1. Partial fix for NIHVIVO-2130. Now the downloadable csv file properly prints out all the authors, with same name. The right hand side bar still prints wrong values in case of authors with duplicate names.

2. Solution for 2 stage loading for temporal graph where now when the intial call is made to it, it returns with the markup & js lib includes & then makes an ajax call to get the data file in json format which is the used to render the linegraph & the table.

productMods/css/visualization/entitycomparison/layout.css

@@ -8,6 +8,11 @@
     margin: auto;
     overflow: hidden;
 }
+
+#error-container {
+    display: none;
+}
+
 .easy-deselect-label a.temporal-vis-url {
     float: right;
 }

productMods/js/jquery_plugins/jquery.blockUI.js

@@ -0,0 +1,490 @@
+/*!
+ * jQuery blockUI plugin
+ * Version 2.37 (29-JAN-2011)
+ * @requires jQuery v1.2.3 or later
+ *
+ * Examples at: http://malsup.com/jquery/block/
+ * Copyright (c) 2007-2010 M. Alsup
+ * Dual licensed under the MIT and GPL licenses:
+ * http://www.opensource.org/licenses/mit-license.php
+ * http://www.gnu.org/licenses/gpl.html
+ *
+ * Thanks to Amir-Hossein Sobhi for some excellent contributions!
+ */
+
+;(function($) {
+
+if (/1\.(0|1|2)\.(0|1|2)/.test($.fn.jquery) || /^1.1/.test($.fn.jquery)) {
+	alert('blockUI requires jQuery v1.2.3 or later!  You are using v' + $.fn.jquery);
+	return;
+}
+
+$.fn._fadeIn = $.fn.fadeIn;
+
+var noOp = function() {};
+
+// this bit is to ensure we don't call setExpression when we shouldn't (with extra muscle to handle
+// retarded userAgent strings on Vista)
+var mode = document.documentMode || 0;
+var setExpr = $.browser.msie && (($.browser.version < 8 && !mode) || mode < 8);
+var ie6 = $.browser.msie && /MSIE 6.0/.test(navigator.userAgent) && !mode;
+
+// global $ methods for blocking/unblocking the entire page
+$.blockUI   = function(opts) { install(window, opts); };
+$.unblockUI = function(opts) { remove(window, opts); };
+
+// convenience method for quick growl-like notifications  (http://www.google.com/search?q=growl)
+$.growlUI = function(title, message, timeout, onClose) {
+	var $m = $('<div class="growlUI"></div>');
+	if (title) $m.append('<h1>'+title+'</h1>');
+	if (message) $m.append('<h2>'+message+'</h2>');
+	if (timeout == undefined) timeout = 3000;
+	$.blockUI({
+		message: $m, fadeIn: 700, fadeOut: 1000, centerY: false,
+		timeout: timeout, showOverlay: false,
+		onUnblock: onClose, 
+		css: $.blockUI.defaults.growlCSS
+	});
+};
+
+// plugin method for blocking element content
+$.fn.block = function(opts) {
+	return this.unblock({ fadeOut: 0 }).each(function() {
+		if ($.css(this,'position') == 'static')
+			this.style.position = 'relative';
+		if ($.browser.msie)
+			this.style.zoom = 1; // force 'hasLayout'
+		install(this, opts);
+	});
+};
+
+// plugin method for unblocking element content
+$.fn.unblock = function(opts) {
+	return this.each(function() {
+		remove(this, opts);
+	});
+};
+
+$.blockUI.version = 2.37; // 2nd generation blocking at no extra cost!
+
+// override these in your code to change the default behavior and style
+$.blockUI.defaults = {
+	// message displayed when blocking (use null for no message)
+	message:  '<h1>Please wait...</h1>',
+
+	title: null,	  // title string; only used when theme == true
+	draggable: true,  // only used when theme == true (requires jquery-ui.js to be loaded)
+	
+	theme: false, // set to true to use with jQuery UI themes
+	
+	// styles for the message when blocking; if you wish to disable
+	// these and use an external stylesheet then do this in your code:
+	// $.blockUI.defaults.css = {};
+	css: {
+		padding:	0,
+		margin:		0,
+		width:		'30%',
+		top:		'40%',
+		left:		'35%',
+		textAlign:	'center',
+		color:		'#000',
+		border:		'3px solid #aaa',
+		backgroundColor:'#fff',
+		cursor:		'wait'
+	},
+	
+	// minimal style set used when themes are used
+	themedCSS: {
+		width:	'30%',
+		top:	'40%',
+		left:	'35%'
+	},
+
+	// styles for the overlay
+	overlayCSS:  {
+		backgroundColor: '#000',
+		opacity:	  	 0.6,
+		cursor:		  	 'wait'
+	},
+
+	// styles applied when using $.growlUI
+	growlCSS: {
+		width:  	'350px',
+		top:		'10px',
+		left:   	'',
+		right:  	'10px',
+		border: 	'none',
+		padding:	'5px',
+		opacity:	0.6,
+		cursor: 	'default',
+		color:		'#fff',
+		backgroundColor: '#000',
+		'-webkit-border-radius': '10px',
+		'-moz-border-radius':	 '10px',
+		'border-radius': 		 '10px'
+	},
+	
+	// IE issues: 'about:blank' fails on HTTPS and javascript:false is s-l-o-w
+	// (hat tip to Jorge H. N. de Vasconcelos)
+	iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank',
+
+	// force usage of iframe in non-IE browsers (handy for blocking applets)
+	forceIframe: false,
+
+	// z-index for the blocking overlay
+	baseZ: 1000,
+
+	// set these to true to have the message automatically centered
+	centerX: true, // <-- only effects element blocking (page block controlled via css above)
+	centerY: true,
+
+	// allow body element to be stetched in ie6; this makes blocking look better
+	// on "short" pages.  disable if you wish to prevent changes to the body height
+	allowBodyStretch: true,
+
+	// enable if you want key and mouse events to be disabled for content that is blocked
+	bindEvents: true,
+
+	// be default blockUI will supress tab navigation from leaving blocking content
+	// (if bindEvents is true)
+	constrainTabKey: true,
+
+	// fadeIn time in millis; set to 0 to disable fadeIn on block
+	fadeIn:  200,
+
+	// fadeOut time in millis; set to 0 to disable fadeOut on unblock
+	fadeOut:  400,
+
+	// time in millis to wait before auto-unblocking; set to 0 to disable auto-unblock
+	timeout: 0,
+
+	// disable if you don't want to show the overlay
+	showOverlay: true,
+
+	// if true, focus will be placed in the first available input field when
+	// page blocking
+	focusInput: true,
+
+	// suppresses the use of overlay styles on FF/Linux (due to performance issues with opacity)
+	applyPlatformOpacityRules: true,
+	
+	// callback method invoked when fadeIn has completed and blocking message is visible
+	onBlock: null,
+
+	// callback method invoked when unblocking has completed; the callback is
+	// passed the element that has been unblocked (which is the window object for page
+	// blocks) and the options that were passed to the unblock call:
+	//	 onUnblock(element, options)
+	onUnblock: null,
+
+	// don't ask; if you really must know: http://groups.google.com/group/jquery-en/browse_thread/thread/36640a8730503595/2f6a79a77a78e493#2f6a79a77a78e493
+	quirksmodeOffsetHack: 4,
+
+	// class name of the message block
+	blockMsgClass: 'blockMsg'
+};
+
+// private data and functions follow...
+
+var pageBlock = null;
+var pageBlockEls = [];
+
+function install(el, opts) {
+	var full = (el == window);
+	var msg = opts && opts.message !== undefined ? opts.message : undefined;
+	opts = $.extend({}, $.blockUI.defaults, opts || {});
+	opts.overlayCSS = $.extend({}, $.blockUI.defaults.overlayCSS, opts.overlayCSS || {});
+	var css = $.extend({}, $.blockUI.defaults.css, opts.css || {});
+	var themedCSS = $.extend({}, $.blockUI.defaults.themedCSS, opts.themedCSS || {});
+	msg = msg === undefined ? opts.message : msg;
+
+	// remove the current block (if there is one)
+	if (full && pageBlock)
+		remove(window, {fadeOut:0});
+
+	// if an existing element is being used as the blocking content then we capture
+	// its current place in the DOM (and current display style) so we can restore
+	// it when we unblock
+	if (msg && typeof msg != 'string' && (msg.parentNode || msg.jquery)) {
+		var node = msg.jquery ? msg[0] : msg;
+		var data = {};
+		$(el).data('blockUI.history', data);
+		data.el = node;
+		data.parent = node.parentNode;
+		data.display = node.style.display;
+		data.position = node.style.position;
+		if (data.parent)
+			data.parent.removeChild(node);
+	}
+
+	var z = opts.baseZ;
+
+	// blockUI uses 3 layers for blocking, for simplicity they are all used on every platform;
+	// layer1 is the iframe layer which is used to supress bleed through of underlying content
+	// layer2 is the overlay layer which has opacity and a wait cursor (by default)
+	// layer3 is the message content that is displayed while blocking
