From 778aa3d82189970a5b397db6275452be2fcc562d Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 22 Aug 2011 17:34:08 +0000
Subject: [PATCH] fix: very slow operation of HDF5ContainerReader due to
inappropriate buffer size of IOUtils.copyLarge()
SVN: 22583
---
.../cisd/common/hdf5/HDF5ContainerReader.java | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java
index fe28c5f90f8..4fbd0cff244 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java
@@ -22,8 +22,6 @@ import java.io.InputStream;
import java.io.OutputStream;
import java.util.List;
-import org.apache.commons.io.IOUtils;
-
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
@@ -36,6 +34,8 @@ import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory;
*/
final class HDF5ContainerReader implements IHDF5ContainerReader
{
+ private final byte[] buffer = new byte[HDF5ContainerWriter.BUFFER_SIZE];
+
private final IHDF5Reader innerReader;
HDF5ContainerReader(final File hdf5Container)
@@ -63,13 +63,25 @@ final class HDF5ContainerReader implements IHDF5ContainerReader
return innerReader.getGroupMembers(groupPath);
}
+ private long copy(InputStream input, OutputStream output) throws IOException
+ {
+ long count = 0;
+ int n = 0;
+ while (-1 != (n = input.read(buffer)))
+ {
+ output.write(buffer, 0, n);
+ count += n;
+ }
+ return count;
+ }
+
public void readFromHDF5Container(String objectPath, OutputStream ostream)
{
final InputStream istream = HDF5IOAdapterFactory.asInputStream(innerReader, objectPath);
Exception e = null;
try
{
- IOUtils.copyLarge(istream, ostream);
+ copy(istream, ostream);
} catch (IOException ex)
{
e = ex;
--
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