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From shame...@apache.org
Subject [3/8] airavata git commit: moved commons-utils to commons module
Date Thu, 11 Jun 2015 21:34:44 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DBUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DBUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DBUtil.java
deleted file mode 100644
index bb2ff1d..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DBUtil.java
+++ /dev/null
@@ -1,334 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.commons.dbcp.BasicDataSource;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.sql.DataSource;
-import java.sql.*;
-import java.util.Properties;
-
-/**
- * Database lookup. Abstracts out JDBC operations.
- */
-public class DBUtil {
-
-    private String jdbcUrl;
-    private String databaseUserName;
-    private String databasePassword;
-    private String driverName;
-
-    protected static Logger log = LoggerFactory.getLogger(DBUtil.class);
-
-    private Properties properties;
-
-    public DBUtil(String jdbcUrl, String userName, String password, String driver) throws InstantiationException,
-            IllegalAccessException, ClassNotFoundException {
-
-        this.jdbcUrl = jdbcUrl;
-        this.databaseUserName = userName;
-        this.databasePassword = password;
-        this.driverName = driver;
-
-        init();
-    }
-
-    /**
-     * Initializes and load driver. Must be called this before calling anyother method.
-     * 
-     * @throws ClassNotFoundException
-     *             If DB driver is not found.
-     * @throws InstantiationException
-     *             If unable to create driver class.
-     * @throws IllegalAccessException
-     *             If security does not allow users to instantiate driver object.
-     */
-    private void init() throws ClassNotFoundException, InstantiationException, IllegalAccessException {
-        properties = new Properties();
-
-        properties.put("user", databaseUserName);
-        properties.put("password", databasePassword);
-        properties.put("characterEncoding", "ISO-8859-1");
-        properties.put("useUnicode", "true");
-
-        loadDriver();
-    }
-
-    /**
-     * Generic method to query values in the database.
-     * 
-     * @param tableName
-     *            Table name to query
-     * @param selectColumn
-     *            The column selecting
-     * @param whereValue
-     *            The condition query
-     * @return The value appropriate to the query.
-     * @throws SQLException
-     *             If an error occurred while querying
-     */
-    public String getMatchingColumnValue(String tableName, String selectColumn, String whereValue) throws SQLException {
-        return getMatchingColumnValue(tableName, selectColumn, selectColumn, whereValue);
-    }
-
-    /**
-     * Generic method to query values in the database.
-     * 
-     * @param tableName
-     *            Table name to query
-     * @param selectColumn
-     *            The column selecting
-     * @param whereColumn
-     *            The column which condition should apply
-     * @param whereValue
-     *            The condition query
-     * @return The value appropriate to the query.
-     * @throws SQLException
-     *             If an error occurred while querying
-     */
-    public String getMatchingColumnValue(String tableName, String selectColumn, String whereColumn, String whereValue)
-            throws SQLException {
-
-        StringBuilder stringBuilder = new StringBuilder();
-
-        stringBuilder.append("SELECT ").append(selectColumn).append(" FROM ").append(tableName).append(" WHERE ")
-                .append(whereColumn).append(" = ?");
-
-        String sql = stringBuilder.toString();
-
-        Connection connection = getConnection();
-
-        PreparedStatement ps = connection.prepareStatement(sql);
-        ResultSet rs = null;
-
-        try {
-            ps.setString(1, whereValue);
-            rs = ps.executeQuery();
-
-            if (rs.next()) {
-                return rs.getString(1);
-            }
-
-        } finally {
-            try {
-                if (rs != null) {
-                    rs.close();
-                }
-
-                ps.close();
-                connection.close();
-
-            } catch (Exception ignore) {
-                log.error("An error occurred while closing database connections ", ignore);
-            }
-        }
-
-        return null;
-    }
-
-    /**
-     * Create table utility method.
-     * 
-     * @param sql
-     *            SQL to be executed.
-     * @throws SQLException
-     *             If an error occurred while creating the table.
-     */
-    public void executeSQL(String sql) throws SQLException {
-
-        Connection connection = getConnection();
-
-        PreparedStatement ps = connection.prepareStatement(sql);
-
-        try {
-            ps.executeUpdate();
-            connection.commit();
-        } finally {
-            try {
-                if (ps != null) {
-                    ps.close();
-                }
-
-                connection.close();
-
-            } catch (Exception ignore) {
-                log.error("An error occurred while closing database connections ", ignore);
-            }
-        }
-
-    }
-
-    private void loadDriver() throws ClassNotFoundException, IllegalAccessException, InstantiationException {
-        Class.forName(driverName).newInstance();
-    }
-
-    /**
-     * Gets a new DBCP data source.
-     * 
-     * @return A new data source.
-     */
-    public DataSource getDataSource() {
-        BasicDataSource ds = new BasicDataSource();
-        ds.setDriverClassName(this.driverName);
-        ds.setUsername(this.databaseUserName);
-        ds.setPassword(this.databasePassword);
-        ds.setUrl(this.jdbcUrl);
-
-        return ds;
-    }
-
-    /**
-     * Creates a new JDBC connections based on provided DBCP properties.
-     * 
-     * @return A new DB connection.
-     * @throws SQLException
-     *             If an error occurred while creating the connection.
-     */
-    public Connection getConnection() throws SQLException {
-        Connection connection = DriverManager.getConnection(jdbcUrl, properties);
-        connection.setAutoCommit(false);
-        return connection;
-    }
-
-    /**
-     * Utility method to close statements and connections.
-     * 
-     * @param preparedStatement
-     *            The prepared statement to close.
-     * @param connection
-     *            The connection to close.
-     */
-    public static void cleanup(PreparedStatement preparedStatement, Connection connection) {
-        if (preparedStatement != null) {
-            try {
-                preparedStatement.close();
-            } catch (SQLException e) {
-                log.error("Error closing prepared statement.", e);
-            }
-        }
-        if (connection != null) {
-            try {
-                connection.close();
-            } catch (SQLException e) {
-                log.error("Error closing database connection.", e);
-            }
-        }
-    }
-
-    /**
-     * Utility method to close statements and connections.
-     *
-     * @param preparedStatement
-     *            The prepared statement to close.
-     */
-    public static void cleanup(PreparedStatement preparedStatement) {
-        if (preparedStatement != null) {
-            try {
-                preparedStatement.close();
-            } catch (SQLException e) {
-                log.error("Error closing prepared statement.", e);
-            }
-        }
-    }
-
-    /**
-     * Utility method to close statements and connections.
-     *
-     * @param preparedStatement
-     *            The prepared statement to close.
-     */
-    public static void cleanup(PreparedStatement preparedStatement, ResultSet resultSet) {
-        if (resultSet != null) {
-            try {
-                resultSet.close();
-            } catch (SQLException e) {
-                log.error("Error closing prepared statement.", e);
-            }
-        }
-
-        cleanup(preparedStatement);
-    }
-
-    /**
-     * Cleanup the connection.
-     * @param connection The connection to close.
-     */
-    public static void cleanup(Connection connection) {
-        if (connection != null) {
-            try {
-                connection.close();
-            } catch (SQLException e) {
-                log.debug("Error closing connection.", e);
-                log.warn("Error closing connection.");
-            }
-        }
-    }
-
-    /**
-     * Mainly useful for tests.
-     * 
-     * @param tableName
-     *            The table name.
-     * @param connection
-     *            The connection to be used.
-     */
-    public static void truncate(String tableName, Connection connection) throws SQLException {
-
-        String sql = "delete from " + tableName;
-
-        PreparedStatement preparedStatement = connection.prepareStatement(sql);
-        preparedStatement.executeUpdate();
-
-        connection.commit();
-
-    }
-
-    /**
-     * Creates a DBUtil object based on servlet context configurations.
