https://biasedsignalingatlas.org/static/home/js/citation_tool.js

1function citation_tool(url, cite_id) {
2	// Modal part
3	$('#citation_modal_table tbody').empty();
4    var modal = document.getElementById('citation-tool');
5    var span = document.getElementById("close-citation");
6    modal.classList.add("modal");
7    setTimeout(function(){
8    	modal.style.display = "block";
9    }, 200)
10
11    span.onclick = function() {
12        modal.style.display = "none";
13        $(".article_option").remove();
14        $(".article").remove();
15        $(".cite-submenu").remove();
16    }
17    window.onclick = function(event) {
18        if (event.target == modal) {
19            modal.style.display = "none";
20            $(".article_option").remove();
21            $(".article").remove();
22            $(".cite-submenu").remove();
23        }
24    }
25
26    // Process location
27    var this_site = parse_url_long(url);
28    var highlight_main = false;
29    if (window.location.pathname==='/') {
30    	highlight_main = true
31    }
32
33    // AJAX to create citation list
34    var dropdown_articles = document.getElementById("dropdown_articles");
35    var article_list = document.getElementById("article_list");
36    var env = url.split('//')[1].split('/')[0];
37    var main_ref_id = [];
38    var cit_request = new XMLHttpRequest();
39    var domains = ["gpcrdb.org", "gproteindb.org", "arrestindb.org", "biasedsignalingatlas.org"];
40    var filter_for = false;
41    let cite_id_missing = typeof cite_id === "undefined";
42    if ((cite_id_missing && env==="gpcrdb.org") || cite_id==="cite_gpcrdb") {
43    	filter_for = "gpcrdb";
44    }
45    if ((cite_id_missing && env==="gproteindb.org") || cite_id==="cite_gproteindb") {
46    	filter_for = "gproteindb";
47    }
48    if ((cite_id_missing && env==="arrestindb.org") || cite_id==="cite_arrestindb") {
49    	filter_for = "arrestindb";
50    }
51    if ((cite_id_missing && env==="biasedsignalingatlas.org") || cite_id==="cite_biasedsignalingatlas") {
52    	filter_for = "biasedsignalingatlas";
53    }
54    // Use the current origin; previous splitting logic was fragile (e.g. "http:" + "/citations").
55    cit_request.open('GET', window.location.origin + '/citations');
56    cit_request.onload = function() {
57		if (cit_request.status < 200 || cit_request.status >= 300) {
58			console.warn("Citations request failed:", cit_request.status, cit_request.responseText);
59			return;
60		}
61		let data = [];
62		try {
63			data = JSON.parse(cit_request.responseText);
64		} catch (e) {
65			console.warn("Citations response was not valid JSON:", e, cit_request.responseText);
66			return;
67		}
68		for (let i = 0; i < data.length; i++) {
69			var link = "";
70			if (!domains.includes(env)) {
71				link = "/" + data[i][0].split("//")[1].split("/").slice(1).join("/");
72			}
73			else {
74				link = data[i][0];
75			}
76			if (link[link.length-1]==='/') {
77				link = link.substring(0, link.length-1);
78			}
79			if (link==='/GPCR-Gprotein_Mutations.xlsx') {
80				link = 'https://files.gpcrdb.org/GPCR-Gprotein_Mutations.xlsx'
81			}
82			else if (link==='/mutations.html#mutation-data-submission') {
83				link = 'https://docs.gpcrdb.org/mutations.html#mutation-data-submission'
84			}
85			if ($('a[href="'+link+'"]').first().parent().parent().parent().first().hasClass('dropdown-submenu')) {
86				data[i].push($('a[href="'+link+'"]').first().parent().parent().parent().parent().parent().first().find(">:first-child").text().trim());
87			}
88			else {
89				if (link==="/protein/ste2_yeast") {
90					data[i].push("GPCRdb");
91				}
92				else {
93					data[i].push($('a[href="'+link+'"]').first().parent().parent().parent().first().find(">:first-child").text().trim());
94				}
95			}
96		}
97		// Create HTML once per call
98		var articles = {};
99		var tags = [];
100		for (let i = 0; i < data.length; i++) {
101			if (data[i][11]==='') {
102				continue;
103			}
104			if (filter_for==="gpcrdb" && data[i][11]!=="GPCRdb") {
105				continue;
106			}
107			else if (filter_for==="gproteindb" && data[i][11]!=="GproteinDb" && data[i][7]===2022) {
108				continue;
109			}
110			else if (filter_for==="arrestindb" && data[i][11]!=="ArrestinDb") {
111				continue;
112			}
113			else if (filter_for==="biasedsignalingatlas" && data[i][11]!=="Biased Signaling Atlas") {
114				continue;
115			}
116			else if (filter_for==="arrestindb" && data[i][11]==="ArrestinDb") {
117				data[i][5] = "The arrestin database, ArrestinDb";
