Information for the super user¶
Find out if you have sudo rights¶
To check if you have sudo user rights on awb-webapp01 run
sudo -l -U <username>
If you don't you get 'User
If successful you get the message
...
User <username> may run the following commands on awb-webapp01:
(ALL : ALL) ALL
Creating new users locally on the VM¶
Since the move to the "red zone" within interim services, FreeIPA managed accounts no longer work. Therefore, we can create user accounts ourselves with
sudo adduser <username>
and following the prompts, where the username is either
When new users are needed for the shiny dev, the helpdesks only need to request accounts for the VDI and for that account to be able to connect to the space-rshiny-dev VM. The local user accounts can then be created and passed on by anyone within the support group with sudo rights as needed.
We recommend to add all new (project)users to the table at the bottom of Current User Accounts.
Shared project directories¶
If data analysts want to collaborate on a project
sudo mkdir -p /home/shared/<projectname> //The -p will create the directory and would ignore any errors if the directory already exists.
sudo groupadd <projectname> //Create the new group
sudo chgrp -R <projectname> /home/shared/<projectname> //The -R recursive for subdirectories
sudo chmod -R 2770 /home/shared/<projectname>/ //The 2 inheritence for new subfiles
sudo usermod -a -G <projectname> <username> //The -G a list of supplementary groups which the user is also a member of. Not gid group!
Where to find the server¶
The server 'shinyproxy-2.5.0.jar' is in '/usr/bin/shiny/'.
How and when to (re-)start the server¶
The server needs to be restarted if any changes to the configuration file 'application.yml' are to take effect.
Check the server status: "sudo systemctl status shinyproxy"
To stop the server: "sudo systemctl stop shinyproxy"
(Re-)start the server: "sudo systemctl start shinyproxy". The server must be stopped before restarting for changes to take effect.
The configuration file¶
The configuration file 'application.yml' and the server 'shinyproxy-2.3.1.jar' must be in the same directory, and can both be found in '/usr/bin/shiny/'.
The configuration file should not be readable by 'group' or 'other.
root@space-rshiny-dev:/usr/bin/shiny# ls -lrt
total 99848
....
-rw------- 1 root root 2312 Sep 15 14:39 application.yml
Otherwise this can be changed by the sudo user with the command "chmod go= application.yml".
The configuration file looks like this:
proxy:
title: SPACe Shiny Proxy
logo-url: /home/ebreitmoser/ediunilogo.png
landing-page: /
bind-address:
heartbeat-rate: 10000
heartbeat-timeout: 60000
port: 3939
authentication: simple
admin-groups: scientists
# Example: 'simple' authentication configuration
users:
- name: <user1>
password: <password1>
groups: scientists
- name: <user2>
password: <password2>
groups: maths
# Docker configuration
docker:
cert-path: /home/none
url: http://localhost:2375
port-range-start: 20000
specs:
- id: 01_hello
display-name: Hello Application
description: Application which demonstrates the basics of a Shiny app
container-cmd: ["R", "-e", "shinyproxy::run_01_hello()"]
container-image: openanalytics/shinyproxy-demo
access-groups: scientists
- id: 06_tabsets
container-cmd: ["R", "-e", "shinyproxy::run_06_tabsets()"]
container-image: openanalytics/shinyproxy-demo
access-groups: scientists
- id: euler
display-name: Euler Application
description: Euler Application for Elena
container-cmd: ["R", "-e", "shiny::runApp('/root/shinyproxy-template/euler',host='0.0.0.0',port=3838)"]
container-image: openanalytics/shinyproxy-template
access-groups: scientists, maths
logging:
file:
shinyproxy.log
server:
servlet:
context-path: /eidf.epcc.ed.ac.uk/space-shiny
Please do NOT change anything in the application file below 'server:'.
How to edit the configuration file¶
It's advisable to save a copy of the application.yml before editing, as a state to return to if breaking changes are made.
The file can be edited in the user's choice of editor, the below example is for emacs:
- Run: sudo emacs -nw application.yml
- Make necessary changes (paying close attention to indentation)
- To save changes: Ctrl + x, Ctrl + s
- To exit emacs editor: Ctrl + x, Ctrl + c
How to add new users (aka data analysts)¶
If you want new users to be able to see and interact with the apps on the website https://eidf.epcc.ed.ac.uk/space-shiny/ you need to add them to the configuration file.
- Edit 'application.yml' and add the new user
below 'users'. Note that indentations are important! We recommend NOT to use the same username and password as the one to access awb-webapp01!
users:
- name: <userN>
password: <passwordN>
groups: scientists
- For the changes to become effective, the server has to be restarted.
- You might want to add the new user to the docker group as well (see Howtoaddanewusertothedockergroup of how to do this)
How to add new apps to the VM¶
Any new app needs to be added to the configuration file 'application.yml' to become visible and useable on the website.
- Edit 'application.yml' and add the new app below 'specs'. Note that indentations are important!
- id: myappname
display-name: My new Application
description: The new Application doing x
container-cmd: ["R", "-e", "shiny::runApp('/root/<username>/myappname',host='0.0.0.0',port=3838)"]
container-image: myappname
access-groups: scientists
- For the changes to become effective, the server has to be restarted.
What's different for 'flexdashboard' package/rmarkdown¶
If you are to deploy an app consisting of rmarkdown and making use of the flexdashboard package.
Edit 'application.yml' and add the new app below 'specs'. Note that indentations are important! The only differences between other apps and rmarkdown ones are in the line for 'container-cmd'
- id: myappname
display-name: My new Application using rmarkdown
description: The new Application doing x with rmarkdown
container-cmd: ["R", "-e", "rmarkdown::run('/root/<username>/flexdashboard.Rmd',shiny_args = list(port = 3838, host='0.0.0
.0'))"]
container-image: myappname
access-groups: scientists
For the changes to become effective, the server has to be restarted.
How to make apps visible to certain users only¶
The 'groups' in the configuration file 'application.yml' determines which apps a given user can see and interact with. In our case '
- name: <user2>
password: <password2>
groups: maths
[...]
- id: euler
display-name: Euler Application
description: Euler Application for Elena
container-cmd: ["R", "-e", "shiny::runApp('/root/shinyproxy-template/euler',host='0.0.0.0',port=3838)"]
container-image: openanalytics/shinyproxy-template
access-groups: scientists, maths
How to change the title of the landing page¶
Currently the title of the landing page is 'SPACe Shiny Proxy'. This can be changed in the configuration file 'application.yml' by editing 'title: SPACe Shiny Proxy'.
proxy:
title: SPACe Shiny Proxy
logo-url: /home/ebreitmoser/ediunilogo.png
How to change the logo of the landing page¶
Currently the logo of the landing page is set to the University of Edinburgh one. This is can be changed in the configuration file 'application.yml' by editing 'logo-url: /home/ebreitmoser/ediunilogo.png'.
proxy:
title: SPACe Shiny Proxy
logo-url: /home/ebreitmoser/ediunilogo.png
How to add a new data analyst to the docker group¶
In case a new data analyst hasn't been added to the docker group automatically:
sudo usermod -aG docker <username>
For the changes to take effect the user will have to log off and back in.
To check who is in the docker group either
more /etc/group|grep -in docker
80:docker:x:998:ebreitmoser,sdt,tcrines,mbarnes2,mdrake2,twilliamson2
or
members docker
ebreitmoser sdt tcrines mbarnes2 mdrake2 twilliamson2