def create_patient_resource(resource_id, nhs_number, title, first_name,
last_name, gender, date_of_birth, address_line_1,
city, postcode, place_of_birth):
"""
Helper function to create a basic fhir patient
:return: Patient
"""
pat_address = Address({
'line': [address_line_1],
'city': city,
'postalCode': postcode
})
nhs_number = Identifier({'value': nhs_number})
name = HumanName({
'prefix': [title],
'family': last_name,
'given': [first_name]
})
birth_address = Address({'city': place_of_birth})
place_of_birth = Extension({
'url': 'http://hl7.org/fhir/StructureDefinition/birthPlace',
'valueAddress': birth_address.as_json()
})
patient = Patient({
'id': resource_id,
'identifier': [nhs_number.as_json()],
'gender': gender,
'name': [name.as_json()],
'birthDate': date_of_birth,
'address': [pat_address.as_json()],
'extension': [place_of_birth.as_json()]
})
return patient
def lookup_patient(federated_principal_alias):
""" Queries a patient by FPA.
Args:
federated_principal_alias: ID of a person in Cerner's Identity Federation.
Returns:
{"name": "<patient's name>", "id": <FHIR server's patient ID>}
"""
identifier = f'{CERNER_FPA_URN}|{federated_principal_alias}'
search = Patient.where(struct={'identifier': identifier})
patients = search.perform_resources(demo_fhir_server())
return {'name': patients[0].name[0].text, 'id': patients[0].id}
def create_operation_definition_for_death_registration(free_text=None):
practitioner = create_simple_practitioner()
patient = Patient({
'id': 'patient-1',
'identifier': [{
'value': 'NHSNO22222'
}],
'deceasedBoolean': True,
'deceasedDateTime': '2019-04-20 09:00:04.159338'
})
op_param_interchange_sequence = creators.create_parameter_with_binding(
name=ParameterName.INTERCHANGE_SEQ_NO, value="000001")
op_param_message_sequence = creators.create_parameter_with_binding(
name=ParameterName.MESSAGE_SEQ_NO, value="000001")
op_param_nhais_cypher = creators.create_parameter_with_binding(
name=ParameterName.NHAIS_CYPHER, value="XX1")
op_param_sender_cypher = creators.create_parameter_with_binding(
name=ParameterName.SENDER_CYPHER, value="TES5")
op_param_transaction_number = creators.create_parameter_with_binding(
name=ParameterName.TRANSACTION_NO, value="17")
op_param_practitioner = creators.create_parameter_with_resource_ref(
name=ParameterName.REGISTER_PRACTITIONER,
resource_type=ResourceType.PRACTITIONER,
reference="practitioner-1")
op_param_patient = creators.create_parameter_with_resource_ref(
name=ParameterName.REGISTER_PATIENT,
resource_type=ResourceType.PATIENT,
reference="patient-1")
parameters = [
op_param_interchange_sequence, op_param_message_sequence,
op_param_nhais_cypher, op_param_sender_cypher,
op_param_transaction_number, op_param_practitioner, op_param_patient
]
if free_text:
parameters.append(
creators.create_parameter_with_binding(
name=ParameterName.FREE_TEXT, value=free_text))
op_def = creators.create_operation_definition(
name=OperationName.REGISTER_DEATH,
code="gpc.registerpatient",
date_time="2019-04-23 09:00:04.159338",
contained=[practitioner, patient],
parameters=parameters)
return op_def
def to_fhir_res(self):
data = {
'id': self.id,
'identifier': [{
'value': self.identifier
}],
'name': [{
'given': self.given_name.split(' '),
'family': self.family_name
}],
'gender': {'m': 'male', 'f': 'female', 'u': 'unknown', 'o': 'other'}[self.gender],
'birthDate': self.birthdate.isoformat() if self.birthdate is not None else None,
'address': [{
'text': self.address
}]
}
return Patient(data)
def get_demo_patient(email):
"""
Returns an instance of a FHIR Patient using dummy info for testing
:param email: The email of the testing user
:type email: str
:return: Test Patient resource object
:rtype: Patient
"""
return Patient(
jsondict={
'id':
'TEST',
'identifier': [{
'system': PPMFHIR.patient_email_identifier_system,
'value': email
}]
})
def check_patient(patient_email):
# Prepare the client
fhir = client.FHIRClient(settings={
'app_id': settings.FHIR_APP_ID,
'api_base': settings.FHIR_URL
})
# Set the search parameters
struct = {
'identifier': 'http://schema.org/email|{}'.format(patient_email)
}
# Get the questionnaire
search = Patient.where(struct=struct)
resources = search.perform_resources(fhir.server)
if not resources:
logger.warning('Patient not found: {}'.format(
FHIR._obfuscate_email(patient_email)))
raise FHIR.PatientDoesNotExist
def _get_patient(patient_id):
p = FHIRPatient()
p.id = str(patient_id)
return p
def post_patient_validate(self, pat: patient.Patient):
url = f'{self.base_url}/Patient/$validate'
data = json.dumps(pat.as_json())
return self.session.post(url, data)
from fhirclient.client import FHIRServer
from fhirclient.models.patient import Patient
server = FHIRServer(None, "http://hapi.fhir.org/baseR4")
p = Patient.read("921009", server)
print("-" * 40)
print("Patient Information")
print("-" * 40)
print(f"NAME: {p.name[0].text}")
print(f"BIRTHDATE: {p.birthDate.date.isoformat()}")
from fhirclient.models.condition import Condition
# from fhirclient.models.bundle import Bundle
# conditionBundle = Condition.where( { "subject": "921009" } ).perform( server )
# if conditionBundle.entry is None:
conditions = Condition.where({"subject": "921009"}).perform_resources(server)
if not conditions:
print("PROBLEM LIST: None")
else:
print("PROBLEM LIST:")
i = 1
# for entry in conditionBundle.entry:
for cond in conditions:
# cond = entry.resource
print(
f"{i:>3d}. {cond.code.text:<40s} Severity: {cond.severity.text:<12s}"
)
i += 1
def get_patient_detail(fhir, pat_id):
pat = Patient.read(pat_id, fhir.server)
