r-geno-tools-api

This is a REST api wrapper around "r-geno-tools-engine". For more detailed documentation, please check r-geno-tools-engine's readme.

API documentation

To generate the openapi.json file one can run in R:

source("r-geno-tools-api.R")
spec <- utils::modifyList(list(servers = list(list(url = ""))),
                               genoApi$getApiSpec())
writeLines(jsonlite::toJSON(spec,
                            complex = "list",
                            auto_unbox = TRUE,
                            pretty = T,
                            digits = NA,
                            na = 'string'),
                            con = "openapi.json")

Build and deploy

To this project use docker to build and deploy the API.

Build

To build an image of the api, one can just run this command in the app folder:

docker build -t utbiomet/rgenotoolapi ./

Deploy

docker push utbiomet/rgenotoolapi:latest

Debug

docker run -d --rm --name rgenotoolapi -p 8080:8080 utbiomet/rgenotoolapi

docker exec -u 0 -it rgenotoolapi bash

Tests

To test the API, first launch a local instance of the API on port 8181. This can be done through several ways, for example in R run:

source('r-geno-tools-api.R');
genoApi$run(port = 8080, host = '0.0.0.0')

Or you can run the Docker container (mapping the API on the port 8181):

docker run -d --rm --name rgenotoolapi -p 8080:8080 utbiomet/rgenotoolapi

Then run the script tests/testthat.R:

Rscript tests/testthat.R

For manually testing, you can use these urls when the api is running in docker:

file:///r-geno-tools-api/r-geno-tools-engine/data/results/gwasResult.json
file:///r-geno-tools-api/r-geno-tools-engine/data/geno/testMarkerData01.vcf.gz
file:///r-geno-tools-api/r-geno-tools-engine/data/pheno/testPhenoData01.csv
file:///r-geno-tools-api/r-geno-tools-engine/data/pedigree/testPedData_char.csv

For trait this one is in the pheno file: Flowering.time.at.Arkansas