Adds jupyterhub support

.dockerignore

@@ -0,0 +1 @@
+data/

docker-compose.yml

@@ -48,8 +48,10 @@ services:
       # specific sites
       - ./nginx/etc/nginx/sites-enabled/bmegio.ohsu.edu:/etc/nginx/sites-enabled/bmegio.ohsu.edu:ro
       - ./nginx/etc/nginx/sites-enabled/gen3-ohsu.ddns.net:/etc/nginx/sites-enabled/gen3-ohsu.ddns.net:ro
+      - ./nginx/etc/nginx/sites-enabled/bmeg-jupyter.ddns.net:/etc/nginx/sites-enabled/bmeg-jupyter.ddns.net:ro
       - ./nginx/etc/nginx/sites-enabled/bmeg.io:/etc/nginx/sites-enabled/bmeg.io:ro
 
+
       # for letsencrypt
       - ./data/certbot/conf:/etc/letsencrypt
       - ./data/certbot/www:/var/www/certbot
@@ -59,6 +61,7 @@ services:
 
     depends_on:
       - grip
+      - jupyterhub
 
 
   # for letsencrypt
@@ -86,60 +89,92 @@ services:
       - grip
       - mongo
 
-
-  # https://github.com/jupyterhub/jupyterhub-deploy-docker
-  # jupyterhub database
-  hub-db:
-    image: postgres:9.5
-    container_name: jupyterhub-db
-    restart: always
-    environment:
-      POSTGRES_DB: ${POSTGRES_DB}
-      PGDATA: ${DB_VOLUME_CONTAINER}
-    env_file:
-      - secrets/jupyter.env
-    volumes:
-      - "db:${DB_VOLUME_CONTAINER}"
-
-  # jupyterhub
-  hub:
-    depends_on:
-      - hub-db
-    build:
-      context: jupyterhub
-      args:
-        JUPYTERHUB_VERSION: ${JUPYTERHUB_VERSION}
-    restart: always
-    image: jupyterhub
-    container_name: jupyterhub
-    volumes:
-      # Bind Docker socket on the host so we can connect to the daemon from
-      # within the container
-      - "/var/run/docker.sock:/var/run/docker.sock:rw"
-      # Bind Docker volume on host for JupyterHub database and cookie secrets
-      - "data:${DATA_VOLUME_CONTAINER}"
+  # see https://opendreamkit.org/2018/10/17/jupyterhub-docker/
+  jupyterhub:
+    build: jupyterhub                # Build the container from this folder.
+    container_name: jupyterhub       # The service will use this container name.
+    volumes:                         # Give access to Docker socket.
+      - /var/run/docker.sock:/var/run/docker.sock
+      # - ./data/certbot/conf/live/bmegio.ohsu.edu/cert.pem:/etc/letsencrypt/cert.pem
+      # - ./data/certbot/conf/live/bmegio.ohsu.edu/privkey.pem:/etc/letsencrypt/privkey.pem
+      - ./secrets/userlist:/srv/jupyterhub/userlist
       - ./secrets/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py
-    ports:
-      - "443:443"
-    links:
-      - hub-db
-    environment:
-      POSTGRES_HOST: hub-db
+      - /mnt/data1/bmeg/jupyter-data:/data
+    environment:                     # Env variables passed to the Hub process.
+      DOCKER_NOTEBOOK_IMAGE: jupyterlab_img
+      DOCKER_NETWORK_NAME: deployment_default
+      HUB_IP: jupyterhub
+      # SSL_KEY: /etc/letsencrypt/privkey.pem
+      # SSL_CERT: /etc/letsencrypt/cert.pem
     env_file:
       - secrets/jupyter.env
       - secrets/oauth.env
-    command: >
-      jupyterhub -f /srv/jupyterhub/jupyterhub_config.py
-
-# docker volume create --name=jupyterhub-data
-# docker volume create --name=jupyterhub-db-data
-volumes:
-  data:
-    external:
-      name: ${DATA_VOLUME_HOST}
-  db:
-    external:
-      name: ${DB_VOLUME_HOST}
+    depends_on:
+      - grip
+
+  # notebook image, build via: `dc build jupyterlab`
+  # The extra line command: echo is there so that,
+  # when Docker Compose starts the service, it terminates immediately.
+  # Indeed this image is meant to be loaded by the Hub, not by Compose.
+  jupyterlab:
+    build: jupyterlab
+    image: jupyterlab_img
+    command: echo
+
+
+#   # https://github.com/jupyterhub/jupyterhub-deploy-docker
+#   # jupyterhub database
+#   hub-db:
+#     image: postgres:9.5
+#     container_name: jupyterhub-db
+#     restart: always
+#     environment:
+#       POSTGRES_DB: ${POSTGRES_DB}
+#       PGDATA: ${DB_VOLUME_CONTAINER}
+#     env_file:
+#       - secrets/jupyter.env
+#     volumes:
+#       - "db:${DB_VOLUME_CONTAINER}"
+#
+#   # jupyterhub
+#   hub:
+#     depends_on:
+#       - hub-db
+#     build:
+#       context: jupyterhub
+#       args:
+#         JUPYTERHUB_VERSION: ${JUPYTERHUB_VERSION}
+#     # restart: always
+#     # image: jupyterhub
+#     container_name: jupyterhub
+#     volumes:
+#       # Bind Docker socket on the host so we can connect to the daemon from
+#       # within the container
+#       - "/var/run/docker.sock:/var/run/docker.sock:rw"
+#       # Bind Docker volume on host for JupyterHub database and cookie secrets
+#       - "data:${DATA_VOLUME_CONTAINER}"
+#       # - ./secrets/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py
+#     ports:
+#       - "443:443"
+#     links:
+#       - hub-db
+#     environment:
+#       POSTGRES_HOST: hub-db
+#     env_file:
+#       - secrets/jupyter.env
+#       - secrets/oauth.env
+#     command: >
+#       jupyterhub -f /srv/jupyterhub/jupyterhub_config.py
+#
+# # docker volume create --name=jupyterhub-data
+# # docker volume create --name=jupyterhub-db-data
+# volumes:
+#   data:
+#     external:
+#       name: ${DATA_VOLUME_HOST}
+#   db:
+#     external:
+#       name: ${DB_VOLUME_HOST}
 
