From fe90cd66048ff3d7951526ae71f2bf75eb4d44b9 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Wed, 19 Mar 2008 19:16:41 +0000
Subject: [PATCH] change: CISD formatting conventions: max line length 120 ->
100 (mass formatting)
SVN: 4950
---
.../cisd/ant/common/DummyProjectHandler.java | 4 +-
.../ant/common/EclipseClasspathReader.java | 13 +-
.../FileBaseEclipseClasspathLocation.java | 4 +-
.../ant/common/IEclipseClasspathLocation.java | 4 +-
.../cisd/ant/common/IProjectHandler.java | 13 +-
.../ant/common/RecursiveProjectTraverser.java | 9 +-
.../TextBasedEclipseClasspathLocation.java | 5 +-
.../systemsx/cisd/ant/task/RecursiveJar.java | 10 +-
.../ant/task/SetEclipseClasspathTask.java | 10 +-
.../BuildJavaSubprojectsTask.java | 2 +-
.../AntTaskSimpleLoggerAdapter.java | 13 +-
.../GatherRevisionAndVersionTask.java | 17 +-
.../cisd/ant/task/subversion/ISVNActions.java | 3 +-
.../ant/task/subversion/ISVNCheckout.java | 3 +-
.../cisd/ant/task/subversion/ISVNCopy.java | 4 +-
.../cisd/ant/task/subversion/ISVNInfo.java | 4 +-
.../subversion/ISVNProjectPathProvider.java | 4 +-
.../cisd/ant/task/subversion/SVNActions.java | 46 +++--
.../task/subversion/SVNBranchAndTagTask.java | 73 +++++---
.../cisd/ant/task/subversion/SVNCheckout.java | 4 +-
.../SVNDependentProjectsCollector.java | 10 +-
.../ant/task/subversion/SVNException.java | 4 +-
.../ant/task/subversion/SVNInfoRecord.java | 121 +++++++------
.../subversion/SVNInfoRecordExtractor.java | 39 ++--
.../ant/task/subversion/SVNItemStatus.java | 29 +--
.../subversion/SVNRecursiveCheckoutTask.java | 16 +-
.../SVNRepositoryProjectContext.java | 38 ++--
.../ant/task/subversion/SVNUtilities.java | 46 +++--
.../subversion/SVNWCProjectPathProvider.java | 15 +-
.../ant/task/SetEclipseClasspathTaskTest.java | 46 +++--
.../GatherRevisionAndVersionTaskTest.java | 62 ++++---
.../subversion/SVNBranchAndTagTaskTest.java | 139 ++++++++------
.../SVNDependentProjectCollectorTest.java | 127 ++++++++-----
.../SVNInfoRecordExtractorTest.java | 106 +++++------
.../SVNRecursiveCheckoutTaskTest.java | 46 +++--
.../SVNRepositoryProjectContextTest.java | 43 +++--
.../ant/task/subversion/SVNUtilitiesTest.java | 14 +-
.../SVNWCProjectPathProviderTest.java | 28 +--
.../NullAuthenticationService.java | 4 +-
.../cisd/authentication/Principal.java | 16 +-
.../crowd/CrowdAuthenticationService.java | 96 ++++++----
.../crowd/IRequestExecutor.java | 4 +-
.../crowd/CrowdAuthenticationServiceTest.java | 77 +++++---
.../crowd/RealCrowdAuthenticationTest.java | 10 +-
.../cisd/bds/AbstractFormattedData.java | 7 +-
.../java/ch/systemsx/cisd/bds/Constants.java | 2 +-
.../cisd/bds/DataStructureLoader.java | 10 +-
.../systemsx/cisd/bds/DataStructureV1_0.java | 20 +-
.../cisd/bds/ExperimentIdentifier.java | 9 +-
.../cisd/bds/ExperimentRegistratorDate.java | 3 +-
.../java/ch/systemsx/cisd/bds/Factory.java | 23 ++-
.../java/ch/systemsx/cisd/bds/Format.java | 3 +-
