Fix codecs without config (#34)

* allow no config for BytesCodec

* pretty print json

* testZarrJsonFormat

* add @JsonIgnore annotation to codec name fields for serialization

* remove duplicate 'id' for v2 compressors in .zarray

* JsonInclude.Include.NON_NULL for all json attributes

* JsonInclude.Include.NON_NULL only for v3

---------

Co-authored-by: brokkoli71 <[email protected]>

Author: brokkoli71

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

@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.core;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.utils.MultiArrayUtils;
@@ -16,6 +17,7 @@ public abstract class ArrayMetadata {
 
     public final long[] shape;
 
+    @JsonInclude(JsonInclude.Include.ALWAYS)
     @JsonProperty("fill_value")
     public final Object fillValue;
     @JsonIgnore

src/main/java/dev/zarr/zarrjava/core/codec/core/BytesCodec.java

@@ -1,38 +1,44 @@
 package dev.zarr.zarrjava.core.codec.core;
 
 import com.fasterxml.jackson.annotation.JsonValue;
+import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.codec.ArrayBytesCodec;
 import ucar.ma2.*;
 
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 
 public abstract class BytesCodec extends ArrayBytesCodec {
-    protected abstract ByteOrder getByteOrder();
+    protected abstract ByteOrder getByteOrder() throws ZarrException;
 
     @Override
-public Array decode(ByteBuffer chunkBytes) {
-    chunkBytes.order(getByteOrder());
-    DataType dtype = arrayMetadata.dataType.getMA2DataType();
-    int[] shape = arrayMetadata.chunkShape;
-
-    // Array.factory does not support boolean arrays directly from ByteBuffer
-    if (dtype == DataType.BOOLEAN) {
-        int size = chunkBytes.remaining();
-        boolean[] bools = new boolean[size];
-        for (int i = 0; i < size; i++) {
-            bools[i] = chunkBytes.get(i) != 0;
-        }
+    public Array decode(ByteBuffer chunkBytes) throws ZarrException {
+        ByteOrder order = ByteOrder.BIG_ENDIAN; // Default for 1-byte types
+        if (arrayMetadata.dataType.getByteCount() > 1)
+            order = getByteOrder();
+        chunkBytes.order(order);
+        DataType dtype = arrayMetadata.dataType.getMA2DataType();
+        int[] shape = arrayMetadata.chunkShape;
+
+        // Array.factory does not support boolean arrays directly from ByteBuffer
+        if (dtype == DataType.BOOLEAN) {
+            int size = chunkBytes.remaining();
+            boolean[] bools = new boolean[size];
+            for (int i = 0; i < size; i++) {
+                bools[i] = chunkBytes.get(i) != 0;
+            }
 
-        Index index = Index.factory(shape);
-        return Array.factory(DataType.BOOLEAN, index, bools);
+            Index index = Index.factory(shape);
+            return Array.factory(DataType.BOOLEAN, index, bools);
+        }
+        return Array.factory(dtype, shape, chunkBytes);
     }
 
-    return Array.factory(dtype, shape, chunkBytes);
-}
     @Override
-    public ByteBuffer encode(Array chunkArray) {
-        ByteOrder order = getByteOrder();
+    public ByteBuffer encode(Array chunkArray) throws ZarrException {
+        ByteOrder order = ByteOrder.BIG_ENDIAN; // Default for 1-byte types
+        if (arrayMetadata.dataType.getByteCount() > 1)
+            order = getByteOrder();
 
         // Boolean
         if (chunkArray instanceof ArrayBoolean) {
@@ -94,6 +100,10 @@ public ByteOrder getByteOrder() {
                     throw new RuntimeException("Unreachable");
             }
         }
+
+        public static Endian nativeOrder() {
+            return ByteOrder.nativeOrder() == ByteOrder.LITTLE_ENDIAN ? LITTLE : BIG;
+        }
     }
 
 }

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

@@ -1,6 +1,6 @@
 package dev.zarr.zarrjava.v2;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
@@ -18,6 +18,7 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import static dev.zarr.zarrjava.v2.Node.makeObjectMapper;
+import static dev.zarr.zarrjava.v2.Node.makeObjectWriter;
 
 public class Array extends dev.zarr.zarrjava.core.Array implements Node {
 
@@ -141,8 +142,8 @@ public static Array create(StoreHandle storeHandle, ArrayMetadata arrayMetadata,
           "Trying to create a new array in " + storeHandle + ". But " + metadataHandle
               + " already exists.");
     }
-    ObjectMapper objectMapper = makeObjectMapper();
-    ByteBuffer metadataBytes = ByteBuffer.wrap(objectMapper.writeValueAsBytes(arrayMetadata));
+    ObjectWriter objectWriter = makeObjectWriter();
+    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(arrayMetadata));
     metadataHandle.set(metadataBytes);
     return new Array(storeHandle, arrayMetadata);
   }

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

@@ -1,6 +1,6 @@
 package dev.zarr.zarrjava.v2;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
@@ -14,6 +14,7 @@
 import java.nio.file.Paths;
 import java.util.function.Function;
 import static dev.zarr.zarrjava.v2.Node.makeObjectMapper;
+import static dev.zarr.zarrjava.v2.Node.makeObjectWriter;
 
 public class Group extends dev.zarr.zarrjava.core.Group implements Node{
   public GroupMetadata metadata;
@@ -41,8 +42,8 @@ public static Group open(String path) throws IOException {
   public static Group create(
       @Nonnull StoreHandle storeHandle, @Nonnull GroupMetadata groupMetadata
   ) throws IOException {
-    ObjectMapper objectMapper = makeObjectMapper();
-    ByteBuffer metadataBytes = ByteBuffer.wrap(objectMapper.writeValueAsBytes(groupMetadata));
+    ObjectWriter objectWriter = makeObjectWriter();
+    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(groupMetadata));
     storeHandle.resolve(ZGROUP).set(metadataBytes);
     return new Group(storeHandle, groupMetadata);
   }

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

@@ -1,6 +1,8 @@
 package dev.zarr.zarrjava.v2;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.store.FilesystemStore;
@@ -21,7 +23,11 @@ static ObjectMapper makeObjectMapper() {
     return objectMapper;
   }
 
-  /**
+  static ObjectWriter makeObjectWriter() {
+    return makeObjectMapper().writerWithDefaultPrettyPrinter();
+  }
+
+    /**
    * Opens an existing Zarr array or group at a specified storage location.
    *
    * @param storeHandle the storage location of the Zarr array

src/main/java/dev/zarr/zarrjava/v2/codec/core/BloscCodec.java

@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.v2.codec.core;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonParser;
@@ -22,6 +23,7 @@
 
 public class BloscCodec extends dev.zarr.zarrjava.core.codec.core.BloscCodec implements Codec {
 
+  @JsonIgnore
   public final String id = "blosc";
 
   @Nonnull

src/main/java/dev/zarr/zarrjava/v2/codec/core/BytesCodec.java

@@ -1,8 +1,5 @@
 package dev.zarr.zarrjava.v2.codec.core;
 
-import com.fasterxml.jackson.annotation.JsonCreator;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.ArrayMetadata;
 import dev.zarr.zarrjava.v2.codec.Codec;
 
@@ -14,9 +11,7 @@ public class BytesCodec extends dev.zarr.zarrjava.core.codec.core.BytesCodec imp
     @Nonnull
     public final Endian endian;
 
-    @JsonCreator
-    public BytesCodec(
-        @JsonProperty(value = "endian", defaultValue = "little") Endian endian) {
+    public BytesCodec(Endian endian) {
         this.endian = endian;
     }
 

src/main/java/dev/zarr/zarrjava/v2/codec/core/ZlibCodec.java

@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.v2.codec.core;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.core.ArrayMetadata;
@@ -16,6 +17,7 @@
 
 public class ZlibCodec extends BytesBytesCodec implements Codec {
 
+    @JsonIgnore
     public final String id = "zlib";
     public final int level;
 

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

@@ -1,6 +1,6 @@
 package dev.zarr.zarrjava.v3;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectWriter;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
@@ -17,6 +17,7 @@
 import java.util.stream.Collectors;
 import javax.annotation.Nonnull;
 import static dev.zarr.zarrjava.v3.Node.makeObjectMapper;
+import static dev.zarr.zarrjava.v3.Node.makeObjectWriter;
 
 public class Array extends dev.zarr.zarrjava.core.Array implements Node {
 
@@ -136,8 +137,8 @@ public static Array create(StoreHandle storeHandle, ArrayMetadata arrayMetadata,
           "Trying to create a new array in " + storeHandle + ". But " + metadataHandle
               + " already exists.");
     }
-    ObjectMapper objectMapper = makeObjectMapper();
-    ByteBuffer metadataBytes = ByteBuffer.wrap(objectMapper.writeValueAsBytes(arrayMetadata));
+    ObjectWriter objectWriter = makeObjectWriter();
+    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(arrayMetadata));
     metadataHandle.set(metadataBytes);
     return new Array(storeHandle, arrayMetadata);
   }
@@ -182,8 +183,8 @@ public static ArrayMetadataBuilder metadataBuilder(ArrayMetadata existingMetadat
   }
 
   private Array writeMetadata(ArrayMetadata newArrayMetadata) throws ZarrException, IOException {
-    ObjectMapper objectMapper = makeObjectMapper();
-    ByteBuffer metadataBytes = ByteBuffer.wrap(objectMapper.writeValueAsBytes(newArrayMetadata));
+    ObjectWriter objectWriter = makeObjectWriter();
+    ByteBuffer metadataBytes = ByteBuffer.wrap(objectWriter.writeValueAsBytes(newArrayMetadata));
     storeHandle.resolve(ZARR_JSON)
         .set(metadataBytes);
     return new Array(storeHandle, newArrayMetadata);

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

@@ -73,6 +73,12 @@ public ArrayMetadataBuilder withDefaultChunkKeyEncoding(Separator separator) {
     return this;
   }
 
+    public ArrayMetadataBuilder withDefaultChunkKeyEncoding() {
+        this.chunkKeyEncoding = new DefaultChunkKeyEncoding(
+            new DefaultChunkKeyEncoding.Configuration(Separator.SLASH));
+        return this;
+    }
+
   public ArrayMetadataBuilder withDefaultChunkKeyEncoding(String separator) {
     this.chunkKeyEncoding =
         new DefaultChunkKeyEncoding(
@@ -85,6 +91,12 @@ public ArrayMetadataBuilder withV2ChunkKeyEncoding(Separator separator) {
     return this;
   }
 
+  public ArrayMetadataBuilder withV2ChunkKeyEncoding() {
+    this.chunkKeyEncoding = new V2ChunkKeyEncoding(
+        new V2ChunkKeyEncoding.Configuration(Separator.DOT));
+    return this;
+  }
+
   public ArrayMetadataBuilder withV2ChunkKeyEncoding(String separator) {
     this.chunkKeyEncoding =
         new V2ChunkKeyEncoding(new V2ChunkKeyEncoding.Configuration(Separator.valueOf(separator)));