Application logs to stdout with Shiny Server and Docker

Question

I have a Docker container running a shiny app ( Dockerfile here ).

Shiny server logs are output to stdout and application logs are written to /var/log/shiny-server . I'm deploying this container to AWS Fargate and logging applications only display stdout which makes debugging an application when deployed challenging. I'd like to write the application logs to stdout .

I've tried a number of potential solutions:

1. I've tried the solution provided here, but have had no luck. . I added the exec xtail /var/log/shiny-server/ to my shiny-server.sh as the last line in the file. App logs are not written to stdout

2. I noticed that writing application logs to stdout is now the default behavior in rocker/shiny , but as I'm using rocker/verse:3.6.2 (upgraded from 3.6.0 today ) along with RUN export ADD=shiny , I don't think this is standard behavior for the rocker/verse:3.6.2 container with Shiny add-on. As a result, I don't get the default behavior out of the box.

3. This issue on github suggests an alternative method of forcing application logging to stdout by way of an environment variable SHINY_LOG_STDERR=1 set at runtime but I'm not Linux-savvy enough to know where that env variable needs to be set to be effective. I found this documentation from Shiny Server v1.5.13 which gave suggestions in which file to set the environment variable depending on Linux distro; however, the output from my container when I run cat /etc/os-release is:

which doesn't really line up with any of the distributions in the Shiny Server documentation, thus making the documentation unhelpful.

4. I tried adding adding the environment variable from the github issue above in the docker run command, ie,

   docker run --rm -e SHINY_LOG_STDERR=1 -p 3838:3838 [my image]

as well as

    docker run --rm -e APPLICATION_LOGS_TO_STDOUT=true -p 3838:3838 [my image]

and am still not getting the logs to stdout .

I must be missing something here. Can someone help me identify how to successfully get application logs to stdout successfully?

Answer 1

You can add the line ENV SHINY_LOG_STDERR=1 to your Dockerfile (at least, this works with rocker/shiny , not sure about rocker/verse ), such as with your Dockerfile:

FROM rocker/verse:3.6.2

## Add shiny capabilities to container
RUN export ADD=shiny && bash /etc/cont-init.d/add

## Install curl and xtail
RUN apt-get update && apt-get install -y \
    curl \
    xtail

## Add pip3 and other Python packages
RUN sudo apt-get update -y && apt-get install -y python3-pip
RUN pip3 install boto3

## Add R packages
RUN R -e "install.packages(c('shiny', 'tidyverse', 'tidyselect', 'knitr', 'rmarkdown', 'jsonlite', 'odbc', 'dbplyr', 'RMySQL', 'DBI', 'pander', 'sciplot', 'lubridate', 'zoo', 'stringr', 'stringi', 'openxlsx', 'promises', 'future', 'scales', 'ggplot2', 'zip', 'Cairo', 'tinytex', 'reticulate'), repos = 'https://cran.rstudio.com/')"

## Update and install 
RUN tlmgr update --self --all
RUN tlmgr install ms
RUN tlmgr install beamer
RUN tlmgr install pgf

#Copy app dir and theme dirs to their respective locations
COPY iarr /srv/shiny-server/iarr
COPY iarr/reports/interim_annual_report/theme/SwCustom /opt/TinyTeX/texmf-dist/tex/latex/beamer/
  
#Force texlive to find my custom beamer theme
RUN texhash

EXPOSE 3838

## Add shiny-server information
COPY shiny-server.sh /usr/bin/shiny-server.sh
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf

## Add dos2unix to eliminate Win-style line-endings and run
RUN apt-get update -y && apt-get install -y dos2unix
RUN dos2unix /usr/bin/shiny-server.sh && apt-get --purge remove -y dos2unix && rm -rf /var/lib/apt/lists/*

# Enable Logging from stdout
ENV SHINY_LOG_STDERR=1

RUN ["chmod", "+x", "/usr/bin/shiny-server.sh"]

CMD ["/usr/bin/shiny-server.sh"]