From 45b6e5154c06a9f6b1e08d9a01d8f7217d0c8e83 Mon Sep 17 00:00:00 2001
From: ribeaudc <ribeaudc>
Date: Fri, 30 Nov 2007 07:32:31 +0000
Subject: [PATCH] [LMS-128] change: - 'tryTo*' renamed to 'try*' add: -
'ILinkMaker' interface and its implementation 'HardLinkMaker'
SVN: 2863
---
.../systemsx/cisd/bds/DataStructureV1_0.java | 14 +-
.../java/ch/systemsx/cisd/bds/Format.java | 6 +-
.../java/ch/systemsx/cisd/bds/Utilities.java | 6 +-
.../cisd/bds/handler/MappingFileHandler.java | 5 +-
.../cisd/bds/hcs/IHCSFormattedData.java | 16 ++-
.../cisd/bds/hcs/ImageHCSFormattedData.java | 83 ++++++++++--
.../systemsx/cisd/bds/storage/IDirectory.java | 16 ++-
.../ch/systemsx/cisd/bds/storage/IFile.java | 3 +
.../ch/systemsx/cisd/bds/storage/INode.java | 6 +-
.../bds/storage/filesystem/Directory.java | 36 ++++-
.../cisd/bds/storage/filesystem/File.java | 10 +-
.../bds/storage/filesystem/HardLinkMaker.java | 123 ++++++++++++++++++
.../bds/storage/filesystem/ILinkMaker.java | 57 ++++++++
.../cisd/bds/storage/filesystem/Link.java | 6 +-
.../storage/filesystem/LinkMakerProvider.java | 51 ++++++++
.../bds/storage/filesystem/NodeFactory.java | 6 +-
.../bds/hcs/HCSDataStructureV1_0Test.java | 8 +-
.../bds/storage/filesystem/DirectoryTest.java | 6 +-
.../storage/filesystem/HardLinkMakerTest.java | 102 +++++++++++++++
19 files changed, 503 insertions(+), 57 deletions(-)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMaker.java
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/ILinkMaker.java
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/LinkMakerProvider.java
create mode 100644 bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMakerTest.java
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index 532c330053a..0304ac73034 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -277,27 +277,27 @@ public class DataStructureV1_0 extends AbstractDataStructure
throw new DataStructureException("Empty original data directory.");
}
IDirectory metaDataDirectory = getMetaDataDirectory();
- if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null && format == null)
+ if (metaDataDirectory.tryGetNode(Format.FORMAT_DIR) == null && format == null)
{
throw new DataStructureException("Unspecified format.");
}
- if (metaDataDirectory.tryToGetNode(ExperimentIdentifier.FOLDER) == null)
+ if (metaDataDirectory.tryGetNode(ExperimentIdentifier.FOLDER) == null)
{
throw new DataStructureException("Unspecified experiment identifier.");
}
- if (metaDataDirectory.tryToGetNode(ExperimentRegistratorDate.FILE_NAME) == null)
+ if (metaDataDirectory.tryGetNode(ExperimentRegistratorDate.FILE_NAME) == null)
{
throw new DataStructureException("Unspecified experiment registration date.");
}
- if (metaDataDirectory.tryToGetNode(ExperimentRegistrator.FOLDER) == null)
+ if (metaDataDirectory.tryGetNode(ExperimentRegistrator.FOLDER) == null)
{
throw new DataStructureException("Unspecified experiment registrator.");
}
- if (metaDataDirectory.tryToGetNode(MeasurementEntity.FOLDER) == null)
+ if (metaDataDirectory.tryGetNode(MeasurementEntity.FOLDER) == null)
{
throw new DataStructureException("Unspecified measurement entity.");
}
- if (metaDataDirectory.tryToGetNode(ProcessingType.PROCESSING_TYPE) == null)
+ if (metaDataDirectory.tryGetNode(ProcessingType.PROCESSING_TYPE) == null)
{
throw new DataStructureException("Unspecified processing type.");
}
@@ -318,7 +318,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
super.performClosing();
final IDirectory metaDataDirectory = getMetaDataDirectory();
formatParameters.saveTo(getParametersDirectory());
- if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null && format != null)
+ if (metaDataDirectory.tryGetNode(Format.FORMAT_DIR) == null && format != null)
{
format.saveTo(metaDataDirectory);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Format.java b/bds/source/java/ch/systemsx/cisd/bds/Format.java
index 8e477ca9984..ec569b375ae 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Format.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Format.java
@@ -40,13 +40,13 @@ public class Format implements IStorable
*/
static Format loadFrom(IDirectory directory)
{
- INode dir = directory.tryToGetNode(FORMAT_DIR);
+ INode dir = directory.tryGetNode(FORMAT_DIR);
if (dir instanceof IDirectory == false)
{
throw new DataStructureException("Not a directory: " + dir);
}
IDirectory formatDir = (IDirectory) dir;
- INode file = formatDir.tryToGetNode(FORMAT_CODE_FILE);
+ INode file = formatDir.tryGetNode(FORMAT_CODE_FILE);
if (file instanceof IFile == false)
{
throw new DataStructureException("Not a plain file: " + file);
@@ -55,7 +55,7 @@ public class Format implements IStorable
String formatCode = codeFile.getStringContent().trim();
Version formatVersion = Version.loadFrom(formatDir);
String variant = null;
- file = formatDir.tryToGetNode(FORMAT_VARIANT_FILE);
+ file = formatDir.tryGetNode(FORMAT_VARIANT_FILE);
if (file != null)
{
if (file instanceof IFile == false)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index ba177890da0..012b32ad31d 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -36,7 +36,7 @@ public class Utilities
*/
public static IDirectory getOrCreateSubDirectory(IDirectory directory, String name)
{
- INode node = directory.tryToGetNode(name);
+ INode node = directory.tryGetNode(name);
if (node == null)
{
return directory.makeDirectory(name);
@@ -58,7 +58,7 @@ public class Utilities
*/
public final static IDirectory getSubDirectory(final IDirectory directory, final String name)
{
- INode node = directory.tryToGetNode(name);
+ INode node = directory.tryGetNode(name);
if (node == null)
{
throw new DataStructureException(String.format("No directory named '%s' found in directory '%s'.", name,
@@ -111,7 +111,7 @@ public class Utilities
{
assert directory != null : String.format("Given directory can not be null.");
assert name != null : String.format("Given name can not be null.");
- final INode node = directory.tryToGetNode(name);
+ final INode node = directory.tryGetNode(name);
if (node == null)
{
throw new DataStructureException("File '" + name + "' missing in '" + directory + "'.");
diff --git a/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java b/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
index 405643b6445..d0222927db5 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
@@ -44,9 +44,11 @@ public final class MappingFileHandler implements IDataStructureHandler
private final IDirectory mappingDirectory;
/** The root of {@link Reference#getPath()}. Usually the path to <code>standard</code> directory. */
+ @SuppressWarnings("unused")
private final IDirectory pathRoot;
/** The root of {@link Reference#getOriginalPath()}. Usually the path to <code>original</code> directory. */
+ @SuppressWarnings("unused")
private final IDirectory originalPathRoot;
/**
@@ -119,7 +121,8 @@ public final class MappingFileHandler implements IDataStructureHandler
standardOriginalMapping.put(path, new Reference(path, referenceDefinition.substring(i2 + 1), type));
}
}
-
+
+ // TODO 2007-11-30, Christian Ribeaud: list all nodes present in the standard directory.
private final String createMappingFile()
{
final StringWriter writer = new StringWriter();
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
index 8549e0f1f7e..0b408224a6a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
@@ -35,9 +35,17 @@ public interface IHCSFormattedData extends IFormattedData
* corresponding <code>INode</code> (found in <code>data/standard</code> directory).
*
* @return this could be, for instance, a {@link ILink} pointing to the <code>data/original</code> directory or a
- * {@link IFile} that can be extracted somewhere. Never returns <code>null</code>.
- * @throws DataStructureException if a problem occurs while trying to find out the node in the whole data structure.
+ * {@link IFile} that can be extracted somewhere. Might return <code>null</code>.
*/
- public INode getNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
- throws DataStructureException;
+ public INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation);
+
+ /**
+ * Adds a new node at given coordinates and returns it.
+ *
+ * @return the new <code>INode</code> just added. Never returns <code>null</code>.
+ * @param originalFileName name of the <code>original</code> directory file that is going to be added in the
+ * <code>standard</code> directory.
+ */
+ public INode addStandardNode(final String originalFileName, final int channel, final Location plateLocation,
+ final Location wellLocation) throws DataStructureException;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
index 32c8fb762dc..fbdbd1dfe5a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.bds.IFormattedData;
import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.INode;
+import ch.systemsx.cisd.bds.storage.StorageException;
/**
* {@link IFormattedData} implementation for <i>HCS (High-Content Screening) with Images</i>. It is associated with
@@ -58,6 +59,11 @@ public final class ImageHCSFormattedData extends AbstractFormattedData implement
super(context);
}
+ private final boolean containsOriginalData()
+ {
+ return (Boolean) getFormatParameters().getValue(ImageHCSFormat1_0.CONTAINS_ORIGINAL_DATA);
+ }
+
private final Geometry getWellGeometry()
{
return (Geometry) getFormatParameters().getValue(WellGeometry.WELL_GEOMETRY);
@@ -108,27 +114,86 @@ public final class ImageHCSFormattedData extends AbstractFormattedData implement
return ROW + wellLocation.y + "_" + COLUMN + wellLocation.x + ".tiff";
}
+ private final IDirectory getStandardDataDirectory()
+ {
+ return Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_STANDARD);
+ }
+
+ private final IDirectory getOriginalDataDirectory()
+ {
+ return Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_ORIGINAL);
+ }
+
+ private final static String getPlateColumnDir(final Location plateLocation)
+ {
+ return COLUMN + plateLocation.x;
+ }
+
+ private final static String getPlateRowDirName(final Location plateLocation)
+ {
+ return ROW + plateLocation.y;
+ }
+
+ private final static String getChannelName(final int channel)
+ {
+ return Channel.CHANNEL + channel;
+ }
+
//
// IHCSFormattedData
//
- public final INode getNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
- throws DataStructureException
+ public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
{
checkChannel(channel);
checkLocation(getPlateGeometry(), plateLocation);
checkLocation(getWellGeometry(), wellLocation);
- final IDirectory standardDir = Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_STANDARD);
- final IDirectory channelDir = Utilities.getSubDirectory(standardDir, Channel.CHANNEL + channel);
- final IDirectory plateRowDir = Utilities.getSubDirectory(channelDir, ROW + plateLocation.y);
- final IDirectory plateColumnDir = Utilities.getSubDirectory(plateRowDir, COLUMN + plateLocation.x);
- final INode node = plateColumnDir.tryToGetNode(createWellFileName(wellLocation));
- if (node == null)
+ final IDirectory standardDir = getStandardDataDirectory();
+ final IDirectory channelDir = Utilities.getSubDirectory(standardDir, getChannelName(channel));
+ final IDirectory plateRowDir = Utilities.getSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ final IDirectory plateColumnDir = Utilities.getSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
+ return plateColumnDir.tryGetNode(createWellFileName(wellLocation));
+ }
+
+ public final INode addStandardNode(final String originalFileName, int channel, final Location plateLocation,
+ final Location wellLocation)
+ {
+ // This will check all parameters but originalFileName.
+ INode node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
+ if (node != null)
{
throw new DataStructureException(String.format(
- "No node could be found at channel %d, plate location '%s' and well location '%s'.", channel,
+ "A node already exists at channel %d, plate location '%s' and well location '%s'.", channel,
plateLocation, wellLocation));
}
+ assert originalFileName != null : "Given original file name can not be null.";
+ final IDirectory standardDir = getStandardDataDirectory();
+ final IDirectory channelDir = Utilities.getOrCreateSubDirectory(standardDir, getChannelName(channel));
+ final IDirectory plateRowDir = Utilities.getOrCreateSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ final IDirectory plateColumnDir =
+ Utilities.getOrCreateSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
+ final String wellFileName = createWellFileName(wellLocation);
+ final INode originalNode = getOriginalDataDirectory().tryGetNode(originalFileName);
+ if (originalNode == null)
+ {
+ throw new DataStructureException(String.format("No original node with name '%s' could be found.",
+ originalFileName));
+ }
+ if (containsOriginalData())
+ {
+ node = plateColumnDir.tryAddLink(wellFileName, originalNode);
+ } else
+ {
+ node = plateColumnDir.tryAddNode(wellFileName, originalNode);
+ }
+ if (node == null)
+ {
+ throw new StorageException(
+ String
+ .format(
+ "Original file name '%s' could not be added at channel %d, plate location '%s' and well location '%s'.",
+ originalFileName, channel, plateLocation, wellLocation));
+ }
return node;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
index 7f0ef500185..90195b00029 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
@@ -30,7 +30,7 @@ public interface IDirectory extends INode, Iterable<INode>
*
* @return <code>null</code> if there is no child node named <code>name</code>.
*/
- public INode tryToGetNode(final String name);
+ public INode tryGetNode(final String name);
/**
* Makes a new subdirectory in this directory. Does nothing if the subdirectory already exists.
@@ -38,7 +38,7 @@ public interface IDirectory extends INode, Iterable<INode>
* @param name Name of the new subdirectory.
* @return the new subdirectory.
*/
- public IDirectory makeDirectory(String name);
+ public IDirectory makeDirectory(final String name);
/**
* Adds the specified real file to this directory. The content of <code>file</code> will be copied. If it is a
@@ -62,6 +62,16 @@ public interface IDirectory extends INode, Iterable<INode>
/**
* Adds the link named <code>name</code> to this directory which refers to the specified node.
+ *
+ * @return <code>null</code> if the operation did not succeed.
+ */
+ public ILink tryAddLink(final String name, final INode node);
+
+ /**
+ * Adds given <code>node</code> to this <code>IDirectory</code> and returns a new node with given
+ * <code>name</code> (rename operation).
+ *
+ * @return <code>null</code> if the operation did not succeed.
*/
- public ILink addLink(final String name, final INode node);
+ public INode tryAddNode(final String name, final INode node);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java
index 1fce846462f..05bbdcb129e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IFile.java
@@ -43,6 +43,9 @@ public interface IFile extends INode
/**
* Returns the content of this file node as a list of <code>String</code> objects.
+ * <p>
+ * This is useful when you know that the file content is composed of several lines.
+ * </p>
*/
public List<String> getStringContentList();
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 24de1be2923..6496d08bc0d 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.bds.storage;
-import java.io.File;
-
/**
* Abstraction of a node in a hierarchical data structure.
*
@@ -46,11 +44,11 @@ public interface INode
* All descendants are also extracted. This is a copy operation.
* </p>
*/
- public void extractTo(final File directory);
+ public void extractTo(final java.io.File directory);
/**
* Moves this node and all descendants to the specified directory of the file system. This node will be
* automatically removed from its parent.
*/
- public void moveTo(final File directory);
+ public void moveTo(final java.io.File directory);
}
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 c51790b7ba9..6729aadf881 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
@@ -27,7 +27,6 @@ import ch.systemsx.cisd.bds.storage.ILink;
import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
@@ -38,7 +37,7 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
final class Directory extends AbstractNode implements IDirectory
{
- Directory(java.io.File directory)
+ Directory(final java.io.File directory)
{
super(directory);
if (directory.isDirectory() == false)
@@ -47,11 +46,17 @@ final class Directory extends AbstractNode implements IDirectory
}
}
+ private final static java.io.File getNodeFile(final INode node)
+ {
+ assert node instanceof AbstractNode : "Must be an instance of AbstractNode.";
+ return ((AbstractNode) node).nodeFile;
+ }
+
//
// IDirectory
//
- public final INode tryToGetNode(final String name)
+ public final INode tryGetNode(final String name)
{
assert name != null : "Given name can not be null.";
final java.io.File[] files = FileUtilities.listFiles(nodeFile);
@@ -122,9 +127,19 @@ final class Directory extends AbstractNode implements IDirectory
return NodeFactory.createNode(newFile);
}
- public final ILink addLink(final String name, final INode node)
+ public final ILink tryAddLink(final String name, final INode node)
{
- throw new NotImplementedException();
+ assert node != null : "Node can not be null.";
+ assert name != null : "Name can not be null.";
+ final java.io.File file = getNodeFile(node);
+ final java.io.File fileLink = LinkMakerProvider.getDefaultLinkMaker().tryCreateLink(file, nodeFile, name);
+ if (fileLink != null)
+ {
+ final Link link = NodeFactory.createLinkNode(fileLink);
+ link.setParent(this);
+ return link;
+ }
+ return null;
}
public final Iterator<INode> iterator()
@@ -170,11 +185,18 @@ final class Directory extends AbstractNode implements IDirectory
}
}
+ public final INode tryAddNode(final String name, final INode node)
+ {
+ assert node != null : "Node can not be null";
+ assert name != null : "Name can not be null.";
+ final java.io.File file = getNodeFile(node);
+ return addFile(file, true);
+ }
+
public final void removeNode(final INode node)
{
assert node != null : "Node could not be null";
- AbstractNode abstractNode = (AbstractNode) node;
- final java.io.File file = abstractNode.nodeFile;
+ final java.io.File file = getNodeFile(node);
if (file.isDirectory())
{
if (FileUtilities.deleteRecursively(file, null) == false)
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 559e0c5c98b..791d86e8828 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
@@ -34,15 +34,19 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
*
* @author Franz-Josef Elmer
*/
-class File extends AbstractNode implements IFile
+final class File extends AbstractNode implements IFile
{
- File(java.io.File file)
+ File(final java.io.File file)
{
super(file);
assert file.isFile() : "Not a file " + file.getAbsolutePath();
}
- public byte[] getBinaryContent()
+ //
+ // IFile
+ //
+
+ public final byte[] getBinaryContent()
{
InputStream inputStream = getInputStream();
try
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMaker.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMaker.java
new file mode 100644
index 00000000000..a3e52766485
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMaker.java
@@ -0,0 +1,123 @@
+/*
+ * Copyright 2007 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.bds.storage.filesystem;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.logging.BufferedAppender;
+import ch.systemsx.cisd.common.utilities.OSUtilities;
+import ch.systemsx.cisd.common.utilities.ProcessExecutionHelper;
+
+/**
+ * An <code>ILinkMaker</code> implementation which is able to make hard links using the operating system.
+ * <p>
+ * Note that the current implementation only works for files.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class HardLinkMaker implements ILinkMaker
+{
+ static final String ALREADY_EXISTS_FORMAT = "Given file '%s' already exists.";
+
+ private static final String HARD_LINK_EXEC = "ln";
+
+ private static HardLinkMaker instance;
+
+ private final String linkExecPath;
+
+ private final BufferedAppender loggerRecorder;
+
+ private HardLinkMaker(final String linkExecPath)
+ {
+ this.linkExecPath = linkExecPath;
+ loggerRecorder = new BufferedAppender("%m", Level.ERROR);
+ }
+
+ private final List<String> createLnCmdLine(final File srcFile, final File destFile)
+ {
+ List<String> tokens = new ArrayList<String>();
+ tokens.add(linkExecPath);
+ tokens.add(srcFile.getAbsolutePath());
+ // The destination file does not yet exist. Is going to be created and is the link.
+ tokens.add(destFile.getAbsolutePath());
+ return tokens;
+ }
+
+ /**
+ * Returns the unique instance of this class.
+ */
+ static synchronized final HardLinkMaker getInstance() throws EnvironmentFailureException
+ {
+ if (instance == null)
+ {
+ final File lnExec = OSUtilities.findExecutable(HARD_LINK_EXEC);
+ if (lnExec == null)
+ {
+ throw EnvironmentFailureException.fromTemplate(
+ "No hard link executable '%s' could be found in path '%s'.", HARD_LINK_EXEC, OSUtilities
+ .getSafeOSPath());
+ }
+ instance = new HardLinkMaker(lnExec.getAbsolutePath());
+ }
+ return instance;
+ }
+
+ //
+ // ILinkMaker
+ //
+
+ public final File tryCreateLink(final java.io.File file, final java.io.File destDir, final String nameOrNull)
+ throws EnvironmentFailureException
+ {
+ assert file != null && file.isFile() : "Given file can not be null and must be a file.";
+ assert destDir != null && destDir.isDirectory() : "Given destination directory can not be null and must be a directory.";
+ final String destName;
+ if (nameOrNull == null)
+ {
+ destName = file.getName();
+ } else
+ {
+ destName = nameOrNull;
+ }
+ final File destFile = new File(destDir, destName);
+ if (destFile.exists())
+ {
+ throw new IllegalArgumentException(String.format(ALREADY_EXISTS_FORMAT, destFile.getAbsolutePath()));
+ }
+ final List<String> cmd = createLnCmdLine(file, destFile);
+ final Logger rootLogger = Logger.getRootLogger();
+ loggerRecorder.resetLogContent();
+ final boolean ok = ProcessExecutionHelper.runAndLog(cmd, rootLogger, rootLogger);
+ if (ok == false)
+ {
+ String message = loggerRecorder.getLogContent();
+ if (message.length() == 0)
+ {
+ return null;
+ }
+ throw new EnvironmentFailureException(message);
+ }
+ return destFile;
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/ILinkMaker.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/ILinkMaker.java
new file mode 100644
index 00000000000..81d1e80d612
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/ILinkMaker.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2007 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.bds.storage.filesystem;
+
+import java.io.File;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+
+/**
+ * Kind of strategy how to 'serialize' a <code>ILink</code> implementation.
+ *
+ * @author Christian Ribeaud
+ */
+public interface ILinkMaker
+{
+
+ /**
+ * An default <code>ILinkMaker</code> implementation which always returns <code>null</code> without trying to do
+ * anything.
+ */
+ public final static ILinkMaker DEFAULT = new ILinkMaker()
+ {
+
+ //
+ // ILinkMaker
+ //
+
+ public final File tryCreateLink(final File file, final File destDir, final String nameOrNull)
+ throws EnvironmentFailureException
+ {
+ return null;
+ }
+ };
+
+ /**
+ * Tries to create a link to given <var>file</var> in given <var>destDir</var>.
+ *
+ * @param nameOrNull the link name in the destination directory.
+ * @return might returns <code>null</code> if the application was not able to create the link.
