Add cli wrapper

.github/workflows/conformance.yml

@@ -0,0 +1,39 @@
+name: Zarr Conformance Tests
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '17 3 * * 0'
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  conformance-tests:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+          cache: maven
+
+      - name: Build
+        run: mvn package -DskipTests
+
+      - name: Prepare JAR for testing
+        run: |
+          # Find the JAR
+          JAR_PATH=$(ls target/zarr-java-*.jar | grep -v original | grep -v javadoc | grep -v sources | head -1)
+          FULL_JAR_PATH="${GITHUB_WORKSPACE}/${JAR_PATH}"
+          echo "JAR_PATH=${FULL_JAR_PATH}" >> $GITHUB_ENV
+          echo "Found JAR at: ${FULL_JAR_PATH}"
+
+      - name: Run Conformance Tests
+        uses: brokkoli71/zarr-conformance-tests@main
+        with:
+          zarr-cli: "java -jar ${{ env.JAR_PATH }}"

pom.xml

@@ -126,6 +126,12 @@
             <artifactId>commons-compress</artifactId>
             <version>1.28.0</version>
         </dependency>
+
+        <dependency>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
+            <version>4.7.6</version>
+        </dependency>
     </dependencies>
 
     <repositories>
@@ -240,6 +246,26 @@
                     <tokenAuth>true</tokenAuth>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.5.0</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>dev.zarr.zarrjava.cli.Main</mainClass>
+                                </transformer>
+                            </transformers>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 </project>

src/main/java/dev/zarr/zarrjava/cli/Main.java

@@ -0,0 +1,44 @@
+package dev.zarr.zarrjava.cli;
+
+import dev.zarr.zarrjava.core.Array;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Option;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.concurrent.Callable;
+
+@Command(name = "zarr-java-cli", mixinStandardHelpOptions = true, version = "1.0", description = "CLI wrapper for zarr-java conformance tests.")
+public class Main implements Callable<Integer> {
+
+    @Option(names = { "--array_path" }, description = "Path to the Zarr array", required = true)
+    private String arrayPath;
+
+    @Override
+    public Integer call() throws Exception {
+        try {
+            Path path = Paths.get(arrayPath);
+            // Attempt to open the array. This should throw if the array is invalid or
+            // cannot be opened.
+            Array array = Array.open(path);
+
+            // Read the entire array
+            ucar.ma2.Array data = array.read();
+
+            // Print the array values using ucar.ma2.Array's string representation.
+            System.out.println(data.toString());
+
+            return 0;
+        } catch (Exception e) {
+            System.err.println("Failed to open array at " + arrayPath);
+            e.printStackTrace();
+            return 1;
+        }
+    }
+
+    public static void main(String[] args) {
+        int exitCode = new CommandLine(new Main()).execute(args);
+        System.exit(exitCode);
+    }
+}

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

@@ -0,0 +1,41 @@
+package dev.zarr.zarrjava.core.codec.core;
+
+import com.github.luben.zstd.Zstd;
+import com.github.luben.zstd.ZstdCompressCtx;
+import dev.zarr.zarrjava.ZarrException;
+import dev.zarr.zarrjava.core.codec.BytesBytesCodec;
+import dev.zarr.zarrjava.utils.Utils;
+
+import java.nio.ByteBuffer;
+
+public abstract class ZstdCodec extends BytesBytesCodec {
+
+    protected abstract int getLevel();
+
+    protected abstract boolean getChecksum();
+
+    @Override
+    public ByteBuffer decode(ByteBuffer compressedBytes) throws ZarrException {
+        byte[] compressedArray = Utils.toArray(compressedBytes);
+
+        long originalSize = Zstd.getFrameContentSize(compressedArray);
+        if (originalSize == 0) {
+            throw new ZarrException("Failed to get decompressed size");
+        }
+
+        byte[] decompressed = Zstd.decompress(compressedArray, (int) originalSize);
+        return ByteBuffer.wrap(decompressed);
+    }
+
+    @Override
+    public ByteBuffer encode(ByteBuffer chunkBytes) throws ZarrException {
+        byte[] arr = Utils.toArray(chunkBytes);
+        byte[] compressed;
+        try (ZstdCompressCtx ctx = new ZstdCompressCtx()) {
+            ctx.setLevel(getLevel());
+            ctx.setChecksum(getChecksum());
+            compressed = ctx.compress(arr);
+        }
+        return ByteBuffer.wrap(compressed);
+    }
+}

