[e988c2]: / tests / integration / measures / test_calculate.py

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import random
from collections import defaultdict
from datetime import date, timedelta
from unittest import mock
import pytest
from ehrql import months, years
from ehrql.measures import INTERVAL, Measures, get_measure_results
from ehrql.measures.calculate import MeasuresTimeout
from ehrql.tables import EventFrame, PatientFrame, Series, table
@table
class patients(PatientFrame):
sex = Series(str)
@table
class addresses(EventFrame):
date = Series(date)
region = Series(str)
@table
class events(EventFrame):
date = Series(date)
code = Series(str)
value = Series(int)
def test_get_measure_results(engine):
events_in_interval = events.where(events.date.is_during(INTERVAL))
event_count = events_in_interval.count_for_patient()
foo_event_count = events_in_interval.where(events.code == "foo").count_for_patient()
had_event = events_in_interval.exists_for_patient()
event_value = events_in_interval.value.sum_for_patient()
region = addresses.sort_by(addresses.date).last_for_patient().region
intervals = years(3).starting_on("2020-01-01")
measures = Measures()
measures.define_measure(
"foo_events_by_sex",
numerator=foo_event_count,
denominator=event_count,
group_by=dict(sex=patients.sex),
intervals=intervals,
)
measures.define_measure(
"foo_events_by_region",
numerator=foo_event_count,
denominator=event_count,
group_by=dict(region=region),
intervals=intervals,
)
measures.define_measure(
"had_event_by_sex",
numerator=had_event,
denominator=patients.exists_for_patient(),
group_by=dict(sex=patients.sex),
intervals=intervals,
)
measures.define_measure(
"event_value_by_region",
numerator=event_value,
denominator=patients.exists_for_patient(),
group_by=dict(region=region),
intervals=intervals,
)
measures.define_measure(
"had_event_by_sex_and_region",
numerator=had_event,
denominator=patients.exists_for_patient(),
group_by=dict(
sex=patients.sex,
region=region,
),
intervals=intervals,
)
measures.define_measure(
"foo_events",
numerator=foo_event_count,
denominator=event_count,
intervals=intervals,
)
patient_data, address_data, event_data = generate_data(intervals)
engine.populate(
{patients: patient_data, addresses: address_data, events: event_data}
)
results = get_measure_results(engine.query_engine(), measures)
results = list(results)
# Verify that we don't get any duplicate rows in the results
assert len(results) == len(set(results))
expected = calculate_measure_results(
intervals, patient_data, address_data, event_data
)
expected = list(expected)
# We don't care about the order of the results
assert set(results) == set(expected)
def test_get_measures_interval_dependent_denominator(engine):
# Test results when an interval denominator is dependent on the specific interval
# (i.e. values in other intervals affect the inclusion in this interval population)
# i.e. the union of all measure denominators will exclude some patients
intervals = years(2).starting_on("2020-01-01")
measures = Measures()
is_female = patients.sex == "female"
had_event_in_interval = events.where(
events.date.is_during(INTERVAL)
).exists_for_patient()
had_event_outside_interval = events.where(
events.date.is_before(INTERVAL.start_date)
| events.date.is_after(INTERVAL.end_date)
).exists_for_patient()
measures.define_measure(
"female_by_events_outside_interval_only",
numerator=is_female,
denominator=had_event_outside_interval & ~(had_event_in_interval),
intervals=intervals,
)
patient_data = [
dict(patient_id=1, sex="male"),
dict(patient_id=2, sex="female"),
dict(patient_id=3, sex="male"),
dict(patient_id=4, sex="female"),
]
event_data = [
# Interval 1 includes only patient 2 (female) in the population (has an event in interval 2 only)
# Interval 2 includes only patient 1 (male) in the population (has an event in interval 1 only)
dict(patient_id=1, code="abc", date=date(2020, 2, 1)),
dict(patient_id=2, code="abc", date=date(2021, 2, 1)),
# Patient 3 and 4 have events in both intervals, so aren't included in the population for
# either
dict(patient_id=3, code="abc", date=date(2020, 2, 1)),
dict(patient_id=4, code="abc", date=date(2020, 2, 1)),
