NIHVIVO-3196 suppression of additional unnecessary log messages related to connection timeout and associated improvements

webapp/config/default.log4j.properties

@@ -38,6 +38,7 @@ log4j.logger.edu.cornell.mannlib.vitro.webapp.controller.freemarker.BrowseContro
 log4j.logger.edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener=WARN
 log4j.logger.edu.cornell.mannlib.vitro.webapp.dao.jena.RDBGraphGenerator=WARN
 # suppress odd warnings from libraries
+log4j.logger.com.hp.hpl.jena.sdb.layout2.LoaderTuplesNodes=FATAL
 log4j.logger.com.hp.hpl.jena.db.impl.PSet_TripleStore_RDB=FATAL
 log4j.logger.com.hp.hpl.jena.sdb.sql.SDBConnection=ERROR
 log4j.logger.org.openjena.riot=FATAL

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/GraphGenerator.java

@@ -8,4 +8,6 @@ public interface GraphGenerator {
 
 	public Graph generateGraph();
 	
+	public boolean isGraphClosed();
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/MemToDBModelSynchronizer.java

@@ -11,22 +11,23 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 
 /**
- * This listener will open and close RDB models as it performs edits to avoid
+ * This listener will open and close DB models as it performs edits to avoid
  * wasting DB connections
  * @author bjl23
  *
  */
-public class MemToRDBModelSynchronizer extends StatementListener {
+public class MemToDBModelSynchronizer extends StatementListener {
 
-	private static long IDLE_MILLIS = 2000; // how long to let a model site idle after an edit has been performed
+	private static long IDLE_MILLIS = 2000; // how long to let a model site idle
+	                                        // after an edit has been performed
 	
-	RDBGraphGenerator generator;
+	SQLGraphGenerator generator;
 	Model model;
 	boolean editInProgress;
 	boolean cleanupThreadActive;
 	long lastEditTimeMillis;
 	
-	public MemToRDBModelSynchronizer(RDBGraphGenerator generator) {
+	public MemToDBModelSynchronizer(SQLGraphGenerator generator) {
 		this.generator = generator;
 	}
 	
@@ -49,7 +50,8 @@ public class MemToRDBModelSynchronizer extends StatementListener {
 			lastEditTimeMillis = System.currentTimeMillis();
 			this.editInProgress = false;
 			if (!cleanupThreadActive) {
-				(new Thread(new Cleanup(this), "MemToRDBModelSynchronizer")).start();
+				(new Thread(
+						new Cleanup(this), "MemToDBModelSynchronizer")).start();
 			}
 		}
 	}
@@ -63,33 +65,39 @@ public class MemToRDBModelSynchronizer extends StatementListener {
 			lastEditTimeMillis = System.currentTimeMillis();
 			this.editInProgress = false;
 			if (!cleanupThreadActive) {
-				(new Thread(new Cleanup(this), "MemToRDBModelSynchronizer")).start();
+				(new Thread(
+						new Cleanup(this), "MemToDBModelSynchronizer")).start();
 			}
 		}
 	}
 	
 	private class Cleanup implements Runnable {
 		
-		private MemToRDBModelSynchronizer s;
+		private MemToDBModelSynchronizer s;
 				
-		public Cleanup(MemToRDBModelSynchronizer s) {
+		public Cleanup(MemToDBModelSynchronizer s) {
 			this.s = s;
 		}
 		
 		public void run() {
 			s.cleanupThreadActive = true;
-			while( (s.editInProgress) || (System.currentTimeMillis() - s.lastEditTimeMillis < IDLE_MILLIS ) ) {
+			while( (s.editInProgress) 
+					|| (System.currentTimeMillis() 
+							- s.lastEditTimeMillis < IDLE_MILLIS ) ) {
 				try {
 					Thread.currentThread().sleep(1000);
 				} catch (InterruptedException e) {
-					throw new RuntimeException("Interrupted cleanup thread in " + this.getClass().getName(), e);
+					throw new RuntimeException(
+							"Interrupted cleanup thread in " 
+							+ this.getClass().getName(), e);
 				}
 			}
 			if (s.model != null) {
 				s.model.close();
 				s.model = null;
 			} else {
-				throw new RuntimeException(this.getClass().getName()+"Model already null");
+				throw new RuntimeException(
+						this.getClass().getName() + "Model already null");
 			}
 			java.sql.Connection c = generator.getConnection();
 			try {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDBGraphGenerator.java

@@ -17,7 +17,7 @@ import com.hp.hpl.jena.graph.Graph;
 
 
 
-public class RDBGraphGenerator implements GraphGenerator {
+public class RDBGraphGenerator implements SQLGraphGenerator {
 
 	private static final Log log = LogFactory.getLog(RDBGraphGenerator.class.getName());
 	
@@ -32,6 +32,14 @@ public class RDBGraphGenerator implements GraphGenerator {
         this.graphID = graphID;
     }
 
+    public boolean isGraphClosed() {
+    	try {
+    		return (connection == null || connection.isClosed());
+        } catch (SQLException e) {
+        	throw new RuntimeException(e);
+        }
+    }
+    
     public Graph generateGraph() {
     	log.info("Regenerate the graph.");
         try {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RDBModelGenerator.java

@@ -1,43 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import com.hp.hpl.jena.db.DBConnection;
-import com.hp.hpl.jena.db.IDBConnection;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.ModelMaker;
-import org.apache.commons.dbcp.BasicDataSource;
-
-import java.sql.SQLException;
-
-public class RDBModelGenerator implements ModelGenerator {
-
-    private BasicDataSource ds = null;
-    private String dbTypeStr = null;
-    private String modelNameStr = null;
-    private OntModelSpec ontModelSpec = null;
-
-    public RDBModelGenerator(BasicDataSource bds, String dbTypeStr, String modelNameStr, OntModelSpec ontModelSpec) {
-        this.ds = bds;
-        this.dbTypeStr = dbTypeStr;
-        this.modelNameStr = modelNameStr;
-        this.ontModelSpec = ontModelSpec;
-    }
-
-    public OntModel generateModel() {
-        try {
-            IDBConnection conn = new DBConnection(ds.getConnection(), dbTypeStr);
-            ModelMaker maker = ModelFactory.createModelRDBMaker(conn);
-            Model model = maker.openModel(modelNameStr);
-            OntModel oModel = ModelFactory.createOntologyModel(ontModelSpec, model);
-            oModel.prepare();
-            return oModel;
-        } catch (SQLException e) {
-            return null;
-        }
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/RegeneratingGraph.java

@@ -2,6 +2,9 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.graph.BulkUpdateHandler;
 import com.hp.hpl.jena.graph.Capabilities;
 import com.hp.hpl.jena.graph.Graph;
@@ -22,6 +25,8 @@ import com.hp.hpl.jena.vocabulary.RDF;
 
 public class RegeneratingGraph implements Graph, Regenerable {
 
+	private final static Log log = LogFactory.getLog(RegeneratingGraph.class);
+	
 	private GraphGenerator generator;
 	private Graph g;
 	
@@ -37,10 +42,14 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public void regenerate() {
 		this.g = generator.generateGraph();
-	}
+	}	
 	
+	/*
+	 * a nonsense query that should never send back actual result data
+	 */
 	private void sendTestQuery() {
-		this.g.contains(DAML_OIL.Thing.asNode(),RDF.type.asNode(),DAML_OIL.Thing.asNode());
+		this.g.contains(
+				DAML_OIL.Thing.asNode(),RDF.type.asNode(),DAML_OIL.Thing.asNode());
 	}
 
 	protected void finalize() {
@@ -61,6 +70,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean contains(Triple arg0) {
 		try {
+			regenerateIfClosed();
             return g.contains(arg0);
         } catch (Exception e) {
             regenerate();
@@ -70,7 +80,8 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean contains(Node arg0, Node arg1, Node arg2) {
 		try {
-            return g.contains(arg0, arg1, arg2);
+			regenerateIfClosed();
+			return g.contains(arg0, arg1, arg2);
         } catch (Exception e) {
             regenerate();
             return g.contains(arg0, arg1, arg2);
@@ -79,6 +90,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public void delete(Triple arg0) throws DeleteDeniedException {
 		try {
+			regenerateIfClosed();			
             g.delete(arg0);
         } catch (Exception e) {
             regenerate();
@@ -88,6 +100,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean dependsOn(Graph arg0) {
 		try {
+			regenerateIfClosed();			
             return g.dependsOn(arg0);
         } catch (Exception e) {
             regenerate();
@@ -97,6 +110,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 
 	public ExtendedIterator find(TripleMatch arg0) {
 		try {
+			regenerateIfClosed();
             return g.find(arg0);
         } catch (Exception e) {
             regenerate();
@@ -106,6 +120,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 
 	public ExtendedIterator find(Node arg0, Node arg1, Node arg2) {
 		try {
+			regenerateIfClosed();
             return g.find(arg0,arg1,arg2);
         } catch (Exception e) {
             regenerate();
@@ -115,6 +130,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public BulkUpdateHandler getBulkUpdateHandler() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getBulkUpdateHandler();
         } catch (Exception e) {
@@ -125,6 +141,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 
 	public Capabilities getCapabilities() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getCapabilities();
         } catch (Exception e) {
@@ -136,6 +153,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public GraphEventManager getEventManager() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getEventManager();
         } catch (Exception e) {
@@ -147,6 +165,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public PrefixMapping getPrefixMapping() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getPrefixMapping();
         } catch (Exception e) {
@@ -158,6 +177,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public Reifier getReifier() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getReifier();
         } catch (Exception e) {
@@ -169,6 +189,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public GraphStatisticsHandler getStatisticsHandler() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getStatisticsHandler();
         } catch (Exception e) {
@@ -180,6 +201,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public TransactionHandler getTransactionHandler() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
             return g.getTransactionHandler();
         } catch (Exception e) {
@@ -191,6 +213,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean isClosed() {
 		try {
+			regenerateIfClosed();
             return g.isClosed();
         } catch (Exception e) {
             regenerate();
@@ -201,6 +224,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean isEmpty() {
 		try {
+			regenerateIfClosed();
             return g.isEmpty();
         } catch (Exception e) {
             regenerate();
@@ -211,6 +235,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public boolean isIsomorphicWith(Graph arg0) {
 		try {
+			regenerateIfClosed();
             return g.isIsomorphicWith(arg0);
         } catch (Exception e) {
             regenerate();
@@ -221,6 +246,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public QueryHandler queryHandler() {
 		try {
+			regenerateIfClosed();
 			sendTestQuery();
 			return g.queryHandler();
 		} catch (Exception e) {
@@ -232,6 +258,7 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public int size() {
 		try {
+			regenerateIfClosed();
             return g.size();
         } catch (Exception e) {
             regenerate();
@@ -242,11 +269,18 @@ public class RegeneratingGraph implements Graph, Regenerable {
 	
 	public void add(Triple arg0) throws AddDeniedException {
 		try {
+			regenerateIfClosed();
             g.add(arg0);
         } catch (Exception e) {
             regenerate();
             g.add(arg0);
         }
 	}
+	
+	private void regenerateIfClosed() {
+		if (generator.isGraphClosed()) {
+			regenerate();
+		}
+	}
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SDBGraphGenerator.java

@@ -13,7 +13,7 @@ import com.hp.hpl.jena.sdb.StoreDesc;
 import java.sql.Connection;
 import java.sql.SQLException;
 
-public class SDBGraphGenerator implements GraphGenerator {
+public class SDBGraphGenerator implements SQLGraphGenerator {
 
 	private static final Log log = LogFactory.getLog(SDBGraphGenerator.class.getName());
 	
@@ -28,6 +28,14 @@ public class SDBGraphGenerator implements GraphGenerator {
     	this.storeDesc = storeDesc;
     	this.graphID = graphID;
     }
+    
+    public boolean isGraphClosed() {
+    	try {
+    		return (connection == null || connection.isClosed());
+        } catch (SQLException e) {
+        	throw new RuntimeException(e);
+        }
+    }
 
     public Graph generateGraph() {
         try {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/SQLGraphGenerator.java

@@ -2,10 +2,10 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import com.hp.hpl.jena.ontology.OntModel;
+import java.sql.Connection;
 
-public interface ModelGenerator {
+public interface SQLGraphGenerator extends GraphGenerator {
-
-    public OntModel generateModel();
 
+	public Connection getConnection();
+	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/VitroJenaModelMaker.java

@@ -346,7 +346,7 @@ public class VitroJenaModelMaker implements ModelMaker {
         Graph g = gen.generateGraph();
         Model m = ModelFactory.createModelForGraph(g);	
         memCache.add(m);
-        memCache.register(new MemToRDBModelSynchronizer(gen));
+        memCache.register(new MemToDBModelSynchronizer(gen));
         m.close();
         try {
             gen.getConnection().close();