def main():
endpoint = 'https://ncpi-api-fhir-service-dev.kidsfirstdrc.org'
# Create an instance
client = SyncFHIRClient(endpoint)
# Search for patients
resources = client.resources('Patient')
resources = resources.search(gender='female').limit(1000)
patients = resources.fetch()
print("# of patients:{}".format(len(patients)))
def main():
endpoint = 'https://ncpi-api-fhir-service-dev.kidsfirstdrc.org'
full_cookie_path = os.path.expanduser('~/.keys/kf_cookies.json')
print(full_cookie_path)
with open(full_cookie_path) as f:
cookies = json.load(f)
client = SyncFHIRClient(endpoint, extra_headers=cookies)
# Search for patients
resources = client.resources('Patient')
resources = resources.search(gender='female').limit(10)
patients = resources.fetch()
print("# of patients:{}".format(len(patients)))
def main():
endpoint = 'https://ncpi-api-fhir-service-dev.kidsfirstdrc.org'
full_cookie_path = os.path.expanduser('~/.keys/kf_cookies.json')
print(full_cookie_path)
with open(full_cookie_path) as f:
cookies = json.load(f)
client = SyncFHIRClient(endpoint, extra_headers=cookies)
document_references = client.resources("DocumentReference")
document_references.search(_profile='http://fhir.ncpi-project-forge.io/StructureDefinition/ncpi-drs-document-reference')
drs_ids = document_references.fetch()
print("# of ids:{}".format(len(drs_ids)))
for d in drs_ids:
print(d['content'][0]['attachment']['url'])
async def init_client(self, config):
basic_auth = BasicAuth(login=config['client']['id'],
password=config['client']['secret'])
self.client = AsyncFHIRClient('{}'.format(config['box']['base-url']),
authorization=basic_auth.encode())
self.sync_client = SyncFHIRClient('{}'.format(
config['box']['base-url']),
authorization=basic_auth.encode())
await self._create_seed_resources()
self._initialized = True
if callable(self._on_ready):
result = self._on_ready()
if asyncio.iscoroutine(result):
await self._on_ready()
from fhirpy import SyncFHIRClient
from fhir.resources.patient import Patient
from fhir.resources.observation import Observation
from fhir.resources.humanname import HumanName
from fhir.resources.contactpoint import ContactPoint
import json
client = SyncFHIRClient(
url='https://dh9fytkn0e.execute-api.eu-west-2.amazonaws.com/dev',
extra_headers={
"x-api-key":
"EzAVxFOjEqagIbYVHK2Mz7RUp1GOpRHMVTTxVQk9",
"Authorization":
"eyJraWQiOiJ2ZXZ0cUNYZitiUzNBM3hNWm5IVFhRbDlucTFZaDloRzJZNkxVXC94bTd0ST0iLCJhbGciOiJSUzI1NiJ9.eyJzdWIiOiJmOWU4YmI3OC04MjRlLTRhZGQtOTZjNS1iZjVmMGY3YTlkNTUiLCJjb2duaXRvOmdyb3VwcyI6WyJwcmFjdGl0aW9uZXIiXSwiZW1haWxfdmVyaWZpZWQiOnRydWUsImlzcyI6Imh0dHBzOlwvXC9jb2duaXRvLWlkcC5ldS13ZXN0LTIuYW1hem9uYXdzLmNvbVwvZXUtd2VzdC0yX0JiTkFoUTVzTSIsImNvZ25pdG86dXNlcm5hbWUiOiJmaGlyYXBpdGVzdCIsIm9yaWdpbl9qdGkiOiIxZWQ0NmU1NS1jNmE1LTQ3MjMtYTEyZi04OTYzOWQzZGVjYWMiLCJhdWQiOiIxdXJkaWlmZjJlbWMzcGgzamdiZ3AxYm43ayIsImV2ZW50X2lkIjoiYjQ4MDM0NjctMjRjYy00OWZlLTg3NTYtNTgzZDEzNDZmOGE3IiwidG9rZW5fdXNlIjoiaWQiLCJhdXRoX3RpbWUiOjE2NTgyNDQ0MDUsImV4cCI6MTY1ODMzMDgwNSwiaWF0IjoxNjU4MjQ0NDA1LCJqdGkiOiJjNjJkNTc3Zi01NWJmLTQwNjQtYjYwOC0xMzA1MTQ1ODM0M2QiLCJlbWFpbCI6ImFsbWE1Lm5oc2RAZ21haWwuY29tIn0.XxflQNEL_N8XWut2MxGNTZfnjei4qCsbvEBs31n1RMemY9DneEU1haYGGaHp4T3CyBy2-eLeaDbfI16dhEnh_5D6qSgRoMPWv5ScZop2uvoqujkufsp-C6lZsRtetyowETrcaSs46jvumqzpONUO5F5i7UdEg2lh9N0iKfUi67MepgMy9gBJMZkKQhTl6S0BRNHfyGhUT5kbN2EeFeDltiSOaDZKk7IbRoUO0OnZYNFcqmDNAjPYzLFKNnYyGcsMlPSKZaULHt3P7EhAS-e5EOG5c8-Sqp7fPOZ3cpq2QHr5RF4hZcyZiUwoyYoeW4_MDvhkdew2tdnyEsFQHwuO2g"
})
patients_resources = client.resources('Patient')
patient0 = Patient.parse_obj(
patients_resources.search(family='Jameson',
given='Matt').first().serialize())
print("Our paitent:", patient0.name)
def setup_class(cls):
cls.client = SyncFHIRClient(
cls.URL,
authorization=FHIR_SERVER_AUTHORIZATION,
extra_headers={'Access-Control-Allow-Origin': '*'}
)
def __init__(self, fhir_server, fhir_port, split='train', input_size=256):
"""
Args:
fhir_server (string): Address of FHIR Server.
fhir_port (string): Port of FHIR Server.
