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ScienceDirect.js
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{
"translatorID": "b6d0a7a-d076-48ae-b2f0-b6de28b194e",
"label": "ScienceDirect",
"creator": "Michael Berkowitz and Aurimas Vinckevicius",
"target": "^https?://[^/]*science-?direct\\.com[^/]*/((science/)?(article/|(journal|bookseries|book|handbook)/\\d)|search[?/]|journal/[^/]+/vol)",
"minVersion": "3.0",
"maxVersion": "",
"priority": 100,
"inRepository": true,
"translatorType": 4,
"browserSupport": "gcsibv",
"lastUpdated": "2024-10-03 14:17:12"
}
function detectWeb(doc, url) {
if (!doc.body.textContent.trim()) return false;
if ((url.includes("_ob=DownloadURL"))
|| doc.title == "ScienceDirect Login"
|| doc.title == "ScienceDirect - Dummy"
|| (url.includes("/science/advertisement/"))) {
return false;
}
if ((url.includes("pdf")
&& !url.includes("_ob=ArticleURL")
&& !url.includes("/article/"))
|| url.search(/\/(?:journal|bookseries|book|handbook)\//) !== -1) {
if (getArticleList(doc).length > 0) {
return "multiple";
}
else {
return false;
}
}
if (url.search(/\/search[?/]/) != -1) {
if (getArticleList(doc).length > 0) {
return "multiple";
}
else if (doc.querySelector('.LoadingOverlay.show')) {
// monitor and update the toolbar icon when results have loaded
Z.monitorDOMChanges(doc.querySelector('.results-container'));
return false;
}
}
if (!new URL(url).pathname.includes("pdf")) {
// Book sections have the ISBN in the URL
if (url.includes("/B978")) {
return "bookSection";
}
else if (getISBN(doc)) {
if (getArticleList(doc).length) {
return "multiple";
}
else {
return "book";
}
}
else {
return "journalArticle";
}
}
return false;
}
async function getPDFLink(doc) {
// No PDF access ("Get Full Text Elsewhere" or "Check for this article elsewhere")
if (doc.querySelector('.accessContent') || doc.querySelector('.access-options-link-text') || doc.querySelector('#check-access-popover')) {
Zotero.debug("PDF is not available");
return false;
}
// Some pages still have the PDF link available
var pdfURL = attr(doc, '#pdfLink', 'href');
if (!pdfURL) pdfURL = attr(doc, '[name="citation_pdf_url"]', 'content');
if (pdfURL && pdfURL != '#') {
Z.debug('Found intermediate URL in head: ' + pdfURL);
return parseIntermediatePDFPage(pdfURL);
}
// If intermediate page URL is available, use that directly
var intermediateURL = attr(doc, '.PdfEmbed > object', 'data');
if (intermediateURL) {
Zotero.debug("Found embedded PDF URL: " + intermediateURL);
if (/[?&]isDTMRedir=(Y|true)/i.test(intermediateURL)) {
return intermediateURL;
}
else {
return parseIntermediatePDFPage(intermediateURL);
}
}
// Simulate a click on the "Download PDF" button to open the menu containing the link with the URL
// for the intermediate page, which doesn't seem to be available in the DOM after the page load.
// This is an awful hack, and we should look out for a better way to get the URL, but it beats
// refetching the original source. Works and should be imperceptible to users
// when run from the browser, does not work from non-browser translation
// environments (e.g. Find Available PDFs in the client). In those cases we
// fall back to approach #3: embedded JSON metadata.
var pdfLink = doc.querySelector('#pdfLink');
if (pdfLink) {
// Just in case
try {
pdfLink.click();
intermediateURL = attr(doc, '.PdfDropDownMenu a', 'href');
doc.body.click();
}
catch (e) {
Zotero.debug(e, 2);
}
if (intermediateURL) {
// Zotero.debug("Intermediate PDF URL from drop-down: " + intermediateURL);
return parseIntermediatePDFPage(intermediateURL);
}
}
// On some institutional networks with access to ScienceDirect, the site
// serves JSON metadata probably used to preload dynamic content without a
// separate network request. If we find it, we can take advantage of it to
// grab the PDF url's parts directly, constructing it in the same way that
// the site's frontend JavaScript would.
var json = text(doc, 'script[type="application/json"]');
if (json) {
try {
json = JSON.parse(json);
Zotero.debug("Trying to construct PDF URL from JSON data");
let urlMetadata = json.article.pdfDownload.urlMetadata;
let path = urlMetadata.path;
let pdfExtension = urlMetadata.pdfExtension;
let pii = urlMetadata.pii;
let md5 = urlMetadata.queryParams.md5;
let pid = urlMetadata.queryParams.pid;
if (path && pdfExtension && pii && md5 && pid){
pdfURL = `/${path}/${pii}${pdfExtension}?md5=${md5}&pid=${pid}`;
Zotero.debug("Created PDF URL from JSON data: " + pdfURL);
return pdfURL;
}
else {
Zotero.debug("Missing elements in JSON data required for URL creation");
}
}
catch (e) {
Zotero.debug(e, 2);
}
}
// In most cases, appending the suffix seen below to the page's canonical URL
// should get us directly to the PDF; it'll yield a URL similar to the one
// created by the JSON but without the md5 and pid parameters. It should be
// enough to get us through even without those parameters.
pdfURL = attr(doc, 'link[rel="canonical"]', 'href');
if (pdfURL) {
pdfURL = pdfURL + '/pdfft?download=true';
Zotero.debug("Trying to construct PDF URL from canonical link: " + pdfURL);
return pdfURL;
}
// If none of that worked for some reason, get the URL from the initial HTML,
// where it is present, by fetching the page source again. Hopefully this is
// never actually used.
var url = doc.location.href;
Zotero.debug("Refetching HTML for PDF link");
let reloadedDoc = await requestDocument(url);
intermediateURL = attr(reloadedDoc, '.pdf-download-btn-link', 'href');
// Zotero.debug("Intermediate PDF URL: " + intermediateURL);
if (intermediateURL) {
return parseIntermediatePDFPage(intermediateURL);
}
return false;
}
async function parseIntermediatePDFPage(url) {
// Get the PDF URL from the meta refresh on the intermediate page
Z.debug('Parsing intermediate page to find redirect: ' + url);
let doc = await requestDocument(url);
var pdfURL = attr(doc, 'meta[HTTP-EQUIV="Refresh"]', 'CONTENT');
var otherRedirect = attr(doc, '#redirect-message a', 'href');
// Zotero.debug("Meta refresh URL: " + pdfURL);
if (pdfURL) {
// Strip '0;URL='
var matches = pdfURL.match(/\d+;URL=(.+)/);
pdfURL = matches ? matches[1] : null;
}
else if (otherRedirect) {
pdfURL = otherRedirect;
}
else if (url.includes('.pdf')) {
// Sometimes we are already on the PDF page here and therefore
// can simply use the original url as pdfURL.
pdfURL = url;
}
return pdfURL;
}
function getISBN(doc) {
var isbn = ZU.xpathText(doc, '//td[@class="tablePubHead-Info"]//span[@class="txtSmall"]');
if (!isbn) return false;
isbn = isbn.match(/ISBN:\s*([-\d]+)/);
if (!isbn) return false;
return isbn[1].replace(/[-\s]/g, '');
}
function getAbstract(doc) {
var p = ZU.xpath(doc, '//div[contains(@class, "abstract") and not(contains(@class, "abstractHighlights"))]/p');
var paragraphs = [];
for (var i = 0; i < p.length; i++) {
paragraphs.push(ZU.trimInternal(p[i].textContent));
}
return paragraphs.join('\n');
}
// mimetype map for supplementary attachments
// intentionally excluding potentially large files like videos and zip files
var suppTypeMap = {
pdf: 'application/pdf',
// 'zip': 'application/zip',
doc: 'application/msword',
docx: 'application/vnd.openxmlformats-officedocument.wordprocessingml.document',
xls: 'application/vnd.ms-excel',
xlsx: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
};
// attach supplementary information
function attachSupplementary(doc, item) {
var links = ZU.xpath(doc, './/span[starts-with(@class, "MMCvLABEL_SRC")]');
var link, title, url, type, snapshot;
var attachAsLink = Z.getHiddenPref("supplementaryAsLink");
for (var i = 0, n = links.length; i < n; i++) {
link = links[i].firstElementChild;
if (!link || link.nodeName.toUpperCase() !== 'A') continue;
url = link.href;
if (!url) continue;
title = ZU.trimInternal(link.textContent);
if (!title) title = 'Supplementary Data';
type = suppTypeMap[url.substr(url.lastIndexOf('.') + 1).toLowerCase()];
snapshot = !attachAsLink && type;
var attachment = {
title: title,
url: url,
mimeType: type,
snapshot: !!snapshot
};
var replaced = false;
if (snapshot && title.search(/Article plus Supplemental Information/i) != -1) {
// replace full text PDF
for (var j = 0, m = item.attachments.length; j < m; j++) {
if (item.attachments[j].title == "ScienceDirect Full Text PDF") {
attachment.title = "Article plus Supplemental Information";
item.attachments[j] = attachment;
replaced = true;
break;
}
}
}
if (!replaced) {
item.attachments.push(attachment);
}
}
}
async function processRIS(doc, text, isSearchResult = false) {
let pdfURL = await getPDFLink(doc);
// T2 doesn't appear to hold the short title anymore.
// Sometimes has series title, so I'm mapping this to T3,
// although we currently don't recognize that in RIS
text = text.replace(/^T2\s/mg, 'T3 ');
// Sometimes PY has some nonsensical value. Y2 contains the correct
// date in that case.
if (text.search(/^Y2\s+-\s+\d{4}\b/m) !== -1) {
text = text.replace(/TY\s+-[\S\s]+?ER/g, function (m) {
if (m.search(/^PY\s+-\s+\d{4}\b/m) === -1
&& m.search(/^Y2\s+-\s+\d{4}\b/m) !== -1
) {
return m.replace(/^PY\s+-.*\r?\n/mg, '')
.replace(/^Y2\s+-/mg, 'PY -');
}
return m;
});
}
// Certain authors sometimes have "role" prefixes or are in the wrong order
// e.g. http://www.sciencedirect.com/science/article/pii/S0065260108602506
text = text.replace(/^((?:A[U\d]|ED)\s+-\s+)(?:Editor-in-Chief:\s+)?(.+)/mg,
function (m, pre, name) {
if (!name.includes(',')) {
name = name.trim().replace(/^(.+?)\s+(\S+)$/, '$2, $1');
}
return pre + name;
}
);
// The RIS sometimes has spaces at the beginning of lines, which break things
// as of 20170121 e.g. on http://www.sciencedirect.com/science/article/pii/B9780123706263000508 for A2
// remove them
text = text.replace(/\n\s+/g, "\n");
// Z.debug(text)
var translator = Zotero.loadTranslator("import");
translator.setTranslator("32d59d2d-b65a-4da4-b0a3-bdd3cfb979e7");
translator.setString(text);
translator.setHandler("itemDone", function (obj, item) {
// If the title on the page contains formatting tags, use it instead of the title from the RIS
let titleElem = doc.querySelector('h1 > .title-text');
if (titleElem && titleElem.childNodes.length > 1) {
item.title = titleToString(titleElem);
}
// issue sometimes is set to 0 for single issue volumes (?)
if (item.issue === 0) delete item.issue;
if (item.volume) item.volume = item.volume.replace(/^\s*volume\s*/i, '');
for (var i = 0, n = item.creators.length; i < n; i++) {
// add spaces after initials
if (item.creators[i].firstName) {
item.creators[i].firstName = item.creators[i].firstName
.replace(/\.\s*(?=\S)/g, '. ')
.replace(/\s/g, ' '); // NBSP, etc -> space
}
if (item.creators[i].lastName) {
item.creators[i].lastName = item.creators[i].lastName
.replace(/\s/g, ' ');
}
// fix all uppercase lastnames
if (item.creators[i].lastName.toUpperCase() == item.creators[i].lastName) {
item.creators[i].lastName = item.creators[i].lastName.charAt(0) + item.creators[i].lastName.slice(1).toLowerCase();
}
}
// abstract is not included with the new export form. Scrape from page
if (!item.abstractNote) {
item.abstractNote = getAbstract(doc);
}
if (item.abstractNote) {
item.abstractNote = item.abstractNote.replace(/^(Abstract|Summary)[\s:\n]*/, "");
}
if (!isSearchResult) {
item.attachments.push({
title: "ScienceDirect Snapshot",
document: doc
});
}
// attach supplementary data
if (Z.getHiddenPref && Z.getHiddenPref("attachSupplementary")) {
try { // don't fail if we can't attach supplementary data
attachSupplementary(doc, item);
}
catch (e) {
Z.debug("Error attaching supplementary information.");
Z.debug(e);
}
}
if (item.notes[0]) {
item.abstractNote = item.notes[0].note;
item.notes = [];
}
if (item.abstractNote) {
item.abstractNote = item.abstractNote.replace(/^\s*(?:abstract|(publisher\s+)?summary)\s+/i, '');
}
if (item.DOI) {
item.DOI = item.DOI.replace(/^doi:\s+/i, '');
}
if (item.ISBN && !ZU.cleanISBN(item.ISBN)) delete item.ISBN;
if (item.ISSN && !ZU.cleanISSN(item.ISSN)) delete item.ISSN;
item.language = item.language || attr(doc, 'article[role="main"]', 'lang');
if (item.url && item.url.substr(0, 2) == "//") {
item.url = "https:" + item.url;
}
if (pdfURL) {
item.attachments.push({
title: 'ScienceDirect Full Text PDF',
url: pdfURL,
mimeType: 'application/pdf',
proxy: false
});
}
item.complete();
});
await translator.translate();
}
function titleToString(titleElem) {
let title = '';
for (let node of titleElem.childNodes) {
// Wrap italics within the title in <i> for CiteProc
if (node.nodeName === 'EM') {
title += '<i>' + node.textContent + '</i>';
}
else {
title += node.textContent;
}
}
return title;
}
function getArticleList(doc) {
let articlePaths = [
'//table[@class="resultRow"]/tbody/tr/td[2]/a',
'//table[@class="resultRow"]/tbody/tr/td[2]/h3/a',
'//td[@class="nonSerialResultsList"]/h3/a',
'//div[@id="bodyMainResults"]//li[contains(@class,"title")]//a',
'//h2//a[contains(@class, "result-list-title-link")]',
'//ol[contains(@class, "article-list") or contains(@class, "article-list-items")]//a[contains(@class, "article-content-title")]',
'//li[contains(@class, "list-chapter")]//h2//a',
'//h4[contains(@class, "chapter-title")]/a'
];
return ZU.xpath(doc, '('
+ articlePaths.join('|')
+ ')[not(contains(text(),"PDF (") or contains(text(), "Related Articles"))]'
);
}
async function doWeb(doc, url) {
if (detectWeb(doc, url) == "multiple") {
// search page
var itemList = getArticleList(doc);
var items = {};
for (var i = 0, n = itemList.length; i < n; i++) {
items[itemList[i].href] = itemList[i].textContent;
}
let selectedItems = await Zotero.selectItems(items);
if (!selectedItems) return;
for (let url of Object.keys(selectedItems)) {
await scrape(await requestDocument(url), url, true);
}
}
else {
await scrape(doc, url);
}
}
function getFormInput(form) {
var inputs = form.elements;
var values = {};
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var form = ZU.xpath(doc, '//form[@name="exportCite"]')[0];
if (form) {
Z.debug("Fetching RIS via POST form");
var values = getFormInput(form);
values['citation-type'] = 'RIS';
values.format = 'cite-abs';
let text = await requestText(form.action, {
body: formValuesToPostData(values)
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await processRIS(doc, text, isSearchResult);
return;
}
// On newer pages, there is an GET formular which is only there if
// the user click on the export button, but we know how the url
// in the end will be built.
form = ZU.xpath(doc, '//div[@id="export-citation"]//button')[0];
if (form) {
Z.debug("Fetching RIS via GET form (new)");
var pii = ZU.xpathText(doc, '//meta[@name="citation_pii"]/@content');
if (!pii) {
Z.debug("not finding pii in metatag; attempting to parse URL");
pii = url.match(/\/pii\/([^#?]+)/);
if (pii) {
pii = pii[1];
}
else {
Z.debug("cannot find pii");
}
}
if (pii) {
let risUrl = '/sdfe/arp/cite?pii=' + pii + '&format=application%2Fx-research-info-systems&withabstract=true';
Z.debug('Fetching RIS using PII: ' + risUrl);
let text = await requestText(risUrl);
await processRIS(doc, text, isSearchResult);
return;
}
}
// On some older article pages, there seems to be a different form
// that uses GET
form = doc.getElementById('export-form');
if (form) {
Z.debug("Fetching RIS via GET form (old)");
let risUrl = form.action
+ '?export-format=RIS&export-content=cite-abs';
let text = await requestText(risUrl);
await processRIS(doc, text, isSearchResult);
return;
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throw new Error("Could not scrape metadata via known methods");
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"abstractNote": "Mitochondrial involvement in yeast apoptosis is probably the most unifying feature in the field. Reports proposing a role for mitochondria in yeast apoptosis present evidence ranging from the simple observation of ROS accumulation in the cell to the identification of mitochondrial proteins mediating cell death. Although yeast is unarguably a simple model it reveals an elaborate regulation of the death process involving distinct proteins and most likely different pathways, depending on the insult, growth conditions and cell metabolism. This complexity may be due to the interplay between the death pathways and the major signalling routes in the cell, contributing to a whole integrated response. The elucidation of these pathways in yeast has been a valuable help in understanding the intricate mechanisms of cell death in higher eukaryotes, and of severe human diseases associated with mitochondria-dependent apoptosis. In addition, the absence of obvious orthologues of mammalian apoptotic regulators, namely of the Bcl-2 family, favours the use of yeast to assess the function of such proteins. In conclusion, yeast with its distinctive ability to survive without respiration-competent mitochondria is a powerful model to study the involvement of mitochondria and mitochondria interacting proteins in cell death.",
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],
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"abstractNote": "The African continent (30.1million km2) extends from 37°17′N to 34°52S and covers a great variety of climates except the polar climate. Although Africa is often associated to extended arid areas as the Sahara (7million km2) and Kalahari (0.9million km2), it is also characterized by a humid belt in its equatorial part and by few very wet regions as in Cameroon and in Sierra Leone. Some of the largest river basins are found in this continent such as the Congo, also termed Zaire, Nile, Zambezi, Orange, and Niger basins. Common features of Africa river basins are (i) warm temperatures, (ii) general smooth relief due to the absence of recent mountain ranges, except in North Africa and in the Rift Valley, (iii) predominance of old shields and metamorphic rocks with very developed soil cover, and (iv) moderate human impacts on river systems except for the recent spread of river damming. African rivers are characterized by very similar hydrochemical and physical features (ionic contents, suspended particulate matter, or SPM) but differ greatly by their hydrological regimes, which are more developed in this article.",
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"ISSN": "0006-3495",
