run_rstudio_server

#!/usr/bin/env bash

USAGE="Usage: run_rstudio_server -i <image> -u <user list> -p <admin password>\n
\n
This command generates docker containers based on a rstudio server container for each user\n
\n
-i image name. If not present yet it will be downloaded from docker hub. Should be based on a rocker/rstudio image. Default: rocker/rstudio\n
-u user list. Tab delimited list of users with three columns: port, user name, password\n
-p admin password. Password used for the admin container.\n
-m maximum memory for the user container. Default: 16g.\n
-c maximum number of cpu for the user container. Default: 4.
-n container name prefix. Default: jupyter \n
-a add admin container[yes/no]. Default: yes \n"

while getopts ":i:u:p:m:c:n:a:" opt
do
  case $opt in
    i)
      IMAGE=$OPTARG
      ;;
    u)
      USERLIST=$OPTARG
      ;;
    p)
      MASTERPW=$OPTARG
      ;;
    m)
      MEMORY=$OPTARG
      ;;
    c)
      CPU=$OPTARG
      ;;
    n)
      CONTAINER_NAME=$OPTARG
      ;;
    a)
      ADD_ADMIN=$OPTARG
      ;;
    \?)
      echo -e "Invalid option: -$OPTARG \n" >&2
      echo -e $USAGE >&2
      exit 1
      ;;
    :)
      echo -e "Option -$OPTARG requires an argument. \n"
      echo -e $USAGE >&2
      exit 1
      ;;
  esac
done

# return usage if no options are passed
if [ $OPTIND -eq 1 ]
then
  echo -e "No options were passed. \n" >&2
  echo -e $USAGE >&2
  exit 1
fi

# required options
if [ "$USERLIST" == "" ]; then echo "option -u is missing, but required">&2 && exit 1; fi
if [ "$MASTERPW" == "" ]; then echo "option -p is missing, but required">&2 && exit 1; fi

# default values
if [ "$IMAGE" == "" ]; then IMAGE=rocker/rstudio; fi
if [ "$MEMORY" == "" ]; then MEMORY=16g; fi
if [ "$CPU" == "" ]; then CPU=4; fi
if [ "$CONTAINER_NAME" == "" ]; then CONTAINER_NAME=rstudio; fi
if [ "$ADD_ADMIN" == "" ]; then ADD_ADMIN=yes; fi

# create general volume that will be populated with read-only data
docker volume create data
# create general volume for group work
docker volume create group

if [ "$ADD_ADMIN" == "yes" ] 
then
  docker run \
  -d \
  -e ROOT=TRUE \
  -p 9000:8787 \
  --name rstudio_admin \
  -e PASSWORD=$MASTERPW \
  --mount source=data,target=/home/rstudio/data \
  --mount source=group,target=/group_work \
  $IMAGE
fi

# remove carriage returns and spaces and pipe to while loop
cat $USERLIST | tr -d '\015\040' | while read port user password
do
    # create user volume. If the container crashes the volume keeps existing.
  docker volume create $user

  # generate container for each user
  # mount user volume, data volume (general, read only) and group work volume (general, read and write)
  # the permissions of general volumes (data and group work) need to be changed with the master container (this can probably be coded as well)


  docker run \
  -d \
  --cpus=$CPU \
  --memory=$MEMORY \
  --restart=on-failure:10 \
  --name "$CONTAINER_NAME"_"$user" \
  -p $port:8787 \
  --name rstudio_"$user" \
  -e PASSWORD=$password \
  --mount source=$user,target=/home/rstudio \
  --mount source=data,target=/data,readonly \
  --mount source=group,target=/group_work \
  $IMAGE
done