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From scnakand...@apache.org
Subject [1/3] airavata git commit: removing registry core and cpi dependencies from Airavata API Server
Date Thu, 11 Aug 2016 16:44:57 GMT
Repository: airavata
Updated Branches:
  refs/heads/develop 63696ffa1 -> b9b2480c5


http://git-wip-us.apache.org/repos/asf/airavata/blob/1eb3b415/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/ReplicaCatalogInitUtil.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/ReplicaCatalogInitUtil.java b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/ReplicaCatalogInitUtil.java
deleted file mode 100644
index 908d82d..0000000
--- a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/ReplicaCatalogInitUtil.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.api.server.util;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.net.InetAddress;
-import java.net.URI;
-import java.sql.Connection;
-import java.sql.SQLException;
-
-public class ReplicaCatalogInitUtil {
-    private static final Logger logger = LoggerFactory.getLogger(ReplicaCatalogInitUtil.class);
-    public static final String REPLICA_CATALOG = "DATA_PRODUCT";
-    public static final String REPLICA_CATALOG_JDBC_DRIVER = "replicacatalog.jdbc.driver";
-    public static final String REPLICA_CATALOG_JDBC_URL = "replicacatalog.jdbc.url";
-    public static final String REPLICA_CATALOG_JDBC_USER = "replicacatalog.jdbc.user";
-    public static final String REPLICA_CATALOG_JDBC_PASSWORD = "replicacatalog.jdbc.password";
-    public static final String START_DERBY_ENABLE = "start.derby.server.mode";
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-    private static NetworkServerControl server;
-    private static JdbcStorage db;
-    private static String jdbcURl;
-    private static String jdbcDriver;
-    private static String jdbcUser;
-    private static String jdbcPassword;
-
-
-    public static void initializeDB() {
-//        System.setProperty("appcatalog.initialize.state", "0");
-        try{
-            jdbcDriver = ServerSettings.getSetting(REPLICA_CATALOG_JDBC_DRIVER);
-            jdbcURl = ServerSettings.getSetting(REPLICA_CATALOG_JDBC_URL);
-            jdbcUser = ServerSettings.getSetting(REPLICA_CATALOG_JDBC_USER);
-            jdbcPassword = ServerSettings.getSetting(REPLICA_CATALOG_JDBC_PASSWORD);
-            jdbcURl = jdbcURl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read airavata server properties", e.getMessage());
-        }
-
-        if (getDBType(jdbcURl).equals("derby") && isDerbyStartEnabled()) {
-            startDerbyInServerMode();
-        }
-        db = new JdbcStorage(10, 50, jdbcURl, jdbcDriver, true);
-
-        Connection conn = null;
-        try {
-            conn = db.connect();
-            if (!DatabaseCreator.isDatabaseStructureCreated(REPLICA_CATALOG, conn)) {
-                DatabaseCreator.createRegistryDatabase("database_scripts/replicacatalog", conn);
-                logger.info("New Database created for Replica Catalog !!! ");
-            } else {
-                logger.info("Database already created for Replica Catalog!!!");
-            }
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new RuntimeException("Database failure", e);
-        } finally {
-            db.closeConnection(conn);
-            try {
-                if(conn != null){
-                    if (!conn.getAutoCommit()) {
-                        conn.commit();
-                    }
-                    conn.close();
-                }
-            } catch (SQLException e) {
-                logger.error("Error while closing database connection...", e.getMessage(), e);
-            }
-        }
-//        System.setProperty("appcatalog.initialize.state", "1");
-    }
-
-    public static String getDBType(String jdbcUrl){
-        try{
-            String cleanURI = jdbcUrl.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getScheme();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return null;
-        }
-    }
-
-    public static boolean isDerbyStartEnabled(){
-        try {
-            String s = ServerSettings.getSetting(START_DERBY_ENABLE);
-            if("true".equals(s)){
-                return true;
-            }
-        }  catch (ApplicationSettingsException e) {
-            logger.error("Unable to read airavata server properties", e.getMessage(), e);
-            return false;
-        }
-        return false;
-    }
-
-    public static void startDerbyInServerMode() {
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
-                    getPort(jdbcURl),
-                    jdbcUser, jdbcPassword);
-            java.io.PrintWriter consoleWriter = new java.io.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");
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether " +
-                    "specified port is available");
-        }
-    }
-    
-    public static void stopDerbyInServerMode() {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "false");
-            if (server!=null){
-            	try {
-					server.shutdown();
-				} catch (Exception e) {
-		            logger.error("Error when stopping the derby server : "+e.getLocalizedMessage());
-				}
-            }
-    }
-
-    public static int getPort(String jdbcURL){
-        try{
