citeclaw 2.0.0

package/vendor/translators-official/Climate Change and Human Health Literature Portal.js

@@ -0,0 +1,283 @@
+{
+	"translatorID": "0722e1d4-3c3b-47b1-b8b2-1ed986030303",
+	"label": "Climate Change and Human Health Literature Portal",
+	"creator": "Sebastian Karcher",
+	"target": "^https?://tools\\.niehs\\.nih\\.gov/cchhl/index\\.cfm",
+	"minVersion": "5.0",
+	"maxVersion": "",
+	"priority": 100,
+	"inRepository": true,
+	"translatorType": 4,
+	"browserSupport": "gcsibv",
+	"lastUpdated": "2023-08-22 04:14:33"
+}
+
+/*
+	***** BEGIN LICENSE BLOCK *****
+
+	Copyright © 2022 Sebastian Karcher
+	
+	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 *****
+*/
+
+
+function detectWeb(doc, url) {
+	if (url.includes('/index.cfm/detail/')) {
+		return 'journalArticle';
+	}
+
+	let appRoot = doc.querySelector("#app"); // Ajax app "mount point"
+	if (appRoot) {
+		// Watch for live filtering of search results)
+		Z.monitorDOMChanges(appRoot);
+	}
+	if (getSearchResults(doc, true)) {
+		return 'multiple';
+	}
+
+	return false;
+}
+
+function getSearchResults(doc, checkOnly) {
+	var items = {};
+	var found = false;
+	var rows = doc.querySelectorAll('#ccpp_results-list .ccpp_result-title>a');
+	for (let row of rows) {
+		let href = row.href;
+		let title = ZU.trimInternal(row.textContent);
+		if (!href || !title) continue;
+		if (checkOnly) return true;
+		found = true;
+		items[href] = title;
+	}
+	return found ? items : false;
+}
+
+async function doWeb(doc, url) {
+	if (detectWeb(doc, url) == 'multiple') {
+		let items = await Zotero.selectItems(getSearchResults(doc, false));
+		if (!items) return;
+		for (let url of Object.keys(items)) {
+			await scrape(await requestDocument(url));
+		}
+	}
+	else {
+		await scrape(doc);
+	}
+}
+
+async function scrape(doc) {
+	var pmid = text(doc, 'li>a[href*="www.ncbi.nlm.nih.gov/pubmed"]');
+	var doi = text(doc, 'li>a[href*="doi.org/10."]');
+	var abstract = text(doc, '#cchh-detail-abstract');
+	Z.debug(pmid);
+	Z.debug(doi);
+	if (pmid) {
+		pmid = pmid.match(/\.gov\/pubmed\/(\d+)/)[1];
+		let translate = Z.loadTranslator('search');
+		translate.setTranslator('3d0231ce-fd4b-478c-b1d3-840389e5b68c');
+		translate.setSearch({ itemType: "journalArticle", PMID: pmid });
+ 
+		await translate.translate();
+	}
+	else if (doi) {
+		let translate = Z.loadTranslator('search');
+		translate.setSearch({ DOI: ZU.cleanDOI(doi) });
+		translate.setTranslator('b28d0d42-8549-4c6d-83fc-8382874a5cb9'); // DOI Content Negotiation
+		translate.setHandler("itemDone", function (obj, item) {
+			// ad abstract from page
+			if (abstract && !item.abstractNote) {
+				item.abstractNote = abstract;
+			}
+			item.complete();
+		});
+		await translate.translate();
+	}
+	else {
+		// scrape if we have to; I couldn't find a live example of this
+		var item = new Zotero.Item("journalArticle");
+		item.title = text(doc, 'h1>span');
+		item.date = ZU.xpathText(doc, '//div[@class="cchh-content_label" and contains(text(), "Year:")]/following-sibling::div');
+		let authors = ZU.xpathText(doc, '//div[@class="cchh-content_label" and contains(text(), "Author(s):")]/following-sibling::div');
+		let publication = ZU.xpathText(doc, '//div[@class="cchh-content_label" and contains(text(), "Journal:")]/following-sibling::div');
+		for (let author of authors.split(", ")) {
+			author = author.replace(/\s([A-Z]+)$/, ", $1");
+			item.creators.push(ZU.cleanAuthor(author, "author", true));
+		}
+		if (publication) {
+			var pubinfo = publication.match(/^(.+?)\.\s*(\d+)\s*(?:\((\d+)\))?:\s*([\d-]+?)$/);
+			if (pubinfo) {
+				item.publicationTitle = pubinfo[1];
+				item.volume = pubinfo[2];
+				item.issue = pubinfo[3];
+				item.pages = pubinfo[4];
+			}
+		}
+		
+		item.complete();
+	}
+}
+
+/** BEGIN TEST CASES **/
+var testCases = [
+	{
+		"type": "web",
+		"url": "https://tools.niehs.nih.gov/cchhl/index.cfm/detail/20124#searchTerm=testing&selectedFacets=&selectedResults=",
+		"items": [
+			{
+				"itemType": "journalArticle",
+				"title": "An analytical heat wave definition based on the impact on buildings and occupants",
+				"creators": [
+					{
+						"creatorType": "author",
+						"firstName": "Alfonso P.",
+						"lastName": "Ramallo-González"
+					},
+					{
+						"creatorType": "author",
+						"firstName": "Matt E.",
+						"lastName": "Eames"
+					},
+					{
+						"creatorType": "author",
+						"firstName": "Sukumar",
+						"lastName": "Natarajan"
+					},
+					{
+						"creatorType": "author",
+						"firstName": "Daniel",
+						"lastName": "Fosas-de-Pando"
+					},
+					{
+						"creatorType": "author",
+						"firstName": "David A.",
+						"lastName": "Coley"
+					}
+				],
+				"date": "06/2020",
+				"DOI": "10.1016/j.enbuild.2020.109923",
+				"ISSN": "03787788",
