CDA2FHIR

Translating Cancer Data Commons (CDA) to 🔥 FHIR (Fast Healthcare Interoperability Resources) format.

Usage

Installation

• from source

# clone repo & setup virtual env
python3 -m venv venv
. venv/bin/activate
pip install -e .

Transform to FHIR

Data

To run the transformer, ensure that CDA raw data is located in the ./data/raw/ directory. If you need to retrieve the raw data, please contact cancerdataaggregator @ gmail.

Usage: cda2fhir transform [OPTIONS]

Options:
  -s, --save               Save FHIR ndjson to CDA2FHIR/data/META folder.
                           [default: True]
  -v, --verbose
  -ns, --n_samples TEXT    Number of samples to randomly select - max 100.
  -nd, --n_diagnosis TEXT  Number of diagnosis to randomly select - max 100.
  -p, --path TEXT          Path to save the FHIR NDJSON files. default is
                           CDA2FHIR/data/META.
  --help                   Show this message and exit.

• example

cda2fhir transform 

Testing

Current integration testing runs on all data and may take approximately 2 hours.

pytest -cov 

FHIR data validation

For FHIR data validation please run:

g3t meta validate <path to data/META folder with ndjson files> 
>>>> resources={'summary': {'Specimen': 715864, 'Observation': 724999, 'ResearchStudy': 423, 'BodyStructure': 180, 'Condition': 95288, 'ResearchSubject': 160662, 'Patient': 137522}}

NOTE: This process may take more than 5 minutes due to the size of the current data.