add:

- new parameter to addFile(File)
change:
- copyFile -> extractFile (back to previous version)
remove:
- removeFile method

SVN: 2220

bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java

@@ -48,10 +48,11 @@ public interface IDirectory extends INode, Iterable<INode>
      * Adds the specified real file to this directory. The content of <code>file</code> will be copied. If it is a
      * folder also its complete content including all subfolders will be copied.
      * 
+     * @param move whether given <var>file</var> should be copied or moved.
      * @return the new node. It will be a {@link ILink} if <code>file</code> is a symbolic link, a {@link IDirectory}
      *         if <code>file</code> is a folder, or {@link IFile} if <code>file</code> is a plain file.
      */
-    public INode addFile(File file) throws UserFailureException, EnvironmentFailureException;
+    public INode addFile(final File file, final boolean move) throws UserFailureException, EnvironmentFailureException;
 
     /**
      * Adds a plain file named <code>key</code> with content <code>value</code> to this directory.

bds/source/java/ch/systemsx/cisd/bds/storage/INode.java

@@ -39,20 +39,14 @@ public interface INode
     public IDirectory tryToGetParent();
 
     /**
-     * Copies this node to the specified directory of the file system. All descendants are also copied.
+     * Extracts this node to the specified directory of the file system.
+     * <p>
+     * All descendants are also extracted. This is a copy operation.
+     * </p>
      * 
      * @throws UserFailureException if this or a descended node is a link referring to a node which is not this node or
      *             a descended node.
      * @throws EnvironmentFailureException if extraction causes an IOException.
      */
-    public void copyTo(File directory) throws UserFailureException, EnvironmentFailureException;
-
-    /**
-     * Moves this node to the specified directory of the file system. All descendants are also moved.
-     * 
-     * @throws UserFailureException if this or a descended node is a link referring to a node which is not this node or
-     *             a descended node.
-     * @throws EnvironmentFailureException if extraction causes an IOException.
-     */
-    public void moveTo(File directory) throws UserFailureException, EnvironmentFailureException;
+    public void extractTo(final File directory) throws UserFailureException, EnvironmentFailureException;
 }

bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java

@@ -27,7 +27,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
  */
 abstract class AbstractNode implements INode
 {
-    protected File nodeFile;
+    protected final File nodeFile;
 
     AbstractNode(File file)
     {

bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java

@@ -20,6 +20,7 @@ import java.io.IOException;
 import java.util.Iterator;
 
 import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
 import ch.systemsx.cisd.bds.storage.IFile;
@@ -27,6 +28,8 @@ import ch.systemsx.cisd.bds.storage.ILink;
 import ch.systemsx.cisd.bds.storage.INode;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.common.utilities.FileUtilities;
 
 /**
@@ -34,6 +37,9 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
  */
 class Directory extends AbstractNode implements IDirectory
 {
+
+    private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, AbstractNode.class);
+
     Directory(java.io.File directory)
     {
         super(directory);
@@ -83,11 +89,31 @@ class Directory extends AbstractNode implements IDirectory
         return new File(file);
     }
 
-    public INode addFile(java.io.File file) throws UserFailureException, EnvironmentFailureException
+    public INode addFile(final java.io.File file, final boolean move) throws UserFailureException,
+            EnvironmentFailureException
     {
-        INode node = NodeFactory.createNode(file);
-        node.moveTo(nodeFile);
-        return node;
+        final java.io.File newFile = new java.io.File(nodeFile, file.getName());
+        if (move)
+        {
+            moveFileToDirectory(file, nodeFile);
+        } else
+        {
+            try
+            {
+                if (file.isDirectory())
+                {
+                    FileUtils.copyDirectory(file, newFile);
+                } else
+                {
+                    FileUtils.copyFile(file, newFile);
+                }
+            } catch (IOException ex)
+            {
+                throw EnvironmentFailureException.fromTemplate(ex, "Couldn't not copy file '%s' to directory '%s'.",
+                        file, nodeFile.getAbsolutePath());
+            }
+        }
+        return NodeFactory.createNode(newFile);
     }
 
     public ILink addLink(String name, INode node)
@@ -125,7 +151,7 @@ class Directory extends AbstractNode implements IDirectory
             };
     }
 
-    public final void copyTo(final java.io.File directory) throws EnvironmentFailureException
+    public final void extractTo(final java.io.File directory) throws EnvironmentFailureException
     {
         assert directory != null;
         try
@@ -138,30 +164,27 @@ class Directory extends AbstractNode implements IDirectory
         }
     }
 
-    public final void moveTo(java.io.File directory) throws EnvironmentFailureException
+    private final static void moveFileToDirectory(final java.io.File source, final java.io.File directory)
+            throws EnvironmentFailureException
     {
-        assert directory != null;
-        directory.mkdirs();
-        final java.io.File destination = new java.io.File(directory, getName());
+        assert source != null;
+        assert directory != null && directory.isDirectory();
+        final java.io.File destination = new java.io.File(directory, source.getName());
         if (destination.exists() == false)
         {
-            // Note that 'renameTo' does not change 'nodeFile' path
-            final boolean successful = nodeFile.renameTo(destination);
+            final boolean successful = source.renameTo(destination);
             if (successful == false)
             {
-                throw EnvironmentFailureException.fromTemplate("Couldn't not move directory '%s' to directory '%s'.",
-                        nodeFile.getAbsolutePath(), directory.getAbsolutePath());
+                throw EnvironmentFailureException.fromTemplate("Couldn't not move file '%s' to directory '%s'.", source
+                        .getAbsolutePath(), directory.getAbsolutePath());
             }
-            assert nodeFile.exists() == false;
-        }
-        if (nodeFile.equals(destination) == false)
+        } else
         {
-            nodeFile = destination;
-        }
-        // Update children
-        for (INode node : this)
-        {
-            node.moveTo(destination);
+            if (operationLog.isInfoEnabled())
+            {
+                operationLog.info(String.format("Destination file '%s' already exists. Will not overwrite", destination
+                        .getAbsolutePath()));
+            }
         }
     }
 }

bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java

@@ -58,8 +58,9 @@ class File extends AbstractNode implements IFile
         return FileUtilities.loadToString(nodeFile);
     }
 
-    public final void copyTo(final java.io.File directory) throws EnvironmentFailureException
+    public final void extractTo(final java.io.File directory) throws EnvironmentFailureException
     {
+        assert directory != null && directory.isDirectory();
         try
         {
             FileUtils.copyFileToDirectory(nodeFile, directory);
@@ -69,24 +70,4 @@ class File extends AbstractNode implements IFile
                     nodeFile.getAbsolutePath(), directory.getAbsolutePath());
         }
     }
-
-    public final void moveTo(java.io.File directory) throws EnvironmentFailureException
-    {
-        assert directory != null;
-        final java.io.File destination = new java.io.File(directory, getName());
-        if (destination.exists() == false)
-        {
-            // Note that 'renameTo' does not change 'nodeFile' path
-            final boolean successful = nodeFile.renameTo(destination);
-            if (successful == false)
-            {
-                throw EnvironmentFailureException.fromTemplate("Couldn't not move file '%s' to directory '%s'.",
-                        nodeFile.getAbsolutePath(), directory.getAbsolutePath());
-            }
-        }
-        if (nodeFile.equals(destination) == false)
-        {
-            nodeFile = destination;
-        }
-    }
 }

bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java

@@ -62,15 +62,8 @@ class Link implements ILink
         return reference;
     }
 
-    public void copyTo(File directory) throws UserFailureException, EnvironmentFailureException
+    public void extractTo(final File directory) throws UserFailureException, EnvironmentFailureException
     {
         // TODO Auto-generated method stub
     }
-
-    public void moveTo(File directory) throws UserFailureException, EnvironmentFailureException
-    {
-        // TODO Auto-generated method stub
-
-    }
-
 }

bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java

@@ -93,7 +93,7 @@ public class DirectoryTest extends StorageTestCase
     }
 
     @Test
-    public void testCopyTo()
+    public void testExtractTo()
     {
         File dir = new File(TEST_DIR, "dir");
         dir.mkdirs();
@@ -103,7 +103,7 @@ public class DirectoryTest extends StorageTestCase
         subdir.addKeyValuePair("p2", "property 2");
         File destination = new File(TEST_DIR, "destination");
         assertFalse(destination.exists());
-        directory.copyTo(destination);
+        directory.extractTo(destination);
         assertTrue(destination.exists());
         File copiedDir = new File(destination, "dir");
         assertTrue(copiedDir.exists());
@@ -115,29 +115,6 @@ public class DirectoryTest extends StorageTestCase
         assertEquals(true, new File(TEST_DIR, "dir").exists());
     }
 
-    @Test
-    public void testMoveTo()
-    {
-        File dir = new File(TEST_DIR, "dir");
-        dir.mkdirs();
-        Directory directory = new Directory(dir);
-        directory.addKeyValuePair("p1", "property 1");
-        IDirectory subdir = directory.makeDirectory("subdir");
-        subdir.addKeyValuePair("p2", "property 2");
-        File destination = new File(TEST_DIR, "destination");
-        assertFalse(destination.exists());
-        directory.moveTo(destination);
-        assertTrue(destination.exists());
-        File copiedDir = new File(destination, "dir");
-        assertTrue(copiedDir.exists());
-        assertEquals("property 1\n", FileUtilities.loadToString(new File(copiedDir, "p1")));
-        File copiedSubDir = new File(copiedDir, "subdir");
-        assertTrue(copiedSubDir.isDirectory());
-        assertEquals("property 2\n", FileUtilities.loadToString(new File(copiedSubDir, "p2")));
-        // Source directory does no longer exist
-        assertEquals(false, new File(TEST_DIR, "dir").exists());
-    }
-
     @Test
     public void testAddFile()
     {
@@ -151,7 +128,7 @@ public class DirectoryTest extends StorageTestCase
         dest.mkdir();
         Directory directory = new Directory(dest);
 
-        INode copiedDir = directory.addFile(dir);
+        INode copiedDir = directory.addFile(dir, false);
 
         assertEquals("dir", copiedDir.getName());
         assertTrue(copiedDir instanceof IDirectory);

bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java

@@ -33,7 +33,7 @@ public class FileTest extends StorageTestCase
         java.io.File file = new java.io.File(TEST_DIR, "test.txt");
         FileUtilities.writeToFile(file, "Hello\nworld!\n");
         File stringFile = new File(file);
-        
+
         assertEquals("test.txt", stringFile.getName());
         assertEquals("Hello\nworld!\n", stringFile.getStringContent());
         assertEquals("Hello\nworld!\n", new String(stringFile.getBinaryContent()));
@@ -47,7 +47,8 @@ public class FileTest extends StorageTestCase
         File stringFile = new File(file);
 
         java.io.File subdir = new java.io.File(TEST_DIR, "subdir");
-        stringFile.copyTo(subdir);
+        subdir.mkdir();
+        stringFile.extractTo(subdir);
         assertEquals("Hello\nworld!\n", FileUtilities.loadToString(new java.io.File(subdir, stringFile.getName())));
     }