VIVO-987 Properly shutdown the TripleSource instances.

When shutting down a ContentTripleSourceSDB instance, attempt to deregister the JDBC driver.
Also, attempt to shut down the AbandonedConnectionCleanupThread.
Each of these produce warning messages if not shut down.

webapp/src/edu/cornell/mannlib/vitro/webapp/application/ApplicationImpl.java

@@ -280,9 +280,11 @@ public class ApplicationImpl implements Application {
 		@Override
 		public void contextDestroyed(ServletContextEvent sce) {
 			Application app = ApplicationUtils.instance();
-			app.getSearchEngine().shutdown(app);
-			app.getImageProcessor().shutdown(app);
+			app.getConfigurationTripleSource().shutdown(app);
+			app.getContentTripleSource().shutdown(app);
 			app.getFileStorage().shutdown(app);
+			app.getImageProcessor().shutdown(app);
+			app.getSearchEngine().shutdown(app);
 		}
 	}
 

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

@@ -16,6 +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.shared.Lock;
 import com.hp.hpl.jena.tdb.TDB;
 import com.hp.hpl.jena.tdb.TDBFactory;
@@ -94,12 +95,7 @@ public class RDFServiceTDB extends RDFServiceJena {
 	@Override
 	public void close() {
 		if (this.dataset != null) {
-			dataset.getLock().enterCriticalSection(Lock.WRITE);
-			try {
-				dataset.close();
-			} finally {
-				dataset.getLock().leaveCriticalSection();
-			}
+			dataset.close();
 		}
 	}
 

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

@@ -4,8 +4,12 @@ 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;
 import java.util.Arrays;
+import java.util.Enumeration;
 
 import javax.servlet.ServletContext;
 import javax.sql.DataSource;
@@ -212,9 +216,62 @@ public class ContentTripleSourceSDB extends ContentTripleSource {
 
 	@Override
 	public void shutdown(Application application) {
+		if (this.modelMaker != null) {
+			this.modelMaker.close();
+		}
+		if (this.dataset != null) {
+			this.dataset.close();
+		}
+		if (this.rdfService != null) {
+			this.rdfService.close();
+		}
 		if (ds != null) {
+			String driverClassName = ds.getDriverClass();
 			ds.close();
+			attemptToDeregisterJdbcDriver(driverClassName);
+			cleanupAbandonedConnectionThread(driverClassName);
 		}
 	}
 
+	private void attemptToDeregisterJdbcDriver(String driverClassName) {
+		ClassLoader cl = Thread.currentThread().getContextClassLoader();
+
+		for (Enumeration<Driver> drivers = DriverManager.getDrivers(); drivers
+				.hasMoreElements();) {
+			Driver driver = drivers.nextElement();
+			if (driver.getClass().getClassLoader() == cl) {
+				// This driver was registered by the webapp's ClassLoader, so
+				// deregister it:
+				try {
+					DriverManager.deregisterDriver(driver);
+				} catch (SQLException ex) {
+					log.error("Error deregistering JDBC driver {" + driver
+							+ "}", ex);
+				}
+			} else {
+				// driver was not registered by the webapp's ClassLoader and may
+				// be in use elsewhere
+			}
+		}
+	}
+
+	/**
+	 * The MySQL driver leaves a thread running after it is deregistered.
+	 * Versions after 5.1.23 provide AbandonedConnectionCleanupThread.shutdown()
+	 * to stop this thread.
+	 * 
+	 * Using reflection to invoke this method means that we don't have a
+	 * hard-coded dependency to MySQL.
+	 */
+	private void cleanupAbandonedConnectionThread(String driverClassName) {
+		if (!driverClassName.contains("mysql")) {
+			return;
+		}
+		try {
+			Class.forName("com.mysql.jdbc.AbandonedConnectionCleanupThread")
+					.getMethod("shutdown").invoke(null);
+		} catch (Exception e) {
+			log.info("Failed to shutdown MySQL connection cleanup thread: " + e);
+		}
+	}
 }