118				data[i][6] = "Jimmy Caroli, Gáspár Pándy-Szekeres, Alexander S. Hauser, György M. Keserű, Albert J. Kooistra and David E. Gloriam";
119				data[i][7] = 2022;
120				data[i][8] = "";
121				data[i][9] = "Manuscript";
122				data[i][10] = "";
123			}
124			else if (filter_for==="biasedsignalingatlas" && data[i][11]==="Biased Signaling Atlas") {
125				data[i][5] = "A community Biased Signaling Atlas";
126				data[i][6] = "Jimmy Caroli, Alibek Mamyrbekov, Kasper Harpsøe, Sahar Gardizi, Linda Dörries, Eshan Ghosh, Alexander S. Hauser, Albert J. Kooistra, and David E. Gloriam";
127				data[i][7] = 2023;
128				data[i][8] = "19, 531–535";
129				data[i][9] = "Nature Chemical Biology";
130				data[i][10] = "https://doi.org/10.1038/s41589-023-01292-8";
131			}
132			var site = parse_url_long(data[i][0]);
133			tags.push(site);
134			// Dropdown menus
135			var a_sub, submenu, submenu_ul;
136			if (document.getElementById(data[i][11])===null) {
137				submenu = document.createElement("li");
138				submenu.setAttribute("id", data[i][11]);
139				submenu.classList.add("dropdown-submenu");
140				submenu.classList.add("cite-submenu");
141				a_sub = document.createElement("a");
142				a_sub.innerHTML = data[i][11];
143				a_sub.setAttribute('tabindex', '0');
144				submenu.appendChild(a_sub);
145				submenu_ul = document.createElement("ul");
146				submenu_ul.classList.add('dropdown-menu');
147				submenu_ul.classList.add('dropdown-auto-overflow')
148				submenu.appendChild(submenu_ul);
149			}
150			else {
151				submenu = document.getElementById(data[i][11])
152				submenu_ul = submenu.getElementsByTagName('ul')[0];
153			}
154
155			// Dropdown options
156			var option = document.createElement("li");
157			var option_link = document.createElement("a");
158			option_link.innerHTML = data[i][4];
159			option_link.classList.add("article_option");
160			option.appendChild(option_link);
161			option.setAttribute("id", site.replace('#', '_').replace('.', '_'));
162			option.setAttribute("role", "button");
163
164			if (site===this_site) {
165				option.setAttribute("selected", "selected");
166				$('#page_select_button').html(data[i][4]);
167			}
168
169			submenu_ul.appendChild(option);
170			dropdown_articles.appendChild(submenu);
171
172			// Reformat data
173			if (!(data[i][5] in articles)) {
174				articles[data[i][5]] = {'tools':{}};
175				articles[data[i][5]]['tools'][site] = option.innerHTML;
176				articles[data[i][5]]['main'] = data[i][3];
177				articles[data[i][5]]['authors'] = data[i][6];
178				articles[data[i][5]]['year'] = data[i][7];
179				articles[data[i][5]]['reference'] = data[i][8];
180				articles[data[i][5]]['journal'] = data[i][9];
181				articles[data[i][5]]['doi'] = data[i][10];
182				articles[data[i][5]]['menu'] = data[i][11];
183				if (data[i][3] === "GPCRdb" || data[i][3] === "GproteinDb") {
184					main_ref_id.push(site);
185				}
186			}
187			else {
188				articles[data[i][5]]['tools'][site] = option.innerHTML;
189				if (data[i][3]=="GPCRdb" || data[i][3]=="GproteinDb") {
190					main_ref_id.push(site);
191				}
192			}
193		}
194
195		// Create HTML
196		for (var key in articles) {
197			var main_ref = false
198			var entry = document.createElement("ul");
199			entry.setAttribute("id", articles[key]['doi']);
200			var entry_holder = document.createElement("div");
201			var tools_list = document.createElement("div");
202			// Loop through tools list to add them with ID
203			var selected = false;

204			for (var tool_key in articles[key]['tools']) {
205				if (tool_key===this_site) {
206					selected = true;
207				}
208				var tool = document.createElement("div");
209				tool.innerHTML = articles[key]['tools'][tool_key].bold();
210				tool.setAttribute("id", tool_key.replace('#', '_').replace('.', '_')+'_tag');
211				tool.style.display = 'none';
212				tools_list.appendChild(tool);
213				// var separator = document.createElement("div");
214				// separator.innerHTML = '\u00A0•\u00A0';
215				// separator.style.display = 'inline-block';
216				// tools_list.appendChild(separator);
217				if (main_ref_id.includes(tool_key)) {
218					main_ref = true;
219				}
220			}
221			// tools_list.removeChild(tools_list.lastChild);
222			tools_list.style.display = 'block';
223
224			var ref = document.createElement("div");
225			var p = document.createElement("p");
226			var d1 = document.createElement("div");
227			var d2 = document.createElement("div");