-     *
-     * @return DBUtil object.
-     * @throws Exception
-     * If an error occurred while reading configurations or while creating database object.
-     */
-    public static DBUtil getCredentialStoreDBUtil() throws ApplicationSettingsException, IllegalAccessException,
-            ClassNotFoundException, InstantiationException {
-        String jdbcUrl = ServerSettings.getCredentialStoreDBURL();
-        String userName = ServerSettings.getCredentialStoreDBUser();
-        String password = ServerSettings.getCredentialStoreDBPassword();
-        String driverName = ServerSettings.getCredentialStoreDBDriver();
-
-        StringBuilder stringBuilder = new StringBuilder("Starting credential store, connecting to database - ");
-        stringBuilder.append(jdbcUrl).append(" DB user - ").append(userName).append(" driver name - ")
-                .append(driverName);
-
-        log.debug(stringBuilder.toString());
-
-        DBUtil dbUtil = new DBUtil(jdbcUrl, userName, password, driverName);
-        dbUtil.init();
-
-        return dbUtil;
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java
deleted file mode 100644
index 6ff528d..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.sql.Connection;
-import java.sql.SQLException;
-
-/**
- * An abstraction for database specific test classes. This will create a database and provides methods to execute SQLs.
- */
-public class DatabaseTestCases {
-
-    private static final Logger logger = LoggerFactory.getLogger(DatabaseTestCases.class);
-
-    protected static String hostAddress = "localhost";
-    protected static int port = 20000;
-    protected static String userName = "admin";
-    protected static String password = "admin";
-    protected static String driver = "org.apache.derby.jdbc.ClientDriver";
-
-    public static String getHostAddress() {
-        return hostAddress;
-    }
-
-    public static int getPort() {
-        return port;
-    }
-
-    public static String getUserName() {
-        return userName;
-    }
-
-    public static String getPassword() {
-        return password;
-    }
-
-    public static String getDriver() {
-        return driver;
-    }
-
-    public static String getJDBCUrl() {
-        return new StringBuilder().append("jdbc:derby://").append(getHostAddress()).append(":").append(getPort())
-                .append("/experiment_catalog;create=true;user=").append(getUserName()).append(";password=")
-                .append(getPassword()).toString();
-    }
-
-    public static void waitTillServerStarts() {
-        DBUtil dbUtil = null;
-
-        try {
-            dbUtil = new DBUtil(getJDBCUrl(), getUserName(), getPassword(), getDriver());
-        } catch (Exception e) {
-           // ignore
-        }
-
-        Connection connection = null;
-        try {
-            if (dbUtil != null) {
-                connection = dbUtil.getConnection();
-            }
-        } catch (Throwable e) {
-            // ignore
-        }
-
-        while (connection == null) {
-            try {
-                Thread.sleep(1000);
-                try {
-                    if (dbUtil != null) {
-                        connection = dbUtil.getConnection();
-                    }
-                } catch (SQLException e) {
-                    // ignore
-                }
-            } catch (InterruptedException e) {
-                // ignore
-            }
-        }
-
-    }
-
-    public static void executeSQL(String sql) throws Exception {
-        DBUtil dbUtil = new DBUtil(getJDBCUrl(), getUserName(), getPassword(), getDriver());
-        dbUtil.executeSQL(sql);
-    }
-
-    public DBUtil getDbUtil () throws Exception {
-        return new DBUtil(getJDBCUrl(), getUserName(), getPassword(), getDriver());
-
-    }
-
-    public Connection getConnection() throws Exception {
-
-        DBUtil dbUtil =  getDbUtil ();
-        Connection connection = dbUtil.getConnection();
-        connection.setAutoCommit(true);
-        return connection;
-
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java
deleted file mode 100644
index fc7792b..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 12/29/13
- * Time: 12:10 PM
- */
-
-public class DefaultKeyStorePasswordCallback implements KeyStorePasswordCallback {
-
-    public DefaultKeyStorePasswordCallback(){
-
-    }
-
-    @Override
-    public char[] getStorePassword() {
-        try {
-            return ApplicationSettings.getCredentialStoreKeyStorePassword().toCharArray();
-        } catch (ApplicationSettingsException e) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    @Override
-    public char[] getSecretKeyPassPhrase(String keyAlias) {
-        try {
-            return ApplicationSettings.getCredentialStoreKeyStorePassword().toCharArray();
-        } catch (ApplicationSettingsException e) {
-            throw new RuntimeException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java
deleted file mode 100644
index 4fb35b9..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.InetAddress;
-import java.sql.DriverManager;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.sql.SQLException;
-
-/**
- * This class includes methods to start stop Derby database. Mainly user for tests.
- */
-public class DerbyUtil {
-
-    private static NetworkServerControl server;
-
-    private static final Logger logger = LoggerFactory.getLogger(DerbyUtil.class);
-
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-
-    /**
-     * Starts new derby server instance with given configurations.
-     * 
-     * @param hostAddress
-     *            The host address start the server.
-     * @param port
-     *            The port number which server is starting.
-     * @param user
-     *            JDBC user name.
-     * @param password
-     *            JDBC password.
-     * @throws Exception
-     *             If an error occurred while starting the server.
-     */
-    public static void startDerbyInServerMode(String hostAddress, int port, String user, String password)
-            throws Exception {
-        PrintWriter consoleWriter = null;
-
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName(hostAddress), port, user, password);
-            consoleWriter = new PrintWriter(System.out, true);
-            server.start(consoleWriter);
-
-        } catch (IOException e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether "
-                    + "specified port is available", e);
-            throw e;
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether "
-                    + "specified port is available", e);
-            throw e;
-        } finally {
-
-            if (consoleWriter != null) {
-                consoleWriter.close();
-            }
-
-        }
-
-    }
-
-    /**
-     * Starts derby server in embedded mode.
-     * 
-     * @throws ClassNotFoundException
-     *             If specified driver not found in the class path.
-     * @throws SQLException
-     *             If an error occurred while creat
-     */
-    public static void startDerbyInEmbeddedMode() throws ClassNotFoundException, SQLException {
-        Class.forName("org.apache.derby.jdbc.EmbeddedDriver");
-        DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close();
-    }
-
-    /**
-     * Shuts down the server.
-     * 
-     * @throws Exception
-     *             If an error occurred while shutting down.
-     */
-    public static void stopDerbyServer() throws Exception {
-        try {
-            server.shutdown();
-        } catch (Exception e) {
-            logger.error("Error shutting down derby server.", e);
-            throw e;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ExecutionMode.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ExecutionMode.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ExecutionMode.java
deleted file mode 100644
index cf17ef0..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ExecutionMode.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-public enum ExecutionMode {
-	CLIENT,
-	SERVER,
-	UNKNOWN
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IOUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IOUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IOUtil.java
deleted file mode 100644
index 9d1d7dd..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IOUtil.java
+++ /dev/null
@@ -1,209 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.Writer;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class IOUtil {
-
-    private static final Logger logger = LoggerFactory.getLogger(IOUtil.class);
-
-    /**
-     * @param path
-     * @param content
-     * @throws IOException
-     */
-    public static void writeToFile(String content, String path) throws IOException {
-        logger.debug("Path:" + path + " Content:" + content);
-
-        FileWriter fw = new FileWriter(path);
-        writeToWriter(content, fw);
-    }
-
-    /**
-     * @param content
-     * @param file
-     * @throws IOException
-     */
-    public static void writeToFile(String content, File file) throws IOException {
-        FileWriter fw = new FileWriter(file);
-        writeToWriter(content, fw);
-    }
-
-    /**
-     * @param inputStream
-     * @param file
-     * @throws IOException
-     */
-    public static void writeToFile(InputStream inputStream, File file) throws IOException {
-        FileOutputStream outputStream = new FileOutputStream(file);
-        byte[] bytes = new byte[1024];
-        int len;
-        while ((len = inputStream.read(bytes)) != -1) {
-            outputStream.write(bytes, 0, len);
-        }
-        outputStream.close();
-    }
-
-    /**
-     * Writes a specified String to a specified Writer.
