[RESOLVED] Issue when running running qunexContainer with scheduler

Description:

When running qunexContainer using the --scheduler flag not scheduling the job. Issue seems to be linked to the --sessions flag.

Call:

  1. FAILED - Running with the specific --sessions flag:
qunexContainer importDICOM \
  --sessions="pb9609" \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
  --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
  --check=any \
  --options="addImageType:1" \
  --scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"
  1. SUCCESS - Running without the --sessions flag:
qunexContainer importDICOM \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
  --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
  --check=any \
  --options="addImageType:1" \
  --scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"
  1. SUCCESS - Running on a node without the --scheduler flag
qunexContainer importDICOM \
  --sessions="pb10122" \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
  --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
  --check=any \
  --options="addImageType:1"
  1. FAILED - Running qunexContainer with the --scheduler flag on a session (pb3924) that was already processed successfully using option 3 above.
qunexContainer importDICOM \
  --sessions="pb3924" \
  --sessionsfolder="/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions" \
  --container="/gpfs/project/fas/n3/software/Singularity/qunex_suite-0.62.5.sif" \
  --check=any \
  --options="addImageType:1" \
  --scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=pi_anticevic"

Logs:

  1. When run with the sessions flag: No logs or terminal output created as no job is submitted.

  2. When running without session flag, slurm output: /gpfs/project/fas/n3/Studies/Longitudinal.R01/processing/logs/batchlogs/slurm-15567730.out
    [job stopped because we did not want to process all the sessions folder at this time]

  3. Terminal output - Successful run through importDICOM. No logs created. Location of session: /gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions/pb10122

  4. Output from terminal:

Quantitative Neuroimaging Environment & Toolbox (Qu|Nex) Suite Version 0.62.5
--------------------==== Qu|Nex failed! ====--------------------
ERROR: Execution of command `importDICOM` failed!
       Please check documentation for the command (`qunex ?importDICOM`)!
The call received was: 
(please note that when run through scheduler, all possible parameters, 
even non relevant ones are passed) 
qunex importDICOM \
    --sessions=pb3924 \
    --sessionsfolder=/gpfs/project/fas/n3/Studies/Longitudinal.R01/sessions \
    --check=any \
    --options=addImageType:1 \
    --sessionids=pb3924 
--------------------------------------------------------------
Here's the error as caught by python:
Traceback (most recent call last):
  File "/opt/qunex/niutilities/gmri", line 558, in <module>
    main()
  File "/opt/qunex/niutilities/gmri", line 526, in main
    runCommand(comm, opts)
  File "/opt/qunex/niutilities/gmri", line 378, in runCommand
    gcom.commands[command]['com'](**args)
TypeError: importDICOM() got an unexpected keyword argument 'sessionids'

Hi Clara, we will assign a developer to this issue and will let you know once it has been resolved.

This has been resolved, the fix will go live in the next QuNex version. @clara.fonteneau if you need the fix earlier contact me offline, there is a hack/workaround that bypasses this bug.