usdm4-fhir 0.12.0

A python package for importing and exporting the CDISC TransCelerate USDM, version 4, using FHIR

USDM4 FHIR

A Python package for converting between CDISC TransCelerate Unified Study Data Model (USDM), version 4, and HL7 FHIR M11 message bundles.

Supports export (USDM to FHIR) and import (FHIR to USDM) for multiple FHIR profile versions, including PRISM2 and PRISM3 message formats, as well as a Madrid export variant.

Features

• Export USDM4 study definitions to FHIR M11 Bundle JSON (PRISM2, PRISM3, Madrid)
• Import FHIR M11 Bundle JSON back to USDM4 study definitions (PRISM2, PRISM3)
• Schedule of Activities export to FHIR
• Round-trip fidelity testing between USDM and FHIR representations
• Built on fhir.resources (Pydantic-based FHIR R5 models)

Installation

pip install usdm4_fhir

Quick Start

Export: USDM to FHIR

from usdm4_fhir.m11.export.export_prism3 import ExportPRISM3

exporter = ExportPRISM3(study, extra)
fhir_bundle_json = exporter.to_message()

Import: FHIR to USDM

from usdm4_fhir.m11.import_.import_prism3 import ImportPRISM3

importer = ImportPRISM3()
wrapper = await importer.from_message("path/to/fhir_bundle.json")
study = wrapper.study

Dependencies

• usdm4 (>=0.18.0) -- USDM4 API model and assembler
• fhir.resources (==7.1.0) -- FHIR R5 resource models
• d4k_ms_base (>=0.3.0) -- shared microservice base

Development

Setup

git clone https://github.com/data4knowledge/usdm4_fhir.git
cd usdm4_fhir
python -m venv .venv
source .venv/bin/activate
pip install -e ".[test]"

Commands

ruff format          # Format code
ruff check           # Lint
pytest               # Run tests

Build and Publish

python3 -m build --sdist --wheel
twine upload dist/*

Project Structure

src/usdm4_fhir/
  factory/        FHIR resource factories (ResearchStudy, PlanDefinition, etc.)
  m11/
    export/       USDM to FHIR export (PRISM2, PRISM3, Madrid)
    import_/      FHIR to USDM import (PRISM2, PRISM3)
    utility/      Shared utilities (address service, HTML parsing, tag references)
  soa/
    export/       Schedule of Activities FHIR export
  utility/        Data store
tests/            Integration test suite with round-trip verification

License

This project is licensed under the GNU General Public License v3.0. See LICENSE for details.