def add_arguments_extended(parser: KGTKArgumentParser, parsed_shared_args: Namespace):
"""
Parse arguments
Args:
parser (argparse.ArgumentParser)
"""
_expert: bool = parsed_shared_args._expert
# This helper function makes it easy to suppress options from
# The help message. The options are still there, and initialize
# what they need to initialize.
def h(msg: str)->str:
if _expert:
return msg
else:
return SUPPRESS
parser.add_argument( "input_kgtk_file", nargs="?", type=Path, default="-",
help="The KGTK file to filter. May be omitted or '-' for stdin (default=%(default)s).")
parser.add_argument("-o", "--output-file", dest="output_kgtk_file", help="The KGTK file to write (default=%(default)s).", type=Path, default="-")
parser.add_argument( "--column", dest="column_name", help="The name of the column to explode. (default=%(default)s).", default=KgtkFormat.NODE2)
fgroup: _MutuallyExclusiveGroup = parser.add_mutually_exclusive_group()
fgroup.add_argument( "--types", dest="type_names", nargs='*',
help="The KGTK data types for which fields should be exploded. (default=%(default)s).",
choices=KgtkFormat.DataType.choices(),
default=KgtkFormat.DataType.choices())
fgroup.add_argument( "--fields", dest="field_names", nargs='*',
help=h("The names of the fields to extract (overrides --types). (default=%(default)s)."),
choices=KgtkValueFields.FIELD_NAMES)
parser.add_argument( "--prefix", dest="prefix", help="The prefix for exploded column names. (default=%(default)s).",
default=KgtkFormat.NODE2 + ";" + KgtkFormat.KGTK_NAMESPACE)
parser.add_argument( "--overwrite", dest="overwrite_columns",
help="Indicate that it is OK to overwrite existing columns. (default=%(default)s).",
type=optional_bool, nargs='?', const=True, default=False)
parser.add_argument( "--expand", dest="expand_list",
help="Expand the source column if it contains a list, else fail. (default=%(default)s).",
type=optional_bool, nargs='?', const=True, default=False)
parser.add_argument( "--show-data-types", dest="show_data_types",
help="Print the list of data types and exit. (default=%(default)s).",
type=optional_bool, nargs='?', const=True, default=False)
KgtkReader.add_debug_arguments(parser, expert=_expert)
KgtkReaderOptions.add_arguments(parser, mode_options=True, expert=_expert)
KgtkValueOptions.add_arguments(parser, expert=_expert)
def add_arguments_extended(parser: KGTKArgumentParser,
parsed_shared_args: Namespace):
"""
Parse arguments
Args:
parser (argparse.ArgumentParser)
"""
from kgtk.kgtkformat import KgtkFormat
from kgtk.io.kgtkreader import KgtkReader, KgtkReaderOptions
from kgtk.io.kgtkwriter import KgtkWriter
from kgtk.utils.argparsehelpers import optional_bool
from kgtk.value.kgtkvalue import KgtkValueFields
from kgtk.value.kgtkvalueoptions import KgtkValueOptions
_expert: bool = parsed_shared_args._expert
# This helper function makes it easy to suppress options from
# The help message. The options are still there, and initialize
# what they need to initialize.
def h(msg: str) -> str:
if _expert:
return msg
else:
return SUPPRESS
parser.add_input_file(positional=True)
parser.add_output_file()
parser.add_argument(
"--column",
dest="column_name",
help="The name of the column to explode. (default=%(default)s).",
default=KgtkFormat.NODE2)
fgroup: _MutuallyExclusiveGroup = parser.add_mutually_exclusive_group()
fgroup.add_argument(
"--types",
dest="type_names",
nargs='*',
help=
"The KGTK data types for which fields should be exploded. (default=%(default)s).",
choices=KgtkFormat.DataType.choices(),
default=KgtkFormat.DataType.choices())
fgroup.add_argument(
"--fields",
dest="field_names",
nargs='*',
help=
h("The names of the fields to extract (overrides --types). (default=%(default)s)."
),
choices=KgtkValueFields.FIELD_NAMES)
parser.add_argument(
"--prefix",
dest="prefix",
help="The prefix for exploded column names. (default=%(default)s).",
default=KgtkFormat.NODE2 + ";" + KgtkFormat.KGTK_NAMESPACE)
parser.add_argument(
"--overwrite",
dest="overwrite_columns",
metavar="True|False",
help=
"Indicate that it is OK to overwrite existing columns. (default=%(default)s).",
type=optional_bool,
nargs='?',
const=True,
default=False)
parser.add_argument(
"--expand",
dest="expand_list",
metavar="True|False",
help=
"Expand the source column if it contains a list, else fail. (default=%(default)s).",
type=optional_bool,
nargs='?',
const=True,
default=False)
parser.add_argument(
"--show-data-types",
dest="show_data_types",
metavar="True|False",
help="Print the list of data types and exit. (default=%(default)s).",
type=optional_bool,
nargs='?',
const=True,
default=False)
parser.add_argument("--output-format",
dest="output_format",
help="The file format (default=kgtk)",
type=str,
choices=KgtkWriter.OUTPUT_FORMAT_CHOICES)
KgtkReader.add_debug_arguments(parser, expert=_expert)
KgtkReaderOptions.add_arguments(parser, mode_options=True, expert=_expert)
KgtkValueOptions.add_arguments(parser, expert=_expert)
