remove duplicate 'id' for v2 compressors in .zarray

brokkoli71 · brokkoli71 · commit 9bb4fc38f698 · 2025-11-10T14:12:51.000+01:00
diff --git a/src/main/java/dev/zarr/zarrjava/v2/Array.java b/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);
   }
diff --git a/src/main/java/dev/zarr/zarrjava/v2/Group.java b/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);
   }
diff --git a/src/main/java/dev/zarr/zarrjava/v2/Node.java b/src/main/java/dev/zarr/zarrjava/v2/Node.java
@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.v2;
 
 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 +22,11 @@ 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
diff --git a/src/main/java/dev/zarr/zarrjava/v2/codec/core/BloscCodec.java b/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
diff --git a/src/main/java/dev/zarr/zarrjava/v2/codec/core/BytesCodec.java b/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;
     }
 
diff --git a/src/main/java/dev/zarr/zarrjava/v2/codec/core/ZlibCodec.java b/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;
 
diff --git a/src/test/java/dev/zarr/zarrjava/ZarrV2Test.java b/src/test/java/dev/zarr/zarrjava/ZarrV2Test.java
@@ -1,23 +1,28 @@
 package dev.zarr.zarrjava;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import dev.zarr.zarrjava.store.FilesystemStore;
 import dev.zarr.zarrjava.store.StoreHandle;
-import dev.zarr.zarrjava.v2.Array;
-import dev.zarr.zarrjava.v2.ArrayMetadata;
-import dev.zarr.zarrjava.v2.DataType;
-import dev.zarr.zarrjava.v2.Group;
-import dev.zarr.zarrjava.v2.Node;
+import dev.zarr.zarrjava.v2.*;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvSource;
+import org.junit.jupiter.params.provider.MethodSource;
 import org.junit.jupiter.params.provider.ValueSource;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static dev.zarr.zarrjava.core.Node.ZARRAY;
 
 public class ZarrV2Test extends ZarrTest {
     @ParameterizedTest
@@ -255,4 +260,32 @@ public void testCreateGroup() throws ZarrException, IOException {
         Group.create(storeHandleString);
         Assertions.assertTrue(Files.exists(Paths.get(storeHandleString).resolve(".zgroup")));
     }
+
+
+    static Stream<Function<ArrayMetadataBuilder, ArrayMetadataBuilder>> compressorBuilder() {
+        return Stream.of(
+                ArrayMetadataBuilder::withBloscCompressor,
+                ArrayMetadataBuilder::withZlibCompressor,
+                b -> b
+        );
+    }
+
+    @ParameterizedTest
+    @MethodSource("compressorBuilder")
+    public void testZarrJsonFormat(Function<ArrayMetadataBuilder, ArrayMetadataBuilder> compressorBuilder) throws ZarrException, IOException {
+        // regression test: ensure that 'id' keyword of codecs is only written once.
+        StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testZarrJsonFormatV2").resolve(String.valueOf(compressorBuilder.hashCode()));
+        ArrayMetadataBuilder builder = Array.metadataBuilder()
+                .withShape(10, 10)
+                .withDataType(DataType.UINT8)
+                .withChunks(6, 6);
+        builder = compressorBuilder.apply(builder);
+        Array.create(storeHandle, builder.build());
+
+        try (BufferedReader reader = Files.newBufferedReader(storeHandle.resolve(ZARRAY).toPath())) {
+            String jsonInString = reader.lines().collect(Collectors.joining(System.lineSeparator()));
+            JsonNode JSON = new ObjectMapper().readTree(jsonInString);
+            Assertions.assertEquals(JSON.toPrettyString(), jsonInString);
+        }
+    }
 }
diff --git a/src/test/java/dev/zarr/zarrjava/ZarrV3Test.java b/src/test/java/dev/zarr/zarrjava/ZarrV3Test.java
@@ -36,6 +36,7 @@
 import java.util.stream.Stream;
 
 import static dev.zarr.zarrjava.core.ArrayMetadata.parseFillValue;
+import static dev.zarr.zarrjava.core.Node.ZARR_JSON;
 import static org.junit.Assert.assertThrows;
 
 public class ZarrV3Test extends ZarrTest {
@@ -624,7 +625,7 @@ public void testZarrJsonFormat(Function<ArrayMetadataBuilder, ArrayMetadataBuild
 
         Array.create(storeHandle, builder.build());
 
-        try (BufferedReader reader = Files.newBufferedReader(storeHandle.resolve("zarr.json").toPath())) {
+        try (BufferedReader reader = Files.newBufferedReader(storeHandle.resolve(ZARR_JSON).toPath())) {
             String jsonInString = reader.lines().collect(Collectors.joining(System.lineSeparator()));
             JsonNode JSON = new ObjectMapper().readTree(jsonInString);
             Assertions.assertEquals(JSON.toPrettyString(), jsonInString);
