index for caseLevelData

EGA-archive · Nov 13, 2024 · 29c29a5 · 29c29a5
1 parent 67d872c
commit 29c29a5
Show file tree

Hide file tree

Showing 3 changed files with 493 additions and 1 deletion.
diff --git a/beacon/connections/mongo/reindex.py b/beacon/connections/mongo/reindex.py
@@ -71,6 +71,7 @@
 client.beacon.genomicVariations.create_index([("identifiers.genomicHGVSId", 1)])
 #client.beacon.genomicVariations.create_index([("datasetId", 1), ("variation.location.interval.start.value", 1), ("variation.referenceBases", 1), ("variation.alternateBases", 1)])
 client.beacon.genomicVariations.create_index([("molecularAttributes.geneIds", 1), ("variation.variantType", 1)])
+client.beacon.caseLevelData.create_index([("id", 1), ("datasetId", 1)])
 #client.beacon.individuals.create_index([("$**", "text")])
 #client.beacon.runs.create_index([("$**", "text")])
 #collection_name = client.beacon.analyses

diff --git a/beacon/connections/mongo/utils.py b/beacon/connections/mongo/utils.py
@@ -114,7 +114,6 @@ def get_docs_by_response_type(self, include: str, query: dict, dataset: str, lim
         queryid={}
         queryid['datasetId']=dataset
         query_count["$or"].append(queryid)
-        LOG.debug(query_count)
         if query_count["$or"]!=[]:
             dataset_count = get_count(self, mongo_collection, query_count)
             if dataset_count == 0: