import textwrap
from datetime import date
import pytest
from ehrql.tables.core import patients
from tests.lib.inspect_utils import function_body_as_string
from tests.lib.orm_utils import make_orm_models
@function_body_as_string
def MEASURE_DEFINITIONS():
from ehrql import INTERVAL, Measures, years
from ehrql.tables.core import patients
measures = Measures()
measures.define_measure(
"births",
numerator=patients.date_of_birth.is_during(INTERVAL),
denominator=patients.exists_for_patient(),
group_by={"sex": patients.sex},
intervals=years(2).starting_on("2020-01-01"),
)
DISABLE_DISCLOSURE_CONTROL = "\n\nmeasures.configure_disclosure_control(enabled=False)"
@pytest.mark.parametrize("disclosure_control_enabled", [False, True])
def test_generate_measures(
in_memory_sqlite_database, tmp_path, disclosure_control_enabled, call_cli
):
in_memory_sqlite_database.setup(
make_orm_models(
{
patients: [
dict(patient_id=1, date_of_birth=date(2020, 6, 1), sex="male"),
dict(patient_id=2, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=3, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=4, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=5, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=6, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=7, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=8, date_of_birth=date(2021, 6, 1), sex="female"),
dict(patient_id=9, date_of_birth=date(2021, 6, 1), sex="female"),
]
}
)
)
measure_definitions = tmp_path / "measures.py"
if disclosure_control_enabled:
measure_definitions.write_text(MEASURE_DEFINITIONS)
else:
measure_definitions.write_text(MEASURE_DEFINITIONS + DISABLE_DISCLOSURE_CONTROL)
output_file = tmp_path / "output.csv"
call_cli(
"generate-measures",
measure_definitions,
"--output",
output_file,
"--dsn",
in_memory_sqlite_database.host_url(),
"--query-engine",
"sqlite",
)
if disclosure_control_enabled:
assert output_file.read_text() == textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,0.0,0,10,female
births,2020-01-01,2020-12-31,,0,0,male
births,2021-01-01,2021-12-31,1.0,10,10,female
births,2021-01-01,2021-12-31,,0,0,male
"""
)
else:
assert output_file.read_text() == textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,0.0,0,8,female
births,2020-01-01,2020-12-31,1.0,1,1,male
births,2021-01-01,2021-12-31,1.0,8,8,female
births,2021-01-01,2021-12-31,0.0,0,1,male
"""
)
@pytest.mark.parametrize("disclosure_control_enabled", [False, True])
def test_generate_measures_dummy_data_generated(
tmp_path, disclosure_control_enabled, call_cli
):
measure_definitions = tmp_path / "measures.py"
measure_definitions.write_text(MEASURE_DEFINITIONS)
output_file = tmp_path / "output.csv"
call_cli(
"generate-measures",
measure_definitions,
"--output",
output_file,
)
assert output_file.read_text().startswith(
"measure,interval_start,interval_end,ratio,numerator,denominator,sex"
)
@pytest.mark.parametrize("disclosure_control_enabled", [False, True])
def test_generate_measures_legacy_dummy_data_generated(
tmp_path, disclosure_control_enabled, call_cli
):
measure_definitions = tmp_path / "measures.py"
measure_definitions.write_text(
MEASURE_DEFINITIONS
+ "\nmeasures.configure_dummy_data(population_size=10, legacy=True)"
)
output_file = tmp_path / "output.csv"
call_cli(
"generate-measures",
measure_definitions,
"--output",
output_file,
)
assert output_file.read_text().startswith(
"measure,interval_start,interval_end,ratio,numerator,denominator,sex"
)
@pytest.mark.parametrize("disclosure_control_enabled", [False, True])
def test_generate_measures_dummy_data_supplied(
tmp_path, disclosure_control_enabled, call_cli
):
measure_definitions = tmp_path / "measures.py"
if disclosure_control_enabled:
measure_definitions.write_text(MEASURE_DEFINITIONS)
else:
measure_definitions.write_text(MEASURE_DEFINITIONS + DISABLE_DISCLOSURE_CONTROL)
output_file = tmp_path / "output.csv"
DUMMY_DATA = textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,0.4,4,10,male
births,2020-01-01,2020-12-31,0.3,6,20,female
births,2021-01-01,2021-12-31,0.6,6,10,male
births,2021-01-01,2021-12-31,0.7,14,20,female
"""
)
dummy_data_file = tmp_path / "dummy.csv"
dummy_data_file.write_text(DUMMY_DATA)
call_cli(
"generate-measures",
measure_definitions,
"--output",
output_file,
"--dummy-data",
dummy_data_file,
)
if disclosure_control_enabled:
assert output_file.read_text() == textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,0.0,0,10,male
births,2020-01-01,2020-12-31,0.0,0,20,female
births,2021-01-01,2021-12-31,0.0,0,10,male
births,2021-01-01,2021-12-31,0.75,15,20,female
"""
)
else:
assert output_file.read_text() == DUMMY_DATA
@pytest.mark.parametrize("disclosure_control_enabled", [False, True])
def test_generate_measures_dummy_tables(tmp_path, disclosure_control_enabled, call_cli):
measure_definitions = tmp_path / "measures.py"
if disclosure_control_enabled:
measure_definitions.write_text(MEASURE_DEFINITIONS)
else:
measure_definitions.write_text(MEASURE_DEFINITIONS + DISABLE_DISCLOSURE_CONTROL)
output_file = tmp_path / "output.csv"
DUMMY_DATA = textwrap.dedent(
"""\
patient_id,date_of_birth,sex
1,2020-06-01,male
2,2021-06-01,female
"""
)
dummy_tables_path = tmp_path / "dummy_tables"
dummy_tables_path.mkdir()
dummy_tables_path.joinpath("patients.csv").write_text(DUMMY_DATA)
call_cli(
"generate-measures",
measure_definitions,
"--output",
output_file,
"--dummy-tables",
dummy_tables_path,
)
if disclosure_control_enabled:
assert output_file.read_text() == textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,,0,0,male
births,2020-01-01,2020-12-31,,0,0,female
births,2021-01-01,2021-12-31,,0,0,male
births,2021-01-01,2021-12-31,,0,0,female
"""
)
else:
assert output_file.read_text() == textwrap.dedent(
"""\
measure,interval_start,interval_end,ratio,numerator,denominator,sex
births,2020-01-01,2020-12-31,1.0,1,1,male
births,2020-01-01,2020-12-31,0.0,0,1,female
births,2021-01-01,2021-12-31,0.0,0,1,male
births,2021-01-01,2021-12-31,1.0,1,1,female
"""
)
