Merge remote-tracking branch 'upstream/dev' into oidc-pipeline-config (c11e7529) · Commits · NDIP / Galaxy

.github/workflows/framework_tools.yaml

+2 −2

Original line number	Diff line number	Diff line
		@@ -67,7 +67,7 @@ jobs:
		uses: actions/cache@v4
		with:
		path: 'galaxy root/.venv'
		key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-tools
		key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
		- name: Run tests
		run: ./run_tests.sh --coverage --framework-tools
		working-directory: 'galaxy root'
		@@ -78,5 +78,5 @@ jobs:
		- uses: actions/upload-artifact@v4
		if: failure()
		with:
		name: Framework test results (${{ matrix.python-version }})
		name: Tool framework test results (${{ matrix.python-version }})
		path: 'galaxy root/run_framework_tests.html'

.github/workflows/framework_workflows.yaml

+5 −3

Original line number	Diff line number	Diff line
		@@ -5,11 +5,13 @@ on:
		- 'client/**'
		- 'doc/**'
		- 'lib/galaxy_test/selenium/**'
		- 'packages/**'
		pull_request:
		paths-ignore:
		- 'client/**'
		- 'doc/**'
		- 'lib/galaxy_test/selenium/**'
		- 'packages/**'
		schedule:
		# Run at midnight UTC every Tuesday
		- cron: '0 0 * * 2'
		@@ -66,16 +68,16 @@ jobs:
		uses: actions/cache@v4
		with:
		path: 'galaxy root/.venv'
		key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework-workflows
		key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
		- name: Run tests
		run: ./run_tests.sh --coverage --framework-workflows
		working-directory: 'galaxy root'
		- uses: codecov/codecov-action@v3
		with:
		flags: framework
		flags: framework-workflows
		working-directory: 'galaxy root'
		- uses: actions/upload-artifact@v4
		if: failure()
		with:
		name: Framework test results (${{ matrix.python-version }})
		name: Workflow framework test results (${{ matrix.python-version }})
		path: 'galaxy root/run_framework_workflows_tests.html'

.github/workflows/main_tools.yaml

0 → 100644

+75 −0

Original line number	Diff line number	Diff line
		name: Main tool tests
		on:
		push:
		paths-ignore:
		- 'client/**'
		- 'doc/**'
		- 'lib/galaxy_test/selenium/**'
		- 'packages/**'
		pull_request:
		paths-ignore:
		- 'client/**'
		- 'doc/**'
		- 'lib/galaxy_test/selenium/**'
		- 'packages/**'
		env:
		GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
		GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
		concurrency:
		group: ${{ github.workflow }}-${{ github.ref }}
		cancel-in-progress: true
		jobs:
		test:
		name: Test
		runs-on: ubuntu-latest
		strategy:
		matrix:
		python-version: ['3.9']
		services:
		postgres:
		image: postgres:17
		env:
		POSTGRES_USER: postgres
		POSTGRES_PASSWORD: postgres
		POSTGRES_DB: postgres
		ports:
		- 5432:5432
		steps:
		- uses: actions/checkout@v4
		with:
		path: 'galaxy root'
		persist-credentials: false
		- name: Read Node.js version
		id: node-version
		run: echo "version=$(cat 'galaxy root/client/.node_version')" >> $GITHUB_OUTPUT
		- uses: actions/setup-node@v4
		with:
		node-version: ${{ steps.node-version.outputs.version }}
		cache: 'yarn'
		cache-dependency-path: 'galaxy root/client/yarn.lock'
		- uses: actions/setup-python@v5
		with:
		python-version: ${{ matrix.python-version }}
		cache: 'pip'
		cache-dependency-path: 'galaxy root/requirements.txt'
		- name: Get full Python version
		id: full-python-version
		shell: bash
		run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
		- name: Cache galaxy venv
		uses: actions/cache@v4
		with:
		path: 'galaxy root/.venv'
		key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
		- name: Run tests
		run: ./run_tests.sh --coverage --main_tools
		working-directory: 'galaxy root'
		- uses: codecov/codecov-action@v3
		with:
		flags: main-tools
		working-directory: 'galaxy root'
		- uses: actions/upload-artifact@v4
		if: failure()
		with:
		name: Main tool test results (${{ matrix.python-version }})
		path: 'galaxy root/run_framework_tests.html'

