https://github.com/galaxyproject/galaxy
Tip revision: c9a57290c0fdfe45a948cec32418ce737946ecaa authored by John Chilton on 28 October 2020, 19:52:32 UTC
Version 20.9.1 of tool-util (tag galaxy-tool-util-20.9.1).
Version 20.9.1 of tool-util (tag galaxy-tool-util-20.9.1).
Tip revision: c9a5729
summarize_timings.py
"""Script to parse timings out of a Galaxy log and summarize."""
from __future__ import print_function
import re
from argparse import ArgumentParser
import numpy
DESCRIPTION = ""
TIMING_LINE_PATTERN = re.compile(r"\((\d+.\d+) ms\)")
def main(argv=None):
"""Entry point for script."""
arg_parser = ArgumentParser(description=DESCRIPTION)
arg_parser.add_argument("--file", default="galaxy.log")
arg_parser.add_argument("--print_lines", default=False, action="store_true")
arg_parser.add_argument("--pattern", default=None)
args = arg_parser.parse_args(argv)
print_lines = args.print_lines
pattern_str = args.pattern
filter_pattern = re.compile(pattern_str) if pattern_str is not None else None
times = []
for line in open(args.file, "r"):
if filter_pattern and not filter_pattern.search(line):
continue
match = TIMING_LINE_PATTERN.search(line)
if not match:
continue
times.append(float(match.group(1)))
if print_lines:
print(line.strip())
template = "Summary (ms) - Mean: %f, Median: %f, Max: %f, Min: %f, StdDev: %f"
message = template % (
numpy.mean(times),
numpy.median(times),
numpy.max(times),
numpy.min(times),
numpy.std(times)
)
print(message)
if __name__ == "__main__":
main()