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Merge pull request #26315 from geneontology/balhoff-patch-2
Add relation-diff action for testing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| name: Relation diff | ||
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| on: | ||
| workflow_dispatch: | ||
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| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| #define RDF_TYPE "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>" | ||
| #define RDFS_SUBCLASS_OF "<http://www.w3.org/2000/01/rdf-schema#subClassOf>" | ||
| #define RDFS_SUBPROPERTY_OF "<http://www.w3.org/2000/01/rdf-schema#subPropertyOf>" | ||
| #define OWL_TRANSITIVE_PROPERTY "<http://www.w3.org/2002/07/owl#TransitiveProperty>" | ||
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| .decl left(s: symbol, p: symbol, o: symbol) | ||
| .decl right(s: symbol, p: symbol, o: symbol) | ||
| .decl left_equivalent(x: symbol, y: symbol) | ||
| .decl left_subClassOf(sub: symbol, super: symbol) | ||
| .decl right_equivalent(x: symbol, y: symbol) | ||
| .decl right_subClassOf(sub: symbol, super: symbol) | ||
| .decl ontrdf(s: symbol, p: symbol, o: symbol) | ||
| .decl transitive(prop: symbol) | ||
| .decl subPropertyOf(sub: symbol, super: symbol) | ||
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| .decl lost_entailment(s: symbol, p: symbol, o: symbol) | ||
| .decl gained_entailment(s: symbol, p: symbol, o: symbol) | ||
| .decl lost_redundant(s: symbol, p: symbol, o: symbol) | ||
| .decl lost(s: symbol, p: symbol, o: symbol, dot: symbol) | ||
| .decl gained_redundant(s: symbol, p: symbol, o: symbol) | ||
| .decl gained(s: symbol, p: symbol, o: symbol, dot: symbol) | ||
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| .input left | ||
| .input right | ||
| .input ontrdf //using right version | ||
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| left_equivalent(x, y) :- left(x, RDFS_SUBCLASS_OF, y), x != y, left(y, RDFS_SUBCLASS_OF, x). | ||
| left_subClassOf(sub, super) :- left(sub, RDFS_SUBCLASS_OF, super), sub != super, !left_equivalent(sub, super). | ||
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| right_equivalent(x, y) :- right(x, RDFS_SUBCLASS_OF, y), x != y, right(y, RDFS_SUBCLASS_OF, x). | ||
| right_subClassOf(sub, super) :- right(sub, RDFS_SUBCLASS_OF, super), sub != super, !right_equivalent(sub, super). | ||
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| transitive(prop) :- ontrdf(prop, RDF_TYPE, OWL_TRANSITIVE_PROPERTY). | ||
| subPropertyOf(sub, super) :- ontrdf(sub, RDFS_SUBPROPERTY_OF, super), sub != super. | ||
| subPropertyOf(sub, supersuper) :- subPropertyOf(sub, super), ontrdf(super, RDFS_SUBPROPERTY_OF, supersuper), super != supersuper, sub != supersuper. | ||
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| lost_entailment(s, p, o) :- left(s, p, o), !right(s, p, o). | ||
| gained_entailment(s, p, o) :- right(s, p, o), !left(s, p, o). | ||
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| lost_redundant(s, p, o) :- left(s, p, other), s != other, !left_equivalent(s, other), left_subClassOf(other, o), lost_entailment(s, p, o). | ||
| lost_redundant(s, p, o) :- lost_entailment(s, p, o), left_subClassOf(s, other), left(other, p, o), other != o, !left_equivalent(other, o). | ||
| lost_redundant(s, p, o) :- lost_entailment(s, p, o), transitive(p), lost_entailment(s, p, other), other != o, lost_entailment(other, p, o). | ||
| lost_redundant(s, p, o) :- lost_entailment(s, p, o), subPropertyOf(sub, p), lost_entailment(s, sub, o). | ||
| lost_redundant(s, RDFS_SUBCLASS_OF, s) :- lost_entailment(s, RDFS_SUBCLASS_OF, s). | ||
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| lost(s, p, o, ".") :- lost_entailment(s, p, o), !lost_redundant(s, p, o). | ||
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| gained_redundant(s, p, o) :- right(s, p, other), s != other, !right_equivalent(s, other), right_subClassOf(other, o), gained_entailment(s, p, o). | ||
| gained_redundant(s, p, o) :- gained_entailment(s, p, o), right_subClassOf(s, other), right(other, p, o), other != o, !right_equivalent(other, o). | ||
| gained_redundant(s, p, o) :- gained_entailment(s, p, o), transitive(p), gained_entailment(s, p, other), other != o, gained_entailment(other, p, o). | ||
| gained_redundant(s, p, o) :- gained_entailment(s, p, o), subPropertyOf(sub, p), gained_entailment(s, sub, o). | ||
| gained_redundant(s, RDFS_SUBCLASS_OF, s) :- gained_entailment(s, RDFS_SUBCLASS_OF, s). | ||
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| gained(s, p, o, ".") :- gained_entailment(s, p, o), !gained_redundant(s, p, o). | ||
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| .output lost | ||
| .output gained |