date:20180129

Eroma created AIRAVATA-2658:
---

 Summary: Specified intermediate output viewing through the PGA 
portal
 Key: AIRAVATA-2658
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2658
 Project: Airavata
  Issue Type: Bug
  Components: GFac, PGA PHP Web Gateway
Affects Versions: 0.18
Reporter: Eroma
Assignee: Shameera Rathnayaka


Gateway user should be able to view output files while the job is running.

Gateway PI, would probably indicate which file or files should be brought back 
and those files should be available fort h user to view while job is executing.

If the output doesn't seem good then the user can cancel the job.



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[jira] [Updated] (AIRAVATA-2615) Experiment view page

2018-01-29 Thread ASF subversion and git services (JIRA)


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2615?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie updated AIRAVATA-2615:
--
Description: 
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * (/) If the experiment isn't completed or failed, poll the experiment
 * (/) Display the job information
 * (/) Redirect from experiment launch to experiment summary page

 

 

  was:
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * (/) If the experiment isn't completed or failed, poll the experiment
 * Display the job information
 * (/) Redirect from experiment launch to experiment summary page

 

 


> Experiment view page
> 
>
> Key: AIRAVATA-2615
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2615
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> TODO
>  * (/) Load the Experiment model data together with the Project data, input 
> and output DataProducts, ApplicationModule and ComputeResourceDescription 
> (what I'm calling a FullExperiment)
>  * (/) If the experiment isn't completed or failed, poll the experiment
>  * (/) Display the job information
>  * (/) Redirect from experiment launch to experiment summary page
>  
>  



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[jira] [Commented] (AIRAVATA-2615) Experiment view page


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2615?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16344028#comment-16344028
 ] 

ASF subversion and git services commented on AIRAVATA-2615:
---

Commit 9289284d07f62afe39a63e690b5fba44d4f2b96b in airavata-django-portal's 
branch refs/heads/master from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=9289284 ]

AIRAVATA-2615 Redirect from launch to experiment summary

'launching' query param/prop added to experiment summary to indicate
that the experiment is currently launching so that experiment summary
knows to poll for status updates until the experiment has launched.


> Experiment view page
> 
>
> Key: AIRAVATA-2615
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2615
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> TODO
>  * (/) Load the Experiment model data together with the Project data, input 
> and output DataProducts, ApplicationModule and ComputeResourceDescription 
> (what I'm calling a FullExperiment)
>  * (/) If the experiment isn't completed or failed, poll the experiment
>  * Display the job information
>  * (/) Redirect from experiment launch to experiment summary page
>  
>  



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[jira] [Commented] (AIRAVATA-2615) Experiment view page

2018-01-29 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2615?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16344027#comment-16344027
 ] 

ASF subversion and git services commented on AIRAVATA-2615:
---

Commit 11c3daccd82d208642dc1d4659e454653cd01440 in airavata-django-portal's 
branch refs/heads/master from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=11c3dac ]

AIRAVATA-2615 experimentStatus is read only


> Experiment view page
> 
>
> Key: AIRAVATA-2615
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2615
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> TODO
>  * (/) Load the Experiment model data together with the Project data, input 
> and output DataProducts, ApplicationModule and ComputeResourceDescription 
> (what I'm calling a FullExperiment)
>  * (/) If the experiment isn't completed or failed, poll the experiment
>  * Display the job information
>  * (/) Redirect from experiment launch to experiment summary page
>  
>  



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[jira] [Commented] (AIRAVATA-2143) Experiments with overridden resource allocation details tries to use qos and reservation from community user

2018-01-29 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2143?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343990#comment-16343990
 ] 

ASF subversion and git services commented on AIRAVATA-2143:
---

Commit a44fa60e5d1cf853b1b7a13a7b3ca779fdf6bd2b in airavata's branch 
refs/heads/master from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=a44fa60 ]

Merge pull request #166 from DImuthuUpe/AIRAVATA-2143

Fixing Airavata-2143

> Experiments with overridden resource allocation details tries to use qos and 
> reservation from  community user
> -
>
> Key: AIRAVATA-2143
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2143
> Project: Airavata
>  Issue Type: Bug
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> Experiments with overridden resource allocation details tries to use qos and 
> reservation from  community user.
> Remote resource login details sent at experiment creation is used to submit 
> jobs but refers to qos and reservation for the community allocation of the 
> remote resource.



