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authorFrederick Muriuki Muriithi2022-05-18 17:37:33 +0300
committerFrederick Muriuki Muriithi2022-05-18 17:37:33 +0300
commit6865d8621e6fadb915813951068ee950c781ee0d (patch)
tree5d0f1caed20f01b336439df33f5ee9b882ea2317 /scripts/qc.py
parent347ca2fe50225b4736e69bb86d8b278818be40ac (diff)
downloadgn-uploader-6865d8621e6fadb915813951068ee950c781ee0d.tar.gz
Update CLI: use new error collection code
Use the new code that collects the errors in the CLI client.
Diffstat (limited to 'scripts/qc.py')
-rw-r--r--scripts/qc.py66
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()