.../systemsx/cisd/bds/FormatParameters.java | 12 +-
.../ch/systemsx/cisd/bds/FormatStore.java | 7 +-
.../cisd/bds/FormattedDataContext.java | 3 +-
.../cisd/bds/FormattedDataFactory.java | 16 +-
.../ch/systemsx/cisd/bds/IAnnotations.java | 2 -
.../ch/systemsx/cisd/bds/IDataStructure.java | 3 +-
.../cisd/bds/IFormatParameterFactory.java | 41 +++--
.../ch/systemsx/cisd/bds/IFormattedData.java | 5 +-
.../ch/systemsx/cisd/bds/IHasVersion.java | 2 +-
.../systemsx/cisd/bds/MeasurementEntity.java | 3 +-
.../systemsx/cisd/bds/UnknownFormatV1_0.java | 4 +-
.../java/ch/systemsx/cisd/bds/Utilities.java | 14 +-
.../java/ch/systemsx/cisd/bds/Version.java | 3 +-
.../bds/exception/DataStructureException.java | 7 +-
.../cisd/bds/handler/ChecksumHandler.java | 32 ++--
.../bds/handler/MD5ChecksumCalculator.java | 1 -
.../cisd/bds/handler/MappingFileHandler.java | 17 +-
.../ch/systemsx/cisd/bds/hcs/Channel.java | 3 +-
.../ch/systemsx/cisd/bds/hcs/ChannelList.java | 3 +-
.../cisd/bds/hcs/FormatParameterFactory.java | 3 +-
.../ch/systemsx/cisd/bds/hcs/Geometry.java | 3 +-
.../cisd/bds/hcs/HCSImageAnnotations.java | 19 +-
.../cisd/bds/hcs/HCSImageFormatV1_0.java | 4 +-
.../cisd/bds/hcs/HCSImageFormattedData.java | 64 ++++---
.../cisd/bds/hcs/IHCSImageFormattedData.java | 8 +-
.../ch/systemsx/cisd/bds/hcs/Location.java | 3 +-
.../systemsx/cisd/bds/storage/IDirectory.java | 3 +-
.../ch/systemsx/cisd/bds/storage/ILink.java | 2 +-
.../systemsx/cisd/bds/storage/IStorage.java | 9 +-
.../cisd/bds/storage/NodeFilters.java | 7 +-
.../bds/storage/filesystem/AbstractNode.java | 12 +-
.../bds/storage/filesystem/Directory.java | 30 +--
.../cisd/bds/storage/filesystem/File.java | 11 +-
.../bds/storage/filesystem/FileStorage.java | 6 +-
.../cisd/bds/storage/filesystem/Link.java | 3 +-
.../bds/storage/filesystem/NodeFactory.java | 10 +-
.../cisd/bds/storage/hdf5/HDF5Storage.java | 4 +-
.../cisd/bds/DataStructureFactoryTest.java | 9 +-
.../cisd/bds/DataStructureLoaderTest.java | 3 +-
.../cisd/bds/DataStructureTestV1_0.java | 41 +++--
.../ch/systemsx/cisd/bds/UtilitiesTest.java | 3 +-
.../bds/handler/MappingFileHandlerTest.java | 13 +-
.../bds/hcs/HCSDataStructureTestV1_0.java | 16 +-
.../bds/hcs/HCSImageFormattedDataTest.java | 21 ++-
.../cisd/bds/hcs/PlateGeometryTest.java | 3 +-
.../cisd/bds/hcs/WellGeometryTest.java | 3 +-
.../cisd/bds/storage/filesystem/FileTest.java | 6 +-
.../storage/filesystem/NodeFactoryTest.java | 4 +-
.../ch/systemsx/cisd/common/Constants.java | 7 +-
.../java/ch/systemsx/cisd/common/Script.java | 10 +-
.../AbstractCollectionDecorator.java | 2 +-
.../cisd/common/collections/CollectionIO.java | 28 +--
.../common/collections/CollectionStyle.java | 4 +-
.../common/collections/CollectionUtils.java | 30 +--
.../collections/FilteredCollection.java | 3 +-
.../common/collections/IKeyExtractor.java | 2 +-
.../cisd/common/collections/TableMap.java | 6 +-
.../collections/TableMapNonUniqueKey.java | 5 +-
.../compression/file/CompressionWorker.java | 19 +-
.../common/compression/file/Compressor.java | 28 ++-
.../compression/file/ICompressionMethod.java | 2 +-
.../file/InPlaceCompressionMethod.java | 29 +--
.../compression/tiff/TiffCompressor.java | 3 +-
.../tiff/TiffZipCompressionMethod.java | 23 ++-
.../concurrent/ConcurrencyUtilities.java | 20 +-
.../cisd/common/converter/ConverterPool.java | 3 +-
.../cisd/common/db/DBRestrictionParser.java | 41 +++--
.../cisd/common/db/ISequenceNameMapper.java | 2 +-
.../common/db/ISqlScriptExecutionLogger.java | 6 +-
.../cisd/common/db/ISqlScriptExecutor.java | 3 +-
.../common/db/OracleSequencerHandler.java | 2 +-
.../cisd/common/db/SQLCommandTokenizer.java | 18 +-
.../cisd/common/db/SQLStateUtils.java | 2 +-
.../cisd/common/db/SqlUnitTestRunner.java | 63 ++++---
.../common/db/StandardSequenceNameMapper.java | 4 +-
.../ConfigurationFailureException.java | 3 +-
.../EnvironmentFailureException.java | 3 +-
.../common/exceptions/HighLevelException.java | 4 +-
.../exceptions/InvalidSessionException.java | 1 -
.../exceptions/NotImplementedException.java | 4 +-
.../RetriableEnvironmentFailureException.java | 7 +-
.../cisd/common/exceptions/Status.java | 4 +-
.../cisd/common/exceptions/StatusFlag.java | 4 +-
.../exceptions/UserFailureException.java | 3 +-
.../systemsx/cisd/common/io/ILinePrinter.java | 2 +-
.../cisd/common/io/SimpleLinePrinter.java | 8 +-
.../cisd/common/logging/ConsoleLogger.java | 2 +-
.../cisd/common/logging/ISimpleLogger.java | 4 +-
.../cisd/common/logging/LogFactory.java | 3 +-
.../cisd/common/logging/LogInitializer.java | 3 +-
.../common/logging/LogInvocationHandler.java | 9 +-
.../common/logging/LoggingContextHandler.java | 2 -
.../cisd/common/mail/IMailClient.java | 3 +-
.../systemsx/cisd/common/mail/MailClient.java | 37 ++--
.../parser/AbstractParserObjectFactory.java | 28 +--
.../cisd/common/parser/BeanAnalyzer.java | 21 ++-
.../parser/ColumnSizeMismatchException.java | 8 +-
.../parser/DefaultAliasPropertyMapper.java | 14 +-
.../common/parser/DefaultLineTokenizer.java | 6 +-
.../cisd/common/parser/DefaultParser.java | 4 +-
.../common/parser/DefaultPropertyMapper.java | 10 +-
.../cisd/common/parser/HeaderLineFilter.java | 4 +-
.../common/parser/IAliasPropertyMapper.java | 2 +-
.../cisd/common/parser/ILineTokenizer.java | 2 +-
.../systemsx/cisd/common/parser/IParser.java | 4 +-
.../common/parser/IParserObjectFactory.java | 3 +-
.../parser/IParserObjectFactoryFactory.java | 3 +-
.../cisd/common/parser/IPropertyMapper.java | 3 +-
.../parser/IndexOutOfBoundsException.java | 3 +-
.../ch/systemsx/cisd/common/parser/Line.java | 3 +-
.../cisd/common/parser/ParserUtilities.java | 9 +-
.../cisd/common/parser/ParsingException.java | 3 +-
.../cisd/common/parser/TabFileLoader.java | 9 +-
.../parser/UnmatchedPropertiesException.java | 12 +-
.../cisd/common/process/CleanUpCallable.java | 1 -
.../cisd/common/process/CleanUpRegistry.java | 3 +-
