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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| name: "Update OWL" | ||
|
|
||
| on: | ||
| push: | ||
| branches: [master] | ||
|
|
||
| jobs: | ||
| generate-owl: | ||
| if: "! contains(github.event.head_commit.message, 'Update OWL file')" | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: write | ||
| pull-requests: write | ||
| steps: | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v3 | ||
| - name: Extract version from OBO | ||
| run: | | ||
| CV_VERSION=`grep data-version psi-ms.obo | grep -oP "(\d+.\d+.\d+)"` | ||
| echo CV_VERSION=${CV_VERSION} | ||
| echo "CV_VERSION=${CV_VERSION}" >> $GITHUB_ENV | ||
| - name: Generate OWL | ||
| run: | | ||
| docker pull obolibrary/robot:v1.8.1 | ||
| # Replace the imports of the UO and PATO ontology .obo files with the equivalent .owl files | ||
| cp psi-ms.obo tmp.obo | ||
| sed -e "s/pato.obo/pato.owl/g" -e "s/uo.obo/uo.owl/g" -i tmp.obo | ||
| head -n 50 tmp.obo | ||
| export JAVA_TOOL_OPTIONS=-Xmx6G | ||
| docker run --rm -v ${{ github.workspace }}:/work obolibrary/robot:v1.8.1 robot convert -vvv -i /work/tmp.obo -o /work/psi-ms.owl --format owl | ||
| rm tmp.obo | ||
| - name: Create pull request | ||
| id: cpr | ||
| uses: peter-evans/create-pull-request@v4 | ||
| with: | ||
| token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }} | ||
| commit-message: Update OWL file | ||
| committer: GitHub <[email protected]> | ||
| author: GitHub <[email protected]> | ||
| branch: update-owl-file | ||
| delete-branch: true | ||
| title: Update OWL file | ||
| body: This automated PR updates the OWL file corresponding to the OBO file | ||
| - name: Approve pull request | ||
| if: (steps.cpr.outputs.pull-request-operation == 'created' || steps.cpr.outputs.pull-request-operation == 'updated') | ||
| uses: juliangruber/approve-pull-request-action@v1 | ||
| with: | ||
| github-token: ${{ secrets.GITHUB_TOKEN }} | ||
| number: ${{ steps.cpr.outputs.pull-request-number }} | ||
| - name: Merge pull request | ||
| if: (steps.cpr.outputs.pull-request-operation == 'created' || steps.cpr.outputs.pull-request-operation == 'updated') | ||
| uses: peter-evans/enable-pull-request-automerge@v2 | ||
| with: | ||
| token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }} | ||
| pull-request-number: ${{ steps.cpr.outputs.pull-request-number }} | ||
| merge-method: squash | ||
| - name: GitHub Tag | ||
| id: new_tag | ||
| uses: mathieudutour/[email protected] | ||
| with: | ||
| github_token: ${{ secrets.PSI_MS_CV_GITHUB_TOKEN }} | ||
| pre_release_branches: test-tag | ||
| custom_tag: ${{ env.CV_VERSION }} |
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