"""Verify dataset integrity"""
import argparse
import pathlib
import sys
from ..rtdc_dataset import check_dataset, fmt_tdms
from .._version import version
from . import common
[docs]
def verify_dataset(path_in=None):
"""Perform checks on experimental datasets"""
if path_in is None:
parser = verify_dataset_parser()
args = parser.parse_args()
path_in = pathlib.Path(args.path).resolve()
if not path_in.exists():
common.print_violation(f"File not found: {path_in}")
return sys.exit(4)
else:
common.print_info(f"Checking {path_in}")
# The exit status of this script. Non-zero exit status means:
# 1: alerts
# 2: violations
# 3: alerts and violations
# 4: other error
exit_status = 4
try:
viol, aler, info = check_dataset(path_in)
except fmt_tdms.InvalidTDMSFileFormatError:
common.print_violation("Invalid tdms file format!")
except fmt_tdms.IncompleteTDMSFileFormatError:
common.print_violation("Incomplete dataset!")
except fmt_tdms.ContourIndexingError:
common.print_violation("Invalid contour data!")
except fmt_tdms.InvalidVideoFileError:
common.print_violation("Invalid image data!")
except BaseException as e:
common.print_violation(f"{e.__class__.__name__}: {', '.join(e.args)}")
else:
for inf in info:
common.print_info(inf)
for ale in aler:
common.print_alert(ale)
for vio in viol:
common.print_violation(vio)
common.print_info(f"Check Complete: {len(viol)} violations and "
+ f"{len(aler)} alerts")
if aler and viol:
exit_status = 3
elif aler:
exit_status = 1
elif viol:
exit_status = 2
else:
# everything is ok
exit_status = 0
finally:
# return sys.exit for testing (monkeypatched)
return sys.exit(exit_status)
def verify_dataset_parser():
descr = "Check experimental datasets for completeness. This command " \
+ "is used e.g. to enforce data integrity with Shape-In. The " \
+ "following exit codes are defined: ``0: valid dataset``, " \
+ "``1: alerts encountered``, ``2: violations encountered``, " \
+ "``3: alerts and violations``, ``4: other error``."
parser = argparse.ArgumentParser(description=descr)
parser.add_argument('path', metavar='PATH', type=str,
help='Path to experimental dataset')
parser.add_argument('--version', action='version',
version=f'dclab-verify-dataset {version}')
return parser