Trans: Change PubMed to support import
This commit is contained in:
Avram Lyon
parent
5ff4bd6326
commit
6958518063
1 changed files with 133 additions and 102 deletions
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@ -1,14 +1,15 @@
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{
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"translatorID":"fcf41bed-0cbc-3704-85c7-8062a0068a7a",
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"translatorType":12,
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"translatorType":13,
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"label":"NCBI PubMed",
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"creator":"Simon Kornblith, Michael Berkowitz, Avram Lyon, and Rintze Zelle",
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"target":"https?://[^/]*(www|preview)\\.ncbi\\.nlm\\.nih\\.gov[^/]*/(pubmed|sites/pubmed|sites/entrez|entrez/query\\.fcgi\\?.*db=PubMed)",
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"minVersion":"2.1b1",
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"maxVersion":"",
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"priority":100,
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"configOptions":{"dataMode":"block"},
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"inRepository":true,
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"lastUpdated":"2010-11-17 10:15:00"
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"lastUpdated":"2011-01-27 10:15:00"
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}
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function detectWeb(doc, url) {
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@ -61,115 +62,145 @@ function detectSearch(item) {
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function lookupPMIDs(ids, doc) {
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var newUri = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=PubMed&tool=Zotero&retmode=xml&rettype=citation&id="+ids.join(",");
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Zotero.debug(newUri);
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Zotero.Utilities.HTTP.doGet(newUri, doImportFromText, function () {Zotero.done()});
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Zotero.wait();
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var newUri = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=PubMed&retmode=xml&rettype=citation&id="+ids.join(",");
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Zotero.Utilities.HTTP.doGet(newUri, function(text) {
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// Remove xml parse instruction and doctype
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text = text.replace(/<!DOCTYPE[^>]*>/, "").replace(/<\?xml[^>]*\?>/, "");
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}
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var xml = new XML(text);
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function doImport() {
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var text = "";
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var line;
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while((line = Zotero.read(4096)) !== false) {
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text += line;
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}
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return doImportFromText(text);
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}
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for(var i=0; i<xml.PubmedArticle.length(); i++) {
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var newItem = new Zotero.Item("journalArticle");
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function detectImport() {
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Zotero.debug("Detecting Pubmed content....");
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var text = "";
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var line;
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while(line = Zotero.read(1000)) {
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text += line;
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// Look for the PubmedArticle tag in the first 1000 characters
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if (text.match(/<PubmedArticle>/)) return "journalArticle";
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else if (text.length > 1000) return false;
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}
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return false;
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}
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var citation = xml.PubmedArticle[i].MedlineCitation;
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function doImportFromText(text) {
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// Remove xml parse instruction and doctype
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text = text.replace(/<!DOCTYPE[^>]*>/, "").replace(/<\?xml[^>]*\?>/, "");
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var PMID = citation.PMID.text().toString();
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newItem.url = "http://www.ncbi.nlm.nih.gov/pubmed/" + PMID;
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newItem.extra = "PMID: "+PMID;
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if (!text.substr(0,1000).match(/<PubmedArticleSet>/)) {
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// Pubmed data in the wild, perhaps copied from the web site's search results,
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// can be missing the <PubmedArticleSet> root tag. Let's add a pair!
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Zotero.debug("No root <PubmedArticleSet> tag found, wrapping in a new root tag.");
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text = "<PubmedArticleSet>" + text + "</PubmedArticleSet>";
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}
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var article = citation.Article;
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if(article.ArticleTitle.length()) {
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var title = article.ArticleTitle.text().toString();
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if(title.substr(-1) == ".") {
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title = title.substring(0, title.length-1);
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}
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newItem.title = title;
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var xml = new XML(text);
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for(var i=0; i<xml.PubmedArticle.length(); i++) {
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var newItem = new Zotero.Item("journalArticle");
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var citation = xml.PubmedArticle[i].MedlineCitation;
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var PMID = citation.PMID.text().toString();
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newItem.url = "http://www.ncbi.nlm.nih.gov/pubmed/" + PMID;
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newItem.extra = "PMID: "+PMID;
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var article = citation.Article;
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if(article.ArticleTitle.length()) {
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var title = article.ArticleTitle.text().toString();
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if(title.substr(-1) == ".") {
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title = title.substring(0, title.length-1);
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}
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if (article.Pagination.MedlinePgn.length()){
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var fullPageRange = article.Pagination.MedlinePgn.text().toString();
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var pageRange = fullPageRange.match(/\d+-\d+/g);
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for (var j in pageRange) {
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var pageRangeStart = pageRange[j].match(/^\d+/)[0];
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var pageRangeEnd = pageRange[j].match(/\d+$/)[0];
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if (pageRangeStart.length > pageRangeEnd.length) {
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pageRangeEnd = pageRangeStart.substring(0,pageRangeStart.length-pageRangeEnd.length) + pageRangeEnd;
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fullPageRange = fullPageRange.replace(pageRange[j],pageRangeStart+"-"+pageRangeEnd);
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}
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}
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newItem.pages = fullPageRange;
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}
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if(article.Journal.length()) {
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var issn = article.Journal.ISSN.text().toString();
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if(issn) {
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newItem.ISSN = issn;
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}
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if(citation.Article.Journal.ISOAbbreviation.length()) {
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newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.Article.Journal.ISOAbbreviation.text().toString());
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} else if(citation.MedlineJournalInfo.MedlineTA.length()) {
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newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.MedlineJournalInfo.MedlineTA.text().toString());
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}
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if(article.Journal.Title.length()) {
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newItem.publicationTitle = Zotero.Utilities.superCleanString(article.Journal.Title.text().toString());
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} else if(newItem.journalAbbreviation.length()) {
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newItem.publicationTitle = newItem.journalAbbreviation;
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}
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if(article.Journal.JournalIssue.length()) {
