validate-bids doesn't report an error on a file with incorrect suffix

[yarikoptic]

$> dandi --version
0.39.4+2.gb73f44d1
(dev3) 1 21468 [1].....................................:Thu 28 Apr 2022 06:08:44 PM EDT:.
lena:/tmp/test
$> dandi validate-bids sub-MITU01/ses-MR/sub-MITU01_ses-MR_SSSPDmap.nii.gz
2022-04-28 18:08:50,698 [ WARNING] BIDSVersion 1.5.0 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.
2022-04-28 18:08:51,321 [    INFO] Logs saved in /home/yoh/.cache/dandi-cli/log/20220428220849Z-1783177.log

there is no SSSPDmap, only PDmap:

(git)lena:~/proj/dandi/dandi-cli-master[master]
$> git grep PDmap
dandi/support/bids/schemadata/1.7.0+012+dandi001/objects/suffixes.yaml:    **Change:** Replaced by `PDw` or `PDmap`.
dandi/support/bids/schemadata/1.7.0+012+dandi001/objects/suffixes.yaml:PDmap:
dandi/support/bids/schemadata/1.7.0+012+dandi001/rules/datatypes/anat.yaml:  - PDmap
dandi/support/bids/schemadata/1.7.0+012/objects/suffixes.yaml:    **Change:** Replaced by `PDw` or `PDmap`.
dandi/support/bids/schemadata/1.7.0+012/objects/suffixes.yaml:PDmap:
dandi/support/bids/schemadata/1.7.0+012/rules/datatypes/anat.yaml:  - PDmap

[yarikoptic]

what does it validate really? doesn't even complain if sub / ses label doesn't match between folders and files:

$> dandi validate-bids sub-MITU02/ses-MR2/sub-MITU01_ses-MR_SSSPDmap.nii.gz
2022-04-28 18:11:09,291 [ WARNING] BIDSVersion 1.5.0 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.
2022-04-28 18:11:09,873 [    INFO] Logs saved in /home/yoh/.cache/dandi-cli/log/20220428221107Z-1784078.log
(dev3) 1 21475 [1].....................................:Thu 28 Apr 2022 06:11:10 PM EDT:.
lena:/tmp/test
$> cat /home/yoh/.cache/dandi-cli/log/20220428221107Z-1784078.log
2022-04-28T18:11:07-0400 [INFO    ] dandi 1784078:140317588195136 dandi v0.39.4+2.gb73f44d1, hdmf v3.1.1, pynwb v2.0.0, h5py v3.6.0
2022-04-28T18:11:07-0400 [INFO    ] dandi 1784078:140317588195136 sys.argv = ['/home/yoh/proj/dandi/dandi-cli-master/venvs/dev3/bin/dandi', 'validate-bids', 'sub-MITU02/ses-MR2/sub-MITU01_ses-MR_SSSPDmap.nii.gz']
2022-04-28T18:11:07-0400 [INFO    ] dandi 1784078:140317588195136 os.getcwd() = /tmp/test
2022-04-28T18:11:08-0400 [DEBUG   ] urllib3.connectionpool 1784078:140317588195136 Starting new HTTPS connection (1): rig.mit.edu:443
2022-04-28T18:11:08-0400 [DEBUG   ] urllib3.connectionpool 1784078:140317588195136 https://rig.mit.edu:443 "GET /et/projects/dandi/dandi-cli HTTP/1.1" 200 579
2022-04-28T18:11:08-0400 [DEBUG   ] dandi 1784078:140317588195136 Running a newer version (0.39.4+2.gb73f44d1) of dandi/dandi-cli than available (0.39.4)
2022-04-28T18:11:08-0400 [DEBUG   ] h5py._conv 1784078:140317588195136 Creating converter from 7 to 5
2022-04-28T18:11:08-0400 [DEBUG   ] h5py._conv 1784078:140317588195136 Creating converter from 5 to 7
2022-04-28T18:11:08-0400 [DEBUG   ] h5py._conv 1784078:140317588195136 Creating converter from 7 to 5
2022-04-28T18:11:08-0400 [DEBUG   ] h5py._conv 1784078:140317588195136 Creating converter from 5 to 7
2022-04-28T18:11:09-0400 [WARNING ] dandi 1784078:140317588195136 BIDSVersion 1.5.0 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.
2022-04-28T18:11:09-0400 [INFO    ] dandi 1784078:140317588195136 Logs saved in /home/yoh/.cache/dandi-cli/log/20220428221107Z-1784078.log

edit: here is the tarball of that "tricky" case -- http://www.onerussian.com/tmp/test-bids.tgz

[TheChymera]

@yarikoptic it marks the file as invalid if there is a mismatch, just that the function only returns a dictionary of the summary, and optionally writes issues it found to the report file via -r.

This should additionally log the errors: #992

[TheChymera]

chymera@decohost ~ $ wget http://www.onerussian.com/tmp/test-bids.tgz -q
chymera@decohost ~ $ tar xvf test-bids.tgz
test/
test/dataset_description.json
test/sub-MITU02/
test/sub-MITU02/ses-MR2/
test/sub-MITU02/ses-MR2/sub-MITU01_ses-MR_SSSPDmap.nii.gz
chymera@decohost ~ $ dandi validate-bids test -r
2022-04-29 08:56:51,060 [ WARNING] A newer version (0.39.4) of dandi/dandi-cli is available. You are using 0.39.2+47.gb73f44d.dirty
2022-04-29 08:56:51,157 [    INFO] Note: NumExpr detected 12 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2022-04-29 08:56:51,158 [    INFO] NumExpr defaulting to 8 threads.
2022-04-29 08:56:52,377 [ WARNING] BIDSVersion 1.5.0 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.
2022-04-29 08:56:53,148 [    INFO] BIDS validation log written to /home/chymera/.cache/dandi-cli/log/bids-validator-report_20220429125653Z-1736.log
2022-04-29 08:56:53,149 [   ERROR] The `.*?/README$` regex pattern file required by BIDS was not found.
2022-04-29 08:56:53,149 [   ERROR] The `.*?/CHANGES$` regex pattern file required by BIDS was not found.
2022-04-29 08:56:53,149 [ WARNING] The `/home/chymera/test/sub-MITU02/ses-MR2/sub-MITU01_ses-MR_SSSPDmap.nii.gz` file was not matched by any regex schema entry.
2022-04-29 08:56:53,149 [    INFO] Logs saved in /home/chymera/.cache/dandi-cli/log/20220429125650Z-1736.log
chymera@decohost ~ $ ppb /home/chymera/.cache/dandi-cli/log/bids-validator-report_20220429125653Z-1736.log
Upload succeeded:
https://ppb.chymera.eu/fe88e3.log

[yarikoptic]

now it is #1037 I think

(git-annex)lena:~/proj/dandi/dandisets/000108[draft]git
$> dandi validate-bids sub-MITU02/ses-20210521h17m17s06/micr/sub-MITU01_ses-20210521h17m17s06_sample-178_stain-NN_run-1_chunk-1_SPIM.ome.zarr                                                    
2022-07-08 19:06:33,800 [ WARNING] A newer version (0.44.1) of dandi/dandi-cli is available. You are using 0.39.6+39.g8139966
2022-07-08 19:06:34,992 [ 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.
2022-07-08 19:06:35,655 [    INFO] Logs saved in /home/yoh/.cache/dandi-cli/log/20220708230633Z-424963.log
Error: list index out of range

while testing the 0.39.6+39.g8139966 of #1011

[TheChymera]

@yarikoptic This is not the same issue as the initial one reported, and that particular issue was just missing reporting which has been fixed a while ago.