Lazy search sets

fhir-py

async/sync FHIR client for python3. This package provides an API for CRUD operations over FHIR resources

pip install fhirpy

or to install the latest dev version:

pip install git+https://github.com/beda-software/fhir-py.git

You can test this library by interactive FHIR course in the repository Aidbox/jupyter-course.

Getting started
Resource and helper methods
Reference
Run integration tests

Getting started

Async example

import asyncio
from fhirpy import AsyncFHIRClient


async def main():
    # Create an instance
    client = AsyncFHIRClient(
        'http://fhir-server/',
        authorization='Bearer TOKEN',
    )

    # Search for patients
    resources = client.resources('Patient')  # Return lazy search set
    resources = resources.search(name='John').limit(10).sort('name')
    patients = await resources.fetch()  # Returns list of AsyncFHIRResource

    # Create Organization resource
    organization = client.resource(
        'Organization',
        name='beda.software',
        active=False
    )
    await organization.save()

    # Update (PATCH) organization. Resource support accessing its elements
    # both as attribute and as a dictionary keys
    if organization['active'] is False:
        organization.active = True
    await organization.save(fields=['active'])
    # `await organization.patch(active=True)` would do the same PATCH operation

    # Get patient resource by reference and delete
    patient_ref = client.reference('Patient', 'new_patient')
    # Get resource from this reference
    # (throw ResourceNotFound if no resource was found)
    patient_res = await patient_ref.to_resource()
    await patient_res.delete()

    # Iterate over search set
    org_resources = client.resources('Organization')
    # Lazy loading resources page by page with page count = 100
    async for org_resource in org_resources.limit(100):
        print(org_resource.serialize())


if __name__ == '__main__':
    loop = asyncio.get_event_loop()
    loop.run_until_complete(main())

Searchset examples

patients = client.resources('Patient')

patients.search(birthdate__gt='1944', birthdate__lt='1964')
# /Patient?birthdate=gt1944&birthdate=lt1964

patients.search(name__contains='John')
# /Patient?name:contains=John

patients.search(name=['John', 'Rivera'])
# /Patient?name=John&name=Rivera

patients.search(name='John,Eva')
# /Patient?name=John,Eva

patients.search(family__exact='Moore')
# /Patient?family:exact=Moore

patients.search(address_state='TX')
# /Patient?address-state=TX

patients.search(active=True, _id='id')
# /Patient?active=true&_id=id

patients.search(gender__not=['male', 'female'])
# /Patient?gender:not=male&gender:not=female

Chained parameters

patients.search(general_practitioner__Organization__name='Hospital')
# /Patient?general-practitioner:Organization.name=Hospital

patients.search(general_practitioner__name='Hospital')
# /Patient?general-practitioner.name=Hospital

Reference

practitioner = client.resources('Practitioner').search(_id='john-smith').first()
patients.search(general_practitioner=practitioner)
# /Patient?general-practitioner=Practitioner/john-smith

Date

import pytz
import datetime


patients.search(birthdate__lt=datetime.datetime.now(pytz.utc))
# /Patient?birthdate=lt2019-11-19T20:16:08Z

patients.search(birthdate__gt=datetime.datetime(2013, 10, 27, tzinfo=pytz.utc))
# /Patient?birthdate=gt2013-10-27T00:00:00Z

Modifiers

conditions = client.resources('Condition')

conditions.search(code__text='headache')
# /Condition?code:text=headache

conditions.search(code__in='http://acme.org/fhir/ValueSet/cardiac-conditions')
# /Condition?code:in=http://acme.org/fhir/ValueSet/cardiac-conditions

conditions.search(code__not_in='http://acme.org/fhir/ValueSet/cardiac-conditions')
# /Condition?code:not-in=http://acme.org/fhir/ValueSet/cardiac-conditions

conditions.search(code__below='126851005')
# /Condition?code:below=126851005

conditions.search(code__above='126851005')
# /Condition?code:above=126851005

Raw parameters

Sometimes you can find that fhir-py does not implement some search parameters from the FHIR specification. In this case, you can use Raw() wrapper without any transformations

from fhirpy.base.searchset import Raw

patients = client.resources('Patient')
patients.search(Raw(**{'general-practitioner.name': 'Hospital'}))
# /Patient?general-practitioner.name=Hospital

Get resource by id

Use reference to get resource by id

patient = await client.reference('Patient', '1').to_resource()
# /Patient/1

Or use FHIR search API with .first() or .get() as described below.

