Update OWL file (#355) #126
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| 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: | | |
| # 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 | |
| python -m pip install fastobo | |
| python scripts/prepare_template.py tmp.obo cv_template.tsv | |
| echo Generated template with `wc -l cv_template.tsv` | |
| wget -nv --no-check-certificate https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar | |
| export JAVA_TOOL_OPTIONS=-Xmx6G | |
| # java -jar robot.jar -vvv template -p "PEFF: http://purl.obolibrary.org/obo/PEFF_" -i psi-ms.obo -t cv_template.tsv convert -f ofn -o psi-ms.owl | |
| java -jar robot.jar convert -v -i tmp.obo -o psi-ms.owl --format owl | |
| rm *robot.jar* | |
| rm *tmp.obo* *cv_template.tsv* | |
| - 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@v3 | |
| 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 }} |