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dandi / dandi-cli

DANDI command line client to facilitate common operations
https://dandi.readthedocs.io/
Apache License 2.0
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dandi validate-bids crashes with IndexError: list index out of range #1037

Closed yarikoptic closed 2 years ago

yarikoptic commented 2 years ago

trying on datalad dandiset of 000108 (note -- is being updated)

(git-annex)lena:~/proj/dandi/dandisets/000108[draft]git
$> dandi --pdb validate-bids sub-MITU01/ses-20210521h17m17s06/micr/sub-MITU01_ses-20210521h17m17s06_sample-178_stain-NN_run-1_chunk-1_SPIM.ome.zarr
2022-06-30 16:37:17,222 [ WARNING] BIDSVersion 1.4.0 is less than the minimal working 1.7.0+012+dandi001. Falling back to 1.7.0+012+dandi001. To force the usage of earlier versions specify them explicitly when calling the validator.
2022-06-30 16:37:18,059 [    INFO] Logs saved in /home/yoh/.cache/dandi-cli/log/20220630203713Z-3420148.log
Traceback (most recent call last):
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/bin/dandi", line 33, in <module>
    sys.exit(load_entry_point('dandi', 'console_scripts', 'dandi')())
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/lib/python3.9/site-packages/click/decorators.py", line 38, in new_func
    return f(get_current_context().obj, *args, **kwargs)
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/cli/base.py", line 102, in wrapper
    return f(*args, **kwargs)
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/cli/cmd_validate.py", line 34, in validate_bids
    validation_result = validate_bids_(
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/validate.py", line 36, in validate_bids
    return validate_bids_(
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/bids_validator_xs.py", line 735, in validate_bids
    validation_result = validate_all(
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/bids_validator_xs.py", line 401, in validate_all
    paths_list = _get_paths(bids_paths)
  File "/home/yoh/proj/dandi/dandi-cli-master/dandi/bids_validator_xs.py", line 81, in _get_paths
    if "\\" in path_list[0]:
IndexError: list index out of range

> /home/yoh/proj/dandi/dandi-cli-master/dandi/bids_validator_xs.py(81)_get_paths()
-> if "\\" in path_list[0]:
yarikoptic commented 2 years ago

any progress resolving this issue @TheChymera ?

TheChymera commented 2 years ago

Just as a general point, IndexError: list index out of range at that point in the logic is caused by _get_paths() not returning any files. The fix is in https://github.com/dandi/dandi-cli/pull/1050 , and it's been fixed upstream for a while:

