1. Added dynamic reload of data instead of page refresh, for temporal graph vis.

2. Added link-textbox for viz of each parameter form the dropdown box in temporal vis.
3. Made sure that the choices are preserved when another option is selected from the dropdown box.
4. Refactor of some legacy front-end code for temporal vis.
5. Added legend for bars drawn below the graph.
6. Formatted the last cached at date time.

productMods/css/visualization/entitycomparison/layout.css

@@ -20,6 +20,55 @@
 .easy-deselect-label a.temporal-vis-url {
     float: right;
 }
+
+.known-bar {
+	display: inline-block;
+	cursor: help;
+}
+
+.unknown-inner-bar {
+	opacity: 0.5;
+	filter:alpha(opacity=50);
+	display: inline-block;
+}
+
+.bar-count-text {
+    padding-right: 3px;
+    vertical-align: super;
+}
+
+img.bar-count-icon {
+	vertical-align: super;
+	cursor: help;
+}
+
+.unknown-bar {
+	background: url("../../../images/visualization/diagonal.png") repeat scroll 50% 50% #666666;
+	cursor: help;
+}
+
+.legend-bar {
+	margin-bottom: 3px;
+}
+
+.unknown-legend-bar {
+	background: url("../../../images/visualization/legend-unknown-bar-dark.png") repeat #B7B7B7;
+}
+
+
+#legend-known-bar-text,
+#legend-unknown-bar-text {
+	font-size: 0.75em;
+}
+
+span#copy-vis-viewlink {
+	display: none;
+}
+
+img#copy-vis-viewlink-icon {
+	cursor: pointer;
+}
+
 a.temporalGraphLinks {
     background-color: #2485AE;
     color: white;

productMods/js/visualization/entitycomparison/constants.js

@@ -37,8 +37,8 @@ var globalDateObject;
 var year;
 
 var colors, prevColor, colorToAssign, 
-	colorToRemove, renderedObjects, labelToEntityRecord,
+	colorToRemove, renderedObjects, URIToEntityRecord,
-	setOfLabels, labelToCheckedEntities, stopWordsToCount;
+	setOfLabels, URIToCheckedEntities, stopWordsToCount;
 
 var graphContainer;
 var tableDiv;
@@ -66,9 +66,9 @@ function initConstants() {
 	prevColor = {};
 	colorToAssign, colorToRemove;
 	renderedObjects = [];
-	labelToEntityRecord = {};
+	URIToEntityRecord = {};
 	setOfLabels = [];
-	labelToCheckedEntities = {};
+	URIToCheckedEntities = {};
 	stopWordsToCount = {};
 	lastCachedAtDateTimes = [];
 	//options for Flot
@@ -100,7 +100,5 @@ function initConstants() {
 				borderColor : "#D9D9D9"
 			}
 	};
-
 	FlotOptions.colors = colorConstantQueue;
-	
 }

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

@@ -3,9 +3,10 @@
 $(document).ready(function() {
 
 	/*
-	 * This will set intitial values of the constants present in constants.js
+	 * This will set initial 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. */
@@ -27,34 +28,45 @@ $(document).ready(function() {
 
         var selectedValue = $("select.comparisonValues option:selected").val();
         
-        var selectedParameter;
+        var selectedDataURL;
         
         $.each(COMPARISON_PARAMETERS_INFO, function(index, parameter) {
         	
             if (parameter.value === selectedValue) {
-            	selectedParameter = parameter;
+            	
-                window.location = parameter.viewLink;
+            	currentParameter = parameter.name;
+            	selectedDataURL = parameter.dataLink;
             }
         	
         });
         
-        //$("#body").empty().html("<div id='loading-comparisons'>Loading " + selectedValue + "&nbsp;&nbsp;<img src='" + loadingImageLink + "' /></div>");
+        options = {
+    			responseContainer: $("div#temporal-graph-response"),
+    			bodyContainer: $("#body"),
+    			errorContainer: $("#error-container"),
+    			dataURL: selectedDataURL	
+    		};
     	
-        /*
+    	setupLoadingScreen(options.responseContainer);
-         * This piece of code is not executed at all because the redirect happens before there is a chance 
-         * to render the below contents.
-         * */
     		
-        /*
+    	$.ajax({
-        
+            url: options.dataURL,
-        $("#comparisonParameter").text("Total Number of " + selectedValue);
+            dataType: "json",
-        $('#yaxislabel').html("Number of " + selectedValue).mbFlipText(false);
+            timeout: 5 * 60 * 1000,
-        $('#yaxislabel').css("color", "#595B5B");
+            success: function (data) {
-        $('#comparisonHeader').html(selectedValue).css('font-weight', 'bold');
-        
-        
-        */
     		
+                if (data.error) {
+                	options.bodyContainer.remove();
+                	options.errorContainer.show();
+                	options.responseContainer.unblock();
+                } else {
+                	options.bodyContainer.show();
+                	options.errorContainer.remove();
+                    temporalGraphProcessor.redoTemporalGraphRenderProcess(graphContainer, data);
+                    options.responseContainer.unblock();
+                }
+            }
+        });
     });
     
 });
@@ -68,8 +80,9 @@ $("input[type=checkbox].easyDeselectCheckbox").live('click', function(){
     
     var checkbox = $(this);
     var checkboxValue = $(this).attr("value");
-    var linkedCheckbox = labelToCheckedEntities[checkboxValue];
+    var linkedCheckbox = URIToCheckedEntities[checkboxValue];
-    var entityToBeRemoved = labelToEntityRecord[checkboxValue];
+    
+    var entityToBeRemoved = URIToEntityRecord[checkboxValue];
 
     if(!checkbox.is(':checked')){
         //console.log("Easy deselect checkbox is unclicked!");
@@ -85,7 +98,6 @@ $("input[type=checkbox].easyDeselectCheckbox").live('click', function(){
     }
 });
 
