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Push PubMed and PubMed Central

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This commit is contained in:
Dan Stillman 2009-12-17 08:09:03 +00:00
parent f5a9dd6812
commit 9c31b10de7
3 changed files with 177 additions and 85 deletions
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2
repotime.txt
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@ -1 +1 @@
2009-11-19 05:05:00
2009-12-17 08:10:00

8
translators/NCBI PubMed.js
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@ -8,7 +8,7 @@
"maxVersion":"",
"priority":100,
"inRepository":true,
"lastUpdated":"2009-10-22 19:00:00"
"lastUpdated":"2009-12-17 08:10:00"
}
function detectWeb(doc, url) {
@ -27,10 +27,10 @@ function detectWeb(doc, url) {
}
}
var uids = doc.evaluate('//input[@type="checkbox" or @name="uid"]', doc,
var uids = doc.evaluate('//input[@type="checkbox" and @name="EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum.uid"]', doc,
nsResolver, XPathResult.ANY_TYPE, null);
if(uids.iterateNext() && doc.title.indexOf("PMC Results") == -1) {
if (uids.iterateNext() && doc.title.indexOf("PMC Results") == -1){
if(uids.iterateNext()) {
if (uids.iterateNext()){
return "multiple";
}
return "journalArticle";

252
translators/PubMed Central.js
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@ -2,95 +2,187 @@
"translatorID":"27ee5b2c-2a5a-4afc-a0aa-d386642d4eed",
"translatorType":4,
"label":"PubMed Central",
"creator":"Michael Berkowitz",
"creator":"Michael Berkowitz and Rintze Zelle",
"target":"http://[^/]*.nih.gov/",
"minVersion":"1.0.0b4.r5",
"maxVersion":"",
"priority":100,
"inRepository":true,
"lastUpdated":"2009-10-02 04:50:00"
"lastUpdated":"2009-12-17 08:10:00"
}
function detectWeb(doc, url) {
if (doc.evaluate('//table[@id="ResultPanel"]//td[2]', doc, null, XPathResult.ANY_TYPE, null).iterateNext()) {
return "multiple";
} else if (url.indexOf("articlerender") != -1) {
return "journalArticle";
}
var namespace = doc.documentElement.namespaceURI;
var nsResolver = namespace ? function(prefix) {
if (prefix == 'x') return namespace; else return null;
} : null;
try {var pmid = url.match(/ncbi\.nlm\.nih\.gov\/pmc\/articles\/PMC([\d]+)/)[1];} catch (e) {}
if (pmid) {
return "journalArticle";
}
var uids = doc.evaluate('//div[@class="toc-pmcid"]', doc, nsResolver, XPathResult.ANY_TYPE, null);
if(uids.iterateNext()) {
if (uids.iterateNext()){
return "multiple";
}
return "journalArticle";
}
}
function lookupPMCIDs(ids, doc) {
Zotero.wait();
var newUri = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&retmode=xml&id=" + ids.join(",");
Zotero.debug(newUri);
Zotero.Utilities.HTTP.doGet(newUri, function (text) {
text = text.replace(/<!DOCTYPE[^>]*>/, "").replace(/<\?xml[^>]*\?>/, ""); // Remove xml parse instruction and doctype
text = text.replace(/(<[^!>][^>]*>)/g, function replacer(str, p1, p2, offset, s) {
return str.replace(/-/gm, "");
}); //Strip hyphens from element names, attribute names and attribute values
text = text.replace(/(<[^!>][^>]*>)/g, function replacer(str, p1, p2, offset, s) {
return str.replace(/:/gm, "");
}); //Strip colons from element names, attribute names and attribute values
text = Zotero.Utilities.trim(text);
XML.prettyPrinting = false;
XML.ignoreWhitespace = false;
var xml = new XML(text);
for (var i = 0; i < xml.article.length(); i++) {
var newItem = new Zotero.Item("journalArticle");
var journal = xml.article[i].front.journalmeta;
if (journal.journalid.(@journalidtype == "nlmta").length()) {
newItem.journalAbbreviation = Zotero.Utilities.superCleanString(journal.journalid.(@journalidtype == "nlmta").text().toString());
}
newItem.publicationTitle = Zotero.Utilities.superCleanString(journal.journaltitle.text().toString());
var issn = journal.issn.(@pubtype == "epub").text().toString();
var issn = journal.issn.(@pubtype == "ppub").text().toString();
if (issn) {
newItem.ISSN = issn;
}
var article = xml.article[i].front.articlemeta;
if (article.abstract.p.length()) {
newItem.abstractNote = Zotero.Utilities.unescapeHTML(article.abstract.p.toXMLString());
}
if (article.articleid.(@pubidtype == "doi").length()) {
newItem.DOI = article.articleid.(@pubidtype == "doi").text().toString();
}
var PMID = article.articleid.(@pubidtype == "pmid").text().toString();
if (PMID) {
newItem.extra = "PMID: " + PMID + "\n";
}
newItem.extra = newItem.extra + "PMCID: " + ids[i];
newItem.title = Zotero.Utilities.unescapeHTML(article.titlegroup.articletitle.toXMLString().split("<xref")[0]);
if (article.volume.length()) {
newItem.volume = article.volume.text().toString();
}
if (article.issue.length()) {
newItem.issue = article.issue.text().toString();
}
if (article.lpage.length()) {
newItem.pages = article.fpage.text().toString() + "-" + article.lpage.text().toString();
} else if (article.fpage.length()) {
newItem.pages = article.fpage.text().toString()
}
var pubdate = article.pubdate. (@pubtype == "ppub");
if (!pubdate) {
var pubdate = article.pubdate. (@pubtype == "epub");
}
if (pubdate) {
if (pubdate.day.text().toString() != "") {
newItem.date = pubdate.year.text().toString() + "-" + pubdate.month.text().toString() + "-" + pubdate.day.text().toString();
} else if (pubdate.month.text().toString() != "") {
newItem.date = pubdate.year.text().toString() + "-" + pubdate.month.text().toString();
} else if (pubdate.year.text().toString() != "") {
newItem.date = pubdate.year.text().toString();
}
}
if (article.contribgroup.contrib.length()) {
var authors = article.contribgroup.contrib. (@contribtype == "author");
for (var j = 0; j < authors.length(); j++) {
var lastName = authors[j].name.surname.text().toString();
var firstName = authors[j].name.givennames.text().toString();
if (firstName || lastName) {
newItem.creators.push({
lastName: lastName,
firstName: firstName
});
}
}
}
var linkurl = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC" + ids[i] + "/";
newItem.attachments = [{
url: linkurl,
title: "PubMed Central Link",
mimeType: "text/html",
snapshot: false
}];
if (article.selfuri.@xlinkhref.length()) {
var pdfFileName = article.selfuri.@xlinkhref.toXMLString();
var pdfurl = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC" + ids[i] + "/pdf/" + pdfFileName;
newItem.attachments.push({
title:"PubMed Central Full Text PDF",
mimeType:"application/pdf",
url:pdfurl
});
}
newItem.complete();
}
Zotero.done();
});
}
function doWeb(doc, url) {
var tagMap = {journal_title:"publicationTitle",
title:"title",
date:"date",
issue:"issue",
volume:"volume",
doi:"DOI",
fulltext_html_url:"url"
};
var URIs = new Array();
var items = new Object();
