Refactor/deprecated

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

@@ -0,0 +1,47 @@
+package org.janelia.saalfeldlab.n5;
+
+import org.janelia.saalfeldlab.n5.readdata.ReadData;
+
+import java.io.*;
+
+class BufferedKvaLockedChannel implements LockedChannel {
+
+    private final KeyValueAccess kva;
+    private final String key;
+    private ByteArrayOutputStream baos = null;
+
+    BufferedKvaLockedChannel(final KeyValueAccess kva, final String key) {
+        this.kva = kva;
+        this.key = key;
+    }
+
+    @Override
+    public Reader newReader() throws N5Exception.N5IOException {
+
+        return new InputStreamReader(newInputStream());
+    }
+
+    @Override
+    public InputStream newInputStream() throws N5Exception.N5IOException {
+        return kva.createReadData(key).inputStream();
+    }
+
+    @Override
+    public Writer newWriter() throws N5Exception.N5IOException {
+
+        return new BufferedWriter(new OutputStreamWriter(newOutputStream()));
+    }
+
+    @Override
+    public OutputStream newOutputStream() throws N5Exception.N5IOException {
+        if (baos == null)
+            baos = new ByteArrayOutputStream();
+        return baos;
+    }
+
+    @Override
+    public void close() throws IOException {
+        if (baos != null && baos.size() > 0)
+            kva.write(key, ReadData.from(baos.toByteArray()));
+    }
+}

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

@@ -34,8 +34,6 @@
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException;
 
-import java.nio.ByteBuffer;
-import java.nio.channels.FileChannel;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.file.attribute.FileAttribute;
@@ -45,11 +43,8 @@
 import java.util.stream.Stream;
 
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
-import org.janelia.saalfeldlab.n5.readdata.LazyRead;
 import org.janelia.saalfeldlab.n5.readdata.VolatileReadData;
 
-import static org.janelia.saalfeldlab.n5.FileKeyLockManager.FILE_LOCK_MANAGER;
-
 /**
  * Filesystem {@link KeyValueAccess}.
  *
@@ -67,11 +62,11 @@ private static IoPolicy getIoPolicy() {
 			return FsIoPolicy.atomicWithFallback;
 
 		switch (property) {
-			case "atomic":
+			case "strict":
 				return new FsIoPolicy.Atomic();
 			case "unsafe":
 				return new FsIoPolicy.Unsafe();
-			case "atomicFallbackUnsafe":
+			case "permissive":
 			default:
 				return FsIoPolicy.atomicWithFallback;
 		}
@@ -100,44 +95,6 @@ public void write(final String normalPath, final ReadData data) throws N5IOExcep
 		}
 	}
 
-	@Override
-	@Deprecated
-	public LockedFileChannel lockForReading(final String normalPath) throws N5IOException {
-
-		return lockForReading(Paths.get(normalPath));
-	}
-
-	@Override
-	@Deprecated
-	public LockedChannel lockForWriting(final String normalPath) throws N5IOException {
-
-		return lockForWriting(Paths.get(normalPath));
-	}
-
-	@Deprecated
-	protected static LockedFileChannel lockForReading(final Path path) throws N5IOException {
-
-		try {
-			return FILE_LOCK_MANAGER.lockForReading(path);
-		} 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);
-		}
-	}
-
-	@Deprecated
-	static LockedFileChannel lockForWriting(final Path path) throws N5IOException {
-
-		try {
-			return FILE_LOCK_MANAGER.lockForWriting(path);
-		} 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
 	public boolean isDirectory(final String normalPath) {
 
@@ -165,17 +122,6 @@ public long size(final String normalPath) {
 		return size(Paths.get(normalPath));
 	}
 
-	protected static long size(final Path path) {
-
-		try {
-			return Files.size(path);
-		} catch (NoSuchFileException e) {
-			throw new N5NoSuchKeyException("No such file", e);
-		} catch (IOException | UncheckedIOException e) {
-			throw new N5IOException(e);
-		}
-	}
-
 	@Override
 	public String[] listDirectories(final String normalPath) throws N5IOException {
 
@@ -346,6 +292,17 @@ public void delete(final String normalPath) throws N5IOException {
 		}
 	}
 
+	protected static long size(final Path path) {
+
+		try {
+			return Files.size(path);
+		} catch (NoSuchFileException e) {
+			throw new N5NoSuchKeyException("No such file", e);
+		} catch (IOException | UncheckedIOException e) {
+			throw new N5IOException(e);
+		}
+	}
+
 	protected static void tryDelete(final Path path) throws IOException {
 
 		try {
@@ -501,88 +458,4 @@ protected static void createAndCheckIsDirectory(
 				throw x;
 		}
 	}
-
-	static class FileLazyRead implements LazyRead {
-
-		private static final Closeable NO_OP = () -> { };
-
-		private final Path path;
-		private Closeable lock;
-
-		FileLazyRead(final Path path) throws IOException {
-			this(path, true);
-		}
-
-		FileLazyRead(final Path path, final boolean requireLock ) throws IOException {
-	        this.path = path;
-			if (requireLock)
-				lock = FILE_LOCK_MANAGER.lockForReading(path);
-			else
-				lock = NO_OP;
-	    }
-
-		@Override
-		public long size() throws N5IOException {
-
-			if (lock == null) {
-				throw new N5IOException("FileLazyRead is already closed.");
-			}
-			return FileSystemKeyValueAccess.size(path);
-		}
-
-		@Override
-	    public ReadData materialize(final long offset, final long length) {
-
-			if (lock == null) {
-				throw new N5IOException("FileLazyRead is already closed.");
-			}
-
-			try (final FileChannel channel = FileChannel.open(path, StandardOpenOption.READ)) {
-
-				channel.position(offset);
-
-	            final long channelSize = channel.size();
-	            if (!validBounds(channelSize, offset, length)) {
-					throw new IndexOutOfBoundsException();
-				}
-
-				final long size = length < 0 ? (channelSize - offset) : length;
-				if (size > Integer.MAX_VALUE) {
-					throw new IndexOutOfBoundsException("Attempt to materialize too large data");
-				}
-
-				final byte[] data = new byte[(int) size];
-				final ByteBuffer buf = ByteBuffer.wrap(data);
-				channel.read(buf);
-				return ReadData.from(data);
-
-			} catch (final NoSuchFileException e) {
-	            throw new N5NoSuchKeyException("No such file", e);
-	        } catch (IOException | UncheckedIOException e) {
-	            throw new N5IOException(e);
-	        }
-	    }
-
-		@Override
-		public void close() throws IOException {
-
-			if (lock != null) {
-				lock.close();
-				lock = null;
-			}
-		}
-	}
-
-	private static boolean validBounds(long channelSize, long offset, long length) {
-
-		if (offset < 0)
-			return false;
-		else if (channelSize > 0 && offset >= channelSize) // offset == 0 and channelSize == 0 is okay
-			return false;
-		else if (length >= 0 && offset + length > channelSize)
-			return false;
-
-		return true;
-	}
-
 }

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

@@ -1,9 +1,13 @@
 package org.janelia.saalfeldlab.n5;
 
+import org.janelia.saalfeldlab.n5.readdata.LazyRead;
 import org.janelia.saalfeldlab.n5.readdata.ReadData;
 import org.janelia.saalfeldlab.n5.readdata.VolatileReadData;
 
+import java.io.Closeable;
 import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.ByteBuffer;
 import java.nio.channels.FileChannel;
 import java.nio.file.*;
 
@@ -13,6 +17,18 @@ public class FsIoPolicy {
 
     static final IoPolicy atomicWithFallback = IoPolicy.withFallback(new Atomic(), new Unsafe());
 
+    private static boolean validBounds(long channelSize, long offset, long length) {
+
+        if (offset < 0)
+            return false;
+        else if (channelSize > 0 && offset >= channelSize) // offset == 0 and channelSize == 0 is okay
+            return false;
+        else if (length >= 0 && offset + length > channelSize)
+            return false;
+
+        return true;
+    }
+
     public static class Unsafe implements IoPolicy {
         @Override
         public void write(String key, ReadData readData) throws IOException {
@@ -23,7 +39,7 @@ public void write(String key, ReadData readData) throws IOException {
         @Override
         public VolatileReadData read(final String key) throws IOException {
             final Path path = Paths.get(key);
-            FileSystemKeyValueAccess.FileLazyRead fileLazyRead = new FileSystemKeyValueAccess.FileLazyRead(path, false);
+            FileLazyRead fileLazyRead = new FileLazyRead(path, false);
             return VolatileReadData.from(fileLazyRead);
         }
 
@@ -46,7 +62,7 @@ public void write(String key, ReadData readData) throws IOException {
         @Override
         public VolatileReadData read(String key) throws IOException {
             final Path path = Paths.get(key);
-            FileSystemKeyValueAccess.FileLazyRead fileLazyRead = new FileSystemKeyValueAccess.FileLazyRead(path, true);
+            FileLazyRead fileLazyRead = new FileLazyRead(path, true);
             return VolatileReadData.from(fileLazyRead);
         }
 
@@ -58,4 +74,75 @@ public void delete(final String key) throws IOException {
             }
         }
     }
+
+    static class FileLazyRead implements LazyRead {
+
+        private static final Closeable NO_OP = () -> { };
+
+        private final Path path;
+        private Closeable lock;
+
+        FileLazyRead(final Path path) throws IOException {
+            this(path, true);
+        }
+
+        FileLazyRead(final Path path, final boolean requireLock ) throws IOException {
+            this.path = path;
+            if (requireLock)
+                lock = FILE_LOCK_MANAGER.lockForReading(path);
+            else
+                lock = NO_OP;
+        }
+
+        @Override
+        public long size() throws N5Exception.N5IOException {
+
+            if (lock == null) {
+                throw new N5Exception.N5IOException("FileLazyRead is already closed.");
+            }
+            return FileSystemKeyValueAccess.size(path);
+        }
+
+        @Override
+        public ReadData materialize(final long offset, final long length) {
+
+            if (lock == null) {
+                throw new N5Exception.N5IOException("FileLazyRead is already closed.");
+            }
+
+            try (final FileChannel channel = FileChannel.open(path, StandardOpenOption.READ)) {
+
+                channel.position(offset);
+
+                final long channelSize = channel.size();
+                if (!validBounds(channelSize, offset, length)) {
+                    throw new IndexOutOfBoundsException();
+                }
+
+                final long size = length < 0 ? (channelSize - offset) : length;
+                if (size > Integer.MAX_VALUE) {
+                    throw new IndexOutOfBoundsException("Attempt to materialize too large data");
+                }
+
+                final byte[] data = new byte[(int) size];
+                final ByteBuffer buf = ByteBuffer.wrap(data);
+                channel.read(buf);
+                return ReadData.from(data);
+
+            } catch (final NoSuchFileException e) {
+                throw new N5Exception.N5NoSuchKeyException("No such file", e);
+            } catch (IOException | UncheckedIOException e) {
+                throw new N5Exception.N5IOException(e);
+            }
+        }
+
+        @Override
+        public void close() throws IOException {
+
+            if (lock != null) {
+                lock.close();
+                lock = null;
+            }
+        }
+    }
 }