Chapter 7 Dockerfile for JAMES

7.1 Objective

This chapter describes how to build and deploy JAMES as a Docker container.

7.2 Pre-requisites

JAMES is currently constructed from a collection of R packages. The top-level package at https://github.com/growthcharts/james also defines a Javascript interface in the inst/www directory. Deployment of JAMES relies on the OpenCPU server. In principle, it is enough to install the james package on the OpenCPU server, and will also install all dependencies.

The following is needed to build and run a JAMES image:

  • Permission to read from the following private repo’s:

    • growthcharts/chartplotter
    • growthcharts/curvematching
    • growthcharts/donorloader
    • growthcharts/jamesdocker

  • If needed, a personal Github token with repo scope from here, Generate a token with only scope repo.

  • Install Docker Desktop on your local machine, and run some tutorials

7.3 Dockerfile

The Dockerfile is at https://raw.githubusercontent.com/growthcharts/jamesdocker/master/Dockerfile, which is located in the private repo https://github.com/growthcharts/jamesdocker. You need authentication to use this resource.

  • Clone the growthcharts/jamesdocker repo to your machine
  • Set working directory to root of jamesdocker
  • If needed: Add the file docker/opencpu_config/Renviron with contents GITHUB_PAT=fa2... with your own GITHUB_PAT.

7.4 Docker commands

Build the james image, type in a terminal

docker build -t james .

This may takes a long time (30 minutes), in which the entire application is downloaded from various web-locations. After (hopefully successful) completion, check the image

docker images -a

If all is well, the top line is called james. Now run the container on your local machine:

docker run -t -d -p 80:80 james

If the ports are already taken by other containers, stop and remove all containers:

docker stop $(docker ps -a -q)
docker rm $(docker ps -a -q)

Reissue the docker run, and the container should now run. Check by

docker ps

which should list a container created from the james image.

If you want to enter the container use

docker exec -i -t 6c /bin/bash

where 6c are the first two characters of the container ID.

Inside the container, check font matching of Arial as

fc-match Arial

7.5 Checks with the browser

http://localhost

should show Apache2 Ubuntu default screen.

http://localhost/ocpu/test/

should show OpenCPU test page.

http://localhost/rstudio/

should start the Rstudio IDE - if installed . Use opencpu:opencpu to log in.

http://localhost/ocpu/library/james/www/

should start the JAMES javascript interface.

See also https://registry.hub.docker.com/r/opencpu/rstudio

7.6 Security

  1. Don’t use the intermediate container, since it will contain your token in /.Renviron. The latest (james) container does not hold your token, and can be shared.
  2. The container is shielded from the machine on which it runs. However, the materials within the container are only protected by R_LIMITS. In general, for production it is wise to add restriction on the OpenCPU server.