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| name: CI | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master, dev ] | |
| jobs: | |
| # First job runs inside the ODKFull container | |
| validate_obo: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: obolibrary/odkfull | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Validate OBO file | |
| run: fastobo-validator --all pride_cv.obo | |
| # Second job runs inside the Robot container | |
| convert_and_validate_owl: | |
| runs-on: ubuntu-latest | |
| needs: validate_obo # Ensures this runs after the previous job | |
| container: | |
| image: obolibrary/robot | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate OWL and validate it | |
| run: | | |
| # 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 | |
| robot convert -vvv -i tmp_pride.obo -o pride_cv.owl --format owl | |
| robot convert -vvv -i tmp_unimod.obo -o unimod.owl --format owl | |
| rm tmp_pride.obo | |
| rm tmp_unimod.obo | |
| - name: Validate the OWL file | |
| run: robot report -vvv --input pride_cv.owl --output report.tsv | |
| - name: Upload report artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: report.tsv | |
| path: report.tsv |