diff --git a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
index fd291b6e5d8d9cdc32941fc24f3da54cb1051d87..892a54390ecb8aa2a92721db0a3147dc0a91933b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
@@ -44,6 +44,11 @@ public interface IFormatParameterFactory
}
return null;
}
+
+ public final FormatParameter createFormatParameter(final String name, final String value)
+ {
+ return null;
+ }
};
/**
@@ -53,4 +58,15 @@ public interface IFormatParameterFactory
* <code>INode</code>.
*/
public FormatParameter createFormatParameter(final INode node);
+
+ /**
+ * Creates a <code>FormatParameter</code> from given <var>value</var>.
+ *
+ * @param name name of the format parameter. Usually it is one of the values returned by
+ * {@link Format#getParameterNames()}.
+ * @param value generic value that should help to construct the <code>FormatParameter</code>.
+ * @return <code>null</code> if no appropriate <code>FormatParameter</code> could be created from given
+ * <code>value</code>.
+ */
+ public FormatParameter createFormatParameter(final String name, final String value);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
index 68a780cb445834bdccb233234e8435782cff9e32..f6266bdf0b80bf95bb1e7411d0876947622aa5cc 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
@@ -30,6 +30,23 @@ import ch.systemsx.cisd.bds.storage.INode;
public final class FormatParameterFactory implements IFormatParameterFactory
{
+ private static IFormatParameterFactory instance;
+
+ private FormatParameterFactory()
+ {
+ // Can not be instantiated.
+ }
+
+ /** Returns the unique instance of this class. */
+ public final synchronized static IFormatParameterFactory getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new FormatParameterFactory();
+ }
+ return instance;
+ }
+
//
// IFormatParameterFactory
//
@@ -58,4 +75,27 @@ public final class FormatParameterFactory implements IFormatParameterFactory
}
return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(node);
}
+
+ public final FormatParameter createFormatParameter(final String name, final String value)
+ {
+ if (name.equals(PlateGeometry.PLATE_GEOMETRY))
+ {
+ final Geometry geometry = Geometry.createFromString(value);
+ if (geometry != null)
+ {
+ return new FormatParameter(name, new PlateGeometry(geometry));
+ }
+ } else if (name.equals(WellGeometry.WELL_GEOMETRY))
+ {
+ final Geometry geometry = Geometry.createFromString(value);
+ if (geometry != null)
+ {
+ return new FormatParameter(name, new WellGeometry(geometry));
+ }
+ } else if (name.equals(ChannelList.NUMBER_OF_CHANNELS))
+ {
+ return new FormatParameter(name, ChannelList.createChannelListFromString(value));
+ }
+ return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(name, value);
+ }
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
index 1b0994e18b8bf8b4ba8972ea93136091e176fe62..f6daf488528f3a59255dd0e79177da31762b0b5e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -20,6 +20,7 @@ import java.util.HashSet;
import java.util.Set;
import ch.systemsx.cisd.bds.AbstractFormattedData;
+import ch.systemsx.cisd.bds.Constants;
import ch.systemsx.cisd.bds.DataStructureV1_0;
import ch.systemsx.cisd.bds.Format;
import ch.systemsx.cisd.bds.FormattedDataContext;
@@ -37,7 +38,7 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Christian Ribeaud
*/
-public final class HCSImageFormattedData extends AbstractFormattedData implements IHCSFormattedData
+public final class HCSImageFormattedData extends AbstractFormattedData implements IHCSImageFormattedData
{
/** The <i>column</i> (or <i>x</i>) coordinate. */
@@ -46,14 +47,6 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
/** The <i>row</i> (or <i>y</i>) coordinate. */
public static final String ROW = "row";
- /**
- * The mandatory format parameters that must be defined so that this implementation is able to work properly.
- */
- final static String[] MANDATORY_FORMAT_PARAMETERS =
- new String[]
- { PlateGeometry.PLATE_GEOMETRY, WellGeometry.WELL_GEOMETRY, ChannelList.NUMBER_OF_CHANNELS,
- HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA, HCSImageFormat1_0.DEVICE_ID };
-
public HCSImageFormattedData(final FormattedDataContext context)
{
super(context);
@@ -157,7 +150,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
return plateColumnDir.tryGetNode(createWellFileName(wellLocation));
}
- public final INode addStandardNode(final String originalFileName, int channel, final Location plateLocation,
+ public final NodePath addStandardNode(final String originalFilePath, int channel, final Location plateLocation,
final Location wellLocation)
{
// This will check all parameters but originalFileName.
