OpenCGA benchmark is a rich test suite to benchmark different storage engine currently supported with OpenCGA for variant storage.
Execution Mode
Benchmark supports the following execution mode :
- Fixed
- Random
Fixed Mode
Its a fixed set of queries written in a YML file, benchmark will take each query (default) or a selection of queries passed as IDs arguments in --query, -q option and execute these as a certain number of users (-c, - -concurrency) for a specific number of time (-r, - - repetition). Common parameters to each query are placed in baseQuery. A sample of fixedQuery is displayed below:
FixedQueries.yml
---
baseQuery :
summary : true
queries :
- id : "RegionAndBiotype"
description : "Purpose of this query"
query :
region : "22:16052853-16054112"
gene : "BRCA2"
biotype : "coding"
populationFrequencyMaf : "1kG_phase3:ALL>0.1"
tolerationThreshold : 300
- id : "Region"
description : "Purpose of this query"
query :
region : "22:16052853-16054112"
tolerationThreshold : 400
.....
sessionIds :
- "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJ0ZXN0IiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTU0MzQwMTU5OCwiZXhwIjozNzU0MzQwMTU5OH0.c0HSb8j9dfB6nzoq3OYZqYmU1sSoRAzN5C-5miJ6UzY"
- "eyJhbGciOiJIUzI1NiJ9.eyJzdWIiOiJ0ZXN0IiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTU0MzQwMTU5OCwiZXhwIjozNzU0MzQwMTU5OH0.c0HSb8j9dfB6nzoq3OYZqYmU1sSoRAzN5C-5miJ6UzY"
Benchmark Query
opencga-storage-admin.sh benchmark variant --concurrency 10 --num-repetition 5 --mode FIXED --connector REST
Complete set of options and default settings are listed in help :
Connection Type
Storage Engine
The following Storage engines are currently supported with OpenGCA :
- Mongo
- HBase