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Structured validation results #1104

Merged
merged 124 commits into from
Oct 28, 2022
Merged

Structured validation results #1104

merged 124 commits into from
Oct 28, 2022

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jwodder
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@jwodder jwodder commented Aug 18, 2022

Closes #943.

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codecov bot commented Aug 18, 2022

Codecov Report

Base: 88.05% // Head: 88.04% // Decreases project coverage by -0.00% ⚠️

Coverage data is based on head (6205109) compared to base (1e43339).
Patch coverage: 82.57% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1104      +/-   ##
==========================================
- Coverage   88.05%   88.04%   -0.01%     
==========================================
  Files          73       73              
  Lines        8586     8727     +141     
==========================================
+ Hits         7560     7684     +124     
- Misses       1026     1043      +17     
Flag Coverage Δ
unittests 88.04% <82.57%> (-0.01%) ⬇️

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

Impacted Files Coverage Δ
dandi/files/zarr.py 86.86% <20.00%> (+1.76%) ⬆️
dandi/files/bases.py 76.72% <58.33%> (+0.94%) ⬆️
dandi/cli/cmd_validate.py 73.86% <63.49%> (-15.03%) ⬇️
dandi/pynwb_utils.py 83.48% <77.77%> (-0.31%) ⬇️
dandi/files/bids.py 93.93% <96.00%> (+0.12%) ⬆️
dandi/cli/tests/test_cmd_validate.py 100.00% <100.00%> (ø)
dandi/tests/fixtures.py 98.19% <100.00%> (+0.11%) ⬆️
dandi/tests/test_files.py 100.00% <100.00%> (ø)
dandi/tests/test_validate.py 100.00% <100.00%> (ø)
dandi/validate.py 100.00% <100.00%> (ø)
... and 2 more

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This pull request introduces 1 alert when merging 72a51fb into ef097cc - view on LGTM.com

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@TheChymera
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@jwodder thank you, yes, the error no longer happens. Apparently there was another one, but I fixed that as well. @yarikoptic ready for merge?

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ok, let's merge and then tune up from there. Thanks @TheChymera and @jwodder for the reviews.

@yarikoptic yarikoptic added the minor Increment the minor version when merged label Oct 28, 2022
@yarikoptic yarikoptic merged commit 48a222f into master Oct 28, 2022
@yarikoptic yarikoptic deleted the gh-943 branch October 28, 2022 14:17
selected_dataset = os.path.join(bids_examples, dataset)
validation_result = validate_bids(selected_dataset, report=True)
for i in validation_result:
assert not hasattr(i, "severtiy")
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@TheChymera Is this typo deliberate? If it is, what's the point? If it's not, shouldn't you instead be testing that the attribute is None?

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@jwodder thank you for spotting this, indeed it was an error, and further, it was giving a false positive arising from an upstream oversight. Will sumbit a fix PR once the reference data is fixed, since currently fixing this would fail due to the data being broken.

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@jwodder fix is here → #1148

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validate: RF to collect/output more informative structured records
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