h5rs (dump, ls, diff, check --data) kept its own lenient VL decoder:
a heap object longer than its element was cut to the element's length
(libhdf5 and h5py refuse it), a null string printed "" where h5dump
prints NULL, the stored element size was trusted, and every heap
collection was kept as an owned copy for the whole run. It now resolves
each element with VlResolver::element / string_element (new: one element
in place, borrowing from the file), and refuses a VL type whose stored
element size is not 4 + offset size + 4, as File does. H5::heap_object
and its cache are gone. h5diff compares a null VL string equal to an
empty one; so does h5rs diff.
clawhdf5-wasm already resolved VL strings with read_vl_strings; it now
uses VlResolver and checks the stored element size before reading, as
File::read_string does.
Tests (h5py writes the files, patched for "a\0b", a null element and
mis-sized heap objects, with 8- and 4-byte offsets):
- h5rs_interop dump_prints_vl_data_like_h5dump: byte-identical to h5dump;
- dump_json_vl_values_match_h5py: h5py's values, errors where h5py fails;
- check_data_flags_mis_sized_vl_heap_objects;
- clawhdf5-wasm tests/vl_strings.rs: wasm, File and h5py agree.
All four fail before. check --data over the 150 cve_hdf5 CVE and fuzzer
files now passes 15 (h5dump rejects 8 of them), was 16 and 9: the
stored-size check flags cve-2024-32608. h5rs-check-ok-files.sh --data:
0 of 422 flagged; h5rs-fuzz.sh: clean on 180 files.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
With the header checks merged, the library refuses truncated files and
misaligned chunk-index keys itself, so check reported only "file cannot
be opened" for a truncated file. It now reports the truncation (stored
end of file vs file length) or the library's error, and the misaligned
chunk test accepts the library's refusal of the key.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The README said check skips only "global heap collections other than
those a value read touches", but read_dataset returns the raw heap IDs,
so no collection was ever read: a file whose global heap collection
claims a 4 GiB object passed `check --data` with no problems, while
h5dump (and h5rs dump/diff) fail on it.
With --data, every variable-length element (strings and sequences, also
inside compounds, arrays and nested sequences) of every dataset and
attribute is followed into its collection. A collection that does not
parse, a missing heap object, or a sequence longer than its heap object
is a problem at the collection's address, once per object; the summary
counts the collections read.
Measured on tank, 2026-09-26: the 418 fully-read conformance ok files
still pass (scripts/h5rs-check-ok-files.sh --data, 0 flagged), and
`check --data` now flags 152 of the 180 CVE-corpus files (was 147); of
the 28 it passes, h5dump 1.14.6 rejects 21 (was 26 of 33).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
New workspace crate clawhdf5-tools with one binary, h5rs, built only on the
clawhdf5 facade and clawhdf5-format (no libhdf5, no C):
- ls [-r] [-v] FILE[/path]: h5ls's listing (same text in its first two
columns) plus the datatype; -v adds address, link count, layout and chunk
index, chunk size, storage, filters, datatype and attributes.
- dump [--json] [-A] [-p] [-d PATH] FILE: h5dump DDL (byte-identical to
h5dump 1.14.6 on the test files) or hdf5-json.
- stat FILE: h5stat's object/link/rank/layout/filter/attribute counts, raw
data and total size.
- diff [-r] [-q] [-d D] [-p R] A B [OBJ1 [OBJ2]]: structural and value
differences, exit 0/1/2 like h5diff.
- check [--data] FILE: walks every object, parses every message, verifies
the checksums of every v2+ structure (including the fractal heap blocks
the library never checks), checks chunk indexes against their datasets
and raw data for out-of-file or overlapping extents; every problem with
its address.
Values over --max-bytes are reported, not read; dense-storage heaps are
verified before objects are read from them; panics are caught (exit 3).
Tests compare with h5ls, h5stat, h5dump and h5diff and with h5py's values,
and flip the checksum of every checksummed structure in a v1.14-format file.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
