diff options
| -rw-r--r-- | scripts/qc.py | 66 |
1 files changed, 45 insertions, 21 deletions
diff --git a/scripts/qc.py b/scripts/qc.py index 688147c..9d57f4b 100644 --- a/scripts/qc.py +++ b/scripts/qc.py @@ -5,12 +5,12 @@ import argparse import magic -from quality_control.errors import ParseError +from quality_control.errors import InvalidValue from quality_control.parsing import ( + take, FileType, - parse_file, strain_names, - parse_errors) + collect_errors) def is_file_mime(filepath, mimetype): @@ -42,28 +42,51 @@ def cli_argument_parser(): default=default_strains_file) parser.add_argument( + "-c", "--count", type=int, + help=( + "Number of errors to display. " + "A negative number means display all errors."), + default=20) + + parser.add_argument( "-v", "--verbose", help="Controls whether to show extra output", default=False, action="store_true") return parser -def check(filepath, filetype, strains, verbose=False): +def progress_indicator(msg): + """Utility to display the progress""" + print(f"LINE: {msg['line_number']} ({msg['percent']:.2f}%)", end="\r") + return msg + +def print_errors(errors, verbose): + """Print out the errors""" + errors_exist = False + starter = "\n" if verbose else "" + print(f"{starter}line(s)\tcolumn(s)\terrors") + for error in errors: + cols = ( + error.column if isinstance(error, InvalidValue) + else ", ".join(str(col) for col in error.columns)) + errors_exist = True + print(f"{starter}{error.line}\t{cols}\t{error.message}") + + if not errors_exist: + print("No errors were found!") + + return errors + +def check(filepath, filetype, strains, count, verbose=False): """Check the file and print out results""" - try: - for line_num, line in enumerate(parse_file( - filepath, filetype, strains), start=1): - if verbose: - print(f"Checked line: {line_num}") - - print(f"Successfully checked the file. No errors found.") - except ParseError as pe: - print("line\terrors") - for line_num, error in enumerate( - parse_errors(filepath, filetype, strains, - pe.args[0]["line_number"]), - start = pe.args[0]["line_number"] + 1): - print(f"{line_num}\t{' '.join(error['message'])}") - + if verbose: + updater = progress_indicator + + if count > 0: + return print_errors( + take(collect_errors(filepath, filetype, strains, updater), count), + verbose) + return print_errors( + collect_errors(filepath, filetype, strains, updater), verbose) def main(): """Entry point function""" @@ -98,10 +121,11 @@ def main(): if args.verbose: print(f"Checking '{filepath}' for errors") - check( + return check( filepath, ( FileType.AVERAGE if args.filetype == "average" - else FileType.STANDARD_ERROR), strains) + else FileType.STANDARD_ERROR), + strains, args.count, verbose=args.verbose) if __name__ == "__main__": main() |