osobhandClaude Opus 5.5
14876b8ae5
An empty AttrValue::String (or a StringArray of empty strings) was
written with a size-0 fixed-length string type. libhdf5 rejects that
("invalid datatype size"), and the failure takes every attribute on the
object with it. Strings are now at least 1 byte, NUL-padded, which is
how h5py stores "" and reads back as "" in both h5py and our reader.
check_encodable also refuses a size-0 string type passed in directly.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
527 lines
18 KiB
Rust
527 lines
18 KiB
Rust
//! Regression tests for writer metadata bugs that produced files libhdf5
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//! refuses (or reads differently from us), plus the reader-side counterparts.
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//!
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//! The plain tests check the bytes we write with our own parser. The
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//! `#[ignore]`d ones are the interop half: they open what we write in h5py
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//! (`CLAWHDF5_PYTHON`, as in `writer_h5py_tests.rs`) and run `h5dump` over it.
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use clawhdf5_format::data_layout::DataLayout;
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use clawhdf5_format::datatype::{Datatype, DatatypeByteOrder, ReferenceType};
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use clawhdf5_format::file_writer::{AttrValue, FileWriter};
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use clawhdf5_format::group_v2::resolve_path_any;
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use clawhdf5_format::message_type::MessageType;
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use clawhdf5_format::object_header::ObjectHeader;
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use clawhdf5_format::signature;
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use clawhdf5_format::superblock::Superblock;
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use clawhdf5_format::type_builders::{FillTime, make_u8_type};
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// ---- helpers ----
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fn header_at(bytes: &[u8], path: &str) -> (Superblock, ObjectHeader) {
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let sig = signature::find_signature(bytes).unwrap();
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let sb = Superblock::parse(bytes, sig).unwrap();
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let addr = if path == "/" {
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sb.root_group_address
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} else {
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resolve_path_any(bytes, &sb, path).unwrap()
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};
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let oh = ObjectHeader::parse(bytes, addr as usize, sb.offset_size, sb.length_size).unwrap();
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(sb, oh)
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}
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fn layout_of(bytes: &[u8], path: &str) -> DataLayout {
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let (sb, oh) = header_at(bytes, path);
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let msg = oh
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.messages
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.iter()
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.find(|m| m.msg_type == MessageType::DataLayout)
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.unwrap();
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DataLayout::parse(&msg.data, sb.offset_size, sb.length_size).unwrap()
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}
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fn python() -> String {
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std::env::var("CLAWHDF5_PYTHON").unwrap_or_else(|_| "python3".to_string())
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}
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fn write_tmp(name: &str, bytes: &[u8]) -> std::path::PathBuf {
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let path = std::env::temp_dir().join(format!("clawhdf5_writer_meta_{name}.h5"));
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std::fs::write(&path, bytes).unwrap();
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path
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}
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/// Run `script` (with `path` bound to the file) under h5py; return stdout.
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fn h5py(path: &std::path::Path, script: &str) -> String {
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let full = format!(
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"import h5py, numpy as np, json\npath = {:?}\n{script}",
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path.display().to_string()
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);
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let o = std::process::Command::new(python())
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.args(["-c", &full])
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.output()
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.expect("python interpreter");
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assert!(
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o.status.success(),
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"h5py failed: {}",
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String::from_utf8_lossy(&o.stderr)
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);
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String::from_utf8(o.stdout).unwrap().trim().to_string()
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}
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/// `h5dump` must read the whole file without error.
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fn h5dump_ok(path: &std::path::Path) {
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let o = std::process::Command::new("h5dump")
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.arg(path)
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.output()
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.expect("h5dump");
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assert!(
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o.status.success(),
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"h5dump failed: {}{}",
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String::from_utf8_lossy(&o.stdout),
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String::from_utf8_lossy(&o.stderr)
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);
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}
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fn u8_ramp(n: usize) -> Vec<u8> {
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(0..n).map(|i| (i % 251) as u8).collect()
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}
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// ---- 1. object header message size limit ----
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#[test]
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fn attribute_too_big_for_a_header_message_is_an_error() {
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// Measured: a 70000-byte attribute was written with its message size
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// wrapped to 16 bits, and libhdf5 refused the whole root group.
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let mut fw = FileWriter::new();
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fw.set_root_attr(
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"a",
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AttrValue::Raw {
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datatype: make_u8_type(),
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shape: vec![70_000],
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data: u8_ramp(70_000),
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},
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);
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assert!(fw.finish().is_err());
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// 65500 bytes still fits and still works.
