FHIR to MIP Schema Conversion

This repository provides a tool to convert FHIR data into MIP schema data models, transforming features and outcomes, adjusting field names, and ensuring proper handling of categorical and numerical variables.

Features

• Converts FHIR JSON data to MIP schema format.
• Transforms boolean fields and handles numeric min/max values.
• Logs rejected features and outcomes based on validation.
• Dynamically set input/output file paths using argparse.

Usage

1. Install dependencies using Poetry:

   poetry install

2. Run the conversion script:

   poetry run python converter/fhir2mip.py <input_path> <output_path> <rejected_file_path>

   Example:

   poetry run python converter/fhir2mip.py data/minimal_fhir.json  transformed_data.json rejected_codes.txt

Testing

Run the tests using pytest:

poetry run pytest

Files

• converter.py: Main script to handle the transformation from FHIR to MIP schema.
• tests/: Contains unit tests for validation of the transformation logic.