-            String cleanURI = jdbcURL.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getPort();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return -1;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/1eb3b415/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/WorkflowCatalogInitUtil.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/WorkflowCatalogInitUtil.java b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/WorkflowCatalogInitUtil.java
deleted file mode 100644
index ea20c63..0000000
--- a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/util/WorkflowCatalogInitUtil.java
+++ /dev/null
@@ -1,162 +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.api.server.util;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.AiravataUtils;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.registry.core.app.catalog.resources.GatewayProfileResource;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-import java.net.InetAddress;
-import java.net.URI;
-import java.sql.Connection;
-import java.sql.SQLException;
-
-public class WorkflowCatalogInitUtil {
-    private static final Logger logger = LoggerFactory.getLogger(WorkflowCatalogInitUtil.class);
-    public static final String WORKFLOW = "WORKFLOW";
-    public static final String WORKFLOWCATALOG_JDBC_DRIVER = "workflowcatalog.jdbc.driver";
-    public static final String WORKFLOWCATALOG_JDBC_URL = "workflowcatalog.jdbc.url";
-    public static final String WORKFLOWCATALOG_JDBC_USER = "workflowcatalog.jdbc.user";
-    public static final String WORKFLOWCATALOG_JDBC_PASSWORD = "workflowcatalog.jdbc.password";
-    public static final String START_DERBY_ENABLE = "start.derby.server.mode";
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-    private static NetworkServerControl server;
-    private static JdbcStorage db;
-    private static String jdbcURl;
-    private static String jdbcDriver;
-    private static String jdbcUser;
-    private static String jdbcPassword;
-
-
-    public static void initializeDB() {
-//        System.setProperty("appcatalog.initialize.state", "0");
-        try{
-            jdbcDriver = ServerSettings.getSetting(WORKFLOWCATALOG_JDBC_DRIVER);
-            jdbcURl = ServerSettings.getSetting(WORKFLOWCATALOG_JDBC_URL);
-            jdbcUser = ServerSettings.getSetting(WORKFLOWCATALOG_JDBC_USER);
-            jdbcPassword = ServerSettings.getSetting(WORKFLOWCATALOG_JDBC_PASSWORD);
-            jdbcURl = jdbcURl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read airavata server properties", e.getMessage());
-        }
-
-        if (getDBType(jdbcURl).equals("derby") && isDerbyStartEnabled()) {
-            startDerbyInServerMode();
-        }
-        db = new JdbcStorage(10, 50, jdbcURl, jdbcDriver, true);
-
-        Connection conn = null;
-        try {
-            conn = db.connect();
-            if (!DatabaseCreator.isDatabaseStructureCreated(WORKFLOW, conn)) {
-                DatabaseCreator.createRegistryDatabase("database_scripts/workflowcatalog", conn);
-                logger.info("New Database created for Workflow Catalog !!! ");
-            } else {
-                logger.info("Database already created for Workflow Catalog!!!");
-            }
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new RuntimeException("Database failure", e);
-        } finally {
-            db.closeConnection(conn);
-            try {
-                if(conn != null){
-                    if (!conn.getAutoCommit()) {
-                        conn.commit();
-                    }
-                    conn.close();
-                }
-            } catch (SQLException e) {
-                logger.error("Error while closing database connection...", e.getMessage(), e);
-            }
-        }
-//        System.setProperty("appcatalog.initialize.state", "1");
-    }
-
-    public static String getDBType(String jdbcUrl){
-        try{
-            String cleanURI = jdbcUrl.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getScheme();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return null;
-        }
-    }
-
-    public static boolean isDerbyStartEnabled(){
-        try {
-            String s = ServerSettings.getSetting(START_DERBY_ENABLE);
-            if("true".equals(s)){
-                return true;
-            }
-        }  catch (ApplicationSettingsException e) {
-            logger.error("Unable to read airavata server properties", e.getMessage(), e);
-            return false;
-        }
-        return false;
-    }
-
-    public static void startDerbyInServerMode() {
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
-                    getPort(jdbcURl),
-                    jdbcUser, jdbcPassword);
-            java.io.PrintWriter consoleWriter = new java.io.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");
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether " +
-                    "specified port is available");
-        }
-    }
-    
-    public static void stopDerbyInServerMode() {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "false");
-            if (server!=null){
-            	try {
-					server.shutdown();
-				} catch (Exception e) {
-		            logger.error("Error when stopping the derby server : "+e.getLocalizedMessage());
-				}
-            }