-
 $(".disabled-checkbox-event-receiver").live("click", function () {
     
     if ($(this).next().is(':disabled')) {
@@ -97,11 +109,32 @@ $(".disabled-checkbox-event-receiver").live("click", function () {
             custom: true,
             expires: false
         });
+    }
+});
 
+$("#copy-vis-viewlink-icon").live('click', function() {
+	
+	if ($("#copy-vis-viewlink").is(':visible')) {
+		
+		$("#copy-vis-viewlink").hide();
+		
+	} else {
+		
+		$("#copy-vis-viewlink").show();
+		
+		var linkTextBox = $("#copy-vis-viewlink input[type='text']");
+		
+		linkTextBox.val(getCurrentParameterVisViewLink());
+		
+		linkTextBox.select();
 	}
 	
 });
 
+function getCurrentParameterVisViewLink() {
+	return location.protocol + "//" + location.host + COMPARISON_PARAMETERS_INFO[currentParameter].viewLink;
+}
+
 function performEntityCheckboxUnselectedActions(entity, checkboxValue, checkbox) {
     
     removeUsedColor(entity);
@@ -121,10 +154,10 @@ function performEntityCheckboxSelectedActions(entity, checkboxValue, checkbox) {
     createLegendRow(entity, $("#bottom"));
 
     renderLineGraph(renderedObjects, entity);
-    labelToCheckedEntities[checkboxValue] = checkbox;
-    labelToCheckedEntities[checkboxValue].entity = entity;
     
-//            console.log(labelToCheckedEntities[checkboxValue], entity);
+    URIToCheckedEntities[checkboxValue] = checkbox;
+    URIToCheckedEntities[checkboxValue].entity = entity;
+    
     
     /*
      * To highlight the rows belonging to selected entities. 
@@ -151,7 +184,7 @@ function loadData(jsonData, dataTableParams) {
 
     $.each(jsonData, function (index, val) {
         setOfLabels.push(val.label);
-        labelToEntityRecord[val.label] = val;
+        URIToEntityRecord[val.entityURI] = val;
         if (val.lastCachedAtDateTime) {
         	lastCachedAtDateTimes[lastCachedAtDateTimes.length] = val.lastCachedAtDateTime;
         }
@@ -164,6 +197,26 @@ function loadData(jsonData, dataTableParams) {
     
 }
 
+/* 
+ *  function to populate the labelToEntityRecord object with the
+ *  values from the json file and
+ *  dynamically generate checkboxes
+ */
+function reloadData(preselectedEntityURIs, jsonData) {
+
+    $.each(jsonData, function (index, val) {
+        setOfLabels.push(val.label);
+        URIToEntityRecord[val.entityURI] = val;
+        if (val.lastCachedAtDateTime) {
+        	lastCachedAtDateTimes[lastCachedAtDateTimes.length] = val.lastCachedAtDateTime;
+        }
+    });
+    
+    reloadDataTablePagination(preselectedEntityURIs, jsonData);
+    setEntityLevel(getEntityVisMode(jsonData));
+}
+
+
 function entityCheckboxOperatedOnEventListener() {
 	
     /*
@@ -174,7 +227,7 @@ function entityCheckboxOperatedOnEventListener() {
 
         var checkbox = $(this);
         var checkboxValue = $(this).attr("value");
-        var entity = labelToEntityRecord[checkboxValue];
+        var entity = URIToEntityRecord[checkboxValue];
         
         if (checkbox.is(':checked')) {
         
@@ -183,13 +236,10 @@ function entityCheckboxOperatedOnEventListener() {
         } else {
         
             performEntityCheckboxUnselectedActions(entity, checkboxValue, checkbox);        
-
         }
         
         performEntityCheckboxClickedRedrawActions();
-
     });
-	
 }
 
 function renderTemporalGraphVisualization(parameters) {
@@ -200,7 +250,6 @@ function renderTemporalGraphVisualization(parameters) {
     					 parameters.bodyContainer,
                          parameters.errorContainer,
                          parameters.responseContainer);
-	
 }
 
 /*
@@ -216,7 +265,7 @@ function setupLoadingScreen(visContainerDIV) {
         
     $.blockUI.defaults.css.width = '500px';
     $.blockUI.defaults.css.border = '0px';
-    $.blockUI.defaults.css.top = '15%';
+    $.blockUI.defaults.css.top = '1%';
 	
     visContainerDIV.block({
         message: '<div id="loading-data-container"><h3><img id="data-loading-icon" src="' + loadingImageLink 
@@ -225,7 +274,9 @@ function setupLoadingScreen(visContainerDIV) {
         			+ '</i></h3></div>'
     });
     
-    setTimeout(function() {
+    clearTimeout(temporalGraphProcessor.loadingScreenTimeout);
+    
+    temporalGraphProcessor.loadingScreenTimeout = setTimeout(function() {
     	$("#loading-data-container")
     		.html('<h3><img id="refresh-page-icon" src="' 
     				+ refreshPageImageLink 
@@ -235,22 +286,8 @@ function setupLoadingScreen(visContainerDIV) {
 	    	.css({'cursor': 'pointer'});
     	
     }, 10 * 1000);
-	
 }
 
-$("#reload-data").live('click', function() {
-	
-	options = {
-			responseContainer: $("div#temporal-graph-response"),
-			bodyContainer: $("#body"),
-			errorContainer: $("#error-container"),
-			dataURL: temporalGraphDataURL	
-		};
-		
-	renderTemporalGraphVisualization(options);
-	
-});
-
 /*
  * This function gets json data for temporal graph & after rendering removes the
  * loading message. It will also display the error container in case of any error.
@@ -274,7 +311,6 @@ function getTemporalGraphData(temporalGraphDataURL,
 	            	graphBodyDIV.remove();
 	            	errorBodyDIV.show();
 	            	visContainerDIV.unblock();
-	                
 	            } else {
 	            	graphBodyDIV.show();
 	            	errorBodyDIV.remove();
@@ -291,25 +327,57 @@ function getTemporalGraphData(temporalGraphDataURL,
 	
