commit 3dcb45d6ac28397780b0308b039bdc762190ed9a
parent 3b2cc93269e8405861d4bb01c75220379d1ed01d
Author: Simon Kornblith <simon@simonster.com>
Date: Fri, 1 Jul 2011 04:21:20 +0000
Add Chrome/Safari-compatible PubMed
Diffstat:
1 file changed, 150 insertions(+), 85 deletions(-)
diff --git a/translators/NCBI PubMed.js b/translators/NCBI PubMed.js
@@ -4,12 +4,13 @@
"label":"NCBI PubMed",
"creator":"Simon Kornblith, Michael Berkowitz, Avram Lyon, and Rintze Zelle",
"target":"https?://[^/]*(www|preview)\\.ncbi\\.nlm\\.nih\\.gov[^/]*/(pubmed|sites/pubmed|sites/entrez|entrez/query\\.fcgi\\?.*db=PubMed)",
- "minVersion":"2.1b1",
+ "minVersion":"2.1.9",
"maxVersion":"",
"priority":100,
+ "browserSupport":"gcs",
"configOptions":{"dataMode":"block"},
"inRepository":true,
- "lastUpdated":"2011-04-25 18:05:00"
+ "lastUpdated":"2011-07-01 04:22:03"
}
function detectWeb(doc, url) {
@@ -91,9 +92,6 @@ function detectImport() {
}
function doImportFromText(text) {
- // Remove xml parse instruction and doctype
- text = text.replace(/<!DOCTYPE[^>]*>/, "").replace(/<\?xml[^>]*\?>/, "");
-
if (!text.substr(0,1000).match(/<PubmedArticleSet>/)) {
// Pubmed data in the wild, perhaps copied from the web site's search results,
// can be missing the <PubmedArticleSet> root tag. Let's add a pair!
@@ -101,28 +99,30 @@ function doImportFromText(text) {
text = "<PubmedArticleSet>" + text + "</PubmedArticleSet>";
}
- var xml = new XML(text);
+ // parse XML with DOMParser
+ var parser = new DOMParser();
+ var doc = parser.parseFromString(text, "text/xml");
- for(var i=0; i<xml.PubmedArticle.length(); i++) {
+ var articles = ZU.xpath(doc, '/PubmedArticleSet/PubmedArticle');
+ for(var i in articles) {
var newItem = new Zotero.Item("journalArticle");
- var citation = xml.PubmedArticle[i].MedlineCitation;
-
- var PMID = citation.PMID.text().toString();
+ var citation = ZU.xpath(articles[i], 'MedlineCitation');
+ var PMID = ZU.xpathText(citation, 'PMID');
newItem.url = "http://www.ncbi.nlm.nih.gov/pubmed/" + PMID;
newItem.extra = "PMID: "+PMID;
- var article = citation.Article;
- if(article.ArticleTitle.length()) {
- var title = article.ArticleTitle.text().toString();
+ var article = ZU.xpath(citation, 'Article');
+ var title = ZU.xpathText(article, 'ArticleTitle');
+ if(title) {
if(title.substr(-1) == ".") {
title = title.substring(0, title.length-1);
}
newItem.title = title;
}
-
- if (article.Pagination.MedlinePgn.length()){
- var fullPageRange = article.Pagination.MedlinePgn.text().toString();
+
+ var fullPageRange = ZU.xpathText(article, 'Pagination/MedlinePgn');
+ if(fullPageRange) {
var pageRange = fullPageRange.match(/\d+-\d+/g);
for (var j in pageRange) {
var pageRangeStart = pageRange[j].match(/^\d+/)[0];
@@ -134,76 +134,88 @@ function doImportFromText(text) {
}
newItem.pages = fullPageRange;
}
-
- if(article.Journal.length()) {
- var issn = article.Journal.ISSN.text().toString();
- if(issn) {
- newItem.ISSN = issn;
+
+ var journal = ZU.xpath(article, 'Journal');
+ if(journal.length) {
+ newItem.ISSN = ZU.xpathText(journal, 'ISSN');
+
+ var abbreviation;
+ if((abbreviation = ZU.xpathText(journal, 'ISOAbbreviation'))) {
+ newItem.journalAbbreviation = abbreviation;
+ } else if((abbreviation = ZU.xpathText(journal, 'MedlineTA'))) {
+ newItem.journalAbbreviation = abbreviation;
}
-
- if(citation.Article.Journal.ISOAbbreviation.length()) {
- newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.Article.Journal.ISOAbbreviation.text().toString());
- } else if(citation.MedlineJournalInfo.MedlineTA.length()) {
- newItem.journalAbbreviation = Zotero.Utilities.superCleanString(citation.MedlineJournalInfo.MedlineTA.text().toString());
- }
-
- if(article.Journal.Title.length()) {
- newItem.publicationTitle = Zotero.Utilities.superCleanString(article.Journal.Title.text().toString());
- } else if(newItem.journalAbbreviation.length()) {
+
+ var title = ZU.xpathText(journal, 'Title');
+ if(title) {
+ newItem.publicationTitle = title;
+ } else if(newItem.journalAbbreviation) {
newItem.publicationTitle = newItem.journalAbbreviation;
}
-
- if(article.Journal.JournalIssue.length()) {
- newItem.volume = article.Journal.JournalIssue.Volume.text().toString();
- newItem.issue = article.Journal.JournalIssue.Issue.text().toString();
- if(article.Journal.JournalIssue.PubDate.length()) { // try to get the date
- if(article.Journal.JournalIssue.PubDate.Day.text().toString() != "") {
- newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Day.text().toString()+", "+article.Journal.JournalIssue.PubDate.Year.text().toString();
- } else if(article.Journal.JournalIssue.PubDate.Month.text().toString() != "") {
- newItem.date = article.Journal.JournalIssue.PubDate.Month.text().toString()+" "+article.Journal.JournalIssue.PubDate.Year.text().toString();
- } else if(article.Journal.JournalIssue.PubDate.Year.text().toString() != "") {
- newItem.date = article.Journal.JournalIssue.PubDate.Year.text().toString();
- } else if(article.Journal.JournalIssue.PubDate.MedlineDate.text().toString() != "") {
- newItem.date = article.Journal.JournalIssue.PubDate.MedlineDate.text().toString();
+
+ var journalIssue = ZU.xpath(journal, 'JournalIssue');
+ if(journalIssue.length) {
+ newItem.volume = ZU.xpathText(journalIssue, 'Volume');
+ newItem.issue = ZU.xpathText(journalIssue, 'Issue');
+ var pubDate = ZU.xpath(journalIssue, 'PubDate');
+ if(pubDate.length) { // try to get the date
+ var day = ZU.xpathText(pubDate, 'Day');
+ var month = ZU.xpathText(pubDate, 'Month');
+ var year = ZU.xpathText(pubDate, 'Year');
+
+ if(day) {
+ newItem.date = month+" "+day+", "+year;
+ } else if(month) {
+ newItem.date = month+" "+year;
+ } else if(year) {
+ newItem.date = year;
+ } else {
+ newItem.date = ZU.xpathText(pubDate, 'MedlineDate');
}
}
}
}
- if(article.AuthorList.length() && article.AuthorList.Author.length()) {
- var authors = article.AuthorList.Author;
- for(var j=0; j<authors.length(); j++) {
- var lastName = authors[j].LastName.text().toString();
- var firstName = authors[j].FirstName.text().toString();
- if(firstName == "") {
- firstName = authors[j].ForeName.text().toString();
- }
- var suffix = authors[j].Suffix.text().toString();
- if(suffix && firstName != "") {
- firstName += ", " + authors[j].Suffix.text().toString();
- }
- if(firstName || lastName) {
- newItem.creators.push({lastName:lastName, firstName:firstName});
- }
+ var authors = ZU.xpath(article, 'AuthorList/Author');
+ for(var j in authors) {
+ var author = authors[j];
+
+ var lastName = ZU.xpathText(author, 'LastName');
+ var firstName = ZU.xpathText(author, 'FirstName');
+ if(!firstName) {
+ firstName = ZU.xpathText(author, 'ForeName');
+ }
+ var suffix = ZU.xpathText(author, 'Suffix');
+ if(suffix && firstName) {
+ firstName += ", " + suffix
+ }
+ if(firstName || lastName) {
+ newItem.creators.push({lastName:lastName, firstName:firstName});
}
}
-
-
- if (citation.MeshHeadingList && citation.MeshHeadingList.MeshHeading) {
- var keywords = citation.MeshHeadingList.MeshHeading;
- for (var k = 0 ; k < keywords.length() ; k++) {
- newItem.tags.push(keywords[k].DescriptorName.text().toString());
+
+
+ var keywords = ZU.xpath(citation, 'MeshHeadingList/MeshHeading');
+ for(var k in keywords) {
+ newItem.tags.push(ZU.xpathText(keywords[k], 'DescriptorName'));
+ }
+
+ var abstractSections = ZU.xpath(article, 'Abstract/AbstractText');
+ var abstractNote = [];
+ for(var j in abstractSections) {
+ var abstractSection = abstractSections[j];
+ if(abstractSection.hasAttribute("Label")) {
+ abstractNote.push(abstractSection.getAttribute("Label"));
}
+ abstractNote.push(abstractSection.textContent+"\n");
+ }
+
+ newItem.abstractNote = abstractNote.join("\n\n");
+ newItem.DOI = ZU.xpathText(articles[i], 'PubmedData/ArticleIdList/ArticleId[@IdType="doi"]');
+ // (do we want this?)
