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Background

This code base to deploy Jupyter Notebooks using JupyterHub is based on the open source reference implementation from https://github.com/jupyterhub/jupyterhub-deploy-docker.

It also uses Docker (https://www.docker.com/) containers to manage the three pieces of software needed to run this set up:

1. JupyterHub - takes care of authentication and spawning of single-user notebook servers (containers)
2. Jupyter Notebooks - notebook environment with Python 3.6 kernel
3. PostgreSQL database backend to store notebook user data (or one can use SQLite instead)

Installation Guide - Quick

First install on localhost machine

1. Install Docker, docker-compose, git. (...or run sudo install-docker-bionic.sh - be sure to change $INSTALL_USER variable to your local username.)
2. Open terminal app and cd to preferred workspace directory
3. git clone this repository: git clone https://github.com/PHI-Toolkit/jupyterhub-deploy-docker-localhost.git
4. cd jupyterhub-deploy-docker-localhost, locate buildhub.sh, make sure it is executable and run this script on command line.
5. Wait for the buildhub.sh script to finish, watch for build errors. Then locate starthub.sh, make sure it is executable, then run ./starthub.sh on a terminal. You will see container logs being displayed as the containers start up. Before running ./starthub.sh you may want to check: 5.1 Built Docker containers: run docker images on the terminal. 5.2 Running containers (after running ./starthub.sh: run docker ps on the terminal.
6. Open Chrome, Chrome-based Edge, Safari, or Firefox browser and proceed to https://localhost. (Look up default login credentials on .env file.)

Changing the UI to Jupyter Notebook Classic

JupyterLab is the default user interface. You can easily switch from the JupyterLab user interface to Jupyter Notebook Classic:

1. Temporarily by editing the URL, and replacing lab with tree.
2. Permanently by switching the .env file entry JUPYTER_UI=/lab with JUPYTER_UI=notebook (slash is important for lab).

First install on remote server

Follow steps 1-6 above and replace localhost with IP address of remote server. See also Four Steps below. If you get a NET::ERR_CERT_INVALID error on Chrome, use Firefox instead or see this Stack Overflow solution for Chrome.

Modifying the .env and userlist files

The .env is automatically created after the first run of the buildhub.sh script. It contains configurable parameters for this application, including:

1. Authentication - includes dummy_authenticator (default), github_authenticator
2. SSL Certificate - self-signed (default) or LetsEncrypt
3. Database for user data - SQLite or PostGreSQL
4. Custom logo (filename pointer to image)
5. Jupyter Notebook UI or JupyterLab
6. Versions of JupyterHub, JupyterLab, Jupyter Notebook, and PostGRESQL Hub backend
7. OAuth, Notebook and Hub, PostGreSQL Authentication Credentials
8. Single-user Notebook server timeout (when idle servers are culled or stopped)

The userlist file is automatically created from userlist-template after the first run of the buildhub.sh script. For GitHub autentication, follow the template entry for recording GitHub username in the userlist file and assigning admin status. This can also be done through the Admin interface of JupyterHub.

Starting and Stopping Containers

1. cd to the folder where you did git clone of the GitHub repository. (This is important to do before running any of the shell scripts below.)
2. To start containers, run ./starthub.sh. Running this script also displays the logs for the running containers as they boot up and/or encounter any launch errors.
3. To stop containers, press ctrl-C if you see log file display on your terminal. When you see the terminal prompt, run ./stophub.sh.
4. You can also use ./restarthub.sh for stopping and restarting containers.

Recommended four steps for remote server install (unmodified .env file to full LetsEncrypt SSL certificate)

Step 1

Follow steps for first install (step 1-6, unmodified .env file after git clone) then test if the JupyterHub server can be accessed at https://<server IP address> using a Chrome or Firefox browser. First install uses default settings - dummy_authenticator, self-signed SSL certificates for running on localhost machine. The localhost IP address can be replaced with the server IP address.

Figure 1. JupyterHub signin page using dummy_authenticator and self-signed SSL certificate

Step 2

Obtain a domain name and assign it to the JupyterHub server IP address. Test if the JupyterHub server can be accessed through the fully qualified domain name (FQDN) using https. Test the domain name by running ./restarthub.sh at the terminal after exiting from logs display with ctrl-C.

