def load_config(self): Configure.load_config(self) self.__ucsc_reader = UcscReader() self.__ucsc_reader.read(self.config_values[combivep_settings.LATEST_UCSC_FILE_NAME]) self.__ljb_reader = LjbReader() self.__ljb_reader.read(self.config_values[combivep_settings.LATEST_LJB_FILE_PREFIX] + '.txt.gz')
def __init__(self): Configure.__init__(self)
def __init__(self): LjbUpdater.__init__(self) Configure.__init__(self) self.chromosome_list = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']
def __init__(self): UcscUpdater.__init__(self) Configure.__init__(self)
class TestConfigure(SafeGeneralTester): def __init__(self, test_name): SafeGeneralTester.__init__(self, test_name) def setUp(self): self.test_class = 'configure' def init_configure_instance(self): self.__configure = Configure() def test_initial(self): #init self.individual_debug = True self.init_test('test_initial') self.init_configure_instance() output_file = os.path.join(self.working_dir, 'out_config.txt') self.__configure.config_file = output_file expected_out_file = os.path.join(self.data_dir, 'expected_update_initial_config_output.txt') #run test self.__configure.write_ljb_config('4.5', '/home/jessada/development/scilifelab/projects/CombiVEP/combivep/refdb/test/data/ljb_controller/dummy_dbNSFP_light1.4') self.assertTrue(filecmp.cmp(output_file, expected_out_file), "Configure cannot update LJB config correctly") def test_load(self): #init self.init_test('test_load') self.init_configure_instance() test_file = os.path.join(self.data_dir, 'test_load.txt') self.__configure.config_file = test_file #run test out = self.__configure.load_config() self.assertEqual(out[combivep_settings.LATEST_UCSC_DATABASE_VERSION], '7.5', "Configure cannot load configuration correctly") self.assertEqual(out[combivep_settings.LATEST_UCSC_FILE_NAME], 'ucsc_file7.5.txt', "Configure cannot load configuration correctly") self.assertEqual(out[combivep_settings.LATEST_LJB_DATABASE_VERSION], '4.4', "Configure cannot load configuration correctly") self.assertEqual(out[combivep_settings.LATEST_LJB_FILE_PREFIX], '/home/jessada/development/scilifelab/projects/CombiVEP/combivep/refdb/test/data/ljb_controller/dummy_dbNSFP_light1.3', "Configure cannot load configuration correctly") def test_update_ljb_config(self): #init self.init_test('test_update_ljb_config') self.init_configure_instance() test_file = os.path.join(self.data_dir, 'test_load.txt') output_file = os.path.join(self.working_dir, 'out_config.txt') self.copy_file(test_file, output_file) self.__configure.config_file = output_file expected_out_file = os.path.join(self.data_dir, 'expected_update_ljb_config_output.txt') #run test self.__configure.write_ljb_config('4.5', '/home/jessada/development/scilifelab/projects/CombiVEP/combivep/refdb/test/data/ljb_controller/dummy_dbNSFP_light1.4') self.assertTrue(filecmp.cmp(output_file, expected_out_file), "Configure cannot update LJB config correctly") def test_update_ucsc_config(self): #init self.init_test('test_update_ucsc_config') self.init_configure_instance() test_file = os.path.join(self.data_dir, 'test_load.txt') output_file = os.path.join(self.working_dir, 'out_config.txt') self.copy_file(test_file, output_file) self.__configure.config_file = output_file expected_out_file = os.path.join(self.data_dir, 'expected_update_ucsc_config_output.txt') #run test self.__configure.write_ucsc_config('7.6', 'ucsc_file7.6.txt') self.assertTrue(filecmp.cmp(output_file, expected_out_file), "Configure cannot update UCSC config correctly") def tearDown(self): self.remove_working_dir()
def init_configure_instance(self): self.__configure = Configure()