re-integrating the branch /branches/iu-vis-dev-branches/vivo-post-1.1

deploy.properties

@@ -0,0 +1,77 @@
+# -----------------------------------------------------------------------------
+#
+# VIVO deployment properties
+#
+# This file is provided as example.deploy.properties.
+#
+# Save a copy of this file as deploy.properties, and edit the properties as 
+# needed for your deployment. 
+#
+# -----------------------------------------------------------------------------
+
+# 
+# This namespace will  be used when generating URIs for objects created in the 
+# editor. Change it to reflect your own domain. For example, Cornell's 
+# namespace is http://vivo.cornell.edu/individual/
+#
+# Note: it is essential that this namespace end with a trailing slash.
+#
+Vitro.defaultNamespace = http://vivo-trunk.indiana.edu/individual/
+
+#
+# Where is the Vitro core directory?
+# In most deployments, this is set to ./vitro-core, but internal developers may
+# prefer to set it to ../vitro
+#   Examples:
+#      vitro.core.dir = ./vitro-core
+#      vitro.core.dir = ../vitro
+#      vitro.core.dir = /usr/local/vitro/trunk
+vitro.core.dir = /usr/local/home/bkoniden/eclipse-workspace/bkoniden-vitro-post-1.1
+
+#
+# The base install directory for your Tomcat server. The VIVO application 
+# will be deployed in the /webapps directory below this base. 
+#
+tomcat.home = /usr/local/tomcat
+
+#
+# The name of the VIVO application. This will be used as the name of the
+# subdirectory within your Tomcat server's /webapps directory. It also appears
+# in the URL for the application. For example, http://my.vivo.server/vivo
+#
+webapp.name = vivo1
+
+#
+# The location where the VIVO application will store uploaded files 
+# (usually images). You should arrange for these files to be backed up in some
+# way.
+#
+upload.directory = /usr/local/vivo1/data-vivo-updated/uploads
+
+#
+# The location where the VIVO application will create its Lucene search 
+# index. 
+#
+LuceneSetup.indexDir = /usr/local/vivo1/data-vivo-updated/luceneIndex
+
+#
+# SMTP host which the "Contact Us" form can use to send mail. If this is left 
+# empty, the "Contact Us" form will be disabled.
+#
+Vitro.smtpHost =
+
+#
+# The basic parameters for a MySQL database connection. Change the end of the 
+# URL to reflect your database name (if it is not "vitro"). Change the username 
+# and password to match the authorized user you created in MySQL.
+#
+VitroConnection.DataSource.url = jdbc:mysql://localhost/vivo1
+VitroConnection.DataSource.username = vivouser1
+VitroConnection.DataSource.password = vivo123
+
+#
+# The name of your first admin user for the VIVO application. The password for
+# for this user is initially set to "defaultAdmin", but you will be asked to 
+# change the password the first time you login.
+#
+initialAdminUser = defaultAdmin

deployVIVOInstance

@@ -0,0 +1,2 @@
+sudo /usr/local/tomcat/bin/shutdown.sh
+ant clean deploy

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

@@ -1,6 +1,5 @@
 <beans xmlns="http://www.springframework.org/schema/beans"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:aop="http://www.springframework.org/schema/aop"
-	xmlns:aop="http://www.springframework.org/schema/aop"
 	xmlns:context="http://www.springframework.org/schema/context"
 	xsi:schemaLocation="http://www.springframework.org/schema/beans
            http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
@@ -10,21 +9,31 @@
            http://www.springframework.org/schema/context/spring-context-2.5.xsd">
 
 
-<bean id="person_pub_count" class="edu.cornell.mannlib.vitro.webapp.visualization.personpubcount.PersonPublicationCountRequestHandler" />
+	<bean id="person_pub_count"
-<bean id="college_pub_count" class="edu.cornell.mannlib.vitro.webapp.visualization.collegepubcount.CollegePublicationCountRequestHandler" />
+		class="edu.cornell.mannlib.vitro.webapp.visualization.personpubcount.PersonPublicationCountRequestHandler" />
-<bean id="coauthorship" class="edu.cornell.mannlib.vitro.webapp.visualization.coauthorship.CoAuthorshipRequestHandler" />
+	<bean id="coauthorship"
-<bean id="person_level" class="edu.cornell.mannlib.vitro.webapp.visualization.personlevel.PersonLevelRequestHandler" />
+		class="edu.cornell.mannlib.vitro.webapp.visualization.coauthorship.CoAuthorshipRequestHandler" />
-<bean id="utilities" class="edu.cornell.mannlib.vitro.webapp.visualization.utilities.UtilitiesRequestHandler" />
+	<bean id="person_level"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.personlevel.PersonLevelRequestHandler" />
+	<bean id="utilities"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.utilities.UtilitiesRequestHandler" />
+	<bean id="entity_comparison"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison.EntityPublicationCountRequestHandler" />
+	<bean id="coprincipalinvestigator"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator.CoPIGrantCountRequestHandler" />
+	<bean id="freemarker"
+		class="edu.cornell.mannlib.vitro.webapp.visualization.freemarker.FreemarkerRequestHandler" />
 		
-<bean id="visualizationInjector" class="edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationInjector">
+		
+
+
+	<bean id="visualizationInjector"
+		class="edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationInjector">
 		<property name="visualizations">
 			<map>
 				<entry key="person_pub_count">
 					<ref bean="person_pub_count"></ref>
 				</entry>
-                <entry key="college_pub_count">
-                	<ref bean="college_pub_count"></ref>
-                </entry>
 				<entry key="coauthorship">
 					<ref bean="coauthorship"></ref>
 				</entry>
@@ -34,6 +43,15 @@
 				<entry key="utilities">
 					<ref bean="utilities"></ref>
 				</entry>
+				<entry key="entity_comparison">
+					<ref bean="entity_comparison"></ref>
+				</entry>
+				<entry key="coprincipalinvestigator">
+					<ref bean="coprincipalinvestigator"></ref>
+				</entry>
+				<entry key="freemarker">
+					<ref bean="freemarker"></ref>
+				</entry>
 			</map>
 		</property>
 

productMods/WEB-INF/web.xml

@@ -1221,7 +1221,6 @@
     <url-pattern>/admin/sparqlquery</url-pattern>
   </servlet-mapping>
   
-  <!-- 
   <servlet>
     <servlet-name>DummyVisClient</servlet-name>
     <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.visualization.DummyVisClientController</servlet-class>
@@ -1231,7 +1230,8 @@
     <servlet-name>DummyVisClient</servlet-name>
     <url-pattern>/admin/dummyVisClient</url-pattern>
   </servlet-mapping>
-   -->
+
+
    
    <servlet>
     <servlet-name>VisualizationController</servlet-name>

productMods/js/visualization/entityComparison/constants.js

@@ -0,0 +1,75 @@
+
+//Hard coded color constants
+var	TURQUOISE = "#8DD3C7";
+var	LIGHT_YELLOW = "#FFFFB3";
+var	LIGHT_VIOLET = "#BEBADA";
+var	LIGHT_RED = "#FB8072";
+var	SKY_BLUE = "#80B1D3";
+var	ORANGE = "#FDB462";
+var	LIGHT_GREEN = "#B3DE69";
+var	LIGHT_PINK = "#FCCDE5";
+var	LIGHT_GREY = "#D9D9D9";
+var	PURPLE = "#BC80BD";                     
+
+var colorConstantQueue = 
+	[
+       TURQUOISE, LIGHT_YELLOW, LIGHT_VIOLET, LIGHT_RED, 
+       SKY_BLUE, ORANGE, LIGHT_GREEN, LIGHT_PINK, LIGHT_GREY,
+       PURPLE
+    ];
+
+var freeColors = [
+                   TURQUOISE, LIGHT_YELLOW, LIGHT_VIOLET, LIGHT_RED, 
+                   SKY_BLUE, ORANGE, LIGHT_GREEN, LIGHT_PINK, LIGHT_GREY,
+                   PURPLE
+                ];
+
+var year = {
+		min: 1998,
+		max: 2018,
+		globalMin: 1995,
+		globalMax: 2025
+};
+
+var colors = {};
+var prevColor = {};
+var colorToAssign, colorToRemove;
+var renderedObjects = [];
+var labelToEntityRecord = {};
+var setOfLabels = [];
+var labelToCheckedEntities = {};
+var stopWordsToCount = {};
+
+var graphContainer;
+var tableDiv;
+var entityLevel;
+
+//options for Flot
+var FlotOptions = {
+		legend : {
+			show : false
+		},
+		lines : {
+			show : true
+		},
+		points : {
+			show : false
+		},
+		xaxis : {
+			tickDecimals : 0,
+			tickSize : 10
+		},
+		series : {
+			lines : {
+				lineWidth : 7
+			}
+		},
+		yaxis : {
+			tickSize : 1,
+			tickDecimals : 0,
+			min : 0
+		}
+};
+
+FlotOptions.colors = colorConstantQueue;
+

productMods/js/visualization/personlevel/person_level.js

@@ -256,6 +256,7 @@ function createTable(tableID, tableContainer, tableData) {
 	$('#' + tableContainer + " #loadingData").remove();
 }
 
+//renderStatsOnNodeClicked, CoRelations, noOfCoRelations
 function nodeClickedJS(json){
 
 	var obj = jQuery.parseJSON(json);
@@ -309,6 +310,11 @@ function nodeClickedJS(json){
 
 }
 
+function encodeURL(url){
+	var domainURL = 'http://vivo-vis-bkoniden.slis.indiana.edu/';
+	return domainURL + url.replace(/&/g,'%26');
+}
+
 function renderCoAuthorshipVisualization() {
 
 	// Version check for the Flash Player that has the ability to start Player
@@ -330,13 +336,13 @@ function renderCoAuthorshipVisualization() {
 		AC_FL_RunContent(
 				"src", "playerProductInstall",
 				"FlashVars", "MMredirectURL="+MMredirectURL+'&MMplayerType='+MMPlayerType+'&MMdoctitle='+MMdoctitle+"",
-				"width", "600",
+				"width", "800",
 				"height", "840",
 				"align", "middle",
-				"id", "CoAuthor",
+				"id", "EgoCentric",
 				"quality", "high",
 				"bgcolor", "#ffffff",
-				"name", "CoAuthor",
+				"name", "EgoCentric",
 				"allowScriptAccess","sameDomain",
 				"type", "application/x-shockwave-flash",
 				"pluginspage", "http://www.adobe.com/go/getflashplayer"
@@ -344,16 +350,17 @@ function renderCoAuthorshipVisualization() {
 	} else if (hasRequestedVersion) {
 		// if we've detected an acceptable version
 		// embed the Flash Content SWF when all tests are passed
+		//coAuthorUrl=/vivo1/visualization?vis=coauthorship%26render_mode=data%26uri=http%3A%2F%2Fvivo.iu.edu%2Findividual%2FBrnerKaty&labelField=label&coPIUrl=/vivo1/visualization?vis=coprincipalinvestigator%26render_mode=data%26uri=http%3A%2F%2Fvivo.iu.edu%2Findividual%2FBrnerKaty&labelField=label
 		AC_FL_RunContent(
 				"src", swfLink,
-				"flashVars", "graphmlUrl=" + egoCoAuthorshipDataFeederURL,			
+				"flashVars", 'coAuthorUrl='+ encodeURL(egoCoAuthorshipDataFeederURL) + '&coPIUrl=' + encodeURL(egoCoPIDataFeederURL) ,			
-				"width", "600",
+				"width", "800",
 				"height", "850",
 				"align", "top",
-				"id", "CoAuthor",
+				"id", "EgoCentric",
 				"quality", "high",
 				"bgcolor", "#ffffff",
-				"name", "CoAuthor",
+				"name", "EgoCentric",
 				"allowScriptAccess","sameDomain",
 				"type", "application/x-shockwave-flash",
 				"pluginspage", "http://www.adobe.com/go/getflashplayer"

productMods/templates/visualization/dummy_vis_client.jsp

@@ -35,7 +35,6 @@
 	<c:param name="uri" value="http://vivo.library.cornell.edu/ns/0.1#individual5611"/>
 </c:url>
 
-
 <c:url var="staticHref3" value="/visualization">
 	<c:param name="vis" value="person_pub_count"/>
 	<c:param name="vis_mode" value="short"/>
@@ -204,13 +203,13 @@
 <c:url var="coAuthorship10" value="/visualization">
 	<c:param name="vis" value="coauthorship"/>
 	<c:param name="render_mode" value="standalone"/>
-	<c:param name="uri" value="http://vivo.library.cornell.edu/ns/0.1#individual12053"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/BrnerKaty"/>
 </c:url>
 
 <c:url var="coAuthorship10Data" value="/visualization">
 	<c:param name="vis" value="coauthorship"/>
 	<c:param name="render_mode" value="data"/>
-	<c:param name="uri" value="http://vivo.library.cornell.edu/ns/0.1#individual12053"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/BrnerKaty"/>
 </c:url>
 
 <c:url var="coAuthorshipSparklineData" value="/visualization">
@@ -229,6 +228,61 @@
 
 <c:url var="loadingImageLink" value="/${themeDir}site_icons/visualization/ajax-loader.gif"></c:url>
 
+<c:url var="departmentPublications" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="standalone"/>
+	<c:param name="vis_mode" value="DEPARTMENT"/>
+	<c:param name="uri" value="http://vivo-trunk.indiana.edu/individual/DepartmentBL-SLIS"/>
+</c:url>
+
+<c:url var="schoolPublications" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="standalone"/>
+	<c:param name="vis_mode" value="SCHOOL"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/SchoolofLibraryandInformationScience"/>
+</c:url>
+
+<c:url var="universityPublications" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="standalone"/>
+	<c:param name="vis_mode" value="UNIVERSITY"/>
+	<c:param name="uri" value="http://vivo-trunk.indiana.edu/individual/n7971"/>
+</c:url>
+
+<c:url var="departmentPublicationsdata" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="data"/>
+	<c:param name="vis_mode" value="DEPARTMENT"/>
+	<c:param name="uri" value="http://vivo-trunk.indiana.edu/individual/DepartmentBL-SLIS"/>
+</c:url>
+
+<c:url var="schoolPublicationsdata" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="data"/>
+	<c:param name="vis_mode" value="SCHOOL"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/SchoolofLibraryandInformationScience"/>
+</c:url>
+
+<c:url var="universityPublicationsdata" value="/visualization">
+	<c:param name="vis" value="entity_comparison"/>
+	<c:param name="render_mode" value="data"/>
+	<c:param name="vis_mode" value="UNIVERSITY"/>
+	<c:param name="uri" value="http://vivo-trunk.indiana.edu/individual/n7971"/>
+</c:url>
+
+<c:url var="coprincipalinvestigatordata" value="/visualization">
+	<c:param name="vis" value="coprincipalinvestigator"/>
+	<c:param name="render_mode" value="data"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/McDonaldRobertH"/>
+</c:url>
+
+<c:url var="freemarkertest" value="/visualization">
+	<c:param name="vis" value="freemarker"/>
+	<c:param name="render_mode" value="standalone"/>
+	<c:param name="uri" value="http://vivo.iu.edu/individual/McDonaldRobertH"/>
+</c:url>
+
+
 <style type="text/css">
 	.get_vis {
 		background-color:Yellow;
@@ -316,7 +370,7 @@ $(document).ready(function() {
 
 <h1 id="test-bed">Visualization Testbed (Not to be seen by eventual end users)</h1>
 
-
+<h2>Hello World!</h2>
 
 <a href='<c:out value="${coAuthorship1}"/>'>vis link for coauthorship -> "Erb, Hollis Nancy"</a>
 &nbsp;&nbsp;<a href='<c:out value="${coAuthorship1Data}"/>'>Data</a>
@@ -342,8 +396,24 @@ $(document).ready(function() {
 <a href='<c:out value="${coAuthorship10}"/>'>vis link for coauthorship -> "Not Working"</a>&nbsp;
 <a href='<c:out value="${coAuthorship10Data}"/>'>Data</a><br />
 
+<a href='<c:out value="${departmentPublications}"/>'>Department Publications</a>
+&nbsp;&nbsp;<a href='<c:out value="${departmentPublicationsdata}"/>'>Data</a><br />
+<a href='<c:out value="${schoolPublications}"/>'>School Publications</a>
+&nbsp;&nbsp;<a href='<c:out value="${schoolPublicationsdata}"/>'>Data</a><br />
+<a href='<c:out value="${universityPublications}"/>'>University Publications</a>
+&nbsp;&nbsp;<a href='<c:out value="${universityPublicationsdata}"/>'>Data</a><br />
+
 <br /><br /><br />
 
