isolate v2 and v3 with common core.chunkkeyencoding

brokkoli71 · brokkoli71 · commit 494b01ae7d63 · 2025-09-17T17:32:46.000+02:00
diff --git a/src/main/java/dev/zarr/zarrjava/core/ArrayMetadata.java b/src/main/java/dev/zarr/zarrjava/core/ArrayMetadata.java
@@ -3,7 +3,7 @@
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.utils.MultiArrayUtils;
 import dev.zarr.zarrjava.utils.Utils;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.ChunkKeyEncoding;
+import dev.zarr.zarrjava.core.chunkkeyencoding.ChunkKeyEncoding;
 import ucar.ma2.Array;
 
 import javax.annotation.Nonnull;
@@ -132,10 +132,10 @@ final class CoreArrayMetadata {
 
     public final long[] shape;
     public final int[] chunkShape;
-    public final dev.zarr.zarrjava.v3.DataType dataType;
+    public final DataType dataType;
     public final Object parsedFillValue;
 
-    public CoreArrayMetadata(long[] shape, int[] chunkShape, dev.zarr.zarrjava.v3.DataType dataType,
+    public CoreArrayMetadata(long[] shape, int[] chunkShape, DataType dataType,
                              Object parsedFillValue) {
       this.shape = shape;
       this.chunkShape = chunkShape;
diff --git a/src/main/java/dev/zarr/zarrjava/core/chunkkeyencoding/ChunkKeyEncoding.java b/src/main/java/dev/zarr/zarrjava/core/chunkkeyencoding/ChunkKeyEncoding.java
@@ -0,0 +1,7 @@
+package dev.zarr.zarrjava.core.chunkkeyencoding;
+
+public interface ChunkKeyEncoding {
+
+  String[] encodeChunkKey(long[] chunkCoords);
+
+}
diff --git a/src/main/java/dev/zarr/zarrjava/core/chunkkeyencoding/Separator.java b/src/main/java/dev/zarr/zarrjava/core/chunkkeyencoding/Separator.java
@@ -1,4 +1,4 @@
-package dev.zarr.zarrjava.v3.chunkkeyencoding;
+package dev.zarr.zarrjava.core.chunkkeyencoding;
 
 import com.fasterxml.jackson.annotation.JsonValue;
 
diff --git a/src/main/java/dev/zarr/zarrjava/core/codec/CodecBuilder.java b/src/main/java/dev/zarr/zarrjava/core/codec/CodecBuilder.java
@@ -1,6 +1,6 @@
 package dev.zarr.zarrjava.core.codec;
 
-import dev.zarr.zarrjava.v3.DataType;
+import dev.zarr.zarrjava.core.DataType;
 
 public abstract class CodecBuilder {
 
diff --git a/src/main/java/dev/zarr/zarrjava/v2/ArrayMetadata.java b/src/main/java/dev/zarr/zarrjava/v2/ArrayMetadata.java
@@ -4,10 +4,10 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.chunkkeyencoding.ChunkKeyEncoding;
 import dev.zarr.zarrjava.utils.MultiArrayUtils;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.ChunkKeyEncoding;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.Separator;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.V2ChunkKeyEncoding;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
+import dev.zarr.zarrjava.v2.chunkkeyencoding.V2ChunkKeyEncoding;
 import dev.zarr.zarrjava.v2.codec.Codec;
 import ucar.ma2.Array;
 
@@ -26,9 +26,8 @@ public class ArrayMetadata implements dev.zarr.zarrjava.core.ArrayMetadata {
   public int[] chunks;
 
   @JsonProperty("dtype")
-  public DataType dataTypeV2;
-  @JsonIgnore
-  public final dev.zarr.zarrjava.v3.DataType dataType;
+  public DataType dataType;
+
   @JsonIgnore
   public final Endianness endianness;
 
