Docker container failing to start with connection to database from shinyproxy - r

Question

I want to connect an individual app within shiny proxy to a docker network.
I have a few apps on shinyproxy, only one needs to connect to the database.
It is a postgresql DB running on the same machine in a docker set up to receive connections though the network my-docker-network
In application.yml Should I use
container-network: my-docker-network
or
container-network-connections: ["my-docker-network"]
?
Even though I don’t need internal networks in shiny proxy do I still need to set ``internal-networking: trueunderdocker:```
At the moment the container isn’t starting, but as the container runs fine by itself using docker run --net my-docker-network --env-file /mypath/.Renviron my_app_image it seems to be a connection issue. The container also works if I run it with --network="host"
I've tried various options of putting the .Renviron in different places and don't think that is the issue.
Full dockerfile (other apps deleted and pseudonomised):
FROM rocker/r-ver:3.6.3
RUN apt-get update --allow-releaseinfo-change && apt-get install -y \
lbzip2 \
libfftw3-dev \
libgdal-dev \
libgeos-dev \
libgsl0-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libhdf4-alt-dev \
libhdf5-dev \
libjq-dev \
liblwgeom-dev \
libpq-dev \
libproj-dev \
libprotobuf-dev \
libnetcdf-dev \
libsqlite3-dev \
libssl-dev \
libudunits2-dev \
netcdf-bin \
postgis \
protobuf-compiler \
sqlite3 \
tk-dev \
unixodbc-dev \
libssh2-1-dev \
r-cran-v8 \
libv8-dev \
net-tools \
libsqlite3-dev \
libxml2-dev
#for whatever reason it wasn't working
#RUN export ADD=shiny && bash /etc/cont-init.d/add
#install packages
RUN R -e "install.packages(c('somepackages'))"
#copy app script and variables into docker
RUN mkdir /home/app
COPY .Renviron /home/app/
COPY global.R /home/app/
COPY ui.R /home/app/
COPY server.R /home/app/
COPY Rprofile.site /usr/lib/R/etc/
#add run script
CMD ["R", "-e", "shiny::runApp('home/app')"]
Useful parts of the application.yml
At the moment I always get "500/container doesn't respond/run" on the shinyproxy side even though it runs on the standalone.
proxy:
title: apps - page
# logo-url: https://link/to/your/logo.png
landing-page: /
favicon-path: favicon.ico
heartbeat-rate: 10000
heartbeat-timeout: 60000
container-wait-time: 40000
port: 8080
authentication: simple
admin-groups: admins
container-log-path: /etc/shinyproxy/logs
# Example: 'simple' authentication configuration
users:
- name: admin
password: password
groups: admins
- name: user
password: password
groups: users
# Docker configuration
docker:
cert-path: /home/none
url: http://localhost:2375
port-range-start: 20000
# internal-networking: true
specs:
- id: 06_rshiny_dashboard_r_ver
display-name: app r_ver container r_app_r_ver
description: using simple rver set up docker and the r_app_r_ver image
container-cmd: ["R", "-e", "shinyrunApp('/home/app')"]
#container-cmd: ["R", "-e", "shiny::runApp('/home/app', shiny.port = 3838, shiny.host = '0.0.0.0')"]
container-image: asela_r_app_r_ver:latest
#container-network: my-docker-network
container-network-connections: [ "my-docker-network" ]
container-env-file: /home/app/.Renviron
access-groups: [admins]
logging:
file:
name: /etc/shinyproxy/shinyproxy.log
Various commented out lines show the current set up but have tried with/without

Answer 1

Fixed it by using a shiny server version of the docker - not sure why but this sorted out some connection issue.
Dockerfile:
FROM rocker/r-ver:3.6.3
RUN apt-get update --allow-releaseinfo-change && apt-get install -y \
lbzip2 \
libfftw3-dev \
libgdal-dev \
libgeos-dev \
libgsl0-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libhdf4-alt-dev \
libhdf5-dev \
libjq-dev \
liblwgeom-dev \
libpq-dev \
libproj-dev \
libprotobuf-dev \
libnetcdf-dev \
libsqlite3-dev \
libssl-dev \
libudunits2-dev \
netcdf-bin \
postgis \
protobuf-compiler \
sqlite3 \
tk-dev \
unixodbc-dev \
libssh2-1-dev \
r-cran-v8 \
libv8-dev \
net-tools \
libsqlite3-dev \
libxml2-dev \
wget \
gdebi
##No version control
#then install shiny
RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
#install packages
RUN R -e "install.packages(c('xtable', 'stringr', 'glue', 'data.table', 'pool', 'RPostgres', 'palettetown', 'deckgl', 'sf', 'shinyWidgets', 'shiny', 'stats', 'graphics', 'grDevices', 'datasets', 'utils', 'methods', 'base'))"
##No version control over
##with version control and renv.lock file
##With version control over
#copy shiny server config over
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
#avoid some errors
#already in there
#RUN echo 'sanitize_errors off;disable_protocols xdr-streaming xhr-streaming iframe-eventsource iframe-htmlfile;' >> /etc/shiny-server/shiny-server.conf
# copy the app to the image
COPY .Renviron /srv/shiny-server/
COPY global.R /srv/shiny-server/
COPY server.R /srv/shiny-server/
COPY ui.R /srv/shiny-server/
# select port
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"]
# run app
CMD ["/usr/bin/shiny-server.sh"]
application.yml:
proxy:
title: apps - page
# logo-url: https://link/to/your/logo.png
landing-page: /
favicon-path: favicon.ico
heartbeat-rate: 10000
heartbeat-timeout: 60000
container-wait-time: 40000
port: 8080
authentication: simple
admin-groups: admins
container-log-path: /etc/shinyproxy/logs
# Example: 'simple' authentication configuration
users:
- name: admin
password: password
groups: admins
- name: user
password: password
groups: users
# Docker configuration
docker:
cert-path: /home/none
url: http://localhost:2375
port-range-start: 20000
# internal-networking: true
- id: 10_asela_rshiny_shinyserv
display-name: ASELA Dash internal shiny server version
description: container has own shinyserver within it functions on docker network only not on host container-network version
container-cmd: ["/usr/bin/shiny-server.sh"]
access-groups: [admins]
container-image: asela_r_app_shinyserv_ver:latest
container-network: asela-docker-net
logging:
file:
name: /etc/shinyproxy/shinyproxy.log