-     * 
-     * @param content
-     *            The content to write
-     * @param writer
-     *            The specified Writer
-     * 
-     * @throws IOException
-     */
-    public static void writeToWriter(String content, Writer writer) throws IOException {
-        writer.write(content);
-        writer.close();
-    }
-
-    /**
-     * Returns the content of a specified file as a String.
-     * 
-     * @param path
-     * @return the content of a specified file as a String
-     * @throws IOException
-     */
-    public static String readFileToString(String path) throws IOException {
-        FileReader read = new FileReader(path);
-        return readToString(read);
-    }
-
-    /**
-     * Returns the content of a specified file as a String.
-     * 
-     * @param file
-     * @return the content of a specified file as a String
-     * @throws IOException
-     */
-    public static String readFileToString(File file) throws IOException {
-        FileReader reader = new FileReader(file);
-        return readToString(reader);
-    }
-
-    /**
-     * Returns a String read from a specified InputStream.
-     * 
-     * @param stream
-     *            The specified InputStream
-     * @return The String read from the specified InputStream
-     * @throws IOException
-     */
-    public static String readToString(InputStream stream) throws IOException {
-        return readToString(new InputStreamReader(stream));
-    }
-
-    /**
-     * Returns a String read from a specified Reader.
-     * 
-     * @param reader
-     *            The specified Reader
-     * @return The String read from the specified Reader
-     * @throws IOException
-     */
-    public static String readToString(Reader reader) throws IOException {
-        char[] cbuf = new char[1024];
-        StringBuilder sbuf = new StringBuilder();
-        int len;
-        while ((len = reader.read(cbuf)) != -1) {
-            sbuf.append(cbuf, 0, len);
-        }
-        return sbuf.toString();
-    }
-
-    /**
-     * @param file
-     * @return The byte array
-     * @throws IOException
-     */
-    public static byte[] readToByteArray(File file) throws IOException {
-        return readToByteArray(new FileInputStream(file));
-    }
-
-    /**
-     * @param inputStream
-     * @return The byte array.
-     * @throws IOException
-     */
-    public static byte[] readToByteArray(InputStream inputStream) throws IOException {
-        byte[] buf = new byte[1024];
-        ByteArrayOutputStream byteArrayStream = new ByteArrayOutputStream();
-        int len;
-        while ((len = inputStream.read(buf)) != -1) {
-            byteArrayStream.write(buf, 0, len);
-        }
-        return byteArrayStream.toByteArray();
-    }
-
-    /**
-     * @param path
-     * @return <code>true</code> if and only if the file or directory is successfully deleted; <code>false</code>
-     *         otherwise
-     */
-    public static boolean deleteDirectory(File path) {
-        if (path.exists()) {
-            File[] files = path.listFiles();
-            for (File file : files) {
-                if (file.isDirectory()) {
-                    deleteDirectory(file);
-                } else {
-                    file.delete();
-                }
-            }
-        }
-        return path.delete();
-    }
-
-    /**
-     * Gets the extension of a specified file.
-     * 
-     * @param file
-     *            the specified file.
-     * @return the extension of the file in lower case if there is an extension; null otherwise
-     */
-    public static String getExtension(File file) {
-        String ext = null;
-        String name = file.getName();
-
-        int index = name.lastIndexOf('.');
-        if (index > 0 && index < name.length() - 1) {
-            ext = name.substring(index + 1).toLowerCase();
-        }
-        return ext;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IServer.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IServer.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IServer.java
deleted file mode 100644
index 867eb45..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/IServer.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.util.Calendar;
-import java.util.Date;
-
-public interface IServer {
-	public enum ServerStatus{
-		STOPING,
-		STOPPED,
-		STARTING,
-		STARTED,
-		FAILED;
-		public void updateTime(){
-			now=Calendar.getInstance().getTime();
-		}
-		private Date now;
-		public Date getTime(){
-			return now;
-		}
-	}
-	public String getName();
-	public String getVersion();
-	public void start() throws Exception;
-	public void stop() throws Exception;
-	public void restart() throws Exception;
-	public void configure() throws Exception;
-	public ServerStatus getStatus() throws Exception;
-//	public void waitForServerToStart() throws Exception;
-//	public void waitForServerToStop() throws Exception;
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/JSONUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/JSONUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/JSONUtil.java
deleted file mode 100644
index 7946acc..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/JSONUtil.java
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
-import com.google.gson.JsonArray;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParser;
-import com.google.gson.JsonPrimitive;
-import com.google.gson.stream.JsonReader;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Reader;
-import java.util.Map;
-import java.util.Set;
-
-public class JSONUtil {
-
-
-    public static void saveJSON(JsonElement jsonElement, File file) throws IOException {
-        IOUtil.writeToFile(jsonElementToString(jsonElement), file);
-    }
-
-    public static JsonObject stringToJSONObject(String workflowString) {
-        JsonParser parser = new JsonParser();
-        return (JsonObject) parser.parse(workflowString);
-    }
-
-    public static JsonObject loadJSON(File file) throws IOException {
-        return loadJSON(new FileReader(file));
-    }
-
-    public static JsonObject loadJSON(Reader reader) throws IOException {
-       JsonParser parser = new JsonParser();
-       JsonElement jsonElement = parser.parse(reader);
-        if (jsonElement instanceof JsonObject) {
-            return (JsonObject) jsonElement;
-        } else {
-            throw new RuntimeException("Error while loading Json from file");
-        }
-
-    }
-
-    public static String jsonElementToString(JsonElement jsonElement) {
-        Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        return gson.toJson(jsonElement);
-    }
-
-    public static boolean isEqual(JsonObject originalJsonObject, JsonObject newJsonObject) {
-        // TODO - Implement this method
-        if (originalJsonObject == null && newJsonObject == null) {
-            return true;
-        }else if (originalJsonObject == null || newJsonObject == null) {
-            return false;
-        } else {
-            // check the number of childs
-            Set<Map.Entry<String , JsonElement>> entrySetOfOriginalJson =  originalJsonObject.entrySet();
-            Set<Map.Entry<String , JsonElement>> entrySetOfNewJson =  newJsonObject.entrySet();
-            if (entrySetOfOriginalJson.size() != entrySetOfNewJson.size()) {
-                return false;
-            }
-
-            for (Map.Entry<String, JsonElement> keyString : entrySetOfOriginalJson) {
-                JsonElement valueOrig = keyString.getValue();
-                JsonElement valueNew = newJsonObject.get(keyString.getKey());
-                if (valueOrig instanceof JsonObject && valueNew instanceof JsonObject &&
-                        !isEqual((JsonObject) valueOrig, (JsonObject) valueNew)) {
-                    return false;
-                }else if (valueOrig instanceof JsonArray && valueNew instanceof JsonArray &&
-                        !isEqual((JsonArray) valueOrig, (JsonArray) valueNew)) {
-                    return false;
-                }else if (valueOrig instanceof JsonPrimitive && valueNew instanceof JsonPrimitive &&
-                        !isEqual((JsonPrimitive) valueOrig, (JsonPrimitive) valueNew)) {
-                    return false;
-                }
-            }
-        }
-        return true;
-    }
-
-    private static boolean isEqual(JsonArray arrayOriginal, JsonArray arrayNew) {
-        if (arrayOriginal == null && arrayNew == null) {
-            return true;
