def test_explicit_bmi_fallback():
session = make_session()
weight_code = "X76C7"
bmi_code = "22K.."
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=weight_code, NumericValue=50, ConsultationDate="2001-06-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=bmi_code, NumericValue=99, ConsultationDate="2001-10-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="1995-01-01",
on_or_before="2005-01-01",
include_measurement_date=True,
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["99.0"]
assert [x["BMI_date_measured"] for x in results] == ["2001-10-01"]
def test_bmi_rounded():
session = make_session()
weight_code = "X76C7"
height_code = "XM01E"
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(
CTV3Code=weight_code, NumericValue=10.12345, ConsultationDate="2001-06-01"
)
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=height_code, NumericValue=10, ConsultationDate="2000-02-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
"2005-01-01",
include_measurement_date=True,
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.1"]
assert [x["BMI_date_measured"] for x in results] == ["2001-06-01"]
def test_no_bmi_when_measurements_of_child():
session = make_session()
bmi_code = "22K.."
patient = Patient(DateOfBirth="2000-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=bmi_code, NumericValue=99, ConsultationDate="2001-01-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="1995-01-01",
on_or_before="2005-01-01",
include_measurement_date=True,
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.0"]
assert [x["BMI_date_measured"] for x in results] == [""]
def test_bmi_when_only_some_measurements_of_child():
session = make_session()
bmi_code = "22K.."
weight_code = "X76C7"
height_code = "XM01E"
patient = Patient(DateOfBirth="1990-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=bmi_code, NumericValue=99, ConsultationDate="1995-01-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=weight_code, NumericValue=50, ConsultationDate="2010-01-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=height_code, NumericValue=10, ConsultationDate="2010-01-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="2005-01-01", on_or_before="2015-01-01",
),
BMI_date_measured=patients.date_of("BMI", date_format="YYYY-MM-DD"),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.5"]
assert [x["BMI_date_measured"] for x in results] == ["2010-01-01"]
def test_to_sql_passes():
session = make_session()
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code="XYZ", NumericValue=50, ConsultationDate="2002-06-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.with_these_clinical_events(codelist(["XYZ"], "ctv3"))
)
sql = "SET NOCOUNT ON; " # don't output count after table output
sql += study.to_sql()
db_dict = study.get_db_dict()
cmd = [
"sqlcmd",
"-S",
db_dict["hostname"] + "," + str(db_dict["port"]),
"-d",
db_dict["database"],
"-U",
db_dict["username"],
"-P",
db_dict["password"],
"-Q",
sql,
"-W", # strip whitespace
]
result = subprocess.run(
cmd, capture_output=True, check=True, encoding="utf8"
).stdout
patient_id = result.splitlines()[-1]
assert patient_id == str(patient.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 test_patients_satisfying_with_hidden_columns():
condition_code = "ASTHMA"
condition_code2 = "COPD"
session = make_session()
patient_1 = Patient(DateOfBirth="1940-01-01", Sex="M")
patient_2 = Patient(DateOfBirth="1940-01-01", Sex="F")
patient_3 = Patient(DateOfBirth="1990-01-01", Sex="M")
patient_4 = Patient(DateOfBirth="1940-01-01", Sex="F")
patient_4.CodedEvents.append(
CodedEvent(CTV3Code=condition_code, ConsultationDate="2010-01-01")
)
patient_5 = Patient(DateOfBirth="1940-01-01", Sex="F")
patient_5.CodedEvents.append(
CodedEvent(CTV3Code=condition_code, ConsultationDate="2010-01-01")
)
patient_5.CodedEvents.append(
CodedEvent(CTV3Code=condition_code2, ConsultationDate="2010-01-01")
)
session.add_all([patient_1, patient_2, patient_3, patient_4, patient_5])
session.commit()
study = StudyDefinition(
population=patients.all(),
sex=patients.sex(),
age=patients.age_as_of("2020-01-01"),
at_risk=patients.satisfying(
"""
(age > 70 AND sex = "M")
OR
(has_asthma AND NOT copd)
""",
has_asthma=patients.with_these_clinical_events(
codelist([condition_code], "ctv3")
),
copd=patients.with_these_clinical_events(
codelist([condition_code2], "ctv3")
),
),
)
results = study.to_dicts()
assert [i["at_risk"] for i in results] == ["1", "0", "0", "1", "0"]
assert "has_asthma" not in results[0].keys()
def test_patient_random_sample():
session = make_session()
sample_size = 1000
for _ in range(sample_size):
patient = Patient()
session.add(patient)
session.commit()
study = StudyDefinition(population=patients.random_sample(percent=20))
results = study.to_dicts()
