I'm learning how to use shinyproxy to deploy R shiny applications but I can't figure out where to place my .Renviron file which contains global variables used to access a database.

The docker image builds without any errors but when I start the container using:

docker run -it -p 3838:3838 shinyproxy-template .

It doesn't find the env variables in the .Renviron file and I end up getting an error on the part of the R code that requires the global variables.

My current folder structure is as follows:

shinyproxy-template/
                   |- app-folder/
                   |- .gitignore
                   |- Dockerfile
                   |- README.md
                   |- app.Rproj
                   |- Rprofile.site
                   |- .Renviron

I tried placing the .Renviron file inside the app-folder/ then built the docker image again but the global variables were still inaccessible.

Where should I place the .Renviron so that the global variables are accessed by the app?

CodePudding user response：

There are multiple options:

Put .Renviron file to the expected location inside the container

You can add a COPY command to the Dockefile to copy your .Renviron file to the expected location - i.e. either a home directory of the user or the WORKDIR location if defined in the Dockerfile. In case of the root user it would be:

COPY .Renviron /root/

Add environment variables from .Renviron to the Dockerfile

Add lines like:

ENV VAR1="value1"
ENV VAR2="value2"

to your Dockerfile

Add environment variables from .Renviron to the shinyproxy configuration

You can define environment variables in the application.yaml configuration file by either using

container-env:
  VAR1: VALUE1
  VAR2: VALUE2

or

container-env-file: /path/to/.Renviron

for your app specification. Note that the path here is on the host and not inside the container.

For docker run

When you do a docker run outside of shinyproxy you can use argument --env-file with something like:

docker run -it -p 3838:3838 shinyproxy-template --env-file /path/to/shinyproxy-template/.Renviron

Releant documentation links:

• https://www.shinyproxy.io/documentation/configuration/#apps
• https://docs.docker.com/engine/reference/commandline/run/#set-environment-variables--e---env---env-file

CodePudding user response：

Edit: Have a look at @Max's solution. We posted at nearly the same time but his instructions are clearer.

---

After lots of trial and error I finally got a solution.

---

First, starting the container outside shinyproxy to check if the shiny app runs normally? Use docker's --env-file flag to specify the .Renviron filepath. In my case since both the Dockerfile and .Renviron are in the same folder so I'd do:

docker run -it --env-file .Renviron -p 3838:3838 shinyproxy-template .

The app will now recognize env vars defined in the .Renviron file and no errors!

---

I then changed into the directory where I had shinyproxy-2.6.1.jar file and ran it again using java -jar shinyproxy-2.6.1.jar. There was an error when I tried to start my shinyapp. It couldn't find the env vars.

So I resorted to adding them directly in the application.yml which is in the same location as shinyproxy-2.6.1.jar:

  - id: app-folder
    display-name: My App
    description: My App's title
    container-cmd: ["R", "-e", "shiny::runApp('/root/app-folder')"]
    container-image: openanalytics/shinyproxy-template
    container-env:
        ENV1: ENV1-VALUE
        ENV2: ENV2-VALUE
        ENV3: ENV3-VALUE
    access-groups: scientists

Replace the necessary parts of the yml section with the corresponding one's on your side depending on your case. The same applies to the env vars.

---

In fact let me just provide a prototype of my whole application.yml file, have a look at the last app I added "wca":

proxy:
  title: Open Analytics Shiny Proxy
  logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
  landing-page: /
  # hide nav bar:
  hide-navbar: true
  heartbeat-rate: 10000
  heartbeat-timeout: 60000
  port: 8080
  authentication: ldap
  admin-groups: scientists
  # Example: 'simple' authentication configuration
  users:
  - name: jack
    password: password
    groups: scientists
  - name: jeff
    password: password
    groups: mathematicians
  # Example: 'ldap' authentication configuration
  ldap:
    url: ldap://ldap.forumsys.com:389/dc=example,dc=com
    user-dn-pattern: uid={0}
    group-search-base:
    group-search-filter: (uniqueMember={0})
    manager-dn: cn=read-only-admin,dc=example,dc=com
    manager-password: password
    # Docker configuration
  docker:
    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, mathematicians]
  - id: 06_tabsets
    container-cmd: ["R", "-e", "shinyproxy::run_06_tabsets()"]
    container-image: openanalytics/shinyproxy-demo
    access-groups: scientists
  - id: euler
    display-name: Euler's number
    description: Adding another app to shinyproxy
    container-cmd: ["R", "-e", "shiny::runApp('/root/euler')"]
    container-image: openanalytics/shinyproxy-template
    access-groups: scientists
  - id: wca
    display-name: Wasanii
    description: WhatsApp Chat Analysis
    container-cmd: ["R", "-e", "shiny::runApp('/root/wca')"]
    container-image: wca
    container-env:
        FIREBASE_API_KEY: myfirebaseapikey
        FIREBASE_PROJECT_ID: myfirebaseprojectid
        FIREBASE_AUTH_DOMAIN: myfirebaseauthdomain
        FIREBASE_STORAGE_BUCKET: myfirebasestoragebucket
        FIREBASE_APP_ID: myfirebaseappid
        FIREBASE_DATABASE_URL: myfirebasedatabaseurl
    access-groups: scientists

logging:
  file:
    shinyproxy.log

---

There's obviously a better solution to refer to the .Renviron file directly but since I can't figure it out this will do.