clawhdf5: FileEditor skips optional filters that fail, as libhdf5 does
The editor stored every chunk through the whole pipeline with filter mask 0. For LZF that did not shrink a chunk, h5py instead stores it raw with the filter's mask bit set. A chunk the editor stored LZF-encoded at exactly the raw size was then rewritten raw by libhdf5 at the same size; libhdf5 does not touch the index entry when the size is unchanged, so the stale mask 0 stayed and h5py (and h5dump) could no longer read the dataset. clawhdf5_format::filters::compress_chunk_masked runs the pipeline as H5Z_pipeline does: an optional filter (H5Z_FLAG_OPTIONAL) that fails is skipped and its bit set, a mandatory one fails the write, and LZF/Blosc output no smaller than the input counts as failure, as in the reference filters (their output buffer is the input's size). Deflate, LZ4, Zstd, bitshuffle and bzip2 never fail on size in libhdf5 and are kept as before. Test: edit_interop optional_filters_that_fail_are_skipped — the reviewer's repro at every libver: the editor stores the chunk exactly as h5py does (mask 1, size 5; shuffle+LZF+fletcher32 mask 2), h5py r+ rewrites and extends the datasets, and h5py, h5dump and our reader read every value. Fails on the previous editor (mask 0; h5dump cannot read /u8). Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
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osobh
@@ -1187,3 +1187,131 @@ fn measure_append_waste() {
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);
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}
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}
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/// Optional filters that fail are skipped as libhdf5 skips them: an LZF
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/// that does not shrink a chunk leaves it stored unfiltered with its mask
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/// bit set, exactly as h5py stores it. Storing the LZF stream with a clear
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/// mask at the raw chunk's size once let a later libhdf5 rewrite of the
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/// chunk (raw, same size) keep the stale mask, and h5py then failed to read
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/// the dataset. After the editor, h5py r+ rewrites and extends the datasets
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/// and h5py, h5dump (on the chunks it can decode: LZF is not in h5dump) and
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/// our reader read every value.
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#[test]
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fn optional_filters_that_fail_are_skipped() {
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if !tools_ok() {
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return;
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}
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for (li, (lv, _)) in LIBVERS.iter().enumerate() {
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let dir = tmpdir();
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let path = dir.path().join(format!("optional_{li}.h5"));
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let p = path.to_str().unwrap();
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py(&format!(
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"import h5py, numpy as np\n\
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with h5py.File({p:?}, 'w', libver={lv}) as f:\n\
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\x20 f.create_dataset('u8', shape=(5,), dtype='u1', chunks=(5,), maxshape=(None,), compression='lzf')\n\
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\x20 f.create_dataset('mix', shape=(32,), dtype='<i4', chunks=(8,), maxshape=(None,), compression='lzf', shuffle=True, fletcher32=True)\n\
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\x20 f.create_dataset('ref', shape=(5,), dtype='u1', chunks=(5,), maxshape=(None,), compression='lzf')\n\
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\x20 f['ref'][...] = [182, 0, 0, 0, 0]\n"
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));
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let mut rng = Rng(li as u64 + 17);
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// Chunks 0 and 2 incompressible, 1 and 3 compressible.
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let mix: Vec<i32> = (0..32)
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.map(|i| {
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if (i / 8) % 2 == 0 {
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rng.next() as i32
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} else {
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7
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}
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})
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.collect();
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let mut ed = FileEditor::open(&path).unwrap();
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ed.write_all("u8", &[182, 0, 0, 0, 0]).unwrap();
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ed.write_values("mix", &Selection::All, &mix).unwrap();
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drop(ed);
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// Stored as h5py stores it: raw, LZF's bit (0; 1 behind shuffle) set.
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let masks = py(&format!(
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"import h5py\n\
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f = h5py.File({p:?}, 'r')\n\
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i = lambda d, k: f[d].id.get_chunk_info(k)\n\
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print(i('u8', 0).filter_mask, i('u8', 0).size, i('ref', 0).filter_mask, i('ref', 0).size,\n\
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\x20 *[(i('mix', k).filter_mask, i('mix', k).size < 36) for k in range(4)])\n"
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));
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assert_eq!(
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masks, "1 5 1 5 (2, False) (0, True) (2, False) (0, True)",
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"{lv}"
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);
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let dump = |ds: &str| {
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let o = Command::new("h5dump")
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.args(["-d", ds, "-y", "-w", "0", p])
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.output()
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.unwrap();
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assert!(o.status.success(), "h5dump -d {ds} {p}:\n{}", text(&o));
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let s = String::from_utf8_lossy(&o.stdout).into_owned();
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s.split_once("DATA {")
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.and_then(|(_, r)| r.split_once('}'))
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.map(|(d, _)| {
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d.split(|c: char| c == ',' || c.is_whitespace())
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.filter(|t| !t.is_empty())
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.map(|t| t.parse::<i64>().unwrap())
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.collect::<Vec<_>>()
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})
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.unwrap_or_default()
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};
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if *lv != "'latest'" {
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assert_eq!(dump("/u8"), [182, 0, 0, 0, 0]);
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}
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// libhdf5 rewrites the chunk raw at the same size, then extends the
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// datasets with more incompressible data.
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py(&format!(
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"import h5py, numpy as np\n\
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with h5py.File({p:?}, 'r+') as f:\n\
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\x20 f['u8'][...] = [182, 0, 0, 0, 1]\n\
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\x20 f['u8'].resize((12,))\n\
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\x20 f['u8'][5:] = [9, 200, 3, 77, 1, 250, 42]\n\
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\x20 m = f['mix']\n\
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\x20 m[8:16] = np.arange(8, dtype='<i4') * 104729 + 12345\n\
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\x20 m[0:8] = 5\n\
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\x20 m.resize((40,))\n\
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\x20 m[32:] = 11\n"
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));
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let u8_want: Vec<u8> = vec![182, 0, 0, 0, 1, 9, 200, 3, 77, 1, 250, 42];
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let mut mix_want = mix.clone();
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mix_want[0..8].fill(5);
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for (k, v) in mix_want[8..16].iter_mut().enumerate() {
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*v = k as i32 * 104_729 + 12_345;
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}
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mix_want.extend([11; 8]);
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let f = File::open(&path).unwrap();
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assert_eq!(
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f.dataset("u8")
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.unwrap()
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.read_selection(&Selection::All)
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.unwrap(),
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u8_want
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);
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assert_eq!(f.dataset("mix").unwrap().read_i32().unwrap(), mix_want);
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drop(f);
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verify(
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&path,
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"mix",
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&Model {
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shape: vec![40],
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data: mix_want,
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},
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);
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py(&format!(
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"import h5py\n\
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f = h5py.File({p:?}, 'r')\n\
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assert f['u8'][()].tolist() == {u8_want:?}, f['u8'][()]\n"
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));
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if *lv != "'latest'" {
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let got: Vec<u8> = dump("/u8").into_iter().map(|v| v as u8).collect();
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assert_eq!(got, u8_want);
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}
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let o = Command::new(env!("CARGO_BIN_EXE_h5rs"))
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.args(["check", "--data", "-q", p])
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.output()
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.unwrap();
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assert!(o.status.success(), "h5rs check --data {p}:\n{}", text(&o));
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}
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}
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