 }
 
-function parseXSDateTime(rawDateTimeString) {
+var lastCachedAtDateTimeParser = {
+		
+	getDateObjectFromRawXSDateTimeString: function(rawDateTimeString) {
 	
 		var dateTime = rawDateTimeString.split("T", 2);
 		var date = dateTime[0].split("-");
 		var time = dateTime[1].split(":");
 		
 		return new Date(date[0], parseInt(date[1], 10) -1, date[2], time[0], time[1], 0);
-}
+	},
 	
-function getReadableDateForLastCachedAtDate(dateObject) {
+	getReadableDateString: function(dateObject) {
 		
-	var day = ['Sunday', 'Monday', 'Tuesday', 'Wednesday', 'Thursday', 'Friday', 'Saturday']
+		if (typeof dateObject === "string") {
-	var month = ['January','February','March','April','May','June','July','August','September','October','November']
+			dateObject = this.getDateObjectFromRawXSDateTimeString(dateObject);
+		}
+		
+		var day = ['Sunday', 'Monday', 'Tuesday', 'Wednesday', 'Thursday', 'Friday', 'Saturday'];
+		var month = ['January','February','March','April','May','June','July','August','September','October','November'];
 		
 		return day[dateObject.getDay()] + ", " + month[dateObject.getMonth()] + " " + dateObject.getDate();
+	},
+	
+	ascendingDateSorter: function(rawDateStringA, rawDateStringB) {
+		
+		var dateA = lastCachedAtDateTimeParser.getDateObjectFromRawXSDateTimeString(rawDateStringA); 
+		var dateB = lastCachedAtDateTimeParser.getDateObjectFromRawXSDateTimeString(rawDateStringB);
+		return dateA-dateB; //sort by date ascending
+   }
+		
+};
+
+var entitySelector = {
+		
+	manuallyTriggerSelectOnDataTableCheckbox: function(checkbox) {
+	
+		checkbox.attr('checked', true);
+	    
+	    var checkboxValue = checkbox.attr("value");
+	    var entity = URIToEntityRecord[checkboxValue];
+	    
+	    performEntityCheckboxSelectedActions(entity, checkboxValue, checkbox);
+	    performEntityCheckboxClickedRedrawActions();
+	
+	}
 }
 
 temporalGraphProcessor = {
 		
+	loadingScreenTimeout: '',
+		
 	initiateTemporalGraphRenderProcess: function(givenGraphContainer, jsonData) {
 		
 		this.dataTableParams = {
@@ -328,11 +396,7 @@ temporalGraphProcessor = {
          * */
         loadData(jsonData, this.dataTableParams);
         
-        lastCachedAtDateTimes.sort(function(a, b) {
+        lastCachedAtDateTimes.sort(lastCachedAtDateTimeParser.ascendingDateSorter);
-        	 var dateA = parseXSDateTime(a); 
-        	 var dateB = parseXSDateTime(b);
-        	 return dateA-dateB; //sort by date ascending
-        });
         
         /*
          * This will make sure that top 3 entities are selected by default when the page loads.
@@ -343,21 +407,75 @@ temporalGraphProcessor = {
                 return false;
             }
         
-                    $(this).attr('checked', true);
+            entitySelector.manuallyTriggerSelectOnDataTableCheckbox($(this));
-                    
-                    var checkboxValue = $(this).attr("value");
-                    var entity = labelToEntityRecord[checkboxValue];
-                    
-                    performEntityCheckboxSelectedActions(entity, checkboxValue, $(this));
-                    
-                    performEntityCheckboxClickedRedrawActions();
                     
         });
 
         if ($("#incomplete-data-disclaimer").length > 0 && lastCachedAtDateTimes.length > 0) {
         	$("#incomplete-data-disclaimer").attr(
         			"title", 
-        			$("#incomplete-data-disclaimer").attr("title") + " as of " + getReadableDateForLastCachedAtDate(parseXSDateTime(lastCachedAtDateTimes[0]))); 
+        			$("#incomplete-data-disclaimer").attr("title") + " as of " 
+        			+ lastCachedAtDateTimeParser.getReadableDateString(lastCachedAtDateTimes[0])); 
         }
+	},
+	
+	redoTemporalGraphRenderProcess: function(givenGraphContainer, jsonData) {
+		
+		var currentSelectedEntityURIs = [];
+		
+		$.each(URIToCheckedEntities, function(index, entity){
+			currentSelectedEntityURIs.push(index);
+		});
+		
+		clearRenderedObjects();
+		initConstants();
+		
+		/*
+         * initial display of the grid when the page loads 
+         * */ 
+        init(givenGraphContainer);
+
+        /*
+         * render the temporal graph per the sent content. 
+         * */
+        reloadData(currentSelectedEntityURIs, jsonData);
+        
+        lastCachedAtDateTimes.sort(lastCachedAtDateTimeParser.ascendingDateSorter);
+
+        if (currentSelectedEntityURIs.length > 0) {
+
+        	$.each(currentSelectedEntityURIs, function(index, uri) {
+
+        		var targetPrevSelectedCheckbox = $('input.' + entityCheckboxSelectorDOMClass + '[value="' + uri + '"]');
+        		
+        		if (targetPrevSelectedCheckbox.length > 0) {
+
+        			entitySelector.manuallyTriggerSelectOnDataTableCheckbox(targetPrevSelectedCheckbox);
+        		}
+        	});
+        } else {
+	        /*
+	         * This will make sure that top 3 entities are selected by default when the page loads.
+	        */      
+	        $.each($("input." + entityCheckboxSelectorDOMClass), function(index, checkbox) {
+	                
+                if (index > 2) {
+                    return false;
+                }
+                entitySelector.manuallyTriggerSelectOnDataTableCheckbox($(this));
+	        });
+        }
+        
+        if ($("#incomplete-data-disclaimer").length > 0 && lastCachedAtDateTimes.length > 0) {
+        	
+        	var disclaimerText = "This information is based solely on " 
+        							+ COMPARISON_PARAMETERS_INFO[currentParameter].value
+        							+ " which have been loaded into the VIVO system"
+        							+ " as of " + lastCachedAtDateTimeParser.getReadableDateString(lastCachedAtDateTimes[0]);
+        	
+        	$("#incomplete-data-disclaimer").attr(
+        			"title", disclaimerText); 
+        }
+        $("#copy-vis-viewlink input[type='text']").val(getCurrentParameterVisViewLink());
 	}	
 }

