1. Removed SOPs from the visualization codebase. Switched it with log.debugs.

2. Added person grant count & coauthorship to the freemarker version of dependency inhection bean.
3. Fixed a bug in garnt count freemarker.
4. Made use of urlbuilder instead of making urls by just encoding/appending parameters.
5. Add co-pi to the freemarker package. Completed the back-end conversion.

productMods/WEB-INF/visualization/visualizations-beans-injection-fm.xml

@@ -15,12 +15,18 @@
 	<bean id="utilities"
 		class="edu.cornell.mannlib.vitro.webapp.visualization.freemarker.utilities.UtilitiesRequestHandler" />
 	
-	<!-- 
+	
 	<bean id="coauthorship"
-		class="edu.cornell.mannlib.vitro.webapp.visualization.coauthorship.CoAuthorshipRequestHandler" />
+		class="edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coauthorship.CoAuthorshipRequestHandler" />
+		
+	<bean id="person_grant_count"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.freemarker.persongrantcount.PersonGrantCountRequestHandler" />
+	
+	<!-- 
 	<bean id="person_level"
 		class="edu.cornell.mannlib.vitro.webapp.visualization.personlevel.PersonLevelRequestHandler" />
 	
+	
 	<bean id="entity_comparison"
 		class="edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison.EntityPublicationCountRequestHandler" />
 	<bean id="coprincipalinvestigator"
@@ -38,10 +44,16 @@
 				<entry key="utilities">
 					<ref bean="utilities"></ref>
 				</entry>
-				<!-- 
+				
 				<entry key="coauthorship">
 					<ref bean="coauthorship"></ref>
 				</entry>
+				
+				<entry key="person_grant_count">
+					<ref bean="person_grant_count"></ref>
+				</entry>
+				
+				<!-- 
 				<entry key="person_level">
 					<ref bean="person_level"></ref>
 				</entry>

productMods/templates/freemarker/visualization/grantSparklineContent.ftl

@@ -69,8 +69,6 @@
         
         <#if sparklineVO.shortVisMode>
          
-        console.log("Yay! Short Vis Mode!");
-         
         <#-- For the short view we only want the last 10 year's view of grant count, hence we filter 
         	the data we actually want to use for render. -->
          
@@ -78,14 +76,10 @@
                 column: 0,
                 minValue: '${sparklineVO.earliestRenderedGrantYear?c}',
                 maxValue: '${sparklineVO.latestRenderedGrantYear?c}'
-                /*minValue: '2001',
-                maxValue: '2011'*/
         }]));
          
         <#else>
          
-        console.log("Yay! Full Vis Mode!");
-         
         </#if>         
         
         <#-- Create the vis object and draw it in the div pertaining to sparkline. -->
@@ -130,6 +124,7 @@
 		 
 		 $('#${sparklineContainerID} td.sparkline_text').html(sparksText);        
         
+        }
         
 	/*
 	 * This will activate the visualization. It takes care of creating 

src/edu/cornell/mannlib/vitro/webapp/visualization/coauthorship/CoAuthorshipQueryRunner.java

@@ -399,23 +399,10 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 								   DataSource dataSource) {
 
         QueryExecution queryExecution = null;
- //       try {
+        Query query = QueryFactory.create(queryText, SYNTAX);
-            Query query = QueryFactory.create(queryText, SYNTAX);
 
-//            QuerySolutionMap qs = new QuerySolutionMap();
+        queryExecution = QueryExecutionFactory.create(query, dataSource);
-//            qs.add("authPerson", queryParam); // bind resource to s
+        return queryExecution.execSelect();
-            
-            queryExecution = QueryExecutionFactory.create(query, dataSource);
-			System.out.println("\n\nquery.isSelectType() is "+ query.isSelectType()+ " \n\n");
-//            if (query.isSelectType()) {
-                return queryExecution.execSelect();
-//            }
-//        } finally {
-//            if (queryExecution != null) {
-//            	queryExecution.close();
-//            }
-//        }
-//		return null;
     }
 
 	private String generateEgoCoAuthorshipSparqlQuery(String queryURI) {
@@ -455,7 +442,7 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 			+ "} " 
 			+ "ORDER BY ?document ?coAuthorPerson";
 
-		System.out.println("COAUTHORSHIP QUERY - " + sparqlQuery);
+		log.debug("COAUTHORSHIP QUERY - " + sparqlQuery);
 		
 		return sparqlQuery;
 	}

src/edu/cornell/mannlib/vitro/webapp/visualization/coprincipalinvestigator/CoPIGrantCountQueryRunner.java

@@ -92,7 +92,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 			+ "?CoPI rdfs:label ?CoPILabel . " 
 			+ " }";
 
-		System.out.println("COPI QUERY - " + sparqlQuery);
+		log.debug("COPI QUERY - " + sparqlQuery);
 		
 		return sparqlQuery;
 	}
@@ -100,20 +100,10 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 	private ResultSet executeQuery(String queryText, DataSource dataSource) {
 
 		QueryExecution queryExecution = null;
-//		try {
+		Query query = QueryFactory.create(queryText, SYNTAX);
-			Query query = QueryFactory.create(queryText, SYNTAX);
 
-			queryExecution = QueryExecutionFactory.create(query, dataSource);
+		queryExecution = QueryExecutionFactory.create(query, dataSource);
-			System.out.println("\n\nquery.isSelectType() is "+ query.isSelectType()+ " \n\n");
+		return queryExecution.execSelect();
-//			if (query.isSelectType()) {
-				return queryExecution.execSelect();
-//			}
-//		} finally {
-//			if (queryExecution != null) {
-//				queryExecution.close();
-//			}
-//		}
-//		return null;
 	}
 	
 	public CoPIData getQueryResult()
@@ -137,7 +127,6 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 
 	ResultSet resultSet	= executeQuery(generateEgoCoPIquery(this.egoURI),
 									   this.dataSource);
-	System.out.println("ResultSet ");
 	return createQueryResult(resultSet);
 	}
 	
@@ -202,8 +191,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 						egoNode.setNodeName(authorLabelNode.toString());
 					}
 				}
-				System.out.println("\n----------------------------------");
+				log.debug("PI: "+ egoNode.getIndividualLabel());
-				System.out.println("PI: "+ egoNode.getIndividualLabel());
 				
 				RDFNode grantNode = solution.get(QueryFieldLabels.GRANT_URL);
 				Grant grant;
@@ -216,7 +204,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 				}
 				
 				egoNode.addGrant(grant);
-				System.out.println("Adding grant: "+ grant.getIndividualLabel());
+				log.debug("Adding grant: "+ grant.getIndividualLabel());
 				
 				/*
 				 * After some discussion we concluded that for the purpose of this visualization
@@ -247,7 +235,7 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 					}
 				}
 				
-				System.out.println("Adding CO-PI: "+ coPINode.getIndividualLabel());
+				log.debug("Adding CO-PI: "+ coPINode.getIndividualLabel());
 				coPINode.addGrant(grant);
 				
 				Set<CoPINode> coPIsForCurrentGrant;
@@ -262,10 +250,9 @@ public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
 				}
 				
 				coPIsForCurrentGrant.add(coPINode);
-				System.out.println("Co-PI for current grant : "+ coPINode.getIndividualLabel());
+				log.debug("Co-PI for current grant : "+ coPINode.getIndividualLabel());
 				
 				CoPIEdge egoCoPIEdge = getExistingEdge(egoNode, coPINode, edgeUniqueIdentifierToVO);
-				System.out.println("\n----------------------------------");
 				/*
 				 * If "egoCoPIEdge" is null it means that no edge exists in between the egoNode 
 				 * & current coPINode. Else create a new edge, add it to the edges set & add 

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

@@ -166,22 +166,11 @@ public class EntityPublicationCountQueryRunner implements QueryRunner<Entity> {
 	private ResultSet executeQuery(String queryURI, DataSource dataSource) {
 
 		QueryExecution queryExecution = null;
-//		try {
+		Query query = QueryFactory.create(
-			Query query = QueryFactory.create(
+				getSparqlQuery(queryURI, this.visMode), SYNTAX);
-					getSparqlQuery(queryURI, this.visMode), SYNTAX);
+		queryExecution = QueryExecutionFactory.create(query, dataSource);
-			queryExecution = QueryExecutionFactory.create(query, dataSource);
+		return queryExecution.execSelect();
-			System.out.println("\n\nquery.isSelectType() is "+ query.isSelectType()+ " \n\n");
+}
-			return queryExecution.execSelect();
-//			if (query.isSelectType()) {
-//				return queryExecution.execSelect();
-//			}
-//		} finally {
-//			if (queryExecution != null) {
-//				queryExecution.close();
-//			}
-//		}
-//		return null;
-	}
 
 	private String getSparqlQuery(String queryURI, String visMode) {
 		String result = "";
@@ -281,7 +270,7 @@ public class EntityPublicationCountQueryRunner implements QueryRunner<Entity> {
 		+ SPARQL_QUERY_COMMON_WHERE_CLAUSE + "}"
 		+ "}";
 		
-		System.out.println("\nThe sparql query is :\n" + sparqlQuery);
+		log.debug("\nThe sparql query is :\n" + sparqlQuery);
 		
 		return sparqlQuery;
 

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

@@ -5,10 +5,10 @@ package edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.HashSet;
 
 import javax.servlet.RequestDispatcher;
 import javax.servlet.ServletException;
@@ -16,17 +16,16 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
-import com.google.gson.Gson;
 
+import com.google.gson.Gson;
 import com.hp.hpl.jena.query.DataSource;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
 import edu.cornell.mannlib.vitro.webapp.controller.visualization.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.valueobjects.BiboDocument;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.JsonObject;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SubEntity;
@@ -45,7 +44,6 @@ public class EntityPublicationCountRequestHandler implements
 	public static String SUB_ENTITY_VIS_MODE;
 
 
-	@SuppressWarnings("null")
 	public void generateVisualization(VitroRequest vitroRequest,
 			HttpServletRequest request, HttpServletResponse response, Log log,
 			DataSource dataSource) {
@@ -91,13 +89,13 @@ public class EntityPublicationCountRequestHandler implements
 			if (VisualizationFrameworkConstants.DATA_RENDER_MODE
 					.equalsIgnoreCase(renderMode)) {
 
-				prepareDataResponse(entity, entity.getSubEntities(),subOrganizationTypesResult, response);
+				prepareDataResponse(entity, entity.getSubEntities(),subOrganizationTypesResult, response, log);
 
 			} else if (VisualizationFrameworkConstants.STANDALONE_RENDER_MODE
 					.equalsIgnoreCase(renderMode)) {
 
 				prepareStandaloneResponse(request, response, vitroRequest,
-						entity, subOrganizationTypesResult);
+						entity, subOrganizationTypesResult, log);
 				requestDispatcher = request
 						.getRequestDispatcher(Controllers.BASIC_JSP);
 			}
@@ -135,9 +133,10 @@ public class EntityPublicationCountRequestHandler implements
 	 * @param subOrganizationTypesResult 
 	 * @param yearToPublicationCount
 	 * @param response
+	 * @param log 
 	 */
 	private void prepareDataResponse(Entity entity, Set<SubEntity> subentities,
-			Map<String, Set<String>> subOrganizationTypesResult, HttpServletResponse response) {
+			Map<String, Set<String>> subOrganizationTypesResult, HttpServletResponse response, Log log) {
 
 		String entityLabel = entity.getEntityLabel();
 
@@ -156,7 +155,7 @@ public class EntityPublicationCountRequestHandler implements
 			 * We are side-effecting responseWriter since we are directly
 			 * manipulating the response object of the servlet.
 			 */
-			responseWriter.append(writePublicationsOverTimeJSON(subentities, subOrganizationTypesResult));
+			responseWriter.append(writePublicationsOverTimeJSON(subentities, subOrganizationTypesResult, log));
 
 			responseWriter.flush();
 			responseWriter.close();
@@ -175,9 +174,10 @@ public class EntityPublicationCountRequestHandler implements
 	 * @param vreq
 	 * @param entity
 	 * @param subOrganizationTypesResult 
+	 * @param log 
 	 */
 	private void prepareStandaloneResponse(HttpServletRequest request,
-			HttpServletResponse response, VitroRequest vreq, Entity entity, Map<String, Set<String>> subOrganizationTypesResult) {
+			HttpServletResponse response, VitroRequest vreq, Entity entity, Map<String, Set<String>> subOrganizationTypesResult, Log log) {
 