-    }
-
-    public static int getPort(String jdbcURL){
-        try{
-            String cleanURI = jdbcURL.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getPort();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return -1;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/1eb3b415/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/AppCatInit.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/AppCatInit.java b/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/AppCatInit.java
deleted file mode 100644
index 86cb1ba..0000000
--- a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/AppCatInit.java
+++ /dev/null
@@ -1,320 +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.api.server.handler.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.InetAddress;
-import java.net.URI;
-import java.sql.*;
-import java.util.StringTokenizer;
-
-public class AppCatInit {
-    private static final Logger logger = LoggerFactory.getLogger(AppCatInit.class);
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-    public  String scriptName = "appcatalog-derby.sql";
-    private NetworkServerControl server;
-    private static final String delimiter = ";";
-    public static final String COMPUTE_RESOURCE_TABLE = "COMPUTE_RESOURCE";
-    private String jdbcUrl = null;
-    private String jdbcDriver = null;
-    private String jdbcUser = null;
-    private String jdbcPassword = null;
-
-    public AppCatInit(String scriptName) {
-        this.scriptName = scriptName;
-    }
-
-    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;
-    }
-
-    private static boolean isServerStarted(NetworkServerControl server, int ntries)
-    {
-        for (int i = 1; i <= ntries; i ++)
-        {
-            try {
-                Thread.sleep(500);
-                server.ping();
-                return true;
-            }
-            catch (Exception e) {
-                if (i == ntries)
-                    return false;
-            }
-        }
-        return false;
-    }
-
-    public void initializeDB() {
-
-        try{
-            jdbcDriver = ServerSettings.getSetting("appcatalog.jdbc.driver");
-            jdbcUrl = ServerSettings.getSetting("appcatalog.jdbc.url");
-            jdbcUser = ServerSettings.getSetting("appcatalog.jdbc.user");
-            jdbcPassword = ServerSettings.getSetting("appcatalog.jdbc.password");
-            jdbcUrl = jdbcUrl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read properties", e);
-        }
-
-        startDerbyInServerMode();
-        if(!isServerStarted(server, 20)){
-           throw new RuntimeException("Derby server cound not started within five seconds...");
-        }
-//      startDerbyInEmbeddedMode();
-
-        Connection conn = null;
-        try {
-            Class.forName(jdbcDriver).newInstance();
-            conn = DriverManager.getConnection(jdbcUrl, jdbcUser, jdbcPassword);
-            if (!isDatabaseStructureCreated(COMPUTE_RESOURCE_TABLE, conn)) {
-                executeSQLScript(conn);
-                logger.info("New Database created for App Catalog !!!");
-            } else {
-                logger.debug("Database already created for App Catalog!");
-            }
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new RuntimeException("Database failure", e);
-        } finally {
-            try {
-                if (conn != null){
-                    if (!conn.getAutoCommit()) {
-                        conn.commit();
-                    }
-                    conn.close();
-                }
-            } catch (SQLException e) {
-                logger.error(e.getMessage(), e);
-            }
-        }
-    }
-
-    public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
-        try {
-            System.out.println("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;
-    }
-
-    private void executeSQLScript(Connection conn) throws Exception {
-        StringBuffer sql = new StringBuffer();
-        BufferedReader reader = null;
-        try{
-
-        InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(scriptName);
-        reader = new BufferedReader(new InputStreamReader(inputStream));
-        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){
-            logger.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();
-            }
-
-        }
-
-    }
-
-    private static void executeSQL(String sql, Connection conn) throws Exception {
-        // Check and ignore empty statements
-        if ("".equals(sql.trim())) {
-            return;
-        }
-
-        Statement statement = null;
-        try {
-            logger.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);
-
-            logger.debug(sql + " : " + updateCountTotal + " rows affected");
-
-            SQLWarning warning = conn.getWarnings();
-            while (warning != null) {
-                logger.warn(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
-                logger.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) {
-                    logger.error("Error occurred while closing result set.", e);
-                }
-            }
-        }
-    }
-
-    private void startDerbyInServerMode() {
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
-                    20000,
