def _update_patient_and_environment(
patient: PatientAgent,
environment: Union[
AandEEnvironmentAgent, EnvironmentAgent, GPEnvironmentAgent, COEnvironmentAgent, OPEnvironmentAgent, IPEnvironmentAgent
],
interactions: List[str],
simulation_step: int,
patient_time: datetime.datetime,
update_data: dict,
patient_record_duplicate_action: str,
main_logger: logging.Logger,
patient_logger: logging.Logger,
) -> None:
supported_fhir_resources = get_supported_fhir_resources()
required_entry_fields = get_required_entry_fields()
new_patient_record_entries = update_data["new_patient_record_entries"]
for entry in new_patient_record_entries:
missing_entry_fields = required_entry_fields - set(entry)
if len(missing_entry_fields) > 0:
raise ValueError(
"Each patient record entry must contain all the following "
f"keys: {required_entry_fields}. Entry {entry} is missing "
f"{missing_entry_fields} generated by interactions "
f"{interactions}"
)
if entry["resource_type"] not in supported_fhir_resources:
raise ValueError(
"Currently can only support the following FHIR resources: "
f"{supported_fhir_resources}. Found {entry['resource_type']}"
)
patient.update(
[
wrap_fhir_resource(
entry,
patient_time,
environment.environment_id,
interactions,
simulation_step,
)
for entry in new_patient_record_entries
],
logger=patient_logger,
skip_existing=patient_record_duplicate_action == "skip",
)
environment.update(patient, update_data.get("patient_data"))
def test_patient_conditions_update():
patient_id = 2468
gender = "female"
birth_date = "1985-05-24"
patient = PatientAgent(
patient_id=patient_id,
gender=gender,
birth_date=birth_date,
)
condition_entry = {
"resource_type": "Condition",
"name": "Fever",
"start": "2021-03-21",
}
patient_time = datetime.datetime.now(patient.tz)
patient.update([wrap_fhir_resource(condition_entry, patient_time)])
def test_initialize_patient_agent_minimal():
patient_id = 2468
gender = "female"
birth_date = "1985-05-24"
start_time = "2020-12-01"
agent_id = 12345
created_at = "2021-03-09"
patient = PatientAgent(
patient_id=patient_id,
gender=gender,
birth_date=birth_date,
start_time=start_time,
id_=agent_id,
created_at=created_at,
)
patient_profile = {
"resource_type": "Patient",
"id": str(patient_id),
"gender": gender,
"birth_date": birth_date,
}
wrapped_entry = wrap_fhir_resource(
patient_profile,
patient_time=string_to_datetime(start_time),
environment_id=-1,
tag="patient_profile",
)
wrapped_entry["real_time"] = string_to_datetime(created_at)
wrapped_entry["record_index"] = 0
wrapped_entry["entry_id"] = patient.record[0].entry_id
initial_patient_resource = PatientRecordEntry(**wrapped_entry)
assert patient.id == agent_id
assert patient.created_at == string_to_datetime(created_at)
assert patient.__repr__() == (
f"PatientAgent(id={agent_id}, "
f"created_at={string_to_datetime(created_at)})")
assert patient.record == [initial_patient_resource]
def test_convert_patient_record_entry_to_fhir():
fhir_handler = FHIRHandler()
patient = PatientAgent(
patient_id="patient-0",
gender="male",
birth_date="1956-07-26",
)
entry_id = "test-entry-0"
record_entry = PatientRecordEntry(
real_time="",
patient_time="",
environment_id=None,
interactions=None,
simulation_step=None,
fhir_resource_time="",
fhir_resource_type="",
fhir_resource={},
record_index=0,
entry_id=entry_id,
entry={},
tag="test-entry",
)
# NOTE: all these keys and more can be in entry but they won't
# all get used in every resource
# TODO: write func to return keys used by resource, also which ones are
# required
entry = {
"name": "some name",
"code": "xxx",
"start": string_to_datetime("2021-01-10 09:00:00"),
"end": string_to_datetime("2021-01-10 09:15:00"),
"reason": "some reason",
"description": "some description",
"dosage": "some dosage",
"duration_value": 10,
"duration_unit": "some duration_unit",
"value": {
"value": 6.3,
"unit": "mmol/l",
"system": "http://unitsofmeasure.org",
"code": "mmol/L",
},
}
record_entry.entry = entry
supported_fhir_resources = get_supported_fhir_resources()
for fhir_resource_type in supported_fhir_resources:
record_entry.fhir_resource_type = fhir_resource_type
resource = convert_patient_record_entry_to_fhir(record_entry,
patient,
environments=None)
assert fhir_handler.validate(resource, fhir_resource_type)
entries = []
for fhir_resource_type in supported_fhir_resources:
entry["resource_type"] = fhir_resource_type
entry["name"] = f"some name in resource {fhir_resource_type}"
entries.append(wrap_fhir_resource(entry, entry["start"]))
patient._update_record(entries)
environments = None
resources = generate_patient_fhir_resources(
patient,
environments,
validate=True,
server_url=None,
)
bundle_path = TEST_DATA_DIR / f"patient_{patient.patient_id}_bundle.json"
generate_patient_fhir_bundle(
patient,
environments,
bundle_type="transaction",
validate=True,
server_url=None,
save_path=bundle_path,
)
