From eae3c0a15129388f468f805899614c8fc0a09445 Mon Sep 17 00:00:00 2001
From: ribeaudc <ribeaudc>
Date: Mon, 5 Nov 2007 12:00:04 +0000
Subject: [PATCH] [LMS-107] add: - HCS image format to BDS library
SVN: 2376
---
.../systemsx/cisd/bds/DataStructureV1_0.java | 11 ++-
.../ch/systemsx/cisd/bds/FormatParameter.java | 6 +-
.../systemsx/cisd/bds/FormatParameters.java | 52 ++++++++---
.../cisd/bds/IFormatParameterFactory.java | 56 ++++++++++++
.../systemsx/cisd/bds/IFormatParameters.java | 2 +-
.../systemsx/cisd/bds/UnknownFormat1_0.java | 3 +-
.../java/ch/systemsx/cisd/bds/Utilities.java | 4 +-
.../systemsx/cisd/bds/{ => hcs}/Channel.java | 5 +-
.../cisd/bds/{ => hcs}/ChannelList.java | 4 +-
.../cisd/bds/hcs/FormatParameterFactory.java | 61 +++++++++++++
.../systemsx/cisd/bds/{ => hcs}/Geometry.java | 7 +-
.../cisd/bds/hcs/ImageHCSFormat1_0.java | 50 +++++++++++
.../cisd/bds/{ => hcs}/PlateGeometry.java | 2 +-
.../cisd/bds/{ => hcs}/WellGeometry.java | 2 +-
.../bds/storage/filesystem/NodeFactory.java | 59 +++++++++---
.../cisd/bds/ChecksumBuilderTest.java | 40 +++------
.../ch/systemsx/cisd/bds/UtilitiesTest.java | 30 ++-----
.../ChannelListTest.java} | 24 ++---
.../cisd/bds/hcs/PlateGeometryTest.java | 89 ++++++++++++++++++
.../cisd/bds/hcs/WellGeometryTest.java | 90 +++++++++++++++++++
.../bds/storage/filesystem/DirectoryTest.java | 43 ++++-----
.../storage/filesystem/FileStorageTest.java | 17 ++--
.../cisd/bds/storage/filesystem/FileTest.java | 30 ++++---
.../storage/filesystem/NodeFactoryTest.java | 9 +-
24 files changed, 543 insertions(+), 153 deletions(-)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
rename bds/source/java/ch/systemsx/cisd/bds/{ => hcs}/Channel.java (94%)
rename bds/source/java/ch/systemsx/cisd/bds/{ => hcs}/ChannelList.java (94%)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
rename bds/source/java/ch/systemsx/cisd/bds/{ => hcs}/Geometry.java (90%)
create mode 100644 bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java
rename bds/source/java/ch/systemsx/cisd/bds/{ => hcs}/PlateGeometry.java (97%)
rename bds/source/java/ch/systemsx/cisd/bds/{ => hcs}/WellGeometry.java (97%)
rename bds/sourceTest/java/ch/systemsx/cisd/bds/{storage/filesystem/StorageTestCase.java => hcs/ChannelListTest.java} (53%)
create mode 100644 bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
create mode 100644 bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
index 1447c1b2330..71899de46da 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -64,7 +64,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
/**
* Creates a new instance relying on the specified storage.
*/
- public DataStructureV1_0(IStorage storage)
+ public DataStructureV1_0(final IStorage storage)
{
super(storage);
}
@@ -257,6 +257,15 @@ public class DataStructureV1_0 extends AbstractDataStructure
standardOriginalMapping.put(path, reference);
}
+ /**
+ * Sets a different <code>IFormatParameterFactory</code> implementation than the default one to encapsulated
+ * <code>FormatParameters</code>.
+ */
+ public void setFormatParametersFactory(final IFormatParameterFactory formatParameterFactory)
+ {
+ formatParameters.setFormatParameterFactory(formatParameterFactory);
+ }
+
@Override
protected void assertValid()
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
index 1f6f40d729a..de2d2315adb 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameter.java
@@ -25,7 +25,7 @@ public final class FormatParameter
{
private final String name;
- private final String value;
+ private final Object value;
/**
* Creates an instance for the specified name and value.
@@ -33,7 +33,7 @@ public final class FormatParameter
* @param name A non-empty string as the name of the parameter.
* @param value A non-<code>null</code> string as the value.
*/
- public FormatParameter(String name, String value)
+ public FormatParameter(final String name, final Object value)
{
assert name != null && name.length() > 0 : "Unspecified parameter name.";
this.name = name;
@@ -52,7 +52,7 @@ public final class FormatParameter
/**
* Returns the value of this parameter.
