import datetime
import pytest
import sqlalchemy
from ehrql import Dataset
from ehrql.backends.base import MappedTable, QueryTable, SQLBackend
from ehrql.query_engines.base_sql import BaseSQLQueryEngine
from ehrql.tables import EventFrame, PatientFrame, Series, table
Base = sqlalchemy.orm.declarative_base()
# Simple schema to test against
@table
class patients(PatientFrame):
date_of_birth = Series(datetime.date)
@table
class covid_tests(EventFrame):
date = Series(datetime.date)
positive = Series(int)
class BackendFixture(SQLBackend):
display_name = "Backend Fixture"
query_engine_class = BaseSQLQueryEngine
patient_join_column = "patient_id"
# Define a table whose name and column names don't match the user-facing schema
patients = MappedTable(
source="patient_record",
columns=dict(
patient_id="PatientId",
date_of_birth="DoB",
),
)
# Define a table which is a VIEW-like representation of data from multuple
# underlying tables
covid_tests = QueryTable(
"""
SELECT patient_id, date, 1 AS positive FROM positive_result
UNION ALL
SELECT patient_id, date, 0 AS positive FROM negative_result
"""
)
class PatientRecord(Base):
__tablename__ = "patient_record"
pk = sqlalchemy.Column(sqlalchemy.Integer, primary_key=True)
PatientId = sqlalchemy.Column(sqlalchemy.Integer)
DoB = sqlalchemy.Column(sqlalchemy.Date)
class PositiveResult(Base):
__tablename__ = "positive_result"
pk = sqlalchemy.Column(sqlalchemy.Integer, primary_key=True)
patient_id = sqlalchemy.Column(sqlalchemy.Integer)
date = sqlalchemy.Column(sqlalchemy.Date)
class NegativeResult(Base):
__tablename__ = "negative_result"
pk = sqlalchemy.Column(sqlalchemy.Integer, primary_key=True)
patient_id = sqlalchemy.Column(sqlalchemy.Integer)
date = sqlalchemy.Column(sqlalchemy.Date)
def test_mapped_table(engine):
if engine.name == "in_memory":
pytest.skip("doesn't apply to non-SQL engines")
engine.setup(
PatientRecord(PatientId=1, DoB=datetime.date(2001, 2, 3)),
)
results = _extract(engine, patients.date_of_birth)
assert results == {1: datetime.date(2001, 2, 3)}
def test_query_table(engine):
if engine.name == "in_memory":
pytest.skip("doesn't apply to non-SQL engines")
engine.setup(
PositiveResult(patient_id=1, date=datetime.date(2020, 6, 1)),
NegativeResult(patient_id=1, date=datetime.date(2020, 7, 1)),
)
results = _extract(
engine, covid_tests.where(covid_tests.positive == 1).date.maximum_for_patient()
)
assert results == {1: datetime.date(2020, 6, 1)}
def _extract(engine, series):
dataset = Dataset()
dataset.define_population(
patients.exists_for_patient() | covid_tests.exists_for_patient()
)
dataset.v = series
return {
r["patient_id"]: r["v"]
for r in engine.extract(dataset, backend=BackendFixture())
}