-                    jdbcUser, jdbcPassword);
-            java.io.PrintWriter consoleWriter = new java.io.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");
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether " +
-                    "specified port is available");
-        }
-
-    }
-
-    public static int getPort(String jdbcURL){
-        try{
-            String cleanURI = jdbcURL.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getPort();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return -1;
-        }
-    }
-
-    private void startDerbyInEmbeddedMode(){
-        try {
-            Class.forName("org.apache.derby.jdbc.EmbeddedDriver");
-            DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close();
-        } catch (ClassNotFoundException e) {
-            logger.error(e.getMessage(), e);
-        } catch (SQLException e) {
-            logger.error(e.getMessage(), e);
-        }
-    }
-
-    public void stopDerbyServer() {
-        try {
-            server.shutdown();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/1eb3b415/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ExpCatInit.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ExpCatInit.java b/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ExpCatInit.java
deleted file mode 100644
index 90bbeeb..0000000
--- a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ExpCatInit.java
+++ /dev/null
@@ -1,330 +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.api.server.handler.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.registry.core.experiment.catalog.ResourceType;
-import org.apache.airavata.registry.core.experiment.catalog.resources.*;
-import org.apache.airavata.registry.cpi.*;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.InetAddress;
-import java.sql.*;
-import java.util.StringTokenizer;
-
-public class ExpCatInit {
-    private static final Logger logger = LoggerFactory.getLogger(ExpCatInit.class);
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-    public  String expCatScript = "expcatalog-derby.sql";
-    private NetworkServerControl server;
-    private static final String delimiter = ";";
-    public static final String PERSISTANT_DATA = "Configuration";
-
-    public ExpCatInit(String scriptName) {
-        this.expCatScript = scriptName;
-    }
-
-    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;
-    }
-
-    private static boolean isServerStarted(NetworkServerControl server, int ntries)
-    {
-        for (int i = 1; i <= ntries; i ++)
-        {
-            try {
-                Thread.sleep(500);
-                server.ping();
-                return true;
-            }
-            catch (Exception e) {
-                if (i == ntries)
-                    return false;
-            }
-        }
-        return false;
-    }
-
-    public void initializeDB() throws SQLException{
-        String jdbcUrl = null;
-        String jdbcUser = null;
-        String jdbcPassword = null;
-        try{
-            jdbcUrl = ServerSettings.getSetting("registry.jdbc.url");
-            jdbcUser = ServerSettings.getSetting("registry.jdbc.user");
-            jdbcPassword = ServerSettings.getSetting("registry.jdbc.password");
-            jdbcUrl = jdbcUrl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read properties", e);
-        }
-        startDerbyInServerMode();
-        if(!isServerStarted(server, 20)){
-           throw new RuntimeException("Derby server cound not started within five seconds...");
-        }
-
-        Connection conn = null;
-        try {
-            Class.forName(Utils.getJDBCDriver()).newInstance();
-            conn = DriverManager.getConnection(jdbcUrl, jdbcUser, jdbcPassword);
-            if (!isDatabaseStructureCreated(PERSISTANT_DATA, conn)) {
-                executeSQLScript(conn);
-                logger.info("New Database created for Exp Catalog");
-            } else {
-                logger.debug("Database already created for Exp Catalog!");
-            }
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new RuntimeException("Database failure", e);
-        } finally {
-            try {
-                if (conn != null){
-                    if (!conn.getAutoCommit()) {
-                        conn.commit();
-                    }
-                    conn.close();
-                }
-            } catch (SQLException e) {
-                logger.error(e.getMessage(), e);
-            }
-        }
-
-        try{
-            GatewayResource gatewayResource = new GatewayResource();
-            gatewayResource.setGatewayId(ServerSettings.getSetting("default.registry.gateway"));
-            gatewayResource.setGatewayName(ServerSettings.getSetting("default.registry.gateway"));
-            gatewayResource.setDomain("test-domain");
-            gatewayResource.setEmailAddress("test-email");
-            gatewayResource.save();
-            
-            UserResource userResource = new UserResource();
-            userResource.setUserName(ServerSettings.getSetting("default.registry.user"));
-            userResource.setPassword(ServerSettings.getSetting("default.registry.password"));
-            userResource.setGatewayId(ServerSettings.getDefaultUserGateway());
-            userResource.save();
-
