diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/CompressingHdf5WriterWrapper.java b/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
similarity index 99%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/CompressingHdf5WriterWrapper.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
index e2677a710e1cb94fd7bfd3df3bbd532fa2eb0de7..8335139b687113793d7a4fbc03a31a39579e01ca 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/CompressingHdf5WriterWrapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/CompressingHdf5WriterWrapper.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.generic.shared.content;
+package ch.systemsx.cisd.common.hdf5;
import java.util.BitSet;
import java.util.Date;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5AwareHierarchicalContentFactory.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5AwareHierarchicalContentFactory.java
similarity index 89%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5AwareHierarchicalContentFactory.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/HDF5AwareHierarchicalContentFactory.java
index 4aad22cdaecfe01f5d669f634e85b4fd0733513c..a8a52b0469f54c71cb205cbf8cf290a46017cb56 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5AwareHierarchicalContentFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5AwareHierarchicalContentFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.generic.shared.content;
+package ch.systemsx.cisd.common.hdf5;
import java.io.File;
import java.util.Arrays;
@@ -38,9 +38,10 @@ public class HDF5AwareHierarchicalContentFactory extends HierarchicalContentFact
public IHierarchicalContentNode asHierarchicalContentNode(IHierarchicalContent rootContent,
File file)
{
- if (FilenameUtils.isExtension(file.getName(), Arrays.asList("h5", "h5r")))
+ if (FilenameUtils.isExtension(file.getName(), Arrays.asList("h5", "h5ar")))
{
- return new HDF5ContainerBasedHierarchicalContentNode(this, rootContent, file);
+ return null;
+ // return new HDF5ContainerBasedHierarchicalContentNode(this, rootContent, file);
} else
{
return super.asHierarchicalContentNode(rootContent, file);
diff --git a/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTraverser.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTraverser.java
new file mode 100644
index 0000000000000000000000000000000000000000..a8beeb893a88310c99fd23af44a6ac9098796d78
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HDF5ContainerTraverser.java
@@ -0,0 +1,71 @@
+/*
+ * 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.util.List;
+
+import ch.systemsx.cisd.common.io.IHierarchicalContent;
+import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
+
+/**
+ * {@link IHierarchicalContent} implementation for an HDF5 container.
+ *
+ * @author Piotr Buczek
+ */
+public class HDF5ContainerTraverser
+{
+ public static void main(String[] args)
+ {
+ File container = new File("container.h5");
+ System.err.println(container.getAbsolutePath());
+ if (container.exists())
+ {
+ Hdf5Container hdf5Container = new Hdf5Container(container);
+ IHDF5SimpleReader reader = hdf5Container.createSimpleReader();
+ try
+ {
+ traverse(reader, "/", "");
+ } finally
+ {
+ reader.close();
+ }
+ }
+ }
+
+ public static void traverse(IHDF5SimpleReader reader, String relativePath, String indent)
+ {
+ System.err.println(indent + "traverse: '" + relativePath + "'");
+ List<String> childPaths = reader.getGroupMembers(relativePath);
+ String newIndent = indent + "\t";
+ for (String childPath : childPaths)
+ {
+ String newRelativePath =
+ (relativePath.equals(File.separator)) ? childPath : relativePath
+ + File.separator + childPath;
+ if (reader.isGroup(newRelativePath))
+ {
+ System.err.println(newIndent + "group: '" + childPath + "'");
+ traverse(reader, newRelativePath, newIndent);
+ } else
+ {
+ System.err.println(newIndent + "file: '" + childPath + "'");
+ }
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/Hdf5Container.java b/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
similarity index 98%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/Hdf5Container.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
index 031396510f4763463a78e93a862da3c10cdaca31..c61c2a5db562a6d55c1ac135f6c91fbadba8bd6b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/Hdf5Container.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/Hdf5Container.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.generic.shared.content;
+package ch.systemsx.cisd.common.hdf5;
import java.io.File;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
similarity index 97%
rename from datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
rename to common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
index 72c620cdc038293e2f8110b16dc0b2fba8db9532..130b73b6191694a75fe743a55456c203bba686a0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
+++ b/common/source/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.etlserver.hdf5;
+package ch.systemsx.cisd.common.hdf5;
import java.io.File;
import java.io.IOException;
@@ -25,7 +25,6 @@ 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;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
/**
* Takes the hierarchical structure of a file and applies it to an HDF5 container.
