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.

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
 	 */

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 {

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) {

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);
 	}
 

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) 

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();

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;
+		}
+		
+	}
+
+}

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;
+		}
+	}
+}

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);
+	}
+	
 }

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;
 

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());
+		}
+	}
+}

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());
 				}
 			}