- hibernate bug fixed and related to a join tables that have some columns with identical name. Bug resolved using JDBC. GetConnection method changed in the SubmitQuery algorithm to create the connection with JDBC.

- timer added in the SubmitQuery algorithm that stops the query execution  after 30 minutes.

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-access/DatabasesResourcesManagerAlgorithms@99396 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQuery.java

@@ -2,13 +2,18 @@ package org.gcube.dataaccess.algorithms.drmalgorithms;
 
 import java.io.File;
 import java.io.IOException;
+import java.sql.Connection;
+import java.sql.DriverManager;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Timer;
+import java.util.TimerTask;
 import java.util.UUID;
 
+import org.apache.commons.httpclient.UsernamePasswordCredentials;
 import org.gcube.common.scope.api.ScopeProvider;
 import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
 import org.gcube.dataaccess.databases.access.DatabasesDiscoverer;
@@ -33,14 +38,15 @@ import com.adventnet.swissqlapi.sql.parser.ParseException;
  * map.
  */
 public class SubmitQuery extends StandardLocalExternalAlgorithm {
-
+	
+	static long maximum_execution_time = 30*60*1000;   //time to stop execution query
 	private LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
 	// object that allows to manage some operations on a database
 	private DatabaseManagement mgt;
 	// variable that keeps track of the database's type
 	private String driverInfo;
 
-	private SessionFactory sf;
+	private Connection dbconnection;
 	// database's parameters specified by the user
 	private String resourceName = null;
 	private String databaseName = null;
@@ -59,6 +65,16 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 	// variable used to filter the disallowed queries
 	private boolean NotAllowedQuery = false;
 
+	//class for the timer to stop execution query
+	private class ExecutionStopper extends TimerTask {
+		@Override
+		public void run() {
+			AnalysisLogger.getLogger().debug("ExecutionStopper: Stopping execution");
+			shutdown();
+		}
+ 	}
+ 
+	
 	@Override
 	public void init() throws Exception {
 
@@ -92,19 +108,22 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 			HibernateException {
 
 		AnalysisLogger.getLogger().debug("In SubmitQuery->Processing");
-
+		
+		Timer stopper = new Timer();
+		stopper.schedule(new ExecutionStopper(),maximum_execution_time); 
+		
 		try {
 			// retrieve information
 			List<String> Info = retrieveInfo();
 
 			// create the connection
-			sf = getConnection(Info);
+			dbconnection = getConnection(Info);
 
 			// submit a query
 			map = submitQuery();
 
 			// close the connection
-			sf.close();
+			dbconnection.close();
 
 		} catch (HibernateException h) {
 
@@ -162,8 +181,18 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 			throw e4;
 
 		} finally {
-			if (sf.isClosed() == false) {
-				mgt.closeConnection();
+			if (dbconnection!=null && dbconnection.isClosed() == false) {
+				dbconnection.close();
+			}
+			//remove the timer if the execution query has already terminated
+			if (stopper!=null){
+				try{
+				stopper.cancel();
+				stopper.purge();
+				AnalysisLogger.getLogger().debug("In SubmitQuery-> Execution stopper terminated");
+				}catch(Exception e){
+					AnalysisLogger.getLogger().debug("In SubmitQuery-> Could not stop execution stopper "+e.getMessage() );
+				}
 			}
 		}
 	}
@@ -265,9 +294,12 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 	public void shutdown() {
 				
 		AnalysisLogger.getLogger().debug("In SubmitQuery->Shutdown");
-		
-		if (sf.isClosed() == false) {
-			mgt.closeConnection();
+		try{
+		if (dbconnection!=null && dbconnection.isClosed() == false) {
+			dbconnection.close();
+		}
+		}catch(Exception e){
+			AnalysisLogger.getLogger().debug("In SubmitQuery->Unable to close connection "+e.getMessage());
 		}
 	}
 
@@ -363,7 +395,7 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 	}
 
 	// create the database's connection
-	private SessionFactory getConnection(List<String> Info) throws IOException {
+	private Connection getConnection(List<String> Info) throws Exception {
 
 		// create the connection
 		Iterator<String> iterator = Info.iterator();
@@ -375,12 +407,15 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 		String DatabaseURL = iterator.next();
 		String DatabaseName = iterator.next();
 
-		SessionFactory sf = mgt.createConnection(DatabaseUserName,
-				DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL,
-				DatabaseName);
-		AnalysisLogger.getLogger().debug(
-				"In SubmitQuery->database " + DatabaseName + ": connected");
-		return sf;
+		// Load the database driver
+		Class.forName(DatabaseDriver) ;
+		// Get a connection to the database
+	    Connection conn = DriverManager.getConnection(DatabaseURL,DatabaseUserName,DatabasePassword) ;
+		if (conn!=null){
+			AnalysisLogger.getLogger().debug(
+					"In SubmitQuery->database " + DatabaseName + ": connected");	
+		}
+		return conn;
 	}
 
 	// Method that allows to submit a query
@@ -504,7 +539,7 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 				// sf, config.getPersistencePath());
 
 				result = mgt
-						.submitQuery(query, sf, config.getPersistencePath());
+						.submitQuery(query, dbconnection, config.getPersistencePath());
 			}
 
 			if (driverInfo.toLowerCase().contains("mysql")) {
@@ -515,7 +550,7 @@ public class SubmitQuery extends StandardLocalExternalAlgorithm {
 				// sf, config.getPersistencePath());
 
 				result = mgt
-						.submitQuery(query, sf, config.getPersistencePath());
+						.submitQuery(query, dbconnection, config.getPersistencePath());
 			}
 
 			if (result == null) {