+
+	var lyr1 = ($.browser.msie || opts.forceIframe) 
+		? $('<iframe class="blockUI" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;position:absolute;width:100%;height:100%;top:0;left:0" src="'+opts.iframeSrc+'"></iframe>')
+		: $('<div class="blockUI" style="display:none"></div>');
+	var lyr2 = $('<div class="blockUI blockOverlay" style="z-index:'+ (z++) +';display:none;border:none;margin:0;padding:0;width:100%;height:100%;top:0;left:0"></div>');
+	
+	var lyr3, s;
+	if (opts.theme && full) {
+		s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:fixed">' +
+				'<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || '&nbsp;')+'</div>' +
+				'<div class="ui-widget-content ui-dialog-content"></div>' +
+			'</div>';
+	}
+	else if (opts.theme) {
+		s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:absolute">' +
+				'<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title || '&nbsp;')+'</div>' +
+				'<div class="ui-widget-content ui-dialog-content"></div>' +
+			'</div>';
+	}
+	else if (full) {
+		s = '<div class="blockUI ' + opts.blockMsgClass + ' blockPage" style="z-index:'+z+';display:none;position:fixed"></div>';
+	}			
+	else {
+		s = '<div class="blockUI ' + opts.blockMsgClass + ' blockElement" style="z-index:'+z+';display:none;position:absolute"></div>';
+	}
+	lyr3 = $(s);
+
+	// if we have a message, style it
+	if (msg) {
+		if (opts.theme) {
+			lyr3.css(themedCSS);
+			lyr3.addClass('ui-widget-content');
+		}
+		else 
+			lyr3.css(css);
+	}
+
+	// style the overlay
+	if (!opts.applyPlatformOpacityRules || !($.browser.mozilla && /Linux/.test(navigator.platform)))
+		lyr2.css(opts.overlayCSS);
+	lyr2.css('position', full ? 'fixed' : 'absolute');
+
+	// make iframe layer transparent in IE
+	if ($.browser.msie || opts.forceIframe)
+		lyr1.css('opacity',0.0);
+
+	//$([lyr1[0],lyr2[0],lyr3[0]]).appendTo(full ? 'body' : el);
+	var layers = [lyr1,lyr2,lyr3], $par = full ? $('body') : $(el);
+	$.each(layers, function() {
+		this.appendTo($par);
+	});
+	
+	if (opts.theme && opts.draggable && $.fn.draggable) {
+		lyr3.draggable({
+			handle: '.ui-dialog-titlebar',
+			cancel: 'li'
+		});
+	}
+
+	// ie7 must use absolute positioning in quirks mode and to account for activex issues (when scrolling)
+	var expr = setExpr && (!$.boxModel || $('object,embed', full ? null : el).length > 0);
+	if (ie6 || expr) {
+		// give body 100% height
+		if (full && opts.allowBodyStretch && $.boxModel)
+			$('html,body').css('height','100%');
+
+		// fix ie6 issue when blocked element has a border width
+		if ((ie6 || !$.boxModel) && !full) {
+			var t = sz(el,'borderTopWidth'), l = sz(el,'borderLeftWidth');
+			var fixT = t ? '(0 - '+t+')' : 0;
+			var fixL = l ? '(0 - '+l+')' : 0;
+		}
+
+		// simulate fixed position
+		$.each([lyr1,lyr2,lyr3], function(i,o) {
+			var s = o[0].style;
+			s.position = 'absolute';
+			if (i < 2) {
+				full ? s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"')
+					 : s.setExpression('height','this.parentNode.offsetHeight + "px"');
+				full ? s.setExpression('width','jQuery.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"')
+					 : s.setExpression('width','this.parentNode.offsetWidth + "px"');
+				if (fixL) s.setExpression('left', fixL);
+				if (fixT) s.setExpression('top', fixT);
+			}
+			else if (opts.centerY) {
+				if (full) s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"');
+				s.marginTop = 0;
+			}
+			else if (!opts.centerY && full) {
+				var top = (opts.css && opts.css.top) ? parseInt(opts.css.top) : 0;
+				var expression = '((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"';
+				s.setExpression('top',expression);
+			}
+		});
+	}
+
+	// show the message
+	if (msg) {
+		if (opts.theme)
+			lyr3.find('.ui-widget-content').append(msg);
+		else
+			lyr3.append(msg);
+		if (msg.jquery || msg.nodeType)
+			$(msg).show();
+	}
+
+	if (($.browser.msie || opts.forceIframe) && opts.showOverlay)
+		lyr1.show(); // opacity is zero
+	if (opts.fadeIn) {
+		var cb = opts.onBlock ? opts.onBlock : noOp;
+		var cb1 = (opts.showOverlay && !msg) ? cb : noOp;
+		var cb2 = msg ? cb : noOp;
+		if (opts.showOverlay)
+			lyr2._fadeIn(opts.fadeIn, cb1);
+		if (msg)
+			lyr3._fadeIn(opts.fadeIn, cb2);
+	}
+	else {
+		if (opts.showOverlay)
+			lyr2.show();
+		if (msg)
+			lyr3.show();
+		if (opts.onBlock)
+			opts.onBlock();
+	}
+
+	// bind key and mouse events
+	bind(1, el, opts);
+
+	if (full) {
+		pageBlock = lyr3[0];
+		pageBlockEls = $(':input:enabled:visible',pageBlock);
+		if (opts.focusInput)
+			setTimeout(focus, 20);
+	}
+	else
+		center(lyr3[0], opts.centerX, opts.centerY);
+
+	if (opts.timeout) {
+		// auto-unblock
+		var to = setTimeout(function() {
+			full ? $.unblockUI(opts) : $(el).unblock(opts);
+		}, opts.timeout);
+		$(el).data('blockUI.timeout', to);
+	}
+};
+
+// remove the block
+function remove(el, opts) {
+	var full = (el == window);
+	var $el = $(el);
+	var data = $el.data('blockUI.history');
+	var to = $el.data('blockUI.timeout');
+	if (to) {
+		clearTimeout(to);
+		$el.removeData('blockUI.timeout');
+	}
+	opts = $.extend({}, $.blockUI.defaults, opts || {});
+	bind(0, el, opts); // unbind events
+	
+	var els;
+	if (full) // crazy selector to handle odd field errors in ie6/7
+		els = $('body').children().filter('.blockUI').add('body > .blockUI');
+	else
+		els = $('.blockUI', el);
+
+	if (full)
+		pageBlock = pageBlockEls = null;
+
+	if (opts.fadeOut) {
+		els.fadeOut(opts.fadeOut);
+		setTimeout(function() { reset(els,data,opts,el); }, opts.fadeOut);
+	}
+	else
+		reset(els, data, opts, el);
+};
+
+// move blocking element back into the DOM where it started
+function reset(els,data,opts,el) {
+	els.each(function(i,o) {
+		// remove via DOM calls so we don't lose event handlers
+		if (this.parentNode)
+			this.parentNode.removeChild(this);
+	});
+
+	if (data && data.el) {
+		data.el.style.display = data.display;
+		data.el.style.position = data.position;
+		if (data.parent)
+			data.parent.appendChild(data.el);
+		$(el).removeData('blockUI.history');
+	}
+
+	if (typeof opts.onUnblock == 'function')
+		opts.onUnblock(el,opts);
+};
+
+// bind/unbind the handler
+function bind(b, el, opts) {
+	var full = el == window, $el = $(el);
+
+	// don't bother unbinding if there is nothing to unbind
+	if (!b && (full && !pageBlock || !full && !$el.data('blockUI.isBlocked')))
+		return;
+	if (!full)
+		$el.data('blockUI.isBlocked', b);
+
+	// don't bind events when overlay is not in use or if bindEvents is false
+	if (!opts.bindEvents || (b && !opts.showOverlay)) 
+		return;
+
+	// bind anchors and inputs for mouse and key events
+	var events = 'mousedown mouseup keydown keypress';
+	b ? $(document).bind(events, opts, handler) : $(document).unbind(events, handler);
+
+// former impl...
+//	   var $e = $('a,:input');
+//	   b ? $e.bind(events, opts, handler) : $e.unbind(events, handler);
+};
+
+// event handler to suppress keyboard/mouse events when blocking
+function handler(e) {
+	// allow tab navigation (conditionally)
+	if (e.keyCode && e.keyCode == 9) {
+		if (pageBlock && e.data.constrainTabKey) {
+			var els = pageBlockEls;
+			var fwd = !e.shiftKey && e.target === els[els.length-1];
+			var back = e.shiftKey && e.target === els[0];
+			if (fwd || back) {
+				setTimeout(function(){focus(back)},10);
+				return false;
+			}
+		}
+	}
+	var opts = e.data;
+	// allow events within the message content
+	if ($(e.target).parents('div.' + opts.blockMsgClass).length > 0)
+		return true;
+
+	// allow events for content that is not being blocked
+	return $(e.target).parents().children().filter('div.blockUI').length == 0;
+};
+
+function focus(back) {
+	if (!pageBlockEls)
+		return;
+	var e = pageBlockEls[back===true ? pageBlockEls.length-1 : 0];
+	if (e)
+		e.focus();
+};
+
+function center(el, x, y) {
+	var p = el.parentNode, s = el.style;
+	var l = ((p.offsetWidth - el.offsetWidth)/2) - sz(p,'borderLeftWidth');
+	var t = ((p.offsetHeight - el.offsetHeight)/2) - sz(p,'borderTopWidth');
+	if (x) s.left = l > 0 ? (l+'px') : '0';
+	if (y) s.top  = t > 0 ? (t+'px') : '0';
+};
+
+function sz(el, p) {
+	return parseInt($.css(el,p))||0;
+};
+
+})(jQuery);

