def run(
input_file: KGTKFiles,
output_file: KGTKFiles,
output_format: str,
errors_to_stdout: bool = False,
errors_to_stderr: bool = True,
show_options: bool = False,
verbose: bool = False,
very_verbose: bool = False,
**kwargs # Whatever KgtkFileOptions and KgtkValueOptions want.
) -> int:
# import modules locally
from kgtk.exceptions import KGTKException
input_file_path: Path = KGTKArgumentParser.get_input_file(input_file)
output_file_path: Path = KGTKArgumentParser.get_output_file(output_file)
# Select where to send error messages, defaulting to stderr.
error_file: typing.TextIO = sys.stdout if errors_to_stdout else sys.stderr
# TODO: check that at most one input file is stdin?
# Build the option structures.
reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(kwargs)
value_options: KgtkValueOptions = KgtkValueOptions.from_dict(kwargs)
# Show the final option structures for debugging and documentation.
if show_options:
print("--input-file=%s" % str(input_file_path),
file=error_file,
flush=True)
print("--output-file=%s" % str(output_file_path),
file=error_file,
flush=True)
reader_options.show(out=error_file)
value_options.show(out=error_file)
print("=======", file=error_file, flush=True)
try:
kc: KgtkCat = KgtkCat(input_file_paths=[input_file_path],
output_path=output_file_path,
output_format=output_format,
reader_options=reader_options,
value_options=value_options,
error_file=error_file,
verbose=verbose,
very_verbose=very_verbose)
kc.process()
return 0
except SystemExit as e:
raise KGTKException("Exit requested")
except Exception as e:
raise KGTKException(str(e))
def run(input_files: KGTKFiles,
output_file: KGTKFiles,
output_format: typing.Optional[str],
output_column_names: typing.Optional[typing.List[str]],
old_column_names: typing.Optional[typing.List[str]],
new_column_names: typing.Optional[typing.List[str]],
errors_to_stdout: bool = False,
errors_to_stderr: bool = True,
show_options: bool = False,
verbose: bool = False,
very_verbose: bool = False,
**kwargs # Whatever KgtkFileOptions and KgtkValueOptions want.
)->int:
# import modules locally
from kgtk.exceptions import KGTKException
from kgtk.join.kgtkcat import KgtkCat
from kgtk.io.kgtkreader import KgtkReader, KgtkReaderOptions
from kgtk.io.kgtkwriter import KgtkWriter
from kgtk.value.kgtkvalueoptions import KgtkValueOptions
input_file_paths: typing.List[Path] = KGTKArgumentParser.get_input_file_list(input_files)
output_file_path: Path = KGTKArgumentParser.get_output_file(output_file)
# Select where to send error messages, defaulting to stderr.
error_file: typing.TextIO = sys.stdout if errors_to_stdout else sys.stderr
# print("cat running", file=error_file, flush=True) # ***
# TODO: check that at most one input file is stdin?
# Build the option structures.
reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(kwargs)
value_options: KgtkValueOptions = KgtkValueOptions.from_dict(kwargs)
# Show the final option structures for debugging and documentation.
if show_options:
print("--input-files %s" % " ".join((str(input_file_path) for input_file_path in input_file_paths)), file=error_file, flush=True)
print("--output-file=%s" % str(output_file_path), file=error_file, flush=True)
if output_format is not None:
print("--output-format=%s" % output_format, file=error_file, flush=True)
if output_column_names is not None:
print("--output-coloumns %s" % " ".join(output_column_names), file=error_file, flush=True)
if old_column_names is not None:
print("--old-columns %s" % " ".join(old_column_names), file=error_file, flush=True)
if new_column_names is not None:
print("--new-columns %s" % " ".join(new_column_names), file=error_file, flush=True)
reader_options.show(out=error_file)
value_options.show(out=error_file)
print("=======", file=error_file, flush=True)
# Check for comsistent options. argparse doesn't support this yet.
if output_column_names is not None and len(output_column_names) > 0:
if (old_column_names is not None and len(old_column_names) > 0) or \
(new_column_names is not None and len(new_column_names) > 0):
raise KGTKException("When --output-columns is used, --old-columns and --new-columns may not be used.")
