def setUp(self):
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_app_identity_stub()
self.testbed.init_memcache_stub()
self.testbed.init_urlfetch_stub()
self.testbed.init_blobstore_stub()
self.testbed.init_datastore_v3_stub()
self.project_id = bq_utils.app_identity.get_application_id()
self.hpo_ids = [NYC_HPO_ID, PITT_HPO_ID]
self.input_dataset_id = bq_utils.get_dataset_id()
self.output_dataset_id = bq_utils.get_unioned_dataset_id()
self._empty_hpo_buckets()
test_util.delete_all_tables(self.input_dataset_id)
test_util.delete_all_tables(self.output_dataset_id)
# TODO Generalize to work for all foreign key references
# Collect all primary key fields in CDM tables
mapped_fields = []
for table in cdm.tables_to_map():
field = table + '_id'
mapped_fields.append(field)
self.mapped_fields = mapped_fields
self.implemented_foreign_keys = [
eu_constants.VISIT_OCCURRENCE_ID, eu_constants.CARE_SITE_ID,
eu_constants.LOCATION_ID
]
def tearDownClass(cls):
ehr_dataset_id = bq_utils.get_dataset_id()
rdr_dataset_id = bq_utils.get_rdr_dataset_id()
test_util.delete_all_tables(ehr_dataset_id)
test_util.delete_all_tables(rdr_dataset_id)
cls.testbed.deactivate()
logger.handlers = []
def setUp(self):
super(CombineEhrRdrTest, self).setUp()
self.APP_ID = bq_utils.app_identity.get_application_id()
self.ehr_dataset_id = bq_utils.get_dataset_id()
self.rdr_dataset_id = bq_utils.get_rdr_dataset_id()
self.combined_dataset_id = bq_utils.get_ehr_rdr_dataset_id()
self.drc_bucket = gcs_utils.get_drc_bucket()
test_util.delete_all_tables(self.combined_dataset_id)
def setUp(self):
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_app_identity_stub()
self.testbed.init_memcache_stub()
self.testbed.init_urlfetch_stub()
self.testbed.init_blobstore_stub()
self.testbed.init_datastore_v3_stub()
self.hpo_bucket = gcs_utils.get_hpo_bucket(test_util.FAKE_HPO_ID)
test_util.empty_bucket(self.hpo_bucket)
test_util.delete_all_tables(bq_utils.get_dataset_id())
def setUp(self):
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_app_identity_stub()
self.testbed.init_memcache_stub()
self.testbed.init_urlfetch_stub()
self.testbed.init_blobstore_stub()
self.testbed.init_datastore_v3_stub()
self.hpo_bucket = gcs_utils.get_hpo_bucket(FAKE_HPO_ID)
self.person_table_id = bq_utils.get_table_id(FAKE_HPO_ID, PERSON)
test_util.delete_all_tables(self.EHR_DATASET_ID)
self._empty_bucket()
def setUpClass(cls):
cls.testbed = testbed.Testbed()
cls.testbed.activate()
cls.testbed.init_app_identity_stub()
cls.testbed.init_memcache_stub()
cls.testbed.init_urlfetch_stub()
cls.testbed.init_blobstore_stub()
cls.testbed.init_datastore_v3_stub()
fake_bucket = gcs_utils.get_hpo_bucket(test_util.FAKE_HPO_ID)
dataset_id = bq_utils.get_dataset_id()
test_util.delete_all_tables(dataset_id)
test_util.get_synpuf_results_files()
test_util.populate_achilles(fake_bucket)
def setUp(self):
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_app_identity_stub()
self.testbed.init_memcache_stub()
self.testbed.init_urlfetch_stub()
self.testbed.init_blobstore_stub()
self.testbed.init_datastore_v3_stub()
self.app_id = os.environ.get('APPLICATION_ID')
self.dataset_id = os.environ.get('BIGQUERY_DATASET_ID')
self.bucket = os.environ.get('DRC_BUCKET_NAME')
test_util.empty_bucket(self.bucket)
test_util.delete_all_tables(self.dataset_id)
self.load_test_data(hpo_id=HPO_NYC)
def setUp(self):
super(EhrUnionTest, self).setUp()
self.testbed = testbed.Testbed()
self.testbed.activate()
self.testbed.init_app_identity_stub()
self.testbed.init_memcache_stub()
self.testbed.init_urlfetch_stub()
self.testbed.init_blobstore_stub()
self.testbed.init_datastore_v3_stub()
self.project_id = bq_utils.app_identity.get_application_id()
self.hpo_ids = [CHS_HPO_ID, PITT_HPO_ID]
self.input_dataset_id = bq_utils.get_dataset_id()
self.output_dataset_id = bq_utils.get_unioned_dataset_id()
self._empty_hpo_buckets()
test_util.delete_all_tables(self.input_dataset_id)
test_util.delete_all_tables(self.output_dataset_id)
def setUpClass(cls):
# TODO base class this
logger.level = logging.INFO
stream_handler = logging.StreamHandler(sys.stdout)
logger.addHandler(stream_handler)
cls.testbed = testbed.Testbed()
cls.testbed.activate()
cls.testbed.init_app_identity_stub()
cls.testbed.init_memcache_stub()
cls.testbed.init_urlfetch_stub()
cls.testbed.init_blobstore_stub()
cls.testbed.init_datastore_v3_stub()
ehr_dataset_id = bq_utils.get_dataset_id()
rdr_dataset_id = bq_utils.get_rdr_dataset_id()
test_util.delete_all_tables(ehr_dataset_id)
test_util.delete_all_tables(rdr_dataset_id)
cls.load_dataset_from_files(ehr_dataset_id, test_util.NYC_FIVE_PERSONS_PATH)
cls.load_dataset_from_files(rdr_dataset_id, test_util.RDR_PATH)
def setUpClass(cls):
fake_bucket = gcs_utils.get_hpo_bucket(test_util.FAKE_HPO_ID)
dataset_id = bq_utils.get_dataset_id()
test_util.delete_all_tables(dataset_id)
test_util.get_synpuf_results_files()
test_util.populate_achilles(fake_bucket)
def tearDownClass(cls):
dataset_id = bq_utils.get_dataset_id()
test_util.delete_all_tables(dataset_id)
def tearDown(self):
test_util.delete_all_tables(self.EHR_DATASET_ID)
self._empty_bucket()
self.testbed.deactivate()
def tearDown(self):
test_util.empty_bucket(self.bucket)
test_util.delete_all_tables(self.dataset_id)
self.testbed.deactivate()
def tearDown(self):
test_util.delete_all_tables(bq_utils.get_dataset_id())
test_util.empty_bucket(self.hpo_bucket)
self.testbed.deactivate()
def tearDownClass(cls):
dataset_id = bq_utils.get_dataset_id()
test_util.delete_all_tables(dataset_id)
cls.testbed.deactivate()
def tearDown(self):
self._empty_hpo_buckets()
test_util.delete_all_tables(self.input_dataset_id)
test_util.delete_all_tables(self.output_dataset_id)
self.testbed.deactivate()
def tearDown(self):
test_util.delete_all_tables(self.combined_dataset_id)