From ae432163967564e017479579a17d51f974e8381a Mon Sep 17 00:00:00 2001
From: cdtank <cdtank"@43c2fc9b-1942-4403-87b2-35b4218f7473>
Date: Tue, 12 Apr 2011 17:49:53 +0000
Subject: [PATCH] 1. In Temporal vis developed vis drilling up from lower
 level. (see http://issues.library.cornell.edu/browse/NIHVIVO-1800) 2.
 Refactored client-side code for temporal vis.

---
 .../visualization/entitycomparison/layout.css |   5 +
 .../entitycomparison/gui-event-manager.js     | 122 +++++++++++-------
 .../js/visualization/entitycomparison/util.js |  15 +--
 .../entitycomparison/entityComparisonBody.ftl |   5 +
 .../entityComparisonOnGrantsStandalone.ftl    |   4 +-
 ...tityComparisonOnPublicationsStandalone.ftl |   4 +-
 .../entityComparisonSetup.ftl                 |  13 +-
 .../constants/QueryFieldLabels.java           |   6 +
 .../EntityComparisonUtilityFunctions.java     |  14 +-
 ...poralGrantVisualizationRequestHandler.java |  20 ++-
 ...ublicationVisualizationRequestHandler.java |  17 ++-
 .../ModelConstructorUtilities.java            |   2 +
 ...OrganizationModelWithTypesConstructor.java |   2 -
 ...SubOrganizationWithinModelConstructor.java | 111 ++++++++++++++++
 .../SubOrganizationWithinModelFactory.java    |  42 ++++++
 .../freemarker/valueobjects/Entity.java       |  15 ++-
 .../freemarker/valueobjects/JsonObject.java   |   2 -
 .../valueobjects/SubjectEntityJSON.java       |  47 +++++++
 .../visutils/SelectOnModelUtilities.java      |  81 +++++++++++-
 19 files changed, 449 insertions(+), 78 deletions(-)
 create mode 100644 src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/SubOrganizationWithinModelConstructor.java
 create mode 100644 src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/factory/SubOrganizationWithinModelFactory.java
 create mode 100644 src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/SubjectEntityJSON.java

diff --git a/productMods/css/visualization/entitycomparison/layout.css b/productMods/css/visualization/entitycomparison/layout.css
index 381646e6..ae99242c 100644
--- a/productMods/css/visualization/entitycomparison/layout.css
+++ b/productMods/css/visualization/entitycomparison/layout.css
@@ -13,6 +13,10 @@
     display: none;
 }
 
+#subject-parent-entity {
+	display: none;
+}
+
 #error-container {
     display: none;
 }
@@ -49,6 +53,7 @@ img.bar-count-icon {
 
 .legend-bar {
 	margin-bottom: 3px;
+	cursor:default;
 }
 
 .unknown-legend-bar {
diff --git a/productMods/js/visualization/entitycomparison/gui-event-manager.js b/productMods/js/visualization/entitycomparison/gui-event-manager.js
index c9f0a8b8..d46ef482 100644
--- a/productMods/js/visualization/entitycomparison/gui-event-manager.js
+++ b/productMods/js/visualization/entitycomparison/gui-event-manager.js
@@ -24,7 +24,7 @@ $(document).ready(function() {
      * update the status accordingly.   
      */         
 
-    $("select.comparisonValues").change(function(){
+    $("select.comparisonValues").change(function() {
 
         var selectedValue = $("select.comparisonValues option:selected").val();
         
@@ -36,6 +36,8 @@ $(document).ready(function() {
             	
             	currentParameter = parameter.name;
             	selectedDataURL = parameter.dataLink;
+            	temporalGraphCommonURL = parameter.viewBaseLink;
+            	csvDownloadURL = parameter.csvLink;
             }
         	
         });
@@ -175,47 +177,79 @@ function performEntityCheckboxClickedRedrawActions() {
 
 }
 
-/* 
- *  function to populate the labelToEntityRecord object with the
- *  values from the json file and
- *  dynamically generate checkboxes
- */
-function loadData(jsonData, dataTableParams) {
-
-    $.each(jsonData, function (index, val) {
-        setOfLabels.push(val.label);
-        URIToEntityRecord[val.entityURI] = val;
-        if (val.lastCachedAtDateTime) {
-        	lastCachedAtDateTimes[lastCachedAtDateTimes.length] = val.lastCachedAtDateTime;
-        }
-    });
-    
-    prepareTableForDataTablePagination(jsonData, dataTableParams);
-    setEntityLevel(getEntityVisMode(jsonData));
-    
-    entityCheckboxOperatedOnEventListener();
-    
-}
-
-/* 
- *  function to populate the labelToEntityRecord object with the
- *  values from the json file and
- *  dynamically generate checkboxes
- */
-function reloadData(preselectedEntityURIs, jsonData) {
-
-    $.each(jsonData, function (index, val) {
-        setOfLabels.push(val.label);
-        URIToEntityRecord[val.entityURI] = val;
-        if (val.lastCachedAtDateTime) {
-        	lastCachedAtDateTimes[lastCachedAtDateTimes.length] = val.lastCachedAtDateTime;
-        }
-    });
-    
-    reloadDataTablePagination(preselectedEntityURIs, jsonData);
-    setEntityLevel(getEntityVisMode(jsonData));
-}
-
+var processJSONData = {
+		
+	isParentEntityAvailable: false,	
+		
+	setupGlobals: function(jsonContent) {
+		$.each(jsonContent, function (index, val) {
+	        
+	    	/*
+	    	 * We are checking if the "label" attribute is present, because that pertains to 
+	    	 * data used for linegraph visualization.
+	    	 * */
+	    	if (val.label) {
+	    		
+		    	setOfLabels.push(val.label);
+		        URIToEntityRecord[val.entityURI] = val;
+		        if (val.lastCachedAtDateTime) {
+		        	lastCachedAtDateTimes[lastCachedAtDateTimes.length] = val.lastCachedAtDateTime;
+		        }
+	    	} else if (val.subjectEntityLabel) {
+	
+	    		/*
+	    		 * This is to set the drill-up visualization URLs.
+	    		 * */
+	    		$.each(val.parentURIToLabel, function(index, value) {
+	    			
+	    			$("a#subject-parent-entity-temporal-url").attr("href", getTemporalVisURL(index));
+	    			
+	    			$("a#subject-parent-entity-profile-url").attr("href", getVIVOURL(index));
+	    			$("a#subject-parent-entity-profile-url").text(value);
+	    			
+	    			processJSONData.isParentEntityAvailable = true;
+	    		});
+	    	}
+	    });
+		
+		if (processJSONData.isParentEntityAvailable) {
+			$("#subject-parent-entity").show();
+		} else {
+			$("#subject-parent-entity").hide();
+		}
+	},	
+	
+	/* 
+	 *  function to populate the labelToEntityRecord object with the
+	 *  values from the json file and
+	 *  dynamically generate checkboxes
+	 */
+	loadData: function(jsonData, dataTableParams) {
+	    
+		processJSONData.setupGlobals(jsonData);
+		
+	    prepareTableForDataTablePagination(jsonData, dataTableParams);
+	    setEntityLevel(getEntityVisMode(jsonData));
+	    
+	    entityCheckboxOperatedOnEventListener();
+	},
+	
+	/* 
+	 *  function to populate the labelToEntityRecord object with the
+	 *  values from the json file and
+	 *  dynamically generate checkboxes
+	 */
+	reloadData: function(preselectedEntityURIs, jsonData) {
+	    
+		processJSONData.setupGlobals(jsonData);
+		
+	    reloadDataTablePagination(preselectedEntityURIs, jsonData);
+	    setEntityLevel(getEntityVisMode(jsonData));
+	    
+	    $("a#csv").attr("href", csvDownloadURL);
+	}
+		
+};
 
 function entityCheckboxOperatedOnEventListener() {
 	
@@ -394,7 +428,7 @@ temporalGraphProcessor = {
         /*
          * render the temporal graph per the sent content. 
          * */
-        loadData(jsonData, this.dataTableParams);
+        processJSONData.loadData(jsonData, this.dataTableParams);
         
         lastCachedAtDateTimes.sort(lastCachedAtDateTimeParser.ascendingDateSorter);
         
@@ -438,7 +472,7 @@ temporalGraphProcessor = {
         /*
          * render the temporal graph per the sent content. 
          * */
-        reloadData(currentSelectedEntityURIs, jsonData);
+        processJSONData.reloadData(currentSelectedEntityURIs, jsonData);
         
         lastCachedAtDateTimes.sort(lastCachedAtDateTimeParser.ascendingDateSorter);
 
diff --git a/productMods/js/visualization/entitycomparison/util.js b/productMods/js/visualization/entitycomparison/util.js
index aafe6c20..0a7b5cc5 100644
--- a/productMods/js/visualization/entitycomparison/util.js
+++ b/productMods/js/visualization/entitycomparison/util.js
@@ -640,7 +640,7 @@ function createLegendRow(entity, bottomDiv) {
      * there is no drill-down possible, so don't diaply the temporal graph icon.
      * */
     if (entity.visMode !== "PERSON") {
-    	labelDiv.append('<a class="temporal-vis-url" href="' + getTemporalVisURL(entity) + '"><img src = "' + temporalGraphSmallIcon + '"/></a>');	
+    	labelDiv.append('<a class="temporal-vis-url" href="' + getTemporalVisURL(entity.entityURI) + '"><img src = "' + temporalGraphSmallIcon + '"/></a>');	
     }
     
