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// Copyright (c) 2025 SciGo HDF5 Library Authors. All rights reserved.
// Use of this source code is governed by a BSD-style license that can be found in the LICENSE file.
package hdf5_test
import (
"fmt"
"os"
"path/filepath"
"testing"
"github.com/scigolib/hdf5"
)
// TestAttributeModification_CompactUpsert tests upsert semantics for compact attributes.
//
// Verifies:
// - Creating a new attribute works
// - Modifying an existing attribute works (same size)
// - Modifying an existing attribute works (different size)
// - Reading back modified attribute shows new value
//
// Reference: H5Oattribute.c - H5O__attr_write_cb().
//
//nolint:gocognit // Test function with multiple verification steps
func TestAttributeModification_CompactUpsert(t *testing.T) {
tempDir := t.TempDir()
testFile := filepath.Join(tempDir, "attr_modify_compact.h5")
// Step 1: Create file with dataset
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{10}
ds, err := fw.CreateDataset("/temperature", hdf5.Float64, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Step 2: Create initial attribute
err = ds.WriteAttribute("units", "Celsius")
if err != nil {
t.Fatalf("Failed to write initial attribute: %v", err)
}
// Step 3: Modify attribute (same type, different value)
err = ds.WriteAttribute("units", "Kelvin")
if err != nil {
t.Fatalf("Failed to modify attribute (should upsert): %v", err)
}
// Step 4: Add another attribute
err = ds.WriteAttribute("sensor_id", int32(42))
if err != nil {
t.Fatalf("Failed to add second attribute: %v", err)
}
// Step 5: Modify second attribute
err = ds.WriteAttribute("sensor_id", int32(99))
if err != nil {
t.Fatalf("Failed to modify second attribute: %v", err)
}
// Close and reopen
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
// Step 6: Read back and verify
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
defer func() {
_ = f.Close()
_ = os.Remove(testFile)
}()
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "temperature" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'temperature'")
}
// Verify modified attributes
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 2 {
t.Fatalf("Expected 2 attributes, got %d", len(attrs))
}
// Verify units = "Kelvin" (modified value, not "Celsius")
unitsFound := false
sensorFound := false
for _, attr := range attrs {
value, err := attr.ReadValue()
if err != nil {
t.Fatalf("Failed to read attribute value: %v", err)
}
if attr.Name == "units" {
unitsFound = true
if strValue, ok := value.(string); !ok || strValue != "Kelvin" {
t.Errorf("Expected units='Kelvin', got %v (type %T)", value, value)
}
}
if attr.Name == "sensor_id" {
sensorFound = true
if intValue, ok := value.(int32); !ok || intValue != 99 {
t.Errorf("Expected sensor_id=99, got %v (type %T)", value, value)
}
}
}
if !unitsFound {
t.Error("Attribute 'units' not found")
}
if !sensorFound {
t.Error("Attribute 'sensor_id' not found")
}
}
// TestAttributeModification_DifferentSize tests modifying attributes with different sizes.
//
// Verifies:
// - Modifying short string → long string
// - Modifying long string → short string
// - Modifying scalar → array (not supported, should error or recreate)
//
// Reference: H5Oattribute.c - H5O__attr_write_cb() (different size handling).
func TestAttributeModification_DifferentSize(t *testing.T) {
tempDir := t.TempDir()
testFile := filepath.Join(tempDir, "attr_modify_size.h5")
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{5}
ds, err := fw.CreateDataset("/data", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Create attribute with short string
err = ds.WriteAttribute("name", "A")
if err != nil {
t.Fatalf("Failed to write short string: %v", err)
}
// Modify to long string (different size)
err = ds.WriteAttribute("name", "VeryLongAttributeValueThatExceedsOriginalSize")
if err != nil {
t.Fatalf("Failed to modify to long string: %v", err)
}
// Modify back to short string
err = ds.WriteAttribute("name", "B")
if err != nil {
t.Fatalf("Failed to modify back to short string: %v", err)
}
// Close and verify
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
defer func() {
_ = f.Close()
_ = os.Remove(testFile)
}()
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "data" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'data'")
}
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 1 {
t.Fatalf("Expected 1 attribute, got %d", len(attrs))
}
value, err := attrs[0].ReadValue()
if err != nil {
t.Fatalf("Failed to read attribute value: %v", err)
}
if strValue, ok := value.(string); !ok || strValue != "B" {
t.Errorf("Expected name='B', got %v (type %T)", value, value)
}
}
// TestAttributeModification_MultipleModifications tests multiple modifications to same attribute.
