The fractal-heap reader split direct vs indirect block rows using the FRHP
"Starting # of Rows in Root Indirect Block" field (a constant, typically 1),
mislabeled as starting_row_of_indirect_blocks. For any heap whose data spans
more than one direct block — common in libhdf5 files with a large group or
many dense attributes — this treated direct blocks as indirect and walked into
garbage, failing with InvalidFractalHeapSignature.
Derive the split from the heap geometry instead: max_direct_rows =
log2(max_direct_block_size / starting_block_size) + 2. Rows below it hold
direct blocks; rows at/above hold child indirect blocks.
Validated against an h5py-written group with 400 dense attributes (root
indirect block, 4 rows, 13 direct blocks): all values now read correctly.
Regression fixture covers an 80-attribute multi-block heap.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
The readers added this cycle parse untrusted bytes, so malformed/hostile
input must produce errors — never a panic, OOM, or unbounded recursion.
Audited each new surface and fixed the concrete vectors, each covered by an
adversarial regression test:
- Paged Fixed Array: `1 << max_nelmts_bits` shift overflow (u8 up to 255);
element-count bounded by file size; element/page offset multiplies checked.
- H5S selection decoder: ALL/NONE validate they have the 16 bytes they claim
to consume; hyperslab rank capped at 32 (H5S_MAX_RANK); iter_linear
coordinate/stride/product arithmetic uses checked ops.
- VDS mapping parser: drop pre-allocation from the untrusted `nused`;
bounds-check all selection slicing.
- scale-offset / N-Bit filters: `1 << minbits` overflow at minbits==64; N-Bit
`bit_offset + precision` overflow; N-Bit type-tree recursion depth capped to
stop a crafted nested tree from overflowing the stack; element counts bounded
by the chunk's expected decompressed size (threaded the previously-unused
chunk_size into both decoders) so a bogus count can't over-allocate.
- VDS assembly: a virtual dataset whose source is itself virtual (a cycle) now
errors instead of recursing into a stack overflow.
16 new adversarial tests; full format suite (482 lib) + agent + facade green;
clippy clean.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
The HDF5 library does not implement the scale-offset filter's floating-point
E-scale mode. When asked for it (cd_values[0] = 1) it stores the chunk raw
(no minbits/minval header) and sets the chunk filter mask to skip the filter,
so such datasets read back verbatim purely by honoring the per-chunk filter
mask — no E-scale decoder is required.
Add a fixture written via the HDF5 low-level API (exact-representable values)
and a test asserting it reads back verbatim, locking in the filter-mask path.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
VDS sources living in other files were previously unsupported because the
pure-byte read API has no filesystem. Add a resolver seam and wire a default.
clawhdf5-format:
- Add VdsSourceResolver (Fn(&str) -> Option<Vec<u8>>) and
read_raw_data_full_with_resolver. read_virtual_data uses the resolver to
fetch an external source file's bytes by its stored name, then reads the
named source dataset from those bytes and scatters as usual. A resolver
returning None leaves the region at fill (HDF5's missing-source behavior);
an external source with no resolver at all is a clean error. read_raw_data_full
is unchanged (delegates with no resolver).
clawhdf5:
- File now records the directory it was opened from and, for virtual layouts,
reads through a default resolver that loads sibling source files relative to
that directory. So File::open(virt).dataset(d).read_*() transparently
assembles cross-file VDS. In-memory files (from_bytes) have no directory, so
only same-file VDS resolves there.
Tests: format-layer external read with an injected resolver (and the
no-resolver error path), plus facade tests that drop both files in a temp dir
and read through File::open — covering successful resolution and the
missing-source-is-fill case.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
Generalize Selection iteration from 1-D to arbitrary rank: iter_linear(dims)
enumerates a selection's row-major linear indices over a dataspace of the
given shape (ALL, NONE, regular hyperslabs, points), which is the order HDF5
uses to pair virtual and source selections.
read_virtual_data now passes the full virtual/source dimensions instead of a
single extent, so multi-dimensional block mappings scatter to the correct
non-contiguous linear positions. read_named_dataset_raw returns the source
dataset's dimensions. The rank-1 restriction is removed; only external-file
sources remain unsupported.
Tests: 2-D integration fixture (vds_2d_same_file.h5: two 2x2 sources placed
as non-contiguous blocks in a 4x4 virtual) plus N-D iter_linear unit tests
(block, strided, ALL, rank-mismatch). The 1-D path is unchanged.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
A virtual layout previously returned UnsupportedVersion. Implement reading
for the common 1-D, same-file case, reverse-engineered and validated against
HDF5 2.0.
- Rewrite parse_vds_mappings to the real global-heap block format
(version(1) · nused(length_size) · entries · checksum(4)), where each
entry is source-file(null) · source-dataset(null) · source-selection ·
virtual-selection. Block version 1 encodes a same-file source as a single
0x04 marker in place of the file name; version 0 stores an explicit file
name. The selections are H5S-serialized and self-describing in length, so
they are decoded to find entry boundaries. The previous parser used a
guessed layout that did not match real files.
- Extend Selection with decode_serialized() (H5S_select_serialize: ALL,
NONE, and version-3 regular hyperslabs) and iter_linear_1d().
- Add read_virtual_data: resolve the mapping block from the global heap,
read each same-file source dataset, and scatter its selected elements into
the virtual buffer; unmapped regions stay at the zero fill value.
External-file sources and N-D selections return a clean unsupported error.
Tests: real-file integration test (vds_same_file.h5: partial source slice +
fill gap), selection decoder unit tests built from the fixture bytes, and
same-file/external mapping-parser unit tests.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
A filtered, fixed-dimension dataset with more than one Fixed Array
data-block page (>1024 chunks by default) previously failed with
"paged Fixed Array data blocks not yet supported".
Implement the paged data-block layout, reverse-engineered and validated
against an HDF5 2.0 file:
- after the FADB prefix: a page-init bitmap (one bit per page, MSB-first
within each byte), a 4-byte checksum, then the pages;
- each page is a fixed full-size slot of page_nelmts elements plus a
4-byte checksum, with only the final page shorter;
- uninitialized pages still occupy their slot (zero-filled), so the
bitmap — not a 0xFF sentinel — marks a whole page unallocated.
Element parsing is factored into parse_fa_element, shared by the
non-paged and paged paths.
Tests: real-file integration test against a minimal 2-page gzip fixture
(v4_fixed_array_paged.h5) plus a synthetic unit test covering a
multi-byte/MSB-first bitmap, a skipped uninitialized page, and a short
final page.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
