autofill.yml

name: Prepare autofilled template for library metadata
on:
  issue_comment:
    types: [created]

jobs:
  Autofill:
    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
    if: >
      contains(github.event.comment.html_url, '/pull/') &&
      startsWith(github.event.comment.body, '@spaam-bot please autofill') &&
      github.repository == 'SPAAM-community/AncientMetagenomeDir'
    runs-on: ubuntu-latest
    continue-on-error: true
    permissions:
      pull-requests: write
    env:
      PR_NUMBER: ${{ github.event.number }}
    steps:
      - uses: actions/checkout@v4
        with:
          ## from: https://github.com/actions/checkout/issues/331
          ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) }}

      # indication that the autofill is being attempted
      - name: React on comment
        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: eyes
          token: ${{ secrets.GITHUB_TOKEN }}

      # install AMDirT
      - uses: actions/setup-python@v4
        with:
          python-version: "3.9"
          architecture: "x64"
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install amdirt==1.5.0
          pip install jsonschema==4.17.0

      # Get context of PR...
      - name: get context
        run: |
          echo "${{ github.head_ref }}"
          echo "${{ github.event.number }}"
          tail ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv
          git --no-pager log --oneline | head

      # Run the autofill script
      - name: run autofill
        run: |
          table=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 4)
          project=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 5)
          bash assets/utility/autofill-wrapper.sh -t $table -p $project 2>&1 | tee autofill-log.txt

      - uses: actions/upload-artifact@v4
        id: artifact-upload-step
        with:
          name: autofill-results
          path: |
            TEMPLATE_*libraries.tsv
            autofill-log.txt

      # Prepare the results
      - name: prepare results
        run: |
          bash assets/utility/autofill-report.sh -l autofill-log.txt -i ${{ github.run_id }} -u ${{ steps.artifact-upload-step.outputs.artifact-url }}

      # Post results
      - name: comment PR success
        if: always()
        uses: mshick/add-pr-comment@v2
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          message-path: autofill-report.md
          refresh-message-position: true

      # indication that the autofill attempt was completed
      - name: React on succesful comment
        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: +1
          token: ${{ secrets.GITHUB_TOKEN }}