all occurances of UserFailureException replaced by either StorageException or...

all occurances of UserFailureException replaced by either StorageException or DataStructureException

SVN: 2250

bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java

@@ -18,7 +18,6 @@ package ch.systemsx.cisd.bds;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
 import ch.systemsx.cisd.bds.storage.IStorage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Abstract superclass of classes implementing {@link IDataStructure}.
@@ -47,7 +46,7 @@ abstract class AbstractDataStructure implements IDataStructure
         Version loadedVersion = Version.loadFrom(root);
         if (loadedVersion.isBackwardsCompatibleWith(getVersion()) == false)
         {
-            throw new UserFailureException("Version of loaded data structure is " + loadedVersion
+            throw new DataStructureException("Version of loaded data structure is " + loadedVersion
                     + " which is not backward compatible with " + getVersion());
         }
     }

bds/source/java/ch/systemsx/cisd/bds/DataStructureException.java

+/*
+ * 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;
+
+import ch.systemsx.cisd.bds.storage.StorageException;
+
+/**
+ * Exception thrown by manipulations of BDS data structures which can not be classified as {@link StorageException}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStructureException extends RuntimeException
+{
+    private static final long serialVersionUID = 1L;
+    
+    /**
+     *  Creates an instance with the specified message.
+     */
+    public DataStructureException(String message)
+    {
+        super(message);
+    }
+
+    /**
+     * Creates an instance with the specified message and throwable causing this exception.
+     */
+    public DataStructureException(String message, Throwable cause)
+    {
+        super(message, cause);
+    }
+}

bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java

@@ -18,7 +18,6 @@ package ch.systemsx.cisd.bds;
 
 import ch.systemsx.cisd.bds.storage.IStorage;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Factory of data structures.
@@ -39,7 +38,7 @@ public class DataStructureFactory
      * Returns the class of the object returned after invoking {@link #createDataStructure(IStorage, Version)}.
      * 
      * @param version Version of the data structure.
-     * @throws UserFailureException if no data structure can be created for the specified version.
+     * @throws DataStructureException if no data structure can be created for the specified version.
      */
     public static Class<? extends IDataStructure> getDataStructureClassFor(Version version)
     {
@@ -52,7 +51,7 @@ public class DataStructureFactory
      * @param storage Storage behind the data structure.
      * @param version Version of the data structure to be created.
      * @throws EnvironmentFailureException found data structure class has not an appropriated constructor. 
-     * @throws UserFailureException if no data structure can be created for the specified version.
+     * @throws DataStructureException if no data structure can be created for the specified version.
      */
     public static IDataStructure createDataStructure(IStorage storage, Version version)
     {

bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java

@@ -21,7 +21,6 @@ import java.io.File;
 import ch.systemsx.cisd.bds.storage.IStorage;
 import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
 import ch.systemsx.cisd.bds.storage.hdf5.HDF5Storage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Loader for {@link IDataStructure}s from the file system. 
@@ -58,7 +57,7 @@ public class DataStructureLoader
         File file = new File(baseDir, name);
         if (file.exists() == false)
         {
-            throw new UserFailureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
+            throw new DataStructureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
         }
         if (file.isDirectory())
         {
@@ -69,7 +68,7 @@ public class DataStructureLoader
         {
             return new HDF5Storage(hdf5File);
         }
-        throw new UserFailureException("Couldn't found appropriate container named '" + name + "' in "
+        throw new DataStructureException("Couldn't found appropriate container named '" + name + "' in "
                 + baseDir.getAbsolutePath());
         
