crates/clawhdf5-format/src/attribute.rs

@@ -15,6 +15,7 @@ use crate::fractal_heap::FractalHeapHeader;
 use crate::message_type::MessageType;
 use crate::object_header::ObjectHeader;
 use crate::shared_message;
+use crate::storage::{Storage, require_contiguous};
 use crate::vl_data;
 
 /// A parsed HDF5 attribute message.
@@ -65,13 +66,24 @@ impl AttributeMessage {
         offset_size: u8,
         length_size: u8,
     ) -> Result<AttributeMessage, FormatError> {
-        Self::parse_impl(data, length_size, Some((file_data, offset_size)))
+        Self::parse_in_storage(data, &file_data, offset_size, length_size)
+    }
+
+    /// [`AttributeMessage::parse_in_file`] with the file behind any
+    /// [`Storage`].
+    pub fn parse_in_storage(
+        data: &[u8],
+        file: &dyn Storage,
+        offset_size: u8,
+        length_size: u8,
+    ) -> Result<AttributeMessage, FormatError> {
+        Self::parse_impl(data, length_size, Some((file, offset_size)))
     }
 
     fn parse_impl(
         data: &[u8],
         length_size: u8,
-        file: Option<(&[u8], u8)>,
+        file: Option<(&dyn Storage, u8)>,
     ) -> Result<AttributeMessage, FormatError> {
         ensure_len(data, 0, 2)?;
         let version = data[0];
@@ -91,14 +103,14 @@ impl AttributeMessage {
         shared: bool,
         msg_type: MessageType,
         length_size: u8,
-        file: Option<(&[u8], u8)>,
+        file: Option<(&dyn Storage, u8)>,
     ) -> Result<Cow<'a, [u8]>, FormatError> {
         if !shared {
             return Ok(Cow::Borrowed(bytes));
         }
         let (file_data, offset_size) = file.ok_or(FormatError::UnresolvedSharedMessage)?;
         let shared_ref = shared_message::parse_shared_ref_sized(bytes, offset_size, length_size)?;
-        shared_message::resolve_shared_message(
+        shared_message::resolve_shared_message_in(
             file_data,
             &shared_ref,
             msg_type,
@@ -146,7 +158,7 @@ impl AttributeMessage {
     fn parse_v2(
         data: &[u8],
         length_size: u8,
-        file: Option<(&[u8], u8)>,
+        file: Option<(&dyn Storage, u8)>,
     ) -> Result<AttributeMessage, FormatError> {
         // Flags: bit 0 = datatype is shared, bit 1 = dataspace is shared.
         let flags = data.get(1).copied().unwrap_or(0);
@@ -200,7 +212,7 @@ impl AttributeMessage {
     fn parse_v3(
         data: &[u8],
         length_size: u8,
-        file: Option<(&[u8], u8)>,
+        file: Option<(&dyn Storage, u8)>,
     ) -> Result<AttributeMessage, FormatError> {
         // Flags: bit 0 = datatype is shared, bit 1 = dataspace is shared.
         let flags = data.get(1).copied().unwrap_or(0);
@@ -415,7 +427,20 @@ pub fn extract_attributes_full(
     offset_size: u8,
     length_size: u8,
 ) -> Result<Vec<AttributeMessage>, FormatError> {
-    extract_attributes_with(file_data, header, offset_size, length_size, &mut Err)
+    extract_attributes_full_in(&file_data, header, offset_size, length_size)
+}
+
+/// [`extract_attributes_full`] over any [`Storage`]. Dense attribute
+/// storage is indexed by a v2 B-tree, which is not read over [`Storage`]
+/// yet: on a backend without the whole file in memory an object with dense
+/// attributes is [`FormatError::ContiguousStorageRequired`].
+pub fn extract_attributes_full_in(
+    file: &dyn Storage,
+    header: &ObjectHeader,
+    offset_size: u8,
+    length_size: u8,
+) -> Result<Vec<AttributeMessage>, FormatError> {
+    extract_attributes_with(file, header, offset_size, length_size, &mut Err)
 }
 