 # networks:
 #   default:

jupyterhub/Dockerfile

@@ -0,0 +1,14 @@
+# Do not forget to pin down the version
+FROM jupyterhub/jupyterhub:1.0.0
+
+# OLD: Copy the JupyterHub configuration in the container
+  # COPY jupyterhub_config.py .
+# NEW: map as volume -> /srv/jupyterhub/jupyterhub_config.py
+
+# Download script to automatically stop idle single-user servers
+RUN wget https://raw.githubusercontent.com/jupyterhub/jupyterhub/1.0.0/examples/cull-idle/cull_idle_servers.py
+
+# Install dependencies (for advanced authentication and spawning)
+RUN pip install \
+    dockerspawner==0.11.1 \
+    oauthenticator==0.8.2

jupyterlab/Dockerfile

@@ -0,0 +1,9 @@
+FROM jupyter/scipy-notebook:6c3390a9292e
+RUN pip install --pre jupyterhub==1.0.0
+
+# RUN pip install jupyterhub==1.0.0
+
+# RUN conda install --quiet --yes \
+#     'r-base=3.4.1' \
+#     'r-irkernel=0.8*'&& \
+#     conda clean -tipsy

nginx/etc/nginx/grip.conf

@@ -3,7 +3,7 @@
   ##
   lua_ssl_trusted_certificate /etc/ssl/certs/ca-certificates.crt;
   lua_ssl_verify_depth        5;
-	
+
   set_by_lua $ngo_callback_host '
     if os.getenv("NGO_CALLBACK_HOST") then
       return os.getenv("NGO_CALLBACK_HOST")
@@ -54,7 +54,7 @@
   # our protected "landing page"
   location /analyze/access {
     include /etc/nginx/protected.conf;
-    root /usr/share/nginx/html;
+    root /usr/share/nginx/bmegio.ohsu.edu;
     try_files $uri $uri/index.html $uri.html =404;
   }
   location /grip/ {

nginx/etc/nginx/nginx.conf

@@ -92,4 +92,5 @@ http {
 	include /etc/nginx/sites-enabled/bmeg.io;
 	include /etc/nginx/sites-enabled/bmegio.ohsu.edu;
 	include /etc/nginx/sites-enabled/gen3-ohsu.ddns.net;
+	include /etc/nginx/sites-enabled/bmeg-jupyter.ddns.net;
 }

nginx/etc/nginx/sites-enabled/bmeg-jupyter.ddns.net

@@ -0,0 +1,43 @@
+# top-level http config for websocket headers
+# If Upgrade is defined, Connection = upgrade
+# If Upgrade is empty, Connection = close
+map $http_upgrade $connection_upgrade {
+    default upgrade;
+    ''      close;
+}
+
+
+# redirect to https
+server {
+	listen *:80;
+	server_name bmeg-jupyter.ddns.net;
+	return 301 https://$host$request_uri;
+}
+
+server {
+  listen 443 ssl http2;
+  listen [::]:443 ssl http2;
+
+  server_name bmeg-jupyter.ddns.net;
+  ssl_certificate /etc/letsencrypt/live/bmeg-jupyter.ddns.net/fullchain.pem;
+  ssl_certificate_key /etc/letsencrypt/live/bmeg-jupyter.ddns.net/privkey.pem;
+
+
+	# Managing literal requests to the JupyterHub front end
+	location / {
+			proxy_pass http://jupyterhub:8000;
+			proxy_set_header X-Real-IP $remote_addr;
+			proxy_set_header Host $host;
+			proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+
+			# websocket headers
+			proxy_set_header Upgrade $http_upgrade;
+			proxy_set_header Connection $connection_upgrade;
+	}
+
+  # for certbot challenge
+  location /.well-known/acme-challenge/ {
+      root /var/www/certbot;
+  }
+
+}