add core.Node

Author: brokkoli71

.github/workflows/ci.yml

@@ -36,11 +36,6 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v6
 
-      - name: Set up zarr-python
-        run: |
-          uv venv && uv init
-          uv add zarr
-
       - name: Download testdata
         run: |
           mkdir testoutput

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

@@ -14,23 +14,24 @@
 import java.util.Arrays;
 import java.util.stream.Stream;
 
-public interface Array {
+public abstract class Array extends Node {
 
-    ArrayMetadata metadata();
-    
-    StoreHandle storeHandle();
+    protected CodecPipeline codecPipeline;
+    protected abstract ArrayMetadata metadata();
 
-    CodecPipeline codecPipeline();
+    protected Array(StoreHandle storeHandle) throws ZarrException {
+        super(storeHandle);
+    }
 
     /**
      * Writes a ucar.ma2.Array into the Zarr array at a specified offset. The shape of the Zarr array
      * needs be large enough for the write.
      *
-     * @param offset the offset where to write the data
-     * @param array the data to write
+     * @param offset   the offset where to write the data
+     * @param array    the data to write
      * @param parallel utilizes parallelism if true
      */
-    default void write(long[] offset, ucar.ma2.Array array, boolean parallel) {
+    public void write(long[] offset, ucar.ma2.Array array, boolean parallel) {
         ArrayMetadata metadata = metadata();
         if (offset.length != metadata.ndim()) {
             throw new IllegalArgumentException("'offset' needs to have rank '" + metadata.ndim() + "'.");
@@ -82,19 +83,19 @@ default void write(long[] offset, ucar.ma2.Array array, boolean parallel) {
      *
      * @param chunkCoords The coordinates of the chunk as computed by the offset of the chunk divided
      *                    by the chunk shape.
-     * @param chunkArray The data to write into the chunk
+     * @param chunkArray  The data to write into the chunk
      * @throws ZarrException throws ZarrException if the write fails
      */
-    default void writeChunk(long[] chunkCoords, ucar.ma2.Array chunkArray) throws ZarrException {
+    public void writeChunk(long[] chunkCoords, ucar.ma2.Array chunkArray) throws ZarrException {
         ArrayMetadata metadata = metadata();
         String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
-        StoreHandle chunkHandle = storeHandle().resolve(chunkKeys);
+        StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
         Object parsedFillValue = metadata.parsedFillValue();
 
         if (parsedFillValue != null && MultiArrayUtils.allValuesEqual(chunkArray, parsedFillValue)) {
             chunkHandle.delete();
         } else {
-            ByteBuffer chunkBytes = codecPipeline().encode(chunkArray);
+            ByteBuffer chunkBytes = codecPipeline.encode(chunkArray);
             chunkHandle.set(chunkBytes);
         }
     }
@@ -108,22 +109,21 @@ default void writeChunk(long[] chunkCoords, ucar.ma2.Array chunkArray) throws Za
      * @throws ZarrException throws ZarrException if the requested chunk is outside the array's domain or if the read fails
      */
     @Nonnull
-    default ucar.ma2.Array readChunk(long[] chunkCoords)
-        throws ZarrException {
+    public ucar.ma2.Array readChunk(long[] chunkCoords) throws ZarrException {
         ArrayMetadata metadata = metadata();
         if (!chunkIsInArray(chunkCoords)) {
             throw new ZarrException("Attempting to read data outside of the array's domain.");
         }
 
         final String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
-        final StoreHandle chunkHandle = storeHandle().resolve(chunkKeys);
+        final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
 
         ByteBuffer chunkBytes = chunkHandle.read();
         if (chunkBytes == null) {
             return metadata.allocateFillValueChunk();
         }
 
-        return codecPipeline().decode(chunkBytes);
+        return codecPipeline.decode(chunkBytes);
     }
 
 
@@ -134,7 +134,7 @@ default ucar.ma2.Array readChunk(long[] chunkCoords)
      *
      * @param array the data to write
      */
-    default void write(ucar.ma2.Array array) {
+    public void write(ucar.ma2.Array array) {
         write(new long[metadata().ndim()], array);
     }
 
@@ -144,20 +144,20 @@ default void write(ucar.ma2.Array array) {
      * Utilizes no parallelism.
      *
      * @param offset the offset where to write the data
-     * @param array the data to write
+     * @param array  the data to write
      */
-    default void write(long[] offset, ucar.ma2.Array array) {
+    public void write(long[] offset, ucar.ma2.Array array) {
         write(offset, array, false);
     }
 
