Range reads M0/M1 (indexed lookups, Storage trait), ZFP, in-place editing #17

Merged
osobh merged 52 commits from feat/p3-range-zfp-edit into main 2026-09-26 20:42:22 +00:00
6 changed files with 467 additions and 95 deletions
Showing only changes of commit 76c97f6c94 - Show all commits
+48 -20
View File
@@ -12,7 +12,7 @@ use alloc::{format, vec, vec::Vec};
use crate::chunk_grid::ChunkGrid;
use crate::chunked_read::ChunkInfo;
use crate::error::FormatError;
use crate::storage::{Storage, Window, read_exact_at};
use crate::storage::{PAGED_BLOCK_ONE_READ_MAX, Storage, Window, read_exact_at};
/// Verify the Jenkins lookup3 checksum stored immediately after
/// `data[start..end]`, as every Extensible Array structure carries one. `w`
@@ -373,6 +373,9 @@ fn read_data_block_elements<S: Storage + ?Sized>(
.checked_mul(elem_bytes)
.and_then(|b| pos.checked_add(b))
.ok_or_else(|| FormatError::Overflow("Extensible Array data block span".into()))?;
// The checksum's bounds check comes first: make it before reading.
#[cfg(feature = "checksum")]
Window::check_extent(file, db_offset, end, 4)?;
let w = Window::read(file, db_offset, end.saturating_add(4))?;
verify_checksum(&w, 0, end)?;
read_run(&w, pos, nelmts, start_index, &mut chunks)?;
@@ -384,13 +387,26 @@ fn read_data_block_elements<S: Storage + ?Sized>(
// clear were never written; their slot still occupies the file, so stride
// over it rather than reading zeros as addresses.
let npages = nelmts.div_ceil(page);
// The whole data block in one window: every position checked below lies
// inside it (or past the end of the file).
// The whole data block in one window when it is small: every position
// checked below lies inside it (or past the end of the file). A larger
// block is read as its prefix, then each page in use on its own.
let block_len = pos
.saturating_add(4)
.saturating_add(npages.saturating_mul(page.saturating_mul(elem_bytes).saturating_add(4)));
let w = Window::read(file, db_offset, block_len)?;
verify_checksum(&w, 0, pos)?;
let whole = if block_len <= PAGED_BLOCK_ONE_READ_MAX {
Some(Window::read(file, db_offset, block_len)?)
} else {
None
};
let head_w;
let head = match &whole {
Some(w) => w,
None => {
head_w = Window::read(file, db_offset, pos + 4)?;
&head_w
}
};
verify_checksum(head, 0, pos)?;
pos += 4;
let page_stride = page
.checked_mul(elem_bytes)
@@ -405,10 +421,20 @@ fn read_data_block_elements<S: Storage + ?Sized>(
.is_some_and(|byte| byte & (0x80 >> (bit % 8)) != 0);
if initialised {
let count = core::cmp::min(page, nelmts - p * page);
// `w` holds the page from `base` on (positions below are
// relative to it, and `pos` to the data block).
let page_w;
let (w, base) = match &whole {
Some(w) => (w, 0),
None => {
page_w = Window::read(file, db_offset.saturating_add(pos as u64), page_stride)?;
(&page_w, pos)
}
};
// Each page carries its own checksum, over a full page's worth of
// slots even when the last one holds fewer live elements.
verify_checksum(&w, pos, pos + page * elem_bytes)?;
read_run(&w, pos, count, start_index + p * page, &mut chunks)?;
verify_checksum(w, pos - base, pos - base + page * elem_bytes)?;
read_run(w, pos - base, count, start_index + p * page, &mut chunks)?;
}
pos = pos
.checked_add(page_stride)
@@ -544,6 +570,9 @@ pub fn read_extensible_array_chunks_in<S: Storage + ?Sized>(
.ok_or_else(|| FormatError::Overflow("Extensible Array index block span".into()))?;
// The whole index block in one window: every position read below is
// before `ib_end`.
// The checksum's bounds check comes first: make it before reading.
