diff --git a/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5 b/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5
new file mode 100644
index 0000000000000000000000000000000000000000..26b6d1d2b811814c1db75f7dd008cede7d4b01fb
Binary files /dev/null and b/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5 differ
diff --git a/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5ar b/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5ar
new file mode 100644
index 0000000000000000000000000000000000000000..194bcd2d1cf5157fda61ec28344ed1992ca761ed
Binary files /dev/null and b/common/resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest/thumbnails.h5ar differ
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 e1d55337195838f2af58c9d266c429beb3e4fcb9..668d6b2c53aafeaecf08d28de0c2c57d501934b0 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
@@ -321,7 +321,7 @@ public class HDF5ContainerBasedHierarchicalContentNode extends
int entryChecksum = entry.getCrc32();
if (entryChecksum != 0)
{
- checksum = (long) entryChecksum;
+ checksum = entryChecksum & 0xffffffffL;
} else
{
checksum = IOUtilities.getChecksumCRC32(doGetInputStream());
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/IOUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/IOUtilitiesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0a1c83781a9a489a9c3bfe28caa49fdf56eab286
--- /dev/null
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/IOUtilitiesTest.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2012 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.io;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.util.Random;
+import java.util.zip.CRC32;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class IOUtilitiesTest extends AssertJUnit
+{
+ private static final class CloseDetectingByteArrayInputStream extends ByteArrayInputStream
+ {
+ private boolean closeInvoked;
+
+ public CloseDetectingByteArrayInputStream(byte[] bytes)
+ {
+ super(bytes);
+ }
+
+ @Override
+ public void close() throws IOException
+ {
+ closeInvoked = true;
+ super.close();
+ }
+ }
+
+ @Test
+ public void test()
+ {
+ Random random = new Random(37);
+ byte[] exampleData = new byte[1000];
+ for (int i = 0; i < exampleData.length; i++)
+ {
+ exampleData[i] = (byte) random.nextInt();
+ }
+ CRC32 crc32 = new CRC32();
+ crc32.update(exampleData);
+ long expectedChecksum = crc32.getValue();
+ CloseDetectingByteArrayInputStream inputStream =
+ new CloseDetectingByteArrayInputStream(exampleData);
+
+ long checksum = IOUtilities.getChecksumCRC32(inputStream);
+
+ assertEquals(expectedChecksum, checksum);
+ assertEquals(true, inputStream.closeInvoked);
+ }
+
+}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
index 09cd68e2c485fa3f14e7abe3e6b415963c2e4b82..4bde6c2cf01726f75d8911092244d70318f1bdd2 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/AbstractHierarchicalContentNodeTest.java
@@ -42,6 +42,7 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
// check only that no exception is thrown
fileNode.getFileLength();
+ fileNode.getChecksumCRC32();
fileNode.getFileContent();
fileNode.getInputStream();
}
@@ -81,6 +82,13 @@ public class AbstractHierarchicalContentNodeTest extends AssertJUnit
dirNode.getFileLength();
}
});
+ assertUnsupportedFileOperationOnAction(new IDelegatedAction()
+ {
+ public void execute()
+ {
+ dirNode.getChecksumCRC32();
+ }
+ });
assertUnsupportedFileOperationOnAction(new IDelegatedAction()
{
public void execute()
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 bf4f46190e74c6632b484640de6e7515e0ff81e4..c9b11ba1c35af6ab87e26f3883e7bd7f7d03ce7a 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.common.io.hierarchical_content;
import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
@@ -37,6 +38,7 @@ 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.HierarchicalStructureDuplicatorFileToHDF5.DuplicatorWriterClient;
+import ch.systemsx.cisd.common.io.IOUtilities;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
import ch.systemsx.cisd.common.utilities.HierarchicalContentUtils;
import ch.systemsx.cisd.common.utilities.IDelegatedAction;
@@ -544,6 +546,8 @@ public class DefaultFileBasedHierarchicalContentTest extends AbstractFileSystemT
// file info access
assertEquals("File: " + expectedFile, expectedFile.getName(), fileNode.getName());
assertEquals("File: " + expectedFile, expectedFile.length(), fileNode.getFileLength());
+ long expectedChecksum = IOUtilities.getChecksumCRC32(new FileInputStream(expectedFile));
+ assertEquals("File: " + expectedFile, expectedChecksum, fileNode.getChecksumCRC32());
assertTrue("File: " + expectedFile,
fileNode.getLastModified() >= expectedFile.lastModified());
assertTrue("File: " + expectedFile,
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNodeTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNodeTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..5f0dbbf77a5bcf83363d14748a6b6a29d570aa31
--- /dev/null
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/io/hierarchical_content/HDF5ContainerBasedHierarchicalContentNodeTest.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright 2012 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.io.hierarchical_content;
+
+import java.io.File;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class HDF5ContainerBasedHierarchicalContentNodeTest extends AssertJUnit
+{
+ private static final File TEST_DATA_FOLDER = new File(
+ "resource/test-data/HDF5ContainerBasedHierarchicalContentNodeTest");
+
+ @Test
+ public void testH5File()
+ {
+ IHierarchicalContent content =
+ new DefaultFileBasedHierarchicalContentFactory().asHierarchicalContent(
+ TEST_DATA_FOLDER, null);
+ IHierarchicalContentNode node = content.getNode("thumbnails.h5");
+ List<IHierarchicalContentNode> nodes = getSortedChildren(node);
+
+ assertEquals("3361fd20 24242 PLATE1_A01_01_Cy3.png\n" +
+ "609f3183 29353 PLATE1_A01_01_DAPI.png\n" +
+ "b68f97cf 27211 PLATE1_A01_01_GFP.png\n" +
+ "b312b087 31570 PLATE1_A01_02_Cy3.png\n" +
+ "e7082b23 28267 PLATE1_A01_02_DAPI.png\n" +
+ "fb7f320e 26972 PLATE1_A01_02_GFP.png\n" +
+ "a97cff4e 28916 PLATE1_A01_03_Cy3.png\n" +
+ "6f0abf6f 30079 PLATE1_A01_03_DAPI.png\n" +
+ "5ba6ae39 28072 PLATE1_A01_03_GFP.png\n" +
+ "e2c7c34f 28279 PLATE1_A01_04_Cy3.png\n" +
+ "1bf73b61 22246 PLATE1_A01_04_DAPI.png\n" +
+ "58e14da9 22227 PLATE1_A01_04_GFP.png\n" +
+ "d367dd9d 34420 PLATE1_A01_05_Cy3.png\n" +
+ "15e1f3b0 28070 PLATE1_A01_05_DAPI.png\n" +
+ "34bcde32 27185 PLATE1_A01_05_GFP.png\n" +
+ "f8d4cfc7 26367 PLATE1_A01_06_Cy3.png\n" +
+ "aeb12b1a 25086 PLATE1_A01_06_DAPI.png\n" +
+ "ced4332a 22199 PLATE1_A01_06_GFP.png", getNamesChecksumsAndSizes(nodes));
+ }
+
+ @Test
+ public void testH5arFile()
+ {
+ IHierarchicalContent content =
+ new DefaultFileBasedHierarchicalContentFactory().asHierarchicalContent(
+ TEST_DATA_FOLDER, null);
+ IHierarchicalContentNode node = content.getNode("thumbnails.h5ar");
+ List<IHierarchicalContentNode> nodes = getSortedChildren(node);
+
+ assertEquals("3361fd20 24242 wA1_d1-1_cCy3.png\n" +
+ "609f3183 29353 wA1_d1-1_cDAPI.png\n" +
+ "b68f97cf 27211 wA1_d1-1_cGFP.png\n" +
+ "e2c7c34f 28279 wA1_d1-2_cCy3.png\n" +
+ "1bf73b61 22246 wA1_d1-2_cDAPI.png\n" +
+ "58e14da9 22227 wA1_d1-2_cGFP.png\n" +
+ "b312b087 31570 wA1_d2-1_cCy3.png\n" +
+ "e7082b23 28267 wA1_d2-1_cDAPI.png\n" +
+ "fb7f320e 26972 wA1_d2-1_cGFP.png\n" +
+ "d367dd9d 34420 wA1_d2-2_cCy3.png\n" +
+ "15e1f3b0 28070 wA1_d2-2_cDAPI.png\n" +
+ "34bcde32 27185 wA1_d2-2_cGFP.png\n" +
+ "a97cff4e 28916 wA1_d3-1_cCy3.png\n" +
+ "6f0abf6f 30079 wA1_d3-1_cDAPI.png\n" +
+ "5ba6ae39 28072 wA1_d3-1_cGFP.png\n" +
+ "f8d4cfc7 26367 wA1_d3-2_cCy3.png\n" +
+ "aeb12b1a 25086 wA1_d3-2_cDAPI.png\n" +
+ "ced4332a 22199 wA1_d3-2_cGFP.png", getNamesChecksumsAndSizes(nodes));
+ }
+
+ private String getNamesChecksumsAndSizes(List<IHierarchicalContentNode> nodes)
+ {
+ StringBuilder builder = new StringBuilder();
+ for (IHierarchicalContentNode node : nodes)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append("\n");
+ }
+ builder.append(Long.toHexString(node.getChecksumCRC32()));
+ builder.append(" ").append(node.getFileLength());
+ builder.append(" ").append(node.getName());
+ }
+ return builder.toString();
+ }
+
+ private List<IHierarchicalContentNode> getSortedChildren(IHierarchicalContentNode node)
+ {
+ List<IHierarchicalContentNode> nodes = node.getChildNodes();
+ Collections.sort(nodes, new Comparator<IHierarchicalContentNode>()
+ {
+ public int compare(IHierarchicalContentNode n1, IHierarchicalContentNode n2)
+ {
+ return n1.getName().compareTo(n2.getName());
+ }
+ });
+ return nodes;
+ }
+
+}