.../common/process/FileRenamingProcess.java | 13 +-
.../cisd/common/process/ICleanUpRegistry.java | 4 +-
.../process/ProcessExecutionHelper.java | 60 +++---
.../cisd/common/process/ProcessResult.java | 21 ++-
.../common/test/InterfaceForRMIChecker.java | 28 +--
.../common/utilities/AbstractHashable.java | 4 +-
.../cisd/common/utilities/BeanUtils.java | 126 ++++++++-----
.../cisd/common/utilities/ClassUtils.java | 29 +--
.../utilities/DirectoryScanningTimerTask.java | 21 ++-
.../cisd/common/utilities/ExceptionUtils.java | 9 +-
.../common/utilities/ExtendedProperties.java | 6 +-
.../cisd/common/utilities/FileUtilities.java | 111 +++++++-----
.../cisd/common/utilities/FileWatcher.java | 6 +-
.../utilities/FileWatcherSynchronizer.java | 24 ++-
.../cisd/common/utilities/IExitHandler.java | 4 +-
.../cisd/common/utilities/ITriggerable.java | 6 +-
.../ModifiedShortPrefixToStringStyle.java | 17 +-
.../utilities/NamePrefixFileFilter.java | 4 +-
.../cisd/common/utilities/OSUtilities.java | 14 +-
.../common/utilities/PasswordGenerator.java | 20 +-
.../common/utilities/PathPrefixPrepender.java | 14 +-
.../utilities/RecursiveHardLinkMaker.java | 62 ++++---
.../common/utilities/RegexFileFilter.java | 3 +-
.../common/utilities/StringUtilities.java | 63 ++++---
.../utilities/SynchronizationMonitor.java | 6 +-
.../cisd/common/utilities/Template.java | 89 +++++----
.../cisd/common/utilities/TimerHelper.java | 4 +-
.../common/utilities/TriggeringTimerTask.java | 14 +-
.../common/collections/CollectionIOTest.java | 10 +-
.../collections/CollectionUtilsTest.java | 6 +-
.../common/collections/FilteredListTest.java | 2 +-
.../collections/TableMapNonUniqueKeyTest.java | 33 ++--
.../cisd/common/collections/TableMapTest.java | 8 +-
.../collections/ValidatorUtilsTest.java | 12 +-
.../file/CompressionWorkerTest.java | 4 +-
.../concurrent/ConcurrencyUtilitiesTest.java | 85 ++++-----
.../common/db/DBRestrictionParserTest.java | 48 +++--
.../common/db/SQLCommandTokenizerTest.java | 6 +-
.../cisd/common/db/SqlUnitTestRunnerTest.java | 126 +++++++------
.../exceptions/UserFailureExceptionTest.java | 12 +-
.../common/logging/LogMonitoringAppender.java | 13 +-
.../cisd/common/mail/MailClientTest.java | 13 +-
.../AbstractParserObjectFactoryTest.java | 17 +-
.../cisd/common/parser/DefaultParserTest.java | 18 +-
.../common/parser/HeaderLineFilterTest.java | 31 ++--
.../common/parser/ParserUtilitiesTest.java | 10 +-
.../cisd/common/parser/TabFileLoaderTest.java | 8 +-
.../process/ProcessExecutionHelperTest.java | 53 +++---
.../test/InterfaceForRMICheckerTest.java | 90 +++++----
.../test/StoringUncaughtExceptionHandler.java | 4 +-
.../cisd/common/utilities/BeanUtilsTest.java | 66 ++++---
.../cisd/common/utilities/ClassUtilsTest.java | 26 ++-
.../DirectoryScanningTimerTaskTest.java | 51 ++++--
.../common/utilities/ExceptionUtilsTest.java | 52 +++---
.../FileUtilitiesDeleteRecursivelyTest.java | 3 +-
.../FileUtilitiesLastChangedTest.java | 35 ++--
