Bergfeldt 2024 #95
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| 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 }} |