Uberon integration #3
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| name: Uberon integration | |
| on: | |
| # Manual triggering only | |
| workflow_dispatch: | |
| jobs: | |
| uberon_integration: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.4.3 | |
| steps: | |
| - name: Checkout current FBbt | |
| uses: actions/checkout@v4 | |
| with: | |
| path: fbbt | |
| - name: Checkout current Uberon | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: obophenotype/uberon | |
| path: uberon | |
| - name: Checkout current CL | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: obophenotype/cell-ontology | |
| path: cl | |
| - name: Build FBbt | |
| run: | | |
| cd fbbt/src/ontology | |
| make fbbt.owl mappings.sssom.tsv MIR=false IMP=false PAT=false | |
| - name: Build Uberon | |
| run: | | |
| cd uberon/src/ontology | |
| make uberon.owl MIR=false IMP=false PAT=false BRI=false GH_ACTION=true | |
| - name: Build CL | |
| run: | | |
| cd cl/src/ontology | |
| make cl.owl MIR=false IMP=false PAT=false | |
| - name: Merge all ontologies together | |
| env: | |
| ROBOT_PLUGINS_DIRECTORY: uberon/src/ontology/tmp/plugins | |
| run: | | |
| robot merge -i fbbt/src/ontology/fbbt.owl \ | |
| -i uberon/src/ontology/uberon.owl \ | |
| -i cl/src/ontology/cl.owl \ | |
| sssom:inject --sssom fbbt/src/ontology/mappings.sssom.tsv \ | |
| --ruleset fbbt/src/scripts/bridging.rules \ | |
| annotate --ontology-iri http://purl.obolibrary.org/obo/fbbt/fbbt-uberon-cl-merge.owl \ | |
| --output fbbt-uberon-cl-merge.owl \ | |
| reason --reasoner ELK | tee merge.log | |
| - name: Upload merged ontology | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: merged-ontology | |
| path: fbbt-uberon-cl-merge.owl | |
| - name: Check and explain unsats | |
| run: | | |
| if grep -q unsat merge.log ; then | |
| robot explain -i fbbt-uberon-cl-merge.owl \ | |
| --reasoner ELK \ | |
| --mode unsatisfiability \ | |
| --unsatisfiable all \ | |
| --explanation unsats.md | |
| exit 1 | |
| fi | |
| - name: Upload explanations | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: explanations | |
| path: unsats.md |