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From scnakand...@apache.org
Subject [16/17] airavata git commit: renaming directory names
Date Wed, 05 Oct 2016 08:21:07 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java
deleted file mode 100644
index 259e22c..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java
+++ /dev/null
@@ -1,98 +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.sharing.registry.db.repositories;
-
-import org.apache.airavata.sharing.registry.db.entities.GroupMembershipEntity;
-import org.apache.airavata.sharing.registry.db.entities.GroupMembershipEntityPK;
-import org.apache.airavata.sharing.registry.db.entities.UserEntity;
-import org.apache.airavata.sharing.registry.db.entities.UserGroupEntity;
-import org.apache.airavata.sharing.registry.db.utils.DBConstants;
-import org.apache.airavata.sharing.registry.models.*;
-
-import java.util.*;
-
-public class GroupMembershipRepository extends AbstractRepository<GroupMembership, GroupMembershipEntity, GroupMembershipEntityPK> {
-
-    public GroupMembershipRepository() {
-        super(GroupMembership.class, GroupMembershipEntity.class);
-    }
-
-    public List<GroupMembership> getChildMembershipsOfGroup(String parentId) throws GovRegistryException {
-        Map<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.GroupMembershipTable.PARENT_ID, parentId);
-        return select(filters, 0, -1);
-    }
-
-    public List<User> getAllChildUsers(String groupId) throws GovRegistryException {
-        String queryString = "SELECT U FROM " + UserEntity.class.getSimpleName() + " U, " + GroupMembershipEntity.class.getSimpleName()
-                + " GM WHERE GM." + DBConstants.GroupMembershipTable.CHILD_ID + " = U." + DBConstants.UserTable.USER_ID + " AND " +
-                "gm." + DBConstants.GroupMembershipTable.PARENT_ID+"='"+groupId + "' AND gm." + DBConstants.GroupMembershipTable.CHILD_TYPE
-                + "='" + GroupChildType.USER.toString() + "'";
-        UserRepository userRepository = new UserRepository();
-        List<User> users = userRepository.select(queryString, 0, -1);
-        return users;
-    }
-
-    public List<UserGroup> getAllChildGroups(String groupId) throws GovRegistryException {
-        String queryString = "SELECT G FROM " + UserGroupEntity.class.getSimpleName() + " G, " + GroupMembershipEntity.class.getSimpleName()
-                + " GM WHERE GM." + DBConstants.GroupMembershipTable.CHILD_ID + " = G." + DBConstants.UserGroupTable.GROUP_ID + " AND " +
-                "GM." + DBConstants.GroupMembershipTable.PARENT_ID+"='"+groupId + "' AND GM." + DBConstants.GroupMembershipTable.CHILD_TYPE
-                + "='" + GroupChildType.GROUP.toString() + "'";
-        UserGroupRepository userGroupRepository = new UserGroupRepository();
-        List<UserGroup> groups = userGroupRepository.select(queryString, 0, -1);
-        return groups;
-    }
-
-    public List<GroupMembership> getAllParentMembershipsForChild(String childId) throws GovRegistryException {
-        List<GroupMembership> finalParentGroups = new ArrayList<>();
-        Map<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.GroupMembershipTable.CHILD_ID, childId);
-        LinkedList<GroupMembership> temp = new LinkedList<>();
-        select(filters, 0, -1).stream().forEach(m -> temp.addLast(m));
-        while (temp.size() > 0){
-            GroupMembership gm = temp.pop();
-            filters = new HashMap<>();
-            filters.put(DBConstants.GroupMembershipTable.CHILD_ID, gm.parentId);
-            select(filters, 0, -1).stream().forEach(m -> temp.addLast(m));
-            finalParentGroups.add(gm);
-        }
-        return finalParentGroups;
-    }
-
-    public List<UserGroup> getAllParentGroupsForChild(String childId) throws GovRegistryException {
-        List<UserGroup> finalParentGroups = new ArrayList<>();
-        Map<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.GroupMembershipTable.CHILD_ID, childId);
-        LinkedList<GroupMembership> temp = new LinkedList<>();
-        select(filters, 0, -1).stream().forEach(m -> temp.addLast(m));
-        UserGroupRepository userGroupRepository = new UserGroupRepository();
-        while (temp.size() > 0){
-            GroupMembership gm = temp.pop();
-            filters = new HashMap<>();
-            filters.put(DBConstants.GroupMembershipTable.CHILD_ID, gm.parentId);
-            select(filters, 0, -1).stream().forEach(m -> temp.addLast(m));
-            finalParentGroups.add(userGroupRepository.get(gm.parentId));
-        }
-        return finalParentGroups;
-    }
-
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java
deleted file mode 100644
index e61f1ec..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java
+++ /dev/null
@@ -1,52 +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.sharing.registry.db.repositories;
-
-import org.apache.airavata.sharing.registry.db.entities.PermissionTypeEntity;
-import org.apache.airavata.sharing.registry.db.utils.DBConstants;
-import org.apache.airavata.sharing.registry.models.GovRegistryException;
-import org.apache.airavata.sharing.registry.models.PermissionType;
-import org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.HashMap;
-import java.util.List;
-
-public class PermissionTypeRepository extends AbstractRepository<PermissionType, PermissionTypeEntity, String> {
-    private final static Logger logger = LoggerFactory.getLogger(PermissionTypeRepository.class);
-
-    public PermissionTypeRepository() {
-        super(PermissionType.class, PermissionTypeEntity.class);
-    }
-
-    public String getGlobalPermissionTypeIdForDomain(String domainId) throws GovRegistryException {
-        HashMap<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.PermissionTypeTable.DOMAIN_ID, domainId);
-        filters.put(DBConstants.PermissionTypeTable.NAME, SharingRegistryServerHandler.GLOBAL_PERMISSION_NAME);
-        List<PermissionType> permissionTypeList = select(filters, 0, -1);
-        if(permissionTypeList.size() != 1){
-            throw new GovRegistryException("GLOBAL Permission inconsistency. Found " + permissionTypeList.size()
-                    + " records with " + SharingRegistryServerHandler.GLOBAL_PERMISSION_NAME + " name");
-        }
-        return permissionTypeList.get(0).getPermissionTypeId();
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java
deleted file mode 100644
index 27f9e0e..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java
+++ /dev/null
@@ -1,74 +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.sharing.registry.db.repositories;
-
-import org.apache.airavata.sharing.registry.db.entities.SharingEntity;
-import org.apache.airavata.sharing.registry.db.entities.SharingEntityPK;
-import org.apache.airavata.sharing.registry.db.utils.DBConstants;
-import org.apache.airavata.sharing.registry.models.GovRegistryException;
-import org.apache.airavata.sharing.registry.models.Sharing;
-import org.apache.airavata.sharing.registry.models.SharingType;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.HashMap;
-import java.util.List;
-
-public class SharingRepository extends AbstractRepository<Sharing, SharingEntity, SharingEntityPK> {
-    private final static Logger logger = LoggerFactory.getLogger(SharingRepository.class);
-
-    public SharingRepository() {
-        super(Sharing.class, SharingEntity.class);
-    }
-
-    public List<Sharing> getIndirectSharedChildren(String parentId, String permissionTypeId) throws GovRegistryException {
-        HashMap<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.SharingTable.INHERITED_PARENT_ID, parentId);
-        filters.put(DBConstants.SharingTable.SHARING_TYPE, SharingType.INHERITED.toString());
-        filters.put(DBConstants.SharingTable.PERMISSION_TYPE_ID, permissionTypeId);
-
-        return select(filters, 0, -1);
-    }
-
-    public List<Sharing> getPermissionsForEntity(String entityId) throws GovRegistryException {
-        HashMap<String, String> filters = new HashMap<>();
-        filters.put(DBConstants.SharingTable.ENTITY_ID, entityId);
-        return select(filters, 0, -1);
-    }
-
-    public boolean hasAccess(String entityId, List<String> groupIds, List<String> permissionTypeIds) throws GovRegistryException {
-        String query = "SELECT p from " + SharingEntity.class.getSimpleName() + " as p";
-        query += " WHERE ";
-        query += "p." + DBConstants.SharingTable.ENTITY_ID + " = '" + entityId + "' AND ";
-        String permissionTypeIdString = "'";
-        for(String permissionId : permissionTypeIds)
-            permissionTypeIdString += permissionId + "','";
-        permissionTypeIdString = permissionTypeIdString.substring(0, permissionTypeIdString.length()-2);
-        query += "p." + DBConstants.SharingTable.PERMISSION_TYPE_ID + " IN(" + permissionTypeIdString + ") AND ";
-        String groupIdString = "'";
-        for(String groupId : groupIds)
-            groupIdString += groupId + "','";
-        groupIdString = groupIdString.substring(0, groupIdString.length()-2);
-        query += "p." + DBConstants.SharingTable.GROUP_ID + " IN(" + groupIdString + ") ";
-        query += " ORDER BY p.createdTime DESC";
-        return select(query, 0, -1).size() > 0;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java
deleted file mode 100644
index 170b1fd..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java
+++ /dev/null
@@ -1,34 +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.sharing.registry.db.repositories;
-
-import org.apache.airavata.sharing.registry.db.entities.UserGroupEntity;
-import org.apache.airavata.sharing.registry.models.UserGroup;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class UserGroupRepository extends AbstractRepository<UserGroup, UserGroupEntity, String> {
-    private final static Logger logger = LoggerFactory.getLogger(UserGroupRepository.class);
-
-    public UserGroupRepository() {
-        super(UserGroup.class, UserGroupEntity.class);
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java
deleted file mode 100644
index f4ec03f..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java
+++ /dev/null
@@ -1,35 +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.sharing.registry.db.repositories;
-
-
-import org.apache.airavata.sharing.registry.db.entities.UserEntity;
-import org.apache.airavata.sharing.registry.models.User;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class UserRepository extends AbstractRepository<User, UserEntity, String> {
-    private final static Logger logger = LoggerFactory.getLogger(UserRepository.class);
-
-    public UserRepository() {
-        super(User.class, UserEntity.class);
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java
deleted file mode 100644
index ed8c9b3..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java
+++ /dev/null
@@ -1,27 +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.sharing.registry.db.utils;
-
-@FunctionalInterface
-public interface Committer<T, R>  {
-
-    R commit(T t);
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ConnectionPool.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ConnectionPool.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ConnectionPool.java
deleted file mode 100644
index 02484f7..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ConnectionPool.java
+++ /dev/null
@@ -1,382 +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.sharing.registry.db.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.sql.DataSource;
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Stack;
-import java.util.concurrent.Semaphore;
-
-
-/**
- * A class for preallocating, recycling, and managing JDBC connections.
