diff --git a/templates/favourite/css/custom.css b/templates/favourite/css/custom.css index f09c2799b..0b4960cd0 100644 --- a/templates/favourite/css/custom.css +++ b/templates/favourite/css/custom.css @@ -808,6 +808,73 @@ video.responsive-vid { } /* ### END TWITTER WIDGET ### */ +/** ### CSS for the citation project ### **/ +.radio-button input[type="radio"], +input.radio { + float: left; + clear: none; + margin: 2px 0 0 2px; +} + +.radio-button label { + float: left; + clear: none; + display: block; + padding: 0px 1em 0px 8px; + font-weight: normal; +} + +#exportCitationButton[disabled] { + cursor: not-allowed; +} + +@-moz-document url-prefix() { + .radio-button label { + margin: 2px 0 0 0; + } +} + +/* class for citation button on big screens */ +.citation-button-large { + position:fixed; + top:50%; + display: block; + background-color:#2F9EC2; + color:white; + padding: 16px; + border-radius: 0 10px 10px 0; + transition: 0.5s; +} + +.citation-button-large i { + padding: 1px 2px 1px 2px; +} + +.citation-button-large span { + font-family: Arial; + font-weight: 700; + display: none; + font-size: 25px; +} + +.citation-button-large:hover { + padding-right: 25px; + color: white; +} + +.citation-button-large:hover span { + display: inline-block; + color: white; +} + +.citation-button-large:hover img { + display: none; +} + + +/* ### CSS for Citation Project Ends Here ###*/ + + @media only screen and (max-width: 1024px) { .fav2buttons div[id^="favglyph-box"] i, .fav2buttons div[id*=" favglyph-box"] i { diff --git a/templates/favourite/images/reactome/citation.png b/templates/favourite/images/reactome/citation.png new file mode 100644 index 000000000..b6aafb8f0 Binary files /dev/null and b/templates/favourite/images/reactome/citation.png differ diff --git a/templates/favourite/index.php b/templates/favourite/index.php index d91dc84e6..0c1114550 100644 --- a/templates/favourite/index.php +++ b/templates/favourite/index.php @@ -26,6 +26,9 @@ JHtml::_('jquery.framework'); $doc->addStyleSheet($this->baseurl. '/templates/' .$this->template. '/bootstrap/favth-bootstrap.css'); $doc->addScript($this->baseurl. '/templates/' .$this->template. '/bootstrap/favth-bootstrap.js'); +//Custom: adding the js files for the citation project +$doc->addScript($this->baseurl. '/templates/' .$this->template. '/js/clipboard.min.js'); +$doc->addScript($this->baseurl. '/templates/' .$this->template. '/js/citation-query.js'); // Custom: Adding autocomplete javascript JHtml::_('script', 'jui/jquery.autocomplete.min.js', array('version' => 'auto', 'relative' => true)); @@ -85,7 +88,7 @@ - + @@ -521,7 +524,6 @@ function gtag(){dataLayer.push(arguments)}; - + + countModules('cite-us')) { ?> + + + Cite Us! + + + + + + + + + + +
- +
diff --git a/templates/favourite/js/citation-query.js b/templates/favourite/js/citation-query.js new file mode 100644 index 000000000..1a35efd85 --- /dev/null +++ b/templates/favourite/js/citation-query.js @@ -0,0 +1,352 @@ +/* + This script powers the citation functionality on the Joomla website + + To have the citation button `visible` on a new page, add the `Cite Us` module to that particular page from Joomla admin dashboard + + To control which citation appears on which page, the `CITATIONS` object is used alongside the variables with the matching regex + + For example, to add a new citation `foo` which will appear on all pages where the url contains the string `bar`: + + 1) add FOO_CITATION: {id: , fallback: } to CITATIONS constant + 2) create a new variable fooCitation = [/bar/], with the (list of) matching regexes to display FOO_CITATION + 3) add the appropriate condition in parseURL function +*/ + + + +// constants declaration +var BASE_URL = window.location.origin; + +// the various endpoints we query +var PATHWAY_CITATION_ENDPOINT = "/ContentService/citation/pathway/"; +var DOWNLOAD_CITATION_ENDPOINT = "/ContentService/citation/download/"; +var STATIC_CITATION_ENDPOINT = "/ContentService/citation/static/"; +var EXPORT_CITATION_ENDPOINT = "/ContentService/citation/export?"; +var CONTENT_SERVICE_QUERY_ENDPOINT = "/ContentService/data/query/"; +var CONTENT_SERVICE_QUERY_ATTRIBUTE = "/schemaClass"; + +// we cam query pathway and static citations to get +// vanilla text or to export them in bib, ris or txt formats +var QUERY_MODES = { + EXPORT: "export", + TEXT: "text" +} + +// export formats +var EXPORT_FORMATS = { + BIBTEX: "bib", + TEXT: "txt", + RIS: "ris" +}; + + +// the request-response cycle for static citations +// for both exporting and getting as text +var STATIC_CITATION_REQUEST_RESPONSE = { + export : { + callFunction: function(citation, ext) { + var d = jQuery.get(BASE_URL.concat(EXPORT_CITATION_ENDPOINT, jQuery.param({id:citation["id"], ext: ext, isPathway: "false", dateAccessed: new Date().toDateString()}))) + .then(function(response) { + downloadFile(response, ext, "reactome_citation_".concat(citation["id"],".",ext)); + }) + return d; + } + }, + text: { + callFunction: function(citation) { + var d = jQuery.get(BASE_URL.concat(STATIC_CITATION_ENDPOINT, citation["id"])) + .then( + function(response) { + return response; + }, + function() { + return citation["fallback"]; + } + ) + return d; + } + } +} + +// the request-response cycle for pathway citations +// for both exporting and getting as text +var PATHWAY_CITATION_REQUEST_RESPONSE = { + export: { + callFunction: function(id, ext) { + var d = jQuery.get(BASE_URL.concat(EXPORT_CITATION_ENDPOINT, jQuery.param({id:id, ext: ext, isPathway: "true", dateAccessed: new Date().toDateString()}))) + .then(function(response) { + downloadFile(response, ext, "reactome_citation_".concat(id,".",ext)); + }) + return d; + } + }, + text: { + callFunction: function(id) { + var d = jQuery.get(BASE_URL.concat(PATHWAY_CITATION_ENDPOINT, id, "?", jQuery.param({dateAccessed: new Date().toDateString()}))) + .then(function(response) { + + var citation = ""; + if (response) { + var pathwayCitation = "
Pathway Citation:
".concat(response["pathwayCitation"]); + var imageCitation = "
Image Citation:
".concat(response["imageCitation"]); + citation = pathwayCitation.concat("\n", imageCitation); + } + else { + citation = "Not a pathway" + } + + return citation; + }) + return d; + } + } +} + +// note that all fallbacks are texts from the `Citing Us` page +// that is except for the ORCID_CITATION fallback, as we don't have a citation for that on the `Citing Us` page. The fallback citation for that was taken from Europe PMC (http://europepmc.org/article/MED/31802127) +var CITATIONS = { + GENERAL_CITATION: {id: "31691815", fallback: "Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815"}, + ICON_CITATION: {id: "29077811", fallback: "Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A. Reactome enhanced pathway visualization. Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441. PubMed PMID: 29077811"}, + PATHWAY_ANALYSIS_CITATION: {id: "28249561", fallback: "Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H. Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinformatics. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2. PubMed PMID: 28249561"}, + FIVIZ_CITATION: {id: "28150241", fallback: "Wu G, Haw R. Functional Interaction Network Construction and Analysis for Disease Discovery. Methods Mol Biol. 2017;1558:235-253. doi: 10.1007/978-1-4939-6783-4_11. PubMed PMID: 28150241"}, + GRAPH_DATABASE_CITATION: {id: "29377902", fallback: "Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H. Reactome graph database: Efficient accessto complex pathway data. PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan. PubMed PMID: 29377902"}, + ORCID_CITATION: {id: "31802127", fallback: "Viteri G, Matthews L, Varusai T, et al. Reactome and ORCID-fine-grained credit attribution for community curation. Database : the Journal of Biological Databases and Curation. 