Merge pull request #110 from PRIDE-Archive/update-owl-file #23
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| name: "Update OWL" | |
| on: | |
| push: | |
| branches: [master] | |
| jobs: | |
| generate-owl: | |
| if: "! contains(github.event.head_commit.message, 'Update PRIDE 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 pride_cv.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 pride_cv.obo tmp_pride.obo | |
| cp unimod.obo tmp_unimod.obo | |
| sed -e "s/pato.obo/pato.owl/g" -e "s/uo.obo/uo.owl/g" -i tmp_pride.obo | |
| sed -e "s/pato.obo/pato.owl/g" -e "s/uo.obo/uo.owl/g" -i tmp_unimod.obo | |
| head -n 50 tmp_pride.obo | |
| export JAVA_TOOL_OPTIONS=-Xmx6G | |
| docker run --rm -v ${{ github.workspace }}:/work obolibrary/robot:v1.8.1 robot convert -vvv -i /work/tmp_pride.obo -o /work/pride_cv.owl --format owl | |
| docker run --rm -v ${{ github.workspace }}:/work obolibrary/robot:v1.8.1 robot convert -vvv -i /work/tmp_unimod.obo -o /work/unimod.owl --format owl | |
| rm tmp_pride.obo | |
| rm tmp_unimod.obo | |
| - name: Create pull request | |
| id: cpr | |
| uses: peter-evans/create-pull-request@v4 | |
| with: | |
| token: ${{ secrets.PRIDE_CV_GITHUB_TOKEN }} | |
| commit-message: Update PRIDE 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.PRIDE_CV_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.PRIDE_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.PRIDE_CV_GITHUB_TOKEN }} | |
| pre_release_branches: test-tag | |
| custom_tag: ${{ env.CV_VERSION }} |