def test_vaccination_events_sql():
session = make_session()
session.add_all(
[
# This patient is too old and should be ignored
Patient(
DateOfBirth="2002-05-04",
Vaccinations=[
Vaccination(
VaccinationName="Infanrix Hexa", VaccinationDate="2002-06-01",
)
],
),
# This patient is too young and should be ignored
Patient(
DateOfBirth="2019-10-04",
Vaccinations=[
Vaccination(
VaccinationName="Infanrix Hexa", VaccinationDate="2019-11-04",
)
],
),
Patient(
DateOfBirth="2018-10-28",
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()
sql = vaccination_events_sql(
date_of_birth_range=("2012-01-01", "2019-06-01"),
tpp_vaccination_codelist=codelist(
[("Infanrix Hexa", "dtap_hex")], system="tpp_vaccines",
),
ctv3_codelist=codelist([("abc", "menb")], system="ctv3"),
snomed_codelist=codelist([("123", "rotavirus")], system="snomed"),
)
results = sql_to_dicts(sql)
result_tuples = [(x["date_given"], x["vaccine_name"]) for x in results]
# Results are ordered by patient ID but within each patient's results the
# order is arbitrary. To make testing easier we sort them here.
result_tuples = sorted(result_tuples)
assert result_tuples == [
("2018-11-01", "dtap_hex"),
("2019-01-01", "rotavirus"),
("2019-06-01", "menb"),
]
def test_meds_with_count():
session = make_session()
asthma_medication = MedicationDictionary(
FullName="Asthma Drug", DMD_ID="0", MultilexDrug_ID="0"
)
patient_with_med = Patient()
patient_with_med.MedicationIssues = [
MedicationIssue(
MedicationDictionary=asthma_medication, ConsultationDate="2010-01-01"
),
MedicationIssue(
MedicationDictionary=asthma_medication, ConsultationDate="2015-01-01"
),
MedicationIssue(
MedicationDictionary=asthma_medication, ConsultationDate="2018-01-01"
),
MedicationIssue(
MedicationDictionary=asthma_medication, ConsultationDate="2020-01-01"
),
]
patient_without_med = Patient()
session.add(patient_with_med)
session.add(patient_without_med)
session.commit()
study = StudyDefinition(
population=patients.all(),
asthma_meds=patients.with_these_medications(
codelist(asthma_medication.DMD_ID, "snomed"),
on_or_after="2012-01-01",
return_number_of_matches_in_period=True,
),
)
results = study.to_dicts()
assert [x["asthma_meds"] for x in results] == ["3", "0"]
def test_meds():
session = make_session()
asthma_medication = MedicationDictionary(
FullName="Asthma Drug", DMD_ID="0", MultilexDrug_ID="0"
)
patient_with_med = Patient()
patient_with_med.MedicationIssues = [
MedicationIssue(MedicationDictionary=asthma_medication)
]
patient_without_med = Patient()
session.add(patient_with_med)
session.add(patient_without_med)
session.commit()
study = StudyDefinition(
population=patients.all(),
asthma_meds=patients.with_these_medications(
codelist(asthma_medication.DMD_ID, "snomed")
),
)
results = study.to_dicts()
assert [x["asthma_meds"] for x in results] == ["1", "0"]
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": "",
},
]