@@ -168,18 +161,18 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
"A node already exists at channel %d, plate location '%s' and well location '%s'.", channel,
plateLocation, wellLocation));
}
- assert originalFileName != null : "Given original file name can not be null.";
+ assert originalFilePath != null : "Given original file name can not be null.";
final IDirectory standardDir = getStandardDataDirectory();
final IDirectory channelDir = Utilities.getOrCreateSubDirectory(standardDir, getChannelName(channel));
final IDirectory plateRowDir = Utilities.getOrCreateSubDirectory(channelDir, getPlateRowDirName(plateLocation));
final IDirectory plateColumnDir =
Utilities.getOrCreateSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
final String wellFileName = createWellFileName(wellLocation);
- final INode originalNode = getOriginalDataDirectory().tryGetNode(originalFileName);
+ final INode originalNode = getOriginalDataDirectory().tryGetNode(originalFilePath);
if (originalNode == null)
{
throw new DataStructureException(String.format("No original node with name '%s' could be found.",
- originalFileName));
+ originalFilePath));
}
if (containsOriginalData())
{
@@ -194,9 +187,12 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
String
.format(
"Original file name '%s' could not be added at channel %d, plate location '%s' and well location '%s'.",
- originalFileName, channel, plateLocation, wellLocation));
+ originalFilePath, channel, plateLocation, wellLocation));
}
- return node;
+ final char sep = Constants.PATH_SEPARATOR;
+ final String standardNodePath = channelDir.getName() + sep + plateRowDir.getName() + sep + plateColumnDir + sep
+ + wellFileName;
+ return new NodePath(node, standardNodePath);
}
//
@@ -214,7 +210,7 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
super.assertValidFormatAndFormatParameters();
final IFormatParameters formatParameters = getFormatParameters();
final Set<String> notPresent = new HashSet<String>();
- for (final String formatParameterName : MANDATORY_FORMAT_PARAMETERS)
+ for (final String formatParameterName : format.getParameterNames())
{
if (formatParameters.containsParameter(formatParameterName) == false)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
similarity index 63%
rename from bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
rename to bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
index a0247918ff4e33d2d328fed09031858d4beee3b3..afe3b7712909b57abaf715971546d0eb4796f45f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Christian Ribeaud
*/
-public interface IHCSFormattedData extends IFormattedData
+public interface IHCSImageFormattedData extends IFormattedData
{
/**
@@ -40,12 +40,32 @@ public interface IHCSFormattedData extends IFormattedData
public INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation);
/**
- * Adds a new node at given coordinates and returns it.
+ * Adds a new node at given coordinates.
*
- * @return the new <code>INode</code> just added. Never returns <code>null</code>.
- * @param originalFileName name of the <code>original</code> directory file that is going to be added in the
+ * @return the new <code>INode</code> just added (encapsulated in returned <code>NodePath</code>) with its path
+ * in the <code>standard</code> directory. Never returns <code>null</code>.
+ * @param originalFilePath name of the <code>original</code> directory file path that is going to be added in the
* <code>standard</code> directory.
*/
- public INode addStandardNode(final String originalFileName, final int channel, final Location plateLocation,
+ public NodePath addStandardNode(final String originalFilePath, final int channel, final Location plateLocation,
final Location wellLocation) throws DataStructureException;
+
+ //
+ // Helper classes
+ //
+
+ public final static class NodePath
+ {
+ public final INode node;
+
+ public final String path;
+
+ public NodePath(final INode node, final String path)
+ {
+ assert node != null : "Given node could not be null.";
+ assert path != null : "Given path could not be null.";
+ this.node = node;
+ this.path = path;
+ }
+ }
}
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 bbbd9474cfbefcd40530bef074f4b0d04a0a9cdf..8241204d9381b8b76e89fc9691fff6d1b8db0e1e 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
@@ -101,11 +101,11 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
}
setFormatAndFormatParameters();
final IFormattedData formattedData = dataStructure.getFormattedData();
- assertTrue(formattedData instanceof IHCSFormattedData);
+ assertTrue(formattedData instanceof IHCSImageFormattedData);
assertEquals(format, formattedData.getFormat());
}
- @Test(dependsOnMethods="testGetFormattedData")
+ @Test(dependsOnMethods = "testGetFormattedData")
public final void testHCSImageDataStructure()
{
// Creating...
