First commit

2024-12-21 12:28:12 +00:00 · 2018-05-20 20:14:00 +02:00 · 2018-05-20 20:14:00 +02:00 · 3f287c88b3
commit 3f287c88b3
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--- a/.gitignore
+++ b/.gitignore
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+.*
+ssl-custom
--- a/README.md
+++ b/README.md
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+# Your data science lab, in a box
+
+This repository contains two example deployments of a multi-user isolated environments using Jupyterhub.
+It is aimed towards small research or data science teams.
+
+The first one authenticates users using GitHub OAuth.
+
+The second one also contains a self-hosted GitLab instance, which can be used for authentication and every else (e.g. CI/CD and docker registry).
+It also contains an Nginx service as a reverse proxy
+
+Although these deployments have been tested on a single machine, it can be scaled to multiple nodes using swarm (see https://github.com/jupyterhub/dockerspawner/pull/216).
+
+Note that this is not meant as a guide or complete tutorial.
+If you want to learn more about Jupyter(hub)'s architecture and configuration options, check out:
+
+* https://github.com/jupyterhub/jupyterhub-deploy-docker
+* https://z2jh.jupyter.org
+
+# What's Jupyter?
+
+
+Most people associate the Jupyter project (formerly known as ipython server) to the notebooks.
+But it is way more than that: it is FANTASTIC project and community!
+It includes many actively developed open source projects that go way beyond the original idea of notebooks and kernels.
+Moreover, most of these projects are cloud-oriented.
+Just to name a few:
+
+* Jupyterhub: http://jupyterhub.readthedocs.io/en/latest/
+* Jupyterlab: https://jupyterlab.readthedocs.io/en/stable/
+* nbgrader: https://nbgrader.readthedocs.io/en/stable/
+* Binder: https://mybinder.org/
+
+In this repository we set up jupyterhub, which extends jupyter by providing multi-user support, authentication and different isolation/deployment options.
+
+# Requirements
+
+* Docker
+* Docker-compose
+* Docker-machine (recommended)
+
+# Setup
+
+* Create a machine
+* Add SSH key
+* Configure a DNS wildcard for your domain (if you don't own a domain, check out http://nip.io/ or http://xip.io)
+* For convenience, change the SSH port to something other than 22 (e.g. 2222):
+```
+vi /etc/sshd_config
+systemctl restart sshd
+```
+* Install docker. The easiest way is to use docker-machine:
+
+```
+docker-machine create --driver generic --generic-ip-address=lab.todevnull.com  --generic-ssh-key ~/.ssh/id_rsa --generic-ssh-port 2222  labinabox
+```
+* Set up your environment to start using the remote docker:
+```
+eval $(docker-machine env labinabox) 
+docker info
+```
+* The docker spawner does not fetch the single-user image automatically, so you will have to pull it manually:
+```
+docker pull jupyter/scipy-notebook:latest
+```
+* Create a folder for user homes (workspaces) and give the docker image write permissions:
+```
+docker-machine ssh labinabox 'mkdir /mnt/home'
+docker-machine ssh labinabox 'chown -R 1000:100 -R /mnt/home'
+```
+
+# SSL
+
+This demo assumes you have a valid certificate (`/etc/ssl/ssl-custom/cert.pem`) and a key (`/etc/ssl/ssl-custom/key.pem`) for your domain.
+
+
+## Certbot
+You're encouraged to use a valid certificate authority such as letsencrypt.
+Using certbot is pretty straightforward.
