nano-lazar 1.1.0

data/public/ui/small-white/slides.js

@@ -0,0 +1,558 @@
+// S5 v1.1 slides.js -- released into the Public Domain
+// Modified for Docutils (http://docutils.sf.net) by David Goodger
+//
+// Please see http://www.meyerweb.com/eric/tools/s5/credits.html for
+// information about all the wonderful and talented contributors to this code!
+
+var undef;
+var slideCSS = '';
+var snum = 0;
+var smax = 1;
+var slideIDs = new Array();
+var incpos = 0;
+var number = undef;
+var s5mode = true;
+var defaultView = 'slideshow';
+var controlVis = 'visible';
+
+var isIE = navigator.appName == 'Microsoft Internet Explorer' ? 1 : 0;
+var isOp = navigator.userAgent.indexOf('Opera') > -1 ? 1 : 0;
+var isGe = navigator.userAgent.indexOf('Gecko') > -1 && navigator.userAgent.indexOf('Safari') < 1 ? 1 : 0;
+
+function hasClass(object, className) {
+	if (!object.className) return false;
+	return (object.className.search('(^|\\s)' + className + '(\\s|$)') != -1);
+}
+
+function hasValue(object, value) {
+	if (!object) return false;
+	return (object.search('(^|\\s)' + value + '(\\s|$)') != -1);
+}
+
+function removeClass(object,className) {
+	if (!object) return;
+	object.className = object.className.replace(new RegExp('(^|\\s)'+className+'(\\s|$)'), RegExp.$1+RegExp.$2);
+}
+
+function addClass(object,className) {
+	if (!object || hasClass(object, className)) return;
+	if (object.className) {
+		object.className += ' '+className;
+	} else {
+		object.className = className;
+	}
+}
+
+function GetElementsWithClassName(elementName,className) {
+	var allElements = document.getElementsByTagName(elementName);
+	var elemColl = new Array();
+	for (var i = 0; i< allElements.length; i++) {
+		if (hasClass(allElements[i], className)) {
+			elemColl[elemColl.length] = allElements[i];
+		}
+	}
+	return elemColl;
+}
+
+function isParentOrSelf(element, id) {
+	if (element == null || element.nodeName=='BODY') return false;
+	else if (element.id == id) return true;
+	else return isParentOrSelf(element.parentNode, id);
+}
+
+function nodeValue(node) {
+	var result = "";
+	if (node.nodeType == 1) {
+		var children = node.childNodes;
+		for (var i = 0; i < children.length; ++i) {
+			result += nodeValue(children[i]);
+		}		
+	}
+	else if (node.nodeType == 3) {
+		result = node.nodeValue;
+	}
+	return(result);
+}
+
+function slideLabel() {
+	var slideColl = GetElementsWithClassName('*','slide');
+	var list = document.getElementById('jumplist');
+	smax = slideColl.length;
+	for (var n = 0; n < smax; n++) {
+		var obj = slideColl[n];
+
+		var did = 'slide' + n.toString();
+		if (obj.getAttribute('id')) {
+			slideIDs[n] = obj.getAttribute('id');
+		}
+		else {
+			obj.setAttribute('id',did);
+			slideIDs[n] = did;
+		}
+		if (isOp) continue;
+
+		var otext = '';
+		var menu = obj.firstChild;
+		if (!menu) continue; // to cope with empty slides
+		while (menu && menu.nodeType == 3) {
+			menu = menu.nextSibling;
+		}
+	 	if (!menu) continue; // to cope with slides with only text nodes
+
+		var menunodes = menu.childNodes;
+		for (var o = 0; o < menunodes.length; o++) {
+			otext += nodeValue(menunodes[o]);
+		}
+		list.options[list.length] = new Option(n + ' : '  + otext, n);
+	}
+}
+
+function currentSlide() {
+	var cs;
+	var footer_nodes;
+	var vis = 'visible';
+	if (document.getElementById) {
+		cs = document.getElementById('currentSlide');
+		footer_nodes = document.getElementById('footer').childNodes;
+	} else {
+		cs = document.currentSlide;
+		footer = document.footer.childNodes;
+	}
+	cs.innerHTML = '<span id="csHere">' + snum + '<\/span> ' + 
+		'<span id="csSep">\/<\/span> ' + 
+		'<span id="csTotal">' + (smax-1) + '<\/span>';
+	if (snum == 0) {
+		vis = 'hidden';
+	}
+	cs.style.visibility = vis;
+	for (var i = 0; i < footer_nodes.length; i++) {
+		if (footer_nodes[i].nodeType == 1) {
+			footer_nodes[i].style.visibility = vis;
+		}
+	}		
+}
+
+function go(step) {
+	if (document.getElementById('slideProj').disabled || step == 0) return;
