Clinical Key.js

{
	"translatorID": "a55463ba-e403-415b-80d4-284d5f9b4b15",
	"label": "Clinical Key",
	"creator": "Jaret M. Karnuta, Mike Davidson",
	"target": "^https?://(www\\.|www-)clinicalkey(\\.|-)com",
	"minVersion": "3.0",
	"maxVersion": "",
	"priority": 100,
	"inRepository": true,
	"translatorType": 4,
	"browserSupport": "gcsibv",
	"lastUpdated": "2017-01-30 08:08:52"
}
/*
	***** BEGIN LICENSE BLOCK *****

	Copyright © 2017 Jaret M. Karnuta & Mike Davidson

	This file is part of Zotero.

	Zotero is free software: you can redistribute it and/or modify
	it under the terms of the GNU Affero General Public License as published by
	the Free Software Foundation, either version 3 of the License, or
	(at your option) any later version.

	Zotero 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 Affero General Public License for more details.

	You should have received a copy of the GNU Affero General Public License
	along with Zotero. If not, see <http://www.gnu.org/licenses/>.

	***** END LICENSE BLOCK *****
*/

/*
This translator is designed specifically for use on book section portions and journal articles of
ClinicalKey. It will not work on book overview pages or journal table of contents pages.

NB: url and doc.location.href are different. I think it is because of the way clinicalkey redirects.
Replicate by going to a content page (/content/book/...) and then going to a broswing page (/browse/book/...).
URL remains the page of the previous page (content page) and doc.location.href is the current page (as it should be).

Hence, I never use url and change its content to doc.location.href in detectWeb, the only function that uses the url

To get journal article metadata, Publisher Item Identifier (PIIs) are extracted from the Scopus EID
and queried using the CrossRef REST API. 
Documentation at:
https://github.com/CrossRef/rest-api-doc
CrossReff REST API Return Values at:
https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md
*/

function detectWeb(doc, url) {
	//see NB above for explanation
	url = doc.location.href;

	//contentType depends on url, which is present, but rest of site is loaded via ajax (I think)
	//monitor dom and reset if changes
	var jsession = doc.getElementById('jsessionid');
	if (jsession){
		Zotero.monitorDOMChanges(jsession, {attributes:true});
		if (!jsession.value){
			return;
		}
	}

	var contentType;
	//contains /content/book/ and does not contain login?
	if (url.indexOf("/content/book/") != -1 && url.indexOf("login?") == -1){
		contentType = "bookSection";
	}
	//similar structure to above
	else if (url.indexOf('/browse/book/') != -1 && url.indexOf("login?") == -1){
		contentType = "book";
	}
	// similar structure to above, for journal articles
	else if (url.indexOf('/content/journal/') != -1 && url.indexOf("login?") == -1){
		contentType = "journalArticle";
	}

	//contentType not set
	if (!contentType){
		return;
	}
	return contentType;
}

function doWeb(doc, url){
	var contentType = detectWeb(doc, url);