productMods/js/jquery_plugins/jquery.blockUI.min.js

@@ -0,0 +1,66 @@
+/*!
+  jQuery blockUI plugin
+  Version 2.37 (29-JAN-2011)
+  @requires jQuery v1.2.3 or later
+ 
+  Examples at: http://malsup.com/jquery/block/
+  Copyright (c) 2007-2010 M. Alsup
+  Dual licensed under the MIT and GPL licenses:
+  http://www.opensource.org/licenses/mit-license.php
+  http://www.gnu.org/licenses/gpl.html
+ 
+  Thanks to Amir-Hossein Sobhi for some excellent contributions!
+ */;(function($){if(/1\.(0|1|2)\.(0|1|2)/.test($.fn.jquery)||/^1.1/.test($.fn.jquery)){alert('blockUI requires jQuery v1.2.3 or later!  You are using v'+$.fn.jquery);return;}
+$.fn._fadeIn=$.fn.fadeIn;var noOp=function(){};var mode=document.documentMode||0;var setExpr=$.browser.msie&&(($.browser.version<8&&!mode)||mode<8);var ie6=$.browser.msie&&/MSIE 6.0/.test(navigator.userAgent)&&!mode;$.blockUI=function(opts){install(window,opts);};$.unblockUI=function(opts){remove(window,opts);};$.growlUI=function(title,message,timeout,onClose){var $m=$('<div class="growlUI"></div>');if(title)$m.append('<h1>'+title+'</h1>');if(message)$m.append('<h2>'+message+'</h2>');if(timeout==undefined)timeout=3000;$.blockUI({message:$m,fadeIn:700,fadeOut:1000,centerY:false,timeout:timeout,showOverlay:false,onUnblock:onClose,css:$.blockUI.defaults.growlCSS});};$.fn.block=function(opts){return this.unblock({fadeOut:0}).each(function(){if($.css(this,'position')=='static')
+this.style.position='relative';if($.browser.msie)
+this.style.zoom=1;install(this,opts);});};$.fn.unblock=function(opts){return this.each(function(){remove(this,opts);});};$.blockUI.version=2.37;$.blockUI.defaults={message:'<h1>Please wait...</h1>',title:null,draggable:true,theme:false,css:{padding:0,margin:0,width:'30%',top:'40%',left:'35%',textAlign:'center',color:'#000',border:'3px solid #aaa',backgroundColor:'#fff',cursor:'wait'},themedCSS:{width:'30%',top:'40%',left:'35%'},overlayCSS:{backgroundColor:'#000',opacity:0.6,cursor:'wait'},growlCSS:{width:'350px',top:'10px',left:'',right:'10px',border:'none',padding:'5px',opacity:0.6,cursor:'default',color:'#fff',backgroundColor:'#000','-webkit-border-radius':'10px','-moz-border-radius':'10px','border-radius':'10px'},iframeSrc:/^https/i.test(window.location.href||'')?'javascript:false':'about:blank',forceIframe:false,baseZ:1000,centerX:true,centerY:true,allowBodyStretch:true,bindEvents:true,constrainTabKey:true,fadeIn:200,fadeOut:400,timeout:0,showOverlay:true,focusInput:true,applyPlatformOpacityRules:true,onBlock:null,onUnblock:null,quirksmodeOffsetHack:4,blockMsgClass:'blockMsg'};var pageBlock=null;var pageBlockEls=[];function install(el,opts){var full=(el==window);var msg=opts&&opts.message!==undefined?opts.message:undefined;opts=$.extend({},$.blockUI.defaults,opts||{});opts.overlayCSS=$.extend({},$.blockUI.defaults.overlayCSS,opts.overlayCSS||{});var css=$.extend({},$.blockUI.defaults.css,opts.css||{});var themedCSS=$.extend({},$.blockUI.defaults.themedCSS,opts.themedCSS||{});msg=msg===undefined?opts.message:msg;if(full&&pageBlock)
+remove(window,{fadeOut:0});if(msg&&typeof msg!='string'&&(msg.parentNode||msg.jquery)){var node=msg.jquery?msg[0]:msg;var data={};$(el).data('blockUI.history',data);data.el=node;data.parent=node.parentNode;data.display=node.style.display;data.position=node.style.position;if(data.parent)
+data.parent.removeChild(node);}
+var z=opts.baseZ;var lyr1=($.browser.msie||opts.forceIframe)?$('<iframe class="blockUI" style="z-index:'+(z++)+';display:none;border:none;margin:0;padding:0;position:absolute;width:100%;height:100%;top:0;left:0" src="'+opts.iframeSrc+'"></iframe>'):$('<div class="blockUI" style="display:none"></div>');var lyr2=$('<div class="blockUI blockOverlay" style="z-index:'+(z++)+';display:none;border:none;margin:0;padding:0;width:100%;height:100%;top:0;left:0"></div>');var lyr3,s;if(opts.theme&&full){s='<div class="blockUI '+opts.blockMsgClass+' blockPage ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:fixed">'+'<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title||'&nbsp;')+'</div>'+'<div class="ui-widget-content ui-dialog-content"></div>'+'</div>';}
+else if(opts.theme){s='<div class="blockUI '+opts.blockMsgClass+' blockElement ui-dialog ui-widget ui-corner-all" style="z-index:'+z+';display:none;position:absolute">'+'<div class="ui-widget-header ui-dialog-titlebar ui-corner-all blockTitle">'+(opts.title||'&nbsp;')+'</div>'+'<div class="ui-widget-content ui-dialog-content"></div>'+'</div>';}
+else if(full){s='<div class="blockUI '+opts.blockMsgClass+' blockPage" style="z-index:'+z+';display:none;position:fixed"></div>';}
+else{s='<div class="blockUI '+opts.blockMsgClass+' blockElement" style="z-index:'+z+';display:none;position:absolute"></div>';}
+lyr3=$(s);if(msg){if(opts.theme){lyr3.css(themedCSS);lyr3.addClass('ui-widget-content');}
+else
+lyr3.css(css);}
+if(!opts.applyPlatformOpacityRules||!($.browser.mozilla&&/Linux/.test(navigator.platform)))
+lyr2.css(opts.overlayCSS);lyr2.css('position',full?'fixed':'absolute');if($.browser.msie||opts.forceIframe)
+lyr1.css('opacity',0.0);var layers=[lyr1,lyr2,lyr3],$par=full?$('body'):$(el);$.each(layers,function(){this.appendTo($par);});if(opts.theme&&opts.draggable&&$.fn.draggable){lyr3.draggable({handle:'.ui-dialog-titlebar',cancel:'li'});}
+var expr=setExpr&&(!$.boxModel||$('object,embed',full?null:el).length>0);if(ie6||expr){if(full&&opts.allowBodyStretch&&$.boxModel)
+$('html,body').css('height','100%');if((ie6||!$.boxModel)&&!full){var t=sz(el,'borderTopWidth'),l=sz(el,'borderLeftWidth');var fixT=t?'(0 - '+t+')':0;var fixL=l?'(0 - '+l+')':0;}
+$.each([lyr1,lyr2,lyr3],function(i,o){var s=o[0].style;s.position='absolute';if(i<2){full?s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"'):s.setExpression('height','this.parentNode.offsetHeight + "px"');full?s.setExpression('width','jQuery.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"'):s.setExpression('width','this.parentNode.offsetWidth + "px"');if(fixL)s.setExpression('left',fixL);if(fixT)s.setExpression('top',fixT);}
+else if(opts.centerY){if(full)s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"');s.marginTop=0;}
+else if(!opts.centerY&&full){var top=(opts.css&&opts.css.top)?parseInt(opts.css.top):0;var expression='((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"';s.setExpression('top',expression);}});}
+if(msg){if(opts.theme)
+lyr3.find('.ui-widget-content').append(msg);else
+lyr3.append(msg);if(msg.jquery||msg.nodeType)
+$(msg).show();}
+if(($.browser.msie||opts.forceIframe)&&opts.showOverlay)
+lyr1.show();if(opts.fadeIn){var cb=opts.onBlock?opts.onBlock:noOp;var cb1=(opts.showOverlay&&!msg)?cb:noOp;var cb2=msg?cb:noOp;if(opts.showOverlay)
+lyr2._fadeIn(opts.fadeIn,cb1);if(msg)
+lyr3._fadeIn(opts.fadeIn,cb2);}
+else{if(opts.showOverlay)
+lyr2.show();if(msg)
+lyr3.show();if(opts.onBlock)
+opts.onBlock();}
+bind(1,el,opts);if(full){pageBlock=lyr3[0];pageBlockEls=$(':input:enabled:visible',pageBlock);if(opts.focusInput)
+setTimeout(focus,20);}
+else
+center(lyr3[0],opts.centerX,opts.centerY);if(opts.timeout){var to=setTimeout(function(){full?$.unblockUI(opts):$(el).unblock(opts);},opts.timeout);$(el).data('blockUI.timeout',to);}};function remove(el,opts){var full=(el==window);var $el=$(el);var data=$el.data('blockUI.history');var to=$el.data('blockUI.timeout');if(to){clearTimeout(to);$el.removeData('blockUI.timeout');}
+opts=$.extend({},$.blockUI.defaults,opts||{});bind(0,el,opts);var els;if(full)
+els=$('body').children().filter('.blockUI').add('body > .blockUI');else
+els=$('.blockUI',el);if(full)
+pageBlock=pageBlockEls=null;if(opts.fadeOut){els.fadeOut(opts.fadeOut);setTimeout(function(){reset(els,data,opts,el);},opts.fadeOut);}
+else
+reset(els,data,opts,el);};function reset(els,data,opts,el){els.each(function(i,o){if(this.parentNode)
+this.parentNode.removeChild(this);});if(data&&data.el){data.el.style.display=data.display;data.el.style.position=data.position;if(data.parent)
+data.parent.appendChild(data.el);$(el).removeData('blockUI.history');}
+if(typeof opts.onUnblock=='function')
+opts.onUnblock(el,opts);};function bind(b,el,opts){var full=el==window,$el=$(el);if(!b&&(full&&!pageBlock||!full&&!$el.data('blockUI.isBlocked')))
+return;if(!full)
+$el.data('blockUI.isBlocked',b);if(!opts.bindEvents||(b&&!opts.showOverlay))
+return;var events='mousedown mouseup keydown keypress';b?$(document).bind(events,opts,handler):$(document).unbind(events,handler);};function handler(e){if(e.keyCode&&e.keyCode==9){if(pageBlock&&e.data.constrainTabKey){var els=pageBlockEls;var fwd=!e.shiftKey&&e.target===els[els.length-1];var back=e.shiftKey&&e.target===els[0];if(fwd||back){setTimeout(function(){focus(back)},10);return false;}}}
+var opts=e.data;if($(e.target).parents('div.'+opts.blockMsgClass).length>0)
+return true;return $(e.target).parents().children().filter('div.blockUI').length==0;};function focus(back){if(!pageBlockEls)
+return;var e=pageBlockEls[back===true?pageBlockEls.length-1:0];if(e)
+e.focus();};function center(el,x,y){var p=el.parentNode,s=el.style;var l=((p.offsetWidth-el.offsetWidth)/2)-sz(p,'borderLeftWidth');var t=((p.offsetHeight-el.offsetHeight)/2)-sz(p,'borderTopWidth');if(x)s.left=l>0?(l+'px'):'0';if(y)s.top=t>0?(t+'px'):'0';};function sz(el,p){return parseInt($.css(el,p))||0;};})(jQuery);

productMods/js/visualization/entitycomparison/gui-event-manager.js

@@ -6,23 +6,22 @@ $(document).ready(function() {
 	 * This will set intitial values of the constants present in constants.js
 	 * */
 	initConstants();
-	
 	/* This is used to cache the current state whether the user is allowed to select more entities from 
     the datatable or not. Once Max number of entity selection is reached the user can no longer select 
     more & this variable will be set to false. */
     $("#datatable").data("isEntitySelectionAllowed", true);
     
