146 lines
3.8 KiB
JavaScript
146 lines
3.8 KiB
JavaScript
{
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"translatorID": "cee0cca2-e82a-4618-b6cf-16327970169d",
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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": true,
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"translatorType": 4,
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"browserSupport": "gcv",
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"lastUpdated": "2014-01-05 11:26:46"
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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 xPath = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
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var cites = doc.evaluate(xPath, doc, null, 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 PMIDs = getPMIDs(doc);
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retrievePMIDs(PMIDs, doc);
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}
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function getPMIDs(doc){
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var myPMID = '//cite//*[@class="pmid"] | //cite//a[contains (@href, "pubmed")]';
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var pmids = doc.evaluate(myPMID, doc, null, 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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return pmid_list;
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}
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function retrievePMIDs(PMIDs, doc){
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_numPMIDs = PMIDs.length;
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for (var i=0; i<_numPMIDs; i++){
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(function(doc, PMID) {
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var translate = Zotero.loadTranslator("search");
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translate.setTranslator("fcf41bed-0cbc-3704-85c7-8062a0068a7a");
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var item = {"itemType":"journalArticle", "PMID":PMID};
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translate.setSearch(item);
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// don't save when item is done
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translate.setHandler("itemDone", function(translate, item) {
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item.repository = "CrossRef";
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items[PMID] = item;
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selectArray[PMID] = item.title;
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});
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translate.setHandler("done", function(translate) {
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_numPMIDs--;
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if (numPMIDs <= 0) {
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completePMIDs(doc);
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}
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});
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// Don't throw on error
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translate.setHandler("error", function() {});
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translate.translate();
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})(doc, PMIDs[i]);
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}
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}
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function completePMIDs(doc) {
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// all PMIDs retrieved now
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// check to see if there is more than one DOI
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var numPMIDs = 0;
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for (var PMID in selectArray) {
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numPMIDs++;
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if (numPMIDs == 1) break;
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}
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if (numPMIDs == 0) {
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throw "Could not find PMID";
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} else {
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Zotero.selectItems(selectArray, function(selectedPMIDs) {
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if (!selectedPMIDs) return true;
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for (var PMID in selectedPMIDs) {
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items[PMID].complete();
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}
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});
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}
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}
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/** BEGIN TEST CASES **/
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var testCases = [
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{
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"type": "web",
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"url": "http://www.geneontology.org/GO.cite.shtml",
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"items": "multiple"
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}
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]
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/** END TEST CASES **/ |