ldpm-pubmed
Version:
pubmed as package.jsonld
1,407 lines (1,290 loc) • 50.4 kB
JavaScript
var traverse = require('traverse')
, DOMParser = require('xmldom').DOMParser
, once = require('once')
, crypto = require('crypto')
, fs = require('fs')
, zlib = require('zlib')
, async = require('async')
, path = require('path')
, BASE = require('package-jsonld').BASE.replace('https','http')
, uuid = require('node-uuid');
exports.json2html = json2html;
exports.parseXmlNodesRec = parseXmlNodesRec;
exports.findNodePaths = findNodePaths;
exports.addPubmedAnnotations = addPubmedAnnotations;
exports.matchDOCO = matchDOCO;
exports.extractBetween = extractBetween;
exports.extractKeywords = extractKeywords;
exports.getArtInd = getArtInd;
exports.removeDiacritics = removeDiacritics;
exports.cleanText = cleanText;
function json2html(ldpm,jsonBody,pkg,opts,callback){
// Build the html article, merging information from the pkg and from the jsonBody
// generated from the xml articleBody
if(arguments.length === 4){
callback = opts;
opts = {};
}
var html = "<!doctype html>\n";
var artInd = getArtInd(pkg);
var abstract = pkg.article[artInd].abstract;
html += "<html>\n";
html += "\n<head>\n<title>\n" + pkg.article[artInd].headline + "\n</title>\n<meta charset='UTF-8'>\n";
html += "</head>\n";
html += "\n<body>\n";
html += "<article>\n";
html += "\n<h1>\n" + pkg.article[artInd].headline + "\n</h1>\n";
if(pkg.keyword){
html += '\n<section class="keywords">\n';
html += '<ul>\n';
pkg.keyword.forEach(function(k){
html += '<li>\n';
html += k + '\n';
html += '</li>\n';
})
html += '</ul>\n';
html += '</section>\n';
}
if(pkg.author){
html += '\n<section class="authors" >\n';
html += '<section class="author" >\n';
html += '<span>\n';
html += pkg.author.name + '\n';
html += '</span>\n';
if(pkg.author.email){
html += '<span>\n';
html += pkg.author.email + '\n';
html += '</span>\n';
}
if(pkg.author.affiliation){
html += '<ul>\n';
pkg.author.affiliation.forEach(function(aff){
html += '<li>\n';
html += '<span>\n';
html += aff.description + '\n';
html += '</span>\n';
html += '</li>\n';
})
html += '</ul>\n';
}
html += '</section>\n';
}
if(pkg.contributor){
pkg.contributor.forEach(function(contr){
html += '<section class="contributor">\n';
html += '<span>\n';
html += contr.name + '\n';
html += '</span>\n';
if(contr.email){
html += '<span>\n';
html += contr.email + '\n';
html += '</span>\n';
}
if(contr.affiliation){
html += '<ul>\n';
contr.affiliation.forEach(function(aff){
html += '<li>\n';
html += '<span>\n';
html += aff.description + '\n';
html += '</span>\n';
html += '</li>\n';
})
html += '</ul>\n';
}
html += '</section>\n';
})
}
html += '</section>\n\n';
if(pkg.provider){
html += '\n<section class="provider">\n';
html += '<h3>Provider</h3>\n';
html += pkg.provider.description + '\n';
html += '</section>\n';
}
if(pkg.editor){
html += '\n<section class="editors">\n';
html += '<h3>Editor</h3>\n';
pkg.editor.forEach(function(ed){
html += '<section>\n';
if(ed.name){
html += '<span>\n';
html += ed.name + '\n';
html += '</span>\n';
}
if(ed.affiliation){
html += '<ul>\n';
ed.affiliation.forEach(function(aff){
html += '<li>\n';
html += '<span>\n';
html += aff.description + '\n';
html += '</span>\n';
html += '</li>\n';
})
html += '</ul>\n';
}
html += '</section>\n';
})
html += '</section>\n'
}
if(pkg.journal){
html += '\n<section class="journal">\n';
html += '<h3>Journal</h3>';
if(pkg.journal.name){
html += '<span>\n';
html += pkg.journal.name + '\n';
html += '</span>\n';
}
if(pkg.journal.name){
html += '<span>\n';
html += pkg.journal.issn + '\n';
html += '</span>\n';
}
html += '</section>\n';
}
if(abstract !== undefined){
var id = uuid.v4();
html += '\n<section id="' + id + '" typeof="http://salt.semanticauthoring.org/ontologies/sro#Abstract">\n'; //+ '" resource="' + pkg.name + '/' + id + '">\n';
html += "<h2>Abstract</h2>";
var doc = new DOMParser().parseFromString("<sec>" + abstract + "</sec>",'text/xml');
var abs = doc.getElementsByTagName('sec')[0];
parseJsonNodesRec(ldpm,parseXmlNodesRec(abs,abstract),pkg,3, function(err,newTxt){
if(err) return callback(err);
html += newTxt;
html += "</section>\n\n";
parseJsonNodesRec(ldpm, jsonBody, pkg, 2, function(err,newTxt){
if(err) return callback(err);
html += newTxt;
if(pkg.article[artInd].citation){
html += '\n<section typeof="http://purl.org/spar/deo/BibliographicReference">\n';
html += '<h2>Bibliography</h2>\n';
html += '<ol>\n';
pkg.article[artInd].citation.forEach(function(cit,i){
html += '<li id="ref_' + parseInt(i+1,10) + '">\n';
html += cit.description;
html += '<br>\n';
if(cit.doi){
html += 'doi:' + cit.doi + '\n';
}
if(cit.pmid){
html += 'pmid:' + cit.pmid + '\n';
}
if(cit.url){
html += '<a href="' + cit.url +'">link</a>' + '\n';
}
html += '</li>\n';
});
html += '</ol>\n';
html += '</section>\n';
}
html += '\n</article>\n';
html += '</body>\n';
html += '</html>';
