def test_error_message_retrieval(self):
sq = sqlClient(self.testDB)
sq.create_conn()
response = sq.get_error_message_from_code(1)
self.assertEqual(response,
"The summary statistics file cannot be found")
response = sq.get_error_message_from_code(0)
self.assertIsNone(response)
def setUp(self):
self.testDB = "./tests/study_meta.db"
self.test_storepath = "./tests/data"
config.STORAGE_PATH = self.test_storepath
config.BROKER_PORT = 5682
config.BROKER_HOST = "localhost"
sq = sqlClient(self.testDB)
sq.create_conn()
sq.cur.executescript(config.DB_SCHEMA)
def setUp(self):
self.testDB = "./tests/study_meta.db"
self.test_storepath = "./tests/data"
config.STORAGE_PATH = self.test_storepath
config.DB_PATH = self.testDB
sq = sqlClient(self.testDB)
sq.create_conn()
sq.cur.executescript(config.DB_SCHEMA)
self.valid_url = "file://{}".format(
os.path.abspath("./tests/test_sumstats_file.tsv"))
def setup_method(self, method):
self.testDB = "./tests/study_meta.db"
self.test_storepath = "./tests/data"
config.STORAGE_PATH = self.test_storepath
config.DB_PATH = self.testDB
celery.conf['CELERY_ALWAYS_EAGER'] = True
sq = sqlClient(self.testDB)
sq.create_conn()
sq.cur.executescript(config.DB_SCHEMA)
self.valid_url = "file://{}".format(os.path.abspath("./tests/test_sumstats_file.tsv"))
def test_cannot_insert_same_study_twice(self):
sq = sqlClient(self.testDB)
sq.create_conn()
sq.insert_new_study([
VALID_POST["requestEntries"][0]["id"], "callback123",
VALID_POST["requestEntries"][0]["filePath"],
VALID_POST["requestEntries"][0]["md5"],
VALID_POST["requestEntries"][0]["assembly"],
VALID_POST["requestEntries"][0]["readme"],
VALID_POST["requestEntries"][0]["entryUUID"]
])
response = sq.get_study_count()
self.assertEqual(response, 1)
def test_insert_new_study(self):
sq = sqlClient(self.testDB)
sq.create_conn()
sq.insert_new_study([
VALID_POST["requestEntries"][0]["id"], "callback123",
VALID_POST["requestEntries"][0]["filePath"],
VALID_POST["requestEntries"][0]["md5"],
VALID_POST["requestEntries"][0]["assembly"],
VALID_POST["requestEntries"][0]["readme"],
VALID_POST["requestEntries"][0]["entryUUID"]
])
response = sq.get_study_metadata("abc123")
self.assertTrue(response)
def setUp(self):
self.testDB = "./tests/study_meta.db"
self.test_storepath = "./tests/data"
config.STORAGE_PATH = self.test_storepath
config.DB_PATH = self.testDB
config.BROKER_PORT = 5682
config.BROKER_HOST = "localhost"
sq = sqlClient(self.testDB)
sq.create_conn()
sq.cur.executescript(config.DB_SCHEMA)
self.study_id = "123abc123"
self.callback_id = "abc123xyz"
self.file_path = "file/path.tsv"
self.md5 = "b1d7e0a58d36502d59d036a17336ddf5"
self.assembly = "GRCh38"
def test_update_retrieved_status(self):
sq = sqlClient(self.testDB)
sq.create_conn()
sq.insert_new_study([
VALID_POST["requestEntries"][0]["id"], "callback123",
VALID_POST["requestEntries"][0]["filePath"],
VALID_POST["requestEntries"][0]["md5"],
VALID_POST["requestEntries"][0]["assembly"],
VALID_POST["requestEntries"][0]["readme"],
VALID_POST["requestEntries"][0]["entryUUID"]
])
sq.update_retrieved_status(VALID_POST["requestEntries"][0]["id"], 1)
response = sq.get_study_metadata(VALID_POST["requestEntries"][0]["id"])
self.assertEqual(response[5], 1)
sq.update_retrieved_status(VALID_POST["requestEntries"][0]["id"], 0)
response = sq.get_study_metadata(VALID_POST["requestEntries"][0]["id"])
self.assertEqual(response[5], 0)
def test_select_from_callback_id(self):
sq = sqlClient(self.testDB)
sq.create_conn()
sq.insert_new_study([
VALID_POST["requestEntries"][0]["id"], "callback123",
VALID_POST["requestEntries"][0]["filePath"],
VALID_POST["requestEntries"][0]["md5"],
VALID_POST["requestEntries"][0]["assembly"],
VALID_POST["requestEntries"][0]["readme"],
VALID_POST["requestEntries"][0]["entryUUID"]
])
sq.insert_new_study([
VALID_POST["requestEntries"][1]["id"], "callback123",
VALID_POST["requestEntries"][0]["filePath"],
VALID_POST["requestEntries"][0]["md5"],
VALID_POST["requestEntries"][0]["assembly"],
VALID_POST["requestEntries"][0]["readme"],
VALID_POST["requestEntries"][0]["entryUUID"]
])
response = sq.get_data_from_callback_id("callback123")
self.assertIsNotNone(response)
self.assertEqual(len(response), 2)
self.assertEqual(response[0][0], VALID_POST["requestEntries"][0]["id"])
self.assertEqual(response[1][0], VALID_POST["requestEntries"][1]["id"])