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From lah...@apache.org
Subject svn commit: r1383138 - in /incubator/airavata/trunk/modules/registry/airavata-registry-service: ./ src/ src/main/ src/main/java/ src/main/java/org/ src/main/java/org/apache/ src/main/java/org/apache/airavata/ src/main/java/org/apache/airavata/registry/...
Date Mon, 10 Sep 2012 22:31:09 GMT
Author: lahiru
Date: Mon Sep 10 22:31:08 2012
New Revision: 1383138

URL: http://svn.apache.org/viewvc?rev=1383138&view=rev
Log:
adding new regstry-service to handle regisry initialization.

Added:
    incubator/airavata/trunk/modules/registry/airavata-registry-service/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/pom.xml
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/RegistryService.java
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/ConnectionPool.java
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/DatabaseCreator.java
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/JdbcStorage.java
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/
    incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/services.xml

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/pom.xml
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/pom.xml?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/pom.xml (added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/pom.xml Mon Sep 10
22:31:08 2012
@@ -0,0 +1,84 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license
agreements. See the NOTICE file 
+    distributed with this work for additional information regarding copyright ownership.
The ASF licenses this file to you under 
+    the Apache License, Version 2.0 (theÏ "License"); you may not use this file except
in compliance with the License. You may 
+    obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required
by applicable law or agreed to 
+    in writing, software distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF 
+    ANY ~ KIND, either express or implied. See the License for the specific language governing
permissions and limitations under 
+    the License. -->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <groupId>org.apache.airavata</groupId>
+        <artifactId>airavata</artifactId>
+        <version>0.5-incubating-SNAPSHOT</version>
+        <relativePath>../../pom.xml</relativePath>
+    </parent>
+
+    <modelVersion>4.0.0</modelVersion>
+    <artifactId>airavata-registry-service</artifactId>
+    <name>Airavata Registry Service</name>
+    <description>Registry Service to expose Registry as a web service</description>
+    <dependencies>
+<dependency>
+            <groupId>org.apache.axis2</groupId>
+            <artifactId>axis2-adb</artifactId>
+            <version>${axis2.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.axis2</groupId>
+            <artifactId>axis2-kernel</artifactId>
+            <version>${axis2.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-api</artifactId>
+            <version>1.2.8</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-impl</artifactId>
+            <version>1.2.8</version>
+        </dependency>
+<dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>jcl-over-slf4j</artifactId>
+            <version>${org.slf4j.version}</version>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+            <version>${org.slf4j.version}</version>
+            <scope>runtime</scope>
+        </dependency>
+
+	</dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-antrun-plugin</artifactId>
+                <version>1.6</version>
+                <executions>
+                    <execution>
+                        <id>restore-persistence</id>
+                        <phase>prepare-package</phase>
+                        <configuration>
+                            <tasks>
+                                <copy file="${project.build.outputDirectory}/services.xml"
tofile="${project.build.outputDirectory}/META-INF/services.xml" />
+                            </tasks>
+                        </configuration>
+                        <goals>
+                            <goal>run</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/RegistryService.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/RegistryService.java?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/RegistryService.java
(added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/RegistryService.java
Mon Sep 10 22:31:08 2012
@@ -0,0 +1,69 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.registry.services;
+
+import com.sun.tools.corba.se.idl.toJavaPortable.StringGen;
+import org.apache.airavata.registry.services.utils.DatabaseCreator;
+import org.apache.airavata.registry.services.utils.JdbcStorage;
+import org.apache.axis2.context.ConfigurationContext;
+import org.apache.axis2.description.AxisService;
+import org.apache.axis2.engine.ServiceLifeCycle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Connection;
+
+public class RegistryService implements ServiceLifeCycle {
+    private static final Logger logger = LoggerFactory.getLogger(RegistryService.class);
+
+    public static final String PERSISTANT_DATA = "persistant_data";
+    private JdbcStorage db;
+
+    @Override
+    public void startUp(ConfigurationContext configurationContext, AxisService axisService)
{
+        //todo have to read these properties from some configuration
+        String jdbcUrl = null;
+        String jdbcDriver = null;
+
+        db = new JdbcStorage(10, 50, jdbcUrl, jdbcDriver, true);
+
+        Connection conn = null;
+        try {
+            conn = db.connect();
+            if (!DatabaseCreator.isDatabaseStructureCreated(PERSISTANT_DATA, conn)) {
+                DatabaseCreator.createMsgBoxDatabase(conn);
+                logger.info("New Database created for Registry");
+            } else {
+                logger.info("Database already created for Registry!");
+            }
+        } catch (Exception e) {
+            logger.error(e.getMessage(), e);
+            throw new RuntimeException("Database failure");
+        } finally {
+            db.closeConnection(conn);
+        }
+    }
+
+    @Override
+    public void shutDown(ConfigurationContext configurationContext, AxisService axisService)
{
+        //To change body of implemented methods use File | Settings | File Templates.
+    }
+}

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/ConnectionPool.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/ConnectionPool.java?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/ConnectionPool.java
(added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/ConnectionPool.java
Mon Sep 10 22:31:08 2012
@@ -0,0 +1,382 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.registry.services.utils;
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.sql.DataSource;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Stack;
+import java.util.concurrent.Semaphore;
+
+
+/**
+ * A class for preallocating, recycling, and managing JDBC connections.
+ */
+public class ConnectionPool {
+    private static final Logger logger = LoggerFactory.getLogger(ConnectionPool.class);
+
+    private long MAX_IDLE_TIME = 5 * 60 * 1000; // 5 minutes
+
+    private String driver;
+    private String url;
+    private String username;
+    private String password;
+    private String jdbcUrl;
+
+    private int maxConnections;
+
+    private boolean autoCommit = true;
+    private boolean waitIfBusy;
+
+    private Semaphore needConnection = new Semaphore(0);
+    private boolean stop;
+
+    private Stack<Connection> availableConnections;
+    private Stack<Connection> busyConnections;
+
+    private HashMap<Connection, Long> lastAccessTimeRecord = new HashMap<Connection,
Long>();
+
+    private String urlType = "";
+
+    private DataSource datasource;
+
+    private int transactionIsolation = Connection.TRANSACTION_NONE;
+
+    private Thread clenupThread;
+    private Thread producerThread;
+
+    public ConnectionPool(String driver, String url, String username, String password, int
initialConnections,
+            int maxConnections, boolean waitIfBusy) throws SQLException {
+        this.driver = driver;
+        this.url = url;
+        this.username = username;
+        this.password = password;
+        this.urlType = "speratedURL";
+        initialize(initialConnections, maxConnections, waitIfBusy);
+    }
+
+    public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections,
+            boolean waitIfBusy, boolean autoCommit, int transactionIsolation) throws SQLException
{
+        this.driver = driver;
+        this.jdbcUrl = jdbcUrl;
+        this.urlType = "simpleURL";
+        this.autoCommit = autoCommit;
+        this.transactionIsolation = transactionIsolation;
+        initialize(initialConnections, maxConnections, waitIfBusy);
+    }
+
+    public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections,
boolean waitIfBusy)
+            throws SQLException {
+        this.driver = driver;
+        this.jdbcUrl = jdbcUrl;
+        this.urlType = "simpleURL";
+        initialize(initialConnections, maxConnections, waitIfBusy);
+    }
+
+    public ConnectionPool(DataSource dataSource, int initialConnections, int maxConnections,
boolean waitIfBusy)
+            throws SQLException {
+        this.urlType = "dataSource";
+        this.datasource = dataSource;
+        initialize(initialConnections, maxConnections, waitIfBusy);
+    }
+
+    /**
+     * Check if this connection pool is auto commit or not
+     *
+     * @return
+     */
+    public boolean isAutoCommit() {
+        return this.autoCommit;
+    }
+
+    private void initialize(int initialConnections, int maxConnections, boolean waitIfBusy)
throws SQLException {
+        this.maxConnections = maxConnections;
+        this.waitIfBusy = waitIfBusy;
+
+        int sizeOfConnections = (initialConnections > maxConnections) ? maxConnections
: initialConnections;
+
+        availableConnections = new Stack<Connection>();
+        busyConnections = new Stack<Connection>();
+
+        for (int i = 0; i < sizeOfConnections; i++) {
+            Connection con = makeNewConnection();
+            setTimeStamp(con);
+            availableConnections.push(con);
+
+        }
+
+        producerThread = new Thread(new FillUpThread());
+        producerThread.start();
+
+        clenupThread = new Thread(new CleanUpThread());
+        clenupThread.start();
+    }
+
+    public synchronized Connection getConnection() throws SQLException {
+        if (!availableConnections.isEmpty()) {
+            Connection existingConnection = availableConnections.pop();
+
+            // If connection on available list is closed (e.g.,
+            // it timed out), then remove it from available list
+            // and race for a connection again.
+            if (existingConnection.isClosed()) {
+                lastAccessTimeRecord.remove(existingConnection);
+                // notifyAll for fairness
+                notifyAll();
+            } else {
+                busyConnections.push(existingConnection);
+                setTimeStamp(existingConnection);
+                return existingConnection;
+            }
+        } else if (!waitIfBusy && busyConnections.size() >= maxConnections) {
+            // You reached maxConnections limit and waitIfBusy flag is false.
+            // Throw SQLException in such a case.
+            throw new SQLException("Connection limit reached");
+        } else {
+
+            if (busyConnections.size() < maxConnections) {
+                // available connection is empty, but total number of connection
+                // doesn't reach maxConnection. Request for more connection
+                needConnection.release();
+            }
+
+            try {
+                // wait for free connection
+                wait();
+            } catch (InterruptedException ie) {
+            }
+        }
+        // always race for connection forever
+        return getConnection();
+    }
+
+    // This explicitly makes a new connection. Called in
+    // the foreground when initializing the ConnectionPool,
+    // and called in the background when running.
+    private Connection makeNewConnection() throws SQLException {
+        try {
+            // Load database driver if not already loaded
+            Class.forName(driver);
+            Connection connection;
+            // Establish network connection to database
+            if (urlType.equals("speratedURL")) {
+                connection = DriverManager.getConnection(url, username, password);
+            } else if (urlType.equals("simpleURL")) {
+                connection = DriverManager.getConnection(jdbcUrl);
+            } else { // if(urlType.equals("dataSource")){
+                connection = datasource.getConnection();
+            }
+            connection.setTransactionIsolation(this.transactionIsolation);
+            connection.setAutoCommit(this.autoCommit);
+            return connection;
+        } catch (ClassNotFoundException cnfe) {
+            // Simplify try/catch blocks of people using this by
+            // throwing only one exception type.
+            throw new SQLException("Can't find class for driver: " + driver);
+        }
+    }
+
+    private synchronized void fillUpConnection(Connection conn) {
+        setTimeStamp(conn);
+        availableConnections.push(conn);
+
+        // notify all since new connection is created
+        notifyAll();
+    }
+
+    private void setTimeStamp(Connection connection) {
+        lastAccessTimeRecord.put(connection, System.currentTimeMillis());
+    }
+
+    // The database connection cannot be left idle for too long, otherwise TCP
+    // connection will be broken.
+    /**
+     * From http://forums.mysql.com/read.php?39,28450,57460#msg-57460 Okay, then it looks
like wait_timeout on the
+     * server is killing your connection (it is set to 8 hours of idle time by default).
Either set that value higher on
+     * your server, or configure your connection pool to not hold connections idle that long
(I prefer the latter). Most
+     * folks I know that run MySQL with a connection pool in high-load production environments
only let connections sit
+     * idle for a matter of minutes, since it only takes a few milliseconds to open a connection,
and the longer one
+     * sits idle the more chance it will go "bad" because of a network hiccup or the MySQL
server being restarted.
+     *
+     * @throws SQLException
+     */
+    private boolean isConnectionStale(Connection connection) {
+        long currentTime = System.currentTimeMillis();
+        long lastAccess = lastAccessTimeRecord.get(connection);
+        if (currentTime - lastAccess > MAX_IDLE_TIME) {
+            return true;
+        } else
+            return false;
+    }
+
+    private synchronized void closeStaleConnections() {
+        // close idle connections
+        Iterator<Connection> iter = availableConnections.iterator();
+        while (iter.hasNext()) {
+            Connection existingConnection = iter.next();
+            if (isConnectionStale(existingConnection)) {
+                try {
+                    existingConnection.close();
+                    iter.remove();
+                } catch (SQLException sql) {
+                    logger.error(sql.getMessage(), sql);
+                }
+            }
+        }
+        // close busy connections that have been checked out for too long.
+        // This should not happen since this means program has bug for not
+        // releasing connections .
+        iter = busyConnections.iterator();
+        while (iter.hasNext()) {
+            Connection busyConnection = iter.next();
+            if (isConnectionStale(busyConnection)) {
+                try {
+                    busyConnection.close();
+                    iter.remove();
+                    logger.warn("****Connection has checked out too long. Forced release.
Check the program for calling release connection [free(Connection) method]");
+                } catch (SQLException sql) {
+                    logger.error(sql.getMessage(), sql);
+                }
+            }
+        }
+    }
+
+    public synchronized void free(Connection connection) {
+        busyConnections.removeElement(connection);
+        availableConnections.addElement(connection);
+        // Wake up threads that are waiting for a connection
+        notifyAll();
+    }
+
+    /**
+     * Close all the connections. Use with caution: be sure no connections are in use before
calling. Note that you are
+     * not <I>required</I> to call this when done with a ConnectionPool, since
connections are guaranteed to be closed
+     * when garbage collected. But this method gives more control regarding when the connections
are closed.
+     */
+    public synchronized void dispose() {
+        logger.info("Connection Pool Shutting down");
+
+        // stop clean up thread
+        this.stop = true;
+        this.clenupThread.interrupt();
+
+        // stop producer up thread
+        this.producerThread.interrupt();
+
+        // close all connection
+        closeConnections(availableConnections);
+        availableConnections = new Stack<Connection>();
+        closeConnections(busyConnections);
+        busyConnections = new Stack<Connection>();
+        lastAccessTimeRecord.clear();
+
+        logger.info("All connection is closed");
+
+        try {
+            this.clenupThread.join();
+            this.producerThread.join();
+        } catch (Exception e) {
+            logger.error("Cannot shutdown cleanup thread", e);
+        }
+
+        logger.info("Connection Pool Shutdown");
+    }
+
+    private void closeConnections(Stack<Connection> connections) {
+        while (!connections.isEmpty()) {
+            Connection connection = connections.pop();
+            try {
+                if (!connection.isClosed()) {
+                    connection.close();
+                }
+            } catch (SQLException sqle) {
+                // Ignore errors; garbage collect anyhow
+                logger.warn(sqle.getMessage());
+            }
+        }
+    }
+
+    public synchronized String toString() {
+        String info = "ConnectionPool(" + url + "," + username + ")" + ", available=" + availableConnections.size()
+                + ", busy=" + busyConnections.size() + ", max=" + maxConnections;
+        return (info);
+    }
+
+    class CleanUpThread implements Runnable {
+        public void run() {
+            while (!stop) {
+                try {
+                    Thread.sleep(MAX_IDLE_TIME);
+                    closeStaleConnections();
+                } catch (InterruptedException e) {
+                    logger.info("Clean up thread is interrupted to close");
+                }
+            }
+        }
+    }
+
+    class FillUpThread implements Runnable {
+        public void run() {
+            while (!stop) {
+                try {
+                    // block until get
+                    needConnection.acquire();
+
+                    Connection conn = makeNewConnection();
+                    fillUpConnection(conn);
+                } catch (SQLException e) {
+                    // cannot create connection (increase semaphore value back)
+                    needConnection.release();
+                    logger.error(e.getMessage(), e);
+                } catch (InterruptedException e) {
+                    logger.info("Fill up thread is interrupted to close");
+                    break;
+                }
+            }
+        }
+    }
+}

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/DatabaseCreator.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/DatabaseCreator.java?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/DatabaseCreator.java
(added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/DatabaseCreator.java
Mon Sep 10 22:31:08 2012
@@ -0,0 +1,348 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.registry.services.utils;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.sql.Connection;
+import java.sql.DatabaseMetaData;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.SQLWarning;
+import java.sql.Statement;
+import java.util.StringTokenizer;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * This class creates the database tables required for messagebox and messagebroker with
default configuration this
+ * class creates embedded derby database in local file system. User can specify required
database in appropriate
+ * properties files.