- */
-public class ConnectionPool {
-    private static final Logger logger = LoggerFactory.getLogger(ConnectionPool.class);
-
-    private long MAX_IDLE_TIME = 5 * 60 * 1000; // 5 minutes
-
-    private String driver;
-    private String url;
-    private String username;
-    private String password;
-    private String jdbcUrl;
-
-    private int maxConnections;
-
-    private boolean autoCommit = true;
-    private boolean waitIfBusy;
-
-    private Semaphore needConnection = new Semaphore(0);
-    private boolean stop;
-
-    private Stack<Connection> availableConnections;
-    private Stack<Connection> busyConnections;
-
-    private HashMap<Connection, Long> lastAccessTimeRecord = new HashMap<Connection, Long>();
-
-    private String urlType = "";
-
-    private DataSource datasource;
-
-    private int transactionIsolation = Connection.TRANSACTION_NONE;
-
-    private Thread clenupThread;
-    private Thread producerThread;
-
-    public ConnectionPool(String driver, String url, String username, String password, int initialConnections,
-                          int maxConnections, boolean waitIfBusy) throws SQLException {
-        this.driver = driver;
-        this.url = url;
-        this.username = username;
-        this.password = password;
-        this.urlType = "speratedURL";
-        initialize(initialConnections, maxConnections, waitIfBusy);
-    }
-
-    public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections,
-                          boolean waitIfBusy, boolean autoCommit, int transactionIsolation) throws SQLException {
-        this.driver = driver;
-        this.jdbcUrl = jdbcUrl;
-        this.urlType = "simpleURL";
-        this.autoCommit = autoCommit;
-        this.transactionIsolation = transactionIsolation;
-        initialize(initialConnections, maxConnections, waitIfBusy);
-    }
-
-    public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections, boolean waitIfBusy)
-            throws SQLException {
-        this.driver = driver;
-        this.jdbcUrl = jdbcUrl;
-        this.urlType = "simpleURL";
-        initialize(initialConnections, maxConnections, waitIfBusy);
-    }
-
-    public ConnectionPool(DataSource dataSource, int initialConnections, int maxConnections, boolean waitIfBusy)
-            throws SQLException {
-        this.urlType = "dataSource";
-        this.datasource = dataSource;
-        initialize(initialConnections, maxConnections, waitIfBusy);
-    }
-
-    /**
-     * Check if this connection pool is auto commit or not
-     *
-     * @return
-     */
-    public boolean isAutoCommit() {
-        return this.autoCommit;
-    }
-
-    private void initialize(int initialConnections, int maxConnections, boolean waitIfBusy) throws SQLException {
-        this.maxConnections = maxConnections;
-        this.waitIfBusy = waitIfBusy;
-
-        int sizeOfConnections = (initialConnections > maxConnections) ? maxConnections : initialConnections;
-
-        availableConnections = new Stack<Connection>();
-        busyConnections = new Stack<Connection>();
-
-        for (int i = 0; i < sizeOfConnections; i++) {
-            Connection con = makeNewConnection();
-            setTimeStamp(con);
-            availableConnections.push(con);
-
-        }
-
-        producerThread = new Thread(new FillUpThread());
-        producerThread.start();
-
-        clenupThread = new Thread(new CleanUpThread());
-        clenupThread.start();
-    }
-
-    public synchronized Connection getConnection() throws SQLException {
-        if (!availableConnections.isEmpty()) {
-            Connection existingConnection = availableConnections.pop();
-
-            // If connection on available list is closed (e.g.,
-            // it timed out), then remove it from available list
-            // and race for a connection again.
-            if (existingConnection.isClosed()) {
-                lastAccessTimeRecord.remove(existingConnection);
-                // notifyAll for fairness
-                notifyAll();
-            } else {
-                busyConnections.push(existingConnection);
-                setTimeStamp(existingConnection);
-                return existingConnection;
-            }
-        } else if (!waitIfBusy && busyConnections.size() >= maxConnections) {
-            // You reached maxConnections limit and waitIfBusy flag is false.
-            // Throw SQLException in such a case.
-            throw new SQLException("Connection limit reached");
-        } else {
-
-            if (busyConnections.size() < maxConnections) {
-                // available connection is empty, but total number of connection
-                // doesn't reach maxConnection. Request for more connection
-                needConnection.release();
-            }
-
-            try {
-                // wait for free connection
-                wait();
-            } catch (InterruptedException ie) {
-            }
-        }
-        // always race for connection forever
-        return getConnection();
-    }
-
-    // This explicitly makes a new connection. Called in
-    // the foreground when initializing the ConnectionPool,
-    // and called in the background when running.
-    private Connection makeNewConnection() throws SQLException {
-        try {
-            // Load database driver if not already loaded
-            Class.forName(driver);
-            Connection connection;
-            // Establish network connection to database
-            if (urlType.equals("speratedURL")) {
-                connection = DriverManager.getConnection(url, username, password);
-            } else if (urlType.equals("simpleURL")) {
-                connection = DriverManager.getConnection(jdbcUrl);
-            } else { // if(urlType.equals("dataSource")){
-                connection = datasource.getConnection();
-            }
-            connection.setTransactionIsolation(this.transactionIsolation);
-            connection.setAutoCommit(this.autoCommit);
-            return connection;
-        } catch (ClassNotFoundException cnfe) {
-            // Simplify try/catch blocks of people using this by
-            // throwing only one exception type.
-            throw new SQLException("Can't find class for driver: " + driver);
-        }
-    }
-
-    private synchronized void fillUpConnection(Connection conn) {
-        setTimeStamp(conn);
-        availableConnections.push(conn);
-
-        // notify all since new connection is created
-        notifyAll();
-    }
-
-    private void setTimeStamp(Connection connection) {
-        lastAccessTimeRecord.put(connection, System.currentTimeMillis());
-    }
-
-    // The database connection cannot be left idle for too long, otherwise TCP
-    // connection will be broken.
-    /**
-     * From http://forums.mysql.com/read.php?39,28450,57460#msg-57460 Okay, then it looks like wait_timeout on the
-     * server is killing your connection (it is set to 8 hours of idle time by default). Either set that value higher on
-     * your server, or configure your connection pool to not hold connections idle that long (I prefer the latter). Most
-     * folks I know that run MySQL with a connection pool in high-load production environments only let connections sit
-     * idle for a matter of minutes, since it only takes a few milliseconds to open a connection, and the longer one
-     * sits idle the more chance it will go "bad" because of a network hiccup or the MySQL server being restarted.
-     *
-     * @throws java.sql.SQLException
-     */
-    private boolean isConnectionStale(Connection connection) {
-        long currentTime = System.currentTimeMillis();
-        long lastAccess = lastAccessTimeRecord.get(connection);
-        if (currentTime - lastAccess > MAX_IDLE_TIME) {
-            return true;
-        } else
-            return false;
-    }
-
-    private synchronized void closeStaleConnections() {
-        // close idle connections
-        Iterator<Connection> iter = availableConnections.iterator();
-        while (iter.hasNext()) {
-            Connection existingConnection = iter.next();
-            if (isConnectionStale(existingConnection)) {
-                try {
-                    existingConnection.close();
-                    iter.remove();
-                } catch (SQLException sql) {
-                    logger.error(sql.getMessage(), sql);
-                }
-            }
-        }
-        // close busy connections that have been checked out for too long.
-        // This should not happen since this means program has bug for not
-        // releasing connections .
-        iter = busyConnections.iterator();
-        while (iter.hasNext()) {
-            Connection busyConnection = iter.next();
-            if (isConnectionStale(busyConnection)) {
-                try {
-                    busyConnection.close();
-                    iter.remove();
-                    logger.warn("****Connection has checked out too long. Forced release. Check the program for calling release connection [free(Connection) method]");
-                } catch (SQLException sql) {
-                    logger.error(sql.getMessage(), sql);
-                }
-            }
-        }
-    }
-
-    public synchronized void free(Connection connection) {
-        busyConnections.removeElement(connection);
-        availableConnections.addElement(connection);
-        // Wake up threads that are waiting for a connection
-        notifyAll();
-    }
-
-    /**
-     * Close all the connections. Use with caution: be sure no connections are in use before calling. Note that you are
-     * not <I>required</I> to call this when done with a ConnectionPool, since connections are guaranteed to be closed
-     * when garbage collected. But this method gives more control regarding when the connections are closed.
-     */
-    public synchronized void dispose() {
-        logger.info("Connection Pool Shutting down");
-
-        // stop clean up thread
-        this.stop = true;
-        this.clenupThread.interrupt();
-
-        // stop producer up thread
-        this.producerThread.interrupt();
-
-        // close all connection
-        closeConnections(availableConnections);
-        availableConnections = new Stack<Connection>();
-        closeConnections(busyConnections);
-        busyConnections = new Stack<Connection>();
-        lastAccessTimeRecord.clear();
-
-        logger.info("All connection is closed");
-
-        try {
-            this.clenupThread.join();
-            this.producerThread.join();
-        } catch (Exception e) {
-            logger.error("Cannot shutdown cleanup thread", e);
-        }
-
-        logger.info("Connection Pool Shutdown");
-    }
-
-    private void closeConnections(Stack<Connection> connections) {
-        while (!connections.isEmpty()) {
-            Connection connection = connections.pop();
-            try {
-                if (!connection.isClosed()) {
-                    connection.close();
-                }
-            } catch (SQLException sqle) {
-                // Ignore errors; garbage collect anyhow
-                logger.warn(sqle.getMessage());
-            }
-        }
-    }
-
-    public synchronized String toString() {
-        String info = "ConnectionPool(" + url + "," + username + ")" + ", available=" + availableConnections.size()
-                + ", busy=" + busyConnections.size() + ", max=" + maxConnections;
-        return (info);
-    }
-
-    class CleanUpThread implements Runnable {
-        public void run() {
-            while (!stop) {
-                try {
-                    Thread.sleep(MAX_IDLE_TIME);
-                    closeStaleConnections();
-                } catch (InterruptedException e) {
-                    logger.info("Clean up thread is interrupted to close");
-                }
-            }
-        }
-    }
-
-    class FillUpThread implements Runnable {
-        public void run() {
-            while (!stop) {
-                try {
-                    // block until get
-                    needConnection.acquire();
-
-                    Connection conn = makeNewConnection();
-                    fillUpConnection(conn);
-                } catch (SQLException e) {
-                    // cannot create connection (increase semaphore value back)
-                    needConnection.release();
-                    logger.error(e.getMessage(), e);
-                } catch (InterruptedException e) {
-                    logger.info("Fill up thread is interrupted to close");
-                    break;
-                }
-            }
-        }
-    }
-
-    public void shutdown() throws SQLException{
-        for (Connection c : availableConnections) {
-            try {
-                c.close();
-            } catch (SQLException e) {
-                logger.error("Error while closing the connection", e);
-                throw new SQLException("Error while closing the connection", e);
-            }
-        }
-
-        for (Connection c : busyConnections) {
-            try {
-                c.close();
-            } catch (SQLException e) {
-                logger.error("Error while closing the connection", e);
-                throw new SQLException("Error while closing the connection", e);
-            }
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java
deleted file mode 100644
index f963de2..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java
+++ /dev/null
@@ -1,85 +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.sharing.registry.db.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class DBConstants {
-    private final static Logger logger = LoggerFactory.getLogger(DBConstants.class);
-
-    public static int SELECT_MAX_ROWS = 10000;
-
-    public static class DomainTable {
-        public static String DOMAIN_ID = "domainId";
-        public static String NAME = "name";
-        public static String DESCRIPTION = "description";
-    }
-
-    public static class UserTable {
-        public static String USER_ID = "userId";
-        public static String DOMAIN_ID = "domainId";
-        public static String USER_NAME = "userName";
-    }
-
-    public static class UserGroupTable {
-        public static String GROUP_ID = "groupId";
-        public static String DOMAIN_ID = "domainId";
-        public static String NAME = "name";
-        public static String DESCRIPTION = "description";
-        public static String OWNER_ID = "ownerId";
-        public static String GROUP_TYPE = "groupType";
-    }
-
-    public static class GroupMembershipTable {
-        public static String PARENT_ID = "parentId";
-        public static String CHILD_ID = "childId";
-        public static String CHILD_TYPE = "childType";
-    }
-
-    public static class EntityTypeTable {
-        public static String ENTITY_TYPE_ID = "entityTypeId";
-        public static String DOMAIN_ID = "domainId";
-    }
-
-    public static class PermissionTypeTable {
-        public static String ENTITY_TYPE_ID = "permissionTypeId";
-        public static String DOMAIN_ID = "domainId";
-        public static String NAME = "name";
-    }
-
-    public static class EntityTable {
-        public static String ENTITY_ID = "entityId";
-        public static String PARENT_ENTITY_ID = "parentEntityId";
-        public static String ENTITY_TYPE_ID = "entityTypeId";
-        public static String NAME = "name";
-        public static String DESCRIPTION = "description";
-        public static String FULL_TEXT = "fullText";
-    }
-
-    public static class SharingTable {
-        public static String PERMISSION_TYPE_ID = "permissionTypeId";
-        public static String ENTITY_ID = "entityId";
-        public static String GROUP_ID = "groupId";
-        public static String INHERITED_PARENT_ID = "inheritedParentId";
-        public static final String SHARING_TYPE = "sharingType";
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DatabaseCreator.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DatabaseCreator.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DatabaseCreator.java
deleted file mode 100644
index 5aa423c..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/DatabaseCreator.java
+++ /dev/null
@@ -1,353 +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.sharing.registry.db.utils;
-
-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.sql.*;
-import java.util.StringTokenizer;
-
-/**
- * This class creates the database tables required for airavata with default configuration this
- * class creates derby database in server mode. User can specify required database in appropriate
- * properties files.
- */
-public class DatabaseCreator {
-    private final static Logger logger = LoggerFactory.getLogger(DatabaseCreator.class);
-
-    public enum DatabaseType {
-        derby("(?i).*derby.*"), mysql("(?i).*mysql.*"), other("");
-
-        private String pattern;
-
-        private DatabaseType(String matchingPattern) {
-            this.pattern = matchingPattern;
-        }
-
-        public String getMatchingPattern() {
-            return this.pattern;
-        }
-    }
-
-    private static DatabaseType[] supportedDatabase = new DatabaseType[] { DatabaseType.derby, DatabaseType.mysql };
-
-    private static Logger log = LoggerFactory.getLogger(DatabaseCreator.class);
-    private static final String delimiter = ";";
-
-    /**
-     * Creates database
-     *
-     * @throws Exception
-     */
-    public static void createRegistryDatabase(String prefix, Connection conn) throws Exception {
-        createDatabase(prefix, conn);
-    }
-
-
-
-    /**
-     * Checks whether database tables are created by using select * on given table name
-     *
-     * @param tableName
-     *            Table which should be existed
-     * @return <code>true</core> if checkSQL is success, else <code>false</code> .
-     */
-    public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
-        try {
-
-            log.debug("Running a query to test the database tables existence.");
-
-            // check whether the tables are already created with a query
-            Statement statement = null;
-            try {
-                statement = conn.createStatement();
-                ResultSet rs = statement.executeQuery("select * from " + tableName);
-                if (rs != null) {
-                    rs.close();
-                }
-            } finally {
-                try {
-                    if (statement != null) {
-                        statement.close();
-                    }
-                } catch (SQLException e) {
-                    return false;
-                }
-            }
-        } catch (SQLException e) {
-            return false;
-        }
-
-        return true;
-    }
-
-    /**
-     * executes given sql
-     *
-     * @param sql
-     * @throws Exception
-     */
-    private static void executeSQL(String sql, Connection conn) throws Exception {
-        // Check and ignore empty statements
-        if ("".equals(sql.trim())) {
-            return;
-        }
-
-        Statement statement = null;
-        try {
-            log.debug("SQL : " + sql);
-
-            boolean ret;
-            int updateCount = 0, updateCountTotal = 0;
-            statement = conn.createStatement();
-            ret = statement.execute(sql);
-            updateCount = statement.getUpdateCount();
-            do {
-                if (!ret) {
-                    if (updateCount != -1) {
-                        updateCountTotal += updateCount;
-                    }
-                }
-                ret = statement.getMoreResults();
-                if (ret) {
-                    updateCount = statement.getUpdateCount();
-                }
-            } while (ret);
-
-            log.debug(sql + " : " + updateCountTotal + " rows affected");
-
-            SQLWarning warning = conn.getWarnings();
-            while (warning != null) {
-                log.info(warning + " sql warning");
-                warning = warning.getNextWarning();
-            }
-            conn.clearWarnings();
-        } catch (SQLException e) {
-            if (e.getSQLState().equals("X0Y32")) {
-                // eliminating the table already exception for the derby
-                // database
-                log.info("Table Already Exists", e);
-            } else {
-                throw new Exception("Error occurred while executing : " + sql, e);
-            }
-        } finally {
-            if (statement != null) {
-                try {
-                    statement.close();
-                } catch (SQLException e) {
-                    log.error("Error occurred while closing result set.", e);
-                }
-            }
-        }
-    }
-
-    /**
-     * computes relatational database type using database name
-     *
-     * @return DatabaseType
-     * @throws Exception
-     *
-     */
-    public static DatabaseType getDatabaseType(Connection conn) throws Exception {
-        try {
-            if (conn != null && (!conn.isClosed())) {
-                DatabaseMetaData metaData = conn.getMetaData();
-                String databaseProductName = metaData.getDatabaseProductName();
-                return checkType(databaseProductName);
-            }
-        } catch (SQLException e) {
-            String msg = "Failed to create Airavata database." + e.getMessage();
-            log.error(msg, e);
-            throw new Exception(msg, e);
-        }
-        return DatabaseType.other;
-    }
-
-    /**
-     * Overloaded method with String input
-     *
-     * @return DatabaseType
-     * @throws Exception
-     *
-     */
-    public static DatabaseType getDatabaseType(String dbUrl) throws Exception {
-        return checkType(dbUrl);
-    }
-
-    private static DatabaseType checkType(String text) throws Exception {
-        try {
-            if (text != null) {
-                for (DatabaseType type : supportedDatabase) {
-                    if (text.matches(type.getMatchingPattern()))
-                        return type;
-                }
-            }
-            String msg = "Unsupported database: " + text
-                    + ". Database will not be created automatically by the Airavata. "
-                    + "Please create the database using appropriate database scripts for " + "the database.";
-            throw new Exception(msg);
-
-        } catch (SQLException e) {
-            String msg = "Failed to create Airavatadatabase." + e.getMessage();
-            log.error(msg, e);
-            throw new Exception(msg, e);
-        }
-    }
-
-    /**
-     * Get scripts location which is prefix + "-" + databaseType + ".sql"
-     *
-     * @param prefix
-     * @param databaseType
-     * @return script location
-     */
-    private static String getScriptLocation(String prefix, DatabaseType databaseType) {
-        String scriptName = prefix + "-" + databaseType + ".sql";
-        log.debug("Loading database script from :" + scriptName);
-        return  scriptName;
-    }
-
-    private static void createDatabase(String prefix, Connection conn) throws Exception {
-        Statement statement = null;
-        try {
-            conn.setAutoCommit(false);
-            statement = conn.createStatement();
-            executeSQLScript(getScriptLocation(prefix, DatabaseCreator.getDatabaseType(conn)), conn);
-            conn.commit();
-            log.debug("Tables are created successfully.");
-        } catch (SQLException e) {
-            String msg = "Failed to create database tables for Airavata resource store. " + e.getMessage();
-            log.error(msg, e);
-            conn.rollback();
-            throw new Exception(msg, e);
-        } finally {
-            conn.setAutoCommit(true);
-            try {
-                if (statement != null) {
-                    statement.close();
-                }
-            } catch (SQLException e) {
-                log.error("Failed to close statement.", e);
-            }
-        }
-    }
-
-    private static void executeSQLScript(String dbscriptName, Connection conn) throws Exception {
-        StringBuffer sql = new StringBuffer();
-        BufferedReader reader = null;
-
-        try {
-            InputStream is = DatabaseCreator.class.getClassLoader().getResourceAsStream(dbscriptName);
-            if(is == null) {
-                logger.info("Script file not found at " + dbscriptName + ". Uses default database script file");
-                DatabaseType databaseType = DatabaseCreator.getDatabaseType(conn);
-                if(databaseType.equals(DatabaseType.derby)){
-                    is = DatabaseCreator.class.getClassLoader().getResourceAsStream("experiment-derby.sql");
-                }else if(databaseType.equals(DatabaseType.mysql)){
-                    is = DatabaseCreator.class.getClassLoader().getResourceAsStream("experiment-mysql.sql");
-                }
-            }
-            reader = new BufferedReader(new InputStreamReader(is));
-            String line;
-            while ((line = reader.readLine()) != null) {
-                line = line.trim();
-                if (line.startsWith("//")) {
-                    continue;
-                }
-                if (line.startsWith("--")) {
-                    continue;
-                }
-                StringTokenizer st = new StringTokenizer(line);
-                if (st.hasMoreTokens()) {
-                    String token = st.nextToken();
-                    if ("REM".equalsIgnoreCase(token)) {
-                        continue;
-                    }
-                }
-                sql.append(" ").append(line);
-
-                // SQL defines "--" as a comment to EOL
-                // and in Oracle it may contain a hint
-                // so we cannot just remove it, instead we must end it
-                if (line.indexOf("--") >= 0) {
-                    sql.append("\n");
-                }
-                if ((checkStringBufferEndsWith(sql, delimiter))) {
-                    executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn);
-                    sql.replace(0, sql.length(), "");
-                }
-            }
-            // Catch any statements not followed by ;
-            if (sql.length() > 0) {
-                executeSQL(sql.toString(), conn);
-            }
-        } catch (IOException e) {
-            log.error("Error occurred while executing SQL script for creating Airavata database", e);
-            throw new Exception("Error occurred while executing SQL script for creating Airavata database", e);
-
-        } finally {
-            if (reader != null) {
-                reader.close();
-            }
-        }
-    }
-
-    /**
-     * Checks that a string buffer ends up with a given string. It may sound trivial with the existing JDK API but the
-     * various implementation among JDKs can make those methods extremely resource intensive and perform poorly due to
-     * massive memory allocation and copying. See
-     *
-     * @param buffer
-     *            the buffer to perform the check on
-     * @param suffix
-     *            the suffix
-     * @return <code>true</code> if the character sequence represented by the argument is a suffix of the character
-     *         sequence represented by the StringBuffer object; <code>false</code> otherwise. Note that the result will
-     *         be <code>true</code> if the argument is the empty string.