 		Portal portal = vreq.getPortal();
 		String jsonContent = "";
@@ -185,7 +185,7 @@ public class EntityPublicationCountRequestHandler implements
 		 * We are side-effecting responseWriter since we are directly
 		 * manipulating the response object of the servlet.
 		 */
-		jsonContent = writePublicationsOverTimeJSON(entity.getSubEntities(), subOrganizationTypesResult);
+		jsonContent = writePublicationsOverTimeJSON(entity.getSubEntities(), subOrganizationTypesResult, log);
 
 		request.setAttribute("JsonContent", jsonContent);
 
@@ -201,15 +201,16 @@ public class EntityPublicationCountRequestHandler implements
 	/**
 	 * function to generate a json file for year <-> publication count mapping
 	 * @param subOrganizationTypesResult 
+	 * @param log 
 	 * 
 	 * @param yearToPublicationCount
 	 * @param responseWriter
 	 * @param visMode
 	 */
-	private String writePublicationsOverTimeJSON(Set<SubEntity> subentities, Map<String, Set<String>> subOrganizationTypesResult) {
+	private String writePublicationsOverTimeJSON(Set<SubEntity> subentities, Map<String, Set<String>> subOrganizationTypesResult, Log log) {
 //		System.out.println("\nsub entity vis mode ------>"
 //				+ SUB_ENTITY_VIS_MODE + "\n");
-		System.out.println("Creating JSONObject \n-----------------------");
+		log.debug("Creating JSONObject \n-----------------------");
 		Gson json = new Gson();
 		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
 
@@ -239,7 +240,7 @@ public class EntityPublicationCountRequestHandler implements
 			entityJson.setEntityURI(subentity.getIndividualURI());
 			setEntityVisMode(entityJson);
 			//entityJson.setVisMode(SUB_ENTITY_VIS_MODE);
-			System.out.println("Adding object with uri: "
+			log.debug("Adding object with uri: "
 					+ entityJson.getEntityURI() + " vismode: "
 					+ entityJson.getVisMode() + " label: "
 					+ entityJson.getLabel() + " type: "

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

@@ -74,20 +74,10 @@ public class EntitySubOrganizationTypesQueryRunner implements QueryRunner<Map<St
 	private ResultSet executeQuery(String queryURI, DataSource dataSource) {
 
 		QueryExecution queryExecution = null;
-//		try {
+		Query query = QueryFactory.create(
-			Query query = QueryFactory.create(
+				getSparqlQuery(queryURI), SYNTAX);
-					getSparqlQuery(queryURI), SYNTAX);
+		queryExecution = QueryExecutionFactory.create(query, dataSource);
-			queryExecution = QueryExecutionFactory.create(query, dataSource);
+			return queryExecution.execSelect();
-			System.out.println("\n\nquery.isSelectType() is "+ query.isSelectType()+ " \n\n");
-//			if (query.isSelectType()) {
-				return queryExecution.execSelect();
-//			}
-//		} finally {
-//			if (queryExecution != null) {
-//				queryExecution.close();
-//			}
-//		}
-//		return null;
 	}
 	
 	private String getSparqlQuery(String queryURI) {
@@ -133,7 +123,7 @@ public class EntitySubOrganizationTypesQueryRunner implements QueryRunner<Map<St
 							+ " ?personType rdfs:label ?personTypeLabel ."
 							+ "}";;
 		}
-		System.out.println("\nThe sparql query is :\n" + sparqlQuery);
+		log.debug("\nThe sparql query is :\n" + sparqlQuery);
 		return sparqlQuery;
 
 	}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coauthorship/CoAuthorshipGraphMLWriter.java

@@ -2,15 +2,14 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coauthorship;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.StandardVisualizationController;
+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.visualization.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoAuthorshipData;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Edge;
@@ -29,13 +28,7 @@ public class CoAuthorshipGraphMLWriter {
 	private final String GRAPHML_FOOTER = "</graphml>";
 	
 	public CoAuthorshipGraphMLWriter(CoAuthorshipData visVOContainer) {
-		
 		coAuthorshipGraphMLContent = createCoAuthorshipGraphMLContent(visVOContainer);
-		
-	}
-
-	public StringBuilder getCoAuthorshipGraphMLContent() {
-		return coAuthorshipGraphMLContent;
 	}
 
 	private StringBuilder createCoAuthorshipGraphMLContent(
@@ -63,6 +56,10 @@ public class CoAuthorshipGraphMLWriter {
 		return graphMLContent;
 	}
 	
+	public StringBuilder getCoAuthorshipGraphMLContent() {
+		return coAuthorshipGraphMLContent;
+	}
+
 	private void generateGraphContent(CoAuthorshipData coAuthorshipData,
 			StringBuilder graphMLContent) {
 
@@ -77,10 +74,6 @@ public class CoAuthorshipGraphMLWriter {
 		}
 		
 		graphMLContent.append("</graph>\n");
-		  
-		
-		
-		
 	}
 
 	private void generateEdgeSectionContent(CoAuthorshipData coAuthorshipData,
@@ -101,9 +94,7 @@ public class CoAuthorshipGraphMLWriter {
 			 * is being side-effected. 
 			 * */
 			getEdgeContent(graphMLContent, currentEdge);
-			
 		}
-		
 	}
 
 	private void getEdgeContent(StringBuilder graphMLContent, Edge currentEdge) {
@@ -212,16 +203,11 @@ public class CoAuthorshipGraphMLWriter {
 
 	private void getNodeContent(StringBuilder graphMLContent, Node node) {
 
-		String profileURL = null;
+		ParamMap individualProfileURLParams = new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
-		try {
+														   node.getNodeURI());
-			profileURL = VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX + "?" 
+
-								+ VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
+		String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX,
-								+ "=" + URLEncoder.encode(node.getNodeURI(),
+			individualProfileURLParams);
-														  StandardVisualizationController
-														  		.URL_ENCODING_SCHEME).toString();
-		} catch (UnsupportedEncodingException e) {
-			System.err.println("URL Encoding ERRor. Move this to use log.error ASAP");
-		}
 		
 		graphMLContent.append("<node id=\"" + node.getNodeID() + "\">\n");
 		graphMLContent.append("\t<data key=\"url\">" + node.getNodeURI() + "</data>\n");

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coauthorship/CoAuthorshipQueryRunner.java

@@ -399,23 +399,10 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 								   DataSource dataSource) {
 
         QueryExecution queryExecution = null;
- //       try {
+        Query query = QueryFactory.create(queryText, SYNTAX);
-            Query query = QueryFactory.create(queryText, SYNTAX);
 
-//            QuerySolutionMap qs = new QuerySolutionMap();
+        queryExecution = QueryExecutionFactory.create(query, dataSource);
-//            qs.add("authPerson", queryParam); // bind resource to s
+        return queryExecution.execSelect();
-            
-            queryExecution = QueryExecutionFactory.create(query, dataSource);
-			System.out.println("\n\nquery.isSelectType() is "+ query.isSelectType()+ " \n\n");
-//            if (query.isSelectType()) {
-                return queryExecution.execSelect();
-//            }
-//        } finally {
-//            if (queryExecution != null) {
-//            	queryExecution.close();
-//            }
-//        }
-//		return null;
     }
 
 	private String generateEgoCoAuthorshipSparqlQuery(String queryURI) {

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coauthorship/CoAuthorshipRequestHandler.java

@@ -190,10 +190,6 @@ public class CoAuthorshipRequestHandler implements VisualizationRequestHandler {
 	 */
 	private Map<String, String> prepareNetworkDataResponse(CoAuthorshipData authorNodesAndEdges) {
 	
-		/*
-		 * We are side-effecting responseWriter since we are directly manipulating the response 
-		 * object of the servlet.
-		 * */
 		CoAuthorshipGraphMLWriter coAuthorshipGraphMLWriter = 
 				new CoAuthorshipGraphMLWriter(authorNodesAndEdges);
 		

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIEdgeComparator.java

@@ -0,0 +1,22 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.util.Comparator;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIEdge;
+
+
+/**
+ * This Comparator is used to sort the edges based on their IDs in ascending order.
+ * @author bkoniden
+ *
+ */
+public class CoPIEdgeComparator implements Comparator<CoPIEdge> {
+
+	@Override
+	public int compare(CoPIEdge arg0, CoPIEdge arg1) {
+		return arg0.getEdgeID() - arg1.getEdgeID();
+	}
+
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIGrantCountQueryRunner.java

@@ -0,0 +1,437 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.util.ArrayList;
+import java.util.Collections;
+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.StringUtils;
+import org.apache.commons.logging.Log;
+
+import com.hp.hpl.jena.iri.IRI;
+import com.hp.hpl.jena.iri.IRIFactory;
+import com.hp.hpl.jena.iri.Violation;
+import com.hp.hpl.jena.query.DataSource;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.Syntax;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIEdge;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Grant;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPINode;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.QueryRunner;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UniqueIDGenerator;
+/**
+ * @author bkoniden
+ * Deepak Konidena
+ */
+public class CoPIGrantCountQueryRunner implements QueryRunner<CoPIData> {
+	
+	private static final int MAX_PI_PER_GRANT_ALLOWED = 100;
+	
+	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
+	
+	private String egoURI;
+	
+	private DataSource dataSource;
+
+	private Log log;
+
+	private UniqueIDGenerator nodeIDGenerator;
+
+	private UniqueIDGenerator edgeIDGenerator;
+	
+	public CoPIGrantCountQueryRunner(String egoURI,
+			DataSource dataSource, Log log) {
+
+		this.egoURI = egoURI;
+		this.dataSource = dataSource;
+		this.log = log;
+		
+		this.nodeIDGenerator = new UniqueIDGenerator();
+		this.edgeIDGenerator = new UniqueIDGenerator();
+
+	}
+	
+	private String generateEgoCoPIquery(String queryURI) {
+
+
+		String sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+			+ "SELECT "
+			+ "		(str(<" + queryURI + ">) as ?" + QueryFieldLabels.PI_URL + ") " 
+			+ "		(str(?PILabel) as ?" + QueryFieldLabels.PI_LABEL + ") " 
+			+ "		(str(?Grant) as ?"	+ QueryFieldLabels.GRANT_URL + ") "	
+			+ "		(str(?GrantLabel) as ?" + QueryFieldLabels.GRANT_LABEL + ") " 
+			+ "		(str(?GrantStartDate) as ?" + QueryFieldLabels.GRANT_START_DATE + ") "
+			+ "		(str(?GrantEndDate) as ?" + QueryFieldLabels.GRANT_END_DATE + ") "
+			+ "		(str(?CoPI) as ?" + QueryFieldLabels.CO_PI_URL + ") "
+			+ "		(str(?CoPILabel) as ?" + QueryFieldLabels.CO_PI_LABEL + ") "
+			+ "WHERE { "
+			+ "<" + queryURI + "> rdfs:label ?PILabel ;" 
+								+ " core:hasCo-PrincipalInvestigatorRole ?Role . " 
+			+ "?Role core:roleIn ?Grant . " 
+			+ "?Grant rdfs:label ?GrantLabel ; " 
+			+ "core:startDate ?GrantStartDate ; " 
+			+ "core:endDate ?GrantEndDate ;" 
+			+ "core:relatedRole ?RelatedRole . "
+			+ "?RelatedRole core:co-PrincipalInvestigatorRoleOf ?CoPI . " 
+			+ "?CoPI rdfs:label ?CoPILabel . " 
+			+ " }";
+
+		log.debug("COPI QUERY - " + sparqlQuery);
+		
+		return sparqlQuery;
+	}
+	
+	private ResultSet executeQuery(String queryText, DataSource dataSource) {
+
+		QueryExecution queryExecution = null;
+		Query query = QueryFactory.create(queryText, SYNTAX);
+
+		queryExecution = QueryExecutionFactory.create(query, dataSource);
+		return queryExecution.execSelect();
+	}
+	
+	public CoPIData getQueryResult()
+	throws MalformedQueryParametersException {
+
+	if (StringUtils.isNotBlank(this.egoURI)) {
+		/*
+    	 * To test for the validity of the URI submitted.
+    	 * */
+    	IRIFactory iRIFactory = IRIFactory.jenaImplementation();
+		IRI iri = iRIFactory.create(this.egoURI);
+        if (iri.hasViolation(false)) {
+            String errorMsg = ((Violation) iri.violations(false).next()).getShortMessage();
+            log.error("Ego Co-PI Vis Query " + errorMsg);
+            throw new MalformedQueryParametersException(
+            		"URI provided for an individual is malformed.");
+        }
+    } else {
+        throw new MalformedQueryParametersException("URI parameter is either null or empty.");
+    }
+
+	ResultSet resultSet	= executeQuery(generateEgoCoPIquery(this.egoURI),
+									   this.dataSource);
+	return createQueryResult(resultSet);
+	}
+	
+	
+	private CoPIEdge getExistingEdge(
+			CoPINode collaboratingNode1, 
+			CoPINode collaboratingNode2, 
+			Map<String, CoPIEdge> edgeUniqueIdentifierToVO) {
+
+		String edgeUniqueIdentifier = getEdgeUniqueIdentifier(collaboratingNode1.getNodeID(), 
+				collaboratingNode2.getNodeID());
+
+		return edgeUniqueIdentifierToVO.get(edgeUniqueIdentifier);
+
+	}
+
+	private String getEdgeUniqueIdentifier(int nodeID1, int nodeID2) {
+
+		String separator = "*"; 
+
+		if (nodeID1 < nodeID2) {
+			return nodeID1 + separator + nodeID2;
+		} else {
+			return nodeID2 + separator + nodeID1;
+		}
+
+	}
+	
+	private CoPIData createQueryResult(ResultSet resultSet) {
+		
+		Set<CoPINode> nodes = new HashSet<CoPINode>();
+		
+		Map<String, Grant> grantURLToVO = new HashMap<String, Grant>();
+		Map<String, Set<CoPINode>> grantURLToCoPIs = new HashMap<String, Set<CoPINode>>();
+		Map<String, CoPINode> nodeURLToVO = new HashMap<String, CoPINode>();
+		Map<String, CoPIEdge> edgeUniqueIdentifierToVO = new HashMap<String, CoPIEdge>();
+		
+		CoPINode egoNode = null;
+
+		Set<CoPIEdge> edges = new HashSet<CoPIEdge>();
+
+			while (resultSet.hasNext()) {
+				QuerySolution solution = resultSet.nextSolution();
+				
+				/*
+				 * We only want to create only ONE ego node.
+				 * */
+				RDFNode egoPIURLNode = solution.get(QueryFieldLabels.PI_URL);
+				if (nodeURLToVO.containsKey(egoPIURLNode.toString())) {
+	
+					egoNode = nodeURLToVO.get(egoPIURLNode.toString());
+					
+				} else {
+					
+					egoNode = new CoPINode(egoPIURLNode.toString(), nodeIDGenerator);
+					nodes.add(egoNode);
+					nodeURLToVO.put(egoPIURLNode.toString(), egoNode);
+					
+					
+					RDFNode authorLabelNode = solution.get(QueryFieldLabels.PI_LABEL);
+					if (authorLabelNode != null) {
+						egoNode.setNodeName(authorLabelNode.toString());
+					}
+				}
+				log.debug("PI: "+ egoNode.getIndividualLabel());
+				
+				RDFNode grantNode = solution.get(QueryFieldLabels.GRANT_URL);
+				Grant grant;
+				
+				if (grantURLToVO.containsKey(grantNode.toString())) {
+					grant = grantURLToVO.get(grantNode.toString());
+				} else {
+					grant = createGrantVO(solution, grantNode.toString());
+					grantURLToVO.put(grantNode.toString(), grant);	
+				}
+				
+				egoNode.addGrant(grant);
+				log.debug("Adding grant: "+ grant.getIndividualLabel());
+				
+				/*
+				 * After some discussion we concluded that for the purpose of this visualization
+				 * we do not want a co-pi node or edge if the grant has only one
+				 * pi and that happens to be the ego.
+				 * */
+				if (solution.get(QueryFieldLabels.PI_URL).toString().equalsIgnoreCase(
+						solution.get(QueryFieldLabels.CO_PI_URL).toString())) {
+					continue;
+				}
+				
+				CoPINode coPINode;
+				
+				RDFNode coPIURLNode = solution.get(QueryFieldLabels.CO_PI_URL);
+				if (nodeURLToVO.containsKey(coPIURLNode.toString())) {
+	
+					coPINode = nodeURLToVO.get(coPIURLNode.toString());
+					
+				} else {
+					
+					coPINode = new CoPINode(coPIURLNode.toString(), nodeIDGenerator);
+					nodes.add(coPINode);
+					nodeURLToVO.put(coPIURLNode.toString(), coPINode);
+					
+					RDFNode coPILabelNode = solution.get(QueryFieldLabels.CO_PI_LABEL);
+					if (coPILabelNode != null) {
+						coPINode.setNodeName(coPILabelNode.toString());
+					}
+				}
+				
+				log.debug("Adding CO-PI: "+ coPINode.getIndividualLabel());
+				coPINode.addGrant(grant);
+				
+				Set<CoPINode> coPIsForCurrentGrant;
+				
+				if (grantURLToCoPIs.containsKey(grant.getGrantURL())) {
+					coPIsForCurrentGrant = grantURLToCoPIs
+															.get(grant.getGrantURL());
+				} else {
+					coPIsForCurrentGrant = new HashSet<CoPINode>();
+					grantURLToCoPIs.put(grant.getGrantURL(), 
+												   coPIsForCurrentGrant);
+				}
+				
+				coPIsForCurrentGrant.add(coPINode);
+				log.debug("Co-PI for current grant : "+ coPINode.getIndividualLabel());
+				
+				CoPIEdge egoCoPIEdge = getExistingEdge(egoNode, coPINode, edgeUniqueIdentifierToVO);
+				/*
+				 * If "egoCoPIEdge" is null it means that no edge exists in between the egoNode 
+				 * & current coPINode. Else create a new edge, add it to the edges set & add 
+				 * the collaborator grant to it.
+				 * */
+				if (egoCoPIEdge != null) {
+					egoCoPIEdge.addCollaboratorGrant(grant);
+				} else {
+					egoCoPIEdge = new CoPIEdge(egoNode, coPINode, grant, edgeIDGenerator);
+					edges.add(egoCoPIEdge);
+					edgeUniqueIdentifierToVO.put(
+							getEdgeUniqueIdentifier(egoNode.getNodeID(),
+													coPINode.getNodeID()), 
+							egoCoPIEdge);
+				}
+				
+		}
+		
+			
+			/*
+			 * This method takes out all the PIs & edges between PIs that belong to grants 
+			 * that have more than 100 PIs. We conjecture that these grants do not provide much 
+			 * insight. However, we have left the grants be.
+			 * 
+			 * This method side-effects "nodes" & "edges".  
+			 * */
+			removeLowQualityNodesAndEdges(nodes, 
+					  grantURLToVO, 
+					  grantURLToCoPIs, 
+					  edges);
+			/*
+			 * We need to create edges between 2 co-PIs. E.g. On a grant there were 3 PI
+			 * ego, A & B then we have already created edges like,
+			 * 		ego - A
+			 * 		ego - B
+			 * The below sub-routine will take care of,
+			 * 		A - B 
+			 * 
+			 * We are side-effecting "edges" here. The only reason to do this is because we are adding 
+			 * edges en masse for all the co-PIs on all the grants considered so far. The 
+			 * other reason being we dont want to compare against 2 sets of edges (edges created before 
+			 * & co-PI edges created during the course of this method) when we are creating a new 
+			 * edge.
+			 * */
+			createCoPIEdges(grantURLToVO, 
+								grantURLToCoPIs,
+								edges,
+								edgeUniqueIdentifierToVO);
+			
+			
+			return new CoPIData(egoNode, nodes, edges);
+	}
+
+	private void createCoPIEdges(Map<String, Grant> grantURLToVO,
+			Map<String, Set<CoPINode>> grantURLToCoPIs, Set<CoPIEdge> edges,
+			Map<String, CoPIEdge> edgeUniqueIdentifierToVO) {
+		
+		for (Map.Entry<String, Set<CoPINode>> currentGrantEntry 
+				: grantURLToCoPIs.entrySet()) {
+		
+		/*
+		 * If there was only one co-PI (other than ego) then we dont have to create any 
+		 * edges. so the below condition will take care of that.
+		 * 
+		 * We are restricting edges between co-PI if a particular grant has more than
+		 * 100 co-PIs. Our conjecture is that such edges do not provide any good insight
+		 * & causes unnecessary computations causing the server to time-out.
+		 * */
+		if (currentGrantEntry.getValue().size() > 1 
+				&& currentGrantEntry.getValue().size() 
+						<= MAX_PI_PER_GRANT_ALLOWED) {
+			
+			
+			Set<CoPIEdge> newlyAddedEdges = new HashSet<CoPIEdge>();
+		
+			/*
+			 * In order to leverage the nested "for loop" for making edges between all the 
+			 * co-PIs we need to create a list out of the set first. 
+			 * */
+			List<CoPINode> coPINodes = new ArrayList<CoPINode>(currentGrantEntry.getValue());
+			Collections.sort(coPINodes, new CoPINodeComparator());
+			
+			int numOfCoPIs = coPINodes.size();
+			
+			for (int ii = 0; ii < numOfCoPIs - 1; ii++) {
+				for (int jj = ii + 1; jj < numOfCoPIs; jj++) {
+					
+					CoPINode coPI1 = coPINodes.get(ii);
+					CoPINode coPI2 = coPINodes.get(jj);
+					
+					CoPIEdge coPI1_2Edge = getExistingEdge(coPI1, 
+														   coPI2, 
+														   edgeUniqueIdentifierToVO);
+					
+					Grant currentGrant = grantURLToVO.get(currentGrantEntry.getKey());
+		
+					if (coPI1_2Edge != null) {
+						coPI1_2Edge.addCollaboratorGrant(currentGrant);
+					} else {
+						coPI1_2Edge = new CoPIEdge(coPI1, 
+												   coPI2, 
+												   currentGrant, 
+												   edgeIDGenerator);
+						newlyAddedEdges.add(coPI1_2Edge);
+						edgeUniqueIdentifierToVO.put(
+								getEdgeUniqueIdentifier(coPI1.getNodeID(),
+														coPI2.getNodeID()), 
+								coPI1_2Edge);
+					}
+				}
+			}
+			edges.addAll(newlyAddedEdges);
+		}
+		
+	}
+		
+	}
+
+	private void removeLowQualityNodesAndEdges(Set<CoPINode> nodes,
+			Map<String, Grant> grantURLToVO,
+			Map<String, Set<CoPINode>> grantURLToCoPIs, Set<CoPIEdge> edges) {
+		
+		Set<CoPINode> nodesToBeRemoved = new HashSet<CoPINode>();
+		for (Map.Entry<String, Set<CoPINode>> currentGrantEntry 
+					: grantURLToCoPIs.entrySet()) {
+				
+				if (currentGrantEntry.getValue().size() > MAX_PI_PER_GRANT_ALLOWED) {
+					
+					Grant currentGrant = grantURLToVO.get(currentGrantEntry.getKey());
+					
+					Set<CoPIEdge> edgesToBeRemoved = new HashSet<CoPIEdge>();
+					
+					for (CoPIEdge currentEdge : edges) {
+						Set<Grant> currentCollaboratorGrants = 
+									currentEdge.getCollaboratorGrants();
+						
+						if (currentCollaboratorGrants.contains(currentGrant)) {
+							currentCollaboratorGrants.remove(currentGrant);
+							if (currentCollaboratorGrants.isEmpty()) {
+								edgesToBeRemoved.add(currentEdge);
+							}
+						}
+					}
+						
+					edges.removeAll(edgesToBeRemoved);
+
+					for (CoPINode currentCoPI : currentGrantEntry.getValue()) {
+						currentCoPI.getInvestigatedGrants().remove(currentGrant);
+						if (currentCoPI.getInvestigatedGrants().isEmpty()) {
+							nodesToBeRemoved.add(currentCoPI);
+						}
+					}
+				}
+		}
+		nodes.removeAll(nodesToBeRemoved);
+		
+	}
+
+	private Grant createGrantVO(QuerySolution solution, String grantURL) {
+		
+		Grant grant = new Grant(grantURL);
+
+		RDFNode grantLabelNode = solution.get(QueryFieldLabels.GRANT_LABEL);
+		if (grantLabelNode != null) {
+			grant.setIndividualLabel(grantLabelNode.toString());
+		}
+
+
+		RDFNode grantStartYear = solution.get(QueryFieldLabels.GRANT_START_DATE);
+		if (grantStartYear != null) {
+			grant.setGrantStartDate(grantStartYear.toString());
+		}
+		
+		RDFNode grantEndDate = solution.get(QueryFieldLabels
+															.GRANT_END_DATE);
+		if (grantEndDate != null) {
+			grant.setGrantEndDate(grantEndDate.toString());
+		}
+		
+		return grant;
+	}
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIGrantCountRequestHandler.java

