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Trans: Adding Gene Ontology translator. Thanks to Amelia Ireland for submitting!

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Avram Lyon 2011-01-29 10:26:36 +00:00
parent e1c770bef7
commit 5336df69c3
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translators/GeneOntology.org.js Normal file
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{
"translatorID":"cee0cca2-e82a-4618-b6cf-16327970169d",
"translatorType":4,
"label":"Gene Ontology",
"creator":"Amelia Ireland",
"target":"^https?:\/\/.*\\.geneontology\\.org",
"minVersion":"2.0",
"maxVersion":"",
"priority":100,
"inRepository":false,
"lastUpdated":"2011-01-27 21:28:58"
}
/*
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 namespace = doc.documentElement.namespaceURI;
var nsResolver = namespace ? function(prefix) {
if (prefix == "x" ) return namespace; else return null;
} : null;
var xPath = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
var cites = doc.evaluate(xPath, doc, nsResolver, XPathResult.ANY_TYPE, null).iterateNext();
if (cites)
{ Zotero.debug("Found some cites!");
return "multiple";
}
}
function doWeb(doc, url) {
var namespace = doc.documentElement.namespaceURI;
var nsResolver = namespace ? function(prefix) {
if (prefix == 'x') return namespace; else return null;
} : null;
var myPMID = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
var pmids = doc.evaluate(myPMID, doc, nsResolver, 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!" );
}
// get the data from the NCBI server
var pmids = pmid_list.join(",");
var url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=" + pmids;
Zotero.Utilities.HTTP.doGet(url, function(text) {
// load translator for PubMed
var translator = Zotero.loadTranslator("import");
// var translator = Zotero.Translate.Import;
translator.setTranslator("fcf41bed-0cbc-3704-85c7-8062a0068a7a");
translator.setString(text);
// don't save when item is done
translator.setHandler("itemDone", function(obj, item) {
items[item.extra] = item;
selectArray[item.extra] = item.title;
});
translator.translate();
// all pmids retrieved now
selectArray = Zotero.selectItems(selectArray);
for(var PMID in selectArray) {
items[PMID].complete();
}
Zotero.done();
});
Zotero.wait();
}