-        }else if (arrayOriginal == null || arrayNew == null) {
-            return false;
-        }else {
-            // check the number of element
-            if (arrayOriginal.size() != arrayNew.size()) {
-                return false;
-            }else if (arrayOriginal.size() == 0) {
-                return true;
-            } else {
-                for (int i = 0; i < arrayOriginal.size(); i++) {
-                    JsonElement valueOrig = arrayOriginal.get(i);
-                    JsonElement valueNew = arrayNew.get(i);
-                    if (valueOrig instanceof JsonObject && valueNew instanceof JsonObject) {
-                        if (!isEqual((JsonObject) valueOrig, (JsonObject) valueNew)) {
-                            return false;
-                        }
-                    }else if (valueOrig instanceof JsonPrimitive && valueNew instanceof JsonPrimitive) {
-                        if (!isEqual((JsonPrimitive) valueOrig, (JsonPrimitive) valueNew)) {
-                            return false;
-                        }
-                    }
-                }
-            }
-        }
-        return true;
-    }
-
-    private static boolean isEqual(JsonPrimitive primitiveOrig, JsonPrimitive primitiveNew) {
-        if (primitiveOrig == null && primitiveNew == null) {
-            return true;
-        }else if (primitiveOrig == null || primitiveNew == null) {
-            return false;
-        } else {
-            if (primitiveOrig.isString() && primitiveNew.isString()){
-                if(!primitiveOrig.getAsString().equals(primitiveNew.getAsString())) {
-                    return false;
-                }
-            }else if (primitiveOrig.isBoolean() && primitiveNew.isBoolean()) {
-                if ((Boolean.valueOf(primitiveOrig.getAsBoolean()).compareTo(primitiveNew.getAsBoolean()) != 0)) {
-                    return false;
-                }
-            }else if (primitiveOrig.isNumber() && primitiveNew.isNumber() ) {
-                if (new Double(primitiveOrig.getAsDouble()).compareTo(primitiveNew.getAsDouble()) != 0) {
-                    return false;
-                }
-            }else {
-                return primitiveOrig.isJsonNull() && primitiveNew.isJsonNull();
-            }
-        }
-        return true;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java
deleted file mode 100644
index bafaff3..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package org.apache.airavata.common.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.
- *
- */
-
-/**
- * User: AmilaJ (amilaj@apache.org)
- * Date: 10/11/13
- * Time: 11:30 AM
- */
-
-/**
- * An interface to get keystore password in a form of a callback.
- */
-public interface KeyStorePasswordCallback {
-
-    /**
-     * Caller should implement the interface. Should return the password for
-     * the keystore. This should return the keystore password. i.e. password used to open the keystore.
-     * Instead of the actual file.
-     * @return The password to open the keystore.
-     */
-    char[] getStorePassword() throws RuntimeException;
-
-    /**
-     * Caller should implement the interface. Should return the pass phrase for
-     * the secret key.
-     * Instead of the actual file.
-     * @param keyAlias The alias of the key
-     * @return The pass phrase for the secret key.
-     */
-    char[] getSecretKeyPassPhrase(String keyAlias);
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/MonitorPublisher.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/MonitorPublisher.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/MonitorPublisher.java
deleted file mode 100644
index 7f64e86..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/MonitorPublisher.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import com.google.common.eventbus.EventBus;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class MonitorPublisher{
-    private final static Logger logger = LoggerFactory.getLogger(MonitorPublisher.class);
-    private EventBus eventBus;
-    
-    public MonitorPublisher(EventBus eventBus) {
-        this.eventBus = eventBus;
-    }
-
-    public void registerListener(Object listener) {
-        eventBus.register(listener);
-    }
-    
-    public void unregisterListener(Object listener) {
-        eventBus.unregister(listener);
-    }
-
-    public void publish(Object o) {
-        eventBus.post(o);
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/NameValidator.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/NameValidator.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/NameValidator.java
deleted file mode 100644
index 98530cf..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/NameValidator.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class NameValidator {
-
-    /**
-     * @param name
-     * @return Is it valid name?
-     */
-    public static boolean validate(String name) {
-        // Set the name pattern string
-        Pattern p = Pattern.compile("([a-zA-Z]){1,}([0-9]|_|\\.|[a-zA-Z]){0,}$");
-
-        // Match the given string with the pattern
-        Matcher m = p.matcher(name);
-
-        // Check whether match is found
-        boolean matchFound = m.matches();
-
-        return matchFound;
-    }
-
-    /**
-     * @param args
-     * @Description some quick tests
-     */
-    public static void main(String[] args) {
-        System.out.println(validate("abc90_90abc")); // true
-
-        System.out.println(validate("abc_abc_123")); // true
-
-        System.out.println(validate("abc_abc_")); // true
-
-        System.out.println(validate("abc_abc")); // true
-
-        System.out.println(validate("abc.abc")); // true
-
-        System.out.println(validate("9abc_abc")); // false, name cannot start with number
-
-        System.out.println(validate("_abc_abc")); // false, name cannot start with "_"
-
-        System.out.println(validate("\\abc_abc")); // false, name cannot start with "\"
-
-        System.out.println(validate("abc\\_abc")); // false, name cannot contain "\"
-    }
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/Pair.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/Pair.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/Pair.java
deleted file mode 100644
index ee24360..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/Pair.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-public class Pair<L, R> {
-
-    private L left;
-
-    private R right;
-
-    /**
-     * Constructs a Pair.
-     * 
-     * @param left
-     * @param right
-     */
-    public Pair(L left, R right) {
-        this.left = left;
-        this.right = right;
-    }
-
-    /**
-     * Returns the left.
-     * 
-     * @return The left
-     */
-    public L getLeft() {
-        return this.left;
-    }
-
-    /**
-     * Sets left.
-     * 
-     * @param left
-     *            The left to set.
-     */
-    public void setLeft(L left) {
-        this.left = left;
-    }
-
-    /**
-     * Returns the right.
-     * 
-     * @return The right
-     */
-    public R getRight() {
-        return this.right;
-    }
-
-    /**
-     * Sets right.
-     * 
-     * @param right
-     *            The right to set.
-     */
-    public void setRight(R right) {
-        this.right = right;
-    }
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
deleted file mode 100644
index aeec807..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.crypto.Cipher;
-import javax.crypto.spec.IvParameterSpec;
-import javax.crypto.spec.SecretKeySpec;
-import java.io.*;
-import java.security.*;
-import java.security.cert.CertificateException;
-
-/**
- * Class which includes security utilities.
- */
-public class SecurityUtil {
-
-    public static final String PASSWORD_HASH_METHOD_PLAINTEXT = "PLAINTEXT";
-
-    public static final String CHARSET_ENCODING = "UTF-8";
-    public static final String ENCRYPTION_ALGORITHM = "AES";
-    public static final String PADDING_MECHANISM = "AES/CBC/PKCS5Padding";
-
-    private static final Logger logger = LoggerFactory.getLogger(SecurityUtil.class);
-
-    /**
-     * Creates a hash of given string with the given hash algorithm.
-     * 
-     * @param stringToDigest
-     *            The string to digest.
-     * @param digestingAlgorithm
-     *            Hash algorithm.
-     * @return The digested string.
-     * @throws NoSuchAlgorithmException
-     *             If given hash algorithm doesnt exists.
