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 ea865fc9c27ed036c0b9344460b8bc0641deab84..d734dde6b11f847a980e248335873a19c7f49935 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -142,6 +142,25 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
checkLocation(getWellGeometry(), wellLocation);
}
+ private final IDirectory getImageRootDirectoryNode(final File imageRootDirectory)
+ {
+ final IDirectory originalDataDirectory = getOriginalDataDirectory();
+ final String imageRootDirName = imageRootDirectory.getName();
+ // If not already present, move the 'imageRootDirectory' to 'original' data directory.
+ if (originalDataDirectory.tryGetNode(imageRootDirName) == null)
+ {
+ originalDataDirectory.addFile(imageRootDirectory, null, true);
+ }
+ final INode imageRootNode = originalDataDirectory.tryGetNode(imageRootDirName);
+ if (imageRootNode == null)
+ {
+ throw new DataStructureException(String.format(
+ "No image root directory named '%s' could be found in the original directory.", imageRootDirName));
+ }
+ assert imageRootNode instanceof IDirectory : "Image root node must be a directory.";
+ return (IDirectory) imageRootNode;
+ }
+
//
// IHCSFormattedData
//
@@ -162,9 +181,11 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
}
}
- public final NodePath addStandardNode(final File imageFile, int channel, final Location plateLocation,
- final Location wellLocation) throws DataStructureException
+ public final NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath,
+ final int channel, final Location plateLocation, final Location wellLocation) throws DataStructureException
{
+ assert imageRootDirectory != null : "Given image root directory can not be null.";
+ assert imageRelativePath != null : "Given image relative path can not be null.";
INode node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
if (node != null)
{
@@ -172,7 +193,6 @@ 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 imageFile != 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));
@@ -181,16 +201,18 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
final String wellFileName = createWellFileName(wellLocation);
if (containsOriginalData())
{
- final INode originalNode = getOriginalDataDirectory().addFile(imageFile, null, true);
- if (originalNode == null)
+ final IDirectory imageRootDirectoryNode = getImageRootDirectoryNode(imageRootDirectory);
+ final INode imageNode = imageRootDirectoryNode.tryGetNode(imageRelativePath);
+ if (imageNode == null)
{
- throw new DataStructureException(String.format("No original node with name '%s' could be found.",
- imageFile));
+ throw new DataStructureException(String.format(
+ "No image node with path '%s' could be found in the original directory.", imageRelativePath));
}
- node = plateColumnDir.tryAddLink(wellFileName, originalNode);
+ node = plateColumnDir.tryAddLink(wellFileName, imageNode);
} else
{
- node = plateColumnDir.addFile(imageFile, wellFileName, true);
+ // Copies the file. So we are able to undo the operation.
+ node = plateColumnDir.addFile(new File(imageRootDirectory, imageRelativePath), wellFileName, false);
}
if (node == null)
{
@@ -198,7 +220,7 @@ 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'.",
- imageFile, channel, plateLocation, wellLocation));
+ imageRelativePath, channel, plateLocation, wellLocation));
}
final char sep = Constants.PATH_SEPARATOR;
final String standardNodePath =
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
index bd3eaf39cecf45ed7e219529e6443aba983253cd..7e42df5d01e144a124c10525cb541a2237a1e8f1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -44,13 +44,16 @@ public interface IHCSImageFormattedData extends IFormattedData
/**
* Adds a new image file at given coordinates.
*
+ * @param imageRootDirectory the root directory where the image is located. This usually is the incoming data set
+ * directory.
+ * @param imageRelativePath relative path (to <var>imageRootDirectory</var>) name of the image file that is going
+ * to be added in the <code>standard</code> directory.
* @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 imageFile name of the image file that is going to be added in the <code>standard</code> directory.
* @throws DataStructureException if a node already exists at given coordinates.
*/
- public NodePath addStandardNode(final File imageFile, final int channel, final Location plateLocation,
- final Location wellLocation) throws DataStructureException;
+ public NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath, final int channel,
+ final Location plateLocation, final Location wellLocation) throws DataStructureException;
//
// Helper classes
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 9edccc78314479b636265ff049ced8019c87b3fb..a5b54ec75bb9e8fd8aa63019943fba03628ac931 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
@@ -54,6 +54,10 @@ import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
{
+ private static final String IMAGE_ROOT_DIRECTORY_NAME = "CP001-1";
+
+ private static final String ORIGINAL_TIFF = "original.tiff";
+
static final Location PLATE_LOCATION = new Location(2, 1);
static final Location WELL_LOCATION = new Location(1, 2);
@@ -68,7 +72,11 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
private IDirectory standardNode;
- private IDirectory leafDirectory;
+ private IDirectory originalNode;
+
+ private IDirectory standardLeafDirectory;
+
+ private File imageRootDirectory;
private final void prepareAndCreateFormattedData()
{
@@ -92,10 +100,19 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
private final void prepareStandardNode()
{
- standardNode = NodeFactory.createDirectoryNode(workingDirectory);
+ final File standardDirectory = new File(workingDirectory, DataStructureV1_0.DIR_STANDARD);
+ standardDirectory.mkdir();
+ standardNode = NodeFactory.createDirectoryNode(standardDirectory);
final IDirectory channel1 = standardNode.makeDirectory(Channel.CHANNEL + "1");
final IDirectory row1 = channel1.makeDirectory(HCSImageFormattedData.ROW + "1");
- leafDirectory = row1.makeDirectory(HCSImageFormattedData.COLUMN + "2");
+ standardLeafDirectory = row1.makeDirectory(HCSImageFormattedData.COLUMN + "2");
+ }
+
+ private final void prepareOriginalNode()
+ {
+ final File originalDirectory = new File(workingDirectory, DataStructureV1_0.DIR_ORIGINAL);
+ originalDirectory.mkdir();
+ originalNode = NodeFactory.createDirectoryNode(originalDirectory);
}
private final void addParameterCheckExpectations(final Expectations exp)
@@ -110,6 +127,14 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
exp.will(exp.returnValue(geometry));
}
+ private final void prepareImageRootDirectory() throws IOException
+ {
+ imageRootDirectory = new File(workingDirectory, IMAGE_ROOT_DIRECTORY_NAME);
+ imageRootDirectory.mkdir();
+ final File originalFile = new File(imageRootDirectory, ORIGINAL_TIFF);
+ FileUtils.writeStringToFile(originalFile, "This is my original file...");
+ }
+
//
// AbstractFileSystemTestCase
//
@@ -122,6 +147,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
context = new Mockery();
prepareAndCreateFormattedData();
prepareStandardNode();
+ prepareOriginalNode();
}
@AfterMethod
@@ -169,11 +195,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
@Test
public final void testAddStandardNodeWithOriginalData() throws IOException
{
- final String originalFilePath = "original.txt";
- final File originalFile = new File(workingDirectory, originalFilePath);
- FileUtils.writeStringToFile(originalFile, "This is my original file...");
+ prepareImageRootDirectory();
final int channelIndex = 1;
- final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
{
{
@@ -190,29 +213,27 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
final NodePath nodePath =
- formattedData.addStandardNode(originalFile, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ formattedData.addStandardNode(imageRootDirectory, ORIGINAL_TIFF, channelIndex, PLATE_LOCATION,
+ WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
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);
+ final INode standardFile = standardLeafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
// Node should still be in the 'original' directory.
- assertNotNull(originalNode.tryGetNode(originalFilePath));
+ assertNotNull(((IDirectory) originalNode.tryGetNode(IMAGE_ROOT_DIRECTORY_NAME)).tryGetNode(ORIGINAL_TIFF));
context.assertIsSatisfied();
}
@Test
public final void testAddStandardNodeWithoutOriginalData() throws IOException
{
- final String originalFilePath = "original.tiff";
- final File originalFile = new File(workingDirectory, originalFilePath);
- FileUtils.writeStringToFile(originalFile, "This is my original file...");
+ prepareImageRootDirectory();
final int channelIndex = 1;
- final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
{
{
@@ -226,18 +247,19 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
final NodePath nodePath =
- formattedData.addStandardNode(originalFile, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ formattedData.addStandardNode(imageRootDirectory, ORIGINAL_TIFF, channelIndex, PLATE_LOCATION,
+ WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
assertNotNull(nodePath);
assertTrue(nodePath.node instanceof IFile);
assertEquals(standardFileName, nodePath.node.getName());
// Look at the standard leaf directory if the node is there as well.
- final INode standardFile = leafDirectory.tryGetNode(standardFileName);
+ final INode standardFile = standardLeafDirectory.tryGetNode(standardFileName);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
// Node should no longer be in the 'original' directory.
- assertNull(originalNode.tryGetNode(originalFilePath));
+ assertNull(originalNode.tryGetNode(IMAGE_ROOT_DIRECTORY_NAME));
context.assertIsSatisfied();
}
@@ -265,7 +287,7 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
{
final File file = new File(workingDirectory, "row2_column1.tiff");
FileUtils.writeStringToFile(file, "This is my original file...");
- leafDirectory.addFile(file, null, true);
+ standardLeafDirectory.addFile(file, null, true);
final int channelIndex = 1;
context.checking(new Expectations()
{