cubids apply renaming variants bug

[B-Sevchik]

Summary

Running cubids apply is not re-naming variants explicitly for the fmap variants. Case where cubids failed:

• original name of entity set: acquisition-dwi_datatype-fmap_direction-AP_fmap-epi_run-01_suffix-epi; acquisition-dwi_datatype-fmap_direction-PA_fmap-epi_run-01_suffix-epi; acquisition-fmri_datatype-fmap_direction-AP_fmap-epi_run-01_suffix-epi; acquisition-fmri_datatype-fmap_direction-PA_fmap-epi_run-01_suffix-epi
• suggested new name entity set: acquisition-dwiVARIANTObliquity_datatype-fmap_direction-AP_fmap-epi_run-01_suffix-epi; acquisition-dwiVARIANTObliquity_datatype-fmap_direction-PA_fmap-epi_run-01_suffix-epi; acquisition-fmriVARIANTObliquity_datatype-fmap_direction-AP_fmap-epi_run-01_suffix-epi; acquisition-fmriVARIANTObliquity_datatype-fmap_direction-PA_fmap-epi_run-01_suffix-epi
• original name of file example: /sub-20812/ses-3/fmap/sub-20812_ses-3_acq-dwi_dir-AP_run-01_epi.nii.gz
• suggested rename of file example: /sub-20812/ses-3/fmap/sub-20812_ses-3_acq-VARIANTObliquity_dwi_dir-AP_run-01_epi.nii.gz

Additional details

• CuBIDS version: 1.1.1.dev137+g89792af
• Datalad version: datalad 1.1.5

What were you trying to do?

I was trying to re-name the fmap variants according to the suggested rename in the summary tsv file.

What did you expect to happen?

I expected that running cubids apply would successfully re-name the fmap variants, and the new summary tsv file that would be produced would not have any suggested renames, but rather the variant re-name would show up successfully in the new KeyParamGroup and EntitySet columns.

What actually happened?

Running cubids apply did not change the names of the fmap scans, and the suggested rename is still in RenameEntitySet column.

Reproducing the bug

cd /cbica/projects/executive_function/data/bids/
/cbica/projects/executive_function/miniforge3/envs/cubids/bin/cubids apply \
    /cbica/projects/executive_function/data/bids/EF_bids_data_DataLad \
    /cbica/projects/executive_function/data/bids/EF_bids_data_DataLad/code/CuBIDS/v24_edited_summary.tsv \
    /cbica/projects/executive_function/data/bids/EF_bids_data_DataLad/code/CuBIDS/v24_files.tsv \
    v25 

command above is from cubids_apply.sh, the script that submits cubids apply to be run as a job on cubic

[tsalo]

Under "Reproducing the bug", can you replace your script with the cubids apply command in the script?