def app_combivep_reference_updater():
#update LJB reference database
ljb_controller = LjbController()
ljb_controller.update()
#update UCSC reference database
ucsc_controller = UcscController()
ucsc_controller.update()
def init_ucsc_controller_instance(self):
self.__ucsc_controller = UcscController()
class TestUcscController(SafeRefDBTester):
def __init__(self, test_name):
SafeRefDBTester.__init__(self, test_name)
def setUp(self):
self.test_class = 'ucsc_controller'
def init_ucsc_controller_instance(self):
self.__ucsc_controller = UcscController()
# def test_clean_raw_database(self):
# #initialize variables
## self.individual_debug = True
# self.init_test('test_clean_raw_database')
# self.init_ucsc_controller_instance()
# test_file = os.path.join(self.data_dir, 'test_clean_raw_database.txt')
# working_file = os.path.join(self.working_dir, 'test_clean_raw_database.txt')
# out_file = os.path.join(self.working_dir, 'clean_database.txt')
# expected_out_file = os.path.join(self.data_dir, 'expected_clean_database.txt')
# self.copy_file(test_file, working_file)
#
# self.__ucsc_controller.clean_raw_database(working_file, out_file)
# self.assertTrue(filecmp.cmp(out_file, expected_out_file), "Raw UCSC database haven't been clean properly");
#
def test_tabix_database(self):
#init
self.init_test('test_tabix_database')
self.init_ucsc_controller_instance()
test_file = os.path.join(self.data_dir, 'test_tabix_database.txt')
working_file = os.path.join(self.working_dir, 'test_tabix_database.txt')
expected_out_file = os.path.join(self.working_dir, 'test_tabix_database.txt.gz')
self.copy_file(test_file, working_file)
#test if the 'tabix' files are produced
out_file = self.__ucsc_controller.tabix_database(working_file)
self.assertEqual(expected_out_file, out_file, "Tabix doesn't work correctly")
self.assertTrue(os.path.exists(out_file), "Tabix doesn't work correctly")
self.assertTrue(os.path.exists(out_file+'.tbi'), "Tabix doesn't work correctly")
#test if it is readable
ucsc_reader = UcscReader()
ucsc_reader.read(out_file)
readable = False
for rec in ucsc_reader.fetch_array_snps('chr3', 108572604, 108572605):
readable = True
self.assertEqual(rec[combivep_settings.UCSC_0_INDEX_START_POS], '108572604', "Database tabixing doesn't work correctly")
break
self.assertTrue(readable, "Tabixed ucsc database is not readable")
@unittest.skip("temporary disable due to high bandwidth usage")
def test_not_update(self):
#init
self.init_test('test_not_update')
self.init_ucsc_controller_instance()
self.__ucsc_controller.config_file = os.path.join(self.data_dir, 'test_not_update_config_file.txt')
#run test
self.assertFalse(self.__ucsc_controller.update(), "UCSC controller cannot identify correct update status")
def tearDown(self):
self.remove_working_dir()