+ */
+public class DatabaseCreator {
+
+    public enum DatabaseType {
+        derby("(?i).*derby.*"), mysql("(?i).*mysql.*"), other("");
+
+        private String pattern;
+
+        private DatabaseType(String matchingPattern) {
+            this.pattern = matchingPattern;
+        }
+
+        public String getMatchingPattern() {
+            return this.pattern;
+        }
+    }
+
+    private static DatabaseType[] supportedDatabase = new DatabaseType[] { DatabaseType.derby,
DatabaseType.mysql };
+
+    private static Logger log = LoggerFactory.getLogger(DatabaseCreator.class);
+    private static final String delimiter = ";";
+
+    /**
+     * Creates database
+     *
+     * @throws Exception
+     */
+    public static void createMsgBoxDatabase(Connection conn) throws Exception {
+        createDatabase("data", conn);
+    }
+
+
+
+    /**
+     * Checks whether database tables are created by using select * on given table name
+     *
+     * @param tableName
+     *            Table which should be existed
+     * @return <code>true</core> if checkSQL is success, else <code>false</code>
.
+     */
+    public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
+        try {
+
+            log.debug("Running a query to test the database tables existence.");
+
+            // check whether the tables are already created with a query
+            Statement statement = null;
+            try {
+                statement = conn.createStatement();
+                ResultSet rs = statement.executeQuery("select * from " + tableName);
+                if (rs != null) {
+                    rs.close();
+                }
+            } finally {
+                try {
+                    if (statement != null) {
+                        statement.close();
+                    }
+                } catch (SQLException e) {
+                    return false;
+                }
+            }
+        } catch (SQLException e) {
+            return false;
+        }
+
+        return true;
+    }
+
+    /**
+     * executes given sql
+     *
+     * @param sql
+     * @throws Exception
+     */
+    private static void executeSQL(String sql, Connection conn) throws Exception {
+        // Check and ignore empty statements
+        if ("".equals(sql.trim())) {
+            return;
+        }
+
+        Statement statement = null;
+        try {
+            log.debug("SQL : " + sql);
+
+            boolean ret;
+            int updateCount = 0, updateCountTotal = 0;
+            statement = conn.createStatement();
+            ret = statement.execute(sql);
+            updateCount = statement.getUpdateCount();
+            do {
+                if (!ret) {
+                    if (updateCount != -1) {
+                        updateCountTotal += updateCount;
+                    }
+                }
+                ret = statement.getMoreResults();
+                if (ret) {
+                    updateCount = statement.getUpdateCount();
+                }
+            } while (ret);
+
+            log.debug(sql + " : " + updateCountTotal + " rows affected");
+
+            SQLWarning warning = conn.getWarnings();
+            while (warning != null) {
+                log.info(warning + " sql warning");
+                warning = warning.getNextWarning();
+            }
+            conn.clearWarnings();
+        } catch (SQLException e) {
+            if (e.getSQLState().equals("X0Y32")) {
+                // eliminating the table already exception for the derby
+                // database
+                log.info("Table Already Exists", e);
+            } else {
+                throw new Exception("Error occurred while executing : " + sql, e);
+            }
+        } finally {
+            if (statement != null) {
+                try {
+                    statement.close();
+                } catch (SQLException e) {
+                    log.error("Error occurred while closing result set.", e);
+                }
+            }
+        }
+    }
+
+    /**
+     * computes relatational database type using database name
+     *
+     * @return DatabaseType
+     * @throws Exception
+     *
+     */
+    public static DatabaseType getDatabaseType(Connection conn) throws Exception {
+        try {
+            if (conn != null && (!conn.isClosed())) {
+                DatabaseMetaData metaData = conn.getMetaData();
+                String databaseProductName = metaData.getDatabaseProductName();
