Task #4217

Project WP #629: WP4 - VREs Deployment and Operation [Months: 1-30]

Project Task #631: T4.2 VREs Creation and Deployment [Months: 1-30]

Tuna Atlas VRE: extensions to support

Added by Julien Barde over 3 years ago. Updated about 3 years ago.

Status:ClosedStart date:Jun 09, 2016
Priority:NormalDue date:
Assignee:Massimiliano Assante% Done:

100%

Category:Default
Sprint:WP05
Infrastructure:
Milestones:
Duration:

Description

As already done for the StockAssesment VRE (#2111), we would like to add new services in the upper menu of the Tuna Atlas VRE:
- Statistical Manager with the following name " Data and Processing Services "
- Rstudio with the same name

Once set up, in the left menu of the statistical manager, we would like to get 4 categories in which algoritms will be grouped:
- "Transform and load Tuna Atlas data"
- "Access Tuna Atlas data"
- "Process Tuna Atlas data"
- "Automated report"

Once the categories are set sup we will write a new ticket to indicate which algorithms in the development environment we would like to get of each category. As an example, the "Tuna_Atlas_Data_Access_Form_1" algorithm (in the devVRE for now) should be made available in the "Access Tuna Atlas data" category of the left menu.

Last point, the Sardara database hosted in the infrastructure (#1899) should be available within this VRE as well.

Let me know if you need some clarifications, thanks for your help.


Related issues

Related to D4Science Infrastructure - Task #4416: Enable Statistical Manager service and algorithms on gCub... Closed Jun 23, 2016 Jun 24, 2016
Related to D4Science Infrastructure - Task #4417: Add Sardara database service endpoint to gCubeApps/FAO_Tu... Closed Jun 23, 2016 Jun 24, 2016
Related to D4Science Infrastructure - Task #4418: Add RConnector service to gCubeApps/FAO_TunaAtlas Closed Jun 23, 2016 Jun 24, 2016
Related to D4Science Infrastructure - Task #4446: Add DBManager-portlet to gCubeApps/FAO_TunaAtlas Closed Jun 24, 2016

History

#1 Updated by Pasquale Pagano over 3 years ago

  • Category set to Default
  • Tracker changed from Support to Task

@massimiliano.assante@isti.cnr.it could you report an update on this activity?

#2 Updated by Massimiliano Assante over 3 years ago

  • Related to Task #4416: Enable Statistical Manager service and algorithms on gCubeApps/FAO_TunaAtlas added

#3 Updated by Massimiliano Assante over 3 years ago

  • Related to Task #4417: Add Sardara database service endpoint to gCubeApps/FAO_TunaAtlas added

#4 Updated by Massimiliano Assante over 3 years ago

  • Related to Task #4418: Add RConnector service to gCubeApps/FAO_TunaAtlas added

#5 Updated by Massimiliano Assante over 3 years ago

Tickets #4416, #4417 and #4418 have been opened to perform the necessary actions in the underlying infrastructure to support this request. As soon as they will be complete we can perform this change in the VRE pages.

#6 Updated by Massimiliano Assante over 3 years ago

  • Status changed from New to In Progress

#7 Updated by Massimiliano Assante over 3 years ago

  • Description updated (diff)

#8 Updated by Gianpaolo Coro over 3 years ago

Currently we are far away from having the Tuna Atlas algorithms available on StatMan, as far as I know.

We are still working on the integration of the VPA Workflow for the Stock Assessment VRE.

The Sardara DB can be made available in the scope, but is this meant to be available to the StatMan algorithm only? Why don't we deploy the DB manager portlet in the Tuna Atlas VRE so that every user can browse the content of the DB in a read-only mode?

#9 Updated by Julien Barde over 3 years ago

I think your suggestion is related to a recent question of Paul who wanted to get an application like "pgadmin" to browse the content of the database. So this is a good idea as we didn't know it was possible.
We will be able to deplot Tuna Atlas algorithms soon. However ICCAT BFT algorithms will not be part of Tuna Atlas VRE for now, they will stay in the StockAssessment VRE.
Thanks

#10 Updated by Julien Barde over 3 years ago

Can we access a VRE where this DB manager portlet has been deployed ?

#11 Updated by Roberto Cirillo over 3 years ago

  • Related to Task #4446: Add DBManager-portlet to gCubeApps/FAO_TunaAtlas added

#12 Updated by Massimiliano Assante over 3 years ago

  • % Done changed from 0 to 100
  • Status changed from In Progress to Feedback

RStudio, DB Mananager and Statman portlets are available un Tuna Atlas VRE, please note that the Staman Page is called Data and Processing Services as requirement

https://i-marine.d4science.org/group/fao_tunaatlas/fao_tunaatlas

#13 Updated by Gianpaolo Coro over 3 years ago

There is still some issue in the visualisation of buttons in the Database Manager due to some stretch of the page.

#14 Updated by Julien Barde over 3 years ago

Thanks for the configuration of the VREs. I am not sure you are done already but here is some feedback.
I have been trying the DB manager and it looks ok for me. I let Paul add some comments regarding additional functionalities if needed.
At this stage I think there is too much information in the DB manager, Sardara database would be enough for now. We will ask you (step by step) if we need new databases to be made accessible.
Same comment for the "Data and Processing Services" (which is still using Statman and not Dataminer) where we would like to get only specific processes as described above:

Once set up, in the left menu of the statistical manager, we would like to get 4 categories in which algoritms will be grouped:
- "Transform and load Tuna Atlas data"
- "Access Tuna Atlas data"
- "Process Tuna Atlas data"
- "Automated report"

Once the categories are set sup we will write a new ticket to indicate which algorithms in the development environment we would like to get of each category. As an example, the "Tuna_Atlas_Data_Access_Form_1" algorithm (in the devVRE for now) should be made available in the "Access Tuna Atlas data" category of the left menu.

#15 Updated by Gianpaolo Coro over 3 years ago

Hi Julien, thanks for the feedback, although we are finalising the installation. As for the algorithms, I have added also other algorithms that had been explicitly requested by FAO for the Tuna Atlas use case (e.g FAOMSY).

As for the databases, the current version of DB Manager allows visualising the list of all the databases available for the VRE. Not all of them can be browsed. Indeed, this was originally conceived for VRE managers, but can be a useful tool to you too with further adjustment we can add in the future. It is a bit slow at the beginning, because it is still based on the Statistical Manager, but the more you use it the faster it gets thanks to caching mechanisms.

Also here, apart from Sardara, I added other DBs that were requested by FAO. I think it would be better if you discussed with Anton about the resources and the algorithms you need there. Apart from these, I will add the categories you requested.

#16 Updated by Julien Barde over 3 years ago

Ok thanks for your explanations.
Let us know once you the VRE is ready.
Regarding algorithms we will discuss with FAO and other partners to set up the list of needed algorithms.
However we want it to be empty first and add algorithms one by one. We want to use the dataminer for few algorithms only and we think that being used in the tabular manager or elsewhere in the VRE doesn't imply for an algorithm that it has to be made available as well in dataminer. Same for databases.
Indeed, we are convinced that users will be lost if we don't minimize the list of algorithms and if we can't choose the labels of items in the menu.
We will make a demo thursday to some of our colleagues here in S├Ęte.

julien

#17 Updated by Roberto Cirillo over 3 years ago

The VRE is ready.

#18 Updated by Julien Barde over 3 years ago

ok thanks.
As I said we prefer to get remove all algorithms from the Statistical manager (and get the dataminer instead whenever possible) to get the following content:
Once set up, in the left menu of the statistical manager, we would like to get 4 categories in which algoritms will be grouped:
- "Transform and load Tuna Atlas data"
- "Access Tuna Atlas data"
- "Process Tuna Atlas data"
- "Automated report"

Once the categories are set sup we will write a new ticket to indicate which algorithms in the development environment we would like to get of each category. As an example, the "Tuna_Atlas_Data_Access_Form_1" algorithm (in the devVRE for now) should be made available in the "Access Tuna Atlas data" category of the left menu.

#19 Updated by Gianpaolo Coro over 3 years ago

Hi Julien, currently you are using a production environment interface. This does not support the creation of empty categories, i.e. the categories are visualised only if there is at least one algorithm inside. If there are already available algorithms that you want in those categories, please let us know.

We are going to remove the other algorithms from the VRE as you say. Anyway, currently we do not support custom visualisation for VREs and I think this will be a task for WP5 (stock assessment = Engineering) and not for WP9 (enabling services = CNR).

#20 Updated by Gianpaolo Coro over 3 years ago

Hi Julien, I have removed the algorithms and the auxiliary databases from the VRE. Currently, you only find the Sardara DB (press the refresh button on the DB Manager) and the Database algorithms, plus other system databases that are available in the VRE. As I said, currently we don't have an option to hide the visualisation of these resources, but the most sensible ones cannot be browsed.
Please, tell me if you want some legacy algorithms to appear on the StatMan interface.

#21 Updated by Pasquale Pagano over 3 years ago

Could you please update this ticket and close it if all extensions have been implemented?

#22 Updated by Massimiliano Assante over 3 years ago

  • Status changed from Feedback to Closed

We are still missing the feature allowing to remove all algorithms from the Statistical manager (and get the dataminer instead whenever possible), but this requires a new Feature Request ticket to the StatMan (or DataMiner) to be created. I am going yo close the ticket and ask @gianpaolo.coro@isti.cnr.it to create a new Feature Request ticket on gCube for tracking/evaluating the implementation of the missing feature.

#23 Updated by Gianpaolo Coro over 3 years ago

Hi Massi, I think that we should wait for Julien to answer if what we have provided so far is good and if he wants legacy algorithms in the VRE.

#24 Updated by Massimiliano Assante over 3 years ago

  • Status changed from Closed to In Progress

ok then, I'll set the status to feedback again and wait for @julien.barde@ird.fr feedback

#25 Updated by Massimiliano Assante over 3 years ago

  • Status changed from In Progress to Feedback

#26 Updated by Massimiliano Assante about 3 years ago

  • Status changed from Feedback to Closed

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