def handle_logs(test_paths, force_overwrite):
print "***Handling stdout/sterr logs and determining failed tests."
settings = Settings.instance()
wrangler = FileWrangler(test_paths, "output/output.gd")
for job_id, run_id, test_gd in wrangler:
# Create log path string, depending on if the run completed or not.
log_path = "log.txt" if os.path.exists(test_gd) else "error_log.txt"
log_path = os.path.join(settings.job_paths(job_id, run_id)[3], log_path)
# Copy log to above path
shutil.copy2(settings.log_fmt.format(job_id, run_id), log_path)
def handle_gds(test_paths, force_overwrite):
# *** Attempt at parallelization.
# pool = Pool(multiprocessing.cpu_count())
# job_paths = list()
# args = list()
# for job_id, run_id, test_gd in wrangler:
# ctrl_gd = settings.ctrl_gd_fmt.format(run_id)
# ref_seqs = GenomeDiff(ctrl_gd).ref_sequence_file_paths(settings.downloads)
# results = settings.job_paths(job_id, run_id)
# args.append((ctrl_gd, test_gd, ref_seqs, results, force_overwrite))
# job_paths.append(results[3])
#
# pool.map(handle_gd, args)
print "***Begin normalizing and comparing genome diffs."
settings = Settings.instance()
print "Searching output/output.gd in paths:"
for path in test_paths:
print "\t", path
wrangler = FileWrangler(test_paths, "output/output.gd")
assert len(wrangler.data_list), "No GDs found from, check REGEX expression in FileWrangler."
print "Found files:"
for job_id, run_id, test_gd in wrangler:
print "[job_id]: {} [run_id]: {} [file]: {}".format(job_id, run_id, test_gd)
if not os.path.exists(settings.job_dir):
os.makedirs(settings.job_dir)
job_paths = list()
for job_id, run_id, test_gd in wrangler:
ctrl_gd = settings.ctrl_gd_fmt.format(run_id)
ref_seqs = GenomeDiff(ctrl_gd).ref_sequence_file_paths(settings.downloads)
results = settings.job_paths(job_id, run_id)
handle_gd(ctrl_gd, test_gd, ref_seqs, results, force_overwrite)
job_paths.append(results[3])
print "***End normalizing and comparing genome diffs."
return job_paths
def __init__(self):
self.settings = Settings.instance()