SP-3: IHierachicalContentNode extend by method getChecksumCRC32(). Implemented...

SP-3: IHierachicalContentNode extend by method getChecksumCRC32(). Implemented for all implementing classes except PathInfoProviderBasedHierarchicalContent. IOUtilities introduced. No new unit tests.

SVN: 25145

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
     {

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
     {

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
     {

common/source/java/ch/systemsx/cisd/common/io/IOUtilities.java

+/*
+ * 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();
+    }
+}

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();

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()
     {

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()
     {

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()
         {

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
         {

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. *

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()
                 {

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
                 {

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();

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
         {