dict(patient_id=3, code="abc", date=date(2021, 2, 1)),
dict(patient_id=4, code="abc", date=date(2021, 2, 1)),
]
engine.populate({patients: patient_data, events: event_data})
results = get_measure_results(engine.query_engine(), measures)
expected = [
# interval 1 has 1 female patient in the population - numerator 1, denominator 1
(
"female_by_events_outside_interval_only",
date(2020, 1, 1),
date(2020, 12, 31),
1.0,
1,
1,
),
# interval 2 has 1 male patient in the population - numerator 0, denominator 1
(
"female_by_events_outside_interval_only",
date(2021, 1, 1),
date(2021, 12, 31),
0.0,
0,
1,
),
]
assert set(results) == set(expected)
def test_get_measures_same_numerator_and_denominator(engine):
# Ensure that calculations are handled correctly when the same column
# is used as both numerator and denominator
intervals = years(2).starting_on("2020-01-01")
measures = Measures()
measures.define_measure(
"test",
numerator=patients.exists_for_patient(),
denominator=patients.exists_for_patient(),
intervals=intervals,
)
patient_data = [dict(patient_id=1), dict(patient_id=2)]
engine.populate({patients: patient_data})
results = set(get_measure_results(engine.query_engine(), measures))
expected = {
("test", date(2020, 1, 1), date(2020, 12, 31), 1.0, 2, 2),
("test", date(2021, 1, 1), date(2021, 12, 31), 1.0, 2, 2),
}
assert results == expected
def test_get_measures_duplicate_group_bys(engine):
# Ensure that calculations are handled correctly when there are measures
# in the same group (sharing a denominator and intervals) with the same
# group bys. These can be handled by a single grouping set in the SQL
# query; duplicate grouping sets in the query result in duplicate
# rows in the result
events_in_interval = events.where(events.date.is_during(INTERVAL))
event_count = events_in_interval.count_for_patient()
foo_event_count = events_in_interval.where(events.code == "foo").count_for_patient()
bar_event_count = events_in_interval.where(events.code == "bar").count_for_patient()
intervals = years(1).starting_on("2020-01-01")
measures = Measures()
measures.define_measure(
"foo_events",
numerator=foo_event_count,
denominator=event_count,
intervals=intervals,
)
measures.define_measure(
"foo_events_by_sex",
numerator=foo_event_count,
denominator=event_count,
group_by=dict(sex=patients.sex),
intervals=intervals,
)
measures.define_measure(
"bar_events",
numerator=bar_event_count,
denominator=event_count,
intervals=intervals,
)
measures.define_measure(
"bar_events_by_sex",
numerator=bar_event_count,
denominator=event_count,
group_by=dict(sex=patients.sex),
intervals=intervals,
)
patient_data = [dict(patient_id=1, sex="male"), dict(patient_id=2, sex="female")]
address_data = [
dict(patient_id=1, date=date(2020, 1, 1), region="London"),
dict(patient_id=1, date=date(2020, 1, 1), region="The North"),
]
event_data = [
dict(patient_id=1, date=date(2020, 2, 1), code="foo"),
dict(patient_id=1, date=date(2020, 2, 1), code="bar"),
dict(patient_id=2, date=date(2020, 2, 1), code="foo"),
dict(patient_id=2, date=date(2020, 2, 1), code="bar"),
]
engine.populate(
{patients: patient_data, addresses: address_data, events: event_data}
)
results = list(get_measure_results(engine.query_engine(), measures))
# Verify that we don't get any duplicate rows in the results
assert len(results) == len(set(results))
expected = {
("foo_events", date(2020, 1, 1), date(2020, 12, 31), 0.5, 2, 4, None),
("foo_events_by_sex", date(2020, 1, 1), date(2020, 12, 31), 0.5, 1, 2, "male"),
(
"foo_events_by_sex",
date(2020, 1, 1),
date(2020, 12, 31),
0.5,
1,
2,
"female",
),
("bar_events", date(2020, 1, 1), date(2020, 12, 31), 0.5, 2, 4, None),
("bar_events_by_sex", date(2020, 1, 1), date(2020, 12, 31), 0.5, 1, 2, "male"),
(
"bar_events_by_sex",
date(2020, 1, 1),
date(2020, 12, 31),
0.5,
1,
2,
"female",
),
}
assert set(results) == expected
@mock.patch("ehrql.measures.calculate.time")
def test_get_measure_results_with_timeout(patched_time, in_memory_engine):
events_in_interval = events.where(events.date.is_during(INTERVAL))
event_count = events_in_interval.count_for_patient()
foo_event_count = events_in_interval.where(events.code == "foo").count_for_patient()
