Visualisation caching improvements

productMods/css/visualization/visualization.css

@@ -23,9 +23,6 @@ span.incomplete-data-holder,
     margin-top: 1.6em;
     font-size: 1em;
 }
-#incomplete-data-small {
-    margin-top: 1.6em;
-}
 .collaboratorship-icon {
     float: left;
     padding-right: 8px;
@@ -90,6 +87,21 @@ span.incomplete-data-holder,
 .infoIcon {
     padding-right:30px;
 }
+.cache-info-small {
+    padding: 5px;
+    font-size: .8em;
+    color: #444;
+    border: dotted 1px #eee;
+    background-color: #ffb;
+    float: right;
+}
+.cache-info-vis {
+    padding: 5px;
+    color: #444;
+    border: dotted 1px #eee;
+    background-color: #ffb;
+    float: right;
+}
 
 /* ---------------------------*/
 /* Visualization Tools -------*/

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnGrantsStandalone.ftl

@@ -46,6 +46,9 @@ $(document).ready(function () {
 <#assign currentParameterObject = grantParameter>
 
 <div id="temporal-graph-response">
+<#if (builtFromCacheTime??) >
+    <div class="cache-info-small">${i18n().using_cache_time} ${builtFromCacheTime?time} (${builtFromCacheTime?date?string("MMM dd yyyy")})</div>
+</#if>
 
 <#include "entityComparisonBody.ftl">
 

productMods/templates/freemarker/visualization/entitycomparison/entityComparisonOnPublicationsStandalone.ftl

@@ -46,6 +46,9 @@ $(document).ready(function () {
 <#assign currentParameterObject = publicationParameter>
 
 <div id="temporal-graph-response">
+<#if (builtFromCacheTime??) >
+    <div class="cache-info-small">${i18n().using_cache_time} ${builtFromCacheTime?time} (${builtFromCacheTime?date?string("MMM dd yyyy")})</div>
+</#if>
 
 <#include "entityComparisonBody.ftl">
 

productMods/templates/freemarker/visualization/mapOfScience/mapOfScienceStandalone.ftl

@@ -7,6 +7,9 @@ corresponding changes in the included Templates. -->
 <#include "mapOfScienceSetup.ftl">
 
 <div id="map-of-science-response">
+	<#if (builtFromCacheTime??) >
+		<div class="cache-info-vis">${i18n().using_cache_time} ${builtFromCacheTime?time} (${builtFromCacheTime?date?string("MMM dd yyyy")})</div>
+	</#if>
 
 <#--
 <div id="subject-parent-entity" class="hide-dom-on-init">
@@ -84,3 +87,5 @@ corresponding changes in the included Templates. -->
 </div>
 
 ${headScripts.add('<script type="text/javascript" src="${urls.base}/js/jquery_plugins/qtip/jquery.qtip-1.0.0-rc3.min.js"></script>')}
+
+${stylesheets.add('<link rel="stylesheet" type="text/css" href="${urls.base}/css/visualization/visualization.css" />')}

productMods/templates/freemarker/visualization/personlevel/coAuthorPersonLevel.ftl

@@ -151,6 +151,9 @@ $(document).ready(function(){
         </div>
     </div>
 
+    <#if (builtFromCacheTime??) >
+        <div class="cache-info-small">${i18n().using_cache_time} ${builtFromCacheTime?time} (${builtFromCacheTime?date?string("MMM dd yyyy")})</div>
+    </#if>
     <div style="clear:both;"></div>
     
     <#if (numOfAuthors?? && numOfAuthors > 0) >

productMods/templates/freemarker/visualization/personlevel/coAuthorPersonLevelD3.ftl

@@ -266,6 +266,9 @@ $(document).ready(function(){
         </div>
     </div>
     
+    <#if (builtFromCacheTime??) >
+        <div class="cache-info-small">${i18n().using_cache_time} ${builtFromCacheTime?time} (${builtFromCacheTime?date?string("MMM dd yyyy")})</div>
+    </#if>
     <div style="clear:both;"></div>
 
     <#if (numOfAuthors?? && numOfAuthors > 0) >

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

@@ -2,7 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.coauthorship;
 
-import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Date;
@@ -15,14 +14,12 @@ import java.util.concurrent.ConcurrentHashMap;
 
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
-import net.sf.jga.algorithms.Unique;
+import edu.cornell.mannlib.vitro.webapp.visualization.utilities.VisualizationCaches;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.jena.iri.IRI;
@@ -34,7 +31,6 @@ import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 
 import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CoAuthorshipData;
-import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaborationData;
 import edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils.CollaboratorComparator;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
 import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryFieldLabels;
@@ -58,6 +54,8 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 
 	protected static final Syntax SYNTAX = Syntax.syntaxARQ;
 
+	private static boolean preferCaches = false;
+
 	private String egoURI;
 
 	private RDFService rdfService;
@@ -90,34 +88,46 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 
 		@Override
 		protected void processQuerySolution(QuerySolution qs) {
+			RDFNode egoAuthorURLNode = qs.get(QueryFieldLabels.AUTHOR_URL);
+			RDFNode authorLabelNode = qs.get(QueryFieldLabels.AUTHOR_LABEL);
+			RDFNode documentNode = qs.get(QueryFieldLabels.DOCUMENT_URL);
+			RDFNode coAuthorURLNode = qs.get(QueryFieldLabels.CO_AUTHOR_URL);
+			RDFNode coAuthorLabelNode = qs.get(QueryFieldLabels.CO_AUTHOR_LABEL);
+			RDFNode publicationDateNode = qs.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
+
+			String authorURI    = egoAuthorURLNode == null ? null : egoAuthorURLNode.asLiteral().getString();
+			String authorName   = authorLabelNode == null ? null : authorLabelNode.asLiteral().getString();
+			String documentURI  = documentNode == null ? null : documentNode.asLiteral().getString();
+			String documentDate = publicationDateNode == null ? null : publicationDateNode.asLiteral().getString();
+			String coAuthorURI  = coAuthorURLNode == null ? null : coAuthorURLNode.asLiteral().getString();
+			String coAuthorName = coAuthorLabelNode == null ? null : coAuthorLabelNode.asLiteral().getString();
+
+			processEntry(authorURI, authorName, documentURI, documentDate, coAuthorURI, coAuthorName);
+		}
+
+		public void processEntry(String authorURI, String authorName, String documentURI, String documentDate, String coAuthorURI, String coAuthorName) {
 			/*
 			 * We only want to create only ONE ego node.
 			 * */
-			RDFNode egoAuthorURLNode = qs.get(QueryFieldLabels.AUTHOR_URL);
+			if (nodeURLToVO.containsKey(authorURI)) {
-			if (nodeURLToVO.containsKey(egoAuthorURLNode.toString())) {
+				egoNode = nodeURLToVO.get(authorURI);
-
-				egoNode = nodeURLToVO.get(egoAuthorURLNode.toString());
-
 			} else {
-
+				egoNode = new Collaborator(authorURI, nodeIDGenerator);
-				egoNode = new Collaborator(egoAuthorURLNode.toString(), nodeIDGenerator);
 				nodes.add(egoNode);
-				nodeURLToVO.put(egoAuthorURLNode.toString(), egoNode);
+				nodeURLToVO.put(authorURI, egoNode);
 
-				RDFNode authorLabelNode = qs.get(QueryFieldLabels.AUTHOR_LABEL);
+				if (authorName != null) {
-				if (authorLabelNode != null) {
+					egoNode.setCollaboratorName(authorName);
-					egoNode.setCollaboratorName(authorLabelNode.toString());
 				}
 			}
 
-			RDFNode documentNode = qs.get(QueryFieldLabels.DOCUMENT_URL);
 			Activity biboDocument;
 