#[cfg(feature = "checksum")]
Window::check_extent(file, ib_offset, ib_end, 4)?;
let w = Window::read(file, ib_offset, ib_end.saturating_add(4))?;
verify_checksum(&w, 0, ib_end)?;
@@ -682,26 +711,25 @@ fn read_super_block<S: Storage + ?Sized>(
// Positions below are relative to the super block, whose bytes (up to
// its checksum) are all in one window.
let bitmap_start = sb_header_size;
let w = Window::read(
file,
sb_offset,
bitmap_start
.saturating_add(bitmap_bytes)
.saturating_add(ndblks.saturating_mul(os))
.saturating_add(4),
)?;
w.ensure(bitmap_start, bitmap_bytes)?;
let bitmap = &w.bytes[bitmap_start..bitmap_start + bitmap_bytes];
// The bitmap's bounds check, then (with checksums) the checksum's, come
// before anything else is read from the block: make them before reading
// it, so size fields stretching it past the end of the file cost no read.
Window::check_extent(file, sb_offset, bitmap_start, bitmap_bytes)?;
let mut pos = bitmap_start + bitmap_bytes;
let mut chunks = Vec::new();
let mut global_idx = start_index;
// One checksum covers the prefix, the bitmap and every data block address.
let sb_end = ndblks
.checked_mul(os)
.and_then(|b| pos.checked_add(b))
.ok_or_else(|| FormatError::Overflow("Extensible Array super block span".into()))?;
#[cfg(feature = "checksum")]
Window::check_extent(file, sb_offset, sb_end, 4)?;
let w = Window::read(file, sb_offset, sb_end.saturating_add(4))?;
w.ensure(bitmap_start, bitmap_bytes)?;
let bitmap = &w.bytes[bitmap_start..bitmap_start + bitmap_bytes];
let mut chunks = Vec::new();
let mut global_idx = start_index;
verify_checksum(&w, 0, sb_end)?;
for i in 0..ndblks {
+62 -18
View File
@@ -9,7 +9,7 @@ use alloc::{format, vec, vec::Vec};
use crate::chunk_grid::ChunkGrid;
use crate::chunked_read::ChunkInfo;
use crate::error::FormatError;
use crate::storage::{Storage, Window, len_usize, read_exact_at};
use crate::storage::{PAGED_BLOCK_ONE_READ_MAX, Storage, Window, len_usize, read_exact_at};
/// Verify the Jenkins lookup3 checksum stored immediately after
/// `data[start..end]`, as every Fixed Array structure carries one. `w` is
@@ -278,6 +278,9 @@ pub fn read_fixed_array_chunks_in<S: Storage + ?Sized>(
// then a checksum over both. One window holds all of it (or ends at
// the end of the file), so its bounds checks are the whole-file ones.
let end = elem_at(elements_start, num_elements)?;
// The checksum's bounds check comes first: make it before reading.
#[cfg(feature = "checksum")]
Window::check_extent(file, db_offset as u64, end - db_offset, 4)?;
let w = Window::read(file, db_offset as u64, end.saturating_add(4) - db_offset)?;
verify_checksum(&w, 0, end - db_offset)?;
for i in 0..num_elements {
@@ -310,21 +313,34 @@ pub fn read_fixed_array_chunks_in<S: Storage + ?Sized>(
available: file_len,
});
}
// The whole data block in one window: every page slot is at most
// `page_stride` bytes, so every position checked below lies inside it
// (or past the end of the file).
// The whole data block in one window when it is small: every page slot
// is at most `page_stride` bytes, so every position checked below lies
// inside it (or past the end of the file). A larger block is read as its
// prefix and bitmap, then each page in use on its own.
let block_len = (pages_start - db_offset).saturating_add(npages.saturating_mul(page_stride));
let w = Window::read(file, db_offset as u64, block_len)?;
let whole = if block_len <= PAGED_BLOCK_ONE_READ_MAX {
Some(Window::read(file, db_offset as u64, block_len)?)
