vanderbilt: store raw_data with gzip in the four files ClamAV flags

#86
by tristan-deep - opened

Stores tracks/track_0/data/raw_data with shuffle + gzip (level 4) instead of Blosc in the four data/Fundamental/ files that the Hub's ClamAV scan marks unsafe (Win.Exploit.CVE_2016_4332_1-6028013-0):

  • 126987_3_Focused_Uncoded_TX.hdf5
  • 559277_2_Focused_Uncoded_TX.hdf5
  • 729304_2_Focused_Uncoded_TX.hdf5
  • 829312_1_Focused_Uncoded_TX.hdf5

The matching bytes sit inside Blosc-compressed raw_data chunks, not in the HDF5 object headers the CVE is about, so this is a false positive (reported to ClamAV). Re-encoding with Blosc at another level or shuffle mode only clears some files (#82). gzip changes the chunk bytes completely and is the same fix as #83 for UBC session_01_f0374.hdf5.

Files changed: 4. Only the compression filter of raw_data changed. Its values, dtype, shape, chunk shape and fill value, every other dataset (still Blosc) and every attribute are untouched. The Sept 26 subject-ID fix (#74) is kept, since the files were rewritten from current main.

Checks, each file against current main (source SHA-256 matched the Hub):

  • All 24 datasets compared byte-for-byte after decompression, including all 32 raw_data frames; all 53 attributes compared by name, order, dtype and value; dtype, shape, maxshape, chunks and fill value compared for every dataset. 0 differences.
  • zea 0.1.7: File.validate() succeeds, and scan, metadata, load_parameters() and a full raw_data read run with no warnings (same as the originals).
  • ClamAV 1.4.3, daily 28140 (--allmatch --max-filesize=1900M --max-scansize=2000M --max-scantime=0 --alert-exceeds-max=yes): all four originals are flagged, all four replacements are clean.
File Original bytes Replacement bytes
126987_3_Focused_Uncoded_TX.hdf5 1171259392 1163677695
559277_2_Focused_Uncoded_TX.hdf5 1043398656 1019994734
729304_2_Focused_Uncoded_TX.hdf5 1061224448 1026541803
829312_1_Focused_Uncoded_TX.hdf5 1111031808 1080546952

Diff (h5_diff against main: file hashes differ, no structure, dtype, shape, attribute or metadata change):

vanderbilt/data/Fundamental/126987_3_Focused_Uncoded_TX.hdf5: differs (main)
vanderbilt/data/Fundamental/559277_2_Focused_Uncoded_TX.hdf5: differs (main)
vanderbilt/data/Fundamental/729304_2_Focused_Uncoded_TX.hdf5: differs (main)
vanderbilt/data/Fundamental/829312_1_Focused_Uncoded_TX.hdf5: differs (main)

Storage of raw_data, before -> after:

  ~ tracks/track_0/data/raw_data: filters [blosc (zstd, clevel 7, bitshuffle)] -> [shuffle, gzip 4]

Hugging Face's own scan of the new files should be checked before merging.

Replacement SHA-256 hashes
  • vanderbilt/data/Fundamental/126987_3_Focused_Uncoded_TX.hdf5: 2c205f460bfd00eee82e7ebc13c84e44208658104548434c58f59a3822fa171c
  • vanderbilt/data/Fundamental/559277_2_Focused_Uncoded_TX.hdf5: 09026325a76ec701c1f25ac17e267ec4850c6a1dfb090a6525cefbac3a4871a4
  • vanderbilt/data/Fundamental/729304_2_Focused_Uncoded_TX.hdf5: 6c3c4f8717107a98e64d76f1dfae29f93cb11aaa3db0f97d1b9986581cb00773
  • vanderbilt/data/Fundamental/829312_1_Focused_Uncoded_TX.hdf5: a0c549afe4ad4f61a9d96ea50d5dcc57de3f149898f593a8daf4bc697795267e

Confirmed with:

zea process \
  --dataset hf://nvidia/OpenH-RF/vanderbilt/data/Fundamental/729304_2_Focused_Uncoded_TX.hdf5 \
  --config hf://nvidia/OpenH-RF/vanderbilt/pipeline.yaml \
  --revision a82787d61de80bcd14e7742c3b52dd2ed6dd0262 --config-revision main \
  --n-frames 10

Looks good to me! Thank you Tristan!

🙏

wsimson changed pull request status to merged

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