1. Changed icon for map of science.

2. Bug fixes for map of science edge cases.
3. Included a default error message when there are no publications to be found.
4. Improved text for map of sience info.

productMods/css/visualization/mapofscience/layout.css

@@ -210,4 +210,26 @@ a.map-of-science-links {
 
 .paginatedtabs {
 	font-size: 0.81em;
+}
+
+/* -------------------------------------------------------------->  */
+/* SPECIAL STYLES FOR THE error  */
+/* -------------------------------------------------------------->  */
+#error-container {
+    display: none;
+}
+
+#noPublications-header {
+    font-size: 1.375em;
+    color: #2485ae;
+    line-height: 1.3em;
+    padding-top:15px;
+    padding-bottom:10px;
+}
+#noPublications-span  {
+    font-size:22px;
+}
+#noPublications-span a {
+    color: #84a655;
+    font-size:16px;
 }

productMods/js/visualization/mapofscience/DataTableWidget.js

@@ -237,7 +237,7 @@ var DataTableWidget = Class.extend({
 			}
 			me.currentSelectedFilter = SCIMAP_TYPE.SUBDISCIPLINE;
 			$("a#csv").attr("href", entityMapOfScienceSubDisciplineCSVURL);
-			$("a#csv").html("Export All Sub-Displines");
+			$("a#csv").html("Export All Sub-Disciplines");
 			
 		} else {
 			
@@ -247,7 +247,7 @@ var DataTableWidget = Class.extend({
 				me.widget.fnSettings()._iDisplayLength = 13;
 			}
 			$("a#csv").attr("href", entityMapOfScienceDisciplineCSVURL);
-			$("a#csv").html("Export All Displines");
+			$("a#csv").html("Export All Disciplines");
 			