} else {
None
};
let head_w;
let head = match &whole {
Some(w) => w,
None => {
head_w = Window::read(file, db_offset as u64, pages_start - db_offset)?;
&head_w
}
};
// The prefix and page bitmap are covered by their own checksum, and each
// initialised page by one of its own.
verify_checksum(&w, 0, bitmap_start + bitmap_size - db_offset)?;
verify_checksum(head, 0, bitmap_start + bitmap_size - db_offset)?;
for p in 0..npages {
let page_first = p * page_nelmts; // < num_elements, cannot overflow
let page_count = core::cmp::min(page_nelmts, num_elements - page_first);
// Check the page-init bit (MSB-first within each byte).
let bit_byte = w.bytes[bitmap_start + p / 8 - db_offset];
let bit_byte = head.bytes[bitmap_start + p / 8 - db_offset];
let bit_mask = 1u8 << (7 - (p % 8));
if bit_byte & bit_mask == 0 {
continue; // entire page unallocated
@@ -334,18 +350,21 @@ pub fn read_fixed_array_chunks_in<S: Storage + ?Sized>(
.checked_mul(page_stride)
.and_then(|o| pages_start.checked_add(o))
.ok_or_else(stride_overflow)?;
verify_checksum(
&w,
page_off - db_offset,
elem_at(page_off, page_count)? - db_offset,
)?;
let page_end = elem_at(page_off, page_count)?;
// `w` holds the page from `base` on (positions below are relative
// to it).
let page_w;
let (w, base) = match &whole {
Some(w) => (w, db_offset),
None => {
page_w =
Window::read(file, page_off as u64, page_end.saturating_add(4) - page_off)?;
(&page_w, page_off)
}
};
verify_checksum(w, page_off - base, page_end - base)?;
for e in 0..page_count {
push_element(
&w,
page_first + e,
elem_at(page_off, e)? - db_offset,
&mut chunks,
)?;
push_element(w, page_first + e, elem_at(page_off, e)? - base, &mut chunks)?;
}
}
@@ -949,4 +968,29 @@ mod tests {
}
}
}
/// A header whose element count stretches its data block (one checksum
/// over the whole block) far past the end of a 16 MiB file: the
/// checksum's bounds check fails before the block is read, with the
/// slice read's error.
#[cfg(feature = "checksum")]
#[test]
fn oversized_block_fails_before_reading() {
use crate::storage::CountingStorage;
let mut f = build_fixed_array(3, false, 10);
f.resize(16 << 20, 0);
let mut h = FixedArrayHeader::parse(&f, 0x100, 8, 8).unwrap();
h.max_nelmts_bits = 30;
h.num_elements = 4 << 20;
let dims = [h.num_elements * 20];
let want = read_fixed_array_chunks(&f, &h, &dims, None, &[20], 8, 8, 8);
assert!(
matches!(want, Err(FormatError::UnexpectedEof { .. })),
"{want:?}"
);
let storage = CountingStorage::new(f);
let got = read_fixed_array_chunks_in(&storage, &h, &dims, None, &[20], 8, 8, 8);
assert_eq!(format!("{got:?}"), format!("{want:?}"));
assert!(storage.bytes_read() < 64, "{} bytes", storage.bytes_read());
}
}
+201 -40
View File
@@ -669,15 +669,20 @@ impl FractalHeapHeader {
let iblock_header = 5 + offset_size as usize + block_offset_bytes;
let tw = self.table_width as u64;
let nrows_usize = nrows as usize;
let mut current_heap_offset = iblock_heap_offset;
// Rows below max_direct_rows hold direct blocks; rows at/above hold
// child indirect blocks. (NOT the FRHP "starting rows" field.)
let start_indirect = self.max_direct_rows();
let max_direct_rows = nrows_usize.min(start_indirect);
// The block up to its last child entry, in one window: every
// position read below lies inside it, so its bounds checks are the
// The block up to its last child entry. The walk below reads
// entries in order and stops at the one covering the target, which
// the geometry alone locates, so the first window ends there: a
// header claiming a huge table costs a read of the entries in front
// of the target, not of the rest of the file. Only when that entry
// is unallocated (or none covers the target) does the walk go on,
// over the whole block. Either window holds what it was asked for or
// ends at the end of the file, so its bounds checks are the
// whole-file ones.
let direct_entry = usize::from(offset_size)
+ if self.filter_pipeline.is_some() {
@@ -685,21 +690,129 @@ impl FractalHeapHeader {
} else {
0
};
let entries =
|rows: usize, entry: usize| rows.saturating_mul(tw as usize).saturating_mul(entry);
let block_len = iblock_header
.saturating_add(entries(max_direct_rows, direct_entry))
.saturating_add(entries(
nrows_usize.saturating_sub(start_indirect),
usize::from(offset_size),
));
let w = Window::read(file, iblock_addr as u64, block_len)?;
let direct_entries = max_direct_rows.saturating_mul(tw as usize);
let entries_len = |n: usize| {
n.min(direct_entries)
.saturating_mul(direct_entry)
.saturating_add(
n.saturating_sub(direct_entries)
.saturating_mul(usize::from(offset_size)),
)
};
let all_entries = direct_entries.saturating_add(
nrows_usize
.saturating_sub(start_indirect)
.saturating_mul(tw as usize),
);
let block_len = iblock_header.saturating_add(entries_len(all_entries));
let target_entry = self.indirect_entry_for(nrows_usize, iblock_heap_offset, target_offset);
let first_len = target_entry.map_or(block_len, |i| {
iblock_header
.saturating_add(entries_len(i.saturating_add(1)))
.min(block_len)
});
let mut next = self.walk_indirect_block(
&Window::read(file, iblock_addr as u64, first_len)?,
nrows_usize,
iblock_heap_offset,
target_offset,
offset_size,
target_entry.map_or(usize::MAX, |i| i.saturating_add(1)),
)?;
if next.is_none() && first_len < block_len {
next = self.walk_indirect_block(
&Window::read(file, iblock_addr as u64, block_len)?,
nrows_usize,
iblock_heap_offset,
target_offset,
offset_size,
usize::MAX,
)?;
}
match next {
Some(IndirectChild::Direct(block)) => {
self.read_from_direct_block(file, block, target_offset, length)
}
Some(IndirectChild::Indirect {
addr,
nrows,
heap_offset,
}) => self.read_from_indirect_block(
file,
addr,
nrows,
heap_offset,
target_offset,
length,
offset_size,
depth_remaining - 1,
),
None => Err(FormatError::UnexpectedEof {
expected: target_offset as usize + length,
available: len_usize(file),
}),
}
}
/// Which child entry of an indirect block (numbered in walk order:
/// direct rows, then indirect rows) covers `target_offset`, from the
/// doubling-table geometry alone — the entry
/// [`Self::walk_indirect_block`] stops at if it is allocated. `None`
/// when no entry does.
fn indirect_entry_for(&self, nrows: usize, heap_offset: u64, target: u64) -> Option<usize> {
// The walk adds block sizes with saturation; in u128 the same test
// is `cur <= target < cur + size` without it (a target of u64::MAX
// is never inside a saturated range).
if target == u64::MAX {
return None;
}
let (tw, target) = (u128::from(self.table_width), u128::from(target));
let mut cur = u128::from(heap_offset);
let mut before = 0usize;
for row in 0..nrows {
if target < cur {
return None;
}
// Direct and indirect rows alike span this row's block size per
// entry.
let size = u128::from(self.block_size_for_row(row));
let span = size * tw;
if size > 0 && target < cur + span {
let col = usize::try_from((target - cur) / size).ok()?;
return before.checked_add(col);
}
cur += span;
before = before.saturating_add(self.table_width as usize);
}
None
}
/// Walk an indirect block's child entries in order, in the window `w`
/// (the block from its signature on), and return the allocated child
/// covering `target_offset`, or `None` when no entry among the first
/// `limit` does.
fn walk_indirect_block(
&self,
w: &Window<'_>,
nrows: usize,
iblock_heap_offset: u64,
target_offset: u64,
offset_size: u8,
limit: usize,
) -> Result<Option<IndirectChild>, FormatError> {
let ensure_len = |_: &[u8], pos: usize, needed: usize| w.ensure(pos, needed);
let read_offset = |_: &[u8], pos: usize, size: u8| {
w.ensure(pos, usize::from(size))?;
read_offset(&w.bytes, pos, size)
};
let file_data: &[u8] = &w.bytes;
let block_offset_bytes = (self.max_heap_size as usize).div_ceil(8);
let iblock_header = 5 + offset_size as usize + block_offset_bytes;
let tw = self.table_width as u64;
let mut current_heap_offset = iblock_heap_offset;
let start_indirect = self.max_direct_rows();
let max_direct_rows = nrows.min(start_indirect);
let mut walked = 0usize;
// Parse indirect block header
ensure_len(file_data, 0, 4)?;
@@ -712,6 +825,10 @@ impl FractalHeapHeader {
let block_size = self.block_size_for_row(row);
for _col in 0..tw {
if walked == limit {
return Ok(None);
}
walked += 1;
let child_addr = read_offset(file_data, pos, offset_size)?;
pos += offset_size as usize;
@@ -738,18 +855,13 @@ impl FractalHeapHeader {
&& target_offset >= current_heap_offset
&& target_offset < block_end
{
return self.read_from_direct_block(
file,
DirectBlock {
addr: child_addr as usize,
size: block_size,
heap_offset: current_heap_offset,
filtered_size,
filter_mask,
},
target_offset,
length,
);
return Ok(Some(IndirectChild::Direct(DirectBlock {
addr: child_addr as usize,
size: block_size,
heap_offset: current_heap_offset,
filtered_size,
filter_mask,
})));
}
current_heap_offset = block_end;
}
@@ -758,11 +870,15 @@ impl FractalHeapHeader {
// Rows at and above `start_indirect` hold child indirect blocks. A
// child in row r spans exactly that row's block size of heap space,
// so it has as many rows as a table of that total size needs.
for row in start_indirect..nrows_usize {
for row in start_indirect..nrows {
let child_space = self.block_size_for_row(row);
let child_nrows = self.rows_for_size(child_space);
for _col in 0..tw {
if walked == limit {
return Ok(None);
}
walked += 1;
let child_addr = read_offset(file_data, pos, offset_size)?;
pos += offset_size as usize;
@@ -771,25 +887,16 @@ impl FractalHeapHeader {
&& target_offset >= current_heap_offset
&& target_offset < block_end
{
return self.read_from_indirect_block(
file,
child_addr as usize,
child_nrows,
current_heap_offset,
target_offset,
length,
offset_size,
depth_remaining - 1,
);
return Ok(Some(IndirectChild::Indirect {
addr: child_addr as usize,
nrows: child_nrows,
heap_offset: current_heap_offset,
}));
}
current_heap_offset = block_end;
}
}
Err(FormatError::UnexpectedEof {
expected: target_offset as usize + length,
available: len_usize(file),
})
Ok(None)
}
/// Number of rows in the doubling table whose block size is at most the
@@ -833,6 +940,16 @@ impl FractalHeapHeader {
/// A managed direct block's location, extent and (for a filtered heap) its
/// stored size and filter mask.
/// The child of an indirect block that covers a heap offset.
enum IndirectChild {
Direct(DirectBlock),
Indirect {
addr: usize,
nrows: u16,
heap_offset: u64,
},
}
struct DirectBlock {
addr: usize,
size: u64,
@@ -1151,6 +1268,50 @@ mod tests {
}
}
/// A header claiming a huge doubling table (width 0xFFFF, 0xFFFF rows in
/// the root indirect block) in a 16 MiB file: reading an object from the
/// table's first block reads the entries up to it, not the rest of the
/// file, and gives what the slice read gives. When the covering entry is
/// unallocated the walk goes on over the whole block, still identically.
#[test]
fn huge_table_claims_read_only_what_the_walk_needs() {
use crate::storage::CountingStorage;
let (mut file, _) = build_simple_heap(8, 8);
file.resize(16 << 20, 0);
file[600..604].copy_from_slice(b"FHIB");
let first_entry = 600 + 5 + 8 + 2;
file[first_entry..first_entry + 8].copy_from_slice(&256u64.to_le_bytes());
let mut hdr = FractalHeapHeader::parse(&file, 0, 8, 8).unwrap();
hdr.table_width = 0xFFFF;
hdr.root_block_address = 600;
hdr.current_rows_in_root_indirect_block = 0xFFFF;
let managed_id = |offset: u64, len: u64| {
let payload = offset | (len << 16);
let mut id = vec![0u8];
id.extend_from_slice(&payload.to_le_bytes()[..6]);
id
};
let storage = CountingStorage::new(file.clone());
let id = managed_id(15, 13);
let want = hdr.read_managed_object(&file, &id, 8);
assert!(want.is_ok(), "{want:?}");
storage.reset();
assert_eq!(hdr.read_managed_object_in(&storage, &id, 8), want);
assert!(
storage.bytes_read() < 1024,
"{} bytes in {} reads",
storage.bytes_read(),
storage.reads()
);
// The second entry (heap offsets 128..256) is unallocated (zero is
// not the undefined address, so make it all ones).