228			var d3 = document.createElement("div");
229			d1.innerHTML = key;
230			d2.innerHTML = articles[key]['authors'];
231
232			// Link
233			var a = document.createElement("a");
234			a.innerHTML = articles[key]['journal'].italics() + ", " + articles[key]['year'] + ", " + articles[key]['reference'];
235  			a.title = key;
236  			a.href = "https://doi.org/"+articles[key]['doi'];
237  			a.target = "_blank";
238  			d3.appendChild(a);
239			p.appendChild(d1);
240			p.appendChild(d2);
241			p.appendChild(d3);
242			ref.appendChild(p);
243			ref.style.display = 'block';
244
245			entry_holder.appendChild(tools_list);
246			entry_holder.appendChild(ref);
247			entry.appendChild(entry_holder);
248			entry.classList.add('article');
249			if (selected) {
250				entry.classList.add('highlight_reference');
251			}
252			if (main_ref) {
253				var main_ref_list = document.getElementById("main_reference");
254
255				main_ref_list.appendChild(entry);
256			}
257			else {
258				article_list.appendChild(entry);
259			}
260		}
261		if (env=="gproteindb.org") {
262			main_ref_id = main_ref_id[0];
263		}
264		else {
265			main_ref_id = main_ref_id[1];
266		}
267		/*var color = "#BE00BE";
268		if (filter_for==="gproteindb") {
269			color = "#F46615";
270		}
271		else if (filter_for==="arrestindb") {
272			color = "#55AE35";
273		}
274		$(".article").first().css("border-top","4px solid "+color);*/
275		// $(".article").eq(1).css("border-top","4px solid #BE00BE");
276		if (highlight_main || $('.highlight_reference').length==0) {
277			highlight_article(main_ref_id);
278			$('#dropdown_articles option#'+main_ref_id).attr('selected', 'selected');
279		}
280    };
281    cit_request.send();
282}
283
284function highlight_article(key) {
285	$('.highlight_reference').removeClass('highlight_reference');
286	$('#'+key+'_tag').parent().parent().parent().addClass('highlight_reference');
287}
288
289function parse_url(url) {
290	var url_split = url.split('/');
291	if (url_split[url_split.length-1]==="") {
292    	var this_site = url_split[url_split.length-2];
293    	if (this_site==='targetselection') {
294    		this_site = url_split[url_split.length-3]+'-'+this_site;
295    	}
296    }
297    else {
298    	var this_site = url_split[url_split.length-1];
299    	if (this_site==='targetselection') {
300    		this_site = url_split[url_split.length-2]+'-'+this_site;
301    	}
302    }
303    return this_site
304}
305
306function parse_url_long(url) {
307	var url_split = url.split('/');
308	if (url_split[url_split.length-1]==="") {
309		if (url_split.length>5) {
310			return url_split[3]+"-"+url_split[4];
311		}
312		else {
313			return url_split[3];
314		}
315	}
316	else if (url_split.length===4) {
317		return url_split[3];
318	}
319	else {
320		return url_split[3]+"-"+url_split[4];
321	}
322}
323
324function toggle_widget() {
325	$("#ref_widget").animate({width: "toggle"});
326    if ($("#widget_chevron").hasClass("glyphicon glyphicon-chevron-left")) {
327        $("#widget_chevron").removeClass("glyphicon glyphicon-chevron-left");
328        $("#widget_chevron").addClass("glyphicon glyphicon-chevron-right");
329        $("#widget_infosign").show();
330    }
331    else {
332        $("#widget_chevron").removeClass("glyphicon glyphicon-chevron-right");
333        $("#widget_chevron").addClass("glyphicon glyphicon-chevron-left");
334        $("#widget_infosign").hide();
335        setTimeout(function() {
336        	$("#ref_widget").animate({width: "toggle"});
337        	$("#widget_chevron").removeClass("glyphicon glyphicon-chevron-left");
338        	$("#widget_chevron").addClass("glyphicon glyphicon-chevron-right");
339        	$("#widget_infosign").show();
340        }, 8000)
341    }
342}
343
344async function check_for_video(url) {
345	var this_site = parse_url_long(url);
346	var cit_request = new XMLHttpRequest();
347    cit_request.open('GET', window.location.origin + '/citations');
348    cit_request.onload = function() {
349		if (cit_request.status < 200 || cit_request.status >= 300) {
350			return;
351		}
352		let data = [];
353		try {
354			data = JSON.parse(cit_request.responseText);
355		} catch (e) {
356			return;
357		}
358		var video = false;

359		for (i = 0; i < data.length; i++) {
360			var site = parse_url_long(data[i][0]);
361			if (site===this_site && data[i][1]!=null) {
362				video = data[i][1];
363				$('#icon_video').attr('href', video);
364				$('#icon_video').css('display','inline');
365			}
366		}
367	}
368	cit_request.send();
369}