ldpm-pubmed/index.js

pubmed as package.jsonld

var url = require('url')
  , request = require('request')
  , pubmed = require('./lib/pubmed').pubmed
  , oapmc = require('./lib/oapmc').oapmc
  , jats = require('./lib/jats');

/**
 * 'this' is an Ldpm instance
 */
function convert(id, opts, callback){

  var that = this;

  if(arguments.length === 2){
    callback = opts;
    opts = {};
  }

  var uri = "http://www.pubmedcentral.nih.gov/utils/idconv/v1.0/?ids=" + id + '&format=json';
  that.logHttp('GET', uri);
  request(uri,function(error, response, body){
    if(error) return callback(error);
    that.logHttp(response.statusCode, uri);
    
    if(response.statusCode >= 400){
      var err = new Error(body);
      err.code = response.statusCode;
      return callback(err);
    }

    //if error pubmedcentral display a webpage with 200 return code :( so we are cautious...
    try{
      body = JSON.parse(body);
    } catch(e){
      return callback(new Error(url.parse(uri).hostname + ' did not returned valid JSON'));
    }

    if(body.records && body.records.length){
      var pmcid = body.records[0].pmcid;
      var pmid = body.records[0].pmid;
      var doi = body.records[0].doi;
      if (pmcid){
        oapmc.call(that, pmcid, { pmid: pmid, doi: doi }, callback); //passing a pmid (if not undefined => add pubmed annotation)
      } else if(pmid){
        pubmed.call(that, pmid, opts, callback);
      } else {
        callback(new Error('the id cannot be recognized'));      
      }
    } else {
      callback(new Error('the id cannot be recognized'));      
    }
  });

};

exports.convert = convert;
exports.jats = jats;