Merge pull request #634 from biolink/go-site-895-gorule-0000039-prote…

…in-containing-complex-desc

Check if annotated term is in the complex closure

ontobio/io/qc.py

@@ -514,15 +514,27 @@ class GoRule39(GoRule):
 
     def __init__(self):
         super().__init__("GORULE:0000039", "Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants", FailMode.HARD)
+        self.protein_containing_complex_descendents = None
+
+    def make_protein_complex_descendents_if_not_present(self, ontology: Optional[ontol.Ontology]) -> Set:
+        if ontology is not None and self.protein_containing_complex_descendents is None:
+            closure = gafparser.protein_complex_sublcass_closure(ontology)
+            self.protein_containing_complex_descendents = closure
+
+        return {} if self.protein_containing_complex_descendents is None else self.protein_containing_complex_descendents    
 
     def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
-        # An implementation note: This is done by testing if the DB (column 1) is ComplexPortal.
-        # This will grab a subset of all actual Protein Complexes. This is noted in the rule description
+        # An implementation note: This is done by testing if the DB (column 1) is ComplexPortal or DB Object type (column 12) is protein_complex
         db = annotation.subject.id.namespace
+        objecttype = annotation.subject.type
         goterm = str(annotation.object.id)
-
-        fails = (db == "ComplexPortal" and goterm == "GO:0032991")
-        return self._result(not fails)
+        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)
+        return self._result(True)    
 
 
 class GoRule42(GoRule):

tests/test_qc.py

@@ -431,18 +431,33 @@ def test_gorule37():
     assert test_result.result_type == qc.ResultType.ERROR
 
 def test_gorule39():
+    config = all_rules_config(ontology=ontology)
     assoc = make_annotation(db="ComplexPortal", goid="GO:0032991").associations[0]
 
-    test_result = qc.GoRule39().test(assoc, all_rules_config())
+    test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.ERROR
 
+    # 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")
+    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")
+    test_result = qc.GoRule39().test(assoc,  config)
+    assert test_result.result_type == qc.ResultType.ERROR   
+
     assoc.subject.id = association.Curie("FB", "1234")
-    test_result = qc.GoRule39().test(assoc, all_rules_config())
+    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
 
     assoc.subject.id = association.Curie("ComplexPortal", "12345")
     assoc.object.id = association.Curie("GO", "0000023")
-    test_result = qc.GoRule39().test(assoc, all_rules_config())
+    test_result = qc.GoRule39().test(assoc,  config)
     assert test_result.result_type == qc.ResultType.PASS
 
 def test_gorule42():