JupyterLab

Bench workspaces require setting a docker image to use as the image for the workspace. Illumina Connected Analytics (ICA) provides a default docker image with JupyterLab installed.

JupyterLab supports Jupyter Notebook documents (.ipynb). Notebook documents consist of a sequence of cells which may contain executable code, markdown, headers, and raw text.

The JupyterLab docker image contains the following environment variables:

• ICA_URL set to the ICA server URL https://ica.illumina.com/ica

• ICA_PROJECT (OBSOLETE) set to the current ICA project ID

• ICA_PROJECT_UUID set to the current ICA project UUID

• ICA_SNOWFLAKE_ACCOUNT set to the ICA Snowflake (Base) Account ID

• ICA_SNOWFLAKE_DATABASE set to the ICA Snowflake (Base) Database ID

• ICA_PROJECT_TENANT_NAME set to the tenant name of the owning tenant of the project where the workspace is created

• ICA_STARTING_USER_TENANT_NAME set to the tenant name of the tenant of the user which last started the workspace

• ICA_COHORTS_URL set to the URL of the Cohorts web application used to support the Cohorts view

To export data from your workspace to your local machine, it is best practice to move the data in your workspace to the /data/project/ folder so that it becomes available in your project under projects > your_project > Data.

ICA Python Library

Included in the default JupyterLab docker image is a python library with APIs to perform actions in ICA, such as add data, launch pipelines, and operate on Base tables. The python library is generated from the ICA Open API specification using openapi-generator.

The ICA Python library API documentation can be found in folder /etc/ica/data/ica_v2_api_docs within the JupyterLab docker image.

See the Bench ICA Python Library Tutorial for examples on using the ICA Python library.