Handling FileNotFoundError in BIDSLayout Initialization when is_derivative=True and validate=False, also resolves #1050 #1049
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Description of the "is_derivative" parameter of BIDSLayout states that this parameter "can be enabled along with validate=False to index derivatives without dataset_description.json." However, the initialization method of BIDSLayout calls "validate_derivative_path(root)" on line 141, which eventually leads to a "FileNotFoundError" as the this function then tries to read a dataset_description.json file that does not exist. This commit fixes this issue by catching this FileNotFoundError and restores intended functionality.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1049 +/- ##
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Coverage 89.80% 89.80%
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Files 63 63
Lines 7178 7178
Branches 1374 1374
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Hits 6446 6446
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effigies
reviewed
May 5, 2024
bids/layout/index.py
Outdated
| @@ -265,6 +265,7 @@ def _index_metadata(self): | |||
| # ensure we are returning objects | |||
| filters['return_type'] = 'object' | |||
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| ext_key = 'extensions' if 'extensions' in filters else 'extension' | |||
There was a problem hiding this comment.
This was correctly removed, but ext_key failed to get changed to 'extension' in the next 5 lines. Could you apply that?
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Just to make sure I understand correctly, would you like me to remove the line I added and change the next 5 lines to this instead:
if filters.get('extension'):
filters['extension'] = listify(filters['extension'])
# ensure json files are being indexed
if '.json' not in filters['extension']:
filters['extension'].append('.json')
alperkent
changed the title
effigies
approved these changes
May 10, 2024
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This pull request addresses an issue encountered when initializing a
BIDSLayoutwith a derivatives directory that does not contain adataset_description.jsonfile. Previously, aFileNotFoundErrorwould be raised in such cases, even whenvalidate=Falsewas set.The proposed change allows for a
FileNotFoundErrorto be caught and handled gracefully during the initialization of aBIDSLayout. This allows for the indexing of derivatives without adataset_description.jsonfile, aligning with the description ofis_derivativeparameter that states this parameter "can be enabled along with validate=False to index derivatives without dataset_description.json."The specific change involves modifying the exception handling at line 142 in
layout.pyto catch bothBIDSValidationErrorandFileNotFoundError. This ensures that the initialization process can continue even if thedataset_description.jsonfile is missing.