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Nature Publishing Group.js
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{
"translatorID": "6614a99-479a-4524-8e30-686e4d66663e",
"label": "Nature Publishing Group",
"creator": "Aurimas Vinckevicius",
"target": "^https?://(www\\.)?nature\\.com/([^?/]+/)?(journal|archive|research|topten|search|full|abs|current_issue\\.htm|most\\.htm|articles/)",
"minVersion": "3.0",
"maxVersion": "",
"priority": 100,
"inRepository": true,
"translatorType": 4,
"browserSupport": "gcsibv",
"lastUpdated": "2024-02-29 20:21:02"
}
/**
Copyright (c) 2012 Aurimas Vinckevicius
This program 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.
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
Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public
License along with this program. If not, see
<http://www.gnu.org/licenses/>.
*/
// mimetype map for supplementary attachments
var suppTypeMap = {
pdf: 'application/pdf',
// 'zip': 'application/zip',
doc: 'application/msword',
xls: 'application/vnd.ms-excel',
excel: 'application/vnd.ms-excel'
};
function attachSupplementary(doc, item, next) {
// nature's new website
var attachAsLink = Z.getHiddenPref("supplementaryAsLink");
var suppDiv = doc.getElementById("supplementary-information");
if (suppDiv) {
var fileClasses = ZU.xpath(suppDiv, './/div[contains(@class, "supp-info")]/h2');
for (var i = 0, n = fileClasses.length; i < n; i++) {
var type = fileClasses[i].classList.item(0);
if (type) type = suppTypeMap[type];
if (!fileClasses[i].nextElementSibling) continue;
var dls = fileClasses[i].nextElementSibling.getElementsByTagName('dl');
for (var j = 0, m = dls.length; j < m; j++) {
var link = ZU.xpath(dls[j], './dt/a')[0];
if (!link) {
continue;
}
var title = dls[j].getElementsByTagName('dd')[0];
if (title) {
title = title.textContent.replace(
/^[\s\r\n]*(?:Th(?:is|e) )?file (?:contains|shows)\s+(\S+)/i,
function (m, firstWord) { // fix capitalization of first word
if (firstWord.toLowerCase() == firstWord) { // lower case word
return firstWord.charAt(0).toUpperCase() + firstWord.substr(1);
}
return firstWord;
}
).trim();
}
// add the heading from link
title = link.textContent.replace(/\s+\([^()]+\)\s*$/g, '').trim() // strip off the file size info
+ ". " + (title || '');
// fallback if we fail miserably
if (!title) title = "Supplementary file";
var attachment = {
title: title,
url: link.href
};
if (type) attachment.mimeType = type;
if (attachAsLink || !type) { // don't download unknown file types
attachment.snapshot = false;
}
item.attachments.push(attachment);
}
}
return;
}
// older websites, e.g. http://www.nature.com/onc/journal/v31/n6/full/onc2011282a.html
var suppLink = doc.getElementById('articlenav') || doc.getElementById('extranav');
if (suppLink) {
suppLink = ZU.xpath(suppLink, './ul/li//a[text()="Supplementary info"]')[0]; // unfortunately, this is the best we can do
if (!suppLink) return;
if (attachAsLink) { // we don't need to find links to individual files
item.attachments.push({
title: "Supplementary info",
url: suppLink.href,
mimeType: 'text/html',
snapshot: false
});
}
else {
ZU.processDocuments(suppLink.href, function (newDoc) {
var content = newDoc.getElementById('content');
if (content) {
var links = ZU.xpath(content, './div[@class="container-supplementary" or @id="general"]//a');
for (var i = 0, n = links.length; i < n; i++) {
var title = ZU.trimInternal(links[i].textContent);
var type = title.match(/\((\w+)\s+\d+[^)]+\)\s*$/);
if (type) type = suppTypeMap[type[1]];
if (!type) {
type = links[i].classList;
type = type.item(type.length - 1);
if (type) type = suppTypeMap[type.replace(/^(?:i|all)-/, '')];
}
// clean up title a bit
title = title.replace(/\s*\([^()]+\)$/, '')
.replace(/\s*-\s*download\b.*/i, '');
item.attachments.push({
title: title,
url: links[i].href,
mimeType: type,
snapshot: !!type // don't download unknown file types
});
}
}
next(doc, item);
});
return;
}
return;
}
// e.g. http://www.nature.com/ng/journal/v38/n11/full/ng1901.html
suppLink = ZU.xpath(doc, '(//a[text()="Supplementary info"])[last()]')[0];
if (suppLink) {
if (attachAsLink) { // we don't need to find links to individual files
item.attachments.push({
title: "Supplementary info",
url: suppLink.href,
mimeType: 'text/html',
snapshot: false
});
}
else {
Z.debug(suppLink.href);
ZU.processDocuments(suppLink.href, function (newDoc) {
var links = ZU.xpath(newDoc, './/p[@class="articletext"]');
Z.debug("Found " + links.length + " links");
for (var i = 0, n = links.length; i < n; i++) {
var link = links[i].getElementsByTagName('a')[0];
if (!link) continue;
var title = ZU.trimInternal(link.textContent);
var type = title.match(/\((\w+)\s+\d+[^)]+\)\s*$/);
if (type) type = suppTypeMap[type[1]];
// clean up title a bit
title = title.replace(/\s*\([^()]+\)$/, '')
.replace(/\s*-\s*download\b.*/i, '');
// maybe we can attach description to title
// can this be too long? I would probably make more sense to attach these as notes on the files
// how do we do that?
var desc = ZU.xpathText(links[i], './node()[last()][not(name())]'); // last text node
if (desc && (desc = ZU.trimInternal(desc))) {
title += '. ' + desc;
}
item.attachments.push({
title: title,
url: links[i].href,
mimeType: type,
snapshot: !!type // don't download unknown file types
});
}
next(doc, item);
});
}
}
}
// unescape Highwire's special html characters
function HWunescape(str) {
if (!str || !str.includes('[')) return str;
return str.replace(/\|?\[([^\]]+)\]\|?/g, function (s, p1) {
if (ISO8879CharMap[p1] !== undefined) {
return ISO8879CharMap[p1];
}
else {
return s;
}
});
}
// fix capitalization if all in upper case
function fixCaps(str) {
if (str && str == str.toUpperCase()) {
return ZU.capitalizeTitle(str.toLowerCase(), true);
}
else {
return str;
}
}
// get abstract
function getAbstract(doc) {
var abstractLocations = [
// e.g. https://www.nature.com/articles/onc2011282
'//*[@id="abstract-content"]',
// e.g. 'lead' http://www.nature.com/emboj/journal/v31/n1/full/emboj2011343a.html
// e.g. 'first_paragraph' http://www.nature.com/emboj/journal/vaop/ncurrent/full/emboj201239a.html
'//p[contains(@class,"lead") or contains(@class,"first_paragraph")]',
// e.g. http://www.nature.com/nprot/journal/v8/n11/full/nprot.2013.143.html
'//div[@id="abstract"]/div[@class="content"]/p',
// e.g.