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

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.databind.jsontype.NamedType;
 import dev.zarr.zarrjava.v2.codec.core.BloscCodec;
 import dev.zarr.zarrjava.v2.codec.core.ZlibCodec;
+import dev.zarr.zarrjava.v2.codec.core.ZstdCodec;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -14,6 +15,7 @@ public class CodecRegistry {
     static {
         addType("blosc", BloscCodec.class);
         addType("zlib", ZlibCodec.class);
+        addType("zstd", ZstdCodec.class);
     }
 
     public static void addType(String name, Class<? extends Codec> codecClass) {

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

@@ -0,0 +1,43 @@
+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;
+
+public class ZstdCodec extends dev.zarr.zarrjava.core.codec.core.ZstdCodec implements Codec {
+
+    @JsonIgnore
+    public final String id = "zstd";
+    public final int level;
+    public final boolean checksum;
+
+    @JsonCreator(mode = JsonCreator.Mode.PROPERTIES)
+    public ZstdCodec(
+            @JsonProperty(value = "level", defaultValue = "0") int level,
+            @JsonProperty(value = "checksum", defaultValue = "false") boolean checksum)
+            throws ZarrException {
+        if (level < -131072 || level > 22) {
+            throw new ZarrException("'level' needs to be between -131072 and 22.");
+        }
+        this.level = level;
+        this.checksum = checksum;
+    }
+
+    @Override
+    protected int getLevel() {
+        return level;
+    }
+
+    @Override
+    protected boolean getChecksum() {
+        return checksum;
+    }
+
+    @Override
+    public Codec evolveFromCoreArrayMetadata(ArrayMetadata.CoreArrayMetadata arrayMetadata) {
+        return this;
+    }
+}

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

@@ -3,18 +3,13 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.github.luben.zstd.Zstd;
-import com.github.luben.zstd.ZstdCompressCtx;
 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.nio.ByteBuffer;
 
-public class ZstdCodec extends BytesBytesCodec implements Codec {
+public class ZstdCodec extends dev.zarr.zarrjava.core.codec.core.ZstdCodec implements Codec {
 
     @JsonIgnore
     public final String name = "zstd";
@@ -28,28 +23,13 @@ public ZstdCodec(
     }
 
     @Override
-    public ByteBuffer decode(ByteBuffer compressedBytes) throws ZarrException {
-        byte[] compressedArray = Utils.toArray(compressedBytes);
-
-        long originalSize = Zstd.getFrameContentSize(compressedArray);
-        if (originalSize == 0) {
-            throw new ZarrException("Failed to get decompressed size");
-        }
-
-        byte[] decompressed = Zstd.decompress(compressedArray, (int) originalSize);
-        return ByteBuffer.wrap(decompressed);
+    protected int getLevel() {
+        return configuration.level;
     }
 
     @Override
-    public ByteBuffer encode(ByteBuffer chunkBytes) throws ZarrException {
-        byte[] arr = Utils.toArray(chunkBytes);
-        byte[] compressed;
-        try (ZstdCompressCtx ctx = new ZstdCompressCtx()) {
-            ctx.setLevel(configuration.level);
-            ctx.setChecksum(configuration.checksum);
-            compressed = ctx.compress(arr);
-        }
-        return ByteBuffer.wrap(compressed);
+    protected boolean getChecksum() {
+        return configuration.checksum;
     }
 
     @Override