-     */
-    public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) {
-        if (suffix.length() > buffer.length()) {
-            return false;
-        }
-        // this loop is done on purpose to avoid memory allocation performance
-        // problems on various JDKs
-        // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and
-        // implementation is ok though does allocation/copying
-        // StringBuffer.toString().endsWith() does massive memory
-        // allocation/copying on JDK 1.5
-        // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169
-        int endIndex = suffix.length() - 1;
-        int bufferIndex = buffer.length() - 1;
-        while (endIndex >= 0) {
-            if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) {
-                return false;
-            }
-            bufferIndex--;
-            endIndex--;
-        }
-        return true;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java
deleted file mode 100644
index f2f7c3a..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java
+++ /dev/null
@@ -1,230 +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.sharing.registry.db.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.sharing.registry.models.GovRegistryException;
-import org.apache.derby.drda.NetworkServerControl;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.*;
-import java.io.IOException;
-import java.net.InetAddress;
-import java.net.URI;
-import java.sql.Connection;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-public class JPAUtils {
-    private final static Logger logger = LoggerFactory.getLogger(JPAUtils.class);
-
-    private static final String PERSISTENCE_UNIT_NAME = "airavata-sharing-registry";
-    private static final String SHARING_REG_JDBC_DRIVER = "sharingcatalog.jdbc.driver";
-    private static final String SHARING_REG_JDBC_URL = "sharingcatalog.jdbc.url";
-    private static final String SHARING_REG_JDBC_USER = "sharingcatalog.jdbc.user";
-    private static final String SHARING_REG_JDBC_PWD = "sharingcatalog.jdbc.password";
-    private static final String SHARING_REG_VALIDATION_QUERY = "sharingcatalog.validationQuery";
-    private static final String JPA_CACHE_SIZE = "jpa.cache.size";
-    private static final String JPA_CACHE_ENABLED = "cache.enable";
-
-    public static final String CONFIGURATION = "CONFIGURATION";
-    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;
-
-
-    @PersistenceUnit(unitName = PERSISTENCE_UNIT_NAME)
-    protected static EntityManagerFactory factory;
-    @PersistenceContext(unitName = PERSISTENCE_UNIT_NAME)
-    private static EntityManager entityManager;
-
-    public static EntityManager getEntityManager() {
-        if (factory == null) {
-//            String connectionProperties = "DriverClassName=" + readServerProperties(SHARING_REG_JDBC_DRIVER) + "," +
-//                    "Url=" + readServerProperties(SHARING_REG_JDBC_URL) + "?autoReconnect=true," +
-//                    "Username=" + readServerProperties(SHARING_REG_JDBC_USER) + "," +
-//                    "Password=" + readServerProperties(SHARING_REG_JDBC_PWD) +
-//                    ",validationQuery=" + readServerProperties(SHARING_REG_VALIDATION_QUERY);
-//
-
-            String connectionProperties = "DriverClassName=com.mysql.jdbc.Driver," +
-                    "Url=jdbc:mysql://localhost:3306/airavata_sharing_catalog?autoReconnect=true," +
-                    "Username=root," +
-                    "Password=," +
-                    ",validationQuery=SELECT 1 FROM CONFIGURATION";
-
-            Map<String, String> properties = new HashMap<String, String>();
-            properties.put("openjpa.ConnectionDriverName", "org.apache.commons.dbcp.BasicDataSource");
-            properties.put("openjpa.ConnectionProperties", connectionProperties);
-            properties.put("openjpa.DynamicEnhancementAgent", "true");
-            properties.put("openjpa.RuntimeUnenhancedClasses", "unsupported");
-            // For app catalog, we don't need caching
-//            properties.put("openjpa.DataCache","" + readServerProperties(JPA_CACHE_ENABLED) + "(CacheSize=" + Integer.valueOf(readServerProperties(JPA_CACHE_SIZE)) + ", SoftReferenceSize=0)");
-//            properties.put("openjpa.QueryCache","" + readServerProperties(JPA_CACHE_ENABLED) + "(CacheSize=" + Integer.valueOf(readServerProperties(JPA_CACHE_SIZE)) + ", SoftReferenceSize=0)");
-            properties.put("openjpa.RemoteCommitProvider", "sjvm");
-            properties.put("openjpa.Log", "DefaultLevel=INFO, Runtime=INFO, Tool=INFO, SQL=INFO");
-            properties.put("openjpa.jdbc.SynchronizeMappings", "buildSchema(ForeignKeys=true)");
-            properties.put("openjpa.jdbc.QuerySQLCache", "false");
-            properties.put("openjpa.ConnectionFactoryProperties", "PrettyPrint=true, PrettyPrintLineLength=72," +
-                    " PrintParameters=true, MaxActive=10, MaxIdle=5, MinIdle=2, MaxWait=31536000,  autoReconnect=true");
-            properties.put("openjpa.RuntimeUnenhancedClasses", "warn");
-            factory = Persistence.createEntityManagerFactory(PERSISTENCE_UNIT_NAME, properties);
-        }
-        entityManager = factory.createEntityManager();
-        return entityManager;
-    }
-
-    public static <R> R execute(Committer<EntityManager, R> committer) throws GovRegistryException {
-        EntityManager entityManager = JPAUtils.getEntityManager();
-        try {
-            entityManager.getTransaction().begin();
-            R r = committer.commit(entityManager);
-            entityManager.getTransaction().commit();
-            return  r;
-        }finally {
-            if (entityManager != null && entityManager.isOpen()) {
-                if (entityManager.getTransaction().isActive()) {
-                    entityManager.getTransaction().rollback();
-                }
-                entityManager.close();
-            }
-        }
-    }
-
-    public static void initializeDB() throws GovRegistryException {
-        jdbcDriver = readServerProperties(SHARING_REG_JDBC_DRIVER);
-        jdbcURl = readServerProperties(SHARING_REG_JDBC_URL);
-        jdbcUser = readServerProperties(SHARING_REG_JDBC_USER);
-        jdbcPassword = readServerProperties(SHARING_REG_JDBC_PWD);
-        jdbcURl = jdbcURl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
-
-        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(CONFIGURATION, conn)) {
-                DatabaseCreator.createRegistryDatabase("database_scripts/sharing-registry", conn);
-                logger.info("New Database created for Sharing Catalog !!! ");
-            } else {
-                logger.info("Database already created for Sharing 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);
-            }
-        }
-    }
-
-    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;
-        }
-    }
-