+                return checkType(databaseProductName);
+            }
+        } catch (SQLException e) {
+            String msg = "Failed to create Airavatadatabase." + e.getMessage();
+            log.error(msg, e);
+            throw new Exception(msg, e);
+        }
+        return DatabaseType.other;
+    }
+
+    /**
+     * Overloaded method with String input
+     *
+     * @return DatabaseType
+     * @throws Exception
+     *
+     */
+    public static DatabaseType getDatabaseType(String dbUrl) throws Exception {
+        return checkType(dbUrl);
+    }
+
+    private static DatabaseType checkType(String text) throws Exception {
+        try {
+            if (text != null) {
+                for (DatabaseType type : supportedDatabase) {
+                    if (text.matches(type.getMatchingPattern()))
+                        return type;
+                }
+            }
+            String msg = "Unsupported database: " + text
+                    + ". Database will not be created automatically by the Airavata. "
+                    + "Please create the database using appropriate database scripts for
" + "the database.";
+            throw new Exception(msg);
+
+        } catch (SQLException e) {
+            String msg = "Failed to create Airavatadatabase." + e.getMessage();
+            log.error(msg, e);
+            throw new Exception(msg, e);
+        }
+    }
+
+    /**
+     * Get scripts location which is prefix + "-" + databaseType + ".sql"
+     *
+     * @param prefix
+     * @param databaseType
+     * @return script location
+     */
+    private static String getScriptLocation(String prefix, DatabaseType databaseType) {
+        String scriptName = prefix + "-" + databaseType + ".sql";
+        log.debug("Loading database script from :" + scriptName);
+        return "database_scripts" + File.separator + scriptName;
+    }
+
+    private static void createDatabase(String prefix, Connection conn) throws Exception {
+        Statement statement = null;
+        try {
+            conn.setAutoCommit(false);
+            statement = conn.createStatement();
+            executeSQLScript(getScriptLocation(prefix, DatabaseCreator.getDatabaseType(conn)),
conn);
+            conn.commit();
+            log.debug("Tables are created successfully.");
+        } catch (SQLException e) {
+            String msg = "Failed to create database tables for Airavata resource store. "
+ e.getMessage();
+            log.error(msg, e);
+            conn.rollback();
+            throw new Exception(msg, e);
+        } finally {
+            conn.setAutoCommit(true);
+            try {
+                if (statement != null) {
+                    statement.close();
+                }
+            } catch (SQLException e) {
+                log.error("Failed to close statement.", e);
+            }
+        }
+    }
+
+    private static void executeSQLScript(String dbscriptName, Connection conn) throws Exception
{
+        StringBuffer sql = new StringBuffer();
+        BufferedReader reader = null;
+
+        try {
+            InputStream is = DatabaseCreator.class.getClassLoader().getResourceAsStream(dbscriptName);
+            reader = new BufferedReader(new InputStreamReader(is));
+            String line;
+            while ((line = reader.readLine()) != null) {
+                line = line.trim();
+                if (line.startsWith("//")) {
+                    continue;
+                }
+                if (line.startsWith("--")) {
+                    continue;
+                }
+                StringTokenizer st = new StringTokenizer(line);
+                if (st.hasMoreTokens()) {
+                    String token = st.nextToken();
+                    if ("REM".equalsIgnoreCase(token)) {
+                        continue;
+                    }
+                }
+                sql.append(" ").append(line);
+
+                // SQL defines "--" as a comment to EOL
+                // and in Oracle it may contain a hint
+                // so we cannot just remove it, instead we must end it
+                if (line.indexOf("--") >= 0) {
+                    sql.append("\n");
+                }
+                if ((checkStringBufferEndsWith(sql, delimiter))) {
+                    executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn);
+                    sql.replace(0, sql.length(), "");
+                }
+            }
+            // Catch any statements not followed by ;
+            if (sql.length() > 0) {
+                executeSQL(sql.toString(), conn);
+            }
+        } catch (IOException e) {
+            log.error("Error occurred while executing SQL script for creating Airavata database",
e);
+            throw new Exception("Error occurred while executing SQL script for creating Airavata
database", e);
+
+        } finally {
+            if (reader != null) {
+                reader.close();
+            }
+        }
+    }
+
+    /**
+     * Checks that a string buffer ends up with a given string. It may sound trivial with
the existing JDK API but the
+     * various implementation among JDKs can make those methods extremely resource intensive
and perform poorly due to
+     * massive memory allocation and copying. See
+     *
+     * @param buffer
+     *            the buffer to perform the check on
+     * @param suffix
+     *            the suffix
+     * @return <code>true</code> if the character sequence represented by the
argument is a suffix of the character
+     *         sequence represented by the StringBuffer object; <code>false</code>
otherwise. Note that the result will
+     *         be <code>true</code> if the argument is the empty string.
+     */
+    public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) {
+        if (suffix.length() > buffer.length()) {
+            return false;
+        }
+        // this loop is done on purpose to avoid memory allocation performance
+        // problems on various JDKs
+        // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and
+        // implementation is ok though does allocation/copying
+        // StringBuffer.toString().endsWith() does massive memory
+        // allocation/copying on JDK 1.5
+        // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169
+        int endIndex = suffix.length() - 1;
+        int bufferIndex = buffer.length() - 1;
+        while (endIndex >= 0) {
+            if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) {
+                return false;
+            }
+            bufferIndex--;
+            endIndex--;
+        }
+        return true;
+    }
+}

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/JdbcStorage.java
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/JdbcStorage.java?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/JdbcStorage.java
(added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/java/org/apache/airavata/registry/services/utils/JdbcStorage.java
Mon Sep 10 22:31:08 2012
@@ -0,0 +1,176 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.registry.services.utils;
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class JdbcStorage {
+    private static Logger log = LoggerFactory.getLogger(JdbcStorage.class);
+
+    private ConnectionPool connectionPool;
+
+    public JdbcStorage(String jdbcUrl, String jdbcDriver) {
+        // default init connection and max connection
+        this(3, 50, jdbcUrl, jdbcDriver, true);
+    }
+
+    public JdbcStorage(int initCon, int maxCon, String url, String driver, boolean enableTransactions)
{
+        try {
+            if (enableTransactions) {
+                connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true, false,
+                        Connection.TRANSACTION_SERIALIZABLE);
+            } else {
+                connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true);
+            }
+        } catch (Exception e) {
+            throw new RuntimeException("Failed to create database connection pool.", e);
+        }
+    }
+
+    /**
+     * Check if this connection pool is auto commit or not
+     *
+     * @return
+     */
+    public boolean isAutoCommit() {
+        return connectionPool.isAutoCommit();
+    }
+
+    public void commit(Connection conn) {
+        try {
+            if (conn != null && !conn.getAutoCommit()) {
+                conn.commit();
+            }
+        } catch (SQLException sqle) {
+            log.error("Cannot commit data", sqle);
+        }
+    }
+
+    public void commitAndFree(Connection conn) {
+        commit(conn);
+        closeConnection(conn);
+    }
+
+    public void rollback(Connection conn) {
+        try {
+            if (conn != null && !conn.getAutoCommit()) {
+                conn.rollback();
+            }
+        } catch (SQLException sqle) {
+            log.error("Cannot Rollback data", sqle);
+        }
+    }
+
+    public void rollbackAndFree(Connection conn) {
+        rollback(conn);