-            WorkerResource workerResource = (WorkerResource) gatewayResource.create(ResourceType.GATEWAY_WORKER);
-            workerResource.setUser(userResource.getUserName());
-            workerResource.save();
-            
-            ProjectResource projectResource = (ProjectResource)workerResource.create(ResourceType.PROJECT);
-            projectResource.setGatewayId(gatewayResource.getGatewayId());
-            projectResource.setId("default");
-            projectResource.setName("default");
-            projectResource.setWorker(workerResource);
-            projectResource.save();
-        
-          
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read properties", e);
-            throw new SQLException(e.getMessage(), e);
-        } catch (RegistryException e) {
-            logger.error("Unable to save data to registry", e);
-            throw new SQLException(e.getMessage(), e);
-        }
-    }
-
-    public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
-        try {
-            System.out.println("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;
-    }
-
-    private void executeSQLScript(Connection conn) throws Exception {
-        StringBuffer expCatsql = new StringBuffer();
-        BufferedReader expCatReader = null;
-        try{
-
-        InputStream expCatStream = this.getClass().getClassLoader().getResourceAsStream(expCatScript);
-        expCatReader = new BufferedReader(new InputStreamReader(expCatStream));
-        String line;
-        while ((line = expCatReader.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;
-                }
-            }
-            expCatsql.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) {
-                expCatsql.append("\n");
-            }
-            if ((checkStringBufferEndsWith(expCatsql, delimiter))) {
-                executeSQL(expCatsql.substring(0, expCatsql.length() - delimiter.length()), conn);
-                expCatsql.replace(0, expCatsql.length(), "");
-            }
-        }
-        // Catch any statements not followed by ;
-        if (expCatsql.length() > 0) {
-            executeSQL(expCatsql.toString(), conn);
-        }
-        }catch (IOException e){
-            logger.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 (expCatReader != null) {
-                expCatReader.close();
-            }
-
-        }
-
-    }
-
-    private static void executeSQL(String sql, Connection conn) throws Exception {
-        // Check and ignore empty statements
-        if ("".equals(sql.trim())) {
-            return;
-        }
-
-        Statement statement = null;
-        try {
-            logger.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);
-
-            logger.debug(sql + " : " + updateCountTotal + " rows affected");
-
-            SQLWarning warning = conn.getWarnings();
-            while (warning != null) {
-                logger.warn(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
-                logger.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) {
-                    logger.error("Error occurred while closing result set.", e);
-                }
-            }
-        }
-    }
-
-    private void startDerbyInServerMode() {
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName(Utils.getHost()),
-                    20000,
-                    Utils.getJDBCUser(), Utils.getJDBCPassword());
-            java.io.PrintWriter consoleWriter = new java.io.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");
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether " +
-                    "specified port is available");
-        }
-
-    }
-
-    public void stopDerbyServer() throws SQLException{
-        try {
-            server.shutdown();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new SQLException("Error while stopping derby server", e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/1eb3b415/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ReplicaCatInit.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ReplicaCatInit.java b/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ReplicaCatInit.java
deleted file mode 100644
index 977454a..0000000
--- a/airavata-api/airavata-api-server/src/test/java/org/apache/airavata/api/server/handler/utils/ReplicaCatInit.java
+++ /dev/null
@@ -1,315 +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.api.server.handler.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.registry.core.replica.catalog.utils.ReplicaCatalogConstants;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.InetAddress;
-import java.net.URI;
-import java.sql.*;
-import java.util.StringTokenizer;
-
-public class ReplicaCatInit {
-    private static final Logger logger = LoggerFactory.getLogger(ReplicaCatInit.class);
-    public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
-    public  String scriptName = "replicacatalog-derby.sql";
-    private NetworkServerControl server;
-    private static final String delimiter = ";";
-    private String jdbcUrl = null;
-    private String jdbcDriver = null;
-    private String jdbcUser = null;
-    private String jdbcPassword = null;
-
-    public ReplicaCatInit(String scriptName) {
-        this.scriptName = scriptName;
-    }
-
-    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;
-    }
-
