Task #9012

Shiny application for ICCAT BFT-E VRE

Added by Julien Barde about 2 years ago. Updated over 1 year ago.

Status:ClosedStart date:Jun 23, 2017
Priority:HighDue date:Jun 28, 2017
Assignee:Andrea Dell'Amico% Done:

100%

Category:-
Sprint:WP05
Infrastructure:Development
Milestones:
Duration: 4

Description

As done in #7492, in the following WS folder: https://goo.gl/4PdPoa , we are storing two shiny applications developed by @taha.imzilen@ird.fr and Sylvain Bonhommeau (one of them is hosted here https://taha-chatrooms.shinyapps.io/shinyapp_BFT-E_retrosTable/) which can be used to test the Docker deployment.
Let us know if you can't access the folder and if you need additional information.

History

#1 Updated by Julien Barde about 2 years ago

The two applications can be hosted by the same container as they are related to the same VRE.

- name: shinyapp_BFT-E_retrosTable
    display-name: ICCAT BFT-E retrosTable shiny app
    description: Shiny application to visualize the content of retros tables according to the different runs and parameterizations. 

Please @taha.imzilen@ird.fr : can you specify the expected R packages and give similar information for the second shiny application ?

#2 Updated by Andrea Dell'Amico about 2 years ago

  • Assignee changed from Andrea Dell'Amico to Daniele Pavia

@daniele.pavia@eng.it let me know how we can proceed, maybe we want a build machine different from the shinyproxy server.

#3 Updated by Pasquale Pagano about 2 years ago

  • Due date set to Jun 28, 2017
  • Tracker changed from Support to Task

#4 Updated by Julien Barde almost 2 years ago

  • Priority changed from Normal to High
  • Infrastructure Development added

Is there a plan to assist us to deploy our shiny apps with Docker ?
We developed the shiny apps since long but we still don't understand how to proceed to host them in the VREs...
I changed the priority because we expected the shiny apps in the stock assessment VRE to present the work to the RFMOs working groups.

#5 Updated by Nathan Vaughan almost 2 years ago

Hi Julien, Scott passed this along to me as I was able to get his LBI tool working on Docker. Do you have these apps up on github, if so could you share the link. Using dockerhub I was able to link to create an automated build linked to a github shiny app and all I had to add was the docker control file. I can probably modify the one for LBI tool to work. Cheers, Nathan.

#6 Updated by Julien Barde almost 2 years ago

thanks @nathan.vaughan1@gmail.com and @scott.large@ices.dk
We don't have the code on github (just on the workspace) but we can do it if it helps.

I don't know of this is what @daniele.pavia@eng.it wanted to do ?

#7 Updated by Nathan Vaughan almost 2 years ago

If you could put them up on github that would be a great help and then I will work on getting them linked to dockerhub.

#8 Updated by Daniele Pavia almost 2 years ago

  • Status changed from New to In Progress

@julien.barde@ird.fr Yes, the right way to go is having the apps on github and linked on docker hub.

About the deployment: since we know that the shinyapps won't be changing all that much in time we think that deploying a shinyproxy instance and updating the apps on a per-request basis should be enough to serve them to the community.

With the help of @nathan.vaughan1@gmail.com, @andrea.dellamico@isti.cnr.it actually has deployed a shinyproxy instance at CNR that runs other shinyapps that are hosted on github and automatically containerized at dockerhub, please refer to issue #5823 for more info.

#9 Updated by Julien Barde almost 2 years ago

Could you please share the URLs of github repositories with the shiny apps you deployed ? We want to be sure that we will provide the same file structure. I guess it is the usual shiny app file structure...but it would help us to have examples.
Thanks

#10 Updated by Andrea Dell'Amico almost 2 years ago

Julien Barde wrote:

Could you please share the URLs of github repositories with the shiny apps you deployed ? We want to be sure that we will provide the same file structure. I guess it is the usual shiny app file structure...but it would help us to have examples.
Thanks

You can find the information you need here: #7492.
You can add your application to that image, maybe?

#11 Updated by Nathan Vaughan almost 2 years ago

I had an issue with the link in the old thread here is the lbi tool github

https://github.com/nathanvaughan1/shinyproxy-LBI/tree/master/LBI_shiny
It has a link to docker hub in the readme. If you could copy that repository and replace the LBI_shiny folder with your app I can modify the docket file and link to a docker hub automated build for you. Then Andrea can import to the infrastructure. Sorry I'm slow to respond I'm in Miami and currently evacuating for hurricane Irma.

#12 Updated by Julien Barde almost 2 years ago

please find below the codes of Shiny apps developped by @taha.imzilen@ird.fr on github repositories:

Is it sufficient or are you expecting us to "dockerize" these applications as well ?

As indicated by @scott.large@ices.dk I gave a look at https://www.shinyproxy.io/getting-started/ but I don't have Java 8 on my PC and didn't really understand if this part is automated (in order to keep it quite simple for the users).
Please @andrea.dellamico@isti.cnr.it let us know how to proceed.

