Update tests to run properly (#536)

* Remove references to CL:0000003. * Replace CHEBI term for validation. * Update ShEx. * Update test model.
geneontology · Jan 11, 2024 · c77400c · c77400c
1 parent a6a9d0b
commit c77400c
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Showing 5 changed files with 121 additions and 38 deletions.
diff --git a/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java
@@ -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);
@@ -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

diff --git a/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap b/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap
@@ -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>,