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translators/Gene Ontology.js
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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 **/ |