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let mut fw = FileWriter::new();
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fw.set_root_attr(
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"a",
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AttrValue::Raw {
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datatype: make_u8_type(),
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shape: vec![65_500],
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data: u8_ramp(65_500),
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},
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);
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let bytes = fw.finish().unwrap();
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let (sb, oh) = header_at(&bytes, "/");
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let attrs = clawhdf5_format::attribute::extract_attributes(&oh, sb.length_size).unwrap();
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assert_eq!(attrs[0].raw_data, u8_ramp(65_500));
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}
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#[test]
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fn compact_layout_falls_back_to_contiguous_past_the_message_limit() {
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// Layout message = 4 bytes + data; data may be at most 65531 bytes.
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for (n, compact) in [(65_531, true), (65_532, false), (65_534, false)] {
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let mut fw = FileWriter::new();
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fw.create_dataset("d").with_u8_data(&u8_ramp(n)).compact();
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let bytes = fw.finish().unwrap();
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match layout_of(&bytes, "d") {
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DataLayout::Compact { data } => {
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assert!(compact, "{n} bytes must not be compact");
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assert_eq!(data, u8_ramp(n));
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}
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DataLayout::Contiguous { .. } => assert!(!compact, "{n} bytes should be compact"),
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other => panic!("unexpected layout {other:?}"),
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}
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}
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}
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#[test]
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#[ignore = "requires Python h5py module and h5dump"]
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fn h5py_reads_compact_datasets_at_the_limit() {
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for n in [65_531usize, 65_534] {
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let mut fw = FileWriter::new();
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fw.create_dataset("d").with_u8_data(&u8_ramp(n)).compact();
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let path = write_tmp(&format!("compact_{n}"), &fw.finish().unwrap());
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let out = h5py(
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&path,
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"f = h5py.File(path, 'r'); v = f['d'][()]\n\
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print(bool((v == (np.arange(v.size) % 251).astype(np.uint8)).all()), v.size)",
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);
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assert_eq!(out, format!("True {n}"));
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h5dump_ok(&path);
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}
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}
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// ---- 2. Time / BitField / Opaque / Reference datatypes ----
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fn exotic_types() -> Vec<(&'static str, Datatype, Vec<u8>)> {
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// Four elements each. The object references point at the root group,
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// which a v3-superblock file without an extension puts at address 48.
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let refs: Vec<u8> = (0..4).flat_map(|_| 48u64.to_le_bytes()).collect();
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vec![
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(
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"bits",
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Datatype::BitField {
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size: 1,
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byte_order: DatatypeByteOrder::LittleEndian,
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bit_offset: 0,
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bit_precision: 8,
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},
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vec![1, 2, 4, 8],
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),
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(
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"opaque",
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Datatype::Opaque {
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size: 4,
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tag: b"mytag".to_vec(),
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},
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(0..16).collect(),
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),
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(
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"ref",
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Datatype::Reference {
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size: 8,
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ref_type: ReferenceType::Object,
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},
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refs,
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),
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(
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"time",
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Datatype::Time {
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size: 4,
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bit_precision: 32,
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},
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(0..16).collect(),
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),
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]
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}
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fn exotic_file() -> Vec<u8> {
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let mut fw = FileWriter::new();
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for (name, dt, raw) in exotic_types() {
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fw.create_dataset(name)
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.with_compound_data(dt.clone(), raw.clone(), 4);
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fw.set_root_attr(
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name,
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AttrValue::Raw {
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datatype: dt,
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shape: vec![4],
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data: raw,
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},
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);
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}
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fw.finish().unwrap()
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}
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#[test]
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fn exotic_datatypes_are_written_not_emptied() {
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let bytes = exotic_file();
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let (sb, root) = header_at(&bytes, "/");
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assert_eq!(sb.root_group_address, 48);
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let attrs = clawhdf5_format::attribute::extract_attributes(&root, sb.length_size).unwrap();
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for (name, dt, raw) in exotic_types() {
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let (_, oh) = header_at(&bytes, name);
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let msg = oh
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.messages
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.iter()
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.find(|m| m.msg_type == MessageType::Datatype)
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.unwrap();
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assert_eq!(msg.data, dt.serialize(), "{name}");
