fhir.resources 6.0.0b4

FHIR® Version Info

FHIR® (Release R4, version 4.0.1) is available as default. Also previous versions are available as Python sub-package (each release name string becomes sub-package name, i.e STU3 ).

Available Previous Versions:

• STU3 (3.0.2)

• DSTU2 (1.0.2) [partially see issue#13]

Installation

Just a simple pip install fhir.resources or easy_install fhir.resources is enough. But if you want development version, just clone from https://github.com/nazrulworld/fhir.resources and pip install -e .[all].

Usages

Example: 1: Construct Resource Model object:

>>> from fhir.resources.organization import Organization
>>> from fhir.resources.address import Address
>>> data = {
...     "id": "f001",
...     "active": True,
...     "name": "Acme Corporation",
...     "address": [{"country": "Swizterland"}]
... }
>>> org = Organization(**data)
>>> org.resource_type == "Organization"
True
>>> isinstance(org.address[0], Address)
>>> True
>>> org.address[0].country == "Swizterland"
True
>>> org.dict()['active'] is True
True

Example: 2: Resource object created from json string:

>>> from fhir.resources.organization import Organization
>>> from fhir.resources.address import Address
>>> json_str = '''{"resourceType": "Organization",
...     "id": "f001",
...     "active": True,
...     "name": "Acme Corporation",
...     "address": [{"country": "Swizterland"}]
... }'''
>>> org = Organization.parse_raw(json_str)
>>> isinstance(org.address[0], Address)
>>> True
>>> org.address[0].country == "Swizterland"
True
>>> org.dict()['active'] is True
True

Example: 3: Resource object created from json object(py dict):

>>> from fhir.resources.patient import Patient
>>> from fhir.resources.humanname import HumanName
>>> from datetime import date
>>> json_obj = {"resourceType": "Patient",
...     "id": "p001",
...     "active": True,
...     "name": [
...         {"text": "Adam Smith"}
...      ],
...     "birthDate": "1985-06-12"
... }
>>> pat = Patient.parse_obj(json_obj)
>>> isinstance(pat.name[0], HumanName)
>>> True
>>> org.birthDate == date(year=1985, month=6, day=12)
True
>>> org.active is True
True

Example: 4: Construct Resource object from json file:

>>> from fhir.resources.patient import Patient
>>> import os
>>> import pathlib
>>> filename = pathlib.Path("foo/bar.json")
>>> pat = Patient.parse_file(filename)
>>> pat.resource_type == "Patient"
True

Example: 5: Construct resource object in python way:

>>> from fhir.resources.organization import Organization
>>> from fhir.resources.address import Address
>>> json_obj = {"resourceType": "Organization",
...     "id": "f001",
...     "active": True,
...     "name": "Acme Corporation",
...     "address": [{"country": "Swizterland"}]
... }

>>> org = Organization.construct()
>>> org.id = "f001"
>>> org.active = True
>>> org.name = "Acme Corporation"
>>> org.address = list()
>>> address = Address.construct()
>>> address.country = "Swizterland"
>>> org.address.append(address)
>>> org.dict() == json_obj
True

Example: 4: Using Resource Factory Function:

>>> from fhir.resources import construct_fhir_element
>>> json_dict = {"resourceType": "Organization",
...     "id": "mmanu",
...     "active": True,
...     "name": "Acme Corporation",
...     "address": [{"country": "Swizterland"}]
... }
>>> org = construct_fhir_element('Organization', json_dict)
>>> org.address[0].country == "Swizterland"
True
>>> org.dict()['active'] is True
True

Example: 5: Auto validation while providing wrong datatype:

>>> try:
...     org = Organization({"id": "fmk", "address": ["i am wrong type"]})
...     raise AssertionError("Code should not come here")
... except ValueError:
...     pass

Advanced Usages

from typing import Dict
from fhir.resources.patient import Patient

import datetime

def validate_birthdate(cls, values: Dict):
    if not values:
        return values
    if "birthDate" not in values:
        raise ValueError("Patient's ``birthDate`` is required.")

