1. Fix for incorrect error response in case of DataVisualization request. see http://issues.library.cornell.edu/browse/NIHVIVO-2200

2. Also fix for incorrect logic flow in resolving the highest level org.

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

@@ -79,13 +79,9 @@ public class DataVisualizationController extends VitroHttpServlet {
 				
 			} catch (MalformedQueryParametersException e) {
 
-	    		UtilityFunctions.handleMalformedParameters("Visualization Query Error",
+	    		UtilityFunctions.handleMalformedParameters(e.getMessage(),
-						   e.getMessage(),
-						   vreq,
-						   request,
 						   response,
 						   log);
-				
 			}
 			
             return;
@@ -93,10 +89,7 @@ public class DataVisualizationController extends VitroHttpServlet {
     	} else {
     		
     		UtilityFunctions.handleMalformedParameters(
-    								"Visualization Query Error",
     								"Inappropriate query parameters were submitted.",
-    								vreq,
-    								request,
     								response,
     								log);
     		

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

@@ -140,8 +140,6 @@ public class EntityComparisonUtilityFunctions {
 			Dataset dataset, VitroRequest vitroRequest)
 			throws MalformedQueryParametersException {
 		
-		String finalHighestLevelOrganizationURI = "";
-		
 		String staffProvidedHighestLevelOrganization = ConfigurationProperties.getBean(vitroRequest)
 					.getProperty("visualization.topLevelOrg");
 		
@@ -157,13 +155,15 @@ public class EntityComparisonUtilityFunctions {
 			IRIFactory iRIFactory = IRIFactory.jenaImplementation();
 			IRI iri = iRIFactory.create(staffProvidedHighestLevelOrganization);
 		    
-			if (iri.hasViolation(false)) {
+			
-				finalHighestLevelOrganizationURI = EntityComparisonUtilityFunctions
+			if (!iri.hasViolation(false)) {
-					.getHighestLevelOrganizationURI(log, dataset);
+		    	return staffProvidedHighestLevelOrganization;
-		    } else {
-		    	finalHighestLevelOrganizationURI = staffProvidedHighestLevelOrganization;
 		    }
 		} 
-		return finalHighestLevelOrganizationURI;
+		
+		/*
+		 * If the provided value was not proper compute it yourself.
+		 * */
+		return EntityComparisonUtilityFunctions.getHighestLevelOrganizationURI(log, dataset);
 	}
 }

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

@@ -51,6 +51,7 @@ public class EntityPublicationCountRequestHandler implements
 											log, 
 											dataset, 
 											vitroRequest);
+			
 		}
 		return prepareStandaloneMarkupResponse(vitroRequest, entityURI);
 	}

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

@@ -11,7 +11,6 @@ import java.util.TreeMap;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang.StringUtils;
@@ -19,6 +18,8 @@ import org.apache.commons.logging.Log;
 import org.joda.time.DateTime;
 import org.joda.time.format.DateTimeFormatter;
 
+import com.google.gson.Gson;
+
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -26,12 +27,14 @@ import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.ParamMap;
 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.freemarker.collaborationutils.CollaborationData;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Collaborator;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.GenericQueryMap;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
 
 public class UtilityFunctions {
@@ -142,30 +145,18 @@ public class UtilityFunctions {
         return new TemplateResponseValues(VisualizationFrameworkConstants.ERROR_TEMPLATE, body);
     }
     
-    public static void handleMalformedParameters(String errorPageTitle,
+    public static void handleMalformedParameters(String errorMessage,
-    											 String errorMessage,
+    											 HttpServletResponse response,
-												 VitroRequest vitroRequest,
-												 HttpServletRequest request,
-												 HttpServletResponse response,
 												 Log log)
-		throws ServletException, IOException {
+		throws IOException {
 		
-		Portal portal = vitroRequest.getPortal();
+		GenericQueryMap errorDataResponse = new GenericQueryMap();
+		errorDataResponse.addEntry("error", errorMessage);
 		
-		request.setAttribute("error", errorMessage);
+		Gson jsonErrorResponse = new Gson();
 		
-		RequestDispatcher requestDispatcher = request.getRequestDispatcher(Controllers.BASIC_JSP);
+    	response.setContentType("application/octet-stream");
-		request.setAttribute("bodyJsp", "/templates/visualization/visualization_error.jsp");
+    	response.getWriter().write(jsonErrorResponse.toJson(errorDataResponse));
-		request.setAttribute("portalBean", portal);
-		request.setAttribute("title", errorPageTitle);
-		
-		try {
-			requestDispatcher.forward(request, response);
-		} catch (Exception e) {
-			log.error("EntityEditController could not forward to view.");
-			log.error(e.getMessage());
-			log.error(e.getStackTrace());
-		}
 	}
     
 	public static DateTime getValidParsedDateTimeObject(String unparsedDateTime) {