productMods/js/visualization/entitycomparison/util.js

@@ -221,9 +221,11 @@ function init(graphContainer) {
 	
 	var optionSelected = $("select.comparisonValues option:selected").val();
 	// TODO: make use of the id on the select field instead of a generic one.
-	$("#comparisonParameter").text("Total Number of " + $("select.comparisonValues option:selected").val());
+	$("#comparisonParameter").text("Total Number of " + optionSelected);
 	$('#yaxislabel').html("Number of " + optionSelected).mbFlipText(false);
 	$('#comparisonHeader').html(optionSelected).css('font-weight', 'bold');
+	$('#legend-known-bar-text').text("Known " + COMPARISON_PARAMETERS_INFO[currentParameter].name + " year");
+	$('#legend-unknown-bar-text').text("Unknown " + COMPARISON_PARAMETERS_INFO[currentParameter].name + " year");
 	
 	
 	var defaultFlotOptions = {
@@ -455,11 +457,8 @@ function calcMinandMaxYears(jsonObject, year) {
 		}
 		
 	});
-	
-	
 	year.min = Math.min.apply(Math, validYearsInData);
 	year.max = Math.max.apply(Math, validYearsInData);
-	
 }
 
 /**
@@ -473,7 +472,8 @@ function calcMaxOfComparisonParameter(allEntities) {
 	var validCountsInData = new Array();
 	
 	$.each(allEntities, function(key, currentEntity) {
-		validCountsInData.push(calcSumOfComparisonParameter(currentEntity));
+		combinedCount = calcSumOfComparisonParameter(currentEntity);
+		validCountsInData.push(combinedCount.knownYearCount + combinedCount.unknownYearCount);
 	});
 
 	return Math.max.apply(Math, validCountsInData);
@@ -510,12 +510,26 @@ function calcMaxWithinComparisonParameter(jsonObject){
  */
 function calcSumOfComparisonParameter(entity) {
 
-	var sum = 0;
+	var known = 0;
+	var unknown = 0;
 
 	$.each(entity.data, function(index, data){
-		sum += this[1];
+		
+		if (this[0] === -1) {
+			unknown += this[1];
+		} else {
+			known += this[1];
+		}
+		
+		
+		
 	});
 
+	sum = {
+		knownYearCount: known,
+		unknownYearCount: unknown
+	};
+	
 	return sum;
 }
 
@@ -539,47 +553,39 @@ function contains(objectArray, object) {
 	return flag;
 }
 
-/**
+var LineWidth = {
- * Dynamically change the linewidth and ticksize based on input year range.
- * 
- * @param {Object}
- *            yearRange
- */
-function setLineWidthAndTickSize(yearRange, flotOptions) {
 
-	if (yearRange > 0 && yearRange < 15) {
+	getLineWidth: function(tickSize) {
-		flotOptions.series.lines.lineWidth = 3;
+		if (tickSize >= 0 && tickSize < 10) {
-		flotOptions.xaxis.tickSize = 1;
+			return 3;
-	} else if (yearRange > 15 && yearRange < 70) {
+		} else if (tickSize >= 10 && tickSize < 50) {
-		flotOptions.series.lines.lineWidth = 2;
+			return 2;
-		flotOptions.xaxis.tickSize = 5;
-	} else if (yearRange == 0 ) {
-		flotOptions.series.lines.lineWidth = 3;
-		flotOptions.xaxis.tickSize = 1;
 		} else {
-		flotOptions.series.lines.lineWidth = 1;
+			return 1;
-		flotOptions.xaxis.tickSize = 10;
+		}
 	}
 		
-}
+};
 
 var TickSize = {
 		
 	maxValue: 0.0,	
 	
 	maxTicks: {
-		yAxis: 12.0 
+		yAxis: 12.0,
+		xAxis: 12.0
 	},
 	
 	tickSizeUnits: {
-		yAxis: [1.0, 2.5, 5.0]
+		yAxis: [1.0, 2.5, 5.0],
+		xAxis: [1.0, 2, 5.0]
 	},
 	
 	getApproximateTickSize: function(allowedMaxTicks) {
 		return Math.max(Math.ceil(parseFloat(this.maxValue) / allowedMaxTicks), 1.0);
 	},
 	
-	getFinalTickSizeForYaxis: function(unitTickSizeGenerator) {
+	getFinalTickSize: function(unitTickSizeGenerator) {
 		tickSizeMultiplier = 1.0;
 		finalTickSize = 1.0;
 		approximateTickSize = this.getApproximateTickSize(this.maxTicks.yAxis);
@@ -599,14 +605,15 @@ var TickSize = {
 			}
 			tickSizeMultiplier *= 10.0;
 		}
-		
 		return finalTickSize;
 	},
 	
 	getTickSize: function(value, onAxis) {
 		this.maxValue = value;
 		if (onAxis.trim().toLowerCase() === 'y') {
-			return this.getFinalTickSizeForYaxis(this.tickSizeUnits.yAxis);
+			return this.getFinalTickSize(this.tickSizeUnits.yAxis);
+		} else if (onAxis.trim().toLowerCase() === 'x') {
+			return this.getFinalTickSize(this.tickSizeUnits.xAxis);
 		}
 	} 
 };
@@ -622,7 +629,7 @@ var TickSize = {
 function createLegendRow(entity, bottomDiv) {
 
     var parentP = $('<p>');
-    parentP.attr('id', slugify(entity.label));
+    parentP.attr('id', slugify(entity.entityURI));
 
     var labelDiv = $('<div>');
     labelDiv.attr('class', 'easy-deselect-label');
@@ -651,8 +658,23 @@ function createLegendRow(entity, bottomDiv) {
     var barDiv = $('<div>');
     barDiv.attr('id', 'bar');
     
+    var knownBar = $('<span>');
+    knownBar.attr('class', 'known-bar');
+
+    var unknownBar = $('<span>');
+    unknownBar.attr('class', 'unknown-bar');
+    
+    var unknownBarInnerSpan = $('<span>');
+    unknownBarInnerSpan.attr('class', 'unknown-inner-bar');
+    unknownBarInnerSpan.html('&nbsp;');
+    
+    unknownBar.append(unknownBarInnerSpan);
+    
+    barDiv.append(knownBar);
+    barDiv.append(unknownBar);
+    
     var numAttributeText = $('<span>');
-    numAttributeText.attr('id', 'text');
+    numAttributeText.attr('class', 'bar-count-text');
 
     parentP.append(checkbox);
     parentP.append(labelDiv);
@@ -660,7 +682,13 @@ function createLegendRow(entity, bottomDiv) {
     parentP.append(barDiv);
     parentP.append(numAttributeText);
     
+    if (bottomDiv.children('p.displayCounter').nextAll().last().length > 0) {
+    	bottomDiv.children('p.displayCounter').nextAll().last().after(parentP);
+    } else {
     	bottomDiv.children('p.displayCounter').after(parentP);
+    }
+    
+    
 
     renderBarAndLabel(entity, barDiv, labelDiv, numAttributeText);
 }
@@ -672,19 +700,35 @@ function createLegendRow(entity, bottomDiv) {
 
 function renderBarAndLabel(entity, divBar, divLabel, spanElement) {
 
-    var sum = calcSumOfComparisonParameter(entity);
+	var combinedCount = calcSumOfComparisonParameter(entity);
-    var normalizedWidth = getNormalizedWidth(entity, sum);
 	
-    divBar.css("background-color", colorToAssign);
+	var sum = combinedCount.knownYearCount + combinedCount.unknownYearCount;
-    divBar.css("width", normalizedWidth);
+    
+    var normalizedWidth = getNormalizedWidth(entity, sum);
+    var knownNormalizedWidth = getNormalizedWidth(entity, combinedCount.knownYearCount);
+    
+    if (combinedCount.unknownYearCount) {
+    	var unknownNormalizedWidth = getNormalizedWidth(entity, combinedCount.unknownYearCount);
+    } else {
+    	var unknownNormalizedWidth = 0;
+    }
+    
+    divBar.css("width", normalizedWidth + 5);
+    divBar.children(".known-bar").html("&nbsp;").css("background-color", colorToAssign).css("width", knownNormalizedWidth);
+    divBar.children(".unknown-bar").children(".unknown-inner-bar").html("&nbsp;").css("background-color", colorToAssign).css("width", unknownNormalizedWidth);
 
     var entityLabelForLegend = divLabel.find(".entity-label-url");
     entityLabelForLegend.html(entity.label);
     entityLabelForLegend.ellipsis();
     entityLabelForLegend.wrap("<a class='entity-url' title='" + entity.label + "' href='" + getVIVOURL(entity) + "'></a>");
 
-    spanElement.text(sum).css("font-size", "0.8em").css("color", "#595B5B");
+    var countExplanation = 'VIVO knows the ' + COMPARISON_PARAMETERS_INFO[currentParameter].name + ' year for ' 
+    							+ combinedCount.knownYearCount + ' out of ' 
+    							+ sum + ' of these ' + COMPARISON_PARAMETERS_INFO[currentParameter].pluralName;
     
+    divBar.attr("title", countExplanation);
+    
+    spanElement.text(sum).css("font-size", "0.8em").css("color", "#595B5B");
 }
 
 function getVIVOURL(entity){
@@ -826,7 +870,7 @@ function getNextFreeColor(entity){
 
 function getNormalizedWidth(entity, sum){
 	
-	 var maxValueOfComparisonParameter = calcMaxOfComparisonParameter(labelToEntityRecord);
+	 var maxValueOfComparisonParameter = calcMaxOfComparisonParameter(URIToEntityRecord);
 	 var normalizedWidth = 0;
 	 
 	 normalizedWidth = Math.floor(225 * (sum / maxValueOfComparisonParameter));
@@ -906,18 +950,19 @@ function generateCheckBoxes(label, checkedFlag, fontFlag){
 
 function clearRenderedObjects(){
 	
-	$.each(labelToCheckedEntities, function(index, val){
+	$.each(URIToCheckedEntities, function(index, val){
 		if($(val).is(':checked')){
 			$(val).attr("checked", false);
 			updateRowHighlighter(val);
-			removeUsedColor(labelToEntityRecord[$(val).attr("value")]);
+			removeUsedColor(URIToEntityRecord[$(val).attr("value")]);
-			removeEntityUnChecked(renderedObjects, labelToEntityRecord[$(val).attr("value")]);
+			removeEntityUnChecked(renderedObjects, URIToEntityRecord[$(val).attr("value")]);
 			removeLegendRow(val);
 			displayLineGraphs();
 		}
 	});
 	
-	labelToCheckedEntities = {};
+	URIToCheckedEntities = {};
+	
 	checkIfColorLimitIsReached();
 	updateCounter();
 