-     */
-    public static String digestString(String stringToDigest, String digestingAlgorithm) throws NoSuchAlgorithmException {
-
-        if (digestingAlgorithm == null || digestingAlgorithm.equals(PASSWORD_HASH_METHOD_PLAINTEXT)) {
-            return stringToDigest;
-        }
-
-        MessageDigest messageDigest = MessageDigest.getInstance(digestingAlgorithm);
-        try {
-            return new String(messageDigest.digest(stringToDigest.getBytes("UTF-8")));
-        } catch (UnsupportedEncodingException e) {
-            logger.error("Error encoding password string when creating digest", e);
-            throw new RuntimeException("Error encoding password string when creating digest", e);
-        }
-    }
-
-    /**
-     * Sets the truststore for application. Useful when communicating over HTTPS.
-     * 
-     * @param trustStoreFilePath
-     *            Where trust store is located.
-     * @param trustStorePassword
-     *            The trust store password.
-     */
-    public static void setTrustStoreParameters(String trustStoreFilePath, String trustStorePassword) {
-
-        if (System.getProperty("javax.net.ssl.trustStrore") == null) {
-            logger.info("Setting Java trust store to " + trustStoreFilePath);
-            System.setProperty("javax.net.ssl.trustStrore", trustStoreFilePath);
-        }
-
-        if (System.getProperty("javax.net.ssl.trustStorePassword") == null) {
-            System.setProperty("javax.net.ssl.trustStorePassword", trustStoreFilePath);
-        }
-
-    }
-
-    public static byte[] encryptString(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, String value)
-            throws GeneralSecurityException, IOException {
-        return encrypt(keyStorePath, keyAlias, passwordCallback, value.getBytes(CHARSET_ENCODING));
-    }
-
-    public static byte[] encrypt(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, byte[] value)
-            throws GeneralSecurityException, IOException {
-
-        Key secretKey = getSymmetricKey(keyStorePath, keyAlias, passwordCallback);
-
-        Cipher cipher = Cipher.getInstance(PADDING_MECHANISM);
-        cipher.init(Cipher.ENCRYPT_MODE, secretKey,
-                new IvParameterSpec(new byte[16]));
-        return cipher.doFinal(value);
-    }
-
-    private static Key getSymmetricKey(String keyStorePath, String keyAlias,
-                                       KeyStorePasswordCallback passwordCallback)
-            throws CertificateException, NoSuchAlgorithmException, KeyStoreException, IOException,
-            UnrecoverableKeyException {
-
-        KeyStore ks = SecurityUtil.loadKeyStore(keyStorePath, "jceks", passwordCallback);
-
-        if (ks == null) {
-            throw new IOException("Unable to load Java keystore " + keyStorePath);
-        }
-
-        return ks.getKey(keyAlias, passwordCallback.getSecretKeyPassPhrase(keyAlias));
-
-    }
-
-    public static byte[] decrypt(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, byte[] encrypted)
-            throws GeneralSecurityException, IOException {
-
-        Key secretKey = getSymmetricKey(keyStorePath, keyAlias, passwordCallback);
-
-        Cipher cipher = Cipher.getInstance(PADDING_MECHANISM);
-        cipher.init(Cipher.DECRYPT_MODE, secretKey,
-                new IvParameterSpec(new byte[16]));
-
-        return cipher.doFinal(encrypted);
-    }
-
-    public static String decryptString(String keyStorePath, String keyAlias,
-                                       KeyStorePasswordCallback passwordCallback, byte[] encrypted)
-            throws GeneralSecurityException, IOException {
-
-        byte[] decrypted = decrypt(keyStorePath, keyAlias, passwordCallback, encrypted);
-        return new String(decrypted, CHARSET_ENCODING);
-    }
-
-    public static KeyStore loadKeyStore(String keyStoreFilePath, String keyStoreType,
-                                        KeyStorePasswordCallback passwordCallback)
-            throws KeyStoreException, IOException, CertificateException, NoSuchAlgorithmException {
-
-        java.io.FileInputStream fis = null;
-        try {
-            fis = new java.io.FileInputStream(keyStoreFilePath);
-            return loadKeyStore(fis, keyStoreType, passwordCallback);
-        } finally {
-            if (fis != null) {
-                fis.close();
-            }
-        }
-    }
-
-    public static KeyStore loadKeyStore(InputStream inputStream, String keyStoreType,
-                                        KeyStorePasswordCallback passwordCallback)
-            throws KeyStoreException, IOException, CertificateException, NoSuchAlgorithmException {
-
-        if (keyStoreType == null) {
-            keyStoreType = KeyStore.getDefaultType();
-        }
-
-        KeyStore ks = KeyStore.getInstance(keyStoreType);
-        ks.load(inputStream, passwordCallback.getStorePassword());
-
-        return ks;
-    }
-
-
-
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServerSettings.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
deleted file mode 100644
index 8370e40..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
+++ /dev/null
@@ -1,270 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-
-public class ServerSettings extends ApplicationSettings {
-
-    private static final String DEFAULT_USER = "default.registry.user";
-    private static final String DEFAULT_USER_PASSWORD = "default.registry.password";
-    private static final String DEFAULT_USER_GATEWAY = "default.registry.gateway";
-
-    private static final String SERVER_CONTEXT_ROOT = "server.context-root";
-    public static final String EMBEDDED_ZK = "embedded.zk";
-    public static final String IP = "ip";
-
-    private static final String CREDENTIAL_STORE_DB_URL = "credential.store.jdbc.url";
-    private static final String CREDENTIAL_STORE_DB_USER = "credential.store.jdbc.user";
-    private static final String CREDENTIAL_STORE_DB_PASSWORD = "credential.store.jdbc.password";
-    private static final String CREDENTIAL_STORE_DB_DRIVER = "credential.store.jdbc.driver";
-
-    private static final String REGISTRY_DB_URL = "registry.jdbc.url";
-    private static final String REGISTRY_DB_USER = "registry.jdbc.user";
-    private static final String REGISTRY_DB_PASSWORD = "registry.jdbc.password";
-    private static final String REGISTRY_DB_DRIVER = "registry.jdbc.driver";
-    private static final String ENABLE_HTTPS = "enable.https";
-    private static final String HOST_SCHEDULER = "host.scheduler";
-    private static final String MY_PROXY_SERVER = "myproxy.server";
-    private static final String MY_PROXY_USER = "myproxy.user";
-    private static final String MY_PROXY_PASSWORD = "myproxy.password";
-    private static final String MY_PROXY_LIFETIME = "myproxy.life";
-    private static final String STATUS_PUBLISHER = "status.publisher";
-    private static final String TASK_LAUNCH_PUBLISHER = "task.launch.publisher";
-    private static final String ACTIVITY_LISTENERS = "activity.listeners";
-    public static final String JOB_NOTIFICATION_ENABLE = "job.notification.enable";
-    public static final String JOB_NOTIFICATION_EMAILIDS = "job.notification.emailids";
-    public static final String JOB_NOTIFICATION_FLAGS = "job.notification.flags";
-    public static final String GFAC_PASSIVE = "gfac.passive"; // by default this is desabled
-    public static final String LAUNCH_QUEUE_NAME = "launch.queue.name";
-    public static final String CANCEL_QUEUE_NAME = "cancel.queue.name";
-
-
-    //    Workflow Enactment Service component configuration.
