ldpm-pubmed/test/test-oapmc.js

pubmed as package.jsonld

var path = require('path')
  , util = require('util')
  , tar = require('tar')
  , zlib = require('zlib')
  , assert = require('assert')
  , fs = require('fs')
  , temp = require('temp')
  , Ldpm = require('ldpm')
  , DOMParser = require('xmldom').DOMParser
  , oapmc = require('../lib/oapmc');

temp.track();

var root = path.join(path.dirname(__filename), 'fixtures', 'oapmc');

var conf = {
  protocol: 'http',
  port: 3000,
  hostname: 'localhost',
  strictSSL: false,
  sha:true,
  name: "user_a",
  email: "user@domain.com",
  password: "user_a"
};

function getPkg(pmcid, pmid, callback){
  if(arguments.length === 2){
    callback = pmid;
    pmid = undefined;
  }

  temp.mkdir('__tests', function(err, dirPath) {
    if(err) throw err;
    var ldpm = new Ldpm(conf, dirPath);
    
    var tgzStream = fs.createReadStream(path.join(root, pmcid.toLowerCase() + '.tar.gz'))
      .pipe(zlib.Unzip())
      .pipe(tar.Extract({ path: dirPath, strip: 1 }));
    
    tgzStream.on('end', function() {
      oapmc._pkg(pmcid, ldpm, dirPath, {pmid: pmid}, callback);
    });
  });
};

describe('pubmed central', function(){

  this.timeout(4000);

  describe('metadata', function(){

    //http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:2924383&metadataPrefix=pmc
    it('should create a package.jsonld for a ms with a movie zipped and not treat it as a code bundle', function(done){
      getPkg('PMC2924383', function(err, pkg){
        if(err) throw err;
        //fs.writeFileSync(path.join(root, 'pmc2924383.json'), JSON.stringify(pkg, null, 2));
        fs.readFile(path.join(root, 'pmc2924383.json'), function(err, expected){
          if(err) throw err;
          assert.deepEqual(JSON.parse(JSON.stringify(pkg)), JSON.parse(expected)); //JSON.parse(JSON.stringify) so that NaN are taken into account...
          done();
        });
      });
    });

    //http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:2958805&metadataPrefix=pmc
    it('should create a package.jsonld for a ms with a lot of inline formulaes AND add pubmed annotation', function(done){
      getPkg('PMC2958805', 2958805, function(err, pkg){
        if(err) throw err;
        //fs.writeFileSync(path.join(root, 'pmc2958805.json'), JSON.stringify(pkg, null, 2));
        fs.readFile(path.join(root, 'pmc2958805.json'), function(err, expected){
          if(err) throw err;
          assert.deepEqual(JSON.parse(JSON.stringify(pkg)), JSON.parse(expected)); //JSON.parse(JSON.stringify) so that NaN are taken into account...
          done();
        });
      });
    });

    //http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:3532326&metadataPrefix=pmc
    it('should create a package.jsonld for a ms with a codeBundle and an HTML table with footnotes', function(done){
      getPkg('PMC3532326', function(err, pkg){
        if(err) throw err;      
        //fs.writeFileSync(path.join(root, 'pmc3532326.json'), JSON.stringify(pkg, null, 2));
        fs.readFile(path.join(root, 'pmc3532326.json'), function(err, expected){
          if(err) throw err;
          pkg = JSON.parse(JSON.stringify(pkg));
          var expected = JSON.parse(expected);
          delete pkg.sourceCode[0].targetProduct[0].filePath;
          delete expected.sourceCode[0].targetProduct[0].filePath;
          assert.deepEqual(pkg, expected);
          done();
        });
      });
    });

  });

  describe('html body', function(){  
    it('should parse body', function(done){
      getPkg('PMC3532326', function(err, pkg, files, inlines, $doc){
        oapmc._html(pkg, files, inlines, $doc, function(err, html){
          if(err) throw err;          
          //          var $HOME = process.env.HOME || process.env.HOMEPATH || process.env.USERPROFILE;
          //          fs.writeFileSync(path.join($HOME, 'Desktop/pm.html'), html, {encoding: 'utf8'});
          //          console.log(html);
          done();
        });
      });      
    });
  });

});