def test_column_name_clashes_produce_errors():
with pytest.raises(ValueError):
StudyDefinition(
population=patients.all(),
age=patients.age_as_of("2020-01-01"),
status=patients.satisfying(
"age > 70 AND sex = 'M'",
sex=patients.sex(),
age=patients.age_as_of("2010-01-01"),
),
)
def test_patient_characteristics_for_covid_status():
session = make_session()
old_patient_with_covid = Patient(
DateOfBirth="1900-01-01",
CovidStatus=CovidStatus(Result="COVID19", AdmittedToITU=True),
Sex="M",
)
young_patient_1_with_covid = Patient(
DateOfBirth="2000-01-01",
CovidStatus=CovidStatus(Result="COVID19", Died=True),
Sex="F",
)
young_patient_2_without_covid = Patient(DateOfBirth="2001-01-01", Sex="F")
session.add(old_patient_with_covid)
session.add(young_patient_1_with_covid)
session.add(young_patient_2_without_covid)
session.commit()
study = StudyDefinition(
population=patients.with_positive_covid_test(),
age=patients.age_as_of("2020-01-01"),
sex=patients.sex(),
died=patients.have_died_of_covid(),
)
results = study.to_dicts()
assert [x["sex"] for x in results] == ["M", "F"]
assert [x["died"] for x in results] == ["0", "1"]
assert [x["age"] for x in results] == ["120", "20"]
def test_age_dtype_generation():
study = StudyDefinition(
# This line defines the study population
population=patients.all(),
age=patients.age_as_of("2020-02-01"),
)
result = _converters_to_names(study.pandas_csv_args)
assert result == {
"dtype": {"age": "int"},
"parse_dates": [],
"date_col_for": {},
"converters": {},
}
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_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_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"]
),
died_date_ons=patients.died_from_any_cause(
on_or_after="2020-03-01",
returning="date_of_death",
include_month=True,
include_day=True,
return_expectations={"date": {
"earliest": "2020-03-01"
}},
),
## DEMOGRAPHIC INFORMATION
age=patients.age_as_of(
"2020-02-29",
return_expectations={
"rate": "universal",
"int": {
"distribution": "population_ages"
},
},
),
sex=patients.sex(return_expectations={
"rate": "universal",
"category": {
"ratios": {
"M": 0.49,
"F": 0.51
}
},
}),
stp=patients.registered_practice_as_of(
"2020-02-29",
died_ons_covid_flag_any=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=False
),
died_ons_covid_flag_underlying=patients.with_these_codes_on_death_certificate(
covid_codelist, on_or_before="2020-06-01", match_only_underlying_cause=True
),
died_date_ons=patients.died_from_any_cause(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
# The rest of the lines define the covariates with associated GitHub issues
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/33
age=patients.age_as_of("2020-02-01"),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/46
sex=patients.sex(),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/52
imd=patients.address_as_of(
"2020-02-01", returning="index_of_multiple_deprivation", round_to_nearest=100
),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/37
rural_urban=patients.address_as_of(
"2020-02-01", returning="rural_urban_classification"
),
# https://github.com/ebmdatalab/tpp-sql-notebook/issues/54