@@ -948,16 +993,18 @@ function displayLineGraphs(){
     }
 }
 
-
-
 function removeCheckBoxFromGlobalSet(checkbox){
     //remove checkbox object from the globals
 	var value = $(checkbox).attr("value");
-	if(labelToCheckedEntities[value]){
+	/*if (labelToCheckedEntities[value]) {
 		delete labelToCheckedEntities[value];
-	}
+	}*/
-}
 	
+	if (URIToCheckedEntities[value]) {
+		delete URIToCheckedEntities[value];
+	}
+	
+}
 
 /*
  * function to create a table to be 
@@ -967,7 +1014,7 @@ function removeCheckBoxFromGlobalSet(checkbox){
 function prepareTableForDataTablePagination(jsonData, dataTableParams){
 	
 	resetStopWordCount();
-	var checkboxCount = 0;
+	
 	var table = $('<table>');
 	table.attr('cellpadding', '0');
 	table.attr('cellspacing', '0');
@@ -985,19 +1032,20 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
 	var entityLabelTH = $('<th>');
 	entityLabelTH.html('Entity Name');
 	
-	var publicationCountTH = $('<th>');
+	var activityCountTH = $('<th>');
 	if ($("select.comparisonValues option:selected").text() === "by Publications") {
-		publicationCountTH.html('Publication Count');
+		activityCountTH.html('Publication Count');
 	} else {
-		publicationCountTH.html('Grant Count');		
+		activityCountTH.html('Grant Count');		
 	}
+	activityCountTH.attr("id", "activity-count-column");
 
 	var entityTypeTH = $('<th>');
 	entityTypeTH.html('Entity Type');
 
 	tr.append(checkboxTH);
 	tr.append(entityLabelTH);
-	tr.append(publicationCountTH);
+	tr.append(activityCountTH);
 	tr.append(entityTypeTH);
 	
 	thead.append(tr);
@@ -1005,20 +1053,26 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
 	table.append(thead);
 	
 	var tbody = $('<tbody>');
+	var checkboxCount = 0;
 	
-	$.each(labelToEntityRecord, function(index, val){
+	$.each(URIToEntityRecord, function(index, val) {
 		var entityTypesWithoutStopWords = removeStopWords(val);
 		var row = $('<tr>'); 
 		
 		var checkboxTD = $('<td>');
-		checkboxTD.html('<div class="disabled-checkbox-event-receiver">&nbsp;</div><input type="checkbox" class="' + entityCheckboxSelectorDOMClass + '" value="' + index + '"'+'/>');
+		checkboxTD.html('<div class="disabled-checkbox-event-receiver">&nbsp;</div><input type="checkbox" class="' 
+								+ entityCheckboxSelectorDOMClass + '" value="' 
+								+ val.entityURI + '"'+'/>');
 		
 		var labelTD =  $('<td>');
 		labelTD.css("width", "100px");
-		labelTD.html(index);
+		labelTD.html(val.label);
 		
 		var publicationCountTD =  $('<td>');
-		publicationCountTD.html(calcSumOfComparisonParameter(val));
+		
+		var combinedCount = calcSumOfComparisonParameter(val);
+		
+		publicationCountTD.html(combinedCount.knownYearCount + combinedCount.unknownYearCount);
 		
 		var entityTypeTD =  $('<td>');
 		entityTypeTD.html(entityTypesWithoutStopWords);
@@ -1076,6 +1130,91 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
 	
 }
 
+
+/*
+ * function to create a table to be 
+ * used by jquery.dataTables. The JsonObject 
+ * returned is used to populate the pagination table.
+ */	
+function reloadDataTablePagination(preselectedEntityURIs, jsonData){
+
+	resetStopWordCount();
+	
+	/*
+	 * In case no entities are selected, we want that redraw should happen so that top entities are 
+	 * pre-selected.
+	 * */
+	var shouldRedraw = preselectedEntityURIs.length ? false : true;
+	
+	var currentDataTable = $('#datatable').dataTable();
+	
+	currentDataTable.fnClearTable();
+	
+	if ($("select.comparisonValues option:selected").text() === "by Publications") {
+		$("#activity-count-column").html('Publication Count');
+	} else {
+		$("#activity-count-column").html('Grant Count');		
+	}
+	
+	function addNewRowAfterReload(entity) {
+		
+		var checkboxTD = '<div class="disabled-checkbox-event-receiver">&nbsp;</div><input type="checkbox" class="' 
+			+ entityCheckboxSelectorDOMClass 
+			+ '" value="' 
+			+ entity.entityURI + '"' +'/>';
+
+		var labelTD =  entity.label;
+		
+		var combinedCount = calcSumOfComparisonParameter(entity);
+		var publicationCountTD = combinedCount.knownYearCount + combinedCount.unknownYearCount;
+		
+		var entityTypeTD =  removeStopWords(entity);
+		
+		var newRow = [checkboxTD,
+		  labelTD,
+		  publicationCountTD,
+		  entityTypeTD];
+		
+		/*
+		 * Dont redraw the table, so no sorting, no filtering.
+		 * */
+		currentDataTable.fnAddData(newRow, shouldRedraw);
+		
+		/*
+		 * Dont redraw the table, so no sorting, no filtering.
+		 * */
+		currentDataTable.fnDraw(shouldRedraw);
+
+	}
+	
+	/*
+	 * This will ensure that currently selected entities are added first in the table,
+	 * to make sure that they are "visible" in the DOM. This so that our manual trigger
+	 * for selecting this checkboxes on page load, actually works.  
+	 * */
+	$.each(preselectedEntityURIs, function(index, uri) {
+		if (URIToEntityRecord[uri]) {
+			addNewRowAfterReload(URIToEntityRecord[uri]);
+		}
+	});
+	
+	
+	$.each(URIToEntityRecord, function(index, val) {
+		
+		/*
+		 * Don't consider already added pre-selected entities. 
+		 * */
+		if ($.inArray(index, preselectedEntityURIs) < 0) {
+			addNewRowAfterReload(val);
+		}
+	});
+	
+	/*
+	 * We should change to the first page so that checkboxes are selectable.
+	 * */
+	currentDataTable.fnPageChange('first');
+}
+
 function updateRowHighlighter(linkedCheckBox){
 	linkedCheckBox.closest("tr").removeClass('datatablerowhighlight');
 }
@@ -1097,12 +1236,10 @@ function removeStopWords(val){
 			typeStringWithoutStopWords += ', '+ value; 
 		}
 	});
-	//console.log(stopWordsToCount["Person"],stopWordsToCount["Organization"]);
 	return typeStringWithoutStopWords.substring(1, typeStringWithoutStopWords.length);
 }
 
 function setEntityLevel(entityLevel){
-	//$('#entitylevelheading').text(' - ' + toCamelCase(entityLevel) + ' Level').css('font-style', 'italic');
 	$('#entityleveltext').text('  ' + entityLevel.toLowerCase()).css('font-style', 'italic');
 	$('#entityHeader').text(entityLevel).css('font-weight', 'bold');
 	$('#headerText').css("color", "#2485ae");
@@ -1195,7 +1332,7 @@ function enableUncheckedEntities(){
 
 function checkIfColorLimitIsReached(){
 	
-	if (getSize(labelToCheckedEntities) >= 10) {
+	if (getSize(URIToCheckedEntities) >= 10) {
 		disableUncheckedEntities();
 	} else {
 		enableUncheckedEntities();
@@ -1207,15 +1344,17 @@ function setTickSizeOfAxes(){
 	var checkedLabelToEntityRecord = {};
 	var yearRange;
 	
-	$.each(labelToCheckedEntities, function(index, val){
+	$.each(URIToCheckedEntities, function(index, val){
-		checkedLabelToEntityRecord[index] = labelToEntityRecord[index];
+		checkedLabelToEntityRecord[index] = URIToEntityRecord[index];
 	});
 	
 	var normalizedYearRange = getNormalizedYearRange();
 	
-    setLineWidthAndTickSize(normalizedYearRange.normalizedRange, FlotOptions);     
+    FlotOptions.xaxis.tickSize = 
+		TickSize.getTickSize(normalizedYearRange.normalizedRange, 'x');
+
+    FlotOptions.series.lines.lineWidth = LineWidth.getLineWidth(FlotOptions.xaxis.tickSize);
     
 	FlotOptions.yaxis.tickSize = 
 			TickSize.getTickSize(calcMaxWithinComparisonParameter(checkedLabelToEntityRecord), 'y');
-	
 }

productMods/js/visualization/visualization-helper-functions.js

@@ -95,3 +95,12 @@ function constructVisualizationURLForSparkline(dataString, visualizationOptions)
     			+ chartColor + parameterDifferentiator 
     			+ "chd=" + dataString
 }
+
+/*
+ * In IE trim() is not supported.
+ * */
+if (typeof String.prototype.trim !== 'function') {
+	String.prototype.trim = function() {
+		return this.replace(/^\s+|\s+$/g, '');
+	}
+}

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

@@ -13,10 +13,13 @@
                 
                 <select class="comparisonValues" style="margin-bottom: 20px;">
                 
+                <#assign currentViewLink = "no view link">
+                
                 <#list parameterOptions as parameter>
                     <#if currentParameter = parameter.name>
                     
                         <#assign selectedText = "selected='selected'">
+                        <#assign currentViewLink = parameter.viewLink>
 
                     <#else>
                     
@@ -28,6 +31,9 @@
 
                 </select>
                 
+                <img id="copy-vis-viewlink-icon" title="Link to visualization" class="middle" src="${urls.images}/individual/uriIcon.gif" alt="uri icon" />
+                <span id="copy-vis-viewlink"><input type="text" size="21" value="${currentViewLink}" /></span>
+                
                 </div>
             </div>
                         
@@ -84,5 +90,9 @@
             </p>
         
             </div>
+            
+            <p class="displayCounter">Legend</p>
+            <span style="background-color: #B7B7B7; width: 25px;" class="known-bar legend-bar">&nbsp;</span> <span id="legend-known-bar-text">Known ${currentParameterObject.name} year</span><br />
+            <span class="legend-bar unknown-legend-bar"><span style="width: 25px;" class="unknown-inner-bar">&nbsp;</span></span> <span id="legend-unknown-bar-text">Unknown ${currentParameterObject.name} year</span>
         </div>      
 </div>

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

@@ -5,6 +5,12 @@ corresponding changes in the included Templates. -->
 
 <#assign currentParameter = "grant">
 
+<script language="JavaScript" type="text/javascript">
+
+var currentParameter = "${currentParameter}";
+
+</script>
+
 <#include "entityComparisonSetup.ftl">
 
 <#assign temporalGraphDownloadFileLink = '${temporalGraphDownloadCSVCommonURL}&vis=entity_grant_count'>

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

@@ -5,6 +5,12 @@ corresponding changes in the included Templates. -->
 
 <#assign currentParameter = "publication">
 
+<script language="JavaScript" type="text/javascript">
+
+var currentParameter = "${currentParameter}";
+
+</script>
+
 <#include "entityComparisonSetup.ftl">
 
 <#assign temporalGraphDownloadFileLink = '${temporalGraphDownloadCSVCommonURL}&vis=entity_comparison'>

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

@@ -13,20 +13,27 @@
 <#assign subOrganizationPublicationTemporalGraphCommonURL = "${urls.base}${standardVisualizationURLRoot}?vis=entity_comparison">
 
 <#assign organizationPublicationTemporalGraphURL = "${urls.base}${standardVisualizationURLRoot}?vis=entity_comparison&uri=${organizationURI}">
+<#assign organizationPublicationTemporalGraphDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=entity_comparison&uri=${organizationURI}&vis_mode=json">
+
 <#assign organizationGrantTemporalGraphURL = "${urls.base}${standardVisualizationURLRoot}?vis=entity_grant_count&uri=${organizationURI}">
+<#assign organizationGrantTemporalGraphDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=entity_grant_count&uri=${organizationURI}&vis_mode=json">
 
 <#assign temporalGraphSmallIcon = '${urls.images}/visualization/temporal_vis_small_icon.jpg'>
 
 <#assign temporalGraphDownloadCSVCommonURL = '${urls.base}${dataVisualizationURLRoot}?uri=${organizationURI}&labelField=label'>
 
 <#assign publicationParameter = {   "name": "publication",
+									"pluralName": "publications",
                                     "dropDownText": "by Publications", 
                                     "viewLink": "${organizationPublicationTemporalGraphURL}",
+                                    "dataLink": "${organizationPublicationTemporalGraphDataURL}", 
                                     "value": "Publications" }>
                                     
 <#assign grantParameter = {   "name": "grant",
+							  "pluralName": "grants",
                               "dropDownText": "by Grants", 
                               "viewLink": "${organizationGrantTemporalGraphURL}", 
+                              "dataLink": "${organizationGrantTemporalGraphDataURL}",
                               "value": "Grants" }>
                               
 <#assign parameterOptions = [publicationParameter, grantParameter]>
@@ -42,6 +49,15 @@ we will default to using the stable version unless the request comes from IE 9 i
 we will use rev 293 (dev build version) of the flot & excanvas files.
 -->
 
+<script language="JavaScript" type="text/javascript">
+
+var activitiesLabel = {
+    	singular: 'activity',
+    	plural: 'activities'
+    };
+    
+</script>
+
 ${scripts.add('<!--[if IE]><script type="text/javascript" src="${urls.base}/js/visualization/entitycomparison/jquery_plugins/flot/r293/excanvas.min.js"></script><![endif]-->',
               '<script type="text/javascript" src="${urls.base}/js/visualization/entitycomparison/jquery_plugins/flot/r293/jquery.flot.min.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/visualization/entitycomparison/jquery_plugins/fliptext/jquery.mb.flipText.js"></script>',
@@ -50,6 +66,7 @@ ${scripts.add('<!--[if IE]><script type="text/javascript" src="${urls.base}/js/v
               '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.dataTables.min.js"></script>', 
               '<script type="text/javascript" src="${urls.base}/js/visualization/entitycomparison/util.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/visualization/entitycomparison/constants.js"></script>',
+              '<script type="text/javascript" src="${urls.base}/js/visualization/visualization-helper-functions.js"></script>',
               '<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.notify.min.js"></script>')}              
 
 <#-- CSS files -->

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

@@ -15,7 +15,6 @@ import org.apache.commons.logging.Log;
 
 import com.google.gson.Gson;
 import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.rdf.model.Model;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -27,7 +26,6 @@ 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;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
-import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.ConstructedModelTracker;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.JsonObject;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
@@ -58,11 +56,11 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		}
 		
 		
-		System.out.println("current models in the system are");
+//		System.out.println("current models in the system are");
-		for (Map.Entry<String, Model> entry : ConstructedModelTracker.getAllModels().entrySet()) {
+//		for (Map.Entry<String, Model> entry : ConstructedModelTracker.getAllModels().entrySet()) {
-			System.out.println(entry.getKey() + " -> " + entry.getValue().size());
+//			System.out.println(entry.getKey() + " -> " + entry.getValue().size());
-		}
+//		}
-		
+//		
 		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
 	}
 
@@ -71,7 +69,6 @@ public class TemporalPublicationVisualizationRequestHandler implements
 			String subjectEntityURI, EntityComparisonConstants.DataVisMode visMode)
 			throws MalformedQueryParametersException {
 		
-
 		Entity organizationEntity = SelectOnModelUtilities
 				.getSubjectOrganizationHierarchy(dataset, subjectEntityURI);
 		

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

@@ -205,7 +205,7 @@ public class SelectOnModelUtilities {
 																	OrganizationToPublicationsForSubOrganizationsModelConstructor.MODEL_TYPE,
 																	dataset);
 			
-			System.out.println("getting publications for " + subOrganization.getIndividualLabel());
+//			System.out.println("getting publications for " + subOrganization.getIndividualLabel());
 			
 			Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
 			fieldLabelToOutputFieldLabel.put("document", QueryFieldLabels.DOCUMENT_URL);
@@ -352,7 +352,7 @@ public class SelectOnModelUtilities {
 		
 		for (SubEntity subOrganization : organizationEntity.getSubEntities()) {
 			
-			System.out.println("constructing grants for " + subOrganization.getIndividualLabel() + " :: " + subOrganization.getIndividualURI());
+//			System.out.println("constructing grants for " + subOrganization.getIndividualLabel() + " :: " + subOrganization.getIndividualURI());
 			
 			long before = System.currentTimeMillis();
 			
@@ -362,7 +362,7 @@ public class SelectOnModelUtilities {
 																	OrganizationToGrantsForSubOrganizationsModelConstructor.MODEL_TYPE,
 																	dataset);
 			
-			System.out.println("\t construct -> " + (System.currentTimeMillis() - before));
+//			System.out.println("\t construct -> " + (System.currentTimeMillis() - before));
 			
 			before = System.currentTimeMillis();
 			
@@ -419,7 +419,7 @@ public class SelectOnModelUtilities {
 			
 			subOrganization.setLastCachedAtDateTime(lastCachedAtForEntity);
 			
-			System.out.println("\t select -> " + (System.currentTimeMillis() - before));
+//			System.out.println("\t select -> " + (System.currentTimeMillis() - before));
 		}
 		return allGrantURIToVO;
 	}