-    private static String readServerProperties(String propertyName) throws GovRegistryException {
-        try {
-            return ServerSettings.getSetting(propertyName);
-        } catch (ApplicationSettingsException e) {
-            logger.error("Unable to read airavata-server.properties...", e);
-            throw new GovRegistryException("Unable to read airavata-server.properties...");
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JdbcStorage.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JdbcStorage.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JdbcStorage.java
deleted file mode 100644
index 377c50b..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/JdbcStorage.java
+++ /dev/null
@@ -1,175 +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.sharing.registry.db.utils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.sql.*;
-
-public class JdbcStorage {
-    private static Logger log = LoggerFactory.getLogger(JdbcStorage.class);
-
-    private ConnectionPool connectionPool;
-
-    public JdbcStorage(String jdbcUrl, String jdbcDriver) {
-        // default init connection and max connection
-        this(3, 50, jdbcUrl, jdbcDriver, true);
-    }
-
-    public JdbcStorage(int initCon, int maxCon, String url, String driver, boolean enableTransactions) {
-        try {
-            if (enableTransactions) {
-                connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true, false,
-                        Connection.TRANSACTION_SERIALIZABLE);
-            } else {
-                connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true);
-            }
-        } catch (Exception e) {
-            throw new RuntimeException("Failed to create database connection pool.", e);
-        }
-    }
-
-    /**
-     * Check if this connection pool is auto commit or not
-     *
-     * @return
-     */
-    public boolean isAutoCommit() {
-        return connectionPool.isAutoCommit();
-    }
-
-    public void commit(Connection conn) {
-        try {
-            if (conn != null && !conn.getAutoCommit()) {
-                conn.commit();
-            }
-        } catch (SQLException sqle) {
-            log.error("Cannot commit data", sqle);
-        }
-    }
-
-    public void commitAndFree(Connection conn) {
-        commit(conn);
-        closeConnection(conn);
-    }
-
-    public void rollback(Connection conn) {
-        try {
-            if (conn != null && !conn.getAutoCommit()) {
-                conn.rollback();
-            }
-        } catch (SQLException sqle) {
-            log.error("Cannot Rollback data", sqle);
-        }
-    }
-
-    public void rollbackAndFree(Connection conn) {
-        rollback(conn);
-        closeConnection(conn);
-    }
-
-    public Connection connect() {
-
-        Connection conn = null;
-        try {
-            conn = connectionPool.getConnection();
-        } catch (SQLException e) {
-            log.error(e.getMessage(), e);
-        }
-        return conn;
-    }
-
-    /**
-     * This method is provided so that you can have better control over the statement. For example: You can use
-     * stmt.setString to convert quotation mark automatically in an UPDATE statement
-     *
-     * NOTE: Statement is closed after execution
-     */
-    public int executeUpdateAndClose(PreparedStatement stmt) throws SQLException {
-        int rows = 0;
-        try {
-            rows = stmt.executeUpdate();
-            if (rows == 0) {
-                log.info("Problem: 0 rows affected by insert/update/delete statement.");
-            }
-        } finally {
-            stmt.close();
-        }
-        return rows;
-    }
-
-    public int countRow(String tableName, String columnName) throws SQLException {
-        String query = new String("SELECT COUNT(" + columnName + ") FROM " + tableName);
-        int count = -1;
-        Connection conn = null;
-        PreparedStatement stmt = null;
-        try {
-            conn = connectionPool.getConnection();
-            stmt = conn.prepareStatement(query);
-            ResultSet rs = stmt.executeQuery();
-            rs.next();
-            count = rs.getInt(1);
-            commit(conn);
-        } catch (SQLException sql) {
-            rollback(conn);
-            throw sql;
-        } finally {
-            try {
-                if (stmt != null && !stmt.isClosed()) {
-                    stmt.close();
-                }
-            } finally {
-                closeConnection(conn);
-            }
-        }
-        return count;
-    }
-
-    public void quietlyClose(Connection conn, Statement... stmts) {
-        if (stmts != null) {
-            for (Statement stmt : stmts) {
-                try {
-                    if (stmt != null && !stmt.isClosed()) {
-                        stmt.close();
-                    }
-                } catch (SQLException sql) {
-                    log.error(sql.getMessage(), sql);
-                }
-            }
-        }
-        closeConnection(conn);
-    }
-
-    public void closeConnection(Connection conn) {
-        if (conn != null) {
-            connectionPool.free(conn);
-        }
-    }
-
-    public void closeAllConnections() {
-        if (connectionPool != null)
-            connectionPool.dispose();
-    }
-
-    public void shutdown() throws SQLException {
-        connectionPool.shutdown();
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java
deleted file mode 100644
index de6bea9..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java
+++ /dev/null
@@ -1,39 +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.sharing.registry.db.utils;
-
-import org.dozer.DozerBeanMapper;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class ObjectMapperSingleton extends DozerBeanMapper{
-    private final static Logger logger = LoggerFactory.getLogger(ObjectMapperSingleton.class);
-
-    private static ObjectMapperSingleton instance;
-
-    private ObjectMapperSingleton(){}
-
-    public static ObjectMapperSingleton getInstance(){
-        if(instance == null)
-            instance = new ObjectMapperSingleton();
-        return instance;
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/43f228fc/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.java
----------------------------------------------------------------------
diff --git a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.java b/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.java
deleted file mode 100644
index 96fdb90..0000000
--- a/modules/airavata-sharing-registry/airavata-sharing-registry-core/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.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.sharing.registry.server;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SharingRegistryServer {
-    private final static Logger logger = LoggerFactory.getLogger(SharingRegistryServer.class);
-}
\ No newline at end of file


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