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Removes JXON use for native DOMParser for Pubmed abstract parsing #685

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Removes JXON use for native DOMParser for Pubmed abstract parsing #685

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e37c143
Removes JXON use for native DOMParser for Pubmed abstract parsing
AlexanderNull May 19, 2023
b0231ff
Merge branch 'master' into reference-formatting-655
kltm Dec 13, 2023
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80 changes: 37 additions & 43 deletions javascript/web/ReferenceDetails.js
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,6 @@ var golr_response = require('bbop-response-golr');
// And a basic response.
var rest_response = require('bbop-rest-response').base;

// // XML.
// var xpath = require('xpath');
// var dom = require('xmldom').DOMParser;
var jxon = require('jxon');

// Aliases.
var dlimit = defs.download_limit;

Expand Down Expand Up @@ -273,51 +268,41 @@ function ReferenceDetailsInit(){
// Run.
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);
// Previous check for string vs json unneeded due to request parameters always being XML.
var xml = xmlParser.parseFromString(resp.raw(), 'text/xml');
console.log(xml);

var BASE_ARTICLE_PATH = 'PubmedArticleSet PubmedArticle';
var FULL_ARTICLE_PATH = BASE_ARTICLE_PATH + ' MedlineCitation Article';
// Our operating object.
if( ! jx.PubmedArticleSet.PubmedArticle ){
if( ! xml.querySelector(BASE_ARTICLE_PATH) ){
UnableToMakeContact('<b>No such PubMed ID</b>.');
}else if( ! jx.PubmedArticleSet.PubmedArticle.MedlineCitation.Article ){
}else if( ! xml.querySelector(FULL_ARTICLE_PATH) ){
UnableToMakeContact('<b>No such Article</b>.');
}else{
var op = jx.PubmedArticleSet.PubmedArticle.MedlineCitation.Article;
var op = xml.querySelector(FULL_ARTICLE_PATH);

// Title.
var title = 'n/a';
if( op.ArticleTitle ){
title = op.ArticleTitle;
}
var title = getXmlContent(op, 'ArticleTitle', 'n/a');

// Date.
var date = 'n/a';
if( op.ArticleDate ){
var year = op.ArticleDate.Year || '???';
var month = op.ArticleDate.Month || '???';
var day = op.ArticleDate.Day || '???';
if( op.querySelector('AritcleDate') ){
var missingValue = '???';
var year = getXmlContent(op, 'ArticleDate.Year', missingValue);
var month = getXmlContent(op, 'ArticleDate.Month', missingValue);
var day = getXmlContent(op, 'ArticleDate.Day', missingValue);
date = [year, month, day].join('-');
}

// Authors.
var authors = 'n/a';
if( op.AuthorList && op.AuthorList.Author ){
if( op.querySelector('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);
us.each(op.querySelectorAll('AuthorList Author'), function(auth){
var name = [getXmlContent(auth, 'ForeName', ''), getXmlContent(auth, 'LastName', '')].join(' ').trim();
acache.push(name);
});
if( ! us.isEmpty(acache) ){
authors = acache.join(', ');
Expand All @@ -326,19 +311,17 @@ function ReferenceDetailsInit(){

// Abstract; list or string.
var abstract = 'n/a';
if( op.Abstract && op.Abstract.AbstractText ){
if( us.isArray(op.Abstract.AbstractText) ){

var abstractXml = op.querySelectorAll('Abstract AbstractText');
if( abstractXml.length > 1 ){
var abscache = [];
us.each(op.Abstract.AbstractText, function(abs){
if( abs._ ){ abscache.push(abs._); }
us.each(asbtractXml, function(abs){
if( abs.textContent ){ abscache.push(abs.textContent); }
});
if( ! us.isEmpty(abscache) ){
abstract = abscache.join('<br />');
abstract = abscache.join('<br />');
}
}else if( us.isString(op.Abstract.AbstractText) ){
abstract = op.Abstract.AbstractText;
}
}else if( abstractXml.length === 1 ){
abstract = abstractXml[0].textContent;
}

// Render.
Expand Down Expand Up @@ -422,7 +405,6 @@ function ReferenceDetailsInit(){
'db': 'pubmed',
'id': id_part
};
var meth = 'GET';
ncbi_engine.start(url + path, pay, 'GET');

}catch (e) {
Expand Down Expand Up @@ -555,3 +537,15 @@ function _shrink_wrap(elt_id){
}
}
}

// Not certain what minimal browser support here is so avoided default parameter values (Chrome 49, Firefox 15, IE 11, Opera 36, Safari 9).
function getXmlContent(xml, path, default_value){
var content = xml.querySelector(path);
if( content ){
return content.textContent;
}else if(default_value === undefined){
return null;
}else{
return default_value;
}
}
1 change: 0 additions & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,6 @@
"express": "4.16.3",
"golr-conf": "0.0.3",
"jquery": "3.3.1",
"jxon": "2.0.0-beta.5",
"markdown": "0.5.0",
"marked": "0.3.19",
"minerva-requests": "0.0.15",
Expand Down