VRE #4846

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

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

VRE Creation for ICCAT BFT-E

Added by Julien Barde over 3 years ago. Updated 10 months ago.

Status:ReleasedStart date:Sep 08, 2016
Priority:HighDue date:Sep 12, 2016
Assignee:Roberto Cirillo% Done:


VRE_Policy:Restricted Invite_Policy:VRE_Manager
Duration: 3


We need to create a new VRE for the ICCAT working group related to Bluefin Tuna stock assessment (BFT-E).

The Stock Assessment VRE can be used as a template to set it up:
- Tabular Data Manager should be removed,
- Data Miner should be renamed "Data and Processing services",
- Stat. Alg. Importer should be renamed "Import a new process",
- Data Catalog should be removed and be added later only when netCDF files generated by the VRE will be stored and accessible within a dedicated catalog of Thredds server and metadata extracted from netCDF (non gridded data), same with automated reports and html files generated by the VRE will be documented in CKAN,
- We expect to get a direct access to the dedicated Thredds catalog from the VRE

We would like to see in the menu the following order for application: Rstudio | "Data and Processing services" | "Import a new process" | Administration

Screen Shot 2016-09-07 at 10.59.22.png - Current requests (22.2 KB) Leonardo Candela, Sep 07, 2016 11:00 AM



D4Science Infrastructure - Support #4977: publishing the "parallelized_STEP1_VPA_ICCAT_BFT_E_Retros...ClosedTAHA IMZILEN

D4Science Infrastructure - Support #4998: publishing the "Step_4_Vpa_Iccat_Bft_E_Report" algorithm ...ClosedGianpaolo Coro

Project Activity #5087: Develop a logo for ICCAT BFT VREClosedJulien Barde

Support #5113: packages uninstalledClosedAndrea Dell'Amico


#1 Updated by Roberto Cirillo over 3 years ago

  • Tracker changed from Support to Task

#2 Updated by Pasquale Pagano over 3 years ago

  • Invite_Policy set to VRE_Manager
  • VRE_Policy set to Restricted
  • Due date set to Sep 15, 2016
  • Tracker changed from Task to VRE

Is it to have it by September 15th? Moreover please clarify the policy regulating the access. So far I specified restricted meaning that the VRE Manager has to approve any request of participation. Is it ok?

#3 Updated by Julien Barde over 3 years ago

The working group will take place in Madrid the last week of september, so it would be good to validate the VRE before.
Yes it's better to restrict the VRE access as I don't think it should be accessible out of the WG participants.

#4 Updated by Pasquale Pagano over 3 years ago

  • Due date changed from Sep 15, 2016 to Sep 07, 2016

#5 Updated by Massimiliano Assante over 3 years ago

  • Status changed from New to Planned

#6 Updated by Massimiliano Assante over 3 years ago

  • Status changed from Planned to In Progress

#7 Updated by Pasquale Pagano over 3 years ago

  • % Done changed from 0 to 50

#8 Updated by Gianpaolo Coro over 3 years ago

The resources have been added and Dataminer is working. I have tested the STEP_1 algorithm. Only STEP 1-2-3 algorithms have been left. @julien.barde@ird.fr I was wondering if also other algorithms like the legacy ICCAT_VPA and KnitR Compiler should be added.

#9 Updated by Julien Barde over 3 years ago

I sent a request to become a user...once ok I would like to become an adminsitrator to manage users requests and send invitations..Taha as well.
Yesterday we sent a request for the Stock Assessment VRE and I can't see the pending request for my collaeague

#10 Updated by Leonardo Candela over 3 years ago

@julien.barde@ird.fr I do not see your request for membership in ICCAT_BFT-E ... there are only 2 pending requests (see screenshot). Who is expected to be the manager of this VRE (e.g. approve membership requests)? More managers are allowed.

Re the Stock Assessment VRE membership request I'm going to add a specific ticket, I do not see any pending request too.

#11 Updated by Julien Barde over 3 years ago

I was looking for Tristan Rouyer in Stock Assessment VRE but I guess that we didn't realize that we asked a membership for ICCAT BFT-E instead (which was actually more appropriate for Tristan).

Perhaps I made this mistake by clicking on the wrong VRE because the logo is the same (which is OK as the logo is nice) so I was looking for a pending request for Tristan in Stock Assessment and it was in ICCAT BFT-E.

Anyway I checked in both VREs and Tristan is now a member of both.

However, RStudio doesn't work in ICCAT BFT-E.
Below is the error message in the web browser:


Error (400) : this resource cannot process this request because it is malformed
org.gcube.smartgears.handlers.application.request.RequestException: RConnector cannot be called in scope /d4science.research-infrastructures.eu/gCubeApps/ICCAT_BFT-E
at org.gcube.smartgears.handlers.application.request.RequestError.toException(RequestError.java:110)
at org.gcube.smartgears.handlers.application.request.RequestError.fire(RequestError.java:94)
at org.gcube.smartgears.handlers.application.request.RequestValidator.validateScope(RequestValidator.java:90)
at org.gcube.smartgears.handlers.application.request.RequestValidator.retreiveAndSetInfo(RequestValidator.java:161)
at org.gcube.smartgears.handlers.application.request.RequestValidator.validateToken(RequestValidator.java:126)
at org.gcube.smartgears.handlers.application.request.RequestValidator.handleRequest(RequestValidator.java:49)
at org.gcube.smartgears.handlers.application.RequestHandler.onEvent(RequestHandler.java:56)
at org.gcube.smartgears.handlers.application.RequestHandler.onEvent(RequestHandler.java:21)
at org.gcube.smartgears.handlers.Pipeline.forward(Pipeline.java:69)
at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

#12 Updated by Pasquale Pagano over 3 years ago

  • Status changed from In Progress to Available

#13 Updated by Pasquale Pagano about 3 years ago

  • Assignee changed from Massimiliano Assante to Roberto Cirillo

We did not authorize the VRE to exploit RStudio. Sorry. @roberto.cirillo@isti.cnr.it please can you fix it asap. Thanks

#14 Updated by Roberto Cirillo about 3 years ago

I've added the rstudio gCoreEndpoint . Now it works.

#15 Updated by Julien Barde about 3 years ago

Yes it works now. Thanks.

#16 Updated by Leonardo Candela about 3 years ago

  • Status changed from Available to Released

#17 Updated by Julien Barde about 3 years ago

As I said in #4846#note-9, I wanted to be able to send invitations to facilitate the registration process but I couldn't find out where invitations can be sent. I just found the "Invite Friends" section in the home page but it was not obvious for me.

Indeed, I was looking for it in the Administration / "manage users and requests" or "See Invites" items

It would be useful to replicate the service to send invitations in "See invites" which could be rename "Manage invites". Sending invitations to a whole mailing list would be useful too (if not already possible).

#18 Updated by Leonardo Candela about 3 years ago

@julien.barde@ird.fr please let us know if the comments you are posting are pre-requisites (blicking issues) for the release of the VRE or they are simply requests for enhancement. In the second case we will open specific requests.

The portlet for "inviting" users in a VRE is exactly ("Invite Friends"), the title can be easily changed (please let me know). The "placement of the portlet can be easly reconsidered, e.g. if you are willing to have it in the Admin menu (and available for managers only) please let us know.

As you recognise by yuourself, the "See invites" offers only facilities for monitoring the status of invitations sent. Changing its logic requires development activity and it availability cannot be immediate.

Re the last point, please do notice that "Invite Friends" enable to invite "any entity" having an email. Of course we do not manage "shared accounts" (e.g. for accounting purposes) this implies that mailing list members have to create their own account.

#19 Updated by Julien Barde about 3 years ago

It's not a blocking issue at all since I know now how to invite people. However, I was expecting it in the "manage members" item and yes, if possible, I guess that replicating the portlet here would help managers to send invitations. For managers, I would say that renaming it "Invite new members" would make more sens than "Friends". I was perhaps wrong when saying "mailing list". What I foresee for working groups or training sessions is that we will get a list of emails which are expected members and I would like to be able to copy paste all the emails in the portlet to send multiple invitations at once (to avoid to do it as many times as different emails).
In other words: can I use (or would it be possible to use) the portlet by enumerating multipe emails (eg separated by a comma) ?
So no need to change the logic of "See invites" but perhaps adding another item like "Send invites" might be useful when you have time for it.
I think this is worth for any VRE not only in this case.

#20 Updated by Leonardo Candela about 3 years ago

The request for changes suggested by @julien.barde@ird.fr are in place, namely:

  • Invite friends in the home page of the VRE has been renamed;
  • The same "invite friends" portlet is now in the Admin menu also;
  • A new portlet enabling a VRE Manager to actually create a new user (to be a VRE member) is available in the Admin menu. This portlet make it possible to register a new user directly in the VRE;

For bulk invitation I just created #5002

#21 Updated by Julien Barde about 3 years ago

Could you please add Taha to the list of administrators (I asked it in https://support.d4science.org/issues/4846#note-9) ?
It's urgent, ICCAT meeting is next week..he needs the rights to manage members. Same question with Tristan Rouyer and Sylvain Bonhommeau to be sure the can all manage users.

#22 Updated by Massimiliano Assante about 3 years ago

If, for list of Administrators, you mean VR-Managers (I suppose so), since you are a VRE-Manager you can do it your own https://i-marine.d4science.org/group/iccat_bft-e/manage-user-and-requests

#23 Updated by Pasquale Pagano about 3 years ago

To all users specified by @julien.barde@ird.fr have been granted the VRE Manager role.

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