From ebe69754e947df1a5869bbfd0dbaff60e56ddf23 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 3 May 2012 08:18:10 +0000
Subject: [PATCH] SP-3: IHierachicalContentNode extend by method
getChecksumCRC32(). Implemented for all implementing classes except
PathInfoProviderBasedHierarchicalContent. IOUtilities introduced. No new unit
tests.
SVN: 25145
---
.../common/io/ByteArrayBasedContentNode.java | 11 ++++
.../cisd/common/io/FileBasedContentNode.java | 14 +++++
...ntentNodeBasedHierarchicalContentNode.java | 10 ++++
.../systemsx/cisd/common/io/IOUtilities.java | 56 +++++++++++++++++++
.../AbstractHierarchicalContentNode.java | 9 +++
...tractHierarchicalDirectoryContentNode.java | 6 ++
...faultFileBasedHierarchicalContentNode.java | 15 +++++
...ContainerBasedHierarchicalContentNode.java | 20 +++++++
.../VirtualHierarchicalContent.java | 5 ++
.../api/IHierarchicalContentNode.java | 9 +++
.../AbstractHierarchicalContentNodeTest.java | 12 ++++
...faultFileBasedHierarchicalContentTest.java | 5 ++
...hInfoProviderBasedHierarchicalContent.java | 7 +++
.../generic/shared/utils/ImageUtilTest.java | 5 ++
14 files changed, 184 insertions(+)
create mode 100644 common/source/java/ch/systemsx/cisd/common/io/IOUtilities.java
diff --git a/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContentNode.java
index 33c6d6920a5..4f3da04d574 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/ByteArrayBasedContentNode.java
@@ -40,6 +40,8 @@ public class ByteArrayBasedContentNode implements IHierarchicalContentNode
private final String nameOrNull;
private long lastModified;
+
+ private Long checksum;
/**
* Creates an instance for the specified byte array.
@@ -114,6 +116,15 @@ public class ByteArrayBasedContentNode implements IHierarchicalContentNode
return byteArray.length;
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ if (checksum == null)
+ {
+ checksum = IOUtilities.getChecksumCRC32(new ByteArrayInputStream(byteArray));
+ }
+ return checksum;
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/FileBasedContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/FileBasedContentNode.java
index dcaa21daf37..1d94123442a 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/FileBasedContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/FileBasedContentNode.java
@@ -20,9 +20,12 @@ import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.io.InputStream;
import java.util.List;
+import org.apache.commons.io.FileUtils;
+
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
@@ -121,6 +124,17 @@ public class FileBasedContentNode implements IHierarchicalContentNode
return file.length();
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ try
+ {
+ return FileUtils.checksumCRC32(file);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentNodeBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentNodeBasedHierarchicalContentNode.java
index 412b4e3bf43..5c898ac4fdd 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentNodeBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentNodeBasedHierarchicalContentNode.java
@@ -72,6 +72,11 @@ public class HierarchicalContentNodeBasedHierarchicalContentNode implements
return 0;
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ return 0;
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
@@ -172,6 +177,11 @@ public class HierarchicalContentNodeBasedHierarchicalContentNode implements
return getContent().getFileLength();
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ return getContent().getChecksumCRC32();
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/IOUtilities.java b/common/source/java/ch/systemsx/cisd/common/io/IOUtilities.java
new file mode 100644
index 00000000000..7bef4b9d6a6
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/io/IOUtilities.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.io;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.zip.CRC32;
+import java.util.zip.CheckedInputStream;
+import java.util.zip.Checksum;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.output.NullOutputStream;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+
+/**
+ * Useful utility methods.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class IOUtilities
+{
+ /**
+ * Calculates the CRC32 checksum of specified input stream.
+ * Note, that the input stream is closed after invocation of this method.
+ */
+ public static long getChecksumCRC32(InputStream inputStream)
+ {
+ Checksum checksummer = new CRC32();
+ InputStream in = null;
+ try {
+ in = new CheckedInputStream(inputStream, checksummer);
+ IOUtils.copy(in, new NullOutputStream());
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } finally {
+ IOUtils.closeQuietly(in);
+ }
+ return checksummer.getValue();
+ }
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNode.java
index 61e7f9ce7df..67b68893952 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNode.java
@@ -47,6 +47,9 @@ public abstract class AbstractHierarchicalContentNode implements IHierarchicalCo
/** Returns size of a node known NOT to be a directory. */
abstract protected long doGetFileLength();
+ /** Returns checksum of a node known NOT to be a directory. */
+ abstract protected long doGetChecksumCRC32();
+
/** Returns {@link IRandomAccessFile} of a node known NOT to be a directory. */
abstract protected IRandomAccessFile doGetFileContent();
@@ -92,6 +95,12 @@ public abstract class AbstractHierarchicalContentNode implements IHierarchicalCo
return doGetFileLength();
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ failOnDirectory();
+ return doGetChecksumCRC32();
+ }
+
public final IRandomAccessFile getFileContent()
{
failOnDirectory();
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalDirectoryContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalDirectoryContentNode.java
index c53211cca47..22d9261b50c 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalDirectoryContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalDirectoryContentNode.java
@@ -34,6 +34,12 @@ public abstract class AbstractHierarchicalDirectoryContentNode extends
throw new UnsupportedOperationException(OPERATION_NOT_SUPPORTED_FOR_A_DIRECTORY);
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ throw new UnsupportedOperationException(OPERATION_NOT_SUPPORTED_FOR_A_DIRECTORY);
+ }
+
@Override
protected final IRandomAccessFile doGetFileContent()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentNode.java
index fac958829ef..4655beb189c 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentNode.java
@@ -19,10 +19,13 @@ package ch.systemsx.cisd.common.io.hierarchical_content;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
+import org.apache.commons.io.FileUtils;
+
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
@@ -119,6 +122,18 @@ class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalConten
return file.length();
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ try
+ {
+ return FileUtils.checksumCRC32(file);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
@Override
public IRandomAccessFile doGetFileContent()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
index 234cdf081e5..e1d55337195 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.base.io.AdapterIInputStreamToInputStream;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.common.hdf5.HDF5Container;
import ch.systemsx.cisd.common.hdf5.IHDF5ContainerReader;
+import ch.systemsx.cisd.common.io.IOUtilities;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.hdf5.h5ar.ArchiveEntry;
@@ -259,6 +260,8 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
private HDF5DataSetBasedContent contentOrNull;
private final HDF5ContainerBasedHierarchicalContentNode containerNode;
+
+ private Long checksum;
public HDF5FileNode(HDF5ContainerBasedHierarchicalContentNode containerNode,
ArchiveEntry entry)
@@ -310,6 +313,23 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
return entry.getSize();
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ if (checksum == null)
+ {
+ int entryChecksum = entry.getCrc32();
+ if (entryChecksum != 0)
+ {
+ checksum = (long) entryChecksum;
+ } else
+ {
+ checksum = IOUtilities.getChecksumCRC32(doGetInputStream());
+ }
+ }
+ return checksum;
+ }
+
@Override
protected IRandomAccessFile doGetFileContent()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/VirtualHierarchicalContent.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/VirtualHierarchicalContent.java
index fc1fe9c6b3c..9037e3a6244 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/VirtualHierarchicalContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/VirtualHierarchicalContent.java
@@ -437,6 +437,11 @@ class VirtualHierarchicalContent implements IHierarchicalContent
}
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ return lastExistingNode().getChecksumCRC32();
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/api/IHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/api/IHierarchicalContentNode.java
index 4e18a1e3cc4..0022b9e3c34 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/api/IHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/api/IHierarchicalContentNode.java
@@ -91,6 +91,15 @@ public interface IHierarchicalContentNode
* @throws UnsupportedOperationException if the node is an abstraction of a directory.
*/
long getFileLength() throws UnsupportedOperationException;
+
+ /**
+ * Returns the CRC32 checksum of a file abstracted by this node.
+ * <p>
+ * NOTE: Call {@link #isDirectory()} first to make sure this node is NOT a directory.
+ *
+ * @throws UnsupportedOperationException if the node is an abstraction of a directory.
+ */
+ long getChecksumCRC32() throws UnsupportedOperationException;
/**
* Returns a read only {@link IRandomAccessFile} with file content of the node. *
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
index f45da3dbb92..09cd68e2c48 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
@@ -171,6 +171,12 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
return 0;
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ return 0;
+ }
+
@Override
protected IRandomAccessFile doGetFileContent()
{
@@ -238,6 +244,12 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
return 0;
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ return 0;
+ }
+
@Override
protected IRandomAccessFile doGetFileContent()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
index 1070487d7bf..bf4f46190e7 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
@@ -659,6 +659,11 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
throw new UnsupportedOperationException(METHOD_NOT_IMPLEMENTED);
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ throw new UnsupportedOperationException(METHOD_NOT_IMPLEMENTED);
+ }
+
public InputStream getInputStream() throws UnsupportedOperationException,
IOExceptionUnchecked
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
index 60998aad20f..16a1a5e7a0a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
@@ -237,6 +237,13 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return pathInfo.getSizeInBytes();
}
+ @Override
+ protected long doGetChecksumCRC32()
+ {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
public File getFile() throws UnsupportedOperationException
{
File result = doGetFile();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index c20da02064b..e5c728592c4 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -94,6 +94,11 @@ public class ImageUtilTest extends AssertJUnit
throw new UnsupportedOperationException();
}
+ public long getChecksumCRC32() throws UnsupportedOperationException
+ {
+ throw new UnsupportedOperationException();
+ }
+
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
--
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