Add Chrome/Safari-compatible PubMed
This commit is contained in:
Simon Kornblith
parent
3b2cc93269
commit
3dcb45d6ac
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@ -4,12 +4,13 @@
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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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"minVersion":"2.1.9",
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"maxVersion":"",
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"priority":100,
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"browserSupport":"gcs",
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"configOptions":{"dataMode":"block"},
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"inRepository":true,
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"lastUpdated":"2011-04-25 18:05:00"
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"lastUpdated":"2011-07-01 04:22:03"
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}
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function detectWeb(doc, url) {
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@ -91,9 +92,6 @@ function detectImport() {
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}
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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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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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@ -101,28 +99,30 @@ function doImportFromText(text) {
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text = "<PubmedArticleSet>" + text + "</PubmedArticleSet>";
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}
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var xml = new XML(text);
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// parse XML with DOMParser
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var parser = new DOMParser();
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var doc = parser.parseFromString(text, "text/xml");
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for(var i=0; i<xml.PubmedArticle.length(); i++) {
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var articles = ZU.xpath(doc, '/PubmedArticleSet/PubmedArticle');
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for(var i in articles) {
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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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var citation = ZU.xpath(articles[i], 'MedlineCitation');
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var PMID = ZU.xpathText(citation, 'PMID');
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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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var article = ZU.xpath(citation, 'Article');
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var title = ZU.xpathText(article, 'ArticleTitle');
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if(title) {
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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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}
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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 fullPageRange = ZU.xpathText(article, 'Pagination/MedlinePgn');
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if(fullPageRange) {
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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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@ -135,75 +135,87 @@ function doImportFromText(text) {
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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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var journal = ZU.xpath(article, 'Journal');
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if(journal.length) {
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newItem.ISSN = ZU.xpathText(journal, 'ISSN');
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var abbreviation;
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if((abbreviation = ZU.xpathText(journal, 'ISOAbbreviation'))) {
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newItem.journalAbbreviation = abbreviation;
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} else if((abbreviation = ZU.xpathText(journal, 'MedlineTA'))) {
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newItem.journalAbbreviation = abbreviation;
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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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var title = ZU.xpathText(journal, 'Title');
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if(title) {
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newItem.publicationTitle = title;
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} else if(newItem.journalAbbreviation) {
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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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var journalIssue = ZU.xpath(journal, 'JournalIssue');
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if(journalIssue.length) {
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newItem.volume = ZU.xpathText(journalIssue, 'Volume');
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newItem.issue = ZU.xpathText(journalIssue, 'Issue');
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var pubDate = ZU.xpath(journalIssue, 'PubDate');
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if(pubDate.length) { // try to get the date
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var day = ZU.xpathText(pubDate, 'Day');
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var month = ZU.xpathText(pubDate, 'Month');
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var year = ZU.xpathText(pubDate, 'Year');
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if(day) {
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newItem.date = month+" "+day+", "+year;
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} else if(month) {
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newItem.date = month+" "+year;
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} else if(year) {
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newItem.date = year;
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} else {
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newItem.date = ZU.xpathText(pubDate, 'MedlineDate');
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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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var authors = ZU.xpath(article, 'AuthorList/Author');
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for(var j in authors) {
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var author = authors[j];
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var lastName = ZU.xpathText(author, 'LastName');
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var firstName = ZU.xpathText(author, 'FirstName');
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if(!firstName) {
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firstName = ZU.xpathText(author, 'ForeName');
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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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var suffix = ZU.xpathText(author, 'Suffix');
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if(suffix && firstName) {
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firstName += ", " + suffix
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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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var keywords = ZU.xpath(citation, 'MeshHeadingList/MeshHeading');
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for(var k in keywords) {
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newItem.tags.push(ZU.xpathText(keywords[k], 'DescriptorName'));
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}
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}
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// We use a regex to remove the section labels
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// also, we have entities to clear up
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newItem.abstractNote = Zotero.Utilities.unescapeHTML(
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article.Abstract.AbstractText.toString()
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.replace(/<\/?AbstractText\s*(?:Label=")?([^">]+)?[^>]*>/g, "$1\n")
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);
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newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId.(@IdType == "doi" ).text().toString();
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var abstractSections = ZU.xpath(article, 'Abstract/AbstractText');
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var abstractNote = [];
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for(var j in abstractSections) {
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var abstractSection = abstractSections[j];
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if(abstractSection.hasAttribute("Label")) {
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abstractNote.push(abstractSection.getAttribute("Label"));
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}
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abstractNote.push(abstractSection.textContent+"\n");
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}
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newItem.abstractNote = abstractNote.join("\n\n");
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newItem.DOI = ZU.xpathText(articles[i], 'PubmedData/ArticleIdList/ArticleId[@IdType="doi"]');
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// (do we want this?)
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if(newItem.publicationTitle) {
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newItem.publicationTitle = Zotero.Utilities.capitalizeTitle(newItem.publicationTitle);
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}
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newItem.complete();
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}
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}
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@ -238,8 +250,7 @@ function doWeb(doc, url) {
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items[uid.value] = article.textContent;
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}
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items = Zotero.selectItems(items);
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Zotero.selectItems(items, function(items) {
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if(!items) {
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return true;
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}
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@ -249,6 +260,7 @@ function doWeb(doc, url) {
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}
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lookupPMIDs(ids);
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});
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} else {
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ids.push(uid.value);
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lookupPMIDs(ids, doc);
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@ -293,3 +305,55 @@ function doSearch(item) {
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// pmid was defined earlier in detectSearch
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lookupPMIDs([getPMID(item.contextObject)]);
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}
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/** BEGIN TEST CASES **/
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var testCases = [
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{
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"type": "web",
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"url": "http://www.ncbi.nlm.nih.gov/pubmed/20729678",
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"items": [
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{
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"itemType": "journalArticle",
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"creators": [
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{
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"lastName": "Coar",
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"firstName": "Jaekea T"
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},
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{
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"lastName": "Sewell",
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"firstName": "Jeanne P"
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}
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],
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"notes": [],
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"tags": [
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"Bibliography as Topic",
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"Database Management Systems",
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"Humans"
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],
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"seeAlso": [],
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"attachments": [],
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"url": "http://www.ncbi.nlm.nih.gov/pubmed/20729678",
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"extra": "PMID: 20729678",
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"title": "Zotero: harnessing the power of a personal bibliographic manager",
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"pages": "205-207",
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"ISSN": "1538-9855",
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"journalAbbreviation": "Nurse Educ",
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"publicationTitle": "Nurse Educator",
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"volume": "35",
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"issue": "5",
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"date": "2010 Sep-Oct",
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"abstractNote": "Zotero is a powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the writer to focus on content, rather than the tedious details of formatting citations and references. Zotero 2.0 (http://www.zotero.org) has new features including the ability to synchronize citations with the off-site Zotero server and the ability to collaborate and share with others. An overview on how to use the software and discussion about the strengths and limitations are included.\u000a",
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"DOI": "10.1097/NNE.0b013e3181ed81e4",
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"libraryCatalog": "NCBI PubMed",
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"shortTitle": "Zotero"
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}
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]
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},
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{
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"type": "web",
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"url": "http://www.ncbi.nlm.nih.gov/pubmed?term=zotero",
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"items": "multiple"
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}
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]
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/** END TEST CASES **/
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