*/
- public final String getValue()
+ public final Object getValue()
{
return value;
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
index 317734aa8de..4d4eefc7bf5 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
@@ -21,7 +21,6 @@ import java.util.LinkedHashMap;
import java.util.Map;
import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
/**
@@ -29,19 +28,27 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Franz-Josef Elmer
*/
-class FormatParameters implements IFormatParameters, IStorable
+final class FormatParameters implements IFormatParameters, IStorable
{
private final Map<String, FormatParameter> parameters = new LinkedHashMap<String, FormatParameter>();
- void loadFrom(IDirectory directory)
+ /**
+ * The <code>IFormatParameterFactory</code> implementation used here.
+ * <p>
+ * Initialized with the default implementation {@link IFormatParameterFactory#DEFAULT_FORMAT_PARAMETER_FACTORY}.
+ * </p>
+ */
+ private IFormatParameterFactory formatParameterFactory = IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY;
+
+ final void loadFrom(final IDirectory directory)
{
parameters.clear();
for (INode node : directory)
{
- if (node instanceof IFile)
+ final FormatParameter formatParameter = formatParameterFactory.createFormatParameter(node);
+ if (formatParameter != null)
{
- IFile file = (IFile) node;
- addParameter(new FormatParameter(file.getName(), file.getStringContent().trim()));
+ addParameter(formatParameter);
}
}
}
@@ -52,18 +59,36 @@ class FormatParameters implements IFormatParameters, IStorable
public final void saveTo(final IDirectory directory)
{
- for (FormatParameter parameter : parameters.values())
+ for (final FormatParameter parameter : parameters.values())
{
- directory.addKeyValuePair(parameter.getName(), parameter.getValue());
+ final Object value = parameter.getValue();
+ assert value != null : "Parameter value can not be null.";
+ if (value instanceof String)
+ {
+ directory.addKeyValuePair(parameter.getName(), (String) value);
+ } else if (value instanceof IStorable)
+ {
+ ((IStorable) value).saveTo(directory);
+ } else
+ {
+ throw new IllegalArgumentException(String.format(
+ "Parameter value '%s' must be a String or an IStorable implementation.", value));
+ }
}
}
+ /** Sets a different <code>IFormatParameterFactory</code> implementation than the default one. */
+ final void setFormatParameterFactory(final IFormatParameterFactory formatParameterFactory)
+ {
+ this.formatParameterFactory = formatParameterFactory;
+ }
+
/**
* Adds the specified parameter.
*
* @throws IllegalArgumentException if they is already a parameter with same name as <code>parameter</code>.
*/
- void addParameter(FormatParameter parameter)
+ final void addParameter(final FormatParameter parameter)
{
String name = parameter.getName();
if (parameters.containsKey(name))
@@ -73,7 +98,11 @@ class FormatParameters implements IFormatParameters, IStorable
parameters.put(name, parameter);
}
- public String getValue(String parameterName)
+ //
+ // IFormatParameters
+ //
+
+ public final Object getValue(final String parameterName)
{
FormatParameter formatParameter = parameters.get(parameterName);
if (formatParameter == null)
@@ -83,9 +112,8 @@ class FormatParameters implements IFormatParameters, IStorable
return formatParameter.getValue();
}
- public Iterator<FormatParameter> iterator()
+ public final Iterator<FormatParameter> iterator()
{
return parameters.values().iterator();
}
-
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
new file mode 100644
index 00000000000..fd291b6e5d8
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2007 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.bds;
+
+import ch.systemsx.cisd.bds.storage.IFile;
+import ch.systemsx.cisd.bds.storage.INode;
+
+/**
+ * Interface to be implemented if you want to set a different <code>IFormatParameterFactory</code> in
+ * {@link FormatParameters}.
+ *
+ * @author Christian Ribeaud
+ */
+public interface IFormatParameterFactory
+{
+
+ public final static IFormatParameterFactory DEFAULT_FORMAT_PARAMETER_FACTORY = new IFormatParameterFactory()
+ {
+
+ //
+ // IFormatParameterFactory
+ //
+
+ public final FormatParameter createFormatParameter(final INode node)
+ {
+ if (node instanceof IFile)
+ {
+ final IFile file = (IFile) node;
+ return new FormatParameter(file.getName(), file.getStringContent().trim());
+ }
+ return null;
+ }
+ };
+
+ /**
+ * Creates a <code>FormatParameter</code> from given <var>node</var>.
+ *
+ * @return <code>null</code> if no appropriate <code>FormatParameter</code> could be created from given
+ * <code>INode</code>.
+ */
+ public FormatParameter createFormatParameter(final INode node);
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameters.java b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameters.java
index 50b36d2701a..398b81d8322 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameters.java
@@ -28,5 +28,5 @@ public interface IFormatParameters extends Iterable<FormatParameter>
*
* @throws IllegalArgumentException if there is no parameter named as specified.
*/
- public String getValue(String parameterName);
+ public Object getValue(final String parameterName);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java
index cec05c6e51c..d4610298bb6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormat1_0.java
@@ -23,6 +23,7 @@ package ch.systemsx.cisd.bds;
*/
public final class UnknownFormat1_0 extends Format
{
+ private static final String FORMAT_CODE = "UNKNOWN";
/**
* The one and only one instance.
*/
@@ -30,7 +31,7 @@ public final class UnknownFormat1_0 extends Format
private UnknownFormat1_0()
{
- super("UNKNOWN", new Version(1, 0), null);
+ super(FORMAT_CODE, new Version(1, 0), null);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index a4943f6174f..89eabf7e6c6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -107,13 +107,13 @@ public class Utilities
public final static int getNumber(final IDirectory directory, final String name)
{
// No assertion here as 'getString(IDirectory, String)' already does it.
- String value = getTrimmedString(directory, name);
+ final String value = getTrimmedString(directory, name);
try
{
return Integer.parseInt(value);
} catch (NumberFormatException ex)
{
- throw new DataStructureException("Value of " + name + " version file is not a number: " + value);
+ throw new DataStructureException("Value of '" + name + "' version file is not a number: " + value);
}
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Channel.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
similarity index 94%
rename from bds/source/java/ch/systemsx/cisd/bds/Channel.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
index 72b6d170c55..0620cdc5c1f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Channel.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
@@ -14,8 +14,11 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds;
+package ch.systemsx.cisd.bds.hcs;
+import ch.systemsx.cisd.bds.DataStructureException;
+import ch.systemsx.cisd.bds.IStorable;
+import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ChannelList.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
similarity index 94%
rename from bds/source/java/ch/systemsx/cisd/bds/ChannelList.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
index e13741a1d9f..a724bb74054 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ChannelList.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
@@ -14,12 +14,14 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds;
+package ch.systemsx.cisd.bds.hcs;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
+import ch.systemsx.cisd.bds.DataStructureException;
+import ch.systemsx.cisd.bds.IStorable;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.INode;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
new file mode 100644
index 00000000000..68a780cb445
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright 2007 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.bds.hcs;
+
+import ch.systemsx.cisd.bds.FormatParameter;
+import ch.systemsx.cisd.bds.IFormatParameterFactory;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.INode;
+
+/**
+ * A customized <code>IFormatParameterFactory</code> implementation suitable for <i>HCS (High-Content Screening) with
+ * Images</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class FormatParameterFactory implements IFormatParameterFactory
+{
+
+ //
+ // IFormatParameterFactory
+ //
+
+ public final FormatParameter createFormatParameter(final INode node)
+ {
+ assert node != null : "Given node can not be null.";
+ final String nodeName = node.getName();
+ if (node instanceof IDirectory)
+ {
+ final IDirectory directory = (IDirectory) node;
+ if (nodeName.equals(PlateGeometry.PLATE_GEOMETRY))
+ {
+ return new FormatParameter(nodeName, PlateGeometry.loadFrom(directory));
+ } else if (nodeName.equals(WellGeometry.WELL_GEOMETRY))
+ {
+ return new FormatParameter(nodeName, WellGeometry.loadFrom(directory));
+ } else if (nodeName.equals(ChannelList.NUMBER_OF_CHANNELS))
+ {
+ return new FormatParameter(nodeName, ChannelList.loadFrom(directory));
+ } else
+ {
+ // Probably 'channelN'. As already loaded, returns null here.
+ return null;
+ }
+ }
+ return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(node);
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Geometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
similarity index 90%
rename from bds/source/java/ch/systemsx/cisd/bds/Geometry.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
index abafed7aa27..d4e13d270ba 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Geometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
@@ -14,8 +14,10 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds;
+package ch.systemsx.cisd.bds.hcs;
+import ch.systemsx.cisd.bds.IStorable;
+import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
@@ -73,6 +75,8 @@ public class Geometry implements IStorable
*/
final static Geometry loadFrom(final IDirectory directory, final String geometryDirectoryName)
{
+ assert directory != null : "Given directory can not be null.";
+ assert geometryDirectoryName != null && geometryDirectoryName.trim().length() > 0 : "Given subdirectory name can not be empty.";
final IDirectory geometryFolder = Utilities.getSubDirectory(directory, geometryDirectoryName);
return new Geometry(Utilities.getNumber(geometryFolder, ROWS), Utilities.getNumber(geometryFolder, COLUMNS));
}
@@ -83,6 +87,7 @@ public class Geometry implements IStorable
public final void saveTo(final IDirectory directory)
{
+ assert directory != null : "Given directory can not be null.";
final IDirectory geometryDirectory = directory.makeDirectory(getGeometryDirectoryName());
geometryDirectory.addKeyValuePair(ROWS, toString(getRows()));
geometryDirectory.addKeyValuePair(COLUMNS, toString(getColumns()));
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java
new file mode 100644
index 00000000000..6ad2a41c4ec
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2007 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.bds.hcs;
+
+import ch.systemsx.cisd.bds.Format;
+import ch.systemsx.cisd.bds.Version;
+
+/**
+ * <code>Format</code> extension for <i>HCS (High-Content Screening) with Images</i>.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ImageHCSFormat1_0 extends Format
+{
+
+ private static final String FORMAT_CODE = "IMAGE_HCS";
+
+ /** Key for setting the measurement device that was used to take the data of this data set. */
+ public final static String DEVICE_ID = "device_id";
+
+ /**
+ * Flag ({@link Boolean#TRUE} or {@link Boolean#FALSE}) specifying whether the data directory contains the
+ * original data or not.
+ */
+ public final static String CONTAINS_ORIGINAL_DATA = "contains_original_data";
+
+ /**
+ * The one and only one instance.
+ */
+ public static final Format UNKNOWN_1_0 = new ImageHCSFormat1_0();
+
+ private ImageHCSFormat1_0()
+ {
+ super(FORMAT_CODE, new Version(1, 0), null);
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java
similarity index 97%
rename from bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java
index bbb35951e68..c1d862af86b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/PlateGeometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/PlateGeometry.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds;
+package ch.systemsx.cisd.bds.hcs;
import ch.systemsx.cisd.bds.storage.IDirectory;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java
similarity index 97%
rename from bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java
index 893e9b6ef06..5dc44524530 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/WellGeometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/WellGeometry.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds;
+package ch.systemsx.cisd.bds.hcs;
import ch.systemsx.cisd.bds.storage.IDirectory;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
index f851a4c3d93..9e394e94777 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.bds.storage.filesystem;
import java.io.IOException;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -39,25 +41,58 @@ public final class NodeFactory
public static INode createNode(final java.io.File file) throws EnvironmentFailureException
{
assert file != null : "Unspecified node";
- String absolutePath = file.getAbsolutePath();
+ final String absolutePath = file.getAbsolutePath();
+ final String canonicalPath = getCanonicalPath(file);
+ if (absolutePath.equals(canonicalPath) == false)
+ {
+ return createLinkNode(file);
+ }
+ if (file.isDirectory())
+ {
+ return createDirectoryNode(file);
+ }
+ return createFileNode(file);
+ }
+
+ private final static String getCanonicalPath(final java.io.File file)
+ {
+ assert file != null : "Unspecified node";
try
{
- String canonicalPath = file.getCanonicalPath();
- if (absolutePath.equals(canonicalPath) == false)
- {
- return new Link(file.getName(), createNode(new java.io.File(canonicalPath)));
- }
- if (file.isDirectory())
- {
- return new Directory(file);
- }
- return new File(file);
+ return file.getCanonicalPath();
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't get canonical path of file " + absolutePath, ex);
+ throw new EnvironmentFailureException("Couldn't get canonical path of file '" + file.getAbsolutePath()
+ + "'", ex);
}
}
+ private static Link createLinkNode(final java.io.File file) throws EnvironmentFailureException
+ {
+ final String absolutePath = file.getAbsolutePath();
+ final String canonicalPath = getCanonicalPath(file);
+ assert absolutePath.equals(canonicalPath) == false : "Given file must be a link";
+ return new Link(file.getName(), createNode(new java.io.File(getCanonicalPath(file))));
+ }
+
+ /**
+ * Creates a <code>IFile</code> from given <var>file</var>.
+ */
+ public final static IFile createFileNode(final java.io.File file)
+ {
+ assert file != null && file.isFile() : "Given file must be a file";
+ return new File(file);
+ }
+
+ /**
+ * Creates a <code>IDirectory</code> from given <var>file</var>.
+ */
+ public final static IDirectory createDirectoryNode(final java.io.File file)
+ {
+ assert file != null && file.isDirectory() : "Given file must be a directory";
+ return new Directory(file);
+ }
+
private NodeFactory()
{
// Can not be instantiated.
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/ChecksumBuilderTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/ChecksumBuilderTest.java
index 56291627349..a2806d8ffa1 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/ChecksumBuilderTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/ChecksumBuilderTest.java
@@ -25,11 +25,10 @@ import java.io.IOException;
import java.util.Random;
import org.apache.commons.io.IOUtils;
-import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
-import ch.systemsx.cisd.common.logging.LogInitializer;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
@@ -37,43 +36,28 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
*
* @author Christian Ribeaud
*/
-public class ChecksumBuilderTest
+public class ChecksumBuilderTest extends AbstractFileSystemTestCase
{
- private static final File UNIT_TEST_ROOT_DIRECTORY = new File("targets" + File.separator + "unit-test-wd");
-
- private static final File WORKING_DIRECTORY =
- new File(UNIT_TEST_ROOT_DIRECTORY, ChecksumBuilderTest.class.getSimpleName());
-
- private ChecksumBuilder checksumBuilder;
-
- @BeforeMethod
- public final void setUp()
- {
- checksumBuilder = new ChecksumBuilder(new MD5ChecksumCalculator());
- LogInitializer.init();
- WORKING_DIRECTORY.mkdirs();
- assert WORKING_DIRECTORY.isDirectory();
- WORKING_DIRECTORY.deleteOnExit();
- }
+ private ChecksumBuilder checksumBuilder = new ChecksumBuilder(new MD5ChecksumCalculator());
@Test
public final void testBuildChecksumsForAllFilesIn() throws Exception
{
- FileUtilities.writeToFile(new File(WORKING_DIRECTORY, "file1"), "This is my first file.");
- FileUtilities.writeToFile(new File(WORKING_DIRECTORY, "abracadabra"), "This is my second file.");
- fillWithRandomBytes(new File(WORKING_DIRECTORY, "bigBinaryFile"));
-
- File dir = new File(WORKING_DIRECTORY, "dir");
+ FileUtilities.writeToFile(new File(workingDirectory, "file1"), "This is my first file.");
+ FileUtilities.writeToFile(new File(workingDirectory, "abracadabra"), "This is my second file.");
+ fillWithRandomBytes(new File(workingDirectory, "bigBinaryFile"));
+
+ File dir = new File(workingDirectory, "dir");
dir.mkdir();
FileUtilities.writeToFile(new File(dir, "file2"), "This is my fourth file.");
FileUtilities.writeToFile(new File(dir, "escargot.png"), "This is my fifth file.");
FileUtilities.writeToFile(new File(dir, "barbapapa"), "This is my sixth file.");
-
- FileStorage fileStorage = new FileStorage(WORKING_DIRECTORY);
+
+ FileStorage fileStorage = new FileStorage(workingDirectory);
fileStorage.mount();
-
+
String checksums = checksumBuilder.buildChecksumsForAllFilesIn(fileStorage.getRoot());
-
+
assertEquals("31b98e3c4af8d09595dcef2ce8232fbd abracadabra" + LINE_SEPARATOR
+ "90d87b30f70e265e9653356917320679 bigBinaryFile" + LINE_SEPARATOR
+ "23b541115335bbe719c447bb9c942b1a dir/barbapapa" + LINE_SEPARATOR
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
index d16f1db54a4..908ba9ce5f4 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
@@ -16,49 +16,33 @@
package ch.systemsx.cisd.bds;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.fail;
+
import java.io.File;
-import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.common.utilities.FileUtilities;
-
-import static org.testng.AssertJUnit.*;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
/**
* Test cases for corresponding {@link Utilities} class.
*
* @author Christian Ribeaud
*/
-public class UtilitiesTest
+public class UtilitiesTest extends AbstractFileSystemTestCase
{
- private static final File UNIT_TEST_ROOT_DIRECTORY = new File("targets" + File.separator + "unit-test-wd");
-
- private static final File WORKING_DIRECTORY =
- new File(UNIT_TEST_ROOT_DIRECTORY, UtilitiesTest.class.getSimpleName());
-
- @BeforeMethod
- public final void setUp()
- {
- LogInitializer.init();
- FileUtilities.deleteRecursively(WORKING_DIRECTORY);
- WORKING_DIRECTORY.mkdirs();
- assert WORKING_DIRECTORY.isDirectory() && WORKING_DIRECTORY.listFiles().length == 0;
- WORKING_DIRECTORY.deleteOnExit();
- }
-
@Test
public final void testGetNumber()
{
- final IDirectory directory = (IDirectory) NodeFactory.createNode(WORKING_DIRECTORY);
+ final IDirectory directory = (IDirectory) NodeFactory.createNode(workingDirectory);
final String key = "age";
final String value = "35";
final IFile file = directory.addKeyValuePair(key, value);
- final File[] listFiles = WORKING_DIRECTORY.listFiles();
+ final File[] listFiles = workingDirectory.listFiles();
assertEquals(1, listFiles.length);
assertEquals(key, listFiles[0].getName());
assertEquals(value, file.getStringContent().trim());
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ChannelListTest.java
similarity index 53%
rename from bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java
rename to bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ChannelListTest.java
index ef403ea8980..8612226cba7 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/StorageTestCase.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ChannelListTest.java
@@ -14,28 +14,14 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.bds.storage.filesystem;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.commons.io.FileUtils;
-import org.testng.annotations.BeforeMethod;
+package ch.systemsx.cisd.bds.hcs;
/**
- * An <code>abtract</code> storage test case.
+ * Test cases for corresponding {@link ChannelList} class.
*
- * @author Franz-Josef Elmer
+ * @author Christian Ribeaud
*/
-public abstract class StorageTestCase
+public final class ChannelListTest
{
- static final File TEST_DIR = new File("targets" + File.separator + "unit-test-wd");
-
- @BeforeMethod
- public void setup() throws IOException
- {
- TEST_DIR.mkdirs();
- FileUtils.cleanDirectory(TEST_DIR);
- }
-}
+}
\ No newline at end of file
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
new file mode 100644
index 00000000000..46169eda698
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
@@ -0,0 +1,89 @@
+/*
+ * Copyright 2007 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.bds.hcs;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.*;
+
+import java.io.File;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
+
+/**
+ * Test cases for corresponding {@link PlateGeometry} class.
+ *
+ * @author Christian Ribeaud
+ */
+public final class PlateGeometryTest extends AbstractFileSystemTestCase
+{
+
+ private final Geometry geometry = new PlateGeometry(2, 3);
+
+ @Test
+ public final void testConstructor()
+ {
+ try
+ {
+ new PlateGeometry(-1, 0);
+ fail("Rows and columns must be > 0.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here.
+ }
+ }
+
+ @Test
+ public final void testEquals()
+ {
+ assertEquals(new PlateGeometry(2, 3), geometry);
+ assertFalse(new PlateGeometry(3, 2).equals(geometry));
+ assertFalse(geometry.equals(null));
+ }
+
+ @Test
+ public final void testSaveTo()
+ {
+ final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
+ geometry.saveTo(dir);
+ File[] files = workingDirectory.listFiles();
+ assertEquals(1, files.length);
+ final File geometryDir = files[0];
+ assertTrue(geometryDir.isDirectory());
+ assertEquals(PlateGeometry.PLATE_GEOMETRY, geometryDir.getName());
+ files = geometryDir.listFiles();
+ assertEquals(2, files.length);
+ assertEquals(PlateGeometry.COLUMNS, files[0].getName());
+ assertEquals(PlateGeometry.ROWS, files[1].getName());
+ }
+
+ @Test(dependsOnMethods = "testSaveTo")
+ public final void testLoadFrom()
+ {
+ testSaveTo();
+ final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
+ final Geometry loaded = PlateGeometry.loadFrom(dir);
+ assertNotNull(loaded);
+ assertTrue(loaded.getRows() == 2);
+ assertTrue(loaded.getColumns() == 3);
+ }
+}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
new file mode 100644
index 00000000000..142d4f763a1
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2007 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.bds.hcs;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
+
+import java.io.File;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
+
+/**
+ * Test cases for corresponding {@link WellGeometry} class.
+ *
+ * @author Christian Ribeaud
+ */
+public final class WellGeometryTest extends AbstractFileSystemTestCase
+{
+ private final Geometry geometry = new WellGeometry(2, 3);
+
+ @Test
+ public final void testConstructor()
+ {
+ try
+ {
+ new WellGeometry(-1, 0);
+ fail("Rows and columns must be > 0.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here.
+ }
+ }
+
+ @Test
+ public final void testEquals()
+ {
+ assertEquals(new WellGeometry(2, 3), geometry);
+ assertFalse(new WellGeometry(3, 2).equals(geometry));
+ assertFalse(geometry.equals(null));
+ }
+
+ @Test
+ public final void testSaveTo()
+ {
+ final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
+ geometry.saveTo(dir);
+ File[] files = workingDirectory.listFiles();
+ assertEquals(1, files.length);
+ final File geometryDir = files[0];
+ assertTrue(geometryDir.isDirectory());
+ assertEquals(WellGeometry.WELL_GEOMETRY, geometryDir.getName());
+ files = geometryDir.listFiles();
+ assertEquals(2, files.length);
+ assertEquals(WellGeometry.COLUMNS, files[0].getName());
+ assertEquals(WellGeometry.ROWS, files[1].getName());
+ }
+
+ @Test(dependsOnMethods = "testSaveTo")
+ public final void testLoadFrom()
+ {
+ testSaveTo();
+ final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
+ final Geometry loaded = WellGeometry.loadFrom(dir);
+ assertNotNull(loaded);
+ assertTrue(loaded.getRows() == 2);
+ assertTrue(loaded.getColumns() == 3);
+ }
+
+}
\ No newline at end of file
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
index ef286616652..597de4c2dfd 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/DirectoryTest.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
import ch.systemsx.cisd.bds.storage.StorageException;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
@@ -38,18 +39,18 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
*
* @author Franz-Josef Elmer
*/
-public class DirectoryTest extends StorageTestCase
+public final class DirectoryTest extends AbstractFileSystemTestCase
{
private final void testInternalAddFile(final boolean move)
{
- File dir = new File(TEST_DIR, "dir");
+ File dir = new File(workingDirectory, "dir");
dir.mkdirs();
FileUtilities.writeToFile(new File(dir, "p1"), "property 1");
File subDir = new File(dir, "subdir");
subDir.mkdir();
FileUtilities.writeToFile(new File(subDir, "p2"), "property 2");
- File dest = new File(TEST_DIR, "destination");
+ File dest = new File(workingDirectory, "destination");
dest.mkdir();
Directory directory = new Directory(dest);
INode copiedDir = directory.addFile(dir, move);
@@ -74,24 +75,24 @@ public class DirectoryTest extends StorageTestCase
assertTrue(node instanceof IFile);
assertEquals("property 2\n", ((IFile) node).getStringContent());
