Add HDF5 integrity checks, permissive data format, and robust merging#40
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Jozefov merged 12 commits intopluskal-lab:mainfrom Apr 8, 2026
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Add a permissive DataFormatAll data format class that accepts essentially all spectra (wide ranges for charge, m/z, intensity). Update assign_dformat() to return 'ALL' instead of '-' when no standard format matches, and add the 'ALL' case to DataFormatBuilder.
Add MSLevelsOrder.MISSING_MS1 enum value to detect files lacking MS1 precursor spectra. Add a check in get_order_of_spectra() that returns MISSING_MS1 when MS1 level is absent. Wrap get_instrument_props() in try/except to gracefully handle files where TBXIC computation fails.
Add verify_hdf5_integrity() to detect corrupted/truncated HDF5 files. Rewrite merge_lcmsms_hdf5s() with a two-pass approach: first validate and collect union keys from all input files, then merge with proper handling of heterogeneous datasets, metadata collection into a dedicated HDF5 group, and output integrity verification. Add helper functions for dataset appending, metadata coercion, and fill-array generation. Handle MISSING_MS1 files in read_lcmsms().
…provements' into merging_func
io.read_mzml update
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Improvements to HDF5 merging and LC-MS/MS processing robustness, developed for the GeMS dataset construction pipeline.
Key changes:
DataFormatAllpermissive format class and'ALL'fallback inassign_dformat()MSLevelsOrder.MISSING_MS1for files lacking MS1 spectra; makeget_instrument_props()exception-safeverify_hdf5_integrity()to detect corrupted/truncated filesmerge_lcmsms_hdf5s()with two-pass union-key handling, per-file metadata group, and output integrity verification