def test_clinical_event_with_category():
session = make_session()
session.add_all(
[
Patient(),
Patient(
CodedEvents=[
CodedEvent(CTV3Code="foo1", ConsultationDate="2018-01-01"),
CodedEvent(CTV3Code="foo2", ConsultationDate="2020-01-01"),
]
),
Patient(
CodedEvents=[CodedEvent(CTV3Code="foo3", ConsultationDate="2019-01-01")]
),
]
)
session.commit()
codes = codelist([("foo1", "A"), ("foo2", "B"), ("foo3", "C")], "ctv3")
study = StudyDefinition(
population=patients.all(),
code_category=patients.with_these_clinical_events(
codes,
returning="category",
find_last_match_in_period=True,
include_date_of_match=True,
),
)
results = study.to_dicts()
assert [x["code_category"] for x in results] == ["", "B", "C"]
assert [x["code_category_date"] for x in results] == ["", "2020", "2019"]
def test_patients_died_from_any_cause():
session = make_session()
session.add_all(
[
# Not dead
Patient(),
# Died after date cutoff
Patient(ONSDeath=[ONSDeaths(dod="2021-01-01")]),
# Died
Patient(ONSDeath=[ONSDeaths(dod="2020-02-01")]),
]
)
session.commit()
study = StudyDefinition(
population=patients.all(),
died=patients.died_from_any_cause(on_or_before="2020-06-01"),
date_died=patients.died_from_any_cause(
on_or_before="2020-06-01",
returning="date_of_death",
include_month=True,
include_day=True,
),
)
results = study.to_dicts()
assert [i["died"] for i in results] == ["0", "0", "1"]
assert [i["date_died"] for i in results] == ["", "", "2020-02-01"]
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_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_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",
date_format="YYYY-MM-DD",
),
)
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_patients_categorised_as():
session = make_session()
session.add_all(
[
Patient(
Sex="M",
CodedEvents=[
CodedEvent(CTV3Code="foo1", ConsultationDate="2000-01-01")
],
),
Patient(
Sex="F",
CodedEvents=[
CodedEvent(CTV3Code="foo2", ConsultationDate="2000-01-01"),
CodedEvent(CTV3Code="bar1", ConsultationDate="2000-01-01"),
],
),
Patient(
Sex="M",
CodedEvents=[
CodedEvent(CTV3Code="foo2", ConsultationDate="2000-01-01")
],
),
Patient(
Sex="F",
CodedEvents=[
CodedEvent(CTV3Code="foo3", ConsultationDate="2000-01-01")
],
),
]
)
session.commit()
foo_codes = codelist([("foo1", "A"), ("foo2", "B"), ("foo3", "C")], "ctv3")
bar_codes = codelist(["bar1"], "ctv3")
study = StudyDefinition(
population=patients.all(),
category=patients.categorised_as(
{
"W": "foo_category = 'B' AND female_with_bar",
"X": "sex = 'F' AND (foo_category = 'B' OR foo_category = 'C')",
"Y": "sex = 'M' AND foo_category = 'A'",
"Z": "DEFAULT",
},
sex=patients.sex(),
foo_category=patients.with_these_clinical_events(
foo_codes, returning="category", find_last_match_in_period=True
),
female_with_bar=patients.satisfying(
"has_bar AND sex = 'F'",
has_bar=patients.with_these_clinical_events(bar_codes),
),
),
)
results = study.to_dicts()
assert [x["category"] for x in results] == ["Y", "W", "Z", "X"]
# Assert that internal columns do not appear
assert "foo_category" not in results[0].keys()
assert "female_with_bar" not in results[0].keys()
assert "has_bar" not in results[0].keys()
def test_number_of_episodes():
session = make_session()
session.add_all(
[
Patient(
CodedEvents=[
CodedEvent(CTV3Code="foo1", ConsultationDate="2010-01-01"),
# Throw in some irrelevant events
CodedEvent(CTV3Code="mto1", ConsultationDate="2010-01-02"),
CodedEvent(CTV3Code="mto2", ConsultationDate="2010-01-03"),
# These two should be merged in to the previous event
# because there's not more than 14 days between them
CodedEvent(CTV3Code="foo2", ConsultationDate="2010-01-14"),
CodedEvent(CTV3Code="foo3", ConsultationDate="2010-01-20"),
# This is just outside the limit so should count as another event
CodedEvent(CTV3Code="foo1", ConsultationDate="2010-02-04"),
# This shouldn't count because there's an "ignore" event on
# the same day (though at a different time)
CodedEvent(CTV3Code="foo1", ConsultationDate="2012-01-01T10:45:00"),
CodedEvent(CTV3Code="bar2", ConsultationDate="2012-01-01T16:10:00"),
# This should be another episode
CodedEvent(CTV3Code="foo1", ConsultationDate="2015-03-05"),
# This "ignore" event should have no effect because it occurs
# on a different day
CodedEvent(CTV3Code="bar1", ConsultationDate="2015-03-06"),
# This is after the time limit and so shouldn't count
CodedEvent(CTV3Code="foo1", ConsultationDate="2020-02-05"),
]
),
# This patient doesn't have any relevant events
Patient(
CodedEvents=[
CodedEvent(CTV3Code="mto1", ConsultationDate="2010-01-01"),
CodedEvent(CTV3Code="mto2", ConsultationDate="2010-01-14"),
CodedEvent(CTV3Code="mto3", ConsultationDate="2010-01-20"),
CodedEvent(CTV3Code="mto1", ConsultationDate="2010-02-04"),
CodedEvent(CTV3Code="mto1", ConsultationDate="2012-01-01T10:45:00"),
CodedEvent(CTV3Code="mtr2", ConsultationDate="2012-01-01T16:10:00"),
CodedEvent(CTV3Code="mto1", ConsultationDate="2015-03-05"),
CodedEvent(CTV3Code="mto1", ConsultationDate="2020-02-05"),
]
),
]
)
session.commit()
foo_codes = codelist(["foo1", "foo2", "foo3"], "ctv3")
bar_codes = codelist(["bar1", "bar2"], "ctv3")
study = StudyDefinition(
population=patients.all(),
episode_count=patients.with_these_clinical_events(
foo_codes,
on_or_before="2020-01-01",
ignore_days_where_these_codes_occur=bar_codes,
returning="number_of_episodes",
episode_defined_as="series of events each <= 14 days apart",
),
)
results = study.to_dicts()
assert [i["episode_count"] for i in results] == ["3", "0"]
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_minimal_study_to_csv():
session = make_session()
patient_1 = Patient(DateOfBirth="1900-01-01", Sex="M")
patient_2 = Patient(DateOfBirth="1900-01-01", Sex="F")
session.add_all([patient_1, patient_2])
session.commit()
study = StudyDefinition(population=patients.all(), sex=patients.sex())
with tempfile.NamedTemporaryFile(mode="w+") as f:
study.to_csv(f.name)
results = list(csv.DictReader(f))
assert results == [
{"patient_id": str(patient_1.Patient_ID), "sex": "M"},
{"patient_id": str(patient_2.Patient_ID), "sex": "F"},
]
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_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_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",
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",
include_measurement_date=True,
include_month=True,
include_day=True,
),
)
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_bmi_with_zero_values():
session = make_session()
weight_code = "X76C7"
height_code = "XM01E"
patient = Patient(DateOfBirth="1950-01-01")
patient.CodedEvents.append(
CodedEvent(CTV3Code=weight_code, NumericValue=0, ConsultationDate="2001-06-01")
)
patient.CodedEvents.append(
CodedEvent(CTV3Code=height_code, NumericValue=0, ConsultationDate="2001-06-01")
)
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",
),
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] == ["2001-06-01"]
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_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_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_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_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_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",
),
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
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_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]