[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF subversion and git services (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16420595#comment-16420595
 ] 

ASF subversion and git services commented on AIRAVATA-2657:
---

Commit 11efe8a64baf365dc96f4193f57977a7a76e635d in airavata's branch 
refs/heads/group-based-auth from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=11efe8a ]

Merge pull request #167 from tilaks26/registry-refactoring

[AIRAVATA-2657] Refactoring App Catalog Implementation - ApplicationDeployment 
and ApplicationInterface Modules

> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16418194#comment-16418194
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-377055235
 
 
   @DImuthuUpe Yes, I have included tests for the new methods that I have 
included.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16418102#comment-16418102
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-377035909
 
 
   +1 @tilaks26 Code looks good to me. Did you add enough test cases to verify 
the functionality of the changes that you have done?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16418057#comment-16418057
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r177879417
 
 

 ##
 File path: 
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java
 ##
 @@ -3589,8 +3586,7 @@ public String registerApplicationDeployment(String 
gatewayId, ApplicationDeploym
 @Override
 public boolean updateApplicationModule(String appModuleId, 
ApplicationModule applicationModule) throws RegistryServiceException, 
TException {
 try {
-appCatalog = RegistryFactory.getAppCatalog();
-
appCatalog.getApplicationInterface().updateApplicationModule(appModuleId, 
applicationModule);
+new 
ApplicationInterfaceRepository().updateApplicationModule(appModuleId, 
applicationModule);
 
 Review comment:
   @sachinkariyattin yeah, I don't know. I don't see any reason why they 
couldn't be instantiated just once since they have no state.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16413184#comment-16413184
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

sachinkariyattin commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176953397
 
 

 ##
 File path: 
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java
 ##
 @@ -3589,8 +3586,7 @@ public String registerApplicationDeployment(String 
gatewayId, ApplicationDeploym
 @Override
 public boolean updateApplicationModule(String appModuleId, 
ApplicationModule applicationModule) throws RegistryServiceException, 
TException {
 try {
-appCatalog = RegistryFactory.getAppCatalog();
-
appCatalog.getApplicationInterface().updateApplicationModule(appModuleId, 
applicationModule);
+new 
ApplicationInterfaceRepository().updateApplicationModule(appModuleId, 
applicationModule);
 
 Review comment:
   @machristie @DImuthuUpe Same thing has been followed in here in the 
SharingRegistryServerHandler https://git.io/vx0vX. Wonder what the reason could 
be


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412044#comment-16412044
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-375794359
 
 
   @DImuthuUpe @machristie Thank you for the review. I've made the requested 
changes.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411995#comment-16411995
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-375786828
 
 
   @DImuthuUpe I can't find any documentation about it. The description here is 
pretty succinct: https://issues.apache.org/jira/browse/AIRAVATA-2618. Let me 
know if you have any questions.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411984#comment-16411984
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176851411
 
 

 ##
 File path: 
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java
 ##
 @@ -3589,8 +3586,7 @@ public String registerApplicationDeployment(String 
gatewayId, ApplicationDeploym
 @Override
 public boolean updateApplicationModule(String appModuleId, 
ApplicationModule applicationModule) throws RegistryServiceException, 
TException {
 try {
-appCatalog = RegistryFactory.getAppCatalog();
-
appCatalog.getApplicationInterface().updateApplicationModule(appModuleId, 
applicationModule);
+new 
ApplicationInterfaceRepository().updateApplicationModule(appModuleId, 
applicationModule);
 
 Review comment:
   My understanding is that we can reuse them since they are stateless and 
hence threadsafe. +1 for just instantiating these once in RegistryServerHandler 
and reusing them.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411786#comment-16411786
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176816330
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,159 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
 
 Review comment:
   Just print the message mentioning why that block is executing


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411722#comment-16411722
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176800876
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,159 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
 
 Review comment:
   Sure @DImuthuUpe 
   Do you want me to just add a message or include the object as well?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411632#comment-16411632
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-375716872
 
 
   @tilaks26 Code looks good. There are few areas that need improvements
   Add more debug or info level logs in the complex if conditions. This will 
benefit when we are doing debugging. 
   Improve the readability of the code. One option is to add new lines 
logically when there are too much lines together.
   Do null checks and the availability to the items in the lists before 
accessing them. Handle them properly and always try to avoid 
NullPointerExceptions.
   
