pr.yaml

name: Galaxy Tool Linting and Tests for push and PR
on: [push, pull_request]
env:
  GALAXY_REPO: https://github.com/galaxyproject/galaxy
  GALAXY_RELEASE: release_21.05
  MAX_CHUNKS: 4
jobs:
  # the setup job does two things:
  # 1. cache the pip cache and .planemo
  # 2. determine the list of changed repositories
  # it produces one artifact which contains
  # - a file with the latest SHA from the chosen branch of the Galaxy repo
  # - a file containing the list of changed repositories
  # which are needed in subsequent steps.
  setup:
    name: Setup cache and determine changed repositories
    runs-on: ubuntu-latest
    outputs:
      galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
      commit_range: ${{ steps.get-commit-range.outputs.commit_range }}
      nchunks: ${{ steps.get-chunks.outputs.nchunks }}
      chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
    strategy:
      matrix:
        python-version: [3.7]
    steps:
    - name: Print github context properties
      run: |
        echo 'event: ${{ github.event_name }}'
        echo 'sha: ${{ github.sha }}'
        echo 'ref: ${{ github.ref }}'
        echo 'head_ref: ${{ github.head_ref }}'
        echo 'base_ref: ${{ github.base_ref }}'
        echo 'event.before: ${{ github.event.before }}'
        echo 'event.after: ${{ github.event.after }}'
    - name: Determine latest commit in the Galaxy repo
      id: get-galaxy-sha
      run: echo "::set-output name=galaxy_head_sha::$(git ls-remote ${{ env.GALAXY_REPO }} refs/heads/${{ env.GALAXY_RELEASE }} | 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_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ 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 and flake8
      run: pip install planemo flake8 flake8-import-order
    - name: Fake a Planemo run to update cache
      if: steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.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 $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
    # The range of commits to check for changes is:
    # - `origin/master...` for all events happening on a feature branch
    # - for events on the master branch we compare against the sha before the event
    #   (note that this does not work for feature branch events since we want all
    #   commits on the feature branch and not just the commits of the last event)
    # - for pull requests we compare against the 1st ancestor, given the current
    #   HEAD is the merge between the PR branch and the base branch
    - name: Set commit range (push to the feature branch)
      if: github.ref != 'refs/heads/master' && github.event_name == 'push'
      run: |
        git fetch origin master
        echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV
    - name: Set commit range (push to the master branch, e.g. merge)
      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
      run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV
    - name: Set commit range (pull request)
      if: github.event_name == 'pull_request'
      run: echo "COMMIT_RANGE=HEAD~.." >> $GITHUB_ENV
    - id: get-commit-range
      run: echo "::set-output name=commit_range::$COMMIT_RANGE"
    - name: Planemo ci_find_repos for the commit range
      run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --exclude_from .tt_skip --output repository_list.txt
    - name: Show repository list
      run: cat repository_list.txt
    - uses: actions/upload-artifact@v2
      with:
        name: Workflow artifacts
        path: repository_list.txt
    - name: Planemo ci_find_tools for the repository list
      run: |
        touch tool_list.txt
        if [ -s repository_list.txt ]; then
            planemo ci_find_tools --output tool_list.txt $(cat repository_list.txt)
        fi
    - name: Show tool list
      run: cat tool_list.txt
    - name: Compute chunks
      id: get-chunks
      run: |
        nchunks=$(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 }})'

  # Planemo lint the changed repositories
  lint:
    name: Lint tools
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.7]
    steps:
    # checkout the repository
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install Planemo
      run: pip install planemo
    - name: Planemo lint
      run: |
        set -e
        while read -r DIR; do
            planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR";
        done < ../workflow_artifacts/repository_list.txt
    - name: Planemo ci_find_tools for the commit range
      run: planemo ci_find_tools --changed_in_commit_range ${{ needs.setup.outputs.commit_range }} --exclude packages --exclude deprecated --exclude_from .tt_skip --output tool_list.txt
    - name: Check if each changed tool is in the list of changed repositories
      run: |
        set -e
        while read -r TOOL; do
            # Check if any changed repo dir is a substring of $TOOL
            if ! echo $TOOL | grep -qf ../workflow_artifacts/repository_list.txt; then
                echo "Tool $TOOL not in changed repositories list: .shed.yml file missing" >&2
                exit 1
            fi
        done < tool_list.txt

