diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
index e4b5baa0e31e39cab03774a3ea8e5adb42596e57..d7e4b8c220ba79f08f0c15aa96baf20ebf2027b8 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureFactory.java
@@ -20,45 +20,45 @@ import ch.systemsx.cisd.bds.storage.IStorage;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
- * Factory of data structures.
- * Currently only structures compatible with Version 1.0 can be created.
- *
+ * Factory of data structures. Currently only structures compatible with Version 1.0 can be created.
+ *
* @author Franz-Josef Elmer
*/
public class DataStructureFactory
{
private static final Factory<IDataStructure> factory = new Factory<IDataStructure>();
-
+
static
{
factory.register(new Version(1, 0), DataStructureV1_0.class);
}
-
+
/**
* Returns the class of the object returned after invoking {@link #createDataStructure(IStorage, Version)}.
*
* @param version Version of the data structure.
* @throws DataStructureException if no data structure can be created for the specified version.
*/
- public static Class<? extends IDataStructure> getDataStructureClassFor(Version version)
+ public static Class<? extends IDataStructure> getDataStructureClassFor(final Version version)
{
return factory.getClassFor(version);
}
-
+
/**
* Creates a data structure for the specified version.
*
* @param storage Storage behind the data structure.
* @param version Version of the data structure to be created.
- * @throws EnvironmentFailureException found data structure class has not an appropriated constructor.
+ * @throws EnvironmentFailureException found data structure class has not an appropriated constructor.
* @throws DataStructureException if no data structure can be created for the specified version.
*/
- public static IDataStructure createDataStructure(IStorage storage, Version version)
+ public static IDataStructure createDataStructure(final IStorage storage, final Version version)
{
return factory.create(IStorage.class, storage, version);
}
private DataStructureFactory()
{
+ // Can not be instantiated
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
index 9f6ddd0e4bdfa4fdd6f6a80abf13bcfb0d226ca8..8783190a7ac990d80aa8885e2925932232dbca82 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
@@ -23,8 +23,8 @@ import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
import ch.systemsx.cisd.bds.storage.hdf5.HDF5Storage;
/**
- * Loader for {@link IDataStructure}s from the file system.
- *
+ * Loader for {@link IDataStructure}s from the file system.
+ *
* @author Franz-Josef Elmer
*/
public class DataStructureLoader
@@ -34,7 +34,7 @@ public class DataStructureLoader
/**
* Creates an instance for the specified base directory where all data structures to be loaded have to exist.
*/
- public DataStructureLoader(File baseDir)
+ public DataStructureLoader(final File baseDir)
{
assert baseDir != null : "Unspecified base directory.";
assert baseDir.isDirectory() : "Is not a directory : " + baseDir.getAbsolutePath();
@@ -44,19 +44,19 @@ public class DataStructureLoader
/**
* Loads the data structure with specified name.
*/
- public IDataStructure load(String name)
+ public final IDataStructure load(final String name)
{
- IStorage storage = createStorage(name);
+ final IStorage storage = createStorage(name);
storage.mount();
- Version version = Version.loadFrom(storage.getRoot());
- IDataStructure dataStructure = DataStructureFactory.createDataStructure(storage, version);
+ final Version version = Version.loadFrom(storage.getRoot());
+ final IDataStructure dataStructure = DataStructureFactory.createDataStructure(storage, version);
dataStructure.open();
return dataStructure;
}
-
- private IStorage createStorage(String name)
+
+ private final IStorage createStorage(final String name)
{
- File file = new File(baseDir, name);
+ final File file = new File(baseDir, name);
if (file.exists() == false)
{
throw new DataStructureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
@@ -65,13 +65,13 @@ public class DataStructureLoader
{
return new FileStorage(file);
}
- File hdf5File = new File(baseDir, name + ".hdf5");
+ final File hdf5File = new File(baseDir, name + ".hdf5");
if (hdf5File.exists())
{
return new HDF5Storage(hdf5File);
}
throw new DataStructureException("Couldn't found appropriate container named '" + name + "' in "
+ baseDir.getAbsolutePath());
-
+
}
}
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 71899de46daf2ed1557d625cba0f61ac313ccf0b..79f7f406f632decac59ae2017cb97280fcc5a953 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -39,17 +39,17 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
*/
public class DataStructureV1_0 extends AbstractDataStructure
{
- static final String CHECKSUM_DIRECTORY = "md5sum";
+ public static final String CHECKSUM_DIRECTORY = "md5sum";
- static final String DIR_METADATA = "metadata";
+ public static final String DIR_METADATA = "metadata";
- static final String DIR_PARAMETERS = "parameters";
+ public static final String DIR_PARAMETERS = "parameters";
- static final String DIR_DATA = "data";
+ public static final String DIR_DATA = "data";
- static final String DIR_ORIGINAL = "original";
+ public static final String DIR_ORIGINAL = "original";
- static final String MAPPING_FILE = "standard_original_mapping";
+ public static final String MAPPING_FILE = "standard_original_mapping";
private static final Version VERSION = new Version(1, 0);
@@ -106,11 +106,12 @@ public class DataStructureV1_0 extends AbstractDataStructure
/**
* Sets the data format of this structure.
