Jupyter Notebook Images

This repo contains definitions of Jupyter notebook images for deploying to an OpenRiskNet Virtual Environment (VE). Instructions for deploying Jupyter to an ORN VE can be found here.

Typically each sub-directory contains the definitions (e.g. a Dockerfile) for a single notebook image.

All images currently are standard Jupyter notebook images that need to run with relaxed OpenShift security specifications. It is preferable to convert these to s2i builds along the lines found here.

Deploying a Jupyter project derived notebook image to the Jupyter project in an ORN VE

This approach is used for notebooks based on base images from the Jupyter project and use a Dockerfile that extends one of those base images. And example is the simple-rdkit notebook that we use as an example. Other notebook images should be similar. The process for s2i builds from Graham Dumpleton's builds is described below. You should be able to do this as the developer user. All the acton takes place in the jupyter project.

Step 1: Creating the build

From within the jupyter project:

oc new-build --name simple-rdkit --strategy=docker https://github.com/OpenRiskNet/jupyter-notebook-images.git --context-dir=simple-rdkit

Change the name and context-dir parameters if using a different notebook.

This creates a new BuildConfig and starts the build. The container images is built and pushed to the OpenShift registry. Subsequent changes to the GitHub repo will be detected and the image re-built.

Step 2: Adding the image to the JupyterHub configuration

Edit the jupyterhub-cfg ConfigMap in the jupyter project and add the defintion of your image to the c.KubeSpawner.profile_list List. You will add something like this:

{
  'display_name': 'Simple RDKit',
  'kubespawner_override': {
    'image_spec': 'simple-rdkit:latest',
    'supplemental_gids': [100],
    'volume_mounts': [
       {
         'name': 'data',
         'mountPath': '/home/jovyan'
       }
    ]
  }
}

The supplemental_gids parameter is needed because the image needs to run as a predefined goroup ID. The volume_mounts specifies where to mount the user's PVC and needs to be where Jupyter is looking for its notebooks.

Step 3: Redeploy JuputerHub

Run a new deployment of the jupyterhub deployment.

Deploying a s2i derived notebook image to the Jupyter project in an ORN VE

See also the deployment for JupyterHub and the standard notebooks.

We use the sparql notebook as an example.

Step 1: Creating the build

From the sparql directory:

oc create -f templates/build-config.yaml

Step 2: Adding the image to the JupyterHub configuration

Edit the jupyterhub-cfg ConfigMap in the jupyter project and add the defintion of your image to the c.KubeSpawner.profile_list List. You will add something like this:

{
    'display_name': 'SPARQL Notebook (CentOS 7 / Python 3.6 / SPARQL)',
    'kubespawner_override': {
        'image_spec': 's2i-sparql-notebook:latest'
    }
}

Step 3: Redeploy JuputerHub

Run a new deployment of the jupyterhub deployment.