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From chath...@apache.org
Subject [13/22] airavata git commit: adding registry changes
Date Fri, 05 Jun 2015 15:03:12 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/WorkflowResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/WorkflowResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/WorkflowResource.java
deleted file mode 100644
index 3e52019..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/resources/WorkflowResource.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.aiaravata.application.catalog.data.resources;
-
-import org.airavata.appcatalog.cpi.AppCatalogException;
-import org.apache.aiaravata.application.catalog.data.model.Workflow;
-import org.apache.aiaravata.application.catalog.data.util.AppCatalogJPAUtils;
-import org.apache.aiaravata.application.catalog.data.util.AppCatalogQueryGenerator;
-import org.apache.aiaravata.application.catalog.data.util.AppCatalogResourceType;
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.AiravataUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.EntityManager;
-import javax.persistence.Query;
-import java.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.List;
-
-public class WorkflowResource extends AbstractResource {
-    private final static Logger logger = LoggerFactory.getLogger(WorkflowResource.class);
-    private String wfName;
-    private String createdUser;
-    private String graph;
-    private String wfTemplateId;
-    private Timestamp createdTime;
-    private Timestamp updatedTime;
-    private String image;
-    private String gatewayId;
-
-    public Timestamp getCreatedTime() {
-        return createdTime;
-    }
-
-    public void setCreatedTime(Timestamp createdTime) {
-        this.createdTime = createdTime;
-    }
-
-    public Timestamp getUpdatedTime() {
-        return updatedTime;
-    }
-
-    public void setUpdatedTime(Timestamp updatedTime) {
-        this.updatedTime = updatedTime;
-    }
-
-    public String getImage() {
-        return image;
-    }
-
-    public void setImage(String image) {
-        this.image = image;
-    }
-
-    public String getGatewayId() {
-        return gatewayId;
-    }
-
-    public void setGatewayId(String gatewayId) {
-        this.gatewayId = gatewayId;
-    }
-
-    @Override
-    public void remove(Object identifier) throws AppCatalogException {
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            generator.setParameter(WorkflowConstants.WF_TEMPLATE_ID, identifier);
-            Query q = generator.deleteQuery(em);
-            q.executeUpdate();
-            em.getTransaction().commit();
-            em.close();
-        } catch (ApplicationSettingsException e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    @Override
-    public Resource get(Object identifier) throws AppCatalogException {
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            generator.setParameter(WorkflowConstants.WF_TEMPLATE_ID, identifier);
-            Query q = generator.selectQuery(em);
-            Workflow workflow = (Workflow) q.getSingleResult();
-            WorkflowResource workflowResource = (WorkflowResource) AppCatalogJPAUtils.getResource(AppCatalogResourceType.WORKFLOW, workflow);
-            em.getTransaction().commit();
-            em.close();
-            return workflowResource;
-        } catch (ApplicationSettingsException e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    @Override
-    public List<Resource> get(String fieldName, Object value) throws AppCatalogException {
-        List<Resource> workflowResources = new ArrayList<Resource>();
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            Query q;
-            if ((fieldName.equals(WorkflowConstants.WF_NAME)) || (fieldName.equals(WorkflowConstants.CREATED_USER)) || (fieldName.equals(WorkflowConstants.GRAPH)) || (fieldName.equals(WorkflowConstants.WF_TEMPLATE_ID))) {
-                generator.setParameter(fieldName, value);
-                q = generator.selectQuery(em);
-                List<?> results = q.getResultList();
-                for (Object result : results) {
-                    Workflow workflow = (Workflow) result;
-                    WorkflowResource workflowResource = (WorkflowResource) AppCatalogJPAUtils.getResource(AppCatalogResourceType.WORKFLOW, workflow);
-                    workflowResources.add(workflowResource);
-                }
-            } else {
-                em.getTransaction().commit();
-                em.close();
-                logger.error("Unsupported field name for Workflow Resource.", new IllegalArgumentException());
-                throw new IllegalArgumentException("Unsupported field name for Workflow Resource.");
-            }
-            em.getTransaction().commit();
-            em.close();
-        } catch (ApplicationSettingsException e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return workflowResources;
-    }
-
-    @Override
-    public List<Resource> getAll() throws AppCatalogException {
-        List<Resource> workflows = new ArrayList<Resource>();
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            generator.setParameter(WorkflowConstants.GATEWAY_ID, gatewayId);
-            Query q = generator.selectQuery(em);
-            List results = q.getResultList();
-            if (results.size() != 0) {
-                for (Object result : results) {
-                    Workflow workflow = (Workflow) result;
-                    WorkflowResource wfResource =
-                            (WorkflowResource) AppCatalogJPAUtils.getResource(AppCatalogResourceType.WORKFLOW, workflow);
-                    workflows.add(wfResource);
-                }
-            }
-            em.getTransaction().commit();
-            em.close();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return workflows;
-    }
-
-    @Override
-    public List<String> getAllIds() throws AppCatalogException {
-        List<String> workflowIds = new ArrayList<String>();
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            generator.setParameter(WorkflowConstants.GATEWAY_ID, gatewayId);
-            Query q = generator.selectQuery(em);
-            List results = q.getResultList();
-            if (results.size() != 0) {
-                for (Object result : results) {
-                    Workflow workflow = (Workflow) result;
-                    workflowIds.add(workflow.getWfTemplateId());
-                }
-            }
-            em.getTransaction().commit();
-            em.close();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return workflowIds;
-    }
-
-    @Override
-    public List<String> getIds(String fieldName, Object value) throws AppCatalogException {
-        List<String> workflowResourceIDs = new ArrayList<String>();
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            AppCatalogQueryGenerator generator = new AppCatalogQueryGenerator(WORKFLOW);
-            Query q;
-            if ((fieldName.equals(WorkflowConstants.WF_NAME)) || (fieldName.equals(WorkflowConstants.CREATED_USER)) || (fieldName.equals(WorkflowConstants.GRAPH)) || (fieldName.equals(WorkflowConstants.WF_TEMPLATE_ID))) {
-                generator.setParameter(fieldName, value);
-                q = generator.selectQuery(em);
-                List<?> results = q.getResultList();
-                for (Object result : results) {
-                    Workflow workflow = (Workflow) result;
-                    WorkflowResource workflowResource = (WorkflowResource) AppCatalogJPAUtils.getResource(AppCatalogResourceType.WORKFLOW, workflow);
-                    workflowResourceIDs.add(workflowResource.getWfTemplateId());
-                }
-            } else {
-                em.getTransaction().commit();
-                em.close();
-                logger.error("Unsupported field name for Workflow Resource.", new IllegalArgumentException());
-                throw new IllegalArgumentException("Unsupported field name for Workflow Resource.");
-            }
-            em.getTransaction().commit();
-            em.close();
-        } catch (ApplicationSettingsException e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return workflowResourceIDs;
-    }
-
-    @Override
-    public void save() throws AppCatalogException {
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            Workflow existingWorkflow = em.find(Workflow.class, wfTemplateId);
-            em.close();
-            Workflow workflow;
-            em = AppCatalogJPAUtils.getEntityManager();
-            em.getTransaction().begin();
-            if (existingWorkflow == null) {
-                workflow = new Workflow();
-                workflow.setCreationTime(AiravataUtils.getCurrentTimestamp());
-            } else {
-                workflow = existingWorkflow;
-                workflow.setUpdateTime(AiravataUtils.getCurrentTimestamp());
-            }
-            workflow.setWfName(getWfName());
-            workflow.setCreatedUser(getCreatedUser());
-            workflow.setGatewayId(gatewayId);
-            if (getGraph() != null){
-                workflow.setGraph(getGraph().toCharArray());
-            }
-            if (image != null){
-                workflow.setImage(image.getBytes());
-            }
-            workflow.setWfTemplateId(getWfTemplateId());
-            if (existingWorkflow == null) {
-                em.persist(workflow);
-            } else {
-                em.merge(workflow);
-            }
-            em.getTransaction().commit();
-            em.close();
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    @Override
-    public boolean isExists(Object identifier) throws AppCatalogException {
-        EntityManager em = null;
-        try {
-            em = AppCatalogJPAUtils.getEntityManager();
-            Workflow workflow = em.find(Workflow.class, identifier);
-            em.close();
-            return workflow != null;
-        } catch (ApplicationSettingsException e) {
-            logger.error(e.getMessage(), e);
-            throw new AppCatalogException(e);
-        } finally {
-            if (em != null && em.isOpen()) {
-                if (em.getTransaction().isActive()) {
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    public String getWfName() {
-        return wfName;
-    }
-
-    public String getCreatedUser() {
-        return createdUser;
-    }
-
-    public String getGraph() {
-        return graph;
-    }
-
-    public String getWfTemplateId() {
-        return wfTemplateId;
-    }
-
-    public void setWfName(String wfName) {
-        this.wfName=wfName;
-    }
-
-    public void setCreatedUser(String createdUser) {
-        this.createdUser=createdUser;
-    }
-
-    public void setGraph(String graph) {
-        this.graph=graph;
-    }
-
-    public void setWfTemplateId(String wfTemplateId) {
-        this.wfTemplateId=wfTemplateId;
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentCatalogImpl.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentCatalogImpl.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentCatalogImpl.java
index 88fbe29..6a7f723 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentCatalogImpl.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentCatalogImpl.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
index 1178461..35605f8 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.logger.AiravataLogger;
 import org.apache.airavata.common.logger.AiravataLoggerFactory;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/GatewayRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/GatewayRegistry.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/GatewayRegistry.java
index 1aa165c..d97f0d4 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/GatewayRegistry.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/GatewayRegistry.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/LoggingExperimentCatalogImpl.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/LoggingExperimentCatalogImpl.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/LoggingExperimentCatalogImpl.java
index d45c4c5..4849385 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/LoggingExperimentCatalogImpl.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/LoggingExperimentCatalogImpl.java
@@ -18,7 +18,7 @@
  * under the License.
  *
 */
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.registry.cpi.*;
 import org.slf4j.Logger;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ProjectRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ProjectRegistry.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ProjectRegistry.java
index c045a93..f0c4965 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ProjectRegistry.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ProjectRegistry.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.utils.AiravataUtils;
 import org.apache.airavata.model.workspace.Project;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/RegistryFactory.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/RegistryFactory.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/RegistryFactory.java
index 5b8ce18..b54e0cf 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/RegistryFactory.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/RegistryFactory.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/UserReg.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/UserReg.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/UserReg.java
index c7f80c7..e720df0 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/UserReg.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/UserReg.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.apache.airavata.experiment.catalog.impl;
+package org.apache.airavata.registry.core.experiment.catalog.impl;
 
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import org.apache.airavata.common.utils.ServerSettings;

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/JPAConstants.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/JPAConstants.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/JPAConstants.java
deleted file mode 100644
index b558d03..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/JPAConstants.java
+++ /dev/null
@@ -1,33 +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.experiment.catalog;
-
-public class JPAConstants {
-	public static final String KEY_JDBC_URL = "registry.jdbc.url";
-	public static final String KEY_JDBC_USER = "registry.jdbc.user";
-	public static final String KEY_JDBC_PASSWORD = "registry.jdbc.password";
-	public static final String KEY_JDBC_DRIVER = "registry.jdbc.driver";
-	public static final String KEY_DERBY_START_ENABLE = "start.derby.server.mode";
-    public static final String VALIDATION_QUERY = "validationQuery";
-    public static final String JPA_CACHE_SIZE = "jpa.cache.size";
-    public static final String ENABLE_CACHING = "cache.enable";
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/Resource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/Resource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/Resource.java
deleted file mode 100644
index bdfd948..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/Resource.java
+++ /dev/null
@@ -1,71 +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.experiment.catalog;
-
-import org.apache.airavata.registry.cpi.RegistryException;
-
-import java.util.List;
-
-public interface Resource {
-    /**
-     * This method will create associate resource objects for the given resource type.