diff --git a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java
index dbcd6471597d4028ec42bab4ad841357be518f1a..6c7b62ff46060ddc9a5b010205c87fd7fd80dc90 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java
@@ -61,7 +61,7 @@ class DefaultFileBasedHierarchicalContent implements IHierarchicalContent
public IHierarchicalContentNode getNode(String relativePath)
{
- return asNode(new File(root, relativePath)); // FIXME
+ return asNode(new File(root, relativePath)); // FIXME traverse HDF5 container
}
private IHierarchicalContentNode asNode(File file)
@@ -162,6 +162,7 @@ class DefaultFileBasedHierarchicalContent implements IHierarchicalContent
*/
private static void findFiles(File startingPoint, FileFilter filter, List<File> result)
{
+ // TODO 2011-04-12, Piotr Buczek: make HDF5 aware
File[] filteredFiles = startingPoint.listFiles(filter);
if (filteredFiles != null)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
index e71ea38d949979783541ee5db470f1639b9b0d64..1a9cecaa17b8a4dd02f40eac37a16c18033994cc 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
*
* @author Piotr Buczek
*/
-public class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalContentNode
+class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalContentNode
{
protected final IHierarchicalContent root;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5ContainerBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
similarity index 91%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5ContainerBasedHierarchicalContentNode.java
rename to common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
index c7928dc9eb20d0961590fbfd99fb8388d05ecdca..3a6ff0c943b4fe1ec7fd9f6f124729c26deda946 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/HDF5ContainerBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.generic.shared.content;
+package ch.systemsx.cisd.common.io;
import java.io.File;
import java.io.InputStream;
@@ -22,14 +22,7 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
-import ch.systemsx.cisd.common.io.AbstractHierarchicalDirectoryContentNode;
-import ch.systemsx.cisd.common.io.AbstractHierarchicalFileContentNode;
-import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
-import ch.systemsx.cisd.common.io.DefaultFileBasedHierarchicalContentNode;
-import ch.systemsx.cisd.common.io.IContent;
-import ch.systemsx.cisd.common.io.IHierarchicalContent;
-import ch.systemsx.cisd.common.io.IHierarchicalContentFactory;
-import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
+import ch.systemsx.cisd.common.hdf5.Hdf5Container;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
/**
@@ -258,12 +251,13 @@ class HDF5ContainerBasedHierarchicalContentNode extends DefaultFileBasedHierarch
{
if (contentOrNull == null)
{
- contentOrNull = extractFileContent(reader, relativePath);
+ contentOrNull = extractFileContent(file, relativePath);
}
return contentOrNull;
}
}
+ @SuppressWarnings("unused")
private static IContent extractFileContent(IHDF5SimpleReader reader, String path)
{
byte[] content = reader.readAsByteArray(path);
@@ -271,4 +265,8 @@ class HDF5ContainerBasedHierarchicalContentNode extends DefaultFileBasedHierarch
return new ByteArrayBasedContent(content, index < 0 ? path : path.substring(index + 1));
}
+ private static IContent extractFileContent(File hdf5File, String dataSetPath)
+ {
+ return new HDF5DataSetBasedContent(hdf5File, dataSetPath);
+ }
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentFactory.java b/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentFactory.java
index a1629b91cb5a05b35f3ccc22ac92e66ceeab98c8..bcba8746318a7e5c60f8a4a126d74ab394b71891 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HierarchicalContentFactory.java
@@ -35,6 +35,11 @@ public class HierarchicalContentFactory implements IHierarchicalContentFactory
public IHierarchicalContentNode asHierarchicalContentNode(IHierarchicalContent rootContent,
File file)
{
+ // TODO 2011-04-12, Piotr Buczek: uncomment when HDF5 abstraction is fully implemented
+ // if (FilenameUtils.isExtension(file.getName(), Arrays.asList("h5", "h5ar")))
+ // {
+ // return new HDF5ContainerBasedHierarchicalContentNode(this, rootContent, file);
+ // }
return new DefaultFileBasedHierarchicalContentNode(this, rootContent, file);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/FileToHdf5DuplicationVerifier.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
similarity index 93%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/FileToHdf5DuplicationVerifier.java
rename to common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
index 152413bd17a5184dddffad69703fc02040428064..49c836356a0f51a0827d9626dadb5ffefbae91e1 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/FileToHdf5DuplicationVerifier.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/FileToHdf5DuplicationVerifier.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.etlserver.hdf5;
+package ch.systemsx.cisd.common.hdf5;
import java.io.File;
import java.io.IOException;
@@ -22,16 +22,15 @@ 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.hdf5.IHDF5SimpleReader;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5ReaderClient;
/**
* Helper class that verifies that a file structure is matched by the HDF5 structure.