@@ -0,0 +1,205 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.logging.Log;
+
+import com.hp.hpl.jena.query.DataSource;
+
+import edu.cornell.mannlib.vitro.webapp.beans.Portal;
+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.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPINode;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.QueryRunner;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
+/**
+ * @author bkoniden
+ * Deepak Konidena
+ */
+public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler{
+	
+
+	@Override
+	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
+			DataSource dataSource) throws MalformedQueryParametersException {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public Map<String, String> generateDataVisualization(
+			VitroRequest vitroRequest, Log log, DataSource dataSource)
+			throws MalformedQueryParametersException {
+		
+		String egoURI = vitroRequest.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		String visMode = vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
+		
+		QueryRunner<CoPIData> queryManager = new CoPIGrantCountQueryRunner(egoURI, dataSource, log);
+		
+		CoPIData PINodesAndEdges = queryManager.getQueryResult();
+		
+			if (VisualizationFrameworkConstants.COPI_VIS_MODE
+					.equalsIgnoreCase(visMode)) { 
+
+					return prepareCoPIDataResponse(PINodesAndEdges);
+	    		
+			} else {
+	    			/*
+	    			 * When the graphML file is required - based on which copi network 
+	    			 * visualization will be rendered.
+	    			 * */
+	    			return prepareNetworkDataResponse(PINodesAndEdges);
+					
+			}
+	}
+	
+	@Override
+	public ResponseValues generateStandardVisualization(
+			VitroRequest vitroRequest, Log log, DataSource dataSource)
+			throws MalformedQueryParametersException {
+		
+		String egoURI = vitroRequest.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		
+		QueryRunner<CoPIData> queryManager = new CoPIGrantCountQueryRunner(egoURI, dataSource, log);
+		
+		CoPIData PINodesAndEdges = queryManager.getQueryResult();
+		
+		return prepareStandaloneResponse(egoURI,
+				 						  PINodesAndEdges,
+				 						  vitroRequest);
+	}
+	
+	/**
+	 * When the page for person level visualization is requested.
+	 * @param egoURI
+	 * @param vitroRequest
+	 * @param coPIVO
+	 */
+	private TemplateResponseValues prepareStandaloneResponse(String egoURI,
+			CoPIData pINodesAndEdges, VitroRequest vitroRequest) {
+		
+        Portal portal = vitroRequest.getPortal();
+        
+        String title = "";
+        Map<String, Object> body = new HashMap<String, Object>();
+
+
+        if (pINodesAndEdges.getNodes() != null
+				&& pINodesAndEdges.getNodes().size() > 0) {
+        	body.put("numOfAuthors", pINodesAndEdges.getNodes().size());
+			
+			title = pINodesAndEdges.getEgoNode().getNodeName() + " - ";
+		}
+
+		if (pINodesAndEdges.getEdges() != null
+				&& pINodesAndEdges.getEdges().size() > 0) {
+			body.put("numOfCoPIs", pINodesAndEdges.getEdges().size());
+		}
+
+		String standaloneTemplate = "/visualization/coauthorship/coAuthorship.ftl";
+		
+        body.put("portalBean", portal);
+        body.put("egoURIParam", egoURI);
+        body.put("title", title + "Co-PI Visualization");
+        
+        return new TemplateResponseValues(standaloneTemplate, body);
+	}
+
+	/**
+	 * Provides a response when graphml formatted co-pi network is requested, typically by 
+	 * the flash vis.
+	 * @param pINodesAndEdges
+	 */
+	private Map<String, String> prepareNetworkDataResponse(CoPIData pINodesAndEdges) {
+		
+		CoPIGraphMLWriter coPIGraphMLWriter = 
+				new CoPIGraphMLWriter(pINodesAndEdges);
+		
+	    Map<String, String> fileData = new HashMap<String, String>();
+		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
+					 "text/xml");
+		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
+					 coPIGraphMLWriter.getCoPIGraphMLContent().toString());
+	
+		return fileData;
+	}
+	
+	/**
+	 * Provides response when a csv file containing number & names of unique co-pis per 
+	 * year is requested. 
+	 * @param pINodesAndEdges
+	 */
+	private Map<String, String> prepareCoPIDataResponse(CoPIData pINodesAndEdges) {
+		
+		String outputFileName;
+		Map<String, Set<CoPINode>> yearToCoPI = new TreeMap<String, Set<CoPINode>>();
+		
+		if (pINodesAndEdges.getNodes() != null && pINodesAndEdges.getNodes().size() > 0) {
+			
+			outputFileName = UtilityFunctions.slugify(pINodesAndEdges
+									.getEgoNode().getNodeName())
+			+ "_copis-per-year" + ".csv";
+			
+			yearToCoPI = UtilityFunctions.getGrantYearToCoPI(pINodesAndEdges);
+			
+		} else {
+			
+			outputFileName = "no_copis-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, 
+					 getCoPIsPerYearCSVContent(yearToCoPI));
+
+		return fileData;
+	}
+
+	private String getCoPIsPerYearCSVContent(Map<String, Set<CoPINode>> yearToCoPI) {
+
+		StringBuilder csvFileContent = new StringBuilder();
+		
+		csvFileContent.append("Year, Count, Co-PI(s)\n");
+
+		for (Map.Entry<String, Set<CoPINode>> currentEntry : yearToCoPI.entrySet()) {
+			
+			csvFileContent.append(StringEscapeUtils.escapeCsv(currentEntry.getKey()));
+			csvFileContent.append(",");
+			csvFileContent.append(currentEntry.getValue().size());
+			csvFileContent.append(",");
+			csvFileContent.append(StringEscapeUtils.escapeCsv(getCoPINamesAsString(currentEntry.getValue())));
+			csvFileContent.append("\n");
+		}
+		
+		return csvFileContent.toString();
+	}
+
+	private String getCoPINamesAsString(Set<CoPINode> CoPIs) {
+		
+		StringBuilder coPIsMerged = new StringBuilder();
+		
+		String coPISeparator = ";";
+		for(CoPINode currentCoPI : CoPIs){
+			coPIsMerged.append(currentCoPI.getNodeName() + coPISeparator);
+		}
+		
+		return StringUtils.removeEnd(coPIsMerged.toString(), coPISeparator);
+	}
+
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIGraphMLWriter.java

@@ -0,0 +1,319 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+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.visualization.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPIEdge;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPINode;
+/**
+ * @author bkoniden
+ * Deepak Konidena
+ */
+public class CoPIGraphMLWriter {
+	
+	private StringBuilder coPIGraphMLContent;
+	
+	private final String GRAPHML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" 
+		+ "	<graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n"
+		+ "  xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n"
+        + "  xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\n"
+        + "  http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">\n\n";
+	
+	private final String GRAPHML_FOOTER = "</graphml>";
+	
+	public CoPIGraphMLWriter(CoPIData coPIData){
+		coPIGraphMLContent = createCoPIGraphMLContent(coPIData);
+	}
+
+	private StringBuilder createCoPIGraphMLContent(CoPIData coPIData) {
+		
+		StringBuilder graphMLContent = new StringBuilder();
+		
+		graphMLContent.append(GRAPHML_HEADER);
+		
+		/*
+		 * We are side-effecting "graphMLContent" object in this method since creating 
+		 * another String object to hold key definition data will be redundant & will
+		 * not serve the purpose.
+		 * */
+		generateKeyDefinitionContent(coPIData, graphMLContent);
+		
+		/*
+		 * Used to generate graph content. It will contain both the nodes & edge information.
+		 * We are side-effecting "graphMLContent".
+		 * */
+		generateGraphContent(coPIData, graphMLContent);
+		
+		graphMLContent.append(GRAPHML_FOOTER);
+		
+		return graphMLContent;
+	}
+	
+	public StringBuilder getCoPIGraphMLContent(){
+		return coPIGraphMLContent;
+	}
+
+	private void generateGraphContent(CoPIData coPIData,
+			StringBuilder graphMLContent) {
+		
+		graphMLContent.append("\n<graph edgedefault=\"undirected\">\n");
+		
+		if (coPIData.getNodes() != null & coPIData.getNodes().size() > 0) {
+			generateNodeSectionContent(coPIData, graphMLContent);
+		}
+		
+		if (coPIData.getEdges() != null & coPIData.getEdges().size() > 0) {
+			generateEdgeSectionContent(coPIData, graphMLContent);
+		}
+		
+		graphMLContent.append("</graph>\n");
+	}
+
+	private void generateEdgeSectionContent(CoPIData coPIData,
+			StringBuilder graphMLContent) {
+		
+		graphMLContent.append("<!-- edges -->\n");
+		
+		Set<CoPIEdge> edges = coPIData.getEdges();
+		
+		List<CoPIEdge> orderedEdges = new ArrayList<CoPIEdge>(edges);
+		
+		Collections.sort(orderedEdges, new CoPIEdgeComparator());
+
+		for (CoPIEdge currentEdge : orderedEdges) {
+			
+			/*
+			 * This method actually creates the XML code for a single edge. "graphMLContent"
+			 * is being side-effected. 
+			 * */
+			getEdgeContent(graphMLContent, currentEdge);
+		}
+	}
+	
+	private void getEdgeContent(StringBuilder graphMLContent, CoPIEdge currentEdge) {
+		
+		graphMLContent.append("<edge " 
+									+ "id=\"" + currentEdge.getEdgeID() + "\" " 
+									+ "source=\"" + currentEdge.getSourceNode().getNodeID() + "\" "
+									+ "target=\"" + currentEdge.getTargetNode().getNodeID() + "\" "
+									+ ">\n");
+		
+		graphMLContent.append("\t<data key=\"collaborator1\">" 
+								+ currentEdge.getSourceNode().getNodeName() 
+								+ "</data>\n");
+		
+		graphMLContent.append("\t<data key=\"collaborator2\">" 
+								+ currentEdge.getTargetNode().getNodeName() 
+								+ "</data>\n");
+		
+		graphMLContent.append("\t<data key=\"number_of_coinvestigated_grants\">" 
+								+ currentEdge.getNumberOfCoInvestigatedGrants()
+							+ "</data>\n");
+		
+		if (currentEdge.getEarliestCollaborationYearCount() != null) {
+			
+			/*
+			 * There is no clean way of getting the map contents in java even though
+			 * we are sure to have only one entry on the map. So using the for loop.
+			 * */
+			for (Map.Entry<String, Integer> publicationInfo
+						: currentEdge.getEarliestCollaborationYearCount().entrySet()) {
+				
+				graphMLContent.append("\t<data key=\"earliest_collaboration\">" 
+											+ publicationInfo.getKey() 
+										+ "</data>\n");
+
+				graphMLContent.append("\t<data key=\"num_earliest_collaboration\">" 
+											+ publicationInfo.getValue() 
+										+ "</data>\n");
+			}
+			
+		}
+		
+		if (currentEdge.getLatestCollaborationYearCount() != null) {
+			
+			for (Map.Entry<String, Integer> publicationInfo 
+						: currentEdge.getLatestCollaborationYearCount().entrySet()) {
+				
+				graphMLContent.append("\t<data key=\"latest_collaboration\">" 
+											+ publicationInfo.getKey() 
+										+ "</data>\n");
+
+				graphMLContent.append("\t<data key=\"num_latest_collaboration\">" 
+											+ publicationInfo.getValue() 
+										+ "</data>\n");
+			}
+			
+		}
+		
+		if (currentEdge.getUnknownCollaborationYearCount() != null) {
+			
+				graphMLContent.append("\t<data key=\"num_unknown_collaboration\">" 
+											+ currentEdge.getUnknownCollaborationYearCount() 
+										+ "</data>\n");
+				
+		}
+		
+		graphMLContent.append("</edge>\n");
+	}
+
+	
+	private void generateNodeSectionContent(CoPIData coPIData,
+			StringBuilder graphMLContent) {
+		
+		graphMLContent.append("<!-- nodes -->\n");
+		
+		CoPINode egoNode = coPIData.getEgoNode();
+		Set<CoPINode> piNodes = coPIData.getNodes();
+		
+		/*
+		 * This method actually creates the XML code for a single node. "graphMLContent"
+		 * is being side-effected. The egoNode is added first because this is the "requirement"
+		 * of the co-pi vis. Ego should always come first.
+		 * 
+		 * */
+		getNodeContent(graphMLContent, egoNode);
+		
+		List<CoPINode> orderedPINodes = new ArrayList<CoPINode>(piNodes);
+		orderedPINodes.remove(egoNode);
+		
+		Collections.sort(orderedPINodes, new CoPINodeComparator());
+		
+		
+		for (CoPINode currNode : orderedPINodes) {
+			
+			/*
+			 * We have already printed the Ego Node info.
+			 * */
+			if (currNode != egoNode) {
+				
+				getNodeContent(graphMLContent, currNode);
+				
+			}
+			
+		}
+		
+	}
+
+	private void getNodeContent(StringBuilder graphMLContent, CoPINode node) {
+		
+		ParamMap individualProfileURLParams = new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
+				   node.getNodeURI());
+
+		String profileURL = UrlBuilder.getUrl(VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX,
+		individualProfileURLParams);
+		
+		graphMLContent.append("<node id=\"" + node.getNodeID() + "\">\n");
+		graphMLContent.append("\t<data key=\"url\">" + node.getNodeURI() + "</data>\n");
+		graphMLContent.append("\t<data key=\"label\">" + node.getNodeName() + "</data>\n");
+		
+		if (profileURL != null) {
+			graphMLContent.append("\t<data key=\"profile_url\">" + profileURL + "</data>\n");
+		}
+		
+		
+		graphMLContent.append("\t<data key=\"number_of_investigated_grants\">" 
+								+ node.getNumberOfInvestigatedGrants() 
+							+ "</data>\n");
+		
+		if (node.getEarliestGrantYearCount() != null) {
+			
+			/*
+			 * There is no clean way of getting the map contents in java even though
+			 * we are sure to have only one entry on the map. So using the for loop.
+			 * I am feeling dirty just about now. 
+			 * */
+			for (Map.Entry<String, Integer> publicationInfo 
+						: node.getEarliestGrantYearCount().entrySet()) {
+				
+				graphMLContent.append("\t<data key=\"earliest_grant\">" 
+											+ publicationInfo.getKey() 
+										+ "</data>\n");
+
+				graphMLContent.append("\t<data key=\"num_earliest_grant\">" 
+											+ publicationInfo.getValue() 
+										+ "</data>\n");
+			}
+			
+		}
+		
+		if (node.getLatestGrantYearCount() != null) {
+			
+			for (Map.Entry<String, Integer> publicationInfo 
+						: node.getLatestGrantYearCount().entrySet()) {
+				
+				graphMLContent.append("\t<data key=\"latest_grant\">" 
+											+ publicationInfo.getKey() 
+										+ "</data>\n");
+
+				graphMLContent.append("\t<data key=\"num_latest_grant\">" 
+											+ publicationInfo.getValue() 
+										+ "</data>\n");
+			}
+			
+		}
+		
+		if (node.getUnknownGrantYearCount() != null) {
+			
+				graphMLContent.append("\t<data key=\"num_unknown_grant\">" 
+											+ node.getUnknownGrantYearCount() 
+										+ "</data>\n");
+				
+		}
+		
+		graphMLContent.append("</node>\n");
+	}
+
+	private void generateKeyDefinitionContent(CoPIData coPIData,
+			StringBuilder graphMLContent) {
+		/*
+		 * Generate the key definition content for node. 
+		 * */
+		getKeyDefinitionFromSchema(coPIData.getNodeSchema(), graphMLContent);
+		
+		/*
+		 * Generate the key definition content for edge. 
+		 * */
+		getKeyDefinitionFromSchema(coPIData.getEdgeSchema(), graphMLContent);
+	}
+	
+	private void getKeyDefinitionFromSchema(Set<Map<String, String>> schema,
+			StringBuilder graphMLContent) {
+		
+		for (Map<String, String> currentNodeSchemaAttribute : schema) {
+			
+			graphMLContent.append("\n<key ");
+			
+			for (Map.Entry<String, String> currentAttributeKey 
+						: currentNodeSchemaAttribute.entrySet()) {
+				
+				graphMLContent.append(currentAttributeKey.getKey() 
+										+ "=\"" + currentAttributeKey.getValue() 
+										+ "\" ");
+
+			}
+			
+			if (currentNodeSchemaAttribute.containsKey("default")) {
+				
+				graphMLContent.append(">\n");
+				graphMLContent.append("<default>");
+				graphMLContent.append(currentNodeSchemaAttribute.get("default"));
+				graphMLContent.append("</default>\n");
+				graphMLContent.append("</key>\n");
+				
+			} else {
+				graphMLContent.append("/>\n");
+			}
+		}
+	}
+
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPINodeComparator.java

