patient_intake_extraction_baml

Extract structured data from patient intake forms with BAML (v1)

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This example shows how to use BAML to extract structured data from patient intake PDFs using CocoIndex v1. BAML provides type-safe structured data extraction with native PDF support.

• BAML Schema (baml_src/patient.baml) - Defines the data structure and extraction function
• CocoIndex v1 App (main.py) - Wraps BAML in a custom function, processes files incrementally, and writes results to JSON files

Run

1. Install dependencies

Install from the project's pyproject.toml:

pip install -e .

2. Generate BAML client code

This is a required step that generates the Python client code from your BAML schema:

baml generate

This will create a baml_client/ directory with the generated Python code.

3. Set up environment variables

Create a .env file in the example directory:

echo "GEMINI_API_KEY=your_api_key_here" > .env

Replace your_api_key_here with your actual Gemini API key.

4. Run the application

cocoindex update main.py

This will:

1. Read all PDF files from data/patient_forms/
2. Extract patient information using BAML
3. Write the extracted data as JSON files to output_patients/

5. Verify the output

After running, check the output_patients/ directory:

ls -la output_patients/

You should see JSON files such as:

• Patient_Intake_Form_David_Artificial.json
• Patient_Intake_Form_Emily_Artificial.json
• Patient_Intake_Form_Joe_Artificial.json
• Patient_Intake_Form_Jane_Artificial.json