*/
- public void setFormat(Format format)
+ public final void setFormat(final Format format)
{
assert format != null : "Unspecified format.";
assertOpenOrCreated();
this.format = format;
+ formatParameters.setFormatParameterFactory(format.getFormatParameterFactory());
}
/**
@@ -118,7 +119,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
*
* @throws IllegalArgumentException if they is already a parameter with same name as <code>parameter</code>.
*/
- public void addFormatParameter(FormatParameter formatParameter)
+ public void addFormatParameter(final FormatParameter formatParameter)
{
assert formatParameter != null : "Unspecified format parameter.";
formatParameters.addParameter(formatParameter);
@@ -257,15 +258,6 @@ 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/Format.java b/bds/source/java/ch/systemsx/cisd/bds/Format.java
index ed66c35b628860f156e32e9d2b0c60facfdf7cd3..8e477ca9984a8ff5ae4e7c57ab4ad69583d7de36 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Format.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Format.java
@@ -21,7 +21,7 @@ import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.INode;
/**
- * Inmutable value object of a versioned format.
+ * Immutable value object of a versioned format.
*
* @author Franz-Josef Elmer
*/
@@ -64,7 +64,12 @@ public class Format implements IStorable
}
variant = ((IFile) file).getStringContent().trim();
}
- return new Format(formatCode, formatVersion, variant);
+ Format format = FormatStore.getFormat(formatCode, formatVersion, variant);
+ if (format == null)
+ {
+ format = new Format(formatCode, formatVersion, variant);
+ }
+ return format;
}
private final String code;
@@ -76,7 +81,7 @@ public class Format implements IStorable
/**
* Creates a new instance based on the specified format code, format variant (optional), and version.
*/
- public Format(String code, Version version, String variantOrNull)
+ public Format(final String code, final Version version, final String variantOrNull)
{
assert code != null : "Unspecified format code.";
assert version != null : "Unpsecified version.";
@@ -111,6 +116,14 @@ public class Format implements IStorable
return variant;
}
+ /**
+ * Returns the <code>IFormatParameterFactory</code> implementation for this <code>Format</code>.
+ */
+ public IFormatParameterFactory getFormatParameterFactory()
+ {
+ return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY;
+ }
+
//
// IStorable
//
@@ -126,6 +139,10 @@ public class Format implements IStorable
}
}
+ //
+ // Object
+ //
+
@Override
public boolean equals(Object obj)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
index 4d4eefc7bf57a2965fe88d9ecbdb1af90b5ecfdd..15fde98566cc501a288d723e022ee22828794ccf 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
@@ -63,16 +63,12 @@ final class FormatParameters implements IFormatParameters, IStorable
{
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)
+ 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));
+ directory.addKeyValuePair(parameter.getName(), value.toString());
}
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
new file mode 100644
index 0000000000000000000000000000000000000000..10c6a9922963758898430e295dbc061ad6015414
--- /dev/null
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
@@ -0,0 +1,72 @@
+/*
+ * 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 java.util.HashMap;
+import java.util.Map;
+
+import ch.systemsx.cisd.bds.hcs.ImageHCSFormat1_0;
+
+/**
+ * A store of all active formats.
+ *
+ * @author Christian Ribeaud
+ */
+public final class FormatStore
+{
+
+ private final static Map<String, Format> formats = createFormats();
+
+ private FormatStore()
+ {
+ // Can not be instantiated.
