openmetaanalysis.js

var n = location.pathname.indexOf("/",1);
var sub_domain = location.hostname.split('.').shift();
if (n == 0){n = location.pathname.length};
var pagename = location.pathname.split('/').slice(-1);
if (pagename == ""){pagename = "index.html"};
var repo_dir = location.pathname.substring(1,n);
var repo_name = repo_dir.replace(/\-/gi, ' '); 
var subgroup = false;
var metagression = false;
var network = false;
var blobbogram = false;
var r_code = false;
function showtip(tiptext, trigger, width){
	$("#tip").css('display','block');
        $("#tip").html("<div style = 'background-color:white;opacity:1;border-style: solid; border-width: medium;padding:10px'>" + tiptext + '</div>');
	$("#tip").css('width', width);
	$("#tip").css({"background-color":"#6DC6E7"});
	$("#tip").css({"color":"#0022B4"});
	$("#tip").css({"opacity":"1"});
	var pos_left = trigger.position().left;
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            pos_left = $(window).width() - $("#tip").width() - 10;
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        if ((pos_top + $("#tip").height()) > $(window).height()){
            pos_top = pos_top + 20 - $("#tip").height();
		}
        $("#tip").offset({top: pos_top, left: pos_left});
}  
$(document).ready(function(){
	//Display the repo_name in all the correct spots
	$(".repo_name").text(repo_name);
	//Is this a meta-regression?
	if (repo_dir == "Early-goal-directed-therapy-for-septic-shock"){
		//code for testing a specific repository
	}
	$("#subgroup_figure").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#subgroup_figure").attr('src'))
	$("#subgroup_figure").load(function() {
		subgroup = true;
		$("#subgroup").show();
	});
	$("#metaregression_figure").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#metaregression_figure").attr('src'))
	$("#metaregression_figure").load(function() {
		metaregression = true;
		$("#metaregression").show();
	});
	$("#network_figure").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#network_figure").attr('src'))
	$("#network_figure").load(function() {
		network = true;
		$("#network").show();
	});
	$("#blobbogram_figure").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#blobbogram_figure").attr('src'))
	$("#blobbogramfigure").load(function() {
		blobbogram = true;
		$("#blobbogram").show();
	});
	$("#r_code").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/r-code')
	$("#r_code").load(function() {
		r_code = true;
		$("#r-code").show();
	});
	//Customize src for images based on repo name
	$("#forest").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#forest").attr('src'))
	$("#grade").attr('src', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $("#grade").attr('src'))
	//Link rewrites
	$("body").find('a.main').each(function(){
		// main (root) directory for project
		$(this).attr('href', 'https://github.com/openMetaAnalysis//' + repo_dir + '/' + $(this).attr("href"));
		})
	$("body").find('a.gh-pages-dir').each(function(){
		//For directories on gh-pages
		$(this).attr('href', 'https://github.com/' + sub_domain + '/' + repo_dir + '/tree/gh-pages/' + $(this).attr("href"));
		})
	$("body").find('a.gh-pages-files').each(function(){
		//For directories on gh-pages
		$(this).attr('href', '/' + repo_dir + '/' + $(this).attr("href"));
		})
	$("body").find('a.master-home').each(function(){
		//For directories on master
		$(this).attr('href', 'https://github.com/' + sub_domain + '/' + repo_dir + '/tree/master/');
		//$(this).attr('href', 'https://github.com/' + sub_domain + '/' + repo_dir + '/blob/master/README.md');
		})
	$("body").find('a.master-dir').each(function(){
		//For directories on master
		$(this).attr('href', 'https://github.com/' + sub_domain + '/' + repo_dir + '/tree/master/files/' + $(this).attr("href"));
		})
	$("body").find('a.master-file').each(function(){
		//For specific files on master
