def setUp(self):
self.project_id = 'foo'
self.dataset_id = 'bar'
self.sandbox_id = 'baz'
self.query_class = ObservationSourceConceptIDRowSuppression(
self.project_id, self.dataset_id, self.sandbox_id)
self.assertEqual(self.query_class.get_project_id(), self.project_id)
self.assertEqual(self.query_class.get_dataset_id(), self.dataset_id)
self.assertEqual(self.query_class.get_sandbox_dataset_id(),
self.sandbox_id)
def setUp(self):
self.project_id = 'foo'
self.dataset_id = 'bar'
self.sandbox_id = 'baz'
self.client = None
self.rule_instance = ObservationSourceConceptIDRowSuppression(
self.project_id, self.dataset_id, self.sandbox_id)
self.assertEqual(self.rule_instance.project_id, self.project_id)
self.assertEqual(self.rule_instance.dataset_id, self.dataset_id)
self.assertEqual(self.rule_instance.sandbox_dataset_id,
self.sandbox_id)
def setUpClass(cls):
print('**************************************************************')
print(cls.__name__)
print('**************************************************************')
super().initialize_class_vars()
cls.insert_fake_participants_tmpls = [
cls.jinja_env.from_string("""
INSERT INTO `{{fq_table_name}}`
(observation_id, person_id, observation_concept_id, observation_date,
observation_type_concept_id, observation_source_concept_id)
VALUES
(801, 337361, 1585899, date('2016-05-01'), 45905771, {{age_prediabetes}}),
(802, 129884, 1585899, date('2016-05-01'), 45905771, {{meds_prediabetes}}),
(803, 337361, 1585899, date('2016-05-01'), 45905771, {{now_prediabetes}}),
(804, 129884, 1585899, date('2016-05-01'), 45905771, null),
(805, 337361, 1585899, date('2016-05-01'), 45905771, 45),
(806, 129884, 1585899, date('2016-05-01'), 45905771, {{prefer_not_to_ans}})
""")
]
# set the test project identifier
project_id = os.environ.get(PROJECT_ID)
cls.project_id = project_id
# set the expected test datasets
dataset_id = os.environ.get('RDR_DATASET_ID')
cls.dataset_id = dataset_id
sandbox_id = dataset_id + '_sandbox'
cls.sandbox_id = sandbox_id
cls.rule_instance = ObservationSourceConceptIDRowSuppression(
project_id, dataset_id, sandbox_id)
sb_table_names = cls.rule_instance.get_sandbox_tablenames()
for table_name in sb_table_names:
cls.fq_sandbox_table_names.append(
f'{project_id}.{sandbox_id}.{table_name}')
cls.fq_table_names = [f"{project_id}.{dataset_id}.observation"]
