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

@@ -211,3 +211,25 @@ 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

@@ -177,8 +177,8 @@ var DisciplineMarkerManager = ScimapMarkerManager.extend({
 		marker.setContent( 
 				'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
 				+ 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;
 	}
@@ -198,8 +198,8 @@ var SubdisciplineMarkerManager = ScimapMarkerManager.extend({
 		marker.setContent(
 			'<div style="font-size: 80%; padding: 5px; text-align: left;"><b>'
 			+ 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;

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

@@ -55,10 +55,8 @@ public class EntityPublicationCountRequestHandler implements
 		if (StringUtils.isBlank(entityURI)) {
 
 			entityURI = OrganizationUtilityFunctions
-								.getStaffProvidedOrComputedHighestLevelOrganization(
+					.getStaffProvidedOrComputedHighestLevelOrganization(log,
-											log, 
+							dataset, vitroRequest);
-											dataset, 
-											vitroRequest);
 
 		}
 
@@ -72,17 +70,20 @@ 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 = 
+		ModelConstructor constructQueryRunner = new EntityPublicationCountConstructQueryRunner(
-				new EntityPublicationCountConstructQueryRunner(subjectEntityURI, dataset, log);
+				subjectEntityURI, dataset, log);
 
 		Model constructedModel = constructQueryRunner.getConstructedModel();
 
@@ -93,13 +94,13 @@ public class EntityPublicationCountRequestHandler implements
 
 		if (entity.getEntityLabel().equals("no-label")) {
 
-			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
+			return prepareStandaloneDataErrorResponse(vitroRequest,
+					subjectEntityURI);
 
 		} else {
 
-			return getSubEntityTypesAndComputeDataResponse(
+			return getSubEntityTypesAndComputeDataResponse(vitroRequest, log,
-					vitroRequest, log, dataset,
+					dataset, subjectEntityURI, entity);
-					subjectEntityURI, entity);
 		}
 	}
 
@@ -110,7 +111,8 @@ public class EntityPublicationCountRequestHandler implements
 
 		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
 				"application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+		fileData
+				.put(DataVisualizationController.FILE_CONTENT_KEY,
 						"{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
 		return fileData;
 	}
@@ -120,12 +122,11 @@ public class EntityPublicationCountRequestHandler implements
 			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.getSubEntities(),
+		return prepareStandaloneDataResponse(vitroRequest, entity, entity
-				subOrganizationTypesResult);
+				.getSubEntities(), subOrganizationTypesResult);
 	}
 
 	@Override
@@ -137,19 +138,17 @@ public class EntityPublicationCountRequestHandler implements
 				.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(
@@ -158,18 +157,16 @@ public class EntityPublicationCountRequestHandler implements
 						dataset,
 						OrganizationUtilityFunctions
 								.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();
 
@@ -178,39 +175,41 @@ public class EntityPublicationCountRequestHandler implements
 
 			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";
 		}
@@ -218,49 +217,50 @@ public class EntityPublicationCountRequestHandler implements
 		String outputFileName = UtilityFunctions.slugify(entityLabel)
 				+ "_publications-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,
 				"application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-				getEntityPublicationsPerYearCSVContent(subentities, subOrganizationTypesResult));
+				getEntityPublicationsPerYearCSVContent(subentities,
-		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, 
-					 "application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-					 writePublicationsOverTimeJSON(vitroRequest, 
-							 					   entity.getSubEntities(), 
 						subOrganizationTypesResult));
 		return fileData;
 	}
 
-	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
+	private Map<String, String> prepareStandaloneDataResponse(
-																   String entityURI) {
+			VitroRequest vitroRequest, Entity entity,
+			Set<SubEntity> subentities,
+			Map<String, Set<String>> subOrganizationTypesResult)
+			throws MalformedQueryParametersException {
+
+		Map<String, String> fileData = new HashMap<String, String>();
+
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
+				"application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
+				writePublicationsOverTimeJSON(vitroRequest, entity
+						.getSubEntities(), subOrganizationTypesResult));
+		return fileData;
+	}
+
+	private TemplateResponseValues prepareStandaloneMarkupResponse(
+			VitroRequest vreq, String entityURI) {
 
 		String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
 
 		String organizationLabel = OrganizationUtilityFunctions
-        									.getEntityLabelFromDAO(vreq,
+				.getEntityLabelFromDAO(vreq, entityURI);
-        														   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);
@@ -268,21 +268,23 @@ public class EntityPublicationCountRequestHandler implements
 
 	/**
 	 * Function to generate a json file for year <-> publication count mapping.
+	 * 
 	 * @param vreq
 	 * @param subentities
 	 * @param subOrganizationTypesResult
+	 * @throws MalformedQueryParametersException
 	 */
 	private String writePublicationsOverTimeJSON(VitroRequest vreq,
 			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>>();
 
@@ -291,7 +293,8 @@ 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()));
@@ -307,7 +310,8 @@ public class EntityPublicationCountRequestHandler implements
 
 			entityJson.setEntityURI(subentity.getIndividualURI());
 
-			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI());
+			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity
+					.getIndividualURI());
 
 			if (isPerson) {
 				entityJson.setVisMode("PERSON");
@@ -329,7 +333,8 @@ public class EntityPublicationCountRequestHandler implements
 
 		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(", ");
@@ -341,7 +346,8 @@ public class EntityPublicationCountRequestHandler implements
 				joinedTypes.append(subOrganizationType + "; ");
 			}
 
-			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes.toString()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes
+					.toString()));
 			csvFileContent.append("\n");
 		}
 		return csvFileContent.toString();

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

@@ -34,7 +34,6 @@ 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 {
 
@@ -56,10 +55,8 @@ public class EntityGrantCountRequestHandler implements
 		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));
 
 	}
 
@@ -84,19 +85,17 @@ public class EntityGrantCountRequestHandler implements
 				.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
 						.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
 
 			if (StringUtils.isNotBlank(entityURI)) {
 
-				return getSubjectEntityAndGenerateDataResponse(
+				return getSubjectEntityAndGenerateDataResponse(vitroRequest,
-								vitroRequest, 
+						log, dataset, entityURI);
-								log,
-								dataset, 
-								entityURI);
 			} else {
 
 				return getSubjectEntityAndGenerateDataResponse(
@@ -105,17 +104,15 @@ public class EntityGrantCountRequestHandler implements
 						dataset,
 						OrganizationUtilityFunctions
 								.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();
 
@@ -124,12 +121,11 @@ public class EntityGrantCountRequestHandler implements
 
 			Entity entity = queryManager.getQueryResult();
 
+			Map<String, Set<String>> subOrganizationTypesResult = OrganizationUtilityFunctions
+					.getSubEntityTypes(log, dataset, entityURI);
 
-		Map<String, Set<String>> subOrganizationTypesResult = 
+			return prepareDataResponse(entity, entity.getSubEntities(),
-				OrganizationUtilityFunctions.getSubEntityTypes(
+					subOrganizationTypesResult);
-						log, dataset, entityURI);
-
-		return prepareDataResponse(entity, entity.getSubEntities(), subOrganizationTypesResult);
 
 		}
 
@@ -145,11 +141,10 @@ public class EntityGrantCountRequestHandler implements
 
 	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
-			String subjectEntityURI)
+			String subjectEntityURI) throws MalformedQueryParametersException {
-			throws MalformedQueryParametersException {
 
-		ModelConstructor constructQueryRunner = 
+		ModelConstructor constructQueryRunner = new EntityGrantCountConstructQueryRunner(
-				new EntityGrantCountConstructQueryRunner(subjectEntityURI, dataset, log);
+				subjectEntityURI, dataset, log);
 
 		Model constructedModel = constructQueryRunner.getConstructedModel();
 
@@ -159,12 +154,12 @@ public class EntityGrantCountRequestHandler implements
 		Entity entity = queryManager.getQueryResult();
 
 		if (entity.getEntityLabel().equals("no-label")) {
-			return prepareStandaloneDataErrorResponse(vitroRequest, subjectEntityURI);
+			return prepareStandaloneDataErrorResponse(vitroRequest,
+					subjectEntityURI);
 		} else {
 
-			return getSubEntityTypesAndComputeDataResponse(
+			return getSubEntityTypesAndComputeDataResponse(vitroRequest, log,
-					vitroRequest, log, dataset,
+					dataset, subjectEntityURI, entity);
-					subjectEntityURI, entity);
 		}
 	}
 
@@ -173,14 +168,13 @@ public class EntityGrantCountRequestHandler implements
 			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, subOrganizationTypesResult);
+		return prepareStandaloneDataResponse(vitroRequest, entity,
+				subOrganizationTypesResult);
 	}
 
-	
 	private Map<String, String> prepareStandaloneDataErrorResponse(
 			VitroRequest vitroRequest, String subjectEntityURI) {
 
@@ -188,24 +182,23 @@ public class EntityGrantCountRequestHandler implements
 
 		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY,
 				"application/octet-stream");
-		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+		fileData
+				.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,
 				"application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-					 writeGrantsOverTimeJSON(vitroRequest, 
+				writeGrantsOverTimeJSON(vitroRequest, entity.getSubEntities(),
-							 				 entity.getSubEntities(), 
 						subOrganizationTypesResult));
 		return fileData;
 	}
@@ -218,14 +211,16 @@ 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";
 		}
@@ -233,32 +228,34 @@ public class EntityGrantCountRequestHandler implements
 		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,
 				"application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
-				getEntityGrantsPerYearCSVContent(subentities, subOrganizationTypesResult));
+				getEntityGrantsPerYearCSVContent(subentities,
+						subOrganizationTypesResult));
 		return fileData;
 	}
 
-
+	private TemplateResponseValues prepareStandaloneMarkupResponse(
-	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
+			VitroRequest vreq, String entityURI) {
-			   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);
@@ -266,20 +263,23 @@ public class EntityGrantCountRequestHandler implements
 
 	/**
 	 * Function to generate a json file for year <-> grant count mapping.
+	 * 
 	 * @param vreq
 	 * @param subentities
 	 * @param subOrganizationTypesResult
+	 * @throws MalformedQueryParametersException
 	 */
 	private String writeGrantsOverTimeJSON(VitroRequest vreq,
 			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>>();
 
@@ -288,8 +288,7 @@ 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()));
@@ -305,7 +304,8 @@ public class EntityGrantCountRequestHandler implements
 
 			entityJson.setEntityURI(subentity.getIndividualURI());
 
-			if (UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI())) {
+			if (UtilityFunctions.isEntityAPerson(vreq, subentity
+					.getIndividualURI())) {
 				entityJson.setVisMode("PERSON");
 			} else {
 				entityJson.setVisMode("ORGANIZATION");
@@ -318,8 +318,7 @@ public class EntityGrantCountRequestHandler implements
 
 	}
 
-	private String getEntityGrantsPerYearCSVContent(
+	private String getEntityGrantsPerYearCSVContent(Set<SubEntity> subentities,
-					Set<SubEntity> subentities, 
 			Map<String, Set<String>> subOrganizationTypesResult) {
 
 		StringBuilder csvFileContent = new StringBuilder();
@@ -328,7 +327,8 @@ public class EntityGrantCountRequestHandler implements
 
 		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(", ");
@@ -340,7 +340,8 @@ public class EntityGrantCountRequestHandler implements
 				joinedTypes.append(subOrganizationType + "; ");
 			}
 
-			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes.toString()));
+			csvFileContent.append(StringEscapeUtils.escapeCsv(joinedTypes
+					.toString()));
 			csvFileContent.append("\n");
 		}
 

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;
@@ -262,12 +263,18 @@ 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 {
+		Individual individualByURI = vreq.getWebappDaoFactory()
 						.getIndividualDao()
-					.getIndividualByURI(individualURI)
+						.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.");
+		}
+		
 	}