-        $("#organizationLabel").text(organizationLabel).css("color", "#2485ae");
-        $("#organizationMoniker").text(organizationLabel);
-        $("#organizationMoniker").attr("href", organizationVIVOProfileURL);
-        
     $notificationContainer = $("#notification-container").notify();
     
     graphContainer = $("#graphContainer");
     tableDiv = $('#paginatedTable');
     
+    //temporalGraphProcessor.initiateTemporalGraphRenderProcess(graphContainer, jsonString);
+    
+});
+        
 //click event handler for clear button
-        $("a.clear-selected-entities").click(function(){
+$("a.clear-selected-entities").live('click', function(){
     clearRenderedObjects();
 }); 
 
@@ -31,7 +30,7 @@ $(document).ready(function() {
  * update the status accordingly.   
  */         
 
-        $("select.comparisonValues").change(function(){
+$("select.comparisonValues").live('change', function(){
 
     var selectedValue = $("select.comparisonValues option:selected").val();
     
@@ -86,6 +85,23 @@ $(document).ready(function() {
     }
 });
 
+
+$(".disabled-checkbox-event-receiver").live("click", function () {
+    
+    if ($(this).next().is(':disabled')) {
+
+        createNotification("warning-notification", {
+            title: 'Error',
+            text: 'A Maximum 10 entities can be compared. Please remove some & try again.'
+        }, {
+            custom: true,
+            expires: false
+        });
+
+    }
+
+});
+
 function performEntityCheckboxUnselectedActions(entity, checkboxValue, checkbox) {
     
     removeUsedColor(entity);
@@ -141,21 +157,11 @@ $(document).ready(function() {
     prepareTableForDataTablePagination(jsonData);
     setEntityLevel(getEntityVisMode(jsonData));
     
-            $(".disabled-checkbox-event-receiver").live("click", function () {
+    entityCheckboxOperatedOnEventListener();
-        
-                if ($(this).next().is(':disabled')) {
-        
-                    createNotification("warning-notification", {
-                        title: 'Error',
-                        text: 'A Maximum 10 entities can be compared. Please remove some & try again.'
-                    }, {
-                        custom: true,
-                        expires: false
-                    });
     
 }
 
-            });
+function entityCheckboxOperatedOnEventListener() {
 	
     /*
      * When the elements in the paginated div
@@ -180,9 +186,18 @@ $(document).ready(function() {
         performEntityCheckboxClickedRedrawActions();
 
     });
+	
 }
 
-        function initiateTemporalGraphRenderProcess(givenGraphContainer, jsonData) {
+function getTemporalGraphDataFromServer() {
+	
+	
+	
+}
+
+temporalGraphProcessor = {
+		
+	initiateTemporalGraphRenderProcess: function(givenGraphContainer, jsonData) {
 		
 		/*
          * initial display of the grid when the page loads 
@@ -192,7 +207,7 @@ $(document).ready(function() {
         /*
          * render the temporal graph per the sent content. 
          * */
-            loadData(jQuery.parseJSON(jsonData));
+        loadData(jsonData);
         
         /*
          * This will make sure that top 3 entities are selected by default when the page loads.
@@ -216,5 +231,4 @@ $(document).ready(function() {
 		
 	}	
 		
-        initiateTemporalGraphRenderProcess(graphContainer, jsonString);
+}
-});

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl

@@ -2,7 +2,7 @@
 
 <div id="body">
 
-        <h2><span id="header-entity-label"><a id="organizationMoniker" href="#"></a></span></h2>
+        <h2><span id="header-entity-label"><a id="organizationMoniker" href="${organizationVivoProfileURL}">${organizationLabel}</a></span></h2>
         
         <div id="leftblock">
             <div id="leftUpper">
@@ -65,7 +65,7 @@
         
         <div id="rightblock">
         
-            <h3 id="headerText">Comparing <span id="comparisonHeader">${currentParameterObject.value}</span> of <span id="entityHeader">Institutions</span> in <span id="organizationLabel"></span></h3>
+            <h3 id="headerText">Comparing <span id="comparisonHeader">${currentParameterObject.value}</span> of <span id="entityHeader">Institutions</span> in ${organizationLabel}</h3>
             
             <div id="temporal-graph">
                 <div id="yaxislabel"></div>

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonErrorCommonBody.ftl

@@ -5,6 +5,8 @@
 <#assign organizationVivoProfileURL = "${urls.base}/individual?uri=${organizationURI?url}">
 <#assign temporalGraphURL = '${urls.base}${standardVisualizationURLRoot}?vis=${otherVisType}&uri=${organizationURI}&labelField=label'>
 
+<div id="error-container">
+
 <h1 id="noPubsOrGrants-header">${organizationLabel}</h1>
 
     <h3>${textForCurrentEntityComparisonType?capitalize} Temporal Graph 
@@ -13,3 +15,5 @@
     <div id="error-body">
         <p>This organization has neither sub-organizations nor people with ${textForCurrentEntityComparisonType} in the system. Please visit the full ${organizationLabel} <a href="${organizationVivoProfileURL}">profile page</a> for a more complete overview.</p>
     </div>
+
+</div>

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl

@@ -8,17 +8,61 @@ corresponding changes in the included Templates. -->
 <#include "entityComparisonSetup.ftl">
 
 <#assign temporalGraphDownloadFileLink = '${temporalGraphDownloadCSVCommonURL}&vis=entity_grant_count'>
+<#assign temporalGraphDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=entity_grant_count&uri=${organizationURI}&vis_mode=json">
 
 <#-- variables passed from server-side code -->
 <script language="JavaScript" type="text/javascript">
+<!--
 
 /*
 This is used in util.js to print grant temporal graph links for all sub-organizations.
 */    
 var subOrganizationTemporalGraphURL = "${subOrganizationGrantTemporalGraphCommonURL}";
 
+$(document).ready(function () {
+
+    $.blockUI.defaults.overlayCSS = { 
+        backgroundColor: '#fff', 
+        opacity:         1.0 
+    };
+    
+    $.blockUI.defaults.css.width = '500px';
+    $.blockUI.defaults.css.border = '0px';
+     
+    $("div#body").block({
+        message: '<h3><img src="' + loadingImageLink + '" />&nbsp;Loading data for <i>${organizationLabel}</i></h3>'
+    });
+
+    $.ajax({
+        url: '${temporalGraphDataURL}',
+        dataType: "json",
+        success: function (data) {
+
+            if (data.error) {
+                $("#error-container").show();
+                $("#body").remove();
+            } else {
+                temporalGraphProcessor.initiateTemporalGraphRenderProcess(graphContainer, data);
+                $("#error-container").remove();
+            }
+        }
+    });
+
+    // unblock when ajax activity stops    
+    $(document).ajaxStop($("div#body").unblock());
+
+});
+
+// -->
 </script>
 
 <#assign currentParameterObject = grantParameter>
 
 <#include "entityComparisonBody.ftl">
+
+<#-- 
+Right now we include the error message by default becuae currently I could not devise any more smarted solution. By default
+the CSS of the #error-container is display:none; so it will be hidden unless explicitly commanded to be shown which we do in 
+via JavaScript.
+-->
+<#include "entityGrantComparisonError.ftl">

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl

@@ -8,17 +8,69 @@ corresponding changes in the included Templates. -->
 <#include "entityComparisonSetup.ftl">
 
 <#assign temporalGraphDownloadFileLink = '${temporalGraphDownloadCSVCommonURL}&vis=entity_comparison'>
+<#assign temporalGraphDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=entity_comparison&uri=${organizationURI}&vis_mode=json">
 
 <#-- variables passed from server-side code -->
 <script language="JavaScript" type="text/javascript">
+<!--
 
 /*
 This is used in util.js to print grant temporal graph links for all sub-organizations.
 */    
 var subOrganizationTemporalGraphURL = "${subOrganizationPublicationTemporalGraphCommonURL}";
 
+$(document).ready(function () {
+
+    $.blockUI.defaults.overlayCSS = { 
+        backgroundColor: '#fff', 
+        opacity:         1.0 
+    };
+    
+    $.blockUI.defaults.css.width = '500px';
+    $.blockUI.defaults.css.border = '0px';
+    $.blockUI.defaults.css.top = '15%';
+     
+    $("div#temporal-graph-response").block({
+        message: '<h3><img src="' + loadingImageLink + '" />&nbsp;Loading data for <i>${organizationLabel}</i></h3>'
+    });
+
+    $.ajax({
+        url: '${temporalGraphDataURL}',
+        dataType: "json",
+        success: function (data) {
+
+            if (data.error) {
+                $("#body").remove();
+                $("#error-container").show();
+                $("div#temporal-graph-response").unblock();
+                
+            } else {
+                temporalGraphProcessor.initiateTemporalGraphRenderProcess(graphContainer, data);
+                $("#error-container").remove();
+                $("div#temporal-graph-response").unblock();
+            }
+        }
+    });
+
+    // unblock when ajax activity stops    
+    //$(document).ajaxStop($("div#temporal-graph-response").unblock());
+
+});
+
+// -->
 </script>
 
 <#assign currentParameterObject = publicationParameter>
 
+<div id="temporal-graph-response">
+
 <#include "entityComparisonBody.ftl">
+
+<#-- 
+Right now we include the error message by default becuae currently I could not devise any more smarted solution. By default
+the CSS of the #error-container is display:none; so it will be hidden unless explicitly commanded to be shown which we do in 
+via JavaScript.
+-->
+<#include "entityPublicationComparisonError.ftl">
+
+</div>

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl

@@ -5,8 +5,6 @@
 <#assign dataVisualizationURLRoot ="/visualizationData">
 
 <#assign organizationURI ="${organizationURI?url}">
-<#assign jsonContent ="${jsonContent}">
-<#assign organizationLabel = "${organizationLabel}">
 <#assign organizationVivoProfileURL = "${urls.base}/individual?uri=${organizationURI}">
 
 <#assign subOrganizationVivoProfileURL = "${urls.base}/individual?">
@@ -49,6 +47,7 @@ we will use rev 293 (dev build version) of the flot & excanvas files.
 