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assert_eq!(Datatype::parse(&msg.data).unwrap().0, dt, "{name}");
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let attr = attrs.iter().find(|a| a.name == name).unwrap();
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assert_eq!(attr.datatype, dt, "{name}");
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assert_eq!(attr.raw_data, raw, "{name}");
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}
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}
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#[test]
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#[ignore = "requires Python h5py module and h5dump"]
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fn h5py_reads_exotic_datatypes() {
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let path = write_tmp("exotic", &exotic_file());
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let out = h5py(
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&path,
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"from h5py import h5t, h5s\n\
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f = h5py.File(path, 'r')\n\
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r = {}\n\
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buf = np.zeros(4, dtype='V4')\n\
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f['opaque'].id.read(h5s.ALL, h5s.ALL, buf, mtype=f['opaque'].id.get_type())\n\
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r['bits'] = f['bits'][()].tolist(), f.attrs['bits'].tolist()\n\
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r['opaque'] = (f['opaque'].id.get_type().get_tag().decode(),\n\
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\x20 f.attrs.get_id('opaque').get_type().get_tag().decode(),\n\
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\x20 buf.tobytes().hex())\n\
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r['ref'] = [f[x].name for x in f['ref'][()]] + [f[x].name for x in f.attrs['ref']]\n\
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r['time'] = (f['time'].id.get_type().get_class() == h5t.TIME,\n\
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\x20 f.attrs.get_id('time').get_type().get_class() == h5t.TIME)\n\
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print(json.dumps(r))",
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);
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let v: serde_json::Value = serde_json::from_str(&out).unwrap();
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assert_eq!(v["bits"], serde_json::json!([[1, 2, 4, 8], [1, 2, 4, 8]]));
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assert_eq!(
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v["opaque"],
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serde_json::json!(["mytag", "mytag", "000102030405060708090a0b0c0d0e0f"])
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);
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assert_eq!(v["ref"], serde_json::json!(vec!["/"; 8]));
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assert_eq!(v["time"], serde_json::json!([true, true]));
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h5dump_ok(&path);
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}
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#[test]
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#[ignore = "requires Python h5py module and h5dump"]
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fn raw_attributes_copied_from_h5py_survive_a_rewrite() {
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// Read Raw attributes of the exotic classes out of an h5py file and write
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// them back: this used to emit empty datatype messages.
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let src = std::env::temp_dir().join("clawhdf5_writer_meta_exotic_src.h5");
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h5py(
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&src,
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"from h5py import h5t, h5s, h5a\n\
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f = h5py.File(path, 'w')\n\
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f.attrs['ref'] = np.array([f.ref, f.ref], dtype=h5py.ref_dtype)\n\
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f.attrs.create('opaque', np.frombuffer(b'abcdefgh', dtype='V4'))\n\
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t = h5t.STD_B16BE.copy()\n\
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a = h5a.create(f.id, b'bits', t, h5s.create_simple((2,)))\n\
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a.write(np.array([0x0102, 0x0304], dtype='>u2'), mtype=t)\n\
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a.close()\n\
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f.close()",
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);
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let src_bytes = std::fs::read(&src).unwrap();
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let (sb, root) = header_at(&src_bytes, "/");
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let attrs = clawhdf5_format::attribute::extract_attributes(&root, sb.length_size).unwrap();
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assert_eq!(attrs.len(), 3);
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let mut fw = FileWriter::new();
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for a in &attrs {
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let data = if a.name == "ref" {
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// Re-target the references at our root group.
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48u64.to_le_bytes().repeat(2)
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} else {
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a.raw_data.clone()
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};
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fw.set_root_attr(
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&a.name,
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AttrValue::Raw {
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datatype: a.datatype.clone(),
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shape: a.dataspace.dimensions.clone(),
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data,
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},
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);
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}
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let path = write_tmp("exotic_copy", &fw.finish().unwrap());
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let out = h5py(
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&path,
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"f = h5py.File(path, 'r')\n\
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print(json.dumps([[f[x].name for x in f.attrs['ref']],\n\
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\x20 f.attrs['opaque'].tobytes().decode(),\n\
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\x20 f.attrs.get_id('bits').get_type().get_order(),\n\
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\x20 f.attrs['bits'].tolist()]))",
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);
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assert_eq!(out, r#"[["/", "/"], "abcdefgh", 1, [258, 772]]"#);
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h5dump_ok(&path);
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}
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// ---- 3. paged file-space strategy ----
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fn paged_file(page_size: u32) -> Vec<u8> {
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let mut fw = FileWriter::new();
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fw.with_page_size(page_size);
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fw.create_dataset("d").with_f64_data(&[1.0, 2.0, 3.0]);
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fw.create_dataset("c")
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.with_i32_data(&(0..100).collect::<Vec<_>>())
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.with_chunks(&[10]);
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fw.set_root_attr("a", AttrValue::I64(7));
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let mut g = fw.create_group("g");
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g.create_dataset("e").with_u8_data(&[9; 5000]);
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fw.add_group(g.finish());
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fw.finish().unwrap()
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}
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#[test]
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fn paged_file_has_a_real_superblock() {
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// Measured: `with_page_size` wrote superblock version 4, which does not
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// exist ("bad superblock version number" in libhdf5).