	//if book section
	if (contentType == 'bookSection'){
		var newItem = new Zotero.Item(contentType);
		newItem = scrapeBookSection(doc, newItem);
		//pdf (if present)
		var pdfLink = getPDFLink(doc);
		if (pdfLink) {
			newItem.attachments.push({
				url:pdfLink,
				title:"Book Section PDF",
				mimeType:"application/pdf"
			});
		}
		//populate common attributes
		//url, see NB above for explanation as to why url is NOT used
		newItem.url = doc.location.href;
		newItem.complete();
	}
	//if book, use ISBN translator
	//borrowed from amazon translator
	else if (contentType == 'book'){
		var isbn = ZU.xpath(doc, "//button/@data-metadata-isbn");
		if (!isbn){
			return;
		}
		isbn = ZU.cleanISBN(isbn[0].value);
		//use search translator to get metadata from isbn
		var search = Zotero.loadTranslator("search");
		//set translators and search
		search.setHandler("translators", function(obj, translators) {
			search.setTranslator(translators);
			search.setHandler("itemDone", function(obj, lookupItem) {
				newItem=lookupItem;
				//update ISBN
				newItem.ISBN = ZU.cleanISBN(isbn);
				//Override library catalog
				newItem.libraryCatalog = "Clinical Key";
				//update url, see NB for rationale why url not used
				newItem.url = doc.location.href;
			});
			search.translate();
		});
		//no need to override error handler
		//save item
		search.setHandler("done", function() {
			newItem.complete();
		});
		search.setSearch({ ISBN: isbn });
		search.getTranslators();
	}
	else if (contentType == 'journalArticle') {
		var eid; 
		var pii;
		try {
			eid = url.split('/');
			pii = eid.pop().slice(7);
			if (!/^S(\d{15}X|\d{16})/.test(pii)){
				throw new Error('PII from url failed. Trying Xpath');
			}
			} catch(e) {
				Zotero.debug(e);
				eid = ZU.xpathText(doc, "//ul/@data-eid");
				pii = eid.slice(7);
				if (!/^S(\d{15}X|\d{16})/.test(pii)){
					throw new Error('PII from Xpath failed');
				}
			}
		queryCrossRef(pii, doc);
	}
	
}

//Search & Processing based on CrossRef.js translator
function queryCrossRef (pii, doc){
	crossRefQuery = 'http://api.crossref.org/works?query=' + pii;
	//TODO: implement API version request
	//acceptHeader = {'Accept': 'application/vnd.crossref-api-message+json; version=1.0'}
	ZU.doGet(crossRefQuery, function(responseText) {
		processCrossRefREST(responseText, doc);
		});
}

function processCrossRefREST(jsonOutput, doc){
	var jsonParsed = JSON.parse(jsonOutput);
	
	if (jsonParsed['message']['total-results'] > 1) {
		// Multiple results shouldn't occur as pii is unique
		// handle only first returned object just in case
		Zotero.debug('Returned multiple results. Continue processing first');
	}
	else if (jsonParsed['message']['total-results'] == 0) {
		// If the search failed to find results
		Zotero.debug('Crossref API failed to find query match');
		return;
	}
	
	if (!/^1/.test(jsonParsed['message-version'])){
		// check that the API version is compatible with this translator
		// translator currently written according to v1
		Zotero.debug('Request returned wrong API version');
	}
	
	// shorten JSON to the single reference
	var ref = jsonParsed['message']['items'][0];
	
	if (ref['type'] == 'journal-article') {
		// prep for CSL JSON translator
		ref['type'] = 'article-journal';
	} else if (ref['type'] != 'journal-article') {
		// log the unexpected
		Zotero.debug('Returned unexpected reference type');
	}
	
	// use CSL JSON translator
	var text = JSON.stringify(ref);
	var trans = Zotero.loadTranslator('import');
	trans.setTranslator('bc03b4fe-436d-4a1f-ba59-de4d2d7a63f7');
	trans.setString(text);
	
	//Attempt to download fulltext PDF
	var pdfLink = getPDFLink(doc);
		
	trans.setHandler('itemDone', function(obj, item) {
		if (pdfLink)
			item.attachments.push({
				url:pdfLink,
				title:"Full Text PDF",
				mimeType:"application/pdf"
			});
		item.complete();
	});
	
	trans.translate();
}

function getPDFLink(doc) {
	var pdfLink = doc.getElementsByClassName('x-pdf')[0].href;
	if (!pdfLink) {
		pdfLink = ZU.xpathText(doc, './/*[@data-action="pdfDownload"]/@href');
	} else if (!pdfLink) {
		pdfLink = ZU.xpathText(doc, './/*[@action="download"]/@href');
	}
	return pdfLink;
}

function scrapeBookSection(doc, item){
	//book title
	var bookTitle = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.title"]');
	item.bookTitle = bookTitle;
	//section title
	var title  = ZU.xpathText(doc, '//*[@ng-bind-html="ContentCtrl.title"]');
	item.title = title;
	//authors
	var authorsList  = ZU.xpath(doc, '//ul[@ng-bind-html="XocsCtrl.authorsHtml"]/li/a');
	for (var i = 0;i<authorsList.length;i++){
		var author = authorsList[i].innerHTML;
		if (author.indexOf("<") != -1){
			author = author.split("<")[0];
		}
		item.creators.push(Zotero.Utilities.cleanAuthor(author, 'author'));
	}

	//chapter and page metadata
	var chapterAndPages = ZU.xpathText(doc,'//p[@class="source ng-binding"]');
	//make pattern that should capter pages if present
	//matches both xxx-xxx (length of #s not important)
	//and xxx-xxx.eY
	var pagesPattern = /\s\d+-\d+(\.e\d+)?/;
	var pagesMatch = chapterAndPages.match(pagesPattern);
	if (pagesMatch){
		//get whole regex match
		item.pages = pagesMatch[0];
	}
	//make pattern that will match to the chapter number
	var chapterPattern = /chapter\s(\d+)/i
	var chapterMatch = chapterAndPages.match(chapterPattern);
	if (chapterMatch){
		//get match within first group
		var chapterNumber = chapterMatch[1];
		item.notes.push({note:"Chapter: "+chapterNumber});
	}


	//ISBN metadata
	var isbn = ZU.xpath(doc, "//button/@data-metadata-isbn");
	if (isbn){
		var isbnNo = isbn[0].value;
		item.ISBN = isbn;
	}
	//edition metadata
	var edition = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.edition"]').split(/edition/i)[0].trim();
	//convert to number for correct zotero citation handling
	item.edition = textToNumber(edition);

	//publisher metadata
	var datePub = ZU.xpathText(doc, '//*[@data-once-text="XocsCtrl.copyright"]');
	var datePattern = /\d{4}/g;
	var dateMatch = datePub.match(datePattern);
	if (dateMatch){
		item.date = dateMatch[0];
	}

	if (datePub.indexOf("imprint") != -1){
		var imprintPattern = /by\s(.*),.*imprint\sof\s(.*)\sInc/i;
		var imprintMatch = datePub.match(imprintPattern);
		if (imprintMatch){
			//expected number of matches
			if (imprintMatch.length == 3){
				item.publisher = imprintMatch[2]+"/"+imprintMatch[1];
			}
			//added for robustness
			else {
				var imprintPublisher=imprintMatch[0].replace("by","").trim();
				item.publisher=imprintPublisher;
			}
		}
	}
	else {
		var publisherPattern = /by\s(.*?)(,)?\s/;
		var publisherMatch = datePub.match(publisherPattern);
		if (publisherMatch){
			//get first matched group, between by and , or whitespace
			item.publisher=publisherMatch[1];
		}
	}
	if (datePub.match(/elsevier/i)){
		item.place = "Philadelphia, PA";
	}

	return item;
}

//Converts ordinal text to number
//Only converting up to 31
//E.g., text=first -> 1
//E.g., Twenty-Second -> 22
function textToNumber(text){
	var textarr = [
		"first",
		"second",
		"third",
		"fourth",
		"fifth",
		"sixth",
		"seventh",
		"eighth",
		"ninth",
		"tenth",
		"eleventh",
		"twelfth",
		"thirteenth",
		"fourteenth",
		"fifteenth",
		"sixteenth",
		"seventeenth",
		"eighteenth",
		"nineteenth",
		"twentieth",
		"twenty-first",
		"twenty-second",
		"twenty-third",
		"twenty-fourth",
		"twenty-fifth",
		"twenty-sixth",
		"twenty-seventh",
		"twenty-eighth",
		"twenty-ninth",
		"thirtieth",
		"thirty-first"
	];
	var number = textarr.indexOf(text.toLowerCase());
	//shift from 0 to 1 based indexing
	return (number != -1)? number + 1 : text;
}