if (doc.title.indexOf("PMC Results") != -1) {
var titlex = '//div[@class="toc-entry"]/div/div[@class="toc-title"]';
var linkx = '//div[@class="toc-entry"]/div/a[@class="toc-link"][1]';
var titles = doc.evaluate(titlex, doc, null, XPathResult.ANY_TYPE, null);
var next_title = titles.iterateNext();
var links = doc.evaluate(linkx, doc, null, XPathResult.ANY_TYPE, null);
var next_link = links.iterateNext();
while (next_title && next_link) {
items[next_link.href] = next_title.textContent;
next_title = titles.iterateNext();
next_link = links.iterateNext();
}
items = Zotero.selectItems(items);
if(!items) return true;
for (var i in items) {
URIs.push(i);
}
} else {
URIs.push(url);
}
Zotero.Utilities.HTTP.doGet(URIs, function(text) {
var tags = new Object();
var meta = text.match(/<meta[^>]*>/gi);
for (var i in meta) {
var item = meta[i].match(/=\"([^"]*)\"/g);
if (item[0].substring(2, 10) == 'citation') {
tags[item[0].substring(11, item[0].length - 1)] = item[1].substring(2, item[1].length - 1);
}
}
var newItem = new Zotero.Item("journalArticle");
for (var tag in tagMap) {
newItem[tagMap[tag]] = Zotero.Utilities.unescapeHTML(tags[tag]);
}
for (var i in meta) {
if (meta[i].match(/DC.Contributor/)) {
newItem.creators.push(Zotero.Utilities.cleanAuthor(Zotero.Utilities.unescapeHTML(meta[i].match(/content=\"([^"]*)\">/)[1]), "author"));
}
}
newItem.attachments.push({url:tags["fulltext_html_url"], title:"PubMed Central Snapshot", mimeType:"text/html"});
if (tags["pdf_url"]) {
newItem.attachments.push({url:tags["pdf_url"], title:"PubMed Central Full Text PDF", mimeType:"application/pdf"});
}
newItem.url = tags["fulltext_html_url"];
if (!newItem.url) newItem.url = tags["abstract_html_url"];
try {
newItem.extra = "PMCID: " + text.match(/PMCID: <\/span>(PMC\d+)/)[1];
} catch(e){
}
newItem.journalAbbreviation = text.match(/span class=\"citation-abbreviation\">([^<]+)</)[1];
newItem.pages = text.match(/span class=\"citation-flpages\">([^<]+)</)[1].replace(/[\.:\s]/g, "");
if (text.match(/Abstract<\/div>([^<]+)</)) {
var abstract = text.match(/Abstract<\/div>([^<]+)</)[1];
} else if (text.match(/\"section-content\"><!\-\-article\-meta\-\->([^<]+)/)) {
var abstract = text.match(/\"section-content\"><!\-\-article\-meta\-\->([^<]+)/)[1];
}
if (abstract) newItem.abstractNote = abstract;
newItem.complete();
}, function(){ Zotero.done();}
);
Zotero.wait();
var namespace = doc.documentElement.namespaceURI;
var nsResolver = namespace ?
function (prefix) {
if (prefix == 'x') return namespace;
else return null;
} : null;
var ids = new Array();
var pmcid;
var resultsCount = 0;
try {
pmcid = url.match(/ncbi\.nlm\.nih\.gov\/pmc\/articles\/PMC([\d]+)/)[1];
} catch(e) {}
if (pmcid) {
ids.push(pmcid);
lookupPMCIDs(ids, doc);
} else {
var pmcids = doc.evaluate('//div[@class="toc-pmcid"]', doc, nsResolver, XPathResult.ANY_TYPE, null);
var titles = doc.evaluate('//div[@class="toc-title"]', doc, nsResolver, XPathResult.ANY_TYPE, null);
var title;
while (pmcid = pmcids.iterateNext()) {
title = titles.iterateNext();
ids[pmcid.textContent.match(/PMC([\d]+)/)[1]] = title.textContent;
resultsCount = resultsCount + 1;
}
if (resultsCount > 1) {
ids = Zotero.selectItems(ids);
}
if (!ids) {
return true;
}
var pmcids = new Array();
for (var i in ids) {
pmcids.push(i);
}
lookupPMCIDs(pmcids, doc);
}
}