Providing path to .d directory does not work

[Cajac102]

Hello,

I'm trying to convert a diaPASEF .d directory to mzml. Running timsconvert on one directory

timsconvert --input LFQ_timsTOFPro_diaPASEF_Condition_B_Sample_Alpha_01.d
throws the following error:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/caro/miniconda3/envs/timsconvert/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/home/caro/miniconda3/envs/timsconvert/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
           ^^^^^^^^^^^^^^^^
  File "/home/caro/miniconda3/envs/timsconvert/lib/python3.11/site-packages/timsconvert/convert.py", line 22, in convert_raw_file
    if run_args['outdir'] == '' and os.path.isdir(run_args['input']) and os.path.splitext(run_args['input'])[
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen genericpath>", line 42, in isdir
TypeError: stat: path should be string, bytes, os.PathLike or integer, not list
"""

The same happens when putting the directory path in quotation marks.

However, running timsconvert on the directory containing the .d directories works:

timsconvert --input . (ran inside the directory that contains LFQ_timsTOFPro_diaPASEF_Condition_B_Sample_Alpha_01.d and other .d folders)

It's a bit of a nonissue since the second way works, but it took me a minute to figure out so I thought I leave this here for people running into the same situation :)

I use Debian/Linux 12, timsconvert v2.0.0, the file is from here.

[Xisong-Feng]

I also encountered this problem at that time. I added .\ before the path then solved the problem.
You can try timsconvert --input .\LFQ_timsTOFPro_diaPASEF_Condition_B_Sample_Alpha_01.d to check whether the code can run.

[leoschwarz]

Adding the leading dot solves the problem of not being able to create the files, but it still raises an error at the end which I'm ignoring for now (since the files do get produced after all)

Traceback (most recent call last):
  File "/app/.venv/bin/timsconvert", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/app/.venv/lib/python3.11/site-packages/bin/cmd.py", line 34, in main
    clean_up_logfiles(args, list_of_logfiles)
  File "/app/.venv/lib/python3.11/site-packages/timsconvert/convert.py", line 267, in clean_up_logfiles
    if args['outdir'] == '' and os.path.isdir(args['input']) and os.path.splitext(args['input'])[-1] != '.d':
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen genericpath>", line 42, in isdir
TypeError: stat: path should be string, bytes, os.PathLike or integer, not list