cubids-group filepath referenced before assignment in get_param_groups_from_key_group

[ericearl]

A very "vanilla" call to cubids-group with a dataset and a prefix leads to:

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Traceback (most recent call last):
  File "/home/earlea/.local/bin/cubids-group", line 8, in <module>
    sys.exit(cubids_group())
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cli.py", line 272, in cubids_group
    bod.get_CSVs(str(opts.output_prefix),)
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 941, in get_CSVs
    big_df, summary = self.get_param_groups_dataframes()
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 783, in get_param_groups_dataframes
    self.get_param_groups_from_key_group(key_group)
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 759, in get_param_groups_from_key_group
    if mod in filepath:
UnboundLocalError: local variable 'filepath' referenced before assignment

It looks like filepath is only defined on line 749 as a variable in a for loop:

for filepath in matching_files:

I think this means that if the iterable of matching_files is empty, then filepath would not be defined. Since matching_files comes from:

matching_files = self.layout.get(return_type="file", scope="self", regex_search=True, **key_entities)

Do you think I might be missing some certainly expected files or metadata?

[ericearl]

If it helps, I added a print('matching_files length', len(matching_files)) to get_param_groups_from_key_group and a print(key_groups) to get_param_groups_dataframes. This is what I got:

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['acquisition-2d_datatype-anat_reconstruction-scic_suffix-FLAIR', 'acquisition-2d_datatype-anat_suffix-FLAIR', 'acquisition-3d_datatype-anat_reconstruction-scic_suffix-FLAIR', 'acquisition-3d_datatype-anat_suffix-FLAIR', 'acquisition-cube_datatype-anat_reconstruction-scic_suffix-T2w', 'acquisition-cube_datatype-anat_suffix-T2w', 'acquisition-dwi_datatype-fmap_fmap-fieldmap_suffix-fieldmap', 'acquisition-dwi_datatype-fmap_suffix-magnitude', 'acquisition-fspgr_datatype-anat_reconstruction-scic_run-1_suffix-T1w', 'acquisition-fspgr_datatype-anat_reconstruction-scic_run-2_suffix-T1w', 'acquisition-fspgr_datatype-anat_reconstruction-scic_suffix-T1w', 'acquisition-highreshippo_datatype-anat_suffix-T1w', 'acquisition-mprage_datatype-anat_reconstruction-scic_suffix-T1w', 'acquisition-mprage_datatype-anat_suffix-T1w', 'acquisition-resting_datatype-fmap_fmap-fieldmap_suffix-fieldmap', 'acquisition-resting_datatype-fmap_suffix-magnitude', 'datatype-anat_reconstruction-scic_suffix-T2starw', 'datatype-dwi_direction-flipped_suffix-dwi', 'datatype-dwi_direction-unflipped_suffix-dwi', 'datatype-dwi_suffix-dwi', 'datatype-func_direction-reverse_suffix-bold_task-rest', 'datatype-func_run-1_suffix-bold_task-rest', 'datatype-func_run-2_suffix-bold_task-rest', 'datatype-func_suffix-bold_task-rest', 'datatype-perf_suffix-asl']
matching_files length 146
matching_files length 151
matching_files length 25
matching_files length 50
matching_files length 89
matching_files length 242
matching_files length 66
matching_files length 66
matching_files length 1
matching_files length 1
matching_files length 63
matching_files length 0
Traceback (most recent call last):
  File "/home/earlea/.local/bin/cubids-group", line 8, in <module>
    sys.exit(cubids_group())
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cli.py", line 272, in cubids_group
    bod.get_CSVs(str(opts.output_prefix),)
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 943, in get_CSVs
    big_df, summary = self.get_param_groups_dataframes()
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 785, in get_param_groups_dataframes
    self.get_param_groups_from_key_group(key_group)
  File "/home/earlea/.local/lib/python3.8/site-packages/cubids/cubids.py", line 760, in get_param_groups_from_key_group
    if mod in filepath:
UnboundLocalError: local variable 'filepath' referenced before assignment

So I think this means my key_group known as "acquisition-highreshippo_datatype-anat_suffix-T1w" is finding nothing with self.layout.get.

[ericearl]

For what it's worth, I found data in the sourcedata/ folder organized much like the BIDS root folder. So while I had no results with an ls of sub-*/ses-*/anat/*highreshippo*, I did have ls results among sourcedata/sub-*/ses-*/anat/*highreshippo*.

I do still think cubids-group should fail or raise an exception more gracefully in a case like this though.

[scovitz]

Flagging this again. Yes our error messages need to be more robust/descriptive, which is flagged in #253, so I'm closing this one.