Orchestrate healthcare data solutions (preview) notebook execution using Fabric pipelines

[This article is prerelease documentation and is subject to change.]

Fabric notebooks rely on the %pip library management magic command to get the wheel (WHL) files into a Spark session. This operation isn't currently supported in the Fabric pipeline. Hence, you can't add the notebooks as activities to a Fabric pipeline or automate notebook execution. To learn more about Fabric magic commands, go to Magic commands in a notebook.

However, you can utilize the Fabric pipelines to manually orchestrate notebook execution. This article explains how to set up this configuration. It includes the following steps:

  1. Set up prerequisites
  2. Configure Fabric environment
  3. Update workspace settings
  4. Update notebooks
  5. Create orchestration pipeline

Set up prerequisites

Download, install, and set up OneLake file explorer to access your Fabric data locally. For instructions, see Use OneLake file explorer to access Fabric data.

Configure Fabric environment

Let's use the guidance in Create, configure, and use an environment in Microsoft Fabric to upload the files to the workspace Spark pool.

  1. From the experience switcher in your Fabric environment, select Data Engineering.

    A screenshot showing how to switch to the data engineering experience.

  2. On the Data Engineering home page, select the Environment tile to create a new environment.

  3. In the newly created environment, set the Runtime value to 1.1 (Spark 3.3, Delta 2.2).

    A screenshot displaying the new runtime value.

  4. In the navigation menu, select Custom Libraries, and then select Upload.

  5. Using the OneLake file explorer, navigate to the following folder path in your workspace:


  6. Upload the following six wheel files:

    A screenshot displaying the wheel files.

  7. Navigate to Public Libraries and add the following packages from the PyPI public library source:

    1. azure-ai-textanalytics, version 5.3.0b2
    2. opencensus-ext-azure, version 1.1.9
    3. typing-extensions, version 4.8.0

    A screenshot displaying the required library packages.


    Copying the values and pasting them might sometimes cause the addition of hidden characters. This behavior can prevent you from adding the feed libraries. To resolve this issue, start typing the names to get an autocomplete list.

  8. Select Save, and then select Publish to apply the changes. The publishing can take a few minutes to complete.

Update workspace settings

After the library changes finish publishing, follow these steps to update the workspace settings:

  1. Navigate to your healthcare data solutions (preview) workspace and select Workspace settings.

  2. In the workspace settings page, expand the Data Engineering/Science drop-down box, and select Spark settings.

    1. On the Environment tab, slide the Set default environment toggle to On.

    2. In the workspace drop-down box, select the environment you created earlier.

    3. Select Save.

    A screenshot displaying the workspace settings.

Update notebooks

After setting up the Fabric environment and uploading the wheel files, you can now update the notebook configuration. Comment out the first %run cell and the first %pip install cell in the following notebooks. You might see either all or only a subset of these notebooks, depending on the capabilities deployed in your environment:

  • healthcare#_msft_fhir_export_service
  • healthcare#_msft_raw_bronze_ingestion
  • healthcare#_msft_bronze_silver_flatten
  • healthcare#_msft_silver_ta4h
  • healthcare#_msft_silver_omop
  • healthcare#_msft_silver_ci_gold_flatten

Use the # character to comment out the cells. Here's an example:

A screenshot displaying how to comment out the cells.


  • The healthcare#_msft_silver_omop notebook contains two additional %pip install cells that you need to comment out.

  • This execution pipeline doesn't currently include the DICOM data ingestion notebooks.

Create orchestration pipeline

After modifying the notebooks, you can now create a Fabric pipeline to orchestrate their execution.

  1. From the Fabric experience switcher, select Data Engineering.

  2. Select the Data pipeline tile to create a new pipeline. This action creates a blank data pipeline.

  3. Add the healthcare data solutions (preview) notebooks as activities to this pipeline using the guidance in Transform data by running a notebook.

  4. When you add the notebooks as activities, they execute in the following sequence, depending on whether you opt to install the corresponding capability:

    • healthcare#_msft_fhir_export_service (only required if you need to export FHIR data from your FHIR service)
    • healthcare#_msft_raw_bronze_ingestion (required)
    • healthcare#_msft_bronze_silver_flatten (required)
    • healthcare#_msft_silver_ta4h (only required if you need to process unstructured data)
    • healthcare#_msft_silver_omop (only required if you installed the OMOP analytics capability)
    • healthcare#_msft_silver_ci_gold_flatten (only required if you installed the Dynamics 365 Customer Insights - Data preparation capability)

See also