callback(null, html);
});
});
} else {
parseJsonNodesRec(ldpm,jsonBody,pkg,2, function(err,newTxt){
if(err) return callback(err);
if(newTxt != '<div>undefined</div>'){
html += newTxt;
} else {
html += '<div>Empty article.</div>\n';
}
if(pkg.article[artInd].citation){
html += '\n<section typeof="http://purl.org/spar/deo/BibliographicReference">\n';
html += '<h2>Bibliography</h2>\n';
html += '<ol>\n';
pkg.article[artInd].citation.forEach(function(cit,i){
html += '<li id="ref_' + parseInt(i+1,10) + '">\n';
html += cit.description;
html += '<br>\n';
if(cit.doi){
html += 'doi:' + cit.doi + '\n';
}
if(cit.pmid){
html += 'pmid:' + cit.pmid + '\n';
}
if(cit.url){
html += '<a href="' + cit.url +'">link</a>' + '\n';
}
html += '</li>\n';
});
html += '</ol>\n';
html += '</section>\n';
}
html += '\n</article>\n';
html += '</body>\n';
html += '</html>';
callback(null,html);
});
}
};
function parseXmlNodesRec(node,xml){
// recursive function that converts xml nodes into json nodes
// generic node structure: tag and children
var tmp = {
tag: node.tagName,
children: []
};
if(node.attributes != undefined){
var tag = '';
Object.keys(node.attributes).forEach(function(att){
// in some cases, the type information is not in
// tagName but in nodeValue
if(node.attributes[att].nodeValue==='image'){
tag = 'img';
}
if(node.attributes[att].nodeValue==='bibr'){
tag = 'bib-ref';
}
if(node.attributes[att].nodeValue==='fig'){
tag = 'fig-ref';
}
if(node.attributes[att].nodeValue==='sec'){
tag = 'sec-ref';
}
if(node.attributes[att].nodeValue==='table'){
tag = 'table-ref';
}
if((node.tagName==='xref') && (node.attributes[att].nodeValue==='supplementary-material')){
tag = 'sup-ref';
}
if(node.attributes[att].localName==='rid'){
if(node.attributes[att].value !== undefined){
tmp.id = node.attributes[att].value;
}
}
if(node.attributes[att].nodeName==='id'){
tmp.id = node.attributes[att].value;
}
});
if(tag!=''){
tmp.tag = tag;
}
if(node.attributes.nodeName==='id'){
tmp.id = node.attributes.value;
}
}
if(node.childNodes != null){
if(node.childNodes.length>0){
Array.prototype.forEach.call(node.childNodes,function(x){
if(x.textContent!='\n'){
if( x.tagName == 'table-wrap' ){
var tab = {
tag: 'table'
};
Object.keys(x.attributes).forEach(function(att){
if(x.attributes[att].localName==='id'){
tab.id = x.attributes[att].value;
}
});
var caption = [];
Array.prototype.forEach.call(x.childNodes,function(y){
if(y.tagName === 'label'){
caption.push({
tag: 'text',
content: y.textContent
});
}
if(y.tagName === 'caption'){
Array.prototype.forEach.call(y.childNodes,function(z){
if( z.tagName == 'title'){
caption.push({
tag: 'text',
content: z.textContent
});
} else {
caption.push(parseXmlNodesRec(z,xml));
}
})
}
});
var txt = extractBetween(xml,'<table-wrap id="'+x.attributes['0'].value+'"','</table-wrap>');
txt = txt.slice(txt.indexOf('>')+1,txt.length);
txt = txt.slice(txt.indexOf('<table'),txt.length);
txt = txt.slice(0,txt.lastIndexOf('</table>')+8);
tab.table = txt;
if(caption.length){
tab.caption= caption;
};
tmp.children.push(tab);
} else if ( x.tagName == 'fig' ){
var fig = {
tag: 'figure'
};
Object.keys(x.attributes).forEach(function(att){
if(x.attributes[att].localName==='id'){
fig.id = x.attributes[att].value;
}
});
var caption = [];
Array.prototype.forEach.call(x.childNodes,function(y){
if(y.tagName === 'label'){
caption.push({
tag: 'text',
content: y.textContent
});
}
if(y.tagName === 'caption'){
Array.prototype.forEach.call(y.childNodes,function(z){
if( z.tagName == 'title'){
caption.push({
tag: 'text',
content: z.textContent
});
} else {
caption.push(parseXmlNodesRec(z,xml));
}
})
}
});
if(caption.length){
fig.caption= caption;
};
tmp.children.push(fig);
} else if ( x.tagName == 'disp-formula' ){
var form = {
tag: 'disp-formula'
}
Array.prototype.forEach.call(x.childNodes,function(y){
if(y.tagName == 'label'){
form.label = y.textContent;
} else if(y.tagName == 'graphic') {
Object.keys(y.attributes).forEach(function(att){
if(y.attributes[att].name==='xlink:href'){
form.id = y.attributes[att].value;
}
});
}
})
tmp.children.push(form);
} else if ( x.tagName == 'supplementary-material' ){
var sup = {
tag: 'supplementary-material'
};
var caption = [];
Array.prototype.forEach.call(x.childNodes,function(y){
if(y.tagName === 'label'){
caption.push({
tag: 'text',
content: y.textContent
});
}
if(y.tagName === 'caption'){
Array.prototype.forEach.call(y.childNodes,function(z){
if( z.tagName == 'title'){
caption.push({
tag: 'text',
content: z.textContent
});
} else {
caption.push(parseXmlNodesRec(z,xml));
}
})
}
if(y.tagName === 'media'){
Object.keys(y.attributes).forEach(function(att){
if(y.attributes[att].name==='xlink:href'){
sup.id = y.attributes[att].value;
}
});
}
});
if(caption.length){
sup.caption= caption;
};
tmp.children.push(sup);
} else {
tmp.children.push(parseXmlNodesRec(x,xml));
}
}
});
return tmp;
} else if(tmp.tag === 'img'){
var img = {
tag: 'inline-graphic'
}
Object.keys(node.attributes).forEach(function(att){
if(node.attributes[att].name==='xlink:href'){
img.id = node.attributes[att].value;
}
});
return img;
} else {
var txt = node.textContent.toString().replace(/(\r\n|\n|\r)/gm,"");
return {
tag: 'text',
content: txt
};
}
} else if(tmp.tag === 'img'){
var img = {
tag: 'inline-graphic'
}
Object.keys(node.attributes).forEach(function(att){
if(y.attributes[att].name==='xlink:href'){
img.id = y.attributes[att].value;
}
});
return img;
} else {
if(node.textContent){
var txt = node.textContent.toString().replace(/(\r\n|\n|\r)/gm,"");
return {
tag: 'text',
content: txt
};
} else {
return {
tag: 'text',
content: ''
};
}
}
};
function parseJsonNodesRec(ldpm, jsonNode, pkg, hlevel, callback){
callback = once(callback);
// recursive exploration of the json representation of the articleBody
var knownTags = {
'disp-quote': 'blockquote',
'sup': 'sup',
'sub': 'sub',
'bold': 'strong',
'italic': 'em',
'underline': ['span class="underline"','span'],
'inline-formula': 'span',
'label':'span',
'named-content':'span'
};
var txt = '';
if( jsonNode.tag === 'body' ){
async.eachSeries(jsonNode.children, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
return callback(null, txt);
});
} else if( jsonNode.tag === 'sec' ){
var id = uuid.v4();
txt += '\n\n<section id="' + id + '"';
var iri = matchDOCO(jsonNode);
if ( iri != ''){
txt += ' typeof="' + iri + '" ';
}
txt += '>\n';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</section>\n';
return callback(null,txt);
});
} else if( jsonNode.tag === 'p' ){
txt += '\n<p>\n';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
if( (x.tag === 'table') || (x.tag === 'figure') ){
txt += '\n</p>';
txt += newTxt;
txt += '\n<p>\n';
} else {
txt += newTxt;
}
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '\n';
txt += '</p>\n';
txt = txt.replace(/<p>\n\n<\/p>/g,'');
return callback(null,txt);
});
} else if( jsonNode.tag === 'title' ){
txt += ' <h' + hlevel + '>\n';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm, x, pkg, hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '\n </h' + hlevel + '>\n';
return callback(null,txt);
});
} else if(Object.keys(knownTags).indexOf(jsonNode.tag)>-1){
if(typeof knownTags[jsonNode.tag] === 'string'){
txt += '\n<'+knownTags[jsonNode.tag]+'>\n';
} else {
txt += '\n<'+knownTags[jsonNode.tag][0]+'>\n';
}
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '\n';
if(typeof knownTags[jsonNode.tag] === 'string'){
txt += '</'+knownTags[jsonNode.tag]+'>\n';
} else {
txt += '</'+knownTags[jsonNode.tag][1]+'>\n';
}
return callback(null, txt);
});
} else if( jsonNode.tag === 'text' ){
if(jsonNode.content.trim() != ''){
if( (jsonNode.content.slice(0,1)==='.') || (jsonNode.content.slice(0,1)===')') ){ // TODO: regexp
txt += jsonNode.content;
} else {
txt += ' '+jsonNode.content;
}
}
return callback(null, txt);
} else if( jsonNode.tag === 'ext-link' ){
txt += ' <a href="'+jsonNode.children[0].content+'">';
txt += jsonNode.children[0].content;
txt += '</a>';
return callback(null, txt);
} else if( jsonNode.tag === 'list' ){
txt += ' <ul>';
async.eachSeries(jsonNode.children, function(ch, cb){
if(ch.tag === 'list-item'){
txt += ' <li>\n';
async.eachSeries(ch.children, function(ch2,cb2){
parseJsonNodesRec(ldpm, ch2, pkg, hlevel,function(err,newTxt){
if(err) return cb2(err);
txt += newTxt;
cb2(null);
});
},function(err){
if(err) return cb(err);
txt += ' </li>\n';
process.nextTick(cb);
});
} else if(ch.tag === 'text'){ //TODO @JDureau can you check that ? I had a bug on ldpm convert PMC3877328
parseJsonNodesRec(ldpm,ch,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
} else {
cb(new Error('unknown tag in list'))
}
}, function(err){
if(err) return callback(err);
txt += jsonNode.children[0].content;
txt += '</ul>\n';
return callback(null,txt);
});
} else if( jsonNode.tag === 'bib-ref' ){
found = false;
pkg.article.forEach(function(art){
if(art.citation){
art.citation.forEach(function(cit){
if(cit.name == jsonNode.id){
found = true;
if(cit.url){
txt += ' <a href="'+cit.url+'" property="http://schema.org/citation" >';
async.eachSeries(jsonNode.children, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</a>';
return callback(null,txt);
});
} else {
if(jsonNode.children[0]['content']!=undefined){
var ind = parseInt(jsonNode.children[0]['content'].slice(1,jsonNode.children[0]['content'].length-1),10);
} else {
var ind = parseInt(jsonNode.children[0].children[0]['content'].slice(1,jsonNode.children[0].children[0]['content'].length-1),10);
}
txt += ' <a href="#ref_' + ind + '" property="http://schema.org/citation">';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</a>';
return callback(null,txt);
});
}
}
});
}
});
if(!found){
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
return callback(null, txt);
});
}
