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367
translators/Clinical Key.js
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367
translators/Clinical Key.js
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{
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"translatorID": "a55463ba-e403-415b-80d4-284d5f9b4b15",
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"label": "Clinical Key",
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"creator": "Jaret M. Karnuta, Mike Davidson",
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"target": "^https?://(www\\.|www-)clinicalkey(\\.|-)com",
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"minVersion": "3.0",
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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": "2017-01-30 08:08:52"
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}
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/*
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***** BEGIN LICENSE BLOCK *****
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Copyright © 2017 Jaret M. Karnuta & Mike Davidson
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This file is part of Zotero.
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Zotero is free software: you can redistribute it and/or modify
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it under the terms of the GNU Affero 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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Zotero 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 Affero General Public License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with Zotero. If not, see <http://www.gnu.org/licenses/>.
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***** END LICENSE BLOCK *****
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*/
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/*
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This translator is designed specifically for use on book section portions and journal articles of
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ClinicalKey. It will not work on book overview pages or journal table of contents pages.
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NB: url and doc.location.href are different. I think it is because of the way clinicalkey redirects.
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Replicate by going to a content page (/content/book/...) and then going to a broswing page (/browse/book/...).
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URL remains the page of the previous page (content page) and doc.location.href is the current page (as it should be).
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Hence, I never use url and change its content to doc.location.href in detectWeb, the only function that uses the url
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To get journal article metadata, Publisher Item Identifier (PIIs) are extracted from the Scopus EID
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and queried using the CrossRef REST API.
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Documentation at:
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https://github.com/CrossRef/rest-api-doc
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CrossReff REST API Return Values at:
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https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md
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*/
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function detectWeb(doc, url) {
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//see NB above for explanation
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url = doc.location.href;
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//contentType depends on url, which is present, but rest of site is loaded via ajax (I think)
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//monitor dom and reset if changes
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var jsession = doc.getElementById('jsessionid');
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if (jsession){
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Zotero.monitorDOMChanges(jsession, {attributes:true});
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if (!jsession.value){
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return;
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}
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}
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var contentType;
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//contains /content/book/ and does not contain login?
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if (url.indexOf("/content/book/") != -1 && url.indexOf("login?") == -1){
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contentType = "bookSection";
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}
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//similar structure to above
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else if (url.indexOf('/browse/book/') != -1 && url.indexOf("login?") == -1){
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contentType = "book";
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}
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// similar structure to above, for journal articles
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else if (url.indexOf('/content/journal/') != -1 && url.indexOf("login?") == -1){
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contentType = "journalArticle";
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}
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//contentType not set
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if (!contentType){
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return;
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}
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return contentType;
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}
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function doWeb(doc, url){
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var contentType = detectWeb(doc, url);
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//if book section
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if (contentType == 'bookSection'){
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var newItem = new Zotero.Item(contentType);
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newItem = scrapeBookSection(doc, newItem);
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//pdf (if present)
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var pdfLink = getPDFLink(doc);
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if (pdfLink) {
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newItem.attachments.push({
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url:pdfLink,
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title:"Book Section PDF",
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mimeType:"application/pdf"
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});
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}
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//populate common attributes
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//url, see NB above for explanation as to why url is NOT used
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newItem.url = doc.location.href;
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newItem.complete();
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}
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//if book, use ISBN translator
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//borrowed from amazon translator
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else if (contentType == 'book'){
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var isbn = ZU.xpath(doc, "//button/@data-metadata-isbn");
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if (!isbn){
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return;
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}
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isbn = ZU.cleanISBN(isbn[0].value);
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//use search translator to get metadata from isbn
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var search = Zotero.loadTranslator("search");
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//set translators and search
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search.setHandler("translators", function(obj, translators) {
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search.setTranslator(translators);
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search.setHandler("itemDone", function(obj, lookupItem) {
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newItem=lookupItem;
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//update ISBN
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newItem.ISBN = ZU.cleanISBN(isbn);
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//Override library catalog
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newItem.libraryCatalog = "Clinical Key";
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//update url, see NB for rationale why url not used
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newItem.url = doc.location.href;
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});
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search.translate();
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});
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//no need to override error handler
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//save item
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search.setHandler("done", function() {
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newItem.complete();
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});
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search.setSearch({ ISBN: isbn });
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search.getTranslators();
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}
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else if (contentType == 'journalArticle') {
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var eid;
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var pii;
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try {
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eid = url.split('/');
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pii = eid.pop().slice(7);
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if (!/^S(\d{15}X|\d{16})/.test(pii)){
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throw new Error('PII from url failed. Trying Xpath');
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}
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} catch(e) {
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Zotero.debug(e);
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eid = ZU.xpathText(doc, "//ul/@data-eid");
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pii = eid.slice(7);
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if (!/^S(\d{15}X|\d{16})/.test(pii)){
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throw new Error('PII from Xpath failed');
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}
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}
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queryCrossRef(pii, doc);
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}
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}
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//Search & Processing based on CrossRef.js translator
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function queryCrossRef (pii, doc){
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crossRefQuery = 'http://api.crossref.org/works?query=' + pii;
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//TODO: implement API version request
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//acceptHeader = {'Accept': 'application/vnd.crossref-api-message+json; version=1.0'}
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ZU.doGet(crossRefQuery, function(responseText) {
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processCrossRefREST(responseText, doc);
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});
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}
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function processCrossRefREST(jsonOutput, doc){
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var jsonParsed = JSON.parse(jsonOutput);
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if (jsonParsed['message']['total-results'] > 1) {
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// Multiple results shouldn't occur as pii is unique
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// handle only first returned object just in case
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Zotero.debug('Returned multiple results. Continue processing first');
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}
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else if (jsonParsed['message']['total-results'] == 0) {
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// If the search failed to find results
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Zotero.debug('Crossref API failed to find query match');
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return;
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}
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if (!/^1/.test(jsonParsed['message-version'])){
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// check that the API version is compatible with this translator
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// translator currently written according to v1
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Zotero.debug('Request returned wrong API version');
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}
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// shorten JSON to the single reference
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var ref = jsonParsed['message']['items'][0];
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if (ref['type'] == 'journal-article') {
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// prep for CSL JSON translator
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ref['type'] = 'article-journal';
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} else if (ref['type'] != 'journal-article') {
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// log the unexpected
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Zotero.debug('Returned unexpected reference type');
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}
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// use CSL JSON translator
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var text = JSON.stringify(ref);
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var trans = Zotero.loadTranslator('import');
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trans.setTranslator('bc03b4fe-436d-4a1f-ba59-de4d2d7a63f7');
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trans.setString(text);
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//Attempt to download fulltext PDF
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var pdfLink = getPDFLink(doc);
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trans.setHandler('itemDone', function(obj, item) {
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if (pdfLink)
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item.attachments.push({
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url:pdfLink,
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title:"Full Text PDF",
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mimeType:"application/pdf"
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});
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item.complete();
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});
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trans.translate();
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}
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function getPDFLink(doc) {
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var pdfLink = doc.getElementsByClassName('x-pdf')[0].href;
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if (!pdfLink) {
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pdfLink = ZU.xpathText(doc, './/*[@data-action="pdfDownload"]/@href');
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} else if (!pdfLink) {
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pdfLink = ZU.xpathText(doc, './/*[@action="download"]/@href');
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}
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return pdfLink;
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}
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function scrapeBookSection(doc, item){
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//book title
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var bookTitle = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.title"]');
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item.bookTitle = bookTitle;
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//section title
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var title = ZU.xpathText(doc, '//*[@ng-bind-html="ContentCtrl.title"]');
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item.title = title;
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//authors
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var authorsList = ZU.xpath(doc, '//ul[@ng-bind-html="XocsCtrl.authorsHtml"]/li/a');
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for (var i = 0;i<authorsList.length;i++){
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var author = authorsList[i].innerHTML;
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if (author.indexOf("<") != -1){
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author = author.split("<")[0];
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}
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item.creators.push(Zotero.Utilities.cleanAuthor(author, 'author'));
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}
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//chapter and page metadata
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var chapterAndPages = ZU.xpathText(doc,'//p[@class="source ng-binding"]');
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//make pattern that should capter pages if present
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//matches both xxx-xxx (length of #s not important)
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//and xxx-xxx.eY
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var pagesPattern = /\s\d+-\d+(\.e\d+)?/;
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var pagesMatch = chapterAndPages.match(pagesPattern);
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if (pagesMatch){
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//get whole regex match
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item.pages = pagesMatch[0];
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}
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//make pattern that will match to the chapter number
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var chapterPattern = /chapter\s(\d+)/i
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var chapterMatch = chapterAndPages.match(chapterPattern);
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if (chapterMatch){
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//get match within first group
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var chapterNumber = chapterMatch[1];
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item.notes.push({note:"Chapter: "+chapterNumber});
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}
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//ISBN metadata
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var isbn = ZU.xpath(doc, "//button/@data-metadata-isbn");
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if (isbn){
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var isbnNo = isbn[0].value;
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item.ISBN = isbn;
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}
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//edition metadata
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var edition = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.edition"]').split(/edition/i)[0].trim();
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//convert to number for correct zotero citation handling
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item.edition = textToNumber(edition);
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//publisher metadata
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var datePub = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.copyright"]');
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var datePattern = /\d{4}/g;
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var dateMatch = datePub.match(datePattern);
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if (dateMatch){
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item.date = dateMatch[0];
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}
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if (datePub.indexOf("imprint") != -1){
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var imprintPattern = /by\s(.*),.*imprint\sof\s(.*)\sInc/i;
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var imprintMatch = datePub.match(imprintPattern);
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if (imprintMatch){
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//expected number of matches
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if (imprintMatch.length == 3){
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item.publisher = imprintMatch[2]+"/"+imprintMatch[1];
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}
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//added for robustness
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else {
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var imprintPublisher=imprintMatch[0].replace("by","").trim();
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item.publisher=imprintPublisher;
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}
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}
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}
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else {
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var publisherPattern = /by\s(.*?)(,)?\s/;
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var publisherMatch = datePub.match(publisherPattern);
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if (publisherMatch){
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//get first matched group, between by and , or whitespace
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item.publisher=publisherMatch[1];
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}
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}
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if (datePub.match(/elsevier/i)){
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item.place = "Philadelphia, PA";
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}
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return item;
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}
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//Converts ordinal text to number
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//Only converting up to 31
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//E.g., text=first -> 1
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//E.g., Twenty-Second -> 22
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function textToNumber(text){
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var textarr = [
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"first",
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"second",
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"third",
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"fourth",
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"fifth",
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"sixth",
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"seventh",
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"eighth",
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"ninth",
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"tenth",
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"eleventh",
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"twelfth",
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"thirteenth",
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"fourteenth",
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"fifteenth",
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"sixteenth",
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"seventeenth",
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"eighteenth",
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"nineteenth",
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"twentieth",
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"twenty-first",
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"twenty-second",
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"twenty-third",
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"twenty-fourth",
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"twenty-fifth",
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"twenty-sixth",
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"twenty-seventh",
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"twenty-eighth",
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"twenty-ninth",
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"thirtieth",
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"thirty-first"
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];
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var number = textarr.indexOf(text.toLowerCase());
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//shift from 0 to 1 based indexing
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return (number != -1)? number + 1 : text;
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}
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