 		}
 		

productMods/js/visualization/mapofscience/MarkerManager.js

@@ -1,207 +1,207 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-/**
+/**
- * The MarkerManager is more like a composite class of Marker. It manages 
+ * The MarkerManager is more like a composite class of Marker. It manages 
- * markers by grouping the markers by keys. 
+ * markers by grouping the markers by keys. 
- */
+ */
-var MarkerManager = Class.extend({
+var MarkerManager = Class.extend({
-	init: function() {
+	init: function() {
-		this.keyToMarker = {};
+		this.keyToMarker = {};
-	},
+	},
-	addMarker: function(key, marker) {
+	addMarker: function(key, marker) {
-		this.keyToMarker[key] = marker;
+		this.keyToMarker[key] = marker;
-	},
+	},
-	length: function() {
+	length: function() {
-		var size = 0;
+		var size = 0;
-		for (var key in this.keyToMarker) {
+		for (var key in this.keyToMarker) {
-			if (this.keyToMarker.hasOwnProperty(key)) size++;
+			if (this.keyToMarker.hasOwnProperty(key)) size++;
-		}
+		}
-		return size;
+		return size;
-	},
+	},
-	getMarker: function(key) {
+	getMarker: function(key) {
-		return this.keyToMarker[key];
+		return this.keyToMarker[key];
-	},
+	},
-	getMarkerArray: function() {
+	getMarkerArray: function() {
-		var array = [];
+		var array = [];
-		$.each(this.keyToMarker, function(i, e){ array.push(e); });
+		$.each(this.keyToMarker, function(i, e){ array.push(e); });
-		return array;
+		return array;
-	},
+	},
-	hasKey: function(key) {
+	hasKey: function(key) {
-		return (this.keyToMarker.hasOwnProperty(key));
+		return (this.keyToMarker.hasOwnProperty(key));
-	},
+	},
-	showMarkers: function() {
+	showMarkers: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.show();
+			marker.show();
-		});
+		});
-	},
+	},
-	hideMarkers: function() {
+	hideMarkers: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.hide();
+			marker.hide();
-		});
+		});
-	},
+	},
-	addMarkersToMap: function() {
+	addMarkersToMap: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.addToMap();
+			marker.addToMap();
-		});
+		});
-	},
+	},
-	removeMarkersFromMap: function() {
+	removeMarkersFromMap: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.removeFromMap();
+			marker.removeFromMap();
-		});
+		});
-	}
+	}
-});
+});
-
+
-/**
+/**
- * Customized Discipline labels MarkerManager for Science map purpose. It is an abstract class 
+ * Customized Discipline labels MarkerManager for Science map purpose. It is an abstract class 
- */
+ */
-var DisciplineLabelsMarkerManager = MarkerManager.extend({
+var DisciplineLabelsMarkerManager = MarkerManager.extend({
-	init: function(map) {
+	init: function(map) {
-		this._super();
+		this._super();
-		this.map = map;
+		this.map = map;
-		this.initMarkers(map);
+		this.initMarkers(map);
-	},
+	},
-	initMarkers: function(map) {
+	initMarkers: function(map) {
-		me = this;
+		me = this;
-		$.each(DISCIPLINES, function(id, discipline) {
+		$.each(DISCIPLINES, function(id, discipline) {
-			var opts = {
+			var opts = {
-					map: map,
+					map: map,
-					position: createNoWrapLatLng(discipline.labelLatitude, discipline.labelLongitude),
+					position: createNoWrapLatLng(discipline.labelLatitude, discipline.labelLongitude),
-					icon: getDisciplineLabelImageURL(id),
+					icon: getDisciplineLabelImageURL(id),
-					clickable: false
+					clickable: false
-				};
+				};
-			me.addMarker(id, new Marker(opts));
+			me.addMarker(id, new Marker(opts));
-		});
+		});
-	},
+	},
-	showMarkers: function() {
+	showMarkers: function() {
-		this._super();
+		this._super();
-	}
+	}
-});
+});
-
+
-/**
+/**
- * Customized MarkerManager for Science map purpose. It is an abstract class 
+ * Customized MarkerManager for Science map purpose. It is an abstract class 
- */
+ */
-var ScimapMarkerManager = MarkerManager.extend({
+var ScimapMarkerManager = MarkerManager.extend({
-	init: function(map, colorStrategy, sizeCoder) {
+	init: function(map, colorStrategy, sizeCoder) {
-		this._super();
+		this._super();
-		this.colorStrategy = colorStrategy;
+		this.colorStrategy = colorStrategy;
-		this.sizeCoder = sizeCoder;
+		this.sizeCoder = sizeCoder;
-		this.map = map;
+		this.map = map;
-		this.maxValue = 1;
+		this.maxValue = 1;
-		this.layer = {};
+		this.layer = {};
-	},
+	},
-	setSizeCoder: function(sizeCoder) {
+	setSizeCoder: function(sizeCoder) {
-		this.sizeCoder = sizeCoder;
+		this.sizeCoder = sizeCoder;
-		this.maxValue = sizeCoder.getMaxValue();
+		this.maxValue = sizeCoder.getMaxValue();
-	},
+	},
-	createMarker: function(key, density) {
+	createMarker: function(key, density) {
-		var me = this;
+		var me = this;
-		var marker;
+		var marker;
-		if (!me.hasKey(key)) {
+		if (!me.hasKey(key)) {
-			var size = me.sizeCoder.getSize(density);
+			var size = me.sizeCoder.getSize(density);
-			var color = me.colorStrategy.getColor(key);
+			var color = me.colorStrategy.getColor(key);
-			var layer = me.layer;
+			var layer = me.layer;
-			var label = layer[key].label;
+			var label = layer[key].label;
-			var latlng = createNoWrapLatLng(layer[key].latitude, layer[key].longitude);
+			var latlng = createNoWrapLatLng(layer[key].latitude, layer[key].longitude);
-			marker = createScinodeMarker(me.map, label, density, size, color, latlng);
+			marker = createScinodeMarker(me.map, label, density, size, color, latlng);
-			me.addMarker(key, marker);
+			me.addMarker(key, marker);
-		} else {
+		} else {
-			marker = me.keyToMarker[key];
+			marker = me.keyToMarker[key];
-			marker.setValue(marker.getValue() + density);
+			marker.setValue(marker.getValue() + density);
-			marker.setSize(me.sizeCoder.getSize(marker.getValue()));
+			marker.setSize(me.sizeCoder.getSize(marker.getValue()));
-		}
+		}
-		return marker;
+		return marker;
-	},
+	},
-	updateMarkerViews: function() {
+	updateMarkerViews: function() {
-		var me = this;
+		var me = this;
-		for (var key in me.keyToMarker) {
+		for (var key in me.keyToMarker) {
-			var marker = me.keyToMarker[key];
+			var marker = me.keyToMarker[key];
-			marker.setSize(me.sizeCodingFunc(marker.getValue()));
+			marker.setSize(me.sizeCodingFunc(marker.getValue()));
-			marker.setColor(me.colorStrategy.getColor(key));
+			marker.setColor(me.colorStrategy.getColor(key));
-		}
+		}
-	},
+	},
-	display: function(numberOfMarkers) {
+	display: function(numberOfMarkers) {
-		var markerArray = this.sortedMarkers;
+		var markerArray = this.sortedMarkers;
-		if (!markerArray || !markerArray.length) {
+		if (!markerArray || !markerArray.length) {
-			markerArray = this.getMarkerArray();
+			markerArray = this.getMarkerArray();
-		}
+		}
-		
+		
-		$.each(markerArray, function() {
+		$.each(markerArray, function() {
-			if (numberOfMarkers >  0) {
+			if (numberOfMarkers >  0) {
-				this.show();
+				this.show();
-				numberOfMarkers--;
+				numberOfMarkers--;
-			} else {
+			} else {
-				this.hide();
+				this.hide();
-			}
+			}
-		});
+		});
-	},
+	},
-	mouseIn: function(key) {
+	mouseIn: function(key) {
-		var marker = this.getMarker(key);
+		var marker = this.getMarker(key);
-		if (marker) {
+		if (marker) {
-			marker.focus();
+			marker.focus();
-		}
+		}
-	},
+	},
-	mouseInAll: function() {
+	mouseInAll: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.focus();
+			marker.focus();
-		});
+		});
-	},
+	},
-	mouseOut: function(key) {
+	mouseOut: function(key) {
-		var marker = this.getMarker(key);
+		var marker = this.getMarker(key);
-		if (marker) {
+		if (marker) {
-			marker.unfocus();
+			marker.unfocus();
-		}
+		}
-	},
+	},
-	mouseOutAll: function() {
+	mouseOutAll: function() {
-		$.each(this.keyToMarker, function(i, marker) {
+		$.each(this.keyToMarker, function(i, marker) {
-			marker.unfocus();
+			marker.unfocus();
-		});
+		});
-	},
+	},
-	sort: function() {
+	sort: function() {
-		this.sortedMarkers = this.getMarkerArray();
+		this.sortedMarkers = this.getMarkerArray();
-		this.sortedMarkers.sort(function(a, b) {
+		this.sortedMarkers.sort(function(a, b) {
-			return b.getValue() -a.getValue();
+			return b.getValue() -a.getValue();
-		});
+		});
-	}
+	}
-});
+});
-
+
-var DisciplineMarkerManager = ScimapMarkerManager.extend({
+var DisciplineMarkerManager = ScimapMarkerManager.extend({
-	init: function(map, colorStrategy, sizeCoder) {
+	init: function(map, colorStrategy, sizeCoder) {
-		this._super(map, colorStrategy, sizeCoder);
+		this._super(map, colorStrategy, sizeCoder);
-		this.layer = DISCIPLINES;
+		this.layer = DISCIPLINES;
-	},
+	},
-	createMarker: function(subdisciplineKey, density) {
+	createMarker: function(subdisciplineKey, density) {
-		var me = this;
+		var me = this;
-		var key = SUBDISCIPLINES[subdisciplineKey].discipline;
+		var key = SUBDISCIPLINES[subdisciplineKey].discipline;
-		var marker = this._super(key, density);
+		var marker = this._super(key, density);
-		var poly = marker.polygon;
+		var poly = marker.polygon;
-		
+		
-		marker.setContent( 
+		marker.setContent( 
-				'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
+				'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
-				+ poly.label +'</b><br />'
+				+ poly.label +'</b><br />'
-				+ addCommasToNumber(poly.value.toFixed(2)) + ' of publications (pubs.)<br />'
+				+ addCommasToNumber(poly.value.toFixed(2)) + ' publications (pubs.)<br />'
-				+ (poly.value * 100 / this.maxValue).toFixed(2) + '% of activity</div>'
+				+ (poly.value * 100 / this.maxValue).toFixed(2) + '% activity</div>'
-		);
+		);
-		return marker;
+		return marker;
-	}
+	}
-});
+});
-
+
-var SubdisciplineMarkerManager = ScimapMarkerManager.extend({
+var SubdisciplineMarkerManager = ScimapMarkerManager.extend({
-	init: function(map, colorStrategy, sizeCoder) {
+	init: function(map, colorStrategy, sizeCoder) {
-		this._super(map, colorStrategy, sizeCoder);
+		this._super(map, colorStrategy, sizeCoder);
-		this.layer = SUBDISCIPLINES;
+		this.layer = SUBDISCIPLINES;
-	},
+	},
-	createMarker: function(subdisciplineKey, density) {
+	createMarker: function(subdisciplineKey, density) {
-		var marker = this._super(subdisciplineKey, density);
+		var marker = this._super(subdisciplineKey, density);
-		var disciplineId = SUBDISCIPLINES[subdisciplineKey].discipline;
+		var disciplineId = SUBDISCIPLINES[subdisciplineKey].discipline;
-		var disciplineLabel = DISCIPLINES[disciplineId].label;
+		var disciplineLabel = DISCIPLINES[disciplineId].label;
-		var poly = marker.polygon;
+		var poly = marker.polygon;
-		/* Override the getContent for Subdiscipline */
+		/* Override the getContent for Subdiscipline */
-		marker.setContent(
+		marker.setContent(
-			'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
+			'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
-			+ poly.label + '</b> in ' + disciplineLabel +'<br />' 
+			+ poly.label + '</b> in ' + disciplineLabel +'<br />' 
-			+ addCommasToNumber(poly.value.toFixed(2)) + ' of publications (pubs.)<br />'
+			+ addCommasToNumber(poly.value.toFixed(2)) + ' publications (pubs.)<br />'
-			+ (poly.value * 100 / this.maxValue).toFixed(2) + '% of activity</div>'
+			+ (poly.value * 100 / this.maxValue).toFixed(2) + '% activity</div>'
-		);
+		);
-		
+		
-		return marker;
+		return marker;
-	}
+	}
-});
+});

productMods/js/visualization/mapofscience/VisModeControllers.js

@@ -61,11 +61,11 @@ var EntityVisModeController = Class.extend({
 		if (me.isUnloaded) {
 			if (sync) {
 				downloader.downloadAndWait(url, function(data) {
-						me.loadJsonData(me, data[0]);
+						me.loadJsonData(me, data);
 				});
 			} else {
 				downloader.download(url, function(data) {
-						me.loadJsonData(me, data[0]);
+						me.loadJsonData(me, data);
 				});
 			}
 		} // end if
@@ -74,12 +74,20 @@ var EntityVisModeController = Class.extend({
 		
 		$("#" + responseContainerID).unblock();
 		
+		if (data.error) {
+			$("#map-of-science-response").hide();
+			$("#error-container").show();
+			return;
+		} 
+		
+		data = data[0];
+		
 		$.each(me.widgets, function(i, widget) {
 			widget.loadJsonData(data);
 		});
 		me.isUnloaded = false;
-		
 		me.initToolTipInfo();
+		
 	},
 	initToolTipInfo: function() {
 

productMods/templates/freemarker/body/partials/individual/individual-visualizationFoafPerson.ftl

@@ -18,7 +18,7 @@
     <section id="visualization" role="region">
         <#if isAuthor>
             <#assign coAuthorIcon = "${urls.images}/visualization/co_author_icon.png">
-            <#assign mapOfScienceIcon = "${urls.images}/visualization/mapofscience/vivo_scimap_icon_v001.png">
+            <#assign mapOfScienceIcon = "${urls.images}/visualization/mapofscience/vivo_scimap.jpg">
             <#assign coAuthorVisUrl = individual.coAuthorVisUrl>
             <#assign mapOfScienceVisUrl = individual.mapOfScienceUrl>
             

productMods/templates/freemarker/body/partials/individual/individual-visualizationMapOfScience.ftl

@@ -3,5 +3,5 @@
 <#-- Map Of Science visualization -->
 
 <div id="map-of-science">
-    <h3><img src="${urls.images}/visualization/mapofscience/vivo_scimap_icon_v001.png" width="25px" height="25px" /><a href="${individual.mapOfScienceUrl}">Map of Science</a></h3>
+    <h3><img src="${urls.images}/visualization/mapofscience/vivo_scimap.jpg" width="25px" height="25px" /><a href="${individual.mapOfScienceUrl}">Map of Science</a></h3>
 </div>

productMods/templates/freemarker/visualization/mapOfScience/mapOfScienceSetup.ftl

@@ -25,7 +25,7 @@
 
 </#if>
 
-<#assign mapOfScienceIcon = '${urls.images}/visualization/mapofscience/vivo_scimap_icon_v001.png'>
+<#assign mapOfScienceIcon = '${urls.images}/visualization/mapofscience/vivo_scimap.jpg'>
 
 <#assign entityMapOfScienceDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=${mapOfScienceVisParam}&uri=${entityURI}&output=json">
 <#assign entityMapOfScienceDisciplineCSVURL = "${urls.base}${dataVisualizationURLRoot}?vis=${mapOfScienceVisParam}&uri=${entityURI}&output=csv&vis_mode=discipline">

productMods/templates/freemarker/visualization/mapOfScience/mapOfScienceStandalone.ftl

@@ -102,12 +102,25 @@ You can hover over a sub-discipline in the table below to show which overlaid ci
 
 <br /><br /> 
 
+<#--
 In the table below, <b># of pubs.</b> column indicates number of publications that fall under a particular field (sub-discipline or 
-discipline). Sometimes this number will be fractional. This happens when a journal in which the publication was published happens 
+discipline). Sometimes this number will be fractional. This happens when a journal in which the publication was published is associated 
-to impact more than one field and hence the publication score is distributed into number of fractions based on the weight scores 
+with more than one (sub)discipline. In these cases, the publication score is fractionally mapped based on the weight scores 
-of the journal in the different fields.<br /><br />
+of the journal.<br /><br />
 
 <b>% activity</b> column indicates the percentage of publications that fall under a particular field.
+-->
+
+The table below summarizes this institution's body of publications as plotted on the map of science.  
+Each row corresponds to a field (discipline or sub-discipline) on the map.
+<br /><br />
+
+The <b># of pubs.</b> column shows how many of the publications were mapped to each field.  
+This count can be fractional because some publication venues are associated with more than one field.  
+Each publication in such a venue contributes fractionally to all associated fields according to a weighting scheme.
+
+<br /><br />
+The <b>% activity</b> column shows what proportion of the publications were mapped to each field.
 
 </div>
 
@@ -122,7 +135,20 @@ may need to be cleaned up before they are recognized. You may contact a VIVO sys
 concern.</div>
 
 <div id="searchInfoTooltipText" style="display:none;">
-	This search box is used to filter the table rows based on the sub-discipline (or discipline) label found in the first column.
+	<!-- Search for specific sub-discipline (or discipline) label in the first column of the table. -->
+	List only map of science areas whose names contain this text.
+</div>
+
+<div id="error-container">
+
+<h1 id="noPublications-header">${entityLabel}</h1>
+
+    <h3 id="alternative-vis-info">Map of Science Visualization</h3>
+    <div id="error-body">
+        <p>This organization has neither sub-organizations nor people with publications in the system. 
+        Please visit the full ${entityLabel} <a href="${entityVivoProfileURL}">profile page</a> for a more complete overview.</p>
+    </div>
+
 </div>
 
 ${headScripts.add('<script type="text/javascript" src="${urls.base}/js/jquery_plugins/qtip/jquery.qtip-1.0.0-rc3.min.js"></script>')}

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

@@ -35,7 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequ
 
 public class EntityPublicationCountRequestHandler implements
 		VisualizationRequestHandler {
-	
+
 	@Override
 	public ResponseValues generateStandardVisualization(
 			VitroRequest vitroRequest, Log log, Dataset dataset)
@@ -43,7 +43,7 @@ public class EntityPublicationCountRequestHandler implements
 
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
-		
+
 		return generateStandardVisualizationForPublicationTemporalVis(
 				vitroRequest, log, dataset, entityURI);
 	}
@@ -51,19 +51,17 @@ public class EntityPublicationCountRequestHandler implements
 	private ResponseValues generateStandardVisualizationForPublicationTemporalVis(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
 			String entityURI) throws MalformedQueryParametersException {
-		
+
 		if (StringUtils.isBlank(entityURI)) {
-			
+
 			entityURI = OrganizationUtilityFunctions
-								.getStaffProvidedOrComputedHighestLevelOrganization(
+					.getStaffProvidedOrComputedHighestLevelOrganization(log,
-											log, 
+							dataset, vitroRequest);
-											dataset, 
+
-											vitroRequest);
-			
 		}
-		
+
 		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
-		
+
 	}
 
 	@Override
@@ -72,46 +70,50 @@ public class EntityPublicationCountRequestHandler implements
 			Dataset dataSource) throws MalformedQueryParametersException {
 
 		return generateStandardVisualizationForPublicationTemporalVis(
-				vitroRequest, log, dataSource,  parameters.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY));
+				vitroRequest,
-		
+				log,
+				dataSource,
+				parameters
+						.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY));
+
 	}
 
 	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
-			String subjectEntityURI)
+			String subjectEntityURI) throws MalformedQueryParametersException {
-			throws MalformedQueryParametersException {
+
-		
+		ModelConstructor constructQueryRunner = new EntityPublicationCountConstructQueryRunner(
-		ModelConstructor constructQueryRunner = 
+				subjectEntityURI, dataset, log);
-				new EntityPublicationCountConstructQueryRunner(subjectEntityURI, dataset, log);
+
-		
 		Model constructedModel = constructQueryRunner.getConstructedModel();
-		
+
 		QueryRunner<Entity> queryManager = new EntityPublicationCountQueryRunner(
 				subjectEntityURI, constructedModel, log);
-		
+
 		Entity entity = queryManager.getQueryResult();
-		
+
 		if (entity.getEntityLabel().equals("no-label")) {
-			
+
-			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
+			return prepareStandaloneDataErrorResponse(vitroRequest,
-			
+					subjectEntityURI);
-		} else {	
+
-		
+		} else {
-			return getSubEntityTypesAndComputeDataResponse(
+
-					vitroRequest, log, dataset,
+			return getSubEntityTypesAndComputeDataResponse(vitroRequest, log,
-					subjectEntityURI, entity);
+					dataset, subjectEntityURI, entity);
 		}
 	}
-	
+
 	private Map<String, String> prepareStandaloneDataErrorResponse(
 			VitroRequest vitroRequest, String subjectEntityURI) {
 
 		Map<String, String> fileData = new HashMap<String, String>();
-		
+
-		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
-					 "application/octet-stream");
+				"application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+		fileData
-					 "{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
+				.put(DataVisualizationController.FILE_CONTENT_KEY,
+						"{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
 		return fileData;
 	}
 
@@ -119,13 +121,12 @@ public class EntityPublicationCountRequestHandler implements
 			VitroRequest vitroRequest, Log log, Dataset dataset,
 			String subjectEntityURI, Entity entity)
 			throws MalformedQueryParametersException {
-		
+
-		Map<String, Set<String>> subOrganizationTypesResult = 
+		Map<String, Set<String>> subOrganizationTypesResult = OrganizationUtilityFunctions
-				OrganizationUtilityFunctions.getSubEntityTypes(
+				.getSubEntityTypes(log, dataset, subjectEntityURI);
-						log, dataset, subjectEntityURI);
+
-		
+		return prepareStandaloneDataResponse(vitroRequest, entity, entity
-		return prepareStandaloneDataResponse(vitroRequest, entity, entity.getSubEntities(),
+				.getSubEntities(), subOrganizationTypesResult);
-				subOrganizationTypesResult);
 	}
 
 	@Override
@@ -135,154 +136,155 @@ 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. 
+		 * This will provide the data in json format mainly used for standalone
-		 * */
+		 * tmeporal vis.
+		 */
 		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
-					.equalsIgnoreCase(vitroRequest.getParameter(
+				.equalsIgnoreCase(vitroRequest
-							VisualizationFrameworkConstants.VIS_MODE_KEY))) {
+						.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
-			
+
 			if (StringUtils.isNotBlank(entityURI)) {
-				
+
-				return getSubjectEntityAndGenerateDataResponse(
+				return getSubjectEntityAndGenerateDataResponse(vitroRequest,
-								vitroRequest, 
+						log, dataset, entityURI);
-								log,
-								dataset, 
-								entityURI);
 			} else {
-				
+
 				return getSubjectEntityAndGenerateDataResponse(
-								vitroRequest, 
+						vitroRequest,
-								log,
+						log,
-								dataset,
+						dataset,
-								OrganizationUtilityFunctions
+						OrganizationUtilityFunctions
-										.getStaffProvidedOrComputedHighestLevelOrganization(
+								.getStaffProvidedOrComputedHighestLevelOrganization(
-												log,
+										log, dataset, vitroRequest));
-												dataset, 
-												vitroRequest));
 			}
-			
+
 		} else {
 			/*
 			 * This provides csv download files for the content in the tables.
-			 * */
+			 */
-			
+
-			ModelConstructor constructQueryRunner = 
+			ModelConstructor constructQueryRunner = new EntityPublicationCountConstructQueryRunner(
-					new EntityPublicationCountConstructQueryRunner(entityURI, dataset, log);
+					entityURI, dataset, log);
-			
+
 			Model constructedModel = constructQueryRunner.getConstructedModel();
-			
+
 			QueryRunner<Entity> queryManager = new EntityPublicationCountQueryRunner(
-					entityURI, constructedModel, log);	
+					entityURI, constructedModel, log);
-			
+
 			Entity entity = queryManager.getQueryResult();
 
-			Map<String, Set<String>> subOrganizationTypesResult = 
+			Map<String, Set<String>> subOrganizationTypesResult = OrganizationUtilityFunctions
-					OrganizationUtilityFunctions.getSubEntityTypes(
+					.getSubEntityTypes(log, dataset, entityURI);
-							log, dataset, entityURI);
+
+			return prepareDataResponse(entity, entity.getSubEntities(),
+					subOrganizationTypesResult);
 
-			return prepareDataResponse(entity, entity.getSubEntities(), subOrganizationTypesResult);
-			
 		}
-		
+
 	}
-	
+
-	
 	@Override
 	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
 			Dataset dataset) throws MalformedQueryParametersException {
-		throw new UnsupportedOperationException("Entity Pub Count does not provide Ajax Response.");
+		throw new UnsupportedOperationException(
+				"Entity Pub Count does not provide Ajax Response.");
 	}
 
 	/**
-	 * Provides response when json file containing the publication count over the
+	 * Provides response when json file containing the publication count over
-	 * years is requested.
+	 * the years is requested.
 	 * 
 	 * @param entity
 	 * @param subentities
 	 * @param subOrganizationTypesResult
 	 */
-	private Map<String, String> prepareDataResponse(Entity entity, Set<SubEntity> subentities,
+	private Map<String, String> prepareDataResponse(Entity entity,
+			Set<SubEntity> subentities,
 			Map<String, Set<String>> subOrganizationTypesResult) {
 
 		String entityLabel = entity.getEntityLabel();
 
 		/*
-		* To make sure that null/empty records for entity names do not cause any mischief.
+		 * To make sure that null/empty records for entity names do not cause
-		* */
+		 * any mischief.
+		 */
 		if (StringUtils.isBlank(entityLabel)) {
 			entityLabel = "no-organization";
 		}
-		
+
 		String outputFileName = UtilityFunctions.slugify(entityLabel)
 				+ "_publications-per-year" + ".csv";
-		
-		
-		Map<String, String> fileData = new HashMap<String, String>();
-		
-		fileData.put(DataVisualizationController.FILE_NAME_KEY, 
-					 outputFileName);
-		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
-					 "application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
-				getEntityPublicationsPerYearCSVContent(subentities, subOrganizationTypesResult));
-		return fileData;
-	}
-	
-	private Map<String, String> prepareStandaloneDataResponse(
-										VitroRequest vitroRequest, 
-										Entity entity, 
-										Set<SubEntity> subentities,
-										Map<String, Set<String>> subOrganizationTypesResult) {
 
 		Map<String, String> fileData = new HashMap<String, String>();
-		
+
-		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+		fileData.put(DataVisualizationController.FILE_NAME_KEY, outputFileName);
-					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
+				"application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-					 writePublicationsOverTimeJSON(vitroRequest, 
+				getEntityPublicationsPerYearCSVContent(subentities,
-							 					   entity.getSubEntities(), 
+						subOrganizationTypesResult));
-							 					   subOrganizationTypesResult));
 		return fileData;
 	}
-	
-	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
-																   String entityURI) {
 
-        String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
+	private Map<String, String> prepareStandaloneDataResponse(
-		
+			VitroRequest vitroRequest, Entity entity,
-        String organizationLabel = OrganizationUtilityFunctions
+			Set<SubEntity> subentities,
-        									.getEntityLabelFromDAO(vreq,
+			Map<String, Set<String>> subOrganizationTypesResult)
-        														   entityURI);
+			throws MalformedQueryParametersException {
-        
+
-        Map<String, Object> body = new HashMap<String, Object>();
+		Map<String, String> fileData = new HashMap<String, String>();
-        body.put("title", organizationLabel + " - Temporal Graph Visualization");
+
-        body.put("organizationURI", entityURI);
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
-        body.put("organizationLocalName", UtilityFunctions.getIndividualLocalName(entityURI, vreq));
+				"application/octet-stream");
-        body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-        body.put("organizationLabel", organizationLabel);
+				writePublicationsOverTimeJSON(vitroRequest, entity
-        
+						.getSubEntities(), subOrganizationTypesResult));
-        return new TemplateResponseValues(standaloneTemplate, body);
+		return fileData;
+	}
+
+	private TemplateResponseValues prepareStandaloneMarkupResponse(
+			VitroRequest vreq, String entityURI) {
+
+		String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
+
+		String organizationLabel = OrganizationUtilityFunctions
+				.getEntityLabelFromDAO(vreq, entityURI);
+
+		Map<String, Object> body = new HashMap<String, Object>();
+		body
+				.put("title", organizationLabel
+						+ " - Temporal Graph Visualization");
+		body.put("organizationURI", entityURI);
+		body.put("organizationLocalName", UtilityFunctions
+				.getIndividualLocalName(entityURI, vreq));
+		body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory()
+				.getDefaultNamespace());
+		body.put("organizationLabel", organizationLabel);
+
+		return new TemplateResponseValues(standaloneTemplate, body);
 	}
 
 	/**
 	 * Function to generate a json file for year <-> publication count mapping.
-	 * @param vreq 
+	 * 
+	 * @param vreq
 	 * @param subentities
-	 * @param subOrganizationTypesResult  
+	 * @param subOrganizationTypesResult
+	 * @throws MalformedQueryParametersException
 	 */
-	private String writePublicationsOverTimeJSON(VitroRequest vreq, 
+	private String writePublicationsOverTimeJSON(VitroRequest vreq,
-												 Set<SubEntity> subentities, 
+			Set<SubEntity> subentities,
-												 Map<String, Set<String>> 
+			Map<String, Set<String>> subOrganizationTypesResult)
-												 subOrganizationTypesResult) {
+			throws MalformedQueryParametersException {
 
 		Gson json = new Gson();
 		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
 
 		for (SubEntity subentity : subentities) {
-			JsonObject entityJson = new JsonObject(
+			JsonObject entityJson = new JsonObject(subentity
-					subentity.getIndividualLabel());
+					.getIndividualLabel());
 
 			List<List<Integer>> yearPubCount = new ArrayList<List<Integer>>();
 
@@ -291,24 +293,26 @@ public class EntityPublicationCountRequestHandler implements
 					.entrySet()) {
 
 				List<Integer> currentPubYear = new ArrayList<Integer>();
-				if (pubEntry.getKey().equals(VOConstants.DEFAULT_PUBLICATION_YEAR)) {
+				if (pubEntry.getKey().equals(
+						VOConstants.DEFAULT_PUBLICATION_YEAR)) {
 					currentPubYear.add(-1);
 				} else {
 					currentPubYear.add(Integer.parseInt(pubEntry.getKey()));
 				}
-					
+
 				currentPubYear.add(pubEntry.getValue());
 				yearPubCount.add(currentPubYear);
 			}
-			
+
 			entityJson.setYearToActivityCount(yearPubCount);
 			entityJson.getOrganizationTypes().addAll(
 					subOrganizationTypesResult.get(entityJson.getLabel()));
-			
+
 			entityJson.setEntityURI(subentity.getIndividualURI());
-			
+
-			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI());
+			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity
-			
+					.getIndividualURI());
+
 			if (isPerson) {
 				entityJson.setVisMode("PERSON");
 			} else {
@@ -320,28 +324,30 @@ public class EntityPublicationCountRequestHandler implements
 	}
 
 	private String getEntityPublicationsPerYearCSVContent(
-							Set<SubEntity> subentities,
+			Set<SubEntity> subentities,
-							Map<String, Set<String>> subOrganizationTypesResult) {
+			Map<String, Set<String>> subOrganizationTypesResult) {
 
 		StringBuilder csvFileContent = new StringBuilder();
-		
+
 		csvFileContent.append("Entity Name, Publication Count, Entity Type\n");
-		
+
 		for (SubEntity subEntity : subentities) {
-			
+
-			csvFileContent.append(StringEscapeUtils.escapeCsv(subEntity.getIndividualLabel()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(subEntity
+					.getIndividualLabel()));
 			csvFileContent.append(", ");
 			csvFileContent.append(subEntity.getActivities().size());
 			csvFileContent.append(", ");
-			
+
 			StringBuilder joinedTypes = new StringBuilder();
-			
+
 			for (String subOrganizationType : subOrganizationTypesResult
-													.get(subEntity.getIndividualLabel())) {
+					.get(subEntity.getIndividualLabel())) {
 				joinedTypes.append(subOrganizationType + "; ");
 			}
-			
+
-			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes.toString()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes
+					.toString()));
 			csvFileContent.append("\n");
 		}
 		return csvFileContent.toString();
@@ -353,4 +359,4 @@ public class EntityPublicationCountRequestHandler implements
 		return null;
 	}
 
-}	
+}

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

@@ -34,18 +34,17 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
 
-
 public class EntityGrantCountRequestHandler implements
 		VisualizationRequestHandler {
-	
+
 	@Override
 	public ResponseValues generateStandardVisualization(
 			VitroRequest vitroRequest, Log log, Dataset dataset)
 			throws MalformedQueryParametersException {
-		
+
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
-		
+
 		return generateStandardVisualizationForGrantTemporalVis(vitroRequest,
 				log, dataset, entityURI);
 	}
@@ -54,13 +53,11 @@ public class EntityGrantCountRequestHandler implements
 			VitroRequest vitroRequest, Log log, Dataset dataset,
 			String entityURI) throws MalformedQueryParametersException {
 		if (StringUtils.isBlank(entityURI)) {
-			
+
 			entityURI = OrganizationUtilityFunctions
-								.getStaffProvidedOrComputedHighestLevelOrganization(
+					.getStaffProvidedOrComputedHighestLevelOrganization(log,
-										log,
+							dataset, vitroRequest);
-										dataset, 
+
-										vitroRequest);
-			
 		}
 		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
 	}
@@ -71,7 +68,11 @@ public class EntityGrantCountRequestHandler implements
 			Dataset dataSource) throws MalformedQueryParametersException {
 
 		return generateStandardVisualizationForGrantTemporalVis(
-				vitroRequest, log, dataSource,  parameters.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY));
+				vitroRequest,
+				log,
+				dataSource,
+				parameters
+						.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY));
 
 	}
 
@@ -82,89 +83,83 @@ public class EntityGrantCountRequestHandler implements
 
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
-		
+
 		/*
-		 * This will provide the data in json format mainly used for standalone temporal vis. 
+		 * This will provide the data in json format mainly used for standalone
-		 * */
+		 * temporal vis.
+		 */
 		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
-					.equalsIgnoreCase(vitroRequest
+				.equalsIgnoreCase(vitroRequest
-							.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
+						.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
-			
+
 			if (StringUtils.isNotBlank(entityURI)) {
-				
+
-				return getSubjectEntityAndGenerateDataResponse(
+				return getSubjectEntityAndGenerateDataResponse(vitroRequest,
-								vitroRequest, 
+						log, dataset, entityURI);
-								log,
-								dataset, 
-								entityURI);
 			} else {
-				
+
 				return getSubjectEntityAndGenerateDataResponse(
-								vitroRequest, 
+						vitroRequest,
-								log,
+						log,
-								dataset,
+						dataset,
-								OrganizationUtilityFunctions
+						OrganizationUtilityFunctions
-										.getStaffProvidedOrComputedHighestLevelOrganization(
+								.getStaffProvidedOrComputedHighestLevelOrganization(
-												log,
+										log, dataset, vitroRequest));
-												dataset, 
-												vitroRequest));
 			}
-			
+
 		} else {
 			/*
 			 * This provides csv download files for the content in the tables.
-			 * */		
+			 */
-		ModelConstructor constructQueryRunner = 
+			ModelConstructor constructQueryRunner = new EntityGrantCountConstructQueryRunner(
-				new EntityGrantCountConstructQueryRunner(entityURI, dataset, log);
+					entityURI, dataset, log);
 
-		Model constructedModel = constructQueryRunner.getConstructedModel();
+			Model constructedModel = constructQueryRunner.getConstructedModel();
-		
+
-		QueryRunner<Entity> queryManager = new EntityGrantCountQueryRunner(
+			QueryRunner<Entity> queryManager = new EntityGrantCountQueryRunner(
-				entityURI, constructedModel, log);	
+					entityURI, constructedModel, log);
-		
+
-		Entity entity = queryManager.getQueryResult();
+			Entity entity = queryManager.getQueryResult();
-		
+
-		
+			Map<String, Set<String>> subOrganizationTypesResult = OrganizationUtilityFunctions
-		Map<String, Set<String>> subOrganizationTypesResult = 
+					.getSubEntityTypes(log, dataset, entityURI);
-				OrganizationUtilityFunctions.getSubEntityTypes(
+
-						log, dataset, entityURI);
+			return prepareDataResponse(entity, entity.getSubEntities(),
+					subOrganizationTypesResult);
 
-		return prepareDataResponse(entity, entity.getSubEntities(), subOrganizationTypesResult);
-		
 		}
 
 	}
-	
+
 	@Override
 	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
 			Dataset dataset) throws MalformedQueryParametersException {
-		
+
-		throw new UnsupportedOperationException("Entity Grant Count " 
+		throw new UnsupportedOperationException("Entity Grant Count "
 				+ "does not provide Ajax response.");
 	}
-	
+
 	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
-			String subjectEntityURI)
+			String subjectEntityURI) throws MalformedQueryParametersException {
-			throws MalformedQueryParametersException {
+
-		
+		ModelConstructor constructQueryRunner = new EntityGrantCountConstructQueryRunner(
-		ModelConstructor constructQueryRunner = 
+				subjectEntityURI, dataset, log);
-				new EntityGrantCountConstructQueryRunner(subjectEntityURI, dataset, log);
+
-		
 		Model constructedModel = constructQueryRunner.getConstructedModel();
-		
+
 		QueryRunner<Entity> queryManager = new EntityGrantCountQueryRunner(
-				subjectEntityURI, constructedModel, log);	
+				subjectEntityURI, constructedModel, log);
 
 		Entity entity = queryManager.getQueryResult();
-		
+
 		if (entity.getEntityLabel().equals("no-label")) {
-			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
+			return prepareStandaloneDataErrorResponse(vitroRequest,
-		} else {	
+					subjectEntityURI);
-		
+		} else {
-			return getSubEntityTypesAndComputeDataResponse(
+
-					vitroRequest, log, dataset,
+			return getSubEntityTypesAndComputeDataResponse(vitroRequest, log,
-					subjectEntityURI, entity);
+					dataset, subjectEntityURI, entity);
 		}
 	}
 
@@ -172,41 +167,39 @@ public class EntityGrantCountRequestHandler implements
 			VitroRequest vitroRequest, Log log, Dataset dataset,
 			String subjectOrganization, Entity entity)
 			throws MalformedQueryParametersException {
-		
+
-		Map<String, Set<String>> subOrganizationTypesResult = 
+		Map<String, Set<String>> subOrganizationTypesResult = OrganizationUtilityFunctions
-				OrganizationUtilityFunctions.getSubEntityTypes(
+				.getSubEntityTypes(log, dataset, subjectOrganization);
-						log, dataset, subjectOrganization);
+
-		
+		return prepareStandaloneDataResponse(vitroRequest, entity,
-		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, 
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
-					 "application/octet-stream");
+				"application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+		fileData
-					 "{\"error\" : \"No Grants for this Organization found in VIVO.\"}");
+				.put(DataVisualizationController.FILE_CONTENT_KEY,
+						"{\"error\" : \"No Grants for this Organization found in VIVO.\"}");
 		return fileData;
 	}
-	
+
-	
 	private Map<String, String> prepareStandaloneDataResponse(
-										VitroRequest vitroRequest, 
+			VitroRequest vitroRequest, Entity entity,
-										Entity entity,
+			Map<String, Set<String>> subOrganizationTypesResult) 
-										Map<String, Set<String>> subOrganizationTypesResult) {
+			throws MalformedQueryParametersException {
 
 		Map<String, String> fileData = new HashMap<String, String>();
-		
+
-		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
-					 "application/octet-stream");
+				"application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-					 writeGrantsOverTimeJSON(vitroRequest, 
+				writeGrantsOverTimeJSON(vitroRequest, entity.getSubEntities(),
-							 				 entity.getSubEntities(), 
+						subOrganizationTypesResult));
-							 				 subOrganizationTypesResult));
 		return fileData;
 	}
 
@@ -218,68 +211,75 @@ public class EntityGrantCountRequestHandler implements
 	 * @param subentities
 	 * @param subOrganizationTypesResult
 	 */
-	private Map<String, String> prepareDataResponse(Entity entity, Set<SubEntity> subentities,
+	private Map<String, String> prepareDataResponse(Entity entity,
+			Set<SubEntity> subentities,
 			Map<String, Set<String>> subOrganizationTypesResult) {
 
 		String entityLabel = entity.getEntityLabel();
 
 		/*
-		* To make sure that null/empty records for entity names do not cause any mischief.
+		 * To make sure that null/empty records for entity names do not cause
-		* */
+		 * any mischief.
+		 */
 		if (StringUtils.isBlank(entityLabel)) {
 			entityLabel = "no-organization";
 		}
-		
+
 		String outputFileName = UtilityFunctions.slugify(entityLabel)
 				+ "_grants-per-year" + ".csv";
-		
+
-		
 		Map<String, String> fileData = new HashMap<String, String>();
-		
+
-		fileData.put(DataVisualizationController.FILE_NAME_KEY, 
+		fileData.put(DataVisualizationController.FILE_NAME_KEY, outputFileName);
-					 outputFileName);
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
-		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+				"application/octet-stream");
-					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+				getEntityGrantsPerYearCSVContent(subentities,
-				getEntityGrantsPerYearCSVContent(subentities, subOrganizationTypesResult));
+						subOrganizationTypesResult));
 		return fileData;
 	}
-	
 
-	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
+	private TemplateResponseValues prepareStandaloneMarkupResponse(
-			   String entityURI) {
+			VitroRequest vreq, String entityURI) {
 
 		String standaloneTemplate = "entityComparisonOnGrantsStandalone.ftl";
-		
+
-		String organizationLabel = OrganizationUtilityFunctions.getEntityLabelFromDAO(vreq,
+		String organizationLabel = OrganizationUtilityFunctions
-											  entityURI);
+				.getEntityLabelFromDAO(vreq, entityURI);
-		
+
 		Map<String, Object> body = new HashMap<String, Object>();
-		body.put("title", organizationLabel + " - Temporal Graph Visualization");
+		body
+				.put("title", organizationLabel
+						+ " - Temporal Graph Visualization");
 		body.put("organizationURI", entityURI);
-		body.put("organizationLocalName", UtilityFunctions.getIndividualLocalName(entityURI, vreq));
+		body.put("organizationLocalName", UtilityFunctions
-		body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
+				.getIndividualLocalName(entityURI, vreq));
+		body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory()
+				.getDefaultNamespace());
 		body.put("organizationLabel", organizationLabel);
-		
+
 		return new TemplateResponseValues(standaloneTemplate, body);
 	}
-	
+
 	/**
 	 * Function to generate a json file for year <-> grant count mapping.
-	 * @param vreq 
+	 * 
+	 * @param vreq
 	 * @param subentities
-	 * @param subOrganizationTypesResult  
+	 * @param subOrganizationTypesResult
+	 * @throws MalformedQueryParametersException
 	 */
-	private String writeGrantsOverTimeJSON(VitroRequest vreq, 
+	private String writeGrantsOverTimeJSON(VitroRequest vreq,
-										   Set<SubEntity> subentities, 
+			Set<SubEntity> subentities,
-										   Map<String, Set<String>> subOrganizationTypesResult) {
+			Map<String, Set<String>> subOrganizationTypesResult)
+			throws MalformedQueryParametersException {
 
