fix!: xrefs should have exactMatch for ConceptMapping.relation (#…

…397) close #396
cancervariants · Jan 28, 2025 · 80bc5d5 · 80bc5d5
1 parent 5c2af55
commit 80bc5d5
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Showing 3 changed files with 21 additions and 18 deletions.
diff --git a/src/gene/query.py b/src/gene/query.py
@@ -440,14 +440,17 @@ def _get_concept_mapping(
             conceptType="Gene",
         )
 
-        # mappings
-        mappings = [
-            _get_concept_mapping(record["concept_id"], relation=Relation.EXACT_MATCH)
+        xrefs = [record["concept_id"], *record.get("xrefs", [])]
+        gene_obj.mappings = [
+            _get_concept_mapping(xref_id, relation=Relation.EXACT_MATCH)
+            for xref_id in xrefs
         ]
-        source_ids = record.get("xrefs", []) + record.get("associated_with", [])
-        mappings.extend(_get_concept_mapping(source_id) for source_id in source_ids)
-        if mappings:
-            gene_obj.mappings = mappings
+
+        associated_with = record.get("associated_with", [])
+        gene_obj.mappings.extend(
+            _get_concept_mapping(associated_with_id, relation=Relation.RELATED_MATCH)
+            for associated_with_id in associated_with
+        )
 
         # extensions
         extensions = []

diff --git a/src/gene/schemas.py b/src/gene/schemas.py
@@ -365,15 +365,15 @@ class NormalizeService(BaseNormalizationService):
                                 "code": "673",
                                 "system": "https://www.ncbi.nlm.nih.gov/gene/",
                             },
-                            "relation": "relatedMatch",
+                            "relation": "exactMatch",
                         },
                         {
                             "coding": {
                                 "id": "ensembl:ENSG00000157764",
                                 "code": "ENSG00000157764",
                                 "system": "https://www.ensembl.org/id/",
                             },
-                            "relation": "relatedMatch",
+                            "relation": "exactMatch",
                         },
                         {
                             "coding": {

diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -51,15 +51,15 @@ def normalized_ache():
                     "code": "ENSG00000087085",
                     "system": "https://www.ensembl.org/id/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "id": "ncbigene:43",
                     "code": "43",
                     "system": "https://www.ncbi.nlm.nih.gov/gene/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
@@ -197,15 +197,15 @@ def normalized_braf():
                     "code": "673",
                     "system": "https://www.ncbi.nlm.nih.gov/gene/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "id": "ensembl:ENSG00000157764",
                     "code": "ENSG00000157764",
                     "system": "https://www.ensembl.org/id/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
@@ -369,15 +369,15 @@ def normalized_abl1():
                     "code": "ENSG00000097007",
                     "system": "https://www.ensembl.org/id/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "id": "ncbigene:25",
                     "code": "25",
                     "system": "https://www.ncbi.nlm.nih.gov/gene/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
@@ -557,15 +557,15 @@ def normalized_p150():
                     "code": "ENSG00000167670",
                     "system": "https://www.ensembl.org/id/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
                     "id": "ncbigene:10036",
                     "code": "10036",
                     "system": "https://www.ncbi.nlm.nih.gov/gene/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {
@@ -1004,7 +1004,7 @@ def normalized_ifnr():
                     "code": "3466",
                     "system": "https://www.ncbi.nlm.nih.gov/gene/",
                 },
-                "relation": "relatedMatch",
+                "relation": "exactMatch",
             },
             {
                 "coding": {