1. Made changes to the value objects structure/inheritance.

2. Removed unnecessary fields from BiboDocument.
3. Changes to the Query & Vis request handlers to incorporate changes to the VOs.

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/TestJava.java

@@ -46,6 +46,9 @@ public class TestJava {
 		yearToPublicationCount.put("2090", 7);
 		yearToPublicationCount.put("2087", 6);
 		
+		String emptyString = "";
+		System.out.println(emptyString.isEmpty());
+
 //		System.out.println(Collections.max(yearToPublicationCount.keySet()));
 //		System.out.println(Collections.min(yearToPublicationCount.keySet()));
 

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/collegepubcount/QueryHandler.java

@@ -120,8 +120,11 @@ public class QueryHandler {
 				currentEmployee.addParentDepartment(currentDepartment);
 			} else {
 				currentEmployee = new VivoEmployee(employeeNode.toString(), currentEmployeeType, currentDepartment);
+				RDFNode authorLabelNode = solution.get(QueryFieldLabels.AUTHOR_LABEL);
+				if (authorLabelNode != null) {
+					currentEmployee.setIndividualLabel(authorLabelNode.toString());
+				}
 				employeeURLToVO.put(employeeNode.toString(), currentEmployee);
-				
 			}
 			
 			RDFNode documentNode = solution.get(QueryFieldLabels.DOCUMENT_URL);
@@ -203,11 +206,6 @@ public class QueryHandler {
 				biboDocument.setPublicationYear(publicationYearNode.toString());
 			}
 			
-			RDFNode authorLabelNode = solution.get(QueryFieldLabels.AUTHOR_LABEL);
-			if (authorLabelNode != null) {
-				biboDocument.setAuthorLabel(authorLabelNode.toString());
-			}
-
 			return biboDocument;
 	}
 	
@@ -278,7 +276,7 @@ public class QueryHandler {
 															  String ontologyHandle) {
 		
 		String sparqlQuery = " {?department " + ontologyHandle + " ?" + employeeHandle + " . " 
-							+ "?" + employeeHandle + " rdf:type foaf:Person; rdfs:label ?authorLabel. " 
+							+ "?" + employeeHandle + " rdf:type foaf:Individual; rdfs:label ?authorLabel. " 
 							+ "OPTIONAL { ?" + employeeHandle + " vivo:authorOf ?document ." +
 										" ?document rdf:type bibo:Document ." +
 										" ?document rdfs:label ?documentLabel ." +

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/collegepubcount/VisualizationRequestHandler.java

@@ -33,6 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.visualization.PDFDocument;
 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.Individual;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoCollegeOrSchool;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoDepartmentOrDivision;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoEmployee;
@@ -132,13 +133,16 @@ public class VisualizationRequestHandler {
 	    	 * It is ugly! 
 	    	 * */
 	    	if (DATA_RENDER_MODE_URL_VALUE.equalsIgnoreCase(renderMode)) { 
-				prepareVisualizationQueryDataResponse(departmentToPublicationsOverTime,
+				prepareVisualizationQueryDataResponse(
+													  departmentToPublicationsOverTime,
 													  queryManager.getCollegeURLToVO());
 				
-				System.out.println(publishedYearsForCollege);
+				log.debug(publishedYearsForCollege);
 				return;
 			}
 	    	
+	    	
+	    	
 	    	/*
 	    	if (PDF_RENDER_MODE_URL_VALUE.equalsIgnoreCase(renderMode)) { 
 				prepareVisualizationQueryPDFResponse(authorDocuments,
@@ -263,7 +267,8 @@ public class VisualizationRequestHandler {
 		return departmentYearToPublicationCount;
 	}
 
-	private void prepareVisualizationQueryPDFResponse(List<BiboDocument> authorDocuments,
+	private void prepareVisualizationQueryPDFResponse(Individual college, 
+													  List<BiboDocument> authorDocuments,
 													  Map<String, Integer> yearToPublicationCount) {
 		