-    private static final String ENACTMENT_THREAD_POOL_SIZE = "enactment.thread.pool.size";
-    private static final int DEFAULT_ENACTMENT_THREAD_POOL_SIZE = 10;
-    private static final String WORKFLOW_PARSER = "workflow.parser";
-
-    // email based monitoring configurations
-    private static final String EMAIL_BASED_MONITORING_PERIOD = "email.based.monitoring.period";
-    private static final String EMAIL_BASED_MONITOR_HOST = "email.based.monitor.host";
-    private static final String EMAIL_BASED_MONITOR_ADDRESS = "email.based.monitor.address";
-    private static final String EMAIL_BASED_MONITOR_PASSWORD = "email.based.monitor.password";
-    private static final String EMAIL_BASED_MONITOR_FOLDER_NAME = "email.based.monitor.folder.name";
-    private static final String EMAIL_BASED_MONITOR_STORE_PROTOCOL = "email.based.monitor.store.protocol";
-    private static final String ENABLE_EMAIL_BASED_MONITORING = "enable.email.based.monitoring";
-
-    private static boolean stopAllThreads = false;
-    private static boolean emailBaseNotificationEnable;
-
-    public static String getDefaultUser() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER);
-    }
-
-    public static String getLaunchQueueName() {
-        return getSetting(LAUNCH_QUEUE_NAME, "launch.queue");
-    }
-
-
-    public static String getCancelQueueName() {
-        return getSetting(CANCEL_QUEUE_NAME, "cancel.queue");
-    }
-
-    public static String getDefaultUserPassword() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER_PASSWORD);
-    }
-
-    public static String getDefaultUserGateway() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER_GATEWAY);
-    }
-
-    public static String getServerContextRoot() {
-        return getSetting(SERVER_CONTEXT_ROOT, "axis2");
-    }
-
-    public static String getCredentialStoreDBUser() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_USER);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_USER);
-        }
-    }
-
-    public static String getCredentialStoreDBPassword() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_PASSWORD);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_PASSWORD);
-        }
-    }
-
-    public static String getCredentialStoreDBDriver() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_DRIVER);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_DRIVER);
-        }
-    }
-
-    public static String getCredentialStoreDBURL() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_URL);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_URL);
-        }
-
-    }
-
-    public static boolean isEnableHttps() {
-        try {
-            return Boolean.parseBoolean(getSetting(ENABLE_HTTPS));
-        } catch (ApplicationSettingsException e) {
-            return false;
-        }
-    }
-
-
-    public static String getHostScheduler() throws ApplicationSettingsException {
-        return getSetting(HOST_SCHEDULER);
-    }
-
-    public static boolean isStopAllThreads() {
-        return stopAllThreads;
-    }
-
-    public static void setStopAllThreads(boolean stopAllThreads) {
-        ServerSettings.stopAllThreads = stopAllThreads;
-    }
-
-    public static String getMyProxyServer() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_SERVER);
-    }
-
-    public static String getMyProxyUser() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_USER);
-    }
-
-    public static String getMyProxyPassword() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_PASSWORD);
-    }
-
-    public static int getMyProxyLifetime() throws ApplicationSettingsException {
-        return Integer.parseInt(getSetting(MY_PROXY_LIFETIME));
-    }
-
-    public static String[] getActivityListeners() throws ApplicationSettingsException {
-        return getSetting(ACTIVITY_LISTENERS).split(",");
-    }
-
-    public static String getStatusPublisher() throws ApplicationSettingsException {
-        return getSetting(STATUS_PUBLISHER);
-    }
-
-    public static String getTaskLaunchPublisher() throws ApplicationSettingsException {
-        return getSetting(TASK_LAUNCH_PUBLISHER);
-    }
-
-    public static boolean isGFacPassiveMode()throws ApplicationSettingsException {
-        String setting = getSetting(GFAC_PASSIVE);
-        return Boolean.parseBoolean(setting);
-    }
-
-    public static boolean isEmbeddedZK() {
-        return Boolean.parseBoolean(getSetting(EMBEDDED_ZK, "true"));
-    }
-
-    public static String getIp() {
-        try {
-            return getSetting(IP);
-        } catch (ApplicationSettingsException e) {
-            try {
-                return InetAddress.getLocalHost().getHostAddress();
-            } catch (UnknownHostException e1) {
-                e1.printStackTrace();
-            }
-        }
-        return null;
-    }
-
-    public static int getEnactmentThreadPoolSize() {
-        String threadPoolSize = null;
-        try {
-            threadPoolSize = getSetting(ENACTMENT_THREAD_POOL_SIZE);
-        } catch (ApplicationSettingsException e) {
-            return DEFAULT_ENACTMENT_THREAD_POOL_SIZE;
-        }
-        return Integer.valueOf(threadPoolSize);
-    }
-
-    public static String getWorkflowParser() throws ApplicationSettingsException {
-        return getSetting(WORKFLOW_PARSER);
-    }
-
-
-    public static int getEmailMonitorPeriod() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(EMAIL_BASED_MONITORING_PERIOD, "100000"));
-
-    }
-
-    public static String getEmailBasedMonitorHost() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_HOST);
-    }
-
-    public static String getEmailBasedMonitorAddress() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_ADDRESS);
-    }
-
-    public static String getEmailBasedMonitorPassword() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_PASSWORD);
-    }
-
-    public static String getEmailBasedMonitorFolderName() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_FOLDER_NAME);
-    }
-
-    public static String getEmailBasedMonitorStoreProtocol() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_STORE_PROTOCOL);
-    }
-
-    public static boolean isEmailBasedNotificationEnable() {
-        return Boolean.valueOf(getSetting(ENABLE_EMAIL_BASED_MONITORING, "false"));
-    }
-
-    public static boolean isAPISecured() throws ApplicationSettingsException {
-        return Boolean.valueOf(getSetting(Constants.IS_API_SECURED));
-    }
-
-    public static String getRemoteOauthServerUrl() throws ApplicationSettingsException {
-        return getSetting(Constants.REMOTE_OAUTH_SERVER_URL);
-    }
-
-    public static String getAdminUsername() throws ApplicationSettingsException {
-        return getSetting(Constants.ADMIN_USERNAME);
-    }
-
-    public static String getAdminPassword() throws ApplicationSettingsException {
-        return getSetting(Constants.ADMIN_PASSWORD);
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
deleted file mode 100644
index 0c54053..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
+++ /dev/null
@@ -1,93 +0,0 @@
-///*
-// *
-// * 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.common.utils;
-//
-//import java.io.IOException;
-//import java.net.SocketException;
-//
-//import org.apache.airavata.common.exception.ApplicationSettingsException;
-//import org.apache.axis2.context.ConfigurationContext;
-//import org.apache.axis2.description.TransportInDescription;
-//import org.apache.axis2.util.Utils;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//public class ServiceUtils {
-//    private static final Logger log = LoggerFactory.getLogger(ServiceUtils.class);
-////    private static final String REPOSITORY_PROPERTIES = "airavata-server.properties";
-//    public static final String IP = "ip";
-//    public static final String PORT = "port";
-//
-//	public static String generateServiceURLFromConfigurationContext(
-//			ConfigurationContext context, String serviceName) throws IOException, ApplicationSettingsException {
-////		URL url = ServiceUtils.class.getClassLoader()
-////				.getResource(REPOSITORY_PROPERTIES);
-//		 String localAddress = null;
-//        String port = null;
-////        Properties properties = new Properties();
-//        try {
