.then(function (myRemoteItemData) {
if ((myRemoteItemData.error &&
myRemoteItemData.statusCode === 200) ||
myRemoteItemData.statusCode === 404) {
console.log(myRemoteItemData.statusCode, 'adding to post queue', localItem.name);
//if the doesn't exist post for first time
queues.postQueue.push(localItemPackage);
} else if (!myRemoteItemData.error && myRemoteItemData.statusCode === 200) {
//so we should compare for deference before putting
console.log('Get Successful.. 200, comparing', localItem.name);
var remoteItemPackage = jxon.stringToJs(_.unescape(myRemoteItemData.body));
var putPackage = getDifferences(localItemPackage, remoteItemPackage);
if (putPackage) {
queues.putQueue.push(putPackage);
}
} else if (myRemoteItemData.statusCode === 302) {
console.log('Get.. 302 ', myRemoteItemData.body);
} else {
console.log('get default', myRemoteItemData.statusCode, localItem.name);
//console.log('got data, ', jxon.stringToJs(_.unescape(myRemoteItemData.body)));
}
}).fail(function (e) {
.then(function(r) {
output(r);
if (r.error) {
throw new Error('Rest API Error: ' + r.statusInfo);
}
var body = jxon.stringToJs(_.unescape(r.body)).import;
if (body.level === 'ERROR') throw new Error(body.message);
name = model.getName() + ' v' + model.getProperty('version');
ok(r, name);
});
fs.readFile(xmlFileName, 'utf8', function (err, xmlData) {
if (!err) {
console.log('\n\n\n\jxon Test - XML ==> JSON');
console.log('\n\n\n\XML');
console.log(xmlData);
var output = jxon.stringToJs(xmlData);
console.log('\n\n\n\Transformed JSON');
console.log(JSON.stringify(output));
}
done();
});
getFiles(_cliOpts.search || path.join(process.cwd(), '*.xml')).forEach(function (item) {
aJXON.push(jxon.stringToJs(item));
});
ncbi_engine.register('success', function(resp, man){
var xml = resp.raw();
//console.log(xml);
var jx = null;
if( typeof xml === 'string' ){
jx = jxon.stringToJs(xml);
}else{
jx = jxon.xmlToJs(xml);
}
console.log(jx);
// Our operating object.
if( ! jx.PubmedArticleSet.PubmedArticle ){
UnableToMakeContact('<b>No such PubMed ID</b>.');
}else if( ! jx.PubmedArticleSet.PubmedArticle.MedlineCitation.Article ){
UnableToMakeContact('<b>No such Article</b>.');
}else{
var op = jx.PubmedArticleSet.PubmedArticle.MedlineCitation.Article;
// Title.
var title = 'n/a';
if( op.ArticleTitle ){
title = op.ArticleTitle;
}
// Date.
var date = 'n/a';
if( op.ArticleDate ){
var year = op.ArticleDate.Year || '???';
var month = op.ArticleDate.Month || '???';
var day = op.ArticleDate.Day || '???';
date = [year, month, day].join('-');
}
// Authors.
var authors = 'n/a';
if( op.AuthorList && op.AuthorList.Author ){
var acache = [];
us.each(op.AuthorList.Author, function(auth){
var name = '';
if( auth.ForeName ){ name += auth.ForeName; }
//if( auth.Initials ){ name+=' '+auth.Initials+'.'; }
if( auth.LastName ){ name +=' '+auth.LastName; }
acache.push(name);
});
if( ! us.isEmpty(acache) ){
authors = acache.join(', ');
}
}
// Abstract; list or string.
var abstract = 'n/a';
if( op.Abstract && op.Abstract.AbstractText ){
if( us.isArray(op.Abstract.AbstractText) ){
var abscache = [];
us.each(op.Abstract.AbstractText, function(abs){
if( abs._ ){ abscache.push(abs._); }
});
if( ! us.isEmpty(abscache) ){
abstract = abscache.join('<br />');
}
}else if( us.isString(op.Abstract.AbstractText) ){
abstract = op.Abstract.AbstractText;
}
}
// Render.
jQuery('#info-area').empty();
var info = [
'<dl class="dl-horizontal amigo-detail-info">',
// Title.
'<dt>Title</dt>',
'<dd>',
title,
'</dd>',
// Date.
'<dt>Date</dt>',
'<dd>',
date,
'</dd>',
// Author.
'<dt>Author(s)</dt>',
'<dd>',
authors,
'</dd>',
// Abstract.
'<dt>Abstract</dt>',
'<dd id="abstract">',
abstract,
'</dd>',
// // Related.
// '<dt id="prob_related" class="hidden">Related</dt>',
// '<dd id="prob_ann" class="hidden">',
// '<a id="prob_ann_href" href="#" class="btn btn-primary btn-xs">Link</a> to all direct and indirect <strong>annotations</strong> to ' + global_acc + '.',
// '</dd>',
// '<dd id="prob_ann_dl" class="hidden">',
// '<a id="prob_ann_dl_href" href="#" class="btn btn-primary btn-xs">Link</a> to all direct and indirect <strong>annotations download</strong> (limited to first 10,000) for ' + global_acc + '.',
// '</dd>',
// Pubmed.
'<dt>PubMed</dt>',
'<dd>',
'<a href="https://www.ncbi.nlm.nih.gov/pubmed/' + bbop.first_split(':', global_acc)[1] + '">' + global_acc + '</a>',
'</dd>',
// // Feedback.
// '<dt>Feedback</dt>',
// '<dd>',
// 'Contact the <a href="http://geneontology.org/form/contact-go" title="GO Helpdesk.">GO Helpdesk</a> if you find mistakes or have concerns about the data you find here.',
// '</dd>',
'</dl>'
];
jQuery('#info-area').append(info.join(' '));
_shrink_wrap('abstract');
// Powered by NCBI.
jQuery('#info-area').append([
'<p>',
'Powered by NCBI\'s <a href="https://eutils.ncbi.nlm.nih.gov">E-utilities</a>.',
'<br />',
'Please read NCBI\'s <a href="https://www.ncbi.nlm.nih.gov/home/about/policies.shtml">Disclaimer and Copyright notice.',
'</p>',
].join(' '));
// Get feedback from viewers.
jQuery('#info-area').append([
'<p>',
'<span class="glyphicon glyphicon-pencil"></span><b>Are you the author</b> (or have a deep understanding) of this paper? If so, <b>do these annotations look okay to you</b>? <a href="http://geneontology.org/form/contact-go">Let us know</a>!',
'</p>'
].join(' '));
// Start the normal GOlr services.
ReferenceDetailsInit();
}
});