date:20180323

[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412206#comment-16412206
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

tilaks26 commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176881067
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/resources/META-INF/persistence.xml
 ##
 @@ -122,6 +122,9 @@
 
org.apache.airavata.registry.core.entities.appcatalog.StorageInterfacePK
 
 Review comment:
   I've removed it. It's a part of the 
[https://github.com/apache/airavata/pull/167] PR.


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412204#comment-16412204
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

tilaks26 commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176880712
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
 ##
 @@ -0,0 +1,227 @@
+/**
+ *
+ * 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.userresourceprofile.UserComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserStoragePreference;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserComputeResourcePreferencePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfileEntity;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfilePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserStoragePreferencePK;
+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.CompositeIdentifier;
+import org.apache.airavata.registry.cpi.UsrResourceProfile;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.*;
+
+public class UserResourceProfileRepository extends 
AppCatAbstractRepository implements UsrResourceProfile {
+private final static Logger logger = 
LoggerFactory.getLogger(UserResourceProfileRepository.class);
+
+public UserResourceProfileRepository() {
+super(UserResourceProfile.class, UserResourceProfileEntity.class);
+}
+
+protected String saveUserResourceProfileData(UserResourceProfile 
userResourceProfile) throws AppCatalogException {
+UserResourceProfileEntity userResourceProfileEntity = 
saveUserResourceProfile(userResourceProfile);
+return userResourceProfileEntity.getUserId();
+}
+
+protected UserResourceProfileEntity 
saveUserResourceProfile(UserResourceProfile userResourceProfile) throws 
AppCatalogException {
+String userId = userResourceProfile.getUserId();
+String gatewayId = userResourceProfile.getGatewayID();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+UserResourceProfileEntity userResourceProfileEntity = 
mapper.map(userResourceProfile, UserResourceProfileEntity.class);
+
+if (userResourceProfileEntity.getUserComputeResourcePreferences() != 
null) {
+logger.debug("Populating the Primary Key 
UserComputeResourcePreferences objects for the User Resource Profile");
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setGatewayId(gatewayId));
+}
+
+if (userResourceProfileEntity.getUserStoragePreferences() != null) {
+logger.debug("Populating the Primary Key UserStoragePreferences 
objects for the User Resource Profile");
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setGatewayId(gatewayId));
+}
+
+

[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412082#comment-16412082
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176863306
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
 ##
 @@ -0,0 +1,227 @@
+/**
+ *
+ * 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.userresourceprofile.UserComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserStoragePreference;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserComputeResourcePreferencePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfileEntity;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfilePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserStoragePreferencePK;
+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.CompositeIdentifier;
+import org.apache.airavata.registry.cpi.UsrResourceProfile;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.*;
+
+public class UserResourceProfileRepository extends 
AppCatAbstractRepository implements UsrResourceProfile {
+private final static Logger logger = 
LoggerFactory.getLogger(UserResourceProfileRepository.class);
+
+public UserResourceProfileRepository() {
+super(UserResourceProfile.class, UserResourceProfileEntity.class);
+}
+
+protected String saveUserResourceProfileData(UserResourceProfile 
userResourceProfile) throws AppCatalogException {
+UserResourceProfileEntity userResourceProfileEntity = 
saveUserResourceProfile(userResourceProfile);
+return userResourceProfileEntity.getUserId();
+}
+
+protected UserResourceProfileEntity 
saveUserResourceProfile(UserResourceProfile userResourceProfile) throws 
AppCatalogException {
+String userId = userResourceProfile.getUserId();
+String gatewayId = userResourceProfile.getGatewayID();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+UserResourceProfileEntity userResourceProfileEntity = 
mapper.map(userResourceProfile, UserResourceProfileEntity.class);
+
+if (userResourceProfileEntity.getUserComputeResourcePreferences() != 
null) {
+logger.debug("Populating the Primary Key 
UserComputeResourcePreferences objects for the User Resource Profile");
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setGatewayId(gatewayId));
+}
+
+if (userResourceProfileEntity.getUserStoragePreferences() != null) {
+logger.debug("Populating the Primary Key UserStoragePreferences 
objects for the User Resource Profile");
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setGatewayId(gatewayId));
+}
+
+

[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412084#comment-16412084
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176863015
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
 ##
 @@ -0,0 +1,227 @@
+/**
+ *
+ * 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.userresourceprofile.UserComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserStoragePreference;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserComputeResourcePreferencePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfileEntity;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfilePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserStoragePreferencePK;
+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.CompositeIdentifier;
+import org.apache.airavata.registry.cpi.UsrResourceProfile;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.*;
+
+public class UserResourceProfileRepository extends 
AppCatAbstractRepository implements UsrResourceProfile {
+private final static Logger logger = 
LoggerFactory.getLogger(UserResourceProfileRepository.class);
+
+public UserResourceProfileRepository() {
+super(UserResourceProfile.class, UserResourceProfileEntity.class);
+}
+
+protected String saveUserResourceProfileData(UserResourceProfile 
userResourceProfile) throws AppCatalogException {
+UserResourceProfileEntity userResourceProfileEntity = 
saveUserResourceProfile(userResourceProfile);
+return userResourceProfileEntity.getUserId();
+}
+
+protected UserResourceProfileEntity 
saveUserResourceProfile(UserResourceProfile userResourceProfile) throws 
AppCatalogException {
+String userId = userResourceProfile.getUserId();
+String gatewayId = userResourceProfile.getGatewayID();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+UserResourceProfileEntity userResourceProfileEntity = 
mapper.map(userResourceProfile, UserResourceProfileEntity.class);
+
+if (userResourceProfileEntity.getUserComputeResourcePreferences() != 
null) {
+logger.debug("Populating the Primary Key 
UserComputeResourcePreferences objects for the User Resource Profile");
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setGatewayId(gatewayId));
+}
+
+if (userResourceProfileEntity.getUserStoragePreferences() != null) {
+logger.debug("Populating the Primary Key UserStoragePreferences 
objects for the User Resource Profile");
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setGatewayId(gatewayId));
+}
+
+

[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412085#comment-16412085
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176859591
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferenceEntity.java
 ##
 @@ -0,0 +1,195 @@
+/*
+ *
+ * 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.entities.appcatalog;
+
+import javax.persistence.*;
+import java.sql.Timestamp;
+
+/**
+ * The persistent class for the user_compute_resource_preference database 
table.
+ */
+@Entity
+@Table(name = "USER_COMPUTE_RESOURCE_PREFERENCE")
+@IdClass(UserComputeResourcePreferencePK.class)
+public class UserComputeResourcePreferenceEntity {
+private static final long serialVersionUID = 1L;
+
+@Id
+@Column(name = "RESOURCE_ID")
+private String computeResourceId;
+
+@Id
+@Column(name = "USER_ID")
+private String userId;
+
+@Id
+@Column(name = "GATEWAY_ID")
+private String gatewayId;
+
+@Column(name = "PREFERED_BATCH_QUEUE")
+private String preferredBatchQueue;
+
+@Column(name = "RESOURCE_CS_TOKEN")
+private String resourceSpecificCredentialStoreToken;
+
+@Column(name = "LOGIN_USERNAME")
+private String loginUserName;
+
+@Column(name = "ALLOCATION_PROJECT_NUMBER")
+private String allocationProjectNumber;
+
+@Column(name = "QUALITY_OF_SERVICE")
+private String qualityOfService;
+
+@Column(name = "RESERVATION")
+private String reservation;
+
+@Column(name = "RESERVATION_START_TIME")
+private Timestamp reservationStartTime;
+
+@Column(name = "RESERVATION_END_TIME")
+private Timestamp reservationEndTime;
+
+@Column(name = "SCRATCH_LOCATION")
+private String scratchLocation;
+
+@Column(name = "VALIDATED")
+private boolean validated;
+
+@ManyToOne(targetEntity = UserResourceProfileEntity.class, cascade = 
CascadeType.MERGE)
+@JoinColumn(name = "USER_ID")
 
