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