bundle = fhir_handler.load(bundle_path,
"Bundle",
server_url=None,
validate=True)
def test_initialize_patient_agent_with_comorbities():
patient_id = 2468
gender = "female"
birth_date = "1985-05-24"
start_time = "2020-12-01"
agent_id = 12345
created_at = "2021-03-09"
comorbidity = {
"resource_type": "Condition",
"name": "Diabetes",
"start": "2018-10-21",
}
wrapped_comorbidity = wrap_fhir_resource(
comorbidity,
patient_time=string_to_datetime(comorbidity["start"]),
environment_id=-1,
tag="comorbidity_diabetes",
)
wrapped_comorbidity["real_time"] = string_to_datetime(created_at)
telecom = {"system": "phone", "value": "555-113-5410", "use": "home"}
age = 35
kwargs = {
"patient__telecom": telecom,
"age": age,
}
initial_record = [wrapped_comorbidity]
patient = PatientAgent(
patient_id=patient_id,
gender=gender,
birth_date=birth_date,
start_time=start_time,
id_=agent_id,
created_at=created_at,
record=initial_record,
**kwargs,
)
patient_profile = {
"resource_type": "Patient",
"id": str(patient_id),
"gender": gender,
"birth_date": birth_date,
"telecom": telecom,
}
wrapped_patient_profile = wrap_fhir_resource(
patient_profile,
patient_time=string_to_datetime(start_time),
environment_id=-1,
tag="patient_profile",
)
wrapped_patient_profile["real_time"] = string_to_datetime(created_at)
wrapped_patient_profile["record_index"] = 0
wrapped_patient_profile["entry_id"] = patient.record[0].entry_id
initial_patient_entry = PatientRecordEntry(**wrapped_patient_profile)
wrapped_comorbidity["real_time"] = string_to_datetime(created_at)
wrapped_comorbidity["record_index"] = 1
wrapped_comorbidity["entry_id"] = patient.record[1].entry_id
comorbidity_entry = PatientRecordEntry(**wrapped_comorbidity)
assert patient.id == agent_id
assert patient.created_at == string_to_datetime(created_at)
assert (patient.__repr__() == f"PatientAgent(id={agent_id}, "
f"created_at={string_to_datetime(created_at)})")
assert patient.age == age
assert patient.patient__telecom == telecom
assert len(patient.record) == 2
assert patient.record[0] == initial_patient_entry
assert patient.record[1] == comorbidity_entry
assert len(patient.conditions) == 1
assert len(patient.medications) == 0
assert len(patient.actions) == 0
def test_update_patient_agent():
patient_id = 2468
gender = "female"
birth_date = "1985-05-24"
patient_start_time = "2020-12-01"
agent_id = 12345
created_at = "2021-03-09"
patient = PatientAgent(
patient_id=patient_id,
gender=gender,
birth_date=birth_date,
patient_start_time=patient_start_time,
id_=agent_id,
created_at=created_at,
)
assert len(patient.record) == 1
assert len(patient.conditions) == 0
comorbidity = {
"resource_type": "Condition",
"name": "Diabetes",
"start": "2018-10-21",
}
wrapped_comorbidity = wrap_fhir_resource(
comorbidity,
patient_time=string_to_datetime(comorbidity["start"]),
environment_id=-1,
tag="comorbidity_diabetes",
)
wrapped_comorbidity["real_time"] = string_to_datetime(created_at)
patient.update([wrapped_comorbidity])
wrapped_comorbidity["record_index"] = 1
wrapped_comorbidity["entry_id"] = patient.record[1].entry_id
assert len(patient.record) == 2
assert len(patient.conditions) == 1
assert asdict(patient.record[-1]) == wrapped_comorbidity
patient.update([wrapped_comorbidity], skip_existing=False)
assert len(patient.record) == 3
assert len(patient.conditions) == 1
assert asdict(patient.record[-1]) == wrapped_comorbidity
patient.update([wrapped_comorbidity], skip_existing=True)
assert len(patient.record) == 3
assert len(patient.conditions) == 1
assert asdict(patient.record[-1]) == wrapped_comorbidity
assert patient.conditions["active"][0]
assert patient.conditions["end"][0] is None
wrapped_comorbidity = copy.deepcopy(wrapped_comorbidity)
wrapped_comorbidity["entry"]["end"] = "2020-10-21"
patient.update([wrapped_comorbidity], skip_existing=True)
assert len(patient.record) == 4
assert len(patient.conditions) == 1
assert asdict(patient.record[-1]) == wrapped_comorbidity
assert not patient.conditions["active"][0]
assert patient.conditions["end"][0] == string_to_datetime(
wrapped_comorbidity["entry"]["end"])
patient_agent_path = TEST_DATA_DIR / "patient_agent.tar"
patient.save(patient_agent_path)
_patient = PatientAgent.load(patient_agent_path)
dfs = ["conditions", "medications", "actions"]
for attr_name in PatientAgent.serialisable_attributes:
if attr_name in dfs:
# NOTE: there is some discreapncy between the two data frames:
# in one, the timestamps can appear with timezone tz="tzutc()"
# whereas in the other they are tz="UTC", and this causes the
# equality check to fail - this is why .astype(str) has been
# applied to both dataframes. We leave it to future work to
# iron out this detail
assert (getattr(patient, attr_name).astype(str).equals(
getattr(_patient, attr_name).astype(str)))
else:
assert getattr(patient, attr_name) == getattr(_patient, attr_name)
patient_agent_path.unlink()