# The method is approximate!
assert len(results) < (sample_size / 2)
def test_patients_with_these_codes_on_death_certificate():
code = "COVID"
session = make_session()
session.add_all(
[
# Not dead
Patient(),
# Died after date cutoff
Patient(ONSDeath=[ONSDeaths(dod="2021-01-01", icd10u=code)]),
# Died of something else
Patient(ONSDeath=[ONSDeaths(dod="2020-02-01", icd10u="MI")]),
# Covid underlying cause
Patient(ONSDeath=[ONSDeaths(dod="2020-02-01", icd10u=code)]),
# Covid not underlying cause
Patient(ONSDeath=[ONSDeaths(dod="2020-03-01", ICD10014=code)]),
]
)
session.commit()
covid_codelist = codelist([code], system="icd10")
study = StudyDefinition(
population=patients.all(),
died_of_covid=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=True
),
died_with_covid=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=False
),
date_died=patients.with_these_codes_on_death_certificate(
covid_codelist,
on_or_before="2020-06-01",
match_only_underlying_cause=False,
returning="date_of_death",
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [i["died_of_covid"] for i in results] == ["0", "0", "0", "1", "0"]
assert [i["died_with_covid"] for i in results] == ["0", "0", "0", "1", "1"]
assert [i["date_died"] for i in results] == ["", "", "", "2020-02-01", "2020-03-01"]
def test_patients_with_death_recorded_in_cpns_raises_error_on_bad_data():
session = make_session()
session.add_all(
# Create a patient with duplicate CPNS entries recording an
# inconsistent date of death
[Patient(CPNS=[CPNS(DateOfDeath="2020-03-01"), CPNS(DateOfDeath="2020-02-01")])]
)
session.commit()
study = StudyDefinition(
population=patients.all(), cpns_death=patients.with_death_recorded_in_cpns()
)
with pytest.raises(Exception):
study.to_dicts()
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_patients_satisfying():
condition_code = "ASTHMA"
session = make_session()
patient_1 = Patient(DateOfBirth="1940-01-01", Sex="M")
patient_2 = Patient(DateOfBirth="1940-01-01", Sex="F")
patient_3 = Patient(DateOfBirth="1990-01-01", Sex="M")
patient_4 = Patient(DateOfBirth="1940-01-01", Sex="F")
patient_4.CodedEvents.append(
CodedEvent(CTV3Code=condition_code, ConsultationDate="2010-01-01")
)
session.add_all([patient_1, patient_2, patient_3, patient_4])
session.commit()
study = StudyDefinition(
population=patients.all(),
sex=patients.sex(),
age=patients.age_as_of("2020-01-01"),
has_asthma=patients.with_these_clinical_events(
codelist([condition_code], "ctv3")
),
at_risk=patients.satisfying("(age > 70 AND sex = 'M') OR has_asthma"),
)
results = study.to_dicts()
assert [i["at_risk"] for i in results] == ["1", "0", "0", "1"]
def test_mean_recorded_value():
code = "2469."
session = make_session()
patient = Patient()
values = [
("2020-02-10", 90),
("2020-02-10", 100),
("2020-02-10", 98),
# This day is outside period and should be ignored
("2020-04-01", 110),
]
for date, value in values:
patient.CodedEvents.append(
CodedEvent(CTV3Code=code, NumericValue=value, ConsultationDate=date)
)
patient_with_old_reading = Patient()
patient_with_old_reading.CodedEvents.append(
CodedEvent(CTV3Code=code, NumericValue=100, ConsultationDate="2010-01-01")
)
patient_with_no_reading = Patient()
session.add_all([patient, patient_with_old_reading, patient_with_no_reading])
session.commit()
study = StudyDefinition(
population=patients.all(),
bp_systolic=patients.mean_recorded_value(
codelist([code], system="ctv3"),
on_most_recent_day_of_measurement=True,
between=["2018-01-01", "2020-03-01"],
include_measurement_date=True,
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
results = [(i["bp_systolic"], i["bp_systolic_date_measured"]) for i in results]
assert results == [("96.0", "2020-02-10"), ("0.0", ""), ("0.0", "")]
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_patients_with_death_recorded_in_cpns():
session = make_session()
session.add_all(
[
# Not dead
Patient(),
# Died after date cutoff
Patient(CPNS=[CPNS(DateOfDeath="2021-01-01")]),
# Patient should be included
Patient(CPNS=[CPNS(DateOfDeath="2020-02-01")]),
# Patient has multple entries but with the same date of death so
# should be handled correctly
Patient(
CPNS=[CPNS(DateOfDeath="2020-03-01"), CPNS(DateOfDeath="2020-03-01")]
),
]
)
session.commit()
study = StudyDefinition(
population=patients.all(),
cpns_death=patients.with_death_recorded_in_cpns(on_or_before="2020-06-01"),