Step 3

Obtain GitHub OAuth credentials and record these in the .env file (around line 67), replacing the GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET and GITHUB_CALLBACK_URL with the correct entries from GitHub. In the .env file (around line 37) make sure you replace JUPYTERHUB_AUTHENTICATOR=dummy_authenticator with this entry, JUPYTERHUB_AUTHENTICATOR=github_authenticator. For high volume access, make sure you also obtain an access token from https://help.github.com/articles/creating-a-personal-access-token-for-the-command-line/ and record the access token using the .env file GITHUB_ACCESS_TOKEN environment variable (around line 73). Other important edits to do at this step:

1. Make sure you add your GitHub username to the userlist file as described above, especially if you see the 403 : Forbidden error in your browser.
2. Run docker-compose build hub to include the revised userlist file in the JupyterHub container. If you have already selected use_ssl_le in the .env file, run docker-compose -f docker-compose-letsencrypt.yml build hub instead.
3. Test GitHub OAuth by restarting the containers using ./restarthub.sh. The display should be similar to Figure 2 below.

Figure 2. JupyterHub sign in page after launching containers.

Step 4

To replace the self-signed SSL certificate with LetsEncrypt certificates, replace the .env file entry JUPYTERHUB_SSL=use_ssl_ss with JUPYTERHUB_SSL=use_ssl_le (around line 86), as well as the JH_FQDN, JH_EMAIL and CERT_SERVER variables in the .env file (around line 92). Leave CERT_SERVER blank for production. Then run ./restarthub.sh on a terminal. The browser display should be similar to Figure 3 below.

Figure 3. JupyterHub sign in page with LetsEncrypt SSL certificate installed.

Installation Guide - Some Details for Remote Servers

Prepare Jupyter Notebook server

Git clone https://github.com/PHI-Toolkit/jupyterhub-deploy-docker-localhost. Change to the jupyterhub-deploy-docker-localhost folder and run the steps below.

JupyterHub Authentication

This build of JupyterHub has three options for Authentication. Go to about Line 18 of the .env file and set the environment variable JUPYTERHUB_AUTHENTICATOR to the selected option.

• tmp_authenticator
• dummy_authenticator (default, see .env-template for details)
• github_authenticator (thru OAuth, requires obtaining GitHub credentials, see below)
• hash_authenticator
• native_authenticator (new)

There is no need to change or update any .env settings for initial one-user (you) launch and testing from a localhost machine. The default setting dummy_authenticator uses the default user jovyan whose password you can set in the .env file before running buildhub.sh.

GitHub authentication

Obtain your GitHub Account Credentials

If you will be using GitHub Oauth to authenticate users to JupyterHub, you need to sign up for a GitHub Account:

1. Go to https://www.github.com and create an account if you do not have one yet.
2. Remember your GitHub user name. You will use this for #3 below.
3. Open the file userlist with your text editor and add your GitHub user name below "jovyan admin" as below:

<github user name> admin

Obtain GitHub OAuth Credentials

• Log in to GitHub
• Go to Developer Settings (https://github.com/settings/developers) - create new Oauth App
• Record the following information:
  • GitHub Client ID
  • GitHub Client Secret
  • GitHub Callback URL: This should be of the form https://"mydomain.com"/hub/oauth_callback if with a domain name (remember to replace "mydomain.com" with your domain name, as obtained from the step above, "Using a Domain Name".)
• Copy-paste each of these to right .env section (about Line 23):

GITHUB_CLIENT_ID=<github client id>

GITHUB_CLIENT_SECRET=<github client secret>

OAUTH_CALLBACK_URL=https://mydomain.com/hub/oauth_callback

If using localhost, replace "mydomain.com" in OAUTH_CALLBACK with "localhost" (i.e., "https://localhost/hub/oauth_callback").

Native Authentication

Quick Start

1. jovyan is the default admin user. You can change this setting in the .env file.
2. On first launch, do not sign in with jovyan and default password. This only works for dummy_authenticator. Instead, go to https://localhost/hub/signup (change localhost to your fully qualified domain name) to sign up as a user.
3. jovyan is the default admin user in userlist and, after sign up, will be authorized by default after log in. Be sure to change the admin user in production. Admin user also needs to sign up.
4. To authorize non-admin users, go to https://localhost/hub/authorize (change localhost to your fully qualified domain name)

Reference for more information

For more information, go to the native authentication documentation.

Renewing LetsEncrypt certificates

The letsencrypt container automatically checks if the LetsEncrypt certificate is about to expire (at 60 days old) and automatically downloads a new certificate as needed.