} else if( jsonNode.tag === 'sec-ref' ){
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
return callback(null,txt);
});
} else if( (jsonNode.tag === 'sup-ref') || (jsonNode.tag === 'fig-ref') || (jsonNode.tag === 'table-ref') ){
found = false;
var typeMap = { 'figure': 'figure', 'audio': 'audio', 'video': 'video', 'code': 'targetProduct', 'dataset': 'distribution', 'article': 'encoding'};
Object.keys(typeMap).forEach(function(type){
if(pkg[type]){
pkg[type].forEach(function(r,cb){
if(jsonNode.id != undefined){
if( (r.name == jsonNode.id.replace(/\./g,'-')) || (r.alternateName == jsonNode.id.replace(/\./g,'-')) ){
found = true;
if(r[typeMap[type]][0].contentUrl){
txt += '<a href="'+r[typeMap[type]][0].contentUrl+'">';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</a>';
return callback(null,txt);
});
} else {
var sha1 = crypto.createHash('sha1');
var size = 0
if(r[typeMap[type]][0].contentPath){ // can be bundlePath
var p = path.resolve(ldpm.root, r[typeMap[type]][0].contentPath);
}
if(type==='dataset'){
var s = fs.createReadStream(p).pipe(zlib.createGzip());
} else if(r[typeMap[type]][0].bundlePath){
var s = fs.createReadStream(r[typeMap[type]][0].bundlePath+'.zip');
} else {
var s = fs.createReadStream(p);
}
s.on('error', function(err){ return callback(err)});
s.on('data', function(d) { size += d.length; sha1.update(d); });
s.on('end', function() {
var sha = sha1.digest('hex');
txt += '<a href="' + BASE + 'r/'+sha+'">';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</a>';
return callback(null,txt);
});
});
}
}
}
});
if(!found){
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
return callback(null,txt);
});
}
}
});
} else if( jsonNode.tag === 'figure' ){
var id = uuid.v4();
txt += '\n\n<figure ';
txt += 'id="' + id + '" resource="' + pkg.name + '/' + id + '"';
txt += '>\n';
pkg.figure.forEach(function(fig){
if( (fig.name == jsonNode.id.replace(/\./g,'-')) || (fig.alternateName == jsonNode.id.replace(/\./g,'-')) ){
var found = false;
fig.figure.forEach(function(enc){
if( (!found) && ( (enc.encodingFormat==='image/jpeg') || (enc.encodingFormat==='image/png') ) ){
found = true;
if(enc.contentUrl){
txt += '<img src="' + enc.contentUrl +'">';
if(jsonNode.caption){
txt += '<figcaption typeof="http://purl.org/spar/deo/Caption">\n';
async.eachSeries(jsonNode.caption, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err,newTxt){
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</figcaption>\n';
txt += '</figure>\n';
return callback(null,txt);
});
} else {
txt += '</figure>\n';
return callback(null,txt);
}
} else {
var sha1 = crypto.createHash('sha1');
var size = 0
var p = path.resolve(ldpm.root, enc.contentPath);
var s = fs.createReadStream(p);
s.on('error', function(err){return callback(err)});
s.on('data', function(d) { size += d.length; sha1.update(d); });
s.on('end', function() {
var sha = sha1.digest('hex');
txt += '<img src="' + BASE + 'r/'+sha+'">';
if(jsonNode.caption){
txt += '<figcaption typeof="http://purl.org/spar/deo/Caption">\n';
async.eachSeries(jsonNode.caption, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err,newTxt){
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</figcaption>\n';
txt += '</figure>\n';
return callback(null,txt);
});
} else {
txt += '</figure>\n';
return callback(null,txt);
}
});
}
}
})
}
});
} else if( jsonNode.tag === 'table' ){
// txt += '<table>\n';
var tabletxt = jsonNode.table;
if(jsonNode.caption){
var caption = '\n<caption typeof="http://purl.org/spar/deo/Caption">\n';
async.eachSeries(jsonNode.caption, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
caption += newTxt;
//cb(null);
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
caption += '</caption>\n';
tabletxt = tabletxt.slice(0,tabletxt.indexOf('>')+1) + caption + tabletxt.slice(tabletxt.indexOf('>')+1,tabletxt.length);
txt += '\n' + tabletxt + '\n';
return callback(null,txt);
});
} else {
txt += jsonNode.table;
return callback(null,txt);
}
} else if( jsonNode.tag === 'supplementary-material' ){
txt += '<div>';
found = false;
var typeMap = { 'figure': 'figure', 'audio': 'audio', 'video': 'video', 'code': 'targetProduct', 'dataset': 'distribution', 'article': 'encoding'};
Object.keys(typeMap).forEach(function(type){
if(pkg[type]){
pkg[type].forEach(
function(r,i){
if( r.name === path.basename(jsonNode.id,path.extname(jsonNode.id)).replace(/\./g,'-')){
found = true;
if(r[typeMap[type]][0].contentUrl){
txt += '<a href="'+r[typeMap[type]][0].contentUrl+'">';
txt += jsonNode.id;
txt += '</a>';
if(jsonNode.caption){
async.eachSeries(jsonNode.caption, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err,newTxt){
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</div>';
return callback(null,txt);
});
} else {
txt += '</div>';
return callback(null,txt);
}
} else if(r[typeMap[type]][0].bundlePath){
var sha1 = crypto.createHash('sha1');
var size = 0