@@ -56,7 +55,7 @@ public ArrayMetadata(
       @JsonProperty(value = "zarr_format", required = true) int zarrFormat,
       @JsonProperty(value = "shape", required = true) long[] shape,
       @JsonProperty(value = "chunks", required = true) int[] chunks,
-      @JsonProperty(value = "dtype", required = true) DataType dataTypeV2,
+      @JsonProperty(value = "dtype", required = true) DataType dataType,
       @Nullable @JsonProperty(value = "fill_value", required = true) Object fillValue, //todo test when null
       @JsonProperty(value = "order", required = true) Order order,
       @Nullable @JsonProperty(value = "dimension_separator") Separator dimensionSeparator,
@@ -70,9 +69,8 @@ public ArrayMetadata(
     }
     this.shape = shape;
     this.chunks = chunks;
-    this.dataTypeV2 = dataTypeV2;
-    this.endianness = dataTypeV2.getEndianness();
-    this.dataType = dataTypeV2.toV3();
+    this.dataType = dataType;
+    this.endianness = dataType.getEndianness();
     this.fillValue = fillValue;
     this.parsedFillValue = parseFillValue(fillValue, this.dataType);
     this.order = order;
@@ -102,7 +100,7 @@ public long[] shape() {
   }
 
   @Override
-  public dev.zarr.zarrjava.v3.DataType dataType() {
+  public DataType dataType() {
     return dataType;
   }
 
@@ -116,7 +114,7 @@ public Array allocateFillValueChunk() {
   @Override
   public ChunkKeyEncoding chunkKeyEncoding() {
     Separator separator = dimensionSeparator == null ? Separator.DOT : dimensionSeparator;
-    return new V2ChunkKeyEncoding(new V2ChunkKeyEncoding.Configuration(separator));
+    return new V2ChunkKeyEncoding(separator);
   }
 
   @Override
diff --git a/src/main/java/dev/zarr/zarrjava/v2/ArrayMetadataBuilder.java b/src/main/java/dev/zarr/zarrjava/v2/ArrayMetadataBuilder.java
@@ -1,7 +1,7 @@
 package dev.zarr.zarrjava.v2;
 
 import dev.zarr.zarrjava.ZarrException;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.Separator;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
 import dev.zarr.zarrjava.v2.codec.Codec;
 import dev.zarr.zarrjava.v2.codec.CodecBuilder;
 
@@ -10,7 +10,7 @@
 public class ArrayMetadataBuilder {
   long[] shape = null;
   int[] chunks = null;
-  DataType dataTypeV2 = null;
+  DataType dataType = null;
   Order order = Order.C;
   Separator dimensionSeparator = Separator.DOT;
   Object fillValue = 0;
@@ -25,7 +25,7 @@ protected static ArrayMetadataBuilder fromArrayMetadata(ArrayMetadata arrayMetad
     ArrayMetadataBuilder builder = new ArrayMetadataBuilder();
     builder.shape = arrayMetadata.shape;
     builder.chunks = arrayMetadata.chunks;
-    builder.dataTypeV2 = arrayMetadata.dataTypeV2;
+    builder.dataType = arrayMetadata.dataType;
     builder.order = arrayMetadata.order;
     builder.dimensionSeparator = arrayMetadata.dimensionSeparator;
     builder.fillValue = arrayMetadata.parsedFillValue;
@@ -45,13 +45,7 @@ public ArrayMetadataBuilder withChunks(int... chunks) {
   }
 
   public ArrayMetadataBuilder withDataType(DataType dataTypeV2) {
-    this.dataTypeV2 = dataTypeV2;
-    return this;
-  }
-
-  //TODO remove v3?
-  public ArrayMetadataBuilder withDataType(dev.zarr.zarrjava.v3.DataType dataType) {
-    this.dataTypeV2 = DataType.fromDataType(dataType);
+    this.dataType = dataTypeV2;
     return this;
   }
 
@@ -76,10 +70,10 @@ public ArrayMetadataBuilder withFilters(Codec... filters) {
   }
 
   public ArrayMetadataBuilder withFilters(Function<CodecBuilder, CodecBuilder> codecBuilder) throws ZarrException {
-    if (dataTypeV2 == null) {
+    if (dataType == null) {
       throw new IllegalStateException("Please call `withDataType` first.");
     }
-    CodecBuilder nestedCodecBuilder = new CodecBuilder(dataTypeV2.toV3());
+    CodecBuilder nestedCodecBuilder = new CodecBuilder(dataType);
     this.filters = codecBuilder.apply(nestedCodecBuilder)
         .build();
     return this;
@@ -91,25 +85,17 @@ public ArrayMetadataBuilder withCompressor(Codec compressor) {
   }
 