-//            localAddress = ServerSettings.getSetting(IP);
-//        } catch (ApplicationSettingsException e) {
-//			//we will ignore this exception since the properties file will not contain the values
-//			//when it is ok to retrieve them from the axis2 context
-//		}
-//        if(localAddress == null){
-//	        try {
-//	            localAddress = Utils.getIpAddress(context
-//	                    .getAxisConfiguration());
-//	        } catch (SocketException e) {
-//	            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-//	        }
-//        }
-//        String protocol="http";
-//        if(ServerSettings.isEnableHttps()){
-//            protocol="https";
-//        }
-//
-//        try {
-//            port = ServerSettings.getTomcatPort(protocol);
-//        } catch (ApplicationSettingsException e) {
-//            //we will ignore this exception since the properties file will not contain the values
-//            //when it is ok to retrieve them from the axis2 context
-//        }
-//        if (port == null) {
-//            TransportInDescription transportInDescription = context
-//                .getAxisConfiguration().getTransportsIn()
-//                .get(protocol);
-//            if (transportInDescription != null
-//                && transportInDescription.getParameter(PORT) != null) {
-//                port = (String) transportInDescription
-//                    .getParameter(PORT).getValue();
-//            }
-//        }
-//        localAddress = protocol+"://" + localAddress + ":" + port;
-//        localAddress = localAddress + "/"
-//    		//We are not using axis2 config context to get the context root because it is invalid
-//            //+ context.getContextRoot() + "/"
-//    		//FIXME: the context root will be correct after updating the web.xml 
-//            + ServerSettings.getServerContextRoot() + "/"
-//            + context.getServicePath() + "/"
-//            + serviceName;
-//        log.debug("Service Address Configured:" + localAddress);
-//        return localAddress;
-//	}
-//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/8d16d0ec/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/StringUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/StringUtil.java b/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/StringUtil.java
deleted file mode 100644
index 3ce5cda..0000000
--- a/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/StringUtil.java
+++ /dev/null
@@ -1,480 +0,0 @@
-/*
- *
- * 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.common.utils;
-
-import java.io.ByteArrayOutputStream;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.ListIterator;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-
-public class StringUtil {
-	public static final String DELIMETER=",";
-	public static final String QUOTE="\"";
-	
-	public static Map<Integer, String> getContainedParameters(String s) {
-		Map<Integer,String> parameterMap=new HashMap<Integer,String>();
-		int i=0;
-		for(i=0;i<s.length();i++){
-			if (s.charAt(i)=='$' && (i+1)<s.length() && s.charAt(i+1)=='{'){
-				int i2=s.indexOf('{', i+2);
-				int e=s.indexOf('}', i+2);
-				if (e!=-1){
-					if (i2==-1 || e<i2){
-						parameterMap.put(i, s.substring(i,e+1));
-						i=e;
-					}
-				}
-			}
-		}
-		return parameterMap;
-	}
-	
-	// Merits for the following function should go to 
-	// http://blog.houen.net/java-get-url-from-string/ 
-	public static List<String> getURLS(String text) {
-		List<String> links = new ArrayList<String>();
-		String regex = "\\(?\\b((http|https|ftp)://|www[.])[-A-Za-z0-9+&@#/%?=~_()|!:,.;]*[-A-Za-z0-9+&@#/%=~_()|]";
-		Pattern p = Pattern.compile(regex);
-		Matcher m = p.matcher(text);
-		while (m.find()) {
-			String urlStr = m.group();
-			if (urlStr.startsWith("(") && urlStr.endsWith(")")) {
-				urlStr = urlStr.substring(1, urlStr.length() - 1);
-			}
-			if (!links.contains(urlStr)) {
-				links.add(urlStr);
-			}
-		}
-		return links;
-	}
-
-	public static String createHTMLUrlTaggedString2(String value, List<String> pullLinks) {
-		for (String url : pullLinks) {
-			String hyperlinkString="<a href='"+url+"'>"+url+"</a>";
-			value=value.replaceAll(Pattern.quote(url), hyperlinkString);
-		}
-		return value;
-	}
-	public static String createHTMLUrlTaggedString(String value) {
-		String urledString = "";
-		int lastIndex=0,index=0;
-		while(index!=-1){
-			index=value.toLowerCase().indexOf("://",lastIndex);
-			if (index!=-1){
-				int beginIndex=value.lastIndexOf(" ",index);
-				urledString+=value.substring(lastIndex,beginIndex+1);
-				int endIndex=value.indexOf(" ",index);
-				if (beginIndex==-1){
-					beginIndex=0;
-				}else{
-					beginIndex++;
-				}
-				if (endIndex==-1){
-					endIndex=value.length();
-				}
-				String url=value.substring(beginIndex, endIndex);
-				urledString+="<a href='"+url+"'>"+url+"</a>";
-				lastIndex=endIndex;
-			}
-		}
-		urledString+=value.substring(lastIndex, value.length());
-		return urledString;
-	}
-	
-	private static boolean isQuoted(String s, String delimiter){
-		//Check if we need quotes
-		if (s.contains(delimiter)){
-			//Check if its already quoted
-			s=s.replaceAll("\"\"", "");
-			return (s.substring(0,1).equals(QUOTE) && s.subSequence(s.length()-1, s.length()).equals(QUOTE));
-		}
-		//no delimiters present, so already in proper form
-		return true;
-	}
-	
-	private static boolean isQuoted(String s){
-		return isQuoted(s, DELIMETER);
-	}
-	
-	/**
-	 * Create a delimiter separated string out of a list
-	 * @param list
-	 * @return
-	 */
-	public static String createDelimiteredString(String[] list) {
-        return createDelimiteredString(list, DELIMETER);
-    }
-
-
-    /**
-	 * Create a delimiter separated string out of a list
-	 * @param list
-	 * @return
-	 */
-	public static String createDelimiteredString(String[] list,String delimiter){
-		String s=null;
-		for (String ss : list) {
-			ss=quoteString(ss, delimiter);
-			if (s==null){
-				s=ss;
-			}else{
-				s+=delimiter +ss;
-			}
-		}
-		return s;
-	}
-
-	/**
-	 * Return a proper quoted string if the string contains the delimiter character
-	 * @param s
-	 * @return
-	 */
-	public static String quoteString(String s) {
-        return quoteString(s, DELIMETER);
-    }
-
-
-    /**
-	 * Return a proper quoted string if the string contains the delimiter character
-	 * @param s
-	 * @return
-	 */
-	public static String quoteString(String s,String delimiter){
-		if (isQuoted(s,delimiter)){
-			return s;
-		}else{
-			return QUOTE+s.replaceAll(QUOTE, QUOTE+QUOTE)+QUOTE;
-		}
-	}
-
-	/**
-	 * Parse the delimitered string and return elements as a string array 
-	 * @param s
-	 * @return
-	 */
-	public static String[] getElementsFromString(String s, String delimeter, String quote) {
-		List<String> list=new ArrayList<String>();
-		String currentItem="";
-		String previousChar=null;
-		boolean insideQuote=false;
-		for(int i=0;i<s.length();i++){
-			String c=s.substring(i,i+1);
-			if (c.equals(delimeter)){
-				//if not inside a quoted string ignore the delimiter character
-				if (insideQuote) {
-					currentItem+=c;
-				}else{
-					list.add(currentItem);
-					currentItem = "";
-				}
-			}else if (c.equals(quote)){
-				if (quote.equals(previousChar)){
-					//which means previousChar was an escape character, not a quote for the string
-					currentItem+=quote;
-					if (insideQuote){
-						//mistakenly thought previous char was opening quote char, thus need to make this false
-						insideQuote=false;
-					}else{
-						//mistakenly thought previous char was closing quote char, thus need to make this true
-						insideQuote=true;
-					}
-				} else{
-					if (insideQuote){
-						//quote ended
-						insideQuote=false;
-					}else{
-						//quote beginning
-						insideQuote=true;
-					}
-				}
-			}else{
-				currentItem+=c;
-			}
-			previousChar=c;
-		}
-		list.add(currentItem);
-		return list.toArray(new String[]{});
-	}
-	
-	/**
-	 * Parse the delimitered string and return elements as a string array 
-	 * @param s
-	 * @return
-	 */
-	public static String[] getElementsFromString(String s) {
-		return getElementsFromString(s, DELIMETER, QUOTE);
-	}
-
-    /**
-     * Converts object to String without worrying about null check.