-			if (biboDocumentURLToVO.containsKey(documentNode.toString())) {
+			if (biboDocumentURLToVO.containsKey(documentURI)) {
-				biboDocument = biboDocumentURLToVO.get(documentNode.toString());
+				biboDocument = biboDocumentURLToVO.get(documentURI);
 			} else {
-				biboDocument = createDocumentVO(qs, documentNode.toString());
+				biboDocument = createDocumentVO(documentURI, documentDate);
-				biboDocumentURLToVO.put(documentNode.toString(), biboDocument);
+				biboDocumentURLToVO.put(documentURI, biboDocument);
 			}
 
 			egoNode.addActivity(biboDocument);
@@ -127,27 +137,21 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 			 * we do not want a co-author node or Collaboration if the publication has only one
 			 * author and that happens to be the ego.
 			 * */
-			if (qs.get(QueryFieldLabels.AUTHOR_URL).toString().equalsIgnoreCase(
+			if (authorURI.equalsIgnoreCase(coAuthorURI)) {
-					qs.get(QueryFieldLabels.CO_AUTHOR_URL).toString())) {
 				return;
 			}
 
 			Collaborator coAuthorNode;
 
-			RDFNode coAuthorURLNode = qs.get(QueryFieldLabels.CO_AUTHOR_URL);
+			if (nodeURLToVO.containsKey(coAuthorURI)) {
-			if (nodeURLToVO.containsKey(coAuthorURLNode.toString())) {
+				coAuthorNode = nodeURLToVO.get(coAuthorURI);
-
-				coAuthorNode = nodeURLToVO.get(coAuthorURLNode.toString());
-
 			} else {
-
+				coAuthorNode = new Collaborator(coAuthorURI, nodeIDGenerator);
-				coAuthorNode = new Collaborator(coAuthorURLNode.toString(), nodeIDGenerator);
 				nodes.add(coAuthorNode);
-				nodeURLToVO.put(coAuthorURLNode.toString(), coAuthorNode);
+				nodeURLToVO.put(coAuthorURI, coAuthorNode);
 
-				RDFNode coAuthorLabelNode = qs.get(QueryFieldLabels.CO_AUTHOR_LABEL);
+				if (coAuthorName != null) {
-				if (coAuthorLabelNode != null) {
+					coAuthorNode.setCollaboratorName(coAuthorName);
-					coAuthorNode.setCollaboratorName(coAuthorLabelNode.toString());
 				}
 			}
 
@@ -225,13 +229,12 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 			return new CoAuthorshipData(egoNode, nodes, edges, biboDocumentURLToVO);
 		}
 
-		private Activity createDocumentVO(QuerySolution solution, String documentURL) {
+		private Activity createDocumentVO(String documentURL, String documentDate) {
 
 			Activity biboDocument = new Activity(documentURL);
 
-			RDFNode publicationDateNode = solution.get(QueryFieldLabels.DOCUMENT_PUBLICATION_DATE);
+			if (documentDate != null) {
-			if (publicationDateNode != null) {
+				biboDocument.setActivityDate(documentDate);
-				biboDocument.setActivityDate(publicationDateNode.toString());
 			}
 
 			return biboDocument;
@@ -487,20 +490,60 @@ public class CoAuthorshipQueryRunner implements QueryRunner<CoAuthorshipData> {
 			throw new MalformedQueryParametersException("URI parameter is either null or empty.");
 		}
 
+		Date cacheTime = null;
+		QueryResultConsumer consumer = new QueryResultConsumer();
+
+		// If we've had long running queries (preferCaches), and the caches are available, use the cache
+		if (preferCaches && VisualizationCaches.personToPublication.isCached()) {
+			cacheTime = VisualizationCaches.personToPublication.cachedWhen();
+
+			Map<String, String>      personLabelsMap         = VisualizationCaches.personLabels.get(rdfService);
+			Map<String, Set<String>> personToPublicationMap  = VisualizationCaches.personToPublication.get(rdfService).personToPublication;
+			Map<String, Set<String>> publicationToPersonMap  = VisualizationCaches.personToPublication.get(rdfService).publicationToPerson;
+			Map<String, String>      publicationToYearMap    = VisualizationCaches.publicationToYear.get(rdfService);
+
+			String authorURI = this.egoURI;
+			String authorName = personLabelsMap.get(authorURI);
+			for (String documentURI : personToPublicationMap.get(authorURI)) {
+				String documentDate = publicationToYearMap.get(documentURI);
+				for (String coAuthorURI : publicationToPersonMap.get(documentURI)) {
+					String coAuthorName = personLabelsMap.get(coAuthorURI);
+					consumer.processEntry(authorURI, authorName, documentURI, documentDate, coAuthorURI, coAuthorName);
+				}
+			}
+			consumer.endProcessing();
+		} else {
+			// Not use the caches, so query the triple store - recording the time it took
+			long queryStart = System.currentTimeMillis();
 			try {
 				Model constructedModel = ModelFactory.createDefaultModel();
 				rdfService.sparqlConstructQuery(generateEgoCoAuthorshipSparqlConstruct(this.egoURI), constructedModel);
-            QueryResultConsumer consumer = new QueryResultConsumer();
 				QueryExecution qe = QueryExecutionFactory.create(generateEgoCoAuthorshipSparqlQuery(this.egoURI), constructedModel);
 				try {
 					consumer.processResultSet(qe.execSelect());
 				} finally {
 					qe.close();
 				}
-			data = consumer.getCollaborationData();
 			} catch (RDFServiceException e) {
 				log.error("Unable to execute query", e);
 				throw new RuntimeException(e);
+			} finally {
+				// If the query took more than 5 seconds, start using the caches
+				if (System.currentTimeMillis() - queryStart > 5000) {
+					// If the caches haven't already been built, request a rebuild
+					if (!preferCaches && !VisualizationCaches.personToPublication.isCached()) {
+						VisualizationCaches.rebuildAll();
+					}
+
+					// Attempt to use caches next time
+					preferCaches = true;
+				}
+			}
+		}
+
+		data = consumer.getCollaborationData();
+		if (cacheTime != null) {
+			data.setBuiltFromCacheTime(cacheTime);
 		}
 
 		CollaborationDataCacheEntry newEntry = new CollaborationDataCacheEntry();

src/edu/cornell/mannlib/vitro/webapp/visualization/collaborationutils/CollaborationData.java

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.collaborationutils;
 
+import java.util.Date;
 import java.util.Map;
 import java.util.Set;
 
@@ -16,6 +17,8 @@ public abstract class CollaborationData {
 	private Set<Map<String, String>> NODE_SCHEMA;
 	private Set<Map<String, String>> EDGE_SCHEMA;
 
+	private Date builtFromCacheTime = null;
+		
 	public CollaborationData(Collaborator egoCollaborator, 
 							Set<Collaborator> collaborators, 
 							Set<Collaboration> collaborations) {
@@ -24,6 +27,8 @@ public abstract class CollaborationData {
 		this.collaborations = collaborations;
 	}
 
+	public Date getBuiltFromCacheTime() { return builtFromCacheTime; }
+
 	public Set<Collaborator> getCollaborators() {
 		return collaborators;
 	}
@@ -60,6 +65,8 @@ public abstract class CollaborationData {
 		return EDGE_SCHEMA;
 	}
 
+	public void setBuiltFromCacheTime(Date time) { this.builtFromCacheTime = time; }
+
 	abstract Set<Map<String, String>> initializeEdgeSchema();
 	
 	abstract Set<Map<String, String>> initializeNodeSchema();	

src/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java

@@ -90,7 +90,7 @@ public class MapOfScienceVisualizationRequestHandler implements VisualizationReq
 
 	private Set<String> getPublicationsForPerson(RDFService rdfService, String personUri) {
 		if (preferCachesForPersonMap() && VisualizationCaches.personToPublication.isCached()) {
-			Map<String, Set<String>> personToPublicationMap = VisualizationCaches.personToPublication.get(rdfService);
+			Map<String, Set<String>> personToPublicationMap = VisualizationCaches.personToPublication.get(rdfService).personToPublication;
 			return personToPublicationMap.get(personUri);
 		} else {
 			final Set<String> queryResults = new HashSet<String>();
@@ -253,7 +253,7 @@ public class MapOfScienceVisualizationRequestHandler implements VisualizationReq
 
 		Map<String, Set<String>> subOrgMap = VisualizationCaches.organizationSubOrgs.get(rdfService);
 		Map<String, Set<String>> organisationToPeopleMap = VisualizationCaches.organisationToPeopleMap.get(rdfService);
-		Map<String, Set<String>> personToPublicationMap = VisualizationCaches.personToPublication.get(rdfService);
+		Map<String, Set<String>> personToPublicationMap = VisualizationCaches.personToPublication.get(rdfService).personToPublication;
 		Map<String, String> publicationToJournalMap = VisualizationCaches.publicationToJournal.get(rdfService);
 
 		Set<String> orgPublications       = new HashSet<String>();
@@ -397,22 +397,22 @@ public class MapOfScienceVisualizationRequestHandler implements VisualizationReq
 				.getIndividualDao()
 				.getIndividualByURI(entityURI);
 
+		try {
 			if (individual != null && individual.isVClass("http://xmlns.com/foaf/0.1/Person")) {
-
 				return getSubjectPersonEntityAndGenerateDataResponse(
 						vitroRequest,
 						entityURI,
 						individual != null ? individual.getDataValue("http://www.w3.org/2000/01/rdf-schema#label") : "",
 						currentDataVisMode);
-			
 			} else {
-
 				return getSubjectEntityAndGenerateDataResponse(
 						vitroRequest,
 						entityURI,
 						individual != null ? individual.getDataValue("http://www.w3.org/2000/01/rdf-schema#label") : "",
 						currentDataVisMode);
-		
+			}
+		} finally {
+			VisualizationCaches.buildMissing();
 		}
 	}
 	
@@ -437,10 +437,16 @@ public class MapOfScienceVisualizationRequestHandler implements VisualizationReq
         
         if (UtilityFunctions.isEntityAPerson(vreq, entityURI)) {
         	body.put("entityType", "PERSON");
-        	
+			if (preferCachesForPersonMap() && VisualizationCaches.personToPublication.isCached()) {
+				body.put("builtFromCacheTime", VisualizationCaches.personToPublication.cachedWhen());
+			}
         } else {
         	body.put("entityType", "ORGANIZATION");
+			if (VisualizationCaches.personToPublication.isCached()) {
+				body.put("builtFromCacheTime", VisualizationCaches.personToPublication.cachedWhen());
 			}
+        }
+
 
         body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
         

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

@@ -254,6 +254,10 @@ public class PersonLevelRequestHandler implements VisualizationRequestHandler {
 		body.put("egoPubSparklineVO", egoPubSparklineVO);
 		body.put("uniqueCoauthorsSparklineVO", uniqueCoauthorsSparklineVO);
 
+		if (coAuthorshipVO.getBuiltFromCacheTime() != null) {
+			body.put("builtFromCacheTime", coAuthorshipVO.getBuiltFromCacheTime());
+		}
+
 		body.put("title",  title + "Person Level Visualization");
 
 		return new TemplateResponseValues(standaloneTemplate, body);

src/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalGrantVisualizationRequestHandler.java

@@ -103,13 +103,16 @@ public class TemporalGrantVisualizationRequestHandler implements
 			
