def validate_and_prepare_common_arguments(args):
# flatten lists of lists to a list containing elements
lists_to_flatten = ["input_files", "blacklisted_parameters"]
for list_to_flatten in lists_to_flatten:
utils.flatten_list_of_lists(args, list_to_flatten)
# if input is a single file, we expect output to be a file (and not a dir that already exists)
if len(args.input_files) == 1:
if os.path.isdir(args.output_destination):
raise ApplicationException(
"If a single input file is provided, output (%s) is expected to be a file "
"and not a folder.\n" % args.output_destination)
# if input is a list of files, we expect output to be a folder
if len(args.input_files) > 1:
if not os.path.isdir(args.output_destination):
raise ApplicationException(
"If several input files are provided, output (%s) is expected to be an "
"existing directory.\n" % args.output_destination)
# check that the provided input files, if provided, contain a valid file path
input_arguments_to_check = [
"xsd_location", "input_files", "hardcoded_parameters"
]
for argument_name in input_arguments_to_check:
utils.validate_argument_is_valid_path(args, argument_name)
# add the parameter hardcoder
args.parameter_hardcoder = utils.parse_hardcoded_parameters(
args.hardcoded_parameters)
def validate_and_prepare_common_arguments(args):
# flatten lists of lists to a list containing elements
lists_to_flatten = ["input_files", "blacklisted_parameters"]
for list_to_flatten in lists_to_flatten:
utils.flatten_list_of_lists(args, list_to_flatten)
# if input is a single file, we expect output to be a file (and not a dir that already exists)
if len(args.input_files) == 1:
if os.path.isdir(args.output_destination):
raise ApplicationException("If a single input file is provided, output (%s) is expected to be a file "
"and not a folder.\n" % args.output_destination)
# if input is a list of files, we expect output to be a folder
if len(args.input_files) > 1:
if not os.path.isdir(args.output_destination):
raise ApplicationException("If several input files are provided, output (%s) is expected to be an "
"existing directory.\n" % args.output_destination)
# check that the provided input files, if provided, contain a valid file path
input_arguments_to_check = ["xsd_location", "input_files", "hardcoded_parameters"]
for argument_name in input_arguments_to_check:
utils.validate_argument_is_valid_path(args, argument_name)
# add the parameter hardcoder
args.parameter_hardcoder = utils.parse_hardcoded_parameters(args.hardcoded_parameters)
def validate_and_prepare_args(args):
# check that only one of skip_tools_file and required_tools_file has been provided
if args.skip_tools_file is not None and args.required_tools_file is not None:
raise ApplicationException(
"You have provided both a file with tools to ignore and a file with required tools.\n"
"Only one of -s/--skip-tools, -r/--required-tools can be provided."
)
# flatten macros_files to make sure that we have a list containing file names and not a list of lists
utils.flatten_list_of_lists(args, "macros_files")
# check that the arguments point to a valid, existing path
input_variables_to_check = [
"skip_tools_file", "required_tools_file", "macros_files",
"formats_file"
]
for variable_name in input_variables_to_check:
utils.validate_argument_is_valid_path(args, variable_name)
# check that the provided output files, if provided, contain a valid file path (i.e., not a folder)
output_variables_to_check = [
"data_types_destination", "tool_conf_destination"
]
for variable_name in output_variables_to_check:
file_name = getattr(args, variable_name)
if file_name is not None and os.path.isdir(file_name):
raise ApplicationException(
"The provided output file name (%s) points to a directory." %
file_name)
if not args.macros_files:
# list is empty, provide the default value
logger.warning("Using default macros from galaxy/macros.xml", 0)
args.macros_files = ["galaxy/macros.xml"]
def validate_and_prepare_args(args):
# check that only one of skip_tools_file and required_tools_file has been provided
if args.skip_tools_file is not None and args.required_tools_file is not None:
raise ApplicationException(
"You have provided both a file with tools to ignore and a file with required tools.\n"
"Only one of -s/--skip-tools, -r/--required-tools can be provided.")
# flatten macros_files to make sure that we have a list containing file names and not a list of lists
utils.flatten_list_of_lists(args, "macros_files")
# check that the arguments point to a valid, existing path
input_variables_to_check = ["skip_tools_file", "required_tools_file", "macros_files", "formats_file"]
for variable_name in input_variables_to_check:
utils.validate_argument_is_valid_path(args, variable_name)
# check that the provided output files, if provided, contain a valid file path (i.e., not a folder)
output_variables_to_check = ["data_types_destination", "tool_conf_destination"]
for variable_name in output_variables_to_check:
file_name = getattr(args, variable_name)
if file_name is not None and os.path.isdir(file_name):
raise ApplicationException("The provided output file name (%s) points to a directory." % file_name)
if not args.macros_files:
# list is empty, provide the default value
logger.warning("Using default macros from galaxy/macros.xml", 0)
args.macros_files = ["galaxy/macros.xml"]