chore!: update downstream dependencies

* update FileSystemKeyValueAccess constructors
* update createS3 change
* add read/writeShard

Author: bogovicj

pom.xml

@@ -111,11 +111,11 @@
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<n5.version>4.0.0-alpha-8</n5.version>
-		<n5-aws-s3.version>4.4.0-alpha-5</n5-aws-s3.version>
-		<n5-google-cloud.version>5.2.0-alpha-4</n5-google-cloud.version>
-		<n5-zarr.version>2.0.0-alpha-5</n5-zarr.version>
-		<n5-hdf5.version>2.3.0-alpha-5</n5-hdf5.version>
+		<n5.version>4.0.0-alpha-9</n5.version>
+		<n5-aws-s3.version>4.4.0-alpha-6</n5-aws-s3.version>
+		<n5-google-cloud.version>5.2.0-alpha-5</n5-google-cloud.version>
+		<n5-zarr.version>2.0.0-alpha-7</n5-zarr.version>
+		<n5-hdf5.version>2.3.0-alpha-6</n5-hdf5.version>
 		<n5-blosc.version>2.0.0-alpha-4</n5-blosc.version>
 		<n5-imglib2.version>7.1.0-alpha-7</n5-imglib2.version>
 		<n5-zstandard.version>2.0.0-alpha-4</n5-zstandard.version>

src/main/java/org/janelia/saalfeldlab/n5/universe/KeyValueAccessBackend.java

@@ -120,12 +120,15 @@ private static AmazonS3KeyValueAccess newAmazonS3KeyValueAccess(final URI uri, f
 		final String uriString = uri.toString();
 		final S3Client s3 = factory.createS3(uriString);
 
+		// throw exception if s3 endpoint is not reachable
+		AmazonS3Utils.ensureS3EndpointIsReachable(s3);
+
 		return new AmazonS3KeyValueAccess(s3, uri, true);
 	}
 
 	private static FileSystemKeyValueAccess newFileSystemKeyValueAccess(final URI uri, final N5Factory factory) {
 
-		return new FileSystemKeyValueAccess(FileSystems.getDefault());
+		return new FileSystemKeyValueAccess();
 	}
 
 	private static HttpKeyValueAccess newHttpKeyValueAccess(final URI uri, final N5Factory factory) {

src/main/java/org/janelia/saalfeldlab/n5/universe/N5Factory.java

@@ -48,10 +48,8 @@
 import org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter;
 import org.janelia.saalfeldlab.n5.zarr.v3.ZarrV3KeyValueReader;
 import org.janelia.saalfeldlab.n5.zarr.v3.ZarrV3KeyValueWriter;
-import software.amazon.awssdk.auth.credentials.AwsCredentials;
-import software.amazon.awssdk.auth.credentials.DefaultCredentialsProvider;
-import software.amazon.awssdk.http.SdkHttpClient;
 import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.S3ClientBuilder;
 
 import javax.annotation.Nullable;
 import java.io.Serializable;
@@ -60,6 +58,7 @@
 import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.function.BiFunction;
+import java.util.function.Consumer;
 import java.util.regex.Pattern;
 
 import static org.janelia.saalfeldlab.n5.universe.StorageFormat.getStorageFromNestedScheme;
@@ -91,11 +90,7 @@ public class N5Factory implements Serializable {
 	private boolean zarrMergeAttributes = true;
 	private String googleCloudProjectId = null;
 	private boolean googleCloudCreateBucket = false;
-	private String s3Region = null;
-	private AwsCredentials s3Credentials = null;
-	private SdkHttpClient.Builder<?> s3ClientBuilder = null;
-	private boolean s3Anonymous = true;
-	private String s3Endpoint;
+	private Consumer<S3ClientBuilder> builderConfig;
 	private StorageFormat preferredStorageFormat = null;
 
 	public N5Factory hdf5DefaultBlockSize(final int... blockSize) {
@@ -152,30 +147,6 @@ public N5Factory googleCloudProjectId(final String projectId) {
 		return this;
 	}
 
-	/**
-	 * This factory will use the {@link DefaultCredentialsProvider} to
-	 * find s3 credentials.
-	 *
-	 * @return this N5Factory
-	 */
-	public N5Factory s3UseCredentials() {
-
-		s3Anonymous = false;
-		return this;
-	}
-
-	public N5Factory s3UseCredentials(final AwsCredentials credentials) {
-
-		this.s3Credentials = credentials;
-		return this;
-	}
-
-	public N5Factory s3ClientConfiguration(final SdkHttpClient.Builder<?> clientBuilder) {
-
-		this.s3ClientBuilder = clientBuilder;
-		return this;
-	}
-
 	/**
 	 * When N5Factory cannot determine the StorageFormat from the URI, it will attempt to
 	 * try and create a reader/writer with all known StorageFormat values.
@@ -191,28 +162,22 @@ public N5Factory preferredStorageFormat(final StorageFormat format) {
 		return this;
 	}
 
-	@Deprecated
-	public N5Factory s3RetryWithCredentials() {
-
-		return this;
-	}
-
-	public N5Factory s3Endpoint(final String s3Endpoint) {
-
-		this.s3Endpoint = s3Endpoint;
-		return this;
-	}
-
-	public N5Factory s3Region(final String s3Region) {
+	/**
+	 * This factory will use the builderConfig to configure the {@link S3ClientBuilder},
+	 * and thereby the {@link S3Client}.
+	 *
+	 * @return this N5Factory
+	 */
+	public N5Factory s3Configuration(final Consumer<S3ClientBuilder> builderConfig) {
 
-		this.s3Region = s3Region;
+		this.builderConfig = builderConfig;
 		return this;
 	}
 
 	protected S3Client createS3(final String uri) {
 
 		try {
-			return AmazonS3Utils.createS3(uri, s3Endpoint, AmazonS3Utils.getS3Credentials(s3Credentials, s3Anonymous), s3ClientBuilder, s3Region);
+			return AmazonS3Utils.createS3(uri, builderConfig);
 		} catch (final Throwable e) {
 			throw new N5Exception("Could not create s3 client from uri: " + uri, e);
 		}

src/main/java/org/janelia/saalfeldlab/n5/universe/container/ContainerMetadataNode.java

@@ -354,6 +354,11 @@ public boolean remove() {
 	public <T> void writeBlock(String pathName, DatasetAttributes datasetAttributes, DataBlock<T> dataBlock) {
 		throw new UnsupportedOperationException("ContainerMetadata does not support writeBlock");
 	}
+	
+	@Override
+	public <T> void writeShard(String pathName, DatasetAttributes datasetAttributes, DataBlock<T> dataBlock) {
+		throw new UnsupportedOperationException("ContainerMetadata does not support writeBlock");
+	}
 
 	@Override
 	public <T> void writeRegion(String datasetPath, DatasetAttributes datasetAttributes, long[] min, long[] size, DataBlockSupplier<T> dataBlocks,
@@ -381,6 +386,11 @@ public boolean deleteBlock(String datasetPath, DatasetAttributes datasetAttribut
 	public DataBlock<?> readBlock(String pathName, DatasetAttributes datasetAttributes, long... gridPosition) {
 		return null;
 	}
+	
+	@Override
+	public DataBlock<?> readShard(String pathName, DatasetAttributes datasetAttributes, long... gridPosition) {
+		return null;
+	}
 
 	@SuppressWarnings("unchecked")
 	public static  <N extends GsonN5Reader & N5Reader > ContainerMetadataNode build(

src/main/java/org/janelia/saalfeldlab/n5/universe/translation/TranslatedN5Reader.java

@@ -68,6 +68,12 @@ public DataBlock<?> readBlock(String pathName, DatasetAttributes datasetAttribut
 		return n5.readBlock( originalPath( pathName ), datasetAttributes, gridPosition);
 	}
 
+	@Override
+	public DataBlock<?> readShard(String pathName, DatasetAttributes datasetAttributes, long... gridPosition) {
+
+		return n5.readShard(originalPath(pathName), datasetAttributes, gridPosition);
+	}
+
 	@Override
 	public boolean exists(String pathName) {
 		return translation.getTranslated().exists(pathName);

src/main/java/org/janelia/saalfeldlab/n5/universe/translation/TranslatedN5Writer.java

@@ -122,6 +122,11 @@ public <T> void writeBlock(String pathName, DatasetAttributes datasetAttributes,
 		writer.writeBlock(originalPath(pathName), datasetAttributes, dataBlock);
 	}
 
+	@Override
+	public <T> void writeShard(String pathName, DatasetAttributes datasetAttributes, DataBlock<T> dataBlock) {
+		writer.writeShard(originalPath(pathName), datasetAttributes, dataBlock);
+	}
+
 	@Override
 	public <T> void writeRegion(String datasetPath, DatasetAttributes datasetAttributes, long[] min, long[] size, DataBlockSupplier<T> dataBlocks,
 			boolean writeFully) throws N5Exception {

src/test/java/org/janelia/saalfeldlab/n5/universe/N5FactoryTests.java

@@ -18,7 +18,6 @@
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
-import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -503,7 +502,7 @@ public void testCachedFactoryKeys() throws IOException {
 	public void testZarr2VsZarr3Disambiguation() throws URISyntaxException {
 
 		final URI uri = new URI("src/test/resources/metadata.zarr");
-		final FileSystemKeyValueAccess kva = new FileSystemKeyValueAccess(FileSystems.getDefault());
+		final FileSystemKeyValueAccess kva = new FileSystemKeyValueAccess();
 
 		final StorageFormat format = StorageFormat.guessStorageFromKeys(uri, kva);
 		assertEquals("zarr 2", StorageFormat.ZARR2, format);

src/test/java/org/janelia/saalfeldlab/n5/universe/benchmarks/BlockReadWriteBenchmarks.java

@@ -129,7 +129,7 @@ public void setup() {
 		File tmpDir;
 		try {
 			tmpDir = Files.createTempDirectory("n5-blockWriteBenchmark-").toFile();
-			FileSystemKeyValueAccess kva = new FileSystemKeyValueAccess(FileSystems.getDefault());
+			FileSystemKeyValueAccess kva = new FileSystemKeyValueAccess();
 			n5 = new N5KeyValueWriter(kva, tmpDir.getAbsolutePath(), new GsonBuilder(), true);
 
 			int[] blockSize = new int[numDimensions];

src/test/java/org/janelia/saalfeldlab/n5/universe/benchmarks/KeyValueAccessBenchmarks.java

@@ -92,7 +92,7 @@ public static void main(String... args) throws RunnerException {
 	public void setup() throws IOException {
 
 		random = new Random();
-		kva = new FileSystemKeyValueAccess(FileSystems.getDefault());
+		kva = new FileSystemKeyValueAccess();
 
 		data = new byte[objectSizeBytes];
 		random.nextBytes(data);

src/test/java/org/janelia/saalfeldlab/n5/universe/benchmarks/PartialReadBenchmarks.java

@@ -76,7 +76,7 @@ public void teardown() {
 	public void setup() {
 
 		random = new Random(1);
-		kva = new FileSystemKeyValueAccess(FileSystems.getDefault());
+		kva = new FileSystemKeyValueAccess();
 
 		File tmpFile;
 		try {