'//div[@id="abs"]/*[self::div[not(contains(@class, "keyw-abbr"))] or self::p]',
// e.g. 'first-paragraph' http://www.nature.com/nature/journal/v481/n7381/full/nature10669.html
// e.g. 'standfirst' http://www.nature.com/nature/journal/v481/n7381/full/481237a.html
'//div[@id="first-paragraph" or @class="standfirst"]/p',
// e.g. http://www.nature.com/nature/journal/v481/n7381/full/nature10728.html
'//div[contains(@id,"abstract")]/div[contains(@class,"content")]/p',
// e.g. http://www.nature.com/ng/journal/v38/n8/abs/ng1845.html
'//span[@class="articletext" and ./preceding-sibling::*[1][name()="a" or name()="A"][@name="abstract"]]'
];
var paragraphs = [];
for (let i = 0, n = abstractLocations.length; i < n && !paragraphs.length; i++) {
paragraphs = Zotero.Utilities.xpath(doc, abstractLocations[i]);
}
if (!paragraphs.length) return null;
var textArr = [];
var p;
for (let i = 0, n = paragraphs.length; i < n; i++) {
// remove superscript references
p = ZU.xpathText(paragraphs[i], "./node()[not(self::sup and ./a)]", null, '');
if (p) p = ZU.trimInternal(p);
if (p) textArr.push(p);
}
return textArr.join("\n").trim() || null;
}
// some journals display keywords
function getKeywords(doc) {
var keywords = Zotero.Utilities.xpathText(doc, '//p[@class="keywords"]') // e.g. http://www.nature.com/onc/journal/v26/n6/full/1209842a.html
|| Zotero.Utilities.xpathText(doc, '//ul[@class="keywords"]//ul/li', null, '') // e.g. http://www.nature.com/emboj/journal/v31/n3/full/emboj2011459a.html
|| Zotero.Utilities.xpathText(doc, '//div[contains(@class,"article-keywords")]/ul/li/a', null, '; '); // e.g. http://www.nature.com/nature/journal/v481/n7382/full/481433a.html
if (!keywords) return null;
return keywords.split(/[;,]\s+/);
}
// get PDF url
function getPdfUrl(doc, url) {
var m = url.match(/(^[^#?]+\/)(?:full|abs)(\/[^#?]+?\.)[a-zA-Z]+(?=$|\?|#)/);
if (m && m.length) return m[1] + 'pdf' + m[2] + 'pdf';
else {
return attr(doc, 'a[data-track-action="download pdf"]', 'href');
}
}
// add using embedded metadata
function scrapeEM(doc, url, next) {
var translator = Zotero.loadTranslator("web");
// Embedded Metadata translator
translator.setTranslator("951c027d-74ac-47d4-a107-9c3069ab7b48");
translator.setDocument(doc);
translator.setHandler("itemDone", function (obj, item) {
// Replace HTML special characters with proper characters
// also remove all caps in Names and Titles
for (let i = 0; i < item.creators.length; i++) {
item.creators[i].lastName = HWunescape(item.creators[i].lastName);
item.creators[i].firstName = HWunescape(item.creators[i].firstName);
item.creators[i].lastName = fixCaps(item.creators[i].lastName);
item.creators[i].firstName = fixCaps(item.creators[i].firstName);
}
item.title = fixCaps(HWunescape(item.title));
if (item.abstractNote) item.abstractNote = ZU.cleanTags(item.abstractNote);
// the date in EM is usually online publication date
// If we can find a publication year, that's better
var year = ZU.xpathText(doc,
'//dd[preceding-sibling::dt[1][text()="Year published:" or text()="Date published:"]]');
if (year && (year = year.match(/\(\s*(.*?)\s*\)/))) {
item.date = year[1];
}
else if ((year = ZU.xpathText(doc, '//p[@id="cite"]'))
&& (year = year.match(/\((\d{4})\)/))) {
item.date = year[1];
}
else if (
(year = ZU.xpathText(doc, '//a[contains(@href,"publicationDate")]/@href'))
&& (year = year.match(/publicationDate=([^&]+)/))
// check that we at least have a year
&& year[1].match(/\d{4}/)) {
item.date = year[1];
}
// sometimes abstract from EM is description for the website.
// ours should always be better
var abstract = getAbstract(doc);
if (abstract
// maybe the abstract from meta tags is more complete
&& !(item.abstractNote
&& item.abstractNote.substr(0, 10) == abstract.substr(0, 10)
&& item.abstractNote.length > abstract.length)) {
item.abstractNote = abstract;
}
item.tags = getKeywords(doc) || item.tags;
if (item.notes) item.notes = [];
if (item.ISSN && ZU.cleanISSN) { // introduced in 3.0.12
var issn = ZU.cleanISSN(item.ISSN);
if (!issn) delete item.ISSN;
else item.ISSN = issn;
}
else if (item.ISSN === "ERROR! NO ISSN") {
delete item.ISSN;
}
next(item);
});
translator.getTranslatorObject(function (trans) {
// Make sure we always import as journal article (sometimes missing from EM)
// e.g. https://www.nature.com/articles/sdata201618
trans.itemType = "journalArticle";
trans.doWeb(doc, url);
});
}
function scrapeRIS(doc, url, next) {
var navBar = doc.getElementById('articlenav') || doc.getElementById('extranav');
var risURL;
if (navBar) {
risURL = doc.evaluate('//li[@class="export"]/a', navBar, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="Export citation" and not(@href="#")]', navBar, null, XPathResult.ANY_TYPE, null).iterateNext();
}
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="RIS" and not(@href="#")]', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//li[@class="download-citation"]/a', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = doc.evaluate('//a[normalize-space(text())="Export citation" and not(@href="#")]', doc, null, XPathResult.ANY_TYPE, null).iterateNext();
if (!risURL) risURL = ZU.xpath(doc, '//ul[@data-component="article-info-list"]//a[@data-track-source="citation-download"]')[0];
if (!risURL) risURL = doc.querySelector('a[data-track-action="download article citation"]');
if (risURL) {
risURL = risURL.href;
ZU.doGet(risURL, function (text) {
if (text.search(/^TY /m) != -1) {
var translator = Zotero.loadTranslator('import');
translator.setTranslator('32d59d2d-b65a-4da4-b0a3-bdd3cfb979e7');
translator.setString(text);
translator.setHandler('itemDone', function (obj, newItem) {
newItem.notes = [];
next(newItem);
});
translator.setHandler('error', function () {
next();
});
translator.translate();
}
else {
next();
}
});
}
else {
Z.debug('Could not find RIS export');
next();
}
}
function getMultipleNodes(doc, url) {
var allHNodes = '*[self::h1 or self::h2 or self::h3 or self::h4 or self::h5]';
var nodex, titlex, linkx;
var nodes = [];
if (url.includes('/search/') || url.includes('/most.htm')) {
// search, "top" lists
nodex = '//ol[@class="results-list" or @id="content-list"]/li';
titlex = './' + allHNodes + '/node()[not(self::span)]';
linkx = './' + allHNodes + '/a';
nodes = Zotero.Utilities.xpath(doc, nodex);
}
else {
// Maybe there's a nice way to figure out which journal uses what style, but for now we'll just try one until it matches
// these seem to be listed in order of frequency
var styles = [
// ToC
{
nodex: '//tr[./td/span[@class="articletitle"]]',
titlex: './td/span[@class="articletitle"]',
linkx: './td/a[@class="contentslink" and substring(@href, string-length(@href)-3) != "pdf"][1]' // abstract or full text
},
// oncogene
{
nodex: '//div[child::*[@class="atl"]]',
titlex: './' + allHNodes + '[last()]/node()[not(self::span)]', // ignore "subheading"
linkx: './p[@class="links" or @class="articlelinks"]/a[contains(text(),"Full Text") or contains(text(),"Full text")]'
},
// embo journal
{
nodex: '//ul[@class="articles"]/li',
titlex: './' + allHNodes + '[@class="article-title"]/node()[not(self::span)]',
linkx: './ul[@class="article-links"]/li/a[contains(text(),"Full Text") or contains(text(),"Full text")]'
},
// nature
{
nodex: '//ul[contains(@class,"article-list") or contains(@class,"collapsed-list")]/li',
titlex: './/' + allHNodes + '/a',
linkx: './/' + allHNodes + '/a'
},
// archive (e.g. http://www.nature.com/bonekey/archive/type.html)
{
nodex: '//table[@class="archive"]/tbody/tr',
titlex: './td/' + allHNodes + '[last()]/a',
linkx: './td/' + allHNodes + '[last()]/a',
},
// some more ToC (e.g. http://www.nature.com/nrcardio/journal/v5/n1s/index.html)
{
nodex: '//div[@class="container"]/div[./h4[@class="norm"] and ./p[@class="journal"]/a[@title]]',
titlex: './h4[@class="norm"]',
linkx: './p[@class="journal"]/a[@title][1]'
},
// some new more ToC (e.g. https://www.nature.com/ng/volumes/38/issues/11)
{
nodex: '//article',
titlex: './div/h3',
linkx: './div/h3/a'
},
{
nodex: '//li[@itemtype="http://schema.org/Article"]',
titlex: './/h2',
linkx: './/h2/a'
}
];
for (var i = 0; i < styles.length && !nodes.length; i++) {
nodex = styles[i].nodex;
titlex = styles[i].titlex;
linkx = styles[i].linkx;
nodes = Zotero.Utilities.xpath(doc, nodex);
}
}
if (nodes.length) Z.debug("multiples found using: " + nodex);
return [nodes, titlex, linkx];
}
function isNature(url) {
return url.search(/^https?:\/\/(?:[^/]+\.)?nature.com/) != -1;
}
function detectWeb(doc, url) {
if (url.endsWith('.pdf')) return false;
if (url.search(/\/(full|abs)\/[^/]+($|\?|#)|\/fp\/.+?[?&]lang=ja(?:&|$)|\/articles\//) != -1) {
return 'journalArticle';
}
else if (doc.title.toLowerCase().includes('table of contents') // single issue ToC. e.g. http://www.nature.com/emboj/journal/v30/n1/index.html or http://www.nature.com/nature/journal/v481/n7381/index.html
|| doc.title.toLowerCase().includes('current issue')
|| url.includes('/research/') || url.includes('/topten/')
|| url.includes('/most.htm')
|| (url.includes('/vaop/') && url.includes('index.html')) // advanced online publication
|| url.includes('sp-q=') // search query
|| url.search(/journal\/v\d+\/n\d+\/index\.html/i) != -1 // more ToC
|| url.search(/volumes\/\d+\/issues\/\d+/i) != -1
|| url.includes('/search?')) { // new more ToC
return getMultipleNodes(doc, url)[0].length ? 'multiple' : null;
}
else if (url.includes('/archive/')) {
if (url.includes('index.htm')) return false; // list of issues
if (url.includes('subject.htm')) return false; // list of subjects
if (url.includes('category.htm') && !url.includes('code=')) return false; // list of categories
return getMultipleNodes(doc, url)[0].length ? 'multiple' : null; // all else should be ok
