Lebrasseur2024 #98
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ${{ secrets.GITHUB_TOKEN }} | |
| # install AMDirT | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install amdirt==1.6.1 | |
| pip install jsonschema==4.17.0 | |
| # Get context of PR... | |
| - name: get context | |
| run: | | |
| echo "${{ 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 }} |