How to convert between FHIR and FHIRflat

How to convert between FHIR and FHIRflat#

FHIR resources can be initialised using a data dictionary:

from fhirflat import Patient
data= {
    "id": "f001",
    "name": [{"text": "Micky Mouse"}],
    "gender": "male",
    "deceasedBoolean": False,
    "address": [{"country": "Switzerland"}],
    "birthDate": "1996-05-30",
}
patient = Patient(**data)

or in bulk from a FHIR export as an .ndjson file.

from fhirflat import Patient

patients = Patient.fhir_bulk_import("patient_export.ndjson")

To FHIRflat#

Once initialised, FHIR resources can be transformed to FHIRflat files using the to_flat() function like this

patient.to_flat("patient_flat.parquet")

which produces a parquet file which can be read in pandas, producing a dataframe with the following structure

resourceType

id

gender

birthDate

deceasedBoolean

Patient

f001

male

1996-05-30

False

or a FHIRflat file can be generated directly from a FHIR .ndjson export file.

from fhirflat import Patient

Patient.fhir_file_to_flat("patient_export.ndjson")

creates a “patient_export.parquet” FHIRflat file. This first initialises a Patient data class for each row to make use of the Pydantic data validation, then creates a FHIRflat file.

From FHIRflat#

FHIR resources can also be created directly from FHIRflat files

Patient.from_flat("patient_flat.parquet")

which returns either a single Patient resource, or a list of Patient resources if the Parquet file contains multiple rows of data.

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