var basename = path.basename(jsonNode.id,path.extname(jsonNode.id));
var extname = path.extname(jsonNode.id);
basename = basename.replace(/\./g, '-')
var p = path.resolve(ldpm.root, basename+extname);
var s = fs.createReadStream(p);
s.on('error', callback);
s.on('data', function(d) { size += d.length; sha1.update(d); });
s.on('end', function() {
var sha = sha1.digest('hex');
txt += '<a href="' + BASE + 'r/'+sha+'">';
txt += jsonNode.id;
txt += '</a>';
if(jsonNode.caption){
async.eachSeries(jsonNode.caption, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err,newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</div>';
return callback(null,txt);
});
} else {
txt += '</div>';
return callback(null,txt);
}
});
} else {
r[typeMap[type]].forEach(function(enc){
if(path.basename(enc.contentPath)===jsonNode.id){
var sha1 = crypto.createHash('sha1');
var size = 0
var p = path.resolve(ldpm.root, enc.contentPath);
if(type==='dataset'){
var s = fs.createReadStream(p).pipe(zlib.createGzip());
} else {
var s = fs.createReadStream(p);
}
s.on('error', callback);
s.on('data', function(d) { size += d.length; sha1.update(d); });
s.on('end', function() {
var sha = sha1.digest('hex');
txt += '<a href="' + BASE + 'r/'+sha+'">';
txt += jsonNode.id;
txt += '</a>';
if(jsonNode.caption){
async.eachSeries(jsonNode.caption, function(x,cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err,newTxt){
if(err) return cb(err);
txt += newTxt;
process.nextTick(cb);
});
}, function(err){
if(err) return callback(err);
txt += '</div>';
return callback(null,txt);
});
} else {
txt += '</div>';
return callback(null,txt);
}
});
}
});
}
}
}
)
}
});
if(!found){
txt += jsonNode.id;
return callback(null,txt);
}
} else if( jsonNode.tag === 'inline-graphic' ){
found = false;
var typeMap = { 'figure': 'figure' };
Object.keys(typeMap).forEach(function(type){
if(pkg[type]){
pkg[type].forEach(function(r){
if(jsonNode.id != undefined){
if( (!found) && (r.name === path.basename(jsonNode.id,path.extname(jsonNode.id)).replace(/\./g,'-'))){
found = true;
var indjpg;
r[typeMap[type]].forEach(function(enc,i){
if(enc.encodingFormat === 'image/jpeg'){
indjpg = i;
}
})
fs.readFile(path.join(ldpm.root,r[typeMap[type]][indjpg].contentPath),function (err, buffer) {
if (err) return callback(err);
var dataUrl = "data:" + 'image/jpg' + ";base64," + buffer.toString('base64');
txt += '<img src="' + dataUrl +'">';
return callback(null,txt);
});
}
}
})
}
});
} else if ( jsonNode.tag === 'disp-formula'){
txt += '\n<div class="formula" ';
if(jsonNode.label){
txt += 'id="' + jsonNode.label + '"';
}
txt += '>\n';
found = false;
var typeMap = { 'figure': 'figure' };
Object.keys(typeMap).forEach(function(type){
if(pkg[type]){
pkg[type].forEach(function(r,cb){
if(jsonNode.id != undefined){
if( (!found) && ( (r.name === jsonNode.id.replace(/\./g,'-')) || (r.name === path.basename(jsonNode.id,path.extname(jsonNode.id)).replace(/\./g,'-')))){
found = true;
var indjpg=0;
r[typeMap[type]].forEach(function(enc,i){
if(enc.encodingFormat === 'image/jpeg'){
indjpg = i;
}
})
fs.readFile(path.join(ldpm.root,r[typeMap[type]][indjpg].contentPath),function (err, buffer) {
if (err) return callback(err);
var dataUrl = "data:" + 'image/jpg' + ";base64," + buffer.toString('base64');
txt += '<img src="' + dataUrl +'">';
if(jsonNode.label){
txt += '\n<span class="eq-label">\n';
txt += jsonNode.label;
txt += '\n</span>\n';
}
return callback(null,txt);
});
}
}
})
}
});
if(!found){
txt += '<span>';
if(jsonNode.children!=undefined){
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</span>';
return callback(null,txt);
});
} else if (jsonNode.label!=undefined){
txt += jsonNode.label;
return callback(null,txt);
} else {
return callback(null,txt);
}
}
} else if( (jsonNode.tag!=undefined) && (jsonNode.tag.slice(0,4)==='mml:math') ){
txt+= '<math xmlns="http://www.w3.org/1998/Math/MathML">';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</math>';
return callback(null,txt);
});
} else if( (jsonNode.tag!=undefined) && (jsonNode.tag.slice(0,4)==='mml:') ){
txt+= '<' + jsonNode.tag.slice(0,4) + '>';
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</' + jsonNode.tag.slice(0,4) + '>';
return callback(null,txt);
});
} else {
txt += '<div class="unknown">';
txt += '<' + jsonNode.tag;
if(jsonNode.id){
txt += ' id =' + jsonNode.id;
}
txt += '>';
if(jsonNode.children != undefined){
async.eachSeries(jsonNode.children, function(x, cb){
parseJsonNodesRec(ldpm,x,pkg,hlevel,function(err, newTxt){
if(err) return cb(err);
txt += newTxt;
cb(null);
});
}, function(err){
if(err) return callback(err);
txt += '</' + jsonNode.tag + '>';
txt += '</div>';
return callback(null,txt);
});
} else {
txt += '</' + jsonNode.tag + '>';
txt += '</div>';
return callback(null,txt);
}
}
}
function addPubmedAnnotations(pkg, pubmedPkg, ldpm, callback){
// Pubmed metadata brings additional Mesh annotations.
