Relation diff #1
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| name: Relation diff | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| reason_pr: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Run relation-graph | |
| run: cd src/ontology; ROBOT_JAVA_ARGS=-Xmx6G robot merge --catalog catalog-v001.xml -i go-edit.obo -o go-merged.ofn; JAVA_OPTS=-Xmx6G relation-graph --ontology-file go-merged.ofn --mode RDF --output-file go-rels.nt --output-subclasses true --reflexive-subclasses false --equivalence-as-subclass false; sed 's/ /\t/' <go-merged.nt | sed 's/ /\t/' | sed 's/ \.$//' >right.facts | |
| - name: Upload PR facts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: right.facts | |
| path: src/ontology/right.facts | |
| retention-days: 1 | |
| reason_master: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: master | |
| - name: Run relation-graph | |
| run: cd src/ontology; ROBOT_JAVA_ARGS=-Xmx6G robot merge --catalog catalog-v001.xml -i go-edit.obo -o go-merged.ofn; JAVA_OPTS=-Xmx6G relation-graph --ontology-file go-merged.ofn --mode RDF --output-file go-rels.nt --output-subclasses true --reflexive-subclasses false --equivalence-as-subclass false; sed 's/ /\t/' <go-merged.nt | sed 's/ /\t/' | sed 's/ \.$//' >left.facts | |
| - name: Upload PR facts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: left.facts | |
| path: src/ontology/left.facts | |
| retention-days: 1 | |
| merge_ontology: | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Create merged ontology | |
| run: cd src/ontology; ROBOT_JAVA_ARGS=-Xmx6G robot merge --catalog catalog-v001.xml -i go-edit.obo -o go-merged.ttl; riot --output=ntriples go-merged.ttl | sed 's/ /\t/' | sed 's/ /\t/' | sed 's/ \.$//' >ontrdf.facts | |
| - name: Upload ontrdf facts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: ontrdf.facts | |
| path: src/ontology/ontrdf.facts | |
| retention-days: 1 | |
| diff: | |
| needs: | |
| - reason_pr | |
| - reason_master | |
| - merge_ontology | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:${{ vars.ODK_VERSION }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download master relations | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: left.facts | |
| path: left.facts | |
| - name: Download PR relations | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: right.facts | |
| path: right.facts | |
| - name: Download merged ontology | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: ontrdf.facts | |
| path: ontrdf.facts | |
| - name: Diff classification | |
| run: cd src/ontology; souffle ../util/relation-diff.dl | |
| - name: Combine output | |
| run: cat lost.csv gained.csv >diff.tsv | |
| - name: Upload diff | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: diff.tsv | |
| path: src/ontology/diff.tsv |