Permalink
Cannot retrieve contributors at this time
Join GitHub today
GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.
Sign up
Fetching contributors…
![](https://scholarlyorphans.org/memento/20200720134642im_/https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif)
{ | |
"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 **/ |