+ }
+
+ private final static Map<String, Format> createFormats()
+ {
+ final Map<String, Format> map = new HashMap<String, Format>();
+ map.put(getKey(UnknownFormat1_0.UNKNOWN_1_0), UnknownFormat1_0.UNKNOWN_1_0);
+ map.put(getKey(ImageHCSFormat1_0.IMAGE_HCS_1_0), ImageHCSFormat1_0.IMAGE_HCS_1_0);
+ return map;
+ }
+
+ /** Constructs an unique key for given <var>format</var>. */
+ private final static String getKey(final Format format)
+ {
+ return getKey(format.getCode(), format.getVersion(), format.getVariant());
+ }
+
+ /** Constructs an unique key for given <var>formatCode</var>, <var>version</var> and <var>variant</var>. */
+ private final static String getKey(final String formatCode, final Version version, final String variant)
+ {
+ String key = formatCode + version.toString();
+ if (variant != null)
+ {
+ key += variant;
+ }
+ return key;
+ }
+
+ /**
+ * Returns corresponding <code>Format</code> for given format code, version and format variant.
+ */
+ public final static Format getFormat(final String formatCode, final Version version, final String formatVariant)
+ throws DataStructureException
+ {
+ return formats.get(getKey(formatCode, version, formatVariant));
+ }
+}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 11721a4366375401ed19ad398a4c3016baa16d32..50d63671a170294034c1be832945bcb4e1a2de72 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Version.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.bds.storage.IDirectory;
*
* @author Franz-Josef Elmer
*/
-public final class Version
+public final class Version implements IStorable
{
static final String VERSION = "version";
@@ -97,7 +97,11 @@ public final class Version
return new Version(major, minor - 1);
}
- void saveTo(IDirectory directory)
+ //
+ // IStorable
+ //
+
+ public final void saveTo(IDirectory directory)
{
IDirectory versionFolder = directory.makeDirectory(VERSION);
versionFolder.addKeyValuePair(MAJOR, Integer.toString(major));
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
index d4e13d270ba8f6352ce4d642d2c94adaa2bd11b1..4ef1d7cc001afc0443dbc167849c0639077a1480 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
@@ -72,13 +72,15 @@ public class Geometry implements IStorable
/**
* Loads the geometry from the specified directory.
+ *
+ * @param directory the geometry directory. Its name must start with given <var>geometryDirectoryName</var>.
*/
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));
+ assert directory.getName().startsWith(geometryDirectoryName) : "Given directory name must start with given '"
+ + geometryDirectoryName + "'.";
+ return new Geometry(Utilities.getNumber(directory, ROWS), Utilities.getNumber(directory, COLUMNS));
}
//
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
index 6ad2a41c4ece4f13c23f22abcd979a9205707011..818b7a221c9bb085a71c41523ccaaad7eda2a818 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormat1_0.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.bds.hcs;
import ch.systemsx.cisd.bds.Format;
+import ch.systemsx.cisd.bds.IFormatParameterFactory;
import ch.systemsx.cisd.bds.Version;
/**
@@ -41,10 +42,21 @@ public final class ImageHCSFormat1_0 extends Format
/**
* The one and only one instance.
*/
- public static final Format UNKNOWN_1_0 = new ImageHCSFormat1_0();
+ public static final Format IMAGE_HCS_1_0 = new ImageHCSFormat1_0();
private ImageHCSFormat1_0()
{
super(FORMAT_CODE, new Version(1, 0), null);
}
+
+ //
+ // Format
+ //
+
+ @Override
+ public final IFormatParameterFactory getFormatParameterFactory()
+ {
+ return new FormatParameterFactory();
+ }
+
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
index 24318085fbb78b823d6b71d4a9c7023dbe0baa69..13899c31b63594812993e55daa3e23af3fc465dd 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
@@ -16,37 +16,28 @@
package ch.systemsx.cisd.bds;
-import static ch.systemsx.cisd.bds.DataStructureV1_0Test.TEST_DIR;
import static org.testng.AssertJUnit.assertEquals;
import java.io.File;
-import java.io.IOException;
import java.util.Date;
-import org.apache.commons.io.FileUtils;
-import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
/**
* Test cases for corresponding {@link DataStructureLoader} class.
