Merge pull request #124 from saalfeldlab/perf/skipIsFile

perf skip isFile check during readBlock
saalfeldlab · Jul 15, 2024 · 1630a27 · 1630a27
2 parents 6b6d4d2 + 6fe8f29
commit 1630a27
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Showing 4 changed files with 43 additions and 24 deletions.
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/CachedGsonKeyValueN5Reader.java b/src/main/java/org/janelia/saalfeldlab/n5/CachedGsonKeyValueN5Reader.java
@@ -25,7 +25,6 @@
  */
 package org.janelia.saalfeldlab.n5;
 
-import java.io.IOException;
 import java.lang.reflect.Type;
 
 import com.google.gson.JsonSyntaxException;
@@ -233,20 +232,6 @@ default String[] listFromContainer(final String normalPathName) {
 		return GsonKeyValueN5Reader.super.list(normalPathName);
 	}
 
-	@Override
-	default String absoluteDataBlockPath(
-			final String normalPath,
-			final long... gridPosition) {
-
-		final String[] components = new String[gridPosition.length + 1];
-		components[0] = normalPath;
-		int i = 0;
-		for (final long p : gridPosition)
-			components[++i] = Long.toString(p);
-
-		return getKeyValueAccess().compose(getURI(), components);
-	}
-
 	/**
 	 * Check for attributes that are required for a group to be a dataset.
 	 *

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/FileSystemKeyValueAccess.java b/src/main/java/org/janelia/saalfeldlab/n5/FileSystemKeyValueAccess.java
@@ -160,7 +160,11 @@ public FileSystemKeyValueAccess(final FileSystem fileSystem) {
 	@Override
 	public LockedFileChannel lockForReading(final String normalPath) throws IOException {
 
-		return new LockedFileChannel(normalPath, true);
+		try {
+			return new LockedFileChannel(normalPath, true);
+		} catch (NoSuchFileException e) {
+			throw new N5Exception.N5NoSuchKeyException("No such file", e);
+		}
 	}
 
 	@Override
@@ -171,7 +175,11 @@ public LockedFileChannel lockForWriting(final String normalPath) throws IOExcept
 
 	public LockedFileChannel lockForReading(final Path path) throws IOException {
 
-		return new LockedFileChannel(path, true);
+		try {
+			return new LockedFileChannel(path, true);
+		} catch (NoSuchFileException e) {
+			throw new N5Exception.N5NoSuchKeyException("No such file", e);
+		}
 	}
 
 	public LockedFileChannel lockForWriting(final Path path) throws IOException {

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/GsonKeyValueN5Reader.java b/src/main/java/org/janelia/saalfeldlab/n5/GsonKeyValueN5Reader.java
@@ -94,11 +94,11 @@ default DataBlock<?> readBlock(
 			final long... gridPosition) throws N5Exception {
 
 		final String path = absoluteDataBlockPath(N5URI.normalizeGroupPath(pathName), gridPosition);
-		if (!getKeyValueAccess().isFile(path))
-			return null;
 
 		try (final LockedChannel lockedChannel = getKeyValueAccess().lockForReading(path)) {
 			return DefaultBlockReader.readBlock(lockedChannel.newInputStream(), datasetAttributes, gridPosition);
+		} catch (final N5Exception.N5NoSuchKeyException e) {
+			return null;
 		} catch (final IOException | UncheckedIOException e) {
 			throw new N5IOException(
 					"Failed to read block " + Arrays.toString(gridPosition) + " from dataset " + path,
@@ -137,14 +137,13 @@ default String absoluteDataBlockPath(
 			final String normalPath,
 			final long... gridPosition) {
 
-		final String[] components = new String[gridPosition.length + 2];
-		components[0] = getURI().getPath();
-		components[1] = normalPath;
-		int i = 1;
+		final String[] components = new String[gridPosition.length + 1];
+		components[0] = normalPath;
+		int i = 0;
 		for (final long p : gridPosition)
 			components[++i] = Long.toString(p);
 
-		return getKeyValueAccess().compose(components);
+		return getKeyValueAccess().compose(getURI(), components);
 	}
 
 	/**

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/N5Exception.java b/src/main/java/org/janelia/saalfeldlab/n5/N5Exception.java
@@ -94,4 +94,31 @@ protected N5ClassCastException(
 			super(message, cause, enableSuppression, writableStackTrace);
 		}
 	}
+
+	public static class N5NoSuchKeyException extends N5IOException {
+
+		public N5NoSuchKeyException(final String message) {
+
+			super(message);
+		}
+
+		public N5NoSuchKeyException(final String message, final Throwable cause) {
+
+			super(message, cause);
+		}
+
+		public N5NoSuchKeyException(final Throwable cause) {
+
+			super(cause);
+		}
+
+		protected N5NoSuchKeyException(
+				final String message,
+				final Throwable cause,
+				final boolean enableSuppression,
+				final boolean writableStackTrace) {
+
+			super(message, cause, enableSuppression, writableStackTrace);
+		}
+	}
 }