Upgrading JupyterHub to a newer version

Upon runnng starthub.sh, if you see an error message saying you need to run jupyterhub upgrade-db, you can do the following:

1. Run stophub.sh.
2. Comment option 1 of the command: section of the docker-compose.yml (if running without LetsEncrypt) or docker-compose-letsencrypt.yml (if running with LetsEncrypt), and uncommenting option 2 lines (this runs jupyterhub upgrade-db)
3. Run docker-compose build.
4. After running the database upgrade, run stophub.sh again, uncomment comment out option 2 lines, uncomment option 1 lines and then run docker-compose build again.
5. Run starthub.sh.

(This is based on https://jupyterhub.readthedocs.io/en/stable/reference/upgrading.html)

Notes for Windows users

Windows 10 users should do the following:

1. To run the bash scripts in a bash shell on Windows 10, install the Linux Subsystem on Windows 10 here: https://docs.microsoft.com/en-us/windows/wsl/install-win10
2. Use "Edge Channel" Docker version for Windows 10: https://download.docker.com/win/edge/Docker%20for%20Windows%20Installer.exe
3. Check "Expose daemon on tcp://localhost:2375 without TLS as follows:

JupyterHub Logs / Launch Issues

Upgrading the miniconda version

• Delete the miniconda.sh file from the cloned directory. Run buildhub.sh to download an updated Miniconda3 version to be included in the Dockerfile.jupyterhub image.

Logs: Old base64 cookie-secret detected in /data/jupyterhub_cookie_secret.

• While jupyterhub is running, type the following commands:

$ docker exec -it jupyterhub /bin/bash

• This brings you to the jupyterhub bash prompt. Type the following command to regenerate a new cookie secret:

# openssl rand -hex 32 > "/data/jupyterhub_cookie_secret"

Browser: 403 : Forbidden

• Add your GitHub username to the userlist file as described above.

JupyterHub Logs: socket.gaierror: [Errno -2] Name or service not known

• If you see this error in the logs it means the JUPYTERHUB_SERVICE_HOST_IP is misconfigured.

Windows user

• There may be slight differences in how Chrome or Firefox behaves compared to installations on Linux or Mac (YMMV).

HTTP Error

If you get the error:

An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. ConnectionError(ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out.",),)

...and the buildhub.sh script is building the user container image (running Dockerfile.custom), just run make notebook_base, then make notebook_body, and lastly make notebook_image to resume rebuilding the Jupyter Notebook singleuser container image (shows up as jupyterhub-user if you run docker images on the terminal).

[Errno 111] Connection Refused or in the JupyterHub logs after running starthub.sh you see the error message error: [ConfigProxy] Proxy error: Error: connect EHOSTUNREACH 172.18.0.3:8080 or tornado.curl_httpclient.CurlError: HTTP 599: Failed to connect to 172.18.0.X port 8080: Connection refused

This error could be due to JUPYTERHUB_SERVICE_HOST_IP changing value after restarting Docker server (after server reboot). To address this error, run the script get_service_host_ip.sh at the command line, which will provide you with the new JUPYTERHUB_SERVICE_HOST_IP value. This script automatically replaces the old value in the .env file with this new IP address.

500 : Internal Server Error, Error in Authenticator.pre_spawn_start: ImageNotFound 404 Client Error: Not Found ("pull access denied for phitoolkit/jupyterhub-user, repository does not exist or may require 'docker login': denied: requested access to the resource is denied"), You can try restarting your server from the home page.

This error could be due to failed execution of buildhub.sh, specifically the section that takes care of building the notebook containers (Docker build commands through Makefile). Check if the notebook server image phitoolkit/jupyterhub-user exists. You can also check the Docker build logs (visible during execution) to see which specific Docker build step failed. Execute any of the following or in sequence:

1. make notebook_base
2. make notebook_body
3. make notebook_image

if not, run make notebook_base, make notebook_body, and make notebook_image, before running starhub.sh.

"--squash" is only supported on a Docker daemon with experimental features enabled

This Docker-related error may be encountered during execution of the last make command in buildhub.sh (see #3 make above). To enable experimental features in Docker:

1. At the command line: sudo nano /etc/docker/daemon.json
2. Enter the following, then save the file:

   { experimental:true }

3. At the command line: sudo systemctl restart docker
4. At the command line: docker version