Merge pull request #577 from biolink/issue-576-obs-term-repair-aspect

Repair obsolete terms before other GO rule tests; for #576
biolink · Jun 16, 2021 · 99f1d55 · 99f1d55
2 parents 2066457 + 5fb109d
commit 99f1d55
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Showing 2 changed files with 38 additions and 7 deletions.
diff --git a/ontobio/io/gpadparser.py b/ontobio/io/gpadparser.py
@@ -155,6 +155,13 @@ def parse_line(self, line):
 
         assoc = parsed.associations[0]
 
+        split_line = assocparser.SplitLine(line=line, values=vals, taxon="")
+
+        valid_goid = self._validate_ontology_class_id(str(assoc.object.id), split_line)
+        if valid_goid is None:
+            return assocparser.ParseResult(line, [], True)
+        assoc.object.id = association.Curie.from_str(valid_goid)
+
         go_rule_results = qc.test_go_rules(assoc, self.config)
         for rule, result in go_rule_results.all_results.items():
             if result.result_type == qc.ResultType.WARNING:
@@ -173,19 +180,12 @@ def parse_line(self, line):
 
         assoc = go_rule_results.annotation  # type: association.GoAssociation
 
-        split_line = assocparser.SplitLine(line=line, values=vals, taxon="")
-
         if not self._validate_id(str(assoc.subject.id), split_line, context=ENTITY):
             return assocparser.ParseResult(line, [], True)
 
         if not self._validate_id(str(assoc.object.id), split_line, context=ANNOTATION):
             return assocparser.ParseResult(line, [], True)
 
-        valid_goid = self._validate_ontology_class_id(str(assoc.object.id), split_line)
-        if valid_goid is None:
-            return assocparser.ParseResult(line, [], True)
-        assoc.object.id = association.Curie.from_str(valid_goid)
-
         if not self._validate_id(str(assoc.evidence.type), split_line):
             return assocparser.ParseResult(line, [], True)
 

diff --git a/tests/test_gpad_parser.py b/tests/test_gpad_parser.py
@@ -2,6 +2,7 @@
 from ontobio.io import assocparser
 from ontobio.model import association
 from ontobio.model.association import ConjunctiveSet, ExtensionUnit, Curie
+from ontobio.ontol_factory import OntologyFactory
 
 import yaml
 
@@ -122,3 +123,33 @@ def test_parse_2_0():
     # Test annotation property retrieval
     contributors = result.associations[0].annotation_property_values(property_key="contributor-id")
     assert set(contributors) == {"http://orcid.org/0000-0003-2689-5511"}
+
+ALT_ID_ONT = "tests/resources/obsolete.json"
+
+def test_aspect_fill_for_obsolete_terms():
+    # Test null aspect on an obsolete term
+    # GO:4 is obsolete and has no aspect (hasOBONamespace) in obsolete.json ontology
+    # GO:3 is it's replacement term
+    # Note that GPAD lines contain no aspect data
+    vals = [
+        "MGI",
+        "MGI:105128",
+        "involved_in",
+        "GO:4",
+        "PMID:25901318",
+        "ECO:0000314",
+        "",
+        "",
+        "20190517",
+        "MGI",
+        "",
+        "contributor=http://orcid.org/0000-0002-9796-7693|model-state=production|noctua-model-id=gomodel:5c4605cc00004132"
+    ]
+    ont = OntologyFactory().create(ALT_ID_ONT)
+    config = assocparser.AssocParserConfig(ontology=ont, rule_set=assocparser.RuleSet.ALL)
+    parser = GpadParser(config=config)
+    result = parser.parse_line("\t".join(vals))
+    assoc = result.associations[0]
+
+    assert assoc.object.id == Curie("GO", "3")  # GO:4 should be repaired to its replacement term, GO:3
+    assert assoc.aspect == 'P'  # Aspect should not be empty