Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/tdb/RDFServiceTDB.java

@@ -16,9 +16,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.shared.JenaException;
+import com.hp.hpl.jena.query.ReadWrite;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.tdb.TDB;
 import com.hp.hpl.jena.tdb.TDBFactory;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
@@ -65,6 +63,7 @@ public class RDFServiceTDB extends RDFServiceJena {
 			return false;
 		}
 
+		dataset.begin(ReadWrite.WRITE);
 		try {
 			insureThatInputStreamsAreResettable(changeSet);
 
@@ -75,23 +74,20 @@ public class RDFServiceTDB extends RDFServiceJena {
 
 			applyChangeSetToModel(changeSet, dataset);
 
-			dataset.getLock().enterCriticalSection(Lock.WRITE);
-			try {
-				TDB.sync(dataset);
-			} finally {
-				dataset.getLock().leaveCriticalSection();
-			}
-
 			notifyListenersOfChanges(changeSet);
 			notifyListenersOfPostChangeEvents(changeSet);
 
+			dataset.commit();
 			return true;
 		} catch (Exception e) {
 			log.error(e, e);
 			throw new RDFServiceException(e);
+		} finally {
+			dataset.end();
 		}
 	}
 
+	
 	@Override
 	public void close() {
 		if (this.dataset != null) {
@@ -102,75 +98,75 @@ public class RDFServiceTDB extends RDFServiceJena {
 	@Override
 	public InputStream sparqlConstructQuery(String query,
 			ModelSerializationFormat resultFormat) throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			return super.sparqlConstructQuery(query, resultFormat);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public InputStream sparqlDescribeQuery(String query,
 			ModelSerializationFormat resultFormat) throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			return super.sparqlDescribeQuery(query, resultFormat);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public InputStream sparqlSelectQuery(String query, ResultFormat resultFormat)
 			throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			return super.sparqlSelectQuery(query, resultFormat);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public boolean sparqlAskQuery(String query) throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			return super.sparqlAskQuery(query);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public List<String> getGraphURIs() throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			return super.getGraphURIs();
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public void serializeAll(OutputStream outputStream)
 			throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			super.serializeAll(outputStream);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 
 	@Override
 	public void serializeGraph(String graphURI, OutputStream outputStream)
 			throws RDFServiceException {
-		dataset.getLock().enterCriticalSection(Lock.READ);
+		dataset.begin(ReadWrite.READ);
 		try {
 			super.serializeGraph(graphURI, outputStream);
 		} finally {
-			dataset.getLock().leaveCriticalSection();
+			dataset.end();
 		}
 	}
 

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/ContentModelSetup.java

@@ -53,24 +53,22 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
     	
     	Model applicationMetadataModel = models.getOntModel(APPLICATION_METADATA);
 		if (applicationMetadataModel.size()== 0) {
-			thisIsFirstStartup();
-		}
-
-
-        OntModel baseABoxModel = models.getOntModel(ABOX_ASSERTIONS);
-        OntModel baseTBoxModel = models.getOntModel(TBOX_ASSERTIONS);
-        
-        if (isFirstStartup()) {
         	initializeApplicationMetadata(ctx, applicationMetadataModel);
-        	RDFFilesLoader.loadFirstTimeFiles("abox", baseABoxModel, true);
-        	RDFFilesLoader.loadFirstTimeFiles("tbox", baseTBoxModel, true);
 		} else {
         	checkForNamespaceMismatch( applicationMetadataModel, ctx );
 		}
-    	RDFFilesLoader.loadEveryTimeFiles("abox", baseABoxModel);
-    	RDFFilesLoader.loadEveryTimeFiles("tbox", baseTBoxModel);
 
-		log.info("Setting up DAO factories");
+        OntModel baseABoxModel = models.getOntModel(ABOX_ASSERTIONS);
+        if (baseABoxModel.size() == 0) {
+        	RDFFilesLoader.loadFirstTimeFiles("abox", baseABoxModel, true);
+        }
+        RDFFilesLoader.loadEveryTimeFiles("abox", baseABoxModel);
+        
+        OntModel baseTBoxModel = models.getOntModel(TBOX_ASSERTIONS);
+        if (baseTBoxModel.size() == 0) {
+        	RDFFilesLoader.loadFirstTimeFiles("tbox", baseTBoxModel, true);
+        }
+    	RDFFilesLoader.loadEveryTimeFiles("tbox", baseTBoxModel);
     }
 
 	private long secondsSince(long startTime) {

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/RDFFilesLoader.java

@@ -67,9 +67,10 @@ public class RDFFilesLoader {
 	public static void loadFirstTimeFiles(String modelPath, Model model,
 			boolean firstTime) {
 		if (firstTime) {
-			Set<Path> paths = getPaths(locateHomeDirectory(), RDF, modelPath,
+			String home = locateHomeDirectory();
-					FIRST_TIME);
+			Set<Path> paths = getPaths(home, RDF, modelPath, FIRST_TIME);
 			for (Path p : paths) {
+				log.info("Loading " + relativePath(p, home));
 				readOntologyFileIntoModel(p, model);
 			}
 		} else {

webapp/src/edu/cornell/mannlib/vitro/webapp/triplesource/impl/BasicCombinedTripleSource.java

@@ -72,14 +72,14 @@ public class BasicCombinedTripleSource implements CombinedTripleSource {
 		sources.put(CONFIGURATION, configurationSource);
 
 		ontModels = new EnumMap<>(WhichService.class);
-		ontModels.put(CONTENT, new ModelMakerOntModelCache(
+		ontModels.put(CONTENT, new UnionModelsOntModelsCache(
-				getModelMaker(CONTENT)));
+				new ModelMakerOntModelCache(getModelMaker(CONTENT)),
+				CONTENT_UNIONS));
 		ontModels.put(CONFIGURATION, new ModelMakerOntModelCache(
 				getModelMaker(CONFIGURATION)));
 
-		ontModelCache = new UnionModelsOntModelsCache(new JoinedOntModelCache(
+		ontModelCache = new JoinedOntModelCache(ontModels.get(CONTENT),
-				ontModels.get(CONTENT), ontModels.get(CONFIGURATION)),
+				ontModels.get(CONFIGURATION));
-				CONTENT_UNIONS);
 	}
 
 	protected OntModelCache getOntModels(WhichService whichService) {

webapp/src/edu/cornell/mannlib/vitro/webapp/triplesource/impl/sdb/ContentTripleSourceSDB.java

@@ -4,7 +4,6 @@ package edu.cornell.mannlib.vitro.webapp.triplesource.impl.sdb;
 
 import static edu.cornell.mannlib.vitro.webapp.triplesource.impl.BasicCombinedTripleSource.CONTENT_UNIONS;
 
-import java.lang.reflect.Method;
 import java.sql.Driver;
 import java.sql.DriverManager;
 import java.sql.SQLException;
@@ -194,6 +193,9 @@ public class ContentTripleSourceSDB extends ContentTripleSource {
 	 * Use models from the short-term RDFService, since there is less contention
 	 * for the database connections that way. The exceptions are the
 	 * memory-mapped models. By keeping them, we also keep their sub-models.
+	 * 
+	 * Set up the Union models again also, so they will reference the short-term
+	 * models.
 	 */
 	@Override
 	public OntModelCache getShortTermOntModels(RDFService shortTermRdfService,

webapp/src/edu/cornell/mannlib/vitro/webapp/triplesource/impl/tdb/ContentTripleSourceTDB.java

@@ -10,6 +10,7 @@ import com.hp.hpl.jena.tdb.TDB;
 
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
+import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.adapters.ListCachingModelMaker;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.adapters.MemoryMappingModelMaker;
 import edu.cornell.mannlib.vitro.webapp.modelaccess.ontmodels.OntModelCache;
@@ -21,6 +22,7 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.tdb.RDFServiceTDB;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFServiceFactory;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 import edu.cornell.mannlib.vitro.webapp.utils.configuration.Property;
 import edu.cornell.mannlib.vitro.webapp.utils.configuration.Validation;
 import edu.cornell.mannlib.vitro.webapp.utils.logging.ToString;
@@ -75,6 +77,7 @@ public class ContentTripleSourceTDB extends ContentTripleSource {
 			this.unclosableRdfService = this.rdfServiceFactory.getRDFService();
 			this.dataset = new RDFServiceDataset(this.unclosableRdfService);
 			this.modelMaker = createModelMaker();
+			checkForFirstTimeStartup();
 			ss.info("Initialized the RDF source for TDB");
 		} catch (IOException e) {
 			throw new RuntimeException(
@@ -102,6 +105,12 @@ public class ContentTripleSourceTDB extends ContentTripleSource {
 						this.unclosableRdfService), SMALL_CONTENT_MODELS)));
 	}
 
+	private void checkForFirstTimeStartup() {
+		if (this.dataset.getNamedModel(ModelNames.TBOX_ASSERTIONS).size() == 0) {
+			JenaDataSourceSetupBase.thisIsFirstStartup();
+		}
+	}
+
 	@Override
 	public RDFServiceFactory getRDFServiceFactory() {
 		return this.rdfServiceFactory;