+				"abstractNote": "Alongside a mean global rise in temperature, climate change predictions point to an increase in heat waves and an associated rise in heat-related mortality. This suggests a growing need to ensure buildings are resilient to such events. Unfortunately, there is no agreed way of doing this, and no standard set of heatwaves for scientists or engineers to use. In addition, in all cases, heat waves are defined in terms of external conditions, yet, as the Paris heat wave of 2003 showed, people die in the industrialised world from the conditions inside buildings, not those outside. In this work, we reverse engineer external temperature time series from monitored conditions within a representative set of buildings during a heat wave. This generates a general probabilistic analytical relationship between internal and external heatwaves and thereby a standard set of events for testing resilience. These heat waves are by their simplicity ideal for discussions between clients and designers, or for the setting of national building codes. In addition, they provide a new framework for the declaration of a health emergency. (C) 2020 Published by Elsevier B.V.",
+				"journalAbbreviation": "Energy and Buildings",
+				"language": "en",
+				"libraryCatalog": "DOI.org (Crossref)",
+				"pages": "109923",
+				"publicationTitle": "Energy and Buildings",
+				"url": "https://linkinghub.elsevier.com/retrieve/pii/S0378778819330622",
+				"volume": "216",
+				"attachments": [],
+				"tags": [],
+				"notes": [],
+				"seeAlso": []
+			}
+		]
+	},
+	{
+		"type": "web",
+		"url": "https://tools.niehs.nih.gov/cchhl/index.cfm/main/search#/params?searchTerm=heat%20pump&selectedFacets=&selectedResults=",
+		"defer": true,
+		"items": "multiple"
+	},
+	{
+		"type": "web",
+		"url": "https://tools.niehs.nih.gov/cchhl/index.cfm/detail/10206#searchTerm=heat%20pump&selectedFacets=&selectedResults=",
+		"items": [
+			{
+				"itemType": "journalArticle",
+				"title": "Heat waves, aging, and human cardiovascular health",
+				"creators": [
+					{
+						"firstName": "W. Larry",
+						"lastName": "Kenney",
+						"creatorType": "author"
+					},
+					{
+						"firstName": "Daniel H.",
+						"lastName": "Craighead",
+						"creatorType": "author"
+					},
+					{
+						"firstName": "Lacy M.",
+						"lastName": "Alexander",
+						"creatorType": "author"
+					}
+				],
+				"date": "2014-10",
+				"DOI": "10.1249/MSS.0000000000000325",
+				"ISSN": "1530-0315",
+				"abstractNote": "This brief review is based on a President's Lecture presented at the Annual Meeting of the American College of Sports Medicine in 2013. The purpose of this review was to assess the effects of climate change and consequent increases in environmental heat stress on the aging cardiovascular system. The earth's average global temperature is slowly but consistently increasing, and along with mean temperature changes come increases in heat wave frequency and severity. Extreme passive thermal stress resulting from prolonged elevations in ambient temperature and prolonged physical activity in hot environments creates a high demand on the left ventricle to pump blood to the skin to dissipate heat. Even healthy aging is accompanied by altered cardiovascular function, which limits the extent to which older individuals can maintain stroke volume, increase cardiac output, and increase skin blood flow when exposed to environmental extremes. In the elderly, the increased cardiovascular demand during heat waves is often fatal because of increased strain on an already compromised left ventricle. Not surprisingly, excess deaths during heat waves 1) occur predominantly in older individuals and 2) are overwhelmingly cardiovascular in origin. Increasing frequency and severity of heat waves coupled with a rapidly growing at-risk population dramatically increase the extent of future untoward health outcomes.",
+				"extra": "PMID: 24598696\nPMCID: PMC4155032",
+				"issue": "10",
+				"journalAbbreviation": "Med Sci Sports Exerc",
+				"language": "eng",
+				"libraryCatalog": "PubMed",
+				"pages": "1891-1899",
+				"publicationTitle": "Medicine and Science in Sports and Exercise",
+				"volume": "46",
+				"attachments": [
+					{
+						"title": "PubMed entry",
+						"mimeType": "text/html",
+						"snapshot": false
+					}
+				],
+				"tags": [
+					{
+						"tag": "Aged"
+					},
+					{
+						"tag": "Aged, 80 and over"
+					},
+					{
+						"tag": "Aging"
+					},
+					{
+						"tag": "Cardiovascular Diseases"
+					},
+					{
+						"tag": "Cardiovascular System"
+					},
+					{
+						"tag": "Cause of Death"
+					},
+					{
+						"tag": "Climate Change"
+					},
+					{
+						"tag": "Heat Stress Disorders"
+					},
+					{
+						"tag": "Humans"
+					},
+					{
+						"tag": "Skin Aging"
+					},
+					{
+						"tag": "Sports Medicine"
+					},
+					{
+						"tag": "Sweating"
+					}
+				],
+				"notes": [],
+				"seeAlso": []
+			}
+		]
+	}
+]
+/** END TEST CASES **/

package/vendor/translators-official/Clinical Key.js

@@ -0,0 +1,367 @@
+{
+	"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;
+}