   @machristie @sachinkariyattin @tilaks26 I do not have a in depth idea of 
what is going inside the registry refactoring. Do we have any resource that we 
can refer in order to have an idea of the proposed changes?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411616#comment-16411616
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176782440
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -0,0 +1,256 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
+import 
org.apache.airavata.model.appcatalog.appinterface.application_interface_modelConstants;
+import org.apache.airavata.model.application.io.InputDataObjectType;
+import org.apache.airavata.model.application.io.OutputDataObjectType;
+import org.apache.airavata.registry.core.utils.*;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationInterface;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationInterfaceRepository extends 
AppCatAbstractRepository implements ApplicationInterface {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationInterfaceRepository.class);
+
+public ApplicationInterfaceRepository () {
+super(ApplicationInterfaceDescription.class, 
ApplicationInterfaceEntity.class);
+}
+
+protected String saveApplicationInterfaceDescriptorData(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationInterfaceEntity applicationInterfaceEntity = 
saveApplicationInterface(applicationInterfaceDescription, gatewayId);
+return applicationInterfaceEntity.getApplicationInterfaceId();
+}
+
+protected ApplicationInterfaceEntity saveApplicationInterface(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+String applicationInterfaceId = 
applicationInterfaceDescription.getApplicationInterfaceId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationInterfaceEntity applicationInterfaceEntity = 
mapper.map(applicationInterfaceDescription, ApplicationInterfaceEntity.class);
+if (gatewayId != null)
+applicationInterfaceEntity.setGatewayId(gatewayId);
+if (applicationInterfaceEntity.getApplicationInputs() != null) {
+
applicationInterfaceEntity.getApplicationInputs().forEach(applicationInputEntity
 -> applicationInputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (applicationInterfaceEntity.getApplicationOutputs() != null) {
+
applicationInterfaceEntity.getApplicationOutputs().forEach(applicationOutputEntity
 -> applicationOutputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (!isApplicationInterfaceExists(applicationInterfaceId))
+applicationInterfaceEntity.setCreationTime(new 
Timestamp(System.currentTimeMillis()));
+applicationInterfaceEntity.setUpdateTime(new 
Timestamp(System.currentTimeMillis()));
+return execute(entityManager -> 
entityManager.merge(applicationInterfaceEntity));
+}
+
+protected String saveApplicationModuleData(
+ApplicationModule applicationModule, String gatewayId) throws 
AppCatalogException {
+ApplicationModuleEntity applicationModuleEntity = 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411612#comment-16411612
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176781978
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -0,0 +1,256 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
+import 
org.apache.airavata.model.appcatalog.appinterface.application_interface_modelConstants;
+import org.apache.airavata.model.application.io.InputDataObjectType;
+import org.apache.airavata.model.application.io.OutputDataObjectType;
+import org.apache.airavata.registry.core.utils.*;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationInterface;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationInterfaceRepository extends 
AppCatAbstractRepository implements ApplicationInterface {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationInterfaceRepository.class);
+
+public ApplicationInterfaceRepository () {
+super(ApplicationInterfaceDescription.class, 
ApplicationInterfaceEntity.class);
+}
+
+protected String saveApplicationInterfaceDescriptorData(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationInterfaceEntity applicationInterfaceEntity = 
saveApplicationInterface(applicationInterfaceDescription, gatewayId);
+return applicationInterfaceEntity.getApplicationInterfaceId();
+}
+
+protected ApplicationInterfaceEntity saveApplicationInterface(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+String applicationInterfaceId = 
applicationInterfaceDescription.getApplicationInterfaceId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationInterfaceEntity applicationInterfaceEntity = 
mapper.map(applicationInterfaceDescription, ApplicationInterfaceEntity.class);
+if (gatewayId != null)
+applicationInterfaceEntity.setGatewayId(gatewayId);
+if (applicationInterfaceEntity.getApplicationInputs() != null) {
+
applicationInterfaceEntity.getApplicationInputs().forEach(applicationInputEntity
 -> applicationInputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (applicationInterfaceEntity.getApplicationOutputs() != null) {
+
applicationInterfaceEntity.getApplicationOutputs().forEach(applicationOutputEntity
 -> applicationOutputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (!isApplicationInterfaceExists(applicationInterfaceId))
+applicationInterfaceEntity.setCreationTime(new 
Timestamp(System.currentTimeMillis()));
+applicationInterfaceEntity.setUpdateTime(new 
Timestamp(System.currentTimeMillis()));
+return execute(entityManager -> 
entityManager.merge(applicationInterfaceEntity));
+}
+
+protected String saveApplicationModuleData(
+ApplicationModule applicationModule, String gatewayId) throws 
AppCatalogException {
+ApplicationModuleEntity applicationModuleEntity = 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411610#comment-16411610
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176781653
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -0,0 +1,256 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
+import 
org.apache.airavata.model.appcatalog.appinterface.application_interface_modelConstants;
+import org.apache.airavata.model.application.io.InputDataObjectType;
+import org.apache.airavata.model.application.io.OutputDataObjectType;
+import org.apache.airavata.registry.core.utils.*;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationInterface;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationInterfaceRepository extends 
AppCatAbstractRepository implements ApplicationInterface {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationInterfaceRepository.class);
+
+public ApplicationInterfaceRepository () {
+super(ApplicationInterfaceDescription.class, 
ApplicationInterfaceEntity.class);
+}
+
+protected String saveApplicationInterfaceDescriptorData(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationInterfaceEntity applicationInterfaceEntity = 
saveApplicationInterface(applicationInterfaceDescription, gatewayId);
+return applicationInterfaceEntity.getApplicationInterfaceId();
+}
+
+protected ApplicationInterfaceEntity saveApplicationInterface(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+String applicationInterfaceId = 
applicationInterfaceDescription.getApplicationInterfaceId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationInterfaceEntity applicationInterfaceEntity = 
mapper.map(applicationInterfaceDescription, ApplicationInterfaceEntity.class);
+if (gatewayId != null)
 
 Review comment:
   Debug logs


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411504#comment-16411504
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176758465
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,159 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
+applicationDeploymentEntity.setGatewayId(gatewayId);
+if (applicationDeploymentEntity.getModuleLoadCmds() != null) {
+
applicationDeploymentEntity.getModuleLoadCmds().forEach(moduleLoadCmdEntity -> 
moduleLoadCmdEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPreJobCommands() != null) {
+
applicationDeploymentEntity.getPreJobCommands().forEach(prejobCommandEntity -> 
prejobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPostJobCommands() != null) {
+
applicationDeploymentEntity.getPostJobCommands().forEach(postjobCommandEntity 
-> postjobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibPrependPaths() != null) {
+
applicationDeploymentEntity.getLibPrependPaths().forEach(libraryPrependPathEntity
 -> libraryPrependPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibAppendPaths() != null) {
+
applicationDeploymentEntity.getLibAppendPaths().forEach(libraryApendPathEntity 
-> libraryApendPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411500#comment-16411500
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176758088
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,159 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
+applicationDeploymentEntity.setGatewayId(gatewayId);
+if (applicationDeploymentEntity.getModuleLoadCmds() != null) {
+
applicationDeploymentEntity.getModuleLoadCmds().forEach(moduleLoadCmdEntity -> 
moduleLoadCmdEntity.setAppdeploymentId(applicationDeploymentId));
+}
 
 Review comment:
   Add a new line after each if block. It will improve the readability 


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411496#comment-16411496
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176757385
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,159 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
 
 Review comment:
   Add debug logs in each if block. Then we can easily track issues without 
remote debugging


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411489#comment-16411489
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176755943
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -122,15 +130,15 @@ public ApplicationModule getApplicationModule(String 
moduleId) throws AppCatalog
 ApplicationModuleRepository applicationModuleRepository = new 
ApplicationModuleRepository();
 Map queryParameters = new HashMap<>();
 
queryParameters.put(DBConstants.ApplicationModule.APPLICATION_MODULE_ID, 
moduleId);
-ApplicationModule applicationModule = (ApplicationModule) 
applicationModuleRepository.select(QueryConstants.FIND_APPLICATION_MODULE, -1, 
0, queryParameters);
+ApplicationModule applicationModule = 
applicationModuleRepository.select(QueryConstants.FIND_APPLICATION_MODULE, -1, 
0, queryParameters).get(0);
 return applicationModule;
 }
 
 @Override
 public ApplicationInterfaceDescription getApplicationInterface(String 
interfaceId) throws AppCatalogException {
 Map queryParameters = new HashMap<>();
 
queryParameters.put(DBConstants.ApplicationInterface.APPLICATION_INTERFACE_ID, 
interfaceId);
-ApplicationInterfaceDescription applicationInterfaceDescription = 
(ApplicationInterfaceDescription) 
select(QueryConstants.FIND_APPLICATION_INTERFACE, -1, 0, queryParameters);
+ApplicationInterfaceDescription applicationInterfaceDescription = 
select(QueryConstants.FIND_APPLICATION_INTERFACE, -1, 0, 
queryParameters).get(0);
 
 Review comment:
   Same here get(0)


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411488#comment-16411488
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176755873
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -122,15 +130,15 @@ public ApplicationModule getApplicationModule(String 
moduleId) throws AppCatalog
 ApplicationModuleRepository applicationModuleRepository = new 
ApplicationModuleRepository();
 Map queryParameters = new HashMap<>();
 
queryParameters.put(DBConstants.ApplicationModule.APPLICATION_MODULE_ID, 
moduleId);
-ApplicationModule applicationModule = (ApplicationModule) 
applicationModuleRepository.select(QueryConstants.FIND_APPLICATION_MODULE, -1, 
0, queryParameters);
+ApplicationModule applicationModule = 
applicationModuleRepository.select(QueryConstants.FIND_APPLICATION_MODULE, -1, 
0, queryParameters).get(0);
 
 Review comment:
   Is it guaranteed this to return at least one value? Otherwise it is risky to 
directly call get(0) 


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411480#comment-16411480
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176755232
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -67,17 +71,21 @@ protected ApplicationInterfaceEntity 
saveApplicationInterface(
 protected String saveApplicationModuleData(
 ApplicationModule applicationModule) throws AppCatalogException {
 ApplicationModuleEntity applicationModuleEntity = 
saveApplicationModule(applicationModule);
-return applicationModuleEntity.getModuleId();
+return applicationModuleEntity.getAppModuleId();
 }
 
 protected ApplicationModuleEntity saveApplicationModule(
 ApplicationModule applicationModule) throws AppCatalogException {
+String applicationModuleId = applicationModule.getAppModuleId();
 Mapper mapper = ObjectMapperSingleton.getInstance();
 ApplicationModuleEntity applicationModuleEntity = 
mapper.map(applicationModule, ApplicationModuleEntity.class);
-if (!applicationModuleEntity.getModuleId().equals("") && 
!applicationModule.getAppModuleId().equals(application_interface_modelConstants.DEFAULT_ID))
 {
-
applicationModuleEntity.setModuleId(applicationModule.getAppModuleId());
+if (!isApplicationModuleExists(applicationModuleId))
 
 Review comment:
   Same here {}


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411483#comment-16411483
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176755369
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -67,17 +71,21 @@ protected ApplicationInterfaceEntity 
saveApplicationInterface(
 protected String saveApplicationModuleData(
 ApplicationModule applicationModule) throws AppCatalogException {
 ApplicationModuleEntity applicationModuleEntity = 
saveApplicationModule(applicationModule);
-return applicationModuleEntity.getModuleId();
+return applicationModuleEntity.getAppModuleId();
 }
 
 protected ApplicationModuleEntity saveApplicationModule(
 ApplicationModule applicationModule) throws AppCatalogException {
+String applicationModuleId = applicationModule.getAppModuleId();
 Mapper mapper = ObjectMapperSingleton.getInstance();
 ApplicationModuleEntity applicationModuleEntity = 
mapper.map(applicationModule, ApplicationModuleEntity.class);
-if (!applicationModuleEntity.getModuleId().equals("") && 
!applicationModule.getAppModuleId().equals(application_interface_modelConstants.DEFAULT_ID))
 {
-
applicationModuleEntity.setModuleId(applicationModule.getAppModuleId());
+if (!isApplicationModuleExists(applicationModuleId))
+applicationModuleEntity.setCreationTime(new 
Timestamp(System.currentTimeMillis()));
+applicationModuleEntity.setUpdateTime(new 
Timestamp(System.currentTimeMillis()));
+if (!applicationModuleEntity.getAppModuleId().equals("") && 
!applicationModule.getAppModuleId().equals(application_interface_modelConstants.DEFAULT_ID))
 {
 
 Review comment:
   Add debug logs in if else block


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411479#comment-16411479
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176755093
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -55,6 +56,9 @@ protected ApplicationInterfaceEntity 
saveApplicationInterface(
 String applicationInterfaceId = 
applicationInterfaceDescription.getApplicationInterfaceId();
 Mapper mapper = ObjectMapperSingleton.getInstance();
 ApplicationInterfaceEntity applicationInterfaceEntity = 
mapper.map(applicationInterfaceDescription, ApplicationInterfaceEntity.class);
+if (!isApplicationInterfaceExists(applicationInterfaceId))
 
 Review comment:
   It is good to have curly braces {} even though you have one line if 
statement. That improves the readability of the code


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411477#comment-16411477
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176754498
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -43,16 +44,24 @@ public ApplicationDeploymentRepository() {
 }
 
 protected String saveApplicationDeploymentDescriptorData(
-ApplicationDeploymentDescription applicationDeploymentDescription) 
throws AppCatalogException {
-ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription);
-return applicationDeploymentEntity.getDeploymentId();
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
 }
 
 protected ApplicationDeploymentEntity saveApplicationDeployment(
-ApplicationDeploymentDescription applicationDeploymentDescription) 
throws AppCatalogException {
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
 String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
 Mapper mapper = ObjectMapperSingleton.getInstance();
 ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
 
 Review comment:
   This logic is bit complex. Better if you can add debug logs in each if 
block. 


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411474#comment-16411474
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176753900
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,160 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
+applicationDeploymentEntity.setGatewayId(gatewayId);
+if (applicationDeploymentEntity.getModuleLoadCmds() != null) {
+
applicationDeploymentEntity.getModuleLoadCmds().forEach(moduleLoadCmdEntity -> 
moduleLoadCmdEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPreJobCommands() != null) {
+
applicationDeploymentEntity.getPreJobCommands().forEach(prejobCommandEntity -> 
prejobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPostJobCommands() != null) {
+
applicationDeploymentEntity.getPostJobCommands().forEach(postjobCommandEntity 
-> postjobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibPrependPaths() != null) {
+
applicationDeploymentEntity.getLibPrependPaths().forEach(libraryPrependPathEntity
 -> libraryPrependPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibAppendPaths() != null) {
+
applicationDeploymentEntity.getLibAppendPaths().forEach(libraryApendPathEntity 
-> libraryApendPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411462#comment-16411462
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176752715
 
 

 ##
 File path: 
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java
 ##
 @@ -3589,8 +3586,7 @@ public String registerApplicationDeployment(String 
gatewayId, ApplicationDeploym
 @Override
 public boolean updateApplicationModule(String appModuleId, 
ApplicationModule applicationModule) throws RegistryServiceException, 
TException {
 try {
-appCatalog = RegistryFactory.getAppCatalog();
-
appCatalog.getApplicationInterface().updateApplicationModule(appModuleId, 
applicationModule);
+new 
ApplicationInterfaceRepository().updateApplicationModule(appModuleId, 
applicationModule);
 
 Review comment:
   @machristie @tilaks26, Just for my knowledge, is this the new way to do 
database operations? Is it required to create a new object of 
ApplicationInterfaceRepository for each call? Can't we re use them?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411451#comment-16411451
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176748684
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepositoryTest.java
 ##
 @@ -161,23 +161,29 @@ public void ApplicationDeploymentRepositoryTest() throws 
AppCatalogException {
 
applicationDeploymentRepository.updateApplicationDeployment(appDeploymentId , 
applicationDeploymentDescription);
 
assertTrue(applicationDeploymentRepository.getApplicationDeployement(appDeploymentId).getDefaultQueueName().equals("queue3"));
 
-
applicationDeploymentRepository.addApplicationDeployment(applicationDeploymentDescription1,
 gatewayId);
+String deploymentId1 = 
applicationDeploymentRepository.addApplicationDeployment(applicationDeploymentDescription1,
 gatewayId);
 List appDeploymentList = 
applicationDeploymentRepository.getAllApplicationDeployements(gatewayId);
 List appDeploymentIds = 
applicationDeploymentRepository.getAllApplicationDeployementIds();
 assertTrue(appDeploymentList.size() == 2);
 assertTrue(appDeploymentIds.size() == 2);
 
-
applicationDeploymentRepository.removeAppDeployment(applicationDeploymentDescription1.getAppDeploymentId());
-
assertFalse(applicationDeploymentRepository.isExists(applicationDeploymentDescription1.getAppDeploymentId()));
-
 Map filters = new HashMap<>();
 filters.put(DBConstants.ApplicationDeployment.APPLICATION_MODULE_ID, 
applicationModule.getAppModuleId());
 filters.put(DBConstants.ApplicationDeployment.COMPUTE_HOST_ID, 
computeResourceDescription.getComputeResourceId());
 appDeploymentList = 
applicationDeploymentRepository.getApplicationDeployements(filters);
 assertEquals(computeResourceDescription.getComputeResourceId(), 
appDeploymentList.get(0).getComputeHostId());
 
 Review comment:
   Is it safe to call appDeploymentList.get(0) ? You might have to check the 
size of the appDeploymentList first and a potential null check of 
appDeploymentList


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411450#comment-16411450
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r176747997
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepositoryTest.java
 ##
 @@ -161,23 +161,29 @@ public void ApplicationDeploymentRepositoryTest() throws 
AppCatalogException {
 
applicationDeploymentRepository.updateApplicationDeployment(appDeploymentId , 
applicationDeploymentDescription);
 
assertTrue(applicationDeploymentRepository.getApplicationDeployement(appDeploymentId).getDefaultQueueName().equals("queue3"));
 
-
applicationDeploymentRepository.addApplicationDeployment(applicationDeploymentDescription1,
 gatewayId);
+String deploymentId1 = 
applicationDeploymentRepository.addApplicationDeployment(applicationDeploymentDescription1,
 gatewayId);
 
 Review comment:
   Shall we rename deploymentId1 into a more user friendly one?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16406516#comment-16406516
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-374643372
 
 
   @DImuthuUpe can you review the Sneha's more recent changes?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16393544#comment-16393544
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173566445
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java
 ##
 @@ -60,6 +60,10 @@
@Column(name="HAS_OPTIONAL_FILE_INPUTS")
private boolean hasOptionalFileInputs;
 
+   @ElementCollection
+   @CollectionTable(name="APPLICATION_MODULE", joinColumns = 
@JoinColumn(name="MODULE_ID"))
+   private List applicationModules;
 
 Review comment:
   This way was just a suggestion by Sachin. 


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16393543#comment-16393543
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173566354
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java
 ##
 @@ -60,6 +60,10 @@
@Column(name="HAS_OPTIONAL_FILE_INPUTS")
private boolean hasOptionalFileInputs;
 
+   @ElementCollection
+   @CollectionTable(name="APPLICATION_MODULE", joinColumns = 
@JoinColumn(name="MODULE_ID"))
+   private List applicationModules;
 
 Review comment:
   applicationModules is in the Thrift module but not in the 
APPLICATION_INTERFACE table. So when we update the ApplicationInterfaceEntity, 
this field won't get persisted in the database.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16393509#comment-16393509
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173561249
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java
 ##
 @@ -60,6 +60,10 @@
@Column(name="HAS_OPTIONAL_FILE_INPUTS")
private boolean hasOptionalFileInputs;
 
+   @ElementCollection
+   @CollectionTable(name="APPLICATION_MODULE", joinColumns = 
@JoinColumn(name="MODULE_ID"))
+   private List applicationModules;
 
 Review comment:
   I'm not sure, where did this even come from?  You could do something like 
this but you would need to use the APP_MODULE_MAPPING table.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390771#comment-16390771
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173065990
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java
 ##
 @@ -60,6 +60,10 @@
@Column(name="HAS_OPTIONAL_FILE_INPUTS")
private boolean hasOptionalFileInputs;
 
+   @ElementCollection
+   @CollectionTable(name="APPLICATION_MODULE", joinColumns = 
@JoinColumn(name="MODULE_ID"))
+   private List applicationModules;
 
 Review comment:
   @machristie There is no corresponding column for this attribute in the 
APPLICATION_INTERFACE table. Also, it is of `List` type. Can you please 
verify if the `@ElementCollection` annotation required here?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390770#comment-16390770
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173065990
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java
 ##
 @@ -60,6 +60,10 @@
@Column(name="HAS_OPTIONAL_FILE_INPUTS")
private boolean hasOptionalFileInputs;
 
+   @ElementCollection
+   @CollectionTable(name="APPLICATION_MODULE", joinColumns = 
@JoinColumn(name="MODULE_ID"))
+   private List applicationModules;
 
 Review comment:
   @machristie There is no corresponding column for this attribute in the 
APPLICATION_INTERFACE table. Also, it is of List type. Can you please 
verify if the `@ElementCollection` annotation required here?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390755#comment-16390755
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on issue #167: [AIRAVATA-2657] Refactoring App Catalog 
Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#issuecomment-371378771
 
 
   @machristie Thank you for the review. I have modified the getAccessible 
methods as requested and updated the PR.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390749#comment-16390749
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173063477
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepositoryTest.java
 ##
 @@ -0,0 +1,168 @@
+package org.apache.airavata.registry.core.repositories.appcatalog;
 
 Review comment:
   @DImuthuUpe thank you for the review. I have added the license header for 
all the files.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390750#comment-16390750
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173063493
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepositoryTest.java
 ##
 @@ -0,0 +1,107 @@
+package org.apache.airavata.registry.core.repositories.appcatalog;
 
 Review comment:
   @DImuthuUpe thank you for the review. I have added the license header.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390701#comment-16390701
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173058307
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepositoryTest.java
 ##
 @@ -0,0 +1,107 @@
+package org.apache.airavata.registry.core.repositories.appcatalog;
 
 Review comment:
   License header


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390700#comment-16390700
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

DImuthuUpe commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173058250
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepositoryTest.java
 ##
 @@ -0,0 +1,168 @@
+package org.apache.airavata.registry.core.repositories.appcatalog;
 
 Review comment:
   License header


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390693#comment-16390693
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173057150
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputEntity.java
 ##
 @@ -20,123 +20,140 @@
 */
 package org.apache.airavata.registry.core.entities.appcatalog;
 
-import javax.persistence.Column;
-import javax.persistence.EmbeddedId;
-import javax.persistence.Entity;
-import javax.persistence.Table;
+import javax.persistence.*;
 import java.io.Serializable;
 
 /**
  * The persistent class for the application_output database table.
  */
 @Entity
-@Table(name = "application_output")
+@Table(name = "APPLICATION_OUTPUT")
+@IdClass(ApplicationOutputPK.class)
 public class ApplicationOutputEntity implements Serializable {
 private static final long serialVersionUID = 1L;
 
-@EmbeddedId
-private ApplicationOutputPK id;
+@Id
+@Column(name="INTERFACE_ID")
+private String interfaceId;
+
+@Id
+@Column(name="OUTPUT_KEY")
+private String name;
 
 @Column(name = "APP_ARGUMENT")
-private String appArgument;
+private String applicationArgument;
 
 @Column(name = "DATA_MOVEMENT")
-private short dataMovement;
+private boolean dataMovement;
 
 @Column(name = "DATA_NAME_LOCATION")
-private String dataNameLocation;
+private String location;
 
 @Column(name = "DATA_TYPE")
-private String dataType;
+private String type;
 
 @Column(name = "IS_REQUIRED")
-private short isRequired;
+private boolean isRequired;
 
 @Column(name = "OUTPUT_STREAMING")
-private short outputStreaming;
+private boolean outputStreaming;
 
 @Column(name = "OUTPUT_VALUE")
-private String outputValue;
+private String value;
 
 @Column(name = "REQUIRED_TO_COMMANDLINE")
-private short requiredToCommandline;
+private boolean requiredToAddedToCommandLine;
 
 @Column(name = "SEARCH_QUERY")
 private String searchQuery;
 
+private String storageResourceId;
 
 Review comment:
   I didn't include a @Column annotation for this because there is no 
corresponding column in the APPLICATION_OUTPUT table for this attribute.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390696#comment-16390696
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173057150
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputEntity.java
 ##
 @@ -20,123 +20,140 @@
 */
 package org.apache.airavata.registry.core.entities.appcatalog;
 
-import javax.persistence.Column;
-import javax.persistence.EmbeddedId;
-import javax.persistence.Entity;
-import javax.persistence.Table;
+import javax.persistence.*;
 import java.io.Serializable;
 
 /**
  * The persistent class for the application_output database table.
  */
 @Entity
-@Table(name = "application_output")
+@Table(name = "APPLICATION_OUTPUT")
+@IdClass(ApplicationOutputPK.class)
 public class ApplicationOutputEntity implements Serializable {
 private static final long serialVersionUID = 1L;
 
-@EmbeddedId
-private ApplicationOutputPK id;
+@Id
+@Column(name="INTERFACE_ID")
+private String interfaceId;
+
+@Id
+@Column(name="OUTPUT_KEY")
+private String name;
 
 @Column(name = "APP_ARGUMENT")
-private String appArgument;
+private String applicationArgument;
 
 @Column(name = "DATA_MOVEMENT")
-private short dataMovement;
+private boolean dataMovement;
 
 @Column(name = "DATA_NAME_LOCATION")
-private String dataNameLocation;
+private String location;
 
 @Column(name = "DATA_TYPE")
-private String dataType;
+private String type;
 
 @Column(name = "IS_REQUIRED")
-private short isRequired;
+private boolean isRequired;
 
 @Column(name = "OUTPUT_STREAMING")
-private short outputStreaming;
+private boolean outputStreaming;
 
 @Column(name = "OUTPUT_VALUE")
-private String outputValue;
+private String value;
 
 @Column(name = "REQUIRED_TO_COMMANDLINE")
-private short requiredToCommandline;
+private boolean requiredToAddedToCommandLine;
 
 @Column(name = "SEARCH_QUERY")
 private String searchQuery;
 
+private String storageResourceId;
 
 Review comment:
   I didn't include a `@Column` annotation for this because there is no 
corresponding column in the APPLICATION_OUTPUT table for this attribute.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390692#comment-16390692
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173056737
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/ReplicaCatalogRepositoryTest.java
 ##
 @@ -61,70 +61,70 @@ public void setupRepository()   {
 @Test
 public void dataProductRepositoryTest() {
 
-DataProductRepository dataProductRepository = new 
DataProductRepository(DataProductModel.class, DataProductEntity.class);
+//DataProductRepository dataProductRepository = new 
DataProductRepository(DataProductModel.class, DataProductEntity.class);
 
 /*
  * Creating Gateway required for UserProfile & Project creation
 */
-Gateway gateway = new Gateway();
-gateway.setGatewayApprovalStatus(GatewayApprovalStatus.ACTIVE);
-gateway.setGatewayId(gatewayId);
-gateway.setDomain(GATEWAY_DOMAIN);
-gateway = gatewayRepository.create(gateway);
-Assert.assertTrue(!gateway.getGatewayId().isEmpty());
+//Gateway gateway = new Gateway();
 
 Review comment:
   Right now, we've only been working on the application catalog. We haven't 
verified or modified the experiment catalog entities and repositories. So, the 
test cases were failing.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390691#comment-16390691
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173056716
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/ExperimentRepositoryTest.java
 ##
 @@ -76,80 +76,80 @@ public void experimentRepositoryTest() {
/*
  * Creating Gateway required for UserProfile & Project creation
 */
-Gateway gateway = new Gateway();
-gateway.setGatewayApprovalStatus(GatewayApprovalStatus.ACTIVE);
-gateway.setGatewayId(gatewayId);
-gateway.setDomain(GATEWAY_DOMAIN);
-gateway = gatewayRepository.create(gateway);
-Assert.assertTrue(!gateway.getGatewayId().isEmpty());
+//Gateway gateway = new Gateway();
 
 Review comment:
   Right now, we've only been working on the application catalog. We haven't 
verified or modified the experiment catalog entities and repositories. So, the 
test cases were failing.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390638#comment-16390638
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173050021
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
 ##
 @@ -0,0 +1,256 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
+import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
+import 
org.apache.airavata.model.appcatalog.appinterface.application_interface_modelConstants;
+import org.apache.airavata.model.application.io.InputDataObjectType;
+import org.apache.airavata.model.application.io.OutputDataObjectType;
+import org.apache.airavata.registry.core.utils.*;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationInterface;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationInterfaceRepository extends 
AppCatAbstractRepository implements ApplicationInterface {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationInterfaceRepository.class);
+
+public ApplicationInterfaceRepository () {
+super(ApplicationInterfaceDescription.class, 
ApplicationInterfaceEntity.class);
+}
+
+protected String saveApplicationInterfaceDescriptorData(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationInterfaceEntity applicationInterfaceEntity = 
saveApplicationInterface(applicationInterfaceDescription, gatewayId);
+return applicationInterfaceEntity.getApplicationInterfaceId();
+}
+
+protected ApplicationInterfaceEntity saveApplicationInterface(
+ApplicationInterfaceDescription applicationInterfaceDescription, 
String gatewayId) throws AppCatalogException {
+String applicationInterfaceId = 
applicationInterfaceDescription.getApplicationInterfaceId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationInterfaceEntity applicationInterfaceEntity = 
mapper.map(applicationInterfaceDescription, ApplicationInterfaceEntity.class);
+if (gatewayId != null)
+applicationInterfaceEntity.setGatewayId(gatewayId);
+if (applicationInterfaceEntity.getApplicationInputs() != null) {
+
applicationInterfaceEntity.getApplicationInputs().forEach(applicationInputEntity
 -> applicationInputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (applicationInterfaceEntity.getApplicationOutputs() != null) {
+
applicationInterfaceEntity.getApplicationOutputs().forEach(applicationOutputEntity
 -> applicationOutputEntity.setInterfaceId(applicationInterfaceId));
+}
+if (!isApplicationInterfaceExists(applicationInterfaceId))
+applicationInterfaceEntity.setCreationTime(new 
Timestamp(System.currentTimeMillis()));
+applicationInterfaceEntity.setUpdateTime(new 
Timestamp(System.currentTimeMillis()));
+return execute(entityManager -> 
entityManager.merge(applicationInterfaceEntity));
+}
+
+protected String saveApplicationModuleData(
+ApplicationModule applicationModule, String gatewayId) throws 
AppCatalogException {
+ApplicationModuleEntity applicationModuleEntity = 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390635#comment-16390635
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173050297
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/ReplicaCatalogRepositoryTest.java
 ##
 @@ -61,70 +61,70 @@ public void setupRepository()   {
 @Test
 public void dataProductRepositoryTest() {
 
-DataProductRepository dataProductRepository = new 
DataProductRepository(DataProductModel.class, DataProductEntity.class);
+//DataProductRepository dataProductRepository = new 
DataProductRepository(DataProductModel.class, DataProductEntity.class);
 
 /*
  * Creating Gateway required for UserProfile & Project creation
 */
-Gateway gateway = new Gateway();
-gateway.setGatewayApprovalStatus(GatewayApprovalStatus.ACTIVE);
-gateway.setGatewayId(gatewayId);
-gateway.setDomain(GATEWAY_DOMAIN);
-gateway = gatewayRepository.create(gateway);
-Assert.assertTrue(!gateway.getGatewayId().isEmpty());
+//Gateway gateway = new Gateway();
 
 Review comment:
   Why are these all commented out?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390639#comment-16390639
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173049764
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
 ##
 @@ -0,0 +1,160 @@
+/**
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.airavata.registry.core.repositories.appcatalog;
+
+import org.apache.airavata.model.appcatalog.appdeployment.*;
+import org.apache.airavata.registry.core.entities.appcatalog.*;
+import org.apache.airavata.registry.core.utils.DBConstants;
+import org.apache.airavata.registry.core.utils.ObjectMapperSingleton;
+import org.apache.airavata.registry.core.utils.QueryConstants;
+import org.apache.airavata.registry.cpi.AppCatalogException;
+import org.apache.airavata.registry.cpi.ApplicationDeployment;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ApplicationDeploymentRepository extends 
AppCatAbstractRepository implements ApplicationDeployment {
+private final static Logger logger = 
LoggerFactory.getLogger(ApplicationDeploymentRepository.class);
+
+public ApplicationDeploymentRepository() {
+super(ApplicationDeploymentDescription.class, 
ApplicationDeploymentEntity.class);
+}
+
+protected String saveApplicationDeploymentDescriptorData(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+ApplicationDeploymentEntity applicationDeploymentEntity = 
saveApplicationDeployment(applicationDeploymentDescription, gatewayId);
+return applicationDeploymentEntity.getAppDeploymentId();
+}
+
+protected ApplicationDeploymentEntity saveApplicationDeployment(
+ApplicationDeploymentDescription applicationDeploymentDescription, 
String gatewayId) throws AppCatalogException {
+String applicationDeploymentId = 
applicationDeploymentDescription.getAppDeploymentId();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+ApplicationDeploymentEntity applicationDeploymentEntity = 
mapper.map(applicationDeploymentDescription, ApplicationDeploymentEntity.class);
+if (gatewayId != null)
+applicationDeploymentEntity.setGatewayId(gatewayId);
+if (applicationDeploymentEntity.getModuleLoadCmds() != null) {
+
applicationDeploymentEntity.getModuleLoadCmds().forEach(moduleLoadCmdEntity -> 
moduleLoadCmdEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPreJobCommands() != null) {
+
applicationDeploymentEntity.getPreJobCommands().forEach(prejobCommandEntity -> 
prejobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getPostJobCommands() != null) {
+
applicationDeploymentEntity.getPostJobCommands().forEach(postjobCommandEntity 
-> postjobCommandEntity.setAppdeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibPrependPaths() != null) {
+
applicationDeploymentEntity.getLibPrependPaths().forEach(libraryPrependPathEntity
 -> libraryPrependPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if (applicationDeploymentEntity.getLibAppendPaths() != null) {
+
applicationDeploymentEntity.getLibAppendPaths().forEach(libraryApendPathEntity 
-> libraryApendPathEntity.setDeploymentId(applicationDeploymentId));
+}
+if 

[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390637#comment-16390637
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173048843
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputEntity.java
 ##
 @@ -20,123 +20,140 @@
 */
 package org.apache.airavata.registry.core.entities.appcatalog;
 
-import javax.persistence.Column;
-import javax.persistence.EmbeddedId;
-import javax.persistence.Entity;
-import javax.persistence.Table;
+import javax.persistence.*;
 import java.io.Serializable;
 
 /**
  * The persistent class for the application_output database table.
  */
 @Entity
-@Table(name = "application_output")
+@Table(name = "APPLICATION_OUTPUT")
+@IdClass(ApplicationOutputPK.class)
 public class ApplicationOutputEntity implements Serializable {
 private static final long serialVersionUID = 1L;
 
-@EmbeddedId
-private ApplicationOutputPK id;
+@Id
+@Column(name="INTERFACE_ID")
+private String interfaceId;
+
+@Id
+@Column(name="OUTPUT_KEY")
+private String name;
 
 @Column(name = "APP_ARGUMENT")
-private String appArgument;
+private String applicationArgument;
 
 @Column(name = "DATA_MOVEMENT")
-private short dataMovement;
+private boolean dataMovement;
 
 @Column(name = "DATA_NAME_LOCATION")
-private String dataNameLocation;
+private String location;
 
 @Column(name = "DATA_TYPE")
-private String dataType;
+private String type;
 
 @Column(name = "IS_REQUIRED")
-private short isRequired;
+private boolean isRequired;
 
 @Column(name = "OUTPUT_STREAMING")
-private short outputStreaming;
+private boolean outputStreaming;
 
 @Column(name = "OUTPUT_VALUE")
-private String outputValue;
+private String value;
 
 @Column(name = "REQUIRED_TO_COMMANDLINE")
-private short requiredToCommandline;
+private boolean requiredToAddedToCommandLine;
 
 @Column(name = "SEARCH_QUERY")
 private String searchQuery;
 
+private String storageResourceId;
 
 Review comment:
   Is there a reason this field doesn't have a `@Column` annotation?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16390636#comment-16390636
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

machristie commented on a change in pull request #167: [AIRAVATA-2657] 
Refactoring App Catalog Implementation - ApplicationDeployment and 
ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167#discussion_r173050259
 
 

 ##
 File path: 
modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/ExperimentRepositoryTest.java
 ##
 @@ -76,80 +76,80 @@ public void experimentRepositoryTest() {
/*
  * Creating Gateway required for UserProfile & Project creation
 */
-Gateway gateway = new Gateway();
-gateway.setGatewayApprovalStatus(GatewayApprovalStatus.ACTIVE);
-gateway.setGatewayId(gatewayId);
-gateway.setDomain(GATEWAY_DOMAIN);
-gateway = gatewayRepository.create(gateway);
-Assert.assertTrue(!gateway.getGatewayId().isEmpty());
+//Gateway gateway = new Gateway();
 
 Review comment:
   Why are these commented out?


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface

[ASF GitHub Bot (JIRA)]

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2657?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16345565#comment-16345565
 ] 

ASF GitHub Bot commented on AIRAVATA-2657:
--

tilaks26 opened a new pull request #167: [AIRAVATA-2657] Refactoring App 
Catalog Implementation - ApplicationDeployment and ApplicationInterface Modules
URL: https://github.com/apache/airavata/pull/167
 
 
   Implementation of ApplicationDeploymentRepository.java and 
ApplicationInterfaceRepository.java instead of the existing Implementation 
class dependency.
   
   Changes made - 
   - Modification of the necessary entity classes.
   
   TODO - 
   - Override all the methods for the 2 repository classes.
   - Write tests.
   - Make necessary changes to the RegistryServerHandler.java class.


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> Refactoring App Catalog implementation - ApplicationDeployment and 
> ApplicationInterface
> ---
>
> Key: AIRAVATA-2657
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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