How to deploy a Plumber docker that writes a log file?

Question

Im trying to deploy a R Plumber test API as a docker container as my main goal is to successfully create a log file everytime the API processes a request. I have tested it locally and it works.

Here are my test files:

plumber.R

# plumber.R
# A simple API to illustrate logging with Plumber

library(plumber)

#* @apiTitle Logging Example

#* @apiDescription Simple example API for implementing logging with Plumber

#* Echo back the input
#* @param msg The message to echo
#* @get /echo
function(msg = "") {
  list(msg = paste0("The message is: '", msg, "'"))
}

entrypoint.R

library(plumber)

# Config
#config <- config::get()

# logging
library(logger)
# Ensure glue is a specific dependency so it's avaible for logger
library(glue)

# Specify how logs are written 
log_dir <- "/app/logs"
if (!fs::dir_exists(log_dir)) fs::dir_create(log_dir)
log_appender(appender_tee(tempfile("plumber_", log_dir, ".log")))

convert_empty <- function(string) {
  if (string == "") {
    "-"
  } else {
    string
  }
}

pr <- plumb("plumber.R")

pr$registerHooks(
  list(
    preroute = function() {
      # Start timer for log info
      tictoc::tic()
    },
    postroute = function(req, res) {
      end <- tictoc::toc(quiet = TRUE)
      # Log details about the request and the response
      # TODO: Sanitize log details - perhaps in convert_empty
      log_info('{convert_empty(req$REMOTE_ADDR)} "{convert_empty(req$HTTP_USER_AGENT)}" {convert_empty(req$HTTP_HOST)} {convert_empty(req$REQUEST_METHOD)} {convert_empty(req$PATH_INFO)} {convert_empty(res$status)} {round(end$toc - end$tic, digits = getOption("digits", 5))}')
    }
  )
)

pr

Dockerfile

# Base image https://hub.docker.com/u/rocker/
FROM rstudio/plumber

# Install R libraries
RUN R -e "install.packages(c('odbc','glue','parsedate','tibble','dplyr','httr','RCurl','jsonlite','rjson','stringr','telegram','R.utils','logger','tictoc'))"

# Run plumber package
CMD ["/app/plumber.R"]

My expected result is to be able to store the log in a shared folder between the container and the host. But so far I havent been able to have the plumber app even to even create a log file with logs inside /app/logs.

docker build -t logger2 .

docker run -d -p 18001:8000 --rm \
-v /home/user/R/projects/logger2/:/app \
-v /tmp/log1:/app/logs \
logger2

Are you able to manually create files in `/app/logs`? i.e. `docker exec logger2 touch /app/logs/foobar` ? — margusl, May 15 '23 at 16:38
Yes. Running that will create the foobar file on the host folder — Andres Mora, May 15 '23 at 16:44

score 2 · Accepted Answer · answered May 15 '23 at 17:30

The problem here is the entrypoint. Your entrypoint.R script is being ignored.

Here's the default entrypoint that the rplumber image comes with:

ENTRYPOINT ["R", "-e", "pr <- plumber::plumb(rev(commandArgs())[1]); args <- list(host = '0.0.0.0', port = 8000); if (packageVersion('plumber') >= '1.0.0') { pr$setDocs(TRUE) } else { args$swagger <- TRUE }; do.call(pr$run, args)"]

Here's what that does:

Load the plumber library.
From the CMD line in your dockerfile, get filename of the file to load.
Plumb that file.
Turn on docs.
Listen on all interfaces on port 8000.

In this case, it loads the /app/plumber.R file, and ignores the /app/entrypoint.R file.

How can you fix that? Define your own entrypoint in the Dockerfile.

FROM rstudio/plumber

# Install R libraries
RUN R -e "install.packages(c('odbc','glue','parsedate','tibble','dplyr','httr','RCurl','jsonlite','rjson','stringr','telegram','R.utils','logger','tictoc'))"

ENTRYPOINT ["Rscript", "/app/entrypoint.R"]

Here I still ran into a few problems:

No fs package. I added RUN R -e "install.packages(c('fs'))" to install it.
Got the error Error in plumb("plumber.R") : File does not exist: plumber.R. This is because the server is running in the wrong directory. I fixed this by adding WORKDIR /app to your Dockerfile.
Had to change last line of entrypoint.R from pr to pr$run(host='0.0.0.0', port=8000) to make it actually run.

Full Dockerfile:

FROM rstudio/plumber

# Install R libraries
RUN R -e "install.packages(c('odbc','glue','parsedate','tibble','dplyr','httr','RCurl','jsonlite','rjson','stringr','telegram','R.utils','logger','tictoc'))"
RUN R -e "install.packages(c('fs'))"

WORKDIR /app
ENTRYPOINT ["Rscript", "/app/entrypoint.R"]

Full entrypoint.R file:

library(plumber)

# Config
#config <- config::get()

# logging
library(logger)
# Ensure glue is a specific dependency so it's avaible for logger
library(glue)

# Specify how logs are written 
log_dir <- "/app/logs"
if (!fs::dir_exists(log_dir)) fs::dir_create(log_dir)
log_appender(appender_tee(tempfile("plumber_", log_dir, ".log")))

convert_empty <- function(string) {
  if (string == "") {
    "-"
  } else {
    string
  }
}

pr <- plumb("plumber.R")

pr$registerHooks(
  list(
    preroute = function() {
      # Start timer for log info
      tictoc::tic()
    },
    postroute = function(req, res) {
      end <- tictoc::toc(quiet = TRUE)
      # Log details about the request and the response
      # TODO: Sanitize log details - perhaps in convert_empty
      log_info('{convert_empty(req$REMOTE_ADDR)} "{convert_empty(req$HTTP_USER_AGENT)}" {convert_empty(req$HTTP_HOST)} {convert_empty(req$REQUEST_METHOD)} {convert_empty(req$PATH_INFO)} {convert_empty(res$status)} {round(end$toc - end$tic, digits = getOption("digits", 5))}')
    }
  )
)

pr$run(host='0.0.0.0', port=8000)

How to deploy a Plumber docker that writes a log file?

1 Answers1