    minimum_date = datetime.date(2002, 1, 1)
    if values["birthDate"] > minimum_date:
        raise ValueError("Minimum 18 years patient is allowed to use this system.")
    return values
# we want this validator to execute after data evaluating by individual field validators.
Patient.add_root_validator(validate_gender, pre=False)

from typing import Dict
from fhir.resources.patient import Patient

def validate_gender(cls, values: Dict):
    if not values:
        return values
    enums = cls.__fields__["gender"].field_info.extra["enum_values"]
    if "gender" in values and values["gender"] not in enums:
        raise ValueError("write your message")
    return values

Patient.add_root_validator(validate_gender, pre=True)

Migration (from later than 6.X.X)

This migration guide states some underlying changes of API and replacement, those are commonly used from later than 6.X.X version.

Release and Version Policy

Starting from version 5.0.0 we are following our own release policy and we although follow Semantic Versioning scheme like FHIR® version. Unlike previous statement (bellow), releasing now is not dependent on FHIR®.

removed statement

This package is following FHIR® release and versioning policy, for example say, FHIR releases next version 4.0.1, we also release same version here.

Credits

All FHIR® Resources (python classes) are generated using fhir-parser which is forked from https://github.com/smart-on-fhir/fhir-parser.git.

This package skeleton was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

© Copyright HL7® logo, FHIR® logo and the flaming fire are registered trademarks owned by Health Level Seven International

6.0.0b4 (2020-09-24)

Improvements

• orjson supports have been available as default json dumps and loads for Model.

• FHIRAbstractModel::get_json_encoder class method now available, which return pydantic compatible json encoder callable, can be used with any json serializer.

• More DSTU2 FHIR Resources have added, https://github.com/nazrulworld/fhir.resources/issues/21. Thanks to [mmabey].

Fixes

• Fixes URL validation in the case where a primitive type is used as URL (which is allowed in StructureDefinition). [simonvadee]

• Fixes Issue#19 Getting validation errors that don’t make sense.

6.0.0b3 (2020-08-07)

• FHIRAbstractModel::get_resource_type class method now available, which returning name of the resource.

6.0.0b2 (2020-07-09)

• FHIRAbstractModel::element_properties class method now available, which returning generator of ModelField, those are elements of the resource.

• Minor fixes on enum_values.

6.0.0b1 (2020-07-05)

Revolutionary evolution has been made, now fully rewritten with modern python, underlying APIs (almost all) have been changed. Please have look at readme section, for howto.

Improvements

• Full support of FHIR Extensibility for Primitive Data Types

Breaking

• Drop support for python 2.7.

5.1.0 (2020-04-11)

Improvements

• FHIR STU3 release version upgraded from 3.0.1 to 3.0.2, Please find changes history here https://www.hl7.org/fhir/history.html.

• FHIR R4 release version upgraded from 4.0.0 to 4.0.1, find changes history here https://www.hl7.org/fhir/history.html.

5.0.1 (2019-07-18)

Bugfixes:

• Issue#5 confusing error message “name ‘self’ is not defined” [nazrulworld]

5.0.0 (2019-06-08)

• Nothing but release stable version.

5.0.0b3 (2019-05-14)

New features

• Isuue#1 Add DSTU2 Support

5.0.0b2 (2019-05-13)

Breaking or Improvments

• elementProperties: element now has extra property type_name. Now format like (name, json_name, type, type_name, is_list, "of_many", not_optional) The type_name refers original type name (code) from FHIR Structure Definition and it would be very helpful while making fhir search, fhirpath navigator.

5.0.0b1 (2019-01-19)

New features

• Implemented own build policy, now previous version of FHIR® resources are available as python sub-package.

Build info

• Default version is R4 (see version info at 4.0.0b1 (2019-01-13) section)

• STU3 (see version info at 3.0.1 (2019-01-13) section)

4.0.0 (2019-01-14)

• see version info at 4.0.0b1 section.

4.0.0b1 (2019-01-13)

Version Info (R4)

[FHIR]
FhirVersion=4.0.0-a53ec6ee1b
version=4.0.0
buildId=a53ec6ee1b
date=20181227223754

3.0.1 (2019-01-13)

Version Info (STU3)

[FHIR]
FhirVersion=3.0.1.11917
version=3.0.1
revision=11917
date=20170419074443