file[first_entry + 8..first_entry + 16].fill(0xFF);
let storage = CountingStorage::new(file.clone());
let id = managed_id(130, 4);
let want = hdr.read_managed_object(&file, &id, 8);
assert_eq!(hdr.read_managed_object_in(&storage, &id, 8), want);
}
/// A huge object found through the huge-object B-tree needs the whole
/// file in memory until the B-tree reader is converted: a clean error
/// on other storage.
+73 -13
View File
@@ -36,6 +36,10 @@ fn read_offset(data: &[u8], pos: usize, size: u8) -> Result<u64, FormatError> {
})
}
/// First read of a name on a backend without the file in memory: most link
/// names are shorter than this.
const NAME_READ_START: usize = 64;
impl LocalHeap {
/// Parse a local heap header at the given offset in the file data.
pub fn parse(
@@ -152,8 +156,9 @@ impl LocalHeap {
self.read_string_in(file_data, string_offset)
}
/// [`Self::read_string`] over any [`Storage`]: one read, from the
/// string to the end of the data segment.
/// [`Self::read_string`] over any [`Storage`]: one read of up to 64
/// bytes for a short name, more (each four times the last) up to the end
/// of the data segment for a longer one.
pub fn read_string_in<S: Storage + ?Sized>(
&self,
file: &S,
@@ -180,19 +185,33 @@ impl LocalHeap {
});
}
// Find null terminator
// Find the null terminator, which lies before the end of the data
// segment (or of the file). In memory that is one borrowed slice;
// otherwise the bytes are read in growing pieces, so a name costs a
// read of about its own length, not of the rest of the segment
// (whose size is an untrusted header field).
let search_end = seg_end.min(file_len);
let rest = read_exact_at(file, str_start as u64, search_end - str_start)?;
let Some(len) = rest.iter().position(|&b| b == 0) else {
return Err(FormatError::UnexpectedEof {
expected: search_end + 1,
available: search_end,
});
let total = search_end - str_start;
let mut want = if file.as_contiguous().is_some() {
total
} else {
total.min(NAME_READ_START)
};
let s = core::str::from_utf8(&rest[..len])
.map_err(|_| FormatError::InvalidLocalHeapSignature)?;
Ok(String::from(s))
loop {
let rest = read_exact_at(file, str_start as u64, want)?;
if let Some(len) = rest.iter().position(|&b| b == 0) {
let s = core::str::from_utf8(&rest[..len])
.map_err(|_| FormatError::InvalidLocalHeapSignature)?;
return Ok(String::from(s));
}
if want == total {
return Err(FormatError::UnexpectedEof {
expected: search_end + 1,
available: search_end,
});
}
want = want.saturating_mul(4).min(total);
}
}
}
@@ -393,4 +412,45 @@ mod tests {
}
}
}
/// Names of every length around the first read's size, and one with no
/// terminator, read identically through a `read_at`-only storage; a
/// short name in a heap whose header claims a huge data segment costs
/// one small read, not a read of the rest of the file.
#[test]
fn long_names_and_hostile_segment_sizes() {
use crate::storage::CountingStorage;
let names: Vec<String> = [0usize, 1, 63, 64, 65, 255, 256, 257, 1000, 5000]
.iter()
.map(|&n| "n".repeat(n))
.collect();
let refs: Vec<&str> = names.iter().map(String::as_str).collect();
let mut file = build_heap_file(0, 64, &refs, 8, 8);
let heap = LocalHeap::parse(&file, 0, 8, 8).unwrap();
let storage = CountingStorage::new(file.clone());
let mut off = 0u64;
for name in &names {
let got = heap.read_string_in(&storage, off);
assert_eq!(got, heap.read_string(&file, off));
assert_eq!(got.unwrap(), *name);
off += name.len() as u64 + 1;
}
// The last name loses its terminator: both report the same error.