assertEquals("property 2\n", FileUtilities.loadToString(new File(copiedRealSubDir, "p2")));
- assertEquals(move == false, new File(TEST_DIR, "dir").exists());
+ assertEquals(move == false, new File(workingDirectory, "dir").exists());
}
@Test
public void testGetName()
{
- Directory directory = new Directory(TEST_DIR);
- assertEquals(TEST_DIR.getName(), directory.getName());
+ Directory directory = new Directory(workingDirectory);
+ assertEquals(workingDirectory.getName(), directory.getName());
}
@Test
public void testMakeDirectory()
{
- Directory directory = new Directory(TEST_DIR);
+ Directory directory = new Directory(workingDirectory);
IDirectory subdirectory = directory.makeDirectory("sub-directory");
assertEquals("sub-directory", subdirectory.getName());
- File subdir = new File(TEST_DIR, "sub-directory");
+ File subdir = new File(workingDirectory, "sub-directory");
assertEquals(true, subdir.exists());
assertEquals(true, subdir.isDirectory());
}
@@ -99,12 +100,12 @@ public class DirectoryTest extends StorageTestCase
@Test
public void testMakeDirectoryTwice()
{
- Directory directory = new Directory(TEST_DIR);
+ Directory directory = new Directory(workingDirectory);
directory.makeDirectory("sub-directory");
IDirectory subdirectory = directory.makeDirectory("sub-directory");
assertEquals("sub-directory", subdirectory.getName());
- File subdir = new File(TEST_DIR, "sub-directory");
+ File subdir = new File(workingDirectory, "sub-directory");
assertEquals(true, subdir.exists());
assertEquals(true, subdir.isDirectory());
}
@@ -112,7 +113,7 @@ public class DirectoryTest extends StorageTestCase
@Test
public void testMakeDirectoryButThereIsAlreadyAFileWithSameName()
{
- Directory directory = new Directory(TEST_DIR);
+ Directory directory = new Directory(workingDirectory);
directory.addKeyValuePair("sub-directory", "value");
try
{
@@ -127,21 +128,21 @@ public class DirectoryTest extends StorageTestCase
@Test
public void testAddKeyValuePair()
{
- IFile stringFile = new Directory(TEST_DIR).addKeyValuePair("answer", "42");
- assertEquals("42\n", FileUtilities.loadToString(new File(TEST_DIR, "answer")));
+ IFile stringFile = new Directory(workingDirectory).addKeyValuePair("answer", "42");
+ assertEquals("42\n", FileUtilities.loadToString(new File(workingDirectory, "answer")));
assertEquals("42\n", stringFile.getStringContent());
}
@Test
public void testExtractTo()
{
- File dir = new File(TEST_DIR, "dir");
+ File dir = new File(workingDirectory, "dir");
dir.mkdirs();
Directory directory = new Directory(dir);
directory.addKeyValuePair("p1", "property 1");
IDirectory subdir = directory.makeDirectory("subdir");
subdir.addKeyValuePair("p2", "property 2");
- File destination = new File(TEST_DIR, "destination");
+ File destination = new File(workingDirectory, "destination");
assertFalse(destination.exists());
directory.extractTo(destination);
assertTrue(destination.exists());
@@ -152,31 +153,31 @@ public class DirectoryTest extends StorageTestCase
assertTrue(copiedSubDir.isDirectory());
assertEquals("property 2\n", FileUtilities.loadToString(new File(copiedSubDir, "p2")));
// Source directory still exists
- assertEquals(true, new File(TEST_DIR, "dir").exists());
+ assertEquals(true, new File(workingDirectory, "dir").exists());
}
@Test
public void testMoveTo()
{
- File dir = new File(TEST_DIR, "dir");
+ File dir = new File(workingDirectory, "dir");
dir.mkdirs();
IDirectory directory = new Directory(dir);
directory.addKeyValuePair("p1", "property 1");
IDirectory subdir = directory.makeDirectory("subdir");
subdir.addKeyValuePair("p2", "property 2");
- subdir.moveTo(TEST_DIR);
-
+ subdir.moveTo(workingDirectory);
+
Iterator<INode> iterator = directory.iterator();
assertEquals(true, iterator.hasNext());
INode node = iterator.next();
assertEquals("p1", node.getName());
assertEquals("property 1", ((IFile) node).getStringContent().trim());
assertEquals(false, iterator.hasNext());
- File subdir2 = new File(TEST_DIR, "subdir");
+ File subdir2 = new File(workingDirectory, "subdir");
assertEquals(true, subdir2.isDirectory());
assertEquals("property 2", FileUtilities.loadToString(new File(subdir2, "p2")).trim());
}
-
+
@Test
public void testAddFileWithCopy()
{
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
index 60dfaf09542..a17ec92b676 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorageTest.java
@@ -22,26 +22,27 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.StorageException;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
/**
+ * Test cases for corresponding {@link FileStorage} class.
*
- *
* @author Franz-Josef Elmer
*/
-public class FileStorageTest extends StorageTestCase
+public final class FileStorageTest extends AbstractFileSystemTestCase
{
@Test
public void testGetRoot()
{
- FileStorage fileStorage = new FileStorage(TEST_DIR);
+ FileStorage fileStorage = new FileStorage(workingDirectory);
fileStorage.mount();
- assertEquals(TEST_DIR.getName(), fileStorage.getRoot().getName());
+ assertEquals(workingDirectory.getName(), fileStorage.getRoot().getName());
}
-
+
@Test
public void testGetRootOfNeverMountedStorage()
{
- FileStorage fileStorage = new FileStorage(TEST_DIR);
+ FileStorage fileStorage = new FileStorage(workingDirectory);
try
{
fileStorage.getRoot();
@@ -51,11 +52,11 @@ public class FileStorageTest extends StorageTestCase
assertEquals("Can not get root of an unmounted storage.", e.getMessage());
}
}
-
+
@Test
public void testGetRootOfUnMountedStorage()
{
- FileStorage fileStorage = new FileStorage(TEST_DIR);
+ FileStorage fileStorage = new FileStorage(workingDirectory);
fileStorage.mount();
fileStorage.unmount();
try
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
index 1de18aeec8e..e834a0f16b9 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
@@ -27,17 +27,20 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
+ * Test cases for corresponding {@link File} class.
+ *
* @author Franz-Josef Elmer
*/
-public class FileTest extends StorageTestCase
+public final class FileTest extends AbstractFileSystemTestCase
{
@Test
public void testGetValueAndGetName()
{
- java.io.File file = new java.io.File(TEST_DIR, "test.txt");
+ java.io.File file = new java.io.File(workingDirectory, "test.txt");
FileUtilities.writeToFile(file, "Hello\nworld!\n");
File stringFile = new File(file);
@@ -49,11 +52,11 @@ public class FileTest extends StorageTestCase
@Test
public void testExtractTo()
{
- java.io.File file = new java.io.File(TEST_DIR, "test.txt");
+ java.io.File file = new java.io.File(workingDirectory, "test.txt");
FileUtilities.writeToFile(file, "Hello\nworld!\n");
File stringFile = new File(file);
- java.io.File subdir = new java.io.File(TEST_DIR, "subdir");
+ java.io.File subdir = new java.io.File(workingDirectory, "subdir");
subdir.mkdir();
stringFile.extractTo(subdir);
assertEquals("Hello\nworld!\n", FileUtilities.loadToString(new java.io.File(subdir, stringFile.getName())));
@@ -62,26 +65,27 @@ public class FileTest extends StorageTestCase
@Test
public void testMoveTo()
{
- java.io.File dir = new java.io.File(TEST_DIR, "dir");
+ java.io.File dir = new java.io.File(workingDirectory, "dir");
dir.mkdirs();
IDirectory directory = new Directory(dir);
IFile file = directory.addKeyValuePair("p1", "property 1");
-
- file.moveTo(TEST_DIR);
-
+
+ file.moveTo(workingDirectory);
+
assertEquals(false, directory.iterator().hasNext());
- assertEquals("property 1", FileUtilities.loadToString(new java.io.File(TEST_DIR, "p1")).trim());
+ assertEquals("property 1", FileUtilities.loadToString(new java.io.File(workingDirectory, "p1")).trim());
}
-
+
@Test
public void testGetInputStream() throws Exception
{
- java.io.File file = new java.io.File(TEST_DIR, "test");
+ java.io.File file = new java.io.File(workingDirectory, "test");
FileOutputStream fileOutputStream = null;
try
{
fileOutputStream = new FileOutputStream(file);
- fileOutputStream.write(new byte[] {1, 2, 3, 4});
+ fileOutputStream.write(new byte[]
+ { 1, 2, 3, 4 });
} catch (IOException ex)
{
throw ex;
@@ -89,7 +93,7 @@ public class FileTest extends StorageTestCase
{
IOUtils.closeQuietly(fileOutputStream);
}
-
+
File binaryFile = new File(file);
InputStream inputStream = binaryFile.getInputStream();
try
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
index ff9b70135ed..330335e396a 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
@@ -24,19 +24,20 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
+ * Test cases for corresponding {@link NodeFactory} class.
*
* @author Franz-Josef Elmer
*/
-public class NodeFactoryTest extends StorageTestCase
+public class NodeFactoryTest extends AbstractFileSystemTestCase
{
@Test
public void testCreateFileNode()
{
- java.io.File file = new java.io.File(TEST_DIR, "text.txt");
+ java.io.File file = new java.io.File(workingDirectory, "text.txt");
FileUtilities.writeToFile(file, "hello");
INode node = NodeFactory.createNode(file);
assertTrue(node instanceof IFile);
@@ -46,7 +47,7 @@ public class NodeFactoryTest extends StorageTestCase
@Test
public void testCreateDirectoryNode()
{
- java.io.File file = new java.io.File(TEST_DIR, "dir");
+ java.io.File file = new java.io.File(workingDirectory, "dir");
file.mkdir();
INode node = NodeFactory.createNode(file);
assertTrue(node instanceof IDirectory);
--
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