elif (old_column_names is not None and len(old_column_names) > 0) ^ \
(new_column_names is not None and len(new_column_names) > 0):
raise KGTKException("Both --old-columns and --new-columns must be used when either is used.")
elif (old_column_names is not None and len(old_column_names) > 0) and \
(new_column_names is not None and len(new_column_names) > 0):
if len(old_column_names) != len(new_column_names):
raise KGTKException("Both --old-columns and --new-columns must have the same number of columns.")
try:
kc: KgtkCat = KgtkCat(input_file_paths=input_file_paths,
output_path=output_file_path,
output_format=output_format,
output_column_names=output_column_names,
old_column_names=old_column_names,
new_column_names=new_column_names,
reader_options=reader_options,
value_options=value_options,
error_file=error_file,
verbose=verbose,
very_verbose=very_verbose
)
kc.process()
# print("cat done", file=error_file, flush=True) # ***
return 0
except SystemExit as e:
raise KGTKException("Exit requested")
except Exception as e:
raise KGTKException(str(e))
def run(
input_file_path: Path,
output_file_path: Path,
output_format: typing.Optional[str],
output_column_names: typing.Optional[typing.List[str]],
old_column_names: typing.Optional[typing.List[str]],
new_column_names: typing.Optional[typing.List[str]],
errors_to_stdout: bool = False,
errors_to_stderr: bool = True,
show_options: bool = False,
verbose: bool = False,
very_verbose: bool = False,
**kwargs # Whatever KgtkFileOptions and KgtkValueOptions want.
) -> int:
# import modules locally
from kgtk.exceptions import KGTKException
# Select where to send error messages, defaulting to stderr.
error_file: typing.TextIO = sys.stdout if errors_to_stdout else sys.stderr
# Build the option structures.
reader_options: KgtkReaderOptions = KgtkReaderOptions.from_dict(kwargs)
value_options: KgtkValueOptions = KgtkValueOptions.from_dict(kwargs)
# Show the final option structures for debugging and documentation.
if show_options:
print("input: %s" % str(input_file_path), file=error_file, flush=True)
print("--output-file=%s" % str(output_file_path),
file=error_file,
flush=True)
if output_format is not None:
print("--output-format=%s" % output_format,
file=error_file,
flush=True)
if output_column_names is not None:
print("--output-columns %s" % " ".join(output_column_names),
file=error_file,
flush=True)
if old_column_names is not None:
print("--old-columns %s" % " ".join(old_column_names),
file=error_file,
flush=True)
if new_column_names is not None:
print("--new-columns %s" % " ".join(new_column_names),
file=error_file,
flush=True)
reader_options.show(out=error_file)
value_options.show(out=error_file)
print("=======", file=error_file, flush=True)
# Check for consistent options. argparse doesn't support this yet.
if output_column_names is not None and len(output_column_names) > 0:
if (old_column_names is not None and len(old_column_names) > 0) or \
(new_column_names is not None and len(new_column_names) > 0):
raise KGTKException(
"When --output-columns is used, --old-columns and --new-columns may not be used."
)
elif old_column_names is not None and len(old_column_names) > 0:
if new_column_names is None or len(new_column_names) == 0:
raise KGTKException(
"Both --old-columns and --new-columns must be used when either is used."
)
if len(old_column_names) != len(new_column_names):
raise KGTKException(
"Both --old-columns and --new-columns must have the same number of columns."
)
elif new_column_names is not None and len(new_column_names) > 0:
if old_column_names is None or len(old_column_names) == 0:
raise KGTKException(
"Both --old-columns and --new-columns must be used when either is used."
)
else:
raise KGTKException(
"You must specify --output-columns or both of --old-columns and --new-columns."
)
try:
kc: KgtkCat = KgtkCat(input_file_paths=[input_file_path],
output_path=output_file_path,
output_format=output_format,
output_column_names=output_column_names,
old_column_names=old_column_names,
new_column_names=new_column_names,
reader_options=reader_options,
value_options=value_options,
error_file=error_file,
verbose=verbose,
very_verbose=very_verbose)
kc.process()
return 0
except SystemExit as e:
raise KGTKException("Exit requested")
except Exception as e:
raise KGTKException(str(e))