jic-csb / dmaudit

Scripts to perform audits of bioinformatics data in a directory tree

dmaudit

Python script to generate a bioinformatics data management audit report.

Only works with Python 3.

Installation:

pip3 dmaudit

Usage:

dmaudit report /path/to/dir/to/audit

dmaudit's Issues

Hitting a permissions error kills whole script

Encountering a PermissionError trying to read a subdirectory will stop the whole script with a stack trace, e.g:

Auditing directory: /jic/scratch/groups/Matthew-Hartley
Traceback (most recent call last):
File "/dmaudit/dmaudit.py", line 262, in
dmaudit()
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/dmaudit/dmaudit.py", line 235, in dmaudit
directory = build_tree(directory, level, 0, check_mimetype=check_mimetype)
File "/dmaudit/dmaudit.py", line 161, in build_tree
check_mimetype=check_mimetype)
File "/dmaudit/dmaudit.py", line 161, in build_tree
check_mimetype=check_mimetype)
File "/dmaudit/dmaudit.py", line 150, in build_tree
for entry in os.scandir(path):
PermissionError: [Errno 13] Permission denied: '[redacted]'

Where we catch FileNotFound, we might also want to catch PermissionError