+ */
+ public File tryCreateLink(final File file, final File destDir, final String nameOrNull)
+ throws EnvironmentFailureException;
+}
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 604de64e9b8..5d11cc79273 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
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.bds.storage.filesystem;
import java.io.File;
import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.ILink;
import ch.systemsx.cisd.bds.storage.INode;
@@ -29,7 +30,6 @@ import ch.systemsx.cisd.bds.storage.INode;
*/
final class Link implements ILink
{
-
private final String name;
private final INode reference;
@@ -40,7 +40,7 @@ final class Link implements ILink
{
assert name != null : "A name must be specified.";
assert reference != null : "Reference can not be null.";
- assert reference instanceof ILink : "Link of link not supported.";
+ assert reference instanceof IFile && reference.isValid() : "Given reference must be a valid IFile implementation";
this.name = name;
this.reference = reference;
}
@@ -88,7 +88,7 @@ final class Link implements ILink
}
if (parent != null)
{
- final INode node = parent.tryToGetNode(name);
+ final INode node = parent.tryGetNode(name);
return node != null && node.isValid();
}
return true;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/LinkMakerProvider.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/LinkMakerProvider.java
new file mode 100644
index 00000000000..290b3f9d437
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/LinkMakerProvider.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright 2007 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.bds.storage.filesystem;
+
+import ch.systemsx.cisd.common.utilities.OSUtilities;
+
+/**
+ * A provider of {@link ILinkMaker} implementations.
+ *
+ * @author Christian Ribeaud
+ */
+public final class LinkMakerProvider
+{
+
+ private LinkMakerProvider()
+ {
+ // This class can not be instantiated.
+ }
+
+ /**
+ * Returns a default <code>ILinkMaker</code> implementation.
+ * <p>
+ * Never returns <code>null</code> but could return the default implementation.
+ * </p>
+ *
+ * @see ILinkMaker#DEFAULT
+ */
+ public final static ILinkMaker getDefaultLinkMaker()
+ {
+ if (OSUtilities.isWindows())
+ {
+ return ILinkMaker.DEFAULT;
+ }
+ return HardLinkMaker.getInstance();
+ }
+
+}
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 9e394e94777..b647b9e5ad1 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
@@ -67,12 +67,12 @@ public final class NodeFactory
}
}
- private static Link createLinkNode(final java.io.File file) throws EnvironmentFailureException
+ public final static Link createLinkNode(final java.io.File file) throws EnvironmentFailureException
{
final String absolutePath = file.getAbsolutePath();
final String canonicalPath = getCanonicalPath(file);
- assert absolutePath.equals(canonicalPath) == false : "Given file must be a link";
- return new Link(file.getName(), createNode(new java.io.File(getCanonicalPath(file))));
+ assert absolutePath.equals(canonicalPath) == false : "Given file must be a link.";
+ return new Link(file.getName(), createNode(new java.io.File(canonicalPath)));
}
/**
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
index a4b19b867d6..7608680e656 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
@@ -126,7 +126,7 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
final IHCSFormattedData formattedData = (IHCSFormattedData) dataStructure.getFormattedData();
try
{
- formattedData.getNodeAt(3, new Location(1, 1), new Location(1, 1));
+ formattedData.tryGetStandardNodeAt(3, new Location(1, 1), new Location(1, 1));
fail("3 > 2");
} catch (IndexOutOfBoundsException ex)
{
@@ -134,7 +134,7 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
}
try
{
- formattedData.getNodeAt(2, new Location(1, 1), new Location(1, 1));
+ formattedData.tryGetStandardNodeAt(2, new Location(1, 1), new Location(1, 1));
fail("No directory named 'channel2' found.");
} catch (DataStructureException ex)
{
@@ -142,13 +142,13 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
}
try
{
- formattedData.getNodeAt(1, new Location(1, 3), new Location(1, 1));
+ formattedData.tryGetStandardNodeAt(1, new Location(1, 3), new Location(1, 1));
fail("Given geometry '2x3' does not contain location '[x=1,y=3]'.");
} catch (IllegalArgumentException ex)
{
assertTrue(ex.getMessage().indexOf("does not contain location") > -1);
}
- final INode node = formattedData.getNodeAt(1, new Location(1, 1), new Location(1, 1));
+ final INode node = formattedData.tryGetStandardNodeAt(1, new Location(1, 1), new Location(1, 1));
assertEquals("row1_column1.tiff", node.getName());
dataStructure.close();
}
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 597de4c2dfd..d06c00f24d2 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
@@ -59,16 +59,16 @@ public final class DirectoryTest extends AbstractFileSystemTestCase
File copiedRealDir = new File(dest, "dir");
assertTrue(copiedRealDir.isDirectory());
IDirectory cd = (IDirectory) copiedDir;
- INode node = cd.tryToGetNode("p1");
+ INode node = cd.tryGetNode("p1");
assertNotNull(node);
assertTrue(node instanceof IFile);
assertEquals("property 1\n", ((IFile) node).getStringContent());
assertEquals("property 1\n", FileUtilities.loadToString(new File(copiedRealDir, "p1")));
- node = cd.tryToGetNode("subdir");
+ node = cd.tryGetNode("subdir");
assertEquals("subdir", node.getName());
assertNotNull(node);
assertTrue(node instanceof IDirectory);
- node = ((IDirectory) node).tryToGetNode("p2");
+ node = ((IDirectory) node).tryGetNode("p2");
File copiedRealSubDir = new File(copiedRealDir, "subdir");
assertTrue(copiedRealSubDir.isDirectory());
assertEquals("p2", node.getName());
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMakerTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMakerTest.java
new file mode 100644
index 00000000000..ed77511f4e3
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/HardLinkMakerTest.java
@@ -0,0 +1,102 @@
+/*
+ * Copyright 2007 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.bds.storage.filesystem;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
+
+/**
+ * Test cases for corresponding {@link HardLinkMaker} class.
+ *
+ * @author Christian Ribeaud
+ */
+@Test(groups =
+ { "requires_unix" })
+public final class HardLinkMakerTest extends AbstractFileSystemTestCase
+{
+
+ private static final String FILE_CONTENT = "This is my content";
+
+ private static final String SOURCE_FILE_NAME = "source.txt";
+
+ private File createFile() throws IOException
+ {
+ final File srcFile = new File(new File(workingDirectory, "dir"), SOURCE_FILE_NAME);
+ assertFalse(srcFile.exists());
+ FileUtils.writeStringToFile(srcFile, FILE_CONTENT);
+ assertTrue(srcFile.exists());
+ return srcFile;
+ }
+
+ @Test
+ public final void testCreateLinkParameters() throws IOException
+ {
+ try
+ {
+ HardLinkMaker.getInstance().tryCreateLink(null, workingDirectory, null);
+ fail("Null value not accepted.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here.
+ }
+ try
+ {
+ HardLinkMaker.getInstance().tryCreateLink(workingDirectory, workingDirectory, null);
+ fail("First parameter must be an existing file.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here.
+ }
+ final File srcFile = createFile();
+ final File destinationDir = new File(workingDirectory, "dir");
+ try
+ {
+ HardLinkMaker.getInstance().tryCreateLink(srcFile, destinationDir, null);
+ fail("File already exits.");
+ } catch (final IllegalArgumentException ex)
+ {
+ assertEquals(String.format(HardLinkMaker.ALREADY_EXISTS_FORMAT, new File(destinationDir, srcFile.getName())
+ .getAbsolutePath()), ex.getMessage());
+ }
+
+ }
+
+ @Test
+ public final void testCreateLink() throws IOException
+ {
+ final File srcFile = createFile();
+ HardLinkMaker.getInstance().tryCreateLink(srcFile, workingDirectory, null);
+ final File destFile = new File(workingDirectory, SOURCE_FILE_NAME);
+ assertTrue(destFile.exists());
+ assertEquals(FILE_CONTENT, FileUtils.readFileToString(destFile));
+ assertTrue(srcFile.delete());
+ assertFalse(srcFile.exists());
+ // We removed the source file but the destination file (the hard link) still persists.
+ assertTrue(destFile.exists());
+ assertEquals(FILE_CONTENT, FileUtils.readFileToString(destFile));
+ }
+}
\ No newline at end of file
--
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