ga4gh-rxjs

Client for Ga4gh APIs in javascript, with Rx

ga4gh-rxjs is a client library for the Ga4gh APIs in javascript, using rxjs.

Ga4gh APIs are methods for exchanging genomic and clinical data. Rx is a library for taming asynchronous code.

Methods

Ga4gh method references are here.

ga4gh-rxjs exports each ga4gh method as a property. Each exported method takes two parameters: the url of the ga4gh server, and a javascript object with the properties of the query. For example,

// url: string
// params: GASearchVariantSetsRequest || undefined
// returns: Observable<GASearchVariantSetsResponse>

ga4gh.variantSets(url, params)

If no parameters are required, params can be omitted.

Example usage

ga4gh.variantSets(url).subscribe(d => console.log('One page of variantSets', d));

Paging

The Ga4gh APIs are paged. To control the page size, include pageSize in the param object, as per the ga4gh docs.

Available ga4gh methods are

ga4gh.variantSets
ga4gh.variants
ga4gh.referenceSets
ga4gh.references
ga4gh.reads
ga4gh.readGroupSets
ga4gh.callSets

Walking all pages

Additionally, utility methods are provided to accumulate all pages of the query results. These methods are under the property all, and return the concatenated data properties from the results (i.e. the page tokens are dropped).

ga4gh.all.variantSets(url).subscribe(d => console.log('All rows of variantSets', d));

Demo

A few queries demonstrated here.

Source here.

Installation

The library is built as a UMD module, and so should work as a CommonJS module, AMD module, or with a <script> tag. If you have a choice, we recommend a build with npm and webpack.

webpack (and browserify?)

> npm install ga4gh-rxjs

var ga4gh = require('ga4gh-rxjs');
ga4gh.variantSets("http://foo.bar").subscribe(console.log.bind(console));

script tag

If including ga4gh-rxjs with a script tag, the methods will be exposed on the ga4gh global. You must include rx.js, rx.experimental.js, rxjs-dom.js, and underscore.js.

<script src="https://rawgit.com/reactive-extensions/rxjs/v2.5.2/dist/rx.js"></script>
<script src="https://rawgit.com/reactive-extensions/rxjs/v2.5.2/dist/rx.experimental.js"></script>
<script src="https://rawgit.com/reactive-extensions/rxjs-dom/v4.0.4/dist/rx.dom.js"></script>
<script src="https://rawgit.com/jashkenas/underscore/1.8.3/underscore.js"></script>
<script src="https://rawgit.com/acthp/ga4gh-rxjs/master/dist/ga4gh-rx.js"></script>

Lint

Use npm run lint to run the lint rules. We lint with eslint and babel-eslint.