ci-core/.github/workflows/test-xetabase.yml at main · opencb/ci-core · GitHub

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name: TEST Xetabase and publish report workflow

# Workflow to run Xetabase-specific tests
# Triggered on push and pull request events
on:
  push:
  pull_request:

jobs:
  test-xetabase:
    runs-on: ubuntu-latest
    steps:
      # Check out the repository
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          fetch-tags: true
      # Set up Python environment
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.x'
      # Install dependencies
      - name: Install dependencies
        run: pip install -r requirements.txt
      # Run Xetabase tests
      - name: Run Xetabase tests
        run: pytest tests/xetabase

  test:
    name: Execute JUnit and Jacoco tests
    runs-on: ${{ vars.UBUNTU_VERSION }}
    steps:
      # Checkout ci-core en la raíz para que las acciones locales estén siempre disponibles
      - name: Checkout ci-core (main)
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          fetch-tags: true
          repository: opencb/ci-core
          path: ci-core
      # Checkout el repo que dispara el workflow en workspace/
      - name: Checkout triggering repo
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          fetch-tags: true
          path: workspace
      - name: Retrieve secrets from Keeper
        id: ksecrets
        uses: Keeper-Security/ksm-action@master
        with:
          keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
          secrets: |
            AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG
            DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER
            DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD
            SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_HOST
            SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_PORT
            SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_USER
            SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_PASS
      - name: Prepare enterprise, OpenCGA and dependencies
        id: prepare
        uses: ./ci-core/.github/actions/prepare-opencga-enterprise
        with:
          enterprise_ref: ${{ inputs.branch != '' && inputs.branch || github.ref_name }}
          clone_dependencies: "true"
        env:
          ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
      - name: Set up Java and Maven cache
        # Uses dependencies_sha to make the cache key sensitive to dependency commits
        uses: ./ci-core/.github/actions/setup-java-maven
        with:
          storage_hadoop: ${{ vars.HADOOP_FLAVOUR }}
          java_version: "8"

      - name: Install Samtools
        run: sudo apt-get install samtools python3-deeptools
      - name: Start MongoDB v6.0
        uses: supercharge/mongodb-github-action@1.8.0
        with:
          mongodb-version: 6.0
          mongodb-replica-set: rs-test
      - name: Install sshpass
        run: sudo apt-get install sshpass
      - name: Add SSH Host to known_hosts
        run: |
          mkdir -p ~/.ssh
          ssh-keyscan -p ${{ env.SSH_PORT }} ${{ env.SSH_HOST }} >> ~/.ssh/known_hosts
        env:
          SSH_HOST: ${{ env.SSH_HOST }}
          SSH_PORT: ${{ env.SSH_PORT }}
      - name: Create opencga-home symlink
        run: |
          ln -s "$GITHUB_WORKSPACE/workspace/opencga" "$GITHUB_WORKSPACE/workspace/opencga-enterprise/opencga-home"
      - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, opencga and opencga-enterprise
        run: |
          cd "$GITHUB_WORKSPACE/workspace/opencga-enterprise"
          ./build.sh --test --test-level runShortTests --prepare-branches --test-save-reports --task ${{ inputs.task }} --storage-hadoop ${{ vars.HADOOP_FLAVOUR }} --prepare-hadoop --github
        env:
          THIRDPARTY_READ_TOKEN: ${{ secrets.THIRDPARTY_READ_TOKEN }}
      - name: Upload reports results to Github
        uses: actions/upload-artifact@v4
        with:
          name: report-test
          path: ${{ github.workspace }}/workspace/opencga-enterprise/reports/
          if-no-files-found: error
      - name: Upload log
        uses: actions/upload-artifact@v4
        if: success() || failure()
        with:
          name: build-log
          path: |
            ${{ github.workspace }}/workspace/opencga-enterprise/build.log
            ${{ github.workspace }}/workspace/opencga-enterprise/reports/*.log.gz
          if-no-files-found: error
      - name: Log summary
        run: |
          cat "$GITHUB_WORKSPACE/workspace/opencga-enterprise/build.log" | tee -a $GITHUB_STEP_SUMMARY