[jira] [Commented] (AIRAVATA-2360) Web-based user interface for Group Management

2017-04-04 Thread Ameya Advankar (JIRA)

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2360?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15955807#comment-15955807
 ] 

Ameya Advankar commented on AIRAVATA-2360:
--

Based on the suggestion in [this 
discussion|https://lists.apache.org/thread.html/2a0645d251e46855e0249185b18150e704a7b8a5f4821b9480323cd4@%3Cdev.airavata.apache.org%3E]
 in the Dev list, either React or Vue would be used for UI.

Also since it has to be plug-able in the PGA, the interfacing layer between UI 
and backend services will be in PHP. 
This PHP layer present in PGA would be responsible for exposing the 
sharing-registry thrift services as web services to be consumed by the UI.

The separate UI & PHP layer will facilitate ease of plugging the UI into other 
Gateways coded in other languages such as Django or Java.

> Web-based user interface for Group Management
> -
>
> Key: AIRAVATA-2360
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2360
> Project: Airavata
>  Issue Type: Task
>  Components: PGA PHP Web Gateway
>Reporter: Ameya Advankar
>Priority: Minor
>  Labels: features
>
> Design a Web-based UI for Group Management which would interface with the 
> APIs provided by the sharing catalog to create and manage groups in Airavata.
> The [Sharing catalog Thrift 
> services|https://github.com/apache/airavata/tree/develop/modules/sharing-registry]
>  are implemented at [sharing 
> catalog|https://gw54.iu.xsede.org/sharing-api-docs/], which could be used as 
> reference.



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[jira] [Created] (AIRAVATA-2360) Web-based user interface for Group Management

2017-04-04 Thread Ameya Advankar (JIRA)
Ameya Advankar created AIRAVATA-2360:


 Summary: Web-based user interface for Group Management
 Key: AIRAVATA-2360
 URL: https://issues.apache.org/jira/browse/AIRAVATA-2360
 Project: Airavata
  Issue Type: Task
  Components: PGA PHP Web Gateway
Reporter: Ameya Advankar
Priority: Minor



Design a Web-based UI for Group Management which would interface with the APIs 
provided by the sharing catalog to create and manage groups in Airavata.

The [Sharing catalog Thrift 
services|https://github.com/apache/airavata/tree/develop/modules/sharing-registry]
 are implemented at [sharing 
catalog|https://gw54.iu.xsede.org/sharing-api-docs/], which could be used as 
reference.



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[jira] [Commented] (AIRAVATA-2329) file staging seem to hang in dev.seagrid desktop client based job launch

2017-04-04 Thread Sudhakar Pamidighantam (JIRA)

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2329?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15955775#comment-15955775
 ] 

Sudhakar Pamidighantam commented on AIRAVATA-2329:
--

I tried sharing a new project and verified it works fine. This particular one 
has some problem... and should be removed from the registry.

> file staging seem to hang in dev.seagrid desktop client based job launch
> 
>
> Key: AIRAVATA-2329
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2329
> Project: Airavata
>  Issue Type: Bug
>Reporter: Sudhakar Pamidighantam
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.17
>
> Attachments: Screen Shot 2017-02-24 at 10.55.04 AM.png
>
>
>   testdev4_b44d936a-b4d0-44bf-a8d3-f405f873a9db is an example of a job 
> that seem to have launched but the file staging progress hangs.. Recent 
> Experiments has an entry, but the main experiments panel is not updated with 
> the new experiment.
> For this job id no response on multiple mouse clicks.
> When I multiple click on an older experiment id I get a exception dialog for 
> some jobs  with the error as follows.. Not sure if these are related 
> ProjectNotFoundException(message:Error while retrieving the project. More 
> info : User does not have permission to access this resource)
>   at 
> org.apache.airavata.api.Airavata$getProject_result$getProject_resultStandardScheme.read(Airavata.java)
>   at 
> org.apache.airavata.api.Airavata$getProject_result$getProject_resultStandardScheme.read(Airavata.java)
>   at 
> org.apache.airavata.api.Airavata$getProject_result.read(Airavata.java)
>   at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86)
>   at 
> org.apache.airavata.api.Airavata$Client.recv_getProject(Airavata.java:4295)
>   at 
> org.apache.airavata.api.Airavata$Client.getProject(Airavata.java:4281)
>   at 
> org.seagrid.desktop.connectors.airavata.AiravataManager.getProject(AiravataManager.java:181)
>   at 
> org.seagrid.desktop.ui.experiment.summary.controller.ExperimentSummaryController.initExperimentInfo(ExperimentSummaryController.java:226)
>   at 
> org.seagrid.desktop.ui.experiment.summary.controller.ExperimentSummaryController.initExperimentInfo(ExperimentSummaryController.java:293)
>   at 
> org.seagrid.desktop.ui.experiment.summary.ExperimentSummaryWindow.getExperimentInfoNode(ExperimentSummaryWindow.java:54)
>   at 
> org.seagrid.desktop.ui.home.controller.HomeController.lambda$null$23(HomeController.java:415)
>   at 
> com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
>   at 
> com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
>   at 
> com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
>   at 
> com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at 
> com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
>   at 
> com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
>   at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
>   at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
>   at javafx.event.Event.fireEvent(Event.java:198)
>   at javafx.scene.Scene$ClickGenerator.postProcess(Scene.java:3470)
>   at javafx.scene.Scene$ClickGenerator.access$8100(Scene.java:3398)
>   at javafx.scene.Scene$MouseHandler.process(Scene.java:3766)
>   at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
>   at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
>   

