🐛__file__ is not defined error on check_for_s3 node

[birajstha]

Describe the bug

Node: cpac_pipeline_ccs-options_anat-only_sub-NDARAD481FXF_ses-1.gather_T1w-brain-template-mask-ccs.check_for_s3
Working directory: /ocean/projects/med250004p/bshresth/projects/surface_pipelines/outputs1/working/pipeline_ccs-options_anat-only/cpac_pipeline_ccs-options_anat-only_sub-NDARAD481FXF_ses-1/gather_T1w-brain-template-mask-ccs/check_for_s3

Node inputs:

creds_path = None
dl_dir = /ocean/projects/med250004p/bshresth/projects/surface_pipelines/outputs1/working/pipeline_ccs-options_anat-only
file_path = /ccs_template/MNI152_T1_1mm_first_brain_mask.nii.gz
function_str = CPAC.utils.datasource.check_for_s3
img_type = other

Traceback (most recent call last):
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/code/CPAC/pipeline/nipype_pipeline_engine/engine.py", line 478, in run
    return super().run(updatehash)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/share/fsl/6.0/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node check_for_s3.

Traceback:
	Traceback (most recent call last):
	  File "/code/CPAC/pipeline/nipype_pipeline_engine/monkeypatch.py", line 40, in run
	    runtime = self._run_interface(runtime)
	  File "/code/CPAC/utils/interfaces/function/function.py", line 332, in _run_interface
	    out = function_handle(**args)
	  File "<string>", line 97, in check_for_s3
	NameError: name '__file__' is not defined

To reproduce

You can run this in the current develop branch

#!/bin/bash
#SBATCH -N 1
#SBATCH -p RM-shared
#SBATCH -t 60:00:00
#SBATCH --ntasks-per-node=2

MED=/ocean/projects/med250004p
DATA=s3://fcp-indi/data/Projects/HBN/MRI/Site-SI
#/ocean/projects/med250004p/bshresth/projects/data
OUTPUT=/ocean/projects/med250004p/bshresth/projects/surface_pipelines/outputs1
IMAGE=/ocean/projects/med250004p/bshresth/projects/cpac_nightly.sif

PIPELINE=/ocean/projects/med250004p/bshresth/projects/surface_pipelines/pipelines/pipeline1.yml

subject=sub-NDARAD481FXF
#sub-NDARINV003RTV85

repo=/ocean/projects/med250004p/bshresth/projects/C-PAC
singularity run \
    -B ${repo}/CPAC:/code/CPAC\
    -B $MED \
    -B $OUTPUT:$OUTPUT $IMAGE $DATA $OUTPUT participant \
    --num_ants_threads 1 \
    --skip_bids_validator \
    --n_cpus 2 \
    --mem_gb 14 \
    --pipeline_file $PIPELINE \
    --participant_label $subject

Preconfig

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

Custom pipeline configuration

Its on all pipeline but, I got when running this

FROM: anat-only
pipeline_setup:
  pipeline_name: ccs-options anat-only
  freesurfer_dir: /ocean/projects/med250004p/bshresth/projects/solo_fs_runs
  system_config:
    maximum_memory_per_participant: 10.0
    random_seed: 1
    raise_insufficient: Off

segmentation:

  # Automatically segment anatomical images into white matter, gray matter,
  # and CSF based on prior probability maps.
  run: On
  tissue_segmentation:

    # using: ['FSL-FAST', 'Template_Based', 'ANTs_Prior_Based', 'FreeSurfer']
    # this is a fork point
    using: [FreeSurfer]
surface_analysis:

  # Run freesurfer_abcd_preproc to obtain preprocessed T1w for reconall
  abcd_prefreesurfer_prep:
    run: off


  freesurfer:
    run_reconall: Off

    # Ingress freesurfer recon-all folder
    ingress_reconall: On



anatomical_preproc:
  run: On

  brain_extraction:
    run: On
    # using: ['3dSkullStrip', 'BET', 'UNet', 'niworkflows-ants', 'FreeSurfer-ABCD', 'FreeSurfer-BET-Tight', 'FreeSurfer-BET-Loose', 'FreeSurfer-Brainmask']
    # this is a fork option
    using: ['FreeSurfer-BET-Tight', 'FreeSurfer-BET-Loose', 'FreeSurfer-Brainmask']

  # N4 bias field correction via ANTs
  n4_bias_field_correction:

    # this is a fork option
    run: [Off]

    # An integer to resample the input image to save computation time. Shrink factors <= 4 are commonly used.
    shrink_factor: 2

Run command

No response

Expected behavior

Error resolved

Acceptance criteria

Error Resolved

Screenshots

No response

C-PAC version

No response

Container platform

No response

Docker and/or Singularity version(s)

No response

Additional context

No response

[shnizzedy]

This is overdue for an update anyway, but I wonder why it suddenly broke? It looks like that section of code is over 5 years old