 		Gson json = new Gson();
 		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
 
 		for (SubEntity subentity : subentities) {
-			JsonObject entityJson = new JsonObject(
+			JsonObject entityJson = new JsonObject(subentity
-					subentity.getIndividualLabel());
+					.getIndividualLabel());
 
 			List<List<Integer>> yearGrantCount = new ArrayList<List<Integer>>();
 
@@ -288,13 +288,12 @@ public class EntityGrantCountRequestHandler implements
 					.entrySet()) {
 
 				List<Integer> currentGrantYear = new ArrayList<Integer>();
-				if (grantEntry.getKey().equals(
+				if (grantEntry.getKey().equals(VOConstants.DEFAULT_GRANT_YEAR)) {
-						VOConstants.DEFAULT_GRANT_YEAR)) {
 					currentGrantYear.add(-1);
 				} else {
 					currentGrantYear.add(Integer.parseInt(grantEntry.getKey()));
 				}
-					
+
 				currentGrantYear.add(grantEntry.getValue());
 				yearGrantCount.add(currentGrantYear);
 			}
@@ -304,45 +303,47 @@ public class EntityGrantCountRequestHandler implements
 					subOrganizationTypesResult.get(entityJson.getLabel()));
 
 			entityJson.setEntityURI(subentity.getIndividualURI());
-			
+
-			if (UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI())) {
+			if (UtilityFunctions.isEntityAPerson(vreq, subentity
+					.getIndividualURI())) {
 				entityJson.setVisMode("PERSON");
 			} else {
 				entityJson.setVisMode("ORGANIZATION");
-			}			
+			}
-			
+
 			subEntitiesJson.add(entityJson);
 		}
-		
+
 		return json.toJson(subEntitiesJson);
 
 	}
 
-	private String getEntityGrantsPerYearCSVContent(
+	private String getEntityGrantsPerYearCSVContent(Set<SubEntity> subentities,
-					Set<SubEntity> subentities, 
+			Map<String, Set<String>> subOrganizationTypesResult) {
-					Map<String, Set<String>> subOrganizationTypesResult) {
 
 		StringBuilder csvFileContent = new StringBuilder();
-		
+
 		csvFileContent.append("Entity Name, Grant Count, Entity Type\n");
-		
+
 		for (SubEntity subEntity : subentities) {
-			
+
-			csvFileContent.append(StringEscapeUtils.escapeCsv(subEntity.getIndividualLabel()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(subEntity
+					.getIndividualLabel()));
 			csvFileContent.append(", ");
 			csvFileContent.append(subEntity.getActivities().size());
 			csvFileContent.append(", ");
-			
+
 			StringBuilder joinedTypes = new StringBuilder();
-			
+
 			for (String subOrganizationType : subOrganizationTypesResult
-													.get(subEntity.getIndividualLabel())) {
+					.get(subEntity.getIndividualLabel())) {
 				joinedTypes.append(subOrganizationType + "; ");
 			}
-			
+
-			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes.toString()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes
+					.toString()));
 			csvFileContent.append("\n");
-		}	
+		}
 
 		return csvFileContent.toString();
 	}
@@ -352,5 +353,5 @@ public class EntityGrantCountRequestHandler implements
 		// TODO Auto-generated method stub
 		return null;
 	}
-	
+
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java

@@ -32,6 +32,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison.Organizat
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Entity;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.GenericQueryMap;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.MapOfScienceActivity;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SubEntity;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.json.MapOfScience;
@@ -261,13 +262,19 @@ public class MapOfScienceVisualizationRequestHandler implements
 	}
 
 	private Map<String, String> prepareStandaloneDataErrorResponse() {
-
+		
+		GenericQueryMap errorDataResponse = new GenericQueryMap();
+		errorDataResponse.addEntry("error", "No Publications for this Entity found in VIVO.");
+		
+		Gson jsonErrorResponse = new Gson();
+		
 		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 Entity found in VIVO.\"}");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, jsonErrorResponse.toJson(errorDataResponse));
+		
 		return fileData;
 	}
 
@@ -326,7 +333,8 @@ public class MapOfScienceVisualizationRequestHandler implements
 
 	private Map<String, String> prepareStandaloneDataResponse(
 										VitroRequest vitroRequest, 
-										Entity entity) {
+										Entity entity) 
+			throws MalformedQueryParametersException {
 
 		Map<String, String> fileData = new HashMap<String, String>();
 		
@@ -362,9 +370,10 @@ public class MapOfScienceVisualizationRequestHandler implements
 	 * @param vreq 
 	 * @param subentities
 	 * @param subOrganizationTypesResult  
+	 * @throws MalformedQueryParametersException 
 	 */
 	private String writeMapOfScienceDataJSON(VitroRequest vreq, 
-										     Entity subjectEntity) {
+										     Entity subjectEntity) throws MalformedQueryParametersException {
 
 		Gson json = new Gson();
 		Set jsonContent = new HashSet();

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

@@ -29,6 +29,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaborationData;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VisConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Collaborator;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.GenericQueryMap;
@@ -251,11 +252,20 @@ public class UtilityFunctions {
 		return collaboratorshipNetworkURL != null ? collaboratorshipNetworkURL : "" ;
 	}
 	
-	public static boolean isEntityAPerson(VitroRequest vreq, String individualURI) {
+	public static boolean isEntityAPerson(VitroRequest vreq, String individualURI) 
-		return vreq.getWebappDaoFactory()
+		throws MalformedQueryParametersException {
-					.getIndividualDao()
+		Individual individualByURI = vreq.getWebappDaoFactory()
-					.getIndividualByURI(individualURI)
+						.getIndividualDao()
-					.isVClass("http://xmlns.com/foaf/0.1/Person");
+						.getIndividualByURI(individualURI);
+		
+		if (individualByURI != null) {
+
+			return individualByURI
+						.isVClass("http://xmlns.com/foaf/0.1/Person");	
+		} else {
+			throw new MalformedQueryParametersException("Individual with " + individualURI + " not found in the system.");
+		}
+		
 	}