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{
"translatorID": "cee0cca2-e82a-4618-b6cf-16327970169d",
"label": "Gene Ontology",
"creator": "Amelia Ireland",
"target": "^https?://.*\\.geneontology\\.org",
"minVersion": "2.0",
"maxVersion": "",
"priority": 100,
"inRepository": true,
"translatorType": 4,
"browserSupport": "gcv",
"lastUpdated": "2014-01-05 11:26:46"
}
/*
Gene Ontology website translator
Copyright (C) 2010-2011 girlwithglasses, amelia.ireland@gmail.com
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
This translator works on cited PubMed references on the Gene Ontology website.
It makes use of the code of the existing PubMed translator; thanks to the
authors of that translator for their premium quality code.
*/
var items = {};
var selectArray = {};
function detectWeb(doc, url) {
var xPath = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
var cites = doc.evaluate(xPath, doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (cites)
{ Zotero.debug("Found some cites!");
return "multiple";
}
}
function doWeb(doc, url) {
var PMIDs = getPMIDs(doc);
retrievePMIDs(PMIDs, doc);
}
function getPMIDs(doc){
var myPMID = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
var pmids = doc.evaluate(myPMID, doc, null, XPathResult.ANY_TYPE, null);
var pmid_list = new Array();
var unknown_list = new Array();
var x;
while (x = pmids.iterateNext()) {
if (x.href && x.href.match('pubmed')) {
// get the number
var n = x.href.lastIndexOf("/");
n++;
pmid_list.push(x.href.substr(n));
// Zotero.debug("Got a pubmed href! " + x.href.substr(n));
}
else {
unknown_list.push(x);
}
}
if (unknown_list.length > 0) {
// Zotero.debug("Couldn't work out what to do with these refs: " + unknown_list.join("\n"));
}
if (pmid_list.length > 0) {
Zotero.debug( "Found " + pmid_list.length + " PMIDs!" );
}
return pmid_list;
}
function retrievePMIDs(PMIDs, doc){
_numPMIDs = PMIDs.length;
for (var i=0; i<_numPMIDs; i++){
(function(doc, PMID) {
var translate = Zotero.loadTranslator("search");
translate.setTranslator("fcf41bed-0cbc-3704-85c7-8062a0068a7a");
var item = {"itemType":"journalArticle", "PMID":PMID};
translate.setSearch(item);
// don't save when item is done
translate.setHandler("itemDone", function(translate, item) {
item.repository = "CrossRef";
items[PMID] = item;
selectArray[PMID] = item.title;
});
translate.setHandler("done", function(translate) {
_numPMIDs--;
if(_numPMIDs <= 0) {
completePMIDs(doc);
}
});
// Don't throw on error
translate.setHandler("error", function() {});
translate.translate();
})(doc, PMIDs[i]);
}
}
function completePMIDs(doc) {
// all PMIDs retrieved now
// check to see if there is more than one DOI
var numPMIDs = 0;
for(var PMID in selectArray) {
numPMIDs++;
if(numPMIDs == 1) break;
}
if(numPMIDs == 0) {
throw "Could not find PMID";
} else {
Zotero.selectItems(selectArray, function(selectedPMIDs) {
if(!selectedPMIDs) return true;
for(var PMID in selectedPMIDs) {
items[PMID].complete();
}
});
}
}
/** BEGIN TEST CASES **/
var testCases = [
{
"type": "web",
"url": "http://www.geneontology.org/GO.cite.shtml",
"items": "multiple"
}
]
/** END TEST CASES **/
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