# call super to set up the client, create datasets, and create
# empty test tables
# NOTE: does not create empty sandbox tables.
super().setUpClass()
class ObservationSourceConceptIDRowSuppressionTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
print('**************************************************************')
print(cls.__name__)
print('**************************************************************')
def setUp(self):
self.project_id = 'foo'
self.dataset_id = 'bar'
self.sandbox_id = 'baz'
self.client = None
self.rule_instance = ObservationSourceConceptIDRowSuppression(
self.project_id, self.dataset_id, self.sandbox_id)
self.assertEqual(self.rule_instance.project_id, self.project_id)
self.assertEqual(self.rule_instance.dataset_id, self.dataset_id)
self.assertEqual(self.rule_instance.sandbox_dataset_id,
self.sandbox_id)
def test_setup_rule(self):
# test
self.rule_instance.setup_rule(self.client)
# no errors are raised, nothing happens
def test_get_query_specs(self):
# pre-conditions
self.assertEqual(self.rule_instance.affected_datasets,
[clean_consts.RDR])
# test
result_list = self.rule_instance.get_query_specs()
# post conditions
expected_list = [{
clean_consts.QUERY:
DROP_SELECTION_QUERY_TMPL.render(
project=self.project_id,
dataset=self.dataset_id,
sandbox=self.sandbox_id,
drop_table=self.rule_instance.get_sandbox_tablenames()[0],
obs_concepts=OBS_SRC_CONCEPTS)
}, {
clean_consts.QUERY:
DROP_QUERY_TMPL.render(project=self.project_id,
dataset=self.dataset_id,
obs_concepts=OBS_SRC_CONCEPTS)
}]
self.assertEqual(result_list, expected_list)
def test_log_queries(self):
# pre-conditions
self.assertEqual(self.rule_instance.affected_datasets,
[clean_consts.RDR])
store_drops = DROP_SELECTION_QUERY_TMPL.render(
project=self.project_id,
dataset=self.dataset_id,
sandbox=self.sandbox_id,
drop_table=self.rule_instance.get_sandbox_tablenames()[0],
obs_concepts=OBS_SRC_CONCEPTS)
select_saves = DROP_QUERY_TMPL.render(project=self.project_id,
dataset=self.dataset_id,
obs_concepts=OBS_SRC_CONCEPTS)
# test
with self.assertLogs(level='INFO') as cm:
self.rule_instance.log_queries()
expected = [
'INFO:cdr_cleaner.cleaning_rules.base_cleaning_rule:Generated SQL Query:\n'
+ store_drops,
'INFO:cdr_cleaner.cleaning_rules.base_cleaning_rule:Generated SQL Query:\n'
+ select_saves
]
# post condition
self.assertEqual(cm.output, expected)
class ObservationSourceConceptIDRowSuppressionTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
print('**************************************************************')
print(cls.__name__)
print('**************************************************************')
def setUp(self):
self.project_id = 'foo'
self.dataset_id = 'bar'
self.sandbox_id = 'baz'
self.query_class = ObservationSourceConceptIDRowSuppression(
self.project_id, self.dataset_id, self.sandbox_id)
self.assertEqual(self.query_class.get_project_id(), self.project_id)
self.assertEqual(self.query_class.get_dataset_id(), self.dataset_id)
self.assertEqual(self.query_class.get_sandbox_dataset_id(),
self.sandbox_id)
def test_setup_rule(self):
# test
self.query_class.setup_rule()
# no errors are raised, nothing happens
def test_get_query_specs(self):
# pre-conditions
self.assertEqual(self.query_class.get_affected_datasets(),
[clean_consts.RDR])
# test
result_list = self.query_class.get_query_specs()
# post conditions
expected_list = [{
clean_consts.QUERY:
DROP_SELECTION_QUERY.format(project=self.project_id,
dataset=self.dataset_id,
sandbox=self.sandbox_id,
drop_table=SAVE_TABLE_NAME)
}, {
clean_consts.QUERY:
DROP_QUERY.format(project=self.project_id,
dataset=self.dataset_id),
clean_consts.DESTINATION_TABLE:
'observation',
clean_consts.DESTINATION_DATASET:
self.dataset_id,
clean_consts.DISPOSITION:
WRITE_TRUNCATE
}]
self.assertEqual(result_list, expected_list)
def test_log_queries(self):
# pre-conditions
self.assertEqual(self.query_class.get_affected_datasets(),
[clean_consts.RDR])
store_drops = DROP_SELECTION_QUERY.format(project=self.project_id,
dataset=self.dataset_id,
sandbox=self.sandbox_id,
drop_table=SAVE_TABLE_NAME)
select_saves = DROP_QUERY.format(project=self.project_id,
dataset=self.dataset_id)
# test
with self.assertLogs(level='INFO') as cm:
self.query_class.log_queries()
expected = [
'INFO:cdr_cleaner.cleaning_rules.base_cleaning_rule:Generated SQL Query:\n'
+ store_drops,
'INFO:cdr_cleaner.cleaning_rules.base_cleaning_rule:Generated SQL Query:\n'
+ select_saves
]
# post condition
self.assertEqual(cm.output, expected)