OpenCGA Benchmark

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:

---
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"

Following command will execute ALL queries written in fixedQueries.yml file as 10 users, five times each on REST server specified in "storage-configuration.yml" :

opencga-storage-admin.sh benchmark variant --concurrency 10 --num-repetition 5 --mode FIXED --connector REST

For complete list of options, default values and explanations please use the - - help option: 

Connection Type

Storage Engine

The following Storage engines are currently supported with OpenGCA :

1. Mongo
2. HBase