Initial Commit

translators/Gene Ontology.js

@@ -0,0 +1,128 @@
+{
+	"translatorID": "cee0cca2-e82a-4618-b6cf-16327970169d",
+	"label": "Gene Ontology",
+	"creator": "Amelia Ireland and Abe Jellinek",
+	"target": "^https?://(amigo\\.)?geneontology\\.org/",
+	"minVersion": "2.0",
+	"maxVersion": "",
+	"priority": 100,
+	"inRepository": true,
+	"translatorType": 4,
+	"browserSupport": "gcsibv",
+	"lastUpdated": "2021-06-18 21:31:51"
+}
+
+/*
+	Copyright (C) 2010-2021 girlwithglasses (amelia.ireland@gmail.com)
+							and Abe Jellinek
+
+	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 choices = {};
+var itemsRemaining = 0;
+
+function detectWeb(doc, _url) {
+	if (getPMIDs(doc, true)) {
+		Zotero.debug("Found some cites!");
+		return "multiple";
+	}
+	return false;
+}
+
+function getPMIDs(doc, checkOnly) {
+	var items = {};
+	var found = false;
+	var rows = doc.querySelectorAll('cite a[title*="PMID:"], cite a[href*="/pubmed/"]');
+	for (let row of rows) {
+		let pmid = (row.href.match(/\/pubmed\/([0-9]+)/) || [])[1];
+		if (!pmid) pmid = (row.textContent.match(/PMID:([0-9]+)/) || [])[1];
+		let title = ZU.trimInternal(row.textContent);
+		if (!pmid || !title) continue;
+		if (checkOnly) return true;
+		found = true;
+		items[pmid] = title;
+	}
+	return found ? items : false;
+}
+
+function doWeb(doc, _url) {
+	choices = getPMIDs(doc, false);
+	items = {};
+	
+	let pmids = Object.keys(choices);
+	itemsRemaining = pmids.length;
+	
+	for (let pmid of pmids) {
+		searchWithPMID(pmid, itemLookupComplete);
+	}
+}
+
+function searchWithPMID(pmid, callback) {
+	var translate = Zotero.loadTranslator("search");
+	translate.setTranslator("3d0231ce-fd4b-478c-b1d3-840389e5b68c"); // PubMed
+	
+	var item = { itemType: "journalArticle", PMID: pmid };
+	translate.setSearch(item);
+	
+	// Don't throw on error
+	translate.setHandler("error", function () {
+		callback(null);
+	});
+
+	// don't save immediately when item is done
+	translate.setHandler("itemDone", function (translate, item) {
+		item.itemID = pmid;
+		callback(item);
+	});
+
+	translate.translate();
+}
+
+function itemLookupComplete(item) {
+	itemsRemaining--;
+	
+	if (item) {
+		choices[item.itemID] = item.title;
+		items[item.itemID] = item;
+	}
+	
+	if (itemsRemaining <= 0) {
+		Zotero.selectItems(choices, function (selected) {
+			if (selected) {
+				for (let selectedPMID of Object.keys(selected)) {
+					items[selectedPMID].complete();
+				}
+			}
+		});
+	}
+}
+
+/** BEGIN TEST CASES **/
+var testCases = [
+	{
+		"type": "web",
+		"url": "http://amigo.geneontology.org/amigo/term/GO:0048003",
+		"items": "multiple"
+	}
+]
+/** END TEST CASES **/