- remove interfaces no longer used

- IDirectory method signatures changed

SVN: 2086

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

@@ -87,10 +87,10 @@ public class ExperimentIdentifier
     
     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);
+        IDirectory folder = directory.makeDirectory(FOLDER);
+        folder.addKeyValuePair(GROUP_CODE, groupCode);
+        folder.addKeyValuePair(PROJECT_CODE, projectCode);
+        folder.addKeyValuePair(EXPERIMENT_CODE, experimentCode);
     }
 
     @Override

bds/source/java/ch/systemsx/cisd/bds/IDataStructure.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.common.exceptions.EnvironmentFailureException;
-
-/**
- * Common interface of all versions of data structures.
- *
- * @author Franz-Josef Elmer
- */
-public interface IDataStructure extends IHasVersion
-{
-    /**
-     * Returns the name of this data structure.
-     */
-    public String getName();
-    
-    /**
-     * Save the current structure.
-     * 
-     * @throws EnvironmentFailureException if it couldn't saved.
-     */
-    public void save() throws EnvironmentFailureException;
-}

bds/source/java/ch/systemsx/cisd/bds/IDataStructureV1_0.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.IDirectory;
-
-/**
- * Data structure interface for Version 1.0.
- *
- * @author Franz-Josef Elmer
- */
-public interface IDataStructureV1_0 extends IDataStructure
-{
-    public IDirectory getOriginalData();
-    
-    public IFormatedData getFormatedData();
-    
-    public ExperimentIdentifier getExperimentIdentifier();
-    
-    public void setExperimentIdentifier(ExperimentIdentifier id);
-    
-    public ProcessingType getProcessingType();
-    
-    public void setProcessingType(ProcessingType type);
-}

bds/source/java/ch/systemsx/cisd/bds/IDirectory.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 java.io.File;
-
-/**
- * 
- *
- * @author Franz-Josef Elmer
- */
-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);
-    
-    public void appendKeyValuePair(String key, String value);
-    
-    public void appendLink(String name, INode node);
-}

bds/source/java/ch/systemsx/cisd/bds/IFile.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;
-
-/**
- * Role of a file with a value (content) of type <code>T</code>.
- *
- * @author Franz-Josef Elmer
- */
-public interface IFile<T> extends INode
-{
-    /**
-     * Returns the value (or content) of this file node.
-     */
-    public T getValue();
-}

bds/source/java/ch/systemsx/cisd/bds/ILink.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;
-
-/**
- * 
- *
- * @author Franz-Josef Elmer
- */
-public interface ILink extends INode
-{
-    public INode getReference();
-}

bds/source/java/ch/systemsx/cisd/bds/INode.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 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.
- *
- * @author Franz-Josef Elmer
- */
-public interface INode
-{
-    /**
-     * Returns the name of this node.
-     */
-    public String getName();
-    
-    /**
-     * Returns the parent directory of this node or <code>null</code> if it is the root node.
-     */
-    public IDirectory tryToGetParent();
-    
-    /**
-     * 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;
-}

bds/source/java/ch/systemsx/cisd/bds/IStorage.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;
-
-/**
- * 
- *
- * @author Franz-Josef Elmer
- */
-public interface IStorage
-{
-    public void load();
-    
-    public IDirectory getRoot();
-    
-    public void save();
-}

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

@@ -48,6 +48,6 @@ public enum ProcessingType
     
     public void saveTo(IDirectory directory)
     {
-        directory.appendKeyValuePair(PROCESSING_TYPE, toString());
+        directory.addKeyValuePair(PROCESSING_TYPE, toString());
     }
 }

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

@@ -106,9 +106,9 @@ public final class Version
     
     public void saveTo(IDirectory directory)
     {
-        IDirectory versionFolder = directory.appendDirectory(VERSION);
-        versionFolder.appendKeyValuePair(MAJOR, Integer.toString(major));
-        versionFolder.appendKeyValuePair(MINOR, Integer.toString(minor));
+        IDirectory versionFolder = directory.makeDirectory(VERSION);
+        versionFolder.addKeyValuePair(MAJOR, Integer.toString(major));
+        versionFolder.addKeyValuePair(MINOR, Integer.toString(minor));
     }
 
     @Override

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

@@ -27,13 +27,13 @@ public interface IDirectory extends INode, Iterable<INode>
 {
     public INode getNode(String name);
     
-    public IDirectory appendDirectory(String name);
+    public IDirectory makeDirectory(String name);
     
-    public void appendNode(INode node);
+    public void addNode(INode node);
     
-    public void appendRealFile(File file);
+    public IFile<File> addRealFile(File file);
     
-    public void appendKeyValuePair(String key, String value);
+    public IFile<String> addKeyValuePair(String key, String value);
     
-    public void appendLink(String name, INode node);
+    public ILink addLink(String name, INode node);
 }

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

@@ -22,6 +22,8 @@ import java.io.IOException;
 import java.util.Iterator;
 
 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.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -45,13 +47,13 @@ class Directory extends AbstractNode implements IDirectory
         return null;
     }
 
-    public IDirectory appendDirectory(String name)
+    public IDirectory makeDirectory(String name)
     {
         // TODO Auto-generated method stub
         return null;
     }
 
-    public void appendKeyValuePair(String key, String value)
+    public IFile<String> addKeyValuePair(String key, String value)
     {
         File file = new File(fileNode, key);
         try
@@ -64,15 +66,16 @@ class Directory extends AbstractNode implements IDirectory
             file.delete();
             throw new EnvironmentFailureException("Can not create " + file.getAbsolutePath() + ": " + ex);
         }
+        return null;
     }
 
-    public void appendNode(INode node)
+    public void addNode(INode node)
     {
         // TODO Auto-generated method stub
 
     }
 
-    public void appendRealFile(File file)
+    public IFile<File> addRealFile(File file)
     {
         File newFile = new File(fileNode, file.getName());
         if (file.renameTo(newFile) == false)
@@ -80,12 +83,13 @@ class Directory extends AbstractNode implements IDirectory
             throw new EnvironmentFailureException("Couldn't move file " + file.getAbsolutePath() + " to "
                     + fileNode.getAbsolutePath());
         }
+        return null;
     }
 
-    public void appendLink(String name, INode node)
+    public ILink addLink(String name, INode node)
     {
         // TODO Auto-generated method stub
-        
+        return null;
     }
 
     public Iterator<INode> iterator()