Fix test to use correct root type for complexes. (#459)

* Fix test to use correct root type for complexes. * Fix lookup test for new protein complex classification.
geneontology · Feb 22, 2022 · 592dca6 · 592dca6
1 parent 8241a3a
commit 592dca6
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Showing 2 changed files with 9 additions and 16 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
@@ -256,26 +256,19 @@ public void testGetUpperTypes() throws IOException {
 		assertTrue("WBGene00000275 not subclass of CHEBI_24431 chemical entity", supers.contains("http://purl.obolibrary.org/obo/CHEBI_24431"));
 	}
 
-	@Test	
+	@Test
 	public void testGetComplexPortalTypes() throws IOException {
 		//make sure its possible to get from leaf to root for the key classes
 		Set<String> uris = new HashSet<String>();
-		String cp1 = "http://purl.obolibrary.org/obo/ComplexPortal_CPX-9";
-		String cp2 = "http://purl.obolibrary.org/obo/ComplexPortal_CPX-4082";
-//this doesn't work now.  It should work while the ones above do not.  this is problem with the neo ontology.  
-//		String cp3 = "https://www.ebi.ac.uk/complexportal/complex/CPX-9";
+		String cp1 = "https://www.ebi.ac.uk/complexportal/complex/CPX-9";
+		String cp2 = "https://www.ebi.ac.uk/complexportal/complex/CPX-4082";
 		uris.add(cp1);
 		uris.add(cp2);
-//		uris.add(cp3);
-
 		Map<String, Set<String>> uri_roots = onto_repo.getSuperCategoryMap(uris);
 		Set<String> supers = uri_roots.get(cp1);
-		assertTrue("ComplexPortal_CPX-9 not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
+		assertTrue("ComplexPortal_CPX-9 should be a protein-containing complex", supers.contains("http://purl.obolibrary.org/obo/GO_0032991"));
 		supers = uri_roots.get(cp2);
-		assertTrue("ComplexPortal_CPX-4082 not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
-//		supers = uri_roots.get(cp3);
-//		assertTrue("ComplexPortal_CPX-9 as https://www.ebi.ac.uk/complexportal/complex/CPX-9 is not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
-
-
+		assertTrue("ComplexPortal_CPX-4082 should be a protein-containing complex", supers.contains("http://purl.obolibrary.org/obo/GO_0032991"));
 	}
+
 }
diff --git a/...a-lookup/src/test/java/org/geneontology/minerva/lookup/GolrExternalLookupServiceTest.java b/...a-lookup/src/test/java/org/geneontology/minerva/lookup/GolrExternalLookupServiceTest.java
@@ -116,14 +116,14 @@ public void testLookupGeneProductCls() throws Exception {
 		assertTrue(e.isa_closure.size() >= 15);
 		assertTrue(e.isa_closure.contains("CHEBI:33695"));
 //		
-//		//example non-gene obo:ComplexPortal_CPX-900  http://purl.obolibrary.org/obo/ComplexPortal_CPX-900
+//		//example non-gene obo:ComplexPortal_CPX-900  https://www.ebi.ac.uk/complexportal/complex/CPX-900
 		gp_iri = handler.getIRI("ComplexPortal:CPX-900");
 		lookup = s.lookup(gp_iri);
 		assertEquals(1, lookup.size());
 		e = lookup.get(0);
 		assertEquals("saga-kat2a_human Hsap", e.label);
-		assertEquals(16, e.isa_closure.size());
-		assertTrue(e.isa_closure.contains("CHEBI:33695"));
+		assertEquals(7, e.isa_closure.size());
+		assertTrue(e.isa_closure.contains("GO:0032991"));
 	}
 
 	@Test