def test_subqueries(self):
hpo_ids = ['chs', 'pitt']
project_id = bq_utils.app_identity.get_application_id()
dataset_id = bq_utils.get_dataset_id()
table = 'measurement'
mapping_msg = 'Expected mapping subquery count %s but got %s'
union_msg = 'Expected union subquery count %s but got %s'
# Should not generate subqueries when HPO tables do not exist
pitt_table_id = self._create_hpo_table('pitt', table, dataset_id)
expected_count = 1
subqueries = ehr_union._mapping_subqueries(table, hpo_ids, dataset_id,
project_id)
actual_count = len(subqueries)
self.assertEqual(expected_count, actual_count,
mapping_msg % (expected_count, actual_count))
subquery = subqueries[0]
self.assertTrue(pitt_table_id in subquery)
subqueries = ehr_union._union_subqueries(table, hpo_ids, dataset_id,
self.output_dataset_id)
self.assertEqual(expected_count, actual_count,
union_msg % (expected_count, actual_count))
subquery = subqueries[0]
self.assertTrue(pitt_table_id in subquery)
# After adding measurement table for chs, should generate subqueries for both
chs_table_id = self._create_hpo_table('chs', table, dataset_id)
expected_count = 2
subqueries = ehr_union._mapping_subqueries(table, hpo_ids, dataset_id,
project_id)
actual_count = len(subqueries)
self.assertEqual(expected_count, actual_count,
mapping_msg % (expected_count, actual_count))
self.assertTrue(any(sq for sq in subqueries if pitt_table_id in sq))
self.assertTrue(any(sq for sq in subqueries if chs_table_id in sq))
subqueries = ehr_union._union_subqueries(table, hpo_ids, dataset_id,
self.output_dataset_id)
actual_count = len(subqueries)
self.assertEqual(expected_count, actual_count,
union_msg % (expected_count, actual_count))
self.assertTrue(any(sq for sq in subqueries if pitt_table_id in sq))
self.assertTrue(any(sq for sq in subqueries if chs_table_id in sq))
def test_mapping_subqueries(self, mock_list_all_table_ids):
"""
Verify the query for loading mapping tables. A constant value should be added to
destination key fields in all tables except for person where the values in
the src_person_id and person_id fields should be equal.
:param mock_list_all_table_ids: simulate tables being returned
"""
# patch list_all_table_ids so that
# for FAKE_SITE_1 and FAKE_SITE_2
# it returns both of their person, visit_occurrence and pii_name tables
# for FAKE_SITE_1 only
# it returns the condition_occurrence table
tables = ['person', 'visit_occurrence', 'pii_name']
fake_table_ids = [
bq_utils.get_table_id(hpo_id, table) for hpo_id in self.hpo_ids
for table in tables
]
fake_table_ids.append(
bq_utils.get_table_id(self.FAKE_SITE_1, 'condition_occurrence'))
mock_list_all_table_ids.return_value = fake_table_ids
hpo_count = len(self.hpo_ids)
# offset is added to the visit_occurrence destination key field
actual = eu._mapping_subqueries('visit_occurrence', self.hpo_ids,
'fake_dataset', 'fake_project')
hpo_unique_identifiers = eu.get_hpo_offsets(self.hpo_ids)
self.assertEqual(hpo_count, len(actual))
for i in range(0, hpo_count):
hpo_id = self.hpo_ids[i]
subquery = actual[i]
hpo_table = bq_utils.get_table_id(hpo_id, 'visit_occurrence')
hpo_offset = hpo_unique_identifiers[hpo_id]
self.assertIn(f"'{hpo_table}' AS src_table_id", subquery)
self.assertIn('visit_occurrence_id AS src_visit_occurrence_id',
subquery)
self.assertIn(
f'visit_occurrence_id + {hpo_offset} AS visit_occurrence_id',
subquery)
# src_person_id and person_id fields both use participant ID value
# (offset is NOT added to the value)
actual = eu._mapping_subqueries('person', self.hpo_ids, 'fake_dataset',
'fake_project')
self.assertEqual(hpo_count, len(actual))
for i in range(0, hpo_count):
hpo_id = self.hpo_ids[i]
subquery = actual[i]
hpo_table = bq_utils.get_table_id(hpo_id, 'person')
self.assertIn(f"'{hpo_table}' AS src_table_id", subquery)
self.assertIn('person_id AS src_person_id', subquery)
self.assertIn('person_id AS person_id', subquery)
# only return queries for tables that exist
actual = eu._mapping_subqueries('condition_occurrence', self.hpo_ids,
'fake_dataset', 'fake_project')
self.assertEqual(1, len(actual))
subquery = actual[0]
hpo_table = bq_utils.get_table_id(self.FAKE_SITE_1,
'condition_occurrence')
hpo_offset = hpo_unique_identifiers[self.FAKE_SITE_1]
self.assertIn(f"'{hpo_table}' AS src_table_id", subquery)
self.assertIn('condition_occurrence_id AS src_condition_occurrence_id',
subquery)
self.assertIn(
f'condition_occurrence_id + {hpo_offset} AS condition_occurrence_id',
subquery)