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.
  -nf, --n_files TEXT      Number of files to randomly select - max 100.
  -f, --transform_files    Transform CDA files to FHIR DocumentReference and Group.
  -p, --path TEXT          Path to save the FHIR NDJSON files. default is
                           CDA2FHIR/data/META.
  --help                   Show this message and exit.

• example

cda2fhir transform 

NOTE: in-case of interest in validating your FHIR data with GEN3, you will need to go through the user-guide, setup, and documentation of GEN3 tracker before running the cda2fhir commands.

FHIR data validation

disable gen3-client

mv ~/.gen3/gen3_client_config.ini ~/.gen3/gen3_client_config.ini-xxx
mv ~/.gen3/gen3-client ~/.gen3/gen3-client-xxx

Run validate

 time cda2fhir validate
{'summary': {'Specimen': 721837, 'Observation': 731005, 'ResearchStudy': 423, 'BodyStructure': 163, 'Condition': 95262, 'ResearchSubject': 160649, 'Patient': 138738}}

real    5m
user    5m
sys     0m5.1s

Restore gen3-client

mv ~/.gen3/gen3-client-xxx ~/.gen3/gen3-client
mv ~/.gen3/gen3_client_config.ini-xxx ~/.gen3/gen3_client_config.ini
  

This command will validate your FHIR entities and their reference relations to each other. It will also generate a summary count of all entities in each ndjson file.

NOTE: This process may take 5 minutes or more, depending on your platform or compute power due to the size of the current data.

Testing

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

pytest -cov