def test_patients_registered_with_one_practice_between():
session = make_session()
patient_registered_in_2001 = Patient()
patient_registered_in_2002 = Patient()
patient_unregistered_in_2002 = Patient()
patient_registered_in_2001.RegistrationHistory = [
RegistrationHistory(StartDate="2001-01-01", EndDate="9999-01-01")
]
patient_registered_in_2002.RegistrationHistory = [
RegistrationHistory(StartDate="2002-01-01", EndDate="9999-01-01")
]
patient_unregistered_in_2002.RegistrationHistory = [
RegistrationHistory(StartDate="2001-01-01", EndDate="2002-01-01")
]
session.add(patient_registered_in_2001)
session.add(patient_registered_in_2002)
session.add(patient_unregistered_in_2002)
session.commit()
study = StudyDefinition(
population=patients.registered_with_one_practice_between(
"2001-12-01", "2003-01-01"
)
)
results = study.to_dicts()
assert [x["patient_id"] for x in results] == [
str(patient_registered_in_2001.Patient_ID)
]
def test_patient_registered_as_of():
session = make_session()
patient_registered_in_2001 = Patient()
patient_registered_in_2002 = Patient()
patient_unregistered_in_2002 = Patient()
patient_registered_in_2001.RegistrationHistory = [
RegistrationHistory(StartDate="2001-01-01", EndDate="9999-01-01")
]
patient_registered_in_2002.RegistrationHistory = [
RegistrationHistory(StartDate="2002-01-01", EndDate="9999-01-01")
]
patient_unregistered_in_2002.RegistrationHistory = [
RegistrationHistory(StartDate="2001-01-01", EndDate="2002-01-01")
]
session.add(patient_registered_in_2001)
session.add(patient_registered_in_2002)
session.add(patient_unregistered_in_2002)
session.commit()
# No date criteria
study = StudyDefinition(population=patients.registered_as_of("2002-03-02"))
results = study.to_dicts()
assert [x["patient_id"] for x in results] == [
str(patient_registered_in_2001.Patient_ID),
str(patient_registered_in_2002.Patient_ID),
]
def test_patients_with_ages_and_practices_sql():
session = make_session()
session.add_all([
# This patient is too old and should be ignored
Patient(DateOfBirth="2002-05-04"),
# This patient is too young and should be ignored
Patient(DateOfBirth="2019-10-04"),
Patient(
DateOfBirth="2018-10-28",
RegistrationHistory=[
RegistrationHistory(
StartDate="2015-01-01",
EndDate="2021-10-01",
Organisation=Organisation(Organisation_ID=456),
),
],
),
Patient(
DateOfBirth="2014-09-14",
RegistrationHistory=[
RegistrationHistory(
StartDate="2010-01-01",
EndDate="2015-10-01",
Organisation=Organisation(Organisation_ID=123),
),
# Deliberately overlapping registration histories
RegistrationHistory(
StartDate="2015-04-01",
EndDate="9999-12-31",
Organisation=Organisation(Organisation_ID=345),
),
],
),
])
session.commit()
sql = patients_with_ages_and_practices_sql(
date_of_birth_range=("2012-01-01", "2019-06-01"),
age_thresholds=[12, 24, 60],
)
results = sql_to_dicts(sql)
# Note this is rounded to start of month
assert [x["date_of_birth"]
for x in results] == ["2018-10-01", "2014-09-01"]
assert [x["practice_id_at_month_12"] for x in results] == ["456", "345"]
assert [x["practice_id_at_month_24"] for x in results] == ["456", "345"]
assert [x["practice_id_at_month_60"] for x in results] == ["0", "345"]
def set_up_patients(event_data):
organisations = [Organisation(Organisation_ID=ix) for ix in range(5)]
# This patient is in the target population, because they're still registered at the
# practice.
current_patient = Patient()
current_patient.RegistrationHistory = [
RegistrationHistory(
StartDate="2000-01-01",
EndDate="2001-01-01",
Organisation=organisations[0],
),
RegistrationHistory(
StartDate="2001-01-01",
EndDate="9999-01-01",
Organisation=organisations[1],
),
]
current_patient.CodedEventsSnomed = [
CodedEventSnomed(ConsultationDate=date, ConceptID=code)
for date, code in event_data
]