+        closeConnection(conn);
+    }
+
+    public Connection connect() {
+
+        Connection conn = null;
+        try {
+            conn = connectionPool.getConnection();
+        } catch (SQLException e) {
+            e.printStackTrace();
+            log.error(e.getMessage(), e);
+        }
+        return conn;
+    }
+
+    /**
+     * This method is provided so that you can have better control over the statement. For
example: You can use
+     * stmt.setString to convert quotation mark automatically in an UPDATE statement
+     *
+     * NOTE: Statement is closed after execution
+     */
+    public int executeUpdateAndClose(PreparedStatement stmt) throws SQLException {
+        int rows = 0;
+        try {
+            rows = stmt.executeUpdate();
+            if (rows == 0) {
+                log.info("Problem: 0 rows affected by insert/update/delete statement.");
+            }
+        } finally {
+            stmt.close();
+        }
+        return rows;
+    }
+
+    public int countRow(String tableName, String columnName) throws SQLException {
+        String query = new String("SELECT COUNT(" + columnName + ") FROM " + tableName);
+        int count = -1;
+        Connection conn = null;
+        PreparedStatement stmt = null;
+        try {
+            conn = connectionPool.getConnection();
+            stmt = conn.prepareStatement(query);
+            ResultSet rs = stmt.executeQuery();
+            rs.next();
+            count = rs.getInt(1);
+            commit(conn);
+        } catch (SQLException sql) {
+            rollback(conn);
+            throw sql;
+        } finally {
+            try {
+                if (stmt != null && !stmt.isClosed()) {
+                    stmt.close();
+                }
+            } finally {
+                closeConnection(conn);
+            }
+        }
+        return count;
+    }
+
+    public void quietlyClose(Connection conn, Statement... stmts) {
+        if (stmts != null) {
+            for (Statement stmt : stmts) {
+                try {
+                    if (stmt != null && !stmt.isClosed()) {
+                        stmt.close();
+                    }
+                } catch (SQLException sql) {
+                    log.error(sql.getMessage(), sql);
+                }
+            }
+        }
+        closeConnection(conn);
+    }
+
+    public void closeConnection(Connection conn) {
+        if (conn != null) {
+            connectionPool.free(conn);
+        }
+    }
+
+    public void closeAllConnections() {
+        if (connectionPool != null)
+            connectionPool.dispose();
+    }
+}

Added: incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/services.xml
URL: http://svn.apache.org/viewvc/incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/services.xml?rev=1383138&view=auto
==============================================================================
--- incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/services.xml
(added)
+++ incubator/airavata/trunk/modules/registry/airavata-registry-service/src/main/resources/services.xml
Mon Sep 10 22:31:08 2012
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+	license agreements. See the NOTICE file distributed with this work for additional 
+	information regarding copyright ownership. The ASF licenses this file to 
+	you under the Apache License, Version 2.0 (theÏ "License"); you may not use 
+	this file except in compliance with the License. You may obtain a copy of 
+	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+	by applicable law or agreed to in writing, software distributed under the 
+	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+	OF ANY ~ KIND, either express or implied. See the License for the specific 
+	language governing permissions and limitations under the License. -->
+<service name="RegistryService" >
+	<Description>
+		Provide Simple Service for Testing Purpose including addition, subtraction, multiplication,
array-generator
+	</Description>
+	<messageReceivers>
+		<messageReceiver mep="http://www.w3.org/2004/08/wsdl/in-only" class="org.apache.axis2.rpc.receivers.RPCInOnlyMessageReceiver"
/>
+		<messageReceiver  mep="http://www.w3.org/2004/08/wsdl/in-out"  class="org.apache.axis2.rpc.receivers.RPCMessageReceiver"/>
+	</messageReceivers>
+	<parameter name="ServiceClass" locked="false">org.apache.airavata.registry.services.RegistryService</parameter>
+</service>



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