def validate_command_line_options(options): # Validate command-line options try: opt.validate_dict_option(options[LOG_LEVEL], log.LEVELS, "Invalid log level") except schema.SchemaError as exc: exit(exc.code)
def validate_command_line_options(options): # Validate command-line options try: opt.validate_dict_option( options[LOG_LEVEL], log.LEVELS, "Invalid log level") except schema.SchemaError as exc: exit(exc.code)
def test_validate_dict_option_exception_message_contains_correct_info(): values_dict = {1: "one", 2: "two"} msg = "dummy" key = 3 with pytest.raises(SchemaError) as exc_info: validate_dict_option(key, values_dict, msg) check_exception_message(exc_info, msg, key)
def validate_command_line_options(options): try: opt.validate_dict_option( options[LOG_LEVEL], log.LEVELS, "Invalid log level") opt.validate_file_option( options[QUANT_FILE], "Could not open Sailfish quantification results file.") except schema.SchemaError as exc: exit("Exiting. " + exc.code)
def validate_command_line_options(options): try: opt.validate_dict_option( options[LOG_LEVEL], log.LEVELS, "Invalid log level") opt.validate_list_option( options[QUANT_METHOD], QUANT_METHODS, "Invalid quantification method") opt.validate_file_option( options[QUANT_FILE], "Could not open Sailfish quantification results file.") options[READ_LENGTH] = opt.validate_int_option( options[READ_LENGTH], "Read length must be a positive integer", min_val=0) options[PAIRED_END] = opt.check_boolean_value(options[PAIRED_END]) except schema.SchemaError as exc: exit("Exiting. " + exc.code)
def validate_command_line_options(options): try: opt.validate_dict_option( options[LOG_LEVEL], log.LEVELS, "Invalid log level") opt.validate_file_option( options[TAQMAN_EXPRESSION_FILE], "Could not open TaqMan expression file.") opt.validate_file_option( options[SYNONYM_FILE], "Could not open synonym file.") for quant_file in options[QUANTIFICATION_FILES]: opt.validate_file_option( quant_file, "Could not open quantification file " + quant_file) except schema.SchemaError as exc: exit(exc.code)
def validate_command_line_options(options): try: opt.validate_dict_option( options[LOG_LEVEL], log.LEVELS, "Invalid log level") opt.validate_file_option( options[TAQMAN_EXPRESSION_FILE], "Could not open TaqMan expression file.") opt.validate_file_option( options[QUANTIFICATION_FILE], "Could not open quantification file.") opt.validate_file_option( options[SYNONYM_FILE], "Could not open synonym file.") options[REF_TYPE] = options[REF_TYPE].lower() opt.validate_list_option( options[REF_TYPE], maqc.REFERENCE_SETS, "Invalid reference type") except schema.SchemaError as exc: exit(exc.code)
def validate_command_line_options(options): try: opt.validate_dict_option(options[LOG_LEVEL], log.LEVELS, "Invalid log level.") opt.validate_file_option(options[REGIONS_FILE], "Could not open region locations file.") except schema.SchemaError as exc: exit("Exiting. " + exc.code)
def test_validate_dict_option_raises_exception_for_non_existent_key(): values_dict = {1: "one", 2: "two"} with pytest.raises(SchemaError): validate_dict_option(3, values_dict, "dummy")
def test_validate_dict_option_returns_correct_dict_value(): values_dict = {1: "one", 2: "two"} assert validate_dict_option(2, values_dict, "dummy") == "two"