}
else {
return false;
}
}
function supplementItem(item, supp, prefer) {
for (var i in supp) {
if (!supp.hasOwnProperty(i)
|| (item.hasOwnProperty(i) && !prefer.includes(i))) {
continue; // this also skips creators, tags, notes, and related
}
Z.debug('Supplementing item.' + i);
item[i] = supp[i];
}
return item;
}
function runScrapers(scrapers, done) {
var items = [];
var args = Array.prototype.splice.call(arguments, 2); // remove scrapers and done handler
var run = function (item) {
items.push(item);
if (scrapers.length) {
(scrapers.shift())(...args);
}
};
args.push(run);
args.push(items);
scrapers.push(function () {
done(items);
});
(scrapers.shift())(...args);
}
function scrape(doc, url) {
runScrapers([scrapeEM, scrapeRIS], function (items) {
var item = items[0];
if (!item) { // EM failed (unlikely)
item = items[1];
}
else if (items[1]) {
var preferredRisFields = ['date', 'abstractNote'];
// palgrave-macmillan journals
if (!isNature(url)) {
preferredRisFields.push('publisher'); // all others are going to be dropped since we only handle journalArticle
if (item.rights.includes('Nature Publishing Group')) {
delete item.rights;
}
}
// for electronic only journals, EM just has 1-page#; we instead get article number from the extra field
var electronicOnly = ['Scientific Data', 'Nature Communications', 'Scientific Reports', 'npj Science of Food', 'Light: Science & Applications'];
if (electronicOnly.includes(item.publicationTitle)) {
preferredRisFields.push('pages');
}
item = supplementItem(item, items[1], preferredRisFields);
if (items[1].tags.length) item.tags = items[1].tags; // RIS doesn't seem to have tags, but we check just in case
if (!item.creators.length) {
// E.g. http://www.nature.com/nprot/journal/v1/n1/full/nprot.2006.52.html
item.creators = items[1].creators;
}
else {
// RIS can properly split first and last name
// but it does not (sometimes?) include accented letters
// We try to get best of both worlds by trying to re-split EM authors correctly
// hopefully the authors match up
for (var i = 0, j = 0, n = item.creators.length, m = items[1].creators.length; i < n && j < m; i++, j++) {
// check if last names match, then we don't need to worry
var risLName = ZU.removeDiacritics(items[1].creators[j].lastName.toUpperCase());
var emLName = ZU.removeDiacritics(item.creators[i].lastName.toUpperCase());
if (emLName == risLName) {
continue;
}
var fullName = item.creators[i].firstName + ' ' + item.creators[i].lastName;
emLName = fullName.substring(fullName.length - risLName.length);
if (ZU.removeDiacritics(emLName.toUpperCase()) != risLName) {
// corporate authors are sometimes skipped in RIS
if (i + 1 < n) {
var nextEMLName = item.creators[i + 1].firstName + ' '
+ item.creators[i + 1].lastName;
nextEMLName = ZU.removeDiacritics(
nextEMLName.substring(nextEMLName.length - risLName.length)
.toUpperCase()
);
if (nextEMLName == risLName) { // this is corporate author and it was skipped in RIS
item.creators[i].lastName = item.creators[i].firstName
+ ' ' + item.creators[i].lastName;
delete item.creators[i].firstName;
item.creators[i].fieldMode = 1;
j--;
Z.debug('It appears that "' + item.creators[i].lastName
+ '" is a corporate author and was skipped in the RIS output.');
continue;
}
}
// authors with same name are sometimes skipped in EM
if (j + 1 < m) {
var nextRisLName = ZU.removeDiacritics(items[1].creators[j + 1].lastName.toUpperCase());
var resplitEmLName = ZU.removeDiacritics(fullName.substring(fullName.length - nextRisLName.length).toUpperCase());
if (resplitEmLName == nextRisLName) {
item.creators.splice(i, 0, items[1].creators[j]); // insert missing author
Z.debug('It appears that "' + item.creators[i].lastName
+ '" was missing from EM.');
continue;
}
}
Z.debug(emLName + ' and ' + risLName + ' do not match');
continue; // we failed
}
if (items[1].creators[j].fieldMode !== 1) {
item.creators[i].firstName = fullName.substring(0, fullName.length - emLName.length).trim();
}
else {
delete item.creators[i].firstName;
item.creators[i].fieldMode = 1;
}
item.creators[i].lastName = emLName;
Z.debug(fullName + ' was split into '
+ item.creators[i].lastName + ', ' + item.creators[i].firstName);
}
}
}
if (!item) {
Z.debug('Could not retrieve metadata.');
return; // both translators failed
}
// small caps become lowercase in EM/RIS, so if the title contains a
// small-caps span, we'll use innerText.
if (doc.querySelector('h1.c-article-title .u-small-caps')) {
item.title = innerText('h1.c-article-title') || item.title;
}
// We prefer the publication date to some online first date
var pubdate = attr(doc, 'meta[name="citation_publication_date"]', 'content');
if (pubdate) {
item.date = ZU.strToISO(pubdate);
}
if (item.date) item.date = ZU.strToISO(item.date);
if (item.pages && !item.pages.includes('-')) {
var start = text(doc, 'span[itemprop="pageStart"]');
var end = text(doc, 'span[itemprop="pageEnd"]');
if (start && end) {
item.pages = start + '-' + end;
}
}
if (!item.pages) {
// For some online-only publications this should be the "Article number"
// but is not present in either EM or RIS. We grab it from page
var page = doc.querySelector('.citation .page');
if (page) {
item.pages = ZU.trimInternal(page.textContent);
}
}
// write 'en' instead of 'En'
if (item.language && item.language == 'En') item.language = 'en';
// journal abbreviations are now all wrong, i.e. the full title of the journal
if (item.journalAbbreviation && !item.publicationTitle) {
item.publicationTitle = 'Nature';// old articles mess this up
}
if (item.journalAbbreviation == item.publicationTitle) {
delete item.journalAbbreviation;
}
if (item.issue && item.number && item.issue == item.number) {
delete item.number;
}
var hasPDF = false;
for (let attach of item.attachments) {
if (attach.mimeType && attach.mimeType == "application/pdf") {
hasPDF = true;
}
}
if (!hasPDF) {
item.attachments = [{
document: doc,
title: 'Snapshot'
}];
var pdf = getPdfUrl(doc, url);
if (pdf) {
item.attachments.push({
url: pdf,
title: 'Full Text PDF',
mimeType: 'application/pdf'
});
}
}
// attach some useful links, like...
