fix: relax catching and rethrowinbg IOExceptions to Throwable

bump to n5-3.1.3
saalfeldlab · Feb 16, 2024 · 378229f · 378229f
1 parent adfcfb2
commit 378229f
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Showing 3 changed files with 16 additions and 17 deletions.
diff --git a/pom.xml b/pom.xml
@@ -138,7 +138,7 @@
 
 		<json-simple.version>1.1.1</json-simple.version>
 
-		<n5.version>3.1.1</n5.version>
+		<n5.version>3.1.3</n5.version>
 		<n5-zstandard.version>1.0.2</n5-zstandard.version>
 
 	</properties>

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java b/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueReader.java
@@ -505,7 +505,7 @@ protected JsonElement zarrToN5DatasetAttributes(final JsonElement elem ) {
 		attrs.add(DatasetAttributes.BLOCK_SIZE_KEY, attrs.get(ZArrayAttributes.chunksKey));
 		attrs.addProperty(DatasetAttributes.DATA_TYPE_KEY, zattrs.getDType().getDataType().toString());
 
-		JsonElement e = attrs.get(ZArrayAttributes.compressorKey);
+		final JsonElement e = attrs.get(ZArrayAttributes.compressorKey);
 		if (e == JsonNull.INSTANCE) {
 			attrs.add(DatasetAttributes.COMPRESSION_KEY, gson.toJsonTree(new RawCompression()));
 		} else {
@@ -636,7 +636,7 @@ public DataBlock<?> readBlock(
 
 		try (final LockedChannel lockedChannel = keyValueAccess.lockForReading(absolutePath)) {
 			return readBlock(lockedChannel.newInputStream(), zarrDatasetAttributes, gridPosition);
-		} catch (final IOException | UncheckedIOException  e) {
+		} catch (final Throwable  e) {
 			throw new N5IOException(
 					"Failed to read block " + Arrays.toString(gridPosition) + " from dataset " + pathName,
 					e);
@@ -685,9 +685,9 @@ protected static DataBlock<?> readBlock(
 		return dataBlock;
 	}
 
-	private static ZarrStringDataBlock readVLenStringBlock(InputStream in, BlockReader reader, ByteArrayDataBlock byteBlock) throws IOException {
+	private static ZarrStringDataBlock readVLenStringBlock(final InputStream in, final BlockReader reader, final ByteArrayDataBlock byteBlock) throws IOException {
 		// read whole chunk and deserialize; this should be improved
-		ZarrStringDataBlock dataBlock = new ZarrStringDataBlock(byteBlock.getSize(), byteBlock.getGridPosition(), new String[0]);
+		final ZarrStringDataBlock dataBlock = new ZarrStringDataBlock(byteBlock.getSize(), byteBlock.getGridPosition(), new String[0]);
 		if (reader instanceof BloscCompression) {
 			// Blosc reader reads actual data and doesn't care about buffer size (but needs special treatment in data block)
 			reader.read(dataBlock, in);

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueWriter.java b/src/main/java/org/janelia/saalfeldlab/n5/zarr/ZarrKeyValueWriter.java
@@ -27,7 +27,6 @@
 
 import java.io.IOException;
 import java.io.OutputStream;
-import java.io.UncheckedIOException;
 import java.util.Arrays;
 import java.util.Map;
 import java.util.function.Supplier;
@@ -45,9 +44,9 @@
 import org.janelia.saalfeldlab.n5.LockedChannel;
 import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
-import org.janelia.saalfeldlab.n5.cache.N5JsonCache;
 import org.janelia.saalfeldlab.n5.N5URI;
 import org.janelia.saalfeldlab.n5.RawCompression;
+import org.janelia.saalfeldlab.n5.cache.N5JsonCache;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
@@ -137,6 +136,7 @@ public ZarrKeyValueWriter(
 		}
 	}
 
+	@Override
 	public void setVersion(final String path) throws N5Exception {
 
 		setVersion(path, false);
@@ -192,7 +192,7 @@ else if ( getCache().isDataset(normalPath, ZARRAY_FILE)){
 		// since the contents is null
 		try {
 			keyValueAccess.createDirectories(absoluteGroupPath(normalPath));
-		} catch (final IOException | UncheckedIOException e) {
+		} catch (final Throwable e) {
 			throw new N5Exception.N5IOException("Failed to create group " + path, e);
 		}
 
@@ -245,7 +245,7 @@ else if (getCache().isGroup(normalPath, ZGROUP_FILE)) {
 		final String absPath = absoluteGroupPath(normalPath);
 		try {
 			keyValueAccess.createDirectories(absPath);
-		} catch (final IOException | UncheckedIOException  e) {
+		} catch (final Throwable e) {
 			throw new N5IOException("Failed to create directories " + absPath, e);
 		}
 
@@ -386,8 +386,8 @@ protected ZArrayAttributes createZArrayAttributes(final DatasetAttributes datase
 
 	/**
 	 * Write the contents of the attributes argument to the .zarray file at
-	 * the given pathName. Overwrites and existing .zarray. 
-	 * 
+	 * the given pathName. Overwrites and existing .zarray.
+	 *
 	 * @param pathName the group / dataset path
 	 * @param attributes ZArray attributes
 	 * @throws N5Exception the exception
@@ -407,7 +407,7 @@ protected void deleteJsonResource(final String normalPath, final String jsonName
 		final String absolutePath = keyValueAccess.compose(uri, normalPath, jsonName);
 		try {
 			keyValueAccess.delete(absolutePath);
-		} catch (IOException | UncheckedIOException  e1) {
+		} catch (final Throwable e1) {
 			throw new N5IOException("Failed to delete " + absolutePath, e1);
 		}
 	}
@@ -423,7 +423,7 @@ protected void writeJsonResource(
 		final String absolutePath = keyValueAccess.compose(uri, normalPath, jsonName);
 		try (final LockedChannel lock = keyValueAccess.lockForWriting(absolutePath)) {
 			GsonUtils.writeAttributes(lock.newWriter(), attributes, gson);
-		} catch (final IOException | UncheckedIOException  e) {
+		} catch (final Throwable e) {
 			throw new N5IOException("Failed to write " + absolutePath, e);
 		}
 	}
@@ -540,7 +540,7 @@ public <T> void writeBlock(
 						zarrDatasetAttributes,
 						dataBlock);
 			}
-		} catch (final IOException | UncheckedIOException  e) {
+		} catch (final Throwable e) {
 			throw new N5IOException(
 					"Failed to write block " + Arrays.toString(dataBlock.getGridPosition()) + " into dataset " + path,
 					e);
@@ -567,7 +567,7 @@ public boolean deleteBlock(
 		try {
 			if (keyValueAccess.exists(absolutePath))
 				keyValueAccess.delete(absolutePath);
-		} catch (final IOException | UncheckedIOException  e) {
+		} catch (final Throwable e) {
 			throw new N5IOException(
 					"Failed to delete block " + Arrays.toString(gridPosition) + " from dataset " + path,
 					e);
@@ -730,7 +730,7 @@ protected static ZarrJsonElements build(final JsonObject obj, final Gson gson )
 	 * <p>
 	 * Used when re-directing attributes to the appropriate zarr metadata files according to
 	 * attribute keys.
-	 * 
+	 *
 	 * @param obj the json attributes object
 	 * @param gson the json
 	 * @param mapN5Attributes if true, map n5 attribute keys to corresponding zarr attribute keys
@@ -856,5 +856,4 @@ static void reorder(final JsonArray array) {
 			array.set(j, a);
 		}
 	}
-
 }