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


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

Sneha Tilak updated AIRAVATA-2657:
--
Summary: Refactoring App Catalog implementation - ApplicationDeployment and 
ApplicationInterface  (was: Refactoring App Catalog implementation - 
ApplicationDeployment)

> 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] [Updated] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment and ApplicationInterface


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

Sneha Tilak updated AIRAVATA-2657:
--
Component/s: (was: Registry API)
 Application Catalog

> 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] [Updated] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment


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

Sneha Tilak updated AIRAVATA-2657:
--
Issue Type: Task  (was: Improvement)

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




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[jira] [Created] (AIRAVATA-2657) Refactoring App Catalog implementation - ApplicationDeployment

Sneha Tilak created AIRAVATA-2657:
-

 Summary: Refactoring App Catalog implementation - 
ApplicationDeployment
 Key: AIRAVATA-2657
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2657
 Project: Airavata
  Issue Type: Improvement
  Components: Registry API
Reporter: Sneha Tilak
Assignee: Sneha Tilak






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[jira] [Comment Edited] (AIRAVATA-2143) Experiments with overridden resource allocation details tries to use qos and reservation from community user

[
https://issues.apache.org/jira/browse/AIRAVATA-2143?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16341508#comment-16341508
]

Eroma edited comment on AIRAVATA-2143 at 1/29/18 8:21 PM:
--

Tested in [https://dev.seagrid.org|https://dev.seagrid.org/]

Test Cases
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu shared queue without QOS or reservation. - PASS
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu compute queue with QOS. - QOS in job script correctly. - PASS
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu compute queue with QOS and reservation (Since the actual
reservation did not exists checked up to the reservation existence in the job
script). – QOS and reservation in job script correctly - PASS
# Submit a job using individual preferences of individual account. Tested
using comet.sdsc.edu compute queue without QOS or reservation. - PASS
# Submit a job using individual preferences of individual account. Tested
using comet.sdsc.edu shared queue with QOS (Since actual QOS did not exist for
the account tested up to the QOS existence in job script). - PASS
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu shared queue with QOS and reservation (Since the actual QOS and
reservation did not exists checked up to the reservation existence in the job
script). – Job script printed correctly. Observation: Although both QOS and
reservation printed in the job script is incorrect, the error is only for the
QOS. - PASS
# Submit a SLURM job to a different SLURM cluster with no QOS or reservation.
Tested with Stamepde2. - PASS
# Submit a PBS job to a PBS cluster using gateway preferences of community
account. Tested with BigRed2 with a project allocation number. - PASS
# Submit a PBS job to a PBS cluster using individual preferences of individual
account. Tested with BigRed2. BigRed2 has no allocation number, QOS or
reservation - PASS
# User shares the experiment with Write access which was executed using
community allocation. Shared user clones and submits using same community
account. - PASS
# User shares the experiment with Write access which was executed using
individual allocation. Shared user clones and submits using community account.
- For the shared user only available option is to use the community login,
since she has no individual account of her own. - PASS
# User shares the experiment with Write access which was executed using
individual allocation. Shared user clones and submits using original user's
account. Should not be able to submit using that user's individual allocation.
– This option is not available for the user. - PASS
# User shares the experiment with Write access which was executed using
individual allocation. Shared user clones and submits using her own allocation
account. - PASS

NOTE: As per current implementation Reservation is applied for all the queues
in the resource fro the given period. Testing with LDAP integration for compute
clusters are not taken into consideration in this testing.

was (Author: eroma_a):
Tested in [https://dev.seagrid.org|https://dev.seagrid.org/]

[jira] [Resolved] (AIRAVATA-2612) Searching for an existing user throws an exception


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2612?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie resolved AIRAVATA-2612.
---
Resolution: Fixed

> Searching for an existing user throws an exception
> --
>
> Key: AIRAVATA-2612
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2612
> Project: Airavata
>  Issue Type: Bug
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.18
> Environment: https://dev.seagrid.org
>Reporter: Eroma
>Assignee: Marcus Christie
>Priority: Major
> Fix For: 0.18
>
>
> When searched for an existing user gets the exception [1] thrown. If searched 
> for a non-existing user (some random text) no exceptions thrown.
> [1]
> ErrorException (E_ERROR)
> HELP
> Undefined property: stdClass::$emailVerified (View: 
> /var/www/portals/dev-seagrid/app/views/admin/manage-users.blade.php)



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[jira] [Created] (AIRAVATA-2656) Display experiment errors on experiment summary

Marcus Christie created AIRAVATA-2656:
-

 Summary: Display experiment errors on experiment summary
 Key: AIRAVATA-2656
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2656
 Project: Airavata
  Issue Type: Sub-task
Reporter: Marcus Christie
Assignee: Marcus Christie






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[jira] [Updated] (AIRAVATA-2615) Experiment view page


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2615?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie updated AIRAVATA-2615:
--
Description: 
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * (/) If the experiment isn't completed or failed, poll the experiment
 * Display the job information
 * (/) Redirect from experiment launch to experiment summary page

 

 

  was:
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * (/) If the experiment isn't completed or failed, poll the experiment
 * Display the job information
 * Redirect from experiment launch to experiment summary page

 

 


> Experiment view page
> 
>
> Key: AIRAVATA-2615
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2615
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> TODO
>  * (/) Load the Experiment model data together with the Project data, input 
> and output DataProducts, ApplicationModule and ComputeResourceDescription 
> (what I'm calling a FullExperiment)
>  * (/) If the experiment isn't completed or failed, poll the experiment
>  * Display the job information
>  * (/) Redirect from experiment launch to experiment summary page
>  
>  



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[jira] [Comment Edited] (AIRAVATA-2143) Experiments with overridden resource allocation details tries to use qos and reservation from community user

[
https://issues.apache.org/jira/browse/AIRAVATA-2143?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16341508#comment-16341508
]

Eroma edited comment on AIRAVATA-2143 at 1/29/18 7:09 PM:
--

Tested in [https://dev.seagrid.org|https://dev.seagrid.org/]

was (Author: eroma_a):
Tested in [https://dev.seagrid.org|https://dev.seagrid.org/]

Test Cases
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu shared queue without qos or reservation. - PASS
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu compute queue with qos. -
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu compute queue with qos and reservation (Since the actual
reservation did not exists checked up to the reservation existence in the job
script). -
# Submit a job using individual preferences of individual account. Tested
using comet.sdsc.edu compute queue without qos or reservation. - PASS
# Submit a job using individual preferences of individual account. Tested
using comet.sdsc.edu shared queue with qos (Since actual qos did not exist for
the account tested up to the qos existence in job script). -
# Submit a job using gateway preferences of community account. Tested using
comet.sdsc.edu shared queue with qos and reservation (Since the actual qos and
reservation did not exists checked up to the reservation existence in the job
script). -
# Submit a SLURM job to a different SLURM cluster. Tested with Stamepde2. -
# Submit a PBS job to a PBS cluster using gateway preferences of community
account. Tested with BigRed2. -
# Submit a PBS job to a PBS cluster using individual preferences of
individual account. Tested with BigRed2. -
# User shares the experiment with Write access which was executed using
community allocation. Shared user clones and submits using same community
account.
# User shares the experiment with Write access which was

[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343834#comment-16343834
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164530073
 
 

 ##
 File path: 
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
 ##
 @@ -187,16 +182,18 @@ public boolean launchExperiment(String experimentId, 
String gatewayId) throws TE
} else {

log.error("Could not find a replica for the URI " + pi.getValue());
}
-   } catch 
(ReplicaCatalogException e) {
-   
log.error(e.getMessage(), e);
-   }
-   } else if 
(pi.getType().equals(DataType.URI_COLLECTION) && 
pi.getValue().contains("airavata-dp://")) {
+   } catch 
(RegistryServiceException e) {
+e.printStackTrace();
 
 Review comment:
   Please wrap these in RuntimeException


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343839#comment-16343839
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164528315
 
 

 ##
 File path: 
modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/StreamData.java
 ##
 @@ -88,13 +89,15 @@ public void run() {
 log.error("expId: {}, processId:{}, taskId: {}:- Couldn't stage 
file {} , Error occurred while connecting with credential store",
 taskContext.getExperimentId(), taskContext.getProcessId(), 
taskContext.getTaskId(),
 taskContext.getProcessOutput().getName());
+} catch (TException e) {
+e.printStackTrace();
 
 Review comment:
   Same as comment above.
   


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343836#comment-16343836
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164530378
 
 

 ##
 File path: 
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
 ##
 @@ -211,14 +208,16 @@ public boolean launchExperiment(String experimentId, 
String gatewayId) throws TE
}
}

pi.setValue(StringUtils.join(filePathList, ','));
-   } catch 
(ReplicaCatalogException e) {
-   
log.error(e.getMessage(), e);
-   }
-   }
+   } catch 
(RegistryServiceException e) {
+e.printStackTrace();
 
 Review comment:
   These too
   


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343832#comment-16343832
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164528055
 
 

 ##
 File path: 
modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/ForkJobSubmissionTask.java
 ##
 @@ -151,6 +142,8 @@ public TaskStatus execute(TaskContext taskContext) {
 errorModel.setActualErrorMessage(e.getMessage());
 errorModel.setUserFriendlyMessage(msg);
 
taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
+} catch (TException e) {
+e.printStackTrace();
 
 Review comment:
   I'd rather see this wrapped in a RuntimeException and re-thrown than 
swallowed here.


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343837#comment-16343837
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164529626
 
 

 ##
 File path: 
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/SimpleOrchestratorImpl.java
 ##
 @@ -189,10 +192,12 @@ public ValidationResults validateProcess(ExperimentModel 
experiment, ProcessMode
 ErrorModel details = new ErrorModel();
 details.setActualErrorMessage(errorMsg);
 
details.setCreationTime(Calendar.getInstance().getTimeInMillis());
-
orchestratorContext.getRegistry().getExperimentCatalog()
-.add(ExpCatChildDataType.PROCESS_ERROR, 
details, processModel.getProcessId());
-} catch (RegistryException e) {
+orchestratorContext.getRegistryClient()
+
.addErrors(OrchestratorConstants.PROCESS_ERROR, details, 
processModel.getProcessId());
+} catch (RegistryServiceException e) {
 logger.error("Error while saving error details to 
registry", e);
+} catch (TException e) {
+e.printStackTrace();
 
 Review comment:
   Same here.


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343833#comment-16343833
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164530931
 
 

 ##
 File path: 
modules/registry/registry-server/registry-api-stubs/src/main/java/org/apache/airavata/registry/api/exception/RegistryServiceException.java
 ##
 @@ -15,15 +15,15 @@
  * limitations under the License.
  */
 /**
- * Autogenerated by Thrift Compiler (0.10.0)
+ * Autogenerated by Thrift Compiler (0.11.0)
  *
  * DO NOT EDIT UNLESS YOU ARE SURE THAT YOU KNOW WHAT YOU ARE DOING
  *  @generated
  */
 package org.apache.airavata.registry.api.exception;
 
 @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked", "unused"})
-@javax.annotation.Generated(value = "Autogenerated by Thrift Compiler 
(0.10.0)")
+@javax.annotation.Generated(value = "Autogenerated by Thrift Compiler 
(0.11.0)")
 
 Review comment:
   We're still on version 0.10.0, right?


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343831#comment-16343831
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164528155
 
 

 ##
 File path: 
modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/LocalJobSubmissionTask.java
 ##
 @@ -136,6 +136,8 @@ public TaskStatus execute(TaskContext taskContext) {
 errorModel.setUserFriendlyMessage(msg);
 
taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
 taskStatus.setState(TaskState.FAILED);
+} catch (TException e) {
+e.printStackTrace();
 
 Review comment:
   Same as comment above.


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343838#comment-16343838
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164529556
 
 

 ##
 File path: 
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/SimpleOrchestratorImpl.java
 ##
 @@ -126,10 +127,12 @@ public ValidationResults 
validateExperiment(ExperimentModel experiment)
 ErrorModel details = new ErrorModel();
 details.setActualErrorMessage(errorMsg);
 
details.setCreationTime(Calendar.getInstance().getTimeInMillis());
-
orchestratorContext.getRegistry().getExperimentCatalog()
-.add(ExpCatChildDataType.EXPERIMENT_ERROR, 
details, experiment.getExperimentId());
-} catch (RegistryException e) {
+orchestratorContext.getRegistryClient()
+
.addErrors(OrchestratorConstants.EXPERIMENT_ERROR, details, 
experiment.getExperimentId());
+} catch (RegistryServiceException e) {
 logger.error("Error while saving error details to 
registry", e);
+} catch (TException e) {
+e.printStackTrace();
 
 Review comment:
   Please rethrow as a RuntimeException.


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2652) Remove registry-core dependency on orchestrator and gfac modules


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2652?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343835#comment-16343835
 ] 

ASF GitHub Bot commented on AIRAVATA-2652:
--

machristie commented on a change in pull request #164: [AIRAVATA-2652] Remove 
registry-core dependency on orchestrator and gfac modules 
URL: https://github.com/apache/airavata/pull/164#discussion_r164530563
 
 

 ##
 File path: 
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
 ##
 @@ -538,9 +521,8 @@ public void onMessage(MessageContext message) {

status.setState(ExperimentState.EXECUTING);

status.setReason("process  started");
}
-   } catch 
(RegistryException e) {
-   
status.setState(ExperimentState.EXECUTING);
-   
status.setReason("process  started");
+   } catch 
(ApplicationSettingsException e) {
+   
e.printStackTrace();
 
 Review comment:
   These too.


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> Remove registry-core dependency on orchestrator and gfac modules
> 
>
> Key: AIRAVATA-2652
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2652
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata Orchestrator, GFac, Registry API
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
> Fix For: 0.18
>
>
> Refactor orchestrator and gfac modules to use registry-api instead of the 
> existing registry-core dependency
>  * Some of the Experiment Catalog methods used by the orchestrator and gfac 
> are not present in the RegistryServerHandler. 
> ex: _experimentCatalog.add(ExpCatChildDataType.EXPERIMENT_ERROR, details, 
> experimentId);_
> Some new methods related to experiment (ERROR, TASK, PROCESS etc) need to be 
> created in the RegistryServerHandler.



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[jira] [Commented] (AIRAVATA-2143) Experiments with overridden resource allocation details tries to use qos and reservation from community user

2018-01-29 Thread Dimuthu Upeksha (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2143?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343809#comment-16343809
 ] 

Dimuthu Upeksha commented on AIRAVATA-2143:
---

Fixed in https://github.com/apache/airavata/pull/166

> Experiments with overridden resource allocation details tries to use qos and 
> reservation from  community user
> -
>
> Key: AIRAVATA-2143
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2143
> Project: Airavata
>  Issue Type: Bug
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> Experiments with overridden resource allocation details tries to use qos and 
> reservation from  community user.
> Remote resource login details sent at experiment creation is used to submit 
> jobs but refers to qos and reservation for the community allocation of the 
> remote resource.



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[jira] [Commented] (AIRAVATA-2601) Adding Groups to Applications


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2601?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343672#comment-16343672
 ] 

ASF GitHub Bot commented on AIRAVATA-2601:
--

tilaks26 closed pull request #146: [AIRAVATA-2601] Adding groups to Applications
URL: https://github.com/apache/airavata/pull/146
 
 
   

This is a PR merged from a forked repository.
As GitHub hides the original diff on merge, it is displayed below for
the sake of provenance:

As this is a foreign pull request (from a fork), the diff is supplied
below (as it won't show otherwise due to GitHub magic):



 


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> Adding Groups to Applications
> -
>
> Key: AIRAVATA-2601
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2601
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2601) Adding Groups to Applications

2018-01-29 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2601?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343664#comment-16343664
 ] 

ASF GitHub Bot commented on AIRAVATA-2601:
--

tilaks26 opened a new pull request #165: [AIRAVATA-2601] Adding groups to 
Applications
URL: https://github.com/apache/airavata/pull/165
 
 
   Filtering of Application Deployments by gateway ID and user name. We first 
get a list of Application Deployment IDs that are accessible by the current 
user and then retrieve the list of Application Deployments. (Similar to how we 
search for Experiments).
   
   Files changed:
   
   AiravataDataMigrator.java -> Included a new Entity Type names APPLICATION
   AiravataServerHandler.java -> Modified getAllApplicationDeployments(), 
getAllAppModules() methods to filter the accessible Application IDs using the 
user name, modified launchExperiment() to first check if the user has access to 
launch an Experiment in the Application Module
   registry-api.thrift -> Modified getAllApplicationDeployments(), 
getAllAppModules() methods' parameter list to include the accessible 
Application IDs
   RegistryService.java -> Regenerated the Thrift stubs which changed the 
Registry Service interface
   ApplicationDeployment.java -> Modified getAllApplicationDeployements() 
method to include accessible Application Deployment IDs
   ApplicationInterface.java -> Modified getAllAppModules() method to include 
accessible Application Module IDs
   RegistryServerHandler.java -> Modified getAllApplicationDeployments(), 
getAllAppModules() methods to reflect the changes in ApplicationDeployment.java 
and RegistryService.java files


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> Adding Groups to Applications
> -
>
> Key: AIRAVATA-2601
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2601
> Project: Airavata
>  Issue Type: Improvement
>  Components: Registry API
>Reporter: Sneha Tilak
>Assignee: Sneha Tilak
>Priority: Major
>




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[jira] [Commented] (AIRAVATA-2619) Refactoring App Catalog implementation


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2619?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16343591#comment-16343591
 ] 

ASF subversion and git services commented on AIRAVATA-2619:
---

Commit e4b0b2cfe93b17169efa9cdb1754172f7dd77c5e in airavata's branch 
refs/heads/registry-refactoring from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=e4b0b2c ]

Merge pull request #159 from sachinkariyattin/registry-refactoring

[AIRAVATA-2619] Refactoring App Catalog implementation - ComputeResource

> Refactoring App Catalog implementation
> --
>
> Key: AIRAVATA-2619
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2619
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Sachin Kariyattin
>Assignee: Sachin Kariyattin
>Priority: Major
>
> The app catalog module contains the following Impl classes.
> {quote}ApplicationDeploymentImpl
>  ApplicationInterfaceImpl
>  ComputeResourceImpl
>  GwyResourceProfileImpl
>  StorageResourceImpl
>  UsrResourceProfileImpl
> {quote}
> This task involves creating a repository class for app catalog and include 
> all the methods from the Impl classes mentioned above. As a modular approach 
> is being followed, to start of, only methods GwyResourceProfileImpl will be 
> considered. So the RegistryServiceHandler methods only with respect to 
> GwyResourceProfileImpl will be modified. Subsequently all methods related to 
> app catalog will be refactored.
> *Progress*:
>  * Implemeted GatewayResourceProfileRepository.
>  * Implemented ComputeResourceRepository.



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[jira] [Assigned] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma reassigned AIRAVATA-2625:
---

Assignee: Dimuthu Upeksha  (was: Suresh Marru)

> Derive and present Text outputs in Experiment summary
> -
>
> Key: AIRAVATA-2625
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2625
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata System
>Affects Versions: 0.18
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
>
> Currently the available application outputs are in the form of stdout, stderr 
> and URI (files). Going forward to have text (String, Integer, Float) outputs 
> directly in the experiment summary.
> These text outputs to be displayed as key+value pairs and when defining 
> should be defined a file to derive from, e.g. stdout
> At a given time from a single file one or many of these key+value pairs could 
> be derived. Also gateway admin can define multiple files to derive multiple 
> of these values.
> These would be displayed to user in experiment summary and in detailed 
> experiment summary in admin dashboard experiment statistics.
> These should also be displayed to any other gateway user it is shared with. 



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[jira] [Updated] (AIRAVATA-2615) Experiment view page


 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2615?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie updated AIRAVATA-2615:
--
Description: 
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * (/) If the experiment isn't completed or failed, poll the experiment
 * Display the job information
 * Redirect from experiment launch to experiment summary page

 

 

  was:
TODO
 * (/) Load the Experiment model data together with the Project data, input and 
output DataProducts, ApplicationModule and ComputeResourceDescription (what I'm 
calling a FullExperiment)
 * If the experiment isn't completed or failed, poll the experiment
 * Display the job information

 


> Experiment view page
> 
>
> Key: AIRAVATA-2615
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2615
> Project: Airavata
>  Issue Type: Sub-task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> TODO
>  * (/) Load the Experiment model data together with the Project data, input 
> and output DataProducts, ApplicationModule and ComputeResourceDescription 
> (what I'm calling a FullExperiment)
>  * (/) If the experiment isn't completed or failed, poll the experiment
>  * Display the job information
>  * Redirect from experiment launch to experiment summary page
>  
>  



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[jira] [Created] (AIRAVATA-2655) Group based authorization: a default "everyone" group

Marcus Christie created AIRAVATA-2655:
-

 Summary: Group based authorization: a default "everyone" group
 Key: AIRAVATA-2655
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2655
 Project: Airavata
  Issue Type: Bug
Reporter: Marcus Christie
Assignee: Marcus Christie


Investigate what it would take to have a default "everyone" group for each 
domain in the Sharing Registry.  Implement.



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[jira] [Resolved] (AIRAVATA-2624) Stampede2 cluster SSH connectivity issue