+It even comes bundled in a docker image, and a standalone server:
+
+```
+LE_VERSION=v0.14.0
+DOMAIN=todevnull.com
+docker run -ti --rm -p 80:80 -p 443:443 --name certbot \
+    -v '/data/letsencrypt/etc/letsencrypt/:/etc/letsencrypt' \
+    -v '/data/letsencrypt/var/lib/letsencrypt:/var/lib/letsencrypt' \
+    -v '/var/www/letsencrypt/:/webroot' \
+    certbot/certbot:$LE_VERSION certonly --standalone \
+    --expand --keep \
+    -d hub.$DOMAIN -d lab.$DOMAIN -d registry.$DOMAIN -d github.$DOMAIN -d chat.$DOMAIN -d github.$DOMAIN
+
+```
+
+Now, simply move the generated certificates to the paths the demos expect:
+
+```
+docker-machine ssh labinabox "cp -L /data/letsencrypt/etc/letsencrypt/live/hub.$DOMAIN/privkey.pem /etc/ssl/ssl-custom/key.pem"
+docker-machine ssh labinabox "cp -L /data/letsencrypt/etc/letsencrypt/live/hub.$DOMAIN/fullchain.pem /etc/ssl/ssl-custom/cert.pem"
+```
+
+## Self-signed
+
+For a simple test, you can also generate your own self-signed certificates using openssl:
+
+```
+export DOMAIN=<YOUR DOMAIN NAME>
+openssl req -x509 -newkey rsa:4096 -keyout ssl-custom/key.pem -out ssl-custom/cert.pem -days 365 -subj "/C=ES/ST=Madrid/L=Madrid/O=Lab in a Box/OU=Org/CN=*.${DOMAIN}"
+
+docker-machine scp -r ssl-custom labinabox:/etc/ssl/
+```
+
+# Notes
+
+* Instead of creating a custom image, nginx should rely on the vanilla nginx docker image with configuration as a bind mount, but that requires syncing configuration files with the server.
+* **Do not even consider deploying an environment like the one in this demo without a backup strategy**: http://www.taobackup.com/
+* Folder permissions should be more restrictive. You can chown the files to the default uid and gid of the jupyter image.
--- a/github/README.md
+++ b/github/README.md
@ -0,0 +1,19 @@
+This deployment contains a single jupyterhub service, with the docker spawner and GitHub Oauth authentication.
+
+Every user will get an isolated docker container after authenticating with GitHub.
+The image for that container is configurable through the `DOCKER_IMAGE` environment variable.
+
+
+# Instructions
+
+Before running docker compose, you need to create a GitHub application: https://developer.github.com/apps/building-github-apps/creating-a-github-app/
+Add the client ID and client secret to your `.env` file, or to your environment.
+
+
+# Example .env file
+
+```
+DOMAIN=todevnull.com
+GITHUB_CLIENT_ID=<CLIENT ID>
+GITHUB_CLIENT_SECRET=<CLIENT_SECRET>
+```
--- a/github/docker-compose.yml
+++ b/github/docker-compose.yml
@ -0,0 +1,34 @@
+version: '3.6'
+services:
+  jupyter:
+    networks:
+      - labinabox
+    ports:
+      - '80:8000'
+      - '443:8000'
+    image: gsiupm/jupyterhub-oauth:0.8.1
+    command: jupyterhub -f /srv/jupyterhub/jupyterhub_config.py
+    hostname: jupyterhub
+    volumes:
+        - "/mnt/home:/mnt/home"
+        - "/var/run/docker.sock:/var/run/docker.sock"
+        - '/etc/ssl/ssl-custom/cert.pem:/srv/oauthenticator/ssl/ssl.cert'
+        - '/etc/ssl/ssl-custom/key.pem:/srv/oauthenticator/ssl/ssl.key'
+    environment:
+        OAUTH_CALLBACK_URL: "https://github.${DOMAIN-?todevnull.com}/hub/oauth_callback"
+        HOST_HOMEDIR: "/mnt/home/{username}"
+        OAUTH_CLASS: "oauthenticator.github.GitHubOAuthenticator"
+        GITHUB_CLIENT_ID: "${GITHUB_CLIENT_ID}"
+        GITHUB_CLIENT_SECRET: "${GITHUB_CLIENT_SECRET}"
+        JPY_COOKIE_SECRET: "${JPY_COOKIE_SECRET}"
+        JPY_API_TOKEN: "${CONFIGPROXY_AUTH_TOKEN}"
+        OAUTH_TLS_VERIFY: 0
+        COMMON_DIR: "/mnt/home/common"
+        DATASETS_DIR: "/mnt/home/datasets"
+        ADMINS: "${HUB_ADMINS-balkian,root}"
+        DOCKER_MEM_LIMIT: '250M'
+        DOCKER_NETWORK: labinabox
+
+networks:
+  labinabox:
+    name: labinabox
--- a/gitlab-selfhosted/README.md
+++ b/gitlab-selfhosted/README.md
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+This deployment contains:
+
+* Gitlab for code and authentication. The omnibus image is an all-in-one package that contains:
+    * Git (`git.domain.com`) and CI/CD 
+    * Docker registry (`registry.domain.com`)
+    * Mattermost (slack clone, `chat.domain.com`)
+    * Postgres db
+* Jupyterhub for multi-user computing (`hub.domain.com`)
+    * Authentication with Gitlab
+    * Every user has an isolated environment (thanks to Docker-spawner)
+    * Based on https://github.com/balkian/jupyterhub-oauth
+* Nginx as a reverse proxy
+
+# Instructions
+
+Set the `DOMAIN` variable in a `.env` file and run this compose.