// GEO, GenBank, etc.
try { // this shouldn't really fail, but... just in case
var accessionDiv = doc.getElementById('accessions');
if (accessionDiv) {
var accessions = ZU.xpath(accessionDiv, './/div[@class="content"]//div[./h3]');
var repo, links;
for (let i = 0, n = accessions.length; i < n; i++) {
repo = accessions[i].getElementsByTagName('h3')[0].textContent;
if (repo) repo += ' entry ';
links = ZU.xpath(accessions[i], './ul[1]//a');
if (links.length) {
for (let j = 0, m = links.length; j < m; j++) {
item.attachments.push({
title: repo + '(' + links[j].textContent + ')',
url: links[j].href,
type: 'text/html',
snapshot: false
});
}
}
}
}
}
catch (e) {
Z.debug("Error attaching useful links.");
Z.debug(e);
}
// attach supplementary data
var async;
if (Z.getHiddenPref && Z.getHiddenPref("attachSupplementary")) {
try { // don't fail if we can't attach supplementary data
async = attachSupplementary(doc, item, function (doc, item) {
item.complete();
});
}
catch (e) {
Z.debug("Error attaching supplementary information.");
Z.debug(e);
if (async) item.complete();
}
if (!async) {
item.complete();
}
}
else {
item.complete();
}
}, doc, url);
}
function doWeb(doc, url) {
if (detectWeb(doc, url) == 'multiple') {
var nodes = getMultipleNodes(doc, url);
var titlex = nodes[1];
var linkx = nodes[2];
nodes = nodes[0];
if (nodes.length == 0) {
Z.debug("no multiples");
// return false; //keep going so we can report this to zotero.org instead of "silently" failing
}
var items = {};
for (var i = 0; i < nodes.length; i++) {
let title = Zotero.Utilities.xpathText(nodes[i], titlex, null, '');
let link = Zotero.Utilities.xpath(nodes[i], linkx);
if (title && link.length == 1) {
items[link[0].href] = title.trim();
}
}
var urls = [];
Zotero.selectItems(items, function (selectedItems) {
if (!selectedItems) return true;
for (var item in selectedItems) {
urls.push(item);
}
Zotero.Utilities.processDocuments(urls, scrape);
return true;
});
}
else {
scrape(doc, url);
}
}
// ISO8879 to unicode character map
var ISO8879CharMap = {
excl: "\u0021", quot: "\u0022", num: "\u0023", dollar: "\u0024",
percnt: "\u0025", amp: "\u0026", apos: "\u0027", lpar: "\u0028",
rpar: "\u0029", ast: "\u002A", plus: "\u002B", comma: "\u002C",
period: "\u002E", sol: "\u002F", colon: "\u003A", semi: "\u003B",
lt: "\u003C", equals: "\u003D", gt: "\u003E", quest: "\u003F",
commat: "\u0040", lsqb: "\u005B", lbrack: "\u005B", bsol: "\u005C",
rsqb: "\u005D", rbrack: "\u005D", lowbar: "\u005F", grave: "\u0060",
DiacriticalGrave: "\u0060", jnodot: "\u006A", lcub: "\u007B", lbrace: "\u007B",
verbar: "\u007C", vert: "\u007C", rcub: "\u007D", rbrace: "\u007D",
nbsp: "\u00A0", NonBreakingSpace: "\u00A0", iexcl: "\u00A1", cent: "\u00A2",
pound: "\u00A3", curren: "\u00A4", yen: "\u00A5", brvbar: "\u00A6",
sect: "\u00A7", die: "\u00A8", uml: "\u00A8",
copy: "\u00A9", ordf: "\u00AA", laquo: "\u00AB",
not: "\u00AC", shy: "\u00AD", reg: "\u00AE", circledR: "\u00AE",
macr: "\u00AF", deg: "\u00B0", plusmn: "\u00B1", pm: "\u00B1",
PlusMinus: "\u00B1", sup2: "\u00B2", sup3: "\u00B3", acute: "\u00B4",
DiacriticalAcute: "\u00B4", micro: "\u00B5", para: "\u00B6", middot: "\u00B7",
centerdot: "\u00B7", CenterDot: "\u00B7", cedil: "\u00B8", Cedilla: "\u00B8",
sup1: "\u00B9", ordm: "\u00BA", raquo: "\u00BB", frac14: "\u00BC",
frac12: "\u00BD", half: "\u00BD",
frac34: "\u00BE", iquest: "\u00BF", Agrave: "\u00C0", Aacute: "\u00C1",
Acirc: "\u00C2", Atilde: "\u00C3", Auml: "\u00C4", Aring: "\u00C5",
AElig: "\u00C6", Ccedil: "\u00C7", Egrave: "\u00C8", Eacute: "\u00C9",
Ecirc: "\u00CA", Euml: "\u00CB", Igrave: "\u00CC", Iacute: "\u00CD",
Icirc: "\u00CE", Iuml: "\u00CF", ETH: "\u00D0", Ntilde: "\u00D1",
Ograve: "\u00D2", Oacute: "\u00D3", Ocirc: "\u00D4", Otilde: "\u00D5",
Ouml: "\u00D6", times: "\u00D7", Oslash: "\u00D8", Ugrave: "\u00D9",
Uacute: "\u00DA", Ucirc: "\u00DB", Uuml: "\u00DC", Yacute: "\u00DD",
THORN: "\u00DE", szlig: "\u00DF", agrave: "\u00E0", aacute: "\u00E1",
acirc: "\u00E2", atilde: "\u00E3", auml: "\u00E4", aring: "\u00E5",
aelig: "\u00E6", ccedil: "\u00E7", egrave: "\u00E8", eacute: "\u00E9",
ecirc: "\u00EA", euml: "\u00EB", igrave: "\u00EC", iacute: "\u00ED",
icirc: "\u00EE", iuml: "\u00EF", eth: "\u00F0", ntilde: "\u00F1",
ograve: "\u00F2", oacute: "\u00F3", ocirc: "\u00F4", otilde: "\u00F5",
ouml: "\u00F6", divide: "\u00F7", div: "\u00F7", oslash: "\u00F8",
ugrave: "\u00F9", uacute: "\u00FA", ucirc: "\u00FB", uuml: "\u00FC",
yacute: "\u00FD", thorn: "\u00FE", yuml: "\u00FF", Amacr: "\u0100",
amacr: "\u0101", Abreve: "\u0102", abreve: "\u0103", Aogon: "\u0104",
aogon: "\u0105", Cacute: "\u0106", cacute: "\u0107", Ccirc: "\u0108",
ccirc: "\u0109", Cdot: "\u010A", cdot: "\u010B", Ccaron: "\u010C",
ccaron: "\u010D", Dcaron: "\u010E", dcaron: "\u010F", Dstrok: "\u0110",
dstrok: "\u0111", Emacr: "\u0112", emacr: "\u0113", Edot: "\u0116",
edot: "\u0117", Eogon: "\u0118", eogon: "\u0119", Ecaron: "\u011A",
ecaron: "\u011B", Gcirc: "\u011C", gcirc: "\u011D", Gbreve: "\u011E",
gbreve: "\u011F", Gdot: "\u0120", gdot: "\u0121", Gcedil: "\u0122",
Hcirc: "\u0124", hcirc: "\u0125", Hstrok: "\u0126", hstrok: "\u0127",
Itilde: "\u0128", itilde: "\u0129", Imacr: "\u012A", imacr: "\u012B",
Iogon: "\u012E", iogon: "\u012F", Idot: "\u0130", IJlig: "\u0132",
ijlig: "\u0133", Jcirc: "\u0134", jcirc: "\u0135", Kcedil: "\u0136",
kcedil: "\u0137", kgreen: "\u0138", Lacute: "\u0139", lacute: "\u013A",
Lcedil: "\u013B", lcedil: "\u013C", Lcaron: "\u013D", lcaron: "\u013E",
Lmidot: "\u013F", lmidot: "\u0140", Lstrok: "\u0141", lstrok: "\u0142",
Nacute: "\u0143", nacute: "\u0144", Ncedil: "\u0145", ncedil: "\u0146",
Ncaron: "\u0147", ncaron: "\u0148", napos: "\u0149", ENG: "\u014A",
eng: "\u014B", Omacr: "\u014C", omacr: "\u014D", Odblac: "\u0150",
odblac: "\u0151", OElig: "\u0152", oelig: "\u0153", Racute: "\u0154",
racute: "\u0155", Rcedil: "\u0156", rcedil: "\u0157", Rcaron: "\u0158",
rcaron: "\u0159", Sacute: "\u015A", sacute: "\u015B", Scirc: "\u015C",
scirc: "\u015D", Scedil: "\u015E", scedil: "\u015F", Scaron: "\u0160",
scaron: "\u0161", Tcedil: "\u0162", tcedil: "\u0163", Tcaron: "\u0164",
tcaron: "\u0165", Tstrok: "\u0166", tstrok: "\u0167", Utilde: "\u0168",
utilde: "\u0169", Umacr: "\u016A", umacr: "\u016B", Ubreve: "\u016C",
ubreve: "\u016D", Uring: "\u016E", uring: "\u016F", Udblac: "\u0170",
udblac: "\u0171", Uogon: "\u0172", uogon: "\u0173", Wcirc: "\u0174",
wcirc: "\u0175", Ycirc: "\u0176", ycirc: "\u0177", Yuml: "\u0178",
Zacute: "\u0179", zacute: "\u017A", Zdot: "\u017B", zdot: "\u017C",
Zcaron: "\u017D", zcaron: "\u017E", gacute: "\u01F5", circ: "\u02C6",
caron: "\u02C7", Hacek: "\u02C7", breve: "\u02D8", Breve: "\u02D8",
dot: "\u02D9", DiacriticalDot: "\u02D9", ring: "\u02DA", ogon: "\u02DB",
tilde: "\u02DC", DiacriticalTilde: "\u02DC", dblac: "\u02DD", DiacriticalDoubleAcute: "\u02DD",
Aacgr: "\u0386", Eacgr: "\u0388", EEacgr: "\u0389", Iacgr: "\u038A",
Oacgr: "\u038C", Uacgr: "\u038E", OHacgr: "\u038F", idiagr: "\u0390",
Agr: "\u0391", Bgr: "\u0392", Ggr: "\u0393", Gamma: "\u0393",
Dgr: "\u0394", Delta: "\u0394", Egr: "\u0395", Zgr: "\u0396",
EEgr: "\u0397", THgr: "\u0398", Theta: "\u0398", Igr: "\u0399",
Kgr: "\u039A", Lgr: "\u039B", Lambda: "\u039B", Mgr: "\u039C",
Ngr: "\u039D", Xgr: "\u039E", Xi: "\u039E", Ogr: "\u039F",
Pgr: "\u03A0", Pi: "\u03A0", Rgr: "\u03A1", Sgr: "\u03A3",
Sigma: "\u03A3", Tgr: "\u03A4", Ugr: "\u03A5", PHgr: "\u03A6",
Phi: "\u03A6", KHgr: "\u03A7", PSgr: "\u03A8", Psi: "\u03A8",
OHgr: "\u03A9", Omega: "\u03A9", Idigr: "\u03AA", Udigr: "\u03AB",
aacgr: "\u03AC", eacgr: "\u03AD", eeacgr: "\u03AE", iacgr: "\u03AF",
udiagr: "\u03B0", agr: "\u03B1", alpha: "\u03B1", bgr: "\u03B2",
beta: "\u03B2", ggr: "\u03B3", gamma: "\u03B3", dgr: "\u03B4",
delta: "\u03B4", egr: "\u03B5", epsiv: "\u03B5", zgr: "\u03B6",
zeta: "\u03B6", eegr: "\u03B7", eta: "\u03B7", thgr: "\u03B8",
thetas: "\u03B8", igr: "\u03B9", iota: "\u03B9", kgr: "\u03BA",
kappa: "\u03BA", lgr: "\u03BB", lambda: "\u03BB", mgr: "\u03BC",
mu: "\u03BC", ngr: "\u03BD", nu: "\u03BD", xgr: "\u03BE",
xi: "\u03BE", ogr: "\u03BF", pgr: "\u03C0", pi: "\u03C0",
rgr: "\u03C1", rho: "\u03C1", sfgr: "\u03C2", sigmav: "\u03C2",
sgr: "\u03C3", sigma: "\u03C3", tgr: "\u03C4", tau: "\u03C4",