   public ArrayMetadataBuilder withBloscCompressor(String cname,  String shuffle, int clevel) {
-    try {
-      this.compressor = new CodecBuilder(dataTypeV2.toV3())
+      this.compressor = new CodecBuilder(dataType)
           .withBlosc(cname, shuffle, clevel)
           .build()[0];
-    } catch (ZarrException e) {
-      throw new RuntimeException(e);
-    }
-    return this;
+      return this;
   }
 
   public ArrayMetadataBuilder withZlibCompressor(int level) {
-    try {
-      this.compressor = new CodecBuilder(dataTypeV2.toV3())
+      this.compressor = new CodecBuilder(dataType)
           .withZlib(level)
           .build()[0];
-    } catch (ZarrException e) {
-      throw new RuntimeException(e);
-    }
-    return this;
+      return this;
   }
 
   public ArrayMetadata build() throws ZarrException {
@@ -119,14 +105,14 @@ public ArrayMetadata build() throws ZarrException {
     if (chunks == null) {
       throw new IllegalStateException("Please call `withChunks` first.");
     }
-    if (dataTypeV2 == null) {
+    if (dataType == null) {
       throw new IllegalStateException("Please call `withDataType` first.");
     }
     return new ArrayMetadata(
         2,
         shape,
         chunks,
-        dataTypeV2,
+        dataType,
         fillValue,
         order,
         dimensionSeparator,
diff --git a/src/main/java/dev/zarr/zarrjava/v2/Codec.java b/src/main/java/dev/zarr/zarrjava/v2/Codec.java
diff --git a/src/main/java/dev/zarr/zarrjava/v2/chunkkeyencoding/V2ChunkKeyEncoding.java b/src/main/java/dev/zarr/zarrjava/v2/chunkkeyencoding/V2ChunkKeyEncoding.java
@@ -0,0 +1,33 @@
+package dev.zarr.zarrjava.v2.chunkkeyencoding;
+
+import dev.zarr.zarrjava.core.chunkkeyencoding.ChunkKeyEncoding;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
+
+import javax.annotation.Nonnull;
+import java.util.Arrays;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class V2ChunkKeyEncoding implements ChunkKeyEncoding {
+
+  public final String name = "v2";
+  @Nonnull
+  public final Separator separator;
+
+  public V2ChunkKeyEncoding(
+      @Nonnull Separator separator
+  ) {
+    this.separator = separator;
+  }
+
+  @Override
+  public String[] encodeChunkKey(long[] chunkCoords) {
+    Stream<String> keys = Arrays.stream(chunkCoords)
+        .mapToObj(Long::toString);
+    if (separator == Separator.SLASH) {
+      return keys.toArray(String[]::new);
+    }
+    return new String[]{keys.collect(Collectors.joining(this.separator.getValue()))};
+  }
+}
+
diff --git a/src/main/java/dev/zarr/zarrjava/v2/codec/CodecBuilder.java b/src/main/java/dev/zarr/zarrjava/v2/codec/CodecBuilder.java
@@ -3,7 +3,7 @@
 import com.scalableminds.bloscjava.Blosc;
 import dev.zarr.zarrjava.ZarrException;
 import dev.zarr.zarrjava.v2.codec.core.ZlibCodec;
-import dev.zarr.zarrjava.v3.DataType;
+import dev.zarr.zarrjava.v2.DataType;
 import dev.zarr.zarrjava.v2.codec.core.*;
 
