GHA Autofill experiment #35
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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 | |
| permissions: | |
| pull-requests: write | |
| env: | |
| PR_NUMBER: ${{ github.event.number }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # 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: ${{ secrets.GITHUB_TOKEN }} | |
| # install AMDirT | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install amdirt==1.5.0 | |
| pip install jsonschema==4.17.0 | |
| # Run the autofill script | |
| - name: run autofill | |
| run: | | |
| table=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 4) | |
| project=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 5) | |
| set -o pipefail | |
| 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 | |
| # Post results | |
| - name: comment PR | |
| if: always() | |
| uses: mshick/add-pr-comment@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| message: | | |
| <h1> | |
| <picture> | |
| <source media="(prefers-color-scheme: dark)" srcset="https://github.com/SPAAM-community/AMDirT/blob/master/assets/logo_rectangular_dark.png?raw=true"> | |
| <img width=30% alt="nf-core/taxprofiler" src="https://github.com/SPAAM-community/AMDirT/blob/master/assets/logo_rectangular.png?raw=true"> | |
| </picture> | |
| </h1> | |
| ### Autofill success! 🎉 | |
| Download the attempted autofilled library file by pressing [this link](${{ steps.artifact-upload-step.outputs.artifact-url }}). | |
| You can now fill in the remainder of the columns, and append to the end of the corresponding library file. | |
| Please remember this service attempts to pull relevant metadata from the ENA, but metadata is not always correct! | |
| > [!WARNING] | |
| > Always check accuracy of pre-filled columns before adding to the library table! | |
| refresh-message-position: true | |
| message-failure: | | |
| ### Something went wrong 😢 | |
| Please check your previous request (correct table, project ID etc.). | |
| Request should be: | |
| `@spaam-bot please autofill <table> <project_id>`. | |
| Where `table` corresponds to an AncientMetagenomeDir, and `project_id` corresponds to the `project_id` you have added in your samples table (requires exact match!) | |
| Otherwise please report on the #ancientmetagenomedir channel on the [SPAAM slack](https://www.spaam-community.org/about/). | |
| Include the following URL: https://github.com/SPAAM-community/AncientMetagenomeDir/actions/runs/${{ github.run_id }} |