@@ -0,0 +1,20 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.util.Comparator;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.CoPINode;
+
+/**
+ * This Comparator is used to sort the CoPINodes based on their IDs in ascending order.
+ * @author bkoniden
+ * Deepak Konidena
+ */
+
+public class CoPINodeComparator implements Comparator<CoPINode>{
+	@Override
+	public int compare(CoPINode arg0, CoPINode arg1) {
+		return arg0.getNodeID() - arg1.getNodeID();
+	}
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/coprincipalinvestigator/CoPIVisCodeGenerator.java

@@ -0,0 +1,623 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.coprincipalinvestigator;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.Calendar;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.apache.commons.logging.Log;
+
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationController;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.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.valueobjects.CoPINode;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SparklineData;
+
+/**
+ * This class contains code for rendering sparklines and displaying tables for 
+ * Co-PI visualization.
+ * @author bkoniden
+ * Deepak Konidena
+ */
+@SuppressWarnings("serial")
+public class CoPIVisCodeGenerator {
+
+	/*
+	 * There are 2 modes of sparkline that are available via this visualization.
+	 * 		1. Short Sparkline - This sparkline will render all the data points (or sparks),
+	 * 			which in this case are the copi(s) over the years, from the last 10 years.
+	 * 
+	 * 		2. Full Sparkline - This sparkline will render all the data points (or sparks) 
+	 * 			spanning the career of the person & last 10 years at the minimum, in case if
+	 * 			the person started his career in the last 10 years.
+	 * */
+	private static final Map<String, String> VIS_DIV_NAMES = new HashMap<String, String>() { {
+
+		put("SHORT_SPARK", "unique_copis_short_sparkline_vis");
+		put("FULL_SPARK", "unique_copis_full_sparkline_vis");
+
+	} };
+	
+	private static final String VISUALIZATION_STYLE_CLASS = "sparkline_style";
+	
+	private static final String DEFAULT_VISCONTAINER_DIV_ID = "unique_copis_vis_container";
+	
+	private Map<String, Set<CoPINode>> yearToUniqueCoPIs;
+
+	private Log log;
+
+	private SparklineData sparklineData;
+
+	private String contextPath;
+
+	private String individualURI;
+
+	public CoPIVisCodeGenerator(String contextPath, 
+			  String individualURI, 
+			  String visMode, 
+			  String visContainer, 
+			  Map<String, Set<CoPINode>> yearToUniqueCoPIs, 
+			  Log log){
+		
+		this.contextPath = contextPath;
+		this.individualURI = individualURI;
+		
+		this.yearToUniqueCoPIs = yearToUniqueCoPIs;
+		this.sparklineData = new SparklineData();
+		
+		this.log = log;
+		
+		generateVisualizationCode(visMode, visContainer);		
+		
+	}
+
+	/**
+	 * This method is used to generate the visualization code (HMTL, CSS &
+	 * JavaScript). There 2 parts to it - 1. Actual Content Code & 2. Context
+	 * Code. 1. Actual Content code in this case is the sparkline image, text
+	 * related to data and the wrapping tables. This is generated via call to
+	 * google vis API through JavaScript. 2. Context code is generally optional
+	 * but contains code pertaining to tabulated data & links to download files
+	 * etc.
+	 * 
+	 * @param visMode
+	 * @param visContainer
+	 */
+	private void generateVisualizationCode(String visMode, String visContainer) {
+
+		sparklineData.setSparklineContent(getMainVisualizationCode(visMode,
+				visContainer));
+
+		sparklineData.setSparklineContext(getVisualizationContextCode(visMode));
+
+	}
+
+	private String getMainVisualizationCode(String visMode,
+			String providedVisContainerID) {
+
+		int numOfYearsToBeRendered = 0;
+		int currentYear = Calendar.getInstance().get(Calendar.YEAR);
+		int shortSparkMinYear = currentYear
+				- VisConstants.MINIMUM_YEARS_CONSIDERED_FOR_SPARKLINE + 1;
+
+		/*
+		 * This is required because when deciding the range of years over which
+		 * the vis was rendered we dont want to be influenced by the
+		 * "DEFAULT_GRANT_YEAR".
+		 */
+		Set<String> investigatedYears = new HashSet<String>(yearToUniqueCoPIs
+				.keySet());
+		investigatedYears.remove(VOConstants.DEFAULT_GRANT_YEAR);
+
+		/*
+		 * We are setting the default value of minGrantYear to be 10 years
+		 * before the current year (which is suitably represented by the
+		 * shortSparkMinYear), this in case we run into invalid set of investigated
+		 * years.
+		 */
+		int minGrantYear = shortSparkMinYear;
+
+		String visContainerID = null;
+
+		StringBuilder visualizationCode = new StringBuilder();
+
+		if (yearToUniqueCoPIs.size() > 0) {
+			try {
+				minGrantYear = Integer.parseInt(Collections
+						.min(investigatedYears));
+			} catch (NoSuchElementException e1) {
+				log.debug("vis: " + e1.getMessage() + " error occurred for "
+						+ yearToUniqueCoPIs.toString());
+			} catch (NumberFormatException e2) {
+				log.debug("vis: " + e2.getMessage() + " error occurred for "
+						+ yearToUniqueCoPIs.toString());
+			}
+		}
+
+		int minGrantYearConsidered = 0;
+
+		/*
+		 * There might be a case that the person investigated his first grant
+		 * within the last 10 years but we want to make sure that the sparkline
+		 * is representative of at least the last 10 years, so we will set the
+		 * minGrantYearConsidered to "currentYear - 10" which is also given by
+		 * "shortSparkMinYear".
+		 */
+		if (minGrantYear > shortSparkMinYear) {
+			minGrantYearConsidered = shortSparkMinYear;
+		} else {
+			minGrantYearConsidered = minGrantYear;
+		}
+
+		numOfYearsToBeRendered = currentYear - minGrantYearConsidered + 1;
+
+		visualizationCode.append("<style type='text/css'>" + "."
+				+ VISUALIZATION_STYLE_CLASS + " table{" + "		margin: 0;"
+				+ "  		padding: 0;" + "  		width: auto;"
+				+ "  		border-collapse: collapse;" + "    	border-spacing: 0;"
+				+ "    	vertical-align: inherit;" + "}"
+				+ ".incomplete-data-holder {" + "" + "}"
+				+ "td.sparkline_number { text-align:right; "
+				+ "padding-right:5px; }"
+				+ "td.sparkline_text   {text-align:left;}" + "</style>\n");
+
+		visualizationCode
+				.append("<script type=\"text/javascript\">\n"
+						+ "function drawUniqueCoPICountVisualization(providedSparklineImgTD) {\n"
+						+ "var data = new google.visualization.DataTable();\n"
+						+ "data.addColumn('string', 'Year');\n"
+						+ "data.addColumn('number', 'Unique Co-PI(s)');\n"
+						+ "data.addRows(" + numOfYearsToBeRendered + ");\n");
+
+		int uniqueCoPICounter = 0;
+		int renderedFullSparks = 0;
+		Set<CoPINode> allCoPIsWithKnownGrantShipYears = new HashSet<CoPINode>();
+
+		for (int grantYear = minGrantYearConsidered; grantYear <= currentYear; grantYear++) {
+
+			String grantYearAsString = String.valueOf(grantYear);
+			Set<CoPINode> currentCoPIs = yearToUniqueCoPIs
+					.get(grantYearAsString);
+
+			Integer currentUniqueCoPIs = null;
+
+			if (currentCoPIs != null) {
+				currentUniqueCoPIs = currentCoPIs.size();
+				allCoPIsWithKnownGrantShipYears.addAll(currentCoPIs);
+			} else {
+				currentUniqueCoPIs = 0;
+			}
+
+			visualizationCode.append("data.setValue(" + uniqueCoPICounter
+					+ ", 0, '" + grantYearAsString + "');\n");
+
+			visualizationCode.append("data.setValue(" + uniqueCoPICounter
+					+ ", 1, " + currentUniqueCoPIs + ");\n");
+			uniqueCoPICounter++;
+		}
+
+		/*
+		 * For the purpose of this visualization I have come up with a term
+		 * "Sparks" which essentially means data points. Sparks that will be
+		 * rendered in full mode will always be the one's which have any year
+		 * associated with it. Hence.
+		 */
+		renderedFullSparks = allCoPIsWithKnownGrantShipYears.size();
+
+		/*
+		 * Total grants will also consider publications that have no year
+		 * associated with them. Hence.
+		 */
+		Integer unknownYearCoPIs = 0;
+		if (yearToUniqueCoPIs.get(VOConstants.DEFAULT_GRANT_YEAR) != null) {
+			unknownYearCoPIs = yearToUniqueCoPIs.get(
+					VOConstants.DEFAULT_GRANT_YEAR).size();
+		}
+
+		String sparklineDisplayOptions = "{width: 65, height: 30, showAxisLines: false, "
+				+ "showValueLabels: false, labelPosition: 'none'}";
+
+		if (providedVisContainerID != null) {
+			visContainerID = providedVisContainerID;
+		} else {
+			visContainerID = DEFAULT_VISCONTAINER_DIV_ID;
+		}
+
+		/*
+		 * By default these represents the range of the rendered sparks. Only in
+		 * case of "short" sparkline mode we will set the Earliest
+		 * RenderedGrant year to "currentYear - 10".
+		 */
+		sparklineData.setEarliestRenderedGrantYear(minGrantYear);
+		sparklineData.setLatestRenderedGrantYear(currentYear);
+
+		/*
+		 * The Full Sparkline will be rendered by default. Only if the url has
+		 * specific mention of SHORT_SPARKLINE_MODE_KEY then we render the short
+		 * sparkline and not otherwise.
+		 */
+
+		/*
+		 * Since building StringBuilder objects (which is being used to store
+		 * the vis code) is essentially a side-effecting process, we have both
+		 * the activators method as side-effecting. They both side-effect
+		 * "visualizationCode"
+		 */
+		if (VisualizationFrameworkConstants.SHORT_SPARKLINE_VIS_MODE
+				.equalsIgnoreCase(visMode)) {
+
+			sparklineData.setEarliestRenderedGrantYear(shortSparkMinYear);
+			
+			generateShortSparklineVisualizationContent(currentYear,
+					shortSparkMinYear, visContainerID, visualizationCode,
+					unknownYearCoPIs, sparklineDisplayOptions);
+		} else {
+			generateFullSparklineVisualizationContent(currentYear,
+					minGrantYearConsidered, visContainerID, visualizationCode,
+					unknownYearCoPIs, renderedFullSparks,
+					sparklineDisplayOptions);
+		}
+
+		log.debug(visualizationCode);
+
+		return visualizationCode.toString();
+	}
+
+	private void generateShortSparklineVisualizationContent(int currentYear,
+			int shortSparkMinYear, String visContainerID,
+			StringBuilder visualizationCode, int unknownYearGrants,
+			String sparklineDisplayOptions) {
+
+		/*
+		 * Create a view of the data containing only the column pertaining to
+		 * grant count.
+		 */
+		visualizationCode.append("var shortSparklineView = "
+				+ "new google.visualization.DataView(data);\n"
+				+ "shortSparklineView.setColumns([1]);\n");
+
+		/*
+		 * For the short view we only want the last 10 year's view of
+		 * grant count, hence we filter the data we actually want to use
+		 * for render.
+		 */
+		visualizationCode.append("shortSparklineView.setRows("
+				+ "data.getFilteredRows([{column: 0, " + "minValue: '"
+				+ shortSparkMinYear + "', " + "maxValue: '" + currentYear
+				+ "'}])" + ");\n");
+
+		/*
+		 * Create the vis object and draw it in the div pertaining to
+		 * short-sparkline.
+		 */
+		visualizationCode
+				.append("var short_spark = new google.visualization.ImageSparkLine("
+						+ "providedSparklineImgTD[0]"
+						+ ");\n"
+						+ "short_spark.draw(shortSparklineView, "
+						+ sparklineDisplayOptions + ");\n");
+
+		/*
+		 * We want to display how many grant counts were considered, so
+		 * this is used to calculate this.
+		 */
+		visualizationCode
+				.append("var shortSparkRows = shortSparklineView.getViewRows();\n"
+						+ "var renderedShortSparks = 0;\n"
+						+ "$.each(shortSparkRows, function(index, value) {"
+						+ "renderedShortSparks += data.getValue(value, 1);"
+						+ "});\n");
+
+		/*
+		 * Generate the text introducing the vis.
+		 */
+
+		String imcompleteDataText = "This information is based solely on grants which "
+				+ "have been loaded into the VIVO system. "
+				+ "This may only be a small sample of the person\\'s "
+				+ "total work.";
+
+		visualizationCode.append("$('#" + VIS_DIV_NAMES.get("SHORT_SPARK")
+				+ " td.sparkline_number').text("
+				+ "parseInt(renderedShortSparks) " + "+ parseInt("
+				+ unknownYearGrants + "));");
+
+		visualizationCode.append("var shortSparksText = ''"
+				+ "+ ' grant(s) within the last 10 years "
+				+ "<span class=\"incomplete-data-holder\" title=\""
+				+ imcompleteDataText + "\">incomplete data</span>'" + "+ '';"
+				+ "$('#" + VIS_DIV_NAMES.get("SHORT_SPARK") + " "
+				+ "td.sparkline_text').html(shortSparksText);");
+
+		visualizationCode.append("}\n ");
+
+		/*
+		 * Generate the code that will activate the visualization. It takes care
+		 * of creating div elements to hold the actual sparkline image and then
+		 * calling the drawUniqueCoPICountVisualization function.
+		 */
+		visualizationCode.append(generateVisualizationActivator(VIS_DIV_NAMES
+				.get("SHORT_SPARK"), visContainerID));
+
+	}
+	
+	private void generateFullSparklineVisualizationContent(
+			int currentYear, 
+			int minGrantYearConsidered, 
+			String visContainerID, 
+			StringBuilder visualizationCode,
+			int unknownYearGrants,
+			int renderedFullSparks,
+			String sparklineDisplayOptions) {
+		
+		String csvDownloadURLHref = ""; 
+		
+		try {
+			if (getCSVDownloadURL() != null) {
+				
+				csvDownloadURLHref = "<a href=\"" + getCSVDownloadURL() 
+											+ "\" class=\"inline_href\">(.CSV File)</a>";
+				
+			} else {
+				csvDownloadURLHref = "";
+			}
+
+		} catch (UnsupportedEncodingException e) {
+			csvDownloadURLHref = "";
+		}
+		
+		
+		visualizationCode.append("var fullSparklineView = " 
+									+ "new google.visualization.DataView(data);\n" 
+									+ "fullSparklineView.setColumns([1]);\n");
+		
+		visualizationCode.append("var full_spark = new google.visualization.ImageSparkLine(" 
+									+ "providedSparklineImgTD[0]" 
+									+ ");\n" 
+									+ "full_spark.draw(fullSparklineView, " 
+									+ sparklineDisplayOptions + ");\n");
+		
+		visualizationCode.append("$('#" + VIS_DIV_NAMES.get("FULL_SPARK") 
+									+ " td.sparkline_number').text('" + (renderedFullSparks 
+									+ unknownYearGrants) + "');");
+		
+		visualizationCode.append("var allSparksText = ''" 
+									+ "+ ' Co-Principal Investigator(s) '" 
+									+ "+ ' from " 
+									+ "<span class=\"sparkline_range\">" 
+									+ "" + minGrantYearConsidered + " to " + currentYear + "" 
+									+ "</span> '" 
+									+ "+ ' " + csvDownloadURLHref + " ';" 
+									+ "$('#" + VIS_DIV_NAMES.get("FULL_SPARK") 
+									+ " td.sparkline_text').html(allSparksText);");
+		
+		visualizationCode.append("}\n ");
+		
+		visualizationCode.append(generateVisualizationActivator(VIS_DIV_NAMES.get("FULL_SPARK"), 
+																visContainerID));
+		
+	}
+	
+	private String generateVisualizationActivator(String sparklineID, String visContainerID) {
+		
+		String sparklineTableWrapper = "\n" 
+				+ "var table = $('<table>');" 
+				+ "table.attr('class', 'sparkline_wrapper_table');" 
+				+ "var row = $('<tr>');" 
+				+ "sparklineImgTD = $('<td>');" 
+				+ "sparklineImgTD.attr('id', '" + sparklineID + "_img');" 
+				+ "sparklineImgTD.attr('width', '65');" 
+				+ "sparklineImgTD.attr('align', 'right');" 
+				+ "sparklineImgTD.attr('class', '" + VISUALIZATION_STYLE_CLASS + "');" 
+				+ "row.append(sparklineImgTD);" 
+				+ "var sparklineNumberTD = $('<td>');" 
+				+ "sparklineNumberTD.attr('width', '30');" 
+				+ "sparklineNumberTD.attr('align', 'right');" 
+				+ "sparklineNumberTD.attr('class', 'sparkline_number');" 
+				+ "row.append(sparklineNumberTD);" 
+				+ "var sparklineTextTD = $('<td>');" 
+				+ "sparklineTextTD.attr('width', '450');" 
+				+ "sparklineTextTD.attr('class', 'sparkline_text');" 
+				+ "row.append(sparklineTextTD);" 
+				+ "table.append(row);" 
+				+ "table.prependTo('#" + sparklineID + "');\n";
+		
+		return "$(document).ready(function() {" 
+				+ "var sparklineImgTD; " 
+		
+				/*
+				 * This is a nuclear option (creating the container in which everything goes)
+				 * the only reason this will be ever used is the API user never submitted a 
+				 * container ID in which everything goes. The alternative was to let the 
+				 * vis not appear in the calling page at all. So now atleast vis appears but 
+				 * appended at the bottom of the body.
+				 * */
+				
+				+ "if ($('#" + visContainerID + "').length === 0) {" 
+				+ "	$('<div/>', {'id': '" + visContainerID + "'" 
+				+ "     }).appendTo('body');" 
+				+ "}" 
+				+ "if ($('#" + sparklineID + "').length === 0) {" 
+				+ "$('<div/>', {'id': '" + sparklineID + "'," 
+				+ "'class': '" + VISUALIZATION_STYLE_CLASS + "'" 
+				+ "}).prependTo('#" + visContainerID + "');" 
+				+ sparklineTableWrapper 
+				+ "}" 
+				+ "drawUniqueCoPICountVisualization(sparklineImgTD);" 
+				+ "});" 
+				+ "</script>\n";
+	}
+	
+	private String getVisualizationContextCode(String visMode) {
+
+		String visualizationContextCode = "";
+		if (VisualizationFrameworkConstants.SHORT_SPARKLINE_VIS_MODE.equalsIgnoreCase(visMode)) {
+			visualizationContextCode = generateShortVisContext();
+		} else {
+			visualizationContextCode = generateFullVisContext();
+		}
+
+		log.debug(visualizationContextCode);
+
+		return visualizationContextCode;
+	}
+	
+	private String generateFullVisContext() {
+		
+		StringBuilder divContextCode = new StringBuilder();
+		
+		String csvDownloadURLHref = ""; 
+		
+		if (yearToUniqueCoPIs.size() > 0) {
+			
+			try {
+				if (getCSVDownloadURL() != null) {
+					
+					csvDownloadURLHref = "Download data as <a href='" 
+											+ getCSVDownloadURL() + "'>.csv</a> file.<br />";
+					sparklineData.setDownloadDataLink(getCSVDownloadURL());
+					
+				} else {
+					csvDownloadURLHref = "";
+				}
+
+			} catch (UnsupportedEncodingException e) {
+				csvDownloadURLHref = "";
+			}
+			
+		} else {
+			csvDownloadURLHref = "No data available to export.<br />";
+		}
+		
+		String tableCode = generateDataTable();
+		
+		divContextCode.append("<p>" + tableCode + csvDownloadURLHref + "</p>");
+		
+		sparklineData.setTable(tableCode);
+		
+		return divContextCode.toString();
+	}
+	
+	private String getCSVDownloadURL() throws UnsupportedEncodingException {
+		
+		if (yearToUniqueCoPIs.size() > 0) {
+			
+		String secondaryContextPath = "";
+		if (!contextPath.contains(VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX)) {
+			secondaryContextPath = VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX;
+		}
+			
+			
+		String downloadURL = contextPath
+			 + secondaryContextPath
+			 + "?" + VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
+			 + "=" + URLEncoder.encode(individualURI, 
+					 				   VisualizationController.URL_ENCODING_SCHEME).toString() 
+			 + "&" + VisualizationFrameworkConstants.VIS_TYPE_KEY 
+			 + "=" + URLEncoder.encode(VisualizationFrameworkConstants
+					 						.CO_PI_VIS, 
+					 				   VisualizationController.URL_ENCODING_SCHEME).toString() 
+			 + "&" + VisualizationFrameworkConstants.VIS_MODE_KEY
+			 + "=" + URLEncoder.encode("sparkline", 
+					 				   VisualizationController.URL_ENCODING_SCHEME).toString()
+			 + "&" + VisualizationFrameworkConstants.RENDER_MODE_KEY 
+			 + "=" + URLEncoder.encode(VisualizationFrameworkConstants.DATA_RENDER_MODE, 
+	 				 				   VisualizationController.URL_ENCODING_SCHEME).toString();
+		
+			return downloadURL;
+		} else {
+			return null;
+		}
+	}
+	private String generateShortVisContext() {
+
+		StringBuilder divContextCode = new StringBuilder();
+		
+		try {
+		
+		String fullTimelineLink;
+		if (yearToUniqueCoPIs.size() > 0) {
+			
+			String secondaryContextPath = "";
+			if (!contextPath.contains(VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX)) {
+				secondaryContextPath = VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX;
+			}
+			
+			String fullTimelineNetworkURL = contextPath
+							+ secondaryContextPath
+							+ "?" 
+							+ VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
+							+ "=" + URLEncoder.encode(individualURI, 
+					 				 VisualizationController.URL_ENCODING_SCHEME).toString()
+					 	    + "&"
+		 				    + VisualizationFrameworkConstants.VIS_TYPE_KEY 
+							+ "=" + URLEncoder.encode("person_level", 
+					 				 VisualizationController.URL_ENCODING_SCHEME).toString()
+					 	    + "&"
+		 				    + VisualizationFrameworkConstants.VIS_CONTAINER_KEY 
+							+ "=" + URLEncoder.encode("ego_sparkline", 
+					 				 VisualizationController.URL_ENCODING_SCHEME).toString()
+		 				    + "&"
+		 				    + VisualizationFrameworkConstants.RENDER_MODE_KEY
+							+ "=" + URLEncoder.encode(
+											VisualizationFrameworkConstants
+													.STANDALONE_RENDER_MODE,
+											VisualizationController.URL_ENCODING_SCHEME).toString();
+			
+			fullTimelineLink = "<a href='" + fullTimelineNetworkURL 
+									+ "'>View full timeline and co-pi network.</a>";
+			
+			sparklineData.setFullTimelineNetworkLink(fullTimelineNetworkURL);
+			
+		} else {
+			fullTimelineLink = "No data available to render full timeline.<br />";
+		}
+		
+		divContextCode.append("<p>" + fullTimelineLink + "</p>");
+		
+		} catch (UnsupportedEncodingException e) {
+			log.error(e);
+		}
+		
+		return divContextCode.toString();
+	}
+	
+	private String generateDataTable() {
+		
+		StringBuilder dataTable = new StringBuilder();
+		
+		dataTable.append("<table id='sparkline_data_table'>" 
+							+ "<caption>Unique Co-PIs per year</caption>" 
+							+ "<thead>" 
+							+ "<tr>" 
+							+ "<th>Year</th>" 
+							+ "<th>Count</th>" 
+							+ "</tr>" 
+							+ "</thead>" 
+							+ "<tbody>");
+		
+		for (Entry<String, Set<CoPINode>> currentEntry : yearToUniqueCoPIs.entrySet()) {
+			dataTable.append("<tr>" 
+								+ "<td>" + currentEntry.getKey() + "</td>" 
+								+ "<td>" + currentEntry.getValue().size() + "</td>" 
+								+ "</tr>");
+		}
+										
+		dataTable.append("</tbody>\n </table>\n");
+		
+		return dataTable.toString();
+	}
+	
+	public SparklineData getValueObjectContainer() {
+		return sparklineData;
+	}
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/persongrantcount/PersonGrantCountQueryRunner.java

@@ -129,7 +129,7 @@ public class PersonGrantCountQueryRunner implements QueryRunner<Set<Grant>>{
 							+ "?Grant rdfs:label ?GrantLabel ; core:startDate ?GrantStartDate ; core:endDate ?GrantEndDate ."
 							+ "}";
 		
-		System.out.println("SPARQL query for person grant count -> \n"+ sparqlQuery);
+		log.debug("SPARQL query for person grant count -> \n"+ sparqlQuery);
 		return sparqlQuery;
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/persongrantcount/PersonGrantCountRequestHandler.java

@@ -2,38 +2,29 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.persongrantcount;
 
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
 import java.util.Map.Entry;
-
+import java.util.Set;
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 
 import com.hp.hpl.jena.query.DataSource;
-import com.itextpdf.text.Document;
-import com.itextpdf.text.DocumentException;
-import com.itextpdf.text.pdf.PdfWriter;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 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.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.DataVisualizationController;
 import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Grant;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Individual;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SparklineData;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.PDFDocument;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
 
 
@@ -54,14 +45,42 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
  */
 public class PersonGrantCountRequestHandler implements VisualizationRequestHandler {
 	
-	public ResponseValues generateVisualization(VitroRequest vitroRequest,
+	@Override
-			Log log, DataSource dataSource) {
+	public Map<String, String> generateDataVisualization(
+			VitroRequest vitroRequest, Log log, DataSource dataSource)
+			throws MalformedQueryParametersException {
+
 
 		String personURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
-		String renderMode = vitroRequest
+		QueryRunner<Set<Grant>> queryManager = new PersonGrantCountQueryRunner(personURI, dataSource, log );
-				.getParameter(VisualizationFrameworkConstants.RENDER_MODE_KEY);
+		
+		Set<Grant> piGrants = queryManager.getQueryResult();
+		
+		/*
+    	 * Create a map from the year to number of grants. Use the Grant's
+    	 * parsedGrantYear to populate the data.
+    	 * */
+    	Map<String, Integer> yearToGrantCount = 
+			UtilityFunctions.getYearToGrantCount(piGrants);
+	
+    	Individual investigator = ((PersonGrantCountQueryRunner) queryManager).getPrincipalInvestigator();
+    	
+    	return prepareDataResponse(investigator,
+				piGrants,
+				yearToGrantCount);
+
+	
+	}
+	
+
+	@Override
+	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
+			DataSource dataSource) throws MalformedQueryParametersException {
+
+		String personURI = vitroRequest
+		.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 
 		String visMode = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
@@ -69,9 +88,8 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
 		String visContainer = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
 		
-	QueryRunner<Set<Grant>> queryManager = new PersonGrantCountQueryRunner(personURI, dataSource, log );
+		QueryRunner<Set<Grant>> queryManager = new PersonGrantCountQueryRunner(personURI, dataSource, log );
 		
-	try{
 		Set<Grant> piGrants = queryManager.getQueryResult();
 		
     	/*
@@ -81,40 +99,62 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
     	Map<String, Integer> yearToGrantCount = 
 			UtilityFunctions.getYearToGrantCount(piGrants);
     	
-    	Individual investigator = ((PersonGrantCountQueryRunner) queryManager).getPrincipalInvestigator();
 
-    	if (VisualizationFrameworkConstants.DATA_RENDER_MODE
+		boolean shouldVIVOrenderVis = 
-    				.equalsIgnoreCase(renderMode)) {
+			yearToGrantCount.size() > 0 ? true : false;
+			
+			/*
+	    	 * Computations required to generate HTML for the sparkline & related context.
+	    	 * */
+	    	PersonGrantCountVisCodeGenerator visualizationCodeGenerator = 
+	    		new PersonGrantCountVisCodeGenerator(personURI,
+	    									   visMode,
+	    									   visContainer,
+	    									   piGrants,
+	    									   yearToGrantCount,
+	    									   log);
 
 
-    		/*
+	    	SparklineData sparklineData = visualizationCodeGenerator
-			return prepareDataResponse(investigator,
+			.getValueObjectContainer();
-					piGrants,
+	    	
-					yearToGrantCount);
+	    	return prepareDynamicResponse(vitroRequest, 
-					*/
+			   		  sparklineData, 
-		}
+			   		shouldVIVOrenderVis);
+
+		
+	}
+	
+	@Override
+	public ResponseValues generateStandardVisualization(
+			VitroRequest vitroRequest, Log log, DataSource dataSource)
+			throws MalformedQueryParametersException {
+		
+		String personURI = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+
+		String visMode = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
+
+		String visContainer = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
+
+		QueryRunner<Set<Grant>> queryManager = new PersonGrantCountQueryRunner(personURI, dataSource, log );
+	
+		Set<Grant> piGrants = queryManager.getQueryResult();
 		
     	/*
-    	 * For now we are disabling the capability to render pdf file.
+    	 * Create a map from the year to number of grants. Use the Grant's
+    	 * parsedGrantYear to populate the data.
     	 * */
-    	/*
+    	Map<String, Integer> yearToGrantCount = 
-    	if (VisualizationFrameworkConstants.PDF_RENDER_MODE
+			UtilityFunctions.getYearToGrantCount(piGrants);
-    				.equalsIgnoreCase(renderMode)) {
-    		
-			preparePDFResponse(investigator,
-												 piGrants,
-												 yearToGrantCount,
-												 response);
-			return;
-		}
-    	*/
 	
     	/*
     	 * Computations required to generate HTML for the sparkline & related context.
     	 * */
     	PersonGrantCountVisCodeGenerator visualizationCodeGenerator = 
-    		new PersonGrantCountVisCodeGenerator(vitroRequest.getContextPath(),
+    		new PersonGrantCountVisCodeGenerator(personURI,
-    									   personURI,
     									   visMode,
     									   visContainer,
     									   piGrants,
@@ -124,30 +164,9 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
     	SparklineData sparklineData = visualizationCodeGenerator
 											.getValueObjectContainer();
     	
-    	/*
-    	 * This is side-effecting because the response of this method is just to redirect to
-    	 * a page with visualization on it.
-    	 * */
-    	RequestDispatcher requestDispatcher = null;
-    	
-		if (VisualizationFrameworkConstants.DYNAMIC_RENDER_MODE
-				.equalsIgnoreCase(renderMode)) {
-
-		return prepareDynamicResponse(vitroRequest, 
-							   		  sparklineData, 
-							   		  yearToGrantCount);
-		
-		} else {
 			return prepareStandaloneResponse(vitroRequest, 
     							  sparklineData);
-		}
-	} catch (MalformedQueryParametersException e) {
-		return UtilityFunctions.handleMalformedParameters(
-				"Visualization Query Error - Individual Grant Count",
-				e.getMessage(), 
-				vitroRequest);
 	}
-  }
 	
 	private String getGrantsOverTimeCSVContent(Map<String, Integer> yearToGrantCount) {
 		
@@ -199,13 +218,15 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
 		String outputFileName = UtilityFunctions.slugify(piName) 
 										+ "_grants-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, 
+					getGrantsOverTimeCSVContent(yearToGrantCount));
 
-        Map<String, Object> fileContents = new HashMap<String, Object>();
+		return fileData;
-        fileContents.put("fileContent", getGrantsOverTimeCSVContent(yearToGrantCount));
-		
-//		return new FileResponseValues(new ContentType(), outputFileName, fileContents);
-		
-		return new HashMap<String, String>();
 	}
 	
 	/**
@@ -226,11 +247,6 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
         body.put("title", "Individual Grant Count visualization");
         body.put("sparklineVO", valueObjectContainer);
 
-        /*
-         * DO NOT DO THIS HERE. Set stylesheets/scripts in the *.ftl instead using $(scripts.add)
-         * */
-//        body.put("scripts", "/templates/visualization/visualization_scripts.jsp");
-        
         return new TemplateResponseValues(standaloneTemplate, body);
         
 	}
@@ -246,7 +262,7 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
 	private TemplateResponseValues prepareDynamicResponse(
 			VitroRequest vreq,
 			SparklineData valueObjectContainer, 
-			Map<String, Integer> yearToGrantCount) {
+			boolean shouldVIVOrenderVis) {
 
         Portal portal = vreq.getPortal();
 
@@ -256,102 +272,10 @@ public class PersonGrantCountRequestHandler implements VisualizationRequestHandl
         Map<String, Object> body = new HashMap<String, Object>();
         body.put("portalBean", portal);
         body.put("sparklineVO", valueObjectContainer);
-
+        body.put("shouldVIVOrenderVis", shouldVIVOrenderVis);
-        /*
-         * DO NOT DO THIS HERE. Set stylesheets/scripts in the *.ftl instead using $(scripts.add)
-         * */
-//        body.put("scripts", "/templates/visualization/visualization_scripts.jsp");
-        
-        if (yearToGrantCount.size() > 0) {
-        	body.put("shouldVIVOrenderVis", true);
-        } else {
-        	body.put("shouldVIVOrenderVis", false);
-        }
         
         return new TemplateResponseValues(dynamicTemplate, body);
         
 	}
 
-	
-	private void preparePDFResponse(Individual investigator,
-			Set<Grant> piGrants,
-			Map<String, Integer> yearToGrantCount,
-			HttpServletResponse response) {
-
-		String piName = null;
-
-		// To protect against cases where there are no PI grants
-		// associated with the
-		// / individual.
-		if (piGrants.size() > 0) {
-			piName = investigator.getIndividualLabel();
-		}
-
-		// To make sure that null/empty records for PI names do not cause
-		// any mischief.
-		if (StringUtils.isBlank(piName)) {
-			piName = "no-principal-investigator";
-		}
-
-		String outputFileName = UtilityFunctions.slugify(piName)
-				+ "_report" + ".pdf";
-
-		response.setContentType("application/pdf");
-		response.setHeader("Content-Disposition", "attachment;filename="
-				+ outputFileName);
-
-		ServletOutputStream responseOutputStream;
-		try {
-			responseOutputStream = response.getOutputStream();
-
-			Document document = new Document();
-			ByteArrayOutputStream baos = new ByteArrayOutputStream();
-			PdfWriter pdfWriter = PdfWriter.getInstance(document, baos);
-			document.open();
-
-			PDFDocument pdfDocument = new PDFDocument(piName,
-					yearToGrantCount, document, pdfWriter);
-
-			document.close();
-
-			// setting some response headers & content type
-			response.setHeader("Expires", "0");
-			response.setHeader("Cache-Control",
-					"must-revalidate, post-check=0, pre-check=0");
-			response.setHeader("Pragma", "public");
-			response.setContentLength(baos.size());
-			// write ByteArrayOutputStream to the ServletOutputStream
-			baos.writeTo(responseOutputStream);
-			responseOutputStream.flush();
-			responseOutputStream.close();
-
-		} catch (IOException e) {
-			e.printStackTrace();
-		} catch (DocumentException e) {
-			e.printStackTrace();
-		}
-	}
-
-	@Override
-	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
-			DataSource dataSource) throws MalformedQueryParametersException {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Map<String, String> generateDataVisualization(
-			VitroRequest vitroRequest, Log log, DataSource dataSource)
-			throws MalformedQueryParametersException {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public ResponseValues generateStandardVisualization(
-			VitroRequest vitroRequest, Log log, DataSource dataSource)
-			throws MalformedQueryParametersException {
-		// TODO Auto-generated method stub
-		return null;
-	}
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/persongrantcount/PersonGrantCountVisCodeGenerator.java

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.persongrantcount;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Collections;
@@ -11,13 +9,14 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.NoSuchElementException;
 import java.util.Set;
-import java.util.Map.Entry;
 
 import org.apache.commons.logging.Log;
 
-import edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker.StandardVisualizationController;
+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.visualization.VisualizationFrameworkConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VisConstants;
@@ -26,7 +25,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Sp
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.YearGrantCountDataElement;
 
 
-
+@SuppressWarnings("serial")
 public class PersonGrantCountVisCodeGenerator {
 	
 	/*
@@ -38,6 +37,7 @@ public class PersonGrantCountVisCodeGenerator {
 	 * 			spanning the career of the person & last 10 years at the minimum, in case if
 	 * 			the person started his career in the last 10 yeras.
 	 * */
+	
 	private static final Map<String, String> VIS_DIV_NAMES = new HashMap<String, String>() { {
 
 		put("SHORT_SPARK", "grant_count_short_sparkline_vis");
@@ -55,16 +55,13 @@ public class PersonGrantCountVisCodeGenerator {
 
 	private SparklineData sparklineData;
 
-	private String contextPath;
-
 	private String individualURI;
 	
-	public PersonGrantCountVisCodeGenerator(String contextPath,
+	public PersonGrantCountVisCodeGenerator(String individualURIParam,
-			String individualURIParam, String visMode, String visContainer,
+			String visMode, String visContainer, Set<Grant> piGrants,
-			Set<Grant> piGrants,
+			Map<String, Integer> yearToGrantCount,
-			Map<String, Integer> yearToGrantCount, Log log) {
+			Log log) {
 
-		this.contextPath = contextPath;
 		this.individualURI = individualURIParam;
 
 		this.yearToGrantCount = yearToGrantCount;
@@ -198,8 +195,7 @@ public class PersonGrantCountVisCodeGenerator {
 		for (int grantYear = minGrantYearConsidered; grantYear <= currentYear; grantYear++) {
 
 			String stringInvestigatedYear = String.valueOf(grantYear);
-			Integer currentGrants = yearToGrantCount
+			Integer currentGrants = yearToGrantCount.get(stringInvestigatedYear);
-					.get(stringInvestigatedYear);
 
 			if (currentGrants == null) {
 				currentGrants = 0;
@@ -385,17 +381,12 @@ public class PersonGrantCountVisCodeGenerator {
 		
 		String csvDownloadURLHref = ""; 
 		
-		try {
+		if (getCSVDownloadURL() != null) {
-			if (getCSVDownloadURL() != null) {
 			
-				csvDownloadURLHref = "<a href=\"" + getCSVDownloadURL() 
+			csvDownloadURLHref = "<a href=\"" + getCSVDownloadURL() 
-											+ "\" class=\"inline_href\">(.CSV File)</a>";
+										+ "\" class=\"inline_href\">(.CSV File)</a>";
 			
-			} else {
+		} else {
-				csvDownloadURLHref = "";
-			}
-
-		} catch (UnsupportedEncodingException e) {
 			csvDownloadURLHref = "";
 		}
 		
@@ -505,18 +496,13 @@ public class PersonGrantCountVisCodeGenerator {
 		
 		if (yearToGrantCount.size() > 0) {
 			
-			try {
+			if (getCSVDownloadURL() != null) {
-				if (getCSVDownloadURL() != null) {
 				
-					csvDownloadURLHref = "Download data as <a href='" 
+				csvDownloadURLHref = "Download data as <a href='" 
-											+ getCSVDownloadURL() + "'>.csv</a> file.<br />";
+										+ getCSVDownloadURL() + "'>.csv</a> file.<br />";
-					sparklineData.setDownloadDataLink(getCSVDownloadURL());
+				sparklineData.setDownloadDataLink(getCSVDownloadURL());
 				
-				} else {
+			} else {
-					csvDownloadURLHref = "";
-				}
-
-			} catch (UnsupportedEncodingException e) {
 				csvDownloadURLHref = "";
 			}
 		} else {
@@ -533,34 +519,18 @@ public class PersonGrantCountVisCodeGenerator {
 	}
 	
 
-	private String getCSVDownloadURL()
+	private String getCSVDownloadURL() {
-			throws UnsupportedEncodingException {
 		
 		if (yearToGrantCount.size() > 0) {
 			
-			String secondaryContextPath = "";
+			ParamMap CSVDownloadURLParams = new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
-			if (!contextPath.contains(VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX)) {
+										 individualURI,
-				secondaryContextPath = VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX;
+										 VisualizationFrameworkConstants.VIS_TYPE_KEY,
-			}
+										 VisualizationFrameworkConstants.PERSON_GRANT_COUNT_VIS);
+
+			return UrlBuilder.getUrl(VisualizationFrameworkConstants.DATA_VISUALIZATION_SERVICE_URL_PREFIX,
+					 CSVDownloadURLParams);
 
-		String downloadURL = contextPath
-							 + secondaryContextPath
-							 + "?" + VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
-							 + "=" + URLEncoder.encode(individualURI, 
-									 				   StandardVisualizationController.URL_ENCODING_SCHEME)
-									 				   .toString() 
-							 + "&" + VisualizationFrameworkConstants.VIS_TYPE_KEY 
-							 + "=" + URLEncoder.encode(
-										 			VisualizationFrameworkConstants
-										 				.PERSON_GRANT_COUNT_VIS,
-										 				StandardVisualizationController.URL_ENCODING_SCHEME)
-								 				.toString() 
-							 + "&" + VisualizationFrameworkConstants.RENDER_MODE_KEY 
-							 + "=" + URLEncoder.encode(VisualizationFrameworkConstants
-									 						.DATA_RENDER_MODE, 
-									 						StandardVisualizationController.URL_ENCODING_SCHEME)
-			 				 				   .toString();
-			return downloadURL;
 		} else {
 			return null;
 		}
@@ -571,46 +541,30 @@ public class PersonGrantCountVisCodeGenerator {
 
 		StringBuilder divContextCode = new StringBuilder();
 		
-		try {
-		
 		String fullTimelineLink;
 		if (yearToGrantCount.size() > 0) {
 			
-			String secondaryContextPath = "";
+			ParamMap fullTimelineNetworkURLParams = new ParamMap(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY,
-			if (!contextPath.contains(VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX)) {
+					 individualURI,
-				secondaryContextPath = VisualizationFrameworkConstants.VISUALIZATION_URL_PREFIX;
+					 VisualizationFrameworkConstants.VIS_TYPE_KEY,
-			}
+					 VisualizationFrameworkConstants.PERSON_LEVEL_VIS);
 
-			String fullTimelineNetworkURL = contextPath
+			String fullTimelineNetworkURL = UrlBuilder.getUrl(
-							+ secondaryContextPath
+											VisualizationFrameworkConstants.FREEMARKERIZED_VISUALIZATION_URL_PREFIX,
-							+ "?" 
+											fullTimelineNetworkURLParams);
-							+ VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
-							+ "=" + URLEncoder.encode(individualURI, 
-									StandardVisualizationController.URL_ENCODING_SCHEME).toString()
-					 	    + "&"
-		 				    + VisualizationFrameworkConstants.VIS_TYPE_KEY 
-							+ "=" + URLEncoder.encode("person_level", 
-									StandardVisualizationController.URL_ENCODING_SCHEME).toString()
-		 				    + "&"
-		 				    + VisualizationFrameworkConstants.RENDER_MODE_KEY
-							+ "=" + URLEncoder.encode(VisualizationFrameworkConstants
-															.STANDALONE_RENDER_MODE, 
-															StandardVisualizationController.URL_ENCODING_SCHEME).toString();
 
 			fullTimelineLink = "<a href='" + fullTimelineNetworkURL + "'>View all VIVO " 
 									+ "grants and corresponding co-pi network.</a>";
 			
 			sparklineData.setFullTimelineNetworkLink(fullTimelineNetworkURL);
 			
+			
+			
 		} else {
 			fullTimelineLink = "No data available to render full timeline.<br />";
 		}
 		
 		divContextCode.append("<span class=\"vis_link\">" + fullTimelineLink + "</span>");
-		
-		} catch (UnsupportedEncodingException e) {
-			log.error(e);
-		}
 		return divContextCode.toString();
 	}
 	
@@ -618,13 +572,9 @@ public class PersonGrantCountVisCodeGenerator {
 		
 		String csvDownloadURLHref = ""; 
 		
-		try {
+		if (getCSVDownloadURL() != null) {
-			if (getCSVDownloadURL() != null) {
+			csvDownloadURLHref = "<a href=\"" + getCSVDownloadURL() + "\">(.CSV File)</a>";
-				csvDownloadURLHref = "<a href=\"" + getCSVDownloadURL() + "\">(.CSV File)</a>";
+		} else {
-			} else {
-				csvDownloadURLHref = "";
-			}
-		} catch (UnsupportedEncodingException e) {
 			csvDownloadURLHref = "";
 		}
 		

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/CoPINode.java

@@ -8,7 +8,7 @@ import java.util.Set;
 import java.util.HashSet;
 
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UniqueIDGenerator;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UniqueIDGenerator;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
 
 /**

src/edu/cornell/mannlib/vitro/webapp/visualization/persongrantcount/PersonGrantCountQueryRunner.java

@@ -128,7 +128,7 @@ public class PersonGrantCountQueryRunner implements QueryRunner<Set<Grant>>{
 							+ "?Grant rdfs:label ?GrantLabel ; core:startDate ?GrantStartDate ; core:endDate ?GrantEndDate ."
 							+ "}";
 		
-		System.out.println("SPARQL query for person grant count -> \n"+ sparqlQuery);
+		log.debug("SPARQL query for person grant count -> \n"+ sparqlQuery);
 		return sparqlQuery;
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/personpubcount/PersonPublicationCountQueryRunner.java

@@ -186,7 +186,7 @@ public class PersonPublicationCountQueryRunner implements QueryRunner<Set<BiboDo
 							+  SPARQL_QUERY_COMMON_WHERE_CLAUSE
 							+ "}";
 
-		System.out.println("SPARQL query for person pub count -> \n" + sparqlQuery);
+		log.debug("SPARQL query for person pub count -> \n" + sparqlQuery);
 		return sparqlQuery;
 	}