 <#assign fliptext = 'js/visualization/entitycomparison/jquery_plugins/fliptext/jquery.mb.flipText.js'>
 <#assign jqueryNotify = 'js/jquery_plugins/jquery.notify.min.js'>
+<#assign jqueryBlockUI = 'js/jquery_plugins/jquery.blockUI.min.js'>
 <#assign jqueryUI = 'js/jquery-ui/js/jquery-ui-1.8.4.custom.min.js'>
 <#assign datatable = 'js/jquery_plugins/jquery.dataTables.min.js'>
 <#assign entityComparisonUtils = 'js/visualization/entitycomparison/util.js'>
@@ -56,9 +55,11 @@ we will use rev 293 (dev build version) of the flot & excanvas files.
 <#assign guiEventManager = 'js/visualization/entitycomparison/gui-event-manager.js'>
 
 
+
 <!--[if IE]><script type="text/javascript" src="${excanvas}"></script><![endif]-->
 ${scripts.add(flot)}
 ${scripts.add(fliptext)}
+${scripts.add(jqueryBlockUI)}
 ${scripts.add(jqueryUI)}
 ${scripts.add(datatable)}
 ${scripts.add(entityComparisonUtils)}
@@ -90,14 +91,16 @@ var contextPath = "${urls.base}";
 var temporalGraphSmallIcon = "${temporalGraphSmallIcon}";
 var subOrganizationVivoProfileURL = "${subOrganizationVivoProfileURL}";
 
-var jsonString = '${jsonContent}';
+var jsonString = '${jsonContent!}';
 var organizationLabel = '${organizationLabel}';
 var organizationVIVOProfileURL = "${organizationVivoProfileURL}";
 
-var loadingImageLink = contextPath + "/images/visualization/ajax-loader.gif";
+var loadingImageLink = contextPath + "/images/visualization/ajax-loader-indicator.gif";
 
 var entityCheckboxSelectorDOMClass = "${entityCheckboxSelectorDOMClass}";
 
+var temporalGraphProcessor;
+
 /*
 This has to be declared before making a call to GUI event manager JS.
 */
@@ -119,4 +122,4 @@ var COMPARISON_PARAMETERS_INFO = {
 
 </script>
 
-${scripts.add(guiEventManager)}
+${headScripts.add(guiEventManager)}

src/edu/cornell/mannlib/vitro/webapp/controller/visualization/freemarker/VisualizationFrameworkConstants.java

@@ -91,7 +91,6 @@ public class VisualizationFrameworkConstants {
 	public static final String DEPARTMENT_COMPARISON_VIS_MODE = "DEPARTMENT";
 	public static final String HIGHEST_LEVEL_ORGANIZATION_VIS_MODE = "HIGHEST_LEVEL_ORGANIZATION";
 
-
 	/*
 	 * These values represent possible visualizations provided as values to the "vis" url key.
 	 * */
@@ -106,4 +105,8 @@ public class VisualizationFrameworkConstants {
 	public static final String CO_PI_VIS = "coprincipalinvestigator";
 	
 	
+	/*
+	 * These values represent possible vis-modes for temporal graph vis 
+	 * */
+	public static final String TEMPORAL_GRAPH_JSON_DATA_VIS_MODE = "json";
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coauthorship/CoAuthorshipRequestHandler.java

@@ -18,8 +18,8 @@ import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
-import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoAuthorshipData;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Node;
@@ -133,17 +133,29 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
 	
 	
 
-	private String getCoauthorsListCSVContent(Map<String, Integer> coAuthorsToCount) {
+	private String getCoauthorsListCSVContent(CoAuthorshipData coAuthorshipData) {
 		
 		StringBuilder csvFileContent = new StringBuilder();
 		
-		csvFileContent.append("Year, Count\n");
+		csvFileContent.append("Co-author, Count\n");
 		
-		for (Entry<String, Integer> currentEntry : coAuthorsToCount.entrySet()) {
+		//for (Entry<String, Integer> currentEntry : coAuthorsToCount.entrySet()) {
-			csvFileContent.append(StringEscapeUtils.escapeCsv(currentEntry.getKey()));
+		for (Node currNode : coAuthorshipData.getNodes()) {			
+			
+			/*
+			 * We have already printed the Ego Node info.
+			 * */
+			if (currNode != coAuthorshipData.getEgoNode()) {
+				
+			
+			csvFileContent.append(StringEscapeUtils.escapeCsv(currNode.getNodeName()));
 			csvFileContent.append(",");
-			csvFileContent.append(currentEntry.getValue());
+			csvFileContent.append(currNode.getNumOfAuthoredWorks());
 			csvFileContent.append("\n");
+			
+			}
+			
+			
 		}
 		
 		return csvFileContent.toString();
@@ -154,7 +166,7 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
 		
 		StringBuilder csvFileContent = new StringBuilder();
 		
-		csvFileContent.append("Year, Count, Co-Author(s)\n");
+		csvFileContent.append("Year, Count, Co-author(s)\n");
 		
 		for (Entry<String, Set<Node>> currentEntry : yearToCoauthors.entrySet()) {
 			csvFileContent.append(StringEscapeUtils.escapeCsv(currentEntry.getKey()));
@@ -225,15 +237,11 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
 	private Map<String, String> prepareCoauthorsListDataResponse(CoAuthorshipData coAuthorshipData) {
 		
 		String outputFileName = "";
-		Map<String, Integer> coAuthorsToCount = new TreeMap<String, Integer>();
 
 		if (coAuthorshipData.getNodes() != null && coAuthorshipData.getNodes().size() > 0) {
 			
 			outputFileName = UtilityFunctions.slugify(coAuthorshipData.getEgoNode().getNodeName()) 
 									+ "_co-authors" + ".csv";
-	
-			coAuthorsToCount = getCoAuthorsList(coAuthorshipData);
-			
 		} else {
 			outputFileName = "no_co-authors" + ".csv";
 		}
@@ -244,29 +252,11 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
 		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
 					 "application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
-					 getCoauthorsListCSVContent(coAuthorsToCount));
+					 getCoauthorsListCSVContent(coAuthorshipData));
 
 		return fileData;
 	}
 	
-	private Map<String, Integer> getCoAuthorsList(CoAuthorshipData coAuthorsipVO) {
-		
-		Map<String, Integer> coAuthorsToCount = new TreeMap<String, Integer>();
-		
-		for (Node currNode : coAuthorsipVO.getNodes()) {
-			
-			/*
-			 * We have already printed the Ego Node info.
-			 * */
-			if (currNode != coAuthorsipVO.getEgoNode()) {
-				
-				coAuthorsToCount.put(currNode.getNodeName(), currNode.getNumOfAuthoredWorks());
-				
-			}
-		}
-		return coAuthorsToCount;
-	}
-	
 	/**
 	 * Provides a response when graphml formatted co-authorship network is requested, typically by 
 	 * the flash vis.

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIGrantCountRequestHandler.java

@@ -153,21 +153,30 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
 	}
 
 
-	private String getCoPIsListCSVContent(Map<String, Integer> coPIsToCount) {
+	private String getCoPIsListCSVContent(CoPIData coPIData) {
 		
 		StringBuilder csvFileContent = new StringBuilder();
 		
-		csvFileContent.append("Year, Count\n");
+		csvFileContent.append("Co-investigator, Count\n");
 		
-		for (Entry<String, Integer> currentEntry : coPIsToCount.entrySet()) {
+//		for (Entry<String, Integer> currentEntry : coPIData.entrySet()) {
-			csvFileContent.append(StringEscapeUtils.escapeCsv(currentEntry.getKey()));
+		for (CoPINode currNode : coPIData.getNodes()) {
+			
+			/*
+			 * We have already printed the Ego Node info.
+			 * */
+			if (currNode != coPIData.getEgoNode()) {
+			
+			csvFileContent.append(StringEscapeUtils.escapeCsv(currNode.getNodeName()));
 			csvFileContent.append(",");
-			csvFileContent.append(currentEntry.getValue());
+			csvFileContent.append(currNode.getNumberOfInvestigatedGrants());
 			csvFileContent.append("\n");
+			
+			}
+			
 		}
 		
 		return csvFileContent.toString();
-			
 	}	
 	
 
@@ -175,7 +184,7 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
 
 		StringBuilder csvFileContent = new StringBuilder();
 		
-		csvFileContent.append("Year, Count, Co-PI(s)\n");
+		csvFileContent.append("Year, Count, Co-investigator(s)\n");
 
 		for (Map.Entry<String, Set<CoPINode>> currentEntry : yearToCoPI.entrySet()) {
 			
@@ -247,15 +256,12 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
 	private Map<String, String> prepareCoPIsListDataResponse(CoPIData coPIData) {
 		
 		String outputFileName = "";
-		Map<String, Integer> coPIsToCount = new TreeMap<String, Integer>();
 		
 		if (coPIData.getNodes() != null && coPIData.getNodes().size() > 0) {
 			
 			outputFileName = UtilityFunctions.slugify(coPIData.getEgoNode().getNodeName()) 
 									+ "_co-investigators" + ".csv";
 	
-			coPIsToCount = getCoPIsList(coPIData);
-			
 		} else {
 			outputFileName = "no_co-investigators" + ".csv";
 		}
@@ -266,7 +272,7 @@ public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler
 		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
 					 "application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
-					 getCoPIsListCSVContent(coPIsToCount));
+					 getCoPIsListCSVContent(coPIData));
 
 		return fileData;
 	}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityComparisonUtilityFunctions.java

@@ -5,14 +5,21 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Set;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 
+import com.hp.hpl.jena.iri.IRI;
+import com.hp.hpl.jena.iri.IRIFactory;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.beans.Individual;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.GenericQueryMap;
@@ -107,4 +114,47 @@ public class EntityComparisonUtilityFunctions {
 		return subOrganizationTypesResult;
 	}
 
