rm vod

cancervariants · Sep 12, 2023 · 6c7cc58 · 6c7cc58
1 parent 9f59e1e
commit 6c7cc58
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Showing 2 changed files with 17 additions and 18 deletions.
diff --git a/disease/query.py b/disease/query.py
@@ -318,15 +318,14 @@ def _add_merged_meta(self, response: Dict) -> Dict:
         response["source_meta_"] = sources_meta
         return response
 
-    def _add_vod(
-        self, response: Dict, record: Dict, query: str, match_type: MatchType
+    def _add_disease(
+        self, response: Dict, record: Dict, match_type: MatchType
     ) -> NormalizationService:
-        """Format received DB record as VOD and update response object.
+        """Format received DB record as core Disease object and update response object.
 
-        :param Dict response: in-progress response object
-        :param Dict record: record as stored in DB
-        :param str query: query string from user request
-        :param MatchType match_type: type of match achieved
+        :param response: in-progress response object
+        :param record: record as stored in DB
+        :param match_type: type of match achieved
         :return: completed normalized response object ready to return to user
         """
         disease_obj = core_models.Disease(
@@ -415,7 +414,7 @@ def normalize(self, query: str) -> NormalizationService:
         # check merged concept ID match
         record = self.db.get_record_by_id(query_str, case_sensitive=False, merge=True)
         if record:
-            return self._add_vod(response, record, query, MatchType.CONCEPT_ID)
+            return self._add_disease(response, record, MatchType.CONCEPT_ID)
 
         non_merged_match = None
 
@@ -429,7 +428,7 @@ def normalize(self, query: str) -> NormalizationService:
                 if merge is None:
                     return self._handle_failed_merge_ref(record, response, query_str)
                 else:
-                    return self._add_vod(response, merge, query, MatchType.CONCEPT_ID)
+                    return self._add_disease(response, merge, MatchType.CONCEPT_ID)
             else:
                 non_merged_match = (record, "concept_id")
 
@@ -457,8 +456,8 @@ def normalize(self, query: str) -> NormalizationService:
                                 record, response, query_str
                             )
                         else:
-                            return self._add_vod(
-                                response, merge, query, MatchType[match_type.upper()]
+                            return self._add_disease(
+                                response, merge, MatchType[match_type.upper()]
                             )
                     else:
                         if not non_merged_match:
@@ -467,6 +466,6 @@ def normalize(self, query: str) -> NormalizationService:
         # if no successful match, try available non-merged match
         if non_merged_match:
             match_type = MatchType[non_merged_match[1].upper()]
-            return self._add_vod(response, non_merged_match[0], query, match_type)
+            return self._add_disease(response, non_merged_match[0], match_type)
 
         return NormalizationService(**response)
diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -136,7 +136,7 @@ def mafd2():
     )
 
 
-def compare_vod(actual, fixture):
+def compare_disease(actual, fixture):
     """Verify correctness of returned Disease core object against test fixture."""
     actual = actual.disease
     actual_keys = actual.model_dump(exclude_none=True).keys()
@@ -253,7 +253,7 @@ def test_normalize_query(query_handler, neuroblastoma, mafd2):
     response = query_handler.normalize("Neuroblastoma")
     assert response.match_type == MatchType.LABEL
     assert response.warnings is None
-    compare_vod(response, neuroblastoma)
+    compare_disease(response, neuroblastoma)
     assert len(response.source_meta_) == 4
     assert SourceName.NCIT in response.source_meta_
     assert SourceName.DO in response.source_meta_
@@ -263,7 +263,7 @@ def test_normalize_query(query_handler, neuroblastoma, mafd2):
     response = query_handler.normalize("MAFD2")
     assert response.match_type == MatchType.ALIAS
     assert response.warnings is None
-    compare_vod(response, mafd2)
+    compare_disease(response, mafd2)
     assert len(response.source_meta_) == 2
     assert SourceName.MONDO in response.source_meta_
 
@@ -273,19 +273,19 @@ def test_normalize_non_mondo(query_handler, skin_myo, neuroblastoma):
     response = query_handler.normalize("Skin Myoepithelioma")
     assert response.match_type == MatchType.LABEL
     assert len(response.source_meta_) == 1
-    compare_vod(response, skin_myo)
+    compare_disease(response, skin_myo)
     assert SourceName.NCIT in response.source_meta_
 
     response = query_handler.normalize("Cutaneous Myoepithelioma")
     assert response.match_type == MatchType.ALIAS
     assert len(response.source_meta_) == 1
-    compare_vod(response, skin_myo)
+    compare_disease(response, skin_myo)
     assert SourceName.NCIT in response.source_meta_
 
     response = query_handler.normalize("orphanet:635")
     assert response.match_type == MatchType.XREF
     assert len(response.source_meta_) == 4
-    compare_vod(response, neuroblastoma)
+    compare_disease(response, neuroblastoma)
     assert SourceName.NCIT in response.source_meta_
     assert SourceName.DO in response.source_meta_
     assert SourceName.MONDO in response.source_meta_