#13 Updated by Nathan Vaughan almost 2 years ago

Thanks Julien, I'll take a look. That should be sufficient, I'll work on the dockerizing and let Andrea know when it is ready for deployment.

#14 Updated by Nathan Vaughan almost 2 years ago

Hey Andrea,

I've finished the docker builds they are available at
https://hub.docker.com/r/nathanvaughan/shinyproxy-bft-e/
docker pull nathanvaughan/shinyproxy-bft-e
and
https://hub.docker.com/r/nathanvaughan/shinyproxy-iccat/
docker pull nathanvaughan/shinyproxy-iccat
build details are in the read-me's
I had some issues with netcdf but think I got it worked out. Let me know if there are any remaining issues and I can clean them up.
Cheers,
Nathan

#15 Updated by Andrea Dell'Amico almost 2 years ago

  • % Done changed from 0 to 70

I reconfigured shinyproxy but there's a problem with the start of the containers. The old application works, the new ones don't. I'll let you know when I have some news.

#16 Updated by Andrea Dell'Amico almost 2 years ago

It seems that the apps do not start because some R packages are missing.

For the BFT-E app:

Error : there is no package called ‘DT’

For the ICCAT app:

Stack trace (innermost first):
    1: shiny::runApp
Error : could not find function "getURL"
Loading required package: rCharts
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rCharts’
Loading required package: RCurl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RCurl’
Loading required package: XML
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘XML’
Warning: Error in ..stacktraceon..: could not find function "getURL"

#17 Updated by Julien Barde almost 2 years ago

please @taha.imzilen@ird.fr give some feedback to Andrea and describe the list of package required to run your shiny apps...

#18 Updated by Andrea Dell'Amico almost 2 years ago

The packages should be the ones listed here: https://support.d4science.org/issues/9012#note-16, I took them from the container logs.

#19 Updated by Nathan Vaughan almost 2 years ago

Hey Andrea,
I added those missing packages to the dockerfiles for each app. The images are building now on dockerhub so should be ready to test soon. No power or internet still at my house so I will only be available intermittently to make further changes. Hopefully, it works this time.
Cheers,
Nathan

#20 Updated by Andrea Dell'Amico almost 2 years ago

  • % Done changed from 70 to 100
  • Assignee changed from Daniele Pavia to Andrea Dell'Amico
  • Status changed from In Progress to Feedback

Thanks Nathan, both the apps now load correctly.

#21 Updated by Andrea Dell'Amico over 1 year ago

  • Status changed from Feedback to Closed

#22 Updated by Julien Barde over 1 year ago

thanks @nathan.vaughan1@gmail.com and @andrea.dellamico@isti.cnr.it for your help.
We plan to deploy new shiny apps in the upcoming IOTC VRE with @anne.elise.nieblas@gmail.com

Where can we see these Shiny apps and is it possible to get them in a dedicated item of the ICCAT BFT-E VRE (https://services.d4science.org/group/iccat_bft-e) ?
If possible, we would like to have these apps under a new item in the upper menu: I would suggest "Interactive Dashboards".
Please @massimiliano.assante@isti.cnr.it let me know if I should open a new ticket for this request.

#23 Updated by Massimiliano Assante over 1 year ago

@julien.barde@ird.fr I can do that, "Interactive Dashboards main menu with the list of shiny apps as children (sub menu).

Please specify which shiny apps and in which order you want them to appear un the sub menu.

#24 Updated by Julien Barde over 1 year ago

That would be perfect like this :

  • we need to discuss with @taha.imzilen@ird.fr and @anne.elise.nieblas@gmail.com regarding the names of the 2 shiny apps (since we need them for both ICCAT and IOTC VREs)
  • how can I see where our shiny apps are deployed on the infra (I probably missed something since Nathan and Andrea managed the dockerization) ? I guess the names are probably "shinyproxy-bft-e" and "shinyproxy-iccat"

#25 Updated by Andrea Dell'Amico over 1 year ago

Julien Barde wrote:

That would be perfect like this :

  • we need to discuss with @taha.imzilen@ird.fr and @anne.elise.nieblas@gmail.com regarding the names of the 2 shiny apps (since we need them for both ICCAT and IOTC VREs)
  • how can I see where our shiny apps are deployed on the infra (I probably missed something since Nathan and Andrea managed the dockerization) ? I guess the names are probably "shinyproxy-bft-e" and "shinyproxy-iccat"

You can access https://shinyproxy.d4science.org and you will find the application listed there. You can log in with the same credentials used on the portal. The authentication steps have not been integrated yet.

#26 Updated by Julien Barde over 1 year ago

Ok, thanks Andrea, I just found them from the link to Shiny Proxy within the new IOTC VRE:

Also available in: Atom PDF