From 2df20ffbb7083e259345028f4f46e604f4d27eb0 Mon Sep 17 00:00:00 2001
From: ribeaudc <ribeaudc>
Date: Mon, 10 Dec 2007 15:12:20 +0000
Subject: [PATCH] [LMS-107] - Separation of concerns.
SVN: 3008
---
.../java/ch/systemsx/cisd/bds/Utilities.java | 1 +
.../cisd/bds/hcs/HCSImageFormattedData.java | 64 ++++++++++---------
.../cisd/bds/hcs/IHCSImageFormattedData.java | 10 +--
.../systemsx/cisd/bds/storage/IDirectory.java | 11 +---
.../bds/storage/filesystem/Directory.java | 22 +++----
.../bds/hcs/HCSDataStructureV1_0Test.java | 9 +--
.../bds/hcs/HCSImageFormattedDataTest.java | 34 +++++-----
.../bds/storage/filesystem/DirectoryTest.java | 2 +-
8 files changed, 74 insertions(+), 79 deletions(-)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index 3adf9dea87a..beda0d1501b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -61,6 +61,7 @@ public class Utilities
* @throws DataStructureException if requested directory not found.
*/
public final static IDirectory getSubDirectory(final IDirectory directory, final String name)
+ throws DataStructureException
{
INode node = directory.tryGetNode(name);
if (node == null)
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 0ee084daf16..ea865fc9c27 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.bds.hcs;
+import java.io.File;
import java.util.HashSet;
import java.util.Set;
@@ -107,12 +108,12 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
return ROW + wellLocation.y + "_" + COLUMN + wellLocation.x + ".tiff";
}
- private final IDirectory getStandardDataDirectory()
+ private final IDirectory getStandardDataDirectory() throws DataStructureException
{
return Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_STANDARD);
}
- private final IDirectory getOriginalDataDirectory()
+ private final IDirectory getOriginalDataDirectory() throws DataStructureException
{
return Utilities.getSubDirectory(dataDirectory, DataStructureV1_0.DIR_ORIGINAL);
}
@@ -132,62 +133,64 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
return Channel.CHANNEL + channel;
}
- //
- // IHCSFormattedData
- //
-
- public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
+ private void checkCoordinates(final int channel, final Location plateLocation, final Location wellLocation)
{
checkChannel(channel);
assert plateLocation != null : "Plate location can not be null.";
assert wellLocation != null : "Well location can not be null.";
checkLocation(getPlateGeometry(), plateLocation);
checkLocation(getWellGeometry(), wellLocation);
- final IDirectory standardDir = getStandardDataDirectory();
- final IDirectory channelDir = Utilities.getSubDirectory(standardDir, getChannelName(channel));
- final IDirectory plateRowDir = Utilities.getSubDirectory(channelDir, getPlateRowDirName(plateLocation));
- final IDirectory plateColumnDir = Utilities.getSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
- return plateColumnDir.tryGetNode(createWellFileName(wellLocation));
}
- public final NodePath addStandardNode(final String originalFilePath, int channel, final Location plateLocation,
- final Location wellLocation)
+ //
+ // IHCSFormattedData
+ //
+
+ public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
{
- // This will check all parameters but originalFilePath.
- INode node = null;
- // TODO 2007-12-05, Christian Ribeaud: Improve this.
+ checkCoordinates(channel, plateLocation, wellLocation);
try
{
- node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
- } catch (DataStructureException ex)
+ final IDirectory standardDir = getStandardDataDirectory();
+ final IDirectory channelDir = Utilities.getSubDirectory(standardDir, getChannelName(channel));
+ final IDirectory plateRowDir = Utilities.getSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ final IDirectory plateColumnDir = Utilities.getSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
+ return plateColumnDir.tryGetNode(createWellFileName(wellLocation));
+ } catch (final DataStructureException e)
{
- // Nothing to do here.
