diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
index 9ef252f6e3dafda864d22741f6df3e39b1edbf04..dca7be2e5bb26dadfd0f2661319562e34fd43db3 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
+++ b/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());
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureException.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureException.java
new file mode 100644
index 0000000000000000000000000000000000000000..6682379e29f0f58931e2ad69588934b77aa41fd7
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureException.java
@@ -0,0 +1,45 @@
+/*
+ * 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);
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
index 9c628089e66d801bcc9e0abd6cc870960ddd8dac..e4b5baa0e31e39cab03774a3ea8e5adb42596e57 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
+++ b/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)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
index 1d8538b58ca24fc23a6784ea5352ca9842d03493..6c23fa41ac0abf2e82ff6abee0d84ee41ab210ce 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
+++ b/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());
}
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 1a1567c122748e19ea2f521d91bc99545c4ca01f..072856244b6d2bb8eb328d152d0d0f5b86d1f55a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/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();
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index b624e68e3d4f31e815b638542176c112137115d9..5a66b75bca27e01502d594867dbe0ffff4a46d11 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/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)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Factory.java b/bds/source/java/ch/systemsx/cisd/bds/Factory.java
index fccbdd3e8a9bc8fccb55254a415e787f34170157..e700c940c5c5033876dbd45246979a39b62df516 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Factory.java
+++ b/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);
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Format.java b/bds/source/java/ch/systemsx/cisd/bds/Format.java
index 12b2b368e6bb866a0e3934188bc0f60272a5377f..06c5bcfd8b05ee85d5c04dc879cd9dbabab6ee5d 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Format.java
+++ b/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();
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatedDataFactory.java b/bds/source/java/ch/systemsx/cisd/bds/FormatedDataFactory.java
index ef32a8a41ddff64805aa3005b7bb76a9770fa732..42505187763c9eb3de59afabcd7604c84baddd0e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatedDataFactory.java
+++ b/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;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
index 953cf557b84a8f05b61a20ac04cd5a4a14cadb32..c7dbd88c5ca54b2c3e80d763a9adb64a818ba8e4 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
+++ b/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.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index 5b2ccfcdf6223b55d299d90bd91686f62a0fee97..bab9c8ae8ed5c340b5e4190c2301102ea5066644 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/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();
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 88cd8c45c126a858784543a45580b990bcffa0f7..58918ab300e16d844fc0cf7e3efd61a94d1d48c6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/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);
}
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 bdafa8e4d38dbe388238567deded1dae2a2770f4..a943effb8a143e33ca2d353059652ee67f7a2e63 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
+++ b/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.
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 56f81212f6682323e8939b78b9703fb87b31692c..b4cc3ea9fd641e514a55fa60034159fef0661ca1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/INode.java
+++ b/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);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
index 98cf5ae759362c9b360f94223aa255af7fc5e1a9..ac018d8f4b1cc12b9b5055b8ef6daa8ddf299110 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
+++ b/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).
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/StorageException.java b/bds/source/java/ch/systemsx/cisd/bds/storage/StorageException.java
new file mode 100644
index 0000000000000000000000000000000000000000..21534198779cd89560bc6560eeaa0c5bdd5bf870
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/StorageException.java
@@ -0,0 +1,47 @@
+/*
+ * 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);
+ }
+
+}
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 c257acf9b410b12d9c0e3d0c051a7f309745352e..435296f62c49eb0eedb2b7a3f6a5be878cd6c414 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
@@ -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;
}
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 25e9c772aab9b1386961c333e9813b09b2cced5f..c694c78cbc22d8b267b56816f19f37d3eaf6e7cf 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
@@ -27,8 +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;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
index 4a51cd3692e8e5bb53a78c029fa23cc3a1980c55..fbde24c79ed03fa3f8b06d6a5686039737d4a1eb 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
+++ b/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;
}
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 8a3f961e48b6496909eb8b0bb4245fcd950aeebc..9debc53f089778a22be6bb0ee282c4e13c4cac1f 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
@@ -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
}
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 9359038b506db64759bd0b0fa0cedc8721f9c2f2..0ae75b1d5f9947a31d329faacfed2da6484cebff 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
@@ -44,7 +44,7 @@ class NodeFactory
return new File(file);
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't get canonical path of file " + absolutePath);
+ throw new EnvironmentFailureException("Couldn't get canonical path of file " + absolutePath, ex);
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
index 6a37f1476d820b46809d1bb3053ee583364a60fa..564fb93fda57bb9a70397a3443b4b103c6c44f69 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
@@ -25,7 +25,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IStorage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
*
@@ -57,8 +56,8 @@ public class DataStructureFactoryTest
try
{
DataStructureFactory.getDataStructureClassFor(new Version(2, 0));
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("No class found for version V2.0", e.getMessage());
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
index cbc6ae1e1df6038ae41dcdab89f847baf3695fd4..6e3a03d0c02c5cd3ac942725fd31e9371cd0267c 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -28,8 +28,8 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
*
@@ -81,8 +81,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.getFormatedData();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Couldn't create formated data because of undefined format.", e.getMessage());
}
@@ -156,8 +156,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.getExperimentIdentifier();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertPartOfString(ExperimentIdentifier.FOLDER, e.getMessage());
}
@@ -183,8 +183,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.save();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Empty original data directory.", e.getMessage());
}
@@ -197,8 +197,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.save();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Unspecified format.", e.getMessage());
}
@@ -212,8 +212,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.save();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Unspecified experiment identifier.", e.getMessage());
}
@@ -228,8 +228,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.save();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Unspecified processing type.", e.getMessage());
}
@@ -250,8 +250,8 @@ public class DataStructureV1_0Test
try
{
storage.getRoot();
- fail("UserFailureException expected because save() should unmount storage.");
- } catch (UserFailureException e)
+ fail("StorageException expected because save() should unmount storage.");
+ } catch (StorageException e)
{
assertEquals("Can not get root of an unmounted storage.", e.getMessage());
}
@@ -270,8 +270,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.load();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertPartOfString(Version.VERSION, e.getMessage());
}
@@ -305,8 +305,8 @@ public class DataStructureV1_0Test
try
{
dataStructure.load();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("Version of loaded data structure is V2.0 which is not backward compatible with V1.0",
e.getMessage());
@@ -335,8 +335,8 @@ public class DataStructureV1_0Test
{
dataStructure.load();
dataStructure.getFormatedData();
- fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ fail("DataStructureException expected.");
+ } catch (DataStructureException e)
{
assertEquals("No class found for version V2.0", e.getMessage());
}
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 43ba575c4f1f5f6376e502f92c40e724b443d066..6e293a12b670c49740d30d6684099052b7914da4 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
@@ -29,7 +29,7 @@ import org.testng.annotations.Test;
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;
+import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
@@ -116,8 +116,8 @@ public class DirectoryTest extends StorageTestCase
try
{
directory.makeDirectory("sub-directory");
- AssertJUnit.fail("UserFailureException expected.");
- } catch (UserFailureException e)
+ AssertJUnit.fail("StorageException expected.");
+ } catch (StorageException e)
{
assertTrue(e.getMessage().indexOf("sub-directory") >= 0);
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
index 67d2f5b687d8d24bf1324ad8fc0a8b3969dd20dd..60dfaf095427637076dba14f560bf37bb0689cd6 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
@@ -21,7 +21,7 @@ import static org.testng.AssertJUnit.assertEquals;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.bds.storage.StorageException;
/**
*
@@ -45,8 +45,8 @@ public class FileStorageTest extends StorageTestCase
try
{
fileStorage.getRoot();
- AssertJUnit.fail("UserFailureException because storage isn't mounted.");
- } catch (UserFailureException e)
+ AssertJUnit.fail("StorageException because storage isn't mounted.");
+ } catch (StorageException e)
{
assertEquals("Can not get root of an unmounted storage.", e.getMessage());
}
@@ -61,8 +61,8 @@ public class FileStorageTest extends StorageTestCase
try
{
fileStorage.getRoot();
- AssertJUnit.fail("UserFailureException because storage isn't mounted.");
- } catch (UserFailureException e)
+ AssertJUnit.fail("StorageException because storage isn't mounted.");
+ } catch (StorageException e)
{
assertEquals("Can not get root of an unmounted storage.", e.getMessage());
}