*
* @author Chandrasekhar Ramakrishnan
*/
-class FileToHdf5DuplicationVerifier extends AssertJUnit
+public class FileToHdf5DuplicationVerifier extends AssertJUnit
{
private final File sourceFolderOrFile;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5ContainerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
similarity index 93%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5ContainerTest.java
rename to common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
index 25380f0cb899c33cb3c96646572638e9d7d062b2..179f4f80e99986ec1267dccff7ca486b35d7a1b9 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/Hdf5ContainerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/Hdf5ContainerTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.etlserver.hdf5;
+package ch.systemsx.cisd.common.hdf5;
import java.io.ByteArrayOutputStream;
import java.io.File;
@@ -24,11 +24,11 @@ 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;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5ReaderClient;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5WriterClient;
/**
* @author Chandrasekhar Ramakrishnan
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
similarity index 95%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
rename to common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
index bfc424a64fe2bfd46c71aafa21e67fe9d05ca220..cada6b1ec726933301c7af1d584cab09bcb91e10 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/hdf5/HierarchicalStructureDuplicatorFileToHdf5Test.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.etlserver.hdf5;
+package ch.systemsx.cisd.common.hdf5;
import java.io.File;
import java.io.IOException;
@@ -23,9 +23,10 @@ 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.HierarchicalStructureDuplicatorFileToHdf5;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5ReaderClient;
/**
* @author Chandrasekhar Ramakrishnan
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
index 8d87700ab57ffdcc9d7ad6f34d696f87b5022fa1..c69a9714a87c6468b3539f9b98ce54f2a351f1fe 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
@@ -20,11 +20,12 @@ 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.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
@@ -116,7 +117,6 @@ public class Hdf5StorageProcessor extends AbstractStorageProcessor
};
}
-
/**
* Given a directory in the store, return the HDF5 container file.
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 f1093af651bdea796e60463318a58f6261ca985d..9ecfb554a103e6d5659b649354ab799d601750e8 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
@@ -21,10 +21,11 @@ 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.etlserver.IStorageProcessorTransactional.IStorageProcessorTransaction;
import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5ReaderClient;
/**
* Tests for {@link Hdf5StorageProcessor}.
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
index aaaae09bd6c97de22cd4607702b9a010202b24d2..2eda6e7f2d8890628b0824aa777d25b02d22f99f 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
@@ -20,6 +20,7 @@ import java.util.Properties;
import org.testng.annotations.Test;
+
/**
* @author Chandrasekhar Ramakrishnan
*/
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
index 5a5512bbf95252a3d84f9f84ef406a5766a8ae2c..fbb100dee2144e84483db3d07c25f02b7482e971 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
@@ -20,6 +20,7 @@ import java.util.Properties;
import org.testng.annotations.Test;
+
/**
* @author Chandrasekhar Ramakrishnan
*/
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 c685677ac405b94522c07e61acbf23a912af3ee2..00654ddcd4d3ebfed6d1a467eb4c605cbc98498b 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
@@ -43,6 +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.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
@@ -53,7 +55,6 @@ import ch.systemsx.cisd.etlserver.AbstractStorageProcessorTransaction;
import ch.systemsx.cisd.etlserver.DispatcherStorageProcessor.IDispatchableStorageProcessor;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.etlserver.hdf5.HierarchicalStructureDuplicatorFileToHdf5;
import ch.systemsx.cisd.etlserver.utils.Unzipper;
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
@@ -67,7 +68,6 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.OriginalDataStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -693,7 +693,8 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
{
IImageTransformerFactory imgTransformerFactory =
imageStorageConfiguraton.getImageTransformerFactory();
- for (AcquiredSingleImage image : images) {
+ for (AcquiredSingleImage image : images)
+ {
image.setImageTransformerFactoryOrNull(imgTransformerFactory);
}
}
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 bce8aeac11a21c8d39fe47f21c366cc8499920a9..aa712d007507c2a7136ab840a64a0c54db62bd9b 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
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
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.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
@@ -39,7 +40,6 @@ 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.api.v1.ThumbnailsStorageFormat;
-import ch.systemsx.cisd.openbis.dss.generic.shared.content.Hdf5Container.IHdf5WriterClient;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
/**