feat: add validation for duplicate structure acronyms#734
Merged
IgorTatarnikov merged 6 commits intobrainglobe:mainfrom Jan 12, 2026
Merged
feat: add validation for duplicate structure acronyms#734IgorTatarnikov merged 6 commits intobrainglobe:mainfrom
IgorTatarnikov merged 6 commits intobrainglobe:mainfrom
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Closes brainglobe#666 Added `validate_unique_acronyms` function that checks for duplicate acronyms in atlas structures during validation. Duplicate acronyms are incompatible with brainglobe-atlasapi as acronyms are used as primary keys to fetch region details. Changes: - Add `validate_unique_acronyms` validation function - Register function in `get_all_validation_functions()` - Add test for failure case with duplicate acronyms
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Pull request overview
This PR adds validation to detect duplicate structure acronyms during atlas generation. Duplicate acronyms are problematic because they're used as primary keys to fetch region details in brainglobe-atlasapi.
Key changes:
- Added
validate_unique_acronyms()function that checks for duplicate acronyms in atlas structures - Integrated the validation into the existing validation pipeline
- Added test coverage for the duplicate detection failure case
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
brainglobe_atlasapi/atlas_generation/validate_atlases.py |
Implements the validate_unique_acronyms() function and adds it to validation function lists |
tests/atlasgen/test_validation.py |
Adds test case for duplicate acronym detection failure scenario |
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This was referenced Jan 9, 2026
IgorTatarnikov
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Jan 12, 2026
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This is great, thank you @thisisrick25!
I had a few comments regarding the implementation. We can decrease the time complexity of this code by adjusting the approach slightly.
IgorTatarnikov
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LGTM 🚀 Thanks @thisisrick25
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Description
What is this PR
Why is this PR needed?
Closes #666
Duplicate structure acronyms are incompatible with the current implementation of
brainglobe-atlasapias acronyms are used as primary keys to fetch region details. This validation catches such issues during atlas generation.What does this PR do?
Adds a validate_unique_acronyms function that checks for duplicate acronyms in atlas structures during validation and raises an
AssertionErrorwith a meaningful error message listing the duplicate acronyms.References
How has this PR been tested?
test_validate_unique_acronyms_failtest that mocks atlas structures with duplicate acronyms and verifies the validation fails with the expected error messagetest_valid_atlas_passes_all_validationstest will automatically verify the function passes on valid atlasesIs this a breaking change?
No!
Does this PR require an update to the documentation?
No, this is an internal validation function used during atlas generation.
Checklist: