export.yaml

name: Export
on:
  schedule:
  # https://crontab.guru/#05_11_*_*_2
  - cron: '05 11 * * 2'
  workflow_dispatch:
    inputs:
      release:
        description: 'Ensembl release number (e.g. 104 or latest)'
        required: true
        default: 'latest'
      overwrite:
        type: boolean
        description: 'Overwrite output on an existing branch.'
        default: false
jobs:
  export:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        species:
        - human
        - mouse
        - rat
    steps:
    - name: Checkout repository
      uses: actions/checkout@v4
    - name: Setup dependencies
      uses: ./.github/actions/setup
    - name: Set parameters
      id: params
      shell: bash
      run: |
        DATE_ISO=$(date --utc --iso)
        echo "Setting parameter date_iso=$DATE_ISO"
        echo "date_iso=$DATE_ISO" >> $GITHUB_OUTPUT

        ENSEMBL_RELEASE=${{ github.event.inputs.release || 'latest' }}
        ENSEMBL_RELEASE=$(poetry run ensembl_genes ensembl_release --release="$ENSEMBL_RELEASE")
        echo "Setting parameter release=$ENSEMBL_RELEASE"
        echo "release=$ENSEMBL_RELEASE" >> $GITHUB_OUTPUT

        ENSEMBL_DATABASE=$(poetry run ensembl_genes ensembl_database --species="${{ matrix.species }}" --release="$ENSEMBL_RELEASE")
        echo "Setting parameter database=$ENSEMBL_DATABASE"
        echo "database=$ENSEMBL_DATABASE" >> $GITHUB_OUTPUT
        # output_path doubles as a hierarchical branch name
        OUTPUT_PATH="output/${ENSEMBL_DATABASE}"
        echo "Setting parameter output_path=$OUTPUT_PATH"
        echo "output_path=$OUTPUT_PATH" >> $GITHUB_OUTPUT

        OUTPUT_EXISTS="true"
        git ls-remote --exit-code origin $OUTPUT_PATH || OUTPUT_EXISTS="false"
        echo "$OUTPUT_PATH branch exists on origin: $OUTPUT_EXISTS"
        echo "output_exists=$OUTPUT_EXISTS" >> $GITHUB_OUTPUT

        OVERWRITE=${{ github.event.inputs.overwrite || 'false' }}
        echo "Setting parameter overwrite=$OVERWRITE"
        echo "overwrite=$OVERWRITE" >> $GITHUB_OUTPUT

        EXPORT="false"
        if [[ $OUTPUT_EXISTS = "false" || $OVERWRITE = "true" ]]; then
          EXPORT="true"
        fi
        echo "Setting parameter export=$EXPORT"
        echo "export=$EXPORT" >> $GITHUB_OUTPUT
    - name: Extract tables
      id: extract
      if: steps.params.outputs.export == 'true'
      run: poetry run ensembl_genes all --species="${{ matrix.species }}" --release=${{ steps.params.outputs.release }}
    - name: Output artifact
      # upload outputs to artifact only when the extraction fails
      if: always() && steps.extract.outcome == 'failure'
      uses: actions/upload-artifact@v3
      with:
        name: failed_output_${{ steps.params.outputs.database }}
        path: ${{ steps.params.outputs.output_path }}
    - name: Deploy
      uses: peaceiris/actions-gh-pages@v3
      if: steps.params.outputs.export == 'true'
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_branch: ${{ steps.params.outputs.output_path }}
        publish_dir: ${{ steps.params.outputs.output_path }}
        # Won't actually enable jekyll because we're not using GitHub Pages.
        # https://github.com/peaceiris/actions-gh-pages/issues/660
        enable_jekyll: true
        full_commit_message: |
          export ${{ steps.params.outputs.database }} on ${{ steps.params.outputs.date_iso }}
          
          code version ${{ github.sha }}
          built by <${{ github.event.repository.html_url }}/actions/runs/${{ github.run_id }}>
        allow_empty_commit: true