+	public static String getEntityLabelFromDAO(VitroRequest vitroRequest,
+			String entityURI) {
+		
+		IndividualDao iDao = vitroRequest.getWebappDaoFactory().getIndividualDao();
+        Individual ind = iDao.getIndividualByURI(entityURI);
+        
+        String organizationLabel = "Unknown Organization"; 
+        
+        if (ind != null) {
+        	organizationLabel = ind.getName();
+        }
+		return organizationLabel;
+	}
+	
+	public static String getStaffProvidedOrComputedHighestLevelOrganization(Log log,
+			Dataset Dataset)
+			throws MalformedQueryParametersException {
+		
+		String finalHighestLevelOrganizationURI = "";
+		
+		String staffProvidedHighestLevelOrganization = ConfigurationProperties.getProperty("visualization.topLevelOrg");
+		
+		/*
+		 * First checking if the staff has provided highest level organization in deploy.properties
+		 * if so use to temporal graph vis.
+		 */
+		if (StringUtils.isNotBlank(staffProvidedHighestLevelOrganization)) {
+			
+			/*
+			 * To test for the validity of the URI submitted.
+			 */
+			IRIFactory iRIFactory = IRIFactory.jenaImplementation();
+			IRI iri = iRIFactory.create(staffProvidedHighestLevelOrganization);
+		    
+			if (iri.hasViolation(false)) {
+				finalHighestLevelOrganizationURI = EntityComparisonUtilityFunctions.getHighestLevelOrganizationURI(log, Dataset);
+		    } else {
+		    	finalHighestLevelOrganizationURI = staffProvidedHighestLevelOrganization;
+		    }
+		}
+		return finalHighestLevelOrganizationURI;
+	}
+	
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityPublicationCountConstructQueryRunner.java

@@ -67,10 +67,7 @@ public class EntityPublicationCountConstructQueryRunner {
 			+	"?Person rdfs:label ?PersonLabel . "
 			+	"?Resource core:linkedInformationResource ?Document . " 
 			+	"?Document rdf:type bibo:Document . "
-			+	"?Document rdfs:label ?DocumentLabel . "
+			+	"?Document rdfs:label ?DocumentLabel "
-			+   "?Document core:dateTimeValue ?dateTimeValue . "
-			+   "?dateTimeValue core:dateTime ?publicationDate . "
-			+   "?Document core:year ?publicationYearUsing_1_1_property "
 			+"}"
 			+ "WHERE { "
 			+	"<"+queryURI+ "> core:hasSubOrganization ?subOrganization . "
@@ -80,18 +77,8 @@ public class EntityPublicationCountConstructQueryRunner {
 			+	"?Person  core:authorInAuthorship ?Resource . "
 			+	"?Person rdfs:label ?PersonLabel . "
 			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Document rdf:type bibo:Document . "
+			+	"?Document rdf:type bibo:Document . "
 			+	"?Document rdfs:label ?DocumentLabel "		
-			
-            +   "{"
-            +   "?Document core:dateTimeValue ?dateTimeValue . "
-            +   "?dateTimeValue core:dateTime ?publicationDate "
-            +   "}"
-            +   "UNION "
-            +   "{"
-            +   "?Document core:year ?publicationYearUsing_1_1_property "
-            +   "}"
-            
 			+ "}" ;
 					
 		
@@ -110,10 +97,7 @@ public class EntityPublicationCountConstructQueryRunner {
 			+	"?Person rdfs:label ?PersonLabel . "
 			+	"?Resource core:linkedInformationResource ?Document . " 
 			+	"?Document rdf:type bibo:Document . "
-			+	"?Document rdfs:label ?DocumentLabel . "
+			+	"?Document rdfs:label ?DocumentLabel "
-            +   "?Document core:dateTimeValue ?dateTimeValue . "
-            +   "?dateTimeValue core:dateTime ?publicationDate . "
-            +   "?Document core:year ?publicationYearUsing_1_1_property ."
 			+"}"
 			+ "WHERE { "
 			+	"<"+queryURI+ "> core:organizationForPosition ?Position . "
@@ -121,9 +105,37 @@ public class EntityPublicationCountConstructQueryRunner {
 			+	"?Person  core:authorInAuthorship ?Resource . "
 			+	"?Person rdfs:label ?PersonLabel . "
 			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Document rdf:type bibo:Document . "
+			+	"?Document rdf:type bibo:Document . "
 			+	"?Document rdfs:label ?DocumentLabel "		
+			+ "}" ;
 					
+		
+		return sparqlQuery;
+	
+	}
+	
+	private String generateConstructQueryForDocumentDateTimeValueOneLevelDeep(String queryURI){
+		
+		String sparqlQuery = 			 
+		
+			"CONSTRUCT { "
+			+	"<"+queryURI+ "> core:hasSubOrganization ?subOrganization . "
+			+ 	"?subOrganization core:organizationForPosition ?Position . "
+			+   "?Position core:positionForPerson ?Person . "
+			+	"?Person  core:authorInAuthorship ?Resource . "
+			+	"?Resource core:linkedInformationResource ?Document . " 
+			+	"?Document rdf:type bibo:Document . "
+			+	"?Document core:dateTimeValue ?dateTimeValue . "
+			+	"?dateTimeValue core:dateTime ?publicationDate . "
+			+	"?Document core:year ?publicationYearUsing_1_1_property "
+			+"}"
+			+ "WHERE { "
+			+	"<"+queryURI+ "> core:hasSubOrganization ?subOrganization . "
+			+ 	"?subOrganization core:organizationForPosition ?Position . "
+			+   "?Position core:positionForPerson ?Person . "
+			+	"?Person  core:authorInAuthorship ?Resource . "
+			+	"?Resource core:linkedInformationResource ?Document . " 
+			+	"?Document rdf:type bibo:Document . "
 			+	"{"
 				+	"?Document core:dateTimeValue ?dateTimeValue . "
 				+	"?dateTimeValue core:dateTime ?publicationDate "
@@ -132,7 +144,6 @@ public class EntityPublicationCountConstructQueryRunner {
 			+	"{"
 				+	"?Document core:year ?publicationYearUsing_1_1_property "
 			+	"}"
-
 			+ "}" ;
 					
 		
@@ -140,90 +151,56 @@ public class EntityPublicationCountConstructQueryRunner {
 	
 	}	
 	
-//	private String generateConstructQueryForDocumentDateTimeValueOneLevelDeep(String queryURI){
+	private String generateConstructQueryForDocumentDateTimeValue(String queryURI){
-//		
-//		String sparqlQuery = 			 
-//		
-//			"CONSTRUCT { "
-//			+	"<"+queryURI+ "> core:hasSubOrganization ?subOrganization . "
-//			+ 	"?subOrganization core:organizationForPosition ?Position . "
-//			+   "?Position core:positionForPerson ?Person . "
-//			+	"?Person  core:authorInAuthorship ?Resource . "
-//			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Document rdf:type bibo:Document . "
-//			+	"?Document core:dateTimeValue ?dateTimeValue . "
-//			+	"?dateTimeValue core:dateTime ?publicationDate . "
-//			+	"?Document core:year ?publicationYearUsing_1_1_property "
-//			+"}"
-//			+ "WHERE { "
-//			+	"<"+queryURI+ "> core:hasSubOrganization ?subOrganization . "
-//			+ 	"?subOrganization core:organizationForPosition ?Position . "
-//			+   "?Position core:positionForPerson ?Person . "
-//			+	"?Person  core:authorInAuthorship ?Resource . "
-//			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Document rdf:type bibo:Document . "
-//			+	"{"
-//				+	"?Document core:dateTimeValue ?dateTimeValue . "
-//				+	"?dateTimeValue core:dateTime ?publicationDate "
-//			+	"}"
-//			+	"UNION "
-//			+	"{"
-//				+	"?Document core:year ?publicationYearUsing_1_1_property "
-//			+	"}"
-//			+ "}" ;
-//					
-//		
-//		return sparqlQuery;
-//	
-//	}	
 		
-//	private String generateConstructQueryForDocumentDateTimeValue(String queryURI){
+		String sparqlQuery = 			 
-//		
+		
-//		String sparqlQuery = 			 
+			"CONSTRUCT { "
-//		
+			+	"<"+queryURI+ "> core:organizationForPosition ?Position . "
-//			"CONSTRUCT { "
+			+   "?Position core:positionForPerson ?Person . "
-//			+	"<"+queryURI+ "> core:organizationForPosition ?Position . "
+			+	"?Person  core:authorInAuthorship ?Resource . "
-//			+   "?Position core:positionForPerson ?Person . "
+			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Person  core:authorInAuthorship ?Resource . "
+			+	"?Document rdf:type bibo:Document . "
-//			+	"?Resource core:linkedInformationResource ?Document . " 
+			+	"?Document core:dateTimeValue ?dateTimeValue . "
-//			+	"?Document rdf:type bibo:Document . "
+			+	"?dateTimeValue core:dateTime ?publicationDate . "
-//			+	"?Document core:dateTimeValue ?dateTimeValue . "
+			+	"?Document core:year ?publicationYearUsing_1_1_property "
-//			+	"?dateTimeValue core:dateTime ?publicationDate . "
+			+"}"
-//			+	"?Document core:year ?publicationYearUsing_1_1_property "
+			+ "WHERE { "
-//			+"}"
+			+	"<"+queryURI+ "> core:organizationForPosition ?Position . "
-//			+ "WHERE { "
+			+   "?Position core:positionForPerson ?Person . "
-//			+	"<"+queryURI+ "> core:organizationForPosition ?Position . "
+			+	"?Person  core:authorInAuthorship ?Resource . "
-//			+   "?Position core:positionForPerson ?Person . "
+			+	"?Resource core:linkedInformationResource ?Document . " 
-//			+	"?Person  core:authorInAuthorship ?Resource . "
+			+	"?Document rdf:type bibo:Document . "
-//			+	"?Resource core:linkedInformationResource ?Document . " 
+			+	"{"
-//			+	"?Document rdf:type bibo:Document . "
+				+	"?Document core:dateTimeValue ?dateTimeValue . "
-//			+	"{"
+				+	"?dateTimeValue core:dateTime ?publicationDate "
-//				+	"?Document core:dateTimeValue ?dateTimeValue . "
+			+	"}"
-//				+	"?dateTimeValue core:dateTime ?publicationDate "
+			+	"UNION "
-//			+	"}"
+			+	"{"
-//			+	"UNION "
+				+	"?Document core:year ?publicationYearUsing_1_1_property "
-//			+	"{"
+			+	"}"
-//				+	"?Document core:year ?publicationYearUsing_1_1_property "
+			+ "}" ;
-//			+	"}"
+					
-//			+ "}" ;
+		
-//					
+		return sparqlQuery;
-//		
+	
-//		return sparqlQuery;
+	}		
-//	
-//	}		
 	
 	private Model executeQuery(Set<String> constructQueries, Dataset Dataset) {
 		
         Model constructedModel = ModelFactory.createDefaultModel();
         