// The target of these annotations needs to be modified, to match the
// uri of the html article on S3
callback = once(callback);
if(pubmedPkg){
var hasBody = {
"@type": ["Tag", "Mesh"],
"@context": BASE + "mesh.jsonld"
};
var graph = [];
var artInd = getArtInd(pkg);
if(pubmedPkg.annotation){
if(pkg.annotation == undefined){
pkg.annotation = [];
}
var sha1 = crypto.createHash('sha1');
var size = 0;
var p = path.resolve(ldpm.root, pkg.article[getArtInd(pkg)].encoding[pkg.article[getArtInd(pkg)].encoding.length-1].contentPath);
var s = fs.createReadStream(p);
s.on('error', callback);
s.on('data', function(d) { size += d.length; sha1.update(d); });
s.on('end', function() {
var sha = sha1.digest('hex');
pubmedPkg.annotation[0].hasTarget = [
{
"@type": "SpecificResource",
hasSource: "r/"+sha,
hasScope: pkg.name + '/' + pkg.version + '/article/' + pkg.article[artInd].name,
hasState: {
"@type": "HttpRequestState",
value: "Accept: text/html"
}
}
]
pkg.annotation = pkg.annotation.concat(pubmedPkg.annotation)
callback(null,pkg);
});
} else {
callback(null,pkg);
}
} else {
callback(null,pkg);
}
};
function matchDOCO(node){
var iris = {
'introduction': 'http://purl.org/spar/deo/Introduction',
'acknowledgements': 'http://purl.org/spar/deo/Acknowledgements',
'discussion': 'http://salt.semanticauthoring.org/ontologies/sro#Discussion',
'materials': 'http://purl.org/spar/deo/Materials',
'methods': 'http://purl.org/spar/deo/Methods',
'results': 'http://purl.org/spar/deo/Results',
'conclusion': 'http://salt.semanticauthoring.org/documentation.html#Conclusion'
}
var iri = ''
node.children.forEach(function(ch){
if(ch.tag==='title'){
ch.children.forEach(function(x){
if(x.tag==='text'){
if( Object.keys(iris).indexOf(x.content.toLowerCase())>-1){
iri = iris[x.content.toLowerCase()];
}
}
})
}
})
return iri;
};
/**
* !!! in case of nested tags only the last one will be reported... e.g. subj-group:
* <article-categories>
* <subj-group subj-group-type="keywords">
* <subject>Biological Sciences</subject>
* <subj-group subj-group-type="keywords">
* <subject>Neuroscience</subject>
* <subj-group subj-group-type="keywords">
* <subject>Cellular and Molecular Biology</subject>
* <subj-group subj-group-type="keywords">
* <subject>Blood–brain barrier</subject>
* </subj-group>
* </subj-group>
* </subj-group>
* </subj-group>
* </article-categories>
* => avoid subj-group and use higher level tag (article-categories)
*/
function findNodePaths(obj,names){
var paths = {};
traverse(obj).forEach(function(x){
if(names.indexOf(this.key)>-1){
paths[this.key] = this.path;
}
});
return paths;
};
function getArtInd(pkg, mainArticleName){
if(pkg.article){
for(var i=0; i<pkg.article.length; i++){
var art = pkg.article[i];
if(mainArticleName && (art.name === mainArticleName)){
return i;
}
if(art['@type']){
if(typeof art['@type'] === 'string'){
if(art['@type']==='ScholarlyArticle'){
return i;
}
} else {
for(var j=0; j<art['@type'].length; j++){
if(art['@type'][j] === 'ScholarlyArticle'){
return i;
}
}
}
}
}
}
return -1;
};
/**
* obj is a node from article-categories http://jats.nlm.nih.gov/publishing/tag-library/1.1d1/index.html
*/
function extractKeywords($el){
var res = [];
if($el.tagName === 'subj-group'){
for(var i=0; i<$el.childNodes.length; i++){
if($el.childNodes[i].tagName === 'subject'){
res.push($el.childNodes[i].textContent);
} else if ($el.childNodes[i].tagName === 'subj-group'){
res = res.concat(extractKeywords($el.childNodes[i]));
}
}
return res;
} else if($el.tagName === 'subject') {
return [$el.textContent];
}
return res;
};
function extractBetween(str, strBeg, strEnd){
var beg = str.indexOf(strBeg) + strBeg.length;
var end;
if(arguments.length === 3){
end = beg + str.slice(beg, str.length).indexOf(strEnd);
} else {
end = str.length;
}
return str.slice(beg, end);
};
var defaultDiacriticsRemovalMap = [