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for ps in [512u32, 4096, 65536] {
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let bytes = paged_file(ps);
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let (sb, _) = header_at(&bytes, "/");
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assert_eq!(sb.version, 3);
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assert_eq!(bytes.len() % ps as usize, 0);
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let (_, e) = header_at(&bytes, "g/e");
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assert!(
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e.messages
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.iter()
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.any(|m| m.msg_type == MessageType::Dataspace)
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);
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}
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}
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#[test]
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#[ignore = "requires Python h5py module and h5dump"]
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fn h5py_opens_paged_files() {
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for ps in [512u32, 4096, 65536] {
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let path = write_tmp(&format!("paged_{ps}"), &paged_file(ps));
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let out = h5py(
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&path,
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"f = h5py.File(path, 'r')\n\
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p = f.id.get_create_plist()\n\
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print(json.dumps([p.get_file_space_strategy()[0], p.get_file_space_page_size(),\n\
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\x20 f['d'][()].tolist(), int(f['c'][()].sum()), int(f.attrs['a']),\n\
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\x20 int(f['g/e'][()].sum())]))",
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);
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assert_eq!(
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out,
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format!("[1, {ps}, [1.0, 2.0, 3.0], 4950, 7, 45000]"),
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"page size {ps}"
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);
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h5dump_ok(&path);
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}
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}
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// ---- 4. fill time and fill value ----
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fn fill_message(bytes: &[u8], path: &str) -> clawhdf5_format::object_header::HeaderMessage {
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let (_, oh) = header_at(bytes, path);
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oh.messages
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.into_iter()
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.find(|m| m.msg_type == MessageType::FillValue)
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.unwrap()
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}
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fn fill_file() -> Vec<u8> {
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let mut fw = FileWriter::new();
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fw.create_dataset("never")
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.with_f64_data(&[1.0, 2.0])
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.fill_time(FillTime::Never);
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fw.create_dataset("alloc")
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.with_f64_data(&[1.0, 2.0])
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.fill_time(FillTime::Alloc);
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fw.create_dataset("ifset")
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.with_f64_data(&[1.0, 2.0])
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.fill_time(FillTime::IfSet);
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fw.create_dataset("default").with_f64_data(&[1.0, 2.0]);
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fw.create_dataset("filled")
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.with_i32_data(&[1, 2, 3, 4])
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.with_chunks(&[2])
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.with_maxshape(&[u64::MAX])
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.with_fill_value(&(-1i32).to_le_bytes());
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fw.finish().unwrap()
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}
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|
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#[test]
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fn fill_time_uses_libhdf5_codes() {
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// H5D_FILL_TIME_ALLOC = 0, NEVER = 1, IFSET = 2, in bits 2-3. Measured:
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// h5py saw our Never as ALLOC, Alloc as IFSET and IfSet as NEVER.
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let bytes = fill_file();
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for (path, code) in [("never", 1), ("alloc", 0), ("ifset", 2), ("default", 2)] {
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let msg = fill_message(&bytes, path);
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assert_eq!((msg.data[1] >> 2) & 3, code, "{path}");
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assert_eq!(msg.data[1] & 3, 2, "{path}: allocation time stays late");
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}
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for ft in [FillTime::Never, FillTime::Alloc, FillTime::IfSet] {
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assert_eq!(FillTime::from_byte(ft.to_byte()), Some(ft));
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}
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assert_eq!(FillTime::default(), FillTime::IfSet);
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}
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#[test]
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fn fill_value_is_written_and_read_back() {
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let bytes = fill_file();
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let msg = fill_message(&bytes, "filled");
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assert_eq!(
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clawhdf5_format::fill_value::parse_fill_value(&msg).unwrap(),
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Some((-1i32).to_le_bytes().to_vec())
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);
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assert_eq!(
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|
clawhdf5_format::fill_value::parse_fill_value(&fill_message(&bytes, "ifset")).unwrap(),
|
|
None
|
|
);
|
|
|
|
// One element's bytes, no more, no less.
|
|
let mut fw = FileWriter::new();
|
|
fw.create_dataset("d")
|
|
.with_f64_data(&[1.0])
|
|
.with_fill_value(&[0; 4]);
|
|
assert!(fw.finish().is_err());
|
|
}
|
|
|
|
#[test]
|
|
#[ignore = "requires Python h5py module and h5dump"]
|
|
fn h5py_sees_our_fill_time_and_fill_value() {
|
|
let path = write_tmp("fill", &fill_file());
|
|
let out = h5py(
|
|
&path,
|
|
"from h5py import h5d\n\
|
|
f = h5py.File(path, 'r')\n\
|
|
names = {h5d.FILL_TIME_NEVER: 'never', h5d.FILL_TIME_ALLOC: 'alloc', h5d.FILL_TIME_IFSET: 'ifset'}\n\
|
|
t = [names[f[n].id.get_create_plist().get_fill_time()] for n in ('never', 'alloc', 'ifset', 'default')]\n\
|
|
print(json.dumps([t, int(f['filled'].fillvalue), f['filled'][()].tolist()]))\n\
|
|
f.close()\n\
|
|
f = h5py.File(path, 'r+')\n\
|
|
f['filled'].resize((7,))\n\
|
|
f.close()\n\
|
|
print(json.dumps(h5py.File(path, 'r')['filled'][()].tolist()))",
|
|
);
|
|
assert_eq!(
|
|
out,
|
|
"[[\"never\", \"alloc\", \"ifset\", \"ifset\"], -1, [1, 2, 3, 4]]\n[1, 2, 3, 4, -1, -1, -1]"
|
|
);
|
|
h5dump_ok(&path);
|
|
}
|
|
|
|
// ---- 5. empty string attributes ----
|
|
|
|
fn empty_string_file() -> Vec<u8> {
|
|
let mut fw = FileWriter::new();
|
|
fw.set_root_attr("empty", AttrValue::String(String::new()));
|
|
fw.set_root_attr("x", AttrValue::String("héllo".into()));
|
|
fw.set_root_attr(
|
|
"empties",
|
|
AttrValue::StringArray(vec![String::new(), String::new()]),
|
|
);
|
|
fw.set_root_attr("n", AttrValue::I64(3));
|
|
fw.finish().unwrap()
|
|
}
|
|
|
|
#[test]
|
|
fn empty_string_attribute_has_a_one_byte_type() {
|
|
// Measured: "" got a size-0 string type, and libhdf5 then refused every
|
|
// attribute on the object ("invalid datatype size").
|
|
let bytes = empty_string_file();
|
|
let (sb, root) = header_at(&bytes, "/");
|
|
let attrs = clawhdf5_format::attribute::extract_attributes(&root, sb.length_size).unwrap();
|
|
for name in ["empty", "empties"] {
|
|
let a = attrs.iter().find(|a| a.name == name).unwrap();
|
|
assert_eq!(a.datatype.type_size(), 1, "{name}");
|
|
let strings = a.read_as_strings().unwrap();
|
|
assert!(strings.iter().all(String::is_empty), "{name}: {strings:?}");
|
|
}
|
|
|
|
// A size-0 string type handed in directly is refused, not written.
|
|
let mut fw = FileWriter::new();
|
|
fw.set_root_attr(
|
|
"raw",
|
|
AttrValue::Raw {
|
|
datatype: Datatype::String {
|
|
size: 0,
|
|
padding: clawhdf5_format::datatype::StringPadding::NullPad,
|
|
charset: clawhdf5_format::datatype::CharacterSet::Ascii,
|
|
},
|
|
shape: vec![],
|
|
data: vec![],
|
|
},
|
|
);
|
|
assert!(fw.finish().is_err());
|
|
}
|
|
|
|
#[test]
|
|
#[ignore = "requires Python h5py module and h5dump"]
|
|
fn h5py_reads_all_attributes_next_to_an_empty_string() {
|
|
let path = write_tmp("empty_str", &empty_string_file());
|
|
let out = h5py(
|
|
&path,
|
|
"f = h5py.File(path, 'r')\n\
|
|
d = lambda v: v.decode() if isinstance(v, bytes) else v\n\
|
|
print(json.dumps([d(f.attrs['empty']), d(f.attrs['x']),\n\
|
|
\x20 [d(s) for s in f.attrs['empties']], int(f.attrs['n'])], ensure_ascii=False))",
|
|
);
|
|
assert_eq!(out, r#"["", "héllo", ["", ""], 3]"#);
|
|
h5dump_ok(&path);
|
|
}
|