-     * 
-     * @param object
-     * @return The object.toString if object is not null; "" otherwise.
-     */
-    public static String toString(Object object) {
-        if (object == null) {
-            return "";
-        } else {
-            return object.toString();
-        }
-    }
-
-    /**
-     * Trims a specified string, and makes it null if the result is empty string.
-     * 
-     * @param string
-     * @return the string processed
-     */
-    public static String trimAndNullify(String string) {
-        if (string != null) {
-            string = string.trim();
-            if (string.equals("")) {
-                string = null;
-            }
-        }
-        return string;
-    }
-
-    /**
-     * @param oldName
-     * @return Trimmed String
-     */
-    public static String trimSpaceInString(String oldName) {
-        if (oldName == null) {
-            return "";
-        }
-        return oldName.replace(" ", "");
-    }
-
-    /**
-     * Converts a specified string to a Java identifier.
-     * 
-     * @param name
-     * @return the Java identifier
-     */
-    public static String convertToJavaIdentifier(String name) {
-
-        final char REPLACE_CHAR = '_';
-
-        if (name == null || name.length() == 0) {
-            return "" + REPLACE_CHAR;
-        }
-
-        StringBuilder buf = new StringBuilder();
-
-        char c = name.charAt(0);
-        if (!Character.isJavaIdentifierStart(c)) {
-            // Add _ at the beggining instead of replacing it to _. This is
-            // more readable if the name is like 3D_Model.
-            buf.append(REPLACE_CHAR);
-        }
-
-        for (int i = 0; i < name.length(); i++) {
-            c = name.charAt(i);
-            if (Character.isJavaIdentifierPart(c)) {
-                buf.append(c);
-            } else {
-                buf.append(REPLACE_CHAR);
-            }
-        }
-
-        return buf.toString();
-    }
-
-    /**
-     * Creates a new name by incrementing the number after the underscore at the end of the old name. If there is no
-     * underscore and number at the end, put "_2" at the end.
-     * 
-     * @param oldName
-     * @return the new name
-     */
-    public static String incrementName(String oldName) {
-
-        final char PREFIX = '_';
-
-        String newName;
-        if (oldName == null || oldName.length() == 0) {
-            newName = "noName";
-        } else {
-            int lastDashIndex = oldName.lastIndexOf(PREFIX);
-            if (lastDashIndex < 0) {
-                newName = oldName + PREFIX + 2;
-            } else {
-                String suffix = oldName.substring(lastDashIndex + 1);
-                try {
-                    int number = Integer.parseInt(suffix);
-                    int newNumber = number + 1;
-                    newName = oldName.substring(0, lastDashIndex + 1) + newNumber;
-                } catch (RuntimeException e) {
-                    // It was not a number
-                    newName = oldName + PREFIX + 2;
-                }
-            }
-        }
-        return newName;
-    }
-
-    /**
-     * Returns the local class name of a specified class.
-     * 
-     * @param klass
-     *            The specified class
-     * @return The local class name
-     */
-    public static String getClassName(Class klass) {
-        String fullName = klass.getName();
-        int index = fullName.lastIndexOf(".");
-        if (index < 0) {
-            return fullName;
-        } else {
-            return fullName.substring(index + 1);
-        }
-    }
-
-    /**
-     * @param throwable
-     * @return The stackTrace in String
-     */
-    public static String getStackTraceInString(Throwable throwable) {
-        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
-        PrintStream printStream = new PrintStream(byteArrayOutputStream);
-        throwable.printStackTrace(printStream);
-        printStream.flush();
-        return byteArrayOutputStream.toString();
-    }
-    
-    private static Options deriveCommandLineOptions(String[] args){
-    	Options options = new Options();
-    	String[] argCopy = getChangedList(args);
-    	int i=0;
-        for (String arg : argCopy) {
-            if (arg.startsWith("--")){
-            	arg=arg.substring(2);
-                int pos = arg.indexOf('=');
-                String opt;
-                boolean hasArgs=true;
-	            if (pos==-1){ //if not of the form --arg=value
-	            	if (i==argCopy.length-1 || argCopy[i+1].startsWith("-")){ // no value specified 
-	            		hasArgs=false;
-	            	}
-	            	opt=arg;
-	            }else{
-	            	opt=arg.substring(0, pos);
-	            }
-                options.addOption(opt, hasArgs, "");
-            }
-            i++;
-        }
-        return options;
-    }
-    
-	public static Map<String, String> parseCommandLineOptions(String[] args) {
-		Map<String,String> commandLineOptions=new HashMap<String,String>();
-		try {
-			CommandLineParameters cmdParameters = getCommandLineParser(args);
-			Map<String, String> parameters = cmdParameters.getParameters();
-			for (String s : parameters.keySet()) {
-				commandLineOptions.put(s, parameters.get(s)==null? "":parameters.get(s));
-			}
-		} catch (ParseException e1) {
-			e1.printStackTrace();
-		}
-		return commandLineOptions;
-	}
-
-	public static CommandLineParameters getCommandLineParser(String[] args)
-			throws ParseException {
-		String[] argCopy = getChangedList(args);
-		CommandLineParser parser = new DynamicOptionPosixParser();
-		CommandLine cmdLine = parser.parse(deriveCommandLineOptions(argCopy), argCopy);
-		return new CommandLineParameters(cmdLine);
-	}
-
-	
-	//commons-cli does not support arg names having the period (".")
-	private static final String ARG_DOT_REPLACE="dot_replacement_value";
-	
-	private static String[] getChangedList(String[] args) {
-		String[] argCopy = Arrays.asList(args).toArray(new String []{});
-		for (int i=0;i<argCopy.length; i++) {
-			argCopy[i]=changeOption(argCopy[i]);
-		}
-		return argCopy;
-	}
-	
-	private static String revertOption(String option){
-		return option==null? option : option.replaceAll(Pattern.quote(ARG_DOT_REPLACE), ".");
-	}
-	
-	private static String changeOption(String option){
-		return option==null? option : option.replaceAll(Pattern.quote("."), ARG_DOT_REPLACE);
-	}
-	
-	private static class DynamicOptionPosixParser extends PosixParser{
-		@Override
-		protected void processOption(String arg0, @SuppressWarnings("rawtypes") ListIterator arg1)
-				throws ParseException {
-			if (getOptions().hasOption(arg0)){
-				super.processOption(arg0, arg1);
-			}
-		}
-	}
-	
-	public static class CommandLineParameters{
-		private Map<String,String> parameters=new HashMap<String, String>();
-		private List<String> arguments=new ArrayList<String>();
-		protected CommandLineParameters(CommandLine cmd){
-			for(Option opt:cmd.getOptions()){
-				parameters.put(revertOption(opt.getOpt()), revertOption(opt.getValue()));
-			}
-			for(String arg:cmd.getArgs()){
-				arguments.add(revertOption(arg));
-			}
-		}
-		public List<String> getArguments() {
-			return arguments;
-		}
-		public void setArguments(List<String> arguments) {
-			this.arguments = arguments;
-		}
-		public Map<String,String> getParameters() {
-			return parameters;
-		}
-		public void setParameters(Map<String,String> parameters) {
-			this.parameters = parameters;
-		}
-	}
-
-}
\ No newline at end of file


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