fixing get_biosamples_from_variants

EGA-archive · Oct 30, 2024 · 53515a7 · 53515a7
1 parent a91b85b
commit 53515a7
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Showing 2 changed files with 1 addition and 9 deletions.
diff --git a/beacon/connections/mongo/g_variants.py b/beacon/connections/mongo/g_variants.py
@@ -77,7 +77,7 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar
     try:
         finalids=[]
         for bioid in biosample_id:
-            finalids.append({"id": bioid})
+            finalids.append({"id": bioid["biosampleId"]})
     except Exception:# pragma: no cover
         finalids=[]
     query = {"$and": [{"$or": finalids}]}

diff --git a/beacon/connections/mongo/reindex.py b/beacon/connections/mongo/reindex.py
@@ -33,14 +33,6 @@
     client.beacon.validate_collection("synonyms")
 except Exception:
     db=client.beacon.create_collection(name="synonyms")
-try:
-    client.beacon.validate_collection("caseLevelData")
-except Exception:
-    db=client.beacon.create_collection(name="caseLevelData")
-try:
-    client.beacon.validate_collection("targets")
-except Exception:
-    db=client.beacon.create_collection(name="targets")
 try:
     client.beacon.drop_collection("counts")
 except Exception: