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Configuration Guide

Modes

Replica Mode

In this mode, the files are transferred by Rucio to a storage mounted to the JupyterLab server. In order to use the extension in this mode, you need to have the following set up:

  • A JupyterLab version 2 installation.
  • At least one Rucio instance.
  • A storage system that is attached to the JupyterLab installation via FUSE.
    • The storage system should be compatible with Rucio and added as a Rucio Storage Element.
    • The storage element will be shared among multiple users, so be sure to allow all users who will be using the extension to have read permission to the path.
    • It's recommended that quotas be disabled, since the extension does not care if the replication fails because of quota error.

Download Mode

In this mode, the extension downloads the files to the user directory. This is used when your JupyterLab installation does not use a storage as an RSE. To use the extension in this mode, you need to have the following set up:

  • A JupyterLab version 2 installation.
  • At least one Rucio instance.
  • Rucio Storage Elements (RSE) that are accessible from the notebook server, with no authentication scheme.

Configuration

The extension can be configured locally or remotely.

Local Configuration

In your Jupyter configuration (could be ~/.jupyter/jupyter_notebook_config.json), add the following snippet:

{
    "RucioConfig": {
        "instances": [
            {
                "name": "experiment.cern.ch",
                "display_name": "Experiment",
                "rucio_base_url": "https://rucio",
                "rucio_auth_url": "https://rucio",
                "rucio_ca_cert": "/path/to/rucio_ca.pem",
                "destination_rse": "SWAN-EOS",
                "rse_mount_path": "/eos/rucio",
                "path_begins_at": 4,
                "mode": "replica"
            }
        ]
    }
}

Remote Configuration

To use remote configuration, use the following snippet:

{
    "RucioConfig": {
        "instances": [
            {
                "name": "experiment.cern.ch",
                "display_name": "Experiment",
                "$url": "https://url-to-rucio-configuration/config.json"
            }
        ]
    }
}

In the JSON file pointed by the value in $url, use the following snippet:

{
    "rucio_base_url": "https://rucio",
    "destination_rse": "SWAN-EOS",
    "rucio_auth_url": "https://rucio",
    "rucio_ca_cert": "/path/to/rucio_ca.pem",
    "rse_mount_path": "/eos/rucio",
    "path_begins_at": 4,
    "mode": "replica"
}

Attributes name, display_name, and mode must be defined locally, while the rest can be defined remotely. If an attribute is defined in both local and remote configuration, the local one is used.

Configuration Items

Name - name

A unique name to identify Rucio instance, should be machine readable. It is recommended to use FQDN. Must be declared locally.

Example: atlas.cern.ch, cms.cern.ch

Display Name - display_name

A name that will be displayed to users in the interface. Must be declared locally.

Example: ATLAS, CMS

Mode - mode

The mode in which the extension operates. Must be declared locally.

  1. Replica mode (replica)
  2. Download mode (download)

Rucio Base URL - rucio_base_url

Base URL for the Rucio instance accessible from the JupyterLab server, without trailing slash.

Example: https://rucio

Rucio Auth URL - rucio_auth_url

Base URL for the Rucio instance handling authentication (if separate) accessible from the JupyterLab server, without trailing slash.

Example: https://rucio-auth

Rucio CA Certificate File Path - rucio_ca_cert

Path to Rucio server certificate file, accessible via filesystem mount. Optional in Replica mode, mandatory in Download mode.

Example: /opt/rucio/rucio_ca.pem

App ID - app_id

Rucio App ID. Optional.

Example: swan

Site Name - site_name

Site name of the JupyterLab instance, optional. It allows Rucio to know whether to serve a proxied PFN or not.

Example: ATLAS

VO Name - vo

VO of the instance. Optional, for use in multi-VO installations only. If VOMS is enabled, this value will be supplied as --voms option when invoking voms-proxy-init.

Example: def

VOMS Enabled - voms_enabled

The extension uses voms-proxy-init to generate a Proxy certificate when downloading a file from an authenticated RSE.

If set to true, vo option is specified, and X.509 User Certificate is used, the extension will invoke voms-proxy-init with the --voms argument set to the extension's vo option.

Optional, with default: false

VOMS certdir Path - voms_certdir_path

If VOMS is enabled and this configuration is set, the extension will set the --certdir option with this value. Refer to voms-proxy-init documentation.

Example: /etc/grid-security/certificates

VOMS vomsdir Path - voms_vomsdir_path

If VOMS is enabled and this configuration is set, the extension will set the --vomsdir option with this value. Refer to voms-proxy-init documentation.

Example: /etc/grid-security/vomsdir

WARNING: In earlier versions, voms-proxy-init does not support the --vomsdir option. In that case, this option must be omitted.

VOMS vomses File Path - voms_vomses_path

If VOMS is enabled and this configuration is set, the extension will set the --vomses option with this value. Refer to voms-proxy-init documentation.

Example: /etc/vomses

WARNING: In earlier versions, voms-proxy-init does not support the --vomsdir option. In that case, this option must be omitted.

Destination RSE - destination_rse

The name of the Rucio Storage Element that is mounted to the JupyterLab server. Mandatory, only applicable in Replica mode.

Example: SWAN-EOS

RSE Mount Path - rse_mount_path

The base path in which the RSE is mounted to the server. Mandatory, only applicable in Replica mode.

Example: /eos/rucio

File Path Starting Index - path_begins_at

This configuration indicates which part of the PFN should be appended to the mount path. Only applicable in Replica mode. Defaults to 0.

Example: let us say that the PFN of a file is root://xrd1:1094//rucio/test/49/ad/f1.txt and the mount path is /eos/rucio. A starting index of 1 means that the path starting from the 2nd slash (index 1) in the PFN will be appended to the mount path. The resulting path would be /eos/rucio/test/49/ad/f1.txt.

Replication Rule Lifetime (in days) - replication_rule_lifetime_days

Replication rule lifetime in days. Optional, only applicable in Replica mode.

Example: 365

Wildcard Search Enabled - wildcard_enabled

Whether or not wildcard DID search is allowed. Optional, defaults to false.

OpenID Connect Auth Source - oidc_auth

Specifies where should the extension gets the OIDC token from. Optional, the value should be file or env.

OpenID Connect Token Filename - oidc_file_name

Specifies an absolute path to a file containing the OIDC access token.

OpenID Connect Token Environment Variable Name - oidc_env_name

Specifies the environment variable name containing the OIDC access token.

IPython Kernel

To allow users to access the paths from within the notebook, a kernel extension must be enabled. The kernel resides in module rucio_jupyterlab.kernels.ipython.

To enable the kernel extension from inside a notebook, use load_ext IPython magic:

%load_ext rucio_jupyterlab.kernels.ipython

Or, if you want to enable it by default, put the following snippet in your IPython configuration (could be ~/.ipython/profile_default/ipython_kernel_config.py).

c.IPKernelApp.extensions = ['rucio_jupyterlab.kernels.ipython']

Enabling OpenID Connect Authentication

Unlike the other authentication methods supported by the extension, which is configurable by users only, OIDC auth should be configured by the admins. Users won't see "OpenID Connect" option if OIDC auth is not configured properly.

This extension does not provide a way for users to authenticate directly from the extension. Instead, the OIDC token must be obtained from an external mechanism.

In a multi-user setup with JupyterHub, admins must make the OIDC token accessible from the single user's container via either a file or an environment variable. Then, they need to configure the oidc_auth and oidc_env_name or oidc_file_name parameters (see above).

Furthermore, the JupyterHub installation must have a mechanism of periodically refreshing the OIDC token so that an expired token is not used.

See the following sections for more details.

Configuring JupyterHub with OIDC: Single user Dockerfile and Variables

The Docker image for the single-user container must include the Rucio extension and the defined OpenID Connect variables. To install the extension, refer to the provided Dockerfile. Additionally, the configure.py script takes care of writing the variables from the environment to the Jupyter configuration.

Configuring JupyterHub with OIDC: JupyterHub Chart

JupyterHub installation is possible through the use of the Helm Chart provided by Zero to JupyterHub with Kubernetes. In order to enable the Rucio extension, add the following customisation to the values.

  1. Add the custom in singleuser.image:
singleuser:
  image: <image-url>:<image-tag>
  1. Add a custom authentication script to hub.extraConfig. For instance, label it as token-exchange and append the script in this format:
hub:
  extraConfig:
    token-exchange: |
      import pprint
      import os
      import warnings
      import requests
      from oauthenticator.generic import GenericOAuthenticator

      # custom authenticator to enable auth_state and get access token to set as env var for rucio extension
      class RucioAuthenticator(GenericOAuthenticator):
          def __init__(self, **kwargs):
            super().__init__(**kwargs)
              self.enable_auth_state = True

          def exchange_token(self, token):
              params = {
                  'client_id': self.client_id,
                  'client_secret': self.client_secret,
                  'grant_type': 'urn:ietf:params:oauth:grant-type:token-exchange',
                  'subject_token': token,
                  'scope': 'openid profile',
                  'audience': 'rucio'
              }
              response = requests.post(self.token_url, data=params)
              rucio_token = response.json()['access_token']
              return rucio_token
        
          async def pre_spawn_start(self, user, spawner):
              auth_state = await user.get_auth_state()
              pprint.pprint(auth_state)
              if not auth_state:
                  # user has no auth state
                  return
            
              # define token environment variable from auth_state
              spawner.environment['RUCIO_ACCESS_TOKEN'] = self.exchange_token(auth_state['access_token'])
              spawner.environment['EOS_ACCESS_TOKEN'] = auth_state['access_token']

      # set the above authenticator as the default
      c.JupyterHub.authenticator_class = RucioAuthenticator

      # enable authentication state
      c.GenericOAuthenticator.enable_auth_state = True

      if 'JUPYTERHUB_CRYPT_KEY' not in os.environ:
          warnings.warn(
              "Need JUPYTERHUB_CRYPT_KEY env for persistent auth_state.\n"
              "    export JUPYTERHUB_CRYPT_KEY=$(openssl rand -hex 32)"
          )
          c.CryptKeeper.keys = [os.urandom(32)]
  1. Add the configuration parameters for the custom authenticator to the hub.config:
hub:
  config:
    RucioAuthenticator:
      client_id: <your-client-id>
      client_secret: <your-client-secret>
      authorize_url: <your-auth-url>
      token_url: <your-token-url>
      userdata_url: <your-userinfo-url>
      username_key: preferred_username
      scope:
        - openid
        - profile
        - email
  1. Add the required extension parameters to the singleuser.extraEnv:
singleuser:
  extraEnv:
    RUCIO_MODE: "replica"
    RUCIO_WILDCARD_ENABLED: "1"
    RUCIO_BASE_URL: "<your-rucio-url>"
    RUCIO_AUTH_URL: "<your-rucio-auth-url>"
    RUCIO_WEBUI_URL: "<your-rucio-ui-url>"
    RUCIO_DISPLAY_NAME: "<your-rucio-instance-display-name>"
    RUCIO_NAME: "<your-rucio-instance-name>"
    RUCIO_SITE_NAME: "<your-rucio-instance-site-name>"
    RUCIO_OIDC_AUTH: "env"
    RUCIO_OIDC_ENV_NAME: "RUCIO_ACCESS_TOKEN"
    RUCIO_DEFAULT_AUTH_TYPE: "oidc"
    RUCIO_OAUTH_ID: "<your-rucio-oauth-id>" # audience
    RUCIO_DEFAULT_INSTANCE: "<your-rucio-instance-name>""
    RUCIO_DESTINATION_RSE: "EOS RSE"
    RUCIO_RSE_MOUNT_PATH: "/eos/eos-rse"
    RUCIO_PATH_BEGINS_AT: "4"
    RUCIO_CA_CERT: "<your-rucio-ca-file-path>"
    OAUTH2_TOKEN: "FILE:/tmp/eos_oauth.token"
  1. Build the Docker image and install the Helm Chart with the specified values.

Note: This configuration works in replica mode and maps an EOS RSE as the target RSE, which is FUSE mounted on the nodes where Jupyterhub is running.