# This patient is in the target population, because they're still registered at the
# practice, but they have no events.
current_patient_no_events = Patient()
current_patient_no_events.RegistrationHistory = [
RegistrationHistory(
StartDate="2001-01-01",
EndDate="9999-01-01",
Organisation=organisations[1],
),
]
# This patient is in the target population, because they died during the timeframe
# we're interested in.
dead_patient = Patient(DateOfDeath="2022-01-15")
dead_patient.RegistrationHistory = [
RegistrationHistory(
StartDate="2001-01-01",
EndDate="2022-01-15",
Organisation=organisations[2],
)
]
dead_patient.CodedEventsSnomed = [
CodedEventSnomed(ConsultationDate=date, ConceptID=code)
for date, code in event_data
]
# This patient is not in the target population, because they were not registered by
# the end of the timeframe we're interested in.
former_patient = Patient()
former_patient.RegistrationHistory = [
RegistrationHistory(
StartDate="2001-01-01",
EndDate="2022-01-15",
Organisation=organisations[3],
)
]
former_patient.CodedEventsSnomed = [
CodedEventSnomed(ConsultationDate=date, ConceptID=code)
for date, code in event_data
]
# This patient is not in the target population, because they died before the
# timeframe we're interested in.
long_dead_patient = Patient(DateOfDeath="2011-12-31")
long_dead_patient.RegistrationHistory = [
RegistrationHistory(
StartDate="2001-01-01",
EndDate="2011-12-31",
Organisation=organisations[4],
)
]
long_dead_patient.CodedEventsSnomed = [
CodedEventSnomed(ConsultationDate=date, ConceptID=code)
for date, code in event_data
]
session = make_session()
session.add(current_patient)
session.add(current_patient_no_events)
session.add(dead_patient)
session.add(former_patient)
session.add(long_dead_patient)
session.commit()
def test_study_definition(tmp_path):
session = make_session()
session.add_all([
# This patient is too old and should be ignored
Patient(Patient_ID=1, DateOfBirth="2002-05-04"),
Patient(
Patient_ID=2,
DateOfBirth="2019-01-01",
RegistrationHistory=[
RegistrationHistory(
StartDate="2019-01-10",
EndDate="9999-12-31",
Organisation=Organisation(Organisation_ID=678),
),
],
),
Patient(
Patient_ID=3,
DateOfBirth="2018-10-28",
RegistrationHistory=[
RegistrationHistory(
StartDate="2010-01-01",
EndDate="2015-10-01",
Organisation=Organisation(Organisation_ID=123),
),
# Deliberately overlapping registration histories
RegistrationHistory(
StartDate="2015-04-01",
EndDate="9999-12-31",
Organisation=Organisation(Organisation_ID=345),
),
],
Vaccinations=[
Vaccination(
VaccinationName="Infanrix Hexa",
VaccinationDate="2018-11-01",
)
],
MedicationIssues=[
MedicationIssue(
MedicationDictionary=MedicationDictionary(
DMD_ID="123", MultilexDrug_ID="123"),
ConsultationDate="2019-01-01",
),
],
CodedEvents=[
CodedEvent(CTV3Code="abc", ConsultationDate="2019-06-01")
],
),
])
session.commit()
study = VaccinationsStudyDefinition(
start_date="2017-06-01",
get_registered_practice_at_months=[12, 24, 60],
tpp_vaccine_codelist=codelist(
[
("Infanrix Hexa", "dtap_hex"),
("Bexsero", "menb"),
("Rotarix", "rotavirus"),
("Prevenar", "pcv"),
("Prevenar - 13", "pcv"),
("Menitorix", "hib_menc"),
("Repevax", "dtap_ipv"),
("Boostrix-IPV", "dtap_ipv"),
("MMRvaxPRO", "mmr"),
("Priorix", "mmr"),
],
system="tpp_vaccines",
),
ctv3_vaccine_codelist=codelist([("abc", "menb")], system="ctv3"),
