diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index c519323e154a2af456d1bfd0d821ea8c35a31abf..948a0623a3929ddbdc73a4f9f354b0c470e6007b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -16,14 +16,17 @@
package ch.systemsx.cisd.bds;
+import java.io.File;
+
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
* Storage utility methods.
- *
+ *
* @author Franz-Josef Elmer
*/
public class Utilities
@@ -31,7 +34,7 @@ public class Utilities
/**
* Returns a subdirectory from the specified directory. If it does not exist it will be created.
*
- * @throws UserFailureException if there is already a node named <code>name</code> but which isn't a directory.
+ * @throws UserFailureException if there is already a node named <code>name</code> but which isn't a directory.
*/
public static IDirectory getOrCreateSubDirectory(IDirectory directory, String name)
{
@@ -46,7 +49,7 @@ public class Utilities
}
throw new UserFailureException("There is already a node named '" + name + "' but which isn't a directory.");
}
-
+
/**
* Returns a subdirectory from the specified directory.
*
@@ -67,7 +70,7 @@ public class Utilities
}
return (IDirectory) node;
}
-
+
/**
* Convenient short cut for <code>{@link #getString(IDirectory, String)}.trim()</code>.
*/
@@ -81,7 +84,7 @@ public class Utilities
*
* @param directory Directory of the requested file.
* @param name Name of the file.
- * @throws UserFailureException if the requested file does not exist.
+ * @throws UserFailureException if the requested file does not exist.
*/
public static String getString(IDirectory directory, String name)
{
@@ -97,9 +100,29 @@ public class Utilities
IFile file = (IFile) node;
return file.getStringContent();
}
-
+
+ /**
+ * Lists files of given <var>directory</var>.
+ * <p>
+ * Throws an <code>EnvironmentFailureException</code> if {@link File#listFiles()} returns <code>null</code>.
+ * </p>
+ *
+ * @param directory must be a directory.
+ */
+ public final static File[] listFiles(final File directory) throws EnvironmentFailureException
+ {
+ assert directory.isDirectory();
+ final File[] fileList = directory.listFiles();
+ if (fileList == null)
+ {
+ throw EnvironmentFailureException.fromTemplate("Was not able to list files of directory '%s'", directory
+ .getAbsolutePath());
+ }
+ return fileList;
+ }
+
private Utilities()
{
}
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java b/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
index c87af614b2079bd3a8ab6e6539dc352dc25be261..191eece28b395640097459fb7a0306f63df8890a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
* Abstraction of a node in a hierarchical data structure.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface INode
@@ -32,18 +32,27 @@ public interface INode
* Returns the name of this node.
*/
public String getName();
-
+
/**
* Returns the parent directory of this node or <code>null</code> if it is the root node.
*/
public IDirectory tryToGetParent();
-
+
+ /**
+ * Copies this node to the specified directory of the file system. All descendants are also copied.
+ *
+ * @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;
+
/**
- * Extracts this node to the specified directory of the file system. All descendants are also extracted.
+ * 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 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 extractTo(File directory) throws UserFailureException, EnvironmentFailureException;
+ public void moveTo(File directory) throws UserFailureException, EnvironmentFailureException;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
index 7da7143c2e58728d539a7e50476b76fe830f45ce..29076c20f2875ff06192ed87d5624029db11a1a6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
@@ -23,13 +23,11 @@ import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- *
- *
* @author Franz-Josef Elmer
*/
abstract class AbstractNode implements INode
{
- protected final File nodeFile;
+ protected File nodeFile;
AbstractNode(File file)
{
@@ -43,7 +41,7 @@ abstract class AbstractNode implements INode
}
this.nodeFile = file;
}
-
+
public String getName()
{
return nodeFile.getName();
@@ -60,7 +58,4 @@ abstract class AbstractNode implements INode
{
return nodeFile.getAbsolutePath();
}
-
-
-
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
index 5580cd1e78cb1085f9f35b4b5e885452cc51f86e..2614c054ffa491520e1b39a987d88416d003034b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
@@ -16,8 +16,12 @@
package ch.systemsx.cisd.bds.storage.filesystem;
+import java.io.IOException;
import java.util.Iterator;
+import org.apache.commons.io.FileUtils;
+
+import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.ILink;
@@ -42,7 +46,7 @@ class Directory extends AbstractNode implements IDirectory
public INode tryToGetNode(String name)
{
- java.io.File[] files = nodeFile.listFiles();
+ final java.io.File[] files = Utilities.listFiles(nodeFile);
for (java.io.File file : files)