+After GitLab is loaded, create an OAuth application in Gitlab: https://docs.gitlab.com/ce/integration/oauth_provider.html
+The redirect URL is: `https://hub.<your domain>/hub/oauth_callback`.
+Click on `API` level and `trusted`.
+
+Write the client ID and client secret to a `.env` file in this folder.
+
+Then, update the Jupyter service.
+
+# Example .env file
+
+```
+DOMAIN=<YOUR DOMAIN>
+GITLAB_CLIENT_ID=<YOUR ID>
+GITLAB_CLIENT_SECRET=<YOUR SECRET>
+```
+
+# Advanced configuration
+
+GitLab's documentation is terrific.
+For a list of configuration options, see https://docs.gitlab.com/omnibus/docker/#install-gitlab-using-docker-compose .
+
+
+# Note
+
+When run as part of the omnibus, mattermost should register an application automatically on Gitlab.
+I've had some issues with authentication, so if I've explicitly added the OAuth parameters in the compose file.
+This way, you can manually register mattermost on your instance.
+The process is similar to jupyter, and the callback URLs are:
+
+
+```
+https://chat.$DOMAIN/signup/gitlab/complete
+https://chat.$DOMAIN/login/gitlab/complete
+```
+
--- a/gitlab-selfhosted/docker-compose.yml
+++ b/gitlab-selfhosted/docker-compose.yml
@ -0,0 +1,118 @@
+version: '3.6'
+services:
+  web:
+    build: nginx
+    networks:
+      - labinabox
+    image: 'custom-nginx'
+    depends_on:
+      - jupyter
+      - gitlab
+    ports:
+      - '80:80'
+      - '443:443'
+    environment:
+      REGISTRY_INTERNAL: http://gitlab:4567
+      LAB_INTERNAL: http://gitlab:80
+      HUB_INTERNAL: http://jupyter:8000
+      DOMAIN: ${DOMAIN-?todevnull.com}
+    volumes:
+      - '/etc/ssl/ssl-custom/cert.pem:/ssl/certs/nginx.crt'
+      - '/etc/ssl/ssl-custom/key.pem:/ssl/private/nginx.key'
+      - '/data/html:/usr/share/nginx/html'
+  gitlab:
+    networks:
+      - labinabox
+    image: 'gitlab/gitlab-ce:10.7.3-ce.0'
+    restart: always
+    hostname: 'lab.${DOMAIN-?todevnull.com}'
+    environment:
+      GITLAB_OMNIBUS_CONFIG: |
+        external_url 'https://lab.${DOMAIN-?todevnull.com}'
+        mattermost_external_url 'https://chat.todevnull.com/'
+        registry_external_url 'https://registry.${DOMAIN-?todevnull.com}'
+
+        nginx['listen_port'] = 80
+        nginx['listen_https'] = false
+        # LFS
+        gitlab_rails['lfs_enabled'] = true
+        gitlab_rails['lfs_storage_path'] = "/mnt/lfs"
+        # Registry
+        gitlab_rails['registry_enabled'] = true
+        gitlab_rails['registry_port'] = "443"
+
+        registry_nginx['redirect_http_to_https'] = false
+        registry_nginx['listen_port'] = 4567
+        registry_nginx['nginx_enable'] = true
+        registry_nginx['listen_https'] = false
+        registry_nginx['https'] = false
+        gitlab_rails['registry_api_url'] = "http://127.0.0.1:5000"
+        registry['registry_http_addr'] = "127.0.0.1:5000" 
+        registry_nginx['proxy_set_headers'] = {
+          "Host" => "registry.${DOMAIN}",
+          "X-Forwarded-Proto" => "https",
+          "X-Forwarded-Ssl" => "on"
+        }
+
+        mattermost['service_use_ssl'] = false
+        mattermost_nginx['listen_port'] = 80
+        mattermost_nginx['listen_https'] = false
+        mattermost['gitlab_enable'] = true
+        mattermost['gitlab_id'] = "${MATTERMOST_ID}"
+        mattermost['gitlab_secret'] = "${MATTERMOST_SECRET}"
+        mattermost['gitlab_scope'] = ""
+        mattermost['gitlab_auth_endpoint'] = "https://lab.${DOMAIN-?todevnull.com}/oauth/authorize"
+        mattermost['gitlab_token_endpoint'] = "https://lab.${DOMAIN-?todevnull.com}/oauth/token"
+        mattermost['gitlab_user_api_endpoint'] = "https://lab.${DOMAIN-?todevnull.com}/api/v4/user"
+
+
+        # Chat
+        mattermost_nginx['redirect_http_to_https'] = false
+    ports:
+      - '8080:80'
+      - '8443:443'
+      - '22:22'
+      - '4567:4567'
+    volumes:
+      - 'gitlab-config:/etc/gitlab'
+      - 'gitlab-logs:/var/log/gitlab'
+      - 'gitlab-data:/var/opt/gitlab'
+      - 'gitlab-lfs:/mnt/lfs' 
+  jupyter:
+    networks:
+      - labinabox
+    image: gsiupm/jupyterhub-oauth:0.8.1
+    command: jupyterhub --no-ssl -f /srv/jupyterhub/jupyterhub_config.py
+    hostname: jupyterhub
+    volumes:
+        - "/mnt/home:/mnt/home"
+        - "/var/run/docker.sock:/var/run/docker.sock"
+    environment:
+        OAUTH_CALLBACK_URL: "https://hub.${DOMAIN-?todevnull.com}/hub/oauth_callback"
+        HOST_HOMEDIR: "/mnt/home/{username}"
+        OAUTH_CLASS: "oauthenticator.gitlab.GitLabOAuthenticator"
+        GITLAB_HOST: "https://lab.${DOMAIN-?todevnull.com}/"
+        GITLAB_CLIENT_ID: "${GITLAB_CLIENT_ID}"
+        GITLAB_CLIENT_SECRET: "${GITLAB_CLIENT_SECRET}"
+        JPY_COOKIE_SECRET: "${JPY_COOKIE_SECRET}"
+        JPY_API_TOKEN: "${CONFIGPROXY_AUTH_TOKEN}"
+        OAUTH_TLS_VERIFY: 0
+        COMMON_DIR: "/mnt/home/common"
+        DATASETS_DIR: "/mnt/home/datasets"
+        ADMINS: "${HUB_ADMINS-balkian,root}"
+        DOCKER_NETWORK: labinabox
+        DOCKER_MEM_LIMIT: '150M'
+
+volumes:
+  gitlab-config:
+    name: gitlab-config
+  gitlab-logs:
+    name: gitlab-logs
+  gitlab-data:
+    name: gitlab-data
+  gitlab-lfs:
+    name: gitlab-lfs
+
+networks:
+  labinabox:
+    name: labinabox
--- a/gitlab-selfhosted/nginx/Dockerfile
+++ b/gitlab-selfhosted/nginx/Dockerfile
@ -0,0 +1,9 @@
+FROM nginx:1.13
+
+ENV DOMAIN="todevnull.com" HUB_INTERNAL="http://jupyter:80" LAB_INTERNAL="gitlab:80" REGISTRY_INTERNAL="gitlab:5000"
+
+COPY init.sh /
+COPY snippets/ /etc/nginx/snippets/
+COPY conf.d /etc/nginx/conf.d/
+
+CMD /init.sh
--- a/gitlab-selfhosted/nginx/conf.d/hub.conf.template
+++ b/gitlab-selfhosted/nginx/conf.d/hub.conf.template
@ -0,0 +1,54 @@
+server {
+	listen 80;
+
+	access_log /var/log/nginx/hub.access.log;
+# add Strict-Transport-Security to prevent man in the middle attacks
+
+   server_name hub.${DOMAIN};
+   
+   root /var/www/html/ ;
+
+   include /etc/nginx/snippets/letsencrypt.conf;
+
+   location / {
+       return 301 https://$host$request_uri;
+   }
+
+
+}
+
+server {
