For #1523 check for unique GO ID

biolink · Nov 9, 2023 · 77d8aa8 · 77d8aa8
1 parent 0b86178
commit 77d8aa8
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -352,15 +352,16 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
 class GoRule16(GoRule):
 
     def __init__(self):
-        super().__init__("GORULE:0000016", "All IC annotations should include a GO ID in the \"With/From\" column", FailMode.SOFT)
+        super().__init__("GORULE:0000016", "All IC annotations should include a GO ID in the \"With/From\" column that is also different from the entry in the \"GO ID\" column", FailMode.SOFT)
 
     def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
         evidence = str(annotation.evidence.type)
         withfrom = annotation.evidence.with_support_from
+        goId = annotation.object.id
 
         okay = True
         if evidence == ic_eco:
-            only_go = [t for conjunctions in withfrom for t in conjunctions.elements if t.namespace == "GO"] # Filter terms that aren't GO terms
+            only_go = [t for conjunctions in withfrom for t in conjunctions.elements if (t.namespace == "GO" and goId is not None and t.identity != goId.identity)] # Filter terms that aren't GO terms and different from GO ID
             okay = len(only_go) >= 1
 
         return self._result(okay)

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -247,9 +247,14 @@ def test_go_rules_15():
     assert test_result.result_type == qc.ResultType.WARNING    
 
 def test_go_rule_16():
+    # GO term same as with/ID
+    assoc = make_annotation(goid="GO:0044419", evidence="IC", withfrom="GO:0044419").associations[0]
+
+    test_result = qc.GoRule16().test(assoc, all_rules_config())
+    assert test_result.result_type == qc.ResultType.WARNING
+
     # No GO term w/ID
     assoc = make_annotation(evidence="IC", withfrom="BLAH:12345").associations[0]
-
     test_result = qc.GoRule16().test(assoc, all_rules_config())
     assert test_result.result_type == qc.ResultType.WARNING