 		} 		
 
+		try {
 			return getSubjectEntityAndGenerateDataResponse(
 					vitroRequest,
 					log,
 					dataset,
 					entityURI,
 					currentDataMode);
-		
+		} finally {
+			VisualizationCaches.buildMissing();
+		}
 	}
 	
 	private Map<String, String> prepareDataErrorResponse() {
@@ -290,6 +293,10 @@ public class TemporalGrantVisualizationRequestHandler implements
 		body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
 		body.put("organizationLabel", organizationLabel);
 
+		if (VisualizationCaches.personToGrant.isCached()) {
+			body.put("builtFromCacheTime", VisualizationCaches.personToGrant.cachedWhen());
+		}
+
 		return new TemplateResponseValues(standaloneTemplate, body);
 	}
 	

src/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/TemporalPublicationVisualizationRequestHandler.java

@@ -92,7 +92,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		Map<String, String> orgMostSpecificLabelMap      = VisualizationCaches.organizationToMostSpecificLabel.get(rdfService);
 		Map<String, String> personMostSpecificLabelMap   = VisualizationCaches.personToMostSpecificLabel.get(rdfService);
 		Map<String, Set<String>> organisationToPeopleMap = VisualizationCaches.organisationToPeopleMap.get(rdfService);
-		Map<String, Set<String>> personToPublicationMap  = VisualizationCaches.personToPublication.get(rdfService);
+		Map<String, Set<String>> personToPublicationMap  = VisualizationCaches.personToPublication.get(rdfService).personToPublication;
 		Map<String, String>      publicationToYearMap    = VisualizationCaches.publicationToYear.get(rdfService);
 
 		Set<String> orgPublications       = new HashSet<String>();
@@ -250,13 +250,16 @@ public class TemporalPublicationVisualizationRequestHandler implements
 			
 		} 
 
+		try {
 			return getSubjectEntityAndGenerateDataResponse(
 					vitroRequest,
 					log,
 					dataset,
 					entityURI,
 					currentDataMode);
-		
+		} finally {
+			VisualizationCaches.buildMissing();
+		}
 	}
 	
 	
@@ -276,6 +279,10 @@ public class TemporalPublicationVisualizationRequestHandler implements
         body.put("vivoDefaultNamespace", vreq.getWebappDaoFactory().getDefaultNamespace());
         body.put("organizationLabel", organizationLabel);
 
+		if (VisualizationCaches.personToPublication.isCached()) {
+			body.put("builtFromCacheTime", VisualizationCaches.personToPublication.cachedWhen());
+		}
+
         return new TemplateResponseValues(standaloneTemplate, body);
 	}
 

src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/CachingRDFServiceExecutor.java

@@ -6,6 +6,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
 
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -35,6 +36,7 @@ public class CachingRDFServiceExecutor<T> {
      * Background task tracker
      */
     private FutureTask<T> backgroundTask = null;
+    private Thread backgroundCompletion = null;
     private long backgroundTaskStartTime = -1;
 
     /**
@@ -50,6 +52,8 @@ public class CachingRDFServiceExecutor<T> {
         return cachedResults != null;
     }
 
+    public Date cachedWhen() { return new Date(lastCacheTime); }
+
     /**
      * Return the cached results if present, or start the task.
      * Will wait for completion if the cache is not already populated, otherwise the refresh will happen in the background.
@@ -100,21 +104,34 @@ public class CachingRDFServiceExecutor<T> {
      *
      * @param rdfService an RDF service to use, if the background RDF service is not set
      */
-    public synchronized void build(RDFService rdfService) {
+    public void build(RDFService rdfService) {
         // First, check if there are results from the previous background task, and update the cache
+        if (backgroundTask != null && backgroundTask.isDone()) {
+            buildComplete();
+        } else if (backgroundTask == null) {
+            buildStart(rdfService);
+        }
+    }
+
+    private synchronized void buildComplete() {
         if (backgroundTask != null && backgroundTask.isDone()) {
             completeBackgroundTask();
         }
+    }
 
+    private synchronized void buildStart(RDFService rdfService) {
+        if (backgroundTask == null) {
             // If we have a background RDF service, we can launch the task in the background and leave it
             if (backgroundRDFService != null) {
                 startBackgroundTask(backgroundRDFService);
+                completeBackgroundTaskAsync();
             } else if (rdfService != null) {
                 // No background service, so use the paassed RDF service, and wait for completion
                 startBackgroundTask(backgroundRDFService);
                 completeBackgroundTask();
             }
         }
+    }
 
     /**
      * Determine if a task is likely to complete with the time frame specified
@@ -186,6 +203,26 @@ public class CachingRDFServiceExecutor<T> {
         }
     }
 
+    /**
+     * Complete the background task
+     */
+    private synchronized void completeBackgroundTaskAsync() {
+        if (backgroundCompletion == null) {
+            backgroundCompletion = new Thread(new Runnable() {
+                @Override
+                public void run() {
+                    try {
+                        Thread.sleep(500);
+                        completeBackgroundTask(-1);
+                    } catch (InterruptedException e) {
+                    }
+                }
+            });
+            backgroundCompletion.setDaemon(true);
+            backgroundCompletion.start();
+        }
+    }
+
     /**
      * Complete the background task
      */
@@ -215,6 +252,7 @@ public class CachingRDFServiceExecutor<T> {
                 // Clear the background task information
                 backgroundTask = null;
                 backgroundTaskStartTime = -1;
+                backgroundCompletion = null;
             }
         } catch (InterruptedException e) {
             // Task was interrupted, so abort it
@@ -307,7 +345,6 @@ public class CachingRDFServiceExecutor<T> {
                     affinity.complete();
                 }
             }
-
         }
 
         /**

src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/PersonPublicationMaps.java

@@ -0,0 +1,33 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+package edu.cornell.mannlib.vitro.webapp.visualization.utilities;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+public class PersonPublicationMaps {
+    public Map<String, Set<String>> personToPublication = new HashMap<String, Set<String>>();
+    public Map<String, Set<String>> publicationToPerson = new HashMap<String, Set<String>>();
+
+    public void put(String person, String document) {
+        Set<String> documentSet = personToPublication.get(person);
+        if (documentSet == null) {
+            documentSet = new HashSet<String>();
+            documentSet.add(document);
+            personToPublication.put(person, documentSet);
+        } else {
+            documentSet.add(document);
+        }
+
+        Set<String> personSet = publicationToPerson.get(document);
+        if (personSet == null) {
+            personSet = new HashSet<String>();
+            personSet.add(person);
+            publicationToPerson.put(document, personSet);
+        } else {
+            personSet.add(person);
+        }
+    }
+}
+

src/edu/cornell/mannlib/vitro/webapp/visualization/utilities/VisualizationCaches.java

@@ -45,6 +45,32 @@ final public class VisualizationCaches {
         grantToYear.build(rdfService);
     }
 
