...
| Code Block | ||
|---|---|---|
| ||
---
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" :
| Code Block | ||||
|---|---|---|---|---|
| ||||
opencga-storage-admin.sh benchmark variant --concurrency 10 --num-repetition 5 --mode FIXED --connector REST |
For complete Complete list of options, default values and explanations please use the can be displayed using - - help option from benchmark script : 
Random Mode
Random mode supports creation of random queries from meta data provided in "randomQueries.yml" and execute these on selected storage engine :
| Code Block | ||
|---|---|---|
| ||
---
baseQuery :
summary : true
exclude : studies
regions :
- chromosome : "1"
start : 1
end : 249250621
gene :
- DKFZP434A062
- GPSM1
ct : []
type :
- "SV"
- "CNV"
study :
- "1kG_phase3"
...
functionalScore :
- id : "cadd_raw"
min : 0
max : 1
- id : "cadd_scaled"
min : -10
max : 40
populationFrequencies :
- id : "1kG_phase3:ALL"
min : 0
max : 0.2
- id : "1kG_phase3:AFR"
min : 0
max : 0.15
proteinSubstitution :
- id : "polyphen"
min : 0.1
max : 0.9
operators : [">", "<"]
- id : "sift"
min : 0.1
max : 0.9
qual :
id : "polyphen"
min : 1
max : 9
operators : [">"]
conservation :
id : "phylop"
min : 0
max : 1
operators : ["=", "!="]
sessionIds :
- ""
- "" |
Connection Type
Storage Engine
...