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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/async_read.rs
+10 -12
View File
@@ -268,28 +268,26 @@ impl AsyncHDF5File {
///
/// Reads the entire file into memory, then parses the superblock.
pub async fn open<R: AsyncHDF5Read>(reader: &R) -> Result<Self, AsyncHDF5Error> {
let data = reader.read_all().await?;
let sig_offset = find_signature(&data)?;
let superblock = Superblock::parse(&data, sig_offset)?;
Ok(Self { data, superblock })
Self::from_bytes(reader.read_all().await?)
}
/// Open an HDF5 file asynchronously from a file path.
pub async fn open_path<P: AsRef<Path>>(path: P) -> Result<Self, AsyncHDF5Error> {
let data = tokio::fs::read(path).await?;
let sig_offset = find_signature(&data)?;
let superblock = Superblock::parse(&data, sig_offset)?;
Ok(Self { data, superblock })
Self::from_bytes(tokio::fs::read(path).await?)
}
/// Open an HDF5 file from bytes already in memory.
pub fn from_bytes(data: Vec<u8>) -> Result<Self, AsyncHDF5Error> {
let sig_offset = find_signature(&data)?;
let superblock = Superblock::parse(&data, sig_offset)?;
pub fn from_bytes(mut data: Vec<u8>) -> Result<Self, AsyncHDF5Error> {
// HDF5 addresses are relative to the superblock: drop any user block
// so they index `data` directly.
let user_block = find_signature(&data)?;
data.drain(..user_block);
let superblock = Superblock::parse(&data, 0)?;
Ok(Self { data, superblock })
}
/// Access the raw file bytes.
/// Access the file bytes from the superblock on (any user block is
/// dropped on open).
pub fn as_bytes(&self) -> &[u8] {
&self.data
}