'enrichment' endpoint

enrichment.js

// const request = require('request');
// const Promise = require('promise-simple');
// const csv = require('csvtojson');
// const fs = require('fs');
// const _ = require('lodash');
const enrichment = function (query) {

  var promise = new Promise(function(resolve, reject) {
    // do a thing, possibly async, then…
  
    if (query) {
      resolve("Stuff worked!");
    }
    else {
      reject(Error("It broke"));
    }
  });

  return promise;

  // var formData = {
  //   "output": "mini",
  //   "organism": "hsapiens",
  //   "significant": "1",
  //   "sort_by_structure": "1",
  //   "ordered_query": "0",
  //   "as_ranges": "0",
  //   "no_iea": "1",
  //   "underrep": "0",
  //   "hierfiltering": "none",
  //   "user_thr": "1",
  //   "min_set_size": "5",
  //   "max_set_size": "200",
  //   "threshold_algo": "fdr",
  //   "domain_size_type": "annotated",
  //   "custbg_cb": "none",
  //   "sf_GO:BP": "1",
  //   "query": query
  // };
  // const d = Promise.defer();
  // request.post({ url: "http://biit.cs.ut.ee/gprofiler/", formData: formData }, function optionalCallback(err, httpResponse, body) {
  //   if (err) {
  //     d.reject(err);
  //   }

  //   // remove the second line
  //   const lines = body.split('\n');
  //   lines.slice(0, 1);
  //   const str1 = body.split('\n').slice(0, 1).join("\n");
  //   let str2 = body.split('\n').slice(2).join("\n"); // concatenate at last

  //   // remove lines starting with #
  //   const str3 = str2.replace(/^#.*$/mg, "");
  //   const str4 = (str1 + '\n').concat(str3);
  //   fs.writeFileSync("outputFile", str4);

  //   // convert csv to json, extract "term id"
  //   let collection = [];
  //   let ret = [];
  //   csv({ delimiter: "\t" })
  //     .fromFile("outputFile")
  //     .on('json', (jsonObj) => {
  //       collection.push(jsonObj);
  //     })
  //     .on('done', (error) => {
  //       _.forEach(collection, function (elem) {
  //         ret.push(elem["term ID"]);
  //       });
  //       d.resolve(ret);
  //     });
  // });
  // return d;
};

module.exports = enrichment;

index.js

const enrichment = require('./enrichment');

module.exports = { enrichment};

rest.js

//Import Depedencies
const express = require('express');
const router = express.Router();

const controller = require('./controller');
const config = require('../../config');

const {validate, proceed } = require('../gene-query');

const enrichment = require("../enrichment");


const isAuthenticated = token => {
  return config.MASTER_PASSWORD != '' && config.MASTER_PASSWORD === token;
};
const errorMsg = {
  error: 'Invalid access token'
};

// Expose a rest endpoint for controller.submitLayout
router.post('/submit-layout', function (req, res) {
  if (isAuthenticated(req.body.token)) {
    controller.submitLayout(req.body.uri, req.body.version, req.body.layout, req.body.user)
      .then((package) => {
        res.json(package);
      });
  } else {
    res.json(errorMsg);
  }
});

// Expose a rest endpoint for controller.submitGraph
router.post('/submit-graph', function (req, res) {
  if (isAuthenticated(req.body.token)) {
    controller.submitGraph(req.body.uri, req.body.version, req.body.graph)
    .then((package) => {
      res.json(package);
    });
  } else {
    res.json(errorMsg);
  }
});

// Expose a rest endpoint for controller.submitDiff
router.post('/submit-diff', function (req, res) {
  if (isAuthenticated(req.body.token)) {
    controller.submitDiff(req.body.uri, req.body.version, req.body.diff, req.body.user)
      .then((package) => {
        res.json(package);
      });
  } else {
    res.json(errorMsg);
  }
});

// Expose a rest endpoint for controller.getGraphAndLayout
router.get('/get-graph-and-layout', function (req, res) {
  controller.getGraphAndLayout(req.query.uri, req.query.version).then((package) => {
    res.json(package);
  });
});

// expose a rest endpoint for validator
router.get('/gene-query/', (req, res) => {
  const genes = req.query.gene;
  console.log("endpoint genes are: "+genes);

  const geneTokens = validate(genes);
  const results = proceed(geneTokens);

  res.json(results);
});

//expose a rest endpoint for enrichment
router.get('/enrichment/', (req, res) => {
  const genes = req.query.gene;
  console.log("endpoint genes are: "+genes);

  console.log(enrichment.enrichment);
  enrichment.enrichment(genes).then(function(results) {
    // res.json(results);
    res.send(results);
  });
});

// Expose a rest endpoint for controller.endSession
router.get('/disconnect', function (req, res) {
  controller.endSession(req.query.uri, req.query.version, req.query.user)
    .then((package) => {
      res.json(package);
    });
});

module.exports = router;