For geneontology/go-site#2392

biolink · Dec 13, 2024 · 9505d48 · 9505d48
1 parent 85dce88
commit 9505d48
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Showing 3 changed files with 56 additions and 3 deletions.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -954,7 +954,31 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
             return self._result(False)
 
         return self._result(True)
+
+class GoRule65(GoRule):
+
+    def __init__(self):
+        super().__init__("GORULE:0000065", "Annotations to term that are candidates for obsoletion should be removed", FailMode.SOFT)
+        self.candidate_for_obsoletion = None
 
+    def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult:
+        # Cache the subsets
+        if config.ontology is None:
+            return self._result(True)
+
+        if self.candidate_for_obsoletion is None and config.ontology is not None:
+            self.candidate_for_obsoletion = set(config.ontology.extract_subset("gocheck_obsoletion_candidate"))
+        elif self.candidate_for_obsoletion is None and config.ontology is None:
+            self.candidate_for_obsoletion = []
+
+        goid = str(annotation.object.id)
+
+        annotated_to_obsoletion_candidate = goid in self.candidate_for_obsoletion
+        not_obsoletion_candidate = not(annotated_to_obsoletion_candidate)
+
+        t = result(not_obsoletion_candidate, self.fail_mode)
+        return TestResult(t, self.title, not_obsoletion_candidate)
+
 GoRules = enum.Enum("GoRules", {
     "GoRule02": GoRule02(),
     "GoRule05": GoRule05(),    
@@ -982,7 +1006,8 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
     "GoRule58": GoRule58(),
     "GoRule61": GoRule61(),
     "GoRule63": GoRule63(),
-    "GoRule64": GoRule64(),    
+    "GoRule64": GoRule64(),
+    "GoRule65": GoRule65(),         
     # GoRule13 at the bottom in order to make all other rules clean up an annotation before reaching 13
     "GoRule13": GoRule13()
 })

diff --git a/tests/resources/goslim_generic.json b/tests/resources/goslim_generic.json
@@ -4834,6 +4834,21 @@
       },
       "type" : "CLASS",
       "lbl" : "hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_0099531",
+      "meta" : {
+        "definition" : {
+          "val" : "The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission.",
+          "xrefs" : [ "GOC:dos" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", "http://purl.obolibrary.org/obo/go#goslim_synapse" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "biological_process"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "presynaptic process involved in chemical synaptic transmission"
     }, {
       "id" : "http://purl.obolibrary.org/obo/GO_0005929",
       "meta" : {

diff --git a/tests/test_qc.py b/tests/test_qc.py
@@ -816,7 +816,20 @@ def test_go_rule_64():
     assoc = make_annotation(evidence="IEA", references="GO_REF:0000118").associations[0]
     assoc.subject.taxon = Curie.from_str("NCBITaxon:7227")
     test_result = qc.GoRule64().test(assoc, config)
-    assert test_result.result_type == qc.ResultType.ERROR 
+    assert test_result.result_type == qc.ResultType.ERROR
+
+def test_go_rule65():
+
+    assoc = make_annotation(goid="GO:0099531").associations[0]
+
+    test_result = qc.GoRule65().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.WARNING
+
+    assoc = make_annotation(goid="GO:0016192").associations[0]
+    test_result = qc.GoRule65().test(assoc, all_rules_config(ontology=ontology))
+    assert test_result.result_type == qc.ResultType.PASS
+
+
 
 def test_all_rules():
     # pass
@@ -833,7 +846,7 @@ def test_all_rules():
     assoc = gafparser.to_association(a).associations[0]
 
     test_results = qc.test_go_rules(assoc, config).all_results
-    assert len(test_results.keys()) == 27
+    assert len(test_results.keys()) == 28
     assert test_results[qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
     assert test_results[qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS