Connect a shiny app inside docker container with external mysql database on Linux

Question

I have created a shiny app connected to a Mysql database running on my Mac OS Catalina. When I run the app in Rstudio it works fine. After doing it locally I will migrate the app to the cloud on a Linux Ubuntu.

When I create a docker image of this app - just the app, not the mysql db - and I run the container, accessing the app on a browser (localhost), it is not connecting to the database.

What is the correct configuration of my app.R or dockerfile to connect to a external mysql database ?

The files I am using are bellow. Appreciate any help.

===============APP.R========================================

## libraries

library(tidyverse)
library(shiny)
library(shinydashboard)
library(ggplot2)
library(DBI)


#shiny dashboard UI
ui <- dashboardPage(
    dashboardHeader(),
    dashboardSidebar(),
    dashboardBody(
        fluidPage(
            plotOutput("plot1")
        )
    )
)

#shiny dashboard server
server <- function(input, output,session) {
    
    #connection to database  
    orders <- dbConnect(RMySQL::MySQL(), user = 'root', password = '#####', 
                        dbname = 'Archenar',host='localhost')
    #check changes
    rigel <- reactivePoll(5000, session,checkFunc = function() {
        query2= "SELECT * FROM SENSOR"
        rs = dbSendQuery(orders,query2)
        dbFetch(rs)
    },
    
    valueFunc = function() {
        query2= "SELECT * FROM SENSOR"  
        rs = dbSendQuery(orders,query2)
        dbFetch(rs)
    }
    )

    #make plot  
    output$plot1 <- renderPlot({
        rigelp <- rigel() %>% as.data.frame()%>% group_by(category) %>% 
            summarize(v=sum(value1))
        ggplot(rigelp,aes(x=category,y=v)) + geom_bar(stat = "identity")
        
    })  
}

shinyApp(ui, server)

=============Dockerfile========================================

# get shiny server plus tidyverse packages image
FROM rocker/shiny:latest
# system libraries of general use
RUN apt-get update && apt-get install -y \
    sudo \
    pandoc \
    pandoc-citeproc \
    libcurl4-gnutls-dev \
    libcairo2-dev \
    libmariadbd-dev \
    libxt-dev \
    libssl-dev \
    libssh2-1-dev
# install R packages required 
# (change it depending on the packages you need)
RUN R -e "install.packages('shiny',repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('tidyverse',repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('shinydashboard',repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('DBI',repos='http://cran.rstudio.com/')"
RUN R -e "install.packages('RMySQL',repos='http://cran.rstudio.com/')"
# Copy configuration files into the Docker image
COPY shiny-server.conf  /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
RUN rm /srv/shiny-server/index.html
# Make the ShinyApp available at port 80
EXPOSE 3838
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
RUN ["chmod", "+x", "/usr/bin/shiny-server.sh"]
CMD ["/usr/bin/shiny-server.sh"]

=========Shiny Server========================================

# Define the user we should use when spawning R Shiny processes
  run_as shiny;
  # Define a top-level server which will listen on a port
  server {
    # Instruct this server to listen on port 80.
    listen 80;
  # Define the location available at the base URL
    location / {
  # Run this location in 'site_dir' mode, which hosts the entire directory
      # tree at '/srv/shiny-server'
      site_dir /srv/shiny-server;
      
      # Define where we should put the log files for this location
      log_dir /var/log/shiny-server;
      
      # Should we list the contents of a (non-Shiny-App) directory when the user 
      # visits the corresponding URL?
      directory_index on;
    }
  }

hello. Docker image and database are running on my computer yes. Later I will install both in a LInux machine, but the database will not be in the image. — Jonathan Livingston Seagull, Sep 08 '21 at 13:51
Are you using host networking in docker container? Maybe you have to do so. — Miguel Suazo, Sep 08 '21 at 13:51
I am not using host networking. But when I migrate to a linux machine how will that work ? — Jonathan Livingston Seagull, Sep 08 '21 at 13:53

score 0 · Answer 1 · answered Sep 08 '21 at 13:58

0

As @Miguel suggested, you need to use host network mode.

R application
docker run your-image --net=host

When you go for Linux machine, you can just use the same. To access your app after running it with --net=host

linux-machine-ip:3838

For more info

answered Sep 08 '21 at 13:58

Sachith Muhandiram

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Connect a shiny app inside docker container with external mysql database on Linux

1 Answers1