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 0ee29e5885408a5b00168725c278b9928aead1a2..691d18834b4164dc97b4b53d1417c606729ec47c 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -91,12 +91,21 @@ public class DataStructureV1_0 extends AbstractDataStructure
/**
* Returns the directory containing the original data.
*/
- public IDirectory getOriginalData()
+ public final IDirectory getOriginalData()
{
assertOpenOrCreated();
return Utilities.getOrCreateSubDirectory(getDataDirectory(), DIR_ORIGINAL);
}
+ /**
+ * Returns the directory containing the standardized data.
+ */
+ public final IDirectory getStandardData()
+ {
+ assertOpenOrCreated();
+ return Utilities.getOrCreateSubDirectory(getDataDirectory(), DIR_STANDARD);
+ }
+
/**
* Returns the formated data. This method can be called only after method {@link #setFormat(Format)} has been
* invoked. If the format is not known {@link UnknownFormat1_0} will be assumed.
@@ -110,8 +119,8 @@ public class DataStructureV1_0 extends AbstractDataStructure
{
throw new DataStructureException("Couldn't create formated data because of unspecified format.");
}
- IDirectory metaData = getMetaDataDirectory();
- return FormatedDataFactory.createFormatedData(metaData, format, UnknownFormat1_0.UNKNOWN_1_0, formatParameters);
+ return FormatedDataFactory.createFormatedData(getDataDirectory(), format, UnknownFormat1_0.UNKNOWN_1_0,
+ formatParameters);
}
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index 74b298c397fea3bf1b0257f7c9252a7abf2a60f4..1dd9765b4d744a2c58752f52cde3c5837cdb5839 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -59,7 +59,8 @@ public class Utilities
INode node = directory.tryToGetNode(name);
if (node == null)
{
- throw new DataStructureException("No directory named '" + name + "' found in " + directory);
+ throw new DataStructureException(String.format("No directory named '%s' found in directory '%s'.", name,
+ directory));
}
if (node instanceof IDirectory == false)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
index b8be51ad8238b848e8fbbfc5c20251dca749f231..8549e0f1f7eaf980e0af46e58ecc2949c2efd6c8 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Christian Ribeaud
*/
-public interface IHCSFormattedData
+public interface IHCSFormattedData extends IFormattedData
{
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
index c155ae38f06b5e4a3026083f544b4149bb0bdc08..32c8fb762dcc64b0c85b413a24e8ea6d54cca9e0 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedData.java
@@ -36,16 +36,14 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Christian Ribeaud
*/
-// TODO 2007-11-15, Christian Ribeaud: Make a test of this class. Maybe we can extract some of
-// 'HCSDataStructureV1_0Test' class.
public final class ImageHCSFormattedData extends AbstractFormattedData implements IHCSFormattedData
{
/** The <i>column</i> (or <i>x</i>) coordinate. */
- private static final String COLUMN = "column";
+ public static final String COLUMN = "column";
/** The <i>row</i> (or <i>y</i>) coordinate. */
- private static final String ROW = "row";
+ public static final String ROW = "row";
/**
* The mandatory format parameters that must be defined so that this implementation is able to work properly.
@@ -103,16 +101,17 @@ public final class ImageHCSFormattedData extends AbstractFormattedData implement
}
}
- private final static String createWellFileName(final Location wellLocation)
+ /** From given <var>wellLocation</var> creates the leaf file name that is found in <code>data/standard</code>. */
+ final static String createWellFileName(final Location wellLocation)
{
- return ROW + wellLocation.y + COLUMN + wellLocation.x + ".tiff";
+ assert wellLocation != null : "Well location can not be null.";
+ return ROW + wellLocation.y + "_" + COLUMN + wellLocation.x + ".tiff";
}
//
// IHCSFormattedData
//
- // TODO 2007-11-15, Christian Ribeaud: Should we consider to use 'standard_original_mapping' here?
public final INode getNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
throws DataStructureException
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
index c667619d9d7e9cd8715e6c2cf6c46a043b5fcf01..f80754a8a5aa839b5bce4057143ae96ddf849127 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/AbstractNode.java
@@ -24,6 +24,8 @@ import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
+ * An abstract implementation of <code>INode</code>.
+ *
* @author Franz-Josef Elmer
*/
abstract class AbstractNode implements INode
@@ -39,8 +41,8 @@ abstract class AbstractNode implements INode
final boolean successful = source.renameTo(destination);
if (successful == false)
{
- throw EnvironmentFailureException.fromTemplate("Couldn't not move file '%s' to directory '%s'.",
- source.getAbsolutePath(), directory.getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate("Couldn't not move file '%s' to directory '%s'.", source
+ .getAbsolutePath(), directory.getAbsolutePath());
}
}
}
@@ -48,36 +50,49 @@ abstract class AbstractNode implements INode
protected final File nodeFile;
AbstractNode(File file)
+ {
+ checkFile(file);
+ this.nodeFile = file;
+ }
+
+ static void checkFile(final File file)
{
if (file == null)
{
- throw new StorageException("Unspecified file");
+ throw new StorageException("Unspecified file.");
}
if (file.exists() == false)
{
- throw new StorageException("Non existing file " + file);
+ throw new StorageException(String.format("Non existing file '%s'.", file.getAbsolutePath()));
}
- this.nodeFile = file;
}
- public String getName()
+ //
+ // INode
+ //
+
+ public final String getName()
{
return nodeFile.getName();
}
- public IDirectory tryToGetParent()
+ public final IDirectory tryToGetParent()
{
File dir = nodeFile.getParentFile();
return dir == null ? null : new Directory(dir);
}
- public void moveTo(File directory)
+ public final void moveTo(final File directory)
{
moveFileToDirectory(nodeFile, directory);
}
+ //
+ // Object
+ //
+
@Override
- public String toString()
+ public final String toString()
{
return nodeFile.getAbsolutePath();
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
index 963379eea42293a396259a6f343754b45004c649..e71d1f7f7897a2381baa6a3e2348e104f177d9c8 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Directory.java
@@ -34,7 +34,7 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
*
* @author Franz-Josef Elmer
*/
-class Directory extends AbstractNode implements IDirectory
+final class Directory extends AbstractNode implements IDirectory
{
Directory(java.io.File directory)
@@ -42,7 +42,7 @@ class Directory extends AbstractNode implements IDirectory
super(directory);
if (directory.isDirectory() == false)
{
- throw new StorageException("Not a directory: " + directory.getAbsolutePath());
+ throw new StorageException(String.format("Not a directory '%s'.", directory.getAbsolutePath()));
}
}
@@ -50,8 +50,9 @@ class Directory extends AbstractNode implements IDirectory
// IDirectory
//
- public INode tryToGetNode(String name)
+ public final INode tryToGetNode(final String name)
{
+ assert name != null : "Given name can not be null.";
final java.io.File[] files = FileUtilities.listFiles(nodeFile);
for (java.io.File file : files)
{
@@ -63,8 +64,9 @@ class Directory extends AbstractNode implements IDirectory
return null;
}
- public IDirectory makeDirectory(String name)
+ public final IDirectory makeDirectory(final String name)
{
+ assert name != null : "Given name can not be null.";
java.io.File dir = new java.io.File(nodeFile, name);
if (dir.exists())
{
@@ -83,15 +85,18 @@ class Directory extends AbstractNode implements IDirectory
return new Directory(dir);
}
- public IFile addKeyValuePair(String key, String value)
+ public final IFile addKeyValuePair(final String key, final String value)
{
+ assert key != null : "Given key can not be null.";
+ assert value != null : "Given value can not be null.";
java.io.File file = new java.io.File(nodeFile, key);
FileUtilities.writeToFile(file, value);
return new File(file);
}
- public INode addFile(final java.io.File file, final boolean move)
+ public final INode addFile(final java.io.File file, final boolean move)
{
+ checkFile(file);
final java.io.File newFile = new java.io.File(nodeFile, file.getName());
if (move)
{
@@ -116,13 +121,13 @@ class Directory extends AbstractNode implements IDirectory
return NodeFactory.createNode(newFile);
}
- public ILink addLink(String name, INode node)
+ public final ILink addLink(final String name, final INode node)
{
// TODO Auto-generated method stub
return null;
}
- public Iterator<INode> iterator()
+ public final Iterator<INode> iterator()
{
return new Iterator<INode>()
{
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 c98844fd8d21043d367f581d16c0ffb398a64888..d4237b1ee297e7a7d7ac7a82b2bdd9ebde734b5a 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureV1_0Test.java
@@ -32,6 +32,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IStorage;
import ch.systemsx.cisd.bds.storage.StorageException;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
@@ -530,7 +531,12 @@ public final class DataStructureV1_0Test extends AbstractFileSystemTestCase
assertEquals(UnknownFormat1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
}
- private void createExampleDataStructure()
+ private final void createExampleDataStructure()
+ {
+ createExampleDataStructure(storage);
+ }
+
+ public final static void createExampleDataStructure(final IStorage storage)
{
storage.mount();
IDirectory root = storage.getRoot();
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
index cd1f917e94a704e574935ae04b5ed31378016488..a4b19b867d689fbb8578303aabf121f0ff62e263 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureV1_0Test.java
@@ -21,33 +21,30 @@ import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Date;
import java.util.List;
+import org.apache.commons.io.FileUtils;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.DataStructureException;
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.DataStructureV1_0Test;
import ch.systemsx.cisd.bds.Format;
import ch.systemsx.cisd.bds.FormatParameter;
import ch.systemsx.cisd.bds.IDataStructure;
import ch.systemsx.cisd.bds.IFormattedData;
-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.INode;
import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
/**
- * Test cases for corresponding {@link DataStructureV1_0} class.
+ * Test cases for corresponding {@link DataStructureV1_0} class specific to <i>HCS (High-Content Screening) with Images</i>.
*
* @author Christian Ribeaud
*/
@@ -57,6 +54,11 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
private DataStructureV1_0 dataStructure;
+ public HCSDataStructureV1_0Test()
+ {
+ super(false);
+ }
+
private final static ChannelList createChannelList()
{
final List<Channel> list = new ArrayList<Channel>();
@@ -65,24 +67,6 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
return new ChannelList(list);
}
- private final 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();
- }
-
private final void setFormatAndFormatParameters()
{
dataStructure.setFormat(ImageHCSFormat1_0.IMAGE_HCS_1_0);
@@ -120,9 +104,53 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
// Nothing to do here
}
setFormatAndFormatParameters();
- final IFormattedData formatedData = dataStructure.getFormattedData();
- assertTrue(formatedData instanceof ImageHCSFormattedData);
- assertEquals(format, formatedData.getFormat());
+ final IFormattedData formattedData = dataStructure.getFormattedData();
+ assertTrue(formattedData instanceof IHCSFormattedData);
+ assertEquals(format, formattedData.getFormat());
+ }
+
+ @Test
+ public final void testGetNodeAt() throws IOException
+ {
+ dataStructure.create();
+ DataStructureV1_0Test.createExampleDataStructure(storage);
+ setFormatAndFormatParameters();
+ final IDirectory standardData = dataStructure.getStandardData();
+ final IDirectory channelDir = standardData.makeDirectory(Channel.CHANNEL + "1");
+ final IDirectory plateRowDir = channelDir.makeDirectory(ImageHCSFormattedData.ROW + "1");
+ final IDirectory plateColumnDir = plateRowDir.makeDirectory(ImageHCSFormattedData.COLUMN + "1");
+ final String wellFileName = ImageHCSFormattedData.createWellFileName(new Location(1, 1));
+ final File wellFile = new File(workingDirectory, wellFileName);
+ FileUtils.writeStringToFile(wellFile, "This is an image...");
+ plateColumnDir.addFile(wellFile, true);
+ final IHCSFormattedData formattedData = (IHCSFormattedData) dataStructure.getFormattedData();
+ try
+ {
+ formattedData.getNodeAt(3, new Location(1, 1), new Location(1, 1));
+ fail("3 > 2");
+ } catch (IndexOutOfBoundsException ex)
+ {
+ // Nothing to do here.
+ }
+ try
+ {
+ formattedData.getNodeAt(2, new Location(1, 1), new Location(1, 1));
+ fail("No directory named 'channel2' found.");
+ } catch (DataStructureException ex)
+ {
+ assertTrue(ex.getMessage().indexOf("'channel2'") > -1);
+ }
+ try
+ {
+ formattedData.getNodeAt(1, new Location(1, 3), new Location(1, 1));
+ fail("Given geometry '2x3' does not contain location '[x=1,y=3]'.");
+ } catch (IllegalArgumentException ex)
+ {
+ assertTrue(ex.getMessage().indexOf("does not contain location") > -1);
+ }
+ final INode node = formattedData.getNodeAt(1, new Location(1, 1), new Location(1, 1));
+ assertEquals("row1_column1.tiff", node.getName());
+ dataStructure.close();
}
@Test
@@ -130,7 +158,7 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
{
// Creating...
dataStructure.create();
- createExampleDataStructure();
+ DataStructureV1_0Test.createExampleDataStructure(storage);
setFormatAndFormatParameters();
dataStructure.close();
// And loading...
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedDataTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedDataTest.java
index f005cf4394c4cdfbc9e087e6e5f263a678e5fb99..5935ac4ad37370d6c3d2e8092a2c18bd309c377c 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/ImageHCSFormattedDataTest.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.bds.hcs;
+import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.*;
+
/**
* Test cases for corresponding {@link ImageHCSFormattedData} class.
*
@@ -24,4 +27,19 @@ package ch.systemsx.cisd.bds.hcs;
public class ImageHCSFormattedDataTest
{
-}
+ @Test
+ public final void testCreateWellFileName()
+ {
+ try
+ {
+ ImageHCSFormattedData.createWellFileName(null);
+ fail("Location can not be null.");
+ } catch (AssertionError ex)
+ {
+ // Nothing to do here.
+ }
+ final Location location = new Location(1, 2);
+ final String expected = "row2_column1.tiff";
+ assertEquals(expected, ImageHCSFormattedData.createWellFileName(location));
+ }
+}
\ No newline at end of file