client/src/api/index.ts

+9 −0

Original line number	Diff line number	Diff line
		@@ -338,3 +338,12 @@ export type CreateNewCollectionPayload = components["schemas"]["CreateNewCollect
		export type UnprivilegedToolResponse = components["schemas"]["UnprivilegedToolResponse"];
		export type UserToolSource = components["schemas"]["UserToolSource-Input"];
		export type DynamicUnprivilegedToolCreatePayload = components["schemas"]["DynamicUnprivilegedToolCreatePayload"];

		export type ShareableItemWithStatus = components["schemas"]["ShareWithStatus"];
		export type ShareableHistoryWithStatus = components["schemas"]["ShareHistoryWithStatus"];
		export type AnyShareableItemWithStatus = ShareableItemWithStatus \| ShareableHistoryWithStatus;
		export type ShareOption = components["schemas"]["SharingOptions"];

		export function isShareableHistoryWithStatus(item: AnyShareableItemWithStatus): item is ShareableHistoryWithStatus {
		return item.extra != null && "accessible_count" in item.extra;
		}

client/src/api/schema/schema.ts

+74 −1

Original line number	Diff line number	Diff line
		@@ -14066,6 +14066,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14108,6 +14113,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14150,6 +14160,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -14306,7 +14321,10 @@ export interface components {
		* @description Parameter name. Used when referencing parameter in workflows or inside command templating.
		*/
		name: string;
		/** Optional */
		/**
		* Optional
		* @default false
		*/
		optional: boolean;
		/**
		* Parameter Type
		@@ -18103,6 +18121,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -18608,6 +18631,11 @@ export interface components {
		* @description The creation time of the file.
		*/
		ctime: string;
		/**
		* Hashes
		* @description List of precomputed hashes for the file, if available.
		*/
		hashes?: components["schemas"]["RemoteFileHash"][] \| null;
		/**
		* Name
		* @description The name of the entry.
		@@ -18629,6 +18657,16 @@ export interface components {
		*/
		uri: string;
		};
		/** RemoteFileHash */
		RemoteFileHash: {
		/**
		* Hash Function
		* @enum {string}
		*/
		hash_function: "MD5" \| "SHA-1" \| "SHA-256" \| "SHA-512";
		/** Hash Value */
		hash_value: string;
		};
		/**
		* RemoteFilesDisableMode
		* @enum {string}
		@@ -20200,6 +20238,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -20729,6 +20772,11 @@ export interface components {
		* @description TODO
		*/
		tool_inputs?: unknown;
		/**
		* Tool UUID
		* @description The universal unique identifier of the tool associated with this step. Takes precedence over tool_id if set.
		*/
		tool_uuid?: string \| null;
		/**
		* Tool Version
		* @description The version of the tool associated with this step.
		@@ -21800,6 +21848,11 @@ export interface components {
		* @enum {string}
		*/
		class: "GalaxyUserTool";
		/**
		* Configfiles
		* @description A list of config files for this tool.
		*/
		configfiles?: components["schemas"]["YamlTemplateConfigFile"][] \| null;
		/**
		* Container
		* @description Container image to use for this tool.
		@@ -21882,6 +21935,11 @@ export interface components {
		* @constant
		*/
		class: "GalaxyUserTool";
		/**
		* Configfiles
		* @description A list of config files for this tool.
		*/
		configfiles?: components["schemas"]["YamlTemplateConfigFile"][] \| null;
		/**
		* Container
		* @description Container image to use for this tool.
		@@ -22797,6 +22855,21 @@ export interface components {
		*/
		namespace: string;
		};
		/** YamlTemplateConfigFile */
		YamlTemplateConfigFile: {
		/** Content */
		content: string;
		/**
		* Eval Engine
		* @default ecmascript
		* @constant
		*/
		eval_engine: "ecmascript";
		/** Filename */
		filename?: string \| null;
		/** Name */
		name?: string \| null;
		};
		/** Organization */
		galaxy__schema__drs__Organization: {
		/**

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