Updated docker files and fixed j-hub configs.

Author: vladd-bit

Dockerfile_singleuser

@@ -172,7 +172,7 @@ RUN pip3 install --no-cache-dir dvc flask GitPython elasticsearch opensearch-py
 RUN pip3 install --no-cache-dir opencv-python torchvision eland plotly
 
 # XNAT
-RUN pip3 install --no-cache-dir xnat
+RUN pip3 install --no-cache-dir xnat    
 
 # medcat & models
 RUN pip3 install --no-cache-dir -U spacy click torch thinc

README.md

@@ -39,8 +39,9 @@ There are two docker compose files:
 Check the [env/general.env](./env/general.env), set the `CPU_ARCHITECTURE` variable to whatever you need, the default for most Laptops/PCs is `amd64`, if you have an ARM laptop/device then set to `arm64`, that should suffice.
 
 Execute the following in the main repo directory:
+
 ```
-    source envs/*
+    bash export_env_vars.sh
     docker compose up -d
 ```
 

config/jupyterhub_config.py

@@ -66,7 +66,7 @@ def pre_spawn_hook(spawner):
 #c.DockerSpawner.notebook_dir = notebook_dir
 # Mount the real user"s Docker volume on the host to the notebook user"s
 # notebook directory in the container
-c.DockerSpawner.volumes = { "jupyterhub-user-{username}": notebook_dir, "jupyter-hub-shared-scratch": shared_content_dir}
+c.DockerSpawner.volumes = {"jupyterhub-user-{username}": notebook_dir, "jupyter-hub-shared-scratch": shared_content_dir}
 # volume_driver is no longer a keyword argument to create_container()
 
 
@@ -134,13 +134,15 @@ def post_spawn_hook(spawner):
 # need an admin approval so they can actually log in the system.
 c.Authenticator.open_signup = False
 
-c.NotebookApp.allow_root=False
+c.NotebookApp.allow_root = False
 
 c.LocalAuthenticator.create_system_users = True
 c.SystemdSpawner.dynamic_users = True
 c.PAMAuthenticator.admin_groups = {"wheel"}
 c.Authenticator.whitelist = whitelist = set()
 
+#c.Authenticator.allow_all = True
+
 curr_dir = os.path.dirname(__file__)
 
 # Get active users
@@ -270,12 +272,12 @@ def start(self):
 c.ConfigurableHTTPProxy.api_url = jupyter_hub_proxy_url + str(jupyter_hub_proxy_api_port)
 # ideally a private network address
 # c.JupyterHub.proxy_api_ip = "10.0.1.4"
-c.JupyterHub.proxy_api_port = jupyter_hub_proxy_api_port
+# c.JupyterHub.proxy_api_port = jupyter_hub_proxy_api_port
 
 # TLS config
 c.JupyterHub.port = jupyter_hub_ssl_port
-c.JupyterHub.ssl_key = os.environ.get("SSL_KEY", "/etc/jupyterhub/root-ca.key")
-c.JupyterHub.ssl_cert = os.environ.get("SSL_CERT", "/etc/jupyterhub/root-ca.pem")
+c.JupyterHub.ssl_key = os.environ.get("SSL_KEY", "/srv/jupyterhub/root-ca.key")
+c.JupyterHub.ssl_cert = os.environ.get("SSL_CERT", "/srv/jupyterhub/root-ca.pem")
 
 # Persist hub data on volume mounted inside container
 data_dir = os.environ.get("DATA_VOLUME_CONTAINER", "./")

docker-compose-dev.yml

@@ -1,7 +1,7 @@
 services:
   cogstack-jupyter-hub:
     build: ./Dockerfile_hub
-    container_name: cogstack-jupyter-hub
+    container_name: cogstack-jupyter-hub-dev
     restart: always
     environment:
       - http_proxy=$HTTP_PROXY
@@ -11,19 +11,19 @@ services:
       - JUPYTERHUB_INTERNAL_PROXY_API_PORT=${JUPYTERHUB_INTERNAL_PROXY_API_PORT:-8887}
       - JUPYTERHUB_SSL_PORT=${JUPYTERHUB_SSL_PORT:-443}
     env_file:
-      - ./env/jupyter.env
       - ./env/general.env
+      - ./env/jupyter.env
     volumes:
       - jupyter-hub-shared-scratch:/home/jovyan/scratch
-      - jupyter-hub-vol:/etc/jupyterhub
+      - jupyter-hub-vol:/srv/jupyterhub
       # Security configs
-      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.key:/etc/jupyterhub/root-ca.key:ro
-      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.pem:/etc/jupyterhub/root-ca.pem:ro
-      - ./config/jupyterhub_cookie_secret:/etc/jupyterhub/jupyterhub_cookie_secret:ro
+      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.key:/srv/jupyterhub/root-ca.key:ro
+      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.pem:/srv/jupyterhub/root-ca.pem:ro
+      - ./config/jupyterhub_cookie_secret:/srv/jupyterhub/jupyterhub_cookie_secret:ro
       # User list and jupyter config
-      - ./config/jupyterhub_config.py:/etc/jupyterhub/jupyterhub_config.py:ro
-      - ./config/userlist:/etc/jupyterhub/userlist:ro
-      - ./config/teamlist:/etc/jupyterhub/teamlist:ro
+      - ./config/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
+      - ./config/userlist:/srv/jupyterhub/userlist:ro
+      - ./config/teamlist:/srv/jupyterhub/teamlist:ro
       # Give access to Docker socket
       - /var/run/docker.sock:/var/run/docker.sock
     ulimits:

docker-compose.yml

@@ -11,19 +11,19 @@ services:
       - JUPYTERHUB_INTERNAL_PROXY_API_PORT=${JUPYTERHUB_INTERNAL_PROXY_API_PORT:-8887}
       - JUPYTERHUB_SSL_PORT=${JUPYTERHUB_SSL_PORT:-443}
     env_file:
-      - ./env/jupyter.env
       - ./env/general.env
+      - ./env/jupyter.env
     volumes:
       - jupyter-hub-shared-scratch:/home/jovyan/scratch
-      - jupyter-hub-vol:/etc/jupyterhub
+      - jupyter-hub-vol:/srv/jupyterhub
       # Security configs
-      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.key:/etc/jupyterhub/root-ca.key:ro
-      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.pem:/etc/jupyterhub/root-ca.pem:ro
-      - ./config/jupyterhub_cookie_secret:/etc/jupyterhub/jupyterhub_cookie_secret:ro
+      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.key:/srv/jupyterhub/root-ca.key:ro
+      - ./${DEFAULT_SECURITY_DIR:-./security/}root-ca.pem:/srv/jupyterhub/root-ca.pem:ro
+      - ./config/jupyterhub_cookie_secret:/srv/jupyterhub/jupyterhub_cookie_secret:ro
       # User list and jupyter config
-      - ./config/jupyterhub_config.py:/etc/jupyterhub/jupyterhub_config.py:ro
-      - ./config/userlist:/etc/jupyterhub/userlist:ro
-      - ./config/teamlist:/etc/jupyterhub/teamlist:ro
+      - ./config/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
+      - ./config/userlist:/srv/jupyterhub/userlist:ro
+      - ./config/teamlist:/srv/jupyterhub/teamlist:ro
       # Give access to Docker socket
       - /var/run/docker.sock:/var/run/docker.sock
     ulimits:

env/general.env

@@ -4,5 +4,5 @@
 # set only CPU_ARCHITECTURE to amd/arm64
 # remove if this causes issues on any other platform
 # possible values: amd64, arm64
-CPU_ARCHITECTURE=amd64
+CPU_ARCHITECTURE=arm64
 DOCKER_DEFAULT_PLATFORM=linux/${CPU_ARCHITECTURE:-amd64}

env/jupyter.env

@@ -31,8 +31,8 @@ DOCKER_NOTEBOOK_IDLE_TIMEOUT=7200
 DATA_VOLUME_CONTAINER="./"
 
 # These don't really need to be changed.
-SSL_KEY="/etc/jupyterhub/root-ca.key"
-SSL_CERT="/etc/jupyterhub/root-ca.pem"
+SSL_KEY="/srv/jupyterhub/root-ca.key"
+SSL_CERT="/srv/jupyterhub/root-ca.pem"
 
 DOCKER_NETWORK_NAME="cogstack-net"
 DOCKER_JUPYTER_HUB_CONTAINER_NAME="cogstack-jupyter-hub"

export_env_vars.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -o allexport
+
+current_dir=$(pwd)
+env_dir="./env/"
+
+env_files=(
+           $env_dir"general.env"
+           $env_dir"jupyter.env"
+           )
+
+set -a
+
+for env_file in ${env_files[@]}; do
+  source $env_file
+done
+
+# for nginx vars
+export DOLLAR="$"
+
+set +a
+
+set +o allexport