+<a href='<c:out value="${coprincipalinvestigatordata}"/>'>Co-PI data </a>
+
+<br /><br /><br />
+
+<a href='<c:out value="${freemarkertest}"/>'>Freemarker Test</a>
+
+<br /><br /><br />
+
+
 <a href='<c:out value="${collegeCSV}"/>'>vis data query for college -> "School of Industrial and Labor Relations (ILR)"</a><br />
 <a href='<c:out value="${collegeCSV2}"/>'>vis data query for college -> "College of Agriculture and Life Sciences (CALS)"</a><br />
 <a href='<c:out value="${collegeCSV3}"/>'>vis data query for college -> "College of Arts and Sciences"</a><br />

productMods/templates/visualization/entity_comparison.jsp

@@ -0,0 +1,189 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+<!--<script type="text/javascript" src="http://orderedlist.com/demos/quicksilverjs/javascripts/quicksilver.js"></script>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>-->
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+
+<c:set var="portalBean" value="${requestScope.portalBean}" />
+<c:set var="themeDir">
+	<c:out value="${portalBean.themeDir}" />
+</c:set>
+<c:set var='jsonContent' value='${requestScope.JsonContent}' />
+<div id="body">
+	<div id="navcontainer">
+		<ul id="navlist">
+			<li><a href="#">Temporal</a></li>
+			<li><a href="#">Geospatial</a></li>
+			<li><a href="#">Scimap</a></li>
+			<li><a href="#">Networks</a></li>
+		</ul>
+	</div>
+		<h1>Temporal Graph Visualization<span id="entitylevelheading"><i> School level</i></span></h1>
+	<div id="leftblock">
+		<div id="leftUpper">
+			<h2 style="background-color:#3D454E; color: white; margin-top: 0px; margin-bottom: 20px; padding-bottom:5px;">How do you want to compare?</h2>
+			<p style="float:left; margin-left:10px; margin-right: 10px; margin-top: 6px;">Select </p>
+			<select class="comparisonValues" style="margin-bottom: 20px;">
+				<option value="Publications" selected="selected">Publications</option>
+				<option value="Grants" disabled="disabled">Grants</option>
+				<option value="People" disabled="disabled">People</option>
+				<option value="Item4" disabled="disabled">Item4</option>
+				<option value="Item5" disabled="disabled">Item5</option>
+			</select>
+		</div>
+		<br/>	
+		<div id="leftLower">
+			<h2 style="background-color:#3D454E; color: white; margin-top: 0px; margin-bottom: 20px; padding-bottom:5px;">Choose</h2>
+			<div id="paginatedTable">
+			</div>
+		</div>
+		<div id = "stopwordsdiv">
+			* The entity types core:Person, foaf:Organization have been excluded as they are too general.
+		</div>	
+	</div>
+		<div id="rightblock">
+			<div id="graphContainer" style="width: 450px; height: 250px;"></div>
+			<div id="yaxislabel"></div>
+			<div id="bottom" style="width: 450px; height: 350px;">
+				<div id="xaxislabel">Year</div>
+				<h3><span id="comparisonParameter"></span></h3>
+			<p class="displayCounter">You have selected <span id="counter">0</span> of a maximum <span
+			id="total">10</span> <span id="entityleveltext"> schools</span> to compare.</p>
+			</div>
+		</div>		
+		<div id="bottomButtons">
+			<button id="clear" class = "metallic" type ="button">Clear</button>
+			<button id="csv" class = "metallic" type ="button">Save as CSV</button>
+			<button id="image" class= "metallic" type="button" onClick="window.print()"> Save as Image</button>				
+		</div>
+</div>
+<script type="text/javascript">
+	
+	$(document).ready(function() {
+
+		var jsonString = '${jsonContent}';
+		var jsonObject = {
+				prepare : function(arg1){
+					loadData(arg1);
+				}
+			};
+		
+		graphContainer = $("#graphContainer");
+		tableDiv = $('#paginatedTable');
+
+ 		// initial display of the grid when the page loads
+ 		init(graphContainer);
+		
+		/*
+		 * When the intra-entity parameters are clicked,
+		 * update the status accordingly.	
+		 */	        
+        $("select.comparisonValues").click(function(){
+            var selectedValue = $("select.comparisonValues option:selected").val();
+			$("#comparisonParameter").text("Total Number of " + selectedValue);
+			$('#yaxislabel').html("Number of " + selectedValue ).mbFlipText(false);
+			$("span#paramdesc").text($("select.comparisonValues option:selected").val() + ' (desc)');	
+			$("span#paramasc").text($("select.comparisonValues option:selected").val() + ' (asc)');	
+        });
+
+		//click event handler for clear button
+		$("button#clear").click(function(){
+			clearRenderedObjects();
+		});
+
+		
+		$("input[type=checkbox].easyDeselectCheckbox").live('click', function(){
+			
+			var checkbox = $(this);
+			var checkboxValue = $(this).attr("value");
+			var linkedCheckbox = labelToCheckedEntities[checkboxValue];
+			//console.log('checkbox value is '+ checkboxValue);
+			var entityToBeRemoved = labelToEntityRecord[checkboxValue];
+
+			if(!checkbox.is(':checked')){
+				//console.log("Easy deselect checkbox is unclicked!");
+				updateRowHighlighter(linkedCheckbox);
+				removeUsedColor(entityToBeRemoved);
+				removeEntityUnChecked(renderedObjects, entityToBeRemoved);                          
+             	removeGraphic(linkedCheckbox);
+             	removeCheckBoxFromGlobalSet(linkedCheckbox);
+             	$(linkedCheckbox).attr('checked', false);
+             	checkIfColorLimitIsReached();
+                displayLineGraphs();
+				updateCounter();				
+    		}
+		});
+							
+		//parse the json object and pass it to loadData
+        jsonObject.prepare(jQuery.parseJSON(jsonString));
+
+        /* 
+         *  function to populate the labelToEntityRecord object with the
+         *  values from the json file and
+         *  dynamically generate checkboxes
+         */
+        function loadData(jsonData){
+            
+           // var yearRange;
+
+            $.each(jsonData, function(index, val){
+                setOfLabels.push(val.label);
+                labelToEntityRecord[val.label] = val;
+            });
+
+			getEntityVisMode(jsonData);
+			prepareTableForDataTablePagination(jsonData);
+			setEntityLevel();
+           // calcMinandMaxYears(labelToEntityRecord, year);
+			//yearRange = (year.max - year.min);
+
+           // setLineWidthAndTickSize(yearRange, FlotOptions);     
+			//setTickSizeOfYAxis(calcMaxOfComparisonParameter(labelToEntityRecord), FlotOptions);
+            /*
+             * When the elements in the paginated div
+             * are clicked this event handler is called
+             */
+            $("input.if_clicked_on_school").live('click', function(){
+            
+                var checkbox = $(this);
+                var checkboxValue = $(this).attr("value");
+                var entity = labelToEntityRecord[checkboxValue];
+                
+				//Dynamically generate the bar, checkbox and label.
+
+                var bottomDiv = $("#bottom");
+                var hiddenLabel = createGraphic(entity, bottomDiv);
+
+                
+                var divBar = hiddenLabel.next();
+                var divLabel = hiddenLabel.prev();
+                var spanElement = divBar.next('span');
+
+                if (checkbox.is(':checked')) {
+                	
+					getNextFreeColor(entity);
+					generateBarAndLabel(entity, divBar, divLabel,checkbox, spanElement) ; 
+					renderLineGraph(renderedObjects, entity);
+					labelToCheckedEntities[checkboxValue] = checkbox;
+					                     
+		        } else if (!checkbox.is(':checked')) {
+		
+					removeUsedColor(entity);
+					removeEntityUnChecked(renderedObjects, entity);                          
+		            removeGraphic(checkbox);
+		            removeCheckBoxFromGlobalSet(checkbox);
+		                     
+		        	}
+				//console.log('Number of checked entities: ' + getSize(labelToCheckedEntities));
+				//disableUncheckedEntities();
+				setTickSizeOfAxes();
+				checkIfColorLimitIsReached();
+		    	//populateMapOfCheckedEntities();                    
+		        displayLineGraphs();
+				updateCounter(); 
+		
+		    });
+        }
+
+	});
+	
+</script>

productMods/templates/visualization/entity_comparison_inject_head.jsp

@@ -0,0 +1,62 @@
+<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
+
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+
+<c:set var="portalBean" value="${requestScope.portalBean}" />
+<c:set var="themeDir"><c:out value="${portalBean.themeDir}" /></c:set>
+<c:set var="contextPath"><c:out value="${pageContext.request.contextPath}" /></c:set>
+
+<c:url var="jquery" value="/js/jquery.js"/>
+<c:url var="flot" value="/js/jquery_plugins/flot/jquery.flot.js"/>
+<c:url var="fliptext" value="/js/jquery_plugins/fliptext/jquery.mb.flipText.js"/>
+<c:url var="jgrowl" value="/js/jquery_plugins/jgrowl/jquery.jgrowl.js"/>
+<c:url var="pagination" value="/js/jquery_plugins/pagination/jquery.pagination.js"/>
+<c:url var="livesearch" value="/js/jquery_plugins/jquery.livesearch.js"/>
+<c:url var="datatable" value="/js/jquery_plugins/datatable/jquery.dataTables.js"/>
+<c:url var="autoellipsis" value="/js/jquery_plugins/jquery.AutoEllipsis.js"/>
+
+
+<c:url var="entityComparisonUtils" value="/js/visualization/entityComparison/util.js" />
+<c:url var="entityComparisonConstants" value="/js/visualization/entityComparison/constants.js" />
+
+<!-- css related to jgrowl and pagination js files. -->
+<c:url var="paginationStyle" value="/js/jquery_plugins/pagination/pagination.css" />
+<c:url var="jgrowlStyle" value="/js/jquery_plugins/jgrowl/jquery.jgrowl.css" />
+
+<!-- css related to dataTable js files. -->
+<c:url var="demopage" value="/js/jquery_plugins/datatable/demo_page.css" />
+<c:url var="demoTable" value="/js/jquery_plugins/datatable/demo_table.css" />
+
+<c:url var="entityComparisonStyle" value="/${themeDir}css/visualization/entityComparison/layout.css" />
+<c:url var="vizStyle" value="/${themeDir}css/visualization/visualization.css" />
+
+<!-- Including jquery, entity comparison related javascript files -->
+
+<script type="text/javascript" src="${jquery}"></script>
+<script type="text/javascript" src="${flot}"></script>
+<script type="text/javascript" src="${fliptext}"></script>
+<script type="text/javascript" src="${jgrowl}"></script>
+<script type="text/javascript" src="${pagination}"></script>
+<script type="text/javascript" src="${livesearch}"></script>
+<script type="text/javascript" src="${datatable}"></script>
+<script type="text/javascript" src="${autoellipsis}"></script>
+<script type="text/javascript" src="${entityComparisonUtils}"></script>
+<script type="text/javascript" src="${entityComparisonConstants}"></script>
+
+
+<link href="${entityComparisonStyle}" rel="stylesheet" type="text/css" />
+<link href="${paginationStyle}" rel="stylesheet" type="text/css" />
+<link href="${jgrowlStyle}" rel="stylesheet" type="text/css" />
+<link href="${demopage}" rel="stylesheet" type="text/css" />
+<link href="${demoTable}" rel="stylesheet" type="text/css" />
+
+
+<link rel="stylesheet" type="text/css" href="${vizStyle}" />
+
+<script language="JavaScript" type="text/javascript">
+<!--
+
+var contextPath = "${contextPath}";
+
+// -->
+</script>

productMods/templates/visualization/person_level.jsp

@@ -18,6 +18,8 @@
 <c:set var='numOfAuthors' value='${requestScope.numOfAuthors}' />
 <c:set var='numOfCoAuthorShips' value='${requestScope.numOfCoAuthorShips}' />
 
+<c:set var='completeURL' value='${requestScope.completeURL}' />
+
 <c:url var="egoVivoProfileURL" value="/individual">
 	<c:param name="uri" value="${requestScope.egoURIParam}" />
 </c:url>
@@ -59,6 +61,7 @@ $(document).ready(function(){
 
 <div id="body">
 
+<div>complete URL = '${completeURL} '</div>
 <!--[if IE]>
 	<style type="text/css">
 	

productMods/templates/visualization/person_level_inject_head.jsp

@@ -13,6 +13,14 @@
 	<c:param name="labelField" value="label" />
 </c:url>
 
+<c:url var="egoCoPIDataFeederURL" value="/visualization">
+	<c:param name="vis" value="coprincipalinvestigator" />
+	<c:param name="render_mode" value="data" />
+	<c:param name="uri" value="${requestScope.egoURIParam}" />
+	<c:param name="labelField" value="label" />
+</c:url>
+
+
 <c:url var="egoCoAuthorsListDataFileURL" value="/visualization">
 	<c:param name="vis" value="person_level" />
 	<c:param name="render_mode" value="data" />
@@ -20,7 +28,7 @@
 	<c:param name="uri" value="${requestScope.egoURIParam}" />
 </c:url>
 
-<c:url var="swfLink" value="/${themeDir}site_icons/visualization/coauthorship/CoAuthor.swf" />
+<c:url var="swfLink" value="/${themeDir}site_icons/visualization/coauthorship/EgoCentric.swf" />
 
 <c:url var="jquery" value="/js/jquery.js"/>
 <c:url var="adobeFlashDetector" value="/js/visualization/coauthorship/AC_OETags.js" />
@@ -48,6 +56,7 @@ var swfLink = "${swfLink}";
 var egoURI = "${requestScope.egoURIParam}";
 var egoCoAuthorshipDataFeederURL = "${egoCoAuthorshipDataFeederURL}";
 var egoCoAuthorsListDataFileURL = "${egoCoAuthorsListDataFileURL}";
+var egoCoPIDataFeederURL = "${egoCoPIDataFeederURL}";
 var contextPath = "${contextPath}";
 
 // -->

src/edu/cornell/mannlib/vitro/webapp/controller/visualization/VisualizationController.java

@@ -13,6 +13,7 @@ import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+
 import org.springframework.beans.factory.BeanFactory;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
@@ -36,14 +37,13 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequ
  *
  * @author cdtank
  */
+@SuppressWarnings("serial")
 public class VisualizationController extends BaseEditController {
 
 	private Map<String, VisualizationRequestHandler> visualizationIDsToClass;
 
 	public static final String URL_ENCODING_SCHEME = "UTF-8";
 
-	private static final long serialVersionUID = 1L;
-
 	private static final Log log = LogFactory.getLog(VisualizationController.class.getName());
 
     protected static final Syntax SYNTAX = Syntax.syntaxARQ;

src/edu/cornell/mannlib/vitro/webapp/controller/visualization/VisualizationFrameworkConstants.java

@@ -46,6 +46,7 @@ public class VisualizationFrameworkConstants {
 	public static final String COAUTHORSLIST_VIS_MODE = "coauthors";
 	public static final String SHORT_SPARKLINE_VIS_MODE = "short";
 	public static final String FULL_SPARKLINE_VIS_MODE = "full";
+	public static final String COPI_VIS_MODE = "copi";
 
 	/*
 	 * These values represent possible utilities vis modes.
@@ -55,6 +56,10 @@ public class VisualizationFrameworkConstants {
 	public static final String COAUTHOR_UTILS_VIS_MODE = "COAUTHORSHIP_URL";
 	public static final String PERSON_LEVEL_UTILS_VIS_MODE = "PERSON_LEVEL_URL";
 	public static final String IMAGE_UTILS_VIS_MODE = "IMAGE_URL";
+	public static final String UNIVERSITY_COMPARISON_VIS_MODE = "UNIVERSITY";
+	public static final String SCHOOL_COMPARISON_VIS_MODE = "SCHOOL";
+	public static final String DEPARTMENT_COMPARISON_VIS_MODE = "DEPARTMENT";
+	
 
 	/*
 	 * These values represent possible visualizations provided as values to the "vis" url key.
@@ -65,5 +70,8 @@ public class VisualizationFrameworkConstants {
 	public static final String COAUTHORSHIP_VIS = "coauthorship";
 	public static final String PERSON_LEVEL_VIS = "person_level";
 	public static final String UTILITIES_VIS = "utilities";
+	public static final String ENTITY_COMPARISON_VIS = "entity_comparison";
+	public static final String CO_PI_VIS = "coprincipalinvestigator";
+	
 
 }

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

@@ -0,0 +1,5 @@
+package edu.cornell.mannlib.vitro.webapp.controller.visualization.freemarker;
+
+public class VisualizationController {
+
+}

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

@@ -33,7 +33,6 @@ import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.BiboDocument;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoAuthorshipData;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Edge;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Node;
-import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoCollegeOrSchool;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
 import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UniqueIDGenerator;
 
@@ -51,8 +50,6 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
 
 	private String egoURI;
-	private Map<String, VivoCollegeOrSchool> collegeURLToVO = 
-			new HashMap<String, VivoCollegeOrSchool>();
 	
 	private DataSource dataSource;
 