 		String authorName = null; 
@@ -273,7 +278,7 @@ public class VisualizationRequestHandler {
 		 * individual. 
 		 * */
 		if (authorDocuments.size() > 0) {
-			authorName = ((BiboDocument) authorDocuments.get(0)).getAuthorLabel();
+			authorName = college.getIndividualLabel();
 		}
 		
 		/*
@@ -298,29 +303,22 @@ public class VisualizationRequestHandler {
 				ByteArrayOutputStream baos = new ByteArrayOutputStream();
 				PdfWriter pdfWriter = PdfWriter.getInstance(document, baos);
 				document.open();
-//				document.add(new Paragraph("JSS Chintan Deepak Tank "));
-//				document.add(Chunk.NEWLINE);
-//				document.add(new Paragraph("The method used to generate this PDF was: TEST OPST"));
-				
-				PDFDocument pdfDocument = new PDFDocument(authorName, yearToPublicationCount, document, pdfWriter);
-				
 				
+				PDFDocument pdfDocument = new PDFDocument(authorName, 
+														  yearToPublicationCount, 
+														  document, 
+														  pdfWriter);
 				document.close();
 
-				// setting some response headers
 				response.setHeader("Expires", "0");
 				response.setHeader("Cache-Control", "must-revalidate, post-check=0, pre-check=0");
 				response.setHeader("Pragma", "public");
-				// setting the content type
-				// the contentlength is needed for MSIE!!!
 				response.setContentLength(baos.size());
-				// write ByteArrayOutputStream to the ServletOutputStream
+				
 				baos.writeTo(responseOutputStream);
 				responseOutputStream.flush();
 				responseOutputStream.close();
 				
-//				System.out.println("done with response o/p stream");
-				
 			} catch (IOException e) {
 				e.printStackTrace();
 			} catch (DocumentException e) {
@@ -340,7 +338,7 @@ public class VisualizationRequestHandler {
 		* */
 //		System.out.println(collegeURLToVO);
 		if (collegeURLToVO.size() > 0) {
-//		collegeName = ((VivoCollegeOrSchool) collegeURLToVO.entrySet().iterator().next()).getCollegeLabel();
+			collegeName = ((VivoCollegeOrSchool) collegeURLToVO.values().iterator().next()).getCollegeLabel();
 		}
 		
 		/*
@@ -350,8 +348,7 @@ public class VisualizationRequestHandler {
 		collegeName = "";
 		}
 		
-		String outputFileName = slugify(collegeName + "depts-pub-count") 
+		String outputFileName = slugify(collegeName + "depts-pub-count") + ".csv";
-		+ ".csv";
 		
 		response.setContentType("application/octet-stream");
 		response.setHeader("Content-Disposition","attachment;filename=" + outputFileName);
@@ -439,7 +436,7 @@ public class VisualizationRequestHandler {
 
         request.setAttribute("bodyJsp", "/templates/visualization/publication_count.jsp");
         request.setAttribute("portalBean", portal);
-        request.setAttribute("title", "Person Publication Count Visualization");
+        request.setAttribute("title", "Individual Publication Count Visualization");
         request.setAttribute("scripts", "/templates/visualization/visualization_scripts.jsp");
 
 	}
@@ -468,7 +465,7 @@ public class VisualizationRequestHandler {
 		RequestDispatcher requestDispatcher = request.getRequestDispatcher(Controllers.BASIC_JSP);
 		request.setAttribute("bodyJsp", "/templates/visualization/visualization_error.jsp");
 		request.setAttribute("portalBean", portal);
-		request.setAttribute("title", "Visualization Query Error - Person Publication Count");
+		request.setAttribute("title", "Visualization Query Error - Individual Publication Count");
 
 		try {
 			requestDispatcher.forward(request, response);

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

@@ -24,6 +24,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryP
 import edu.cornell.mannlib.vitro.webapp.visualization.sparqlutils.QueryConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.sparqlutils.QueryFieldLabels;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.BiboDocument;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Individual;
 
 
 
@@ -39,6 +40,12 @@ public class QueryHandler {
 	private String queryParam, resultFormatParam, rdfResultFormatParam;
 	private DataSource dataSource;
 
+	private Individual author; 
+
+	public Individual getAuthor() {
+		return author;
+	}
+
 	private Log log;
 
 	private static final String SPARQL_QUERY_COMMON_SELECT_CLAUSE = "" +
@@ -106,14 +113,19 @@ public class QueryHandler {
 				biboDocument.setPublicationYear(publicationYearNode.toString());
 			}
 			
+			/*
+			 * Since we are getting publication count for just one author at a time we need
+			 * to create only one "Individual" instance. We test against the null for "author" to
+			 * make sure that it has not already been instantiated. 
+			 * */
 			RDFNode authorURLNode = solution.get(QueryFieldLabels.AUTHOR_URL);
-			if (authorURLNode != null) {
+			if (authorURLNode != null && author == null) {
-				biboDocument.setAuthorURL(authorURLNode.toString());
+				author = new Individual(authorURLNode.toString());
-			}
-
 				RDFNode authorLabelNode = solution.get(QueryFieldLabels.AUTHOR_LABEL);
 				if (authorLabelNode != null) {
-				biboDocument.setAuthorLabel(authorLabelNode.toString());
+					author.setIndividualLabel(authorLabelNode.toString());
+				}
+				
 			}
 
 			authorDocuments.add(biboDocument);
@@ -154,7 +166,7 @@ public class QueryHandler {
 							+ SPARQL_QUERY_COMMON_SELECT_CLAUSE
 							+ "(str(<" + queryURI + ">) as ?authPersonLit) "
 							+ "WHERE { "
-							+ "<" + queryURI + "> rdf:type foaf:Person ; vivo:authorOf ?document ; rdfs:label ?authorLabel.  "
+							+ "<" + queryURI + "> rdf:type foaf:Individual ; vivo:authorOf ?document ; rdfs:label ?authorLabel.  "
 							+  SPARQL_QUERY_COMMON_WHERE_CLAUSE
 							+ "}";
 

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

@@ -31,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.PDFDocument;
 import edu.cornell.mannlib.vitro.webapp.visualization.VisualizationCodeGenerator;
 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.Individual;
 
 public class VisualizationRequestHandler {
 
@@ -104,14 +105,16 @@ public class VisualizationRequestHandler {
 	    	 * It is ugly! 
 	    	 * */
 	    	if (DATA_RENDER_MODE_URL_VALUE.equalsIgnoreCase(renderMode)) { 
-				prepareVisualizationQueryDataResponse(authorDocuments,
+				prepareVisualizationQueryDataResponse(queryManager.getAuthor(),
+													  authorDocuments,
 													  yearToPublicationCount);
 				return;
 			}
 	    	
 	    	
 	    	if (PDF_RENDER_MODE_URL_VALUE.equalsIgnoreCase(renderMode)) { 
-				prepareVisualizationQueryPDFResponse(authorDocuments,
+				prepareVisualizationQueryPDFResponse(queryManager.getAuthor(),
+													 authorDocuments,
 													 yearToPublicationCount);
 				return;
 			}
@@ -182,7 +185,7 @@ public class VisualizationRequestHandler {
 
 	}
 
-	private void prepareVisualizationQueryPDFResponse(List<BiboDocument> authorDocuments,
+	private void prepareVisualizationQueryPDFResponse(Individual author, List<BiboDocument> authorDocuments,
 													   Map<String, Integer> yearToPublicationCount) {
 		
 		String authorName = null; 
@@ -192,7 +195,7 @@ public class VisualizationRequestHandler {
 		 * individual. 
 		 * */
 		if (authorDocuments.size() > 0) {
-			authorName = ((BiboDocument) authorDocuments.get(0)).getAuthorLabel();
+			authorName = author.getIndividualLabel();
 		}
 		
 		/*
@@ -239,7 +242,7 @@ public class VisualizationRequestHandler {
 			}
 	}
 
-	private void prepareVisualizationQueryDataResponse(List<BiboDocument> authorDocuments,
+	private void prepareVisualizationQueryDataResponse(Individual author, List<BiboDocument> authorDocuments,
 			   Map<String, Integer> yearToPublicationCount) {
 
 		String authorName = null; 
@@ -249,7 +252,7 @@ public class VisualizationRequestHandler {
 		* individual. 
 		* */
 		if (authorDocuments.size() > 0) {
-		authorName = ((BiboDocument) authorDocuments.get(0)).getAuthorLabel();
+		authorName = author.getIndividualLabel();
 		}
 		
 		/*
@@ -323,7 +326,7 @@ public class VisualizationRequestHandler {
 
         request.setAttribute("bodyJsp", "/templates/visualization/publication_count.jsp");
         request.setAttribute("portalBean", portal);
-        request.setAttribute("title", "Person Publication Count visualization");
+        request.setAttribute("title", "Individual Publication Count visualization");
         request.setAttribute("scripts", "/templates/visualization/visualization_scripts.jsp");
 
 	}
@@ -352,7 +355,7 @@ public class VisualizationRequestHandler {
 		RequestDispatcher requestDispatcher = request.getRequestDispatcher(Controllers.BASIC_JSP);
 		request.setAttribute("bodyJsp", "/templates/visualization/visualization_error.jsp");
 		request.setAttribute("portalBean", portal);
-		request.setAttribute("title", "Visualization Query Error - Person Publication Count");
+		request.setAttribute("title", "Visualization Query Error - Individual Publication Count");
 
 		try {
 			requestDispatcher.forward(request, response);

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/BiboDocument.java

@@ -4,50 +4,24 @@ import java.util.Calendar;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-public class BiboDocument {
+public class BiboDocument extends Individual{
 
 	public static final String DEFAULT_PUBLICATION_YEAR = "Unknown";
 	public static final int MINIMUM_PUBLICATION_YEAR = 1800;
 	private static final int CURRENT_YEAR = Calendar.getInstance().get(Calendar.YEAR);
 
-	private String authorURL;
-	private String authorLabel;
-	private String documentURL;
 	private String documentMoniker;
-	private String documentLabel;
 	private String documentBlurb;
 	private String documentDescription;
 	private String publicationYear;
 	private String parsedPublicationYear = DEFAULT_PUBLICATION_YEAR;
 
-
-
 	public BiboDocument(String documentURL) {
-		this.documentURL = documentURL;
+		super(documentURL);
-	}
-	
-	public String getAuthorURL() {
-		return authorURL;
-	}
-	
-	public void setAuthorURL(String authorURL) {
-		this.authorURL = authorURL;
-	}
-	
-	public String getAuthorLabel() {
-		return authorLabel;
-	}
-	
-	public void setAuthorLabel(String authorLabel) {
-		this.authorLabel = authorLabel;
 	}
 	
 	public String getDocumentURL() {
-		return documentURL;
+		return this.getIndividualURL();
-	}
-	
-	public void setDocumentURL(String documentURL) {
-		this.documentURL = documentURL;
 	}
 	
 	public String getDocumentMoniker() {
@@ -59,11 +33,11 @@ public class BiboDocument {
 	}
 	
 	public String getDocumentLabel() {
-		return documentLabel;
+		return this.getIndividualLabel();
 	}
 	
 	public void setDocumentLabel(String documentLabel) {
-		this.documentLabel = documentLabel;
+		this.setIndividualLabel(documentLabel);
 	}
 	
 	public String getDocumentBlurb() {

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/Individual.java

@@ -0,0 +1,30 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+public class Individual {
+	
+	private String individualLabel;
+	private String individualURL;
+	
+	public Individual(String individualURL, String individualLabel) {
+		this.individualLabel = individualLabel;
+		this.individualURL = individualURL;
+	}
+	
+	public Individual(String individualURL) {
+		this(individualURL, "");
+	}
+	
+	public String getIndividualLabel() {
+		return individualLabel;
+	}
+	
+	public void setIndividualLabel(String individualLabel) {
+		this.individualLabel = individualLabel;
+	}
+
+	public String getIndividualURL() {
+		return individualURL;
+	}
+	
+
+}

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/VivoCollegeOrSchool.java

@@ -9,14 +9,12 @@ import java.util.Set;
  * @author cdtank
  *
  */
-public class VivoCollegeOrSchool {
+public class VivoCollegeOrSchool extends Individual {
 
-	private String collegeURL;
-	private String collegeLabel;
 	private Set<VivoDepartmentOrDivision> departments = new HashSet<VivoDepartmentOrDivision>();
 
 	public VivoCollegeOrSchool(String collegeURL) {
-		this.collegeURL = collegeURL;
+		super(collegeURL);
 	}
 	
 	public Set<VivoDepartmentOrDivision> getDepartments() {
@@ -28,19 +26,15 @@ public class VivoCollegeOrSchool {
 	}
 
 	public String getCollegeURL() {
-		return collegeURL;
+		return this.getIndividualURL();
 	}
 
 	public String getCollegeLabel() {
-		if (collegeLabel != null) {
+		return this.getIndividualLabel();
-			return collegeLabel;
-		} else {
-			return "";
-		}
 	}
 
 	public void setCollegeLabel(String collegeLabel) {
-		this.collegeLabel = collegeLabel;
+		this.setIndividualLabel(collegeLabel);
 	}
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/VivoDepartmentOrDivision.java

@@ -9,14 +9,12 @@ import java.util.Set;
  * @author cdtank
  *
  */
-public class VivoDepartmentOrDivision {
+public class VivoDepartmentOrDivision extends Individual {
 
-	private String departmentURL;
-	private String departmentLabel;
 	private Set<VivoCollegeOrSchool> parentColleges = new HashSet<VivoCollegeOrSchool>();
 
 	public VivoDepartmentOrDivision(String departmentURL, VivoCollegeOrSchool parentCollege) {
-		this.departmentURL = departmentURL;
+		super(departmentURL);
 		addParentCollege(parentCollege);
 	}
 
@@ -29,19 +27,15 @@ public class VivoDepartmentOrDivision {
 	}
 
 	public String getDepartmentURL() {
-		return departmentURL;
+		return this.getIndividualURL();
 	}
 
 	public String getDepartmentLabel() {
-		if (departmentLabel != null) {
+		return this.getIndividualLabel();
-			return departmentLabel;
-		} else {
-			return "";
-		}
 	}
 
 	public void setDepartmentLabel(String departmentLabel) {
-		this.departmentLabel = departmentLabel;
+		this.setIndividualLabel(departmentLabel);
 	}
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/VivoEmployee.java

@@ -11,24 +11,25 @@ import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VOConstants.E
  * @author cdtank
  *
  */
-public class VivoEmployee {
+public class VivoEmployee extends Individual{
 
-	private String employeeURL;
 	private EmployeeType employeeType; 
 	private Set<VivoDepartmentOrDivision> parentDepartments = new HashSet<VivoDepartmentOrDivision>();
 	private Set<BiboDocument> authorDocuments = new HashSet<BiboDocument>();
 
-	public VivoEmployee(String employeeURL, EmployeeType employeeType, VivoDepartmentOrDivision parentDepartment) {
+	public VivoEmployee(String employeeURL, 
-		this.employeeURL = employeeURL;
+						EmployeeType employeeType, 
+						VivoDepartmentOrDivision parentDepartment) {
+		super(employeeURL);
 		addParentDepartment(parentDepartment);
 	}
 
 	public String getEmployeeURL() {
-		return employeeURL;
+		return this.getIndividualURL();
 	}
 
-	public void setEmployeeURL(String employeeURL) {
+	public String getEmployeeName() {
-		this.employeeURL = employeeURL;
+		return this.getIndividualLabel();
 	}
 	
 	public EmployeeType getEmployeeType() {