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newItem.volume = article.Journal.JournalIssue.Volume.text().toString();
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newItem.issue = article.Journal.JournalIssue.Issue.text().toString();
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if(article.Journal.JournalIssue.PubDate.length()) { // try to get the date
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if(article.Journal.JournalIssue.PubDate.Day.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Day.text().toString()+", "+article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.Month.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.Year.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.MedlineDate.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.MedlineDate.text().toString();
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}
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}
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}
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}
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if(article.AuthorList.length() && article.AuthorList.Author.length()) {
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var authors = article.AuthorList.Author;
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for(var j=0; j<authors.length(); j++) {
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var lastName = authors[j].LastName.text().toString();
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var firstName = authors[j].FirstName.text().toString();
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if(firstName == "") {
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firstName = authors[j].ForeName.text().toString();
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}
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var suffix = authors[j].Suffix.text().toString();
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if(suffix && firstName != "") {
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firstName += ", " + authors[j].Suffix.text().toString();
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}
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if(firstName || lastName) {
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newItem.creators.push({lastName:lastName, firstName:firstName});
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}
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}
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}
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if (citation.MeshHeadingList && citation.MeshHeadingList.MeshHeading) {
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var keywords = citation.MeshHeadingList.MeshHeading;
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for (var k = 0 ; k < keywords.length() ; k++) {
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newItem.tags.push(keywords[k].DescriptorName.text().toString());
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}
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}
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newItem.abstractNote = article.Abstract.AbstractText.toString()
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newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId.(@IdType == "doi" ).text().toString();
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newItem.publicationTitle = Zotero.Utilities.capitalizeTitle(newItem.publicationTitle);
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newItem.complete();
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newItem.title = title;
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}
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Zotero.done();
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});
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if (article.Pagination.MedlinePgn.length()){
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var fullPageRange = article.Pagination.MedlinePgn.text().toString();
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var pageRange = fullPageRange.match(/\d+-\d+/g);
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for (var j in pageRange) {
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var pageRangeStart = pageRange[j].match(/^\d+/)[0];
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var pageRangeEnd = pageRange[j].match(/\d+$/)[0];
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if (pageRangeStart.length > pageRangeEnd.length) {
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pageRangeEnd = pageRangeStart.substring(0,pageRangeStart.length-pageRangeEnd.length) + pageRangeEnd;
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fullPageRange = fullPageRange.replace(pageRange[j],pageRangeStart+"-"+pageRangeEnd);
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}
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}
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newItem.pages = fullPageRange;
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}
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if(article.Journal.length()) {
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var issn = article.Journal.ISSN.text().toString();
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if(issn) {
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newItem.ISSN = issn;
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}
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if(citation.Article.Journal.ISOAbbreviation.length()) {
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newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.Article.Journal.ISOAbbreviation.text().toString());
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} else if(citation.MedlineJournalInfo.MedlineTA.length()) {
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newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.MedlineJournalInfo.MedlineTA.text().toString());
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}
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if(article.Journal.Title.length()) {
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newItem.publicationTitle = Zotero.Utilities.superCleanString(article.Journal.Title.text().toString());
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} else if(newItem.journalAbbreviation.length()) {
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newItem.publicationTitle = newItem.journalAbbreviation;
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}
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if(article.Journal.JournalIssue.length()) {
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newItem.volume = article.Journal.JournalIssue.Volume.text().toString();
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newItem.issue = article.Journal.JournalIssue.Issue.text().toString();
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if(article.Journal.JournalIssue.PubDate.length()) { // try to get the date
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if(article.Journal.JournalIssue.PubDate.Day.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Day.text().toString()+", "+article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.Month.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.Year.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.Year.text().toString();
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} else if(article.Journal.JournalIssue.PubDate.MedlineDate.text().toString() != "") {
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newItem.date = article.Journal.JournalIssue.PubDate.MedlineDate.text().toString();
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}
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}
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}
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}
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if(article.AuthorList.length() && article.AuthorList.Author.length()) {
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var authors = article.AuthorList.Author;
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for(var j=0; j<authors.length(); j++) {
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var lastName = authors[j].LastName.text().toString();
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var firstName = authors[j].FirstName.text().toString();
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if(firstName == "") {
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firstName = authors[j].ForeName.text().toString();
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}
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var suffix = authors[j].Suffix.text().toString();
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if(suffix && firstName != "") {
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firstName += ", " + authors[j].Suffix.text().toString();
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}
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if(firstName || lastName) {
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newItem.creators.push({lastName:lastName, firstName:firstName});
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}
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}
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}
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if (citation.MeshHeadingList && citation.MeshHeadingList.MeshHeading) {
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var keywords = citation.MeshHeadingList.MeshHeading;
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for (var k = 0 ; k < keywords.length() ; k++) {
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newItem.tags.push(keywords[k].DescriptorName.text().toString());
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}
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}
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newItem.abstractNote = article.Abstract.AbstractText.toString()
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newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId.(@IdType == "doi" ).text().toString();
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newItem.publicationTitle = Zotero.Utilities.capitalizeTitle(newItem.publicationTitle);
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newItem.complete();
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}
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}
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function doWeb(doc, url) {
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