chymera@darkhost ~/src/bids-specification/tools/schemacode $ python -c "from bidsschematools import validator; validator.validate_bids('/home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/', debug=True)"
2022-07-26 20:29:07,181 [ WARNING] BIDSVersion `1.7.0` is less than the minimal working `schema`. Falling back to `schema`. To force the usage of earlier versions specify them explicitly when calling the validator.
Checking file `/home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/`.
Trying file types:
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star|FLASH|PD)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_(T1map|T2map|T2starmap|R1map|R2map|R2starmap|PDmap|MTRmap|MTsat|UNIT1|T1rho|MWFmap|MTVmap|PDT2map|Chimap|S0map|M0map)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_mod-(?P<modality>[0-9a-zA-Z]+))_defacemask(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_echo-(?P<echo>[0-9]*[1-9]+[0-9]*)(|_part-(?P<part>mag|phase|real|imag))_(MESE|MEGRE)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))_flip-(?P<flip>[0-9]*[1-9]+[0-9]*)(|_part-(?P<part>mag|phase|real|imag))_VFA(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*)(|_part-(?P<part>mag|phase|real|imag))_IRT1(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))(|_flip-(?P<flip>[0-9]*[1-9]+[0-9]*))_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*)(|_part-(?P<part>mag|phase|real|imag))_MP2RAGE(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))_flip-(?P<flip>[0-9]*[1-9]+[0-9]*)_mt-(?P<mtransfer>on|off)(|_part-(?P<part>mag|phase|real|imag))_(MPM|MTS)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_mt-(?P<mtransfer>on|off)(|_part-(?P<part>mag|phase|real|imag))_MTR(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)beh/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(stim|physio)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)beh/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_(events|beh)(\.tsv|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)dwi/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_dwi(\.nii\.gz|\.nii|\.json|\.bvec|\.bval)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)dwi/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_sbref(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)dwi/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(physio|stim)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_eeg(\.json|\.edf|\.vhdr|\.vmrk|\.eeg|\.set|\.fdt|\.bdf)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_channels(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_space-(?P<space>[0-9a-zA-Z]+))_coordsystem\.json$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_space-(?P<space>[0-9a-zA-Z]+))_electrodes(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_events(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_photo(\.jpg|\.png|\.tif)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)eeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(physio|stim)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_(phasediff|phase1|phase2|magnitude1|magnitude2|magnitude|fieldmap)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))_dir-(?P<direction>[0-9a-zA-Z]+)(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_(epi|m0scan)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_flip-(?P<flip>[0-9]*[1-9]+[0-9]*)(|_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_TB1DAM(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_echo-(?P<echo>[0-9]*[1-9]+[0-9]*)_flip-(?P<flip>[0-9]*[1-9]+[0-9]*)(|_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_TB1EPI(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))(|_flip-(?P<flip>[0-9]*[1-9]+[0-9]*))(|_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_(TB1AFI|TB1TFL|TB1RFM|RB1COR)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))_flip-(?P<flip>[0-9]*[1-9]+[0-9]*)_inv-(?P<inversion>[0-9]*[1-9]+[0-9]*)(|_part-(?P<part>mag|phase|real|imag))_TB1SRGE(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)fmap/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_(TB1map|RB1map)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)func/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))(|_part-(?P<part>mag|phase|real|imag))_(bold|cbv|sbref)(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)func/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_echo-(?P<echo>[0-9]*[1-9]+[0-9]*))_phase(\.nii\.gz|\.nii|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)func/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_events(\.tsv|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)func/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_dir-(?P<direction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(physio|stim)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_ieeg(\.mefd/|\.json|\.edf|\.vhdr|\.eeg|\.vmrk|\.set|\.fdt|\.nwb)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_channels(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_space-(?P<space>[0-9a-zA-Z]+))_coordsystem\.json$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_space-(?P<space>[0-9a-zA-Z]+))_electrodes(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_events(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_photo(\.jpg|\.png|\.tif)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)ieeg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(physio|stim)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_proc-(?P<processing>[0-9a-zA-Z]+))(|_split-(?P<split>[0-9]*[1-9]+[0-9]*))_meg(/|\.ds/|\.json|\.fif|\.sqd|\.con|\.raw|\.ave|\.mrk|\.kdf|\.mhd|\.trg|\.chn)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_meg\.dat$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_meg\.fif$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_headshape(\..*?|\.pos)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_task-(?P<task>[0-9a-zA-Z]+))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_space-(?P<space>[0-9a-zA-Z]+))_markers(\.sqd|\.mrk)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_coordsystem\.json$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_proc-(?P<processing>[0-9a-zA-Z]+))_channels(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))_events(\.json|\.tsv)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))_photo(\.jpg|\.png|\.tif)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)meg/sub-(?P=subject)(|_ses-(?P=session))_task-(?P<task>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_proc-(?P<processing>[0-9a-zA-Z]+))(|_recording-(?P<recording>[0-9a-zA-Z]+))_(physio|stim)(\.tsv\.gz|\.json)$
    * /home/chymera/src/bids-examples/micr_SEMzarr/sub-01/ses-01/micr/sub-01_ses-01_sample-A_SPIM.ome.zarr/, with pattern: .*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)micr/sub-(?P=subject)(|_ses-(?P=session))_sample-(?P<sample>[0-9a-zA-Z]+)(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_stain-(?P<stain>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9]*[1-9]+[0-9]*))(|_chunk-(?P<chunk>[0-9]*[1-9]+[0-9]*))_(TEM|SEM|uCT|BF|DF|PC|DIC|FLUO|CONF|PLI|CARS|2PE|MPE|SR|NLO|OCT|SPIM)(\.ome\.tif|\.ome\.btf|\.ome\.zarr/|\.png|\.tif|\.json)$
Match identified.
2022-07-26 20:29:08,101 [   ERROR] The `.*?/README(|\.md|\.rst|\.txt)$` regex pattern file required by BIDS was not found.
2022-07-26 20:29:08,102 [   ERROR] The `.*?/dataset_description(\.json)$` regex pattern file required by BIDS was not found.