     }

bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java

@@ -65,13 +65,13 @@ public class DataStructureV1_0 extends AbstractDataStructure
      * Returns the formated data. This method can be called only after method {@link #setFormat(Format)} has been
      * invoked. If the format is not known {@link UnknownFormat1_0} will be assumed.
      * 
-     * @throws UserFailureException if this method has been invoked before the format has been set.
+     * @throws DataStructureException if this method has been invoked before the format has been set.
      */
     public IFormattedData getFormatedData()
     {
         if (format == null)
         {
-            throw new UserFailureException("Couldn't create formated data because of undefined format.");
+            throw new DataStructureException("Couldn't create formated data because of undefined format.");
         }
         return FormatedDataFactory.createFormatedData(getMetaDataDirectory(), format, UnknownFormat1_0.UNKNOWN_1_0);
     }
@@ -88,7 +88,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
     /**
      * Returns the experiment identifier.
      * 
-     * @throws UserFailureException if the experiment identifier hasn't be loaded nor hasn't be set by
+     * @throws DataStructureException if the experiment identifier hasn't be loaded nor hasn't be set by
      *             {@link #setExperimentIdentifier(ExperimentIdentifier)}.
      */
     public ExperimentIdentifier getExperimentIdentifier()
@@ -108,7 +108,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
     /**
      * Returns the processing type.
      * 
-     * @throws UserFailureException if the processing type hasn't be loaded nor hasn't be set by
+     * @throws DataStructureException if the processing type hasn't be loaded nor hasn't be set by
      *             {@link #setProcessingType(ProcessingType)}.
      */
     public ProcessingType getProcessingType()
@@ -136,28 +136,28 @@ public class DataStructureV1_0 extends AbstractDataStructure
     }
 
     @Override
-    public void save() throws UserFailureException
+    public void save()
     {
         if (getOriginalData().iterator().hasNext() == false)
         {
-            throw new UserFailureException("Empty original data directory.");
+            throw new DataStructureException("Empty original data directory.");
         }
         IDirectory metaDataDirectory = getMetaDataDirectory();
         if (metaDataDirectory.tryToGetNode(Format.FORMAT_DIR) == null)
         {
             if (format == null)
             {
-                throw new UserFailureException("Unspecified format.");
+                throw new DataStructureException("Unspecified format.");
             }
             format.saveTo(metaDataDirectory);
         }
         if (metaDataDirectory.tryToGetNode(ExperimentIdentifier.FOLDER) == null)
         {
-            throw new UserFailureException("Unspecified experiment identifier.");
+            throw new DataStructureException("Unspecified experiment identifier.");
         }
         if (metaDataDirectory.tryToGetNode(ProcessingType.PROCESSING_TYPE) == null)
         {
-            throw new UserFailureException("Unspecified processing type.");
+            throw new DataStructureException("Unspecified processing type.");
         }
         super.save();
     }

bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java

@@ -17,7 +17,6 @@
 package ch.systemsx.cisd.bds;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Identifier of the experiment which corresponds to the data. This is an immutable but extendable value object class.
@@ -35,7 +34,7 @@ public class ExperimentIdentifier
     /**
      * Loads the experiment identifier from the specified directory.
      * 
-     * @throws UserFailureException if file missing.
+     * @throws DataStructureException if file missing.
      */
     static ExperimentIdentifier loadFrom(IDirectory directory)
     {

bds/source/java/ch/systemsx/cisd/bds/Factory.java

@@ -22,7 +22,6 @@ import java.util.HashMap;
 import java.util.Map;
 
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * General purpose factory for versioned classes with one-argument constructors.
@@ -51,7 +50,7 @@ class Factory<T>
             }
             if (v.getMinor() == 0)
             {
-                throw new UserFailureException("No class found for version " + version);
+                throw new DataStructureException("No class found for version " + version);
             }
             v = v.getPreviousMinorVersion();
         }
@@ -74,11 +73,11 @@ class Factory<T>
             return constructor.newInstance(new Object[] {argument});
         } catch (InvocationTargetException ex)
         {
-            throw new UserFailureException("Couldn't create instance of " + clazz + " for version " + version, ex
+            throw new DataStructureException("Couldn't create instance of " + clazz + " for version " + version, ex
                     .getCause());
         } catch (Exception ex)
         {
-            throw new UserFailureException("Couldn't create instance of " + clazz + " for version " + version, ex);
+            throw new DataStructureException("Couldn't create instance of " + clazz + " for version " + version, ex);
         }
     }
 

bds/source/java/ch/systemsx/cisd/bds/Format.java

@@ -19,7 +19,6 @@ package ch.systemsx.cisd.bds;
 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.UserFailureException;
 
 /**
  * Inmutable value object of a versioned format.
@@ -34,20 +33,20 @@ public class Format
     /**
      * Loads the format from the specified directory.
      * 
-     * @throws UserFailureException if the format could be loaded.
+     * @throws DataStructureException if the format could be loaded.
      */
     static Format loadFrom(IDirectory directory)
     {
         INode dir = directory.tryToGetNode(FORMAT_DIR);
         if (dir instanceof IDirectory == false)
         {
-            throw new UserFailureException("Not a directory: " + dir);
+            throw new DataStructureException("Not a directory: " + dir);
         }
         IDirectory formatDir = (IDirectory) dir;
         INode file = formatDir.tryToGetNode(FORMAT_CODE_FILE);
         if (file instanceof IFile == false)
         {
-            throw new UserFailureException("Not a plain file: " + file);
+            throw new DataStructureException("Not a plain file: " + file);
         }
         IFile codeFile = (IFile) file;
         String formatCode = codeFile.getStringContent().trim();

bds/source/java/ch/systemsx/cisd/bds/FormatedDataFactory.java

@@ -20,7 +20,6 @@ import java.util.HashMap;
 import java.util.Map;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 
 /**
@@ -75,7 +74,7 @@ class FormatedDataFactory
             {
                 return getFactory(defaultFormat, null);
             }
-            throw new UserFailureException("Unknown format code: " + code);
+            throw new DataStructureException("Unknown format code: " + code);
         }
         return factory;
     }

bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java

@@ -16,7 +16,6 @@
 
 package ch.systemsx.cisd.bds;
 
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Common interface of all data structures.
@@ -28,7 +27,7 @@ public interface IDataStructure extends IHasVersion
     /**
      * Loads the data structure.
      */
-    public void load() throws UserFailureException;
+    public void load();
 
     /**
      * Saves the data structure.

bds/source/java/ch/systemsx/cisd/bds/Utilities.java

@@ -20,7 +20,6 @@ package ch.systemsx.cisd.bds;
 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.UserFailureException;
 
 /**
  * Storage utility methods.
@@ -32,7 +31,7 @@ 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 DataStructureException if there is already a node named <code>name</code> but which isn't a directory.
      */
     public static IDirectory getOrCreateSubDirectory(IDirectory directory, String name)
     {
@@ -45,7 +44,7 @@ public class Utilities
         {
             return (IDirectory) node;
         }
-        throw new UserFailureException("There is already a node named '" + name + "' but which isn't a directory.");
+        throw new DataStructureException("There is already a node named '" + name + "' but which isn't a directory.");
     }
 
     /**
@@ -53,18 +52,18 @@ public class Utilities
      * 
      * @param directory Parent directory of the requested directory.
      * @param name Name of the requested directory.
-     * @throws UserFailureException if requested directory not found.
+     * @throws DataStructureException if requested directory not found.
      */
     public static IDirectory getSubDirectory(IDirectory directory, String name)
     {
         INode node = directory.tryToGetNode(name);
         if (node == null)
         {
-            throw new UserFailureException("No directory named '" + name + "' found in " + directory);
+            throw new DataStructureException("No directory named '" + name + "' found in " + directory);
         }
         if (node instanceof IDirectory == false)
         {
-            throw new UserFailureException("Is not a directory: " + node);
+            throw new DataStructureException("Is not a directory: " + node);
         }
         return (IDirectory) node;
     }
@@ -82,18 +81,18 @@ 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 DataStructureException if the requested file does not exist.
      */
     public static String getString(IDirectory directory, String name)
     {
         INode node = directory.tryToGetNode(name);
         if (node == null)
         {
-            throw new UserFailureException("File '" + name + "' missing in " + directory);
+            throw new DataStructureException("File '" + name + "' missing in " + directory);
         }
         if (node instanceof IFile == false)
         {
-            throw new UserFailureException(node + " is not a file.");
+            throw new DataStructureException(node + " is not a file.");
         }
         IFile file = (IFile) node;
         return file.getStringContent();

bds/source/java/ch/systemsx/cisd/bds/Version.java

@@ -17,7 +17,6 @@
 package ch.systemsx.cisd.bds;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Immutable value object for the version of something.        
@@ -47,7 +46,7 @@ public final class Version
             return Integer.parseInt(value);
         } catch (NumberFormatException ex)
         {
-            throw new UserFailureException("Value of " + name + " version file is not a number: " + value);
+            throw new DataStructureException("Value of " + name + " version file is not a number: " + value);
         }
     }
     
@@ -96,13 +95,13 @@ public final class Version
     /**
      * Returns the previous minor version.
      * 
-     * @throws UserFailureException if minor version is 0.
+     * @throws DataStructureException if minor version is 0.
      */
     public Version getPreviousMinorVersion()
     {
         if (minor == 0)
         {
-            throw new UserFailureException("There is no previous minor version of " + this);
+            throw new DataStructureException("There is no previous minor version of " + this);
         }
         return new Version(major, minor - 1);
     }

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

@@ -18,9 +18,6 @@ package ch.systemsx.cisd.bds.storage;
 
 import java.io.File;
 
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
 /**
  * Node representing a directory.
  * 
@@ -40,9 +37,8 @@ public interface IDirectory extends INode, Iterable<INode>
      * 
      * @param name Name of the new subdirectory.
      * @return the new subdirectory.
-     * @throws EnvironmentFailureException if the subdirectory cannot be created because of some other reason.
      */
-    public IDirectory makeDirectory(String name) throws UserFailureException, EnvironmentFailureException;
+    public IDirectory makeDirectory(String name);
 
     /**
      * Adds the specified real file to this directory. The content of <code>file</code> will be copied. If it is a
@@ -52,14 +48,12 @@ public interface IDirectory extends INode, Iterable<INode>
      * @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(final File file, final boolean move) throws UserFailureException, EnvironmentFailureException;
+    public INode addFile(final File file, final boolean move);
 
     /**
      * Removes given <var>node</var> from this directory.
-     * 
-     * @throws EnvironmentFailureException if given <var>node</var> could be removed for some other reason.
      */
-    public void removeNode(final INode node) throws UserFailureException, EnvironmentFailureException;
+    public void removeNode(final INode node);
 
     /**
      * 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

@@ -18,9 +18,6 @@ package ch.systemsx.cisd.bds.storage;
 
 import java.io.File;
 
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-
 /**
  * Abstraction of a node in a hierarchical data structure.
  * 
@@ -43,10 +40,6 @@ public interface INode
      * <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 extractTo(final File directory) throws UserFailureException, EnvironmentFailureException;
+    public void extractTo(final File directory);
 }

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

@@ -16,7 +16,6 @@
 
 package ch.systemsx.cisd.bds.storage;
 
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
  * Abstraction of a hierarchical storage.
@@ -33,9 +32,9 @@ public interface IStorage
     /**
      * Returns root directory of this storage. 
      * 
-     * @throws UserFailureException if invoked before {@link #mount()} or after {@link #unmount()}.
+     * @throws StorageException if invoked before {@link #mount()} or after {@link #unmount()}.
      */
-    public IDirectory getRoot() throws UserFailureException;
+    public IDirectory getRoot();
     
     /**
      * Unmounts this storage. May perform some finalization (e.g. make cached data persistent).

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

+/*
+ * 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;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+
+/**
+ * Exception thrown if some problem occured during operations in the Storage API which can not be classified
+ * convincingly as an {@link EnvironmentFailureException}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class StorageException extends RuntimeException
+{
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Creates an instance with the specified message.
+     */
+    public StorageException(String message)
+    {
+        super(message);
+    }
+
+    /**
+     * Creates an instance with the specified message and throwable causing this exception.
+     */
+    public StorageException(String message, Throwable cause)
+    {
+        super(message, cause);
+    }
+
+}

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

@@ -20,7 +20,7 @@ import java.io.File;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
 import ch.systemsx.cisd.bds.storage.INode;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.bds.storage.StorageException;
 
 /**
  * @author Franz-Josef Elmer
@@ -33,11 +33,11 @@ abstract class AbstractNode implements INode
     {
         if (file == null)
         {
-            throw new UserFailureException("Unspecified file");
+            throw new StorageException("Unspecified file");
         }
         if (file.exists() == false)
         {
-            throw new UserFailureException("Non existing file " + file);
+            throw new StorageException("Non existing file " + file);
         }
         this.nodeFile = file;
     }

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

@@ -27,8 +27,8 @@ 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;
+import ch.systemsx.cisd.bds.storage.StorageException;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
 import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
@@ -49,7 +49,7 @@ class Directory extends AbstractNode implements IDirectory
         super(directory);
         if (directory.isDirectory() == false)
         {
-            throw new UserFailureException("Not a directory: " + directory.getAbsolutePath());
+            throw new StorageException("Not a directory: " + directory.getAbsolutePath());
         }
     }
 
@@ -101,7 +101,7 @@ class Directory extends AbstractNode implements IDirectory
         {
             if (dir.isDirectory() == false)
             {
-                throw new UserFailureException("There already exists a file named '" + name + "' in directory " + this);
+                throw new StorageException("There already exists a file named '" + name + "' in directory " + this);
             }
             return new Directory(dir);
         }
@@ -121,8 +121,7 @@ class Directory extends AbstractNode implements IDirectory
         return new File(file);
     }
 
-    public INode addFile(final java.io.File file, final boolean move) throws UserFailureException,
-            EnvironmentFailureException
+    public INode addFile(final java.io.File file, final boolean move)
     {
         final java.io.File newFile = new java.io.File(nodeFile, file.getName());
         if (move)
@@ -197,7 +196,7 @@ class Directory extends AbstractNode implements IDirectory
         }
     }
 
-    public final void removeNode(final INode node) throws UserFailureException, EnvironmentFailureException
+    public final void removeNode(final INode node)
     {
         assert node != null : "Node could not be null";
         AbstractNode abstractNode = (AbstractNode) node;

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

@@ -20,7 +20,7 @@ import java.io.File;
 
 import ch.systemsx.cisd.bds.storage.IDirectory;
 import ch.systemsx.cisd.bds.storage.IStorage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.bds.storage.StorageException;
 
 /**
  * Implementation of {@link IStorage} based on the file system.
@@ -36,7 +36,7 @@ public class FileStorage implements IStorage
     /**
      * Creates an instance with the specified folder as the root directory.
      * 
-     * @throws UserFailureException if <code>folder</code> does not exist or is not a directory in the file system.
+     * @throws StorageException if <code>folder</code> does not exist or is not a directory in the file system.
      */
     public FileStorage(File folder)
     {
@@ -47,7 +47,7 @@ public class FileStorage implements IStorage
     {
         if (mounted == false)
         {
-            throw new UserFailureException("Can not get root of an unmounted storage.");
+            throw new StorageException("Can not get root of an unmounted storage.");
         }
         return root;
     }

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

@@ -21,8 +21,6 @@ import java.io.File;
 import ch.systemsx.cisd.bds.storage.IDirectory;
 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;
 
 /**
  * @author Franz-Josef Elmer
@@ -62,7 +60,7 @@ class Link implements ILink
         return reference;
     }
 
-    public void extractTo(final File directory) throws UserFailureException, EnvironmentFailureException
+    public void extractTo(final File directory)
     {
         // TODO Auto-generated method stub
     }