"""
self.fhir_server = fhir_server
self.fhir_port = fhir_port
self.split = split
self.input_size = input_size
# Create an instance
client = SyncFHIRClient('http://{}:{}/fhir'.format(
fhir_server, fhir_port))
# Search for patients
patients = client.resources('Patient') # Return lazy search set
patients_data = []
for patient in patients:
patient_birthDate = None
try:
patient_birthDate = patient.birthDate
except:
pass
# patinet_id, gender, birthDate
patients_data.append(
[patient.id, patient.gender, patient_birthDate])
patients_df = pd.DataFrame(
patients_data, columns=["patient_id", "gender", "birthDate"])
# Search for media
media_list = client.resources('Media').include('Patient', 'subject')
media_data = []
for media in media_list:
media_bodySite = None
media_reasonCode = None
media_note = None
try:
media_bodySite = media.bodySite.text
except:
pass
try:
media_reasonCode = media.reasonCode[0].text
except:
pass
try:
media_note = media.note[0].text
except:
pass
media_data.append([
media.subject.id, media.id, media_bodySite, media_reasonCode,
media_note, media.content.url
])
media_df = pd.DataFrame(media_data,
columns=[
"patient_id", "media_id", "bodySite",
"reasonCode", "note", "image_url"
])
self.data_df = pd.merge(patients_df,
media_df,
on='patient_id',
how='outer')
self.data_df = self.data_df[self.data_df['note'].notna()].reset_index()
self.trans = transforms.Compose([
transforms.RandomHorizontalFlip(),
transforms.RandomVerticalFlip(),
transforms.ColorJitter(brightness=32. / 255., saturation=0.5),
transforms.Resize(self.input_size),
transforms.ToTensor()
])
import pytest
from fhirpy import SyncFHIRClient, AsyncFHIRClient
from fhirpy.lib import BaseFHIRReference
from fhirpy.base.utils import AttrDict, SearchList
@pytest.mark.parametrize(
'client',
[SyncFHIRClient('mock'), AsyncFHIRClient('mock')])
class TestLibBase(object):
def test_to_reference_for_reference(self, client):
reference = client.reference('Patient', 'p1')
reference_copy = reference.to_reference(display='patient')
assert isinstance(reference_copy, BaseFHIRReference)
assert reference_copy.serialize() == {
'reference': 'Patient/p1',
'display': 'patient',
}
def test_serialize(self, client):
practitioner1 = client.resource('Practitioner', id='pr1')
practitioner2 = client.resource('Practitioner', id='pr2')
patient = client.resource(
'Patient',
id='patient',
generalPractitioner=[
practitioner1.to_reference(display='practitioner'),
practitioner2
])
assert patient.serialize() == {
def setup_class(cls):
cls.client = SyncFHIRClient(
cls.URL,
authorization=_basic_auth_str('root', 'secret'),
extra_headers={'Access-Control-Allow-Origin': '*'})
import pytest
from fhirpy import SyncFHIRClient, AsyncFHIRClient
from fhirpy.lib import BaseFHIRReference
from fhirpy.base.utils import AttrDict, SearchList, parse_pagination_url
@pytest.mark.parametrize(
"client",
[SyncFHIRClient("mock"), AsyncFHIRClient("mock")])
class TestLibBase(object):
def test_to_reference_for_reference(self, client):
reference = client.reference("Patient", "p1")
reference_copy = reference.to_reference(display="patient")
assert isinstance(reference_copy, BaseFHIRReference)
assert reference_copy.serialize() == {
"reference": "Patient/p1",
"display": "patient",
}
def test_serialize(self, client):
practitioner1 = client.resource("Practitioner", id="pr1")
practitioner2 = client.resource("Practitioner", id="pr2")
patient = client.resource(
"Patient",
id="patient",
generalPractitioner=[
practitioner1.to_reference(display="practitioner"),
practitioner2,
],
)
fhir_server = str(os.environ['FHIR_SERVER'])
fhir_port = str(os.environ['FHIR_PORT'])
## Load aggregated results from previous stations
# if run_id > 0:
# prev_experiment_dir = osp.join(out_dir, 'run_{}'.format(str(run_id - 1)))
# if osp.exists(osp.join(prev_experiment_dir, '')):
# pass
# else:
# pass
# else:
# pass
## Collect Data Statistic
# Create an instance
client = SyncFHIRClient('http://{}:{}/fhir'.format(fhir_server, fhir_port))
# Search for patients
patients = client.resources('Patient') # Return lazy search set
patients_data = []
for patient in patients:
patient_birthDate = None
try:
patient_birthDate = patient.birthDate
except:
pass
# patinet_id, gender, birthDate
patients_data.append([patient.id, patient.gender, patient_birthDate])
patients_df = pd.DataFrame(patients_data,
columns=["patient_id", "gender", "birthDate"])
# Search for media
media_list = client.resources('Media').include('Patient', 'subject')