		$(this).attr('href', 'https://raw.githubusercontent.com/' + sub_domain + '/' + repo_dir + '/master/files/' + $(this).attr("href"));
		})
	$("body").find('a.Reconciliation-of-conclusions').each(function(){
		//For specific files on master
		$(this).attr('href', 'https://github.com/openMetaAnalysis/' + repo_dir + '/blob/master/files/reconciliation-tables/Reconciliation%20of%20conclusions.csv');
		})
	$("body").find('a').each(function(){
		try{
		//For PDFs
		if ($(this).attr('href').toLowerCase().indexOf(".pdf") > 1){
			$(this).after( " <span style='background:#CB0606;opacity:0.5;color:white;font-weight:bolder;border-radius: 2px;padding:1px;font-size:75%'>PDF</span>")
			}
			}
			catch(e){
				//catch and just suppress error
			}
		})
	//Tips
	$("body").find('GRADE').each(function(){
		//For GRADE
		//$(this).attr("id","grade_quality_definition")
		//$(this).attr("class","hastip")
		//$(this).attr("href","#")
		//$(this).attr('href', "http://www.ncbi.nlm.nih.gov/pubmed/" + $(this).text());
		$(this).replaceWith($("<a href=\"#\" class=\"hastip\" id=\"grade_quality_definition\">" + $(this).text() + '</a>'));
		})
	$("body").find('SoF').each(function(){
		//For Summary of Findings Tables
		$(this).replaceWith($("<a href=\"#\" class=\"hastip\" id=\"SoF_explanation\">" + $(this).text() + '</a>'));
		})
	//For eligibility criteria
	$("CRITERIA").css("display","none")
	$("#criteria_display").html($("CRITERIA").html())
	
	$("body").find('RED').each(function(){
		//For red font
		$(this).replaceWith($("<span style=\"color:red;font-weight:normal\">" + $(this).text() + '</span>'));
		})
	$("body").find('FOREST_PLOTS').each(function(){
		//Link to directory of forest plots
		$(this).replaceWith($("<a href=\"https://github.com/" + sub_domain + '/' + repo_dir + "/tree/master/files/forest-plots/\" title=\"forest plots\">" + $(this).text() + '</a>'));
		})
		//Replace line feeds {'\n') in link labels with space (' ')
	$("body").find('a.pmid').each(function(){
		//For PMIDs
		$(this).attr('href', "http://www.ncbi.nlm.nih.gov/pubmed/" + $(this).text());
		})
	$("body").find('pmid').each(function(){
		//For PMIDs
		//$(this).attr('href', "http://www.ncbi.nlm.nih.gov/pubmed/" + $(this).text());
		$(this).replaceWith($("<a href=\"http://pubmed.gov/" + $(this).text() + "\">" + $(this).text(text.replace('\n', ' ')) + '</a>'));
		})
	$("body").find('PMID').each(function(){
		//For PMIDs
		//$(this).attr('href', "http://www.ncbi.nlm.nih.gov/pubmed/" + $(this).text());
		$(this).replaceWith($("<a href=\"http://pubmed.gov/" + $(this).text() + "\">" + $(this).text(text.replace('\n', ' ')) + '</a>'));
		})
	$("body").find('ol').each(function(){
		//For references
		var str = $(this).html();
		//remove PubMed's citation numbers and colon placed by PubMed
		var regex = /\n\d{1,}\:\s/ig;
    		str = str.replace(regex, "");
		//remove double line feeds and replace with LI elements
		var regex = /\n\s{0,}\n/ig;
		str = str.replace(regex, "</li>\n<li>");
		var regex = /(\n){2,}/ig;
    		str = str.replace(regex, "</li>\n<li>");
		$(this).replaceWith('<ol>' + str + '</ol>');
		//Replace only the first line feed between list items
		var regex = /<\/li>\n<li>/i;
		str = str.replace(regex, '');
		//Remove last <li> from http://jsfiddle.net/dubeynee/PgzrU/64/
		var regex = /<li>([^(<li>)]*)$/
		str = str.replace(regex,''+'$1');
		})
	if ($("#references").length){
		var replaced_text = $("#references").html();
		//alert("Testing:\n\n" + $("#references").html())
		//remove line feeds and replace with space
		//regex = /\r?\n|\r/g
		//replaced_text = replaced_text.replace(regex, " ");
		//Remove extra words PubMed likes
		regex = /PubMed PMID|\r/g
		replaced_text = replaced_text.replace(regex, 'PMID');
		regex = /PubMed Central PMCID|\r/g
		replaced_text = replaced_text.replace(regex, 'PMCID');
		// Replace plain text links by hyperlinks by using regular expressions
