fix array.setAttributes

Author: brokkoli71

src/main/java/dev/zarr/zarrjava/core/Attributes.java

@@ -6,13 +6,20 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.function.Function;
 
 public class Attributes extends HashMap<String, Object> {
 
     public Attributes() {
         super();
     }
 
+    public Attributes (Function<Attributes, Attributes> attributeMapper) {
+        super();
+        attributeMapper.apply(this);
+    }
+
+
     public Attributes(Map<String, Object> attributes) {
         super(attributes);
     }
@@ -90,7 +97,7 @@ public Attributes getAttributes(String key) {
 
     public <T> T[] getArray(String key, Class<T> clazz) throws ZarrException {
     Object value = this.get(key);
-    if (value instanceof Object[] && ( ((Object[]) value).length == 0 || clazz.isInstance(((Object[]) value)[0]) )) {
+    if (value instanceof Object[] && (((Object[]) value).length == 0 || clazz.isInstance(((Object[]) value)[0]) )) {
         return (T[]) value;
     }
     if (value instanceof List) {

src/main/java/dev/zarr/zarrjava/v2/Array.java

@@ -191,7 +191,6 @@ private Array writeMetadata(ArrayMetadata newArrayMetadata) throws ZarrException
    * @throws IOException throws IOException if the new metadata cannot be serialized
    */
   public Array resize(long[] newShape) throws ZarrException, IOException {
-    //TODO: test
     if (newShape.length != metadata.ndim()) {
       throw new IllegalArgumentException(
           "'newShape' needs to have rank '" + metadata.ndim() + "'.");
@@ -213,7 +212,7 @@ public Array resize(long[] newShape) throws ZarrException, IOException {
    */
   public Array setAttributes(Attributes newAttributes) throws ZarrException, IOException {
     ArrayMetadata newArrayMetadata =
-        ArrayMetadataBuilder.fromArrayMetadata(metadata)
+        ArrayMetadataBuilder.fromArrayMetadata(metadata, false)
             .withAttributes(newAttributes)
             .build();
     return writeMetadata(newArrayMetadata);

src/main/java/dev/zarr/zarrjava/v2/ArrayMetadataBuilder.java

@@ -24,6 +24,10 @@ protected ArrayMetadataBuilder() {
   }
 
   protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetadata) {
+    return fromArrayMetadata(arrayMetadata, true);
+  }
+
+  protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetadata, boolean withAttributes) {
     ArrayMetadataBuilder builder = new ArrayMetadataBuilder();
     builder.shape = arrayMetadata.shape;
     builder.chunks = arrayMetadata.chunks;
@@ -33,6 +37,9 @@ protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetad
     builder.fillValue = arrayMetadata.parsedFillValue;
     builder.filters = arrayMetadata.filters;
     builder.compressor = arrayMetadata.compressor;
+    if (withAttributes) {
+      builder.attributes = arrayMetadata.attributes;
+    }
     return builder;
   }
 

src/main/java/dev/zarr/zarrjava/v3/Array.java

@@ -12,8 +12,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import javax.annotation.Nonnull;
@@ -217,7 +215,7 @@ public Array resize(long[] newShape) throws ZarrException, IOException {
    */
   public Array setAttributes(Attributes newAttributes) throws ZarrException, IOException {
     ArrayMetadata newArrayMetadata =
-        ArrayMetadataBuilder.fromArrayMetadata(metadata)
+        ArrayMetadataBuilder.fromArrayMetadata(metadata, false)
             .withAttributes(newAttributes)
             .build();
     return writeMetadata(newArrayMetadata);

src/main/java/dev/zarr/zarrjava/v3/ArrayMetadataBuilder.java

@@ -35,16 +35,22 @@ protected ArrayMetadataBuilder() {
   }
 
   protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetadata) {
+    return fromArrayMetadata(arrayMetadata, true);
+  }
+
+  protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetadata, boolean withAttributes) {
     ArrayMetadataBuilder builder = new ArrayMetadataBuilder();
     builder.shape = arrayMetadata.shape;
     builder.dataType = arrayMetadata.dataType;
     builder.chunkGrid = arrayMetadata.chunkGrid;
     builder.chunkKeyEncoding = arrayMetadata.chunkKeyEncoding;
     builder.fillValue = arrayMetadata.parsedFillValue;
     builder.codecs = arrayMetadata.codecs;
-    builder.attributes = arrayMetadata.attributes;
     builder.dimensionNames = arrayMetadata.dimensionNames;
     builder.storageTransformers = arrayMetadata.storageTransformers;
+    if (withAttributes) {
+      builder.attributes = arrayMetadata.attributes;
+    }
     return builder;
   }
 

src/test/java/dev/zarr/zarrjava/ZarrTest.java

@@ -65,6 +65,7 @@ protected Attributes defaultTestAttributes() {
             put("long_array", new long[]{1, 2, 3});
             put("double_array", new double[]{1.0, 2.0, 3.0});
             put("float_array", new float[]{1.0f, 2.0f, 3.0f});
+            put("boolean_array", new boolean[]{true, false, true});
             put("nested", new Attributes() {{
                 put("element", "value");
             }});
@@ -96,6 +97,7 @@ protected void assertContainsTestAttributes(Attributes attributes) throws ZarrEx
         Assertions.assertArrayEquals(new long[]{1, 2, 3}, attributes.getLongArray("long_array"));
         Assertions.assertArrayEquals(new double[]{1, 2, 3}, attributes.getDoubleArray("double_array"));
         Assertions.assertArrayEquals(new float[]{1, 2, 3}, attributes.getFloatArray("float_array"));
+        Assertions.assertArrayEquals(new boolean[]{true, false, true}, attributes.getBooleanArray("boolean_array"));
         Assertions.assertEquals("value", attributes.getAttributes("nested").getString("element"));
         Assertions.assertArrayEquals(
             new Attributes[]{

src/test/java/dev/zarr/zarrjava/ZarrV2Test.java

@@ -288,12 +288,15 @@ public void testSetAndUpdateAttributes() throws IOException, ZarrException {
             .withShape(10, 10)
             .withDataType(DataType.UINT8)
             .withChunks(5, 5)
+            .withAttributes(new Attributes(b -> b.add("some", "value")))
             .build();
 
         Array array = Array.create(storeHandle, arrayMetadata);
+        Assertions.assertEquals("value", array.metadata().attributes().getString("some"));
         array.setAttributes(defaultTestAttributes());
         array = Array.open(storeHandle);
         assertContainsTestAttributes(array.metadata().attributes());
+        Assertions.assertNull(array.metadata().attributes().get("some"));
 
         // add attribute
         array = array.updateAttributes(b -> b.add("new_attribute", "new_value"));

src/test/java/dev/zarr/zarrjava/ZarrV3Test.java

@@ -602,12 +602,15 @@ public void testSetAndUpdateAttributes() throws IOException, ZarrException {
             .withShape(10, 10)
             .withDataType(DataType.UINT8)
             .withChunkShape(5, 5)
+            .withAttributes(new Attributes(b -> b.add("some", "value")))
             .build();
 
         Array array = Array.create(storeHandle, arrayMetadata);
+        Assertions.assertEquals("value", array.metadata().attributes().getString("some"));
         array.setAttributes(defaultTestAttributes());
         array = Array.open(storeHandle);
         assertContainsTestAttributes(array.metadata().attributes());
+        Assertions.assertNull(array.metadata().attributes().get("some"));
 
         // add attribute
         array = array.updateAttributes(b -> b.add("new_attribute", "new_value"));