ci.yaml

name: Weekly global Tool Linting and Tests
on:
  schedule:
    # Run at midnight every monday
    - cron: '0 0 * * 1'
  repository_dispatch:
    types: [run-all-tool-tests-command]
env:
  GALAXY_RELEASE: release_20.09
  GALAXY_FORK: galaxyproject
  MAX_CHUNKS: 40
jobs:
  setup:
    name: Setup cache
    if: github.repository_owner == 'ASaiM'
    runs-on: ubuntu-latest
    outputs:
      branch: ${{ steps.get-fork-branch.outputs.branch }}
      fork: ${{ steps.get-fork-branch.outputs.fork }}
      galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
      nchunks: ${{ steps.get-chunks.outputs.nchunks }}
      chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
    strategy:
      matrix:
        python-version: [3.7]
    steps:
    - name: Add reaction
      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
      uses: peter-evans/create-or-update-comment@v1
      with:
        token: ${{ secrets.PAT }}
        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
        comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
        reaction-type: hooray
    - name: Set galaxy fork and branch
      id: get-fork-branch
      run: |
        TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
        echo "::set-output name=fork::${TMP:-$GALAXY_FORK}"
        TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
        echo "::set-output name=branch::${TMP:-$GALAXY_RELEASE}"
    - name: Determine latest commit in the Galaxy repo
      id: get-galaxy-sha
      run: echo "::set-output name=galaxy_head_sha::$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)"
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
    # Install the `wheel` package so that when installing other packages which
    # are not available as wheels, pip will build a wheel for them, which can be cached.
    - name: Install wheel
      run: pip install wheel
    - name: Install Planemo
      run: pip install planemo
    - name: Fake a Planemo run to update cache
      if: steps.cache-pip.outputs.cache-hit != 'true'
      run: |
        touch tool.xml
        PIP_QUIET=1 planemo test --galaxy_python_version ${{ matrix.python-version }} --no_conda_auto_init --galaxy_source 'https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy' --galaxy_branch "${{ steps.get-fork-branch.outputs.branch }}" --galaxy_python_version ${{ matrix.python-version }}
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - name: Planemo ci_find_repos
      run: planemo ci_find_repos --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
    - name: Show repository list
      run: cat repository_list.txt
    - name: Planemo ci_find_tools for the repository list
      run: planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt)
    - name: Show tool list
      run: cat tool_list.txt
    - name: Compute chunks
      id: get-chunks
      run: |
        nchunks=$(wc -l < tool_list.txt)
        if [ "$nchunks" -gt "$MAX_CHUNKS" ]; then
            nchunks=$MAX_CHUNKS
        elif [ "$nchunks" -eq 0 ]; then
            nchunks=1
        fi
        echo "::set-output name=nchunks::$nchunks"
        echo "::set-output name=chunk_list::[$(seq -s ", " 0 $(($nchunks - 1)))]"
    - name: Show chunks
      run: |
        echo 'Using ${{ steps.get-chunks.outputs.nchunks }} chunks (${{ steps.get-chunks.outputs.chunk_list }})'

  test:
    name: Test tools
    # This job runs on Linux
    runs-on: ubuntu-latest
    needs: setup
    strategy:
      fail-fast: false
      matrix:
        chunk: ${{ fromJson(needs.setup.outputs.chunk_list) }}
        python-version: [3.7]
    services:
      postgres:
        image: postgres:11
        env:
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
          POSTGRES_DB: postgres
        ports:
          - 5432:5432
    steps:
    # checkout the repository
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install Planemo
      run: pip install planemo
    - name: Planemo ci_find_tools, chunked
      run: planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --exclude test_repositories --exclude packages --exclude deprecated --exclude_from .tt_skip --group_tools --output tool_list_chunk.txt
    - name: Show tool list chunk
      run: cat tool_list_chunk.txt
    - name: Planemo test tools
      run: |
        mkdir json_output
        while read -r TOOL_GROUP; do
            # Check if any of the lines in .tt_biocontainer_skip is a substring of $TOOL_GROUP
            if echo $TOOL_GROUP | grep -qf .tt_biocontainer_skip; then
                PLANEMO_OPTIONS=""
            else
                PLANEMO_OPTIONS="--biocontainers --no_dependency_resolution --no_conda_auto_init"
            fi
            json=$(mktemp -u -p json_output --suff .json)
            PIP_QUIET=1 planemo test --database_connection postgresql://postgres:postgres@localhost:5432/galaxy $PLANEMO_OPTIONS --galaxy_source "https://github.com/${{ needs.setup.outputs.fork }}/galaxy" --galaxy_branch "${{ needs.setup.outputs.branch }}" --galaxy_python_version ${{ matrix.python-version }} --test_output_json "$json" $TOOL_GROUP || true
            docker system prune --all --force --volumes || true
        done < tool_list_chunk.txt
        if [ ! -s tool_list_chunk.txt ]; then
            echo '{"tests":[]}' > "$(mktemp -u -p json_output --suff .json)"
        fi
    - name: Merge tool_test_output.json files
      run: planemo merge_test_reports json_output/*.json tool_test_output.json
    - name: Create tool_test_output.html
      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
    - name: Copy artifacts into place
      run: |
        mkdir upload
        mv tool_test_output.json tool_test_output.html upload/
    - uses: actions/upload-artifact@v2
      with:
        name: 'Tool test output ${{ matrix.chunk }}'
        path: upload

  # - combine the results of the test chunks (which will never fail due
  #   to `|| true`) and create a global test report as json and html which
  #   is provided as artifact
  # - check if any tool test actually failed (by lookup in the combined json)
  #   and fail this step if this is the case
  combine_outputs:
    name: Combine chunked test results
    needs: [setup, test]
    strategy:
      matrix:
        python-version: [3.7]
    # This job runs on Linux
    runs-on: ubuntu-latest
    steps:
    - uses: actions/download-artifact@v2
      with:
        path: artifacts
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install Planemo
      run: pip install planemo
    - name: Install jq
      run: sudo apt-get install jq
    - name: Combine outputs
      run: find artifacts/ -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
    - name: Create tool_test_output.html
      run: planemo test_reports tool_test_output.json --test_output tool_test_output.html
    - name: Copy artifacts into place
      run: |
        mkdir upload
        mv tool_test_output.json tool_test_output.html upload/
    - uses: actions/upload-artifact@v2
      with:
        name: 'All tool test results'
        path: upload

    - name: Create URL to the run output
      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
      id: vars
      run: echo ::set-output name=run-url::https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID

    - name: Gather statistics
      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
      id: stats
      run: echo ::set-output name=statistics::$(jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | sed 's/"//g' | sort | uniq -c)

    - name: Create comment
      if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
      uses: peter-evans/create-or-update-comment@v1
      with:
        token: ${{ secrets.PAT }}
        repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
        issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
        body: |
          Summary:

          ${{ steps.stats.outputs.statistics }}

          [Find all tool test results here][1]

          [1]: ${{ steps.vars.outputs.run-url }}
    - name: Check status of combined outputs
      run: |
        if jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success"; then
            echo "Unsuccessful tests found, inspect the 'All tool test results' artifact for details."
            exit 1
        fi