  # flake8 of Python scripts in the changed repositories
  flake8:
    name: Lint Python scripts
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.7]
    steps:
    # checkout the repository to master
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install flake8
      run: pip install flake8 flake8-import-order
    - name: Flake8
      run: |
        if [ -s ../workflow_artifacts/repository_list.txt ]; then
            flake8 $(cat ../workflow_artifacts/repository_list.txt)
        fi

  lintr:
    name: Lint R scripts
    needs: setup
    runs-on: ubuntu-latest
    strategy:
      matrix:
        r-version: [4.0.1]
    steps:
    # checkout the repository to master
    # and use it as the current working directory
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - uses: r-lib/actions/setup-r@master
      with:
        r-version: ${{ matrix.r-version }}
    - name: Cache R packages
      uses: actions/cache@v2
      with:
        path: ${{ env.R_LIBS_USER }}
        key: r_cache_${{ matrix.r-version }}
    - name: Install non-R lintr dependencies
      run: sudo apt-get install libcurl4-openssl-dev
    - name: Install lintr
      run: |
        install.packages('remotes')
        remotes::install_cran("lintr")
      shell: Rscript {0}
    - name: lintr
      run: |
        library(lintr)
        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL,
          object_name_linter = NULL, object_usage_linter=NULL)
        con <- file("../workflow_artifacts/repository_list.txt", "r")
        status <- 0
        while (TRUE) {
          repo <- readLines(con, n = 1)
          if (length(repo) == 0) {
             break
          }
          lnt <- lint_dir(repo, relative_path=T, linters=linters)
          if (length(lnt) > 0) {
            status <- 1
            for (l in lnt) {
              rel_path <- paste(repo, l$filename, sep="/")
              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
            }
          }
        }
        quit(status = status)
      shell: Rscript {0}

  # Planemo test the changed repositories, each chunk creates an artifact
  # containing HTML and JSON reports for the executed tests
  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: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Cache .planemo
      uses: actions/cache@v2
      id: cache-planemo
      with:
        path: ~/.planemo
        key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install Planemo
      run: pip install planemo
    - name: Planemo ci_find_tools for the repository list, chunked
      run: |
        touch tool_list_chunk.txt
        if [ -s ../workflow_artifacts/repository_list.txt ]; then
          planemo ci_find_tools --chunk_count ${{ needs.setup.outputs.nchunks }} --chunk ${{ matrix.chunk }} --group_tools --output tool_list_chunk.txt $(cat ../workflow_artifacts/repository_list.txt)
        fi
    - 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 $GALAXY_REPO --galaxy_branch $GALAXY_RELEASE --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: 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

  # deploy the tools to the toolsheds (first TTS for testing)
  deploy:
    name: Deploy
    needs: [setup, lint, flake8, lintr, combine_outputs]
    strategy:
      matrix:
        python-version: [3.7]
    runs-on: ubuntu-latest
    if: github.ref == 'refs/heads/master' && github.repository_owner == 'abims-sbr'
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/download-artifact@v2
      with:
        name: Workflow artifacts
        path: ../workflow_artifacts/
    - name: Cache .cache/pip
      uses: actions/cache@v2
      id: cache-pip
      with:
        path: ~/.cache/pip
        key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy_head_sha }}
    - name: Install Planemo
      run: pip install planemo
    - name: Deploy on testtoolshed
      env:
        SHED_KEY: ${{ secrets.TTS_API_KEY }}
      run: |
        while read -r DIR; do
            planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
        done < ../workflow_artifacts/repository_list.txt
      continue-on-error: true
    - name: Deploy on toolshed
      env:
        SHED_KEY: ${{ secrets.TS_API_KEY }}
      run: |
        while read -r DIR; do
            planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
        done < ../workflow_artifacts/repository_list.txt