*
* @author Franz-Josef Elmer
*/
-public class DataStructureLoaderTest
+public final class DataStructureLoaderTest extends AbstractFileSystemTestCase
{
- @BeforeMethod
- public void setUp() throws IOException
- {
- TEST_DIR.mkdirs();
- FileUtils.cleanDirectory(TEST_DIR);
- }
@Test
- public void testOpen()
+ public final void testOpen()
{
- File dir = new File(TEST_DIR, "ds");
+ File dir = new File(workingDirectory, "ds");
assert dir.mkdir();
DataStructureV1_0 dataStructure = new DataStructureV1_0(new FileStorage(dir));
dataStructure.create();
@@ -61,7 +52,7 @@ public class DataStructureLoaderTest
dataStructure.setProcessingType(ProcessingType.RAW_DATA);
dataStructure.close();
- IDataStructure ds = new DataStructureLoader(TEST_DIR).load("ds");
+ IDataStructure ds = new DataStructureLoader(workingDirectory).load("ds");
assertEquals(DataStructureV1_0.class, ds.getClass());
assertEquals(experimentIdentifier, ((DataStructureV1_0) ds).getExperimentIdentifier());
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
index 2e6a3ed0553a660a6beccca5bec1c757fc4ad339..de45734868d8b8dea319aee6e84711e3886a636d 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -23,29 +23,26 @@ import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
-import java.io.File;
import java.io.IOException;
import java.util.Date;
import java.util.Iterator;
import java.util.Map;
-import org.apache.commons.io.FileUtils;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
/**
* Test cases for corresponding {@link DataStructureV1_0} class.
*
* @author Franz-Josef Elmer
*/
-public class DataStructureV1_0Test
+public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
{
- static final File TEST_DIR = new File("targets" + File.separator + "unit-test-wd" + File.separator + "ds");
-
private static void assertPartOfString(String part, String string)
{
assertTrue("Expected <" + part + "> is part of <" + string + ">", string.indexOf(part) >= 0);
@@ -55,12 +52,16 @@ public class DataStructureV1_0Test
private DataStructureV1_0 dataStructure;
+ //
+ // AbstractFileSystemTestCase
+ //
+
+ @Override
@BeforeMethod
- public void setup() throws IOException
+ public final void setup() throws IOException
{
- TEST_DIR.mkdirs();
- FileUtils.cleanDirectory(TEST_DIR);
- storage = new FileStorage(TEST_DIR);
+ super.setup();
+ storage = new FileStorage(workingDirectory);
dataStructure = new DataStructureV1_0(storage);
}
@@ -409,11 +410,11 @@ public class DataStructureV1_0Test
assertEquals(ReferenceType.TRANSFORMED, reference.getReferenceType());
assertEquals("a b/x\tt", reference.getOriginalPath());
checkFormattedData(reloadedDataStructure.getFormattedData());
-
+
IDirectory metaDataDir = Utilities.getSubDirectory(root, DIR_METADATA);
IDirectory checksumDir = Utilities.getSubDirectory(metaDataDir, CHECKSUM_DIRECTORY);
- assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n",
- Utilities.getString(checksumDir, DataStructureV1_0.DIR_ORIGINAL));
+ assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n", Utilities.getString(checksumDir,
+ DataStructureV1_0.DIR_ORIGINAL));
}
private void checkFormattedData(IFormattedData formattedData)
@@ -546,6 +547,5 @@ public class DataStructureV1_0Test
metaData.addKeyValuePair(DataStructureV1_0.MAPPING_FILE, "");
ProcessingType.COMPUTED_DATA.saveTo(metaData);
storage.unmount();
-
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
new file mode 100644
index 0000000000000000000000000000000000000000..77de45b922026deaec137aff2f09e75e92a83385
--- /dev/null
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
@@ -0,0 +1,111 @@
+/*
+ * 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.assertNotNull;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.bds.DataStructureLoader;
+import ch.systemsx.cisd.bds.DataStructureV1_0;
+import ch.systemsx.cisd.bds.ExperimentIdentifier;
+import ch.systemsx.cisd.bds.ExperimentRegistrator;
+import ch.systemsx.cisd.bds.ExperimentRegistratorDate;
+import ch.systemsx.cisd.bds.FormatParameter;
+import ch.systemsx.cisd.bds.IDataStructure;
+import ch.systemsx.cisd.bds.MeasurementEntity;
+import ch.systemsx.cisd.bds.ProcessingType;
+import ch.systemsx.cisd.bds.Version;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
+import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
+
+/**
+ * Test cases for corresponding {@link DataStructureV1_0} class.