let seg_end = 64 + heap.data_segment_size as usize;
file[seg_end - 1] = b'n';
let storage = CountingStorage::new(file.clone());
let last = off - names[names.len() - 1].len() as u64 - 1;
let want = heap.read_string(&file, last);
assert!(want.is_err());
assert_eq!(heap.read_string_in(&storage, last), want);
// A 64 MiB file whose heap claims a data segment reaching its end.
let mut big = build_heap_file(0, 64, &["short", "names"], 8, 8);
big.resize(64 << 20, 0);
big[8..16].copy_from_slice(&((64u64 << 20) - 64).to_le_bytes());
let heap = LocalHeap::parse(&big, 0, 8, 8).unwrap();
let storage = CountingStorage::new(big.clone());
assert_eq!(heap.read_string_in(&storage, 6).unwrap(), "names");
assert_eq!((storage.reads(), storage.bytes_read()), (1, 64));
}
}
+28
View File
@@ -235,6 +235,12 @@ fn short_read() -> FormatError {
)
}
/// Largest paged data block (fixed or extensible array) read in one piece.
/// A bigger one is read as its prefix and then page by page, only the pages
/// in use, so a block whose size fields claim more than the file holds
/// costs no more than the pages it really has.
pub(crate) const PAGED_BLOCK_ONE_READ_MAX: usize = 1 << 20;
/// A window of the file: up to `max` bytes read at `base`, fewer only at
/// the end of the file. Its [`Window::ensure`] reports a bounds failure
/// exactly as the whole-file check `ensure_len(file_data, base + rel, n)`
@@ -272,6 +278,28 @@ impl<'a> Window<'a> {
}
}
/// [`Window::ensure`] for a window at `base` that has not been read:
/// whether `[rel, rel + needed)` lies in the file, with the same error.
/// Lets a parser whose first step is to check a structure's whole extent
/// (a checksum at its end) fail before reading a structure that a
/// hostile size field has stretched past the end of the file.
pub fn check_extent<S: Storage + ?Sized>(
file: &S,
base: u64,
rel: usize,
needed: usize,
) -> Result<(), FormatError> {
let base = usize::try_from(base).unwrap_or(usize::MAX);
let file_len = len_usize(file);
match base.checked_add(rel).and_then(|p| p.checked_add(needed)) {
Some(end) if end <= file_len => Ok(()),
_ => Err(FormatError::UnexpectedEof {
expected: base.saturating_add(rel).saturating_add(needed),
available: file_len,
}),
}
}
/// Check that `[rel, rel + needed)` (relative to `base`) is in the file.
#[inline]
pub fn ensure(&self, rel: usize, needed: usize) -> Result<(), FormatError> {
@@ -113,6 +113,10 @@ struct Tally {
contiguous_required: usize,
reads: u64,
bytes: u64,
/// Chunk indexes (fixed and extensible arrays) read, and the most bytes
/// one of them took through the storage.
