🔥 Transform FHIR JSON to CSV

This repository contains Python classes which use the fhirpath-py library to transform FHIR JSON into CSV rows.

A developer writes FHIR Path expressions to extract the value of a field from the JSON object.

🏁 Quick Start

Define a Transformer

Define a transformer class in: radiant_fhir_transform_cli/transform/classes

This should fairly simple, as the only real implementation is the transform dictionary transform_dict:

TRANSFORM_DICT = {
    "given_name": "name.where(use='official').given.first()",
    "family_name": "name.where(use='official').family",
    "active": "active",
    "birth_date": "birthDate",
    "gender": "gender",
}


class PatientTransformer(FhirResourceTransformer):
    def __init__(self):
        super().__init__("Patient", TRANSFORM_DICT)

FHIR Path

The values in the transform dictionary should be strings containing valid FHIR path expressions. These expressions provide a way to extract the value of a particular field in the FHIR JSON.

The keys of the transform dictionary should be strings containing the names of columns in a CSV file.

It is often helpful to use the web site fhirpath.js while you are writing FHIR path expressions to test them out in real time.

Test Transformer

You can quickly test your transformer against data by running the following CLI command.

$ radiant fhir transform --resource-type Patient --input-filepath=patient.json

If your patient.json file looked something like this:

{
    "resourceType": "Patient",
    "id": "eNuTIJvJoX5g5enjtR.Ul4ASEfAlFvJjiahhGyW1xd8x43",
    "active": True,
    "name": [
        {
            "use": "official",
            "text": "Testing Careeverywhere",
            "family": "Wong",
            "given": ["Jason"],
        },
        {
            "use": "usual",
            "text": "Testing Careeverywhere",
            "family": "Wong",
            "given": ["Jason Sr"],
        },
    ],
    "gender": "Male",
    "birthDate": "2019-10-17",
    ...
}

Your CSV file should show something like:

given_name	family_name	active	birth_date	gender
Jason	Wong	True	2019-10-17	Male

👩‍💻 Developer Guide

The developer guide is for individuals that want to modify existing transformers or add new ones. This guide will provide all of the information necessary to make changes to the CLI code, and tests.