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FHIR Resources as Model Class

Project description

FHIR® Resources (R4, STU3, DSTU2)

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Powered by pydantic, all FHIR Resources are available as python class with built-in data validation, faster in performance and optionally orjson support has been included as a performance booster! Written in modern python.

  • Easy to construct, easy to extended validation, easy to export.
  • By inheriting behaviour from pydantic, compatible with ORM.
  • Full support of FHIR® Extensibility for Primitive Data Types are available.
  • Previous release of FHIR® Resources are available.
  • Free software: BSD license

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) [see issue#13][don’t have full tests coverage]

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

FHIR Comments (JSON)

It is possible to add comments inside json like xml, but need to follow some convention, what is suggested by Grahame Grieve; is implemented here.

Also it is possible to generate json string output without comments.

Examples:

>>> observation_str = b"""{
...  "resourceType": "Observation",
...  "id": "f001",
...    "fhir_comments": [
...      "   a specimen identifier - e.g. assigned when the specimen was taken by the orderer/placer  use the accession number for the filling lab   ",
...      "  Placer ID  "
...    ],
...  "text": {
...      "fhir_comments": [
...      "   a specimen identifier - e.g. assigned when the specimen was taken by the orderer/placer  use the accession number for the filling lab   ",
...      "  Placer ID  "
...    ],
...    "status": "generated",
...    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">.........</div>"
...  },
...  "identifier": [
...    {
...      "use": "official",
...      "system": "http://www.bmc.nl/zorgportal/identifiers/observations",
...      "value": "6323"
...    }
...  ],
...  "status": "final",
...  "_status": {
...      "fhir_comments": [
...            "  EH: Note to balloters  - lots of choices for whole blood I chose this.  "
...          ]
...  },
...  "code": {
...    "coding": [
...      {
...        "system": "http://loinc.org",
...        "code": "15074-8",
...        "display": "Glucose [Moles/volume] in Blood"
...      }
...    ]
...  },
...  "subject": {
...    "reference": "Patient/f001",
...    "display": "P. van de Heuvel"
...  },
...  "effectivePeriod": {
...    "start": "2013-04-02T09:30:10+01:00"
...  },
...  "issued": "2013-04-03T15:30:10+01:00",
...  "performer": [
...    {
...      "reference": "Practitioner/f005",
...      "display": "A. Langeveld"
...    }
...  ],
...  "valueQuantity": {
...    "value": 6.3,
...    "unit": "mmol/l",
...    "system": "http://unitsofmeasure.org",
...    "code": "mmol/L"
...  },
...  "interpretation": [
...    {
...      "coding": [
...        {
...          "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
...          "code": "H",
...          "display": "High"
...        }
...      ]
...    }
...  ],
...  "referenceRange": [
...    {
...      "low": {
...        "value": 3.1,
...        "unit": "mmol/l",
...        "system": "http://unitsofmeasure.org",
...        "code": "mmol/L"
...      },
...      "high": {
...        "value": 6.2,
...        "unit": "mmol/l",
...        "system": "http://unitsofmeasure.org",
...        "code": "mmol/L"
...      }
...    }
...  ]
... }"""
>>> from fhir.resources.observation import Observation
>>> obj = Observation.parse_raw(observation_str)
>>> "fhir_comments" in obj.json()
>>> # Test comments filtering
>>> "fhir_comments" not in obj.json(exclude_comments=True)

Unfortunately comments filtering is not available for FHIRAbstractModel::dict

Special Case: Missing data

In some cases, implementers might find that they do not have appropriate data for an element with minimum cardinality = 1. In this case, the element must be present, but unless the resource or a profile on it has made the actual value of the primitive data type mandatory, it is possible to provide an extension that explains why the primitive value is not present. Example (required intent element is missing but still valid because of extension):

>>> json_str = b"""{
...    "resourceType": "MedicationRequest",
...    "id": "1620518",
...    "meta": {
...        "versionId": "1",
...        "lastUpdated": "2020-10-27T11:04:42.215+00:00",
...        "source": "#z072VeAlQWM94jpc",
...        "tag": [
...            {
...                "system": "http://www.alpha.alp/use-case",
...                "code": "EX20"
...            }
...        ]
...    },
...    "status": "completed",
...    "_intent": {
...        "extension": [
...            {
...                "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
...                "valueCode": "unknown"
...            }
...        ]
...    },
...    "medicationReference": {
...        "reference": "Medication/1620516",
...        "display": "Erythromycin 250 MG Oral Tablet"
...    },
...    "subject": {
...        "reference": "Patient/1620472"
...    },
...    "encounter": {
...        "reference": "Encounter/1620506",
...        "display": "Follow up encounter"
...    },
...    "authoredOn": "2018-06-16",
...    "requester": {
...        "reference": "Practitioner/1620502",
...        "display": "Dr. Harold Hippocrates"
...    },
...    "reasonReference": [
...        {
...            "reference": "Condition/1620514",
...            "display": "Otitis Media"
...        }
...    ],
...    "dosageInstruction": [
...        {
...            "text": "250 mg 4 times per day for 10 days",
...            "timing": {
...                "repeat": {
...                    "boundsDuration": {
...                        "value": 10,
...                        "unit": "day",
...                        "system": "http://unitsofmeasure.org",
...                        "code": "d"
...                    },
...                    "frequency": 4,
...                    "period": 1,
...                    "periodUnit": "d"
...                }
...            },
...            "doseAndRate": [
...                {
...                    "doseQuantity": {
...                        "value": 250,
...                        "unit": "mg",
...                        "system": "http://unitsofmeasure.org",
...                        "code": "mg"
...                    }
...                }
...            ]
...        }
...    ],
...    "priorPrescription": {
...        "reference": "MedicationRequest/1620517",
...        "display": "Amoxicillin prescription"
...    }
... }"""
>>> from fhir.resources.medicationrequest import MedicationRequest
>>> obj = MedicationRequest.parse_raw(json_str)
>>> "intent" not in obj.dict()

Custom Validators

fhir.resources is providing the extensive API to create and attach custom validator into any model. See more about root validator Some convention you have to follow though, while creating a root validator.

  1. Number of arguments are fixed, as well as names are also. i.e (cls, values).
  2. Should return values, unless any exception need to be raised.
  3. Validator should be attached only one time for individual Model. Update [from now, it’s not possible to attach multiple time same name validator on same class]

Example 1: Validator for Patient:

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)

Example 2: Validator for Patient from Validator Class:

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

import datetime

class MyValidator:
    @classmethod
    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(MyValidator.validate_gender, pre=False)

important notes It is possible add root validator into any base class like DomainResource. In this case you have to make sure root validator is attached before any import of derived class, other than validator will not trigger for successor class (if imported before) by nature.

ENUM Validator

fhir.resources is providing API for enum constraint for each field (where applicable), but it-self doesn’t enforce enum based validation! see discussion here. If you want to enforce enum constraint, you have to create a validator for that.

Example: Gender Enum:

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)

Reference Validator

fhir.resources is also providing enum like list of permitted resource types through field property enum_reference_types. You can get that list by following above (Enum) approaches resource_types = cls.__fields__["managingOrganization"].field_info.extra["enum_reference_types"]

Usages of orjson

orjson is one of the fastest Python library for JSON and is more correct than the standard json library (according to their docs). Good news is that fhir.resource has an extensive support for orjson and it’s too easy to enable it automatically. What you need to do, just make orjson as your project dependency!

pydantic Field Type Support

All available fhir resources (types) can be use as pydantic’s Field’s value types. See issue#46 Support for FastAPI pydantic response models. The module fhirtypes.py contains all fhir resources related types and should trigger validator automatically.

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.

fhir.resources.fhirelementfactory.FHIRElementFactory::instantiate

Replacement: fhir.resources.construct_fhir_element

  • First parameter value is same as previous, the Resource name.
  • Second parameter is more flexible than previous! it is possible to provide not only json dict but also json string or json file path.
  • No third parameter, what was in previous version.

fhir.resources.fhirabstractbase.FHIRAbstractBase::__init__

Replacement: fhir.resources.fhirabstractmodel.FHIRAbstractModel::parse_obj<classmethod>

  • First parameter value is same as previous, json dict.
  • No second parameter, what was in previous version.

fhir.resources.fhirabstractbase.FHIRAbstractBase::as_json

Replacement: fhir.resources.fhirabstractmodel.FHIRAbstractModel::dict

  • Output are almost same previous, but there has some difference in case of some date type, for example py date, datetime, Decimal are in object representation.
  • It is possible to use fhir.resources.fhirabstractmodel.FHIRAbstractModel::json as replacement, when json string is required (so not need further, json dumps from dict)

Note:

All resources/classes are derived from fhir.resources.fhirabstractmodel.FHIRAbstractModel what was previously from fhir.resources.fhirabstractbase.FHIRAbstractBase.

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

History

6.0.0 (2020-12-17)

  • Issue #21 Remaining resources are added. [iatechicken]

6.0.0b11 (2020-11-25)

  • Fixes: wrong ClaimResponseAddItemAdjudicationType resource type name into DTSU2.

6.0.0b10 (2020-11-15)

Improvements

  • FHIRAbstractModel::add_root_validator is more improved and practical with proper validation, more now possible provide class method as root validator.

Bugfixes

  • Issue #41 pydantic.errors.ConfigError: duplicate validator function.

6.0.0b9 (2020-11-05)

Improvements

  • Now supports of simplejson is available automatically (depends on importable) along side with orjson and default json library. Order of json serializer available (orjson -> simplejson(as fallback) -> json(as default)).

Breaking

  • orjson is not available by default, have to use extra_require orjson to available that.

6.0.0b8 (2020-11-02)

  • pydantic minimum version has been set to 1.7.2.

6.0.0b7 (2020-10-31)

If you face import error ``from pydantic.utils import ROOT_KEY``, please upgrade your pydnatic version to <1.7

Fixes

  • Issue #39 added compatibility with pydantic version between 1.6.x and 1.7.x [nazrulworld]

Improvements

6.0.0b6 (2020-10-24)

Improvements

  • FHIRAbstractModel::json now takes additional parameter return_bytes, indicates json string would be bytes. [nazrulworld]
  • Issue#38 Add support for FHIR comments. As per suggestion of comments in json from Grahame Grieve, now fhir_comments is accepted. [nazrulworld]
  • FHIR comments filter option is added in FHIRAbstractModel::json, means it is possible to exclude any comments while generating json string by providing parameter exclude_comments value. [nazrulworld]
  • More FHIR DSTU2 resources have been added. [Itay Goren]

6.0.0b5 (2020-10-04)

Improvements

  • visionprescription and supplyrequest resources added for DSTU2 [iatechicken]

Fixes

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

Breaking

  • Drop support for python 2.7.

5.1.0 (2020-04-11)

Improvements

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

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

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