 
@@ -649,7 +649,7 @@ function createLegendRow(entity, bottomDiv) {
     checkbox.attr('checked', true);
     checkbox.attr('id', 'checkbox');
     checkbox.attr('class', 'easyDeselectCheckbox');
-    checkbox.attr('value', entity.label);
+    checkbox.attr('value', entity.entityURI);
 
     var hiddenLabel = $('<label>');
     hiddenLabel.attr('type', 'hidden');
@@ -720,7 +720,7 @@ function renderBarAndLabel(entity, divBar, divLabel, spanElement) {
     var entityLabelForLegend = divLabel.find(".entity-label-url");
     entityLabelForLegend.html(entity.label);
     entityLabelForLegend.ellipsis();
-    entityLabelForLegend.wrap("<a class='entity-url' title='" + entity.label + "' href='" + getVIVOURL(entity) + "'></a>");
+    entityLabelForLegend.wrap("<a class='entity-url' title='" + entity.label + "' href='" + getVIVOURL(entity.entityURI) + "'></a>");
 
     var countExplanation = 'VIVO knows the ' + COMPARISON_PARAMETERS_INFO[currentParameter].name + ' year for ' 
     							+ combinedCount.knownYearCount + ' out of ' 
@@ -731,16 +731,15 @@ function renderBarAndLabel(entity, divBar, divLabel, spanElement) {
     spanElement.text(sum).css("font-size", "0.8em").css("color", "#595B5B");
 }
 
-function getVIVOURL(entity){
+function getVIVOURL(entityURI){
 	
-	var result  = subOrganizationVivoProfileURL + "uri="+entity.entityURI;
+	return subOrganizationVivoProfileURL + "uri=" + entityURI;
 	
-	return result;
 }
 
-function getTemporalVisURL(entity) {
+function getTemporalVisURL(entityURI) {
 	
-	return subOrganizationTemporalGraphURL + "&uri=" + entity.entityURI ;
+	return temporalGraphCommonURL + "&uri=" + entityURI ;
 }
 
 function getVIVOProfileURL(given_uri) {
diff --git a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl
index bbe48759..3d8211e0 100644
--- a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl
+++ b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonBody.ftl
@@ -2,6 +2,11 @@
 
 <div id="body">
 
+		<div id="subject-parent-entity">
+			<a id="subject-parent-entity-profile-url" href="#"></a>&nbsp;
+			<a id="subject-parent-entity-temporal-url" href="#"><img src="${temporalGraphSmallIcon}" width="15px" height="15px"/></a>
+		</div>
+		
         <h2 id="header-entity-label"><span><a id="organizationMoniker" href="${organizationVivoProfileURL}">${organizationLabel}</a>&nbsp;
         <img id="incomplete-data-disclaimer" class="infoIcon" src="${urls.images}/iconInfo.png" alt="information icon" title="This information is based solely on ${currentParameterObject.value} which have been loaded into the VIVO system" /></span></h2>
         
diff --git a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl
index dd88f20d..4a50cc05 100644
--- a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl
+++ b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl
@@ -23,7 +23,7 @@ var currentParameter = "${currentParameter}";
 /*
 This is used in util.js to print grant temporal graph links for all sub-organizations.
 */    
-var subOrganizationTemporalGraphURL = "${subOrganizationGrantTemporalGraphCommonURL}";
+var temporalGraphCommonURL = subOrganizationGrantTemporalGraphCommonURL;
 
 var temporalGraphDataURL = '${temporalGraphDataURL}';
 
@@ -50,7 +50,7 @@ $(document).ready(function () {
 <#include "entityComparisonBody.ftl">
 
 <#-- 
-Right now we include the error message by default becuae currently I could not devise any more smarted solution. By default
+Right now we include the error message by default because currently I could not devise any more smarted solution. By default
 the CSS of the #error-container is display:none; so it will be hidden unless explicitly commanded to be shown which we do in 
 via JavaScript.
 -->
diff --git a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl
index abd59d55..da47d15b 100644
--- a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl
+++ b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl
@@ -23,7 +23,7 @@ var currentParameter = "${currentParameter}";
 /*
 This is used in util.js to print grant temporal graph links for all sub-organizations.
 */    
-var subOrganizationTemporalGraphURL = "${subOrganizationPublicationTemporalGraphCommonURL}";
+var temporalGraphCommonURL = subOrganizationPublicationTemporalGraphCommonURL;
 
 var temporalGraphDataURL = '${temporalGraphDataURL}';
 
@@ -50,7 +50,7 @@ $(document).ready(function () {
 <#include "entityComparisonBody.ftl">
 
 <#-- 
-Right now we include the error message by default becuae currently I could not devise any more smarted solution. By default
+Right now we include the error message by default because currently I could not devise any more smarted solution. By default
 the CSS of the #error-container is display:none; so it will be hidden unless explicitly commanded to be shown which we do in 
 via JavaScript.
 -->
diff --git a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl
index c8a46376..cb858d88 100644
--- a/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl
+++ b/productMods/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl
@@ -26,14 +26,18 @@
 									"pluralName": "publications",
                                     "dropDownText": "by Publications", 
                                     "viewLink": "${organizationPublicationTemporalGraphURL}",
-                                    "dataLink": "${organizationPublicationTemporalGraphDataURL}", 
+                                    "viewBaseLink": "${subOrganizationPublicationTemporalGraphCommonURL}",
+                                    "dataLink": "${organizationPublicationTemporalGraphDataURL}",
+                                    "csvLink": "${temporalGraphDownloadCSVCommonURL}&vis=entity_comparison", 
                                     "value": "Publications" }>
                                     
 <#assign grantParameter = {   "name": "grant",
 							  "pluralName": "grants",
                               "dropDownText": "by Grants", 
-                              "viewLink": "${organizationGrantTemporalGraphURL}", 
+                              "viewLink": "${organizationGrantTemporalGraphURL}",
+                              "viewBaseLink": "${subOrganizationGrantTemporalGraphCommonURL}", 
                               "dataLink": "${organizationGrantTemporalGraphDataURL}",
+                              "csvLink": "${temporalGraphDownloadCSVCommonURL}&vis=entity_grant_count",
                               "value": "Grants" }>
                               
 <#assign parameterOptions = [publicationParameter, grantParameter]>
@@ -86,6 +90,9 @@ var contextPath = "${urls.base}";
 var temporalGraphSmallIcon = "${temporalGraphSmallIcon}";
 var subOrganizationVivoProfileURL = "${subOrganizationVivoProfileURL}";
 
+var subOrganizationGrantTemporalGraphCommonURL = "${subOrganizationGrantTemporalGraphCommonURL}";
+var subOrganizationPublicationTemporalGraphCommonURL = "${subOrganizationPublicationTemporalGraphCommonURL}";
+
 var jsonString = '${jsonContent!}';
 var organizationLabel = '${organizationLabel}';
 var organizationVIVOProfileURL = "${organizationVivoProfileURL}";
@@ -97,7 +104,7 @@ var entityCheckboxSelectorDOMClass = "${entityCheckboxSelectorDOMClass}";
 
 var isDataRequestSentViaAJAX = false;
 
-var temporalGraphProcessor;
+var csvDownloadURL, temporalGraphProcessor;
 
 /*
 This has to be declared before making a call to GUI event manager JS.
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryFieldLabels.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryFieldLabels.java
index ef1e37fb..9b98a9f0 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryFieldLabels.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/constants/QueryFieldLabels.java
@@ -93,6 +93,12 @@ public class QueryFieldLabels {
 	public static final String SUBORGANIZATION_URL = "subOrganizationLit";
 	public static final String SUBORGANIZATION_LABEL = "subOrganizationLabelLit";
 	
+	/*
+	 * Parent Organization related field labels
+	 */
+	public static final String PARENT_ORGANIZATION_URL = "parentOrganizationLit";
+	public static final String PARENT_ORGANIZATION_LABEL = "parentOrganizationLabelLit";
+	
 	/*
 	 * Sub Organization related field labels
 	 */
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityComparisonUtilityFunctions.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityComparisonUtilityFunctions.java
index 44edd3cf..129d6a90 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityComparisonUtilityFunctions.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/EntityComparisonUtilityFunctions.java
@@ -172,11 +172,23 @@ public class EntityComparisonUtilityFunctions {
 		
 		if (StringUtils.equalsIgnoreCase(entityA.getEntityURI(), entityB.getEntityURI())) {
 			
-			Entity mergedEntity = new Entity(entityA.getEntityURI(), entityA.getEntityLabel());
+			Entity mergedEntity = new Entity(entityA.getEntityURI());
+			
+			if (StringUtils.isNotBlank(entityA.getEntityLabel())) {
+				
+				mergedEntity.setEntityLabel(entityA.getEntityLabel());
+				
+			} else if (StringUtils.isNotBlank(entityB.getEntityLabel())) {
+				
+				mergedEntity.setEntityLabel(entityB.getEntityLabel());
+			}
 			
 			mergedEntity.addSubEntitities(entityA.getSubEntities());
 			mergedEntity.addSubEntitities(entityB.getSubEntities());
 			
+			mergedEntity.addParents(entityA.getParents());
+			mergedEntity.addParents(entityB.getParents());
+			
 			return mergedEntity;
 			
 		} else {
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalGrantVisualizationRequestHandler.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalGrantVisualizationRequestHandler.java
index 5835a854..baf2fce5 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalGrantVisualizationRequestHandler.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalGrantVisualizationRequestHandler.java
@@ -31,6 +31,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Co
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.JsonObject;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubjectEntityJSON;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.SelectOnModelUtilities;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
@@ -221,7 +222,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 					 "application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
 					 writeGrantsOverTimeJSON(vitroRequest, 
-							 				 entity.getSubEntities()));
+							 				 entity));
 		return fileData;
 	}
 
@@ -285,12 +286,12 @@ public class TemporalGrantVisualizationRequestHandler implements
 	 * @param subOrganizationTypesResult  
 	 */
 	private String writeGrantsOverTimeJSON(VitroRequest vreq, 
-										   Set<SubEntity> subentities) {
+										   Entity subjectEntity) {
 
 		Gson json = new Gson();
-		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
+		Set jsonifiedResponse = new HashSet();
 
-		for (SubEntity subentity : subentities) {
+		for (SubEntity subentity : subjectEntity.getSubEntities()) {
 			JsonObject entityJson = new JsonObject(
 					subentity.getIndividualLabel());
 
@@ -326,10 +327,17 @@ public class TemporalGrantVisualizationRequestHandler implements
 				entityJson.setVisMode("ORGANIZATION");
 			}		
 			
-			subEntitiesJson.add(entityJson);
+			jsonifiedResponse.add(entityJson);
 		}
 		
-		return json.toJson(subEntitiesJson);
+		
+		SubjectEntityJSON subjectEntityJSON = new SubjectEntityJSON(subjectEntity.getEntityLabel(),
+																	subjectEntity.getEntityURI(),
+																	subjectEntity.getParents());
+		
+		jsonifiedResponse.add(subjectEntityJSON);
+		
+		return json.toJson(jsonifiedResponse);
 	}
 
 	private String getEntityGrantsPerYearCSVContent(Entity entity) {
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalPublicationVisualizationRequestHandler.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalPublicationVisualizationRequestHandler.java
index 8179fd46..9fd0f5e5 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalPublicationVisualizationRequestHandler.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/entitycomparison/cached/TemporalPublicationVisualizationRequestHandler.java
@@ -29,6 +29,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Ac
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.JsonObject;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubjectEntityJSON;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.SelectOnModelUtilities;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.UtilityFunctions;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.VisualizationRequestHandler;
@@ -88,7 +89,6 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		
 		Entity organizationWithAssociatedPeople = SelectOnModelUtilities
 				.getSubjectOrganizationAssociatedPeople(dataset, subjectEntityURI);
-
 		
 		if (organizationWithAssociatedPeople.getSubEntities() !=  null) {
 			
@@ -247,7 +247,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 					 "application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY,
 					 writePublicationsOverTimeJSON(vitroRequest, 
-							 					   entity.getSubEntities()));
+							 					   entity));
 		return fileData;
 	}
 	
@@ -277,12 +277,12 @@ public class TemporalPublicationVisualizationRequestHandler implements
 	 * @param subOrganizationTypesResult  
 	 */
 	private String writePublicationsOverTimeJSON(VitroRequest vreq, 
-												 Set<SubEntity> subentities) {
+												 Entity subjectEntity) {
 
 		Gson json = new Gson();
-		Set<JsonObject> subEntitiesJson = new HashSet<JsonObject>();
+		Set subEntitiesJson = new HashSet();
 
-		for (SubEntity subentity : subentities) {
+		for (SubEntity subentity : subjectEntity.getSubEntities()) {
 			
 			JsonObject entityJson = new JsonObject(
 					subentity.getIndividualLabel());
@@ -320,6 +320,13 @@ public class TemporalPublicationVisualizationRequestHandler implements
 			
 			subEntitiesJson.add(entityJson);
 		}
+		
+		SubjectEntityJSON subjectEntityJSON = new SubjectEntityJSON(subjectEntity.getEntityLabel(),
+																	subjectEntity.getEntityURI(),
+																	subjectEntity.getParents());
+		
+		subEntitiesJson.add(subjectEntityJSON);
+		
 		return json.toJson(subEntitiesJson);
 	}
 
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/ModelConstructorUtilities.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/ModelConstructorUtilities.java
index c169ad3a..39669842 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/ModelConstructorUtilities.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/ModelConstructorUtilities.java
@@ -17,6 +17,7 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructo
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.factory.PeopleToPublicationsFactory;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.factory.PersonToGrantsFactory;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.factory.PersonToPublicationsFactory;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.factory.SubOrganizationWithinModelFactory;
 
 public class ModelConstructorUtilities {
 	
@@ -30,6 +31,7 @@ public class ModelConstructorUtilities {
 		put(OrganizationToGrantsForSubOrganizationsModelConstructor.MODEL_TYPE, new OrganizationToGrantsForSubOrganizationsFactory());
 		put(OrganizationAssociatedPeopleModelWithTypesConstructor.MODEL_TYPE, new OrganizationAssociatedPeopleModelWithTypesFactory());
 		put(OrganizationModelWithTypesConstructor.MODEL_TYPE, new OrganizationModelWithTypesFactory());
+		put(SubOrganizationWithinModelConstructor.MODEL_TYPE, new SubOrganizationWithinModelFactory());
 	}};
 	
 	public static Model getOrConstructModel(String uri, String modelType, Dataset dataset) 
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/OrganizationModelWithTypesConstructor.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/OrganizationModelWithTypesConstructor.java
index d310bb7e..df624e90 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/OrganizationModelWithTypesConstructor.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/OrganizationModelWithTypesConstructor.java
@@ -70,8 +70,6 @@ public class OrganizationModelWithTypesConstructor implements ModelConstructor {
 	
 	private Model executeQuery(String constructQuery) {
 		
-		System.out.println("in constructed model fior organization");
-		
 		Model constructedModel = ModelFactory.createDefaultModel();
 
 		before = System.currentTimeMillis();
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/SubOrganizationWithinModelConstructor.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/SubOrganizationWithinModelConstructor.java
new file mode 100644
index 00000000..e4905874
--- /dev/null
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/SubOrganizationWithinModelConstructor.java
@@ -0,0 +1,111 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.query.Dataset;
+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.Syntax;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.ModelConstructor;
+
+public class SubOrganizationWithinModelConstructor implements ModelConstructor {
+	
+	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
+	
+	public static final String MODEL_TYPE = "SUBORGANIZATION_WITHIN_HIERARCHY_MODEL"; 
+	
+	private Dataset dataset;
+	
+	private Model constructedModel;
+	
+	private Log log = LogFactory.getLog(SubOrganizationWithinModelConstructor.class.getName());
+	
+	private long before, after;
+	
+	public SubOrganizationWithinModelConstructor(Dataset dataset) {
+		this.dataset = dataset;
+	}
+	
+	/**
+	 * This constructor is present so that we can abstract out the model construction process.
+	 * @param uri
+	 * @param dataset
+	 */
+	public SubOrganizationWithinModelConstructor(String uri, Dataset dataset) {
+		this.dataset = dataset;
+	}
+	
+	private String constructAllSubOrganizationsWithinQuery() {
+		return ""
+		+ " CONSTRUCT { "
+		+ "     ?organization rdf:type foaf:Organization . "
+		+ "     ?organization rdfs:label ?organizationLabel . "
+		+ "     ?organization core:subOrganizationWithin ?parentOrganization . "
+		+ "     ?parentOrganization rdfs:label ?parentOrganizationLabel .     "
+		+ " }  "
+		+ " WHERE { "
+		+ "     ?organization rdf:type foaf:Organization . "
+		+ "     ?organization rdfs:label ?organizationLabel . "
+		+ "      "
+		+ "     OPTIONAL { "
+		+ "         ?organization core:subOrganizationWithin ?parentOrganization . "
+		+ "         ?parentOrganization rdfs:label ?parentOrganizationLabel . "
+		+ "     }     "
+		+ " } ";
+		
+	}
+	
+	private Model executeQuery(String constructQuery) {
+		
+		Model constructedModel = ModelFactory.createDefaultModel();
+
+		before = System.currentTimeMillis();
+		log.debug("CONSTRUCT query string : " + constructQuery);
+
+		Query query = null;
+
+		try {
+			query = QueryFactory.create(QueryConstants.getSparqlPrefixQuery()
+					+ constructQuery, SYNTAX);
+		} catch (Throwable th) {
+			log.error("Could not create CONSTRUCT SPARQL query for query "
+					+ "string. " + th.getMessage());
+			log.error(constructQuery);
+		}
+
+		QueryExecution qe = QueryExecutionFactory.create(query, dataset);
+
+		try {
+			qe.execConstruct(constructedModel);
+		} finally {
+			qe.close();
+		}
+
+		after = System.currentTimeMillis();
+		log.debug("Time taken to execute the CONSTRUCT queries is in milliseconds: "
+				+ (after - before));
+
+		return constructedModel;
+	}	
+	
+	public Model getConstructedModel() throws MalformedQueryParametersException {
+	
+		if (constructedModel != null && !constructedModel.isEmpty()) {
+			return constructedModel;
+		} else {
+			constructedModel = executeQuery(constructAllSubOrganizationsWithinQuery());
+			return constructedModel;
+		}
+		
+	}
+
+}
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/factory/SubOrganizationWithinModelFactory.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/factory/SubOrganizationWithinModelFactory.java
new file mode 100644
index 00000000..e1e07979
--- /dev/null
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/modelconstructor/factory/SubOrganizationWithinModelFactory.java
@@ -0,0 +1,42 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.factory;
+
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.rdf.model.Model;
+
+import edu.cornell.mannlib.vitro.webapp.visualization.exceptions.MalformedQueryParametersException;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.SubOrganizationWithinModelConstructor;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.ConstructedModelTracker;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.visutils.ModelConstructor;
+
+public class SubOrganizationWithinModelFactory implements ModelFactoryInterface {
+
+	@Override
+	public Model getOrCreateModel(String uri, Dataset dataset) throws MalformedQueryParametersException {
+		
+		Model candidateModel = ConstructedModelTracker.getModel(
+					ConstructedModelTracker
+					.generateModelIdentifier(
+							null, 
+							SubOrganizationWithinModelConstructor.MODEL_TYPE));
+
+		if (candidateModel != null) {
+		
+			return candidateModel;
+		
+		} else {
+		
+			ModelConstructor model = new SubOrganizationWithinModelConstructor(dataset);
+			Model constructedModel = model.getConstructedModel();
+			
+			ConstructedModelTracker.trackModel(
+					ConstructedModelTracker
+						.generateModelIdentifier(
+								null, 
+								SubOrganizationWithinModelConstructor.MODEL_TYPE),
+								constructedModel);
+			
+			return constructedModel;
+		}
+	}
+}
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/Entity.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/Entity.java
index 812574b2..08ce73d9 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/Entity.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/Entity.java
@@ -11,6 +11,7 @@ import java.util.Set;
  */
 public class Entity extends Individual {
 	
+	private Set<Individual> parents = new LinkedHashSet<Individual>();
 	private Set<SubEntity> children = new LinkedHashSet<SubEntity>();
 	
 	public Entity(String entityURI, String entityLabel) {
@@ -28,10 +29,18 @@ public class Entity extends Individual {
 	public String getEntityLabel() {
 		return this.getIndividualLabel();
 	}
+	
+	public void setEntityLabel(String label) {
+		this.setIndividualLabel(label);
+	}
 
 	public Set<SubEntity> getSubEntities() {
 		return children;
 	}
+	
+	public Set<Individual> getParents() {
+		return parents;
+	}
 
 	public void addSubEntity(SubEntity subEntity) {
 		this.children.add(subEntity);
@@ -40,5 +49,9 @@ public class Entity extends Individual {
 	public void addSubEntitities(Collection<SubEntity> subEntities) {
 		this.children.addAll(subEntities);
 	}
-
+	
+	public void addParents(Collection<Individual> parents) {
+		this.parents.addAll(parents);
+	}
+	
 }
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/JsonObject.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/JsonObject.java
index c6e0f922..44c58118 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/JsonObject.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/JsonObject.java
@@ -2,8 +2,6 @@
 package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects;
 
 import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/SubjectEntityJSON.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/SubjectEntityJSON.java
new file mode 100644
index 00000000..58f94a52
--- /dev/null
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/valueobjects/SubjectEntityJSON.java
@@ -0,0 +1,47 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+public class SubjectEntityJSON {
+	
+	private String subjectEntityLabel;
+	private String subjectEntityURI;
+	private Map<String, String> parentURIToLabel = new HashMap<String, String>();
+	
+	public SubjectEntityJSON(String subjectEntityURI, String label,
+			Set<Individual> parentOrganizations) {
+		this.subjectEntityURI = subjectEntityURI;
+		this.subjectEntityLabel = label;
+		
+		this.setParentURIToLabel(parentOrganizations);
+	}
+
+	public String getSubjectEntityURI() {
+		return subjectEntityURI;
+	}
+
+	public void setSubjectEntityURI(String subjectEntityURI) {
+		this.subjectEntityURI = subjectEntityURI;
+	}
+
+	public String getSubjectEntityLabel() {
+		return subjectEntityLabel;
+	}
+
+	public void setSubjectEntityLabel(String label) {
+		this.subjectEntityLabel = label;
+	}
+
+	public Map<String, String> getParentURIToLabel() {
+		return parentURIToLabel;
+	}
+
+	public void setParentURIToLabel(Set<Individual> parentOrganizations) {
+		for (Individual parentOrganization : parentOrganizations) {
+			this.parentURIToLabel.put(parentOrganization.getIndividualURI(), parentOrganization.getIndividualLabel());
+		}
+	}
+}
diff --git a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/visutils/SelectOnModelUtilities.java b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/visutils/SelectOnModelUtilities.java
index 63e46cf7..c86954c6 100644
--- a/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/visutils/SelectOnModelUtilities.java
+++ b/src/edu/cornell/mannlib/vitro/webapp/visualization/freemarker/visutils/SelectOnModelUtilities.java
@@ -25,8 +25,10 @@ import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructo
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.OrganizationToPublicationsForSubOrganizationsModelConstructor;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PeopleToGrantsModelConstructor;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.PeopleToPublicationsModelConstructor;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.modelconstructor.SubOrganizationWithinModelConstructor;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Activity;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Entity;
+import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.Individual;
 import edu.cornell.mannlib.vitro.webapp.visualization.freemarker.valueobjects.SubEntity;
 
 public class SelectOnModelUtilities {
@@ -59,8 +61,82 @@ public class SelectOnModelUtilities {
 									"",
 									organizationModel);
 		
-		return getEntityWithSubOrganizations(subjectEntityURI, 
+		Entity entityWithSubOrganizations = getEntityWithSubOrganizations(subjectEntityURI, 
 												   subOrganizationsWithTypesQuery.getQueryResult());
+		
+		Entity entityWithParentOrganizations = getAllParentOrganizations(dataset, subjectEntityURI);
+		
+		entityWithSubOrganizations.addParents(entityWithParentOrganizations.getParents());
+		
+		return entityWithSubOrganizations;
+	}
+	
+	public static Entity getAllParentOrganizations(Dataset dataset,
+			String subjectEntityURI) throws MalformedQueryParametersException {
+		Model organizationModel = ModelConstructorUtilities
+										.getOrConstructModel(
+												null, 
+												SubOrganizationWithinModelConstructor.MODEL_TYPE, 
+												dataset);
+		
+		Map<String, String> fieldLabelToOutputFieldLabel = new HashMap<String, String>();
+		fieldLabelToOutputFieldLabel.put("organizationLabel", QueryFieldLabels.ORGANIZATION_LABEL);
+		fieldLabelToOutputFieldLabel.put("parentOrganization", QueryFieldLabels.PARENT_ORGANIZATION_URL);
+		fieldLabelToOutputFieldLabel.put("parentOrganizationLabel", QueryFieldLabels.PARENT_ORGANIZATION_LABEL);
+		
+		String whereClause = ""
+			+ " <" + subjectEntityURI + "> rdfs:label ?organizationLabel . "
+			+ " <" + subjectEntityURI + "> core:subOrganizationWithin ?parentOrganization . "
+			+ " ?parentOrganization rdfs:label ?parentOrganizationLabel . ";
+		
+		QueryRunner<ResultSet> parentOrganizationsQuery = 
+			new GenericQueryRunnerOnModel(fieldLabelToOutputFieldLabel,
+									"",
+									whereClause,
+									"",
+									organizationModel);
+		
+		return getEntityWithParentOrganizations(subjectEntityURI, 
+												   parentOrganizationsQuery.getQueryResult());
+	}
+	
+	private static Entity getEntityWithParentOrganizations(String subjectEntityURI, ResultSet queryResult) {
+
+		Entity entity = new Entity(subjectEntityURI);
+		Map<String, Individual> parentOrganizationURIToVO = new HashMap<String, Individual>();
+		
+		while (queryResult.hasNext()) {
+			
+			QuerySolution solution = queryResult.nextSolution();
+			
+			if (StringUtils.isEmpty(entity.getEntityLabel())) {
+				
+				RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
+				if (organizationLabelNode != null) {
+					entity.setIndividualLabel(organizationLabelNode.toString());
+				}
+			}
+			
+			RDFNode parentOrganizationNode = solution.get(QueryFieldLabels.PARENT_ORGANIZATION_URL);
+			
+			Individual parent;
+			
+			if (!parentOrganizationURIToVO.containsKey(parentOrganizationNode.toString())) {
+				
+				parent = new Individual(parentOrganizationNode.toString());
+				
+				parentOrganizationURIToVO.put(parentOrganizationNode.toString(), parent);
+				
+				RDFNode parentOrganizationLabelNode = solution.get(QueryFieldLabels.PARENT_ORGANIZATION_LABEL);
+				if (parentOrganizationLabelNode != null) {
+					parent.setIndividualLabel(parentOrganizationLabelNode.toString());
+				}
+			}
+		}
+		
+		entity.addParents(parentOrganizationURIToVO.values());
+		
+		return entity;
 	}
 	
 	private static Entity getEntityWithSubOrganizations(String subjectEntityURI, ResultSet queryResult) {
@@ -76,7 +152,8 @@ public class SelectOnModelUtilities {
 				
 				RDFNode organizationLabelNode = solution.get(QueryFieldLabels.ORGANIZATION_LABEL);
 				if (organizationLabelNode != null) {
-					entity.setIndividualLabel(organizationLabelNode.toString());
+					
+					entity.setEntityLabel(organizationLabelNode.toString());
 				}
 			}