+ return null;
}
+ }
+
+ public final NodePath addStandardNode(final File imageFile, int channel, final Location plateLocation,
+ final Location wellLocation) throws DataStructureException
+ {
+ INode node = tryGetStandardNodeAt(channel, plateLocation, wellLocation);
if (node != null)
{
throw new DataStructureException(String.format(
"A node already exists at channel %d, plate location '%s' and well location '%s'.", channel,
plateLocation, wellLocation));
}
- assert originalFilePath != null : "Given original file name can not be null.";
+ 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));
final IDirectory plateColumnDir =
Utilities.getOrCreateSubDirectory(plateRowDir, getPlateColumnDir(plateLocation));
final String wellFileName = createWellFileName(wellLocation);
- final INode originalNode = getOriginalDataDirectory().tryGetNode(originalFilePath);
- if (originalNode == null)
- {
- throw new DataStructureException(String.format("No original node with name '%s' could be found.",
- originalFilePath));
- }
if (containsOriginalData())
{
+ final INode originalNode = getOriginalDataDirectory().addFile(imageFile, null, true);
+ if (originalNode == null)
+ {
+ throw new DataStructureException(String.format("No original node with name '%s' could be found.",
+ imageFile));
+ }
node = plateColumnDir.tryAddLink(wellFileName, originalNode);
} else
{
- node = plateColumnDir.tryAddNode(wellFileName, originalNode);
+ node = plateColumnDir.addFile(imageFile, wellFileName, true);
}
if (node == null)
{
@@ -195,11 +198,12 @@ 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'.",
- originalFilePath, channel, plateLocation, wellLocation));
+ imageFile, channel, plateLocation, wellLocation));
}
final char sep = Constants.PATH_SEPARATOR;
final String standardNodePath =
- channelDir.getName() + sep + plateRowDir.getName() + sep + plateColumnDir.getName() + sep + wellFileName;
+ channelDir.getName() + sep + plateRowDir.getName() + sep + plateColumnDir.getName() + sep
+ + wellFileName;
return new NodePath(node, 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 afe3b771290..bd3eaf39cec 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.bds.hcs;
+import java.io.File;
+
import ch.systemsx.cisd.bds.IFormattedData;
import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.storage.IFile;
@@ -40,14 +42,14 @@ public interface IHCSImageFormattedData extends IFormattedData
public INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation);
/**
- * Adds a new node at given coordinates.
+ * Adds a new image file at given coordinates.
*
* @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.
+ * @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 String originalFilePath, final int channel, final Location plateLocation,
+ public NodePath addStandardNode(final File imageFile, final int channel, final Location plateLocation,
final Location wellLocation) throws DataStructureException;
//
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
index 4965eb31033..fbe2ab1bd94 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
@@ -44,6 +44,7 @@ public interface IDirectory extends INode, Iterable<INode>
* Adds the specified real file to this directory. The content of <code>file</code> will be copied. If it is a
* folder also its complete content including all subfolders will be copied.
*
+ * @param nameOrNull the name of the returned node. If <code>null</code>, then given <var>file</var> name is taken.
* @param move whether given <var>file</var> should be copied or moved.
* @return the new node. It will be a {@link ILink} if <code>file</code> is a symbolic link, a {@link IDirectory}
* if <code>file</code> is a folder, or {@link IFile} if <code>file</code> is a plain file.
@@ -51,7 +52,7 @@ public interface IDirectory extends INode, Iterable<INode>
// TODO 2007-12-03 Tomasz Pylak review: this generic interface should not use java.io.File. Is the 'move' parameter
// possible to implement in HDF5? Maybe those operations should be done before, depending on the implementation
// which is used?
- public INode addFile(final File file, final boolean move);
+ public INode addFile(final File file, final String nameOrNull, final boolean move);
/**
* Removes given <var>node</var> from this directory.
@@ -69,12 +70,4 @@ public interface IDirectory extends INode, Iterable<INode>
* @return <code>null</code> if the operation did not succeed.
*/
public ILink tryAddLink(final String name, final INode node);
-
- /**
- * Adds given <code>node</code> to this <code>IDirectory</code> and returns a new node with given
- * <code>name</code> (rename operation).
- *
- * @return <code>null</code> if the operation did not succeed.
