From 5c4a820bd8076a95224de0541f33fbd7c18a3b91 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Wed, 9 Nov 2011 16:34:40 +0000
Subject: [PATCH] [LMS-2481] add 'image-datasets-original-dir-name'
configuration property for screening dropboxes. The property must be
configured directly on the jython thread.
SVN: 23618
---
.../cisd/common/filesystem/FileUtilities.java | 34 ++++++++++++++++++
.../common/filesystem/FileUtilitiesTest.java | 10 ++++++
.../etl/jython/JythonPlateDataSetHandler.java | 35 ++++++++++++++++---
3 files changed, 75 insertions(+), 4 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java b/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
index 162a31e0904..625f8354b93 100644
--- a/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
@@ -2014,4 +2014,38 @@ public final class FileUtilities
}
}
+ private static String getTempDir()
+ {
+ return System.getProperty("java.io.tmpdir");
+ }
+
+ /**
+ * Return true if <code>fileName</code> is a valid filename.
+ * <p>
+ * The methods works by trying to create a file with the specified name. Thus, the method should
+ * not be called where performance matters.
+ */
+ public static boolean isValidFileName(String fileName)
+ {
+ if (StringUtils.isBlank(fileName) || fileName.contains(File.separator))
+ {
+ return false;
+ }
+
+ File tmpFile = new File(getTempDir(), fileName);
+ try
+ {
+ if (tmpFile.createNewFile())
+ {
+ tmpFile.delete();
+ return true;
+ }
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+
+ return tmpFile.exists();
+ }
+
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/filesystem/FileUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/filesystem/FileUtilitiesTest.java
index 2e8419fdd91..df21eec7274 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/filesystem/FileUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/filesystem/FileUtilitiesTest.java
@@ -500,4 +500,14 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
assertTrue(FileUtilities.isSymbolicLink(linkRelative));
}
+ @Test
+ public void testValidFileName()
+ {
+ assertTrue(FileUtilities.isValidFileName("valid-name1"));
+ assertTrue(FileUtilities.isValidFileName("valid with space and tab\t"));
+ assertTrue(FileUtilities.isValidFileName("valid.dot"));
+ assertFalse(FileUtilities.isValidFileName(""));
+ assertFalse(FileUtilities.isValidFileName("a/b"));
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index 1d0731ee386..849abd1231f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -11,8 +11,11 @@ import java.util.Properties;
import org.python.util.PythonInterpreter;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
@@ -49,9 +52,29 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
*/
public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
{
+
+ private final String ORIGINAL_DIRNAME_KEY = "image-datasets-original-dir-name";
+
+ private final String originalDirName;
+
public JythonPlateDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState)
{
super(globalState);
+ originalDirName = parseOriginalDir(globalState.getThreadParameters().getThreadProperties());
+ }
+
+ private String parseOriginalDir(Properties threadProperties)
+ {
+ String originalDir =
+ PropertyUtils.getProperty(threadProperties, ORIGINAL_DIRNAME_KEY,
+ ScreeningConstants.ORIGINAL_DATA_DIR);
+ if (false == FileUtilities.isValidFileName(originalDir))
+ {
+ throw ConfigurationFailureException.fromTemplate(
+ "Invalid folder name specified in '%s': '%s'.", ORIGINAL_DIRNAME_KEY,
+ originalDir);
+ }
+ return originalDir;
}
/**
@@ -278,7 +301,8 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
IDataSetRegistrationDetailsFactory<DataSetInformation> registrationDetailsFactory)
{
return new ImagingDataSetRegistrationTransaction(rollBackStackParentFolder,
- workingDirectory, stagingDirectory, this, registrationDetailsFactory);
+ workingDirectory, stagingDirectory, this, registrationDetailsFactory,
+ originalDirName);
}
};
}
@@ -292,10 +316,13 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
{
private final JythonPlateDatasetFactory registrationDetailsFactory;
+ private final String originalDirName;
+
public ImagingDataSetRegistrationTransaction(File rollBackStackParentFolder,
File workingDirectory, File stagingDirectory,
DataSetRegistrationService<DataSetInformation> registrationService,
- IDataSetRegistrationDetailsFactory<DataSetInformation> registrationDetailsFactory)
+ IDataSetRegistrationDetailsFactory<DataSetInformation> registrationDetailsFactory,
+ String originalDirName)
{
super(rollBackStackParentFolder, workingDirectory, stagingDirectory,
registrationService, registrationDetailsFactory);
@@ -305,6 +332,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
this.registrationDetailsFactory =
(JythonPlateDatasetFactory) registrationDetailsFactory;
+ this.originalDirName = originalDirName;
}
public IDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
@@ -343,8 +371,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
// create main dataset (with original images)
IDataSet mainDataset = super.createNewDataSet(imageRegistrationDetails);
String originalDatasetPathPrefix =
- ScreeningConstants.ORIGINAL_DATA_DIR + File.separator
- + incomingDirectory.getName();
+ originalDirName + File.separator + incomingDirectory.getName();
moveFile(incomingDirectory.getAbsolutePath(), mainDataset, originalDatasetPathPrefix);
containedDataSetCodes.add(mainDataset.getDataSetCode());
--
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