update handling ids

cancervariants · Sep 13, 2023 · 35ae54a · 35ae54a
1 parent 9f9e7b0
commit 35ae54a
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/disease/query.py b/disease/query.py
@@ -329,7 +329,7 @@ def _add_disease(
         :return: completed normalized response object ready to return to user
         """
         disease_obj = core_models.Disease(
-            id=record["concept_id"], label=record["label"]
+            id=f"normalize.disease.{record['concept_id']}", label=record["label"]
         )
 
         source_ids = record.get("xrefs", []) + record.get("associated_with", [])
@@ -360,6 +360,7 @@ def _add_disease(
 
         response["match_type"] = match_type
         response["disease"] = disease_obj
+        response["normalized_id"] = record["concept_id"]
         response = self._add_merged_meta(response)
         return NormalizationService(**response)
 

diff --git a/disease/schemas.py b/disease/schemas.py
@@ -295,6 +295,7 @@ class NormalizationService(BaseModel):
     query: StrictStr
     warnings: Optional[Dict] = None
     match_type: MatchType
+    normalized_id: Optional[str] = None
     disease: Optional[core_models.Disease] = None
     source_meta_: Optional[Dict[SourceName, SourceMeta]] = None
     service_meta_: ServiceMeta
@@ -305,8 +306,9 @@ class NormalizationService(BaseModel):
                 "query": "childhood leukemia",
                 "warnings": None,
                 "match_type": 80,
+                "normalized_id": "ncit:C4989",
                 "disease": {
-                    "id": "ncit:C4989",
+                    "id": "normalize.disease.ncit:C4989",
                     "type": "Disease",
                     "label": "Childhood Leukemia",
                     "aliases": [

diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -20,7 +20,7 @@ def neuroblastoma():
     return core_models.Disease(
         **{
             "type": "Disease",
-            "id": "ncit:C3270",
+            "id": "normalize.disease.ncit:C3270",
             "label": "Neuroblastoma",
             "mappings": [
                 {
@@ -94,7 +94,7 @@ def skin_myo():
     return core_models.Disease(
         **{
             "type": "Disease",
-            "id": "ncit:C167370",
+            "id": "normalize.disease.ncit:C167370",
             "label": "Skin Myoepithelioma",
             "aliases": ["Cutaneous Myoepithelioma"],
         }
@@ -109,7 +109,7 @@ def mafd2():
     return core_models.Disease(
         **{
             "type": "Disease",
-            "id": "mondo:0010648",
+            "id": "normalize.disease.mondo:0010648",
             "label": "major affective disorder 2",
             "aliases": [
                 "MAFD2",
@@ -138,6 +138,7 @@ def mafd2():
 
 def compare_disease(actual, fixture):
     """Verify correctness of returned Disease core object against test fixture."""
+    assert actual.normalized_id == fixture.id.split("normalize.disease.")[-1]
     actual = actual.disease
     actual_keys = actual.model_dump(exclude_none=True).keys()
     fixture_keys = fixture.model_dump(exclude_none=True).keys()