def compute(allPaths, counter, human_readable, output, filter_zero=False):
for (path, isfile) in allPaths:
if isfile:
analyzeFile(path, counter)
else:
util.process_directory(path, lambda file, printInfo: analyzeFile(file, counter))
list = counter.keys()
if filter_zero:
list = [ k for k in list if counter[k] > 0 ]
list.sort(key = lambda k: counter[k])
padding = len(str(counter[list[len(list) - 1]])) if list else 0
total = 0
try:
for id in list:
num = counter[id]
total += num
if human_readable:
print('{0:{width}}'.format(num, width=padding) + ' ' + id, file=output)
else:
print(id, file=output)
if human_readable:
print('', file=output)
print('time: '+str(time.clock() - starttime)+'s', file=output)
print('ids: '+str(len(list)), file=output)
print('entries: '+str(total), file=output)
print('mean: '+str(total / len(list)), file=output)
except IOError as e:
if e.errno != 32:
raise
def compute(allPaths, counter, human_readable, output, filter_zero=False):
for (path, isfile) in allPaths:
if isfile:
analyzeFile(path, counter)
else:
util.process_directory(
path, lambda file, printInfo: analyzeFile(file, counter))
list = counter.keys()
if filter_zero:
list = [k for k in list if counter[k] > 0]
list.sort(key=lambda k: counter[k])
padding = len(str(counter[list[len(list) - 1]])) if list else 0
total = 0
try:
for id in list:
num = counter[id]
total += num
if human_readable:
print('{0:{width}}'.format(num, width=padding) + ' ' + id,
file=output)
else:
print(id, file=output)
if human_readable:
print('', file=output)
print('time: ' + str(time.clock() - starttime) + 's', file=output)
print('ids: ' + str(len(list)), file=output)
print('entries: ' + str(total), file=output)
print('mean: ' + str(total / len(list)), file=output)
except IOError as e:
if e.errno != 32:
raise
def processAll(qm, cohort, path_tuples):
candidates = {}
id_column = cms_get_patient.input_format["patient_id"]
for (path, isfile) in path_tuples:
if isfile:
processFile(path, id_column, qm, candidates, not debug_inspect)
else:
util.process_directory(path, lambda file, printInfo: processFile(file, id_column, qm, candidates, not debug_inspect and printInfo), not debug_inspect)
for c in candidates.values():
if qm.isMatch(c):
cohort.append(c.getPid())
cohort.sort()
def main(file):
"""Start the localization cleanup program.
For more information, do `python localization.py --help`.
"""
directory = os.path.join(MOD_DIRECTORY, "localisation")
process_directory(directory, EXTENSIONS, clean_localization)
localization_group.set_prompt_file(file)
try:
localization_group.filter()
except click.Abort:
click.echo()
try:
localization_group.prompt_export()
except click.Abort:
pass
def clean_style(lines: List[str]) -> bool:
"""Adjust the file information to be stylistically cleaner.
This leaves no newlines at the start of the file and only one
at the end of the file.
"""
style_changed = False
# remove any extra newlines at the start of the file
while lines and lines[0].isspace():
del lines[0]
style_changed = True
# remove any extra newlines at the end of the file.
while lines and lines[-1].isspace():
del lines[-1]
style_changed = True
# add a newline to the end of the file if not exists.
if lines and not lines[-1].endswith(b"\n"):
lines[-1] += "\n"
style_changed = True
return style_changed
if __name__ == '__main__':
process_directory(MOD_DIRECTORY, EXTENSIONS, clean_file)