+    listen 443 ssl;
+    listen [::]:443 ssl;
+
+    server_name hub.${DOMAIN} ; 
+
+    access_log /var/log/nginx/hub.access.log;
+    error_log /var/log/nginx/hub.error.log;
+    # add Strict-Transport-Security to prevent man in the middle attacks
+    #add_header Strict-Transport-Security "max-age=31536000"; 
+    client_max_body_size 100M;
+
+    ssl_certificate /ssl/certs/nginx.crt;
+    ssl_certificate_key /ssl/private/nginx.key;
+   
+	location / {
+		proxy_set_header        Host $host;
+		proxy_set_header        X-Real-IP $remote_addr;
+		proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;
+		proxy_set_header        X-Forwarded-Proto $scheme;
+
+		proxy_pass ${HUB_INTERNAL};
+	}
+
+    location ~* /user/([a-zA-Z0-9]+)/(api/kernels/[^/]+/(channels|iopub|shell|stdin)|terminals/websocket)/? {
+
+        proxy_set_header      Host $host;
+        # websocket support
+        proxy_http_version    1.1;
+        proxy_set_header      Upgrade "websocket";
+        proxy_set_header      Connection "Upgrade";
+
+        proxy_pass ${HUB_INTERNAL};
+    }
+}
--- a/gitlab-selfhosted/nginx/conf.d/lab.conf.template
+++ b/gitlab-selfhosted/nginx/conf.d/lab.conf.template
@ -0,0 +1,79 @@
+server {
+   listen 80;
+
+   server_name lab.${DOMAIN} chat.${DOMAIN};
+   
+   root /var/www/html/ ;
+
+   include /etc/nginx/snippets/letsencrypt.conf;
+
+   location / {
+       return 301 https://$host$request_uri;
+   }
+
+}
+
+server {
+    listen 443 ssl;
+    listen [::]:443 ssl;
+
+    server_name lab.${DOMAIN} chat.${DOMAIN} ;    
+
+    access_log /var/log/nginx/gitlab.access.log;
+    error_log /var/log/nginx/gitlab.error.log;
+    # add Strict-Transport-Security to prevent man in the middle attacks
+    #add_header Strict-Transport-Security "max-age=31536000"; 
+    ssl_certificate /ssl/certs/nginx.crt;
+    ssl_certificate_key /ssl/private/nginx.key;
+
+    root /var/www/html/ ;
+
+   
+    location / {
+      client_max_body_size 0;
+      proxy_set_header        Host $host;
+      proxy_set_header        X-Real-IP $remote_addr;
+      proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header        X-Forwarded-Proto $scheme;
+  
+      proxy_pass ${LAB_INTERNAL} ;
+    }
+
+}
+
+server {
+    listen 443 ssl;
+    listen [::]:443 ssl;
+
+    server_name registry.${DOMAIN} ;    
+
+    access_log /var/log/nginx/gitlab-registry.access.log;
+    error_log /var/log/nginx/gitlab-registry.error.log;
+    # add Strict-Transport-Security to prevent man in the middle attacks
+    #add_header Strict-Transport-Security "max-age=31536000"; 
+    # disable any limits to avoid HTTP 413 for large image uploads
+    client_max_body_size 0;
+
+    # required to avoid HTTP 411: see Issue #1486 (https://github.com/docker/docker/issues/1486)
+    chunked_transfer_encoding on;
+    ssl_protocols TLSv1.1 TLSv1.2;
+    ssl_ciphers 'EECDH+AESGCM:EDH+AESGCM:AES256+EECDH:AES256+EDH';
+    ssl_prefer_server_ciphers on;
+    ssl_session_cache shared:SSL:10m;
+
+   include /etc/nginx/snippets/letsencrypt.conf;
+
+    root /var/www/html/ ;
+   
+    location / {
+
+      proxy_set_header        Host $host;
+      proxy_set_header        X-Real-IP $remote_addr;
+      proxy_set_header        X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header        X-Forwarded-Proto $scheme;
+  
+      proxy_pass ${REGISTRY_INTERNAL};
+      proxy_read_timeout                  900;
+    }
+
+}
--- a/gitlab-selfhosted/nginx/init.sh
+++ b/gitlab-selfhosted/nginx/init.sh
@ -0,0 +1,9 @@
+#!/bin/sh
+cd /etc/nginx/conf.d/
+
+VARIABLES='${HUB_INTERNAL}${DOMAIN}${LAB_INTERNAL}${REGISTRY_INTERNAL}'
+for i in *.template; do
+    target=$(basename $i ".template")
+    envsubst $VARIABLES < $i > $target;
+done || exit 1
+nginx -g 'daemon off;'
--- a/gitlab-selfhosted/nginx/snippets/letsencrypt.conf
+++ b/gitlab-selfhosted/nginx/snippets/letsencrypt.conf
@ -0,0 +1,44 @@
+#############################################################################
+# Configuration file for Let's Encrypt ACME Challenge location
+# This file is already included in listen_xxx.conf files.
+# Do NOT include it separately!
+#############################################################################
+#
+# This config enables to access /.well-known/acme-challenge/xxxxxxxxxxx
+# on all our sites (HTTP), including all subdomains.
+# This is required by ACME Challenge (webroot authentication).
+# You can check that this location is working by placing ping.txt here:
+# /var/www/letsencrypt/.well-known/acme-challenge/ping.txt
+# And pointing your browser to:
+# http://xxx.domain.tld/.well-known/acme-challenge/ping.txt
+#
+# Sources:
+# https://community.letsencrypt.org/t/howto-easy-cert-generation-and-renewal-with-nginx/3491
+#
+#############################################################################
+
+# Rule for legitimate ACME Challenge requests (like /.well-known/acme-challenge/xxxxxxxxx)
+# We use ^~ here, so that we don't check other regexes (for speed-up). We actually MUST cancel
+# other regex checks, because in our other config files have regex rule that denies access to files with dotted names.
+location ^~ /.well-known/acme-challenge/ {
+
+    # Set correct content type. According to this:
+    # https://community.letsencrypt.org/t/using-the-webroot-domain-verification-method/1445/29
+    # Current specification requires "text/plain" or no content header at all.
+    # It seems that "text/plain" is a safe option.
+    default_type "text/plain";
+
+    # This directory must be the same as in /etc/letsencrypt/cli.ini
+    # as "webroot-path" parameter. Also don't forget to set "authenticator" parameter
+    # there to "webroot".
+    # Do NOT use alias, use root! Target directory is located here:
+    # /var/www/common/letsencrypt/.well-known/acme-challenge/
+    root         /var/www/letsencrypt;
+}
+
+# Hide /acme-challenge subdirectory and return 404 on all requests.
+# It is somewhat more secure than letting Nginx return 403.
+# Ending slash is important!
+location = /.well-known/acme-challenge/ {
+    return 404;
+}