     /**
      * Writes a ucar.ma2.Array into the Zarr array at the beginning of the Zarr array. The shape of
      * the Zarr array needs be large enough for the write.
      *
-     * @param array the data to write
+     * @param array    the data to write
      * @param parallel utilizes parallelism if true
      */
-    default void write(ucar.ma2.Array array, boolean parallel) {
+    public void write(ucar.ma2.Array array, boolean parallel) {
         write(new long[metadata().ndim()], array, parallel);
     }
 
@@ -168,7 +168,7 @@ default void write(ucar.ma2.Array array, boolean parallel) {
      * @throws ZarrException throws ZarrException if the read fails
      */
     @Nonnull
-    default ucar.ma2.Array read() throws ZarrException {
+    public ucar.ma2.Array read() throws ZarrException {
         return read(new long[metadata().ndim()], Utils.toIntArray(metadata().shape()));
     }
 
@@ -177,11 +177,11 @@ default ucar.ma2.Array read() throws ZarrException {
      * Utilizes no parallelism.
      *
      * @param offset the offset where to start reading
-     * @param shape the shape of the data to read
+     * @param shape  the shape of the data to read
      * @throws ZarrException throws ZarrException if the requested data is outside the array's domain or if the read fails
      */
     @Nonnull
-    default ucar.ma2.Array read(final long[] offset, final int[] shape) throws ZarrException {
+    public ucar.ma2.Array read(final long[] offset, final int[] shape) throws ZarrException {
         return read(offset, shape, false);
     }
 
@@ -192,11 +192,11 @@ default ucar.ma2.Array read(final long[] offset, final int[] shape) throws ZarrE
      * @throws ZarrException throws ZarrException if the requested data is outside the array's domain or if the read fails
      */
     @Nonnull
-    default ucar.ma2.Array read(final boolean parallel) throws ZarrException {
+    public ucar.ma2.Array read(final boolean parallel) throws ZarrException {
         return read(new long[metadata().ndim()], Utils.toIntArray(metadata().shape()), parallel);
     }
 
-    default boolean chunkIsInArray(long[] chunkCoords) {
+    boolean chunkIsInArray(long[] chunkCoords) {
         final int[] chunkShape = metadata().chunkShape();
         for (int dimIdx = 0; dimIdx < metadata().ndim(); dimIdx++) {
             if (chunkCoords[dimIdx] < 0
@@ -210,15 +210,14 @@ default boolean chunkIsInArray(long[] chunkCoords) {
     /**
      * Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.
      *
-     * @param offset the offset where to start reading
-     * @param shape the shape of the data to read
+     * @param offset   the offset where to start reading
+     * @param shape    the shape of the data to read
      * @param parallel utilizes parallelism if true
      * @throws ZarrException throws ZarrException if the requested data is outside the array's domain or if the read fails
      */
     @Nonnull
-    default ucar.ma2.Array read(final long[] offset, final int[] shape, final boolean parallel) throws ZarrException {
+    public ucar.ma2.Array read(final long[] offset, final int[] shape, final boolean parallel) throws ZarrException {
         ArrayMetadata metadata = metadata();
-        CodecPipeline codecPipeline = codecPipeline();
         if (offset.length != metadata.ndim()) {
             throw new IllegalArgumentException("'offset' needs to have rank '" + metadata.ndim() + "'.");
         }
@@ -258,7 +257,7 @@ default ucar.ma2.Array read(final long[] offset, final int[] shape, final boolea
                     }
 
                     final String[] chunkKeys = metadata.chunkKeyEncoding().encodeChunkKey(chunkCoords);
-                    final StoreHandle chunkHandle = storeHandle().resolve(chunkKeys);
+                    final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
                     if (!chunkHandle.exists()) {
                         return;
                     }
@@ -281,11 +280,11 @@ default ucar.ma2.Array read(final long[] offset, final int[] shape, final boolea
         return outputArray;
     }
 
-    default ArrayAccessor access() {
+    public ArrayAccessor access() {
         return new ArrayAccessor(this);
     }
 
-    final class ArrayAccessor {
+    public static final class ArrayAccessor {
         @Nullable
         long[] offset;
         @Nullable

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

@@ -0,0 +1,25 @@
+package dev.zarr.zarrjava.core;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
+import dev.zarr.zarrjava.store.StoreHandle;
+import dev.zarr.zarrjava.v3.codec.CodecRegistry;
+import javax.annotation.Nonnull;
+
+public abstract class Node {
+
+  @Nonnull
+  public final StoreHandle storeHandle;
+
+  protected Node(@Nonnull StoreHandle storeHandle) {
+    this.storeHandle = storeHandle;
+  }
+
+  public static ObjectMapper makeObjectMapper() {
+    ObjectMapper objectMapper = new ObjectMapper();
+    objectMapper.registerModule(new Jdk8Module());
+    objectMapper.registerSubtypes(CodecRegistry.getNamedTypes());
+    return objectMapper;
+  }
+
+}

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

@@ -17,15 +17,17 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
-public class Array implements dev.zarr.zarrjava.core.Array {
+public class Array extends dev.zarr.zarrjava.core.Array {
 
   static final String ZARRAY = ".zarray";
   public ArrayMetadata metadata;
-  public StoreHandle storeHandle;
-  CodecPipeline codecPipeline;
+
+  protected ArrayMetadata metadata() {
+      return metadata;
+  }
 
   protected Array(StoreHandle storeHandle, ArrayMetadata arrayMetadata) throws IOException, ZarrException {
-    this.storeHandle = storeHandle;
+    super(storeHandle);
     this.metadata = arrayMetadata;
     this.codecPipeline = new CodecPipeline(Utils.concatArrays(
         new Codec[]{},
@@ -127,20 +129,4 @@ public String toString() {
         metadata.dataType
     );
   }
-
-  @Override
-  public ArrayMetadata metadata() {
-    return metadata;
-  }
-
-  @Override
-  public StoreHandle storeHandle() {
-    return storeHandle;
-  }
-
-  @Override
-  public CodecPipeline codecPipeline() {
-    return codecPipeline;
-  }
-
 }

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

@@ -14,13 +14,15 @@
 import java.util.stream.Collectors;
 import javax.annotation.Nonnull;
 
-public class Array extends Node implements dev.zarr.zarrjava.core.Array {
+public class Array extends dev.zarr.zarrjava.core.Array implements Node {
 
   public ArrayMetadata metadata;
-  CodecPipeline codecPipeline;
 
-  protected Array(StoreHandle storeHandle, ArrayMetadata arrayMetadata)
-      throws ZarrException {
+  protected ArrayMetadata metadata(){
+    return metadata;
+  }
+
+  protected Array(StoreHandle storeHandle, ArrayMetadata arrayMetadata) throws ZarrException {
     super(storeHandle);
     this.metadata = arrayMetadata;
     this.codecPipeline = new CodecPipeline(arrayMetadata.codecs, arrayMetadata.coreArrayMetadata);
@@ -113,21 +115,6 @@ public static ArrayMetadataBuilder metadataBuilder(ArrayMetadata existingMetadat
     return ArrayMetadataBuilder.fromArrayMetadata(existingMetadata);
   }
 
-  @Override
-  public CodecPipeline codecPipeline() {
-    return codecPipeline;
-  }
-
-
-
-
-  @Override
-  public ArrayMetadata metadata() {
-    return metadata;
-  }
-
-
-
   private Array writeMetadata(ArrayMetadata newArrayMetadata) throws ZarrException, IOException {
     ObjectMapper objectMapper = makeObjectMapper();
     ByteBuffer metadataBytes = ByteBuffer.wrap(objectMapper.writeValueAsBytes(newArrayMetadata));

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

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.Node;
 import dev.zarr.zarrjava.store.StoreHandle;
 import dev.zarr.zarrjava.utils.Utils;
 import java.io.IOException;
@@ -13,6 +14,8 @@
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 
+import static dev.zarr.zarrjava.v3.Node.ZARR_JSON;
+
 public class Group extends Node {
 
   public GroupMetadata metadata;

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

@@ -1,31 +1,6 @@
 package dev.zarr.zarrjava.v3;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
-import dev.zarr.zarrjava.store.StoreHandle;
-import dev.zarr.zarrjava.v3.codec.CodecRegistry;
-import javax.annotation.Nonnull;
-
-public class Node {
-
-  public final static String ZARR_JSON = "zarr.json";
-
-  @Nonnull
-  public final StoreHandle storeHandle;
-
-  protected Node(@Nonnull StoreHandle storeHandle) {
-    this.storeHandle = storeHandle;
-  }
-
-  public static ObjectMapper makeObjectMapper() {
-    ObjectMapper objectMapper = new ObjectMapper();
-    objectMapper.registerModule(new Jdk8Module());
-    objectMapper.registerSubtypes(CodecRegistry.getNamedTypes());
-    return objectMapper;
-  }
-
-  public StoreHandle storeHandle() {
-    return storeHandle;
-  }
+public interface Node {
+  String ZARR_JSON = "zarr.json";
 
 }