Get exactly one resource

practitioners = client.resources('Practitioner')

try:
    await practitioners.search(active=True, _id='id').get()
    # /Practitioner?active=true&_id=id
except ResourceNotFound:
    pass
except MultipleResourcesFound:
    pass

Get first result

await practitioners.search(name='Jack').first()
# /Practitioner?name=Jack&_count=1

await patients.sort('active', '-birthdate').first()
# /Patient?_sort=active,-birthdate&_count=1

Get total count

await practitioners.search(active=True).count()

await patients.count()

Fetch one page

await practitioners.fetch()
# /Practitioner

await patients.elements('name', 'telecom').fetch()
# /Patient?_elements=resourceType,name,id,telecom

Fetch all resources on all pages

Keep in mind that this method as well as .fetch() doesn't return any included resources. Use fetch_raw() if you want to get all included resources.

# Returns a list of `Practitioner` resources
await practitioners.search(address_city='Krasnoyarsk').fetch_all()

await patients.fetch_all()

Page count (_count)

# Get 100 resources
await practitioners.limit(100).fetch()

Sort (_sort)

observations = client.resources('Observation')

observations.sort('status', '-date', 'category')
# /Observation?_sort=status,-date,category

Elements (_elements)

# Get only specified set of elements for each resource
patients.elements('identifier', 'active', 'link')
# /Patient?_elements=identifier,active,link

# Get all elements except specified set
practitioners.elements('address', 'telecom', exclude=True)

Include

result = await client.resources('EpisodeOfCare') \
    .include('EpisodeOfCare', 'patient').fetch_raw()
# /EpisodeOfCare?_include=EpisodeOfCare:patient
for entry in result.entry:
    print(entry.resource)

await client.resources('MedicationRequest') \
    .include('MedicationRequest', 'patient', target_resource_type='Patient') \
    .fetch_raw()
# /MedicationRequest?_include=MedicationRequest:patient:Patient

Modifier :iterate (or :recurse in some previous versions of FHIR)

# For FHIR version >= 3.5 we can also use modifier :iterate
await client.resources('MedicationRequest') \
    .include('MedicationDispense', 'prescription') \
    .include('MedicationRequest', 'performer', iterate=True) \
    .fetch_raw()
# /MedicationRequest?_include=MedicationDispense:prescription
#    &_include:iterate=MedicationRequest:performer

# For FHIR version 3.0-3.3 use modifier :recurse
await client.resources('MedicationDispense') \
    .include('MedicationRequest', 'prescriber', recursive=True) \
    .fetch_raw()
# /MedicationDispense?_include:recurse=MedicationRequest:prescriber

Wild card (any search parameter of type=reference be included)

await client.resources('Encounter').include('*') \
    .fetch_raw()
# /Encounter?_include=*

Revinclude

await practitioners.revinclude('Group', 'member').fetch_raw()
# /Practitioner?_revinclude=Group:member

or

await practitioners.include('Group', 'member', reverse=True).fetch_raw()
# /Practitioner?_revinclude=Group:member

Wild card (any search parameter of type=reference be included)

await client.resources('EpisodeOfCare').revinclude('*') \
    .fetch_raw()
# /EpisodeOfCare?_revinclude=*

Conditional operations

Conditional create

FHIR spec: Conditional create

For resource

# resource.create(search_params)
# executes POST /Patient?identifier=fhirpy

patient = client.resource("Patient",
    identifier=[{"system": "http://example.com/env", "value": "fhirpy"}],
    name=[{"text": "Mr. Smith"}],
)
await patient.create(identifier="other")

For SearchSet

# searchset.get_or_create(resource)
# executes POST /Patient?identifier=fhirpy

patient, created = await client.resources("Patient").search(identifier="fhirpy").get_or_create(patient_to_save)

# no match -> created is True
# one match -> created is False, return existing resource
# multiple matches -> 412 'MultipleResourcesFound'

Conditional update

FHIR spec: Conditional update

# resource, created: bool = searchset.patch(resource)
# executes PUT /Patient?identifier=fhirpy

patient_to_update = client.resource("Patient", 
                                    identifier=[{"system": "http://example.com/env", "value": "fhirpy"}],
                                    active=False)
new_patient, created = await client.resources("Patient").search(identifier="fhirpy").update(patient_to_update)

# no match -> created is True
# one match -> created is False, the matched resource is overwritten
# multiple matches -> 412 'MultipleResourcesFound'

Conditional patch

FHIR spec: Conditional patch

# patched_resource = searchset.patch(resource)
# executes PATCH /Patient?identifier=fhirpy

patient_to_patch = client.resource("Patient", 
                                    identifier=[{"system": "http://example.com/env", "value": "fhirpy"}], 
                                    name=[{"text": "Mr. Smith"}])
patched_patient = await client.resources("Patient").search(identifier="fhirpy").patch(patient_to_patch)

# no match -> 404 'ResourceNotFound'
# multiple matches -> 412 'MultipleResourcesFound'

Conditional delete

FHIR spec: Conditional delete

response_data, status_code = await self.client.resources("Patient").search(identifier="abc").delete()

# no match -> status_code = 204 'No Content'
# one match -> status_code = 200 'OK'
# multiple matches -> status_code = 412 'MultipleResourcesFound' (implementation specific)

Resource and helper methods

Validate resource using operation $validate

try:
    await client.resource('Patient', birthDate='date', custom_prop='123', telecom=True) \
        .is_valid(raise_exception=True)
except OperationOutcome as e:
    print('Error: {}'.format(e))

patient = client.resource('Patient', birthDate='1998-01-01')
if (await patient.is_valid()):
    pass

Accessing resource attributes

patient = await client.resources('Patient').first()

# Work with the resource as a dictionary
patient_family = patient['name'][0]['family']

# Or access value by an attribute
patient_given_name = patient.name[0].given[0]

Static type checking with mypy and fhir-py-types

from fhir_py_types.generated.resources import Patient

patient: Patient = await client.resources('Patient').first()

# Works only with dictionary-like resource access
patient_family = patient['name'][0]['family1']
# 'TypedDict "HumanName" has no key "family1" note: Did you mean "family"?'

Check fhir-py-types for more details on generating type definitions from FHIR StructureDefintion

get_by_path(path, default=None)

patient_postal = patient.get_by_path(['resource', 'address', 0, 'postalCode'])

# get_by_path can be also used on any nested attribute
patient_name = patient.name[0]
patient_fullname = '{} {}'.format(
    patient_name.get_by_path(['given', 0]),
    patient_name.get_by_path(['family'])
)

# Get identifier value by specified system or empty string
uid = patient.get_by_path([
        'resource', 'identifier',
        {'system':'http://example.com/identifier/uid'},
        'value'
    ], '')

# Get base value amount or 0
invoice = await client.resources('Invoice').first()
base_value = invoice.get_by_path([
    'totalPriceComponent',
    {'type': 'base'},
    'amount', 'value'], 0)

set_by_path(obj, path, value)

resource = {
    "name": [{"given": ["Firstname"], "family": "Lastname"}],
}

set_by_path(resource, ["name", 0, "given", 0], "FirstnameUpdated")

# resource
# {"name": [{"given": ["FirstnameUpdated"], "family": "Lastname"}]}

serialize()

# Returns resources as dict
patient = await client.reference('Patient', '1').to_resource()
patient.serialize()
# Or 
await client.reference('Patient', '1').to_resource().serialize()
# {'resourceType': 'Patient', 'id': '1', 'meta': {'versionId': '1', 'lastUpdated': '2021-11-13T11:50:24.685719Z'}, ...}

Reference

Main class structure

Both async and sync clients have identical sets of classes and methods.

	Sync	Async
Client	SyncFHIRClient	AsyncFHIRClient
SearchSet	SyncFHIRSearchSet	AsyncFHIRSearchSet
Resource	SyncFHIRResource	AsyncFHIRResource
Reference	SyncFHIRReference	AsyncFHIRReference

Acync client (based on aiohttp) – AsyncFHIRClient

Import library:

from fhirpy import AsyncFHIRClient

To create AsyncFHIRClient instance use:

AsyncFHIRClient(url, authorization='', extra_headers={})

Returns an instance of the connection to the server which provides:

.reference(resource_type, id, reference, **kwargs) - returns AsyncFHIRReference to the resource
.resource(resource_type, **kwargs) - returns AsyncFHIRResource which described below
.resources(resource_type) - returns AsyncFHIRSearchSet
.execute(path, method='post', data=None, params=None) - returns a result of FHIR operation

Aiohttp request parameters

Sometimes you need more control over the way http request is made and provide additional aiohttp session's request parameters like ssl, proxy, cookies, timeout etc. It's possible by providing aiohttp_config dict for AsyncFHIRClient:

client = AsyncFHIRClient(
    FHIR_SERVER_URL,
    aiohttp_config={
        "ssl": ssl.create_default_context(),
        "timeout": aiohttp.ClientTimeout(total=100),
    }
)

Be careful and don't override other request values like params, json, data, auth, because it'll interfere with the way fhir-py works and lead to an incorrect behavior.

AsyncFHIRResource

provides:

.serialize() - serializes resource
.get_by_path(path, default=None) – gets the value at path of resource
async .save(fields=[]) - creates or updates or patches (with fields=[...]) resource instance
async .update() - overrides resource instance
async .patch(**kwargs) - patches resource instance
async .delete() - deletes resource instance
async .refresh() - reloads resource from a server
async .to_reference(**kwargs) - returns AsyncFHIRReference for this resource
async .execute(operation, method='post', data=None, params=None) - returns a result of FHIR operation on the resource

AsyncFHIRReference

provides:

async .to_resource() - returns AsyncFHIRResource for this reference
async .execute(operation, method='post', data=None, params=None) - returns a result of FHIR operation on the resource

AsyncFHIRSearchSet

provides:

.search(param=value)
.limit(count)
.sort(*args)
.elements(*args, exclude=False)
.include(resource_type, attr=None, recursive=False, iterate=False)
.revinclude(resource_type, attr=None, recursive=False, iterate=False)
.has(*args, **kwargs)
async .fetch() - makes query to the server and returns a list of Resource filtered by resource type
async .fetch_all() - makes query to the server and returns a full list of Resource filtered by resource type
async .fetch_raw() - makes query to the server and returns a raw Bundle Resource
async .first() - returns Resource or None
async .get(id=None) - returns Resource or raises ResourceNotFound when no resource found or MultipleResourcesFound when more than one resource found (parameter 'id' is deprecated)
async .count() - makes query to the server and returns the total number of resources that match the SearchSet
async .get_or_create(resource) - conditional create
async .update(resource) - conditional update
async .patch(resource) - conditional patch

Sync client (based on requests) – SyncFHIRClient

Import library:

from fhirpy import SyncFHIRClient

To create SyncFHIRClient instance use:

SyncFHIRClient(url, authorization='', extra_headers={})

Returns an instance of the connection to the server which provides:

.reference(resource_type, id, reference, **kwargs) - returns SyncFHIRReference to the resource
.resource(resource_type, **kwargs) - returns SyncFHIRResource which described below
.resources(resource_type) - returns SyncFHIRSearchSet

Requests request parameters

Pass requests_config parameter to SyncFHIRClient if you want to provide additional parameters for a request like verify, cert, timeout etc.

client = SyncFHIRClient(
    FHIR_SERVER_URL,
    requests_config={
        "verify": False,
        "allow_redirects": True,
        "timeout": 60,
    }
)

Be careful and don't override other request values like params, json, data, headers, which may interfere with the way fhir-py works and lead to an incorrect behavior.

SyncFHIRResource

The same as AsyncFHIRResource but with sync methods

SyncFHIRReference

provides: The same as AsyncFHIRReference but with sync methods

SyncFHIRSearchSet

The same as AsyncFHIRSearchSet but with sync methods

Run integration tests

(need some test FHIR server to run with, e.g. https://docs.aidbox.app/installation/setup-aidbox.dev)

Clone this repository: https://github.com/beda-software/fhir-py.git
Go to fhir-py folder and install dev dependencies:

cd fhir-py
pip install -r requirements.txt

If you've already installed fhir-py library and want to test the last changes, reinstall it by running python setup.py install (or uninstall pip uninstall fhirpy)

Provide ENV variables FHIR_SERVER_URL and FHIR_SERVER_AUTHORIZATION, or edit tests/config.py
Run pytest

If you've found any bugs or think that some part of fhir-py is not compatible with FHIR spec, feel free to create an issue/pull request.

beda-software / fhir-py Goto Github PK

fhir-py's Introduction

fhir-py

Getting started

Async example

Searchset examples

Chained parameters

Reference

Date

Modifiers

Raw parameters

Get resource by id

Get exactly one resource

Get first result

Get total count

Fetch one page

Fetch all resources on all pages

Page count (_count)

Sort (_sort)

Elements (_elements)

Include

Modifier :iterate (or :recurse in some previous versions of FHIR)

Wild card (any search parameter of type=reference be included)

Revinclude

Wild card (any search parameter of type=reference be included)

Conditional operations

Conditional create

For resource

For SearchSet

Conditional update

Conditional patch

Conditional delete

Resource and helper methods

Validate resource using operation $validate

Accessing resource attributes

Static type checking with mypy and fhir-py-types

get_by_path(path, default=None)

set_by_path(obj, path, value)

serialize()

Reference

Main class structure

Acync client (based on aiohttp) – AsyncFHIRClient

Aiohttp request parameters

AsyncFHIRResource

AsyncFHIRReference

AsyncFHIRSearchSet

Sync client (based on requests) – SyncFHIRClient

Requests request parameters

SyncFHIRResource

SyncFHIRReference

SyncFHIRSearchSet

Run integration tests

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