intervals = months(60).starting_on("2000-01-01")
measures = Measures()
measures.define_measure(
"foo_events",
numerator=foo_event_count,
denominator=event_count,
intervals=intervals,
group_by=dict(
sex=patients.sex,
),
)
patient_data, _, event_data = generate_data(intervals)
in_memory_engine.populate({patients: patient_data, events: event_data})
patched_time.time.side_effect = [0.0, 1000.0, 1000000.0]
results = get_measure_results(in_memory_engine.query_engine(), measures)
with pytest.raises(MeasuresTimeout, match="time limit"):
results = list(results)
def generate_data(intervals):
rnd = random.Random(20230518)
# Generate some random patients
patient_data = [
dict(
patient_id=patient_id,
sex=rnd.choice(["male", "female"]),
)
for patient_id in range(1, 50)
]
# Generate some addresses (at least one) for each patient
# Make sure that address dates for the same patient are different; otherwise
# we can't be sure which region will be returned as the last
address_data = []
interval_range = (intervals[0][0], intervals[-1][1])
for patient in patient_data:
address_dates = set()
for _ in range(rnd.randint(1, 3)):
address_dates.add(random_date_in_interval(rnd, interval_range))
for address_date in address_dates:
address_data.append(
dict(
patient_id=patient["patient_id"],
date=address_date,
region=rnd.choice(["London", "The North", "The Countryside"]),
)
)
# For each interval and patient, generate some events (possibly zero)
event_data = []
for interval in intervals:
for patient in patient_data:
# Choose a number of events, biased towards zero
event_count = max(rnd.randint(-10, 10), 0)
event_data.extend(
dict(
patient_id=patient["patient_id"],
code=rnd.choice(["abc", "def", "foo"]),
date=random_date_in_interval(rnd, interval),
value=rnd.randint(0, 10),
)
for _ in range(event_count)
)
return patient_data, address_data, event_data
def random_date_in_interval(rnd, interval):
days_in_interval = (interval[1] - interval[0]).days
offset = rnd.randint(0, days_in_interval)
return interval[0] + timedelta(days=offset)
def calculate_measure_results(intervals, patient_data, address_data, event_data):
nums = defaultdict(int)
dens = defaultdict(int)
for interval, patient, address, events in group_events(
intervals, patient_data, address_data, event_data
):
event_count = len(events)
foo_count = len([e for e in events if e["code"] == "foo"])
had_event = 1 if events else 0
event_value = sum([e["value"] for e in events], start=0)
nums[("foo_events_by_sex", interval, patient["sex"], None)] += foo_count
dens[("foo_events_by_sex", interval, patient["sex"], None)] += event_count
nums[("foo_events_by_region", interval, None, address["region"])] += foo_count
dens[("foo_events_by_region", interval, None, address["region"])] += event_count
nums[("had_event_by_sex", interval, patient["sex"], None)] += had_event
dens[("had_event_by_sex", interval, patient["sex"], None)] += 1
nums[("event_value_by_region", interval, None, address["region"])] += (
event_value
)
dens[("event_value_by_region", interval, None, address["region"])] += 1
nums[
("had_event_by_sex_and_region", interval, patient["sex"], address["region"])
] += had_event
dens[
("had_event_by_sex_and_region", interval, patient["sex"], address["region"])
] += 1
nums[("foo_events", interval, None, None)] += foo_count
dens[("foo_events", interval, None, None)] += event_count
for key, numerator in nums.items():
measure, interval, sex, region = key
denominator = dens[key]
ratio = numerator / denominator
yield (
measure,
interval[0],
interval[1],
ratio,
numerator,
denominator,
sex,
region,
)
def group_events(intervals, patient_data, address_data, event_data):
"Group events by interval and patient"
for patient in patient_data:
patient_events = [
e for e in event_data if e["patient_id"] == patient["patient_id"]
]
patient_addresses = sorted(
[a for a in address_data if a["patient_id"] == patient["patient_id"]],
key=lambda a: a["date"],
)
address = patient_addresses[-1]
for interval in intervals:
interval_events = [
e for e in patient_events if interval[0] <= e["date"] <= interval[1]
]
yield interval, patient, address, interval_events