Merge pull request #155 from saalfeldlab/readDataN5IOExceptions

Migrate IOExceptions to N5IOExceptions for ReadData and related logic

Author: bogovicj

src/main/java/org/janelia/saalfeldlab/n5/Bzip2Compression.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -58,6 +58,7 @@
 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream;
 import org.janelia.saalfeldlab.n5.Compression.CompressionType;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 @CompressionType("bzip2")
@@ -88,9 +89,12 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData) throws IOException {
-
-		return ReadData.from(new BZip2CompressorInputStream(readData.inputStream()));
+	public ReadData decode(final ReadData readData) throws N5IOException {
+		try {
+			return ReadData.from(new BZip2CompressorInputStream(readData.inputStream()));
+		} catch (IOException e) {
+			throw new N5IOException(e);
+		}
 	}
 
 	@Override

src/main/java/org/janelia/saalfeldlab/n5/CachedGsonKeyValueN5Writer.java

@@ -74,11 +74,7 @@ else if (getCache().exists(normalPath, N5KeyValueReader.ATTRIBUTES_JSON)) {
 		 * the lines below duplicate the single line above but would have to call
 		 * normalizeGroupPath again the below duplicates code, but avoids extra work
 		 */
-		try {
-			getKeyValueAccess().createDirectories(absoluteGroupPath(normalPath));
-		} catch (final IOException | UncheckedIOException e) {
-			throw new N5Exception.N5IOException("Failed to create group " + path, e);
-		}
+		getKeyValueAccess().createDirectories(absoluteGroupPath(normalPath));
 
 		if (cacheMeta()) {
 			// check all nodes that are parents of the added node, if they have
@@ -148,12 +144,9 @@ default boolean remove(final String path) throws N5Exception {
 		 */
 		final String normalPath = N5URI.normalizeGroupPath(path);
 		final String groupPath = absoluteGroupPath(normalPath);
-		try {
-			if (getKeyValueAccess().isDirectory(groupPath))
-				getKeyValueAccess().delete(groupPath);
-		} catch (final IOException | UncheckedIOException e) {
-			throw new N5IOException("Failed to remove " + path, e);
-		}
+
+		if (getKeyValueAccess().isDirectory(groupPath))
+			getKeyValueAccess().delete(groupPath);
 
 		if (cacheMeta()) {
 			final String parentPath = getKeyValueAccess().parent(normalPath);

src/main/java/org/janelia/saalfeldlab/n5/Compression.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -60,6 +60,8 @@
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
 import java.lang.annotation.Target;
+
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 import org.scijava.annotations.Indexable;
 
@@ -116,10 +118,10 @@ default String getType() {
 	 *
 	 * @return decoded ReadData
 	 *
-	 * @throws IOException
+	 * @throws N5IOException
 	 * 		if any I/O error occurs
 	 */
-	ReadData decode(ReadData readData) throws IOException;
+	ReadData decode(ReadData readData) throws N5IOException;
 
 	/**
 	 * Encode the given {@code readData}.
@@ -132,9 +134,9 @@ default String getType() {
 	 *
 	 * @return encoded ReadData
 	 *
-	 * @throws IOException
+	 * @throws N5IOException
 	 * 		if any I/O error occurs
 	 */
-	ReadData encode(ReadData readData) throws IOException;
+	ReadData encode(ReadData readData) throws N5IOException;
 
 }

src/main/java/org/janelia/saalfeldlab/n5/DefaultBlockReader.java

@@ -55,6 +55,8 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.codec.DataBlockCodec;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
@@ -76,13 +78,13 @@ public interface DefaultBlockReader {
 	 * @param gridPosition
 	 *            the grid position
 	 * @return the block
-	 * @throws IOException
+	 * @throws N5IOException
 	 *             the exception
 	 */
 	static DataBlock<?> readBlock(
 			final InputStream in,
 			final DatasetAttributes datasetAttributes,
-			final long[] gridPosition) throws IOException {
+			final long[] gridPosition) throws N5IOException {
 
 		final DataBlockCodec<?> codec = datasetAttributes.getDataBlockCodec();
 		return codec.decode(ReadData.from(in), gridPosition);

src/main/java/org/janelia/saalfeldlab/n5/DefaultBlockWriter.java

@@ -55,6 +55,8 @@
 
 import java.io.IOException;
 import java.io.OutputStream;
+
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.codec.DataBlockCodec;
 
 /**
@@ -75,13 +77,13 @@ public interface DefaultBlockWriter {
 	 *            the dataset attributes
 	 * @param dataBlock
 	 *            the data block the block data type
-	 * @throws IOException
+	 * @throws N5IOException
 	 *             the exception
 	 */
 	static <T> void writeBlock(
 			final OutputStream out,
 			final DatasetAttributes datasetAttributes,
-			final DataBlock<T> dataBlock) throws IOException {
+			final DataBlock<T> dataBlock) throws N5IOException {
 
 		final DataBlockCodec<T> codec = datasetAttributes.getDataBlockCodec();
 		codec.encode(dataBlock).writeTo(out);

src/main/java/org/janelia/saalfeldlab/n5/FileSystemKeyValueAccess.java

@@ -53,11 +53,15 @@
  */
 package org.janelia.saalfeldlab.n5;
 
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException;
+
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.io.Reader;
+import java.io.UncheckedIOException;
 import java.io.Writer;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -141,29 +145,40 @@ protected LockedFileChannel(final Path path, final boolean readOnly) throws IOEx
 			}
 		}
 
+		private void truncateChannel(int size) {
+
+			try {
+				channel.truncate(size);
+			} catch (NoSuchFileException e) {
+				throw new N5NoSuchKeyException("No such file", e);
+			} catch (IOException | UncheckedIOException e ) {
+				throw new N5IOException("Failed to truncate locked file channel", e);
+			}
+		}
+
 		@Override
-		public Reader newReader() throws IOException {
+		public Reader newReader() throws N5IOException {
 
 			return Channels.newReader(channel, StandardCharsets.UTF_8.name());
 		}
 
 		@Override
-		public Writer newWriter() throws IOException {
+		public Writer newWriter() throws N5IOException {
 
-			channel.truncate(0);
+			truncateChannel(0);
 			return Channels.newWriter(channel, StandardCharsets.UTF_8.name());
 		}
 
 		@Override
-		public InputStream newInputStream() throws IOException {
+		public InputStream newInputStream() throws N5IOException {
 
 			return Channels.newInputStream(channel);
 		}
 
 		@Override
-		public OutputStream newOutputStream() throws IOException {
+		public OutputStream newOutputStream() throws N5IOException {
 
-			channel.truncate(0);
+			truncateChannel(0);
 			return Channels.newOutputStream(channel);
 		}
 
@@ -187,33 +202,49 @@ public FileSystemKeyValueAccess(final FileSystem fileSystem) {
 	}
 
 	@Override
-	public LockedFileChannel lockForReading(final String normalPath) throws IOException {
+	public LockedChannel lockForReading(final String normalPath) throws N5IOException {
 
 		try {
 			return new LockedFileChannel(normalPath, true);
-		} catch (NoSuchFileException e) {
-			throw new N5Exception.N5NoSuchKeyException("No such file", e);
+		} catch (final NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to lock file for reading: " + normalPath, e);
 		}
 	}
 
 	@Override
-	public LockedFileChannel lockForWriting(final String normalPath) throws IOException {
+	public LockedChannel lockForWriting(final String normalPath) throws N5IOException {
 
-		return new LockedFileChannel(normalPath, false);
+		try {
+			return new LockedFileChannel(normalPath, false);
+		} catch (final NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to lock file for writing: " + normalPath, e);
+		}
 	}
 
-	public LockedFileChannel lockForReading(final Path path) throws IOException {
+	public LockedChannel lockForReading(final Path path) throws N5IOException {
 
 		try {
 			return new LockedFileChannel(path, true);
-		} catch (NoSuchFileException e) {
-			throw new N5Exception.N5NoSuchKeyException("No such file", e);
+		} catch (final NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to lock file for reading: " + path, e);
 		}
 	}
 
-	public LockedFileChannel lockForWriting(final Path path) throws IOException {
+	public LockedChannel lockForWriting(final Path path) throws N5IOException {
 
-		return new LockedFileChannel(path, false);
+		try {
+			return new LockedFileChannel(path, false);
+		} catch (final NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to lock file for writing: " + path, e);
+		}
 	}
 
 	@Override
@@ -238,25 +269,33 @@ public boolean exists(final String normalPath) {
 	}
 
 	@Override
-	public String[] listDirectories(final String normalPath) throws IOException {
+	public String[] listDirectories(final String normalPath) throws N5IOException {
 
 		final Path path = fileSystem.getPath(normalPath);
 		try (final Stream<Path> pathStream = Files.list(path)) {
 			return pathStream
 					.filter(a -> Files.isDirectory(a))
 					.map(a -> path.relativize(a).toString())
 					.toArray(n -> new String[n]);
+		} catch (NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to list directories", e);
 		}
 	}
 
 	@Override
-	public String[] list(final String normalPath) throws IOException {
+	public String[] list(final String normalPath) throws N5IOException {
 
 		final Path path = fileSystem.getPath(normalPath);
 		try (final Stream<Path> pathStream = Files.list(path)) {
 			return pathStream
 					.map(a -> path.relativize(a).toString())
 					.toArray(n -> new String[n]);
+		} catch (NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to list files", e);
 		}
 	}
 
@@ -362,32 +401,42 @@ public String compose(final String... components) {
 	}
 
 	@Override
-	public void createDirectories(final String normalPath) throws IOException {
+	public void createDirectories(final String normalPath) throws N5IOException {
 
-		createDirectories(fileSystem.getPath(normalPath));
+		try {
+			createDirectories(fileSystem.getPath(normalPath));
+		} catch (NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to create directories", e);
+		}
 	}
 
 	@Override
-	public void delete(final String normalPath) throws IOException {
+	public void delete(final String normalPath) throws N5IOException {
 
-		final Path path = fileSystem.getPath(normalPath);
+		try {
+			final Path path = fileSystem.getPath(normalPath);
 
-		if (Files.isRegularFile(path))
-			try (final LockedChannel channel = lockForWriting(path)) {
-				Files.delete(path);
-			}
-		else {
-			try (final Stream<Path> pathStream = Files.walk(path)) {
-				for (final Iterator<Path> i = pathStream.sorted(Comparator.reverseOrder()).iterator(); i.hasNext();) {
-					final Path childPath = i.next();
-					if (Files.isRegularFile(childPath))
-						try (final LockedChannel channel = lockForWriting(childPath)) {
-							Files.delete(childPath);
-						}
-					else
-						tryDelete(childPath);
+			if (Files.isRegularFile(path))
+				try (final LockedChannel channel = lockForWriting(path)) {
+					Files.delete(path);
+				}
+			else {
+				try (final Stream<Path> pathStream = Files.walk(path)) {
+					for (final Iterator<Path> i = pathStream.sorted(Comparator.reverseOrder()).iterator(); i.hasNext();) {
+						final Path childPath = i.next();
+						if (Files.isRegularFile(childPath))
+							try (final LockedChannel channel = lockForWriting(childPath)) {
+								Files.delete(childPath);
+							}
+						else
+							tryDelete(childPath);
+					}
 				}
 			}
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException("Failed to delete file at " + normalPath, e);
 		}
 	}