		// Set regular expression the regex string for PMCIDs
		var regex = /(\s{1,})(pmc\d{7,})/ig;
		replaced_text = replaced_text.replace(regex, "$1<a href='https://www.ncbi.nlm.nih.gov/pmc/articles/$2/'>$2</a>");
		// Set the regex string for NCTs
		regex = /(\s{1,})(NCT\d{7,})/ig;
		replaced_text = replaced_text.replace(regex, "$1<a href='https://clinicaltrials.gov/ct2/show/study/$2'>$2</a>");
		// Set the regular expression regex string for DOIs
		// var = regex = 'https://www.crossref.org/blog/dois-and-matching-regular-expressions/';
		// var regex = '/^10.\d{4,9}/[-._;()/:A-Z0-9]+$/i';
		// based on http://stackoverflow.com/questions/27910/finding-a-doi-in-a-document-or-page
		// var regex = '\b10\.(\d+\.*)+[\/](([^\s\.])+\.*)+\b';
		var regex = /(\b10\.\d+\.*)+[\/](([^\s])+\.*)+\b/ig;
		replaced_text = replaced_text.replace(regex, "<a href='http://dx.doi.org/$1\/$2'>$1\/$2</a>");
		// Set the regular expression regex string for PMIDs
		regex = /(\s{1,})(\d{7,})/ig;
		replaced_text = replaced_text.replace(regex, "$1<a href='http://pubmed.gov/$2'>$2</a>");
		// Set the regex string for line
		// try 1: regex = /([^>]\n{1,}\s{0,})/ig;
		//regex = /([^>])(\n{1,}\s{0,})/ig;
		// Replace plain text line feeds with <br>
		// try 1: replaced_text = replaced_text.replace(regex, "<br>");
		//replaced_text = replaced_text.replace(regex, "$1<br>\n");
		}
	// Echo content
	$('#references').html(replaced_text);
	//write footer business
	//write to div business in the footer
	//Resuse
	$("#business").append("<div style='text-align:center'><a href='https://github.com/openMetaAnalysis/openMetaAnalysis.github.io/blob/master/reusing.MD'>Cite &amp; use this content</a> - <a href=\"https://github.com/" + sub_domain + '/' + repo_dir + "/tree/master/files/LICENSE.md\">License</a></div>")
	//Edit and issues/comments
	$("#business").append("<div style='text-align:center'><a href='https://github.com/" + sub_domain + '/' + repo_dir + "/blob/gh-pages/" + pagename + "'>Edit this page</a> - <a href='https://github.com/" + sub_domain + '/' + repo_dir + "/issues?q=is%3Aboth+is%3Aissue'>Issues and comments</a></div>")
	//Version date...
	lastmod = document.lastModified     // get string of last modified date
	lastmoddate = Date.parse(lastmod)   // convert modified string to date
	if (lastmoddate == 0) {               // unknown date (or January 1, 1970 GMT)
		$("#business").append("<div style='text-align:center'>You need a new browser</div>")
	} else {
		$("#business").append("<div style='text-align:center'>Updated: " + lastmod + " - <a href='https://github.com/" + sub_domain + '/' + repo_dir + "/commits/gh-pages/" + pagename + "'>History</a></div>")
	}
	//Event handlers
	$('#tip').mouseleave(function(event){
		$( "#tip" ).css('display', 'none');
		});
	$('a.hastip_intitle').mouseenter(function(event){
		var tiptext = $(this).attr('title')
		trigger = $(this);
		width = "200px"
		showtip(tiptext, trigger, width);
		});
	$('a.hastip').mouseenter(function(event){
		var tipname = $(this).attr("id");
		trigger = $(this);
		width = "400px"
		$("#tip").load("/tips.xml", function(responseTxt,statusTxt,xhr){
			if(statusTxt=="success"){
				//alert("Success: "+xhr.status+": "+xhr.statusText);
				var xmlDoc = $.parseXML(responseTxt)
				var tiptext = '';
				var temp =$(xmlDoc).find("[name= " + tipname + "]").each(function(){
					$(this).find('p').each(function(){
						tiptext += $(this).text() + "<br>"
					})
					$(this).find('href').each(function(){
						if ($(this).text().length> 5){
							tiptext += "From: <a href='" +  $(this).text() + "' style='align:center'>"
							$(this).find('text').each(function(){
								tiptext += $(this).text() + "</a>"
								})
							}
						})
				     });
				showtip(tiptext, trigger, width)
			}
			if(statusTxt=="error"){
				alert("Error: "+xhr.status+": "+xhr.statusText);
			}
			});


	});
})