-        for (String queryString : constructQueries) {
         before = System.currentTimeMillis();
+
+        for (String queryString : constructQueries) {
+            
         	log.debug("CONSTRUCT query string : " + queryString);
             
         	Query query = null;
         	
         	try{
         		query = QueryFactory.create(QueryConstants.getSparqlPrefixQuery() + queryString, SYNTAX);
+        		//log.info("query: "+ queryString);
         	}catch(Throwable th){
                 log.error("Could not create CONSTRUCT SPARQL query for query " +
                         "string. " + th.getMessage());
@@ -232,16 +209,16 @@ public class EntityPublicationCountConstructQueryRunner {
         	
             QueryExecution qe = QueryExecutionFactory.create(
                     query, Dataset);
-            
             try {
                 qe.execConstruct(constructedModel);
             } finally {
                 qe.close();
             }
         	
-            after = System.currentTimeMillis();
-            log.debug("Time taken to execute the CONSTRUCT queries is in milliseconds: " + (after - before) );
         }	
+
+        after = System.currentTimeMillis();
+        log.info("Time taken to execute the CONSTRUCT queries is in milliseconds: " + (after - before) );        
        // constructedModel.write(System.out);
         return constructedModel;
 	}	
@@ -281,8 +258,8 @@ public class EntityPublicationCountConstructQueryRunner {
 		constructQueries.add(generateConstructQueryForOrganizationLabel(this.egoURI));
 		constructQueries.add(generateConstructQueryForSubOrganizations(this.egoURI));
 		constructQueries.add(generateConstructQueryForPersons(this.egoURI));
-//		constructQueries.add(generateConstructQueryForDocumentDateTimeValueOneLevelDeep(this.egoURI));
+		constructQueries.add(generateConstructQueryForDocumentDateTimeValueOneLevelDeep(this.egoURI));
-//		constructQueries.add(generateConstructQueryForDocumentDateTimeValue(this.egoURI));
+		constructQueries.add(generateConstructQueryForDocumentDateTimeValue(this.egoURI));
 		
 	}	
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityPublicationCountRequestHandler.java

@@ -17,20 +17,16 @@ import org.apache.commons.logging.LogFactory;
 import com.google.gson.Gson;
 import com.hp.hpl.jena.iri.IRI;
 import com.hp.hpl.jena.iri.IRIFactory;
-import com.hp.hpl.jena.iri.Violation;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.Model;
 
-
 import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
@@ -40,6 +36,10 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.QueryR
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
 
+/**
+ * @author cdtank
+ *
+ */
 public class EntityPublicationCountRequestHandler implements
 		VisualizationRequestHandler {
 	
@@ -53,49 +53,15 @@ public class EntityPublicationCountRequestHandler implements
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
-		if (StringUtils.isNotBlank(entityURI)){
+		if (StringUtils.isBlank(entityURI)){
 			
-			return getSubjectEntityAndGenerateResponse(vitroRequest, log,
+			entityURI = EntityComparisonUtilityFunctions
-					Dataset, entityURI);
+								.getStaffProvidedOrComputedHighestLevelOrganization(log, Dataset);
-		} else {
-			
-			String staffProvidedHighestLevelOrganization = ConfigurationProperties.getProperty("visualization.topLevelOrg");
-			
-			/*
-			 * First checking if the staff has provided highest level organization in deploy.properties
-			 * if so use to temporal graph vis.
-			 */
-			if (StringUtils.isNotBlank(staffProvidedHighestLevelOrganization)) {
-				
-				/*
-	        	 * To test for the validity of the URI submitted.
-	        	 */
-	        	IRIFactory iRIFactory = IRIFactory.jenaImplementation();
-	    		IRI iri = iRIFactory.create(staffProvidedHighestLevelOrganization);
-	            
-	    		if (iri.hasViolation(false)) {
-	            	
-	                String errorMsg = ((Violation) iri.violations(false).next()).getShortMessage();
-	                log.error("Highest Level Organization URI provided is invalid " + errorMsg);
-	                
-	            } else {
-	            	
-	    			return getSubjectEntityAndGenerateResponse(vitroRequest,
-							log, Dataset,
-							staffProvidedHighestLevelOrganization);
 		}
+		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
 	}
 
-			String highestLevelOrgURI = EntityComparisonUtilityFunctions.getHighestLevelOrganizationURI(log,
+	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
-					Dataset);
-			
-			return getSubjectEntityAndGenerateResponse(vitroRequest, log,
-					Dataset, highestLevelOrgURI);
-		}
-	
-	}
-	
-	private ResponseValues getSubjectEntityAndGenerateResponse(
 			VitroRequest vitroRequest, Log log, Dataset Dataset,
 			String subjectEntityURI)
 			throws MalformedQueryParametersException {
@@ -106,24 +72,32 @@ public class EntityPublicationCountRequestHandler implements
 		QueryRunner<Entity> queryManager = new EntityPublicationCountQueryRunner(
 				subjectEntityURI, constructedModel, log);
 		
-		
 		Entity entity = queryManager.getQueryResult();
 		
-		
 		if (entity.getEntityLabel().equals("no-label")) {
 			
-			return prepareStandaloneErrorResponse(vitroRequest, subjectEntityURI);
+			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
 			
 		} else {	
 		
-			return getSubEntityTypesAndRenderStandaloneResponse(
+			return getSubEntityTypesAndComputeDataResponse(
 					vitroRequest, log, Dataset,
 					subjectEntityURI, entity);
 		}
 	}
 	
+	private Map<String, String> prepareStandaloneDataErrorResponse(
+			VitroRequest vitroRequest, String subjectEntityURI) {
 
-	private ResponseValues getSubEntityTypesAndRenderStandaloneResponse(
+		Map<String, String> fileData = new HashMap<String, String>();
+		
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, "{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
+		return fileData;
+	}
+
+	private Map<String, String> getSubEntityTypesAndComputeDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset Dataset,
 			String subjectEntityURI, Entity entity)
 			throws MalformedQueryParametersException {
@@ -131,11 +105,10 @@ public class EntityPublicationCountRequestHandler implements
 		Map<String, Set<String>> subOrganizationTypesResult = EntityComparisonUtilityFunctions.getSubEntityTypes(
 				log, Dataset, subjectEntityURI);
 		
-		return prepareStandaloneResponse(vitroRequest, entity, subjectEntityURI,
+		return prepareStandaloneDataResponse(vitroRequest, entity, entity.getSubEntities(),
 				subOrganizationTypesResult);
 	}
 
-
 	@Override
 	public Map<String, String> generateDataVisualization(
 			VitroRequest vitroRequest, Log log, Dataset Dataset)
@@ -144,6 +117,36 @@ public class EntityPublicationCountRequestHandler implements
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
+		/*
+		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
+		 * */
+		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+					.equalsIgnoreCase(vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
+			
+			if (StringUtils.isNotBlank(entityURI)){
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								Dataset, 
+								entityURI);
+			} else {
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								Dataset,
+								EntityComparisonUtilityFunctions
+										.getStaffProvidedOrComputedHighestLevelOrganization(
+												log,
+												Dataset));
+			}
+			
+		} else {
+			/*
+			 * This provides csv download files for the content in the tables.
+			 * */
+			
 			EntityPublicationCountConstructQueryRunner constructQueryRunner = new EntityPublicationCountConstructQueryRunner(entityURI, Dataset, log);
 			Model constructedModel = constructQueryRunner.getConstructedModel();
 			
@@ -159,6 +162,8 @@ public class EntityPublicationCountRequestHandler implements
 			
 		}
 		
+	}
+	
 	
 	@Override
 	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
@@ -201,39 +206,47 @@ public class EntityPublicationCountRequestHandler implements
 		return fileData;
 	}
 	
-	/**
+	private Map<String, String> prepareStandaloneDataResponse(
-	 * 
+										VitroRequest vitroRequest, 
-	 * @param vreq
+										Entity entity, 
-	 * @param valueObjectContainer
+										Set<SubEntity> subentities,
-	 * @return
+										Map<String, Set<String>> subOrganizationTypesResult) {
-	 */
+
-	private TemplateResponseValues prepareStandaloneResponse(VitroRequest vreq,
+		Map<String, String> fileData = new HashMap<String, String>();
-			Entity entity, String entityURI, Map<String, Set<String>> subOrganizationTypesResult) {
+		
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+				writePublicationsOverTimeJSON(vitroRequest, entity.getSubEntities(), subOrganizationTypesResult));
+		return fileData;
+	}
+	
+	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
+																   String entityURI) {
 
         Portal portal = vreq.getPortal();
         String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
 		
-        String jsonContent = "";
+        String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vreq,
-		jsonContent = writePublicationsOverTimeJSON(vreq, entity.getSubEntities(), subOrganizationTypesResult);
+																						  entityURI);
-
-		String title = "";
-		
-		if (StringUtils.isNotBlank(entity.getEntityLabel())) {
-			title = entity.getEntityLabel() + " - ";
-		}
         
         Map<String, Object> body = new HashMap<String, Object>();
         body.put("portalBean", portal);
-        body.put("title", title + "Temporal Graph Visualization");
+        body.put("title", organizationLabel + " - Temporal Graph Visualization");
         body.put("organizationURI", entityURI);
-        body.put("organizationLabel", entity.getEntityLabel());
+        body.put("organizationLabel", organizationLabel);
-        body.put("jsonContent", jsonContent);
         
         return new TemplateResponseValues(standaloneTemplate, body);
-        
 	}
 
 	
+	/**
+	 * @deprecated This method should not be called anymore although the templates being 
+	 * called by this method are still in use, so we should not get rid of it.
+	 * @param vitroRequest
+	 * @param entityURI
+	 * @return
+	 */
 	private ResponseValues prepareStandaloneErrorResponse(
 			VitroRequest vitroRequest, String entityURI) {
 		
@@ -241,14 +254,8 @@ public class EntityPublicationCountRequestHandler implements
         String standaloneTemplate = "entityPublicationComparisonError.ftl";
         Map<String, Object> body = new HashMap<String, Object>();
         