 import java.util.ArrayList;
diff --git a/src/main/java/dev/zarr/zarrjava/v3/ArrayMetadataBuilder.java b/src/main/java/dev/zarr/zarrjava/v3/ArrayMetadataBuilder.java
@@ -5,7 +5,7 @@
 import dev.zarr.zarrjava.v3.chunkgrid.RegularChunkGrid;
 import dev.zarr.zarrjava.v3.chunkkeyencoding.ChunkKeyEncoding;
 import dev.zarr.zarrjava.v3.chunkkeyencoding.DefaultChunkKeyEncoding;
-import dev.zarr.zarrjava.v3.chunkkeyencoding.Separator;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
 import dev.zarr.zarrjava.v3.chunkkeyencoding.V2ChunkKeyEncoding;
 import dev.zarr.zarrjava.v3.codec.Codec;
 import dev.zarr.zarrjava.v3.codec.CodecBuilder;
diff --git a/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/ChunkKeyEncoding.java b/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/ChunkKeyEncoding.java
@@ -9,7 +9,7 @@
     @JsonSubTypes.Type(value = DefaultChunkKeyEncoding.class, name = "default"),
     @JsonSubTypes.Type(value = V2ChunkKeyEncoding.class, name = "v2")
 })
-public abstract class ChunkKeyEncoding {
+public abstract class ChunkKeyEncoding implements dev.zarr.zarrjava.core.chunkkeyencoding.ChunkKeyEncoding {
 
 
   public abstract String[] encodeChunkKey(long[] chunkCoords);
diff --git a/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/DefaultChunkKeyEncoding.java b/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/DefaultChunkKeyEncoding.java
@@ -2,6 +2,8 @@
 
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
+
 import java.util.Arrays;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
diff --git a/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/V2ChunkKeyEncoding.java b/src/main/java/dev/zarr/zarrjava/v3/chunkkeyencoding/V2ChunkKeyEncoding.java
@@ -2,6 +2,8 @@
 
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import dev.zarr.zarrjava.core.chunkkeyencoding.Separator;
+
 import java.util.Arrays;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
diff --git a/src/main/java/dev/zarr/zarrjava/v3/codec/CodecBuilder.java b/src/main/java/dev/zarr/zarrjava/v3/codec/CodecBuilder.java
@@ -125,7 +125,7 @@ public CodecBuilder withSharding(int[] chunkShape,
 
   public CodecBuilder withSharding(int[] chunkShape,
                                    Function<CodecBuilder, CodecBuilder> codecBuilder, String indexLocation) {
-    CodecBuilder nestedBuilder = new CodecBuilder(dataType);
+    CodecBuilder nestedBuilder = new CodecBuilder((DataType) dataType);
     try {
       codecs.add(new ShardingIndexedCodec(
               new ShardingIndexedCodec.Configuration(chunkShape,
diff --git a/src/test/java/dev/zarr/zarrjava/ZarrPythonTests.java b/src/test/java/dev/zarr/zarrjava/ZarrPythonTests.java
@@ -183,7 +183,7 @@ public void testReadFromZarrPythonV2(String compressor, String compressorParam)
 
         //for expected values see zarr_python_write.py
         Assertions.assertArrayEquals(new int[]{16, 16, 16}, result.getShape());
-        Assertions.assertEquals(DataType.INT32, array.metadata.dataType);
+        Assertions.assertEquals(dev.zarr.zarrjava.v2.DataType.INT32, array.metadata.dataType);
         Assertions.assertArrayEquals(new int[]{2, 4, 8}, array.metadata.chunkShape());
 //        Assertions.assertEquals(42, array.metadata.attributes.get("answer"));
 
@@ -208,7 +208,7 @@ public void testWriteReadWithZarrPythonV2(String compressor, String compressorPa
 
         dev.zarr.zarrjava.v2.ArrayMetadataBuilder builder = dev.zarr.zarrjava.v2.Array.metadataBuilder()
             .withShape(16, 16, 16)
-            .withDataType(DataType.UINT32)
+            .withDataType(dev.zarr.zarrjava.v2.DataType.UINT32)
             .withChunks(2, 4, 8)
 //            .withAttributes(attributes)
             .withFillValue(0);
@@ -235,7 +235,7 @@ public void testWriteReadWithZarrPythonV2(String compressor, String compressorPa
         ucar.ma2.Array result = readArray.read();
 
         Assertions.assertArrayEquals(new int[]{16, 16, 16}, result.getShape());
-        Assertions.assertEquals(DataType.UINT32, readArray.metadata.dataType);
+        Assertions.assertEquals(dev.zarr.zarrjava.v2.DataType.UINT32, readArray.metadata.dataType);
         Assertions.assertArrayEquals(new int[]{2, 4, 8}, readArray.metadata.chunkShape());
 //        Assertions.assertEquals("test_value", readArray.metadata.attributes.get("test_key"));
 
diff --git a/src/test/java/dev/zarr/zarrjava/ZarrTest.java b/src/test/java/dev/zarr/zarrjava/ZarrTest.java
@@ -528,7 +528,7 @@ public void testV2createBlosc(String cname, String shuffle, int clevel) throws I
             new FilesystemStore(TESTOUTPUT).resolve("v2_create_blosc", cname + "_" + shuffle + "_" + clevel),
             dev.zarr.zarrjava.v2.Array.metadataBuilder()
                 .withShape(10, 10)
-                .withDataType(DataType.UINT8)
+                .withDataType(dev.zarr.zarrjava.v2.DataType.UINT8)
                 .withChunks(5, 5)
                 .withFillValue(1)
                 .withBloscCompressor(cname, shuffle, clevel)
@@ -537,13 +537,13 @@ public void testV2createBlosc(String cname, String shuffle, int clevel) throws I
         array.write(new long[]{2, 2}, ucar.ma2.Array.factory(ucar.ma2.DataType.UBYTE, new int[]{8, 8}));
 
         ucar.ma2.Array outArray = array.read(new long[]{2, 2}, new int[]{8, 8});
-        Assertions.assertEquals(outArray.getSize(), 8 * 8);
-        Assertions.assertEquals(outArray.getByte(0), 0);
+        Assertions.assertEquals(8 * 8, outArray.getSize());
+        Assertions.assertEquals(0, outArray.getByte(0));
     }
 
     @Test
     public void testV2create() throws IOException, ZarrException {
-        DataType dataType = DataType.UINT32;
+        dev.zarr.zarrjava.v2.DataType dataType = dev.zarr.zarrjava.v2.DataType.UINT32;
 
         dev.zarr.zarrjava.v2.Array array = dev.zarr.zarrjava.v2.Array.create(
             new FilesystemStore(TESTOUTPUT).resolve("v2_create"),
@@ -557,8 +557,8 @@ public void testV2create() throws IOException, ZarrException {
         array.write(new long[]{2, 2}, ucar.ma2.Array.factory(dataType.getMA2DataType(), new int[]{8, 8}));
 
         ucar.ma2.Array outArray = array.read(new long[]{2, 2}, new int[]{8, 8});
-        Assertions.assertEquals(outArray.getSize(), 8 * 8);
-        Assertions.assertEquals(outArray.getByte(0), 0);
+        Assertions.assertEquals(8 * 8, outArray.getSize());
+        Assertions.assertEquals(0, outArray.getByte(0));
     }
 
     @ParameterizedTest
@@ -568,7 +568,7 @@ public void testV2createZlib(int level) throws IOException, ZarrException {
             new FilesystemStore(TESTOUTPUT).resolve("v2_create_zlib", String.valueOf(level)),
             dev.zarr.zarrjava.v2.Array.metadataBuilder()
                 .withShape(15, 10)
-                .withDataType(DataType.UINT8)
+                .withDataType(dev.zarr.zarrjava.v2.DataType.UINT8)
                 .withChunks(4, 5)
                 .withFillValue(5)
                 .withZlibCompressor(level)
@@ -577,7 +577,7 @@ public void testV2createZlib(int level) throws IOException, ZarrException {
         array.write(new long[]{2, 2}, ucar.ma2.Array.factory(ucar.ma2.DataType.UBYTE, new int[]{7, 6}));
 
         ucar.ma2.Array outArray = array.read(new long[]{2, 2}, new int[]{7, 6});
-        Assertions.assertEquals(outArray.getSize(), 7 * 6);
-        Assertions.assertEquals(outArray.getByte(0), 0);
+        Assertions.assertEquals(7 * 6, outArray.getSize());
+        Assertions.assertEquals(0, outArray.getByte(0));
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-package dev.zarr.zarrjava.v3.chunkkeyencoding;`
	`1`	`+package dev.zarr.zarrjava.core.chunkkeyencoding;`
`2`	`2`
`3`	`3`	`import com.fasterxml.jackson.annotation.JsonValue;`
`4`	`4`