@@ -356,9 +353,9 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 			
 	}
 
-	public Map<String, VivoCollegeOrSchool> getCollegeURLToVO() {
+//	public Map<String, VivoCollegeOrSchool> getCollegeURLToVO() {
-		return collegeURLToVO;
+//		return collegeURLToVO;
-	}
+//	}
 
 	private BiboDocument createDocumentVO(QuerySolution solution, String documentURL) {
 

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

@@ -1,322 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.collegepubcount;
-
-import java.util.HashMap;
-import java.util.HashSet;
-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.constants.VOConstants.EmployeeType;
-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.VivoCollegeOrSchool;
-import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoDepartmentOrDivision;
-import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.VivoEmployee;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
-
-
-
-/**
- * @author cdtank
- */
-public class CollegePublicationCountQueryRunner implements QueryRunner<Set<VivoEmployee>> {
-
-	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
-
-	private String collegeURI;
-	private Map<String, VivoCollegeOrSchool> collegeURLToVO = 
-			new HashMap<String, VivoCollegeOrSchool>();
-	private DataSource dataSource;
-
-	private Log log;
-
-	public CollegePublicationCountQueryRunner(String collegeURI,
-			DataSource dataSource, Log log) {
-
-		this.collegeURI = collegeURI;
-		this.dataSource = dataSource;
-		this.log = log;
-
-	}
-
-	private Set<VivoEmployee> createJavaValueObjects(ResultSet resultSet) {
-		
-		Set<VivoEmployee> collegeAcademicEmployees = new HashSet<VivoEmployee>();
-		
-		Map<String, VivoDepartmentOrDivision> departmentURLToVO = 
-				new HashMap<String, VivoDepartmentOrDivision>();
-		Map<String, VivoEmployee> employeeURLToVO = new HashMap<String, VivoEmployee>();
-		
-		while (resultSet.hasNext()) {
-			QuerySolution solution = resultSet.nextSolution();
-
-			String collegeURL = solution.get(QueryFieldLabels.COLLEGE_URL).toString();
-			
-			VivoCollegeOrSchool currentCollege;
-			
-			if (collegeURLToVO.containsKey(collegeURL)) {
-				currentCollege = collegeURLToVO.get(collegeURL);
-			} else {
-				currentCollege = new VivoCollegeOrSchool(collegeURL);
-				collegeURLToVO.put(collegeURL, currentCollege);
-				
-				RDFNode collegeLabelNode = solution.get(QueryFieldLabels.COLLEGE_LABEL);
-				if (collegeLabelNode != null) {
-					currentCollege.setCollegeLabel(collegeLabelNode.toString());
-				}
-			}
-
-			String departmentURL = solution.get(QueryFieldLabels.DEPARTMENT_URL).toString();
-			
-			VivoDepartmentOrDivision currentDepartment;
-			
-			if (departmentURLToVO.containsKey(departmentURL)) {
-				currentDepartment = departmentURLToVO.get(departmentURL);
-				currentDepartment.addParentCollege(currentCollege);
-			} else {
-				currentDepartment = new VivoDepartmentOrDivision(departmentURL, currentCollege);
-				departmentURLToVO.put(departmentURL, currentDepartment);
-
-				RDFNode departmentLabelNode = solution.get(QueryFieldLabels.DEPARTMENT_LABEL);
-				if (departmentLabelNode != null) {
-					currentDepartment.setDepartmentLabel(departmentLabelNode.toString());
-				}
-			}
-
-			currentCollege.addDepartment(currentDepartment);
-			
-			RDFNode employeeNode = solution.get(QueryFieldLabels.ACADEMIC_FACULTY_EMPLOYEE_URL);
-			EmployeeType currentEmployeeType;
-			VivoEmployee currentEmployee;
-			
-			if (employeeNode != null) {
-				currentEmployeeType = EmployeeType.ACADEMIC_FACULTY_EMPLOYEE;
-			} else {
-				currentEmployeeType = EmployeeType.ACADEMIC_STAFF_EMPLOYEE;
-				employeeNode = solution.get(QueryFieldLabels.ACADEMIC_STAFF_EMPLOYEE_URL);
-			}
-			
-			if (employeeURLToVO.containsKey(employeeNode.toString())) {
-				currentEmployee = employeeURLToVO.get(employeeNode.toString());
-				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);
-			if (documentNode != null) {
-				
-				/*
-				 * A document can have multiple authors but if the same author serves in 
-				 * multiple departments then we need to account for "An Authored Document" 
-				 * only once. This check will make sure that a document by same author is 
-				 * not added twice just because that author serves in 2 distinct department.
-				 * */
-				boolean isNewDocumentAlreadyAdded = testForDuplicateEntryOfDocument(
-															currentEmployee, 
-															documentNode);
-				
-				if (!isNewDocumentAlreadyAdded) {
-					currentEmployee.addAuthorDocument(
-							createAuthorDocumentsVO(solution, 
-													documentNode.toString()));
-				}
-				
-			}
-			
-			collegeAcademicEmployees.add(currentEmployee);
-		}
-		
-		return collegeAcademicEmployees;
-	}
-
-	private boolean testForDuplicateEntryOfDocument(
-			VivoEmployee currentEmployee, RDFNode documentNode) {
-		boolean isNewDocumentAlreadyAdded = false;
-		
-		for (BiboDocument currentAuthoredDocument : currentEmployee.getAuthorDocuments()) {
-			if (currentAuthoredDocument.getDocumentURL()
-					.equalsIgnoreCase(documentNode.toString())) {
-				isNewDocumentAlreadyAdded = true;
-				break;
-			}
-		}
-		return isNewDocumentAlreadyAdded;
-	}
-
-	public Map<String, VivoCollegeOrSchool> getCollegeURLToVO() {
-		return collegeURLToVO;
-	}
-
-	private BiboDocument createAuthorDocumentsVO(QuerySolution solution, String documentURI) {
-
-			BiboDocument biboDocument = new BiboDocument(documentURI);
-
-			RDFNode documentLabelNode = solution.get(QueryFieldLabels.DOCUMENT_LABEL);
-			if (documentLabelNode != null) {
-				biboDocument.setDocumentLabel(documentLabelNode.toString());
-			}
-
-			RDFNode documentBlurbNode = solution.get(QueryFieldLabels.DOCUMENT_BLURB);
-			if (documentBlurbNode != null) {
-				biboDocument.setDocumentBlurb(documentBlurbNode.toString());
-			}
-
-			RDFNode documentMonikerNode = solution.get(QueryFieldLabels.DOCUMENT_MONIKER);
-			if (documentMonikerNode != null) {
-				biboDocument.setDocumentMoniker(documentMonikerNode.toString());
-			}
-
-			RDFNode documentDescriptionNode = solution.get(QueryFieldLabels.DOCUMENT_DESCRIPTION);
-			if (documentDescriptionNode != null) {
-				biboDocument.setDocumentDescription(documentDescriptionNode.toString());
-			}
-
-			RDFNode publicationYearNode = solution.get(QueryFieldLabels.DOCUMENT_PUBLICATION_YEAR);
-			if (publicationYearNode != null) {
-				biboDocument.setPublicationYear(publicationYearNode.toString());
-			}
-			
-			RDFNode publicationYearMonthNode = solution.get(
-													QueryFieldLabels
-															.DOCUMENT_PUBLICATION_YEAR_MONTH);
-			if (publicationYearMonthNode != null) {
-				biboDocument.setPublicationYearMonth(publicationYearMonthNode.toString());
-			}
-			
-			RDFNode publicationDateNode = solution.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
-			if (publicationDateNode != null) {
-				biboDocument.setPublicationDate(publicationDateNode.toString());
-			}
-			
-			return biboDocument;
-	}
-	
-	private ResultSet executeQuery(String queryText,
-								   DataSource dataSource) {
-
-        QueryExecution queryExecution = null;
-        try {
-            Query query = QueryFactory.create(queryText, SYNTAX);
-
-//            QuerySolutionMap qs = new QuerySolutionMap();
-//            qs.add("authPerson", queryParam); // bind resource to s
-            
-            queryExecution = QueryExecutionFactory.create(query, dataSource);
-
-            if (query.isSelectType()) {
-                return queryExecution.execSelect();
-            }
-        } finally {
-            if (queryExecution != null) {
-            	queryExecution.close();
-            }
-        }
-		return null;
-    }
-
-	private String generateCollegeEmployeeSparqlQuery(String queryURI) {
-//		Resource uri1 = ResourceFactory.createResource(queryURI);
-
-		String sparqlQuery = QueryConstants.getSparqlPrefixQuery()
-							+ "SELECT (str(?collegeLabel) as ?" + QueryFieldLabels.COLLEGE_LABEL + ") " 
-							+ "		(str(?department) as ?" + QueryFieldLabels.DEPARTMENT_URL + ") " 
-							+ "		(str(?departmentLabel) as ?" + QueryFieldLabels.DEPARTMENT_LABEL + ") " 
-							+ "		(str(?academicFacultyEmployee) as ?" + QueryFieldLabels.ACADEMIC_FACULTY_EMPLOYEE_URL + ") " 
-							+ "		(str(?academicStaffEmployee) as ?" + QueryFieldLabels.ACADEMIC_STAFF_EMPLOYEE_URL + ") "
-							+ "		(str(<" + queryURI + ">) as ?" + QueryFieldLabels.COLLEGE_URL + ") "
-							+ "		(str(?authorLabel) as ?" + QueryFieldLabels.AUTHOR_LABEL + ") "
-							+ "		(str(?document) as ?" + QueryFieldLabels.DOCUMENT_URL + ") "
-							+ "		(str(?documentMoniker) as ?" + QueryFieldLabels.DOCUMENT_MONIKER + ") "
-							+ "		(str(?documentLabel) as ?" + QueryFieldLabels.DOCUMENT_LABEL + ") "
-							+ "		(str(?documentBlurb) as ?" + QueryFieldLabels.DOCUMENT_BLURB + ") "
-							+ "		(str(?documentDescription) as ?" + QueryFieldLabels.DOCUMENT_DESCRIPTION + ") "
-							+ "		(str(?publicationYear) as ?" + QueryFieldLabels.DOCUMENT_PUBLICATION_YEAR + ") "
-							+ "WHERE { "
-							+ "<" + queryURI + "> rdf:type vivo:CollegeOrSchoolWithinUniversity; " +
-									"rdfs:label ?collegeLabel; " +
-									"vivo:hasAcademicDepartmentOrDivision ?department . "
-							+ "?department rdfs:label ?departmentLabel ."
-							+ "{ "
-							+ getAcademicEmployeePublicationsSparqlQuery("academicFacultyEmployee", "vivo:hasEmployeeAcademicFacultyMember")
-							+ " UNION " 
-							+ getAcademicEmployeePublicationsSparqlQuery("academicStaffEmployee", "vivo:hasEmployeeAcademicStaffMember")
-							+ "}"
-							+ "}";
-
-//		System.out.println(sparqlQuery);
-		
-		return sparqlQuery;
-	}
-
-	
-	private String getAcademicEmployeePublicationsSparqlQuery(String employeeHandle, 
-															  String ontologyHandle) {
-		
-		String sparqlQuery = " {?department " + ontologyHandle + " ?" + employeeHandle + " . " 
-							+ "?" + employeeHandle + " rdf:type foaf:Person; rdfs:label ?authorLabel. " 
-							+ "OPTIONAL { ?" + employeeHandle + " vivo:authorOf ?document ." +
-										" ?document rdfs:label ?documentLabel ." +
-										" OPTIONAL { ?document vitro:moniker ?documentMoniker } ." +
-										" OPTIONAL { ?document vitro:blurb ?documentBlurb } ." +
-										" OPTIONAL { ?document vitro:description ?documentDescription } ." +
-										" OPTIONAL { ?document vivo:publicationYear ?publicationYear } ." +
-										"}" +
-								"} ";
-		
-		return sparqlQuery;
-		
-	}
-	
-	public Set<VivoEmployee> getQueryResult()
-		throws MalformedQueryParametersException {
-
-		if (StringUtils.isNotBlank(this.collegeURI)) {
-        	/*
-        	 * To test for the validity of the URI submitted.
-        	 * */
-        	IRIFactory iRIFactory = IRIFactory.jenaImplementation();
-    		IRI iri = iRIFactory.create(this.collegeURI);
-            if (iri.hasViolation(false)) {
-                String errorMsg = ((Violation) iri.violations(false).next()).getShortMessage();
-                log.error("Pub Count 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(generateCollegeEmployeeSparqlQuery(this.collegeURI),
-										   this.dataSource);
-
-		return createJavaValueObjects(resultSet);
-	}
-
-}

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

@@ -1,394 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.collegepubcount;
-
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-import java.util.Map.Entry;
-
-import javax.servlet.ServletException;
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.skife.csv.CSVWriter;
-import org.skife.csv.SimpleWriter;
-
-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.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.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;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.PDFDocument;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
-import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
-
-public class CollegePublicationCountRequestHandler implements VisualizationRequestHandler {
-
-	public void generateVisualization(VitroRequest vitroRequest,
-									  HttpServletRequest request, 
-									  HttpServletResponse response, 
-									  Log log, 
-									  DataSource dataSource) {
-
-		String collegeURIParam = vitroRequest.getParameter(
-										VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
-
-        String renderMode = vitroRequest.getParameter(
-        								VisualizationFrameworkConstants.RENDER_MODE_KEY);
-        
-        String visMode = vitroRequest.getParameter(
-        								VisualizationFrameworkConstants.VIS_MODE_KEY);
-
-        String visContainer = vitroRequest.getParameter(
-        								VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
-
-		QueryRunner<Set<VivoEmployee>> queryManager =
-        	new CollegePublicationCountQueryRunner(collegeURIParam,
-						     dataSource,
-						     log);
-
-		try {
-			
-			Set<VivoEmployee> employees = queryManager.getQueryResult();
-			
-			Map<VivoDepartmentOrDivision, Map<String, Integer>> departmentToPublicationsOverTime = 
-				new HashMap<VivoDepartmentOrDivision, Map<String, Integer>>();
-			
-			Set<String> publishedYearsForCollege = new HashSet<String>();
-			
-			for (VivoEmployee currentEmployee : employees) {
-				
-				Map<String, Integer> currentEmployeeYearToPublicationCount = 
-					UtilityFunctions.getYearToPublicationCount(
-							currentEmployee.getAuthorDocuments());
-				
-				if (currentEmployeeYearToPublicationCount.size() > 0) {
-					
-					
-					publishedYearsForCollege.addAll(currentEmployeeYearToPublicationCount.keySet());
-				
-					for (VivoDepartmentOrDivision currentDepartment 
-								: currentEmployee.getParentDepartments()) {
-						
-						departmentToPublicationsOverTime
-								.put(currentDepartment, 
-										 getUpdatedDepartmentPublicationsOverTime(
-												 currentEmployeeYearToPublicationCount,
-												 departmentToPublicationsOverTime
-												 		.get(currentDepartment)));
-						
-					}
-				}
-			}
-
-	    	/*
-	    	 * In order to avoid unneeded computations we have pushed this "if" condition up.
-	    	 * This case arises when the render mode is data. In that case we dont want to generate 
-	    	 * HTML code to render sparkline, tables etc. Ideally I would want to avoid this flow.
-	    	 * It is ugly! 
-	    	 * */
-	    	if (VisualizationFrameworkConstants.DATA_RENDER_MODE.equalsIgnoreCase(renderMode)) { 
-				prepareDataResponse(
-						departmentToPublicationsOverTime,
-						((CollegePublicationCountQueryRunner) queryManager).getCollegeURLToVO(),
-						response);
-				
-				log.debug(publishedYearsForCollege);
-				return;
-			}
-	    	
-	    	
-	    	
-	    	/*
-	    	if (PDF_RENDER_MODE_URL_VALUE.equalsIgnoreCase(renderMode)) { 
-				prepareVisualizationQueryPDFResponse(authorDocuments,
-													  yearToPublicationCount);
-				return;
-			}
-	    	*/
-	    	
-	    	/*
-	    	 * Computations required to generate HTML for the sparklines & related context.
-	    	 * */
-	    	
-	    	/*
-	    	 * 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_PUBLICATION_YEAR".
-	    	 * */
-	    	publishedYearsForCollege.remove(VOConstants.DEFAULT_PUBLICATION_YEAR);
-
-		} catch (MalformedQueryParametersException e) {
-			try {
-				UtilityFunctions.handleMalformedParameters(
-						e.getMessage(), 
-						"Visualization Query Error - College Publication Count", 
-						vitroRequest, 
-						request, 
-						response, 
-						log);
-			} catch (ServletException e1) {
-				log.error(e1.getStackTrace());
-			} catch (IOException e1) {
-				log.error(e1.getStackTrace());
-			}
-			return;
-		}
-
-	}
-
-	private Map<String, Integer> getUpdatedDepartmentPublicationsOverTime(
-					Map<String, Integer> currentEmployeeYearToPublicationCount,
-					Map<String, Integer> currentDepartmentYearToPublicationCount) {
-		
-		Map<String, Integer> departmentYearToPublicationCount;
-		
-		/*
-		 * In case this is the first time we are consolidating publication counts 
-		 * over time for a department.
-		 * */
-		if (currentDepartmentYearToPublicationCount == null) {
-
-			departmentYearToPublicationCount = new TreeMap<String, Integer>();
-			
-		} else {
-			departmentYearToPublicationCount = currentDepartmentYearToPublicationCount;
-		}
-		
-		
-		Iterator employeePubCountIterator = currentEmployeeYearToPublicationCount
-													.entrySet().iterator();
-		
-		while (employeePubCountIterator.hasNext()) {
-			Map.Entry<String, Integer> employeePubCountEntry = 
-				(Map.Entry) employeePubCountIterator.next();
-			
-			String employeePublicationYear = employeePubCountEntry.getKey();
-			Integer employeePublicationCount = employeePubCountEntry.getValue();
-			
-			try {
-			if (departmentYearToPublicationCount.containsKey(employeePublicationYear)) {
-				departmentYearToPublicationCount.put(employeePublicationYear,
-															departmentYearToPublicationCount
-																.get(employeePublicationYear) 
-															+ employeePublicationCount);
-
-    		} else {
-    			
-    			departmentYearToPublicationCount.put(employeePublicationYear, 
-    												 employeePublicationCount);
-    			
-    		}	
-			} catch (Exception e) {
-				e.printStackTrace();
-			}
-		}
-		
-		return departmentYearToPublicationCount;
-	}
-
-	private void preparePDFResponse(Individual college, 
-													  List<BiboDocument> authorDocuments,
-													  Map<String, Integer> yearToPublicationCount, 
-													  HttpServletResponse response) {
-		
-		String authorName = null; 
-		
-		/*
-		 * To protect against cases where there are no author documents associated with the
-		 * individual. 
-		 * */
-		if (authorDocuments.size() > 0) {
-			authorName = college.getIndividualLabel();
-		}
-		
-		/*
-		 * To make sure that null/empty records for author names do not cause any mischief.
-		 * */
-		if (authorName == null) {
-			authorName = "";
-		}
-		
-		String outputFileName = UtilityFunctions.slugify(authorName + "-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(authorName, 
-														  yearToPublicationCount, 
-														  document, 
-														  pdfWriter);
-				document.close();
-
-				response.setHeader("Expires", "0");
-				response.setHeader("Cache-Control", "must-revalidate, post-check=0, pre-check=0");
-				response.setHeader("Pragma", "public");
-				response.setContentLength(baos.size());
-				
-				baos.writeTo(responseOutputStream);
-				responseOutputStream.flush();
-				responseOutputStream.close();
-				
-			} catch (IOException e) {
-				e.printStackTrace();
-			} catch (DocumentException e) {
-				e.printStackTrace();
-			}
-	}
-
-	private void prepareDataResponse(
-			Map<VivoDepartmentOrDivision, Map<String, Integer>> departmentToPublicationsOverTime,
-			Map<String, VivoCollegeOrSchool> collegeURLToVO, HttpServletResponse response) {
-
-		String collegeName = null; 
-		
-		/*
-		* To protect against cases where there are no author documents associated with the
-		* individual. 
-		* */
-
-		if (collegeURLToVO.size() > 0) {
-			
-			collegeName = ((VivoCollegeOrSchool) collegeURLToVO.values()
-									.iterator().next()).getCollegeLabel();
-			
-		}
-		
-		/*
-		* To make sure that null/empty records for author names do not cause any mischief.
-		* */
-		if (collegeName == null) {
-		collegeName = "";
-		}
-		
-		String outputFileName = UtilityFunctions.slugify(collegeName) + "depts-pub-count" + ".csv";
-		
-		response.setContentType("application/octet-stream");
-		response.setHeader("Content-Disposition", "attachment;filename=" + outputFileName);
-		
-		try {
-		
-		PrintWriter responseWriter = response.getWriter();
-		
-		/*
-		 * We are side-effecting responseWriter since we are directly manipulating the response 
-		 * object of the servlet.
-		 * */
-		generateCsvFileBuffer(departmentToPublicationsOverTime, 
-							  collegeURLToVO, 
-							  responseWriter);
-
-		responseWriter.close();
-		
-		} catch (IOException e) {
-		e.printStackTrace();
-		}
-	}
-	
-	private void generateCsvFileBuffer(
-			Map<VivoDepartmentOrDivision, Map<String, Integer>> departmentToPublicationsOverTime,
-			Map<String, VivoCollegeOrSchool> collegeURLToVO, PrintWriter printWriter) {
-		
-        CSVWriter csvWriter = new SimpleWriter(printWriter);
-        
-        try {
-			csvWriter.append(new String[]{"School", "Department", "Year", "Publications"});
-			
-			Iterator<VivoCollegeOrSchool> collegeIterator = collegeURLToVO.values().iterator();
-			
-			while (collegeIterator.hasNext()) {
-				VivoCollegeOrSchool college = collegeIterator.next();
-				String collegeLabel = college.getCollegeLabel();
-				for (VivoDepartmentOrDivision currentDepartment : college.getDepartments()) {
-					
-					Map<String, Integer> currentDepartmentPublicationsOverTime = 
-							departmentToPublicationsOverTime.get(currentDepartment);
-					
-					/*
-					 * This because many departments might not have any publication.
-					 * */
-					if (currentDepartmentPublicationsOverTime != null) {
-						
-					for (Entry<String, Integer> currentEntry 
-								: currentDepartmentPublicationsOverTime.entrySet()) {
-						csvWriter.append(new Object[]{collegeLabel,
-													  currentDepartment.getDepartmentLabel(),
-													  currentEntry.getKey(), 
-													  currentEntry.getValue()});
-					}
-					
-					}
-					
-				}
-			}
-	        
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-		
-		printWriter.flush();
-		
-	}
-
-	private void prepareStandaloneResponse(HttpServletRequest request,
-			HttpServletResponse response, VitroRequest vreq,
-			String visContentCode, String visContextCode) {
-
-        Portal portal = vreq.getPortal();
-
-        request.setAttribute("visContentCode", visContentCode);
-        request.setAttribute("visContextCode", visContextCode);
-
-        request.setAttribute("bodyJsp", "/templates/visualization/publication_count.jsp");
-        request.setAttribute("portalBean", portal);
-        request.setAttribute("title", "Individual Publication Count Visualization");
-        request.setAttribute("scripts", "/templates/visualization/visualization_scripts.jsp");
-
-	}
-
-	private void prepareDynamicResponse(HttpServletRequest request,
-			HttpServletResponse response, VitroRequest vreq,
-			String visContentCode, String visContextCode) {
-
-        Portal portal = vreq.getPortal();
-
-        request.setAttribute("visContentCode", visContentCode);
-        request.setAttribute("visContextCode", visContextCode);
-
-        request.setAttribute("portalBean", portal);
-        request.setAttribute("bodyJsp", "/templates/visualization/ajax_vis_content.jsp");
-
-	}
-
-}

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

@@ -51,11 +51,7 @@ public class QueryFieldLabels {
 	public static final String COLLEGE_URL = "collegeLit";
 	public static final String COLLEGE_LABEL = "collegeLabelLit";
 	
-	/*
+
-	 * Department related field labels 
-	 * */
-	public static final String DEPARTMENT_URL = "departmentLit";
-	public static final String DEPARTMENT_LABEL = "departmentLabelLit";
 	
 	/*
 	 * Employee related field labels 
@@ -63,4 +59,62 @@ public class QueryFieldLabels {
 	public static final String ACADEMIC_FACULTY_EMPLOYEE_URL = "academicFacultyEmployeeLit";
 	public static final String ACADEMIC_STAFF_EMPLOYEE_URL = "academicStaffEmployeeLit";
 	
+	/*
+	 * Person related field Labels
+	 */
+	public static final String PERSON_URL = "personLit";
+	public static final String PERSON_LABEL = "personLabelLit";
+	public static final String PERSON_TYPE = "personTypeLit";
+	public static final String PERSON_TYPE_LABEL = "personTypeLabelLit";
+	
+	
+	/*
+	 * Position related field labels
+	 */
+	public static final String SECONDARY_POSITION_LABEL = "SecondaryPositionLabelLit";
+	
+	/*
+	 * start year related field labels
+	 */
+	public static final String START_YEAR_LABEL = "StartYearLit";
+	
+	
+	/*
+	 * Organization related field Labels
+	 */
+	public static final String ORGANIZATION_URL = "organizationLit";
+	public static final String ORGANIZATION_LABEL = "organizationLabelLit";
+	
+	
+	/*
+	 * Sub Organization related field labels
+	 */
+	public static final String SUBORGANIZATION_URL = "subOrganizationLit";
+	public static final String SUBORGANIZATION_LABEL = "subOrganizationLabelLit";
+	
+	/*
+	 * Sub Organization related field labels
+	 */
+	public static final String SUBORGANIZATION_TYPE = "subOrganizationTypeLit";
+	public static final String SUBORGANIZATION_TYPE_LABEL = "subOrganizationTypeLabelLit";
+	
+	
+	/*
+	 * Department related field labels 
+	 * */
+	public static final String DEPARTMENT_URL = "departmentLit";
+	public static final String DEPARTMENT_LABEL = "departmentLabelLit";	
+	
+	/*
+	 * Co-PI related field labels
+	 */
+	public static final String PI_URL = "PILit";
+	public static final String PI_LABEL = "PILabelLit";
+	public static final String CO_PI_URL = "coPILit";
+	public static final String CO_PI_LABEL = "coPILabelLit";
+	public static final String GRANT_URL = "grantLit";
+	public static final String GRANT_LABEL = "grantLabelLit";
+	public static final String GRANT_START_DATE = "grantStartDateLit";
+	public static final String GRANT_END_DATE = "grantEndDateLit";
+	
 }

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

@@ -11,6 +11,7 @@ import java.util.Calendar;
 public class VOConstants {
 	
 	public static final String DEFAULT_PUBLICATION_YEAR = "Unknown";
+	public static final String DEFAULT_GRANT_YEAR = "Unknown";
 	
 	/*
 	 * Employee related constants 

src/edu/cornell/mannlib/vitro/webapp/visualization/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.coprincipalinvestigator;
+
+import java.util.Comparator;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.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/coprincipalinvestigator/CoPIGrantCountQueryRunner.java

@@ -0,0 +1,438 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.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.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPIEdge;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Grant;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPINode;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UniqueIDGenerator;
+
+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 . " 
+			+ " }";
+
+		System.out.println("COPI QUERY - " + sparqlQuery);
+		
+		return sparqlQuery;
+	}
+	
+	private ResultSet executeQuery(String queryText, DataSource dataSource) {
+
+		QueryExecution queryExecution = null;
+		try {
+			Query query = QueryFactory.create(queryText, SYNTAX);
+
+			queryExecution = QueryExecutionFactory.create(query, dataSource);
+
+			if (query.isSelectType()) {
+				return queryExecution.execSelect();
+			}
+		} finally {
+			if (queryExecution != null) {
+				queryExecution.close();
+			}
+		}
+		return null;
+	}
+	
+	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());
+					}
+				}
+				
+				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);
+				
+				/*
+				 * 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());
+					}
+				}
+				
+				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);
+				
+				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/coprincipalinvestigator/CoPIGrantCountRequestHandler.java

@@ -0,0 +1,240 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.commons.lang.StringUtils;
+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.Controllers;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPINode;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
+
+public class CoPIGrantCountRequestHandler implements VisualizationRequestHandler{
+	
+	public void generateVisualization(VitroRequest vitroRequest, HttpServletRequest request, HttpServletResponse response, Log log, DataSource dataSource){
+		
+		String egoURI = vitroRequest.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		String renderMode = vitroRequest.getParameter(VisualizationFrameworkConstants.RENDER_MODE_KEY);
+		String visMode = vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
+		
+		QueryRunner<CoPIData> queryManager = new CoPIGrantCountQueryRunner(egoURI, dataSource, log);
+		
+		try{
+			CoPIData PINodesAndEdges = queryManager.getQueryResult();
+			
+			if (VisualizationFrameworkConstants.DATA_RENDER_MODE
+					.equalsIgnoreCase(renderMode)) {
+				
+				if (VisualizationFrameworkConstants.COPI_VIS_MODE
+						.equalsIgnoreCase(visMode)) { 
+
+						prepareCoPIDataResponse(PINodesAndEdges, response);
+						return;
+		    		
+				} else {
+		    			/*
+		    			 * When the graphML file is required - based on which copi network 
+		    			 * visualization will be rendered.
+		    			 * */
+		    			prepareNetworkDataResponse(PINodesAndEdges, response);
+						return;
+				}
+			}else {
+				
+				RequestDispatcher requestDispatcher = null;
+
+				prepareStandaloneResponse(
+						egoURI, 
+						PINodesAndEdges,
+		    			vitroRequest,
+		    			request);
+
+				requestDispatcher = request.getRequestDispatcher(Controllers.BASIC_JSP);
+
+		    	try {
+		            requestDispatcher.forward(request, response);
+		        } catch (Exception e) {
+		            log.error("EntityEditController could not forward to view.");
+		            log.error(e.getMessage());
+		            log.error(e.getStackTrace());
+		        } 
+			}
+			
+		}catch(MalformedQueryParametersException e){
+			try {
+				UtilityFunctions.handleMalformedParameters(
+						e.getMessage(), 
+						"Visualization Query Error - Co-authorship Network",
+						vitroRequest, 
+						request, 
+						response, 
+						log);
+			} catch (ServletException e1) {
+				log.error(e1.getStackTrace());
+			} catch (IOException e1) {
+				log.error(e1.getStackTrace());
+			}
+			return;
+		}
+	}
+	
+	/**
+	 * When the page for person level visualization is requested.
+	 * @param egoURI
+	 * @param coPIVO
+	 * @param vitroRequest
+	 * @param request
+	 */
+	private void prepareStandaloneResponse(String egoURI,
+			CoPIData pINodesAndEdges, VitroRequest vitroRequest,
+			HttpServletRequest request) {
+		
+		Portal portal = vitroRequest.getPortal();
+
+		request.setAttribute("egoURIParam", egoURI);
+
+		String title = "";
+		if (pINodesAndEdges.getNodes() != null
+				&& pINodesAndEdges.getNodes().size() > 0) {
+			request.setAttribute("numOfAuthors", pINodesAndEdges.getNodes()
+					.size());
+			title = pINodesAndEdges.getEgoNode().getNodeName() + " - ";
+		}
+
+		if (pINodesAndEdges.getEdges() != null
+				&& pINodesAndEdges.getEdges().size() > 0) {
+			request.setAttribute("numOfCoPIs", pINodesAndEdges
+					.getEdges().size());
+		}
+
+		request.setAttribute("title", title + "Co-PI Visualization");
+		request.setAttribute("portalBean", portal);
+		request.setAttribute("scripts",
+				"/templates/visualization/person_level_inject_head.jsp");
+		request.setAttribute("bodyJsp",
+				"/templates/visualization/co_authorship.jsp");
+	}
+
+	/**
+	 * Provides a response when graphml formatted co-pi network is requested, typically by 
+	 * the flash vis.
+	 * @param pINodesAndEdges
+	 * @param response
+	 */
+	private void prepareNetworkDataResponse(CoPIData pINodesAndEdges,
+			HttpServletResponse response) {
+		
+		response.setContentType("text/xml");
+		
+		try {
+		
+		PrintWriter responseWriter = response.getWriter();
+		
+		/*
+		 * We are side-effecting responseWriter since we are directly manipulating the response 
+		 * object of the servlet.
+		 * */
+		CoPIGraphMLWriter coPIGraphMLWriter = 
+				new CoPIGraphMLWriter(pINodesAndEdges);
+		
+		responseWriter.append(coPIGraphMLWriter.getCoPIGraphMLContent());
+		
+		responseWriter.close();
+		
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		
+	}
+	
+	/**
+	 * Provides response when a csv file containing number & names of unique co-pis per 
+	 * year is requested. 
+	 * @param pINodesAndEdges
+	 * @param response
+	 */
+	private void prepareCoPIDataResponse(CoPIData pINodesAndEdges,
+			HttpServletResponse response) {
+		
+		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";			
+		}
+		
+		response.setContentType("application/octet-stream");
+		response.setHeader("Content-Disposition", 
+									  "attachment;filename=" + outputFileName);
+		
+		try {
+			
+			PrintWriter responseWriter = response.getWriter();
+			
+			/*
+			 * We are side-effecting responseWriter since we are directly manipulating the response 
+			 * object of the servlet.
+			 * */
+			writeCoPIsPerYearCSV(yearToCoPI, responseWriter);
+		
+			responseWriter.close();
+			
+			} catch (IOException e) {
+			e.printStackTrace();
+			}
+		
+	}
+
+	private void writeCoPIsPerYearCSV(Map<String, Set<CoPINode>> yearToCoPI,
+			PrintWriter responseWriter) {
+		responseWriter.append("Year, Count, Co-PI(s)\n");
+		for (Map.Entry<String, Set<CoPINode>> currentEntry : yearToCoPI.entrySet()) {
+			
+			responseWriter.append("\"" + currentEntry.getKey() + "\"," 
+							   + "\"" + currentEntry.getValue().size() + "\","
+							   + "\"" + getCoPINamesAsString(currentEntry.getValue()) 
+							   + "\"\n");
+		}
+		
+	}
+
+	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/coprincipalinvestigator/CoPIGraphMLWriter.java

@@ -0,0 +1,324 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
+
+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.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPIEdge;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPINode;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+import java.util.Map;
+
+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) {
+		
+		String profileURL = null;
+		try {
+			profileURL = VisualizationFrameworkConstants.INDIVIDUAL_URL_PREFIX + "?" 
+								+ VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY 
+								+ "=" + URLEncoder.encode(node.getNodeURI(),
+														  VisualizationController
+														  		.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");
+		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/coprincipalinvestigator/CoPINodeComparator.java

@@ -0,0 +1,17 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.coprincipalinvestigator;
+
+import java.util.Comparator;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPINode;
+
+/**
+ * This Comparator is used to sort the CoPINodes based on their IDs in ascending order.
+ * @author bkoniden
+ */
+
+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/entitycomparison/EntityPublicationCountQueryRunner.java

@@ -0,0 +1,280 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison;
+
+import java.util.HashMap;
+import java.util.Map;
+
+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.valueobjects.BiboDocument;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Entity;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.SubEntity;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
+
+/**
+ * This query runner is used to execute a sparql query that will fetch all the
+ * publications defined by bibo:Document property for a particular
+ * department/school/university.
+ * 
+ * @author bkoniden
+ */
+public class EntityPublicationCountQueryRunner implements QueryRunner<Entity> {
+
+	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
+
+	private String entityURI;
+	private DataSource dataSource;
+	private Log log;
+	private String visMode;
+
+	private static final String SPARQL_QUERY_COMMON_SELECT_CLAUSE = ""
+			+ "		(str(?Person) as ?personLit) "
+			+ "		(str(?PersonLabel) as ?personLabelLit) "
+			+ "		(str(?SecondaryPositionLabel) as ?SecondaryPositionLabelLit)"
+			+ "		(str(?Document) as ?documentLit) "
+			+ "		(str(?DocumentLabel) as ?documentLabelLit) "
+			+ "		(str(?publicationYear) as ?publicationYearLit) "
+			+ "		(str(?publicationYearMonth) as ?publicationYearMonthLit) "
+			+ "		(str(?publicationDate) as ?publicationDateLit) "
+			+ "		(str(?StartYear) as ?StartYearLit)";
+
+
+	private static final String SPARQL_QUERY_COMMON_WHERE_CLAUSE = ""
+			+ "?Document rdf:type bibo:Document ;"
+			+ " rdfs:label ?DocumentLabel ."
+			+ "OPTIONAL {  ?Document core:year ?publicationYear } ."
+			+ "OPTIONAL {  ?Document core:yearMonth ?publicationYearMonth } ."
+			+ "OPTIONAL {  ?Document core:date ?publicationDate } ."
+			+ "OPTIONAL {  ?SecondaryPosition core:startYear ?StartYear } .";
+
+	private static String ENTITY_LABEL;
+	private static String ENTITY_URL;
+	private static String SUBENTITY_LABEL;
+	private static String SUBENTITY_URL;
+
+	public EntityPublicationCountQueryRunner(String entityURI,
+			DataSource dataSource, Log log, String visMode) {
+
+		this.entityURI = entityURI;
+		this.dataSource = dataSource;
+		this.log = log;
+		this.visMode = visMode;
+
+	}
+
+	private Entity createJavaValueObjects(ResultSet resultSet) {
+
+		Entity entity = null;
+		Map<String, BiboDocument> biboDocumentURLToVO = new HashMap<String, BiboDocument>();
+		Map<String, SubEntity> subentityURLToVO = new HashMap<String, SubEntity>();
+
+		while (resultSet.hasNext()) {
+
+			QuerySolution solution = resultSet.nextSolution();
+
+			if (entity == null) {
+				entity = new Entity(solution.get(ENTITY_URL).toString(),
+						solution.get(ENTITY_LABEL).toString());
+			}
+
+			RDFNode documentNode = solution.get(QueryFieldLabels.DOCUMENT_URL);
+			BiboDocument biboDocument;
+
+			if (biboDocumentURLToVO.containsKey(documentNode.toString())) {
+				biboDocument = biboDocumentURLToVO.get(documentNode.toString());
+
+			} else {
+
+				biboDocument = new BiboDocument(documentNode.toString());
+				biboDocumentURLToVO.put(documentNode.toString(), biboDocument);
+
+				RDFNode documentLabelNode = solution
+						.get(QueryFieldLabels.DOCUMENT_LABEL);
+				if (documentLabelNode != null) {
+					biboDocument.setDocumentLabel(documentLabelNode.toString());
+				}
+
+				RDFNode publicationYearNode = solution
+						.get(QueryFieldLabels.DOCUMENT_PUBLICATION_YEAR);
+				if (publicationYearNode != null) {
+					biboDocument.setPublicationYear(publicationYearNode
+							.toString());
+				}
+
+				RDFNode publicationYearMonthNode = solution
+						.get(QueryFieldLabels.DOCUMENT_PUBLICATION_YEAR_MONTH);
+				if (publicationYearMonthNode != null) {
+					biboDocument
+							.setPublicationYearMonth(publicationYearMonthNode
+									.toString());
+				}
+
+				RDFNode publicationDateNode = solution
+						.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
+				if (publicationDateNode != null) {
+					biboDocument.setPublicationDate(publicationDateNode
+							.toString());
+				}
+
+			}
+
+			RDFNode subEntityURLNode = solution.get(SUBENTITY_URL);
+			
+			if (subEntityURLNode != null) {
+				SubEntity subEntity;
+				if (subentityURLToVO.containsKey(subEntityURLNode.toString())) {
+					subEntity = subentityURLToVO.get(subEntityURLNode
+							.toString());
+				} else {
+					subEntity = new SubEntity(subEntityURLNode.toString());
+					subentityURLToVO
+							.put(subEntityURLNode.toString(), subEntity);
+				}
+
+				RDFNode subEntityLabelNode = solution.get(SUBENTITY_LABEL);
+				if (subEntityLabelNode != null) {
+					subEntity.setIndividualLabel(subEntityLabelNode.toString());
+				}
+				entity.addSubEntity(subEntity);
+				subEntity.addPublications(biboDocument);
+			}
+
+			entity.addPublications(biboDocument);
+		}
+
+		return entity;
+	}
+
+	private ResultSet executeQuery(String queryURI, DataSource dataSource) {
+
+		QueryExecution queryExecution = null;
+		try {
+			Query query = QueryFactory.create(
+					getSparqlQuery(queryURI, this.visMode), SYNTAX);
+			queryExecution = QueryExecutionFactory.create(query, dataSource);
+
+			if (query.isSelectType()) {
+				return queryExecution.execSelect();
+			}
+		} finally {
+			if (queryExecution != null) {
+				queryExecution.close();
+			}
+		}
+		return null;
+	}
+
+	private String getSparqlQuery(String queryURI, String visMode) {
+		String result = "";
+
+		if (visMode.equals("DEPARTMENT")) {
+			result = getSparqlQueryForDepartment(queryURI);
+			ENTITY_URL = QueryFieldLabels.DEPARTMENT_URL;
+			ENTITY_LABEL = QueryFieldLabels.DEPARTMENT_LABEL;
+			SUBENTITY_URL = QueryFieldLabels.PERSON_URL;
+			SUBENTITY_LABEL = QueryFieldLabels.PERSON_LABEL;
+		} else {
+			result = getSparqlQueryForOrganization(queryURI);
+			ENTITY_URL = QueryFieldLabels.ORGANIZATION_URL;
+			ENTITY_LABEL = QueryFieldLabels.ORGANIZATION_LABEL;
+			SUBENTITY_URL = QueryFieldLabels.SUBORGANIZATION_URL;
+			SUBENTITY_LABEL = QueryFieldLabels.SUBORGANIZATION_LABEL;
+		} 
+
+		return result;
+	}
+
+	private String getSparqlQueryForDepartment(String queryURI) {
+
+		String sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+				+ "SELECT (str(?DepartmentLabel) as ?departmentLabelLit) "
+				+ SPARQL_QUERY_COMMON_SELECT_CLAUSE + "		(str(<" + queryURI
+				+ ">) as ?" + QueryFieldLabels.DEPARTMENT_URL + ") "
+				+ "WHERE { " + "<" + queryURI + "> rdf:type core:Department ;"
+				+ " rdfs:label ?DepartmentLabel ;"
+				+ " core:organizationForPosition ?Position .  "
+				+ "	?Position rdf:type core:Position ;"
+				+ " core:positionForPerson ?Person .  "
+				+ "	?Person  core:authorInAuthorship ?Resource ;  "
+				+ " rdfs:label ?PersonLabel ; core:personInPosition ?SecondaryPosition .  "
+				+ " ?Resource core:linkedInformationResource ?Document ."
+				+ "	?SecondaryPosition rdfs:label ?SecondaryPositionLabel ."				
+				+ SPARQL_QUERY_COMMON_WHERE_CLAUSE + "}"
+				+ " ORDER BY ?DocumentLabel";
+		System.out.println("\nThe sparql query is :\n" + sparqlQuery);
+		return sparqlQuery;
+
+	}
+
+	private String getSparqlQueryForOrganization(String queryURI) {
+
+		String sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+				+ "SELECT (str(?organizationLabel) as ?organizationLabelLit) "
+				+ "	 	(str(?subOrganization) as ?subOrganizationLit) "
+				+ "		(str(?subOrganizationLabel) as ?subOrganizationLabelLit) "
+				+ SPARQL_QUERY_COMMON_SELECT_CLAUSE + "		(str(<" + queryURI
+				+ ">) as ?" + QueryFieldLabels.ORGANIZATION_URL + ") "
+				+ "WHERE { " + "<" + queryURI + "> rdf:type foaf:Organization ;"
+				+ " rdfs:label ?organizationLabel ;"
+				+ " core:hasSubOrganization ?subOrganization ."
+				+ " ?subOrganization rdfs:label ?subOrganizationLabel ;"
+				+ " core:organizationForPosition ?Position .  "
+				+ "	?Position rdf:type core:Position ;"
+				+ " core:positionForPerson ?Person .  "
+				+ "	?Person  core:authorInAuthorship ?Resource ;  "
+				+ " rdfs:label ?PersonLabel ; core:personInPosition ?SecondaryPosition .  "
+				+ " ?Resource core:linkedInformationResource ?Document ."
+				+ "	?SecondaryPosition rdfs:label ?SecondaryPositionLabel ."
+				+ SPARQL_QUERY_COMMON_WHERE_CLAUSE + "}"
+				+ " ORDER BY ?DocumentLabel";
+		System.out.println("\nThe sparql query is :\n" + sparqlQuery);
+		return sparqlQuery;
+
+	}
+	
+	public Entity getQueryResult() throws MalformedQueryParametersException {
+
+		if (StringUtils.isNotBlank(this.entityURI)) {
+
+			/*
+			 * To test for the validity of the URI submitted.
+			 */
+			IRIFactory iRIFactory = IRIFactory.jenaImplementation();
+			IRI iri = iRIFactory.create(this.entityURI);
+			if (iri.hasViolation(false)) {
+				String errorMsg = ((Violation) iri.violations(false).next())
+						.getShortMessage();
+				log.error("Entity Comparison vis Query " + errorMsg);
+				throw new MalformedQueryParametersException(
+						"URI provided for an entity is malformed.");
+			}
+
+		} else {
+			throw new MalformedQueryParametersException(
+					"URL parameter is either null or empty.");
+		}
+
+		ResultSet resultSet = executeQuery(this.entityURI, this.dataSource);
+
+		return createJavaValueObjects(resultSet);
+	}
+
+}

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

@@ -0,0 +1,304 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.HashSet;
+
+import javax.servlet.RequestDispatcher;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.commons.logging.Log;
+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.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;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.UtilityFunctions;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
+
+public class EntityPublicationCountRequestHandler implements
+		VisualizationRequestHandler {
+
+	/*
+	 * Vis container holds the "id" of the div on the final response html page
+	 * that the visualization actually appears on.
+	 */
+	public static String ENTITY_VIS_MODE;
+	public static String SUB_ENTITY_VIS_MODE;
+
+
+	@SuppressWarnings("null")
+	public void generateVisualization(VitroRequest vitroRequest,
+			HttpServletRequest request, HttpServletResponse response, Log log,
+			DataSource dataSource) {
+
+		String entityURI = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+
+		String renderMode = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.RENDER_MODE_KEY);
+
+		ENTITY_VIS_MODE = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
+
+		String visContainer = vitroRequest
+				.getParameter(VisualizationFrameworkConstants.VIS_CONTAINER_KEY);
+
+		System.out
+				.println("\nInside EntityPublicationCountRequestHandler! \n----------------------------------------- ");
+		System.out.println("\nEntity URI: " + entityURI + "\nRender Mode: "
+				+ renderMode + "\nVis Mode: " + ENTITY_VIS_MODE
+				+ "\nVis Containter: " + visContainer);
+
+		QueryRunner<Entity> queryManager = new EntityPublicationCountQueryRunner(
+				entityURI, dataSource, log, ENTITY_VIS_MODE);		
+
+		try {
+			Entity entity = queryManager.getQueryResult();
+
+			if (ENTITY_VIS_MODE.equals("DEPARTMENT")) {
+				
+				SUB_ENTITY_VIS_MODE = "PERSON";
+//				System.out
+//						.println("\n\nDocuments within the Entity\n---------------------------------------------");
+//				for (BiboDocument document : entity.getPublications()) {
+//					System.out.println(document.getDocumentLabel() + " > "
+//							+ document.getDocumentURL());
+//				}
+//
+//				System.out
+//						.println("\n\nSubEntities within the Entity\n---------------------------------------------");
+//
+//				for (SubEntity person : entity.getSubEntities()) {
+//					System.out.println(person.getIndividualLabel());
+//				}
+			}else if (ENTITY_VIS_MODE.equals("SCHOOL")) {
+				
+				SUB_ENTITY_VIS_MODE = "DEPARTMENT";
+//				System.out
+//						.println("\nDocuments within the Entity\n---------------------------------------------");
+//				for (BiboDocument document : entity.getPublications()) {
+//					System.out.println(document.getDocumentLabel() + " > "
+//							+ document.getDocumentURL());
+//				}
+//
+//				System.out
+//						.println("\n\nSubEntities within the Entity\n---------------------------------------------");
+//				for (SubEntity department : entity.getSubEntities()) {
+//					System.out.println(department.getIndividualLabel());
+//				}
+			}else {
+				SUB_ENTITY_VIS_MODE = "SCHOOL";
+//				System.out
+//						.println("\nDocuments within the Entity\n---------------------------------------------");
+//				for (BiboDocument document : entity.getPublications()) {
+//					System.out.println(document.getDocumentLabel() + " > "
+//							+ document.getDocumentURL());
+//				}
+//
+//				System.out
+//						.println("\n\nSubEntities within the Entity\n---------------------------------------------");
+//
+//				for (SubEntity school : entity.getSubEntities()) {
+//					System.out.println(school.getIndividualLabel());
+//
+//				}
+			}
+			
+			QueryRunner<Map<String, Set<String>>> queryManagerForsubOrganisationTypes = new EntitySubOrganizationTypesQueryRunner(
+					entityURI, dataSource, log, ENTITY_VIS_MODE);
+			
+			Map<String, Set<String>> subOrganizationTypesResult = queryManagerForsubOrganisationTypes.getQueryResult();
+			
+			System.out.println("Sub Organization Types With Their Labels \n------------------");
+			
+			for(String label: subOrganizationTypesResult.keySet()){
+				System.out.println("Label :"+ label);
+				for(String type : subOrganizationTypesResult.get(label)){
+					System.out.println("type: "+ type);
+				}
+				System.out.println();
+			}
+
+			RequestDispatcher requestDispatcher = null;
+			if (VisualizationFrameworkConstants.DATA_RENDER_MODE
+					.equalsIgnoreCase(renderMode)) {
+
+				prepareDataResponse(entity, entity.getSubEntities(),subOrganizationTypesResult, response);
+
+			} else if (VisualizationFrameworkConstants.STANDALONE_RENDER_MODE
+					.equalsIgnoreCase(renderMode)) {
+
+				prepareStandaloneResponse(request, response, vitroRequest,
+						entity, subOrganizationTypesResult);
+				requestDispatcher = request
+						.getRequestDispatcher(Controllers.BASIC_JSP);
+			}
+
+			try {
+				requestDispatcher.forward(request, response);
+			} catch (Exception e) {
+				log.error("EntityEditController could not forward to view.");
+				log.error(e.getMessage());
+				log.error(e.getStackTrace());
+			}
+			//
+		} catch (MalformedQueryParametersException e) {
+			try {
+				UtilityFunctions
+						.handleMalformedParameters(
+								e.getMessage(),
+								"Visualization Query Error - Individual Publication Count",
+								vitroRequest, request, response, log);
+			} catch (ServletException e1) {
+				log.error(e1.getStackTrace());
+			} catch (IOException e1) {
+				log.error(e1.getStackTrace());
+			}
+			return;
+		}
+	}
+
+	/**
+	 * Provides response when csv file containing the publication count over the
+	 * years is requested.
+	 * 
+	 * @param author
+	 * @param subentities
+	 * @param subOrganizationTypesResult 
+	 * @param yearToPublicationCount
+	 * @param response
+	 */
+	private void prepareDataResponse(Entity entity, Set<SubEntity> subentities,
+			Map<String, Set<String>> subOrganizationTypesResult, HttpServletResponse response) {
+
+		String entityLabel = entity.getEntityLabel();
+
+		String outputFileName = UtilityFunctions.slugify(entityLabel)
+				+ "_publications-per-year" + ".json";
+
+		response.setContentType("text/plain");
+		response.setHeader("Content-Disposition", "attachment;filename="
+				+ outputFileName);
+
+		try {
+
+			PrintWriter responseWriter = response.getWriter();
+
+			/*
+			 * We are side-effecting responseWriter since we are directly
+			 * manipulating the response object of the servlet.
+			 */
+			responseWriter.append(writePublicationsOverTimeJSON(subentities, subOrganizationTypesResult));
+
+			responseWriter.flush();
+			responseWriter.close();
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
+	/**
+	 * Provides response when an entire page dedicated to publication sparkline
+	 * is requested.
+	 * 
+	 * @param request
+	 * @param response
+	 * @param vreq
+	 * @param entity
+	 * @param subOrganizationTypesResult 
+	 */
+	private void prepareStandaloneResponse(HttpServletRequest request,
+			HttpServletResponse response, VitroRequest vreq, Entity entity, Map<String, Set<String>> subOrganizationTypesResult) {
+
+		Portal portal = vreq.getPortal();
+		String jsonContent = "";
+		/*
+		 * We are side-effecting responseWriter since we are directly
+		 * manipulating the response object of the servlet.
+		 */
+		jsonContent = writePublicationsOverTimeJSON(entity.getSubEntities(), subOrganizationTypesResult);
+
+		request.setAttribute("JsonContent", jsonContent);
+
+		request.setAttribute("bodyJsp",
+				"/templates/visualization/entity_comparison.jsp");
+		request.setAttribute("portalBean", portal);
+		request.setAttribute("title", "Entity Comparison visualization");
+		request.setAttribute("scripts",
+				"/templates/visualization/entity_comparison_inject_head.jsp");
+
+	}
+
+	/**
+	 * function to generate a json file for year <-> publication count mapping
+	 * @param subOrganizationTypesResult 
+	 * 
+	 * @param yearToPublicationCount
+	 * @param responseWriter
+	 * @param visMode
+	 */
+	private String writePublicationsOverTimeJSON(Set<SubEntity> subentities, Map<String, Set<String>> subOrganizationTypesResult) {
+//		System.out.println("\nsub entity vis mode ------>"
+//				+ SUB_ENTITY_VIS_MODE + "\n");
+		System.out.println("Creating JSONObject \n-----------------------");
+		Gson json = new Gson();
+		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
+
+		for (SubEntity subentity : subentities) {
+			JsonObject entityJson = new JsonObject(
+					subentity.getIndividualLabel());
+
+			List<List<Integer>> yearPubCount = new ArrayList<List<Integer>>();
+
+			for (Map.Entry<String, Integer> pubEntry : UtilityFunctions
+					.getYearToPublicationCount(subentity.getDocuments())
+					.entrySet()) {
+
+				List<Integer> currentPubYear = new ArrayList<Integer>();
+				if (pubEntry.getKey().equals(
+						VOConstants.DEFAULT_PUBLICATION_YEAR))
+					currentPubYear.add(-1);
+				else
+					currentPubYear.add(Integer.parseInt(pubEntry.getKey()));
+				currentPubYear.add(pubEntry.getValue());
+				yearPubCount.add(currentPubYear);
+			}
+
+			entityJson.setYearToPublicationCount(yearPubCount);
+			entityJson.getOrganizationType().addAll(subOrganizationTypesResult.get(entityJson.getLabel()));
+
+			entityJson.setEntityURI(subentity.getIndividualURI());
+			entityJson.setVisMode(SUB_ENTITY_VIS_MODE);
+			System.out.println("Adding object with uri: "
+					+ entityJson.getEntityURI() + " vismode: "
+					+ entityJson.getVisMode() + " label: "
+					+ entityJson.getLabel() + " type: "
+					+ entityJson.getOrganizationType().toString());
+			subEntitiesJson.add(entityJson);
+		}
+		
+	//	System.out.println("\nStopWords are "+ EntitySubOrganizationTypesQueryRunner.stopWords.toString() + "\n");
+		return json.toJson(subEntitiesJson);
+
+	}
+}

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

@@ -0,0 +1,216 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.entitycomparison;
+
+import java.util.HashMap;
+import java.util.Map;
+
+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.visutils.QueryRunner;
+
+import java.util.Set;
+import java.util.HashSet;
+
+public class EntitySubOrganizationTypesQueryRunner implements QueryRunner<Map<String, Set<String>>> {
+	
+	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
+
+	private String entityURI;
+	private DataSource dataSource;
+	private Log log;
+	private String visMode;
+	static String SUBORGANISATION_LABEL;
+	static String SUBORGANISATION_TYPE_LABEL;
+//	public static Map<String, Integer> subOrganizationTypesToCount = new HashMap<String, Integer>();
+//	public static Set<String> stopWords = new HashSet<String>();
+//	public static Set<String> subOrganizations = new HashSet<String>();
+//	public static Set<String> STOP_WORDS = new HashSet<String>() {
+//		{
+//			add("Person");
+//			add("Organization");
+//		}
+//	};
+	
+	private static final String SPARQL_QUERY_SELECT_CLAUSE = ""
+		+ "		(str(?organizationLabel) as ?"+QueryFieldLabels.ORGANIZATION_LABEL+") "
+		+ "		(str(?subOrganizationLabel) as ?"+QueryFieldLabels.SUBORGANIZATION_LABEL+") "
+		+ "		(str(?subOrganizationType) as ?"+QueryFieldLabels.SUBORGANIZATION_TYPE +")"
+		+ "		(str(?subOrganizationTypeLabel) as ?"+QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL+") ";
+
+	
+	public EntitySubOrganizationTypesQueryRunner(String entityURI,
+			DataSource dataSource, Log log, String visMode){
+		
+		this.entityURI = entityURI;
+		this.dataSource = dataSource;
+		this.log = log;
+		this.visMode = visMode;
+//		stopWords.clear();
+//		subOrganizations.clear();
+//		subOrganizationTypesToCount.clear();
+	}
+	
+	private ResultSet executeQuery(String queryURI, DataSource dataSource) {
+
+		QueryExecution queryExecution = null;
+		try {
+			Query query = QueryFactory.create(
+					getSparqlQuery(queryURI), SYNTAX);
+			queryExecution = QueryExecutionFactory.create(query, dataSource);
+
+			if (query.isSelectType()) {
+				return queryExecution.execSelect();
+			}
+		} finally {
+			if (queryExecution != null) {
+				queryExecution.close();
+			}
+		}
+		return null;
+	}
+	
+	private String getSparqlQuery(String queryURI) {
+		String sparqlQuery = "";
+		
+		if (!this.visMode.equals("DEPARTMENT")) {
+			
+			SUBORGANISATION_LABEL = QueryFieldLabels.SUBORGANIZATION_LABEL;
+			SUBORGANISATION_TYPE_LABEL = QueryFieldLabels.SUBORGANIZATION_TYPE_LABEL;
+			sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+					+ "SELECT "
+					+ SPARQL_QUERY_SELECT_CLAUSE
+					+ " WHERE { "
+					+ "<"
+					+ queryURI
+					+ "> rdf:type foaf:Organization ;"
+					+ " rdfs:label ?organizationLabel ;"
+					+ " core:hasSubOrganization ?subOrganization .  "
+					+ "	?subOrganization rdfs:label ?subOrganizationLabel ;"
+					+ " rdf:type ?subOrganizationType .  "
+					+ " ?subOrganizationType rdfs:label ?subOrganizationTypeLabel ."
+					+ "}";
+			System.out.println("\nThe sparql query is :\n" + sparqlQuery);
+		} else{
+			
+			SUBORGANISATION_LABEL = QueryFieldLabels.PERSON_LABEL;
+			SUBORGANISATION_TYPE_LABEL = QueryFieldLabels.PERSON_TYPE_LABEL;
+			sparqlQuery = QueryConstants.getSparqlPrefixQuery()
+						  + "SELECT "
+							+ "		(str(?departmentLabel) as ?"+QueryFieldLabels.DEPARTMENT_LABEL+") "
+							+ "		(str(?personLabel) as ?"+QueryFieldLabels.PERSON_LABEL+") "
+							+ "		(str(?personType) as ?"+QueryFieldLabels.PERSON_TYPE +")"
+							+ "		(str(?personTypeLabel) as ?"+QueryFieldLabels.PERSON_TYPE_LABEL+") "
+							+ " WHERE { "
+							+ "<"
+							+ queryURI
+							+ "> rdf:type core:Department ;"
+							+ " rdfs:label ?departmentLabel ;"
+							+ " core:organizationForPosition ?position .  "
+							+ " ?position rdf:type core:Position ; core:positionForPerson ?person . "
+							+ "	?person rdfs:label ?personLabel ;"
+							+ " rdf:type ?personType .  "
+							+ " ?personType rdfs:label ?personTypeLabel ."
+							+ "}";;
+		}
+		return sparqlQuery;
+
+	}
+	
+	private Map<String, Set<String>> createJavaValueObjects(ResultSet resultSet) {
+
+		Map<String, Set<String>> subOrganizationLabelToTypes = new HashMap<String, Set<String>>();
+		
+		while(resultSet.hasNext()){
+			
+			QuerySolution solution = resultSet.nextSolution();
+			
+			RDFNode subOrganizationLabel = solution.get(SUBORGANISATION_LABEL);
+			
+			if(subOrganizationLabelToTypes.containsKey(subOrganizationLabel.toString())){
+				RDFNode subOrganizationType = solution.get(SUBORGANISATION_TYPE_LABEL);
+				if(subOrganizationType != null){
+					subOrganizationLabelToTypes.get(subOrganizationLabel.toString()).add(subOrganizationType.toString());
+//					updateSubOrganizationTypesToCount(subOrganizationType.toString());
+//					subOrganizations.add(subOrganizationLabel.toString());
+				}
+			}else{
+				RDFNode subOrganizationType = solution.get(SUBORGANISATION_TYPE_LABEL);
+				if(subOrganizationType != null){
+					subOrganizationLabelToTypes.put(subOrganizationLabel.toString(), new HashSet<String>());
+					subOrganizationLabelToTypes.get(subOrganizationLabel.toString()).add(subOrganizationType.toString());
+//					updateSubOrganizationTypesToCount(subOrganizationType.toString());
+//					subOrganizations.add(subOrganizationLabel.toString());
+				}
+			}
+		}
+		
+//		collectStopWords();
+		
+		return subOrganizationLabelToTypes;
+	}
+
+	
+//	private void collectStopWords() {
+//		System.out.println("Inside collectStopWords \n-----------------------------\n");
+//		for(Map.Entry<String, Integer> typesCount : subOrganizationTypesToCount.entrySet()){
+//			System.out.println(typesCount.getKey() + ": "+ typesCount.getValue());
+//			if(typesCount.getValue() >= subOrganizations.size()){
+//				stopWords.add(typesCount.getKey());
+//			}
+//		}
+//	}
+//
+//	private void updateSubOrganizationTypesToCount(String typeLabel) {
+//		int count = 0;
+//		if(subOrganizationTypesToCount.containsKey(typeLabel)){
+//			count = subOrganizationTypesToCount.get(typeLabel);
+//			subOrganizationTypesToCount.put(typeLabel, ++count);
+//		}else{
+//			subOrganizationTypesToCount.put(typeLabel, 1);
+//		}
+//	}
+
+	public Map<String, Set<String>> getQueryResult() throws MalformedQueryParametersException {
+
+		if (StringUtils.isNotBlank(this.entityURI)) {
+
+			/*
+			 * To test for the validity of the URI submitted.
+			 */
+			IRIFactory iRIFactory = IRIFactory.jenaImplementation();
+			IRI iri = iRIFactory.create(this.entityURI);
+			if (iri.hasViolation(false)) {
+				String errorMsg = ((Violation) iri.violations(false).next())
+						.getShortMessage();
+				log.error("Entity Comparison sub organization types query " + errorMsg);
+				throw new MalformedQueryParametersException(
+						"URI provided for an entity is malformed.");
+			}
+
+		} else {
+			throw new MalformedQueryParametersException(
+					"URL parameter is either null or empty.");
+		}
+
+		ResultSet resultSet = executeQuery(this.entityURI, this.dataSource);
+
+		return createJavaValueObjects(resultSet);
+	}
+
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/VisTestController.java

@@ -0,0 +1,53 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+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.FreemarkerHttpServlet;
+import edu.cornell.mannlib.vitro.webapp.controller.visualization.VisualizationFrameworkConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.visutils.VisualizationRequestHandler;
+
+
+public class VisTestController extends FreemarkerHttpServlet implements VisualizationRequestHandler {
+	
+	private static final String TEMPLATE_DEFAULT = "vistest.ftl";
+	
+	public void generateVisualization(VitroRequest vitroRequest, HttpServletRequest request, HttpServletResponse response, Log log, DataSource dataSource){
+			
+			return;
+		}
+
+	@Override
+	protected ResponseValues processRequest(VitroRequest vitroRequest){
+		
+		Portal portal = vitroRequest.getPortal();
+		Map<String, Object> body = new HashMap<String, Object>();
+		
+		String egoURI = vitroRequest.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
+		String renderMode = vitroRequest.getParameter(VisualizationFrameworkConstants.RENDER_MODE_KEY);
+		String visMode = vitroRequest.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY);
+		
+		List<String> parameters = new ArrayList<String>();
+		
+		parameters.add(egoURI);
+		parameters.add(renderMode);
+		parameters.add(visMode);
+		
+		body.put("parameters", parameters);
+		body.put("title", getTitle("VIVO Vis"));
+		
+		return new TemplateResponseValues(TEMPLATE_DEFAULT, body);
+	}
+	
+}

src/edu/cornell/mannlib/vitro/webapp/visualization/personlevel/PersonLevelRequestHandler.java

@@ -4,6 +4,8 @@ package edu.cornell.mannlib.vitro.webapp.visualization.personlevel;
 
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
@@ -333,6 +335,7 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
 					VitroRequest vitroRequest, 
 					HttpServletRequest request) {
 		
+		String completeURL = "";
         Portal portal = vitroRequest.getPortal();
         
         request.setAttribute("egoURIParam", egoURI);
@@ -348,6 +351,13 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
 		}
 		
         
+		try {
+			completeURL = getCompleteURL(request);
+		} catch (MalformedURLException e) {
+			e.printStackTrace();
+		}
+		
+        request.setAttribute("completeURL", completeURL);
 		request.setAttribute("egoPubSparklineVO", egoPubSparklineVO);
         request.setAttribute("uniqueCoauthorsSparklineVO", uniqueCoauthorsSparklineVO);
         
@@ -360,4 +370,16 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
         request.setAttribute("scripts", "/templates/visualization/person_level_inject_head.jsp");
         request.setAttribute("bodyJsp", "/templates/visualization/person_level.jsp");
 	}
+
+	private String getCompleteURL(HttpServletRequest request) throws MalformedURLException {
+		
+		String file = request.getRequestURI();
+		System.out.println("getRequestURI() = "+ file + "getQueryString() ="+request.getQueryString()+ "getScheme() = "+ request.getScheme());
+		System.out.println("getServerName() = "+ request.getServerName() + "getServerPort() ="+request.getServerPort());
+
+		URL reconstructedURL = new URL(request.getScheme(), request.getServerName(), request.getServerPort(), file);
+		
+		return reconstructedURL.toString();
+	}
+	
 }

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

@@ -0,0 +1,37 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.Set;
+import java.util.HashSet;
+
+public class Child extends Individual {
+
+	Set<BiboDocument> documents = new HashSet<BiboDocument>();
+	
+	public Child(String individualURI) {
+		super(individualURI);
+	}
+	
+	public Set<BiboDocument> getDocuments() {
+		return documents;
+	}
+
+	public Child(String individualURI, String individualLabel) {
+		super(individualURI, individualLabel);
+	}
+	
+	@Override
+	public boolean equals(Object other){
+		boolean result = false;
+		if (other instanceof Child){
+			Child person = (Child) other;
+			result = (this.getIndividualLabel().equals(person.getIndividualLabel())
+						&& this.getIndividualURI().equals(person.getIndividualURI()));
+		}
+		return result;
+	}
+	
+	@Override 
+	public int hashCode(){
+		return(41*(getIndividualLabel().hashCode() + 41*(getIndividualURI().hashCode())));
+	}
+}

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

@@ -0,0 +1,229 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+
+public class CoPIData {
+	
+	private Set<CoPINode> nodes;
+	private Set<CoPIEdge> edges;
+	private CoPINode egoNode;
+	private Set<Map<String, String>> NODE_SCHEMA;
+	private Set<Map<String, String>> EDGE_SCHEMA;
+		
+	public CoPIData(CoPINode egoNode, Set<CoPINode> nodes, Set<CoPIEdge> edges) {
+		this.egoNode = egoNode;
+		this.nodes = nodes;
+		this.edges = edges;
+	}
+	
+	public Set<CoPINode> getNodes() {
+		return nodes;
+	}
+
+	public Set<CoPIEdge> getEdges() {
+		return edges;
+	}	
+	
+	public CoPINode getEgoNode() {
+		return egoNode;
+	}
+	
+	/*
+	 * Node Schema for graphML
+	 * */
+	public Set<Map<String, String>> getNodeSchema() {
+		
+		if (NODE_SCHEMA == null) {
+			NODE_SCHEMA = initializeNodeSchema();			
+		}
+		
+		return NODE_SCHEMA;
+	}
+	
+	/*
+	 * Edge Schema for graphML
+	 * */
+	public Set<Map<String, String>> getEdgeSchema() {
+		
+		if (EDGE_SCHEMA == null) {
+			EDGE_SCHEMA = initializeEdgeSchema();			
+		}
+		
+		return EDGE_SCHEMA;
+	}
+
+	private Set<Map<String, String>> initializeEdgeSchema() {
+
+		Set<Map<String, String>> edgeSchema = new HashSet<Map<String, String>>();
+		
+			Map<String, String> schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "collaborator1");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "collaborator1");
+			schemaAttributes.put("attr.type", "string");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "collaborator2");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "collaborator2");
+			schemaAttributes.put("attr.type", "string");
+		
+		edgeSchema.add(schemaAttributes);		
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "number_of_coinvestigated_grants");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "number_of_coinvestigated_grants");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "earliest_collaboration");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "earliest_collaboration");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_earliest_collaboration");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "num_earliest_collaboration");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "latest_collaboration");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "latest_collaboration");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_latest_collaboration");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "num_latest_collaboration");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_unknown_collaboration");
+			schemaAttributes.put("for", "edge");
+			schemaAttributes.put("attr.name", "num_unknown_collaboration");
+			schemaAttributes.put("attr.type", "int");
+		
+		edgeSchema.add(schemaAttributes);
+		
+		return edgeSchema;
+	}
+	
+
+	private Set<Map<String, String>> initializeNodeSchema() {
+		
+		Set<Map<String, String>> nodeSchema = new HashSet<Map<String, String>>();
+
+			Map<String, String> schemaAttributes = new LinkedHashMap<String, String>();   
+			
+			schemaAttributes.put("id", "url");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "url");
+			schemaAttributes.put("attr.type", "string");
+		
+		nodeSchema.add(schemaAttributes);
+	
+			schemaAttributes = new LinkedHashMap<String, String>();
+		
+			schemaAttributes.put("id", "label");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "label");
+			schemaAttributes.put("attr.type", "string");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+		
+			schemaAttributes.put("id", "profile_url");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "profile_url");
+			schemaAttributes.put("attr.type", "string");
+		
+		nodeSchema.add(schemaAttributes);
+	
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "number_of_investigated_grants");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "number_of_investigated_grants");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "earliest_grant");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "earliest_grant");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_earliest_grant");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "num_earliest_grant");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "latest_grant");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "latest_grant");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_latest_grant");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "num_latest_grant");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+			schemaAttributes = new LinkedHashMap<String, String>();
+			
+			schemaAttributes.put("id", "num_unknown_grant");
+			schemaAttributes.put("for", "node");
+			schemaAttributes.put("attr.name", "num_unknown_grant");
+			schemaAttributes.put("attr.type", "int");
+		
+		nodeSchema.add(schemaAttributes);
+		
+		
+		return nodeSchema;
+	}
+	
+}

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

@@ -0,0 +1,143 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+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.visutils.UtilityFunctions;
+
+/**
+ * This stores edge information for Co-PI vis.
+ * @author bkoniden
+ *
+ */
+public class CoPIEdge {
+	
+	private int edgeID;
+	private Map<String, Integer> yearToGrantCount;
+	private Set<Grant> collaboratorGrants = new HashSet<Grant>();
+	private CoPINode sourceNode;
+	private CoPINode targetNode;
+	
+	public CoPIEdge(CoPINode sourceNode, CoPINode targetNode, Grant seedCoPIedGrant, UniqueIDGenerator uniqueIDGenerator){
+		edgeID = uniqueIDGenerator.getNextNumericID();
+		this.sourceNode = sourceNode;
+		this.targetNode = targetNode;
+		this.collaboratorGrants.add(seedCoPIedGrant);
+	}
+	
+	public int getEdgeID() {
+		return edgeID;
+	}
+	public Set<Grant> getCollaboratorGrants() {
+		return collaboratorGrants;
+	}
+	public CoPINode getSourceNode() {
+		return sourceNode;
+	}
+	public CoPINode getTargetNode() {
+		return targetNode;
+	}
+	
+	public int getNumberOfCoInvestigatedGrants(){
+		return collaboratorGrants.size();
+	}
+	
+	public void addCollaboratorGrant(Grant grant){
+		this.collaboratorGrants.add(grant);
+	}
+	
+	/*
+	 * getEarliest, Latest & Unknown Grant YearCount should only be used after 
+	 * the parsing of the entire sparql is done. Else it will give results based on
+	 * incomplete dataset.
+	 * */
+	@SuppressWarnings("serial")
+	public Map<String, Integer> getEarliestCollaborationYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(collaboratorGrants);
+		}
+		
+		/*
+		 * We do not want to consider the default grant year when we are checking 
+		 * for the min or max grant year. 
+		 * */
+		Set<String> yearsToBeConsidered = new HashSet<String>(yearToGrantCount.keySet());
+		yearsToBeConsidered.remove(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * There can be a case when the only publication the author has no attached year to it
+		 * so essentially an "Unknown". In that case Collections.max or min will throw an 
+		 * NoSuchElementException.
+		 * 
+		 * If there is no maximum year available then we should imply so by returning a "null".
+		 * */
+		if (yearsToBeConsidered.size() > 0) {
+			final String earliestYear = Collections.min(yearsToBeConsidered);
+			final Integer earliestYearGrantCount = yearToGrantCount.get(earliestYear);
+			
+			return new HashMap<String, Integer>() { {
+				put(earliestYear, earliestYearGrantCount);
+			} };
+		} else {
+			return null;
+		}
+	}
+	
+	
+	@SuppressWarnings("serial")
+	public Map<String, Integer> getLatestCollaborationYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(collaboratorGrants);
+		}
+		
+		/*
+		 * We do not want to consider the default grant year when we are checking 
+		 * for the min or max grant year. 
+		 * */
+		Set<String> yearsToBeConsidered = new HashSet<String>(yearToGrantCount.keySet());
+		yearsToBeConsidered.remove(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * There can be a case when the only grant the PI has no attached year to it
+		 * so essentially an "Unknown". In that case Collections.max or min will throw an 
+		 * NoSuchElementException.
+		 * 
+		 * If there is no maximum year available then we should imply so by returning a "null".
+		 * */
+		if (yearsToBeConsidered.size() > 0) {
+			final String latestYear = Collections.max(yearsToBeConsidered);
+			final Integer latestYearGrantCount = yearToGrantCount.get(latestYear);
+			
+			return new HashMap<String, Integer>() { {
+				put(latestYear, latestYearGrantCount);
+			} };
+		} else {
+			return null;
+		}
+		
+	}
+	
+	public Integer getUnknownCollaborationYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(collaboratorGrants);
+		}
+		
+		Integer unknownYearGrantCount = yearToGrantCount
+											.get(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * If there is no unknown year available then we should imply so by returning a "null".
+		 * */
+		if (unknownYearGrantCount != null) {
+			return unknownYearGrantCount;
+		} else {
+			return null;
+		}
+	}
+	
+}

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

@@ -0,0 +1,152 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+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.visutils.UtilityFunctions;
+
+/**
+ * CoPINode is the node in a CoPI vis.
+ * @author bkoniden
+ */
+public class CoPINode extends Individual {
+	
+	private int nodeID;
+	private Map<String, Integer> yearToGrantCount;
+	
+	private Set<Grant> pIGrants = new HashSet<Grant>();
+	
+	public CoPINode(String nodeURI, UniqueIDGenerator uniqueIDGenerator){
+		super(nodeURI);
+		nodeID = uniqueIDGenerator.getNextNumericID();
+	}
+	
+	public int getNodeID(){
+		return nodeID;
+	}
+	
+	public String getNodeURI(){
+		return this.getIndividualURI();
+	}
+	
+	public String getNodeName(){
+		return this.getIndividualLabel();
+	}
+	
+	public void setNodeName(String nodeName) {
+		this.setIndividualLabel(nodeName);
+	}
+	
+	public Set<Grant> getInvestigatedGrants(){
+		return pIGrants;
+	}
+	
+	public int getNumberOfInvestigatedGrants(){
+		return pIGrants.size();
+	}
+	
+	public void addGrant(Grant grant){
+		this.pIGrants.add(grant);
+	}
+	
+	public Map<String, Integer> getYearToGrantCount(){
+		if(yearToGrantCount == null){
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(pIGrants);
+		}
+		return yearToGrantCount;
+	}
+	
+	/*
+	 * getEarliest, Latest & Unknown Grant YearCount should only be used after 
+	 * the parsing of the entire sparql is done. Else it will give results based on
+	 * incomplete dataset.
+	 * */
+	@SuppressWarnings("serial")
+	public Map<String, Integer> getEarliestGrantYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(pIGrants);
+		}
+		
+		/*
+		 * We do not want to consider the default grant year when we are checking 
+		 * for the min or max grant year. 
+		 * */
+		Set<String> yearsToBeConsidered = new HashSet<String>(yearToGrantCount.keySet());
+		yearsToBeConsidered.remove(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * There can be a case when the only publication the author has no attached year to it
+		 * so essentially an "Unknown". In that case Collections.max or min will throw an 
+		 * NoSuchElementException.
+		 * 
+		 * If there is no maximum year available then we should imply so by returning a "null".
+		 * */
+		if (yearsToBeConsidered.size() > 0) {
+			final String earliestYear = Collections.min(yearsToBeConsidered);
+			final Integer earliestYearGrantCount = yearToGrantCount.get(earliestYear);
+			
+			return new HashMap<String, Integer>() { {
+				put(earliestYear, earliestYearGrantCount);
+			} };
+		} else {
+			return null;
+		}
+	}
+	
+	
+	@SuppressWarnings("serial")
+	public Map<String, Integer> getLatestGrantYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(pIGrants);
+		}
+		
+		/*
+		 * We do not want to consider the default grant year when we are checking 
+		 * for the min or max grant year. 
+		 * */
+		Set<String> yearsToBeConsidered = new HashSet<String>(yearToGrantCount.keySet());
+		yearsToBeConsidered.remove(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * There can be a case when the only grant the PI has no attached year to it
+		 * so essentially an "Unknown". In that case Collections.max or min will throw an 
+		 * NoSuchElementException.
+		 * 
+		 * If there is no maximum year available then we should imply so by returning a "null".
+		 * */
+		if (yearsToBeConsidered.size() > 0) {
+			final String latestYear = Collections.max(yearsToBeConsidered);
+			final Integer latestYearGrantCount = yearToGrantCount.get(latestYear);
+			
+			return new HashMap<String, Integer>() { {
+				put(latestYear, latestYearGrantCount);
+			} };
+		} else {
+			return null;
+		}
+		
+	}
+	
+	public Integer getUnknownGrantYearCount() {
+		if (yearToGrantCount == null) {
+			yearToGrantCount = UtilityFunctions.getYearToGrantCount(pIGrants);
+		}
+		
+		Integer unknownYearGrantCount = yearToGrantCount
+											.get(VOConstants.DEFAULT_PUBLICATION_YEAR);
+		
+		/*
+		 * If there is no unknown year available then we should imply so by returning a "null".
+		 * */
+		if (unknownYearGrantCount != null) {
+			return unknownYearGrantCount;
+		} else {
+			return null;
+		}
+	}
+}

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

@@ -0,0 +1,48 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.Set;
+
+public class Department extends Individual{
+	
+	Set<BiboDocument> publication;
+	Set<Person> person;
+	
+	public Department(String departmentURI, String departmentLabel){
+		super(departmentURI, departmentLabel);
+	}
+	
+	public void setDepartmentLabel(String departmentURI){
+		this.setIndividualLabel(departmentURI);
+	}
+	
+	public String getDepartmentURI(){
+		return this.getIndividualURI();
+	}
+	
+	public Set<BiboDocument> getPublication() {
+		return publication;
+	}
+
+	public String getDepartmentLabel(){
+		return this.getIndividualLabel();
+	}
+
+	public Set<Person> getPerson() {
+		return person;
+	}
+
+	public void addPublication(BiboDocument biboDocument) {
+		this.publication.add(biboDocument);
+	}
+
+	public void addPersons(Person person) {
+		this.person.add(person);
+		
+	}
+
+	public void addPerson(Person person) {
+		this.person.add(person);
+		
+	}
+
+}

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

@@ -0,0 +1,45 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.HashSet;
+import java.util.Set;
+import java.util.LinkedHashSet;
+
+public class Entity extends Individual{
+	
+	Set<BiboDocument> publications = new HashSet<BiboDocument>();
+	Set<SubEntity> children = new LinkedHashSet<SubEntity>();
+	
+	public Entity(String departmentURI, String departmentLabel){
+		super(departmentURI, departmentLabel);
+	}
+	
+	public void setDepartmentLabel(String departmentURI){
+		this.setIndividualLabel(departmentURI);
+	}
+	
+	public String getEntityURI(){
+		return this.getIndividualURI();
+	}
+	
+	public Set<BiboDocument> getPublications() {
+		return publications;
+	}
+
+	public String getEntityLabel(){
+		return this.getIndividualLabel();
+	}
+
+	public Set<SubEntity> getSubEntities() {
+		return children;
+	}
+
+	public void addPublications(BiboDocument biboDocument) {
+		this.publications.add(biboDocument);
+	}
+
+	public void addSubEntity(SubEntity subEntity) {
+		this.children.add(subEntity);
+		
+	}
+
+}

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

@@ -0,0 +1,127 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants;
+
+public class Grant extends Individual {
+	
+	private String grantStartYear;
+	private String grantStartYearMonth;
+	private String grantStartDate;
+	private String grantEndYear;
+	private String grantEndYearMonth;
+	private String grantEndDate;
+	
+	public Grant(String grantURL, String grantLabel){
+		super(grantURL, grantLabel);
+	}
+	
+	public Grant(String grantURL){
+		super(grantURL);
+	}
+	
+	public String getGrantURL() {
+		return this.getIndividualURI();
+	}
+	
+	public String getGrantLabel(){
+		return this.getIndividualLabel();
+	}
+	/**
+	 * This method will be called when there is no usable core:year value found
+	 * for the bibo:Document. It will first check & parse core:yearMonth failing
+	 * which it will try core:date
+	 * @return
+	 */
+	public String getParsedGrantStartYear() {
+		
+		/*
+		 * We are assuming that core:yearMonth has "YYYY-MM-DD" format. This is based 
+		 * off of http://www.w3.org/TR/xmlschema-2/#gYearMonth , which is what
+		 * core:yearMonth points to internally.
+		 * */
+		if (grantStartYearMonth != null 
+				&& grantStartYearMonth.length() >= VOConstants.NUM_CHARS_IN_YEAR_FORMAT
+				&& isValidPublicationYear(grantStartYearMonth.substring(
+													0,
+													VOConstants.NUM_CHARS_IN_YEAR_FORMAT))) {
+			
+			return grantStartYearMonth.substring(0, VOConstants.NUM_CHARS_IN_YEAR_FORMAT); 
+			
+		}
+		
+		if (grantStartDate != null 
+				&& grantStartDate.length() >= VOConstants.NUM_CHARS_IN_YEAR_FORMAT
+				&& isValidPublicationYear(grantStartDate
+												.substring(0,
+														   VOConstants.NUM_CHARS_IN_YEAR_FORMAT))) {
+			
+			return grantStartDate.substring(0, VOConstants.NUM_CHARS_IN_YEAR_FORMAT); 
+		}
+		
+		/*
+		 * If all else fails return default unknown year identifier
+		 * */
+		return VOConstants.DEFAULT_GRANT_YEAR;
+	}
+	
+	public String getGrantStartYear() {
+		return grantStartYear;
+	}
+
+	public void setGrantStartYear(String grantStartYear) {
+		this.grantStartYear = grantStartYear;
+	}
+
+	public String getGrantStartYearMonth() {
+		return grantStartYearMonth;
+	}
+
+	public void setGrantStartYearMonth(String grantStartYearMonth) {
+		this.grantStartYearMonth = grantStartYearMonth;
+	}
+
+	public String getGrantStartDate() {
+		return grantStartDate;
+	}
+
+	public void setGrantStartDate(String grantStartDate) {
+		this.grantStartDate = grantStartDate;
+	}
+
+	public String getGrantEndYear() {
+		return grantEndYear;
+	}
+
+	public void setGrantEndYear(String grantEndYear) {
+		this.grantEndYear = grantEndYear;
+	}
+
+	public String getGrantEndYearMonth() {
+		return grantEndYearMonth;
+	}
+
+	public void setGrantEndYearMonth(String grantEndYearMonth) {
+		this.grantEndYearMonth = grantEndYearMonth;
+	}
+
+	public String getGrantEndDate() {
+		return grantEndDate;
+	}
+
+	public void setGrantEndDate(String grantEndDate) {
+		this.grantEndDate = grantEndDate;
+	}
+
+	private boolean isValidPublicationYear(String testGrantYear) {
+		
+		if (testGrantYear.length() != 0 
+				&& testGrantYear.trim().length() == VOConstants.NUM_CHARS_IN_YEAR_FORMAT
+				&& testGrantYear.matches("\\d+")
+				&& Integer.parseInt(testGrantYear) >= VOConstants.MINIMUM_PUBLICATION_YEAR) {
+			return true;
+		}
+		
+		return false;
+	}
+
+}

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

@@ -0,0 +1,75 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * JsonObject is used for creating data in JSON format, 
+ * by just using the fields that are required to be included.
+ * @author bkoniden
+ *
+ */
+public class JsonObject {
+	
+	private String label;
+	private List<List<Integer>> data = new ArrayList<List<Integer>>();
+	private String entityURI;
+	private String visMode;
+	private List<String> organizationType = new ArrayList<String>();
+	private List<String> stopWords = new ArrayList<String>();
+	
+	public List<String> getStopWords() {
+		return stopWords;
+	}
+
+	public void setStopWords(List<String> stopWords) {
+		this.stopWords = stopWords;
+	}
+
+	public List<String> getOrganizationType() {
+		return organizationType;
+	}
+
+	public void setOrganizationType(List<String> organizationType) {
+		this.organizationType = organizationType;
+	}
+
+	public String getEntityURI() {
+		return entityURI;
+	}
+
+	public void setEntityURI(String entityURI) {
+		this.entityURI = entityURI;
+	}
+
+	public String getVisMode() {
+		return visMode;
+	}
+
+	public void setVisMode(String visMode) {
+		this.visMode = visMode;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public void setLabel(String label) {
+		this.label = label;
+	}
+
+	public List<List<Integer>> getYearToPublicationCount() {
+		return data;
+	}
+
+
+	
+	public JsonObject(String label){
+		this.label = label;
+	}
+	
+	public void setYearToPublicationCount(List<List<Integer>> yearToPublicationCount){
+		this.data = yearToPublicationCount;
+	}
+	
+}

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

@@ -0,0 +1,22 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.Set;
+import java.util.HashSet;
+
+public class Person extends Individual {
+
+	Set<BiboDocument> documents = new HashSet<BiboDocument>();
+	
+	public Person(String individualURI) {
+		super(individualURI);
+	}
+	
+	public Set<BiboDocument> getDocuments() {
+		return documents;
+	}
+
+	public Person(String individualURI, String individualLabel) {
+		super(individualURI, individualLabel);
+	}
+
+}

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

@@ -0,0 +1,54 @@
+package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.HashSet;
+
+public class SubEntity extends Individual {
+
+	Set<BiboDocument> publications = new HashSet<BiboDocument>();
+	Map<String, Map<String, String>> personToPositionAndStartYear = new HashMap<String, Map<String, String>>(); 
+	
+	public SubEntity(String individualURI) {
+		super(individualURI);
+	}
+	
+	
+	public Map<String, Map<String, String>> getPersonToPositionAndStartYear() {
+		return personToPositionAndStartYear;
+	}
+
+	public void setPersonToPositionAndStartYear(
+			Map<String, Map<String, String>> personToPositionAndStartYear) {
+		this.personToPositionAndStartYear = personToPositionAndStartYear;
+	}
+
+	public Set<BiboDocument> getDocuments() {
+		return publications;
+	}
+
+	public SubEntity(String individualURI, String individualLabel) {
+		super(individualURI, individualLabel);
+	}
+	
+	@Override
+	public boolean equals(Object other){
+		boolean result = false;
+		if (other instanceof SubEntity){
+			SubEntity person = (SubEntity) other;
+			result = (this.getIndividualLabel().equals(person.getIndividualLabel())
+						&& this.getIndividualURI().equals(person.getIndividualURI()));
+		}
+		return result;
+	}
+	
+	@Override 
+	public int hashCode(){
+		return(41*(getIndividualLabel().hashCode() + 41*(getIndividualURI().hashCode())));
+	}
+
+	public void addPublications(BiboDocument biboDocument) {
+		this.publications.add(biboDocument);
+	}
+}

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

@@ -1,42 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
-
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * 
- * This is equivalent for vivo:CollegeOrSchoolWithinUniversity object type.
- * 
- * @author cdtank
- */
-public class VivoCollegeOrSchool extends Individual {
-
-	private Set<VivoDepartmentOrDivision> departments = new HashSet<VivoDepartmentOrDivision>();
-
-	public VivoCollegeOrSchool(String collegeURI) {
-		super(collegeURI);
-	}
-	
-	public Set<VivoDepartmentOrDivision> getDepartments() {
-		return departments;
-	}
-
-	public void addDepartment(VivoDepartmentOrDivision department) {
-		this.departments.add(department);
-	}
-
-	public String getCollegeURI() {
-		return this.getIndividualURI();
-	}
-
-	public String getCollegeLabel() {
-		return this.getIndividualLabel();
-	}
-
-	public void setCollegeLabel(String collegeLabel) {
-		this.setIndividualLabel(collegeLabel);
-	}
-
-}

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

@@ -1,43 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
-
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * 
- * This is equivalent for vivo:AcademicDepartmentOrDivision object type.
- * 
- * @author cdtank
- */
-public class VivoDepartmentOrDivision extends Individual {
-
-	private Set<VivoCollegeOrSchool> parentColleges = new HashSet<VivoCollegeOrSchool>();
-
-	public VivoDepartmentOrDivision(String departmentURI, VivoCollegeOrSchool parentCollege) {
-		super(departmentURI);
-		addParentCollege(parentCollege);
-	}
-
-	public Set<VivoCollegeOrSchool> getParentCollege() {
-		return parentColleges;
-	}
-
-	public void addParentCollege(VivoCollegeOrSchool parentCollege) {
-		this.parentColleges.add(parentCollege);
-	}
-
-	public String getDepartmentURI() {
-		return this.getIndividualURI();
-	}
-
-	public String getDepartmentLabel() {
-		return this.getIndividualLabel();
-	}
-
-	public void setDepartmentLabel(String departmentLabel) {
-		this.setIndividualLabel(departmentLabel);
-	}
-
-}

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

@@ -1,63 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import edu.cornell.mannlib.vitro.webapp.visualization.constants.VOConstants.EmployeeType;
-
-/**
- * 
- * This is the equivalent for vivo's Employee object type.
- * 
- * @author cdtank
- */
-public class VivoEmployee extends Individual {
-
-	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) {
-		super(employeeURL);
-		addParentDepartment(parentDepartment);
-	}
-
-	public String getEmployeeURI() {
-		return this.getIndividualURI();
-	}
-
-	public String getEmployeeName() {
-		return this.getIndividualLabel();
-	}
-	
-	public EmployeeType getEmployeeType() {
-		return employeeType;
-	}
-
-	public void setEmployeeType(EmployeeType employeeType) {
-		this.employeeType = employeeType;
-	}
-
-	public Set<VivoDepartmentOrDivision> getParentDepartments() {
-		return parentDepartments;
-	}
-
-	public void addParentDepartment(VivoDepartmentOrDivision parentDepartment) {
-		this.parentDepartments.add(parentDepartment);
-	}
-
-	public Set<BiboDocument> getAuthorDocuments() {
-		return authorDocuments;
-	}
-
-	public void addAuthorDocument(BiboDocument authorDocument) {
-		this.authorDocuments.add(authorDocument);
-	}
-
-
-}

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

@@ -22,8 +22,12 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.VisConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.BiboDocument;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoAuthorshipData;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPIData;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Grant;
+import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.CoPINode;
 import edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.Node;
 
+
 public class UtilityFunctions {
 	
 	public static Map<String, Integer> getYearToPublicationCount(
@@ -154,4 +158,86 @@ public class UtilityFunctions {
 		}
 	}
 
+	public static Map<String, Set<CoPINode>> getGrantYearToCoPI(
+			CoPIData pINodesAndEdges) {
+		
+
+		Map<String, Set<CoPINode>> yearToCoPIs = new TreeMap<String, Set<CoPINode>>();
+		
+		CoPINode egoNode = pINodesAndEdges.getEgoNode();
+		
+		for (CoPINode currNode : pINodesAndEdges.getNodes()) {
+					
+				/*
+				 * We have already printed the Ego Node info.
+				 * */
+				if (currNode != egoNode) {
+					
+					for (String year : currNode.getYearToGrantCount().keySet()) {
+						
+						Set<CoPINode> coPINodes;
+						
+						if (yearToCoPIs.containsKey(year)) {
+							
+							coPINodes = yearToCoPIs.get(year);
+							coPINodes.add(currNode);
+							
+						} else {
+							
+							coPINodes = new HashSet<CoPINode>();
+							coPINodes.add(currNode);
+							yearToCoPIs.put(year, coPINodes);
+						}
+						
+					}
+					
+				}
+		}
+		return yearToCoPIs;
+
+	}
+
+	public static Map<String, Integer> getYearToGrantCount(Set<Grant> pIGrants) {
+		
+    	/*
+    	 * Create a map from the year to number of grants. Use the Grant's
+    	 * parsedGrantStartYear to populate the data.
+    	 * */
+    	Map<String, Integer> yearToGrantCount = new TreeMap<String, Integer>();
+
+    	for (Grant curr : pIGrants) {
+
+    		/*
+    		 * Increment the count because there is an entry already available for
+    		 * that particular year.
+    		 * 
+    		 * I am pushing the logic to check for validity of year in "getGrantYear" itself
+    		 * because,
+    		 * 	1. We will be using getGra... multiple times & this will save us duplication of code
+    		 * 	2. If we change the logic of validity of a grant year we would not have to make 
+    		 * changes all throughout the codebase.
+    		 * 	3. We are asking for a grant year & we should get a proper one or NOT at all.
+    		 * */
+    		String grantYear;
+    		if (curr.getGrantStartYear() != null) { 
+    			grantYear = curr.getGrantStartYear();
+    		} else {
+    			grantYear = curr.getParsedGrantStartYear();
+    		}
+    		
+			if (yearToGrantCount.containsKey(grantYear)) {
+    			yearToGrantCount.put(grantYear,
+    									   yearToGrantCount
+    									   		.get(grantYear) + 1);
+
+    		} else {
+    			yearToGrantCount.put(grantYear, 1);
+    		}
+
+    	}
+
+		return yearToGrantCount;
+		
+	}
+
 }

startTomcat

@@ -0,0 +1,2 @@
+sudo /usr/local/tomcat/bin/startup.sh
+tail -f /usr/local/tomcat/logs/catalina.out

themes/vivo-basic/css/visualization/entityComparison/layout.css

@@ -0,0 +1,194 @@
+@CHARSET "UTF-8";
+
+head,#body {
+	font: 0.9em Helvetica;
+}
+
+#body {
+	background-color: #fff;
+	min-height: 800px;
+	width: 100%;
+	min-width: 900px;
+	margin: auto;
+}
+
+h1 {
+	padding-top: 10px;
+	font-size: 1.5em;
+	margin-left: 5%;
+}
+
+h2 {
+	font-size: 1.1em;
+	margin-top: 10px;
+	margin-bottom: 5px;
+}
+
+h3 {
+	font-size: 1.01em;
+}
+
+button{
+	margin-top: 10px;
+	float:right;
+}
+
+form{
+	margin-top:70px;
+	margin-bottom: -50px;	
+}
+#yaxislabel{
+	font-size: 12px;
+	float:right;
+	background-color: white;
+	color:black;
+	display: block;
+
+}
+
+#xaxislabel{
+	font-size: 12px;
+	margin-top: -5px;
+	margin-left: 250px;
+}
+
+#functions{
+	margin-top: 20px;
+	margin-bottom: -40px;	
+}
+#bar {
+	height: 20px;
+	float: left;
+	background-color: #fff;
+	width: 250px;
+	margin-left: 10px;
+}
+#checkbox{
+	float:left;	
+}
+#label {
+	float: left;
+	font-size: 12px;
+	width: 160px;
+	text-align: right;
+}
+
+#searchresult {
+	margin-top: 50px;
+}
+
+#bottom,#graphContainer {
+	float: right;
+}
+
+#graphContainer {
+	margin-bottom: 15px;
+}
+
+#leftblock {
+	float: left;
+	margin-left: 5%;
+	width: 36%;
+}
+
+#text {
+	margin-left: 5px;
+}
+#searchresult a {
+	text-decoration: none;
+	color: black;
+	font-family: Helvetica;
+	font-size: 13px;
+	font-weight: normal;
+}
+
+#label a,#text {
+	text-decoration: none;
+	color: black;
+	font-family: Helvetica;
+	font-size: 1em;
+}
+
+#rightblock {
+	float:right;
+	margin-right:5%;
+	width:54%;
+}
+
+#counter,#total {
+	color: red;
+}
+
+#heading {
+	margin-top: 10px;
+}
+
+li{
+	padding: 5px;
+	list-style: none;
+}
+
+#paginatedTable{
+	margin-top: 10px;
+}
+
+.sDomSearchBar{
+	margin-bottom: 10px;
+	margin-left: 41%;
+}
+
+.datatablerowhighlight {
+	background-color: #ECFFB3 !important;
+}
+
+.metallic{
+	background-color: #212D34;
+	color: white;
+	margin-left: 20px;
+}
+
+#leftUpper{
+	border: 1px #3D454E solid;
+	border-top: 10px #3D454E solid;
+	background-color: #D9D9D9;
+}
+
+#leftLower{
+	border: 1px #3D454E solid;
+	border-top: 10px #3D454E solid;
+}
+
+#navcontainer{
+	background: none repeat scroll 0 0 #3D454E;
+	height: 1%;
+	padding: 8px 22em 8px 20px;
+	position: relative;
+}
+
+#navlist li
+{
+	display: inline;
+	list-style-type: none;
+	padding: 20px;
+	
+}
+
+#navlist li a{
+	color: white;
+	text-decoration: none;
+}
+		
+#bottomButtons{
+	width: 50%;
+	float:right;
+	margin-right: 5%;
+}
+
+#stopwordsdiv{
+	margin-top: 10px;
+}
+
+p.displayCounter{
+	padding-bottom: 4px;
+	border-bottom: 1px solid gray;
+}