From 53b07c02f17bf254dbfeb736a32fbb3a8c991ea6 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 5 Aug 2011 09:11:03 +0000
Subject: [PATCH] refactor Hdf5Container for minimal interface (reader)
SVN: 22349
---
.../cisd/common/hdf5/Hdf5Container.java | 37 +++++++++--
.../common/hdf5/IHDF5ContainerReader.java | 62 +++++++++++++++++++
...ContainerBasedHierarchicalContentNode.java | 12 ++--
.../hdf5/FileToHdf5DuplicationVerifier.java | 7 +--
.../cisd/common/hdf5/Hdf5ContainerTest.java | 5 +-
...icalStructureDuplicatorFileToHdf5Test.java | 3 +-
.../AbstractHdf5StorageProcessorTest.java | 4 +-
7 files changed, 109 insertions(+), 21 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java b/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
index 4787e44af6e..9f14f263cb8 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.common.hdf5;
import java.io.File;
+import java.util.List;
import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
@@ -56,7 +57,7 @@ public class Hdf5Container
/**
* Run code using a reader. Implementations do <b>not</b> need to close the reader.
*/
- public void runWithSimpleReader(IHDF5SimpleReader reader);
+ public void runWithSimpleReader(IHDF5ContainerReader reader);
}
/**
@@ -80,9 +81,37 @@ public class Hdf5Container
*
* @return A new IHDF5SimpleReader
*/
- public IHDF5SimpleReader createSimpleReader()
+ public IHDF5ContainerReader createSimpleReader()
{
- return HDF5FactoryProvider.get().openForReading(hdf5Container);
+ return new IHDF5ContainerReader()
+ {
+ final IHDF5SimpleReader innerReader = HDF5FactoryProvider.get().openForReading(hdf5Container);
+
+ public void close()
+ {
+ innerReader.close();
+ }
+
+ public boolean exists(String objectPath)
+ {
+ return innerReader.exists(objectPath);
+ }
+
+ public boolean isGroup(String objectPath)
+ {
+ return innerReader.isGroup(objectPath);
+ }
+
+ public List<String> getGroupMembers(String groupPath)
+ {
+ return innerReader.getGroupMembers(groupPath);
+ }
+
+ public byte[] readAsByteArray(String objectPath)
+ {
+ return innerReader.readAsByteArray(objectPath);
+ }
+ };
}
/**
@@ -120,7 +149,7 @@ public class Hdf5Container
*/
public void runReaderClient(IHdf5ReaderClient client)
{
- IHDF5SimpleReader reader = createSimpleReader();
+ IHDF5ContainerReader reader = createSimpleReader();
try
{
client.runWithSimpleReader(reader);
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
new file mode 100644
index 00000000000..61759ed72a8
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright 2011 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.common.hdf5;
+
+import java.util.List;
+
+/**
+ * A simple abstraction of the methods needed to read from an HDF5 container.
+ *
+ * @author Bernd Rinn
+ */
+public interface IHDF5ContainerReader
+{
+
+ /**
+ * Closes this object and the file referenced by this object. This object must not be used after
+ * being closed.
+ */
+ public void close();
+
+ /**
+ * Returns the members of <var>groupPath</var>. The order is <i>not</i> well defined.
+ *
+ * @param groupPath The path of the group to get the members for.
+ * @throws IllegalArgumentException If <var>groupPath</var> is not a group.
+ */
+ public List<String> getGroupMembers(final String groupPath);
+
+ /**
+ * Returns <code>true</code>, if <var>objectPath</var> exists and <code>false</code> otherwise.
+ */
+ public boolean exists(final String objectPath);
+
+ /**
+ * Returns <code>true</code> if the <var>objectPath</var> exists and represents a group and
+ * <code>false</code> otherwise.
+ */
+ public boolean isGroup(final String objectPath);
+
+ /**
+ * Reads the data set <var>objectPath</var> as byte array (of rank 1).
+ *
+ * @param objectPath The name (including path information) of the data set object in the file.
+ * @return The data read from the data set.
+ */
+ public byte[] readAsByteArray(final String objectPath);
+
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
index 92d2b7c09e2..b33c9b3e61a 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNode.java
@@ -24,11 +24,11 @@ import java.util.List;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.hdf5.Hdf5Container;
+import ch.systemsx.cisd.common.hdf5.IHDF5ContainerReader;
import ch.systemsx.cisd.common.io.HDF5DataSetBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
* {@link IHierarchicalContent} implementation for HDF5 container.
@@ -47,7 +47,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
this.hdf5Container = new Hdf5Container(hdf5ContainerFile);
}
- private IHDF5SimpleReader createReader()
+ private IHDF5ContainerReader createReader()
{
return hdf5Container.createSimpleReader();
}
@@ -63,7 +63,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
@Override
public List<IHierarchicalContentNode> doGetChildNodes()
{
- IHDF5SimpleReader reader = createReader();
+ IHDF5ContainerReader reader = createReader();
try
{
List<String> childPaths = reader.getGroupMembers("/");
@@ -82,7 +82,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
/** @return child node with given path relative to this container */
public IHierarchicalContentNode getChildNode(String childPath)
{
- IHDF5SimpleReader reader = createReader();
+ IHDF5ContainerReader reader = createReader();
try
{
return getChildNode(reader, childPath);
@@ -92,7 +92,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
}
}
- private IHierarchicalContentNode getChildNode(IHDF5SimpleReader reader, String childPath)
+ private IHierarchicalContentNode getChildNode(IHDF5ContainerReader reader, String childPath)
{
String fileName = FileUtilities.getFileNameFromRelativePath(childPath);
if (reader.isGroup(childPath))
@@ -204,7 +204,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
@Override
protected List<IHierarchicalContentNode> doGetChildNodes()
{
- IHDF5SimpleReader reader = createReader();
+ IHDF5ContainerReader reader = createReader();
try
{
List<IHierarchicalContentNode> result = new ArrayList<IHierarchicalContentNode>();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
index 49c836356a0..c115b7e20ae 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
@@ -23,7 +23,6 @@ import org.apache.commons.io.FileUtils;
import org.testng.AssertJUnit;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
* Helper class that verifies that a file structure is matched by the HDF5 structure.
@@ -37,7 +36,7 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
private final Hdf5Container container;
- private final IHDF5SimpleReader reader;
+ private final IHDF5ContainerReader reader;
public static IHdf5ReaderClient createVerifierClient(File sourceFolderOrFile,
Hdf5Container container)
@@ -57,7 +56,7 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
this.container = container;
}
- public void runWithSimpleReader(IHDF5SimpleReader reader)
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
{
new FileToHdf5DuplicationVerifier(sourceFolderOrFile, container, reader)
.verifyDuplicate();
@@ -65,7 +64,7 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
}
public FileToHdf5DuplicationVerifier(File sourceFolderOrFile, Hdf5Container container,
- IHDF5SimpleReader reader)
+ IHDF5ContainerReader reader)
{
this.sourceFolderOrFile = sourceFolderOrFile;
this.container = container;
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
index 2fb24a3cdf3..e665da188ac 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
@@ -26,7 +26,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5WriterClient;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
* @author Chandrasekhar Ramakrishnan
@@ -58,7 +57,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
hdf5Content.runReaderClient(new IHdf5ReaderClient()
{
- public void runWithSimpleReader(IHDF5SimpleReader reader)
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
{
byte[] readData = reader.readAsByteArray("/test-bytes");
assertEquals(byteArray, readData);
@@ -84,7 +83,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
hdf5Content.runReaderClient(new IHdf5ReaderClient()
{
- public void runWithSimpleReader(IHDF5SimpleReader reader)
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
{
byte[] readData = reader.readAsByteArray("/test-bytes");
assertEquals(byteArray, readData);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
index 861e747bba5..eebcebfdf0c 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
@@ -24,7 +24,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
* @author Chandrasekhar Ramakrishnan
@@ -130,7 +129,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
container.runReaderClient(new IHdf5ReaderClient()
{
- public void runWithSimpleReader(IHDF5SimpleReader reader)
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
{
FileToHdf5DuplicationVerifier verifier =
new FileToHdf5DuplicationVerifier(sourceFolderOrFile, container, reader);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHdf5StorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHdf5StorageProcessorTest.java
index 9ecfb554a10..2f4de9f9d2f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHdf5StorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHdf5StorageProcessorTest.java
@@ -24,8 +24,8 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.hdf5.FileToHdf5DuplicationVerifier;
import ch.systemsx.cisd.common.hdf5.Hdf5Container;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
+import ch.systemsx.cisd.common.hdf5.IHDF5ContainerReader;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional.IStorageProcessorTransaction;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
* Tests for {@link Hdf5StorageProcessor}.
@@ -72,7 +72,7 @@ abstract class AbstractHdf5StorageProcessorTest extends AbstractFileSystemTestCa
container.runReaderClient(new IHdf5ReaderClient()
{
- public void runWithSimpleReader(IHDF5SimpleReader reader)
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
{
FileToHdf5DuplicationVerifier verifier =
new FileToHdf5DuplicationVerifier(incomingDataSetDirectory, container,
--
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