run_jupyter_notebooks

#!/usr/bin/env bash

USAGE="Usage: run_jupyter_notebooks -i <image> -u <user list> -p <admin password>\n
\n
This command generates docker containers based on a jupyter notebook 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 jupyter stacks image. Default: jupyter/base-notebook\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
-n container name prefix. Default: jupyter \n
-a add admin container[yes/no]. Default: yes \n
-d add an additional port at port-2000 [yes/no]. Default: no"

while getopts ":i:u:p:m:c:n:a:d:" 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
      ;;
    d)
      ADD_PORT=$OPTARG
      ;;
    \?)
      echo -e "Invalid option: -$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 [ "$IMAGE" == "" ]; then IMAGE=jupyter/base-notebook; fi
if [ "$MEMORY" == "" ]; then MEMORY=16g; fi
if [ "$CPU" == "" ]; then CPU=4; fi
if [ "$CONTAINER_NAME" == "" ]; then CONTAINER_NAME=jupyter; fi
if [ "$ADD_ADMIN" == "" ]; then ADD_ADMIN=yes; fi
if [ "$ADD_PORT" == "" ]; then ADD_PORT=no; 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

# generate hash for master password
# HASH=`python3 ./generate_pw_hash.py -p $MASTERPW`

# generate admin container
# the option -e GRANT_SUDO=yes is required to e.g. change permissions in the root directory

docker volume create jovyan

if [ "$ADD_ADMIN" == "yes" ] 
then
  docker run \
  -d \
  --name "$CONTAINER_NAME"_admin \
  --mount source=jovyan,target=/home/jovyan/workdir \
  --mount source=data,target=/data \
  --mount source=group,target=/group_work \
  --user root \
  --restart=on-failure:10 \
  -e NB_UMASK=002 \
  -e CHOWN_EXTRA="/group_work" \
  -e GRANT_SUDO=yes \
  -e JUPYTER_ENABLE_LAB=yes \
  -e JUPYTER_TOKEN=$MASTERPW \
  -p 10000:8888 \
  $IMAGE \
  start-notebook.sh
fi

# remove carriage returns and spaces and pipe to while loop
cat $USERLIST | tr -d '\015\040' | while read port user password
do
  # generate hash from password
  # HASH=`python3 ./generate_pw_hash.py -p $password`

  # 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)
  if [ "$ADD_PORT" == "yes" ]
  then 
        ADD_PORT="-p $((port-2000)):$((port-2000))"
  else
        ADD_PORT=""
  fi 

  docker run \
  -d \
  --cpus=$CPU \
  --memory=$MEMORY \
  --restart=on-failure:10 \
  --name "$CONTAINER_NAME"_"$user" \
  --user root \
  -e NB_UMASK=002 \
  -e CHOWN_EXTRA=/home/jovyan/workdir \
  --mount source=$user,target=/home/jovyan/workdir \
  --mount source=data,target=/data,readonly \
  --mount source=group,target=/group_work \
  -e JUPYTER_ENABLE_LAB=yes \
  -e JUPYTER_TOKEN=$password \
  -p $port:8888 \
  $ADD_PORT \
  $IMAGE \
  start-notebook.sh
done

# stop all containers:
# docker stop $(docker ps -aq)
# remove all volumes:
# docker volume rm $(docker volume ls -q)
# check a user-specific volume with:
# USER=user01
# docker run -it --rm --mount source=$USER,target=/$USER -w /$USER ubuntu

# to add https:
# --ServerApp.keyfile=/etc/ssl/notebook/notebook.key \
# --ServerApp.certfile=/etc/ssl/notebook/notebook.pem