Merge pull request #636 from biolink/go-site-1519-gorule-0000006-excl…

…ude-annot-source-goc

For geneontology/go-site#1519 - exclude annotations with source = GOC

ontobio/io/qc.py

@@ -195,8 +195,12 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
         if config.ontology is None:
             return self._result(True)
 
-        go_namespace = [predval for predval in config.ontology.get_graph().nodes.get(str(annotation.object.id), {}).get("meta", {}).get("basicPropertyValues", []) if predval["pred"]=="OIO:hasOBONamespace"]
         evidence = str(annotation.evidence.type)
+        assigned_by = annotation.provided_by
+        #Annotations with code IEP and HEP assigned by GOC are not restricted to Biological Process terms
+        if evidence in [iep_eco, hep_eco] and assigned_by == "GOC":
+            return self._result(True)
+        go_namespace = [predval for predval in config.ontology.get_graph().nodes.get(str(annotation.object.id), {}).get("meta", {}).get("basicPropertyValues", []) if predval["pred"]=="OIO:hasOBONamespace"]
         fails = evidence in [iep_eco, hep_eco] and "biological_process" not in [o["val"] for o in go_namespace]
         return self._result(not fails)
 

tests/test_qc.py

@@ -17,6 +17,7 @@
 ontology = ontol_factory.OntologyFactory().create("tests/resources/goslim_generic.json")
 ecomapping = ecomap.EcoMap()
 iea_eco = ecomapping.coderef_to_ecoclass("IEA")
+hep_eco = ecomapping.coderef_to_ecoclass("HEP")
 ic_eco = ecomapping.coderef_to_ecoclass("IC")
 ikr_eco = ecomapping.coderef_to_ecoclass("IKR")
 iba_eco = ecomapping.coderef_to_ecoclass("IBA")
@@ -104,7 +105,18 @@ def test_go_rule_06():
     assoc.evidence.type = Curie.from_str(iea_eco)
     test_result = qc.GoRule06().test(assoc, all_rules_config(ontology=ontology))
     assert test_result.result_type == qc.ResultType.PASS
+
+    assoc.evidence.type = Curie.from_str(hep_eco)
+    assoc.provided_by = "GOC"
+    assoc.aspect = "F"
+    assoc.object.id = Curie.from_str("GO:0003674");    
+    test_result = qc.GoRule06().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.PASS    
 
+    assoc.provided_by = "WB"  
+    test_result = qc.GoRule06().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.ERROR
+
 def test_go_rule_07():
 
     assoc = make_annotation(goid="GO:0003824", evidence="IPI").associations[0]