-     * @param type child resource type
-     * @return associate child resource
-     */
-    Resource create(ResourceType type) throws RegistryException, RegistryException;
-
-    /**
-     * This method will remove the given child resource from the database
-     * @param type child resource type
-     * @param name child resource name
-     */
-    void remove(ResourceType type, Object name) throws RegistryException;
-
-    /**
-     *  This method will return the given child resource from the database
-     * @param type child resource type
-     * @param name child resource name
-     * @return associate child resource
-     */
-    Resource get(ResourceType type, Object name) throws RegistryException;
-
-    /**
-     * This method will list all the child resources for the given resource type
-     * @param type child resource type
-     * @return list of child resources of the given child resource type
-     */
-    List<Resource> get(ResourceType type) throws RegistryException;
-
-    /**
-     * This method will save the resource to the database.
-     */
-    void save() throws RegistryException;
-
-    /**
-     * This method will check whether an entry from the given resource type and resource name
-     * exists in the database
-     * @param type child resource type
-     * @param name child resource name
-     * @return whether the entry exists in the database or not
-     */
-    boolean isExists(ResourceType type, Object name) throws RegistryException;
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceType.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceType.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceType.java
deleted file mode 100644
index ea66a90..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceType.java
+++ /dev/null
@@ -1,50 +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.experiment.catalog;
-
-public enum ResourceType {
-    GATEWAY,
-    PROJECT,
-    USER,
-    PROJECT_USER,
-    CONFIGURATION,
-    GATEWAY_WORKER,
-    EXPERIMENT,
-    EXPERIMENT_SUMMARY,
-    NOTIFICATION_EMAIL,
-    EXPERIMENT_INPUT,
-    EXPERIMENT_OUTPUT,
-    WORKFLOW_NODE_DETAIL,
-    TASK_DETAIL,
-    ERROR_DETAIL,
-    APPLICATION_INPUT,
-    APPLICATION_OUTPUT,
-    NODE_INPUT,
-    NODE_OUTPUT,
-    JOB_DETAIL,
-    DATA_TRANSFER_DETAIL,
-    STATUS,
-    CONFIG_DATA,
-    COMPUTATIONAL_RESOURCE_SCHEDULING,
-    ADVANCE_INPUT_DATA_HANDLING,
-    ADVANCE_OUTPUT_DATA_HANDLING,
-    QOS_PARAM
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/5a648a60/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceUtils.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceUtils.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceUtils.java
deleted file mode 100644
index a8d8e83..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experimet/catalog/ResourceUtils.java
+++ /dev/null
@@ -1,525 +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.experiment.catalog;
-
-import org.apache.airavata.experiment.catalog.model.*;
-import org.apache.airavata.experiment.catalog.resources.*;
-import org.apache.airavata.experiment.catalog.utils.QueryGenerator;
-import org.apache.airavata.registry.cpi.RegistryException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.EntityManager;
-import javax.persistence.EntityManagerFactory;
-import javax.persistence.Persistence;
-import javax.persistence.Query;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class ResourceUtils {
-    private final static Logger logger = LoggerFactory.getLogger(ResourceUtils.class);
-    private static final String PERSISTENCE_UNIT_NAME = "airavata_data";
-    protected static EntityManagerFactory factory;
-
-    public static void reset(){
-    	factory=null;
-    }
-    
-    public static EntityManager getEntityManager(){
-        if (factory == null) {
-            String connectionProperties = "DriverClassName=" + Utils.getJDBCDriver() + "," + "Url=" + Utils.getJDBCURL() + "?autoReconnect=true,," +
-                    "Username=" + Utils.getJDBCUser() + "," + "Password=" + Utils.getJDBCPassword() + ",validationQuery=" +
-            Utils.getValidationQuery();
-            System.out.println(connectionProperties);
-            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");
-            properties.put("openjpa.DataCache","" + Utils.isCachingEnabled() + "(CacheSize=" + Utils.getJPACacheSize() + ", SoftReferenceSize=0)");
-            properties.put("openjpa.QueryCache","" + Utils.isCachingEnabled() + "(CacheSize=" + Utils.getJPACacheSize() + ", SoftReferenceSize=0)");