{'base':'A', 'letters':/[\u0041\u24B6\uFF21\u00C0\u00C1\u00C2\u1EA6\u1EA4\u1EAA\u1EA8\u00C3\u0100\u0102\u1EB0\u1EAE\u1EB4\u1EB2\u0226\u01E0\u00C4\u01DE\u1EA2\u00C5\u01FA\u01CD\u0200\u0202\u1EA0\u1EAC\u1EB6\u1E00\u0104\u023A\u2C6F]/g},
{'base':'AA','letters':/[\uA732]/g},
{'base':'AE','letters':/[\u00C6\u01FC\u01E2]/g},
{'base':'AO','letters':/[\uA734]/g},
{'base':'AU','letters':/[\uA736]/g},
{'base':'AV','letters':/[\uA738\uA73A]/g},
{'base':'AY','letters':/[\uA73C]/g},
{'base':'B', 'letters':/[\u0042\u24B7\uFF22\u1E02\u1E04\u1E06\u0243\u0182\u0181]/g},
{'base':'C', 'letters':/[\u0043\u24B8\uFF23\u0106\u0108\u010A\u010C\u00C7\u1E08\u0187\u023B\uA73E]/g},
{'base':'D', 'letters':/[\u0044\u24B9\uFF24\u1E0A\u010E\u1E0C\u1E10\u1E12\u1E0E\u0110\u018B\u018A\u0189\uA779]/g},
{'base':'DZ','letters':/[\u01F1\u01C4]/g},
{'base':'Dz','letters':/[\u01F2\u01C5]/g},
{'base':'E', 'letters':/[\u0045\u24BA\uFF25\u00C8\u00C9\u00CA\u1EC0\u1EBE\u1EC4\u1EC2\u1EBC\u0112\u1E14\u1E16\u0114\u0116\u00CB\u1EBA\u011A\u0204\u0206\u1EB8\u1EC6\u0228\u1E1C\u0118\u1E18\u1E1A\u0190\u018E]/g},
{'base':'F', 'letters':/[\u0046\u24BB\uFF26\u1E1E\u0191\uA77B]/g},
{'base':'G', 'letters':/[\u0047\u24BC\uFF27\u01F4\u011C\u1E20\u011E\u0120\u01E6\u0122\u01E4\u0193\uA7A0\uA77D\uA77E]/g},
{'base':'H', 'letters':/[\u0048\u24BD\uFF28\u0124\u1E22\u1E26\u021E\u1E24\u1E28\u1E2A\u0126\u2C67\u2C75\uA78D]/g},
{'base':'I', 'letters':/[\u0049\u24BE\uFF29\u00CC\u00CD\u00CE\u0128\u012A\u012C\u0130\u00CF\u1E2E\u1EC8\u01CF\u0208\u020A\u1ECA\u012E\u1E2C\u0197]/g},
{'base':'J', 'letters':/[\u004A\u24BF\uFF2A\u0134\u0248]/g},
{'base':'K', 'letters':/[\u004B\u24C0\uFF2B\u1E30\u01E8\u1E32\u0136\u1E34\u0198\u2C69\uA740\uA742\uA744\uA7A2]/g},
{'base':'L', 'letters':/[\u004C\u24C1\uFF2C\u013F\u0139\u013D\u1E36\u1E38\u013B\u1E3C\u1E3A\u0141\u023D\u2C62\u2C60\uA748\uA746\uA780]/g},
{'base':'LJ','letters':/[\u01C7]/g},
{'base':'Lj','letters':/[\u01C8]/g},
{'base':'M', 'letters':/[\u004D\u24C2\uFF2D\u1E3E\u1E40\u1E42\u2C6E\u019C]/g},
{'base':'N', 'letters':/[\u004E\u24C3\uFF2E\u01F8\u0143\u00D1\u1E44\u0147\u1E46\u0145\u1E4A\u1E48\u0220\u019D\uA790\uA7A4]/g},
{'base':'NJ','letters':/[\u01CA]/g},
{'base':'Nj','letters':/[\u01CB]/g},
{'base':'O', 'letters':/[\u004F\u24C4\uFF2F\u00D2\u00D3\u00D4\u1ED2\u1ED0\u1ED6\u1ED4\u00D5\u1E4C\u022C\u1E4E\u014C\u1E50\u1E52\u014E\u022E\u0230\u00D6\u022A\u1ECE\u0150\u01D1\u020C\u020E\u01A0\u1EDC\u1EDA\u1EE0\u1EDE\u1EE2\u1ECC\u1ED8\u01EA\u01EC\u00D8\u01FE\u0186\u019F\uA74A\uA74C]/g},
{'base':'OI','letters':/[\u01A2]/g},
{'base':'OO','letters':/[\uA74E]/g},
{'base':'OU','letters':/[\u0222]/g},
{'base':'P', 'letters':/[\u0050\u24C5\uFF30\u1E54\u1E56\u01A4\u2C63\uA750\uA752\uA754]/g},
{'base':'Q', 'letters':/[\u0051\u24C6\uFF31\uA756\uA758\u024A]/g},
{'base':'R', 'letters':/[\u0052\u24C7\uFF32\u0154\u1E58\u0158\u0210\u0212\u1E5A\u1E5C\u0156\u1E5E\u024C\u2C64\uA75A\uA7A6\uA782]/g},
{'base':'S', 'letters':/[\u0053\u24C8\uFF33\u1E9E\u015A\u1E64\u015C\u1E60\u0160\u1E66\u1E62\u1E68\u0218\u015E\u2C7E\uA7A8\uA784]/g},
{'base':'T', 'letters':/[\u0054\u24C9\uFF34\u1E6A\u0164\u1E6C\u021A\u0162\u1E70\u1E6E\u0166\u01AC\u01AE\u023E\uA786]/g},
{'base':'TZ','letters':/[\uA728]/g},
{'base':'U', 'letters':/[\u0055\u24CA\uFF35\u00D9\u00DA\u00DB\u0168\u1E78\u016A\u1E7A\u016C\u00DC\u01DB\u01D7\u01D5\u01D9\u1EE6\u016E\u0170\u01D3\u0214\u0216\u01AF\u1EEA\u1EE8\u1EEE\u1EEC\u1EF0\u1EE4\u1E72\u0172\u1E76\u1E74\u0244]/g},
{'base':'V', 'letters':/[\u0056\u24CB\uFF36\u1E7C\u1E7E\u01B2\uA75E\u0245]/g},
{'base':'VY','letters':/[\uA760]/g},
{'base':'W', 'letters':/[\u0057\u24CC\uFF37\u1E80\u1E82\u0174\u1E86\u1E84\u1E88\u2C72]/g},
{'base':'X', 'letters':/[\u0058\u24CD\uFF38\u1E8A\u1E8C]/g},
{'base':'Y', 'letters':/[\u0059\u24CE\uFF39\u1EF2\u00DD\u0176\u1EF8\u0232\u1E8E\u0178\u1EF6\u1EF4\u01B3\u024E\u1EFE]/g},
{'base':'Z', 'letters':/[\u005A\u24CF\uFF3A\u0179\u1E90\u017B\u017D\u1E92\u1E94\u01B5\u0224\u2C7F\u2C6B\uA762]/g},