{
if (file.getName().equals(name))
@@ -83,7 +87,7 @@ class Directory extends AbstractNode implements IDirectory
public INode addFile(java.io.File file) throws UserFailureException, EnvironmentFailureException
{
INode node = NodeFactory.createNode(file);
- node.extractTo(nodeFile);
+ node.moveTo(nodeFile);
return node;
}
@@ -97,10 +101,14 @@ class Directory extends AbstractNode implements IDirectory
{
return new Iterator<INode>()
{
- private java.io.File[] files = nodeFile.listFiles();
+ private java.io.File[] files = Utilities.listFiles(nodeFile);
private int index;
+ //
+ // Iterator
+ //
+
public void remove()
{
throw new UnsupportedOperationException();
@@ -118,18 +126,43 @@ class Directory extends AbstractNode implements IDirectory
};
}
- public void extractTo(java.io.File directory) throws UserFailureException, EnvironmentFailureException
+ public final void copyTo(final java.io.File directory) throws EnvironmentFailureException
{
- java.io.File destination = new java.io.File(directory, getName());
- if (destination.mkdirs() == false)
+ assert directory != null;
+ try
{
- throw new EnvironmentFailureException("Couldn't create directory for some unknown reason: "
- + destination.getAbsolutePath());
+ FileUtils.copyDirectoryToDirectory(nodeFile, directory);
+ } catch (IOException ex)
+ {
+ throw EnvironmentFailureException.fromTemplate(ex, "Couldn't copy directory '%s' to directory '%s'.",
+ nodeFile.getAbsolutePath(), directory.getAbsolutePath());
}
+ }
+
+ public final void moveTo(java.io.File directory) throws EnvironmentFailureException
+ {
+ assert directory != null;
+ directory.mkdirs();
+ 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 directory '%s' to directory '%s'.",
+ nodeFile.getAbsolutePath(), directory.getAbsolutePath());
+ }
+ assert nodeFile.exists() == false;
+ }
+ if (nodeFile.equals(destination) == false)
+ {
+ nodeFile = destination;
+ }
+ // Update children
for (INode node : this)
{
- node.extractTo(destination);
+ node.moveTo(destination);
}
}
-
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
index 1b3487f3003c745bb88fc3fce39470c31e289c6c..df72cfd9a3adacfd7b13e8f50965cc6119b9d694 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
@@ -17,19 +17,16 @@
package ch.systemsx.cisd.bds.storage.filesystem;
import java.io.FileInputStream;
-import java.io.FileOutputStream;
import java.io.IOException;
+import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
class File extends AbstractNode implements IFile
@@ -39,7 +36,7 @@ class File extends AbstractNode implements IFile
super(file);
assert file.isFile() : "Not a file " + file.getAbsolutePath();
}
-
+
public byte[] getBinaryContent()
{
FileInputStream inputStream = null;
@@ -61,26 +58,35 @@ class File extends AbstractNode implements IFile
return FileUtilities.loadToString(nodeFile);
}
- public void extractTo(java.io.File directory) throws UserFailureException, EnvironmentFailureException
+ public final void copyTo(final java.io.File directory) throws EnvironmentFailureException
{
- FileInputStream inputStream = null;
- FileOutputStream outputStream = null;
try
{
- inputStream = new FileInputStream(nodeFile);
- directory.mkdirs();
- outputStream = new FileOutputStream(new java.io.File(directory, getName()));
- IOUtils.copy(inputStream, outputStream);
+ FileUtils.copyFileToDirectory(nodeFile, directory);
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't extract file '" + this + "' to directory "
- + directory.getAbsolutePath(), ex);
- } finally
- {
- IOUtils.closeQuietly(inputStream);
- IOUtils.closeQuietly(outputStream);
+ throw EnvironmentFailureException.fromTemplate(ex, "Couldn't not copy file '%s' to directory '%s'.",
+ 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;
+ }
+ }
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
index 87deccea4553589f18214cb01c1d7be46ad92ff1..142224cef7d453efb2a17aa2294ce1bae33ec8db 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
@@ -25,15 +25,15 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- *
- *
* @author Franz-Josef Elmer
*/
class Link implements ILink
{
private final String name;
+
private IDirectory parent;
+
private final INode reference;
Link(String name, INode reference)
@@ -51,7 +51,7 @@ class Link implements ILink
{
parent = parentOrNull;
}
-
+
public IDirectory tryToGetParent()
{
return parent;
@@ -62,9 +62,15 @@ class Link implements ILink
return reference;
}
- public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
+ public void copyTo(File directory) throws UserFailureException, EnvironmentFailureException
{
// TODO Auto-generated method stub
}
+ public void moveTo(File directory) throws UserFailureException, EnvironmentFailureException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
index 82169ce3f18ee21545778ba8e7eb004f0d4ed65c..9359038b506db64759bd0b0fa0cedc8721f9c2f2 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
@@ -22,13 +22,11 @@ import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
- *
- *
* @author Franz-Josef Elmer
*/
class NodeFactory
{
- static INode createNode(java.io.File file)
+ static INode createNode(java.io.File file) throws EnvironmentFailureException
{
assert file != null : "Unspecified node";
String absolutePath = file.getAbsolutePath();
@@ -49,7 +47,7 @@ class NodeFactory
throw new EnvironmentFailureException("Couldn't get canonical path of file " + absolutePath);
}
}
-
+
private NodeFactory()
{
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
index 2d87700aa09052b386510d79b705d20a4846c7a2..3391d1b9e06bb2116ee6e0f1ff75dabf634ace77 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
@@ -33,8 +33,6 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class DirectoryTest extends StorageTestCase
@@ -45,32 +43,32 @@ public class DirectoryTest extends StorageTestCase
Directory directory = new Directory(TEST_DIR);
assertEquals(TEST_DIR.getName(), directory.getName());
}
-
+
@Test
public void testMakeDirectory()
{
Directory directory = new Directory(TEST_DIR);
IDirectory subdirectory = directory.makeDirectory("sub-directory");
-
+
assertEquals("sub-directory", subdirectory.getName());
File subdir = new File(TEST_DIR, "sub-directory");
assertEquals(true, subdir.exists());
assertEquals(true, subdir.isDirectory());
}
-
+
@Test
public void testMakeDirectoryTwice()
{
Directory directory = new Directory(TEST_DIR);
directory.makeDirectory("sub-directory");
IDirectory subdirectory = directory.makeDirectory("sub-directory");
-
+
assertEquals("sub-directory", subdirectory.getName());
File subdir = new File(TEST_DIR, "sub-directory");
assertEquals(true, subdir.exists());
assertEquals(true, subdir.isDirectory());
}
-
+
@Test
public void testMakeDirectoryButThereIsAlreadyAFileWithSameName()
{
@@ -85,7 +83,7 @@ public class DirectoryTest extends StorageTestCase
assertTrue(e.getMessage().indexOf("sub-directory") >= 0);
}
}
-
+
@Test
public void testAddKeyValuePair()
{
@@ -93,9 +91,32 @@ public class DirectoryTest extends StorageTestCase
assertEquals("42\n", FileUtilities.loadToString(new File(TEST_DIR, "answer")));
assertEquals("42\n", stringFile.getStringContent());
}
-
+
+ @Test
+ public void testCopyTo()
+ {
+ 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.copyTo(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 still exists
+ assertEquals(true, new File(TEST_DIR, "dir").exists());
+ }
+
@Test
- public void testExtractTo()
+ public void testMoveTo()
{
File dir = new File(TEST_DIR, "dir");
dir.mkdirs();
@@ -105,9 +126,7 @@ public class DirectoryTest extends StorageTestCase
subdir.addKeyValuePair("p2", "property 2");
File destination = new File(TEST_DIR, "destination");
assertFalse(destination.exists());
-
- directory.extractTo(destination);
-
+ directory.moveTo(destination);
assertTrue(destination.exists());
File copiedDir = new File(destination, "dir");
assertTrue(copiedDir.exists());
@@ -115,8 +134,10 @@ public class DirectoryTest extends StorageTestCase
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()
{
@@ -129,9 +150,9 @@ public class DirectoryTest extends StorageTestCase
File dest = new File(TEST_DIR, "destination");
dest.mkdir();
Directory directory = new Directory(dest);
-
+
INode copiedDir = directory.addFile(dir);
-
+
assertEquals("dir", copiedDir.getName());
assertTrue(copiedDir instanceof IDirectory);
File copiedRealDir = new File(dest, "dir");
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
index 29346c1a6180a935c02cb1bc497d70505f795096..43773505c9f59e1630a8b790b836a371b9b55023 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
@@ -23,8 +23,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class FileTest extends StorageTestCase
@@ -40,7 +38,7 @@ public class FileTest extends StorageTestCase
assertEquals("Hello\nworld!\n", stringFile.getStringContent());
assertEquals("Hello\nworld!\n", new String(stringFile.getBinaryContent()));
}
-
+
@Test
public void testExtractTo()
{
@@ -49,7 +47,8 @@ public class FileTest extends StorageTestCase
File stringFile = new File(file);
java.io.File subdir = new java.io.File(TEST_DIR, "subdir");
- stringFile.extractTo(subdir);
+ stringFile.copyTo(subdir);
assertEquals("Hello\nworld!\n", FileUtilities.loadToString(new java.io.File(subdir, stringFile.getName())));
}
+
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java
index 0e2b052ebd1fefbef18bd3433632df288facb2cb..647b3c55b9fb01b72c62a4b099330b09a23d8f9e 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java
@@ -23,19 +23,17 @@ import org.apache.commons.io.FileUtils;
import org.testng.annotations.BeforeMethod;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class StorageTestCase
{
static final File TEST_DIR = new File("targets" + File.separator + "unit-test-wd");
-
+
@BeforeMethod
public void setup() throws IOException
{
TEST_DIR.mkdirs();
FileUtils.cleanDirectory(TEST_DIR);
}
-
+
}