snomed_vaccine_codelist=codelist([("123", "rotavirus")],
system="snomed"),
event_washout_period=14,
vaccination_schedule=[
"dtap_hex_1",
"menb_1",
"rotavirus_1",
"dtap_hex_2",
"pcv_1",
"rotavirus_2",
"dtap_hex_3",
"menb_2",
"hib_menc_1",
"pcv_2",
"mmr_1",
"menb_3",
"dtap_ipv_1",
"mmr_2",
],
)
study.to_csv(tmp_path / "test.csv")
with open(tmp_path / "test.csv", newline="") as f:
reader = csv.DictReader(f)
results = list(reader)
assert results == [
{
"patient_id": "2",
"date_of_birth": "2019-01-01",
"practice_id_at_month_12": "678",
"practice_id_at_month_24": "678",
"practice_id_at_month_60": "678",
"dtap_hex_1": "",
"menb_1": "",
"rotavirus_1": "",
"dtap_hex_2": "",
"pcv_1": "",
"rotavirus_2": "",
"dtap_hex_3": "",
"menb_2": "",
"hib_menc_1": "",
"pcv_2": "",
"mmr_1": "",
"menb_3": "",
"dtap_ipv_1": "",
"mmr_2": "",
},
{
"patient_id": "3",
"date_of_birth": "2018-10-01",
"practice_id_at_month_12": "345",
"practice_id_at_month_24": "345",
"practice_id_at_month_60": "345",
"dtap_hex_1": "2018-11-01",
"menb_1": "2019-06-01",
"rotavirus_1": "2019-01-01",
"dtap_hex_2": "",
"pcv_1": "",
"rotavirus_2": "",
"dtap_hex_3": "",
"menb_2": "",
"hib_menc_1": "",
"pcv_2": "",
"mmr_1": "",
"menb_3": "",
"dtap_ipv_1": "",
"mmr_2": "",
},
]
def test_patients_registered_practice_as_of():
session = make_session()
org_1 = Organisation(
STPCode="123", MSOACode="E0201", Region="East of England", Organisation_ID=1
)
org_2 = Organisation(
STPCode="456", MSOACode="E0202", Region="Midlands", Organisation_ID=2
)
org_3 = Organisation(
STPCode="789", MSOACode="E0203", Region="London", Organisation_ID=3
)
org_4 = Organisation(
STPCode="910", MSOACode="E0204", Region="North West", Organisation_ID=4
)
patient = Patient()
patient.RegistrationHistory.append(
RegistrationHistory(
StartDate="1990-01-01", EndDate="2018-01-01", Organisation=org_1
)
)
# We deliberately create overlapping registration periods so we can check
# that we handle these correctly
patient.RegistrationHistory.append(
RegistrationHistory(
StartDate="2018-01-01", EndDate="2022-01-01", Organisation=org_2
)
)
patient.RegistrationHistory.append(
RegistrationHistory(
StartDate="2019-09-01", EndDate="2020-05-01", Organisation=org_3
)
)
patient.RegistrationHistory.append(
RegistrationHistory(
StartDate="2022-01-01", EndDate="9999-12-31", Organisation=org_4
)
)
patient_2 = Patient()
patient_2.RegistrationHistory.append(
RegistrationHistory(
StartDate="2010-01-01", EndDate="9999-12-31", Organisation=org_1
)
)
patient_3 = Patient()
patient_3.RegistrationHistory.append(
RegistrationHistory(StartDate="2010-01-01", EndDate="9999-12-31")
)
session.add_all([patient, patient_2, patient_3])
session.commit()
study = StudyDefinition(
population=patients.all(),
stp=patients.registered_practice_as_of("2020-01-01", returning="stp_code"),
msoa=patients.registered_practice_as_of("2020-01-01", returning="msoa_code"),
region=patients.registered_practice_as_of(
"2020-01-01", returning="nhse_region_name"
),
pseudo_id=patients.registered_practice_as_of(
"2020-01-01", returning="pseudo_id"
),
)
results = study.to_dicts()
assert [i["stp"] for i in results] == ["789", "123", ""]
assert [i["msoa"] for i in results] == ["E0203", "E0201", ""]
assert [i["region"] for i in results] == ["London", "East of England", ""]
assert [i["pseudo_id"] for i in results] == ["3", "1", "0"]