+	var jl = document.getElementById('jumplist');
+	var cid = slideIDs[snum];
+	var ce = document.getElementById(cid);
+	if (incrementals[snum].length > 0) {
+		for (var i = 0; i < incrementals[snum].length; i++) {
+			removeClass(incrementals[snum][i], 'current');
+			removeClass(incrementals[snum][i], 'incremental');
+		}
+	}
+	if (step != 'j') {
+		snum += step;
+		lmax = smax - 1;
+		if (snum > lmax) snum = lmax;
+		if (snum < 0) snum = 0;
+	} else
+		snum = parseInt(jl.value);
+	var nid = slideIDs[snum];
+	var ne = document.getElementById(nid);
+	if (!ne) {
+		ne = document.getElementById(slideIDs[0]);
+		snum = 0;
+	}
+	if (step < 0) {incpos = incrementals[snum].length} else {incpos = 0;}
+	if (incrementals[snum].length > 0 && incpos == 0) {
+		for (var i = 0; i < incrementals[snum].length; i++) {
+			if (hasClass(incrementals[snum][i], 'current'))
+				incpos = i + 1;
+			else
+				addClass(incrementals[snum][i], 'incremental');
+		}
+	}
+	if (incrementals[snum].length > 0 && incpos > 0)
+		addClass(incrementals[snum][incpos - 1], 'current');
+	ce.style.visibility = 'hidden';
+	ne.style.visibility = 'visible';
+	jl.selectedIndex = snum;
+	currentSlide();
+	number = 0;
+}
+
+function goTo(target) {
+	if (target >= smax || target == snum) return;
+	go(target - snum);
+}
+
+function subgo(step) {
+	if (step > 0) {
+		removeClass(incrementals[snum][incpos - 1],'current');
+		removeClass(incrementals[snum][incpos], 'incremental');
+		addClass(incrementals[snum][incpos],'current');
+		incpos++;
+	} else {
+		incpos--;
+		removeClass(incrementals[snum][incpos],'current');
+		addClass(incrementals[snum][incpos], 'incremental');
+		addClass(incrementals[snum][incpos - 1],'current');
+	}
+}
+
+function toggle() {
+	var slideColl = GetElementsWithClassName('*','slide');
+	var slides = document.getElementById('slideProj');
+	var outline = document.getElementById('outlineStyle');
+	if (!slides.disabled) {
+		slides.disabled = true;
+		outline.disabled = false;
+		s5mode = false;
+		fontSize('1em');
+		for (var n = 0; n < smax; n++) {
+			var slide = slideColl[n];
+			slide.style.visibility = 'visible';
+		}
+	} else {
+		slides.disabled = false;
+		outline.disabled = true;
+		s5mode = true;
+		fontScale();
+		for (var n = 0; n < smax; n++) {
+			var slide = slideColl[n];
+			slide.style.visibility = 'hidden';
+		}
+		slideColl[snum].style.visibility = 'visible';
+	}
+}
+
+function showHide(action) {
+	var obj = GetElementsWithClassName('*','hideme')[0];
+	switch (action) {
+	case 's': obj.style.visibility = 'visible'; break;
+	case 'h': obj.style.visibility = 'hidden'; break;
+	case 'k':
+		if (obj.style.visibility != 'visible') {
+			obj.style.visibility = 'visible';
+		} else {
+			obj.style.visibility = 'hidden';
+		}
+	break;
+	}
+}
+
+// 'keys' code adapted from MozPoint (http://mozpoint.mozdev.org/)
+function keys(key) {
+	if (!key) {
+		key = event;
+		key.which = key.keyCode;
+	}
+	if (key.which == 84) {
+		toggle();
+		return;
+	}
+	if (s5mode) {
+		switch (key.which) {
+			case 10: // return
+			case 13: // enter
+				if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return;
+				if (key.target && isParentOrSelf(key.target, 'controls')) return;
+				if(number != undef) {
+					goTo(number);
+					break;
+				}
+			case 32: // spacebar
+			case 34: // page down
+			case 39: // rightkey
+			case 40: // downkey
+				if(number != undef) {
+					go(number);
+				} else if (!incrementals[snum] || incpos >= incrementals[snum].length) {
+					go(1);
+				} else {
+					subgo(1);
+				}
+				break;
+			case 33: // page up
+			case 37: // leftkey
+			case 38: // upkey
+				if(number != undef) {
+					go(-1 * number);
+				} else if (!incrementals[snum] || incpos <= 0) {
+					go(-1);
+				} else {
+					subgo(-1);
+				}
+				break;
+			case 36: // home
+				goTo(0);
+				break;
+			case 35: // end
+				goTo(smax-1);
+				break;
+			case 67: // c
+				showHide('k');
+				break;
+		}
+		if (key.which < 48 || key.which > 57) {
+			number = undef;
+		} else {
+			if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return;
+			if (key.target && isParentOrSelf(key.target, 'controls')) return;
+			number = (((number != undef) ? number : 0) * 10) + (key.which - 48);
+		}
+	}
+	return false;
+}
+
+function clicker(e) {
+	number = undef;
+	var target;
+	if (window.event) {
+		target = window.event.srcElement;
+		e = window.event;
+	} else target = e.target;
+    if (target.href != null || hasValue(target.rel, 'external') || isParentOrSelf(target, 'controls') || isParentOrSelf(target,'embed') || isParentOrSelf(target, 'object')) return true; 
+	if (!e.which || e.which == 1) {
+		if (!incrementals[snum] || incpos >= incrementals[snum].length) {
+			go(1);
+		} else {
+			subgo(1);
+		}
+	}
+}
+
+function findSlide(hash) {
+	var target = document.getElementById(hash);
+	if (target) {
+		for (var i = 0; i < slideIDs.length; i++) {
+			if (target.id == slideIDs[i]) return i;
+		}
+	}
+	return null;
+}
+
+function slideJump() {
+	if (window.location.hash == null || window.location.hash == '') {
+		currentSlide();
+		return;
+	}
+	if (window.location.hash == null) return;
+	var dest = null;
+	dest = findSlide(window.location.hash.slice(1));
+	if (dest == null) {
+		dest = 0;
+	}
+	go(dest - snum);
+}
+
+function fixLinks() {
+	var thisUri = window.location.href;
+	thisUri = thisUri.slice(0, thisUri.length - window.location.hash.length);
+	var aelements = document.getElementsByTagName('A');
+	for (var i = 0; i < aelements.length; i++) {
+		var a = aelements[i].href;
+		var slideID = a.match('\#.+');
+		if ((slideID) && (slideID[0].slice(0,1) == '#')) {
+			var dest = findSlide(slideID[0].slice(1));
+			if (dest != null) {
+				if (aelements[i].addEventListener) {
+					aelements[i].addEventListener("click", new Function("e",
+						"if (document.getElementById('slideProj').disabled) return;" +
+						"go("+dest+" - snum); " +
+						"if (e.preventDefault) e.preventDefault();"), true);
+				} else if (aelements[i].attachEvent) {
+					aelements[i].attachEvent("onclick", new Function("",
+						"if (document.getElementById('slideProj').disabled) return;" +
+						"go("+dest+" - snum); " +
+						"event.returnValue = false;"));
+				}
+			}
+		}
+	}
+}
+
+function externalLinks() {
+	if (!document.getElementsByTagName) return;
+	var anchors = document.getElementsByTagName('a');
+	for (var i=0; i<anchors.length; i++) {
+		var anchor = anchors[i];
+		if (anchor.getAttribute('href') && hasValue(anchor.rel, 'external')) {
+			anchor.target = '_blank';
+			addClass(anchor,'external');
+		}
+	}
+}
+
+function createControls() {
+	var controlsDiv = document.getElementById("controls");
+	if (!controlsDiv) return;
+	var hider = ' onmouseover="showHide(\'s\');" onmouseout="showHide(\'h\');"';
+	var hideDiv, hideList = '';
+	if (controlVis == 'hidden') {
+		hideDiv = hider;
+	} else {
+		hideList = hider;
+	}
+	controlsDiv.innerHTML = '<form action="#" id="controlForm"' + hideDiv + '>' +
+	'<div id="navLinks">' +
+	'<a accesskey="t" id="toggle" href="javascript:toggle();">&#216;<\/a>' +
+	'<a accesskey="z" id="prev" href="javascript:go(-1);">&laquo;<\/a>' +
+	'<a accesskey="x" id="next" href="javascript:go(1);">&raquo;<\/a>' +
+	'<div id="navList"' + hideList + '><select id="jumplist" onchange="go(\'j\');"><\/select><\/div>' +
+	'<\/div><\/form>';
+	if (controlVis == 'hidden') {
+		var hidden = document.getElementById('navLinks');
+	} else {
+		var hidden = document.getElementById('jumplist');
+	}
+	addClass(hidden,'hideme');
+}
+
+function fontScale() {  // causes layout problems in FireFox that get fixed if browser's Reload is used; same may be true of other Gecko-based browsers
+	if (!s5mode) return false;
+	var vScale = 22;  // both yield 32 (after rounding) at 1024x768
+	var hScale = 32;  // perhaps should auto-calculate based on theme's declared value?
+	if (window.innerHeight) {
+		var vSize = window.innerHeight;
+		var hSize = window.innerWidth;
+	} else if (document.documentElement.clientHeight) {
+		var vSize = document.documentElement.clientHeight;
+		var hSize = document.documentElement.clientWidth;
+	} else if (document.body.clientHeight) {
+		var vSize = document.body.clientHeight;
+		var hSize = document.body.clientWidth;
+	} else {
+		var vSize = 700;  // assuming 1024x768, minus chrome and such
+		var hSize = 1024; // these do not account for kiosk mode or Opera Show
+	}
+	var newSize = Math.min(Math.round(vSize/vScale),Math.round(hSize/hScale));
+	fontSize(newSize + 'px');
+	if (isGe) {  // hack to counter incremental reflow bugs
+		var obj = document.getElementsByTagName('body')[0];
+		obj.style.display = 'none';
+		obj.style.display = 'block';
+	}
+}
+
+function fontSize(value) {
+	if (!(s5ss = document.getElementById('s5ss'))) {
+		if (!isIE) {
+			document.getElementsByTagName('head')[0].appendChild(s5ss = document.createElement('style'));
+			s5ss.setAttribute('media','screen, projection');
+			s5ss.setAttribute('id','s5ss');
+		} else {
+			document.createStyleSheet();
+			document.s5ss = document.styleSheets[document.styleSheets.length - 1];
+		}
+	}
+	if (!isIE) {
+		while (s5ss.lastChild) s5ss.removeChild(s5ss.lastChild);
+		s5ss.appendChild(document.createTextNode('body {font-size: ' + value + ' !important;}'));
+	} else {
+		document.s5ss.addRule('body','font-size: ' + value + ' !important;');
+	}
+}
+
+function notOperaFix() {
+	slideCSS = document.getElementById('slideProj').href;
+	var slides = document.getElementById('slideProj');
+	var outline = document.getElementById('outlineStyle');
+	slides.setAttribute('media','screen');
+	outline.disabled = true;
+	if (isGe) {
+		slides.setAttribute('href','null');   // Gecko fix
+		slides.setAttribute('href',slideCSS); // Gecko fix
+	}
+	if (isIE && document.styleSheets && document.styleSheets[0]) {
+		document.styleSheets[0].addRule('img', 'behavior: url(ui/small-white/iepngfix.htc)');
+		document.styleSheets[0].addRule('div', 'behavior: url(ui/small-white/iepngfix.htc)');
+		document.styleSheets[0].addRule('.slide', 'behavior: url(ui/small-white/iepngfix.htc)');
+	}
+}
+
+function getIncrementals(obj) {
+	var incrementals = new Array();
+	if (!obj) 
+		return incrementals;
+	var children = obj.childNodes;
+	for (var i = 0; i < children.length; i++) {
+		var child = children[i];
+		if (hasClass(child, 'incremental')) {
+			if (child.nodeName == 'OL' || child.nodeName == 'UL') {
+				removeClass(child, 'incremental');
+				for (var j = 0; j < child.childNodes.length; j++) {
+					if (child.childNodes[j].nodeType == 1) {
+						addClass(child.childNodes[j], 'incremental');
+					}
+				}
+			} else {
+				incrementals[incrementals.length] = child;
+				removeClass(child,'incremental');
+			}
+		}
+		if (hasClass(child, 'show-first')) {
+			if (child.nodeName == 'OL' || child.nodeName == 'UL') {
+				removeClass(child, 'show-first');
+				if (child.childNodes[isGe].nodeType == 1) {
+					removeClass(child.childNodes[isGe], 'incremental');
+				}
+			} else {
+				incrementals[incrementals.length] = child;
+			}
+		}
+		incrementals = incrementals.concat(getIncrementals(child));
+	}
+	return incrementals;
+}
+
+function createIncrementals() {
+	var incrementals = new Array();
+	for (var i = 0; i < smax; i++) {
+		incrementals[i] = getIncrementals(document.getElementById(slideIDs[i]));
+	}
+	return incrementals;
+}
+
+function defaultCheck() {
+	var allMetas = document.getElementsByTagName('meta');
+	for (var i = 0; i< allMetas.length; i++) {
+		if (allMetas[i].name == 'defaultView') {
+			defaultView = allMetas[i].content;
+		}
+		if (allMetas[i].name == 'controlVis') {
+			controlVis = allMetas[i].content;
+		}
+	}
+}
+
+// Key trap fix, new function body for trap()
+function trap(e) {
+	if (!e) {
+		e = event;
+		e.which = e.keyCode;
+	}
+	try {
+		modifierKey = e.ctrlKey || e.altKey || e.metaKey;
+	}
+	catch(e) {
+		modifierKey = false;
+	}
+	return modifierKey || e.which == 0;
+}
+
+function startup() {
+	defaultCheck();
+	if (!isOp) createControls();
+	slideLabel();
+	fixLinks();
+	externalLinks();
+	fontScale();
+	if (!isOp) {
+		notOperaFix();
+		incrementals = createIncrementals();
+		slideJump();
+		if (defaultView == 'outline') {
+			toggle();
+		}
+		document.onkeyup = keys;
+		document.onkeypress = trap;
+		document.onclick = clicker;
+	}
+}
+
+window.onload = startup;
+window.onresize = function(){setTimeout('fontScale()', 50);}

data/unicorn.rb

@@ -0,0 +1,2 @@
+#worker_processes 4
+timeout 6000

data/views/layout.haml

@@ -0,0 +1,95 @@
+!!!
+%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
+  %head
+    %meta{'charset'=>"utf-8"}
+    %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
+    %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
+    %title Nano Lazar Toxicity Predictions
+    %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/style.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
+    %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
+    %script{:src=>"/javascripts/jquery.tablesorter.min.js"}
+    %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"}
+    %script{:src=>"/javascripts/jquery.tablesorter.staticrow.min.js"}
+    %script{:src=>"/javascripts/jquery.doubleScroll.js"}
+    %script{:src=>"/javascripts/bootstrap.min.js"}
+    %script{:src=>"/javascripts/nanolazar.js"}
+    %script{:src=>"/javascripts/google_analytics.js"}
+  %body
+    %noscript
+      %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
+      Your web browser must have JavaScript enabled in order for this application to display correctly.
+    %header.page-header{:style=>"margin:20px 0 20px;"}
+      %div.row{:style=>"display:flex;flex-direction:row;align-items:center;justify-content:center"}
+        %div.col-sm-2
+          %a{:href=> to("/predict")}
+            %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo_ist", :width=>"150px", :heigth=>"150px", :style=>"margin:0 0 0 1em;"}
+        %div.col-sm-2
+          %a{:href=> "http://www.enanomapper.net"}
+            %img.media-object{:src=>"/images/enm_logo.png", :width=>"150px", :heigth=>"150px", :alt=>"logo_enm", :style=>"margin:0 0 0 1em;"}
+        %div.col-sm-6
+          %h1.media-heading{:style=>"margin:0 0 0 1em;"} nano-lazar toxicity predictions
+        %div.col-sm-2
+          %h1.media-heading{:style=>"margin:0 0 0 1em;"}
+            %small
+              %a{:href=>"https://lazar.in-silico.ch/predict", :rel=>"external"} lazar
+
+    %div.container-fluid
+      %topline
+        %div.row
+          %div.col-md-8
+            Problems, bugs, ideas for improvements ? Please report at our
+            %a{:href => 'https://github.com/enanomapper/nano-lazar/issues', :rel => "external"} issue tracker
+            or send us an email
+            %a{ :href=>"mailto:info@in-silico.ch?subject=[nano-lazar v#{@version}]", :target=>"_top"}
+              %img.share{:src=>"/images/Email.png"}
+            (version #{@version}).
+          %div.col-md-2
+          %div.col-md-2
+            %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"}
+              %img.share{:src=>"/images/Twitter.png"}
+            %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"}
+              %img.share{:src=>"/images/Google+.png"}
+            %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"}
+              %img.share{:src=>"/images/LinkedIn.png"}
+            %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"}
+              %img.share{:src=>"/images/Facebook.png"}
+      :javascript
+        $(document).ready(function(){
+          $("#back-top").hide();
+        });
+          
+      = yield
+    
+    %footer.footer
+      %div.container-fluid
+        %p.text-muted
+          © 
+          %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2014 - #{Time.now.year.to_s}
+          |
+          %a{:href => to("/license"), :rel => "external"} GPL3 License
+
+    #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
+      %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
+        %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"}
+    :javascript
+      $("#back-top").hide();
+      $(function () {
+        $(window).scroll(function () {
+          if ($(this).scrollTop() > 600) {
+            $('#back-top').fadeIn();
+          } else {
+            $('#back-top').fadeOut();
+          }
+        });
+        // scroll body to 0px on click
+        $('#back-top a').click(function () {
+          $('body,html').animate({
+            scrollTop: 0
+          }, 500);
+          return false;
+        });
+      });

data/views/license.haml

@@ -0,0 +1 @@
+= @license