Docker Image for single server multi user Jupyterhub with R support, Google Auth & Postgresql Backend

.env

GOOGLE_CLIENT_ID=
GOOGLE_CLIENT_SECRET=
GOOGLE_CALLBACK_URL=

POSTGRES_USERNAME=
POSTGRES_PASSWORD=
POSTGRES_HOST=
POSTGRES_DATABASE=

GOOGLE_HOSTED_DOMAIN=example.com
SERVICE_NAME=ACME Inc

README.md

Jupyterhub

Docker image to setup Jupyterhub on a single server for

• Multiple users
• Support for R
• Jupyterlab

Easy to setup and use for a small organisation.

Build

docker build .

Run with docker compose

version: '3'
services:
  jupyter:
    image: jupyterhub-image
    restart: always
    container_name: jupyterhub
    env_file:
      - .env
    ports:
      - "8080:8000"
    volumes:
      - "/var/run/docker.sock:/var/run/docker.sock"
      - "data:/home"

volumes:
  data:
    external:
      name: jupyterhub-data

docker-entrypoint

#!/bin/bash

exec jupyterhub --ip 0.0.0.0

Dockerfile

FROM jupyterhub/jupyterhub

RUN apt-get update && apt-get install -y gnupg2 software-properties-common
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
RUN apt-get update
RUN apt-get install -y curl \
        r-base \
        libopenblas-base \
        apt-utils \
        wget \
        unzip \
        libpq-dev \
        python-dev \
        build-essential \
        postgresql-server-dev-all \
        nano \
        apt-transport-https \
        vim \
        nmap \
        tree \
        libcurl4-openssl-dev \
        libxml2-dev

RUN pip install jupyter_contrib_nbextensions \
        oauthenticator \
        jupyterlab \
        ipyparallel \
        psycopg2 \
        dockerspawner

RUN ipcluster nbextension enable
RUN Rscript -e "install.packages(c('repr', 'IRdisplay', 'IRkernel','tidyverse','DBI','doparallel','RPostgreSQL','googlesheets','foreach','reshape2','jsonlite','httpuv,'gmailr','tableHTML'), type = 'source')"
RUN Rscript -e "IRkernel::installspec(user = FALSE)"

COPY docker-entrypoint docker-entrypoint
COPY jupyterhub_config.py jupyterhub_config.py
COPY requirements.txt requirements.txt

RUN pip install -r requirements.txt
RUN jupyter contrib nbextension install --sys-prefix

RUN jupyter labextension install @krassowski/jupyterlab_go_to_definition \
        @ryantam626/jupyterlab_code_formatter \
        @jupyterlab/github \
        @jupyterlab/git \
        @oriolmirosa/jupyterlab_materialdarker \
        @jupyterlab/toc

RUN chmod +x docker-entrypoint
ENTRYPOINT ["./docker-entrypoint"]

EXPOSE 8000

jupyterhub_config.py

import os

c = get_config()

# Allow CORS
c.NotebookApp.allow_origin = '*'

# Allows multiple single-server per user
c.JupyterHub.allow_named_servers = True

# Use Google OAuthenticator for local users
c.JupyterHub.authenticator_class = 'oauthenticator.LocalGoogleOAuthenticator'
c.LocalGoogleOAuthenticator.oauth_callback_url = os.environ['GOOGLE_CALLBACK_URL']
c.LocalGoogleOAuthenticator.client_id = os.environ['GOOGLE_CLIENT_ID']
c.LocalGoogleOAuthenticator.client_secret = os.environ['GOOGLE_CLIENT_SECRET']

c.LocalGoogleOAuthenticator.hosted_domain = [os.environ['GOOGLE_HOSTED_DOMAIN']]
c.LocalGoogleOAuthenticator.login_service = os.environ['SERVICE_NAME']
c.Authenticator.add_user_cmd = ['adduser', '-q', '--gecos', '""', '--disabled-password', '--force-badname']

# create system users that don't exist yet
c.LocalAuthenticator.create_system_users = True

# Shutdown idle notebooks after 1.5h of inactivity
c.MappingKernelManager.cull_idle_timeout = 5400
c.NotebookApp.shutdown_no_activity_timeout = 5400

# Use jupyterlab by default
c.Spawner.default_url = '/lab'

# Use Postgresql database
c.JupyterHub.db_url = 'postgresql://{}:{}@{}:5432/{}'.format(
    os.environ['POSTGRES_USERNAME'], os.environ['POSTGRES_PASSWORD'], os.environ['POSTGRES_HOST'], os.environ['POSTGRES_DATABASE']
)

requirements.txt

psycopg2==2.7.7
psycopg2-binary==2.7.7
watchdog==0.9.0
SQLAlchemy==1.3.3
alembic==1.0.10
python-json-logger==0.1.10
datetime==4.3
structlog==19.1.0
requests==2.22.0
tensorflow==1.13.1
numpy==1.16.4
scipy==1.1.0
Pillow==5.3.0
tqdm==4.28.0
python-dotenv==0.10.2
json-logging==0.0.13
scikit-image==0.14.2
pandas==0.25.0