- */
- public INode tryAddNode(final String name, final INode node);
}
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 16192f56aa1..39ab104fcb7 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
@@ -146,13 +146,21 @@ final class Directory extends AbstractNode implements IDirectory
return new File(file);
}
- public final INode addFile(final java.io.File file, final boolean move)
+ public final INode addFile(final java.io.File file, final String name, final boolean move)
{
checkFile(file);
- final java.io.File newFile = new java.io.File(nodeFile, file.getName());
+ final String fileName;
+ if (name == null)
+ {
+ fileName = file.getName();
+ } else
+ {
+ fileName = name;
+ }
+ final java.io.File newFile = new java.io.File(nodeFile, fileName);
if (move)
{
- moveFileToDirectory(file, nodeFile, null);
+ moveFileToDirectory(file, nodeFile, name);
} else
{
try
@@ -231,14 +239,6 @@ final class Directory extends AbstractNode implements IDirectory
}
}
- public final INode tryAddNode(final String name, final INode node)
- {
- assert node != null : "Node can not be null";
- assert name != null : "Name can not be null.";
- final java.io.File file = getNodeFile(node);
- return NodeFactory.createNode(moveFileToDirectory(file, nodeFile, name));
- }
-
public final void removeNode(final INode node)
{
assert node != null : "Node could not be null";
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 8241204d938..ef06cdd479b 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
@@ -50,11 +50,6 @@ 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>();
@@ -79,9 +74,9 @@ public final class HCSDataStructureV1_0Test extends AbstractFileSystemTestCase
@Override
@BeforeMethod
- public final void setup() throws IOException
+ public final void setUp() throws IOException
{
- super.setup();
+ super.setUp();
storage = new FileStorage(workingDirectory);
dataStructure = new DataStructureV1_0(storage);
}
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 6ecb02788eb..9edccc78314 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
@@ -116,9 +116,9 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
@Override
@BeforeMethod
- public final void setup() throws IOException
+ public final void setUp() throws IOException
{
- super.setup();
+ super.setUp();
context = new Mockery();
prepareAndCreateFormattedData();
prepareStandardNode();
@@ -170,7 +170,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
public final void testAddStandardNodeWithOriginalData() throws IOException
{
final String originalFilePath = "original.txt";
- FileUtils.writeStringToFile(new File(workingDirectory, originalFilePath), "This is my original file...");
+ final File originalFile = new File(workingDirectory, originalFilePath);
+ FileUtils.writeStringToFile(originalFile, "This is my original file...");
final int channelIndex = 1;
final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
@@ -185,21 +186,22 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
will(returnValue(originalNode));
one(formatParameters).getValue(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA);
- will(returnValue(Boolean.FALSE));
+ will(returnValue(Boolean.TRUE));
}
});
final NodePath nodePath =
- formattedData.addStandardNode(originalFilePath, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ formattedData.addStandardNode(originalFile, 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);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
- // Node should no longer be in original directory
- assertNull(originalNode.tryGetNode(originalFilePath));
+ // Node should still be in the 'original' directory.
+ assertNotNull(originalNode.tryGetNode(originalFilePath));
context.assertIsSatisfied();
}
@@ -207,7 +209,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
public final void testAddStandardNodeWithoutOriginalData() throws IOException
{
final String originalFilePath = "original.tiff";
- FileUtils.writeStringToFile(new File(workingDirectory, originalFilePath), "This is my original file...");
+ final File originalFile = new File(workingDirectory, originalFilePath);
+ FileUtils.writeStringToFile(originalFile, "This is my original file...");
final int channelIndex = 1;
final IDirectory originalNode = NodeFactory.createDirectoryNode(workingDirectory);
context.checking(new Expectations()
@@ -218,26 +221,23 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
exactly(2).of(directory).tryGetNode(DataStructureV1_0.DIR_STANDARD);
will(returnValue(standardNode));
- one(directory).tryGetNode(DataStructureV1_0.DIR_ORIGINAL);
- will(returnValue(originalNode));
-
one(formatParameters).getValue(HCSImageFormat1_0.CONTAINS_ORIGINAL_DATA);
- will(returnValue(Boolean.TRUE));
+ will(returnValue(Boolean.FALSE));
}
});
final NodePath nodePath =
- formattedData.addStandardNode(originalFilePath, channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ formattedData.addStandardNode(originalFile, channelIndex, PLATE_LOCATION, WELL_LOCATION);
final String standardFileName = "row2_column1.tiff";
assertNotNull(nodePath);
- assertTrue(nodePath.node instanceof ILink);
+ 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);
assertNotNull(standardFile);
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
- // Node should still be in original directory
- assertNotNull(originalNode.tryGetNode(originalFilePath));
+ // Node should no longer be in the 'original' directory.
+ assertNull(originalNode.tryGetNode(originalFilePath));
context.assertIsSatisfied();
}
@@ -265,7 +265,7 @@ 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, true);
+ leafDirectory.addFile(file, null, true);
final int channelIndex = 1;
context.checking(new Expectations()
{
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 e59ecc893e6..d3d85b5c910 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
@@ -53,7 +53,7 @@ public final class DirectoryTest extends AbstractFileSystemTestCase
File dest = new File(workingDirectory, "destination");
dest.mkdir();
Directory directory = new Directory(dest);
- INode copiedDir = directory.addFile(dir, move);
+ INode copiedDir = directory.addFile(dir, null, move);
assertEquals("dir", copiedDir.getName());
assertTrue(copiedDir instanceof IDirectory);
File copiedRealDir = new File(dest, "dir");
--
GitLab