{'base':'a', 'letters':/[\u0061\u24D0\uFF41\u1E9A\u00E0\u00E1\u00E2\u1EA7\u1EA5\u1EAB\u1EA9\u00E3\u0101\u0103\u1EB1\u1EAF\u1EB5\u1EB3\u0227\u01E1\u00E4\u01DF\u1EA3\u00E5\u01FB\u01CE\u0201\u0203\u1EA1\u1EAD\u1EB7\u1E01\u0105\u2C65\u0250]/g},
{'base':'aa','letters':/[\uA733]/g},
{'base':'ae','letters':/[\u00E6\u01FD\u01E3]/g},
{'base':'ao','letters':/[\uA735]/g},
{'base':'au','letters':/[\uA737]/g},
{'base':'av','letters':/[\uA739\uA73B]/g},
{'base':'ay','letters':/[\uA73D]/g},
{'base':'b', 'letters':/[\u0062\u24D1\uFF42\u1E03\u1E05\u1E07\u0180\u0183\u0253]/g},
{'base':'c', 'letters':/[\u0063\u24D2\uFF43\u0107\u0109\u010B\u010D\u00E7\u1E09\u0188\u023C\uA73F\u2184]/g},
{'base':'d', 'letters':/[\u0064\u24D3\uFF44\u1E0B\u010F\u1E0D\u1E11\u1E13\u1E0F\u0111\u018C\u0256\u0257\uA77A]/g},
{'base':'dz','letters':/[\u01F3\u01C6]/g},
{'base':'e', 'letters':/[\u0065\u24D4\uFF45\u00E8\u00E9\u00EA\u1EC1\u1EBF\u1EC5\u1EC3\u1EBD\u0113\u1E15\u1E17\u0115\u0117\u00EB\u1EBB\u011B\u0205\u0207\u1EB9\u1EC7\u0229\u1E1D\u0119\u1E19\u1E1B\u0247\u025B\u01DD]/g},
{'base':'f', 'letters':/[\u0066\u24D5\uFF46\u1E1F\u0192\uA77C]/g},
{'base':'g', 'letters':/[\u0067\u24D6\uFF47\u01F5\u011D\u1E21\u011F\u0121\u01E7\u0123\u01E5\u0260\uA7A1\u1D79\uA77F]/g},
{'base':'h', 'letters':/[\u0068\u24D7\uFF48\u0125\u1E23\u1E27\u021F\u1E25\u1E29\u1E2B\u1E96\u0127\u2C68\u2C76\u0265]/g},
{'base':'hv','letters':/[\u0195]/g},
{'base':'i', 'letters':/[\u0069\u24D8\uFF49\u00EC\u00ED\u00EE\u0129\u012B\u012D\u00EF\u1E2F\u1EC9\u01D0\u0209\u020B\u1ECB\u012F\u1E2D\u0268\u0131]/g},
{'base':'j', 'letters':/[\u006A\u24D9\uFF4A\u0135\u01F0\u0249]/g},
{'base':'k', 'letters':/[\u006B\u24DA\uFF4B\u1E31\u01E9\u1E33\u0137\u1E35\u0199\u2C6A\uA741\uA743\uA745\uA7A3]/g},
{'base':'l', 'letters':/[\u006C\u24DB\uFF4C\u0140\u013A\u013E\u1E37\u1E39\u013C\u1E3D\u1E3B\u017F\u0142\u019A\u026B\u2C61\uA749\uA781\uA747]/g},
{'base':'lj','letters':/[\u01C9]/g},
{'base':'m', 'letters':/[\u006D\u24DC\uFF4D\u1E3F\u1E41\u1E43\u0271\u026F]/g},
{'base':'n', 'letters':/[\u006E\u24DD\uFF4E\u01F9\u0144\u00F1\u1E45\u0148\u1E47\u0146\u1E4B\u1E49\u019E\u0272\u0149\uA791\uA7A5]/g},
{'base':'nj','letters':/[\u01CC]/g},
{'base':'o', 'letters':/[\u006F\u24DE\uFF4F\u00F2\u00F3\u00F4\u1ED3\u1ED1\u1ED7\u1ED5\u00F5\u1E4D\u022D\u1E4F\u014D\u1E51\u1E53\u014F\u022F\u0231\u00F6\u022B\u1ECF\u0151\u01D2\u020D\u020F\u01A1\u1EDD\u1EDB\u1EE1\u1EDF\u1EE3\u1ECD\u1ED9\u01EB\u01ED\u00F8\u01FF\u0254\uA74B\uA74D\u0275]/g},
{'base':'oi','letters':/[\u01A3]/g},
{'base':'ou','letters':/[\u0223]/g},
{'base':'oo','letters':/[\uA74F]/g},
{'base':'p','letters':/[\u0070\u24DF\uFF50\u1E55\u1E57\u01A5\u1D7D\uA751\uA753\uA755]/g},
{'base':'q','letters':/[\u0071\u24E0\uFF51\u024B\uA757\uA759]/g},
{'base':'r','letters':/[\u0072\u24E1\uFF52\u0155\u1E59\u0159\u0211\u0213\u1E5B\u1E5D\u0157\u1E5F\u024D\u027D\uA75B\uA7A7\uA783]/g},
{'base':'s','letters':/[\u0073\u24E2\uFF53\u00DF\u015B\u1E65\u015D\u1E61\u0161\u1E67\u1E63\u1E69\u0219\u015F\u023F\uA7A9\uA785\u1E9B]/g},
{'base':'t','letters':/[\u0074\u24E3\uFF54\u1E6B\u1E97\u0165\u1E6D\u021B\u0163\u1E71\u1E6F\u0167\u01AD\u0288\u2C66\uA787]/g},
{'base':'tz','letters':/[\uA729]/g},
{'base':'u','letters':/[\u0075\u24E4\uFF55\u00F9\u00FA\u00FB\u0169\u1E79\u016B\u1E7B\u016D\u00FC\u01DC\u01D8\u01D6\u01DA\u1EE7\u016F\u0171\u01D4\u0215\u0217\u01B0\u1EEB\u1EE9\u1EEF\u1EED\u1EF1\u1EE5\u1E73\u0173\u1E77\u1E75\u0289]/g},
{'base':'v','letters':/[\u0076\u24E5\uFF56\u1E7D\u1E7F\u028B\uA75F\u028C]/g},
{'base':'vy','letters':/[\uA761]/g},
{'base':'w','letters':/[\u0077\u24E6\uFF57\u1E81\u1E83\u0175\u1E87\u1E85\u1E98\u1E89\u2C73]/g},
{'base':'x','letters':/[\u0078\u24E7\uFF58\u1E8B\u1E8D]/g},
{'base':'y','letters':/[\u0079\u24E8\uFF59\u1EF3\u00FD\u0177\u1EF9\u0233\u1E8F\u00FF\u1EF7\u1E99\u1EF5\u01B4\u024F\u1EFF]/g},
{'base':'z','letters':/[\u007A\u24E9\uF