Merge branch 'dev' of https://github.com/BioData-PT/beacon2-ri-api in…

…to dev
BioData-PT · Jun 11, 2024 · b6a14f7 · b6a14f7
2 parents 6728a3f + 8112b99
commit b6a14f7
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/beacon/reindex.py b/beacon/reindex.py
@@ -24,6 +24,9 @@
 client.beacon.individuals.create_index([("$**", "text")])
 client.beacon.runs.create_index([("$**", "text")])
 
+# uncomment this if you want to test the performance of text index
+#print("Ending reindex early!") and exit
+
 # custom indexes
 client.beacon.genomicVariations.create_index([
         ("_info.datasetId", ASCENDING),

diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -31,9 +31,6 @@ services:
     container_name: beacon-training-ui    
     ports:
       - 9500:8080
-    environment:
-      USERNAME: root
-      PASSWORD: ${DB_PASSWD}
     networks:
       - beacon-priv
 

diff --git a/performance-tests/genomic_variants.mongosh b/performance-tests/genomic_variants.mongosh
@@ -0,0 +1,7 @@
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '1'}}, {'_position.start': {'$gte': [69000]}}, {'_position.start': {'$lte': [70000]}}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '2'}}, {'_position.start': 218860}, {'variation.referenceBases': 'G'}, {'variation.alternateBases': 'GT'}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '5'}}, {'_position.start': 692914}, {'variation.referenceBases': 'A'}, {'variation.alternateBases': 'G'}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '20'}}, {'_position.start': 63694303}, {'variation.referenceBases': 'G'}, {'variation.alternateBases': 'GC'}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '1'}}, {'_position.start': {'$gte': [69000]}}, {'_position.start': {'$lte': [70000]}}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '7'}}, {'_position.start': {'$gte': [6000000]}}, {'_position.start': {'$lte': [11000000]}}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')
+db.genomicVariations.find({'$and': [{'_position.refseqId': {'$eq': '19'}}, {'_position.start': {'$gte': [15000000]}}, {'_position.start': {'$lte': [35000000]}}, {'_info.datasetId': {'$eq': 'nature_colorectal_cancer_test'}}]}).explain('executionStats')