www

commit 5336df69c343ed53ac20a1079d4ab4b296126f3c
parent e1c770bef73c62ca1f0b3289d70af234f3e70158
Author: Avram Lyon <ajlyon@gmail.com>
Date:   Sat, 29 Jan 2011 10:26:36 +0000

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


Diffstat:
A
translators/GeneOntology.org.js
 | 
114
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

1 file changed, 114 insertions(+), 0 deletions(-)
diff --git a/translators/GeneOntology.org.js b/translators/GeneOntology.org.js
@@ -0,0 +1,114 @@
+{
+	"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();
+}