-            properties.put("openjpa.RemoteCommitProvider","sjvm");
-            properties.put("openjpa.Log","DefaultLevel=INFO, Runtime=INFO, Tool=INFO, SQL=INFO");
-            properties.put("openjpa.jdbc.DBDictionary","SupportsMultipleNontransactionalResultSets=false");
-//            properties.put("openjpa.ReadLockLevel", "none");
-//            properties.put("openjpa.WriteLockLevel", "none");
-//            properties.put("openjpa.LockTimeout", "30000");
-//            properties.put("openjpa.LockManager", "none");
-            properties.put("openjpa.jdbc.SynchronizeMappings", "buildSchema(ForeignKeys=true)");
-            properties.put("openjpa.ConnectionFactoryProperties", "PrettyPrint=true, PrettyPrintLineLength=72, PrintParameters=true, MaxActive=10, MaxIdle=5, MinIdle=2, MaxWait=31536000,  autoReconnect=true");
-			properties.put("openjpa.jdbc.QuerySQLCache", "false");
-            factory = Persistence.createEntityManagerFactory(PERSISTENCE_UNIT_NAME, properties);
-        }
-		return factory.createEntityManager();
-    }
-
-    /**
-     * @param gatewayId
-     * @return
-     */
-    public static Resource createGateway(String gatewayId) throws RegistryException {
-        if (!isGatewayExist(gatewayId)) {
-            GatewayResource gatewayResource = new GatewayResource();
-            gatewayResource.setGatewayId(gatewayId);
-            return gatewayResource;
-        }else {
-            return getGateway(gatewayId);
-        }
-    }
-
-    public static UserResource createUser(String username, String password) throws RegistryException {
-        if (!isUserExist(username)) {
-            UserResource userResource = new UserResource();
-            userResource.setUserName(username);
-            userResource.setPassword(password);
-            return userResource;
-        }else {
-            return (UserResource)getUser(username);
-        }
-
-    }
-
-    public static Resource getGateway(String gatewayId) throws RegistryException{
-        EntityManager em = null;
-        try {
-            if (isGatewayExist(gatewayId)) {
-                em = getEntityManager();
-                Gateway gateway = em.find(Gateway.class, gatewayId);
-                GatewayResource gatewayResource = (GatewayResource)Utils.getResource(ResourceType.GATEWAY, gateway);
-                em.close();
-                return gatewayResource;
-            }
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return null;
-    }
-
-    public static void addUser (String userName, String password) throws RegistryException{
-        UserResource resource = new UserResource();
-        resource.setUserName(userName);
-        resource.setPassword(password);
-        resource.save();
-    }
-
-    public static boolean isUserExist (String username) throws RegistryException{
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.USERS);
-            generator.setParameter(AbstractResource.UserConstants.USERNAME, username);
-            Query q = generator.selectQuery(em);
-            int size = q.getResultList().size();
-            em.getTransaction().commit();
-            em.close();
-            return size>0;
-        } catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-
-    public static Resource getUser(String userName) throws RegistryException{
-        EntityManager em = null;
-        try {
-            if (isUserExist(userName)) {
-                em = getEntityManager();
-                Users user =  em.find(Users.class, userName);
-                UserResource userResource = (UserResource)Utils.getResource(ResourceType.USER, user);
-                em.close();
-                return userResource;
-            }
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return null;
-
-    }
-
-    public static Resource getWorker(String gatewayId, String userName) throws RegistryException{
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            Gateway_Worker gatewayWorker = em.find(Gateway_Worker.class, new Gateway_Worker_PK(gatewayId, userName));
-            WorkerResource workerResource = (WorkerResource) Utils.getResource(ResourceType.GATEWAY_WORKER, gatewayWorker);
-            em.close();
-            return workerResource;
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-
-
-    }
-
-
-    /**
-     * @param gatewayId
-     * @return
-     */
-    public static boolean isGatewayExist(String gatewayId) throws RegistryException{
