MBM7/anndata-h5ad-sparse-bomb-poc

anndata — .h5ad HDF5 Sparse Data Decompression Bomb (PoC)

Repo: MBM7/anndata-h5ad-sparse-bomb-poc
Status: Responsible disclosure — submitted to Huntr
Severity: High / CWE-789
Packages: anndata + h5py (PyPI) — HDF5 format (.h5ad)

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Summary

A crafted 68 KB .h5ad file causes anndata.read_h5ad() to allocate 2 GB of memory silently — no exception is raised, the returned AnnData object appears completely valid.

File size	Claimed X/data shape	Peak allocation	Amplification
68 KB	(500,000,000,)	2,000 MB	1 : 29,391

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Root Cause

anndata/_io/specs/methods.py, read_sparse():

# No size validation before reading
sparse_dataset(elem).to_memory()
  → h5py: numpy.empty(ds.shape, dtype=ds.dtype)  # ← 2 GB allocated
  #        ds.shape = (500_000_000,) from HDF5 metadata
  → reads actual chunks (only 3 values on disk)

HDF5 chunked datasets support sparse storage — unwritten chunks exist only as metadata. The X/data dataset can claim shape=(500_000_000,) float32 (= 2 GB) while storing only 3 values. h5py pre-allocates numpy.empty(ds.shape) before reading any chunks.

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Distinct from keras/h5py finding

	keras/h5py	anndata
Result	OOM kill (MemoryError)	Silent successful load
File format	.h5	.h5ad
Code path	legacy_h5_format.py	sparse_dataset.py
Detectability	Process crashes	No error — harder to detect

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Reproduce

pip install anndata h5py scipy numpy
python poc_anndata_h5ad_bomb.py

Expected output:

Malicious .h5ad   : 68,048 bytes
X/data claimed    : 2,000,000,000 bytes  (2.0 GB)
Amplification     : 1:29,391
Result            : LOADED — no exception!
Peak memory       : 2000 MB

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Impact

Any service loading user-supplied .h5ad files (HuggingFace single-cell genomics datasets, bioinformatics ML pipelines, spatial transcriptomics tools) can be OOM-killed by a 68 KB payload. The silent load makes the attack harder to detect than typical decompression bombs.

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Suggested Fix

In SparseDataset.to_memory() / read_sparse(), validate before reading:

MAX_ARRAY_BYTES = 512 * 1024 * 1024
for key in ['data', 'indices', 'indptr']:
    ds = elem[key]
    if ds.size * ds.dtype.itemsize > MAX_ARRAY_BYTES:
        raise ValueError(f"Dataset '{key}' too large — possible bomb")

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Environment

Package	Version
anndata	0.13.2
h5py	3.14.0
Python	3.12

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Distinct from keras HDF5 finding — different library, different code path,
different behavior (silent vs crash). anndata is used in HuggingFace Hub
for single-cell ML datasets.