[jira] [Closed] (AIRAVATA-2353) When a defined job output is not generated and not existing exception thrown when user tries to view it

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2353?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma closed AIRAVATA-2353.
---

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

any output file which is configured in application interface, but not generated 
in a job will not be listed as available outputs in experiment summary for the 
users. File which get generated and available will only be available.

> When a defined job output is not generated and not existing exception thrown 
> when user tries to view it
> ---
>
> Key: AIRAVATA-2353
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2353
> Project: Airavata
>  Issue Type: Bug
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: http://149.165.156.11/ (all airavata environments have 
> this issue)
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.17
>
>
> Gateway admins can define application outputs expected in application 
> interface configuration of the gateway.
> If one of those defined outputs are not generated, they will not be available 
> in the user data for user to download. But since it is defined it will appear 
> in experiment summary with a fake link. When clicked getting a 
> FileNotFoundException.
> Ideally if a defined file is not generated/ existing in the data directory 
> that should not appear in the summary.



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[jira] [Resolved] (AIRAVATA-2353) When a defined job output is not generated and not existing exception thrown when user tries to view it

2017-04-04 Thread Supun Chathuranga Nakandala (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2353?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Supun Chathuranga Nakandala resolved AIRAVATA-2353.
---
Resolution: Fixed

> When a defined job output is not generated and not existing exception thrown 
> when user tries to view it
> ---
>
> Key: AIRAVATA-2353
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2353
> Project: Airavata
>  Issue Type: Bug
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: http://149.165.156.11/ (all airavata environments have 
> this issue)
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.17
>
>
> Gateway admins can define application outputs expected in application 
> interface configuration of the gateway.
> If one of those defined outputs are not generated, they will not be available 
> in the user data for user to download. But since it is defined it will appear 
> in experiment summary with a fake link. When clicked getting a 
> FileNotFoundException.
> Ideally if a defined file is not generated/ existing in the data directory 
> that should not appear in the summary.



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[jira] [Updated] (AIRAVATA-2259) When a credential key is deleted while being assigned it is not updated in Compute Resource Preference properly

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2259?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2259:

Fix Version/s: (was: 0.17)
   0.18

> When a credential key is deleted while being assigned it is not updated in 
> Compute Resource Preference properly
> ---
>
> Key: AIRAVATA-2259
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2259
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata System, PGA PHP Web Gateway
> Environment: dev.seagrid.org
>Reporter: Eroma
>Assignee: Anuj Bhandar
> Fix For: 0.18
>
>
> Steps followed
> 1. Generate a key specially for Comet
> 2. Add the key in User settings for Comet
> 3. Delete the above key from credential store 
> 4. Then in UI it shows automatically the default key was assigned to the 
> Comet in Compute resource
> 4. But in the back end the token is not updated.
> 5. So when an experiment is launched it tries the token in the preference but 
> its not there in CREDENTIALS for that user
> When a key is deleted it should be properly removed from COMPUTE RESOURCE 
> PREFERENCES



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[jira] [Updated] (AIRAVATA-2310) Storage resource does not work with gateway profile level credential store token

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2310?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2310:

Fix Version/s: (was: 0.17)
   0.18

> Storage resource does not work with gateway profile level credential store 
> token
> 
>
> Key: AIRAVATA-2310
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2310
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac, PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: https://dev.seagrid.org
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.18
>
>
> Storage resource does not work with gateway profile level credential store 
> token.
> Currently when the generated token is set at gateway level compute resources 
> work using the token for ssh submissions (if individual tokens are not set at 
> resource level).
> But storage resources are only working at individual resource level. If the 
> token is not set at resource level ssh submissions fails. The gateway level 
> set token is not taken into consideration.



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[jira] [Updated] (AIRAVATA-2337) Organize Django source code in repositories

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2337?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2337:

Issue Type: New Feature  (was: Bug)

> Organize Django source code in repositories
> ---
>
> Key: AIRAVATA-2337
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2337
> Project: Airavata
>  Issue Type: New Feature
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> A Django project is made up of many different Django apps.  How best to 
> organize this in source control?
> My initial thought is to have a repo per app as well as a repo for kind of a 
> template Django PGA making use of those apps.  This way the template repo can 
> be cloned and customized as needed for particular Django PGA instances, like 
> the GeoGateway.



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[jira] [Updated] (AIRAVATA-2338) Event-driven database replication for Apache Airavata

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2338?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2338:

Fix Version/s: 0.18

> Event-driven database replication for Apache Airavata
> -
>
> Key: AIRAVATA-2338
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2338
> Project: Airavata
>  Issue Type: Task
>  Components: Application Catalog, Registry API
>Reporter: Gourav Shenoy
>Assignee: Gourav Shenoy
>  Labels: newbie
> Fix For: 0.18
>
>
> Implement an event-driven database replication for Apache Airavata. The 
> motivation is the fact that the current registry module (micro-service) is 
> being refactored and broken down to multiple independent micro-services, 
> which includes:
> - profile-service (consisting of user, tenant and group profiles)
> - sharing-registry
> We have decided to try using different databases per micro-service, which 
> results in the need for replication of certain information across databases, 
> such as user-profile or tenant-profile. An efficient way to perform this 
> replication is to use an event-driven approach, which sync's contents of 
> database via messaging events.



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[jira] [Updated] (AIRAVATA-2352) Orchestrator sometimes stops processing messages from experiment_launch queue

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2352?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2352:

Fix Version/s: 0.18

> Orchestrator sometimes stops processing messages from experiment_launch queue
> -
>
> Key: AIRAVATA-2352
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2352
> Project: Airavata
>  Issue Type: Bug
>Affects Versions: 0.17
>Reporter: Marcus Christie
>Priority: Critical
> Fix For: 0.18
>
>
> This was observed on 3/29 9am for gw153.iu.xsede.org.
> *Workaround*: restart the api-orch server. Once that is done the orchestrator 
> starts picking up events from experiment_launch again.
> I'm not seeing anything in the logs to indicate why the orchestrator stopped 
> processing experiment_launch events.



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[jira] [Updated] (AIRAVATA-2340) [GSoC] Airavata requires a data management module in order to handle all the gateway data requirements. Since airavata is a multi tenanted platform multiple gateways a

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2340?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2340:

Fix Version/s: WISHLIST

> [GSoC] Airavata requires a data management module in order to handle all the 
> gateway data requirements. Since airavata is a multi tenanted platform 
> multiple gateways are linked.
> -
>
> Key: AIRAVATA-2340
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2340
> Project: Airavata
>  Issue Type: Epic
>Reporter: Eroma
>  Labels: GSoC2017
> Fix For: WISHLIST
>
>
> In data management airavata need to look at all the data related requirements 
> currently in place with all the gateway linked to the multi tenanted airavata 
> as a platform service.
> From the simplest level data management should cater for all the data 
> requirements for users to execute their cluster jobs and also manage all the 
> outputs generated with the executions. Users need to have methods to access, 
> share , download the data files.
> Users should be able to upload, download data files to the gateway, Use 3rd 
> party applications to manage data files and link with gateway when required. 
> users should be able to timely clean the storage by removing outdated and 
> non-required data files. 
> Sharing is another capability which would benefit science community. Airavata 
> currently provides sharing capability and downloading of data files which are 
> uploaded into the gateway. Going forward users should be able to share a data 
> file path with other users and user groups would would want to access the 
> data files.



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[jira] [Updated] (AIRAVATA-2356) Cloud Provision of Keycloak

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2356?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2356:

Fix Version/s: 0.18

> Cloud Provision of Keycloak
> ---
>
> Key: AIRAVATA-2356
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2356
> Project: Airavata
>  Issue Type: Sub-task
>  Components: Security
>Reporter: Anuj Bhandar
>Assignee: Anuj Bhandar
> Fix For: 0.18
>
>
> Production grade deployment of Keycloak on jetstream



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[jira] [Updated] (AIRAVATA-2355) production deployment and migration from Wso2IS to Keycloak

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2355?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2355:

Fix Version/s: 0.18

> production deployment and migration from Wso2IS to Keycloak
> ---
>
> Key: AIRAVATA-2355
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2355
> Project: Airavata
>  Issue Type: Epic
>  Components: Security
>Affects Versions: 0.18
>Reporter: Anuj Bhandar
>Assignee: Anuj Bhandar
> Fix For: 0.18
>
>
> As the demo exhibiting Keycloak's integration with Cilogon was a hit, this 
> Epic will track the progress of production deployment of Keycloak and 
> migration from Wso2IS to Keycloak



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[jira] [Updated] (AIRAVATA-2318) Saving Checkpoint files

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2318?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2318:

Fix Version/s: 0.18

> Saving Checkpoint files
> ---
>
> Key: AIRAVATA-2318
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2318
> Project: Airavata
>  Issue Type: New Feature
>Reporter: Sudhakar Pamidighantam
>Assignee: Suresh Marru
> Fix For: 0.18
>
>
> SEAGrid gateway users need checkpoint files for post processing. We need to 
> save these to storage for easy recovery for the users. The current archiving 
> can be used to accomplish this but needs modifications. The archive must 
> exclude saving intermediate (scratch files) files and extract the checkpoint 
> files on the storage device from the archive. 
> Intermediate files are application dependent and should be definable in an 
> extensible fashion by the gateway admin for this purpose.



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[jira] [Updated] (AIRAVATA-2330) Application input parsers for requirement gathering

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2330?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2330:

Fix Version/s: 0.18

> Application input parsers for requirement gathering
> ---
>
> Key: AIRAVATA-2330
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2330
> Project: Airavata
>  Issue Type: Story
>Reporter: Sudhakar Pamidighantam
> Fix For: 0.18
>
>
> Several application input files contain requirements that need to translated 
> to batch scripts such as nodes/cpus/gpus, memory and additional inputs from 
> local at the HPC, local at the users end or a third party storage. 
>  
> Implement configuring node, CPU and core requirements based on applications 
> and resources.
> Currently we can define default values for node and CPU counts. Core number 
> is not taken into consideration. So far based on application and resource the 
> default numbers need to change, If not the execution fails.
> This requires an input parsing system as soon as an input is defined/uploaded 
> at the user interface and parse and populate the fields downstream. The 
> infrastructure should be intelligent enough to determine which application 
> the input refers to if the user interface starts with the input instead of 
> specification of  the application. 
> These parsed values can be used for validation as well as for setting 
> additional requirements such as runtime to be requested. 



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[jira] [Updated] (AIRAVATA-2313) Support third party input file staging

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2313?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2313:

Fix Version/s: 0.18

> Support third party input file staging 
> ---
>
> Key: AIRAVATA-2313
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2313
> Project: Airavata
>  Issue Type: Bug
>Reporter: Sudhakar Pamidighantam
> Fix For: 0.18
>
>
> We should support input file staging for files that are locally available on 
> the host, or from a third party location accessible through http or ftp URLs. 
> Currently the PGA only allows this through a file chooser but the file 
> chooser does not allow specification of such URLs.  On a Mac ⇧⌘G provides a 
> way to go to a finder window where you can type a path but this is not 
> sufficient.



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[jira] [Updated] (AIRAVATA-2354) Deleted user account settings and when tried to launch the experiment it remains in CREATED. No failing or any error

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2354?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2354:

Fix Version/s: (was: 0.17)
   0.18

> Deleted user account settings and when tried to launch the experiment it 
> remains in CREATED. No failing or any error
> 
>
> Key: AIRAVATA-2354
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2354
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata Orchestrator, PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: http://149.165.156.11/
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> Steps taken
> 1. add individual user account settings for a compute resource. 
> 2. Create and save an experiment to use the individual user account
> 3. Delete the user account setting for the above resource
> 4. Launch the experiment.
> 5. Experiment stays in CREATED, no errors, no failures in PGA
> 6. In airavata log there are errors [1]
> 7. These should be reflected in PGA OR automatically the job should use 
> community account if the user setting gets deleted prior to job launch.
> [1]
> 2017-03-29 19:35:09 [pool-15-thread-3] ERROR 
> o.a.a.o.s.OrchestratorServerHandler - Experiment launch failed due to Thrift 
> conversion error, experimentId: 
> Clone_of_Clone_of_Lammps_Stam1_7f3040a4-36d5-4498-a7b3-c29181ba836f, 
> gatewayId: seagrid
> org.apache.thrift.TException: Experiment 
> 'Clone_of_Clone_of_Lammps_Stam1_7f3040a4-36d5-4498-a7b3-c29181ba836f' launch 
> failed. Unable to figureout execution type for application 
> Lammps_1284f9d9-d039-47ec-a885-6792caa26510
> at 
> org.apache.airavata.orchestrator.server.OrchestratorServerHandler.launchExperiment(OrchestratorServerHandler.java:253)
> at 
> org.apache.airavata.orchestrator.server.OrchestratorServerHandler.launchExperiment(OrchestratorServerHandler.java:668)
> at 
> org.apache.airavata.orchestrator.server.OrchestratorServerHandler.access$500(OrchestratorServerHandler.java:78)
> at 
> org.apache.airavata.orchestrator.server.OrchestratorServerHandler$ExperimentHandler.onMessage(OrchestratorServerHandler.java:624)
> at 
> org.apache.airavata.messaging.core.impl.ExperimentConsumer.handleDelivery(ExperimentConsumer.java:85)
> at 
> com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
> at 
> com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
> 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.orchestrator.core.exception.OrchestratorException: Error 
> during creating process
> at 
> org.apache.airavata.orchestrator.cpi.impl.SimpleOrchestratorImpl.createAndSaveTasks(SimpleOrchestratorImpl.java:336)
> at 
> org.apache.airavata.orchestrator.server.OrchestratorServerHandler.launchExperiment(OrchestratorServerHandler.java:221)
> ... 9 common frames omitted
> Caused by: java.lang.NullPointerException: null
> at 
> org.apache.airavata.orchestrator.core.utils.OrchestratorUtils.getScratchLocation(OrchestratorUtils.java:213)
> at 
> org.apache.airavata.orchestrator.cpi.impl.SimpleOrchestratorImpl.createAndSaveEnvSetupTask(SimpleOrchestratorImpl.java:365)
> at 
> org.apache.airavata.orchestrator.cpi.impl.SimpleOrchestratorImpl.createAndSaveTasks(SimpleOrchestratorImpl.java:301)
> ... 10 common frames omitted



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[jira] [Assigned] (AIRAVATA-2019) Managing user profile within PGA

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2019?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma reassigned AIRAVATA-2019:
---

Assignee: Marcus Christie

> Managing user profile within PGA
> 
>
> Key: AIRAVATA-2019
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2019
> Project: Airavata
>  Issue Type: Sub-task
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> PGA should provide its users an interface to manage their user profile.
> In this interface users should be able to change all details provided at 
> account creation except username.
> 1. Changing address
> 2. Password rest
> 3. Changing contact details
> 4. Changing email address
> 5. View user roles assigned
> 6. Upload user image



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[jira] [Assigned] (AIRAVATA-2017) Easy monitoring of new users in gateway admin dashboard

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2017?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma reassigned AIRAVATA-2017:
---

Assignee: Marcus Christie

> Easy monitoring of new users in gateway admin dashboard
> ---
>
> Key: AIRAVATA-2017
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2017
> Project: Airavata
>  Issue Type: Sub-task
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> Currently only way to view activation pending users is to search by
> 1. Individual username
> 2. user-pending role
> If there are number of users to be activated finding users in the list is 
> difficult and somewhat time consuming.
> With above we should also have
> 1. Search by account creation date
> 2. Search by first name, last name



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[jira] [Updated] (AIRAVATA-2017) Easy monitoring of new users in gateway admin dashboard

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2017?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2017:

Fix Version/s: 0.18

> Easy monitoring of new users in gateway admin dashboard
> ---
>
> Key: AIRAVATA-2017
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2017
> Project: Airavata
>  Issue Type: Sub-task
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
> Fix For: 0.18
>
>
> Currently only way to view activation pending users is to search by
> 1. Individual username
> 2. user-pending role
> If there are number of users to be activated finding users in the list is 
> difficult and somewhat time consuming.
> With above we should also have
> 1. Search by account creation date
> 2. Search by first name, last name



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[jira] [Updated] (AIRAVATA-2035) Ability categorize user accounts in the gateway

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2035?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2035:

Fix Version/s: 0.18

> Ability categorize user accounts in the gateway
> ---
>
> Key: AIRAVATA-2035
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2035
> Project: Airavata
>  Issue Type: Sub-task
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
> Fix For: 0.18
>
>
> Currently there is no categorization or grouping of user accounts in the 
> gateway. Going forward
> 1. provide data sharing among group of users
> 2. to tag test accounts as 'test accounts' 
> 3. To give access to specific applications, resources fro a group
> this should be useful.



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[jira] [Updated] (AIRAVATA-2018) Better gateway user experience in managing user profiles and their roles

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2018?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma updated AIRAVATA-2018:

Fix Version/s: 0.18

> Better gateway user experience in managing user profiles and their roles
> 
>
> Key: AIRAVATA-2018
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2018
> Project: Airavata
>  Issue Type: Story
>  Components: PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
> Fix For: 0.18
>
>
> Currently in Airavata reference gateway user accounts are created by the end 
> user it self and afterwards the gateway admins need to provide necessary 
> access to the gateway.
> Once the access provided only the enduser could start using the gateway.
> We currently have few areas to improve in terms of updating user profiles, 
> giving necessary access, etc...



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[jira] [Closed] (AIRAVATA-2339) Default ssh key use for individual user accounts failing. Cannot ssh to compute resource

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2339?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma closed AIRAVATA-2339.
---

tested and verified in 
http://149.165.156.11/ (seagrid PGA in JS)
submitted bigred2 jobs with user account using default key and also with a key 
generated by the user.
Both cases passed.
While having user account set in the gateway also tried submitting jobs with 
the community account by unchecking the checkbox, that also successfully 
launched. 

> Default ssh key use for individual user accounts failing. Cannot ssh to 
> compute resource
> 
>
> Key: AIRAVATA-2339
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2339
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac, PGA PHP Web Gateway
>Affects Versions: 0.17
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.17
>
>
> For individual user settings we can assign the default generated key.
> When it is assigned USER_RESOURCE_PROFILE table gets updated with the 
> relevant token.
> When tried to use it to ssh it is failing.
> But if a new key is generated and assigned then ssh to resource work. When a 
> new key is generated it get saved in to USER_COMPUTE_RESOURCE_PREFERENCE.



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[jira] [Closed] (AIRAVATA-1880) In Application Interface ability to make inputs unchangeable by the end user.

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-1880?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma closed AIRAVATA-1880.
---

tested and verified in PGA (http://149.165.156.11/) in JS
Can set read only flag to true or false in application interface.

When this flag is set for URI, no difference at the experiment create, edit and 
clone. 
When this is set to true for String, Integer or float user cannot change the 
value given by the gateway admin at creation, edit or clone of an experiment

> In Application Interface ability to make inputs unchangeable by the end user.
> -
>
> Key: AIRAVATA-1880
> URL: https://issues.apache.org/jira/browse/AIRAVATA-1880
> Project: Airavata
>  Issue Type: Improvement
>  Components: Airavata System
>Reporter: Eroma
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.17
>
>
> Currently all the interface inputs we add (String and it could be integer, 
> float, etc...) can be changed at Create Experiment by the user.
> There are some string inputs which we don't want to be changed; It would be 
> useful and less room for errors if we could make these types of inputs either 
> unchangeable or if we don't want user to change we can hide them from Create 
> Experiment



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[jira] [Resolved] (AIRAVATA-2063) When QOS added in one gateway (seagrid) it is also taken as the qos of the other gateway (testdrive) linked with airavata

2017-04-04 Thread Eroma (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2063?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Eroma resolved AIRAVATA-2063.
-
Resolution: Fixed

> When QOS added in one gateway (seagrid) it is also taken as the qos of the 
> other gateway (testdrive) linked with airavata
> -
>
> Key: AIRAVATA-2063
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2063
> Project: Airavata
>  Issue Type: Bug
>  Components: Airavata System, PGA PHP Web Gateway
> Environment: dev.seagrid.org
> dev.testdrive.org
>Reporter: Eroma
>Assignee: Shameera Rathnayaka
> Fix For: 0.17
>
>
> Ideally the qos assigned in seagrid gateway comet queues should not be 
> considered by testdrive gateway. qos is gateway specific, resource specific 
> and queue specific.



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[jira] [Commented] (AIRAVATA-2335) Deploy 0.17-SNAPSHOT on Jetstream for testing

2017-04-04 Thread ASF subversion and git services (JIRA)

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2335?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15955542#comment-15955542
 ] 

ASF subversion and git services commented on AIRAVATA-2335:
---

Commit 382e3cb482e78dd319bc1474b999c4de8b64801c in airavata's branch 
refs/heads/master from [~marcuschristie]
[ https://git-wip-us.apache.org/repos/asf?p=airavata.git;h=382e3cb ]

AIRAVATA-2335 Putting real gateway datastore id in testdrive config


> Deploy 0.17-SNAPSHOT on Jetstream for testing
> -
>
> Key: AIRAVATA-2335
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2335
> Project: Airavata
>  Issue Type: Task
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> Use Ansible to deploy Airavata version 0.17-SNAPSHOT for testing before 0.17 
> is released.
> Notes:
> * Airavata is deployed on 149.165.168.5
> * Seagrid PGA is deployed on http://149.165.156.11/
> * Scigap PGA is deployed on http://149.165.156.52/
> * Testdrive PGA is deployed on http://149.165.156.148/
> * DB is deployed on 149.165.172.163



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[GitHub] airavata pull request #93: Adding SQL delta scripts for 0.16-0.17 release mi...

2017-04-04 Thread anujbhan
Github user anujbhan closed the pull request at:

https://github.com/apache/airavata/pull/93


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[jira] [Resolved] (AIRAVATA-2357) dev.seagrid on firefox 52.0.1(64 bit) on Mac does not allow sharing during create project

2017-04-04 Thread Marcus Christie (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2357?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie resolved AIRAVATA-2357.
---
Resolution: Won't Fix

Marking as Won't Fix since this was caused by a Firefox add-on.  I documented 
the workaround.

> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project
> --
>
> Key: AIRAVATA-2357
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2357
> Project: Airavata
>  Issue Type: Bug
>Reporter: Sudhakar Pamidighantam
>Assignee: Marcus Christie
>
> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project
> h3. Workaround
> Configure ad blocker to make exemption for gateway site



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[jira] [Updated] (AIRAVATA-2357) dev.seagrid on firefox 52.0.1(64 bit) on Mac does not allow sharing during create project

2017-04-04 Thread Marcus Christie (JIRA)

 [ 
https://issues.apache.org/jira/browse/AIRAVATA-2357?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marcus Christie updated AIRAVATA-2357:
--
Description: 
dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
create project

h3. Workaround

Configure ad blocker to make exemption for gateway site

  was:dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing 
during create project


> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project
> --
>
> Key: AIRAVATA-2357
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2357
> Project: Airavata
>  Issue Type: Bug
>Reporter: Sudhakar Pamidighantam
>Assignee: Marcus Christie
>
> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project
> h3. Workaround
> Configure ad blocker to make exemption for gateway site



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[jira] [Commented] (AIRAVATA-2357) dev.seagrid on firefox 52.0.1(64 bit) on Mac does not allow sharing during create project

2017-04-04 Thread Marcus Christie (JIRA)

[ 
https://issues.apache.org/jira/browse/AIRAVATA-2357?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15955266#comment-15955266
 ] 

Marcus Christie commented on AIRAVATA-2357:
---

I looked at this with [~spamidig]. The problem was with the Ad Block Plus 
Firefox add-on.  It was preventing the sharing modal dialog from displaying for 
some reason.

The fix we came up with was to tell Ad Block Plus to stop blocking 
dev.seagrid.org.

> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project
> --
>
> Key: AIRAVATA-2357
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2357
> Project: Airavata
>  Issue Type: Bug
>Reporter: Sudhakar Pamidighantam
>Assignee: Marcus Christie
>
> dev.seagrid on firefox 52.0.1(64 bit) on Mac  does not allow sharing during 
> create project



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[GitHub] airavata pull request #104: Temporary fix for mysql-selinux issue

2017-04-04 Thread ECoulter
GitHub user ECoulter opened a pull request:

https://github.com/apache/airavata/pull/104

Temporary fix for mysql-selinux issue

Tmp fix for this issue: https://jira.mariadb.org/browse/MDEV-12231

Adds selinux policy module to allow mysql to set uid/gid. Also
checks for .pp file which should be incuded in future releases
of MariaDB.


You can merge this pull request into a Git repository by running:

$ git pull https://github.com/ECoulter/airavata mysql-selinux-fix

Alternatively you can review and apply these changes as the patch at:

https://github.com/apache/airavata/pull/104.patch

To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:

This closes #104






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[GitHub] airavata pull request #103: Mysql temporary fix in database role

2017-04-04 Thread ECoulter
Github user ECoulter closed the pull request at:

https://github.com/apache/airavata/pull/103


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[GitHub] airavata pull request #103: Mysql temporary fix in database role

2017-04-04 Thread ECoulter
GitHub user ECoulter opened a pull request:

https://github.com/apache/airavata/pull/103

Mysql temporary fix in database role

Fix for the mysql-selinux issue here:
https://jira.mariadb.org/browse/MDEV-12231

This fix includes a check for the update promised by MariaDB packagers. 

You can merge this pull request into a Git repository by running:

$ git pull https://github.com/ECoulter/airavata mysql-tmp-fix

Alternatively you can review and apply these changes as the patch at:

https://github.com/apache/airavata/pull/103.patch

To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:

This closes #103


commit 42fcc66344cdec235d4204450e00ae81940dc6b4
Author: jecoulte 
Date:   2017-03-30T20:55:41Z

added inventory dir for jetstream

commit 97cbbd8608427a11b5155da3be7a425c1099a891
Author: jecoulte 
Date:   2017-03-30T20:56:22Z

become:yes instead of become_user_root

commit 1c44f53e48280b551578a2e33b5926e48191c337
Author: jecoulte 
Date:   2017-03-30T20:57:03Z

spellcheck and become:yes instead of become_user

commit 6729b9617abea0e505c8673d95b482e63d53fc12
Author: jecoulte 
Date:   2017-03-30T20:59:27Z

become:yes instead of become_user:root

commit be1aebb2129eb54acbed9bb1751e72ec2c5e0b65
Author: jecoulte 
Date:   2017-03-30T21:01:54Z

spellcheck and become:yes instead of become_user

commit d6380a98aaca023aa0afeb5b9615d89852d729ac
Author: jecoulte 
Date:   2017-03-30T21:02:25Z

spellcheck

commit 71e993a741b3a030884044738103f2a22311bcb1
Author: jecoulte 
Date:   2017-03-30T21:06:06Z

Added playbooks for building stack in Jetstream

See playbooks ending in _js.yml - all_vms creates openstack
vms, all_deploy deploys the airavata stack on those vms,
and build_all_js calls both of those, using the
inventory/jetstream/openstack.py

commit 7956048e2bb980f0ddbdbf4a6e1f09b960827062
Author: jecoulte 
Date:   2017-03-30T21:20:31Z

copied group_vars over into js inventory

commit 9edbac79b0847cf7b16793efff38c9dff921d879
Author: jecoulte 
Date:   2017-03-31T13:47:43Z

added missing vars to jetstream group_vars

commit a0ee02793915e494e9bde5bf54d67e8a97d1ac30
Author: jecoulte 
Date:   2017-03-31T14:16:10Z

Added steps for Jetstream Deployment to README

commit e1503f4857fcf5907d3af57e774eed13d92ae347
Author: jecoulte 
Date:   2017-03-31T16:15:55Z

added var for Jetstream ssh key

commit c69ce937c445e5c0e530be610ebadf980d776cf0
Author: jecoulte 
Date:   2017-03-31T16:16:05Z

added task for Jetstream ssh key

commit ffcc1469fbaef157f54eac172d4946dcb1b11eeb
Author: jecoulte 
Date:   2017-03-31T16:17:29Z

added directions for cfg files

commit d334cedf005ab2e1772d6fcd45c5ae48a689adfb
Author: jecoulte 
Date:   2017-03-31T16:27:00Z

defined inventory for local VM deploy

commit b4f8b8c98c4829041f14741417a0646dba66c3f2
Author: jecoulte 
Date:   2017-03-31T16:40:54Z

Changed inventory name, added README, hosts

README to explain how to build VirtualBox vms, and edited
host file based on that assumption.

commit b427abb1c26c9524781a9568a3d98c4a97850f38
Author: jecoulte 
Date:   2017-03-31T16:42:00Z

playbook for deployment based on VirtualBox VMs

commit 33aa11c18393e72e53a0cbcde929c7cd7c48de9a
Author: jecoulte 
Date:   2017-03-31T16:42:27Z

Added VBox info, removed bad JS advice

commit 1a21da3062ceacf995c918fe047a06a2045330ea
Author: jecoulte 
Date:   2017-03-31T16:42:41Z

removed non-working JS playbook

commit 67bf972bf09bbc660dd0841053b1fdf9dbcf0898
Author: jecoulte 
Date:   2017-03-31T16:45:01Z

Fixed header

commit 81db8ffa65f5a650d71d40ebc974bdf0742df2a7
Author: jecoulte 
Date:   2017-04-03T17:18:29Z

combined registry w/ api-orch, removed wso2 from site playbooks

commit 0fac2d662a0dad02167bea3a729a68ec9f98ba05
Author: jecoulte 
Date:   2017-04-03T21:52:16Z

Temporary fix for mysql-selinux issue

Tmp fix for this issue: https://jira.mariadb.org/browse/MDEV-12231
Adds selinux policy module to allow mysql to set uid/gid. Also
checks for .pp file which should be incuded in future releases
of MariaDB.




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