114 lines
3.4 KiB
JavaScript
114 lines
3.4 KiB
JavaScript
{
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"translatorID":"cee0cca2-e82a-4618-b6cf-16327970169d",
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"translatorType":4,
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"label":"Gene Ontology",
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"creator":"Amelia Ireland",
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"target":"^https?:\/\/.*\\.geneontology\\.org",
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"minVersion":"2.0",
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"maxVersion":"",
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"priority":100,
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"inRepository":false,
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"lastUpdated":"2011-01-27 21:28:58"
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}
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/*
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Gene Ontology website translator
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Copyright (C) 2010-2011 girlwithglasses, amelia.ireland@gmail.com
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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*/
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/*
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This translator works on cited PubMed references on the Gene Ontology website.
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It makes use of the code of the existing PubMed translator; thanks to the
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authors of that translator for their premium quality code.
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*/
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var items = {};
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var selectArray = {};
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function detectWeb(doc, url) {
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var namespace = doc.documentElement.namespaceURI;
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var nsResolver = namespace ? function(prefix) {
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if (prefix == "x" ) return namespace; else return null;
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} : null;
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var xPath = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
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var cites = doc.evaluate(xPath, doc, nsResolver, XPathResult.ANY_TYPE, null).iterateNext();
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if (cites)
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{ Zotero.debug("Found some cites!");
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return "multiple";
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}
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}
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function doWeb(doc, url) {
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var namespace = doc.documentElement.namespaceURI;
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var nsResolver = namespace ? function(prefix) {
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if (prefix == 'x') return namespace; else return null;
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} : null;
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var myPMID = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
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var pmids = doc.evaluate(myPMID, doc, nsResolver, XPathResult.ANY_TYPE, null);
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var pmid_list = new Array();
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var unknown_list = new Array();
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var x;
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while (x = pmids.iterateNext()) {
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if (x.href && x.href.match('pubmed')) {
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// get the number
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var n = x.href.lastIndexOf("/");
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n++;
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pmid_list.push(x.href.substr(n));
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// Zotero.debug("Got a pubmed href! " + x.href.substr(n));
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}
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else {
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unknown_list.push(x);
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}
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}
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if (unknown_list.length > 0) {
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// Zotero.debug("Couldn't work out what to do with these refs: " + unknown_list.join("\n"));
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}
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if (pmid_list.length > 0) {
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Zotero.debug( "Found " + pmid_list.length + " PMIDs!" );
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}
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// get the data from the NCBI server
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var pmids = pmid_list.join(",");
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var url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=" + pmids;
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Zotero.Utilities.HTTP.doGet(url, function(text) {
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// load translator for PubMed
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var translator = Zotero.loadTranslator("import");
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// var translator = Zotero.Translate.Import;
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translator.setTranslator("fcf41bed-0cbc-3704-85c7-8062a0068a7a");
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translator.setString(text);
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// don't save when item is done
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translator.setHandler("itemDone", function(obj, item) {
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items[item.extra] = item;
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selectArray[item.extra] = item.title;
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});
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translator.translate();
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// all pmids retrieved now
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selectArray = Zotero.selectItems(selectArray);
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for(var PMID in selectArray) {
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items[PMID].complete();
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}
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Zotero.done();
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});
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Zotero.wait();
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}
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