Pathway Commons JS Library

Description

This library is an interface for accessing the Pathway Commons web API, which is designed to make Pathway Commons easier to work with. In addition, it contains useful optimisations to improve efficiency, and various tools which may be useful when working with Pathway Commons data.

The library makes use of promises in order to keep the API clean. Therefore, if you must support browsers which do not natively support promises, please include a polyfill in your project.

We also have a Pathway Commons (cPath2) java client library.

Getting Started

This library can be included directly using a script tag, or it can be imported using several methods. This library is available on NPM.

CommonJS:

var pathwayCommons = require('pathway-commons');

ES6 Imports:

// The entire library can be imported
import pathwayCommons from 'pathway-commons';
// Or only the necessary functions
import {utilities, search} from 'pathway-commons';

Setting a username

We request that our users set a username (or app name), which allows us to analyse how and what kind of different clients use the Pathway Commons web services. If no username is set, then the default username (ID) will be used.

Usage Example

var pathwayCommons = require('pathway-commons'); // Import library

pathwayCommons.utilities.user('my-demo-app'); // Set your user/app name

pathwayCommons.search() // Initialise a new Pathway Commons search request
  .q("insulin") // Set the q parameter
  .datasource(["inoh", "reactome"]) // filter by data source
  .type("pathway") // filter by BioPAX class (includes sub-classes)
  .organism("homo sapiens") // filter by orgamism (currently, Pathway Commons aims to integrate human data only)
  .format("json") // Set the output format
  .fetch() // Send the request to the Pathway Commons service
  .then((obj) => { // Receive the response asynchronously
    console.log(obj);
  });

pathwayCommons.search() // Or use an object containing all request parameters
  .query({
    q: "insulin",
    datasource: [
      "inoh",
      "reactome"
    ],
    type: "pathway",
    organism: "homo sapiens"
  })
  .format("json")
  .fetch()
  .then((obj) => {
    console.log(obj);
  });

See unit tests or documentation for more examples on how the library can be used.

Build

Required Software

• Node.js >=4.0.0. In order to support earlier versions, compile for node and add polyfills for missing features (etc. Promises).

Configuration

The following environment variables can be used to configure the server:

• NODE_ENV : the environment mode, either production or development (default)
• PORT : the port on which the server runs (default 3000)
• PC_URL : Pathway Commons web service endpoint URL (defautl is http://www.pathwaycommons.org/pc2/)

Run targets

• npm run build : build project
• npm run build-prod : build the project for production
• npm run clean : clean the project
• npm run watch : watch mode (debug mode enabled, auto rebuild, livereload)
• npm test : run tests
• npm run lint : lint the project
• npm run docs : Generate documentation and place resulting HTML files in the docs folder

Testing

All files /test will be run by Mocha. You can npm test to run all tests, or you can run mocha -g specific-test-name (prerequisite: npm install -g mocha) to run specific tests.

Chai is included to make the tests easier to read and write.