merge from main

cancervariants · Apr 13, 2021 · 4632d9c · 4632d9c
2 parents 4c347be + b9e023b
commit 4632d9c
Show file tree

Hide file tree

Showing 3 changed files with 26 additions and 12 deletions.
diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py
@@ -44,7 +44,7 @@ def phenobarbital():
         "type": "TherapyDescriptor",
         "value": {
             "type": "Therapy",
-            "therapy_id": "rxcui:8134"
+            "id": "rxcui:8134"
         },
         "label": "Phenobarbital",
         "xrefs": [
@@ -127,7 +127,7 @@ def cisplatin():
         "type": "TherapyDescriptor",
         "value": {
             "type": "Therapy",
-            "therapy_id": "rxcui:2555",
+            "id": "rxcui:2555",
         },
         "label": "cisplatin",
         "xrefs": [
@@ -195,7 +195,7 @@ def spiramycin():
         "type": "TherapyDescriptor",
         "value": {
             "type": "Therapy",
-            "therapy_id": "ncit:C839"
+            "id": "ncit:C839"
         },
         "label": "Spiramycin",
         "xrefs": [
@@ -231,7 +231,7 @@ def timolol():
         "type": "TherapyDescriptor",
         "value": {
             "type": "Therapy",
-            "therapy_id": "rxcui:10600"
+            "id": "rxcui:10600"
         },
         "label": "timolol",
         "alternate_labels": [
@@ -506,6 +506,20 @@ def test_query_merged(merge_query_handler, phenobarbital, cisplatin,
     assert 'record' not in response
     assert response['match_type'] == MatchType.NO_MATCH
 
+    test_query = "APRD00818"
+    response = merge_query_handler.search_groups(test_query)
+    assert response['query'] == test_query
+    assert response['warnings'] is None
+    assert 'record' not in response
+    assert response['match_type'] == MatchType.NO_MATCH
+
+    test_query = "chembl:CHEMBL1200368"
+    response = merge_query_handler.search_groups(test_query)
+    assert response['query'] == test_query
+    assert response['warnings'] is None
+    assert 'record' not in response
+    assert response['match_type'] == MatchType.NO_MATCH
+
 
 def test_merged_meta(merge_query_handler):
     """Test population of source and resource metadata in merged querying."""

diff --git a/therapy/query.py b/therapy/query.py
@@ -334,7 +334,7 @@ def _add_merged_meta(self, response: Dict) -> Dict:
         """
         sources_meta = {}
         vod = response['value_object_descriptor']
-        ids = [vod['value']['therapy_id']] + vod.get('xrefs', [])
+        ids = [vod['value']['id']] + vod.get('xrefs', [])
         for concept_id in ids:
             prefix = concept_id.split(':')[0]
             src_name = PREFIX_LOOKUP[prefix.lower()]
@@ -375,7 +375,7 @@ def _add_vod(self, response: Dict, record: Dict, query: str,
             'type': 'TherapyDescriptor',
             'value': {
                 'type': 'Therapy',
-                'therapy_id': record['concept_id']
+                'id': record['concept_id']
             },
             'label': record['label'],
             'extensions': [],
@@ -447,7 +447,7 @@ def search_groups(self, query: str) -> Dict:
 
         # check concept ID match
         record = self.db.get_record_by_id(query_str, case_sensitive=False)
-        if record:
+        if record and record['src_name'].lower() not in PROHIBITED_SOURCES:
             merge = self.db.get_record_by_id(record['merge_ref'],
                                              case_sensitive=False,
                                              merge=True)
@@ -462,10 +462,10 @@ def search_groups(self, query: str) -> Dict:
         for match_type in ['label', 'trade_name', 'alias', 'other_id']:
             # get matches list for match tier
             matching_refs = self.db.get_records_by_type(query_str, match_type)
-            matching_records = [self.db.get_record_by_id(m['concept_id'],
-                                                         False)
-                                for m in matching_refs
-                                if m['src_name'] not in PROHIBITED_SOURCES]
+            matching_records = \
+                [self.db.get_record_by_id(m['concept_id'], False)
+                 for m in matching_refs
+                 if m['src_name'].lower() not in PROHIBITED_SOURCES]
             matching_records.sort(key=self._record_order)
 
             # attempt merge ref resolution until successful

diff --git a/therapy/schemas.py b/therapy/schemas.py
@@ -397,7 +397,7 @@ def schema_extra(schema: Dict[str, Any],
                     "type": "TherapyDescriptor",
                     "value": {
                         "type": "Therapy",
-                        "therapy_id": "rxcui:2555"
+                        "id": "rxcui:2555"
                     },
                     "label": "cisplatin",
                     "xrefs": [