 Review comment:
   This should join on USER_ID and GATEWAY_ID


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412081#comment-16412081
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176859914
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferenceEntity.java
 ##
 @@ -0,0 +1,118 @@
+/*
+ *
+ * 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.entities.appcatalog;
+
+import javax.persistence.*;
+
+/**
+ * The persistent class for the user_storage_preference database table.
+ */
+@Entity
+@Table(name = "USER_STORAGE_PREFERENCE")
+@IdClass(UserStoragePreferencePK.class)
+public class UserStoragePreferenceEntity {
+private static final long serialVersionUID = 1L;
+
+@Id
+@Column(name = "STORAGE_RESOURCE_ID")
+private String storageResourceId;
+
+@Id
+@Column(name = "USER_ID")
+private String userId;
+
+@Id
+@Column(name = "GATEWAY_ID")
+private String gatewayId;
+
+@Column(name = "RESOURCE_CS_TOKEN")
+private String resourceSpecificCredentialStoreToken;
+
+@Column(name = "FS_ROOT_LOCATION")
+private String fileSystemRootLocation;
+
+@Column(name = "LOGIN_USERNAME")
+private String loginUserName;
+
+@ManyToOne(targetEntity = UserResourceProfileEntity.class, cascade = 
CascadeType.MERGE)
+@JoinColumn(name = "USER_ID")
 
 Review comment:
   This should join on USER_ID and GATEWAY_ID


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412078#comment-16412078
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176859079
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserResourceProfilePK.java
 ##
 @@ -0,0 +1,83 @@
+/*
+ *
+ * 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.entities.appcatalog;
+
+import javax.persistence.Column;
+import javax.persistence.Id;
+import java.io.Serializable;
+
+/**
+ * The primary key class for the user_resource_profile database table.
+ *
+ */
+public class UserResourceProfilePK implements Serializable {
+//default serial version id, required for serializable classes.
+private static final long serialVersionUID = 1L;
+
+@Id
 
 Review comment:
   Same comment as above


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412080#comment-16412080
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176858764
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferencePK.java
 ##
 @@ -0,0 +1,98 @@
+/*
+ *
+ * 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.entities.appcatalog;
+
+import javax.persistence.Column;
+import javax.persistence.Id;
+import java.io.Serializable;
+
+/**
+ * The primary key class for the user_compute_resource_preference database 
table.
+ *
+ */
+public class UserComputeResourcePreferencePK implements Serializable {
+//default serial version id, required for serializable classes.
+private static final long serialVersionUID = 1L;
+
+@Id
 
 Review comment:
   I don't think you need any JPA annotations on an id class. See [Example 
7-4](https://docs.oracle.com/cd/E16439_01/doc.1013/e13981/cmp30cfg001.htm).


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412076#comment-16412076
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176861106
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
 ##
 @@ -0,0 +1,227 @@
+/**
+ *
+ * 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.userresourceprofile.UserComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserStoragePreference;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserComputeResourcePreferencePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfileEntity;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfilePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserStoragePreferencePK;
+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.CompositeIdentifier;
+import org.apache.airavata.registry.cpi.UsrResourceProfile;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.*;
+
+public class UserResourceProfileRepository extends 
AppCatAbstractRepository implements UsrResourceProfile {
+private final static Logger logger = 
LoggerFactory.getLogger(UserResourceProfileRepository.class);
+
+public UserResourceProfileRepository() {
+super(UserResourceProfile.class, UserResourceProfileEntity.class);
+}
+
+protected String saveUserResourceProfileData(UserResourceProfile 
userResourceProfile) throws AppCatalogException {
+UserResourceProfileEntity userResourceProfileEntity = 
saveUserResourceProfile(userResourceProfile);
+return userResourceProfileEntity.getUserId();
+}
+
+protected UserResourceProfileEntity 
saveUserResourceProfile(UserResourceProfile userResourceProfile) throws 
AppCatalogException {
+String userId = userResourceProfile.getUserId();
+String gatewayId = userResourceProfile.getGatewayID();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+UserResourceProfileEntity userResourceProfileEntity = 
mapper.map(userResourceProfile, UserResourceProfileEntity.class);
+
+if (userResourceProfileEntity.getUserComputeResourcePreferences() != 
null) {
+logger.debug("Populating the Primary Key 
UserComputeResourcePreferences objects for the User Resource Profile");
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setUserId(userId));
 
 Review comment:
   No need to forEach twice, you can set both properties. Same on line 68.


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>

[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412087#comment-16412087
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176860039
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferencePK.java
 ##
 @@ -0,0 +1,98 @@
+/*
+ *
+ * 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.entities.appcatalog;
+
+import javax.persistence.Column;
+import javax.persistence.Id;
+import java.io.Serializable;
+
+/**
+ * The primary key class for the user_storage_preference database table.
+ *
+ */
+public class UserStoragePreferencePK implements Serializable {
+//default serial version id, required for serializable classes.
+private static final long serialVersionUID = 1L;
+
+@Id
 
 Review comment:
   Same comment as above.


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412086#comment-16412086
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176863606
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/utils/QueryConstants.java
 ##
 @@ -37,4 +37,26 @@
 "WHERE BQ.groupResourceProfileId LIKE : " + 
DBConstants.GroupResourceProfile.GROUP_RESOURCE_PROFILE_ID;
 String FIND_ALL_GROUP_COMPUTE_RESOURCE_POLICY = "SELECT CR FROM "+ 
ComputeResourcePolicyEntity.class.getSimpleName() + " CR " +
 "WHERE CR.groupResourceProfileId LIKE : " + 
DBConstants.GroupResourceProfile.GROUP_RESOURCE_PROFILE_ID;
+
+String GET_USER_RESOURCE_PROFILE = "SELECT DISTINCT URP FROM " + 
UserResourceProfileEntity.class.getSimpleName() + " URP " +
 
 Review comment:
   GET_USER_RESOURCE_PROFILE, GET_USER_COMPUTE_RESOURCE_PREFERENCE and 
GET_USER_STORAGE_PREFERENCE I don't think are needed if using the `get()` 
repository method as mentioned above.


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412079#comment-16412079
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176863684
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/resources/META-INF/persistence.xml
 ##
 @@ -122,6 +122,9 @@
 
org.apache.airavata.registry.core.entities.appcatalog.StorageInterfacePK
 
 Review comment:
   We can remove these Id classes, right?


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> Refactoring App Catalog Implementation - User Resource Profile
> --
>
> Key: AIRAVATA-2712
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2712
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2712) Refactoring App Catalog Implementation - User Resource Profile

2018-03-23 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2712?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16412083#comment-16412083
 ] 

ASF GitHub Bot commented on AIRAVATA-2712:
--

machristie commented on a change in pull request #185: [AIRAVATA-2712] 
Refactoring App Catalog Implementation - UserResourceProfile
URL: https://github.com/apache/airavata/pull/185#discussion_r176863089
 
 

 ##
 File path: 
modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
 ##
 @@ -0,0 +1,227 @@
+/**
+ *
+ * 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.userresourceprofile.UserComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserStoragePreference;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserComputeResourcePreferencePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfileEntity;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserResourceProfilePK;
+import 
org.apache.airavata.registry.core.entities.appcatalog.UserStoragePreferencePK;
+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.CompositeIdentifier;
+import org.apache.airavata.registry.cpi.UsrResourceProfile;
+import org.dozer.Mapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Timestamp;
+import java.util.*;
+
+public class UserResourceProfileRepository extends 
AppCatAbstractRepository implements UsrResourceProfile {
+private final static Logger logger = 
LoggerFactory.getLogger(UserResourceProfileRepository.class);
+
+public UserResourceProfileRepository() {
+super(UserResourceProfile.class, UserResourceProfileEntity.class);
+}
+
+protected String saveUserResourceProfileData(UserResourceProfile 
userResourceProfile) throws AppCatalogException {
+UserResourceProfileEntity userResourceProfileEntity = 
saveUserResourceProfile(userResourceProfile);
+return userResourceProfileEntity.getUserId();
+}
+
+protected UserResourceProfileEntity 
saveUserResourceProfile(UserResourceProfile userResourceProfile) throws 
AppCatalogException {
+String userId = userResourceProfile.getUserId();
+String gatewayId = userResourceProfile.getGatewayID();
+Mapper mapper = ObjectMapperSingleton.getInstance();
+UserResourceProfileEntity userResourceProfileEntity = 
mapper.map(userResourceProfile, UserResourceProfileEntity.class);
+
+if (userResourceProfileEntity.getUserComputeResourcePreferences() != 
null) {
+logger.debug("Populating the Primary Key 
UserComputeResourcePreferences objects for the User Resource Profile");
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserComputeResourcePreferences().forEach(userComputeResourcePreferenceEntity
 -> userComputeResourcePreferenceEntity.setGatewayId(gatewayId));
+}
+
+if (userResourceProfileEntity.getUserStoragePreferences() != null) {
+logger.debug("Populating the Primary Key UserStoragePreferences 
objects for the User Resource Profile");
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setUserId(userId));
+
userResourceProfileEntity.getUserStoragePreferences().forEach(userStoragePreferenceEntity
 -> userStoragePreferenceEntity.setGatewayId(gatewayId));
+}
+
+

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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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-2717) [GSoC] Resurrect User-Defined Airavata Workflows

2018-03-23 Thread Dimuthu Upeksha (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2717?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411604#comment-16411604
 ] 

Dimuthu Upeksha commented on AIRAVATA-2717:
---

[~marcuschristie] Yeah I guess that's what we want. Sorry for my 
misrepresentation. Let's use a higher level workflow to connect applications 
rather than composing everything in a single workflow. 

> [GSoC] Resurrect User-Defined Airavata Workflows 
> -
>
> Key: AIRAVATA-2717
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2717
> Project: Airavata
>  Issue Type: Epic
>Affects Versions: 0.17
>Reporter: Suresh Marru
>Priority: Major
>  Labels: gsoc2018
>
> Airavata used to support user-defined workflows using an interface XBaya to 
> drag and drop application components to a workspace and define data flow and 
> control flow dependencies among the application nodes. Airavata's workflow 
> system was used for composing, executing, and monitoring workflow graphs 
> primarly web service components. The workflow description was high level 
> abstraction and used to be converted to lower level execution run times like 
> BPEL, SCUFL and Python scripts.
>  
> Airavata has evolved significantly and the current development version is 
> being built-over Apache Helix for DAG orchestration. This provides an 
> opportunity to resurrect workflow capabilities in Airavata. 
> This GSoC project involves finalizing a Airavata Workflow Language; modify 
> the orchestrator to parse user described workflow and translate to equivalent 
> Helix DAG's; execute and monitor the worklfows; develop a simple UI to 
> demonstrate the capabilities. 
> To describe the workflows, you can build on this - 
> [https://docs.google.com/document/d/1eh7BV8CHupxyM2jeqcM2tUG5MnXFt7hNDX4PQDfxCcM/edit]
>  or follow other discussions like - 
> https://issues.apache.org/jira/browse/AIRAVATA-2555 and 
> User community & Impact of the software: Airavata is primarily targeted to 
> build science gateways using computational resources from various 
> disciplines. The initial targeted set of gateways include projects supporting 
> research and education in chemistry, biophysics, and geosciences . The goal 
> of airavata is to enhance productivity of these gateways to utilize 
> cyberinfrastructure of resources (e.g., local lab resources, the Extreme 
> Science and Engineering Discovery Environment (XSEDE), University Clusters, 
> Academic and Commercial Computational Clouds. 



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[jira] [Created] (AIRAVATA-2721) Thirft Models,CPI's and OpenJPA for community requests

2018-03-23 Thread Harsha Phulwani (JIRA)

Harsha Phulwani created AIRAVATA-2721:
-

 Summary: Thirft Models,CPI's and OpenJPA for community requests
 Key: AIRAVATA-2721
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2721
 Project: Airavata
  Issue Type: Sub-task
  Components: Airavata Allocation Manager
Reporter: Harsha Phulwani


Backend changes in the following components - OpenJPA(Entities, Repositories), 
Thrift Model and CPI methods, ServerHandler(For implementing all the methods)



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[jira] [Created] (AIRAVATA-2720) Resource Allocation - Community Requests

2018-03-23 Thread Harsha Phulwani (JIRA)

Harsha Phulwani created AIRAVATA-2720:
-

 Summary: Resource Allocation - Community Requests
 Key: AIRAVATA-2720
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2720
 Project: Airavata
  Issue Type: Task
  Components: Airavata Allocation Manager
Reporter: Harsha Phulwani


A pipeline for PI's to create community requests using the Django-portal.

This includes three dashboard users - PI view, Reviewer view and Admin view 



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[jira] [Commented] (AIRAVATA-2717) [GSoC] Resurrect User-Defined Airavata Workflows

2018-03-23 Thread Marcus Christie (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2717?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411558#comment-16411558
 ] 

Marcus Christie commented on AIRAVATA-2717:
---

[~dimuthuupe], do we need two levels of workflows? The static workflow that the 
orchestrator defines is for running an Application. Do we want a higher level 
workflow for chaining together multiple Applications?  I guess a higher level 
workflow dealing with Applications would be more user friendly.

> [GSoC] Resurrect User-Defined Airavata Workflows 
> -
>
> Key: AIRAVATA-2717
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2717
> Project: Airavata
>  Issue Type: Epic
>Affects Versions: 0.17
>Reporter: Suresh Marru
>Priority: Major
>  Labels: gsoc2018
>
> Airavata used to support user-defined workflows using an interface XBaya to 
> drag and drop application components to a workspace and define data flow and 
> control flow dependencies among the application nodes. Airavata's workflow 
> system was used for composing, executing, and monitoring workflow graphs 
> primarly web service components. The workflow description was high level 
> abstraction and used to be converted to lower level execution run times like 
> BPEL, SCUFL and Python scripts.
>  
> Airavata has evolved significantly and the current development version is 
> being built-over Apache Helix for DAG orchestration. This provides an 
> opportunity to resurrect workflow capabilities in Airavata. 
> This GSoC project involves finalizing a Airavata Workflow Language; modify 
> the orchestrator to parse user described workflow and translate to equivalent 
> Helix DAG's; execute and monitor the worklfows; develop a simple UI to 
> demonstrate the capabilities. 
> To describe the workflows, you can build on this - 
> [https://docs.google.com/document/d/1eh7BV8CHupxyM2jeqcM2tUG5MnXFt7hNDX4PQDfxCcM/edit]
>  or follow other discussions like - 
> https://issues.apache.org/jira/browse/AIRAVATA-2555 and 
> User community & Impact of the software: Airavata is primarily targeted to 
> build science gateways using computational resources from various 
> disciplines. The initial targeted set of gateways include projects supporting 
> research and education in chemistry, biophysics, and geosciences . The goal 
> of airavata is to enhance productivity of these gateways to utilize 
> cyberinfrastructure of resources (e.g., local lab resources, the Extreme 
> Science and Engineering Discovery Environment (XSEDE), University Clusters, 
> Academic and Commercial Computational Clouds. 



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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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

2018-03-23 Thread 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-2717) [GSoC] Resurrect User-Defined Airavata Workflows

2018-03-23 Thread Yasas Gunarathne (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2717?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16411320#comment-16411320
 ] 

Yasas Gunarathne commented on AIRAVATA-2717:


Hi Dimuthu,

Thank you for the detailed answer. I created a new thread at dev mailing list 
to discuss about Airavata Workflow Language.

Regards

> [GSoC] Resurrect User-Defined Airavata Workflows 
> -
>
> Key: AIRAVATA-2717
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2717
> Project: Airavata
>  Issue Type: Epic
>Affects Versions: 0.17
>Reporter: Suresh Marru
>Priority: Major
>  Labels: gsoc2018
>
> Airavata used to support user-defined workflows using an interface XBaya to 
> drag and drop application components to a workspace and define data flow and 
> control flow dependencies among the application nodes. Airavata's workflow 
> system was used for composing, executing, and monitoring workflow graphs 
> primarly web service components. The workflow description was high level 
> abstraction and used to be converted to lower level execution run times like 
> BPEL, SCUFL and Python scripts.
>  
> Airavata has evolved significantly and the current development version is 
> being built-over Apache Helix for DAG orchestration. This provides an 
> opportunity to resurrect workflow capabilities in Airavata. 
> This GSoC project involves finalizing a Airavata Workflow Language; modify 
> the orchestrator to parse user described workflow and translate to equivalent 
> Helix DAG's; execute and monitor the worklfows; develop a simple UI to 
> demonstrate the capabilities. 
> To describe the workflows, you can build on this - 
> [https://docs.google.com/document/d/1eh7BV8CHupxyM2jeqcM2tUG5MnXFt7hNDX4PQDfxCcM/edit]
>  or follow other discussions like - 
> https://issues.apache.org/jira/browse/AIRAVATA-2555 and 
> User community & Impact of the software: Airavata is primarily targeted to 
> build science gateways using computational resources from various 
> disciplines. The initial targeted set of gateways include projects supporting 
> research and education in chemistry, biophysics, and geosciences . The goal 
> of airavata is to enhance productivity of these gateways to utilize 
> cyberinfrastructure of resources (e.g., local lab resources, the Extreme 
> Science and Engineering Discovery Environment (XSEDE), University Clusters, 
> Academic and Commercial Computational Clouds. 



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