Merging validation functions

[TheChymera]

Currently non-working. The main problem seems to be that the old (functional) design ran the validation from validate.py, whereas the new (object-oriented) design runs it as part of the asset instantiation. This makes a lot of things a bit confusing. Currently the immediate issue is that if we validate via BIDS object instantiation, we get the same error reported over and over. Probably has to do with the vanilla validation function using yield versus return... Will continue digging, though comments are appreciated @yarikoptic @jwodder

I'm currently testing this on DANDI:000108 :

(dev) chymera@decohost ~/.local/share/datalad $ dandi validate 000108
2022-11-09 18:57:11,195 [ WARNING] BIDSVersion `1.4.0` 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.
2022-11-09 18:57:12,329 [   ERROR] The `README(?P<extension>|\.md|\.rst|\.txt)` regex pattern file required by BIDS was not found.
..
ValidationResult(id='BIDS.MANDATORY_FILE_MISSING_PLACEHOLDER', origin=ValidationOrigin(name='bidsschematools', version='0.6.0'), scope=<Scope.DATASET: 'dataset'>, asset_paths=None, within_asset_paths=None, dandiset_path=None, dataset_path=None, message='BIDS-required file is not present.', metadata=None, path=None, path_regex='README(?P<extension>|\\.md|\\.rst|\\.txt)', severity=<Severity.ERROR: 'ERROR'>)
ii
ValidationResult(id='BIDS.MANDATORY_FILE_MISSING_PLACEHOLDER', origin=ValidationOrigin(name='bidsschematools', version='0.6.0'), scope=<Scope.DATASET: 'dataset'>, asset_paths=None, within_asset_paths=None, dandiset_path=None, dataset_path=None, message='BIDS-required file is not present.', metadata=None, path=None, path_regex='README(?P<extension>|\\.md|\\.rst|\\.txt)', severity=<Severity.ERROR: 'ERROR'>)
ii
ValidationResult(id='BIDS.MATCH', origin=ValidationOrigin(name='bidsschematools', version='0.6.0'), scope=<Scope.FILE: 'file'>, asset_paths=None, within_asset_paths=None, dandiset_path=PosixPath('/home/chymera/.local/share/datalad/000108'), dataset_path=PosixPath('/home/chymera/.local/share/datalad/000108'), message=None, metadata={}, path=PosixPath('/home/chymera/.local/share/datalad/000108/dataset_description.json'), path_regex=None, severity=None)
kk
ValidationResult(id='BIDS.MATCH', origin=ValidationOrigin(name='bidsschematools', version='0.6.0'), scope=<Scope.FILE: 'file'>, asset_paths=None, within_asset_paths=None, dandiset_path=PosixPath('/home/chymera/.local/share/datalad/000108'), dataset_path=PosixPath('/home/chymera/.local/share/datalad/000108'), message=None, metadata={}, path=PosixPath('/home/chymera/.local/share/datalad/000108/dataset_description.json'), path_regex=None, severity=None)
kk
/home/chymera/.local/share/datalad/000108/dataset_description.json
kk1
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..
Counter({'BIDS.MANDATORY_FILE_MISSING_PLACEHOLDER': 3250})
2022-11-09 18:57:12,835 [    INFO] Logs saved in /home/chymera/.cache/dandi-cli/log/20221109235709Z-11928.log
Error: No active exception to reraise

[lgtm-com]

This pull request introduces 1 alert when merging 7261a91 into c66fd18 - view on LGTM.com

new alerts:

• 1 for Unreachable code

[codecov]

Codecov Report

Base: 88.29% // Head: 89.08% // Increases project coverage by +0.78% 🎉

Coverage data is based on head (9aae3bf) compared to base (c66fd18).
Patch coverage: 84.39% of modified lines in pull request are covered.

❗ Current head 9aae3bf differs from pull request most recent head b4e2e59. Consider uploading reports for the commit b4e2e59 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1154      +/-   ##
==========================================
+ Coverage   88.29%   89.08%   +0.78%     
==========================================
  Files          73       76       +3     
  Lines        8800     9444     +644     
==========================================
+ Hits         7770     8413     +643     
- Misses       1030     1031       +1     

Flag	Coverage Δ
unittests	89.08% <84.39%> (+0.78%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dandi/cli/cmd_validate.py	73.03% <0.00%> (-0.83%)	⬇️
dandi/tests/test_dandiapi.py	100.00% <ø> (ø)
dandi/support/pyout.py	90.00% <50.00%> (ø)
dandi/dandiapi.py	87.11% <59.37%> (-1.56%)	⬇️
dandi/pynwb_utils.py	82.68% <66.66%> (-0.80%)	⬇️
dandi/metadata.py	87.46% <68.00%> (+0.44%)	⬆️
dandi/cli/cmd_ls.py	76.88% <83.33%> (+1.31%)	⬆️
dandi/files/_private.py	98.11% <87.50%> (+0.07%)	⬆️
dandi/organize.py	83.54% <97.29%> (+0.28%)	⬆️
dandi/cli/cmd_organize.py	100.00% <100.00%> (ø)
... and 25 more

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[lgtm-com]

This pull request introduces 1 alert when merging 242be00 into c66fd18 - view on LGTM.com

new alerts:

• 1 for Unreachable code

[yarikoptic]

@TheChymera what is the roadmap for this PR?

[TheChymera]

Merge conflicts after #1164 (which did part of what I was trying to do here but just for ls). After going through open validation issues probably required to proceed on them, so fixing this up.

[TheChymera]

ok, so this blew up in my face :(