cumulus-fhir-support 1.11.0

FHIR support code for the Cumulus project

Cumulus FHIR Support

This library holds FHIR support code for the Cumulus project as a whole.

Installing

pip install cumulus-fhir-support

API

list_multiline_json_in_dir

Lists available multiline JSON files in the target directory (allowing filtering by FHIR resource).

Files with the .jsonl or .ndjson suffixes are supported. Files with an additional .gz suffix will also be returned.

import cumulus_fhir_support as cfs

cfs.list_multiline_json_in_dir("/")
# {
#     "/con1.ndjson.gz": "Condition",
#     "/pat1.jsonl": "Patient",
#     "/random.jsonl": None,
# }

cfs.list_multiline_json_in_dir("/", "Patient")
# {
#     "/pat1.jsonl": "Patient",
# }

cfs.list_multiline_json_in_dir("/", ["Condition", "Patient"])
# {
#     "/con1.ndjson.gz": "Condition",
#     "/pat1.jsonl": "Patient",
# }

cfs.list_multiline_json_in_dir("/does-not-exist/")
# {}

cfs.list_multiline_json_in_dir("s3://mybucket/", fsspec_fs=s3_fs)
# {
#     "/mybucket/procs.ndjson": "Procedure",
# }

read_multiline_json

Iterates over a single multiline JSON file.

Files with the .gz extension are automatically uncompressed.

import cumulus_fhir_support as cfs

list(cfs.read_multiline_json("/pat1.jsonl"))
# [
#     {"resourceType": "Patient", "id": "pat1", "birthDate": "2020-10-16"},
#     {"resourceType": "Patient", "id": "pat2", "birthDate": "2013-04-18"},
# ]

list(cfs.read_multiline_json("/does-not-exist.ndjson"))
# []

list(cfs.read_multiline_json("/mybucket/procs.ndjson", fsspec_fs=s3_fs))
# [
#     {"resourceType": "Procedure", "id": "proc1", "status": "stopped"},
# ]

read_multiline_json_with_details

Lower level function to iterate over a single multiline JSON file, with extra line metadata.

Files with the .gz extension are automatically uncompressed.

import cumulus_fhir_support as cfs

list(cfs.read_multiline_json_with_details("/pat1.jsonl"))
# [
#     {
#         "json": {"resourceType": "Patient", "id": "pat1", "birthDate": "2020-10-16"},
#         "line_num": 0,
#         "byte_offset": 0,
#     },
#     {
#         "json": {"resourceType": "Patient", "id": "pat2", "birthDate": "2013-04-18"},
#         "line_num": 1,
#         "byte_offset": 69,
#     },
# ]

list(cfs.read_multiline_json_with_details("/pat1.jsonl"), offset=69)
# [
#     {
#         "json": {"resourceType": "Patient", "id": "pat2", "birthDate": "2013-04-18"},
#         "line_num": 0,
#         "byte_offset": 0,
#     },
# ]

read_multiline_json_from_dir

Iterates over every JSON object in a directory (allowing filtering by FHIR resource).

Files with the .gz extension are automatically uncompressed.

import cumulus_fhir_support as cfs

list(cfs.read_multiline_json_from_dir("/"))
# [
#     {"resourceType": "Condition", "id": "con1", "onsetDateTime": "2011-11-24"},
#     {"resourceType": "Patient", "id": "pat1", "birthDate": "2020-10-16"},
#     {"resourceType": "Patient", "id": "pat2", "birthDate": "2013-04-18"},
#     {"description": "not a fhir object"},
# ]

list(cfs.read_multiline_json_from_dir("/", "Condition"))
# [
#     {"resourceType": "Condition", "id": "con1", "onsetDateTime": "2011-11-24"},
# ]

list(cfs.read_multiline_json_from_dir("/", ["Condition", "Patient"]))
# [
#     {"resourceType": "Condition", "id": "con1", "onsetDateTime": "2011-11-24"},
#     {"resourceType": "Patient", "id": "pat1", "birthDate": "2020-10-16"},
#     {"resourceType": "Patient", "id": "pat2", "birthDate": "2013-04-18"},
# ]

list(cfs.read_multiline_json_from_dir("/does-not-exist/"))
# []

list(cfs.read_multiline_json_from_dir("/mybucket/", fsspec_fs=s3_fs))
# [
#     {"resourceType": "Procedure", "id": "proc1", "status": "stopped"},
# ]

pyarrow_schema_from_rows

Calculates a schema that can cover a given collection of FHIR objects.

import cumulus_fhir_support as cfs

rows = [
    {
        "resourceType": "Patient",
        "id": "1",
        "extension": [{
            "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
            "extension": [{
                "url": "ombCategory",
                "valueCoding": {
                    "code": "2135-2",
                    "display": "Hispanic or Latino",
                    "system": "urn:oid:2.16.840.1.113883.6.238",
                },
            }],
        }],
    },
]

# The resulting schema will be both wide (every toplevel column)
# and deep enough for every field in `rows`.
# That is, both the non-present toplevel field "telecom" and the deeper
# field "extension.extension.valueCoding.system" will be in the schema.
schema = cfs.pyarrow_schema_from_rows("Patient", rows)

FhirClient

Connect to a FHIR server with a variety of authentication options and retries built-in.

import cumulus_fhir_support as cfs

client = cfs.FhirClient("https://r4.smarthealthit.org", {"Patient"})

async with client:
    response = await client.request("GET", "Patient/2cda5aad-e409-4070-9a15-e1c35c46ed5a")
    print(response.json())