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Update tests to run properly #536

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merged 4 commits into from
Jan 11, 2024
Merged

Update tests to run properly #536

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1a95688
Remove references to CL:0000003.
balhoff Dec 19, 2023
8c0ea00
Replace CHEBI term for validation.
balhoff Dec 19, 2023
ce54e9d
Update ShEx.
balhoff Dec 19, 2023
3c007e6
Update test model.
balhoff Jan 11, 2024
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8 changes: 4 additions & 4 deletions minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -108,10 +108,10 @@ public void testGetSubClasses() throws IOException {
assertTrue("ECO_0000314 not subclass of ECO_0000000", subs.contains("http://purl.obolibrary.org/obo/ECO_0000314"));
//Anatomy
//worm anatomy - note that it needs parts of the cl ontology in there
uri = "http://purl.obolibrary.org/obo/CL_0000003";
uri = "http://purl.obolibrary.org/obo/CL_0000000";
subs = onto_repo.getAllSubClasses(uri);
//GO native cell - used a lot in shex
assertTrue("WBbt_0005753 not subclass of CL_0000003", subs.contains("http://purl.obolibrary.org/obo/WBbt_0005753"));
//GO cell - used a lot in shex
assertTrue("WBbt_0005753 not subclass of CL_0000000", subs.contains("http://purl.obolibrary.org/obo/WBbt_0005753"));
//Cell component
uri = "http://purl.obolibrary.org/obo/GO_0110165";
subs = onto_repo.getAllSubClasses(uri);
Expand Down Expand Up @@ -159,7 +159,7 @@ public void testGetSuperClasses() throws IOException {
uri = "http://purl.obolibrary.org/obo/WBbt_0005753";
supers = onto_repo.getAllSuperClasses(uri);
//GO native cell - used a lot in shex
assertTrue("WBbt_0005753 not subclass of CL_0000003", supers.contains("http://purl.obolibrary.org/obo/CL_0000003"));
assertTrue("WBbt_0005753 not subclass of CL_0000000", supers.contains("http://purl.obolibrary.org/obo/CL_0000000"));
//anatomy - also used a lot in shex
assertTrue("WBbt_0005753 not subclass of UBERON_0001062", supers.contains("http://purl.obolibrary.org/obo/UBERON_0001062"));
//Cell component
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2 changes: 2 additions & 0 deletions minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
SPARQL 'SELECT ?x WHERE { ?x a <http://www.w3.org/2002/07/owl#Ontology> }' @ <http://purl.obolibrary.org/obo/go/shapes/GoCamModel>,
SPARQL 'SELECT ?x WHERE { ?x a/<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/CHEBI_33695> }' @ <http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule>,
SPARQL 'SELECT ?x WHERE { ?x a/<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/NCBITaxon_1> }' @ <http://purl.obolibrary.org/obo/go/shapes/Organism>,
SPARQL 'SELECT ?x WHERE { ?x a/<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/GO_0003674> }' @ <http://purl.obolibrary.org/obo/go/shapes/MolecularFunction>,
SPARQL 'SELECT ?x WHERE { ?x a/<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/GO_0005215> }' @ <http://purl.obolibrary.org/obo/go/shapes/TransporterActivity>,
SPARQL 'SELECT ?x WHERE { ?x a/<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.obolibrary.org/obo/GO_0008150> }' @ <http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess>,
Expand Down
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