-    private static boolean isServerStarted(NetworkServerControl server, int ntries)
-    {
-        for (int i = 1; i <= ntries; i ++)
-        {
-            try {
-                Thread.sleep(500);
-                server.ping();
-                return true;
-            }
-            catch (Exception e) {
-                if (i == ntries)
-                    return false;
-            }
-        }
-        return false;
-    }
-
-    public void initializeDB() {
-        try{
-            jdbcDriver = ServerSettings.getSetting("replicacatalog.jdbc.driver");
-            jdbcUrl = ServerSettings.getSetting("replicacatalog.jdbc.url");
-            jdbcUser = ServerSettings.getSetting("replicacatalog.jdbc.user");
-            jdbcPassword = ServerSettings.getSetting("replicacatalog.jdbc.password");
-            jdbcUrl = jdbcUrl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read properties", e);
-        }
-
-        startDerbyInServerMode();
-        if(!isServerStarted(server, 20)){
-           throw new RuntimeException("Derby server could not started within five seconds...");
-        }
-        Connection conn = null;
-        try {
-            Class.forName(jdbcDriver).newInstance();
-            conn = DriverManager.getConnection(jdbcUrl, jdbcUser, jdbcPassword);
-            if (!isDatabaseStructureCreated(ReplicaCatalogConstants.CONFIGURATION, conn)) {
-                executeSQLScript(conn);
-                logger.info("New Database created for Data Catalog !!!");
-            } else {
-                logger.debug("Database already created for Data Catalog!");
-            }
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new RuntimeException("Database failure", e);
-        } finally {
-            try {
-                if (conn != null){
-                    if (!conn.getAutoCommit()) {
-                        conn.commit();
-                    }
-                    conn.close();
-                }
-            } catch (SQLException e) {
-                logger.error(e.getMessage(), e);
-            }
-        }
-    }
-
-    public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
-        try {
-            System.out.println("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;
-    }
-
-    private void executeSQLScript(Connection conn) throws Exception {
-        StringBuffer sql = new StringBuffer();
-        BufferedReader reader = null;
-        try{
-
-        InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(scriptName);
-        reader = new BufferedReader(new InputStreamReader(inputStream));
-        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){
-            logger.error("Error occurred while executing SQL script for creating Airavata Data Catalog database", e);
-            throw new Exception("Error occurred while executing SQL script for creating Airavata Data Catalog database", e);
-        }finally {
-            if (reader != null) {
-                reader.close();
-            }
-        }
-    }
-
-    private static void executeSQL(String sql, Connection conn) throws Exception {
-        // Check and ignore empty statements
-        if ("".equals(sql.trim())) {
-            return;
-        }
-
-        Statement statement = null;
-        try {
-            logger.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);
-
-            logger.debug(sql + " : " + updateCountTotal + " rows affected");
-
-            SQLWarning warning = conn.getWarnings();
-            while (warning != null) {
-                logger.warn(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
-                logger.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) {
-                    logger.error("Error occurred while closing result set.", e);
-                }
-            }
-        }
-    }
-
-    private void startDerbyInServerMode() {
-        try {
-            System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
-            server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
-                    20000,
-                    jdbcUser, jdbcPassword);
-            java.io.PrintWriter consoleWriter = new java.io.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");
-        } catch (Exception e) {
-            logger.error("Unable to start Apache derby in the server mode! Check whether " +
-                    "specified port is available");
-        }
-
-    }
-
-    public static int getPort(String jdbcURL){
-        try{
-            String cleanURI = jdbcURL.substring(5);
-            URI uri = URI.create(cleanURI);
-            return uri.getPort();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return -1;
-        }
-    }
-
-    private void startDerbyInEmbeddedMode(){
-        try {
-            Class.forName("org.apache.derby.jdbc.EmbeddedDriver");
-            DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close();
-        } catch (ClassNotFoundException e) {
-            logger.error(e.getMessage(), e);
-        } catch (SQLException e) {
-            logger.error(e.getMessage(), e);
-        }
-    }
-
-    public void stopDerbyServer() {
-        try {
-            server.shutdown();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-        }
-    }
-}


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