chunk_indexes: usize,
max_chunk_index_bytes: u64,
}
struct Walk<'a> {
@@ -152,6 +156,12 @@ impl Walk<'_> {
);
}
fn index_read(&mut self, bytes_before: u64) {
self.tally.chunk_indexes += 1;
let bytes = self.storage.bytes_read() - bytes_before;
self.tally.max_chunk_index_bytes = self.tally.max_chunk_index_bytes.max(bytes);
}
fn st(&self) -> &dyn Storage {
self.storage
}
@@ -403,6 +413,7 @@ impl Walk<'_> {
let Ok(h) = h else { return };
let want =
read_fixed_array_chunks(slice, &h, &ds.dimensions, max, dims, es, os, ls);
let before = self.storage.bytes_read();
let got = read_fixed_array_chunks_in(
self.st(),
&h,
@@ -413,6 +424,7 @@ impl Walk<'_> {
os,
ls,
);
self.index_read(before);
self.same("fixed array chunks", &want, &got);
} else {
let h = ExtensibleArrayHeader::parse(slice, *addr as usize, os, ls);
@@ -429,6 +441,7 @@ impl Walk<'_> {
os,
ls,
);
let before = self.storage.bytes_read();
let got = read_extensible_array_chunks_in(
self.st(),
&h,
@@ -439,6 +452,7 @@ impl Walk<'_> {
os,
ls,
);
self.index_read(before);
self.same("extensible array chunks", &want, &got);
}
}
@@ -451,7 +465,11 @@ fn check_file(path: &Path, tally: &mut Tally) {
let Ok(bytes) = std::fs::read(path) else {
return;
};
let Ok((_, hdf5)) = split_user_block(&bytes) else {
check_bytes(&path.display().to_string(), &bytes, tally);
}
fn check_bytes(name: &str, bytes: &[u8], tally: &mut Tally) {
let Ok((_, hdf5)) = split_user_block(bytes) else {
return;
};
let storage = CountingStorage::new(hdf5.to_vec());
@@ -459,7 +477,7 @@ fn check_file(path: &Path, tally: &mut Tally) {
let mut walk = Walk {
slice: hdf5,
storage: &storage,
name: path.display().to_string(),
name: name.to_string(),
tally,
};
walk.run();
@@ -473,7 +491,7 @@ fn check_file(path: &Path, tally: &mut Tally) {
tally.checks - before.0,
storage.reads(),
storage.bytes_read(),
path.display()
name
);
}
}
@@ -581,6 +599,16 @@ with h5py.File(p('v1_groups.h5'), 'w', libver='earliest', userblock_size=512) as
g.attrs['n'] = i
f.create_dataset('x', data=np.arange(10))
# Paged chunk indexes whose data blocks are bigger than the storage reads
# in one piece (1 MiB), with two chunks written: a fixed array of 300 000
# chunks (a 2.4 MB data block) and an extensible array grown to 1.2e9 (its
# last data block holds 131 072 chunks: over 1 MiB).
with h5py.File(p('big_paged.h5'), 'w', libver='latest') as f:
d = f.create_dataset('fa', shape=(300000,), chunks=(1,), dtype='u1')
d[5] = 1; d[250000] = 2
e = f.create_dataset('ea', shape=(1,), maxshape=(None,), chunks=(1,), dtype='u1')
e.resize((1200000000,)); e[10] = 1; e[1100000000] = 3
libs = glob.glob(os.path.join(os.path.dirname(h5py.__file__), '..', 'h5py.libs', 'libhdf5-*.so*'))
if libs:
lib = ctypes.CDLL(libs[0])
@@ -633,7 +661,7 @@ fn h5py_files_parse_identically_through_storage() {
.iter()
.map(|f| f.file_name().unwrap().to_string_lossy().into_owned())
.collect();
for want in ["ea.h5", "v1_groups.h5"] {
for want in ["ea.h5", "v1_groups.h5", "big_paged.h5"] {
assert!(names.iter().any(|n| n == want), "{names:?}");
}
if interop_required() {
@@ -641,6 +669,29 @@ fn h5py_files_parse_identically_through_storage() {
}
let mut tally = Tally::default();
for f in &files {
if f.ends_with("big_paged.h5") {
// Only the pages in use are read, not the whole data blocks:
// read in one piece, the fixed array took 2.4 MB and the
// extensible array 1.2 MB (its super block's page bitmap and
// block addresses are most of what remains).
let mut big = Tally::default();
check_file(f, &mut big);
eprintln!("big paged blocks: {big:?}");
assert_eq!(big.chunk_indexes, 2, "{big:?}");
assert!(big.max_chunk_index_bytes < 256 << 10, "{big:?}");
// Truncated anywhere, the page-by-page reads still agree with
// the slice reads (errors included).
let bytes = std::fs::read(f).unwrap();
for cut in (0..bytes.len()).step_by(bytes.len() / 97) {
check_bytes(
&format!("big_paged.h5 cut at {cut}"),
&bytes[..cut],
&mut big,
);
}
eprintln!("big paged blocks, truncated: {big:?}");
assert!(big.chunk_indexes > 100, "{big:?}");
}
check_file(f, &mut tally);
}
eprintln!("h5py files: {tally:?}");