FHIRflat

fhirflat is a library for transforming FHIR resources in NDJSON or native Python dictionaries to a flat structure that can be written to a Parquet file.

fhirflat is a prototype library, subject to major revisions that is used for the ISARIC 3.0 project and data pipelines. Portions of the code are specific to the ISARIC project, such as ISARIC specific FHIR extensions.

The FHIRflat FHIR resources are derived from the fhir.resources package.

For more information, howtos and tutorials, see the documentation.

Installing

You can use pip to install fhirflat:

pip install git+https://github.com/globaldothealth/fhirflat

If you are using requirements.txt, then add this to your file and rerun pip install -r requirements.txt:

https://github.com/globaldothealth/fhirflat/main.tar.gz

Development

To test and develop fhirflat, from a cloned version of fhirflat use an editable install including the development dependencies(pip install -e ".[dev]"). This will allow you to test the packages, and installs formatting and linting tools, and pre-commit.

Setup pre-commit hooks (pre-commit install) which will do linting checks before commit.