allow fillValue null

Author: brokkoli71

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

@@ -85,8 +85,9 @@ default void writeChunk(long[] chunkCoords, ucar.ma2.Array chunkArray) throws Za
         ArrayMetadata metadata = metadata();
         String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
         StoreHandle chunkHandle = storeHandle().resolve(chunkKeys);
+        Object parsedFillValue = metadata.parsedFillValue();
 
-        if (MultiArrayUtils.allValuesEqual(chunkArray, metadata.parsedFillValue())) {
+        if (parsedFillValue != null && MultiArrayUtils.allValuesEqual(chunkArray, parsedFillValue)) {
             chunkHandle.delete();
         } else {
             ByteBuffer chunkBytes = codecPipeline().encode(chunkArray);

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

@@ -42,6 +42,7 @@ public class ArrayMetadata implements dev.zarr.zarrjava.core.ArrayMetadata {
   @JsonIgnore
   public final Object parsedFillValue;
 
+  @Nullable
   public Codec[] filters;
   @Nullable
   public Codec compressor;
@@ -56,11 +57,11 @@ public ArrayMetadata(
       @JsonProperty(value = "shape", required = true) long[] shape,
       @JsonProperty(value = "chunks", required = true) int[] chunks,
       @JsonProperty(value = "dtype", required = true) DataType dataType,
-      @Nullable @JsonProperty(value = "fill_value", required = true) Object fillValue, //todo test when null
+      @Nullable @JsonProperty(value = "fill_value", required = true) Object fillValue,
       @JsonProperty(value = "order", required = true) Order order,
-      @Nullable @JsonProperty(value = "dimension_separator") Separator dimensionSeparator,
-      @Nullable @JsonProperty(value = "filters") Codec[] filters,
-      @Nullable @JsonProperty(value = "compressor") Codec compressor
+      @Nullable @JsonProperty(value = "filters", required = true) Codec[] filters,
+      @Nullable @JsonProperty(value = "compressor", required = true) Codec compressor,
+      @Nullable @JsonProperty(value = "dimension_separator") Separator dimensionSeparator
   ) throws ZarrException {
     super();
     if (zarrFormat != this.zarrFormat) {
@@ -72,7 +73,11 @@ public ArrayMetadata(
     this.dataType = dataType;
     this.endianness = dataType.getEndianness();
     this.fillValue = fillValue;
-    this.parsedFillValue = parseFillValue(fillValue, this.dataType);
+    if (fillValue == null) {
+      this.parsedFillValue = null;
+    } else {
+      this.parsedFillValue = parseFillValue(fillValue, this.dataType);
+    }
     this.order = order;
     this.dimensionSeparator = dimensionSeparator;
     this.filters = filters;
@@ -107,7 +112,7 @@ public DataType dataType() {
   @Override
   public Array allocateFillValueChunk() {
       ucar.ma2.Array outputArray = ucar.ma2.Array.factory(dataType.getMA2DataType(), chunks);
-      MultiArrayUtils.fill(outputArray, parsedFillValue);
+      if (parsedFillValue != null) MultiArrayUtils.fill(outputArray, parsedFillValue);
       return outputArray;
   }
 

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

@@ -13,7 +13,7 @@ public class ArrayMetadataBuilder {
   DataType dataType = null;
   Order order = Order.C;
   Separator dimensionSeparator = Separator.DOT;
-  Object fillValue = 0;
+  Object fillValue = null;
   Codec[] filters = null;
   Codec compressor = null;
 
@@ -115,9 +115,9 @@ public ArrayMetadata build() throws ZarrException {
         dataType,
         fillValue,
         order,
-        dimensionSeparator,
         filters,
-        compressor
+        compressor,
+        dimensionSeparator
     );
   }
 }

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

@@ -580,4 +580,32 @@ public void testV2createZlib(int level) throws IOException, ZarrException {
         Assertions.assertEquals(7 * 6, outArray.getSize());
         Assertions.assertEquals(0, outArray.getByte(0));
     }
+
+    @ParameterizedTest
+    @ValueSource(strings = {"BOOL", "INT8", "UINT8", "INT16", "UINT16", "INT32", "UINT32", "INT64", "UINT64", "FLOAT32", "FLOAT64"})
+    public void testV2noFillValue(dev.zarr.zarrjava.v2.DataType dataType) throws IOException, ZarrException {
+        StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("v2_no_fillvalue", dataType.name());
+
+        dev.zarr.zarrjava.v2.Array array = dev.zarr.zarrjava.v2.Array.create(
+            storeHandle,
+            dev.zarr.zarrjava.v2.Array.metadataBuilder()
+                .withShape(15, 10)
+                .withDataType(dataType)
+                .withChunks(4, 5)
+                .build()
+        );
+        Assertions.assertNull(array.metadata().fillValue);
+
+        ucar.ma2.Array outArray = array.read(new long[]{0, 0}, new int[]{1, 1});
+        if (dataType == dev.zarr.zarrjava.v2.DataType.BOOL) {
+            Assertions.assertFalse(outArray.getBoolean(0));
+        } else {
+            Assertions.assertEquals(0, outArray.getByte(0));
+        }
+
+        dev.zarr.zarrjava.v2.Array array2 = dev.zarr.zarrjava.v2.Array.open(
+            storeHandle
+        );
+        Assertions.assertNull(array2.metadata().fillValue);
+    }
 }