diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java b/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
deleted file mode 100644
index 1560bfe643061702d41d48b5f837300089aaf7e2..0000000000000000000000000000000000000000
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright 2010 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 ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures;
-import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures;
-import ch.systemsx.cisd.hdf5.IHDF5Writer;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-class CompressingHdf5WriterWrapper implements IHDF5ContainerWriter
-{
- private final IHDF5Writer writer;
-
- // Store this, though I'm not yet using it
- @SuppressWarnings("unused")
- private final HDF5GenericStorageFeatures genericStorageFeatures;
-
- private final HDF5IntStorageFeatures intStorageFeatures;
-
- CompressingHdf5WriterWrapper(Hdf5Container parent, IHDF5Writer writer, boolean compress)
- {
- this.writer = writer;
- if (compress)
- {
- this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_DEFLATE;
- this.intStorageFeatures = HDF5IntStorageFeatures.INT_DEFLATE;
- } else
- {
- this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS;
- this.intStorageFeatures = HDF5IntStorageFeatures.INT_CONTIGUOUS;
- }
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeByteArray(java.lang.String, byte[])
- */
- public void writeByteArray(String objectPath, byte[] data)
- {
- writer.writeByteArray(objectPath, data, intStorageFeatures);
- }
-
- /**
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#close()
- */
- public void close()
- {
- writer.close();
- }
-
-}
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5Container.java
similarity index 69%
rename from common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/HDF5Container.java
index 9f14f263cb84227c61b096be01e64f9173bb47b5..3dd949d3a4777cb070652503286a38e050f24803 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5Container.java
@@ -17,10 +17,9 @@
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;
import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
/**
@@ -30,7 +29,7 @@ import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class Hdf5Container
+public class HDF5Container
{
private final File hdf5Container;
@@ -39,7 +38,7 @@ public class Hdf5Container
*
* @author Chandrasekhar Ramakrishnan
*/
- public static interface IHdf5WriterClient
+ public static interface IHDF5WriterClient
{
/**
* Run code using a writer. Implementations do <b>not</b> need to close the writer.
@@ -52,7 +51,7 @@ public class Hdf5Container
*
* @author Chandrasekhar Ramakrishnan
*/
- public static interface IHdf5ReaderClient
+ public static interface IHDF5ReaderClient
{
/**
* Run code using a reader. Implementations do <b>not</b> need to close the reader.
@@ -66,12 +65,12 @@ public class Hdf5Container
* @param hdf5Container A file designated to be the hdf5 container. The file need not exist --
* it will be created when a writer is accessed.
*/
- public Hdf5Container(File hdf5Container)
+ public HDF5Container(File hdf5Container)
{
this.hdf5Container = hdf5Container;
}
- public File getHdf5File()
+ public File getHDF5File()
{
return hdf5Container;
}
@@ -83,35 +82,7 @@ public class Hdf5Container
*/
public IHDF5ContainerReader createSimpleReader()
{
- 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);
- }
- };
+ return new HDF5ContainerReader(hdf5Container);
}
/**
@@ -123,15 +94,15 @@ public class Hdf5Container
*/
private IHDF5ContainerWriter createSimpleWriter(boolean isContentCompressed)
{
- return new CompressingHdf5WriterWrapper(this, HDF5FactoryProvider.get().open(
- hdf5Container), isContentCompressed);
+ return new HDF5ContainerWriter(this, HDF5FactoryProvider.get().open(hdf5Container),
+ isContentCompressed);
}
/**
* Run a writer client on this Hdf5 container. Ensures that the writer is closed when the client
* finishes running.
*/
- public void runWriterClient(boolean isContentCompressed, IHdf5WriterClient client)
+ public void runWriterClient(boolean isContentCompressed, IHDF5WriterClient client)
{
IHDF5ContainerWriter writer = createSimpleWriter(isContentCompressed);
try
@@ -147,7 +118,7 @@ public class Hdf5Container
* Run a reader client on this Hdf5 container. Ensures that the reader is closed when the client
* finishes running.
*/
- public void runReaderClient(IHdf5ReaderClient client)
+ public void runReaderClient(IHDF5ReaderClient client)
{
IHDF5ContainerReader reader = createSimpleReader();
try
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java
new file mode 100644
index 0000000000000000000000000000000000000000..fe28c5f90f8c41c61ee22b988bd81fec5947eb60
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerReader.java
@@ -0,0 +1,91 @@
+/*
+ * 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.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
+import ch.systemsx.cisd.hdf5.IHDF5Reader;
+import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory;
+
+/**
+ * An implementation of {@link IHDF5ContainerReader}.
+ *
+ * @author Bernd Rinn
+ */
+final class HDF5ContainerReader implements IHDF5ContainerReader
+{
+ private final IHDF5Reader innerReader;
+
+ HDF5ContainerReader(final File hdf5Container)
+ {
+ this.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 void readFromHDF5Container(String objectPath, OutputStream ostream)
+ {
+ final InputStream istream = HDF5IOAdapterFactory.asInputStream(innerReader, objectPath);
+ Exception e = null;
+ try
+ {
+ IOUtils.copyLarge(istream, ostream);
+ } catch (IOException ex)
+ {
+ e = ex;
+ throw new IOExceptionUnchecked(ex);
+ } finally
+ {
+ try
+ {
+ istream.close();
+ } catch (IOException ex)
+ {
+ if (e == null)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerWriter.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerWriter.java
new file mode 100644
index 0000000000000000000000000000000000000000..127cbea8c5c0ff5327e8839944c128752a775ac7
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerWriter.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright 2010 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.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import org.apache.commons.io.IOUtils;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures;
+import ch.systemsx.cisd.hdf5.IHDF5Writer;
+import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory;
+
+/**
+ * An implementation of {@link IHDF5ContainerWriter}.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class HDF5ContainerWriter implements IHDF5ContainerWriter
+{
+ private final static int KB = 1024;
+
+ private final static int MB = 1024 * KB;
+
+ private static final int COMPACT_SIZE_LIMIT = 8 * KB;
+
+ private static final String OPAQUE_TAG_FILE = "FILE";
+
+ final static int BUFFER_SIZE = 10 * MB;
+
+ private final IHDF5Writer writer;
+
+ private final HDF5GenericStorageFeatures genericStorageFeatures;
+
+ HDF5ContainerWriter(HDF5Container parent, IHDF5Writer writer, boolean compress)
+ {
+ this.writer = writer;
+ if (compress)
+ {
+ this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_DEFLATE;
+ } else
+ {
+ this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_CHUNKED;
+ }
+ }
+
+ public void writeToHDF5Container(String objectPath, InputStream istream, long size)
+ throws IOExceptionUnchecked
+ {
+ final OutputStream ostream;
+ if (size <= COMPACT_SIZE_LIMIT)
+ {
+ ostream =
+ HDF5IOAdapterFactory.asOutputStream(writer, objectPath,
+ HDF5GenericStorageFeatures.GENERIC_COMPACT_DELETE, (int) size,
+ OPAQUE_TAG_FILE);
+ } else
+ {
+ ostream =
+ HDF5IOAdapterFactory.asOutputStream(writer, objectPath, genericStorageFeatures,
+ (int) Math.min(size, BUFFER_SIZE), OPAQUE_TAG_FILE);
+ }
+ IOException e = null;
+ try
+ {
+ IOUtils.copyLarge(istream, ostream);
+ } catch (IOException ex)
+ {
+ e = ex;
+ throw new IOExceptionUnchecked(ex);
+ } finally
+ {
+ try
+ {
+ ostream.close();
+ } catch (IOException ex)
+ {
+ if (e == null)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
+ }
+ }
+ }
+
+ /**
+ * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#close()
+ */
+ public void close()
+ {
+ writer.close();
+ }
+
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5.java
similarity index 78%
rename from common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5.java
index b956b85e52081f3bdab6e1cf589004491f78667c..66612878627048b5bae296af756a9b41bf56ac70 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5.java
@@ -17,9 +17,9 @@
package ch.systemsx.cisd.common.hdf5;
import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
-
-import org.apache.commons.io.FileUtils;
+import java.io.InputStream;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class HierarchicalStructureDuplicatorFileToHdf5
+public class HierarchicalStructureDuplicatorFileToHDF5
{
private final File file;
@@ -41,7 +41,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5
*
* @author Chandrasekhar Ramakrishnan
*/
- public static class DuplicatorWriterClient implements Hdf5Container.IHdf5WriterClient
+ public static class DuplicatorWriterClient implements HDF5Container.IHDF5WriterClient
{
private final File file;
@@ -52,7 +52,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5
public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
- HierarchicalStructureDuplicatorFileToHdf5.makeDuplicate(file, writer);
+ HierarchicalStructureDuplicatorFileToHDF5.makeDuplicate(file, writer);
}
}
@@ -68,10 +68,10 @@ public class HierarchicalStructureDuplicatorFileToHdf5
*/
public static void makeDuplicate(File file, IHDF5ContainerWriter writer)
{
- new HierarchicalStructureDuplicatorFileToHdf5(file, writer).makeDuplicate();
+ new HierarchicalStructureDuplicatorFileToHDF5(file, writer).makeDuplicate();
}
- private HierarchicalStructureDuplicatorFileToHdf5(File file, IHDF5ContainerWriter writer)
+ private HierarchicalStructureDuplicatorFileToHDF5(File file, IHDF5ContainerWriter writer)
{
this.file = file;
this.writer = writer;
@@ -97,7 +97,6 @@ public class HierarchicalStructureDuplicatorFileToHdf5
// Mirror the whole file structure
mirrorGroup(file, "/");
}
-
}
private void mirrorGroup(File directory, String groupPath)
@@ -127,13 +126,31 @@ public class HierarchicalStructureDuplicatorFileToHdf5
"Symbolic links are not supported for mirroring in a HDF5 container.");
}
+ InputStream istream = null;
+ IOException e = null;
try
{
- byte[] data = FileUtils.readFileToByteArray(normalFile);
- writer.writeByteArray(hdf5Path, data);
+ istream = new FileInputStream(normalFile);
+ writer.writeToHDF5Container(hdf5Path, istream, normalFile.length());
} catch (IOException ex)
{
+ e = ex;
throw new IOExceptionUnchecked(ex);
+ } finally
+ {
+ if (istream != null)
+ {
+ try
+ {
+ istream.close();
+ } catch (IOException ex)
+ {
+ if (e == null)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
+ }
+ }
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
index 61759ed72a82525169188c85c7aff5bf7fb067d8..9521002511075fa6ce649e47b5eb39b0ebe40553 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerReader.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.common.hdf5;
+import java.io.OutputStream;
import java.util.List;
/**
@@ -52,11 +53,10 @@ public interface IHDF5ContainerReader
public boolean isGroup(final String objectPath);
/**
- * Reads the data set <var>objectPath</var> as byte array (of rank 1).
+ * Reads the data set <var>objectPath</var> into the <var>ostream</var>.
*
* @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);
+ public void readFromHDF5Container(final String objectPath, final OutputStream ostream);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
index 18ec61e7bcfcd4af81e125e6e865ab9740609081..511fd0937faa12cd65255a6b8c8bad7a6cfe85f5 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
@@ -16,21 +16,27 @@
package ch.systemsx.cisd.common.hdf5;
+import java.io.InputStream;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+
/**
* A simple abstraction of the methods needed to write an HDF5 container.
- *
+ *
* @author Bernd Rinn
*/
public interface IHDF5ContainerWriter
{
/**
- * Writes out a <code>byte</code> array (of rank 1). Uses a compact storage layout. Should only
- * be used for small data sets.
+ * Write the given <code>istream</code> to a new data set named <code>objectPath</code>.
*
- * @param objectPath The name (including path information) of the data set object in the file.
- * @param data The data to write. Must not be <code>null</code>.
+ * @param objectPath The path of the data set to write the {@link InputStream} to.
+ * @param istream The stream to get the data from. This method will <i>not</i> close the
+ * <code>istream</code>!</i>
+ * @param size The size of the file represented by the <var>istream</var>.
*/
- public void writeByteArray(final String objectPath, final byte[] data);
+ void writeToHDF5Container(final String objectPath, final InputStream istream, final long size)
+ throws IOExceptionUnchecked;
/**
* Closes this object and the file referenced by this object. This object must not be used after
diff --git a/common/source/java/ch/systemsx/cisd/common/io/HDF5DataSetBasedContent.java b/common/source/java/ch/systemsx/cisd/common/io/HDF5DataSetBasedContent.java
index 116c471dbc0c77584431fbaf420de895102200e2..57339d44bc1ae8d9042ab82e1535052d8f298c0a 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/HDF5DataSetBasedContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HDF5DataSetBasedContent.java
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Reader;
import ch.systemsx.cisd.hdf5.io.HDF5DataSetRandomAccessFile;
+import ch.systemsx.cisd.hdf5.io.HDF5IOAdapterFactory;
/**
* An {@link IContent} implementation based on an HDF5 dataset.
@@ -85,7 +86,7 @@ public class HDF5DataSetBasedContent implements IContent, Closeable
public IRandomAccessFile getReadOnlyRandomAccessFile()
{
final HDF5DataSetRandomAccessFile randomAccessFile =
- HDF5DataSetRandomAccessFile.createForReading(hdf5File, dataSetPath);
+ HDF5IOAdapterFactory.asRandomAccessFileReadOnly(hdf5File, dataSetPath);
randomAccessFiles.add(randomAccessFile);
return randomAccessFile;
}
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 b33c9b3e61a2e4376c41b06174d6de1af0e3d766..a703304c21f813e391fd73ff6ec26efea8a42101 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
@@ -23,7 +23,7 @@ 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.HDF5Container;
import ch.systemsx.cisd.common.hdf5.IHDF5ContainerReader;
import ch.systemsx.cisd.common.io.HDF5DataSetBasedContent;
import ch.systemsx.cisd.common.io.IContent;
@@ -38,13 +38,13 @@ import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentN
public class HDF5ContainerBasedHierarchicalContentNode extends
DefaultFileBasedHierarchicalContentNode
{
- private final Hdf5Container hdf5Container;
+ private final HDF5Container hdf5Container;
public HDF5ContainerBasedHierarchicalContentNode(IHierarchicalContent root,
File hdf5ContainerFile)
{
super(root, hdf5ContainerFile);
- this.hdf5Container = new Hdf5Container(hdf5ContainerFile);
+ this.hdf5Container = new HDF5Container(hdf5ContainerFile);
}
private IHDF5ContainerReader createReader()
@@ -112,7 +112,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
public String toString()
{
return "HDF5ContainerBasedHierarchicalContentNode [root=" + root + ", container="
- + hdf5Container.getHdf5File() + "]";
+ + hdf5Container.getHDF5File() + "]";
}
@Override
@@ -120,7 +120,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
{
final int prime = 31;
int result = 1;
- result = prime * result + hdf5Container.getHdf5File().hashCode();
+ result = prime * result + hdf5Container.getHDF5File().hashCode();
result = prime * result + root.hashCode();
return result;
}
@@ -142,7 +142,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
}
HDF5ContainerBasedHierarchicalContentNode other =
(HDF5ContainerBasedHierarchicalContentNode) obj;
- if (!hdf5Container.getHdf5File().equals(other.hdf5Container.getHdf5File()))
+ if (!hdf5Container.getHDF5File().equals(other.hdf5Container.getHDF5File()))
{
return false;
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHDF5DuplicationVerifier.java
similarity index 77%
rename from common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
rename to common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHDF5DuplicationVerifier.java
index c115b7e20aec2da72a4313f73c439ba47d19b2ce..f1ca3248309292d8293dbc91451f1f4ac46fab03 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHDF5DuplicationVerifier.java
@@ -16,41 +16,42 @@
package ch.systemsx.cisd.common.hdf5;
+import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
import org.testng.AssertJUnit;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
+import ch.systemsx.cisd.common.hdf5.HDF5Container.IHDF5ReaderClient;
/**
* Helper class that verifies that a file structure is matched by the HDF5 structure.
*
* @author Chandrasekhar Ramakrishnan
*/
-public class FileToHdf5DuplicationVerifier extends AssertJUnit
+public class FileToHDF5DuplicationVerifier extends AssertJUnit
{
private final File sourceFolderOrFile;
- private final Hdf5Container container;
+ private final HDF5Container container;
private final IHDF5ContainerReader reader;
- public static IHdf5ReaderClient createVerifierClient(File sourceFolderOrFile,
- Hdf5Container container)
+ public static IHDF5ReaderClient createVerifierClient(File sourceFolderOrFile,
+ HDF5Container container)
{
return new ReaderClient(sourceFolderOrFile, container);
}
- private static class ReaderClient implements IHdf5ReaderClient
+ private static class ReaderClient implements IHDF5ReaderClient
{
private final File sourceFolderOrFile;
- private final Hdf5Container container;
+ private final HDF5Container container;
- private ReaderClient(File sourceFolderOrFile, Hdf5Container container)
+ private ReaderClient(File sourceFolderOrFile, HDF5Container container)
{
this.sourceFolderOrFile = sourceFolderOrFile;
this.container = container;
@@ -58,12 +59,12 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
public void runWithSimpleReader(IHDF5ContainerReader reader)
{
- new FileToHdf5DuplicationVerifier(sourceFolderOrFile, container, reader)
+ new FileToHDF5DuplicationVerifier(sourceFolderOrFile, container, reader)
.verifyDuplicate();
}
}
- public FileToHdf5DuplicationVerifier(File sourceFolderOrFile, Hdf5Container container,
+ public FileToHDF5DuplicationVerifier(File sourceFolderOrFile, HDF5Container container,
IHDF5ContainerReader reader)
{
this.sourceFolderOrFile = sourceFolderOrFile;
@@ -73,7 +74,7 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
public void verifyDuplicate()
{
- assertTrue(container.getHdf5File().length() > 0);
+ assertTrue(container.getHDF5File().length() > 0);
if (sourceFolderOrFile.isFile())
{
@@ -112,7 +113,9 @@ public class FileToHdf5DuplicationVerifier extends AssertJUnit
try
{
byte[] fileContent = FileUtils.readFileToByteArray(file);
- byte[] content = reader.readAsByteArray(hdf5Path);
+ final ByteArrayOutputStream ostream = new ByteArrayOutputStream();
+ reader.readFromHDF5Container(hdf5Path, ostream);
+ byte[] content = ostream.toByteArray();
assertEquals(file.getAbsolutePath() + " does not equal " + hdf5Path, fileContent,
content);
} catch (IOException ex)
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0eb7529da4ae7d305bd8a0f92962bc1ef42493df
--- /dev/null
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTest.java
@@ -0,0 +1,182 @@
+/*
+ * Copyright 2010 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.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+
+import org.testng.annotations.BeforeMethod;
+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;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class HDF5ContainerTest extends AbstractFileSystemTestCase
+{
+ private final static int KB = 1024;
+
+ @Override
+ @BeforeMethod
+ public void setUp() throws IOException
+ {
+ super.setUp();
+ }
+
+ @Test
+ public void testReadWriteUncompressedLarge()
+ {
+ File hdf5File = new File(workingDirectory, "testLarge.h5");
+ hdf5File.delete();
+ HDF5Container hdf5Content = new HDF5Container(hdf5File);
+ final byte[] byteArray = createByteArray(1500 * KB);
+
+ hdf5Content.runWriterClient(false, new IHDF5WriterClient()
+ {
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
+ {
+ writer.writeToHDF5Container("/test-bytes", new ByteArrayInputStream(byteArray),
+ byteArray.length);
+ }
+ });
+
+ hdf5Content.runReaderClient(new IHDF5ReaderClient()
+ {
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
+ {
+ final ByteArrayOutputStream ostream = new ByteArrayOutputStream();
+ reader.readFromHDF5Container("/test-bytes", ostream);
+ byte[] readData = ostream.toByteArray();
+ assertEquals(byteArray, readData);
+ }
+ });
+ }
+
+ @Test
+ public void testReadWriteUncompressed()
+ {
+ File hdf5File = new File(workingDirectory, "test.h5");
+ hdf5File.delete();
+ HDF5Container hdf5Content = new HDF5Container(hdf5File);
+ final byte[] byteArray = createByteArray();
+
+ hdf5Content.runWriterClient(false, new IHDF5WriterClient()
+ {
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
+ {
+ writer.writeToHDF5Container("/test-bytes", new ByteArrayInputStream(byteArray),
+ byteArray.length);
+ }
+ });
+
+ hdf5Content.runReaderClient(new IHDF5ReaderClient()
+ {
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
+ {
+ final ByteArrayOutputStream ostream = new ByteArrayOutputStream();
+ reader.readFromHDF5Container("/test-bytes", ostream);
+ byte[] readData = ostream.toByteArray();
+ assertEquals(byteArray, readData);
+ }
+ });
+ }
+
+ @Test
+ public void testReadWriteCompressed()
+ {
+ File hdf5File = new File(workingDirectory, "test.h5");
+ hdf5File.delete();
+ HDF5Container hdf5Content = new HDF5Container(hdf5File);
+ final byte[] byteArray = createByteArray();
+
+ hdf5Content.runWriterClient(true, new IHDF5WriterClient()
+ {
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
+ {
+ writer.writeToHDF5Container("/test-bytes", new ByteArrayInputStream(byteArray),
+ byteArray.length);
+ }
+ });
+
+ hdf5Content.runReaderClient(new IHDF5ReaderClient()
+ {
+ public void runWithSimpleReader(IHDF5ContainerReader reader)
+ {
+ final ByteArrayOutputStream ostream = new ByteArrayOutputStream();
+ reader.readFromHDF5Container("/test-bytes", ostream);
+ byte[] readData = ostream.toByteArray();
+ assertEquals(byteArray, readData);
+ }
+ });
+ }
+
+ @Test
+ public void testSizeComparison()
+ {
+ final byte[] byteArray = createByteArray();
+
+ File hdf5FileUncompressed = new File(workingDirectory, "test-uncompressed.h5");
+ hdf5FileUncompressed.delete();
+ HDF5Container hdf5ContentUncompressed = new HDF5Container(hdf5FileUncompressed);
+ hdf5ContentUncompressed.runWriterClient(false, new IHDF5WriterClient()
+ {
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
+ {
+ writer.writeToHDF5Container("/test-bytes", new ByteArrayInputStream(byteArray),
+ byteArray.length);
+ }
+ });
+
+ File hdf5FileCompressed = new File(workingDirectory, "test-compressed.h5");
+ HDF5Container hdf5ContentCompressed = new HDF5Container(hdf5FileCompressed);
+ hdf5ContentCompressed.runWriterClient(true, new IHDF5WriterClient()
+ {
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
+ {
+ writer.writeToHDF5Container("/test-bytes", new ByteArrayInputStream(byteArray),
+ byteArray.length);
+ }
+ });
+
+ long uncompressedLength = hdf5FileUncompressed.length();
+ long compressedLength = hdf5FileCompressed.length();
+
+ assertTrue("" + uncompressedLength + " <= " + compressedLength,
+ uncompressedLength > compressedLength);
+ }
+
+ private byte[] createByteArray()
+ {
+ return createByteArray(16 * KB);
+ }
+
+ private byte[] createByteArray(int numberOfBytes)
+ {
+ ByteArrayOutputStream bos = new ByteArrayOutputStream(numberOfBytes);
+ for (int i = 0; i < numberOfBytes; ++i)
+ {
+ bos.write(1);
+ }
+ return bos.toByteArray();
+ }
+
+}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
deleted file mode 100644
index e665da188ac6a06b15b6e2c29cd79d80f12d393f..0000000000000000000000000000000000000000
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*
- * Copyright 2010 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.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-
-import org.testng.annotations.BeforeMethod;
-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;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class Hdf5ContainerTest extends AbstractFileSystemTestCase
-{
- @Override
- @BeforeMethod
- public void setUp() throws IOException
- {
- super.setUp();
- }
-
- @Test
- public void testReadWriteUncompressed()
- {
- File hdf5File = new File(workingDirectory, "test.h5");
- Hdf5Container hdf5Content = new Hdf5Container(hdf5File);
- final byte[] byteArray = createByteArray();
-
- hdf5Content.runWriterClient(false, new IHdf5WriterClient()
- {
- public void runWithSimpleWriter(IHDF5ContainerWriter writer)
- {
- writer.writeByteArray("/test-bytes", byteArray);
-
- }
- });
-
- hdf5Content.runReaderClient(new IHdf5ReaderClient()
- {
- public void runWithSimpleReader(IHDF5ContainerReader reader)
- {
- byte[] readData = reader.readAsByteArray("/test-bytes");
- assertEquals(byteArray, readData);
- }
- });
- }
-
- @Test
- public void testReadWriteCompressed()
- {
- File hdf5File = new File(workingDirectory, "test.h5");
- Hdf5Container hdf5Content = new Hdf5Container(hdf5File);
- final byte[] byteArray = createByteArray();
-
- hdf5Content.runWriterClient(true, new IHdf5WriterClient()
- {
- public void runWithSimpleWriter(IHDF5ContainerWriter writer)
- {
- writer.writeByteArray("/test-bytes", byteArray);
-
- }
- });
-
- hdf5Content.runReaderClient(new IHdf5ReaderClient()
- {
- public void runWithSimpleReader(IHDF5ContainerReader reader)
- {
- byte[] readData = reader.readAsByteArray("/test-bytes");
- assertEquals(byteArray, readData);
- }
- });
- }
-
- @Test
- public void testSizeComparison()
- {
- final byte[] byteArray = createByteArray();
-
- File hdf5FileUncompressed = new File(workingDirectory, "test-uncompressed.h5");
- Hdf5Container hdf5ContentUncompressed = new Hdf5Container(hdf5FileUncompressed);
- hdf5ContentUncompressed.runWriterClient(false, new IHdf5WriterClient()
- {
- public void runWithSimpleWriter(IHDF5ContainerWriter writer)
- {
- writer.writeByteArray("/test-bytes", byteArray);
-
- }
- });
-
- File hdf5FileCompressed = new File(workingDirectory, "test-compressed.h5");
- Hdf5Container hdf5ContentCompressed = new Hdf5Container(hdf5FileCompressed);
- hdf5ContentCompressed.runWriterClient(true, new IHdf5WriterClient()
- {
- public void runWithSimpleWriter(IHDF5ContainerWriter writer)
- {
- writer.writeByteArray("/test-bytes", byteArray);
-
- }
- });
-
- long uncompressedLength = hdf5FileUncompressed.length();
- long compressedLength = hdf5FileCompressed.length();
-
- assertTrue("" + uncompressedLength + " <= " + compressedLength,
- uncompressedLength > compressedLength);
- }
-
- private byte[] createByteArray()
- {
- int numberOfBytes = 1024 * 1024;
- ByteArrayOutputStream bos = new ByteArrayOutputStream(1024);
- for (int i = 0; i < numberOfBytes; ++i)
- {
- bos.write(1);
- }
- return bos.toByteArray();
- }
-
-}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5Test
similarity index 82%
rename from common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
rename to common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5Test
index eebcebfdf0cc532b3ab502c48394793f9bc5ec08..99147a18575b749c6dc6497559eab8ca01d6597c 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHDF5Test
@@ -23,16 +23,16 @@ import org.testng.annotations.BeforeMethod;
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.IHdf5ReaderClient;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileSystemTestCase
+public class HierarchicalStructureDuplicatorFileToHDF5Test extends AbstractFileSystemTestCase
{
private File containerFile;
- private Hdf5Container container;
+ private HDF5Container container;
@BeforeMethod
@Override
@@ -41,7 +41,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
super.setUp();
containerFile = new File(workingDirectory, "test-container.h5");
- container = new Hdf5Container(containerFile);
+ container = new HDF5Container(containerFile);
}
/**
@@ -53,7 +53,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFolder = getTestData("basic-file-structure");
container.runWriterClient(false,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
verifyDuplicate(sourceFolder);
}
@@ -66,7 +66,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFolder = getTestData("basic-file-structure");
container.runWriterClient(true,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
verifyDuplicate(sourceFolder);
}
@@ -78,7 +78,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFolder = getTestData("basic-file-structure/file0.txt");
container.runWriterClient(true,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
verifyDuplicate(sourceFolder);
}
@@ -90,11 +90,11 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFile = getTestData("basic-file-structure/file0.txt");
container.runWriterClient(true,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFile));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFile));
File sourceFolder = getTestData("basic-file-structure");
container.runWriterClient(true,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
verifyDuplicate(sourceFolder);
}
@@ -108,7 +108,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFolder = getTestData("file-structure-with-links");
container.runWriterClient(false,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
}
@Test(expectedExceptions =
@@ -117,7 +117,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
File sourceFolder = getTestData("does-not-exist");
container.runWriterClient(false,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
}
private File getTestData(String folderOrFile)
@@ -131,8 +131,8 @@ public class HierarchicalStructureDuplicatorFileToHdf5Test extends AbstractFileS
{
public void runWithSimpleReader(IHDF5ContainerReader reader)
{
- FileToHdf5DuplicationVerifier verifier =
- new FileToHdf5DuplicationVerifier(sourceFolderOrFile, container, reader);
+ FileToHDF5DuplicationVerifier verifier =
+ new FileToHDF5DuplicationVerifier(sourceFolderOrFile, container, reader);
verifier.verifyDuplicate();
}
});
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
index 71233719c9a2dafb169d6b6075e5b778310383a2..f1c3c81694d907812a0bea5d97d1cc179e5a3f18 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/DefaultFileBasedHierarchicalContentTest.java
@@ -34,10 +34,8 @@ import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container;
-import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHdf5;
-import ch.systemsx.cisd.common.io.hierarchical_content.DefaultFileBasedHierarchicalContent;
-import ch.systemsx.cisd.common.io.hierarchical_content.IHierarchicalContentFactory;
+import ch.systemsx.cisd.common.hdf5.HDF5Container;
+import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHDF5;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.common.utilities.HierarchicalContentUtils;
import ch.systemsx.cisd.common.utilities.IDelegatedAction;
@@ -496,7 +494,10 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
// file info access
assertEquals("File: " + expectedFile, expectedFile.getName(), fileNode.getName());
assertEquals("File: " + expectedFile, expectedFile.length(), fileNode.getFileLength());
- assertEquals("File: " + expectedFile, expectedFile.lastModified(), fileNode.getLastModified());
+ assertTrue("File: " + expectedFile,
+ fileNode.getLastModified() >= expectedFile.lastModified());
+ assertTrue("File: " + expectedFile,
+ fileNode.getLastModified() - expectedFile.lastModified() <= 1000);
final String expectedFileData = expectedFile.getName() + " data";
// check random access to file content
@@ -513,9 +514,9 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
/** creates HDF5 container file with <var>containedDir</var> content */
private static void createHDF5Container(File containerFile, File containedDir)
{
- Hdf5Container container = new Hdf5Container(containerFile);
+ HDF5Container container = new HDF5Container(containerFile);
container.runWriterClient(true,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(containedDir));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(containedDir));
}
private static IHierarchicalContentNode createDummyFileBasedRootNode(final File root)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
similarity index 87%
rename from datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessor.java
rename to datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
index c69a9714a87c6468b3539f9b98ce54f2a351f1fe..bf565e1b5366d80e6146111e4b9dda4de59e4eeb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
@@ -20,8 +20,8 @@ import java.io.File;
import java.util.Properties;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container;
-import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHdf5;
+import ch.systemsx.cisd.common.hdf5.HDF5Container;
+import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHDF5;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
@@ -35,7 +35,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class Hdf5StorageProcessor extends AbstractStorageProcessor
+public class HDF5StorageProcessor extends AbstractStorageProcessor
{
private static final String HDF5_CONTAINER_FILE_NAME = "container.h5";
@@ -48,7 +48,7 @@ public class Hdf5StorageProcessor extends AbstractStorageProcessor
*
* @param properties
*/
- public Hdf5StorageProcessor(Properties properties)
+ public HDF5StorageProcessor(Properties properties)
{
super(properties);
isDataCompressed = PropertyUtils.getBoolean(properties, COMPRESS_DATA_PROPERTY, false);
@@ -75,9 +75,9 @@ public class Hdf5StorageProcessor extends AbstractStorageProcessor
{
checkParameters(incomingDataSetDirectory, rootDir);
- Hdf5Container container = getHdf5Container(rootDir);
+ HDF5Container container = getHdf5Container(rootDir);
container.runWriterClient(isDataCompressed,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(
incomingDataSetDirectory));
fileBeingProcessed = incomingDataSetDirectory;
@@ -88,7 +88,7 @@ public class Hdf5StorageProcessor extends AbstractStorageProcessor
{
// Just delete the file in the store -- no need to touch the incomingDataSet
// because we haven't done anything to it.
- File storedFile = getHdf5ContainerFile(storedDirectory);
+ File storedFile = getHDF5ContainerFile(storedDirectory);
storedFile.delete();
fileBeingProcessed = null;
@@ -123,19 +123,19 @@ public class Hdf5StorageProcessor extends AbstractStorageProcessor
*
* @return A file with HDF5 content
*/
- public static File getHdf5ContainerFile(final File storedDataDirectory)
+ public static File getHDF5ContainerFile(final File storedDataDirectory)
{
return new File(storedDataDirectory, HDF5_CONTAINER_FILE_NAME);
}
/**
- * Given a directory in the store, return an {@link Hdf5Container} object wrapping the file.
+ * Given a directory in the store, return an {@link HDF5Container} object wrapping the file.
*
- * @return An Hdf5Container object.
+ * @return An HDF5Container object.
*/
- public static Hdf5Container getHdf5Container(final File storedDataDirectory)
+ public static HDF5Container getHdf5Container(final File storedDataDirectory)
{
- return new Hdf5Container(getHdf5ContainerFile(storedDataDirectory));
+ return new HDF5Container(getHDF5ContainerFile(storedDataDirectory));
}
}
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
similarity index 81%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHdf5StorageProcessorTest.java
rename to datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHDF5StorageProcessorTest.java
index 2f4de9f9d2f94bfad6b63ec32f48666d54cbef1f..1fd4f29f4541baebf295c5eca20f076f756433ff 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
@@ -21,28 +21,28 @@ import java.util.Properties;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
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.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;
/**
- * Tests for {@link Hdf5StorageProcessor}.
+ * Tests for {@link HDF5StorageProcessor}.
*
* @author Chandrasekhar Ramakrishnan
*/
-abstract class AbstractHdf5StorageProcessorTest extends AbstractFileSystemTestCase
+abstract class AbstractHDF5StorageProcessorTest extends AbstractFileSystemTestCase
{
- protected final Hdf5StorageProcessor storageProcessor;
+ protected final HDF5StorageProcessor storageProcessor;
protected final IStorageProcessorTransaction transaction;
- protected AbstractHdf5StorageProcessorTest(Properties properties)
+ protected AbstractHDF5StorageProcessorTest(Properties properties)
{
super();
- storageProcessor = new Hdf5StorageProcessor(properties);
+ storageProcessor = new HDF5StorageProcessor(properties);
storageProcessor.setStoreRootDirectory(workingDirectory);
transaction = storageProcessor.createTransaction();
}
@@ -63,19 +63,19 @@ abstract class AbstractHdf5StorageProcessorTest extends AbstractFileSystemTestCa
assertTrue(incomingDataSetDirectory.exists());
assertTrue(transaction.getStoredDataDirectory().isDirectory());
- File hdf5ContainerFile = Hdf5StorageProcessor.getHdf5ContainerFile(rootDir);
+ File hdf5ContainerFile = HDF5StorageProcessor.getHDF5ContainerFile(rootDir);
assertTrue(hdf5ContainerFile.exists());
assertTrue(hdf5ContainerFile.isFile());
- final Hdf5Container container = Hdf5StorageProcessor.getHdf5Container(rootDir);
+ final HDF5Container container = HDF5StorageProcessor.getHdf5Container(rootDir);
- container.runReaderClient(new IHdf5ReaderClient()
+ container.runReaderClient(new IHDF5ReaderClient()
{
public void runWithSimpleReader(IHDF5ContainerReader reader)
{
- FileToHdf5DuplicationVerifier verifier =
- new FileToHdf5DuplicationVerifier(incomingDataSetDirectory, container,
+ FileToHDF5DuplicationVerifier verifier =
+ new FileToHDF5DuplicationVerifier(incomingDataSetDirectory, container,
reader);
verifier.verifyDuplicate();
}
@@ -96,7 +96,7 @@ abstract class AbstractHdf5StorageProcessorTest extends AbstractFileSystemTestCa
assertTrue(incomingDataSetDirectory.exists());
assertTrue(transaction.getStoredDataDirectory().isDirectory());
- File hdf5ContainerFile = Hdf5StorageProcessor.getHdf5ContainerFile(rootDir);
+ File hdf5ContainerFile = HDF5StorageProcessor.getHDF5ContainerFile(rootDir);
assertTrue(hdf5ContainerFile.exists());
assertTrue(hdf5ContainerFile.isFile());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorNoCompressionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorNoCompressionTest.java
similarity index 90%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorNoCompressionTest.java
rename to datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorNoCompressionTest.java
index 2eda6e7f2d8890628b0824aa777d25b02d22f99f..fc8a957bc6e83006fe960e534e8c5836cf6b42e5 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorNoCompressionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorNoCompressionTest.java
@@ -24,10 +24,10 @@ import org.testng.annotations.Test;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class Hdf5StorageProcessorNoCompressionTest extends AbstractHdf5StorageProcessorTest
+public class HDF5StorageProcessorNoCompressionTest extends AbstractHDF5StorageProcessorTest
{
- public Hdf5StorageProcessorNoCompressionTest()
+ public HDF5StorageProcessorNoCompressionTest()
{
super(createProperties());
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorWithCompressionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorWithCompressionTest.java
similarity index 87%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorWithCompressionTest.java
rename to datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorWithCompressionTest.java
index fbb100dee2144e84483db3d07c25f02b7482e971..41b226d46172dfd90dcd6161f447efb93913661e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5StorageProcessorWithCompressionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessorWithCompressionTest.java
@@ -24,10 +24,10 @@ import org.testng.annotations.Test;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class Hdf5StorageProcessorWithCompressionTest extends AbstractHdf5StorageProcessorTest
+public class HDF5StorageProcessorWithCompressionTest extends AbstractHDF5StorageProcessorTest
{
- public Hdf5StorageProcessorWithCompressionTest()
+ public HDF5StorageProcessorWithCompressionTest()
{
super(createProperties());
}
@@ -35,7 +35,7 @@ public class Hdf5StorageProcessorWithCompressionTest extends AbstractHdf5Storage
private static Properties createProperties()
{
Properties props = new Properties();
- props.setProperty(Hdf5StorageProcessor.COMPRESS_DATA_PROPERTY, "true");
+ props.setProperty(HDF5StorageProcessor.COMPRESS_DATA_PROPERTY, "true");
return props;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index d3bfa4e9646e82544360e407581931b6c46142af..056a87cbb70d4361af6856cfd15e087b646a6da6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.filesystem.SoftLinkMaker;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container;
-import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHdf5;
+import ch.systemsx.cisd.common.hdf5.HDF5Container;
+import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHDF5;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
@@ -510,9 +510,9 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
private static void saveInHdf5(File sourceFolder, File hdf5DestinationFile,
boolean compressFiles)
{
- Hdf5Container container = new Hdf5Container(hdf5DestinationFile);
+ HDF5Container container = new HDF5Container(hdf5DestinationFile);
container.runWriterClient(compressFiles,
- new HierarchicalStructureDuplicatorFileToHdf5.DuplicatorWriterClient(sourceFolder));
+ new HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient(sourceFolder));
}
private File moveToStore(File incomingDataSetDirectory, File rootDirectory)
@@ -541,7 +541,7 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
imageStorageConfiguraton.getThumbnailsStorageFormat();
if (thumbnailsStorageFormatOrNull != null)
{
- Hdf5Container container = new Hdf5Container(thumbnailsFile);
+ HDF5Container container = new HDF5Container(thumbnailsFile);
ImageLibraryInfo imageLibrary = imageStorageConfiguraton.tryGetImageLibrary();
Hdf5ThumbnailGenerator thumbnailsGenerator =
new Hdf5ThumbnailGenerator(plateImages, imagesInStoreFolder,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
index e5a14d2c714a9e510d73b7c30a2fd3c6cbab8f8d..7f9bbeb72d7a1068ad3ec815a72c210d3c53806d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
import java.awt.image.BufferedImage;
+import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
@@ -35,7 +36,7 @@ import ch.systemsx.cisd.common.concurrent.FailureRecord;
import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5WriterClient;
+import ch.systemsx.cisd.common.hdf5.HDF5Container.IHDF5WriterClient;
import ch.systemsx.cisd.common.hdf5.IHDF5ContainerWriter;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -52,7 +53,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
*
* @author Chandrasekhar Ramakrishnan
*/
-class Hdf5ThumbnailGenerator implements IHdf5WriterClient
+class Hdf5ThumbnailGenerator implements IHDF5WriterClient
{
private static final File convertUtilityOrNull = OSUtilities.findExecutable("convert");
@@ -117,7 +118,8 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
}
synchronized (writer)
{
- writer.writeByteArray(thumbnailPath, byteArray);
+ writer.writeToHDF5Container(thumbnailPath, new ByteArrayInputStream(byteArray),
+ byteArray.length);
}
} catch (IOException ex)
{