# If set, use this to query on a fixed time point.
if REF_DATE:
ref_date = REF_DATE
else:
ref_date = datetime.now()
# Only the last 24 hours are considered.
past24 = ref_date - timedelta(days=1)
# Vital signs for the patient. Includes SBP, HR, RR, satO2, temp
search = Observation.where(struct={
'subject': pat_id,
'category': VITAL_SIGNS_CATEGORY,
'date': {
'$gte': past24.strftime('%Y-%m-%dT%H:%M:%SZ'),
},
})
bp = []
hr = []
rr = []
temp = []
o2 = []
# Implicitly fetches pages on demand.
for r in search.perform_resources(fhir.server):
# Resource code.
system = r.code.coding[0].system
code = r.code.coding[0].code
if system != LOINC_SYSTEM:
continue
# Extract systolic component from blood pressure.
if code == LOINC_BP:
sbp = None
dbp = None
for c in r.component:
if c.code.coding[0].code == LOINC_SBP:
sbp = {
'time': r.effectiveDateTime.isostring,
'value': c.valueQuantity.value,
'unit': c.valueQuantity.unit,
}
elif c.code.coding[0].code == LOINC_DBP:
dbp = {
'time': r.effectiveDateTime.isostring,
'value': c.valueQuantity.value,
'unit': c.valueQuantity.unit,
}
if sbp or dbp:
bp.append({
'systolic': sbp,
'diastolic': dbp,
})
elif code == LOINC_HR:
hr.append({
'time': r.effectiveDateTime.isostring,
'value': r.valueQuantity.value,
'unit': r.valueQuantity.unit,
})
elif code == LOINC_RR:
rr.append({
'time': r.effectiveDateTime.isostring,
'value': r.valueQuantity.value,
'unit': r.valueQuantity.unit,
})
elif code == LOINC_TEMP:
temp.append({
'time': r.effectiveDateTime.isostring,
'value': r.valueQuantity.value,
'unit': r.valueQuantity.unit,
})
elif code == LOINC_O2:
o2.append({
'time': r.effectiveDateTime.isostring,
'value': r.valueQuantity.value,
'unit': r.valueQuantity.unit,
})
mrn = None
if pat.identifier:
mrn = pat.identifier[0].value
return {
'id': pat_id,
'mrn': mrn,
'name': parse_human_name(pat.name[0]),
'birth_date': pat.birthDate.isostring,
'gender': pat.gender,
'measures': {
'heart_rate': hr,
'respiratory_rate': rr,
'temperature': temp,
'pulse_ox': o2,
'blood_pressure': bp,
'mental_status': None,
'eating_status': None,
},
}
from fhirclient.client import FHIRServer
from fhirclient.models.patient import Patient
server = FHIRServer(None, "http://hapi.fhir.org/baseDstu3")
p = Patient.read("2716055", server)
print("-" * 40)
print("Patient Information")
print("-" * 40)
print(f"NAME: {p.name[0].text}")
print(f"BIRTHDATE: {p.birthDate.date.isoformat()}")
from fhirclient.models.condition import Condition
conditions = Condition.where({"subject": "2716055"}).perform_resources(server)
if not conditions:
print("PROBLEM LIST: None")
else:
print("PROBLEM LIST:")
i = 1
for cond in conditions:
print(
f"{i:>3d}. {cond.code.text:<40s} Severity: {cond.severity.text:<12s}"
)
i += 1
from fhirclient.models.encounter import Encounter
encounters = Encounter.where({"subject": "2716055"}).perform_resources(server)
if not encounters:
print("ENCOUNTER LIST: None")
else: