[RESOLVED] Relative paths in createList do not work as expected

Issues
1

Description

listfile parameter in createList command does not work as expected. For example, the following command works; it creates a .list file in folder lists.

qunex createList \
--sessionsfolder='/gpfs/loomis/pi/n3/Studies/Connectome/subjects' \
--sessions='106319,111514' \
--bolds='1,2,3,4' \
--boldtail='.dtseries.nii' \
--listfile='lists/test.list' \
--check='yes' \
--overwrite='yes'

In the following case I would expect the .list file to be created in the current folder. However, I receive an error:

qunex createList \
--sessionsfolder='/gpfs/loomis/pi/n3/Studies/Connectome/subjects' \
--sessions='106319,111514' \
--bolds='1,2,3,4' \
--boldtail='.dtseries.nii' \
--listfile='test.list' \
--check='yes' \
--overwrite='yes'

Error:

Here's the error as caught by python:

Traceback (most recent call last):
  File "/gpfs/project/fas/n3/software/qunex/niutilities/gmri", line 571, in <module>
    main()
  File "/gpfs/project/fas/n3/software/qunex/niutilities/gmri", line 539, in main
    runCommand(comm, opts)
  File "/gpfs/project/fas/n3/software/qunex/niutilities/gmri", line 391, in runCommand
    gcom.commands[command]['com'](**args)
  File "/gpfs/loomis/pi/n3/software/qunex/niutilities/niutilities/g_utilities.py", line 954, in createList
    os.makedirs(targetFolder)
  File "/gpfs/project/fas/n3/software/env/qunex/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 2] No such file or directory: ''

Another weird behavior is produced with the following command. I created folder test in the current folder, then I ran:

qunex createList \
--sessionsfolder='/gpfs/loomis/pi/n3/Studies/Connectome/subjects' \
--sessions='106319,111514' \
--bolds='1,2,3,4' \
--boldtail='.dtseries.nii' \
--listfile='test/test1.list' \
--check='yes' \
--overwrite='yes'

This creates a folder (in this case test) within the study folder (instead of using current directory), which is probably intentional, but I think it is confusing and counterintuitive. This behavior is also not clear from the inline documentation.

I’m using Qunex, version 0.61.0, master branch.

2

Hi Andraž, we have assigned a developer to this issue. We will let you know once it is resolved.

3

The issue has been resolved and will be folded into the next release.