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fix(format): apply the base address of files with a user block

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A file may start with a user block (h5py userblock_size, h5jam), putting
the superblock at 512, 1024, ...; every address in the file is then
relative to the superblock. The signature search found it, but every
reader passed the whole file to the parsers, so addresses landed
userblock bytes early and the root group failed with
InvalidObjectHeaderVersion (twithub.h5, twithub513.h5,
h5clear_fsm_persist_user_*.h5).

Readers now view the file from the superblock on, taking the signature's
position as the base address as libhdf5 does: File (mmap, buffered,
from_bytes), MmapFile, LazyFile, AsyncHDF5File, the VOL and MPI VOL
readers, the HNSW loader and external VDS source files. File, MmapFile
and LazyFile gain user_block_size(). The new signature::split_user_block
returns the two parts, and Superblock::parse refuses a non-zero offset
(UserBlockNotStripped) so a format-level caller cannot silently apply
superblock-relative addresses to the whole file.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
This commit is contained in:
osobh
2026-09-25 22:07:50 -05:00
co-authored by Claude Opus 5.5
parent 0555794850
commit a6e90f3ee3
16 changed files with 540 additions and 79 deletions
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crates/clawhdf5-io/src/vol.rs
+4 -3
View File
@@ -283,12 +283,13 @@ impl VirtualObjectLayer for NativeVol {
use clawhdf5_format::{
data_layout::DataLayout, data_read::read_raw_data_full, dataspace::Dataspace,
datatype::Datatype, filter_pipeline::FilterPipeline, group_v2::resolve_path_any,
message_type::MessageType, object_header::ObjectHeader, signature::find_signature,
message_type::MessageType, object_header::ObjectHeader, signature::split_user_block,
superblock::Superblock,
};
let sig = find_signature(data).map_err(|e| VolError::DataError(e.to_string()))?;
let sb = Superblock::parse(data, sig).map_err(|e| VolError::DataError(e.to_string()))?;
// Addresses are relative to the superblock: skip any user block.
let (_, data) = split_user_block(data).map_err(|e| VolError::DataError(e.to_string()))?;
let sb = Superblock::parse(data, 0).map_err(|e| VolError::DataError(e.to_string()))?;
let addr = resolve_path_any(data, &sb, path)
.map_err(|e| VolError::NotFound(format!("{path}: {e}")))?;