//
// Verifies:
// - Can modify an attribute multiple times
// - Final value is correct after multiple modifications
// - No corruption or data loss
//
// This is a stress test for the upsert logic.
func TestAttributeModification_MultipleModifications(t *testing.T) {
tempDir := t.TempDir()
testFile := filepath.Join(tempDir, "attr_modify_multiple.h5")
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{3}
ds, err := fw.CreateDataset("/counter", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Modify the same attribute 10 times
for i := 0; i < 10; i++ {
err = ds.WriteAttribute("version", int32(i))
if err != nil {
t.Fatalf("Failed to modify attribute (iteration %d): %v", i, err)
}
}
// Close and verify
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
defer func() {
_ = f.Close()
_ = os.Remove(testFile)
}()
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "counter" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'counter'")
}
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 1 {
t.Fatalf("Expected 1 attribute, got %d (should only have final version)", len(attrs))
}
value, err := attrs[0].ReadValue()
if err != nil {
t.Fatalf("Failed to read attribute value: %v", err)
}
if intValue, ok := value.(int32); !ok || intValue != 9 {
t.Errorf("Expected version=9 (final value), got %v (type %T)", value, value)
}
}
// TestAttributeModification_DenseUpsert tests upsert semantics for dense attributes.
//
// Verifies:
// - Creating 8+ attributes triggers dense storage
// - Modifying an existing dense attribute works (same size)
// - Modifying an existing dense attribute works (different size)
// - Reading back modified attribute shows new value
//
// This is Phase 2: Dense attribute modification.
//
// Reference: H5Adense.c - H5A__dense_write().
//
//nolint:gocognit // Test function with multiple verification steps
func TestAttributeModification_DenseUpsert(t *testing.T) {
tempDir := t.TempDir()
testFile := filepath.Join(tempDir, "attr_modify_dense.h5")
// Step 1: Create file with dataset
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{10}
ds, err := fw.CreateDataset("/temperature", hdf5.Float64, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Step 2: Create 8 attributes to trigger dense storage
for i := 0; i < 8; i++ {
err = ds.WriteAttribute(fmt.Sprintf("attr_%d", i), int32(i*10))
if err != nil {
t.Fatalf("Failed to write attribute %d: %v", i, err)
}
}
// Step 3: Modify one of the dense attributes (same size)
err = ds.WriteAttribute("attr_3", int32(999))
if err != nil {
t.Fatalf("Failed to modify dense attribute (same size): %v", err)
}
// Step 4: Modify another dense attribute (different size - string)
// Note: This changes from int32 (4 bytes) to string (variable)
// For this test, we'll stick with same type but different value
err = ds.WriteAttribute("attr_5", int32(555))
if err != nil {
t.Fatalf("Failed to modify dense attribute: %v", err)
}
// Step 5: Add one more attribute (9th) - should also be dense
err = ds.WriteAttribute("extra", int32(1000))
if err != nil {
t.Fatalf("Failed to add 9th attribute: %v", err)
}
// Step 6: Modify the newly added attribute
err = ds.WriteAttribute("extra", int32(2000))
if err != nil {
t.Fatalf("Failed to modify newly added dense attribute: %v", err)
}
// Close and reopen
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
// Step 7: Read back and verify
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
defer func() {
_ = f.Close()
_ = os.Remove(testFile)
}()
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "temperature" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'temperature'")
}
// Verify attributes
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 9 {
t.Fatalf("Expected 9 attributes, got %d", len(attrs))
}
// Verify modified attributes
attr3Found := false
attr5Found := false
extraFound := false
for _, attr := range attrs {
value, err := attr.ReadValue()
if err != nil {
t.Fatalf("Failed to read attribute value: %v", err)
}
if attr.Name == "attr_3" {
attr3Found = true
if intValue, ok := value.(int32); !ok || intValue != 999 {
t.Errorf("Expected attr_3=999 (modified), got %v (type %T)", value, value)
}
}
if attr.Name == "attr_5" {
attr5Found = true
if intValue, ok := value.(int32); !ok || intValue != 555 {
t.Errorf("Expected attr_5=555 (modified), got %v (type %T)", value, value)
}
}
if attr.Name == "extra" {
extraFound = true
if intValue, ok := value.(int32); !ok || intValue != 2000 {
t.Errorf("Expected extra=2000 (modified), got %v (type %T)", value, value)
}
}
}
if !attr3Found {
t.Error("Attribute 'attr_3' not found")
}
if !attr5Found {
t.Error("Attribute 'attr_5' not found")
}
if !extraFound {
t.Error("Attribute 'extra' not found")
}
}
// TestAttributeModification_DenseDifferentSize tests modifying dense attributes with different sizes.
//
// Verifies:
// - Modifying short string → long string in dense storage
// - Modifying long string → short string in dense storage
// - Delete + insert logic works correctly
//
// Reference: H5HF.c - H5HF_remove() + H5HF_insert().
//
//nolint:gocognit // Test function with multiple verification steps
func TestAttributeModification_DenseDifferentSize(t *testing.T) {
tempDir := t.TempDir()
testFile := filepath.Join(tempDir, "attr_modify_dense_size.h5")
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{5}
ds, err := fw.CreateDataset("/data", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Create 8 attributes to trigger dense storage
for i := 0; i < 7; i++ {
err = ds.WriteAttribute(fmt.Sprintf("padding_%d", i), int32(i))
if err != nil {
t.Fatalf("Failed to write padding attribute %d: %v", i, err)
}
}
// Add attribute with short string (8th attribute - triggers dense)
err = ds.WriteAttribute("name", "A")
if err != nil {
t.Fatalf("Failed to write short string: %v", err)
}
// Modify to long string (different size)
err = ds.WriteAttribute("name", "VeryLongAttributeValueThatExceedsOriginalSize")
if err != nil {
t.Fatalf("Failed to modify to long string: %v", err)
}
// Modify back to short string
err = ds.WriteAttribute("name", "B")
if err != nil {
t.Fatalf("Failed to modify back to short string: %v", err)
}
// Close and verify
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
defer func() {
_ = f.Close()
_ = os.Remove(testFile)
}()
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "data" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'data'")
}
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 8 {
t.Fatalf("Expected 8 attributes, got %d", len(attrs))
}
// Find and verify the "name" attribute
nameFound := false
for _, attr := range attrs {
if attr.Name != "name" {
continue
}
nameFound = true
value, err := attr.ReadValue()
if err != nil {
t.Fatalf("Failed to read attribute value: %v", err)
}
if strValue, ok := value.(string); !ok || strValue != "B" {
t.Errorf("Expected name='B', got %v (type %T)", value, value)
}
break
}
if !nameFound {
t.Error("Attribute 'name' not found")
}
}
// TestAttributeDeletion_Dense tests deletion of attributes from dense storage.
//
// Verifies:
// - Creating 10 attributes (triggers dense storage)
// - Deleting 2 attributes
// - Remaining 8 attributes are intact
// - Deleted attributes are not found
//
// Reference: H5Adense.c - H5A__dense_remove(), H5Adelete.c.
//
//nolint:gocognit // Test function with multiple verification steps
func TestAttributeDeletion_Dense(t *testing.T) {
tempDir, err := os.MkdirTemp("", "hdf5_test_*")
if err != nil {
t.Fatalf("Failed to create temp dir: %v", err)
}
defer os.RemoveAll(tempDir)
testFile := filepath.Join(tempDir, "attr_delete_dense.h5")
// Step 1: Create file with dataset
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{5}
ds, err := fw.CreateDataset("/data", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Step 2: Create 10 attributes (triggers dense storage at attr 8)
for i := 0; i < 10; i++ {
attrName := fmt.Sprintf("attr%d", i)
err = ds.WriteAttribute(attrName, int32(i*10))
if err != nil {
t.Fatalf("Failed to write attribute %s: %v", attrName, err)
}
}
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file after creation: %v", err)
}
// Step 3: Reopen file in read-write mode
fw, err = hdf5.OpenForWrite(testFile, hdf5.OpenReadWrite)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
dsw, err := fw.OpenDataset("/data")
if err != nil {
t.Fatalf("Failed to open dataset: %v", err)
}
// Step 4: Delete 2 attributes
err = dsw.DeleteAttribute("attr3")
if err != nil {
t.Fatalf("Failed to delete attr3: %v", err)
}
err = dsw.DeleteAttribute("attr7")
if err != nil {
t.Fatalf("Failed to delete attr7: %v", err)
}
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file after deletion: %v", err)
}
// Step 5: Read back and verify
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file for verification: %v", err)
}
// Access dataset through walk
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "data" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'data'")
}
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
// Should have 8 attributes remaining (10 - 2)
if len(attrs) != 8 {
t.Fatalf("Expected 8 attributes, got %d", len(attrs))
}
// Verify deleted attributes are not present
for _, attr := range attrs {
if attr.Name == "attr3" || attr.Name == "attr7" {
t.Errorf("Deleted attribute %s still exists", attr.Name)
}
}
// Verify remaining attributes are intact
expectedAttrs := map[string]int32{
"attr0": 0,
"attr1": 10,
"attr2": 20,
// attr3 deleted
"attr4": 40,
"attr5": 50,
"attr6": 60,
// attr7 deleted
"attr8": 80,
"attr9": 90,
}
for _, attr := range attrs {
expectedValue, exists := expectedAttrs[attr.Name]
if !exists {
t.Errorf("Unexpected attribute: %s", attr.Name)
continue
}
value, err := attr.ReadValue()
if err != nil {
t.Errorf("Failed to read attribute %s: %v", attr.Name, err)
continue
}
if intValue, ok := value.(int32); !ok || intValue != expectedValue {
t.Errorf("Attribute %s: expected %d, got %v (type %T)",
attr.Name, expectedValue, value, value)
}
}
// Close file before cleanup
if err := f.Close(); err != nil {
t.Errorf("Failed to close file: %v", err)
}
}
// TestAttributeDeletion_DenseDeleteAll tests deleting all attributes from dense storage.