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.GATEWAY);
-            generator.setParameter(AbstractResource.GatewayConstants.GATEWAY_ID, gatewayId);
-            Query q = generator.selectQuery(em);
-            int size = q.getResultList().size();
-            em.getTransaction().commit();
-            em.close();
-            return size>0;
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-
-    }
-
-    public static List<Resource> getAllGateways() throws RegistryException{
-        List<Resource> resourceList = new ArrayList<Resource>();
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.GATEWAY);
-            Query q = generator.selectQuery(em);
-            List results = q.getResultList();
-            if (results.size() != 0) {
-                for (Object result : results) {
-                    Gateway gateway = (Gateway) result;
-                    GatewayResource gatewayResource =
-                            (GatewayResource) Utils.getResource(ResourceType.GATEWAY, gateway);
-                    resourceList.add(gatewayResource);
-                }
-            }
-            em.getTransaction().commit();
-            em.close();
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return resourceList;
-    }
-
-    /**
-     * @param gatewayId
-     * @return
-     */
-    public static boolean removeGateway(String gatewayId) {
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.GATEWAY);
-            generator.setParameter(AbstractResource.GatewayConstants.GATEWAY_ID, gatewayId);
-            Query q = generator.deleteQuery(em);
-            q.executeUpdate();
-            em.getTransaction().commit();
-            em.close();
-            return true;
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return false;
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    /**
-     * @param gatewayResource
-     * @param userResource
-     */
-    public static WorkerResource addGatewayWorker(GatewayResource gatewayResource, UserResource userResource) throws RegistryException{
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            if (!isGatewayExist(gatewayResource.getGatewayName())){
-                gatewayResource.save();
-            }
-            if (!isUserExist(userResource.getUserName())){
-                userResource.save();
-            }
-            Gateway gateway = em.find(Gateway.class, gatewayResource.getGatewayId());
-            Users user = em.find(Users.class, userResource.getUserName());
-            Gateway_Worker gatewayWorker = new Gateway_Worker();
-            gatewayWorker.setGateway(gateway);
-            gatewayWorker.setUser(user);
-            em.persist(gatewayWorker);
-            em.getTransaction().commit();
-            em.close();
-            return (WorkerResource)Utils.getResource(ResourceType.GATEWAY_WORKER, gatewayWorker);
-        } catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    /**
-     * @param gatewayResource
-     * @param userResource
-     * @return
-     */
-    public static boolean removeGatewayWorker(GatewayResource gatewayResource, UserResource userResource) {
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.GATEWAY_WORKER);
-            generator.setParameter(AbstractResource.GatewayWorkerConstants.GATEWAY_ID,
-                    gatewayResource.getGatewayName());
-            generator.setParameter(AbstractResource.UserConstants.USERNAME, userResource.getUserName());
-            Query q = generator.deleteQuery(em);
-            q.executeUpdate();
-            em.getTransaction().commit();
-            em.close();
-            return true;
-        } catch (Exception e) {
-            logger.error(e.getMessage(), e);
-            return false;
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-
-    }
-
-    /**
-     * @param configKey
-     * @return
-     */
-    public static List<ConfigurationResource> getConfigurations(String configKey){
-        List<ConfigurationResource> list = new ArrayList<ConfigurationResource>();
-        EntityManager em = null;
-        try {
-            em = getEntityManager();
-            em.getTransaction().begin();
-            QueryGenerator generator = new QueryGenerator(AbstractResource.CONFIGURATION);
-            generator.setParameter(AbstractResource.ConfigurationConstants.CONFIG_KEY, configKey);
-            Query q = generator.selectQuery(em);
-            List<?> resultList = q.getResultList();
-            if (resultList.size() != 0) {
-                for (Object result : resultList) {
-                    ConfigurationResource configurationResource = createConfigurationResourceObject(result);
-                    list.add(configurationResource);
-                }
-            }
-            em.getTransaction().commit();
-            em.close();
-        }catch (Exception e) {
-            logger.error(e.getMessage(), e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-        return list;
-    }
-
-    /**
-     * @param configKey
-     * @return
-     */
-    public static ConfigurationResource getConfiguration(String configKey){
-        List<ConfigurationResource> configurations = getConfigurations(configKey);
-        return (configurations != null && configurations.size() > 0) ? configurations.get(0) : null;
-    }
-
-    /**
-     * @param configKey
-     * @return
-     */
-    public static boolean isConfigurationExist(String configKey){
-        List<ConfigurationResource> configurations = getConfigurations(configKey);
-        return (configurations != null && configurations.size() > 0);
-    }
-
-    /**
-     * @param configKey
-     * @return
-     */
-    public static ConfigurationResource createConfiguration(String configKey) {
-        ConfigurationResource config = new ConfigurationResource();
-        config.setConfigKey(configKey);
-        return config;
-    }
-
-    /**
-     * @param result
-     * @return
-     */
-    private static ConfigurationResource createConfigurationResourceObject(
-            Object result) {
-        Configuration configuration = (Configuration) result;
-        ConfigurationResource configurationResource = new ConfigurationResource(configuration.getConfig_key(), configuration.getConfig_val());
-        configurationResource.setExpireDate(configuration.getExpire_date());
-        return configurationResource;
-    }
-
-    /**
-     * @param configkey
-     * @param configValue
-     */
-    public static void removeConfiguration(String configkey, String configValue) throws RegistryException{
-        QueryGenerator queryGenerator = new QueryGenerator(AbstractResource.CONFIGURATION);
-        queryGenerator.setParameter(AbstractResource.ConfigurationConstants.CONFIG_KEY, configkey);
-        queryGenerator.setParameter(AbstractResource.ConfigurationConstants.CONFIG_VAL, configValue);
-        EntityManager em = null;
-        try {
-            if(isConfigurationExists(configkey, configValue)){
-                em = getEntityManager();
-                em.getTransaction().begin();
-                Query q = queryGenerator.deleteQuery(em);
-                q.executeUpdate();
-                em.getTransaction().commit();
-                em.close();
-            }
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    /**
-     * @param configkey
-     */
-    public static void removeConfiguration(String configkey) throws RegistryException{
-        QueryGenerator queryGenerator = new QueryGenerator(AbstractResource.CONFIGURATION);
-        queryGenerator.setParameter(AbstractResource.ConfigurationConstants.CONFIG_KEY, configkey);
-        EntityManager em = null;
-        try {
-            if(isConfigurationExist(configkey)){
-                em = getEntityManager();
-                em.getTransaction().begin();
-                Query q = queryGenerator.deleteQuery(em);
-                q.executeUpdate();
-                em.getTransaction().commit();
-                em.close();
-            }
-        }catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-
-    public static boolean isConfigurationExists(String configKey, String configVal) throws RegistryException{
-        EntityManager em = null;
-        try{
-            //Currently categoryID is hardcoded value
-            em = ResourceUtils.getEntityManager();
-            Configuration existing = em.find(Configuration.class, new Configuration_PK(configKey, configVal, AbstractResource.ConfigurationConstants.CATEGORY_ID_DEFAULT_VALUE));
-            em.close();
-            return existing!= null;
-        } catch (Exception e){
-            logger.error(e.getMessage(), e);
-            throw new RegistryException(e);
-        }finally {
-            if (em != null && em.isOpen()){
-                if (em.getTransaction().isActive()){
-                    em.getTransaction().rollback();
-                }
-                em.close();
-            }
-        }
-    }
-}


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