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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, --num-repetition). Common parameters to each query are placed in baseQuery. A sample of fixedQuery is displayed below:
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| 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 :
- ""
- "" |
The following command will generate two queries one with two "ct" values and a gene value and second one with a region value provided in "randomQueries.yml" file and execute as 10 users, five times each on REST server:
| Code Block | ||
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opencga-storage-admin.sh benchmark variant --concurrency 10 --num-repetition 5 --mode RANDOM -q "ct(2),gene;region" |
Connection Type
Storage Engine
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