"abstractNote": "To permit access to DNA-binding proteins involved in the control and expression of the genome, the nucleosome undergoes structural remodeling including unwrapping of nucleosomal DNA segments from the nucleosome core. Here we examine the mechanism of DNA dissociation from the nucleosome using microsecond timescale coarse-grained molecular dynamics simulations. The simulations exhibit short-lived, reversible DNA detachments from the nucleosome and long-lived DNA detachments not reversible on the timescale of the simulation. During the short-lived DNA detachments, 9 bp dissociate at one extremity of the nucleosome core and the H3 tail occupies the space freed by the detached DNA. The long-lived DNA detachments are characterized by structural rearrangements of the H3 tail including the formation of a turn-like structure at the base of the tail that sterically impedes the rewrapping of DNA on the nucleosome surface. Removal of the H3 tails causes the long-lived detachments to disappear. The physical consistency of the CG long-lived open state was verified by mapping a CG structure representative of this state back to atomic resolution and performing molecular dynamics as well as by comparing conformation-dependent free energies. Our results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of the nucleosome remodeling process.",
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"journalAbbreviation": "Biophysical Journal",
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"pages": "849-858",
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"shortTitle": "Unwrapping of Nucleosomal DNA Ends",
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"date": "2014-01-18",
"DOI": "10.1016/S0140-6736(13)62228-X",
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"abstractNote": "Research publication can both communicate and miscommunicate. Unless research is adequately reported, the time and resources invested in the conduct of research is wasted. Reporting guidelines such as CONSORT, STARD, PRISMA, and ARRIVE aim to improve the quality of research reports, but all are much less adopted and adhered to than they should be. Adequate reports of research should clearly describe which questions were addressed and why, what was done, what was shown, and what the findings mean. However, substantial failures occur in each of these elements. For example, studies of published trial reports showed that the poor description of interventions meant that 40–89% were non-replicable; comparisons of protocols with publications showed that most studies had at least one primary outcome changed, introduced, or omitted; and investigators of new trials rarely set their findings in the context of a systematic review, and cited a very small and biased selection of previous relevant trials. Although best documented in reports of controlled trials, inadequate reporting occurs in all types of studies—animal and other preclinical studies, diagnostic studies, epidemiological studies, clinical prediction research, surveys, and qualitative studies. In this report, and in the Series more generally, we point to a waste at all stages in medical research. Although a more nuanced understanding of the complex systems involved in the conduct, writing, and publication of research is desirable, some immediate action can be taken to improve the reporting of research. Evidence for some recommendations is clear: change the current system of research rewards and regulations to encourage better and more complete reporting, and fund the development and maintenance of infrastructure to support better reporting, linkage, and archiving of all elements of research. However, the high amount of waste also warrants future investment in the monitoring of and research into reporting of research, and active implementation of the findings to ensure that research reports better address the needs of the range of research users.",
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{
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"date": "1976-01-01",
"DOI": "10.1016/0584-8539(76)80131-6",
"ISSN": "0584-8539",
"abstractNote": "The absorption spectra between 400 and 50 cm−1 have been measured for the following compounds; 1,2-C6H4F2; 1,4-C6H4F2; 1,2,4-C6H3F3; 1,3,5-C6H3F3; 1,2,4,5-C6H2F4; 1,2,3,4-C6H2F4 (to 200 cm−1 only), 1,2,3,5,-C6H2F4; C6F5H and C6F6. Some new Raman data is also presented. Vibrational assignments have been criticallly examine by seeking consistency between assignments for different molecules and by comparison with predicted frequencies. There is clear evidence for a steady reduction in the force constant for the out-of-plane CH deformation with increasing fluorine substitution.",
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