 /// Like [`extract_attributes_full`], but an attribute that cannot be read
@@ -431,6 +456,17 @@ pub fn extract_attributes_tolerant(
     header: &ObjectHeader,
     offset_size: u8,
     length_size: u8,
+) -> Result<(Vec<AttributeMessage>, Vec<FormatError>), FormatError> {
+    extract_attributes_tolerant_in(&file_data, header, offset_size, length_size)
+}
+
+/// [`extract_attributes_tolerant`] over any [`Storage`] (see
+/// [`extract_attributes_full_in`] for dense storage).
+pub fn extract_attributes_tolerant_in(
+    file_data: &dyn Storage,
+    header: &ObjectHeader,
+    offset_size: u8,
+    length_size: u8,
 ) -> Result<(Vec<AttributeMessage>, Vec<FormatError>), FormatError> {
     let mut errors = Vec::new();
     let attrs = extract_attributes_with(file_data, header, offset_size, length_size, &mut |e| {
@@ -443,7 +479,7 @@ pub fn extract_attributes_tolerant(
 /// Read every attribute; each one that fails goes to `on_error`, which
 /// either stops the read (returns the error) or skips that attribute.
 fn extract_attributes_with(
-    file_data: &[u8],
+    file_data: &dyn Storage,
     header: &ObjectHeader,
     offset_size: u8,
     length_size: u8,
@@ -460,7 +496,7 @@ fn extract_attributes_with(
                 // Shared attribute: resolve the reference to get actual attribute data
                 shared_message::parse_shared_ref_sized(&msg.data, offset_size, length_size)
                     .and_then(|shared_ref| {
-                        shared_message::resolve_shared_message(
+                        shared_message::resolve_shared_message_in(
                             file_data,
                             &shared_ref,
                             MessageType::Attribute,
@@ -469,7 +505,7 @@ fn extract_attributes_with(
                         )
                     })
                     .and_then(|resolved| {
-                        AttributeMessage::parse_in_file(
+                        AttributeMessage::parse_in_storage(
                             &resolved,
                             file_data,
                             offset_size,
@@ -477,7 +513,7 @@ fn extract_attributes_with(
                         )
                     })
             } else {
-                AttributeMessage::parse_in_file(&msg.data, file_data, offset_size, length_size)
+                AttributeMessage::parse_in_storage(&msg.data, file_data, offset_size, length_size)
             };
             let attr = attr.and_then(|a| check_in_header(a, header));
             match attr {
@@ -537,7 +573,7 @@ fn find_attribute_info(
 /// each one's creation order into `orders`.
 #[allow(clippy::too_many_arguments)]
 fn extract_dense_attributes(
-    file_data: &[u8],
+    file_data: &dyn Storage,
     attr_info: &AttributeInfoMessage,
     fh_addr: u64,
     offset_size: u8,
@@ -547,7 +583,7 @@ fn extract_dense_attributes(
     on_error: &mut dyn FnMut(FormatError) -> Result<(), FormatError>,
 ) -> Result<(), FormatError> {
     // Parse fractal heap
-    let fh = FractalHeapHeader::parse(file_data, fh_addr as usize, offset_size, length_size)?;
+    let fh = FractalHeapHeader::parse_in(file_data, fh_addr, offset_size, length_size)?;
 
     // Parse B-tree v2 for name index (type 8)
     let btree_addr = attr_info
@@ -556,8 +592,10 @@ fn extract_dense_attributes(
             expected: 1,
             available: 0,
         })?;
-    let btree_hdr = BTreeV2Header::parse(file_data, btree_addr as usize, offset_size, length_size)?;
-    let records = collect_btree_v2_records(file_data, &btree_hdr, offset_size, length_size)?;
+    let contiguous = require_contiguous(file_data, "dense attribute storage (a v2 B-tree)")?;
+    let btree_hdr =
+        BTreeV2Header::parse(contiguous, btree_addr as usize, offset_size, length_size)?;
+    let records = collect_btree_v2_records(contiguous, &btree_hdr, offset_size, length_size)?;
 
     for record in &records {
         // Per HDF5 spec, both type 8 and type 9 records start with heap_id:
@@ -574,9 +612,9 @@ fn extract_dense_attributes(
 
         // The data in the heap is a complete attribute message
         let attr = fh
-            .read_managed_object(file_data, id_bytes, offset_size)
+            .read_managed_object_in(file_data, id_bytes, offset_size)
             .and_then(|attr_data| {
-                AttributeMessage::parse_in_file(&attr_data, file_data, offset_size, length_size)
+                AttributeMessage::parse_in_storage(&attr_data, file_data, offset_size, length_size)
             });
         match attr {
             Ok(attr) => {
@@ -986,4 +1024,76 @@ mod tests {
         let strs = attr.read_as_strings().unwrap();
         assert_eq!(strs, vec!["abcd", "EFGH"]);
     }
+
+    /// Every object's attributes in h5py-written files read identically
+    /// through a read_at-only CountingStorage — compact ones, shared ones
+    /// and those behind an Attribute Info message — except dense storage,
+    /// whose v2 B-tree index is not read over Storage yet: that is the clean
+    /// ContiguousStorageRequired error, never a partial list. Through a
+    /// slice as Storage every object matches.
+    #[test]
+    fn storage_reads_match_slice_reads() {
+        use crate::storage::CountingStorage;
+        let files: [(&str, &[u8]); 5] = [
+            ("attrs", include_bytes!("../tests/fixtures/attrs.h5")),
+            (
+                "mixed_attrs",
+                include_bytes!("../tests/fixtures/mixed_attrs.h5"),
+            ),
+            (
+                "dense_attrs",
+                include_bytes!("../tests/fixtures/dense_attrs.h5"),
+            ),
+            (
+                "dense_attrs_root",
+                include_bytes!("../tests/fixtures/dense_attrs_root.h5"),
+            ),
+            (
+                "shared_fill_value",
+                include_bytes!("../tests/fixtures/shared_fill_value.h5"),
+            ),
+        ];
+        let (mut same, mut dense, mut attrs) = (0, 0, 0);
+        for (name, file) in files {
+            let sb = crate::superblock::Superblock::parse(file, 0).unwrap();
+            let (os, ls) = (sb.offset_size, sb.length_size);
+            let mut addrs = vec![sb.root_group_address];
+            addrs.extend(
+                crate::group_v2::resolve_group_children(file, &sb, sb.root_group_address)
+                    .unwrap()
+                    .iter()
+                    .map(|e| e.object_header_address),
+            );
+            let storage = CountingStorage::new(file.to_vec());
+            for addr in addrs {
+                let header = ObjectHeader::parse(file, addr as usize, os, ls).unwrap();
+                let want = extract_attributes_full(file, &header, os, ls);
+                let slice_storage = extract_attributes_full_in(&file, &header, os, ls);
+                assert_eq!(format!("{slice_storage:?}"), format!("{want:?}"));
+                let got = extract_attributes_full_in(&storage, &header, os, ls);
+                let got_t = extract_attributes_tolerant_in(&storage, &header, os, ls);
+                let is_dense = find_attribute_info(&header, os)
+                    .unwrap()
+                    .is_some_and(|i| i.fractal_heap_address.is_some());
+                if is_dense {
+                    let e = FormatError::ContiguousStorageRequired(
+                        "dense attribute storage (a v2 B-tree)",
+                    );
+                    assert_eq!(got.unwrap_err(), e, "{name}");
+                    assert_eq!(got_t.unwrap_err(), e, "{name}");
+                    dense += 1;
+                } else {
+                    attrs += want.as_ref().map_or(0, Vec::len);
+                    assert_eq!(format!("{got:?}"), format!("{want:?}"), "{name}");
+                    let want_t = extract_attributes_tolerant(file, &header, os, ls);
+                    assert_eq!(format!("{got_t:?}"), format!("{want_t:?}"), "{name}");
+                    same += 1;
+                }
+            }
+        }
+        assert!(
+            same >= 5 && dense >= 2 && attrs >= 5,
+            "{same} {dense} {attrs}"
+        );
+    }
 }