fix: handle Unicode characters in h5ad metadata without misleading format error#2762
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fresh3nough wants to merge 1 commit into
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fix: handle Unicode characters in h5ad metadata without misleading format error#2762fresh3nough wants to merge 1 commit into
fresh3nough wants to merge 1 commit into
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Summary
Fixes #2754
Loading an h5ad file containing non-ASCII Unicode characters (e.g. Greek letter phi in cell labels like
Interstitial Mφ perivascular) caused a misleading error:File must be in the .h5ad format. The actual file was valid h5ad, but the broadexcept ValueErrorhandler in_load_data()discarded the original error context.Changes
server/data_anndata/anndata_adaptor.pyValueErrorhandling in_load_data()to detect Unicode/encoding-related errors and display a meaningful message instead of the generic format errorValueErrorcases, aiding debugging_normalize_unicode_strings()static method that normalizes all string metadata in obs/var DataFrames to NFC form during_validate_and_initialize(), preventing encoding issues during serializationtest/unit/data_anndata/test_unicode_metadata.pySteps to reproduce the original bug
φ(or similar non-ASCII characters)cellxgene launch anndata.h5adFile must be in the .h5ad formatSteps to verify the fix
All 3 new tests pass, and existing data_anndata tests remain unaffected.