refactor: migrate IOExceptions to N5IOExceptions for ReadData and related logic

Author: cmhulbert

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/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;
 
@@ -119,7 +121,7 @@ default String getType() {
 	 * @throws IOException
 	 * 		if any I/O error occurs
 	 */
-	ReadData decode(ReadData readData) throws IOException;
+	ReadData decode(ReadData readData) throws N5IOException;
 
 	/**
 	 * Encode the given {@code readData}.
@@ -135,6 +137,6 @@ default String getType() {
 	 * @throws IOException
 	 * 		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/FileSystemKeyValueAccess.java

@@ -53,6 +53,8 @@
  */
 package org.janelia.saalfeldlab.n5;
 
+import org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException;
+
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
@@ -191,8 +193,8 @@ public LockedFileChannel lockForReading(final String normalPath) throws IOExcept
 
 		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);
 		}
 	}
 
@@ -206,8 +208,8 @@ public LockedFileChannel lockForReading(final Path path) throws IOException {
 
 		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);
 		}
 	}
 

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

@@ -62,6 +62,7 @@
 import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
 import org.apache.commons.compress.compressors.gzip.GzipParameters;
 import org.janelia.saalfeldlab.n5.Compression.CompressionType;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 @CompressionType("gzip")
@@ -113,13 +114,17 @@ private InputStream decode(final InputStream in) throws IOException {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData) throws IOException {
+	public ReadData decode(final ReadData readData) throws N5IOException {
 
-		return ReadData.from(decode(readData.inputStream()));
+		try {
+			return ReadData.from(decode(readData.inputStream()));
+		} catch (IOException e) {
+			throw new N5IOException(e);
+		}
 	}
 
 	@Override
-	public ReadData encode(final ReadData readData) {
+	public ReadData encode(final ReadData readData)  {
 		if (useZlib) {
 			return readData.encode(out -> new DeflaterOutputStream(out, new Deflater(level)));
 		} else {

src/main/java/org/janelia/saalfeldlab/n5/HttpKeyValueAccess.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
@@ -26,30 +26,11 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-/**
- * Copyright (c) 2017, Stephan Saalfeld All rights reserved.
- * <p>
- * Redistribution and use in source and binary forms, with or without modification, are permitted
- * provided that the following conditions are met:
- * <p>
- * 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.
- * <p>
- * 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 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
- * WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
 package org.janelia.saalfeldlab.n5;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.function.TriFunction;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.http.ListResponseParser;
 
 import java.io.Closeable;
@@ -85,7 +66,7 @@ public class HttpKeyValueAccess implements KeyValueAccess {
 	/**
 	 * Opens an {@link HttpKeyValueAccess}
 	 *
-	 * @throws N5Exception.N5IOException if the access could not be created
+	 * @throws N5IOException if the access could not be created
 	 */
 	public HttpKeyValueAccess() {
 
@@ -296,7 +277,7 @@ private String[] queryListEntries(String normalPath, ListResponseParser parser,
 			final String listResponse = responseToString(http.getInputStream());
 			return parser.parseListResponse(listResponse);
 		} catch (IOException e) {
-			throw new N5Exception.N5IOException("Error listing directory at " + normalPath, e);
+			throw new N5IOException("Error listing directory at " + normalPath, e);
 		}
 	}
 
@@ -324,7 +305,7 @@ private HttpURLConnection requireValidHttpResponse(String uri, String method, Tr
 			code = http.getResponseCode();
 			responseMsg = http.getResponseMessage();
 		} catch (IOException e) {
-			throw new N5Exception.N5IOException("Could not validate HTTP Response", e);
+			throw new N5IOException("Could not validate HTTP Response", e);
 		}
 
 		final N5Exception cause = filterCode.apply(code, responseMsg, http);

src/main/java/org/janelia/saalfeldlab/n5/Lz4Compression.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
@@ -53,10 +53,10 @@
  */
 package org.janelia.saalfeldlab.n5;
 
-import java.io.IOException;
 import net.jpountz.lz4.LZ4BlockInputStream;
 import net.jpountz.lz4.LZ4BlockOutputStream;
 import org.janelia.saalfeldlab.n5.Compression.CompressionType;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 @CompressionType("lz4")
@@ -87,7 +87,7 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData) throws IOException {
+	public ReadData decode(final ReadData readData) throws N5IOException {
 
 		return ReadData.from(new LZ4BlockInputStream(readData.inputStream()));
 	}

src/main/java/org/janelia/saalfeldlab/n5/XzCompression.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
@@ -54,10 +54,10 @@
 package org.janelia.saalfeldlab.n5;
 
 import java.io.IOException;
-import java.io.InputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
 import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream;
 import org.janelia.saalfeldlab.n5.Compression.CompressionType;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 @CompressionType("xz")
@@ -88,9 +88,13 @@ public boolean equals(final Object other) {
 	}
 
 	@Override
-	public ReadData decode(final ReadData readData) throws IOException {
+	public ReadData decode(final ReadData readData) throws N5IOException {
 
-		return ReadData.from(new XZCompressorInputStream(readData.inputStream()));
+		try {
+			return ReadData.from(new XZCompressorInputStream(readData.inputStream()));
+		} catch (IOException e) {
+			throw new N5IOException(e);
+		}
 	}
 
 	@Override

src/main/java/org/janelia/saalfeldlab/n5/codec/DataBlockCodec.java

@@ -28,8 +28,9 @@
  */
 package org.janelia.saalfeldlab.n5.codec;
 
-import java.io.IOException;
 import org.janelia.saalfeldlab.n5.DataBlock;
+import org.janelia.saalfeldlab.n5.N5Exception;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 /**
@@ -40,7 +41,7 @@
  */
 public interface DataBlockCodec<T> {
 
-	ReadData encode(DataBlock<T> dataBlock) throws IOException;
+	ReadData encode(DataBlock<T> dataBlock) throws N5IOException;
 
-	DataBlock<T> decode(ReadData readData, long[] gridPosition) throws IOException;
+	DataBlock<T> decode(ReadData readData, long[] gridPosition) throws N5IOException;
 }