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 3b397d60d7efc514135cf497439f7d0e8ab85eee..8132da599f80da71b4820eb1326f7c5c4ea162e1 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContent.java
@@ -95,8 +95,7 @@ class DefaultFileBasedHierarchicalContent implements IHierarchicalContent
if (existingFile != null && FileUtilities.isHDF5ContainerFile(existingFile))
{
HDF5ContainerBasedHierarchicalContentNode containerNode =
- new HDF5ContainerBasedHierarchicalContentNode(hierarchicalContentFactory, this,
- existingFile);
+ new HDF5ContainerBasedHierarchicalContentNode(this, existingFile);
String relativePath = FileUtilities.getRelativeFile(existingFile, file);
return containerNode.getChildNode(relativePath);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentFactory.java b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentFactory.java
index f418400406e0aac76e3794d31b1a489538cb1337..79d1a54fe1d6f8e681874e0e461ddab03af3efa7 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentFactory.java
@@ -39,7 +39,7 @@ public class DefaultFileBasedHierarchicalContentFactory implements IHierarchical
{
if (FileUtilities.isHDF5ContainerFile(file))
{
- return new HDF5ContainerBasedHierarchicalContentNode(this, rootContent, file);
+ return new HDF5ContainerBasedHierarchicalContentNode(rootContent, file);
}
return new DefaultFileBasedHierarchicalContentNode(this, rootContent, file);
}
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 4cf025088bf96de8893532dc794664c973d9de3d..9618ae7bde42614f6aa5a411e4abbec76a10b81b 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/DefaultFileBasedHierarchicalContentNode.java
@@ -39,16 +39,20 @@ class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalConten
protected final File file;
- protected final IHierarchicalContentFactory hierarchicalContentFactory;
+ private final IHierarchicalContentFactory hierarchicalContentFactoryOrNull;
+
+ protected DefaultFileBasedHierarchicalContentNode(IHierarchicalContent root, File file)
+ {
+ this(null, root, file);
+ }
protected DefaultFileBasedHierarchicalContentNode(
- IHierarchicalContentFactory hierarchicalContentFactory, IHierarchicalContent root,
- File file)
+ IHierarchicalContentFactory hierarchicalContentFactoryOrNull,
+ IHierarchicalContent root, File file)
{
- assert hierarchicalContentFactory != null;
assert root != null;
assert file != null;
- this.hierarchicalContentFactory = hierarchicalContentFactory;
+ this.hierarchicalContentFactoryOrNull = hierarchicalContentFactoryOrNull;
this.root = root;
this.file = file;
}
@@ -82,13 +86,16 @@ class DefaultFileBasedHierarchicalContentNode extends AbstractHierarchicalConten
@Override
public List<IHierarchicalContentNode> doGetChildNodes()
{
+ // if factory is not defined the method should be overriden
+ assert hierarchicalContentFactoryOrNull != null;
+
File[] files = file.listFiles();
List<IHierarchicalContentNode> result = new ArrayList<IHierarchicalContentNode>();
if (files != null)
{
for (File aFile : files)
{
- result.add(hierarchicalContentFactory.asHierarchicalContentNode(root, aFile));
+ result.add(hierarchicalContentFactoryOrNull.asHierarchicalContentNode(root, aFile));
}
}
return result;
diff --git a/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
index 4cdc0ce53551c3e496199f975751a9767936eb01..e870f861fdf76615b0d2deace7730b2ac8fa85d8 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/HDF5ContainerBasedHierarchicalContentNode.java
@@ -31,15 +31,15 @@ import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
*
* @author Piotr Buczek
*/
-class HDF5ContainerBasedHierarchicalContentNode extends DefaultFileBasedHierarchicalContentNode
+public class HDF5ContainerBasedHierarchicalContentNode extends
+ DefaultFileBasedHierarchicalContentNode
{
private final Hdf5Container hdf5Container;
- HDF5ContainerBasedHierarchicalContentNode(
- IHierarchicalContentFactory hierarchicalContentFactory, IHierarchicalContent root,
+ public HDF5ContainerBasedHierarchicalContentNode(IHierarchicalContent root,
File hdf5ContainerFile)
{
- super(hierarchicalContentFactory, root, hdf5ContainerFile);
+ super(root, hdf5ContainerFile);
this.hdf5Container = new Hdf5Container(hdf5ContainerFile);
}
@@ -59,7 +59,6 @@ class HDF5ContainerBasedHierarchicalContentNode extends DefaultFileBasedHierarch
@Override
public List<IHierarchicalContentNode> doGetChildNodes()
{
- // NOTE this is a slow implementation - improve it when information can be retrieved from DB
IHDF5SimpleReader reader = createReader();
try
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ISingleDataSetPathInfoProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ISingleDataSetPathInfoProvider.java
index 71041ff246832d776ced4bcb4f61db232e807c20..469633d56106dcf07330cbf6b16f87ae89e0fb88 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ISingleDataSetPathInfoProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ISingleDataSetPathInfoProvider.java
@@ -31,6 +31,8 @@ public interface ISingleDataSetPathInfoProvider
DataSetPathInfo tryGetPathInfoByRelativePath(String relativePath);
+ // DataSetPathInfo getParentPathInfo(DataSetPathInfo child);
+
List<DataSetPathInfo> listChildrenPathInfos(DataSetPathInfo parent);
List<DataSetPathInfo> listMatchingPathInfos(String relativePathPattern);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
index 802b95dce2f4f0ed0963aad9c7635515624efe0f..1e7c62e86cfed361b8de5a3a39829dbf77bcbe97 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
@@ -26,7 +26,9 @@ import java.util.List;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.io.AbstractHierarchicalContentNode;
+import ch.systemsx.cisd.common.io.HDF5ContainerBasedHierarchicalContentNode;
import ch.systemsx.cisd.common.io.IHierarchicalContent;
import ch.systemsx.cisd.common.io.IHierarchicalContentNode;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
@@ -93,7 +95,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
private IHierarchicalContentNode asNode(DataSetPathInfo pathInfo)
{
- return new PathInfoNode(pathInfo, root, dataSetPathInfoProvider);
+ return new PathInfoNode(pathInfo);
}
private DataSetPathInfo findPathInfo(String relativePath) throws IllegalArgumentException
@@ -187,21 +189,15 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return true;
}
- static class PathInfoNode extends AbstractHierarchicalContentNode
+ class PathInfoNode extends AbstractHierarchicalContentNode
{
-
private final DataSetPathInfo pathInfo;
- private final File root;
-
- private final ISingleDataSetPathInfoProvider dataSetPathInfoProvider;
+ private IFileContentProvider fileContentProviderOrNull;
- PathInfoNode(DataSetPathInfo pathInfo, File root,
- ISingleDataSetPathInfoProvider dataSetPathInfoProvider)
+ PathInfoNode(DataSetPathInfo pathInfo)
{
this.pathInfo = pathInfo;
- this.root = root;
- this.dataSetPathInfoProvider = dataSetPathInfoProvider;
}
public String getName()
@@ -233,7 +229,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
List<IHierarchicalContentNode> result = new ArrayList<IHierarchicalContentNode>();
for (DataSetPathInfo child : pathInfos)
{
- result.add(new PathInfoNode(child, root, dataSetPathInfoProvider));
+ result.add(asNode(child));
}
return result;
}
@@ -244,37 +240,130 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return pathInfo.getSizeInBytes();
}
- // TODO 2011-04-19, Piotr Buczek: use abstraction to get file content
-
public File getFile() throws UnsupportedOperationException
{
- if (StringUtils.isBlank(getRelativePath()))
+ File result = doGetFile();
+ if (result.exists())
{
- return root;
+ return result;
} else
{
- return new File(root, getRelativePath());
+ throw new UnsupportedOperationException("This is not a normal file/directory node.");
}
}
@Override
protected IRandomAccessFile doGetFileContent()
{
- return new RandomAccessFileImpl(getFile(), "r");
+ return getFileContentProvider().getReadOnlyRandomAccessFile();
}
@Override
protected InputStream doGetInputStream()
{
- try
+ return getFileContentProvider().getInputStream();
+ }
+
+ private IFileContentProvider getFileContentProvider()
+ {
+ if (fileContentProviderOrNull == null)
+ {
+ File file = doGetFile();
+ fileContentProviderOrNull = getContent(file);
+ }
+ return fileContentProviderOrNull;
+ }
+
+ /**
+ * Returns a file object with given node's relative path. The file doesn't have to exist on
+ * the file system.
+ */
+ private File doGetFile()
+ {
+ if (StringUtils.isBlank(getRelativePath()))
{
- return new FileInputStream(getFile());
- } catch (FileNotFoundException ex)
+ return root;
+ } else
{
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ return new File(root, getRelativePath());
}
}
+ }
+
+ private IFileContentProvider getContent(File file)
+ {
+ if (file.exists())
+ {
+ return asFileContentProvider(file);
+ }
+
+ // The file doesn't exist in file system but it could be inside a HDF5 container.
+ // Go up in file hierarchy until existing file is found.
+ File existingFile = file;
+ while (existingFile != null && existingFile.exists() == false)
+ {
+ existingFile = existingFile.getParentFile();
+ }
+ if (existingFile != null && FileUtilities.isHDF5ContainerFile(existingFile))
+ {
+ HDF5ContainerBasedHierarchicalContentNode containerNode =
+ new HDF5ContainerBasedHierarchicalContentNode(this, existingFile);
+ String relativePath = FileUtilities.getRelativeFile(existingFile, file);
+ IHierarchicalContentNode node = containerNode.getChildNode(relativePath);
+ return asFileContentProvider(node);
+ }
+ throw new IllegalArgumentException("Resource '" + FileUtilities.getRelativeFile(root, file)
+ + "' does not exist.");
+ }
+
+ private interface IFileContentProvider
+ {
+ public IRandomAccessFile getReadOnlyRandomAccessFile();
+
+ public InputStream getInputStream();
+ }
+
+ private static IFileContentProvider asFileContentProvider(final File existingFile)
+ {
+ assert existingFile.exists();
+ return new IFileContentProvider()
+ {
+
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ return new RandomAccessFileImpl(existingFile, "r");
+ }
+
+ public InputStream getInputStream()
+ {
+ try
+ {
+ return new FileInputStream(existingFile);
+ } catch (FileNotFoundException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+ };
+ }
+
+ private static IFileContentProvider asFileContentProvider(final IHierarchicalContentNode node)
+ {
+ return new IFileContentProvider()
+ {
+
+ public IRandomAccessFile getReadOnlyRandomAccessFile()
+ {
+ return node.getFileContent();
+ }
+
+ public InputStream getInputStream()
+ {
+ return node.getInputStream();
+ }
+ };
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetPathInfo.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetPathInfo.java
index dd4045a5838dd84093507453a9a7d6f9036ae93b..3544dc7fea2793c0bf0e3df98d8236b0d37efe52 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetPathInfo.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetPathInfo.java
@@ -78,6 +78,7 @@ public class DataSetPathInfo
this.sizeInBytes = sizeInBytes;
}
+ @Deprecated
public DataSetPathInfo getParent()
{
return parent;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
index 3d23d3e984f3c10853d0ca78348d22ebb2a63996..82492d9e123794a5d2ea5608907e2a242ee3e912 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
@@ -167,6 +167,7 @@ public class DatabaseBasedDataSetPathInfoProviderTest extends AssertJUnit
assertEquals(2, list.size());
}
+ @SuppressWarnings("deprecation")
private void check(String expectedRelativePath, String expectedFileName,
boolean expectingDirectory, long expectedSize, DataSetPathInfo info)
{
@@ -174,7 +175,6 @@ public class DatabaseBasedDataSetPathInfoProviderTest extends AssertJUnit
assertEquals(expectedFileName, info.getFileName());
assertEquals(expectingDirectory, info.isDirectory());
assertEquals(expectedSize, info.getSizeInBytes());
- @SuppressWarnings("deprecation")
List<DataSetPathInfo> children = info.getChildren();
for (DataSetPathInfo child : children)
{