+ *
+ * @author Christian Ribeaud
+ */
+public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
+{
+ private FileStorage storage;
+
+ private DataStructureV1_0 dataStructure;
+
+ private final static ChannelList createChannelList()
+ {
+ final List<Channel> list = new ArrayList<Channel>();
+ list.add(new Channel(1, 123));
+ list.add(new Channel(2, 456));
+ return new ChannelList(list);
+ }
+
+ private void createExampleDataStructure()
+ {
+ storage.mount();
+ IDirectory root = storage.getRoot();
+ new Version(1, 0).saveTo(root);
+ final IDirectory data = root.makeDirectory(DataStructureV1_0.DIR_DATA);
+ final IDirectory originalDataDir = data.makeDirectory(DataStructureV1_0.DIR_ORIGINAL);
+ originalDataDir.addKeyValuePair("hello", "world");
+ final IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
+ new ExperimentIdentifier("g", "p", "e").saveTo(metaData);
+ new ExperimentRegistratorDate(new Date(0)).saveTo(metaData);
+ new ExperimentRegistrator("john", "doe", "j@doe").saveTo(metaData);
+ new MeasurementEntity("a", "b").saveTo(metaData);
+ metaData.addKeyValuePair(DataStructureV1_0.MAPPING_FILE, "");
+ ProcessingType.COMPUTED_DATA.saveTo(metaData);
+ storage.unmount();
+ }
+
+ //
+ // AbstractFileSystemTestCase
+ //
+
+ @Override
+ @BeforeMethod
+ public final void setup() throws IOException
+ {
+ super.setup();
+ storage = new FileStorage(workingDirectory);
+ dataStructure = new DataStructureV1_0(storage);
+ }
+
+ @Test
+ public final void testHCSImageDataStructure()
+ {
+ // Creating...
+ dataStructure.create();
+ createExampleDataStructure();
+ dataStructure.setFormat(ImageHCSFormat1_0.IMAGE_HCS_1_0);
+ dataStructure.addFormatParameter(new FormatParameter(ImageHCSFormat1_0.DEVICE_ID, "M1"));
+ dataStructure.addFormatParameter(new FormatParameter(ImageHCSFormat1_0.CONTAINS_ORIGINAL_DATA, Boolean.TRUE));
+ dataStructure.addFormatParameter(new FormatParameter("doesNotMatter", createChannelList()));
+ dataStructure.addFormatParameter(new FormatParameter(PlateGeometry.PLATE_GEOMETRY, new PlateGeometry(2, 3)));
+ dataStructure.addFormatParameter(new FormatParameter(WellGeometry.WELL_GEOMETRY, new WellGeometry(7, 5)));
+ dataStructure.close();
+ // And loading...
+ final IDataStructure ds =
+ new DataStructureLoader(workingDirectory.getParentFile()).load(getClass().getSimpleName());
+ assertNotNull(ds);
+ }
+}
\ 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
index 8559a453648adaad44f6322fbae556f594cd88f8..9485681f345426f26012290d00996e7014e537be 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
@@ -25,6 +25,7 @@ import java.io.File;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
@@ -83,7 +84,8 @@ public final class PlateGeometryTest extends AbstractFileSystemTestCase
{
testSaveTo();
final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
- final Geometry loaded = PlateGeometry.loadFrom(dir);
+ final IDirectory geoDir = Utilities.getOrCreateSubDirectory(dir, PlateGeometry.PLATE_GEOMETRY);
+ final Geometry loaded = PlateGeometry.loadFrom(geoDir);
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
index f8e55586654b10f007c6ea1d6f98cbd4bfb1479d..179ef192b9bee023878e88fe94b2a000694ae78a 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
@@ -26,6 +26,7 @@ import java.io.File;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.bds.Utilities;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
@@ -83,7 +84,8 @@ public final class WellGeometryTest extends AbstractFileSystemTestCase
{
testSaveTo();
final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
- final Geometry loaded = WellGeometry.loadFrom(dir);
+ final IDirectory geoDir = Utilities.getOrCreateSubDirectory(dir, WellGeometry.WELL_GEOMETRY);
+ final Geometry loaded = WellGeometry.loadFrom(geoDir);
assertNotNull(loaded);
assertTrue(loaded.getRows() == 2);
assertTrue(loaded.getColumns() == 3);