From 6801969055af9fa0a582d13c684b13f41c0f0288 Mon Sep 17 00:00:00 2001
From: Axel Bocciarelli <axelboc@gmail.com>
Date: Mon, 5 Aug 2024 09:08:32 +0200
Subject: [PATCH] Parse VLEN metadata

---
 src/hdf5_util.cc           |   6 ++++
 src/hdf5_util_helpers.d.ts |   1 +
 test/make_test_files.py    |   9 ++++++
 test/test.mjs              |   2 ++
 test/vlen.h5               | Bin 0 -> 6208 bytes
 test/vlen_test.mjs         |  55 +++++++++++++++++++++++++++++++++++++
 6 files changed, 73 insertions(+)
 create mode 100644 test/vlen.h5
 create mode 100644 test/vlen_test.mjs

diff --git a/src/hdf5_util.cc b/src/hdf5_util.cc
index 0a5191d..b2aadff 100644
--- a/src/hdf5_util.cc
+++ b/src/hdf5_util.cc
@@ -303,6 +303,12 @@ val get_dtype_metadata(hid_t dtype)
         array_type.set("total_size", total_size);
         attr.set("array_type", array_type);
     }
+    else if (dtype_class == H5T_VLEN) {
+        hid_t base_dtype = H5Tget_super(dtype);
+        val vlen_type = get_dtype_metadata(base_dtype);
+        H5Tclose(base_dtype);
+        attr.set("vlen_type", vlen_type);
+    }
     else if (dtype_class == H5T_ENUM) {
         val enum_type = val::object();
         val members = val::object();
diff --git a/src/hdf5_util_helpers.d.ts b/src/hdf5_util_helpers.d.ts
index ea05200..5857432 100644
--- a/src/hdf5_util_helpers.d.ts
+++ b/src/hdf5_util_helpers.d.ts
@@ -23,6 +23,7 @@ export interface Metadata {
     compound_type?: CompoundTypeMetadata,
     cset?: number,
     enum_type?: EnumTypeMetadata,
+    vlen_type?: Metadata,
     littleEndian: boolean,
     maxshape: number[] | null,
     ref_type?: 'object' | 'region',
diff --git a/test/make_test_files.py b/test/make_test_files.py
index 68fccb2..b50a45a 100644
--- a/test/make_test_files.py
+++ b/test/make_test_files.py
@@ -33,3 +33,12 @@
 with h5py.File("empty.h5", "w") as f:
     f.create_dataset("empty_dataset", data=h5py.Empty("f"))
     f.attrs["empty_attr"] = h5py.Empty("f")
+
+with h5py.File("vlen.h5", "w") as f:
+    vlen_scalar = f.create_dataset("int8_scalar", shape=(), dtype=h5py.vlen_dtype(np.int8))
+    vlen_scalar[()] = [0, 1]
+
+    vlen_array = f.create_dataset("float32_oneD", shape=(3,), dtype=h5py.vlen_dtype(np.float32))
+    vlen_array[0] = [0]
+    vlen_array[1] = [0, 1]
+    vlen_array[2] = [0, 1, 2]
diff --git a/test/test.mjs b/test/test.mjs
index 7af6c09..9e69bf7 100644
--- a/test/test.mjs
+++ b/test/test.mjs
@@ -18,6 +18,7 @@ import dimension_scales from './dimension_scales.mjs';
 import references from './create_read_references.mjs';
 import test_throwing_error_handler from './test_throwing_error_handler.mjs';
 import test_empty from './empty_dataset_and_attrs.mjs';
+import vlen_test from './vlen_test.mjs';
 
 let tests = [];
 const add_tests = (tests_in) => { /*global*/ tests = tests.concat(tests_in)}
@@ -39,6 +40,7 @@ add_tests(dimension_scales);
 add_tests(references);
 add_tests(test_throwing_error_handler);
 add_tests(test_empty);
+add_tests(vlen_test);
 
 let passed = true;
 async function run_test(test) {
diff --git a/test/vlen.h5 b/test/vlen.h5
new file mode 100644
index 0000000000000000000000000000000000000000..4fabfdbbab6780b45563fc8b40ba8ecf39670347
GIT binary patch
literal 6208
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z^F@eQPlAw{vYFpqnvZX$Y+pvn@p^l^O)OzZO^ON=j}Mi>rbOT)f31d7y;S`ch~bDo
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zzM}6Xk@r!zR#vi+_x)qQ7G${r%d{b22p9r}fFWQA7y^cXAz%m?0)~JgU<mvb0({@c
S{{ei*=LMhd_PpTpo&FQ{t2@~M

literal 0
HcmV?d00001

diff --git a/test/vlen_test.mjs b/test/vlen_test.mjs
new file mode 100644
index 0000000..e291893
--- /dev/null
+++ b/test/vlen_test.mjs
@@ -0,0 +1,55 @@
+#!/usr/bin/env node
+
+import { strict as assert } from 'assert';
+import h5wasm from 'h5wasm/node';
+
+async function vlen_test() {
+  await h5wasm.ready;
+  var f = new h5wasm.File('./test/vlen.h5', 'r');
+
+  assert.deepEqual(f.get('int8_scalar').metadata, {
+    type: 9,
+    shape: [],
+    maxshape: [],
+    chunks: null,
+    size: 8,
+    total_size: 1,
+    signed: true,
+    littleEndian: true,
+    vlen: false,
+    vlen_type: {
+      type: 0,
+      size: 1,
+      signed: true,
+      littleEndian: true,
+      vlen: false,
+    },
+  });
+
+  assert.deepEqual(f.get('float32_oneD').metadata, {
+    type: 9,
+    shape: [3],
+    maxshape: [3],
+    chunks: null,
+    size: 8,
+    total_size: 3,
+    signed: false,
+    littleEndian: true,
+    vlen: false,
+    vlen_type: {
+      type: 1,
+      size: 4,
+      signed: false,
+      littleEndian: true,
+      vlen: false,
+    },
+  });
+}
+
+export const tests = [
+  {
+    description: 'Read variable-length datasets',
+    test: vlen_test,
+  },
+];
+export default tests;