date:20170125

Github user anujbhan commented on the issue:

https://github.com/apache/airavata/pull/94
  
Working on the review now !


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[jira] [Updated] (AIRAVATA-1718) An Experiment with incorrect batch for the resource has gone through to GFAC; ideally this should be failed at orchestrator level

2017-01-25 Thread Eroma (JIRA)


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-1718?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-1718:

Fix Version/s: (was: 0.16)
   0.18

> An Experiment with incorrect batch for the resource has gone through to GFAC; 
> ideally this should be failed at orchestrator level
> -
>
> Key: AIRAVATA-1718
> URL: https://issues.apache.org/jira/browse/AIRAVATA-1718
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata Orchestrator
>Affects Versions: 0.15
> Environment: 
> http://dev.test-drive.airavata.org/portal/ultrascan-production/public
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.18
>
> Attachments: Screen Shot 2015-06-05 at 12.15.40 PM.png
>
>
> Steps to recreate
> 1. Had an experiment with an incorrect queue and i edited the experiment and 
> saved and launched with the correct queue
> 2. But the experiment failed at both Experiment and job level and got the 
> error message [1] in PGA
> 3. Ideally this should have failed at experiment level; should not proceed to 
> job level.
> Exp ID
> CloneofALAMO_1_0475d607-a95e-4776-9e43-9dea0aa20340
> [1]
> Validation Errors : The specified queuebatchdoes not exist. If you believe 
> this is an error, contact the administrator to verify App-Catalog 
> Configurations Error submitting the job to host lonestar.tacc.utexas.edu 
> message: 2 org.apache.airavata.gfac.GFacException: Error while executing 
> provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. org.apache.airavata.gfac.GFacException: Error launching the 
> Job at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:480)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:179)
>  at 
> org.apache.airavata.gfac.core.utils.InputHandlerWorker.run(InputHandlerWorker.java:47)
>  at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>  at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>  at java.lang.Thread.run(Thread.java:745) Caused by: 
> org.apache.airavata.gfac.GFacException: Error while executing provider 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.launch(BetterGfacImpl.java:718)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:467)
>  ... 5 more Caused by: org.apache.airavata.gfac.GFacException: Error while 
> executing provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.executeProvider(BetterGfacImpl.java:819)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.invokeProviderExecute(BetterGfacImpl.java:728)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.launch(BetterGfacImpl.java:678)
>  ... 6 more Caused by: 
> org.apache.airavata.gfac.core.provider.GFacProviderException: Error 
> submitting the job to host lonestar.tacc.utexas.edu message: 2 at 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider.execute(SSHProvider.java:215)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.executeProvider(BetterGfacImpl.java:817)
>  ... 8 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 2 at 
> org.apache.airavata.gsi.ssh.api.job.UGEOutputParser.parseJobSubmission(UGEOutputParser.java:129)
>  at 
> org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster.submitBatchJobWithScript(GSISSHAbstractCluster.java:279)
>  at 
> org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster.submitBatchJob(GSISSHAbstractCluster.java:319)
>  at 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider.execute(SSHProvider.java:166)
>  ... 9 more 



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[jira] [Reopened] (AIRAVATA-1718) An Experiment with incorrect batch for the resource has gone through to GFAC; ideally this should be failed at orchestrator level

2017-01-25 Thread Eroma (JIRA)


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-1718?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma reopened AIRAVATA-1718:
-
  Assignee: Supun Chathuranga Nakandala  (was: Chathuri Wimalasena)

Steps taken:
1. Create an experiment and edit and change the resource and save before the 
queue is changed according to the new resource.
2. Then launch it.
3. When launched since the queue is not matching with the resource it will 
remain in CREATED without any error messages.
4. User edits the experiment again and then launches the experiment.
5. In PGA user can see correct resource and queue details but the details in 
PROCESS_RESOURCE_SCHEDULE table was as before.
6. So the experiment fails with error messages:
stdout : stderr : qsub: submit error (Unknown queue MSG=requested queue not 
found) org.apache.airavata.gfac.core.GFacException: Error: userFriendly msg 
:Error while executing JOB_SUBMISSION task, actual msg :expId: 
Gauusian_5_d3fe4b73-57cf-469e-955c-56955b57fa50, processId: 
PROCESS_6bfe8385-4934-4405-8761-5fdf2fca72e4, taskId: 
TASK_f4420a74-f33d-4240-849c-cfe003f0763a, type: JOB_SUBMISSION :- 
JOB_SUBMISSION failed. Reason: Job submission command didn't return a jobId at 
org.apache.airavata.gfac.impl.GFacEngineImpl.checkFailures(GFacEngineImpl.java:630)
 at 
org.apache.airavata.gfac.impl.GFacEngineImpl.executeJobSubmission(GFacEngineImpl.java:516)
 at 
org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:388)
 at 
org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:288)
 at 
org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:229) at 
org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:88) at 
org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:21)
 at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) 
at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) 
at java.lang.Thread.run(Thread.java:745)

> An Experiment with incorrect batch for the resource has gone through to GFAC; 
> ideally this should be failed at orchestrator level
> -
>
> Key: AIRAVATA-1718
> URL: https://issues.apache.org/jira/browse/AIRAVATA-1718
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata Orchestrator
>Affects Versions: 0.15
> Environment: 
> http://dev.test-drive.airavata.org/portal/ultrascan-production/public
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.18
>
> Attachments: Screen Shot 2015-06-05 at 12.15.40 PM.png
>
>
> Steps to recreate
> 1. Had an experiment with an incorrect queue and i edited the experiment and 
> saved and launched with the correct queue
> 2. But the experiment failed at both Experiment and job level and got the 
> error message [1] in PGA
> 3. Ideally this should have failed at experiment level; should not proceed to 
> job level.
> Exp ID
> CloneofALAMO_1_0475d607-a95e-4776-9e43-9dea0aa20340
> [1]
> Validation Errors : The specified queuebatchdoes not exist. If you believe 
> this is an error, contact the administrator to verify App-Catalog 
> Configurations Error submitting the job to host lonestar.tacc.utexas.edu 
> message: 2 org.apache.airavata.gfac.GFacException: Error while executing 
> provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. org.apache.airavata.gfac.GFacException: Error launching the 
> Job at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:480)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:179)
>  at 
> org.apache.airavata.gfac.core.utils.InputHandlerWorker.run(InputHandlerWorker.java:47)
>  at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>  at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>  at java.lang.Thread.run(Thread.java:745) Caused by: 
> org.apache.airavata.gfac.GFacException: Error while executing provider 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.launch(BetterGfacImpl.java:718)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:467)
>  ... 5 more Caused by: org.apache.airavata.gfac.GFacException: Error while 
> executing provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.executeProvider(BetterGfacImpl.java:819)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.invokeProviderExecute(BetterGfacImpl.java:728)
>  at 
>

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[jira] [Closed] (AIRAVATA-1718) An Experiment with incorrect batch for the resource has gone through to GFAC; ideally this should be failed at orchestrator level

2017-01-25 Thread Eroma (JIRA)


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-1718?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma closed AIRAVATA-1718.
---

tested and verified in
https://dev.seagrid.org

Currently in PGA when a resource is changed the queue details change 
accordingly. User cannot submit jobs with incorrect resource queue details.

> An Experiment with incorrect batch for the resource has gone through to GFAC; 
> ideally this should be failed at orchestrator level
> -
>
> Key: AIRAVATA-1718
> URL: https://issues.apache.org/jira/browse/AIRAVATA-1718
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata Orchestrator
>Affects Versions: 0.15
> Environment: 
> http://dev.test-drive.airavata.org/portal/ultrascan-production/public
>Reporter: Eroma
>Assignee: Chathuri Wimalasena
> Fix For: 0.16
>
> Attachments: Screen Shot 2015-06-05 at 12.15.40 PM.png
>
>
> Steps to recreate
> 1. Had an experiment with an incorrect queue and i edited the experiment and 
> saved and launched with the correct queue
> 2. But the experiment failed at both Experiment and job level and got the 
> error message [1] in PGA
> 3. Ideally this should have failed at experiment level; should not proceed to 
> job level.
> Exp ID
> CloneofALAMO_1_0475d607-a95e-4776-9e43-9dea0aa20340
> [1]
> Validation Errors : The specified queuebatchdoes not exist. If you believe 
> this is an error, contact the administrator to verify App-Catalog 
> Configurations Error submitting the job to host lonestar.tacc.utexas.edu 
> message: 2 org.apache.airavata.gfac.GFacException: Error while executing 
> provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. org.apache.airavata.gfac.GFacException: Error launching the 
> Job at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:480)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:179)
>  at 
> org.apache.airavata.gfac.core.utils.InputHandlerWorker.run(InputHandlerWorker.java:47)
>  at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>  at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>  at java.lang.Thread.run(Thread.java:745) Caused by: 
> org.apache.airavata.gfac.GFacException: Error while executing provider 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.launch(BetterGfacImpl.java:718)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.submitJob(BetterGfacImpl.java:467)
>  ... 5 more Caused by: org.apache.airavata.gfac.GFacException: Error while 
> executing provider org.apache.airavata.gfac.ssh.provider.impl.SSHProvider 
> functionality. at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.executeProvider(BetterGfacImpl.java:819)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.invokeProviderExecute(BetterGfacImpl.java:728)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.launch(BetterGfacImpl.java:678)
>  ... 6 more Caused by: 
> org.apache.airavata.gfac.core.provider.GFacProviderException: Error 
> submitting the job to host lonestar.tacc.utexas.edu message: 2 at 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider.execute(SSHProvider.java:215)
>  at 
> org.apache.airavata.gfac.core.cpi.BetterGfacImpl.executeProvider(BetterGfacImpl.java:817)
>  ... 8 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 2 at 
> org.apache.airavata.gsi.ssh.api.job.UGEOutputParser.parseJobSubmission(UGEOutputParser.java:129)
>  at 
> org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster.submitBatchJobWithScript(GSISSHAbstractCluster.java:279)
>  at 
> org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster.submitBatchJob(GSISSHAbstractCluster.java:319)
>  at 
> org.apache.airavata.gfac.ssh.provider.impl.SSHProvider.execute(SSHProvider.java:166)
>  ... 9 more 



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[jira] [Closed] (AIRAVATA-2274) Cannot upload multiple optional files in a cloned experiment. Exception thrown

2017-01-25 Thread Eroma (JIRA)


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2274?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma closed AIRAVATA-2274.
---

tested and verified in
https://dev.seagrid.org

Can attach multiple optional files in clone and edit mode of an experiment.
Tested with AutoDock Vina in Comet.

> Cannot upload multiple optional files in a cloned experiment. Exception thrown
> --
>
> Key: AIRAVATA-2274
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2274
> Project: Airavata
>  Issue Type: Bug
>  Components: PGA PHP Web Gateway
> Environment: https://dev.seagrid.org
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.17
>
> Attachments: Screen Shot 2016-12-13 at 4.24.49 PM.png
>
>
> when tried to add multiple optional files getting an exception 
> move_uploaded_file(ZINC0570.pdbqt): failed to open stream: Permission 
> denied. This is when i cloned an experiment which had a single optional file 
> and i was tryign to replace it with multiple.
> But cannot even replace with a single file either
> Error: move_uploaded_file(ZINC1228.pdbqt): failed to open stream: 
> Permission denied



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[GitHub] airavata issue #94: Making corrections to user profile service code

2017-01-25 Thread smarru

Github user smarru commented on the issue:

https://github.com/apache/airavata/pull/94
  
@anujbhan thank you for this contribution and detailed commit and change 
log, very helpful for reviews and provenance.  


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[GitHub] airavata pull request #94: Making corrections to user profile service code

2017-01-25 Thread smarru

Github user smarru commented on a diff in the pull request:

https://github.com/apache/airavata/pull/94#discussion_r97787233
  
--- Diff: 
thrift-interface-descriptions/component-cpis/user-profile-crud-cpi.thrift ---
@@ -0,0 +1,58 @@
+/*
+ * 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.
+ *
+ */
+
+/*
+ * Component Programming Interface definition for Apache Airavata User 
profile registry Service.
+ *
+*/
+
+include "../data-models/user-group-models/user_profile_model.thrift"
+include "registry_api_errors.thrift"
--- End diff --

May be we should move towards service specific exception? so a 
UserProfileService Exception? 


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[GitHub] airavata pull request #94: Making corrections to user profile service code

2017-01-25 Thread smarru

Github user smarru commented on a diff in the pull request:

https://github.com/apache/airavata/pull/94#discussion_r97787375
  
--- Diff: 
thrift-interface-descriptions/component-cpis/user-profile-crud-cpi.thrift ---
@@ -0,0 +1,58 @@
+/*
+ * 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.
+ *
+ */
+
+/*
+ * Component Programming Interface definition for Apache Airavata User 
profile registry Service.
+ *
+*/
+
+include "../data-models/user-group-models/user_profile_model.thrift"
+include "registry_api_errors.thrift"
+
+
+namespace java org.apache.airavata.userprofile.crude.cpi
+
+const string USER_PROFILE_CPI_VERSION = "0.16.0"
+
+service UserProfileCrudeService {
--- End diff --

How about we drop the CRUD all together and rename the service to 
UserProfileService? 


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[GitHub] airavata pull request #94: Making corrections to user profile service code

2017-01-25 Thread machristie

Github user machristie commented on a diff in the pull request:

https://github.com/apache/airavata/pull/94#discussion_r97785195
  
--- Diff: 
thrift-interface-descriptions/component-cpis/user-profile-crud-cpi.thrift ---
@@ -0,0 +1,58 @@
+/*
+ * 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.
+ *
+ */
+
+/*
+ * Component Programming Interface definition for Apache Airavata User 
profile registry Service.
+ *
+*/
+
+include "../data-models/user-group-models/user_profile_model.thrift"
+include "registry_api_errors.thrift"
+
+
+namespace java org.apache.airavata.userprofile.crude.cpi
+
+const string USER_PROFILE_CPI_VERSION = "0.16.0"
+
+service UserProfileCrudeService {
--- End diff --

Rename from "Crude" to "Crud". I'm assuming that it is supposed to be Crud 
like CRUD (Create-Read-Update-Delete).  Also in the namespace and maybe 
elsewhere.


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[GitHub] airavata pull request #94: Making corrections to user profile service code

2017-01-25 Thread machristie

Github user machristie commented on a diff in the pull request:

https://github.com/apache/airavata/pull/94#discussion_r97784766
  
--- Diff: 
thrift-interface-descriptions/component-cpis/user-profile-crud-cpi.thrift ---
@@ -0,0 +1,58 @@
+/*
+ * 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.
+ *
+ */
+
+/*
+ * Component Programming Interface definition for Apache Airavata User 
profile registry Service.
+ *
+*/
+
+include "../data-models/user-group-models/user_profile_model.thrift"
+include "registry_api_errors.thrift"
--- End diff --

Seems like the UserProfile service should have its own error types instead 
of using the registry error types. The way this is set up there are two 
RegistryServiceException classes that are generated.

I'm not sure what to recommend though. Maybe use the common airavata errors 
in airavata_errors.thrift? Or define a new UserProfileServiceException?


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