GeneNetwork3 REST API

Table of Contents

• Introduction
• Install
• Test
• Run

Introduction

At this point GeneNetwork3 (GN3) is a REST API that provides extra end points in addition to the ones in GN2. The main distinction is that GN3 is written in Racket and GN2 in Python ;).

At this point the API caches remote queries (for example to wikidata). To empty the cache simply restart the server.

Enjoy,

Pjotr Prins

Deploy

For GN3 run

alias guix=~/opt/guix/bin/guix
source .guix-deploy
raco pkg install https://github.com/dmac/spin.git
raco pkg install https://github.com/BourgondAries/memo.git
racket rest-api/rest-api.rkt

Test output

curl http://localhost:8000/gene/aliases/BRCA2

Install

Install racket, e.g.

guix package -i racket emacs-racket-mode

Make sure to set the correct GUIX profile where Racket was installed, e.g.

. ~/.guix-profile/etc/profile

or

. ~/opt/racket/etc/profile

(note the leading dot)

Dependencies

raco pkg install https://github.com/dmac/spin.git
raco pkg install https://github.com/BourgondAries/memo.git

Test

Run the tests with

racket test/wikidata-test.rkt

Run

Run the server

racket rest-api/rest-api.rkt

Test output

curl http://localhost:8000/gene/aliases/BRCA2
{ "BRCA2" : [ "BRCC2", "BROVCA2", ... ] }

Web service

The current webservice is running on

curl http://gn2.genenetwork.org/gn3/gene/aliases2/Shh,Brca2