fix!: xrefs should have exactMatch for ConceptMapping.relation

close #222
cancervariants · Jan 28, 2025 · 775e88a · 775e88a
1 parent fcc59a1
commit 775e88a
Showing 3 changed files with 15 additions and 10 deletions.
diff --git a/src/disease/query.py b/src/disease/query.py
@@ -363,12 +363,17 @@ def _create_concept_mapping(
             extensions=[],
         )
 
-        # mappings
+        xrefs = [record["concept_id"], *record.get("xrefs", [])]
         mappings = [
-            _create_concept_mapping(record["concept_id"], relation=Relation.EXACT_MATCH)
+            _create_concept_mapping(xref_id, relation=Relation.EXACT_MATCH)
+            for xref_id in xrefs
         ]
-        source_ids = record.get("xrefs", []) + record.get("associated_with", [])
-        mappings.extend(_create_concept_mapping(source_id) for source_id in source_ids)
+
+        associated_with = record.get("associated_with", [])
+        mappings.extend(
+            _create_concept_mapping(associated_with_id, relation=Relation.RELATED_MATCH)
+            for associated_with_id in associated_with
+        )
         if mappings:
             disease_obj.mappings = mappings
 

diff --git a/src/disease/schemas.py b/src/disease/schemas.py
@@ -324,14 +324,14 @@ class NormalizationService(BaseModel):
                                 "code": "mondo:0004355",
                                 "system": "http://purl.obolibrary.org/obo/mondo.owl",
                             },
-                            "relation": "relatedMatch",
+                            "relation": "exactMatch",
                         },
                         {
                             "coding": {
                                 "code": "DOID:7757",
                                 "system": "http://purl.obolibrary.org/obo/doid.owl",
                             },
-                            "relation": "relatedMatch",
+                            "relation": "exactMatch",
                         },
                         {
                             "coding": {

diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -36,21 +36,21 @@ def neuroblastoma():
                     "code": "mondo:0005072",
                     "system": "http://purl.obolibrary.org/obo/mondo.owl",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "code": "oncotree:NBL",
                     "system": "https://oncotree.mskcc.org",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "code": "DOID:769",
                     "system": "http://purl.obolibrary.org/obo/doid.owl",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
@@ -172,7 +172,7 @@ def mafd2():
             },
             {
                 "coding": {"code": "MIM:309200", "system": "https://www.omim.org"},
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {