pcServices.js

let fetch = require('node-fetch');
const got = require('got');


//Traverse Options
const traverseOptions = {
  method: 'GET',
  headers: {
    'Host' : 'www.pathwaycommons.org',
    'Content-Type': 'application/json',
    'Accept': 'application/json'
  }
};

//Traverse Options
const getOptions = {
  method: 'GET',
  headers: {
    'Content-Type': 'text',
  }
};

//Returns the request file from pathway commons
//Requires uri and format to be valid xml files
function getPC2(uri, format) {
  //Construct query url
  uri = encodeURIComponent(uri);
  let url = 'https://www.pathwaycommons.org/pc2/get?format=' + format + '&uri=' + uri + '&user=pathwaycommons-js-lib%3Apathways-search';
  return fetch(url, getOptions).then(response => response.text());
}

//Queries PC2 using traverse
//Returns metadata for the pathway
//Requires a valid query and uri
function traversePC2(uri, path) {
  //Construct query url
  uri = encodeURIComponent(uri);
  path = encodeURIComponent(path);
  let url = 'https://www.pathwaycommons.org/pc2/traverse?format=json&uri=' + uri + '&path=' + path + '&user=pathwaycommons-js-lib%3Apathways-search';
  let retries = 10; 

  //Use Got instead of fetch due to known issue with fetch  which causes socket hangups
  return got(url, { json: true, retries: retries }).then(response => {
    return response.body;
  }).catch(error => {
    console.log(error);
  });
}

//Generate URL for getting data
function getURL(uri, format) {
  uri = encodeURIComponent(uri);
  let url = 'https://www.pathwaycommons.org/pc2/get?format=' + format + '&uri=' + uri + '&user=pathwaycommons-js-lib%3Apathways-search';
  return url;
}

//Generate URL for a traverse query
function traverseURL(uri, path) {
  uri = encodeURIComponent(uri);
  let url = 'https://www.pathwaycommons.org/pc2/traverse?format=json&uri=' + uri + '&path=' + path;
  return url;
}

//Export Functions
module.exports = {
  getPC2,
  traversePC2,
  getURL,
  traverseURL,
}