2019 Jan;2019 DOI: 10.1093/database/baz123"} +} + +// the regex that must be matched to show the relevant citation +// so for example `ORCID_CITATION` will be used when the page url matches the regex(es) in `orcidCitation` +var generalCitation = [/what-is-reactome/, /about/, /sab/, /license/, /community/]; +var downloadCitation = [/download-data/]; +var iconCitation = [/icon-lib/, /R-ICO/]; +var pathwayAnalysisCitation = [/AnalysisService/]; +var fivizCitation = [/reactome-fiviz/]; +var graphDatabaseCitation = [/ContentService/, /graph-database/]; +var pathwayCitation = [/content\/detail\/R-/]; +var orcidCitation = [/orcid/]; + +// constants declaration end + + +// event based work: +jQuery(document).ready(function() { + + // instantiating the clipboard button here + var clipboard = new ClipboardJS('#clipboardButton', { + container: jQuery('#citationModal').find("#citationText") + }); + + var clipboardButton = jQuery('#clipboardButton'); + + clipboard.on('success', function(e) { + clipboardButton.find("i").removeClass("fa fa-clipboard").addClass("fa fa-check"); + clipboardButton.attr("disabled", true); + + // clears selection and changes icon back to the copy icon after 2 seconds have passed + setTimeout(function() { + clipboardButton.attr("disabled", false); + clipboardButton.find("i").removeClass("fa fa-check").addClass("fa fa-clipboard"); + + e.clearSelection(); + }, 2000); + }); + + clipboard.on('error', function(e) { + console.error("Whoops.Couldn't copy"); + }); + + // showing the backtop button again after the modal closes + jQuery("#citationModal").on("hidden.bs.modal", function (e) { + jQuery("#fav-backtop").css("right", "" ).css("left", "" ); + + }); + + // hiding the backtop button after the modal opens + jQuery("#citationModal").on("show.bs.modal", function (e) { + jQuery("#fav-backtop").css("right", "-1000em" ).css("left", "-1000em"); + + }); + +}); + +// functions being called from the html file + +//main method that gets called when the modal button is clicked +function getCitation() { + var modal = jQuery("#citationModal"); + // passing the current page url to parseURL which will give us a citation promise + // that we can resolve + var d = parseURL(url=window.location.href, mode=QUERY_MODES["TEXT"]); + + d.then( + // on success + function(citation) { + // clearing any radio button selection before modal gets opened + jQuery("input[name=exportOption]:checked").prop("checked", false); + // disabling export buttons + modal.find("#exportCitationButton")[0].disabled = true; + modal.modal("show"); + modal.find("#citationText").html(citation); + }, + // on failure + function(failure) { + // hide the copy to clipboard and mail buttons + modal.find("#clipboardButton").hide(); + modal.find("#mailButton").hide(); + hideExportSection(); + // make warning alert visible + modal.find("#citationWarning").show(); + modal.modal('show'); + + if (!failure) { + // make `help@reactome.org` a mailto link + var helpEmail = jQuery(""); + helpEmail.attr("href", "mailto:help@reactome.org"); + helpEmail.text("help@reactome.org"); + modal.find("#citationText").text("Sorry, we could not process your request. Please email the issue to ").append(helpEmail); + } + else { + modal.find("#citationText").text(failure); + } + } + ); +} + +// handles the mail-to functionality +function sendMail() { + window.location = "mailto:?subject=Reactome Citation&body=" + encodeURIComponent(jQuery('#citationModal').find("#citationText").text()); +} + + +// exports the citation in the selected format +function exportCitation() { + + var exportFormat = jQuery("input[name=exportOption]:checked", "#exportCitationForm").val(); + + if (!exportFormat) { + return; + } + + var modal = jQuery('#citationModal'); + var d = parseURL(url=window.location.href, mode=QUERY_MODES["EXPORT"], exportFormat); +} + + +// enables the export citation button when one of the citation formats is selected +function enableExportCitationButton() { + jQuery("#citationModal").find("#exportCitationButton")[0].disabled = false; + } + +// functions being called from html end + + +// function that does the heavy lifting of figuring out which page we are on, +// and returning the appropriate citation promise +function parseURL(url, mode, ext= EXPORT_FORMATS["TEXT"]) { + if (generalCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["GENERAL_CITATION"], mode, ext); + } + + else if (downloadCitation.some(function(regex) {return regex.test(url)})) { + hideExportSection(); + return getDownloadCitation(); + + } + + else if (iconCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["ICON_CITATION"] + , mode, ext); + } + + else if (pathwayAnalysisCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["PATHWAY_ANALYSIS_CITATION"], mode, ext); + } + + else if (fivizCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["FIVIZ_CITATION"], mode, ext); + } + + else if (graphDatabaseCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["GRAPH_DATABASE_CITATION"], mode, ext); + } + + else if (orcidCitation.some(function(regex) {return regex.test(url)})) { + return getStaticCitation(CITATIONS["ORCID_CITATION"], mode, ext); + } + + else if (pathwayCitation.some(function(regex) {return regex.test(url)})) { + + var pathwayStId = window.location.href.split("/").pop(); + return jQuery.get(BASE_URL.concat(CONTENT_SERVICE_QUERY_ENDPOINT, pathwayStId, CONTENT_SERVICE_QUERY_ATTRIBUTE)).then( + function(response) { + if (response.toLowerCase().indexOf("pathway") != -1) { + // return the promise for pathway citation + return getPathwayCitation(pathwayStId, mode, ext); + } + else { + // return promise for general citation + return getStaticCitation(CITATIONS["GENERAL_CITATION"], mode, ext); + + } + }); + } + + // default case + else { + return getStaticCitation(CITATIONS["GENERAL_CITATION"], mode, ext); + } +} + + +// helper functions + + +function getStaticCitation(citation, mode, ext= EXPORT_FORMATS["TEXT"]) { + if (mode === QUERY_MODES["EXPORT"]) { + return STATIC_CITATION_REQUEST_RESPONSE[mode]["callFunction"](citation, ext); + } + else { + return STATIC_CITATION_REQUEST_RESPONSE[mode]["callFunction"](citation); + } +} + +function getPathwayCitation(id, mode, ext= EXPORT_FORMATS["TEXT"]) { + if (mode === QUERY_MODES["EXPORT"]) { + return PATHWAY_CITATION_REQUEST_RESPONSE[mode]["callFunction"](id, ext); + } + else { + return PATHWAY_CITATION_REQUEST_RESPONSE[mode]["callFunction"](id); + } +} + +function getDownloadCitation() { + var d = jQuery.get(BASE_URL.concat(DOWNLOAD_CITATION_ENDPOINT)).then(function(response) { return response + " (" + new Date().toDateString() + ")";}) + return d; +} + +// download file code taken from here: https://stackoverflow.com/a/33542499/3240056 and https://stackoverflow.com/a/9834261/3240056 +function downloadFile(data, format, filename) { + var blob = new Blob([data], {type: format}); + if(window.navigator.msSaveOrOpenBlob) { + window.navigator.msSaveBlob(blob, filename); + } + else { + var elem = window.document.createElement('a'); + elem.href = window.URL.createObjectURL(blob); + elem.download = filename; + document.body.appendChild(elem); + elem.click(); + document.body.removeChild(elem); + } +} + +function hideExportSection(modal) { + var modal = jQuery("#citationModal"); + // hide the line break before the export form + modal.find("#breakLine").hide(); + // hide the export form as well + jQuery("#exportCitationForm").hide(); +} + +// helper functions end + + diff --git a/templates/favourite/js/clipboard.min.js b/templates/favourite/js/clipboard.min.js new file mode 100644 index 000000000..6989af787 --- /dev/null +++ b/templates/favourite/js/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.4 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return o={},r.m=n=[function(t,e,n){"use strict";var o="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},r=function(t,e,n){return e&&i(t.prototype,e),n&&i(t,n),t};function i(t,e){for(var n=0;n