made gzip work for v2

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

@@ -0,0 +1,42 @@
+package dev.zarr.zarrjava.core.codec.core;
+
+import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.codec.BytesBytesCodec;
+import dev.zarr.zarrjava.utils.Utils;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+
+public abstract class GzipCodec extends BytesBytesCodec {
+
+    @Override
+    public ByteBuffer decode(ByteBuffer chunkBytes) throws ZarrException {
+        try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); GZIPInputStream inputStream = new GZIPInputStream(
+                new ByteArrayInputStream(Utils.toArray(chunkBytes)))) {
+            Utils.copyStream(inputStream, outputStream);
+            inputStream.close();
+            return ByteBuffer.wrap(outputStream.toByteArray());
+        } catch (IOException ex) {
+            throw new ZarrException("Error in decoding gzip.", ex);
+        }
+    }
+
+    protected ByteBuffer encodeInternal(int level, ByteBuffer chunkBytes) throws ZarrException {
+        try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); GZIPOutputStream gzipStream = new GZIPOutputStream(
+                outputStream) {
+            {
+                this.def.setLevel(level);
+            }
+        }) {
+            gzipStream.write(Utils.toArray(chunkBytes));
+            gzipStream.close();
+            return ByteBuffer.wrap(outputStream.toByteArray());
+        } catch (IOException ex) {
+            throw new ZarrException("Error in encoding gzip.", ex);
+        }
+    }
+}

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

@@ -7,6 +7,7 @@
 import dev.zarr.zarrjava.utils.Utils;
 import dev.zarr.zarrjava.v2.codec.Codec;
 import dev.zarr.zarrjava.v2.codec.core.BloscCodec;
+import dev.zarr.zarrjava.v2.codec.core.GzipCodec;
 import dev.zarr.zarrjava.v2.codec.core.ZlibCodec;
 import dev.zarr.zarrjava.v2.codec.core.ZstdCodec;
 
@@ -114,6 +115,19 @@ public ArrayMetadataBuilder withBloscCompressor() {
         return withBloscCompressor("zstd");
     }
 
+    public ArrayMetadataBuilder withGzipCompressor(int level) {
+        try {
+            this.compressor = new GzipCodec(level);
+        } catch (ZarrException e) {
+            throw new RuntimeException(e);
+        }
+        return this;
+    }
+
+    public ArrayMetadataBuilder withGzipCompressor() {
+        return withGzipCompressor(GzipCodec.DEFAULT_LEVEL);
+    }
+
     public ArrayMetadataBuilder withZlibCompressor(int level) {
         try {
             this.compressor = new ZlibCodec(level);

src/main/java/dev/zarr/zarrjava/v2/codec/CodecRegistry.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.databind.jsontype.NamedType;
 import dev.zarr.zarrjava.v2.codec.core.BloscCodec;
+import dev.zarr.zarrjava.v2.codec.core.GzipCodec;
 import dev.zarr.zarrjava.v2.codec.core.ZlibCodec;
 import dev.zarr.zarrjava.v2.codec.core.ZstdCodec;
 
@@ -14,6 +15,7 @@ public class CodecRegistry {
 
     static {
         addType("blosc", BloscCodec.class);
+        addType("gzip", GzipCodec.class);
         addType("zlib", ZlibCodec.class);
         addType("zstd", ZstdCodec.class);
     }

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

@@ -0,0 +1,38 @@
+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;
+import dev.zarr.zarrjava.v2.codec.Codec;
+
+import java.nio.ByteBuffer;
+
+public class GzipCodec extends dev.zarr.zarrjava.core.codec.core.GzipCodec implements Codec {
+
+    public static final int DEFAULT_LEVEL = 1;
+    @JsonIgnore
+    public final String id = "gzip";
+    public final int level;
+
+    @JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
+    public GzipCodec(
+            @JsonProperty(value = "level", defaultValue = "" + DEFAULT_LEVEL) int level)
+            throws ZarrException {
+        if (level < 0 || level > 9) {
+            throw new ZarrException("'level' needs to be between 0 and 9.");
+        }
+        this.level = level;
+    }
+
+    @Override
+    public ByteBuffer encode(ByteBuffer chunkBytes) throws ZarrException {
+        return encodeInternal(this.level, chunkBytes);
+    }
+
+    @Override
+    public Codec evolveFromCoreArrayMetadata(ArrayMetadata.CoreArrayMetadata arrayMetadata) {
+        return this;
+    }
+}

src/main/java/dev/zarr/zarrjava/v3/codec/core/GzipCodec.java

@@ -4,20 +4,13 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ZarrException;
-import dev.zarr.zarrjava.core.codec.BytesBytesCodec;
-import dev.zarr.zarrjava.utils.Utils;
 import dev.zarr.zarrjava.v3.ArrayMetadata;
 import dev.zarr.zarrjava.v3.codec.Codec;
 
 import javax.annotation.Nonnull;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
 import java.nio.ByteBuffer;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
 
-public class GzipCodec extends BytesBytesCodec implements Codec {
+public class GzipCodec extends dev.zarr.zarrjava.core.codec.core.GzipCodec implements Codec {
 
     @JsonIgnore
     public final String name = "gzip";
@@ -30,31 +23,9 @@ public GzipCodec(
         this.configuration = configuration;
     }
 
-
-    @Override
-    public ByteBuffer decode(ByteBuffer chunkBytes)
-            throws ZarrException {
-        try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); GZIPInputStream inputStream = new GZIPInputStream(
-                new ByteArrayInputStream(Utils.toArray(chunkBytes)))) {
-            Utils.copyStream(inputStream, outputStream);
-            inputStream.close();
-            return ByteBuffer.wrap(outputStream.toByteArray());
-        } catch (IOException ex) {
-            throw new ZarrException("Error in decoding gzip.", ex);
-        }
-    }
-
     @Override
-    public ByteBuffer encode(ByteBuffer chunkBytes)
-            throws ZarrException {
-        try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); GZIPOutputStream gzipStream = new GZIPOutputStream(
-                outputStream)) {
-            gzipStream.write(Utils.toArray(chunkBytes));
-            gzipStream.close();
-            return ByteBuffer.wrap(outputStream.toByteArray());
-        } catch (IOException ex) {
-            throw new ZarrException("Error in encoding gzip.", ex);
-        }
+    public ByteBuffer encode(ByteBuffer chunkBytes) throws ZarrException {
+        return encodeInternal(configuration.level, chunkBytes);
     }
 
     @Override
@@ -77,5 +48,3 @@ public Configuration(@JsonProperty(value = "level", defaultValue = "5") int leve
         }
     }
 }
-
-

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

@@ -107,6 +107,8 @@ static Stream<Object[]> compressorAndDataTypeProviderV2() {
                 new Object[]{"blosc", "lz4hc_bitshuffle_3", dev.zarr.zarrjava.v2.DataType.INT32},
                 new Object[]{"blosc", "zlib_shuffle_5", dev.zarr.zarrjava.v2.DataType.INT32},
                 new Object[]{"blosc", "zstd_bitshuffle_9", dev.zarr.zarrjava.v2.DataType.INT32},
+                new Object[]{"gzip", "0", dev.zarr.zarrjava.v2.DataType.INT32},
+                new Object[]{"gzip", "5", dev.zarr.zarrjava.v2.DataType.INT32},
                 new Object[]{"zstd", "0_true", dev.zarr.zarrjava.v2.DataType.INT32},
                 new Object[]{"zstd", "5_false", dev.zarr.zarrjava.v2.DataType.INT32}
         );
@@ -241,6 +243,9 @@ public void testWriteV2(String compressor, String compressorParam, dev.zarr.zarr
                 int clevel_blosc = Integer.parseInt(compressorParam.split("_")[2]);
                 builder = builder.withBloscCompressor(cname, shuffle, clevel_blosc);
                 break;
+            case "gzip":
+                builder = builder.withGzipCompressor(Integer.parseInt(compressorParam));
+                break;
             case "zlib":
                 builder = builder.withZlibCompressor(Integer.parseInt(compressorParam));
                 break;

src/test/python-scripts/parse_codecs.py

@@ -30,6 +30,8 @@ def parse_codecs_zarr_python(codec_string: str, param_string: str, zarr_version:
         compressor = numcodecs.Blosc(typesize=4, cname=cname, shuffle=shuffle, clevel=int(clevel))
     elif codec_string == "zlib" and zarr_version == 2:
         compressor = numcodecs.Zlib(level=int(param_string))
+    elif codec_string == "gzip" and zarr_version == 2:
+        compressor = numcodecs.GZip(level=int(param_string))
     elif codec_string == "gzip" and zarr_version == 3:
         compressor = GzipCodec(level=int(param_string))
     elif codec_string == "zstd" and zarr_version == 3: