From 6b6f53eafb9df4d6f2ab1b1c7940e8fe8a20a487 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 5 Aug 2011 08:59:09 +0000
Subject: [PATCH] refactor Hdf5Container for minimal interface (writer)
SVN: 22348
---
.../hdf5/CompressingHdf5WriterWrapper.java | 479 +-----------------
.../cisd/common/hdf5/Hdf5Container.java | 16 +-
...archicalStructureDuplicatorFileToHdf5.java | 9 +-
.../common/hdf5/IHDF5ContainerWriter.java | 40 ++
.../cisd/common/hdf5/Hdf5ContainerTest.java | 10 +-
.../dss/etl/Hdf5ThumbnailGenerator.java | 8 +-
6 files changed, 72 insertions(+), 490 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java b/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
index 8335139b687..1560bfe6430 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
@@ -16,23 +16,14 @@
package ch.systemsx.cisd.common.hdf5;
-import java.util.BitSet;
-import java.util.Date;
-import java.util.List;
-
-import ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException;
-import ncsa.hdf.hdf5lib.exceptions.HDF5JavaException;
-
-import ch.systemsx.cisd.hdf5.HDF5DataSetInformation;
import ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures;
import ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
/**
* @author Chandrasekhar Ramakrishnan
*/
-class CompressingHdf5WriterWrapper implements IHDF5SimpleWriter
+class CompressingHdf5WriterWrapper implements IHDF5ContainerWriter
{
private final IHDF5Writer writer;
@@ -41,86 +32,19 @@ class CompressingHdf5WriterWrapper implements IHDF5SimpleWriter
private final HDF5GenericStorageFeatures genericStorageFeatures;
private final HDF5IntStorageFeatures intStorageFeatures;
-
- CompressingHdf5WriterWrapper(Hdf5Container parent, IHDF5Writer writer)
+
+ CompressingHdf5WriterWrapper(Hdf5Container parent, IHDF5Writer writer, boolean compress)
{
this.writer = writer;
- this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_DEFLATE;
- this.intStorageFeatures = HDF5IntStorageFeatures.INT_DEFLATE;
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#delete(java.lang.String)
- */
- public void delete(String objectPath)
- {
- writer.delete(objectPath);
- }
-
- /**
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#close()
- */
- public void close()
- {
- writer.close();
- }
-
- /**
- * @param objectPath
- * @param value
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeBoolean(java.lang.String, boolean)
- */
- public void writeBoolean(String objectPath, boolean value)
- {
- writer.writeBoolean(objectPath, value);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#exists(java.lang.String)
- */
- public boolean exists(String objectPath)
- {
- return writer.exists(objectPath);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#isGroup(java.lang.String)
- */
- public boolean isGroup(String objectPath)
- {
- return writer.isGroup(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeBitField(java.lang.String,
- * java.util.BitSet)
- */
- public void writeBitField(String objectPath, BitSet data)
- {
- writer.writeBitField(objectPath, data);
- }
-
- /**
- * @param dataSetPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#getDataSetInformation(java.lang.String)
- */
- public HDF5DataSetInformation getDataSetInformation(String dataSetPath)
- {
- return writer.getDataSetInformation(dataSetPath);
- }
-
- /**
- * @param groupPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#getGroupMembers(java.lang.String)
- */
- public List<String> getGroupMembers(String groupPath)
- {
- return writer.getGroupMembers(groupPath);
+ if (compress)
+ {
+ this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_DEFLATE;
+ this.intStorageFeatures = HDF5IntStorageFeatures.INT_DEFLATE;
+ } else
+ {
+ this.genericStorageFeatures = HDF5GenericStorageFeatures.GENERIC_CONTIGUOUS;
+ this.intStorageFeatures = HDF5IntStorageFeatures.INT_CONTIGUOUS;
+ }
}
/**
@@ -134,384 +58,11 @@ class CompressingHdf5WriterWrapper implements IHDF5SimpleWriter
}
/**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readAsByteArray(java.lang.String)
- */
- public byte[] readAsByteArray(String objectPath)
- {
- return writer.readAsByteArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @param value
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeInt(java.lang.String, int)
- */
- public void writeInt(String objectPath, int value)
- {
- writer.writeInt(objectPath, value);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readBoolean(java.lang.String)
- */
- public boolean readBoolean(String objectPath) throws HDF5JavaException
- {
- return writer.readBoolean(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeIntArray(java.lang.String, int[])
- */
- public void writeIntArray(String objectPath, int[] data)
- {
- writer.writeIntArray(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @throws HDF5DatatypeInterfaceException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readBitField(java.lang.String)
- */
- public BitSet readBitField(String objectPath) throws HDF5DatatypeInterfaceException
- {
- return writer.readBitField(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeIntMatrix(java.lang.String, int[][])
- */
- public void writeIntMatrix(String objectPath, int[][] data)
- {
- writer.writeIntMatrix(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @param value
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeLong(java.lang.String, long)
- */
- public void writeLong(String objectPath, long value)
- {
- writer.writeLong(objectPath, value);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeLongArray(java.lang.String, long[])
- */
- public void writeLongArray(String objectPath, long[] data)
- {
- writer.writeLongArray(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readInt(java.lang.String)
- */
- public int readInt(String objectPath)
- {
- return writer.readInt(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeLongMatrix(java.lang.String, long[][])
- */
- public void writeLongMatrix(String objectPath, long[][] data)
- {
- writer.writeLongMatrix(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readIntArray(java.lang.String)
- */
- public int[] readIntArray(String objectPath)
- {
- return writer.readIntArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @param value
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeFloat(java.lang.String, float)
- */
- public void writeFloat(String objectPath, float value)
- {
- writer.writeFloat(objectPath, value);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readIntMatrix(java.lang.String)
- */
- public int[][] readIntMatrix(String objectPath)
- {
- return writer.readIntMatrix(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeFloatArray(java.lang.String, float[])
- */
- public void writeFloatArray(String objectPath, float[] data)
- {
- writer.writeFloatArray(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readLong(java.lang.String)
- */
- public long readLong(String objectPath)
- {
- return writer.readLong(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeFloatMatrix(java.lang.String, float[][])
- */
- public void writeFloatMatrix(String objectPath, float[][] data)
- {
- writer.writeFloatMatrix(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readLongArray(java.lang.String)
- */
- public long[] readLongArray(String objectPath)
- {
- return writer.readLongArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @param value
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeDouble(java.lang.String, double)
- */
- public void writeDouble(String objectPath, double value)
- {
- writer.writeDouble(objectPath, value);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readLongMatrix(java.lang.String)
- */
- public long[][] readLongMatrix(String objectPath)
- {
- return writer.readLongMatrix(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeDoubleArray(java.lang.String, double[])
- */
- public void writeDoubleArray(String objectPath, double[] data)
- {
- writer.writeDoubleArray(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readFloat(java.lang.String)
- */
- public float readFloat(String objectPath)
- {
- return writer.readFloat(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeDoubleMatrix(java.lang.String, double[][])
- */
- public void writeDoubleMatrix(String objectPath, double[][] data)
- {
- writer.writeDoubleMatrix(objectPath, data);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readFloatArray(java.lang.String)
- */
- public float[] readFloatArray(String objectPath)
- {
- return writer.readFloatArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @param date
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeDate(java.lang.String, java.util.Date)
- */
- public void writeDate(String objectPath, Date date)
- {
- writer.writeDate(objectPath, date);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readFloatMatrix(java.lang.String)
- */
- public float[][] readFloatMatrix(String objectPath)
- {
- return writer.readFloatMatrix(objectPath);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readDouble(java.lang.String)
- */
- public double readDouble(String objectPath)
- {
- return writer.readDouble(objectPath);
- }
-
- /**
- * @param objectPath
- * @param dates
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeDateArray(java.lang.String,
- * java.util.Date[])
- */
- public void writeDateArray(String objectPath, Date[] dates)
- {
- writer.writeDateArray(objectPath, dates);
- }
-
- /**
- * @param objectPath
- * @param timeDuration
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeTimeDuration(java.lang.String, long)
- */
- public void writeTimeDuration(String objectPath, long timeDuration)
- {
- writer.writeTimeDuration(objectPath, timeDuration);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readDoubleArray(java.lang.String)
- */
- public double[] readDoubleArray(String objectPath)
- {
- return writer.readDoubleArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @param timeDurations
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeTimeDurationArray(java.lang.String, long[])
- */
- public void writeTimeDurationArray(String objectPath, long[] timeDurations)
- {
- writer.writeTimeDurationArray(objectPath, timeDurations);
- }
-
- /**
- * @param objectPath
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readDoubleMatrix(java.lang.String)
- */
- public double[][] readDoubleMatrix(String objectPath)
- {
- return writer.readDoubleMatrix(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @param maxLength
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeString(java.lang.String, java.lang.String,
- * int)
- */
- public void writeString(String objectPath, String data, int maxLength)
- {
- writer.writeString(objectPath, data, maxLength);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readDate(java.lang.String)
- */
- public Date readDate(String objectPath) throws HDF5JavaException
- {
- return writer.readDate(objectPath);
- }
-
- /**
- * @param objectPath
- * @param data
- * @param maxLength
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleWriter#writeStringArray(java.lang.String,
- * java.lang.String[], int)
- */
- public void writeStringArray(String objectPath, String[] data, int maxLength)
- {
- writer.writeStringArray(objectPath, data, maxLength);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readDateArray(java.lang.String)
- */
- public Date[] readDateArray(String objectPath) throws HDF5JavaException
- {
- return writer.readDateArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readTimeDuration(java.lang.String)
- */
- public long readTimeDuration(String objectPath) throws HDF5JavaException
- {
- return writer.readTimeDuration(objectPath);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readTimeDurationArray(java.lang.String)
- */
- public long[] readTimeDurationArray(String objectPath) throws HDF5JavaException
- {
- return writer.readTimeDurationArray(objectPath);
- }
-
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readString(java.lang.String)
+ * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#close()
*/
- public String readString(String objectPath) throws HDF5JavaException
+ public void close()
{
- return writer.readString(objectPath);
+ writer.close();
}
- /**
- * @param objectPath
- * @throws HDF5JavaException
- * @see ch.systemsx.cisd.hdf5.IHDF5SimpleReader#readStringArray(java.lang.String)
- */
- public String[] readStringArray(String objectPath) throws HDF5JavaException
- {
- return writer.readStringArray(objectPath);
- }
}
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 c61c2a5db56..4787e44af6e 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
@@ -43,7 +43,7 @@ public class Hdf5Container
/**
* Run code using a writer. Implementations do <b>not</b> need to close the writer.
*/
- public void runWithSimpleWriter(IHDF5SimpleWriter writer);
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer);
}
/**
@@ -92,16 +92,10 @@ public class Hdf5Container
* @param isContentCompressed Pass in true to have byte arrays transparently compressed.
* @return A new IHDF5SimpleWriter
*/
- private IHDF5SimpleWriter createSimpleWriter(boolean isContentCompressed)
+ private IHDF5ContainerWriter createSimpleWriter(boolean isContentCompressed)
{
- if (isContentCompressed)
- {
- return new CompressingHdf5WriterWrapper(this, HDF5FactoryProvider.get().open(
- hdf5Container));
- } else
- {
- return HDF5FactoryProvider.get().open(hdf5Container);
- }
+ return new CompressingHdf5WriterWrapper(this, HDF5FactoryProvider.get().open(
+ hdf5Container), isContentCompressed);
}
/**
@@ -110,7 +104,7 @@ public class Hdf5Container
*/
public void runWriterClient(boolean isContentCompressed, IHdf5WriterClient client)
{
- IHDF5SimpleWriter writer = createSimpleWriter(isContentCompressed);
+ IHDF5ContainerWriter writer = createSimpleWriter(isContentCompressed);
try
{
client.runWithSimpleWriter(writer);
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
index 130b73b6191..b956b85e520 100644
--- a/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
@@ -24,7 +24,6 @@ import org.apache.commons.io.FileUtils;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
/**
* Takes the hierarchical structure of a file and applies it to an HDF5 container.
@@ -35,7 +34,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5
{
private final File file;
- private final IHDF5SimpleWriter writer;
+ private final IHDF5ContainerWriter writer;
/**
* Utility class that adapts to the IHdf5WriterClient interface
@@ -51,7 +50,7 @@ public class HierarchicalStructureDuplicatorFileToHdf5
this.file = file;
}
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
HierarchicalStructureDuplicatorFileToHdf5.makeDuplicate(file, writer);
}
@@ -67,12 +66,12 @@ public class HierarchicalStructureDuplicatorFileToHdf5
* @throws CheckedExceptionTunnel Thrown if an underlying error occurs
* @throws IOExceptionUnchecked Thrown if an underlying error occurs
*/
- public static void makeDuplicate(File file, IHDF5SimpleWriter writer)
+ public static void makeDuplicate(File file, IHDF5ContainerWriter writer)
{
new HierarchicalStructureDuplicatorFileToHdf5(file, writer).makeDuplicate();
}
- private HierarchicalStructureDuplicatorFileToHdf5(File file, IHDF5SimpleWriter writer)
+ private HierarchicalStructureDuplicatorFileToHdf5(File file, IHDF5ContainerWriter writer)
{
this.file = file;
this.writer = writer;
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
new file mode 100644
index 00000000000..18ec61e7bcf
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/IHDF5ContainerWriter.java
@@ -0,0 +1,40 @@
+/*
+ * 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;
+
+/**
+ * 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.
+ *
+ * @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>.
+ */
+ public void writeByteArray(final String objectPath, final byte[] data);
+
+ /**
+ * Closes this object and the file referenced by this object. This object must not be used after
+ * being closed.
+ */
+ public void close();
+}
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 179f4f80e99..2fb24a3cdf3 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
@@ -24,11 +24,9 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.hdf5.Hdf5Container;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5ReaderClient;
import ch.systemsx.cisd.common.hdf5.Hdf5Container.IHdf5WriterClient;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
/**
* @author Chandrasekhar Ramakrishnan
@@ -51,7 +49,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
hdf5Content.runWriterClient(false, new IHdf5WriterClient()
{
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
writer.writeByteArray("/test-bytes", byteArray);
@@ -77,7 +75,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
hdf5Content.runWriterClient(true, new IHdf5WriterClient()
{
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
writer.writeByteArray("/test-bytes", byteArray);
@@ -103,7 +101,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
Hdf5Container hdf5ContentUncompressed = new Hdf5Container(hdf5FileUncompressed);
hdf5ContentUncompressed.runWriterClient(false, new IHdf5WriterClient()
{
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
writer.writeByteArray("/test-bytes", byteArray);
@@ -114,7 +112,7 @@ public class Hdf5ContainerTest extends AbstractFileSystemTestCase
Hdf5Container hdf5ContentCompressed = new Hdf5Container(hdf5FileCompressed);
hdf5ContentCompressed.runWriterClient(true, new IHdf5WriterClient()
{
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
writer.writeByteArray("/test-bytes", byteArray);
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 92c90584203..e5a14d2c714 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
@@ -36,13 +36,13 @@ 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.IHDF5ContainerWriter;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
import ch.systemsx.cisd.common.process.ProcessIOStrategy;
import ch.systemsx.cisd.common.process.ProcessResult;
-import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
@@ -90,7 +90,7 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
* the thumbnail. Using it allows not to allocate memory each time when a thumbnail
* is generated.
*/
- private Status generateThumbnail(IHDF5SimpleWriter writer, AcquiredSingleImage plateImage,
+ private Status generateThumbnail(IHDF5ContainerWriter writer, AcquiredSingleImage plateImage,
ByteArrayOutputStream bufferOutputStream)
{
RelativeImageReference imageReference = plateImage.getImageReference();
@@ -214,7 +214,7 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
}
private ITaskExecutor<AcquiredSingleImage> createThumbnailGenerator(
- final IHDF5SimpleWriter writer)
+ final IHDF5ContainerWriter writer)
{
return new ITaskExecutor<AcquiredSingleImage>()
{
@@ -239,7 +239,7 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
};
}
- public void runWithSimpleWriter(IHDF5SimpleWriter writer)
+ public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
Collection<FailureRecord<AcquiredSingleImage>> errors =
ParallelizedExecutor.process(plateImages, createThumbnailGenerator(writer),
--
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