//
// Verifies:
// - Creating 10 attributes (dense storage)
// - Deleting all 10 attributes
// - Attribute count becomes 0
//
// Reference: H5Adense.c - H5A__dense_remove().
//
//nolint:gocognit // Test function with loop over multiple deletions
func TestAttributeDeletion_DenseDeleteAll(t *testing.T) {
tempDir, err := os.MkdirTemp("", "hdf5_test_*")
if err != nil {
t.Fatalf("Failed to create temp dir: %v", err)
}
defer os.RemoveAll(tempDir)
testFile := filepath.Join(tempDir, "attr_delete_all.h5")
// Step 1: Create file with dataset
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{5}
ds, err := fw.CreateDataset("/data", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Step 2: Create 10 attributes
for i := 0; i < 10; i++ {
attrName := fmt.Sprintf("attr%d", i)
err = ds.WriteAttribute(attrName, int32(i))
if err != nil {
t.Fatalf("Failed to write attribute %s: %v", attrName, err)
}
}
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file after creation: %v", err)
}
// Step 3: Reopen and delete all attributes
fw, err = hdf5.OpenForWrite(testFile, hdf5.OpenReadWrite)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
dsw, err := fw.OpenDataset("/data")
if err != nil {
t.Fatalf("Failed to open dataset: %v", err)
}
// Delete all attributes
for i := 0; i < 10; i++ {
attrName := fmt.Sprintf("attr%d", i)
err = dsw.DeleteAttribute(attrName)
if err != nil {
t.Fatalf("Failed to delete %s: %v", attrName, err)
}
}
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file after deletion: %v", err)
}
// Step 4: Verify no attributes remain
f, err := hdf5.Open(testFile)
if err != nil {
t.Fatalf("Failed to reopen file for verification: %v", err)
}
var dataset *hdf5.Dataset
f.Walk(func(_ string, obj hdf5.Object) {
if ds, ok := obj.(*hdf5.Dataset); ok && ds.Name() == "data" {
dataset = ds
}
})
if dataset == nil {
t.Fatalf("Failed to find dataset 'data'")
}
attrs, err := dataset.Attributes()
if err != nil {
t.Fatalf("Failed to read attributes: %v", err)
}
if len(attrs) != 0 {
t.Errorf("Expected 0 attributes, got %d", len(attrs))
}
// Close file before cleanup
if err := f.Close(); err != nil {
t.Errorf("Failed to close file: %v", err)
}
}
// TestAttributeDeletion_DenseNotFound tests error handling for deleting non-existent attribute.
//
// Verifies:
// - Attempting to delete non-existent attribute returns error
//
// Reference: H5Adelete.c - error handling.
func TestAttributeDeletion_DenseNotFound(t *testing.T) {
tempDir, err := os.MkdirTemp("", "hdf5_test_*")
if err != nil {
t.Fatalf("Failed to create temp dir: %v", err)
}
defer os.RemoveAll(tempDir)
testFile := filepath.Join(tempDir, "attr_delete_notfound.h5")
// Step 1: Create file with dataset and attributes
fw, err := hdf5.CreateForWrite(testFile, hdf5.CreateTruncate)
if err != nil {
t.Fatalf("Failed to create file: %v", err)
}
dims := []uint64{5}
ds, err := fw.CreateDataset("/data", hdf5.Int32, dims)
if err != nil {
t.Fatalf("Failed to create dataset: %v", err)
}
// Create 8 attributes (dense storage)
for i := 0; i < 8; i++ {
attrName := fmt.Sprintf("attr%d", i)
err = ds.WriteAttribute(attrName, int32(i))
if err != nil {
t.Fatalf("Failed to write attribute %s: %v", attrName, err)
}
}
err = fw.Close()
if err != nil {
t.Fatalf("Failed to close file: %v", err)
}
// Step 2: Reopen and try to delete non-existent attribute
fw, err = hdf5.OpenForWrite(testFile, hdf5.OpenReadWrite)
if err != nil {
t.Fatalf("Failed to reopen file: %v", err)
}
dsw, err := fw.OpenDataset("/data")
if err != nil {
t.Fatalf("Failed to open dataset: %v", err)
}
// Try to delete non-existent attribute
err = dsw.DeleteAttribute("nonexistent")
if err == nil {
t.Error("Expected error when deleting non-existent attribute, got nil")
}
_ = fw.Close()
}