Merge pull request #635 from biolink/go-site-895-fix-list-bug

For geneontology/go-site#895 fix list bug
biolink · May 16, 2023 · 046207d · 046207d
2 parents 47cc50a + 864bcd1
commit 046207d
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Showing 2 changed files with 12 additions and 9 deletions.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -528,12 +528,12 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
         db = annotation.subject.id.namespace
         objecttype = annotation.subject.type
         goterm = str(annotation.object.id)
-        namespace = config.ontology.obo_namespace(goterm)
-        
-        if namespace == "cellular_component":
-            if goterm in self.make_protein_complex_descendents_if_not_present(config.ontology):
-                fails = (db == "ComplexPortal" or (objecttype.namespace == "GO" and objecttype.identity == "0032991"))
-                return self._result(not fails)
+        namespace = config.ontology.obo_namespace(goterm)      
+
+        if namespace == "cellular_component" and goterm in self.make_protein_complex_descendents_if_not_present(config.ontology):
+            for ot in objecttype:
+                if db == "ComplexPortal" or (ot.namespace == "GO" and ot.identity == "0032991"):
+                    return self._result(False)
         return self._result(True)    
 
 

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -439,18 +439,18 @@ def test_gorule39():
 
     # test descendant of GO:0032991
     assoc = make_annotation(db="bla", goid="GO:0005840").associations[0]
-    assoc.subject.type = association.map_gp_type_label_to_curie("protein_complex")
+    assoc.subject.type = [association.map_gp_type_label_to_curie("protein_complex")]  
     test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.ERROR    
 
     # test protein complex
     assoc = make_annotation(db="bla", goid="GO:0032991").associations[0]
-    assoc.subject.type=association.map_gp_type_label_to_curie("protein_complex")
+    assoc.subject.type= [association.map_gp_type_label_to_curie("protein_complex")]
     test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.ERROR   
 
     assoc.subject.id = association.Curie("FB", "1234")
-    assoc.subject.type = association.Curie("CHEBI", "33695")
+    assoc.subject.type = [association.Curie("CHEBI", "33695")]
     assoc.object.id = association.Curie("GO", "0032991")       
     test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.PASS
@@ -459,6 +459,9 @@ def test_gorule39():
     assoc.object.id = association.Curie("GO", "0000023")
     test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.PASS
+
+    #test actual GAF file
+
 
 def test_gorule42():
     assoc = make_annotation(qualifier="NOT", evidence="IKR").associations[0]