From d6d17c795a113873d087cd9e6ca6a312b1180cb4 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 9 Oct 2007 15:40:44 +0000
Subject: [PATCH] second approach
SVN: 2076
---
.../cisd/bds/AbstractDataStructure.java | 29 +++++--
.../cisd/bds/DataStructureFactory.java | 83 +++++++++++++++++++
...uctureV1_0.java => DataStructureV1_0.java} | 52 ++++++++----
.../cisd/bds/ExperimentIdentifier.java | 22 +++++
.../cisd/bds/IDataStructureFactory.java | 42 ----------
.../java/ch/systemsx/cisd/bds/IDirectory.java | 4 +
.../java/ch/systemsx/cisd/bds/INode.java | 14 ++++
...ataStructureFactory.java => IStorage.java} | 17 ++--
.../ch/systemsx/cisd/bds/ProcessingType.java | 12 +++
.../java/ch/systemsx/cisd/bds/Utilities.java | 53 ++++++++++++
.../java/ch/systemsx/cisd/bds/Version.java | 56 ++++++++++++-
.../cisd/bds/container/Container.java | 37 ++++++---
.../cisd/bds/fs/DataStructureV1_0.java | 62 --------------
.../ch/systemsx/cisd/bds/fs/Directory.java | 19 +++++
...StructureFactory.java => FileStorage.java} | 28 +++----
.../java/ch/systemsx/cisd/bds/fs/Link.java | 9 ++
.../ch/systemsx/cisd/bds/fs/StringFile.java | 7 ++
...StructureFactory.java => HDF5Storage.java} | 26 +++---
18 files changed, 394 insertions(+), 178 deletions(-)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
rename bds/source/java/ch/systemsx/cisd/bds/{AbstractDataStructureV1_0.java => DataStructureV1_0.java} (53%)
delete mode 100644 bds/source/java/ch/systemsx/cisd/bds/IDataStructureFactory.java
rename bds/source/java/ch/systemsx/cisd/bds/{AbstractDataStructureFactory.java => IStorage.java} (63%)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/Utilities.java
delete mode 100644 bds/source/java/ch/systemsx/cisd/bds/fs/DataStructureV1_0.java
rename bds/source/java/ch/systemsx/cisd/bds/fs/{FileDataStructureFactory.java => FileStorage.java} (51%)
rename bds/source/java/ch/systemsx/cisd/bds/hdf5/{HDF5DataStructureFactory.java => HDF5Storage.java} (59%)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
index b06ae5a928f..48a917329da 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructure.java
@@ -16,24 +16,39 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
/**
*
*
* @author Franz-Josef Elmer
*/
-public abstract class AbstractDataStructure implements IDataStructure
+public abstract class AbstractDataStructure implements IHasVersion
{
- private final String name;
+ protected final IStorage storage;
+ protected final IDirectory root;
- public AbstractDataStructure(String name)
+ AbstractDataStructure(IStorage storage)
{
- assert name != null && name.length() > 0: "Unspecified name";
- this.name = name;
+ assert storage != null: "Unspecified storage.";
+ this.storage = storage;
+ root = storage.getRoot();
}
- public String getName()
+ public void load()
{
- return name;
+ storage.load();
+ Version loadedVersion = Version.loadFrom(root);
+ if (getVersion().isBackwardsCompatibleWith(loadedVersion) == false)
+ {
+ throw new UserFailureException("Version of loaded data structure is " + loadedVersion
+ + " which is not backward compatible with " + getVersion());
+ }
}
+ public void save()
+ {
+ getVersion().saveTo(root);
+ storage.save();
+ }
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
new file mode 100644
index 00000000000..b039165e2e4
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
@@ -0,0 +1,83 @@
+/*
+ * 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 java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.util.HashMap;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStructureFactory
+{
+ private static final Map<Version, Class<? extends AbstractDataStructure>> repository =
+ new HashMap<Version, Class<? extends AbstractDataStructure>>();
+
+ void register(Version version, Class<? extends AbstractDataStructure> clazz)
+ {
+ repository.put(version, clazz);
+ }
+
+ public static Class<? extends AbstractDataStructure> getDataStructureClassFor(Version version)
+ {
+ Class<? extends AbstractDataStructure> clazz = null;
+ for (Version v = version; v.getMinor() >= 0 && clazz == null; v = v.getPreviousMinorVersion())
+ {
+ clazz = repository.get(v);
+ }
+ if (clazz == null)
+ {
+ throw new UserFailureException("No data structure class found for version " + version);
+ }
+ return clazz;
+ }
+
+ public static AbstractDataStructure createDataStructure(IStorage storage, Version version)
+ {
+ Class<? extends AbstractDataStructure> clazz = getDataStructureClassFor(version);
+ Constructor<? extends AbstractDataStructure> constructor;
+ try
+ {
+ constructor = clazz.getConstructor(new Class[] {IStorage.class});
+ } catch (Exception ex1)
+ {
+ throw new EnvironmentFailureException(clazz + " has no constructor with argument of type "
+ + IStorage.class.getCanonicalName());
+ }
+ try
+ {
+ return constructor.newInstance(new Object[] {storage});
+ } catch (InvocationTargetException ex)
+ {
+ throw new UserFailureException("Couldn't create data structure for version " + version, ex.getCause());
+ } catch (Exception ex)
+ {
+ throw new UserFailureException("Couldn't create data structure for version " + version, ex);
+ }
+ }
+
+ private DataStructureFactory()
+ {
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
similarity index 53%
rename from bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureV1_0.java
rename to bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index 8d46c817464..0d3d4e64671 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -16,23 +16,20 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
/**
*
*
* @author Franz-Josef Elmer
*/
-public abstract class AbstractDataStructureV1_0 extends AbstractDataStructure implements IDataStructureV1_0
+public class DataStructureV1_0 extends AbstractDataStructure
{
private static final Version VERSION = new Version(1, 0);
-
- private ExperimentIdentifier experimentIdentifier;
-
- private ProcessingType processingType;
-
- public AbstractDataStructureV1_0(String name)
+ public DataStructureV1_0(IStorage storage)
{
- super(name);
+ super(storage);
}
public Version getVersion()
@@ -40,25 +37,46 @@ public abstract class AbstractDataStructureV1_0 extends AbstractDataStructure im
return VERSION;
}
- public ExperimentIdentifier getExperimentIdentifier()
+ public IDirectory getOriginalData()
{
- return experimentIdentifier;
+ return Utilities.getSubDirectory(getDataDirectory(), "original");
}
+ public IFormatedData getFormatedData()
+ {
+ return null;
+ }
+
+ public ExperimentIdentifier getExperimentIdentifier()
+ {
+ return ExperimentIdentifier.loadFrom(getMetaDataDirectory());
+ }
+
public void setExperimentIdentifier(ExperimentIdentifier id)
{
- experimentIdentifier = id;
+ id.saveTo(getMetaDataDirectory());
}
-
+
public ProcessingType getProcessingType()
{
- return processingType;
+ return ProcessingType.loadFrom(getMetaDataDirectory());
}
-
+
public void setProcessingType(ProcessingType type)
{
- processingType = type;
+ type.saveTo(getMetaDataDirectory());
+ }
+
+ private IDirectory getDataDirectory()
+ {
+ IDirectory subDirectory = Utilities.getSubDirectory(root, "data");
+ return subDirectory;
+ }
+
+ private IDirectory getMetaDataDirectory()
+ {
+ IDirectory subDirectory = Utilities.getSubDirectory(root, "metadata");
+ return subDirectory;
}
-
-
}
+
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index 2020b0cb468..73c4353f586 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
@@ -24,6 +24,20 @@ package ch.systemsx.cisd.bds;
*/
public class ExperimentIdentifier
{
+ private static final String FOLDER = "experiment_identifier";
+ private static final String GROUP_CODE = "group_code";
+ private static final String PROJECT_CODE = "project_code";
+ private static final String EXPERIMENT_CODE = "experiment_code";
+
+ public static ExperimentIdentifier loadFrom(IDirectory directory)
+ {
+ IDirectory idFolder = Utilities.getSubDirectory(directory, FOLDER);
+ String groupCode = Utilities.getString(idFolder, GROUP_CODE);
+ String projectCode = Utilities.getString(idFolder, PROJECT_CODE);
+ String experimentCode = Utilities.getString(idFolder, EXPERIMENT_CODE);
+ return new ExperimentIdentifier(groupCode, projectCode, experimentCode);
+ }
+
private final String groupCode;
private final String projectCode;
private final String experimentCode;
@@ -68,6 +82,14 @@ public class ExperimentIdentifier
{
return experimentCode;
}
+
+ public void saveTo(IDirectory directory)
+ {
+ IDirectory folder = directory.appendDirectory(FOLDER);
+ folder.appendKeyValuePair(GROUP_CODE, groupCode);
+ folder.appendKeyValuePair(PROJECT_CODE, projectCode);
+ folder.appendKeyValuePair(EXPERIMENT_CODE, experimentCode);
+ }
@Override
public boolean equals(Object obj)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructureFactory.java
deleted file mode 100644
index 9ba3ce97725..00000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructureFactory.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * 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.common.exceptions.UserFailureException;
-
-/**
- * Factory of {@link IDataStructure}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IDataStructureFactory
-{
- /**
- * Returns the subinterface of {@link IDataStructure} for the specified version.
- *
- * @throws UserFailureException if this factory can not create a data structure for the specified version.
- */
- public Class<? extends IDataStructure> getDataStructureInterfaceFor(Version version) throws UserFailureException;
-
- /**
- * Creates a new data structure of specified name and version. The return object implements the interface
- * returned by {@link #getDataStructureInterfaceFor(Version)} for the same value of <code>version</code>.
- *
- * @throws UserFailureException if this factory can not create a data structure for the specified version.
- */
- public IDataStructure createDataStructure(String name, Version version) throws UserFailureException;
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDirectory.java b/bds/source/java/ch/systemsx/cisd/bds/IDirectory.java
index 0b515a5c112..dc9c18da657 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDirectory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IDirectory.java
@@ -25,6 +25,10 @@ import java.io.File;
*/
public interface IDirectory extends INode, Iterable<INode>
{
+ public INode getNode(String name);
+
+ public IDirectory appendDirectory(String name);
+
public void appendNode(INode node);
public void appendRealFile(File file);
diff --git a/bds/source/java/ch/systemsx/cisd/bds/INode.java b/bds/source/java/ch/systemsx/cisd/bds/INode.java
index 47d50b1354b..4361171ded5 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/INode.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/INode.java
@@ -16,6 +16,11 @@
package ch.systemsx.cisd.bds;
+import java.io.File;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
/**
* Role of a node in the data structure.
*
@@ -32,4 +37,13 @@ public interface INode
* Returns the parent directory of this node or <code>null</code> if it is the root node.
*/
public IDirectory tryToGetParent();
+
+ /**
+ * Extracts this node to the specified directory of the file system. All descendants are also extracted.
+ *
+ * @throws UserFailureException if this or a descended node is a link referring to a node which is not this
+ * node or a descended node.
+ * @throws EnvironmentFailureException if extraction causes an IOException.
+ */
+ public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/IStorage.java
similarity index 63%
rename from bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureFactory.java
rename to bds/source/java/ch/systemsx/cisd/bds/IStorage.java
index bc9f10dfbf2..8441062e229 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractDataStructureFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IStorage.java
@@ -16,21 +16,16 @@
package ch.systemsx.cisd.bds;
-import java.io.File;
-
/**
*
*
* @author Franz-Josef Elmer
*/
-public abstract class AbstractDataStructureFactory implements IDataStructureFactory
+public interface IStorage
{
- protected final File baseDir;
-
- public AbstractDataStructureFactory(File baseDir)
- {
- assert baseDir != null : "Unspecified base directory.";
- assert baseDir.isDirectory() : "Is not a directory : " + baseDir.getAbsolutePath();
- this.baseDir = baseDir;
- }
+ public void load();
+
+ public IDirectory getRoot();
+
+ public void save();
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
index d4031ad8a37..6717aff94fa 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ProcessingType.java
@@ -26,6 +26,8 @@ public enum ProcessingType
{
OTHER, RAW_DATA, COMPUTED_DATA;
+ private static final String PROCESSING_TYPE = "processing_type";
+
/**
* Resolves the specified string representation of a processing type.
*
@@ -36,4 +38,14 @@ public enum ProcessingType
ProcessingType type = valueOf(processingTypeString);
return type == null ? OTHER : type;
}
+
+ public static ProcessingType loadFrom(IDirectory directory)
+ {
+ return resolve(Utilities.getString(directory, PROCESSING_TYPE));
+ }
+
+ public void saveTo(IDirectory directory)
+ {
+ directory.appendKeyValuePair(PROCESSING_TYPE, toString());
+ }
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
new file mode 100644
index 00000000000..a352ebc55ad
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -0,0 +1,53 @@
+/*
+ * 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.common.exceptions.UserFailureException;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Utilities
+{
+ public static IDirectory getSubDirectory(IDirectory directory, String name)
+ {
+ INode node = directory.getNode(name);
+ if (node instanceof IDirectory == false)
+ {
+ throw new UserFailureException("Is not a directory: " + node);
+ }
+ return (IDirectory) node;
+ }
+
+ public static String getString(IDirectory directory, String name)
+ {
+ INode node = directory.getNode(name);
+ if (node == null)
+ {
+ throw new UserFailureException("File '" + name + "' missing in " + directory);
+ }
+ if (node instanceof IFile<?> == false)
+ {
+ throw new UserFailureException(node + " is not a file.");
+ }
+ IFile<?> file = (IFile<?>) node;
+ return file.getValue().toString();
+ }
+
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 8dbdc15d640..4bc6052125e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Version.java
@@ -16,13 +16,37 @@
package ch.systemsx.cisd.bds;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
/**
- * Immutable value object for the version of something.
+ * Immutable value object for the version of something.
*
* @author Franz-Josef Elmer
*/
public final class Version
{
+ private static final String VERSION = "version";
+ private static final String MAJOR = "major";
+ private static final String MINOR = "minor";
+
+ public static Version loadFrom(IDirectory directory)
+ {
+ IDirectory versionFolder = Utilities.getSubDirectory(directory, VERSION);
+ return new Version(getNumber(versionFolder, MAJOR), getNumber(versionFolder, MINOR));
+ }
+
+ private static int getNumber(IDirectory versionFolder, String name)
+ {
+ String value = Utilities.getString(versionFolder, name);
+ try
+ {
+ return Integer.parseInt(value);
+ } catch (NumberFormatException ex)
+ {
+ throw new UserFailureException("Value of " + name + " version file is not a number: " + value);
+ }
+ }
+
private final int major;
private final int minor;
@@ -55,6 +79,36 @@ public final class Version
{
return minor;
}
+
+ /**
+ * Returns true if this version is backwards compatible to the specified version. That is,
+ * if <code>version.getMajor() == this.getMajor()</code> and <code>version.getMinor() <= this.getMinor()</code>.
+ */
+ public boolean isBackwardsCompatibleWith(Version version)
+ {
+ return version.major == major && version.minor <= minor;
+ }
+
+ /**
+ * Returns the previous minor version.
+ *
+ * @throws UserFailureException if minor version is 0.
+ */
+ public Version getPreviousMinorVersion()
+ {
+ if (minor == 0)
+ {
+ throw new UserFailureException("There is no previous minor version of " + this);
+ }
+ return new Version(major, minor - 1);
+ }
+
+ public void saveTo(IDirectory directory)
+ {
+ IDirectory versionFolder = directory.appendDirectory(VERSION);
+ versionFolder.appendKeyValuePair(MAJOR, Integer.toString(major));
+ versionFolder.appendKeyValuePair(MINOR, Integer.toString(minor));
+ }
@Override
public boolean equals(Object obj)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/container/Container.java b/bds/source/java/ch/systemsx/cisd/bds/container/Container.java
index 0a95d6e76e1..e5437cb0cdd 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/container/Container.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/container/Container.java
@@ -18,10 +18,14 @@ package ch.systemsx.cisd.bds.container;
import java.io.File;
+import ch.systemsx.cisd.bds.AbstractDataStructure;
+import ch.systemsx.cisd.bds.DataStructureFactory;
import ch.systemsx.cisd.bds.IDataStructure;
-import ch.systemsx.cisd.bds.IDataStructureFactory;
-import ch.systemsx.cisd.bds.fs.FileDataStructureFactory;
-import ch.systemsx.cisd.bds.hdf5.HDF5DataStructureFactory;
+import ch.systemsx.cisd.bds.IStorage;
+import ch.systemsx.cisd.bds.Utilities;
+import ch.systemsx.cisd.bds.Version;
+import ch.systemsx.cisd.bds.fs.FileStorage;
+import ch.systemsx.cisd.bds.hdf5.HDF5Storage;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
@@ -40,25 +44,32 @@ public class Container
this.baseDir = baseDir;
}
- public IDataStructure load(String name)
+ public AbstractDataStructure load(String name)
+ {
+ IStorage storage = createStorage(name);
+ storage.load();
+ Version version = Version.loadFrom(storage.getRoot());
+ return DataStructureFactory.createDataStructure(storage, version);
+ }
+
+ private IStorage createStorage(String name)
{
File file = new File(baseDir, name);
if (file.exists() == false)
{
throw new UserFailureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
}
- IDataStructureFactory dataStructureFactory;
if (file.isDirectory())
{
- dataStructureFactory = new FileDataStructureFactory(baseDir);
- } else if (new File(baseDir, name + ".hdf5").exists())
- {
- dataStructureFactory = new HDF5DataStructureFactory(baseDir);
- } else
+ return new FileStorage(file);
+ }
+ File hdf5File = new File(baseDir, name + ".hdf5");
+ if (hdf5File.exists())
{
- throw new UserFailureException("Couldn't found appropriate container named '" + name + "' in "
- + baseDir.getAbsolutePath());
+ return new HDF5Storage(hdf5File);
}
- return dataStructureFactory.createDataStructure(name, null);
+ throw new UserFailureException("Couldn't found appropriate container named '" + name + "' in "
+ + baseDir.getAbsolutePath());
+
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/fs/DataStructureV1_0.java
deleted file mode 100644
index 9cdbc3e726d..00000000000
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/DataStructureV1_0.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * 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.fs;
-
-import java.io.File;
-
-import ch.systemsx.cisd.bds.AbstractDataStructureV1_0;
-import ch.systemsx.cisd.bds.IDirectory;
-import ch.systemsx.cisd.bds.IFormatedData;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class DataStructureV1_0 extends AbstractDataStructureV1_0
-{
- private final File baseDir;
-
- public DataStructureV1_0(String name, File baseDir)
- {
- super(name);
- assert baseDir != null : "Unspecified base directory.";
- assert baseDir.isDirectory() : "Is not a directory: " + baseDir.getAbsolutePath();
- this.baseDir = baseDir;
- }
-
- public IFormatedData getFormatedData()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public IDirectory getOriginalData()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- public void save() throws EnvironmentFailureException
- {
- // TODO Auto-generated method stub
- System.out.println(baseDir);
-
- }
-
-}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java
index 56b3061f354..b7ecbc8c262 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/fs/Directory.java
@@ -24,6 +24,7 @@ import java.util.Iterator;
import ch.systemsx.cisd.bds.IDirectory;
import ch.systemsx.cisd.bds.INode;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
*
@@ -38,6 +39,18 @@ class Directory extends AbstractNode implements IDirectory
assert directory.isDirectory() : "Not a directory: " + directory.getAbsolutePath();
}
+ public INode getNode(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ public IDirectory appendDirectory(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
public void appendKeyValuePair(String key, String value)
{
File file = new File(fileNode, key);
@@ -81,4 +94,10 @@ class Directory extends AbstractNode implements IDirectory
return null;
}
+ public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/FileDataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java
similarity index 51%
rename from bds/source/java/ch/systemsx/cisd/bds/fs/FileDataStructureFactory.java
rename to bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java
index 8d04d284e3a..aefe534501b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/FileDataStructureFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/fs/FileStorage.java
@@ -18,34 +18,34 @@ package ch.systemsx.cisd.bds.fs;
import java.io.File;
-import ch.systemsx.cisd.bds.AbstractDataStructureFactory;
-import ch.systemsx.cisd.bds.IDataStructure;
-import ch.systemsx.cisd.bds.Version;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.bds.IDirectory;
+import ch.systemsx.cisd.bds.IStorage;
/**
*
*
* @author Franz-Josef Elmer
*/
-public class FileDataStructureFactory extends AbstractDataStructureFactory
+public class FileStorage implements IStorage
{
+ private Directory root;
- public FileDataStructureFactory(File baseDir)
+ public FileStorage(File folder)
{
- super(baseDir);
+ root = new Directory(folder);
+ }
+
+ public IDirectory getRoot()
+ {
+ return root;
}
- public Class<? extends IDataStructure> getDataStructureInterfaceFor(Version version) throws UserFailureException
+ public void load()
{
- // TODO Auto-generated method stub
- return null;
}
- public IDataStructure createDataStructure(String name, Version version) throws UserFailureException
+ public void save()
{
- // TODO Auto-generated method stub
- return null;
}
-
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java b/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java
index a1ddf4a6425..09dc58b4e50 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/fs/Link.java
@@ -16,9 +16,13 @@
package ch.systemsx.cisd.bds.fs;
+import java.io.File;
+
import ch.systemsx.cisd.bds.IDirectory;
import ch.systemsx.cisd.bds.ILink;
import ch.systemsx.cisd.bds.INode;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
*
@@ -58,4 +62,9 @@ class Link implements ILink
return reference;
}
+ public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
+ {
+ // TODO Auto-generated method stub
+ }
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java b/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java
index 5e651af966d..1061b43852b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/fs/StringFile.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.bds.fs;
import java.io.File;
import ch.systemsx.cisd.bds.IFile;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
@@ -39,4 +41,9 @@ class StringFile extends AbstractNode implements IFile<String>
return FileUtilities.loadToString(fileNode);
}
+ public void extractTo(File directory) throws UserFailureException, EnvironmentFailureException
+ {
+ // TODO Auto-generated method stub
+ }
+
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5DataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java
similarity index 59%
rename from bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5DataStructureFactory.java
rename to bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java
index 76ef69f2610..04c04c6c3bc 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5DataStructureFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hdf5/HDF5Storage.java
@@ -18,33 +18,37 @@ package ch.systemsx.cisd.bds.hdf5;
import java.io.File;
-import ch.systemsx.cisd.bds.AbstractDataStructureFactory;
-import ch.systemsx.cisd.bds.IDataStructure;
-import ch.systemsx.cisd.bds.Version;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.bds.IDirectory;
+import ch.systemsx.cisd.bds.IStorage;
/**
*
*
* @author Franz-Josef Elmer
*/
-public class HDF5DataStructureFactory extends AbstractDataStructureFactory
+public class HDF5Storage implements IStorage
{
- public HDF5DataStructureFactory(File baseDir)
+ public HDF5Storage(File hdf5File)
{
- super(baseDir);
+ assert hdf5File != null : "Unspecified HDF5 file.";
}
-
- public IDataStructure createDataStructure(String name, Version version) throws UserFailureException
+
+ public IDirectory getRoot()
{
// TODO Auto-generated method stub
return null;
}
- public Class<? extends IDataStructure> getDataStructureInterfaceFor(Version version) throws UserFailureException
+ public void load()
{
// TODO Auto-generated method stub
- return null;
+
+ }
+
+ public void save()
+ {
+ // TODO Auto-generated method stub
+
}
}
--
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