1. refactored code in preparation for adding code structure for map of science vis

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

@@ -0,0 +1,26 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#assign standardVisualizationURLRoot ="/visualization">
+<#assign ajaxVisualizationURLRoot ="/visualizationAjax">
+<#assign dataVisualizationURLRoot ="/visualizationData">
+<#assign shortVisualizationURLRoot ="/vis">
+
+<#assign organizationURI ="${organizationURI?url}">
+<#assign organizationVivoProfileURL = "${urls.base}/individual?uri=${organizationURI}">
+
+<#assign subOrganizationVivoProfileURL = "${urls.base}/individual?">
+
+<#assign subOrganizationMapOfScienceCommonURL = "${urls.base}${shortVisualizationURLRoot}/map-of-science/">
+
+
+<#if organizationLocalName?has_content >
+    
+    <#assign organizationMapOfScienceURL = "${urls.base}${shortVisualizationURLRoot}/map-of-science/${organizationLocalName}">
+    
+<#else>
+
+    <#assign organizationMapOfScienceURL = '${urls.base}${shortVisualizationURLRoot}/map-of-science/?uri=${organizationURI}'>
+
+</#if>
+
+<#assign organizationMapOfScienceDataURL = "${urls.base}${dataVisualizationURLRoot}?vis=map-of-science&uri=${organizationURI}&vis_mode=json">

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

@@ -0,0 +1,38 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#-- The Order of each element in this file is very important. Do not make any changes to it unless making
+corresponding changes in the included Templates. -->
+
+
+<#include "scienceMapSetup.ftl">
+
+<script language="JavaScript" type="text/javascript">
+
+$(document).ready(function() {
+
+var scienceMapDataURL = "${organizationMapOfScienceDataURL}";
+
+
+    	$.ajax({
+            url: scienceMapDataURL
+            dataType: "json",
+            timeout: 5 * 60 * 1000,
+            success: function (data) {
+    		
+                if (data.error) {
+
+					alert("error");
+					alert(data);
+
+                } else {
+                	
+                	alert("success");
+					alert(data);
+                    
+                }
+            }
+        });
+
+});
+
+</script>

src/edu/cornell/mannlib/vitro/webapp/visualization/constants/VisConstants.java

@@ -14,4 +14,8 @@ public class VisConstants {
 	public static final String RESULT_FORMAT_PARAM = "RS_TEXT";
 	public static final String RDF_RESULT_FORMAT_PARAM = "RDF/XML-ABBREV";
 	
+	public static enum DataVisMode {
+		CSV, JSON
+	};
+	
 }

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

@@ -53,7 +53,7 @@ public class EntityPublicationCountRequestHandler implements
 		
 		if (StringUtils.isBlank(entityURI)) {
 			
-			entityURI = EntityComparisonUtilityFunctions
+			entityURI = OrganizationUtilityFunctions
 								.getStaffProvidedOrComputedHighestLevelOrganization(
 											log, 
 											dataset, 
@@ -120,7 +120,7 @@ public class EntityPublicationCountRequestHandler implements
 			throws MalformedQueryParametersException {
 		
 		Map<String, Set<String>> subOrganizationTypesResult = 
-				EntityComparisonUtilityFunctions.getSubEntityTypes(
+				OrganizationUtilityFunctions.getSubEntityTypes(
 						log, dataset, subjectEntityURI);
 		
 		return prepareStandaloneDataResponse(vitroRequest, entity, entity.getSubEntities(),
@@ -155,7 +155,7 @@ public class EntityPublicationCountRequestHandler implements
 								vitroRequest, 
 								log,
 								dataset,
-								EntityComparisonUtilityFunctions
+								OrganizationUtilityFunctions
 										.getStaffProvidedOrComputedHighestLevelOrganization(
 												log,
 												dataset, 
@@ -178,7 +178,7 @@ public class EntityPublicationCountRequestHandler implements
 			Entity entity = queryManager.getQueryResult();
 
 			Map<String, Set<String>> subOrganizationTypesResult = 
-					EntityComparisonUtilityFunctions.getSubEntityTypes(
+					OrganizationUtilityFunctions.getSubEntityTypes(
 							log, dataset, entityURI);
 
 			return prepareDataResponse(entity, entity.getSubEntities(), subOrganizationTypesResult);
@@ -251,7 +251,7 @@ public class EntityPublicationCountRequestHandler implements
 
         String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
 		
-        String organizationLabel = EntityComparisonUtilityFunctions
+        String organizationLabel = OrganizationUtilityFunctions
         									.getEntityLabelFromDAO(vreq,
         														   entityURI);
         

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

@@ -28,7 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.Generi
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.ModelConstructor;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.QueryRunner;
 
-public class EntityComparisonUtilityFunctions {
+public class OrganizationUtilityFunctions {
 
 	public static String getHighestLevelOrganizationURI(ResultSet resultSet,
 			Map<String, String> fieldLabelToOutputFieldLabel) {
@@ -94,7 +94,7 @@ public class EntityComparisonUtilityFunctions {
 				fieldLabelToOutputFieldLabel, aggregationRules, whereClause,
 				groupOrderClause, dataset, log);
 
-		String highestLevelOrgURI = EntityComparisonUtilityFunctions
+		String highestLevelOrgURI = OrganizationUtilityFunctions
 				.getHighestLevelOrganizationURI(
 						highestLevelOrganizationQueryHandler.getQueryResult(),
 						fieldLabelToOutputFieldLabel);
@@ -165,7 +165,7 @@ public class EntityComparisonUtilityFunctions {
 		/*
 		 * If the provided value was not proper compute it yourself.
 		 * */
-		return EntityComparisonUtilityFunctions.getHighestLevelOrganizationURI(log, dataset);
+		return OrganizationUtilityFunctions.getHighestLevelOrganizationURI(log, dataset);
 	}
 	
 	public static Entity mergeEntityIfShareSameURI(Entity entityA, Entity entityB) {

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

@@ -1,11 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.entitycomparison.cached;
-
-public class EntityComparisonConstants {
-	
-	public static enum DataVisMode {
-		CSV, JSON
-	};
-
-}

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

@@ -22,8 +22,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.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.freemarker.entitycomparison.EntityComparisonUtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.entitycomparison.OrganizationUtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.JsonObject;
@@ -55,7 +56,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 			String entityURI) throws MalformedQueryParametersException {
 		if (StringUtils.isBlank(entityURI)) {
 			
-			entityURI = EntityComparisonUtilityFunctions
+			entityURI = OrganizationUtilityFunctions
 								.getStaffProvidedOrComputedHighestLevelOrganization(
 										log,
 										dataset, 
@@ -105,19 +106,19 @@ public class TemporalGrantVisualizationRequestHandler implements
 								log,
 								dataset, 
 								entityURI,
-								EntityComparisonConstants.DataVisMode.JSON);
+								VisConstants.DataVisMode.JSON);
 			} else {
 				
 				return getSubjectEntityAndGenerateDataResponse(
 								vitroRequest, 
 								log,
 								dataset,
-								EntityComparisonUtilityFunctions
+								OrganizationUtilityFunctions
 										.getStaffProvidedOrComputedHighestLevelOrganization(
 												log,
 												dataset, 
 												vitroRequest),
-								EntityComparisonConstants.DataVisMode.JSON);
+								VisConstants.DataVisMode.JSON);
 			}
 			
 		} else {
@@ -129,7 +130,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 					log,
 					dataset,
 					entityURI,
-					EntityComparisonConstants.DataVisMode.CSV);
+					VisConstants.DataVisMode.CSV);
 		}
 	}
 	
@@ -157,7 +158,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 	
 	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
-			String subjectEntityURI, EntityComparisonConstants.DataVisMode visMode)
+			String subjectEntityURI, VisConstants.DataVisMode visMode)
 			throws MalformedQueryParametersException {
 		
 		Entity organizationEntity = SelectOnModelUtilities
@@ -165,7 +166,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 
 		if (organizationEntity.getSubEntities() ==  null) {
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataErrorResponse();
 			} else {
 				return prepareDataErrorResponse();
@@ -194,14 +195,14 @@ public class TemporalGrantVisualizationRequestHandler implements
 			grantURIForAssociatedPeopleToVO = SelectOnModelUtilities
 						.getGrantsForAssociatedPeople(dataset, organizationWithAssociatedPeople.getSubEntities());
 			
-			organizationEntity = EntityComparisonUtilityFunctions.mergeEntityIfShareSameURI(
+			organizationEntity = OrganizationUtilityFunctions.mergeEntityIfShareSameURI(
 										organizationEntity,
 										organizationWithAssociatedPeople);
 		}
 		
 		if (allGrantURIToVO.isEmpty() && grantURIForAssociatedPeopleToVO.isEmpty()) {
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataErrorResponse();
 			} else {
 				return prepareDataErrorResponse();
@@ -209,7 +210,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 			
 		} else {	
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataResponse(vitroRequest, organizationEntity);
 			} else {
 				return prepareDataResponse(organizationEntity);
@@ -283,7 +284,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 
 		String standaloneTemplate = "entityComparisonOnGrantsStandalone.ftl";
 		
-		String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vreq,
+		String organizationLabel = OrganizationUtilityFunctions.getEntityLabelFromDAO(vreq,
 											  entityURI);
 		
 		Map<String, Object> body = new HashMap<String, Object>();

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

@@ -22,8 +22,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.Tem
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.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.freemarker.entitycomparison.EntityComparisonUtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.entitycomparison.OrganizationUtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.JsonObject;
@@ -66,7 +67,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		
 		if (StringUtils.isBlank(entityURI)) {
 			
-			entityURI = EntityComparisonUtilityFunctions
+			entityURI = OrganizationUtilityFunctions
 								.getStaffProvidedOrComputedHighestLevelOrganization(
 											log, 
 											dataset, 
@@ -85,7 +86,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 
 	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
 			VitroRequest vitroRequest, Log log, Dataset dataset,
-			String subjectEntityURI, EntityComparisonConstants.DataVisMode visMode)
+			String subjectEntityURI, VisConstants.DataVisMode visMode)
 			throws MalformedQueryParametersException {
 		
 		Entity organizationEntity = SelectOnModelUtilities
@@ -93,7 +94,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		
 		if (organizationEntity.getSubEntities() ==  null) {
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataErrorResponse();
 			} else {
 				return prepareDataErrorResponse();
@@ -113,14 +114,14 @@ public class TemporalPublicationVisualizationRequestHandler implements
 			documentURIForAssociatedPeopleTOVO = SelectOnModelUtilities
 						.getPublicationsForAssociatedPeople(dataset, organizationWithAssociatedPeople.getSubEntities());
 			
-			organizationEntity = EntityComparisonUtilityFunctions.mergeEntityIfShareSameURI(
+			organizationEntity = OrganizationUtilityFunctions.mergeEntityIfShareSameURI(
 										organizationEntity,
 										organizationWithAssociatedPeople);
 		}
 		
 		if (allDocumentURIToVOs.isEmpty() && documentURIForAssociatedPeopleTOVO.isEmpty()) {
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataErrorResponse();
 			} else {
 				return prepareDataErrorResponse();
@@ -128,7 +129,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 			
 		} else {	
 			
-			if (EntityComparisonConstants.DataVisMode.JSON.equals(visMode)) {
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataResponse(vitroRequest, organizationEntity);
 			} else {
 				return prepareDataResponse(organizationEntity);
@@ -217,19 +218,19 @@ public class TemporalPublicationVisualizationRequestHandler implements
 								log,
 								dataset, 
 								entityURI,
-								EntityComparisonConstants.DataVisMode.JSON);
+								VisConstants.DataVisMode.JSON);
 			} else {
 				
 				return getSubjectEntityAndGenerateDataResponse(
 								vitroRequest, 
 								log,
 								dataset,
-								EntityComparisonUtilityFunctions
+								OrganizationUtilityFunctions
 										.getStaffProvidedOrComputedHighestLevelOrganization(
 												log,
 												dataset, 
 												vitroRequest),
-								EntityComparisonConstants.DataVisMode.JSON);
+								VisConstants.DataVisMode.JSON);
 			}
 			
 		} else {
@@ -242,7 +243,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 						log,
 						dataset,
 						entityURI,
-						EntityComparisonConstants.DataVisMode.CSV);
+						VisConstants.DataVisMode.CSV);
 			
 		}
 		
@@ -274,7 +275,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 
         String standaloneTemplate = "entityComparisonOnPublicationsStandalone.ftl";
 		
-        String organizationLabel = EntityComparisonUtilityFunctions
+        String organizationLabel = OrganizationUtilityFunctions
         									.getEntityLabelFromDAO(vreq,
         														   entityURI);
         

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

@@ -24,7 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.Data
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
 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.entitycomparison.OrganizationUtilityFunctions;
 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;
@@ -54,7 +54,7 @@ public class EntityGrantCountRequestHandler implements
 			String entityURI) throws MalformedQueryParametersException {
 		if (StringUtils.isBlank(entityURI)) {
 			
-			entityURI = EntityComparisonUtilityFunctions
+			entityURI = OrganizationUtilityFunctions
 								.getStaffProvidedOrComputedHighestLevelOrganization(
 										log,
 										dataset, 
@@ -102,7 +102,7 @@ public class EntityGrantCountRequestHandler implements
 								vitroRequest, 
 								log,
 								dataset,
-								EntityComparisonUtilityFunctions
+								OrganizationUtilityFunctions
 										.getStaffProvidedOrComputedHighestLevelOrganization(
 												log,
 												dataset, 
@@ -125,7 +125,7 @@ public class EntityGrantCountRequestHandler implements
 		
 		
 		Map<String, Set<String>> subOrganizationTypesResult = 
-				EntityComparisonUtilityFunctions.getSubEntityTypes(
+				OrganizationUtilityFunctions.getSubEntityTypes(
 						log, dataset, entityURI);
 
 		return prepareDataResponse(entity, entity.getSubEntities(), subOrganizationTypesResult);
@@ -173,7 +173,7 @@ public class EntityGrantCountRequestHandler implements
 			throws MalformedQueryParametersException {
 		
 		Map<String, Set<String>> subOrganizationTypesResult = 
-				EntityComparisonUtilityFunctions.getSubEntityTypes(
+				OrganizationUtilityFunctions.getSubEntityTypes(
 						log, dataset, subjectOrganization);
 		
 		return prepareStandaloneDataResponse(vitroRequest, entity, subOrganizationTypesResult);
@@ -250,7 +250,7 @@ public class EntityGrantCountRequestHandler implements
 
 		String standaloneTemplate = "entityComparisonOnGrantsStandalone.ftl";
 		
-		String organizationLabel = EntityComparisonUtilityFunctions.getEntityLabelFromDAO(vreq,
+		String organizationLabel = OrganizationUtilityFunctions.getEntityLabelFromDAO(vreq,
 											  entityURI);
 		
 		Map<String, Object> body = new HashMap<String, Object>();

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

@@ -0,0 +1,373 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.mapofscience;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.logging.Log;
+
+import com.google.gson.Gson;
+import com.hp.hpl.jena.query.Dataset;
+
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
+import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.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.freemarker.entitycomparison.OrganizationUtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
+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;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubjectEntityJSON;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.SelectOnModelUtilities;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
+
+public class MapOfScienceVisualizationRequestHandler implements
+		VisualizationRequestHandler {
+	
+	@Override
+	public ResponseValues generateStandardVisualization(
+			VitroRequest vitroRequest, Log log, Dataset dataset)
+			throws MalformedQueryParametersException {
+		
+
+		String entityURI = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		
+		return generateStandardVisualizationForScienceMapVis(
+				vitroRequest, log, dataset, entityURI);
+	}
+	
+	@Override
+	public ResponseValues generateVisualizationForShortURLRequests(
+			Map<String, String> parameters, VitroRequest vitroRequest, Log log,
+			Dataset dataset) throws MalformedQueryParametersException {
+
+		
+		return generateStandardVisualizationForScienceMapVis(
+				vitroRequest, log, dataset, parameters.get(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY));
+		
+	}
+
+	private ResponseValues generateStandardVisualizationForScienceMapVis(
+			VitroRequest vitroRequest, Log log, Dataset dataset,
+			String entityURI) throws MalformedQueryParametersException {
+		
+		if (StringUtils.isBlank(entityURI)) {
+			
+			entityURI = OrganizationUtilityFunctions
+								.getStaffProvidedOrComputedHighestLevelOrganization(
+											log, 
+											dataset, 
+											vitroRequest);
+			
+		}
+		
+		
+//		System.out.println("current models in the system are");
+//		for (Map.Entry<String, Model> entry : ConstructedModelTracker.getAllModels().entrySet()) {
+//			System.out.println(entry.getKey() + " -> " + entry.getValue().size());
+//		}
+//		
+		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
+	}
+
+	private Map<String, String> getSubjectEntityAndGenerateDataResponse(
+			VitroRequest vitroRequest, Log log, Dataset dataset,
+			String subjectEntityURI, VisConstants.DataVisMode visMode)
+			throws MalformedQueryParametersException {
+		
+		Entity organizationEntity = SelectOnModelUtilities
+				.getSubjectOrganizationHierarchy(dataset, subjectEntityURI);
+		
+		if (organizationEntity.getSubEntities() ==  null) {
+			
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
+				return prepareStandaloneDataErrorResponse();
+			} else {
+				return prepareDataErrorResponse();
+			}
+		}
+		
+		Map<String, Activity> documentURIForAssociatedPeopleTOVO = new HashMap<String, Activity>();
+		Map<String, Activity> allDocumentURIToVOs = new HashMap<String, Activity>();
+		
+		allDocumentURIToVOs = SelectOnModelUtilities.getPublicationsForAllSubOrganizations(dataset, organizationEntity);
+		
+		Entity organizationWithAssociatedPeople = SelectOnModelUtilities
+				.getSubjectOrganizationAssociatedPeople(dataset, subjectEntityURI);
+		
+		if (organizationWithAssociatedPeople.getSubEntities() !=  null) {
+			
+			documentURIForAssociatedPeopleTOVO = SelectOnModelUtilities
+						.getPublicationsForAssociatedPeople(dataset, organizationWithAssociatedPeople.getSubEntities());
+			
+			organizationEntity = OrganizationUtilityFunctions.mergeEntityIfShareSameURI(
+										organizationEntity,
+										organizationWithAssociatedPeople);
+		}
+		
+		if (allDocumentURIToVOs.isEmpty() && documentURIForAssociatedPeopleTOVO.isEmpty()) {
+			
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
+				return prepareStandaloneDataErrorResponse();
+			} else {
+				return prepareDataErrorResponse();
+			}
+			
+		} else {	
+			
+			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
+				return prepareStandaloneDataResponse(vitroRequest, organizationEntity);
+			} else {
+				return prepareDataResponse(organizationEntity);
+			}
+		}
+	}
+	
+	/**
+	 * Provides response when json file containing the publication count over the
+	 * years is requested.
+	 * 
+	 * @param entity
+	 * @param subentities
+	 * @param subOrganizationTypesResult
+	 */
+	private Map<String, String> prepareDataResponse(Entity entity) {
+
+		String entityLabel = entity.getEntityLabel();
+
+		/*
+		* 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(entity));
+		return fileData;
+	}
+	
+	private Map<String, String> prepareDataErrorResponse() {
+		
+		String outputFileName = "no-organization_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, "");
+		return fileData;
+	}
+
+	private Map<String, String> prepareStandaloneDataErrorResponse() {
+
+		Map<String, String> fileData = new HashMap<String, String>();
+		
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "application/octet-stream");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+					 "{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
+		return fileData;
+	}
+
+	@Override
+	public Map<String, String> generateDataVisualization(
+			VitroRequest vitroRequest, Log log, Dataset dataset)
+			throws MalformedQueryParametersException {
+
+		String entityURI = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		
+		/*
+		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
+		 * */
+		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+					.equalsIgnoreCase(vitroRequest.getParameter(
+							VisualizationFrameworkConstants.VIS_MODE_KEY))) {
+			
+			if (StringUtils.isNotBlank(entityURI)) {
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								dataset, 
+								entityURI,
+								VisConstants.DataVisMode.JSON);
+			} else {
+				
+				return getSubjectEntityAndGenerateDataResponse(
+								vitroRequest, 
+								log,
+								dataset,
+								OrganizationUtilityFunctions
+										.getStaffProvidedOrComputedHighestLevelOrganization(
+												log,
+												dataset, 
+												vitroRequest),
+								VisConstants.DataVisMode.JSON);
+			}
+			
+		} else {
+			/*
+			 * This provides csv download files for the content in the tables.
+			 * */
+			
+				return getSubjectEntityAndGenerateDataResponse(
+						vitroRequest, 
+						log,
+						dataset,
+						entityURI,
+						VisConstants.DataVisMode.CSV);
+			
+		}
+		
+	}
+	
+	
+	@Override
+	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
+			Dataset dataset) throws MalformedQueryParametersException {
+		throw new UnsupportedOperationException("Entity Pub Count does not provide Ajax Response.");
+	}
+
+	private Map<String, String> prepareStandaloneDataResponse(
+										VitroRequest vitroRequest, 
+										Entity entity) {
+
+		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));
+		return fileData;
+	}
+	
+	private TemplateResponseValues prepareStandaloneMarkupResponse(VitroRequest vreq,
+																   String entityURI) {
+
+        String standaloneTemplate = "mapOfScienceStandalone.ftl";
+		
+        String organizationLabel = OrganizationUtilityFunctions
+        									.getEntityLabelFromDAO(vreq,
+        														   entityURI);
+        
+        Map<String, Object> body = new HashMap<String, Object>();
+        body.put("title", organizationLabel + " - Map of Science 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 subentities
+	 * @param subOrganizationTypesResult  
+	 */
+	private String writePublicationsOverTimeJSON(VitroRequest vreq, 
+												 Entity subjectEntity) {
+
+		Gson json = new Gson();
+		Set subEntitiesJson = new HashSet();
+
+		for (SubEntity subentity : subjectEntity.getSubEntities()) {
+			
+			JsonObject entityJson = new JsonObject(
+					subentity.getIndividualLabel());
+
+			List<List<Integer>> yearPubCount = new ArrayList<List<Integer>>();
+
+			for (Map.Entry<String, Integer> pubEntry : UtilityFunctions
+					.getYearToActivityCount(subentity.getActivities())
+					.entrySet()) {
+
+				List<Integer> currentPubYear = new ArrayList<Integer>();
+				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.setOrganizationTypes(subentity.getEntityTypeLabels());
+			
+			entityJson.setEntityURI(subentity.getIndividualURI());
+			
+			entityJson.setLastCachedAtDateTime(subentity.getLastCachedAtDateTime());
+			
+			if (subentity.getEntityClass().equals(VOConstants.EntityClassType.PERSON)) {
+				entityJson.setVisMode("PERSON");
+			} else if (subentity.getEntityClass().equals(VOConstants.EntityClassType.ORGANIZATION)) {
+				entityJson.setVisMode("ORGANIZATION");
+			}
+			
+			subEntitiesJson.add(entityJson);
+		}
+		
+		SubjectEntityJSON subjectEntityJSON = new SubjectEntityJSON(subjectEntity.getEntityLabel(),
+																	subjectEntity.getEntityURI(),
+																	subjectEntity.getParents());
+		
+		subEntitiesJson.add(subjectEntityJSON);
+		
+		return json.toJson(subEntitiesJson);
+	}
+
+	private String getEntityPublicationsPerYearCSVContent(Entity entity) {
+
+		StringBuilder csvFileContent = new StringBuilder();
+		
+		csvFileContent.append("Entity Name, Publication Count, Entity Type\n");
+		
+		for (SubEntity subEntity : entity.getSubEntities()) {
+			
+			csvFileContent.append(StringEscapeUtils.escapeCsv(subEntity.getIndividualLabel()));
+			csvFileContent.append(", ");
+			csvFileContent.append(subEntity.getActivities().size());
+			csvFileContent.append(", ");
+			
+			String allTypes = StringUtils.join(subEntity.getEntityTypeLabels(), "; ");
+			
+			csvFileContent.append(StringEscapeUtils.escapeCsv(allTypes));
+			csvFileContent.append("\n");
+		}
+		return csvFileContent.toString();
+	}
+
+}