Unverified Commit 320aae00 authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #11410 from bernt-matthias/topic/fix-configfile-20.05

parents a11b9943 db1618fc

.ci/minikube-test-setup/deployment.yaml

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+32 −0
Original line number Diff line number Diff line 
apiVersion: apps/v1

kind: Deployment

metadata:

  labels:

    app.kubernetes.io/name: testing

  name: testing

spec:

  replicas: 1

  selector:

    matchLabels:

      app.kubernetes.io/name: test

  template:

    metadata:

      labels:

        app.kubernetes.io/name: test

    spec:

      containers:

      - image: postgres:12

        name: postgres

        ports:

        - containerPort: 5432

        env:

          - name: POSTGRES_DB

            value: postgres

          - name: POSTGRES_USER

            value:  postgres

          - name: POSTGRES_PASSWORD

            value: postgres

      - image: rabbitmq

        name: rabbitmq

        ports:

        - containerPort: 5672

.ci/minikube-test-setup/start_services.sh

0 → 100644
+12 −0
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#!/usr/bin/env bash

set -ex



SCRIPTDIR=$(dirname "${BASH_SOURCE[0]}")

kubectl apply -f "$SCRIPTDIR/deployment.yaml"

kubectl expose deployment testing --type=LoadBalancer --name=testing-service



CLUSTER_IP=$(kubectl get service testing-service -o jsonpath='{.spec.clusterIP}')

GALAXY_TEST_DBURI="postgresql://postgres:postgres@${CLUSTER_IP}:5432/galaxy?client_encoding=utf-8"

GALAXY_TEST_AMQP_URL="amqp://${CLUSTER_IP}:5672)//"

export GALAXY_TEST_DBURI

export GALAXY_TEST_AMQP_URL

.github/workflows/integration.yaml

+49 −36
Original line number Diff line number Diff line
@@ -6,14 +6,15 @@ env: 
jobs:

  test:

    name: Test

    runs-on: ubuntu-18.04

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

        python-version: ['3.7']

        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']

    services:

      postgres:

        image: postgres:11

        image: postgres:13

        env:

          POSTGRES_USER: postgres

          POSTGRES_PASSWORD: postgres
@@ -56,5 +57,17 @@ jobs: 
          path: ~/.cache/pip

          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}

      - name: Run tests

        if: matrix.subset != 'kubernetes'

        run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'

        working-directory: 'galaxy root'

      - name: Run tests

        if: matrix.subset == 'kubernetes'

        run: |

          . .ci/minikube-test-setup/start_services.sh

          ./run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"

        working-directory: 'galaxy root'

      - uses: actions/upload-artifact@v2

        if: failure()

        with:

          name: Integration test results (${{ matrix.python-version }}, ${{ matrix.subset }})

          path: 'galaxy root/run_integration_tests.html'

lib/galaxy/dependencies/pipfiles/default/Pipfile

+1 −1
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@@ -82,7 +82,7 @@ pyparsing = "*" 
"Fabric3" = "*"

paramiko = "*"

cloudbridge = "*"

social_auth_core = {version = "==3.3.0", extras = ['openidconnect']}

social-auth-core = {version = "==3.3.0", extras = ['openidconnect']}

cloudauthz = "==0.6.0"

gxformat2 = "*"

refgenconf = ">=0.7.0"

lib/galaxy/tools/parameters/wrapped_json.py

+6 −3
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@@ -94,10 +94,13 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"): 
    elif input_type == "boolean":

        json_value = _cast_if_not_none(value_wrapper, bool)

    elif input_type == "select":

        if input.multiple and packaging.version.parse(str(profile)) >= packaging.version.parse('20.05'):

            json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]

        else:

        if packaging.version.parse(str(profile)) < packaging.version.parse('20.05'):

            json_value = _cast_if_not_none(value_wrapper, str)

        else:

            if input.multiple:

                json_value = [str(_) for _ in _cast_if_not_none(value_wrapper.value, list)]

            else:

                json_value = _cast_if_not_none(value_wrapper.value, str)

    elif input_type == "data_column":

        # value is a SelectToolParameterWrapper()

        if input.multiple: