For #2002 - Added term to ontology for test; return annotation if tes…

…t fails
biolink · Sep 15, 2023 · 6a9924a · 6a9924a
1 parent c072412
commit 6a9924a
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Showing 2 changed files with 37 additions and 1 deletion.
diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py
@@ -904,7 +904,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP
         else:
             # If we reach here, we're in a weird case where a term is not in either
             # of the three main GO branches, or does not have a namespace defined.
-            return TestResult(repair_result(RepairState.FAILED, self.fail_mode), "{}: {}".format(self.message(repair_state), "GO term has no namespace"), repaired_annotation)
+            return TestResult(repair_result(RepairState.FAILED, self.fail_mode), "{}: {}".format(self.message(repair_state), "GO term has no namespace"), annotation)
 
         allowed_str = ", ".join([str(a) for a in allowed])
         return TestResult(repair_result(repair_state, self.fail_mode), "{}: {} should be one of {}".format(self.message(repair_state), relation, allowed_str), repaired_annotation)

diff --git a/tests/resources/obsolete.json b/tests/resources/obsolete.json
@@ -172,6 +172,42 @@
       "type" : "CLASS",
       "lbl" : "nucleus"
     }, {
+      "id" : "http://purl.obolibrary.org/obo/GO_0007155",
+      "meta" : {
+        "definition" : {
+          "val" : "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.",
+          "xrefs" : [ "GOC:hb", "GOC:pf" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#prokaryote_subset", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_metagenomics" ],
+        "xrefs" : [ {
+          "val" : "Wikipedia:Cell_adhesion"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "single organism cell adhesion",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "cell adhesion molecule activity",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "GO:0098602"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "dos"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-04-15T15:59:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "biological_process"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cell adhesion"
+    },{
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
       "type" : "PROPERTY",
       "lbl" : "has_alternative_id"