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
index 6a1f4b80bbbfa09cc0655f3d945d63a599c0a39a..6ecb02788eb453a7f995b7f304a78f6e253d5b67 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
@@ -35,8 +35,10 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.DataStructureV1_0;
+import ch.systemsx.cisd.bds.Format;
import ch.systemsx.cisd.bds.FormattedDataFactory;
import ch.systemsx.cisd.bds.IFormatParameters;
+import ch.systemsx.cisd.bds.hcs.IHCSImageFormattedData.NodePath;
import ch.systemsx.cisd.bds.storage.IDirectory;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.ILink;
@@ -72,10 +74,11 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
{
directory = context.mock(IDirectory.class);
formatParameters = context.mock(IFormatParameters.class);
+ final Format format = HCSImageFormat1_0.HCS_IMAGE_1_0;
context.checking(new Expectations()
{
{
- for (final String formatParameterName : HCSImageFormattedData.MANDATORY_FORMAT_PARAMETERS)
+ for (final String formatParameterName : format.getParameterNames())
{
one(formatParameters).containsParameter(formatParameterName);
will(returnValue(true));
@@ -83,8 +86,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
formattedData =
- (HCSImageFormattedData) FormattedDataFactory.createFormattedData(directory,
- HCSImageFormat1_0.HCS_IMAGE_1_0, null, formatParameters);
+ (HCSImageFormattedData) FormattedDataFactory.createFormattedData(directory, format, null,
+ formatParameters);
}
private final void prepareStandardNode()
@@ -166,8 +169,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
@Test
public final void testAddStandardNodeWithOriginalData() throws IOException
{
- final String originalFileName = "original.txt";
- FileUtils.writeStringToFile(new File(workingDirectory, originalFileName), "This is my original file...");
+ final String originalFilePath = "original.txt";
+ FileUtils.writeStringToFile(new File(workingDirectory, originalFilePath), "This is my original file...");
final int channelIndex = 1;
final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
@@ -185,25 +188,26 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
will(returnValue(Boolean.FALSE));
}
});
- final INode node = formattedData.addStandardNode(originalFileName, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ final NodePath nodePath =
+ formattedData.addStandardNode(originalFilePath, channelIndex, PLATE_LOCATION, WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
- assertNotNull(node);
- assertEquals(standardFileName, node.getName());
+ assertNotNull(nodePath);
+ assertEquals(standardFileName, nodePath.node.getName());
// Look at the standard leaf directory if the node is there as well.
final INode standardFile = leafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
// Node should no longer be in original directory
- assertNull(originalNode.tryGetNode(originalFileName));
+ assertNull(originalNode.tryGetNode(originalFilePath));
context.assertIsSatisfied();
}
@Test
public final void testAddStandardNodeWithoutOriginalData() throws IOException
{
- final String originalFileName = "original.tiff";
- FileUtils.writeStringToFile(new File(workingDirectory, originalFileName), "This is my original file...");
+ final String originalFilePath = "original.tiff";
+ FileUtils.writeStringToFile(new File(workingDirectory, originalFilePath), "This is my original file...");
final int channelIndex = 1;
final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
@@ -221,18 +225,19 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
will(returnValue(Boolean.TRUE));
}
});
- final INode node = formattedData.addStandardNode(originalFileName, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ final NodePath nodePath =
+ formattedData.addStandardNode(originalFilePath, channelIndex, PLATE_LOCATION, WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
- assertNotNull(node);
- assertTrue(node instanceof ILink);
- assertEquals(standardFileName, node.getName());
+ assertNotNull(nodePath);
+ assertTrue(nodePath.node instanceof ILink);
+ assertEquals(standardFileName, nodePath.node.getName());
// Look at the standard leaf directory if the node is there as well.
final INode standardFile = leafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
// Node should still be in original directory
- assertNotNull(originalNode.tryGetNode(originalFileName));
+ assertNotNull(originalNode.tryGetNode(originalFilePath));
context.assertIsSatisfied();
}