cpns_death_date=patients.with_death_recorded_in_cpns(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [i["cpns_death"] for i in results] == ["0", "0", "1", "1"]
assert [i["cpns_death_date"] for i in results] == [
"",
"",
"2020-02-01",
"2020-03-01",
]
def test_using_expression_in_population_definition():
session = make_session()
session.add_all(
[
Patient(
Sex="M",
DateOfBirth="1970-01-01",
CodedEvents=[
CodedEvent(CTV3Code="foo1", ConsultationDate="2000-01-01")
],
),
Patient(Sex="M", DateOfBirth="1975-01-01"),
Patient(
Sex="F",
DateOfBirth="1980-01-01",
CodedEvents=[
CodedEvent(CTV3Code="foo1", ConsultationDate="2000-01-01")
],
),
Patient(Sex="F", DateOfBirth="1985-01-01"),
]
)
session.commit()
study = StudyDefinition(
population=patients.satisfying(
"has_foo_code AND sex = 'M'",
has_foo_code=patients.with_these_clinical_events(
codelist(["foo1"], "ctv3")
),
sex=patients.sex(),
),
age=patients.age_as_of("2020-01-01"),
)
results = study.to_dicts()
assert results[0].keys() == {"patient_id", "age"}
assert [i["age"] for i in results] == ["50"]
def test_sqlcmd_and_odbc_outputs_match():
session = make_session()
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code="XYZ", NumericValue=50, ConsultationDate="2002-06-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.with_these_clinical_events(codelist(["XYZ"], "ctv3"))
)
with tempfile.NamedTemporaryFile() as input_csv_odbc, tempfile.NamedTemporaryFile() as input_csv_sqlcmd:
# windows line endings
study.to_csv(input_csv_odbc.name, with_sqlcmd=False)
# unix line endings
study.to_csv(input_csv_sqlcmd.name, with_sqlcmd=True)
assert filecmp.cmp(input_csv_odbc.name, input_csv_sqlcmd.name, shallow=False)
def test_simple_bmi(include_dates):
session = make_session()
weight_code = "X76C7"
height_code = "XM01E"
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=weight_code, NumericValue=50, ConsultationDate="2002-06-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=height_code, NumericValue=10, ConsultationDate="2001-06-01")
)
session.add(patient)
session.commit()
if include_dates == "none":
bmi_date = None
bmi_kwargs = {}
elif include_dates == "year":
bmi_date = "2002"
bmi_kwargs = dict(include_measurement_date=True)
elif include_dates == "month":
bmi_date = "2002-06"
bmi_kwargs = dict(include_measurement_date=True, include_month=True)
elif include_dates == "day":
bmi_date = "2002-06-01"
bmi_kwargs = dict(
include_measurement_date=True, include_month=True, include_day=True
)
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="1995-01-01", on_or_before="2005-01-01", **bmi_kwargs
),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.5"]
assert [x.get("BMI_date_measured") for x in results] == [bmi_date]
def test_no_bmi_when_measurement_after_reference_date():
session = make_session()
bmi_code = "22K.."
patient = Patient(DateOfBirth="1900-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=bmi_code, NumericValue=99, ConsultationDate="2001-01-01")
)
session.add(patient)
session.commit()
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="1990-01-01", on_or_before="2000-01-01",
),
BMI_date_measured=patients.date_of("BMI", date_format="YYYY-MM-DD"),
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.0"]
assert [x["BMI_date_measured"] for x in results] == [""]
def test_simple_bmi(include_dates):
session = make_session()
weight_code = "X76C7"
height_code = "XM01E"
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=weight_code, NumericValue=50, ConsultationDate="2002-06-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=height_code, NumericValue=10, ConsultationDate="2001-06-01")
)
session.add(patient)
session.commit()
if include_dates == "none":
bmi_date = None
date_query = None
elif include_dates == "year":
bmi_date = "2002"
date_query = patients.date_of("BMI")
elif include_dates == "month":
bmi_date = "2002-06"
date_query = patients.date_of("BMI", date_format="YYYY-MM")
elif include_dates == "day":
bmi_date = "2002-06-01"
date_query = patients.date_of("BMI", date_format="YYYY-MM-DD")
study = StudyDefinition(
population=patients.all(),
BMI=patients.most_recent_bmi(
on_or_after="1995-01-01", on_or_before="2005-01-01"
),
**dict(BMI_date_measured=date_query) if date_query else {}
)
results = study.to_dicts()
assert [x["BMI"] for x in results] == ["0.5"]
assert [x.get("BMI_date_measured") for x in results] == [bmi_date]
def _make_clinical_events_selection(condition_code, patient_dates=None):
# The default configuration of patients and dates which some tests assume
if patient_dates is None:
patient_dates = ["2001-06-01", "2002-06-01", None]
session = make_session()
for dates in patient_dates:
patient = Patient()
if dates is None:
dates = []
elif isinstance(dates, str):
dates = [dates]
for date in dates:
if isinstance(date, tuple):
date, value = date
else:
value = 0.0
patient.CodedEvents.append(
CodedEvent(
CTV3Code=condition_code, ConsultationDate=date, NumericValue=value
)
)
session.add(patient)
session.commit()
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_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_patients_address_as_of():
session = make_session()
patient = Patient()
patient.Addresses.append(
PatientAddress(
StartDate="1990-01-01",
EndDate="2018-01-01",
ImdRankRounded=100,
RuralUrbanClassificationCode=1,
)
)
# We deliberately create overlapping address periods here to check that we
# handle these correctly
patient.Addresses.append(
PatientAddress(
StartDate="2018-01-01",
EndDate="2020-02-01",
ImdRankRounded=200,
RuralUrbanClassificationCode=1,
)
)
patient.Addresses.append(
PatientAddress(
StartDate="2019-01-01",
EndDate="2022-01-01",
ImdRankRounded=300,
RuralUrbanClassificationCode=2,
)
)
patient.Addresses.append(
PatientAddress(
StartDate="2022-01-01",
EndDate="9999-12-31",
ImdRankRounded=500,
RuralUrbanClassificationCode=3,
)
)
patient_no_address = Patient()
patient_only_old_address = Patient()
patient_only_old_address.Addresses.append(
PatientAddress(
StartDate="2010-01-01",
EndDate="2015-01-01",
ImdRankRounded=100,
RuralUrbanClassificationCode=1,
)
)
session.add_all([patient, patient_no_address, patient_only_old_address])
session.commit()
study = StudyDefinition(
population=patients.all(),
imd=patients.address_as_of(
"2020-01-01",
returning="index_of_multiple_deprivation",
round_to_nearest=100,
),
rural_urban=patients.address_as_of(
"2020-01-01", returning="rural_urban_classification"
),
)
results = study.to_dicts()
assert [i["imd"] for i in results] == ["300", "0", "0"]
assert [i["rural_urban"] for i in results] == ["2", "0", "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": "",
},
]
def test_patients_admitted_to_icu():
session = make_session()
patient_1 = Patient()
patient_1.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-03-01",
OriginalIcuAdmissionDate="2020-03-01",
BasicDays_RespiratorySupport=2,
AdvancedDays_RespiratorySupport=2,
Ventilator=0,
)
)
patient_2 = Patient()
patient_2.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-03-01",
OriginalIcuAdmissionDate="2020-02-01",
BasicDays_RespiratorySupport=1,
AdvancedDays_RespiratorySupport=0,
Ventilator=1,
)
)
patient_3 = Patient()
patient_3.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-03-01",
OriginalIcuAdmissionDate="2020-02-01",
BasicDays_RespiratorySupport=0,
AdvancedDays_RespiratorySupport=0,
Ventilator=0,
)
)
patient_4 = Patient()
patient_4.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-01-01",
OriginalIcuAdmissionDate="2020-01-01",
BasicDays_RespiratorySupport=1,
AdvancedDays_RespiratorySupport=0,
Ventilator=1,
)
)
patient_5 = Patient()
patient_5.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-03-01",
OriginalIcuAdmissionDate=None,
BasicDays_RespiratorySupport=1,
AdvancedDays_RespiratorySupport=0,
Ventilator=1,
)
)
patient_5.ICNARC.append(
ICNARC(
IcuAdmissionDateTime="2020-04-01",
OriginalIcuAdmissionDate=None,
BasicDays_RespiratorySupport=0,
AdvancedDays_RespiratorySupport=0,
Ventilator=1,
)
)
session.add_all([patient_1, patient_2, patient_3, patient_4, patient_5])
session.commit()
study = StudyDefinition(
population=patients.all(),
icu=patients.admitted_to_icu(
on_or_after="2020-02-01",
include_day=True,
returning="date_admitted",
find_first_match_in_period=True,
),
)
results = study.to_dicts()
assert [i["icu"] for i in results] == [
"2020-03-01",
"2020-02-01",
"",
"",
"2020-03-01",
]
study = StudyDefinition(
population=patients.all(),
icu=patients.admitted_to_icu(
on_or_after="2020-02-01",
include_day=True,
returning="date_admitted",
find_last_match_in_period=True,
),
)
results = study.to_dicts()
assert [i["icu"] for i in results] == [
"2020-03-01",
"2020-02-01",
"",
"",
"2020-04-01",
]
study = StudyDefinition(
population=patients.all(),
icu=patients.admitted_to_icu(on_or_after="2020-02-01", returning="binary_flag"),
)
results = study.to_dicts()
assert [i["icu"] for i in results] == ["1", "1", "0", "0", "1"]
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"]