-        IndividualDao iDao = vitroRequest.getWebappDaoFactory().getIndividualDao();
+        String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vitroRequest,
-        Individual ind = iDao.getIndividualByURI(entityURI);
+				entityURI);
-        
-        String organizationLabel = "Unknown Organization"; 
-        
-        if (ind != null) {
-        	organizationLabel = ind.getName();
-        }
         
         body.put("organizationLabel", organizationLabel);
         body.put("portalBean", portal);
@@ -259,7 +266,6 @@ public class EntityPublicationCountRequestHandler implements
 
 	}
 
-	
 	/**
 	 * function to generate a json file for year <-> publication count mapping
 	 * @param vreq 
@@ -302,7 +308,7 @@ public class EntityPublicationCountRequestHandler implements
 			
 			entityJson.setEntityURI(subentity.getIndividualURI());
 			
-			boolean isPerson = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subentity.getIndividualURI()).isVClass("http://xmlns.com/foaf/0.1/Person");
+			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity);
 			
 			if(isPerson){
 				entityJson.setVisMode("PERSON");

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitygrantcount/EntityGrantCountRequestHandler.java

@@ -15,21 +15,15 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.google.gson.Gson;
-import com.hp.hpl.jena.iri.IRI;
-import com.hp.hpl.jena.iri.IRIFactory;
-import com.hp.hpl.jena.iri.Violation;
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.rdf.model.Model;
 
-import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.entitycomparison.EntityComparisonUtilityFunctions;
@@ -54,48 +48,13 @@ public class EntityGrantCountRequestHandler implements
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
-		if (StringUtils.isNotBlank(entityURI)){
+		if (StringUtils.isBlank(entityURI)){
 			
-			return getSubjectEntityAndGenerateResponse(vitroRequest, log,
+			entityURI = EntityComparisonUtilityFunctions
-					Dataset, entityURI);
+								.getStaffProvidedOrComputedHighestLevelOrganization(log, Dataset);
 			
-		} else {
-			
-			String staffProvidedHighestLevelOrganization = ConfigurationProperties.getProperty("visualization.topLevelOrg");
-			
-			/*
-			 * First checking if the staff has provided highest level organization in deploy.properties
-			 * if so use to temporal graph vis.
-			 */
-			if (StringUtils.isNotBlank(staffProvidedHighestLevelOrganization)) {
-				
-				/*
-	        	 * To test for the validity of the URI submitted.
-	        	 */
-	        	IRIFactory iRIFactory = IRIFactory.jenaImplementation();
-	    		IRI iri = iRIFactory.create(staffProvidedHighestLevelOrganization);
-	            
-	    		if (iri.hasViolation(false)) {
-	            	
-	                String errorMsg = ((Violation) iri.violations(false).next()).getShortMessage();
-	                log.error("Highest Level Organization URI provided is invalid " + errorMsg);
-	                
-	            } else {
-	            	
-	    			return getSubjectEntityAndGenerateResponse(vitroRequest,
-							log, Dataset,
-							staffProvidedHighestLevelOrganization);
 		}
-			}
+		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
-			
-			String highestLevelOrgURI = EntityComparisonUtilityFunctions.getHighestLevelOrganizationURI(log,
-					Dataset);
-			
-			return getSubjectEntityAndGenerateResponse(vitroRequest, log,
-					Dataset, highestLevelOrgURI);
-		}
-		
-		
 	}
 
 	@Override
@@ -106,6 +65,36 @@ public class EntityGrantCountRequestHandler implements
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
+		/*
+		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
+		 * */
+		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+					.equalsIgnoreCase(vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
+			
+			if (StringUtils.isNotBlank(entityURI)){
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								Dataset, 
+								entityURI);
+			} else {
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								Dataset,
+								EntityComparisonUtilityFunctions
+										.getStaffProvidedOrComputedHighestLevelOrganization(
+												log,
+												Dataset));
+			}
+			
+		} else {
+			/*
+			 * This provides csv download files for the content in the tables.
+			 * */		
+
 		EntityGrantCountConstructQueryRunner constructQueryRunner = new EntityGrantCountConstructQueryRunner(entityURI, Dataset, log);
 		Model constructedModel = constructQueryRunner.getConstructedModel();
 		
@@ -122,13 +111,15 @@ public class EntityGrantCountRequestHandler implements
 		
 		}
 
+	}
+	
 	@Override
 	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
 			Dataset Dataset) throws MalformedQueryParametersException {
 		throw new UnsupportedOperationException("Entity Grant Count does not provide Ajax Response.");
 	}
 	
-	private ResponseValues getSubjectEntityAndGenerateResponse(
+	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset Dataset,
 			String subjectEntityURI)
 			throws MalformedQueryParametersException {
@@ -142,18 +133,16 @@ public class EntityGrantCountRequestHandler implements
 		Entity entity = queryManager.getQueryResult();
 		
 		if (entity.getEntityLabel().equals("no-label")) {
-			
+			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
-			return prepareStandaloneErrorResponse(vitroRequest, subjectEntityURI);
-			
 		} else {	
 		
-			return getSubEntityTypesAndRenderStandaloneResponse(
+			return getSubEntityTypesAndComputeDataResponse(
 					vitroRequest, log, Dataset,
 					subjectEntityURI, entity);
 		}
 	}
 
-	private ResponseValues getSubEntityTypesAndRenderStandaloneResponse(
+	private Map<String, String> getSubEntityTypesAndComputeDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset Dataset,
 			String subjectOrganization, Entity entity)
 			throws MalformedQueryParametersException {
@@ -161,8 +150,34 @@ public class EntityGrantCountRequestHandler implements
 		Map<String, Set<String>> subOrganizationTypesResult = EntityComparisonUtilityFunctions.getSubEntityTypes(
 				log, Dataset, subjectOrganization);
 		
-		return prepareStandaloneResponse(vitroRequest, entity, subjectOrganization,
+		return prepareStandaloneDataResponse(vitroRequest, entity, subOrganizationTypesResult);
-				subOrganizationTypesResult);
+	}
+	
+	
+	private Map<String, String> prepareStandaloneDataErrorResponse(
+			VitroRequest vitroRequest, String subjectEntityURI) {
+
+		Map<String, String> fileData = new HashMap<String, String>();
+		
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, "{\"error\" : \"No Grants for this Organization found in VIVO.\"}");
+		return fileData;
+	}
+	
+	
+	private Map<String, String> prepareStandaloneDataResponse(
+										VitroRequest vitroRequest, 
+										Entity entity,
+										Map<String, Set<String>> subOrganizationTypesResult) {
+
+		Map<String, String> fileData = new HashMap<String, String>();
+		
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+				writeGrantsOverTimeJSON(vitroRequest, entity.getSubEntities(), subOrganizationTypesResult));
+		return fileData;
 	}
 
 	/**
@@ -200,39 +215,30 @@ public class EntityGrantCountRequestHandler implements
 		return fileData;
 	}
 	
-	/**
+
-	 * 
+	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
-	 * @param vreq
+			   String entityURI) {
-	 * @param valueObjectContainer
-	 * @return
-	 */
-	private TemplateResponseValues prepareStandaloneResponse(VitroRequest vreq,
-			Entity entity, String entityURI, Map<String, Set<String>> subOrganizationTypesResult) {
 
 		Portal portal = vreq.getPortal();
 		String standaloneTemplate = "entityComparisonOnGrantsStandalone.ftl";
 		
-        String jsonContent = "";
+		String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vreq,
-		jsonContent = writeGrantsOverTimeJSON(vreq, entity.getSubEntities(), subOrganizationTypesResult);
+											  entityURI);
-
-		String title = "";
-		
-		if (StringUtils.isNotBlank(entity.getEntityLabel())) {
-			title = entity.getEntityLabel() + " - ";
-		}
-
 		
 		Map<String, Object> body = new HashMap<String, Object>();
 		body.put("portalBean", portal);
-        body.put("title", title + "Temporal Graph Visualization");
+		body.put("title", organizationLabel + " - Temporal Graph Visualization");
 		body.put("organizationURI", entityURI);
-        body.put("organizationLabel", entity.getEntityLabel());
+		body.put("organizationLabel", organizationLabel);
-        body.put("jsonContent", jsonContent);
 		
 		return new TemplateResponseValues(standaloneTemplate, body);
-        
 	}
 	
+	/**
+	 * @deprecated This method should not be called anymore although the templates being 
+	 * called by this method are still in use, so we should not get rid of it.
+	 * @return
+	 */
 	private ResponseValues prepareStandaloneErrorResponse(
 			VitroRequest vitroRequest, String entityURI) {
 		
@@ -240,14 +246,8 @@ public class EntityGrantCountRequestHandler implements
         String standaloneTemplate = "entityGrantComparisonError.ftl";
         Map<String, Object> body = new HashMap<String, Object>();
         
-        IndividualDao iDao = vitroRequest.getWebappDaoFactory().getIndividualDao();
+        String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vitroRequest,
-        Individual ind = iDao.getIndividualByURI(entityURI);
+				entityURI);
-        
-        String organizationLabel = "Unknown Organization"; 
-        
-        if (ind != null) {
-        	organizationLabel = ind.getName();
-        }
         
         body.put("organizationLabel", organizationLabel);
         
@@ -300,7 +300,7 @@ public class EntityGrantCountRequestHandler implements
 
 			entityJson.setEntityURI(subentity.getIndividualURI());
 			
-			boolean isPerson = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subentity.getIndividualURI()).isVClass("http://xmlns.com/foaf/0.1/Person");
+			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity);
 			
 			if(isPerson){
 				entityJson.setVisMode("PERSON");

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/visutils/UtilityFunctions.java

@@ -35,6 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Co
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPINode;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Grant;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Node;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
 
 public class UtilityFunctions {
 	
@@ -321,4 +322,8 @@ public class UtilityFunctions {
 		return collaboratorshipNetworkURL != null ? collaboratorshipNetworkURL : "" ;
 	}
 	
+	public static boolean isEntityAPerson(VitroRequest vreq, SubEntity subentity) {
+		return vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subentity.getIndividualURI()).isVClass("http://xmlns.com/foaf/0.1/Person");
+	}
+
 }