+ if(newItem.publicationTitle) {
+ newItem.publicationTitle = Zotero.Utilities.capitalizeTitle(newItem.publicationTitle);
}
- // We use a regex to remove the section labels
- // also, we have entities to clear up
- newItem.abstractNote = Zotero.Utilities.unescapeHTML(
- article.Abstract.AbstractText.toString()
- .replace(/<\/?AbstractText\s*(?:Label=")?([^">]+)?[^>]*>/g, "$1\n")
- );
-
- newItem.DOI = xml.PubmedArticle[i].PubmedData.ArticleIdList.ArticleId.(@IdType == "doi" ).text().toString();
- newItem.publicationTitle = Zotero.Utilities.capitalizeTitle(newItem.publicationTitle);
newItem.complete();
}
}
@@ -238,17 +250,17 @@ function doWeb(doc, url) {
items[uid.value] = article.textContent;
}
- items = Zotero.selectItems(items);
-
- if(!items) {
- return true;
- }
-
- for(var i in items) {
- ids.push(i);
- }
-
- lookupPMIDs(ids);
+ Zotero.selectItems(items, function(items) {
+ if(!items) {
+ return true;
+ }
+
+ for(var i in items) {
+ ids.push(i);
+ }
+
+ lookupPMIDs(ids);
+ });
} else {
ids.push(uid.value);
lookupPMIDs(ids, doc);
@@ -293,3 +305,55 @@ function doSearch(item) {
// pmid was defined earlier in detectSearch
lookupPMIDs([getPMID(item.contextObject)]);
}
+
+
+/** BEGIN TEST CASES **/
+var testCases = [
+ {
+ "type": "web",
+ "url": "http://www.ncbi.nlm.nih.gov/pubmed/20729678",
+ "items": [
+ {
+ "itemType": "journalArticle",
+ "creators": [
+ {
+ "lastName": "Coar",
+ "firstName": "Jaekea T"
+ },
+ {
+ "lastName": "Sewell",
+ "firstName": "Jeanne P"
+ }
+ ],
+ "notes": [],
+ "tags": [
+ "Bibliography as Topic",
+ "Database Management Systems",
+ "Humans"
+ ],
+ "seeAlso": [],
+ "attachments": [],
+ "url": "http://www.ncbi.nlm.nih.gov/pubmed/20729678",
+ "extra": "PMID: 20729678",
+ "title": "Zotero: harnessing the power of a personal bibliographic manager",
+ "pages": "205-207",
+ "ISSN": "1538-9855",
+ "journalAbbreviation": "Nurse Educ",
+ "publicationTitle": "Nurse Educator",
+ "volume": "35",
+ "issue": "5",
+ "date": "2010 Sep-Oct",
+ "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",
+ "DOI": "10.1097/NNE.0b013e3181ed81e4",
+ "libraryCatalog": "NCBI PubMed",
+ "shortTitle": "Zotero"
+ }
+ ]
+ },
+ {
+ "type": "web",
+ "url": "http://www.ncbi.nlm.nih.gov/pubmed?term=zotero",
+ "items": "multiple"
+ }
+]
+/** END TEST CASES **/
+\ No newline at end of file
