fix(format): resolve shared fill value messages instead of zero-filling

dataset_fill_value treated a shared Fill Value message as "no fill
value", so unwritten storage of a dataset whose fill value lives in the
file's shared-message (SOHM) heap read as zeros rather than its fill
value. libhdf5 shares fill values whenever the file has a SOHM index for
them.

- fill_value::dataset_fill_value_in follows the reference (another object
  header, or the SOHM heap); read_full_with_fill and the facade's
  selection read use it.
- dataset_fill_value, which has no file to follow a reference into, now
  returns UnresolvedSharedMessage for a shared message instead of None.
- shared_message::load_sohm_table / message_data_with_sohm load the SOHM
  table from the superblock extension on demand.
- parse_sohm_table skipped each index's leading version byte, reading
  every field one byte off; SOHM references could never resolve.

Fixture shared_fill_value.h5 (HDF5 2.0, gen_shared_fill.py): sohm_b read
[0,1,2,3,0,0,0,0] and now reads [0,1,2,3,-7,-7,-7,-7], as h5py does.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
This commit is contained in:
osobh
2026-09-25 21:18:12 -05:00
co-authored by Claude Opus 5.5
parent 57e938c438
commit 7c1968a34a
7 changed files with 268 additions and 12 deletions
@@ -597,3 +597,50 @@ fn unknown_message_flags_follow_libhdf5_on_tbogus() {
}
}
}
// ---- 8. shared fill value messages ----
#[test]
fn shared_fill_value_is_resolved_not_zero() {
// gen_shared_fill.py: HDF5 2.0 with a SOHM index for fill values, so each
// dataset's fill value message is a reference into the SOHM heap. It
// used to be read as "no fill value" (zeros) instead of -7.
let bytes = include_bytes!("fixtures/shared_fill_value.h5");
for (name, shared) in [
("sohm_a", false),
("sohm_b", true),
("unwritten_a", false),
("unwritten_b", true),
] {
let (sb, oh) = header_at(bytes, name);
let msg = oh
.messages
.iter()
.find(|m| m.msg_type == MessageType::FillValue)
.unwrap();
assert_eq!(
clawhdf5_format::shared_message::is_shared(msg.flags),
shared,
"{name}: fixture layout"
);
if shared {
// Without the file the reference cannot be followed: an error,
// never a silent default.
assert_eq!(
clawhdf5_format::fill_value::dataset_fill_value(&oh.messages),
Err(clawhdf5_format::error::FormatError::UnresolvedSharedMessage)
);
}
assert_eq!(
clawhdf5_format::fill_value::dataset_fill_value_in(
bytes,
&oh.messages,
sb.offset_size,
sb.length_size
)
.unwrap(),
Some((-7i32).to_le_bytes().to_vec()),
"{name}"
);
}
}