ugr: "\u03C5", upsi: "\u03C5", phgr: "\u03C6", phiv: "\u03C6",
khgr: "\u03C7", chi: "\u03C7", psgr: "\u03C8", psi: "\u03C8",
ohgr: "\u03C9", omega: "\u03C9", idigr: "\u03CA", udigr: "\u03CB",
oacgr: "\u03CC", uacgr: "\u03CD", ohacgr: "\u03CE", thetav: "\u03D1",
vartheta: "\u03D1", Upsi: "\u03D2", phis: "\u03D5", straightphi: "\u03D5",
piv: "\u03D6", varpi: "\u03D6", "b.Gammad": "\u03DC", gammad: "\u03DD",
"b.gammad": "\u03DD", kappav: "\u03F0", varkappa: "\u03F0", rhov: "\u03F1",
varrho: "\u03F1", epsi: "\u03F5", epsis: "\u03F5",
straightepsilon: "\u03F5", bepsi: "\u03F6",
backepsilon: "\u03F6", IOcy: "\u0401", DJcy: "\u0402", GJcy: "\u0403",
Jukcy: "\u0404", DScy: "\u0405", Iukcy: "\u0406", YIcy: "\u0407",
Jsercy: "\u0408", LJcy: "\u0409", NJcy: "\u040A", TSHcy: "\u040B",
KJcy: "\u040C", Ubrcy: "\u040E", DZcy: "\u040F", Acy: "\u0410",
Bcy: "\u0411", Vcy: "\u0412", Gcy: "\u0413", Dcy: "\u0414",
IEcy: "\u0415", ZHcy: "\u0416", Zcy: "\u0417", Icy: "\u0418",
Jcy: "\u0419", Kcy: "\u041A", Lcy: "\u041B", Mcy: "\u041C",
Ncy: "\u041D", Ocy: "\u041E", Pcy: "\u041F", Rcy: "\u0420",
Scy: "\u0421", Tcy: "\u0422", Ucy: "\u0423", Fcy: "\u0424",
KHcy: "\u0425", TScy: "\u0426", CHcy: "\u0427", SHcy: "\u0428",
SHCHcy: "\u0429", HARDcy: "\u042A", Ycy: "\u042B", SOFTcy: "\u042C",
Ecy: "\u042D", YUcy: "\u042E", YAcy: "\u042F", acy: "\u0430",
bcy: "\u0431", vcy: "\u0432", gcy: "\u0433", dcy: "\u0434",
iecy: "\u0435", zhcy: "\u0436", zcy: "\u0437", icy: "\u0438",
jcy: "\u0439", kcy: "\u043A", lcy: "\u043B", mcy: "\u043C",
ncy: "\u043D", ocy: "\u043E", pcy: "\u043F", rcy: "\u0440",
scy: "\u0441", tcy: "\u0442", ucy: "\u0443", fcy: "\u0444",
khcy: "\u0445", tscy: "\u0446", chcy: "\u0447", shcy: "\u0448",
shchcy: "\u0449", hardcy: "\u044A", ycy: "\u044B", softcy: "\u044C",
ecy: "\u044D", yucy: "\u044E", yacy: "\u044F", iocy: "\u0451",
djcy: "\u0452", gjcy: "\u0453", jukcy: "\u0454", dscy: "\u0455",
iukcy: "\u0456", yicy: "\u0457", jsercy: "\u0458", ljcy: "\u0459",
njcy: "\u045A", tshcy: "\u045B", kjcy: "\u045C", ubrcy: "\u045E",
dzcy: "\u045F", ensp: "\u2002", emsp: "\u2003", emsp13: "\u2004",
emsp14: "\u2005", numsp: "\u2007", puncsp: "\u2008", thinsp: "\u2009",
ThinSpace: "\u2009", hairsp: "\u200A", VeryThinSpace: "\u200A", hyphen: "\u2010",
dash: "\u2010", ndash: "\u2013", mdash: "\u2014", horbar: "\u2015",
lsquo: "\u2018", OpenCurlyQuote: "\u2018", rsquo: "\u2019", rsquor: "\u2019",
lsquor: "\u201A", ldquo: "\u201C", OpenCurlyDoubleQuote: "\u201C", rdquo: "\u201D",
rdquor: "\u201D", ldquor: "\u201E", dagger: "\u2020", Dagger: "\u2021",
ddagger: "\u2021", bull: "\u2022", bullet: "\u2022", nldr: "\u2025",
hellip: "\u2026", mldr: "\u2026",
vprime: "\u2032", bprime: "\u2035", backprime: "\u2035", caret: "\u2041",
hybull: "\u2043", incare: "\u2105", planck: "\u210F", hbar: "\u210F",
hslash: "\u210F", ell: "\u2113", numero: "\u2116", copysr: "\u2117",
weierp: "\u2118", wp: "\u2118", real: "\u211C", Re: "\u211C",
realpart: "\u211C", rx: "\u211E", trade: "\u2122", ohm: "\u2126",
beth: "\u2136", gimel: "\u2137", daleth: "\u2138", frac13: "\u2153",
frac23: "\u2154", frac15: "\u2155", frac25: "\u2156", frac35: "\u2157",
frac45: "\u2158", frac16: "\u2159", frac56: "\u215A", frac18: "\u215B",
frac38: "\u215C", frac58: "\u215D", frac78: "\u215E", larr: "\u2190",
leftarrow: "\u2190", LeftArrow: "\u2190", ShortLeftArrow: "\u2190", uarr: "\u2191",
uparrow: "\u2191", UpArrow: "\u2191", ShortUpArrow: "\u2191", rarr: "\u2192",
rightarrow: "\u2192", RightArrow: "\u2192", ShortRightArrow: "\u2192", darr: "\u2193",
downarrow: "\u2193", DownArrow: "\u2193", ShortDownArrow: "\u2193", harr: "\u2194",
leftrightarrow: "\u2194", LeftRightArrow: "\u2194", varr: "\u2195", updownarrow: "\u2195",
UpDownArrow: "\u2195", nwarr: "\u2196", UpperLeftArrow: "\u2196", nwarrow: "\u2196",
nearr: "\u2197", UpperRightArrow: "\u2197", nearrow: "\u2197", drarr: "\u2198",
searrow: "\u2198", LowerRightArrow: "\u2198", dlarr: "\u2199", swarrow: "\u2199",
LowerLeftArrow: "\u2199", nlarr: "\u219A", nleftarrow: "\u219A", nrarr: "\u219B",
nrightarrow: "\u219B", rarrw: "\u219D", rightsquigarrow: "\u219D", Larr: "\u219E",
twoheadleftarrow: "\u219E", Rarr: "\u21A0", twoheadrightarrow: "\u21A0", larrtl: "\u21A2",
leftarrowtail: "\u21A2", rarrtl: "\u21A3", rightarrowtail: "\u21A3", map: "\u21A6",
RightTeeArrow: "\u21A6", mapsto: "\u21A6", larrhk: "\u21A9", hookleftarrow: "\u21A9",
rarrhk: "\u21AA", hookrightarrow: "\u21AA", larrlp: "\u21AB", looparrowleft: "\u21AB",
rarrlp: "\u21AC", looparrowright: "\u21AC", harrw: "\u21AD", leftrightsquigarrow: "\u21AD",
nharr: "\u21AE", nleftrightarrow: "\u21AE", lsh: "\u21B0", Lsh: "\u21B0",
rsh: "\u21B1", Rsh: "\u21B1", cularr: "\u21B6", curvearrowleft: "\u21B6",
curarr: "\u21B7", curvearrowright: "\u21B7", olarr: "\u21BA", circlearrowleft: "\u21BA",
orarr: "\u21BB", circlearrowright: "\u21BB", lharu: "\u21BC", LeftVector: "\u21BC",
leftharpoonup: "\u21BC", lhard: "\u21BD", leftharpoondown: "\u21BD", DownLeftVector: "\u21BD",
uharr: "\u21BE", upharpoonright: "\u21BE", RightUpVector: "\u21BE", uharl: "\u21BF",
upharpoonleft: "\u21BF", LeftUpVector: "\u21BF", rharu: "\u21C0", RightVector: "\u21C0",
rightharpoonup: "\u21C0", rhard: "\u21C1", rightharpoondown: "\u21C1", DownRightVector: "\u21C1",
dharr: "\u21C2", RightDownVector: "\u21C2", downharpoonright: "\u21C2", dharl: "\u21C3",
LeftDownVector: "\u21C3", downharpoonleft: "\u21C3", rlarr2: "\u21C4", rightleftarrows: "\u21C4",
RightArrowLeftArrow: "\u21C4", lrarr2: "\u21C6", leftrightarrows: "\u21C6", LeftArrowRightArrow: "\u21C6",
larr2: "\u21C7", leftleftarrows: "\u21C7", uarr2: "\u21C8", upuparrows: "\u21C8",
rarr2: "\u21C9", rightrightarrows: "\u21C9", darr2: "\u21CA", downdownarrows: "\u21CA",
lrhar2: "\u21CB", ReverseEquilibrium: "\u21CB", leftrightharpoons: "\u21CB", rlhar2: "\u21CC",
rightleftharpoons: "\u21CC", Equilibrium: "\u21CC", nlArr: "\u21CD", nLeftarrow: "\u21CD",
nhArr: "\u21CE", nLeftrightarrow: "\u21CE", nrArr: "\u21CF", nRightarrow: "\u21CF",
uArr: "\u21D1", Uparrow: "\u21D1", DoubleUpArrow: "\u21D1", dArr: "\u21D3",
Downarrow: "\u21D3", DoubleDownArrow: "\u21D3", hArr: "\u21D4", Leftrightarrow: "\u21D4",
DoubleLeftRightArrow: "\u21D4", vArr: "\u21D5", Updownarrow: "\u21D5", DoubleUpDownArrow: "\u21D5",
lAarr: "\u21DA", Lleftarrow: "\u21DA", rAarr: "\u21DB", Rrightarrow: "\u21DB",
comp: "\u2201", complement: "\u2201", nexist: "\u2204", NotExists: "\u2204",
nexists: "\u2204", empty: "\u2205", emptyset: "\u2205", varnothing: "\u2205",
prod: "\u220F", coprod: "\u2210", samalg: "\u2210", sum: "\u2211",
Sum: "\u2211", plusdo: "\u2214", dotplus: "\u2214", setmn: "\u2216",
ssetmn: "\u2216", setminus: "\u2216", Backslash: "\u2216",
vprop: "\u221D",
propto: "\u221D", Proportional: "\u221D", varpropto: "\u221D", ang: "\u2220",
angle: "\u2220", angmsd: "\u2221", measuredangle: "\u2221", mid: "\u2223",
smid: "\u2223", VerticalBar: "\u2223",
nmid: "\u2224", nsmid: "\u2224",
spar: "\u2225", parallel: "\u2225", DoubleVerticalBar: "\u2225",
shortparallel: "\u2225", npar: "\u2226", nspar: "\u2226",
nparallel: "\u2226", NotDoubleVerticalBar: "\u2226",
thksim: "\u223C", Tilde: "\u223C", thicksim: "\u223C",
bsim: "\u223D", backsim: "\u223D", wreath: "\u2240", VerticalTilde: "\u2240",
wr: "\u2240", nsim: "\u2241", NotTilde: "\u2241", nsime: "\u2244",
nsimeq: "\u2244", NotTildeEqual: "\u2244", ncong: "\u2247", NotTildeFullEqual: "\u2247",
asymp: "\u2248", thkap: "\u2248", TildeTilde: "\u2248",
approx: "\u2248",
nap: "\u2249", NotTildeTilde: "\u2249", napprox: "\u2249", ape: "\u224A",
approxeq: "\u224A", bcong: "\u224C", backcong: "\u224C", bump: "\u224E",
HumpDownHump: "\u224E", Bumpeq: "\u224E", bumpe: "\u224F", HumpEqual: "\u224F",
bumpeq: "\u224F", esdot: "\u2250", DotEqual: "\u2250", doteq: "\u2250",
eDot: "\u2251", doteqdot: "\u2251", efDot: "\u2252", fallingdotseq: "\u2252",
erDot: "\u2253", risingdotseq: "\u2253", colone: "\u2254", coloneq: "\u2254",
Assign: "\u2254", ecolon: "\u2255", eqcolon: "\u2255", ecir: "\u2256",
eqcirc: "\u2256", cire: "\u2257", circeq: "\u2257", trie: "\u225C",
triangleq: "\u225C", nequiv: "\u2262", NotCongruent: "\u2262", lE: "\u2266",
LessFullEqual: "\u2266", leqq: "\u2266", nlE: "\u2266\u0338", NotGreaterFullEqual: "\u2266\u0338",