+    public static void buildMissing() {
+        if (!organizationLabels.isCached())              { organizationLabels.build(null); }
+        if (!organizationSubOrgs.isCached())             { organizationSubOrgs.build(null); }
+        if (!organizationToMostSpecificLabel.isCached()) { organizationToMostSpecificLabel.build(null); }
+        if (!organisationToPeopleMap.isCached())         { organisationToPeopleMap.build(null); }
+        if (!personLabels.isCached())                    { personLabels.build(null); }
+        if (!personToMostSpecificLabel.isCached())       { personToMostSpecificLabel.build(null); }
+        if (!personToPublication.isCached())             { personToPublication.build(null); }
+        if (!publicationToJournal.isCached())            { publicationToJournal.build(null); }
+        if (!publicationToYear.isCached())               { publicationToYear.build(null); }
+        if (!personToGrant.isCached())                   { personToGrant.build(null); }
+        if (!grantToYear.isCached())                     { grantToYear.build(null); }
+    }
+
+    /**
+     * Rebuild the specifield caches
+     * @param executors
+     */
+    public static void rebuild(CachingRDFServiceExecutor... executors) {
+        if (executors != null) {
+            for (CachingRDFServiceExecutor e : executors) {
+                e.build(null);
+            }
+        }
+    }
+
     /**
      * Cache of organization labels (uri -> label)
      */
@@ -263,11 +289,11 @@ final public class VisualizationCaches {
     /**
      * Person to publication Map (person uri -> list of publication uri)
      */
-    public static final CachingRDFServiceExecutor<Map<String, Set<String>>> personToPublication =
+    public static final CachingRDFServiceExecutor<PersonPublicationMaps> personToPublication =
-            new CachingRDFServiceExecutor<Map<String, Set<String>>>(
+            new CachingRDFServiceExecutor<PersonPublicationMaps>(
-                    new CachingRDFServiceExecutor.RDFServiceCallable<Map<String, Set<String>>>(visualizationAffinity) {
+                    new CachingRDFServiceExecutor.RDFServiceCallable<PersonPublicationMaps>(visualizationAffinity) {
                         @Override
-                        protected Map<String, Set<String>> callWithService(RDFService rdfService) throws Exception {
+                        protected PersonPublicationMaps callWithService(RDFService rdfService) throws Exception {
                             String query = QueryConstants.getSparqlPrefixQuery() +
                                     "SELECT ?person ?document\n" +
                                     "WHERE\n" +
@@ -276,10 +302,10 @@ final public class VisualizationCaches {
                                     "  ?person core:relatedBy ?authorship .\n" +
                                     "  ?authorship a core:Authorship .\n" +
                                     "  ?authorship core:relates ?document .\n" +
-                                    "  ?document a bibo:Document .\n" +
+                                    "  ?document a <http://purl.obolibrary.org/obo/IAO_0000030> .\n" +
                                     "}\n";
 
-                            final Map<String, Set<String>> map = new HashMap<String, Set<String>>();
+                            final PersonPublicationMaps map = new PersonPublicationMaps();
 
                             rdfService.sparqlSelectQuery(query, new ResultSetConsumer() {
                                 @Override
@@ -289,15 +315,9 @@ final public class VisualizationCaches {
 
                                     if (person != null && document != null) {
                                         String personURI = person.getURI();
+                                        String documentURI = document.getURI();
 
-                                        Set<String> documents = map.get(personURI);
+                                        map.put(personURI, documentURI);
-                                        if (documents == null) {
-                                            documents = new HashSet<String>();
-                                            documents.add(document.getURI());
-                                            map.put(personURI, documents);
-                                        } else {
-                                            documents.add(document.getURI());
-                                        }
                                     }
                                 }
                             });
@@ -319,7 +339,7 @@ final public class VisualizationCaches {
                                     "SELECT ?document ?journalLabel\n" +
                                     "WHERE\n" +
                                     "{\n" +
-                                    "  ?document a bibo:Document .\n" +
+                                    "  ?document a <http://purl.obolibrary.org/obo/IAO_0000030> .\n" +
                                     "  ?document core:hasPublicationVenue ?journal . \n" +
                                     "  ?journal rdfs:label ?journalLabel . \n" +
                                     "}\n";
@@ -353,7 +373,7 @@ final public class VisualizationCaches {
                                     "SELECT ?document ?publicationDate\n" +
                                     "WHERE\n" +
                                     "{\n" +
-                                    "  ?document a bibo:Document .\n" +
+                                    "  ?document a <http://purl.obolibrary.org/obo/IAO_0000030> .\n" +
                                     "  ?document core:dateTimeValue ?dateTimeValue . \n" +
                                     "  ?dateTimeValue core:dateTime ?publicationDate . \n" +
                                     "}\n";

themes/wilma/i18n/all.properties

@@ -885,3 +885,5 @@ researcher_role = Researcher Role
 search_service_btn = Search Service
 through_today = Publications through today's date
 doi_link=Digital Object Identifier (DOI)
+
+using_cache_time=Using information cached at