update examples and documentation

README.md

@@ -32,9 +32,6 @@ dockerspawner to launch a user docker, and a `jupyterhub_config.py` file to conf
 # Do not forget to pin down the version
 FROM jupyterhub/jupyterhub:3.0.0
 
-# Copy the JupyterHub configuration in the container
-COPY jupyterhub_config.py .
-
 # Download script to automatically stop idle single-user servers
 # RUN wget https://raw.githubusercontent.com/jupyterhub/jupyterhub/0.9.3/examples/cull-idle/cull_idle_servers.py
 
@@ -75,7 +72,7 @@ File `docker-compose.yml` contains:
 
 ```
 
-## Build and run
+### Build and run
 
 ```shell
 docker-compose build --no-cache # builds without keeping docker layers in cache
@@ -90,12 +87,58 @@ Then try to sign in from the browser at http://localhost:8000 or http://<server_
 
 __Warning:__ the user containers are persistent so that it is not reinitialized at each start of the hub, 
 which is a pretty nice thing. However, it means that if you want to clean completely the hub __and__ the user containers,
-you need to remove specifically the user containers in addition to setting down the services:
+you need to remove specifically the user containers in addition to setting down the services.
+The following code should remove jupyterhub and user containers respectively.
+
 ```shell
-docker-compose down # should remove the container jupyterhub
-docker rm $(docker ps -qa -f "name=jupyter-") # should remove the jupyter-<username> containers 
+docker-compose down && docker rm $(docker ps -qa -f "name=jupyter-")
 ```
 
+## Rstudio
+
+An Rstudio-session can be launched from inside a jupyterlab session with
+[jupyter-rsession-proxy](https://github.com/jupyterhub/jupyter-rsession-proxy).
+
+The docker image [rocker/binder](https://rocker-project.org/images/versioned/binder.html) and 
+specially script [install_jupyter.sh](https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/install_jupyter.sh)
+gives a good example of how it can be done. Actually it installs JupyterLab, jupyter-rsession-proxy and IRkernel 
+on top of the rocker/geospatial image, and defines the default command with jupyterhub-singleuser 
+making the container controllable by jupyterhub.
+
+The directory `jupyterhub-rstudio` shows an example of such a configuration.
+
+Following [jupyterhub documentation](https://jupyterhub-dockerspawner.readthedocs.io/en/latest/docker-image.html#how-to-build-your-own-docker-image)
+the image rocker/binder is adapted to be spawn by jupyterhub:
+```docker
+FROM rocker/binder:4.2.1
+
+ARG JUPYTERHUB_VERSION=3.0.0
+USER root
+RUN pip3 install --no-cache \
+    jupyterhub==$JUPYTERHUB_VERSION
+
+USER ${NB_USER}
+WORKDIR /home/${NB_USER}
+CMD ["jupyterhub-singleuser"]
+```
+One can notice that no user is created as there is a default user named "rstudio" in rocker images.
+
+A section is then added to `docker-compose.yml` in order to configure the build of rstudio image, named here `rstudio_img`
+and its call by jupyterhub.
+
+Use command lines of section [Build and run] to run and access the server. 
+
+## Adding GitLab OAuth
+
+Directory `jupyterhub-rstudio-gitlab` is showing an example with on the way to configure jupyterhub in order to call GitLab OAuth 
+as authenticator. In order to do so, :
+- package oautenticator is installed in jupyterhub docker image.
+- an application has to be defined in gitlab user settings: it needs scope read_user.
+The URI is defined with https://<jupyterhub server>/hub/oauth_callback.
+- a section is added in jupyterhub_config.py using the URI, the client ID and client secret defined in the gitlab application.
+These variables are stored in .env file and called in jupyterhub_config.py.
+
+
 
 
 # Authors

jupyterhub-rstudio-gitlab/.env

 # Name of our Docker Compose project
-COMPOSE_PROJECT_NAME=rocker_binder
-OAUTH_CALLBACK_URL= # "https://<jupyterhub_server>/hub/oauth_callback", same has to be written in the gitlab application form
+COMPOSE_PROJECT_NAME=rocker_binder_gitlab
+OAUTH_CALLBACK_URL= "https://<jupyterhub_server>/hub/oauth_callback" # the same link has to be written in the gitlab application form in section URI
 GITLAB_CLIENT_ID="xxxxxxxxxxxxxxxxxxxxxxxxxxxxx" # given by gitlab application
-GITLAB_CLIENT_SECRET="xxxxxxxxxxxxxxxxxxxxxxxxx" # iven by gitlab application
+GITLAB_CLIENT_SECRET="xxxxxxxxxxxxxxxxxxxxxxxxxxxxx" # given by gitlab application

jupyterhub-rstudio-gitlab/docker-compose.yml

@@ -8,6 +8,7 @@ services:
     container_name: ${COMPOSE_PROJECT_NAME}_hub    # The service will use this container name.
     volumes:                         # Give access to Docker socket.
       - /var/run/docker.sock:/var/run/docker.sock
+      - ./jupyterhub/jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py
     environment:                     # Env variables passed to the Hub process.
       DOCKER_JUPYTER_IMAGE: rstudio_img
       DOCKER_NETWORK_NAME: ${COMPOSE_PROJECT_NAME}_default

jupyterhub-rstudio-gitlab/jupyterhub/jupyterhub_config.py

@@ -14,7 +14,8 @@ c.GitLabOAuthenticator.oauth_callback_url = os.environ['OAUTH_CALLBACK_URL']
 c.GitLabOAuthenticator.client_id = os.environ['GITLAB_CLIENT_ID']
 c.GitLabOAuthenticator.client_secret = os.environ['GITLAB_CLIENT_SECRET']
 c.GitLabOAuthenticator.scope = ['read_user'] # level necessary for to read users
-c.GitLabOAuthenticator.allowed_users = ['<username1>', '<username2>']
+# c.GitLabOAuthenticator.allowed_users = ['<username1>', '<username2>'] # to allow specific users
+# c.GitLabOAuthenticator.allowed_groups = ['<group1>', '<group2>'] # to allow whole groups
 
 
 

jupyterhub-rstudio/rstudio/Dockerfile

-FROM rocker/binder:a6bef4d6eb4b
+FROM rocker/binder:4.2.1
 
 ARG JUPYTERHUB_VERSION=3.0.0
 USER root
 RUN pip3 install --no-cache \
-    jupyterhub==$JUPYTERHUB_VERSION notebook
-	
+    jupyterhub==$JUPYTERHUB_VERSION
+
 USER ${NB_USER}
 WORKDIR /home/${NB_USER}
 CMD ["jupyterhub-singleuser"]