.../common/utilities/FileUtilitiesTest.java | 43 +++--
.../common/utilities/FileWatcherTest.java | 12 +-
.../utilities/NamePrefixFileFilterTest.java | 6 +-
.../common/utilities/OSUtilitiesTest.java | 3 +-
.../utilities/PathPrefixPrependerTest.java | 11 +-
.../utilities/RecursiveHardLinkMakerTest.java | 6 +-
.../common/utilities/RegexFileFilterTest.java | 41 +++--
.../common/utilities/StringUtilitiesTest.java | 5 +-
.../cisd/common/utilities/TemplateTest.java | 28 ++-
.../ch/systemsx/cisd/datamover/DataMover.java | 26 ++-
.../cisd/datamover/IncomingProcessor.java | 36 ++--
.../cisd/datamover/LocalProcessor.java | 37 ++--
.../java/ch/systemsx/cisd/datamover/Main.java | 36 ++--
.../systemsx/cisd/datamover/Parameters.java | 75 +++++---
.../ch/systemsx/cisd/datamover/SelfTest.java | 18 +-
.../filesystem/FileStoreFactory.java | 6 +-
.../filesystem/FileSysOperationsFactory.java | 19 +-
.../RemoteMonitoredMoverFactory.java | 10 +-
.../filesystem/RetryingPathMover.java | 26 ++-
.../filesystem/RetryingPathRemover.java | 15 +-
.../datamover/filesystem/intf/FileStore.java | 15 +-
.../filesystem/intf/IExtendedFileStore.java | 2 +-
.../datamover/filesystem/intf/IFileStore.java | 2 +-
.../intf/IFileSysOperationsFactory.java | 1 -
.../datamover/filesystem/intf/IPathMover.java | 3 +-
.../intf/IRecoverableTimerTaskFactory.java | 2 +-
.../remote/CopyActivityMonitor.java | 71 +++++---
.../filesystem/remote/RemotePathMover.java | 87 +++++----
.../filesystem/remote/rsync/RsyncCopier.java | 80 ++++----
.../remote/rsync/RsyncVersionChecker.java | 18 +-
.../filesystem/store/FileStoreLocal.java | 33 ++--
.../cisd/datamover/utils/LocalBufferDirs.java | 4 +-
.../utils/QuietPeriodFileFilter.java | 17 +-
.../ch/systemsx/cisd/datamover/MainTest.java | 110 ++++++-----
.../cisd/datamover/ParametersTest.java | 37 ++--
.../systemsx/cisd/datamover/SelfTestTest.java | 24 ++-
.../remote/CopyActivityMonitorTest.java | 44 +++--
.../remote/rsync/RsyncCopierTest.java | 25 ++-
.../utils/QuietPeriodFileFilterTest.java | 9 +-
.../cisd/dbmigration/DBMigrationEngine.java | 43 +++--
.../cisd/dbmigration/DBScriptFormatter.java | 89 ++++-----
.../cisd/dbmigration/DBUtilities.java | 7 +-
.../DatabaseConfigurationContext.java | 6 +-
.../cisd/dbmigration/DatabaseEngine.java | 19 +-
.../dbmigration/DatabaseVersionLogDAO.java | 89 +++++----
.../cisd/dbmigration/IDataSourceFactory.java | 2 +-
.../cisd/dbmigration/IDatabaseAdminDAO.java | 14 +-
.../dbmigration/IDatabaseVersionLogDAO.java | 9 +-
.../systemsx/cisd/dbmigration/LogEntry.java | 41 +++--
.../cisd/dbmigration/MassUploadFileType.java | 10 +-
.../cisd/dbmigration/SqlScriptExecutor.java | 20 +-
.../cisd/dbmigration/SqlScriptProvider.java | 12 +-
.../cisd/dbmigration/h2/H2AdminDAO.java | 26 ++-
.../cisd/dbmigration/h2/H2MassUploader.java | 50 +++--
.../dbmigration/h2/H2StoredProcedures.java | 10 +-
.../postgresql/DumpPreparator.java | 37 ++--
.../postgresql/PostgreSQLAdminDAO.java | 36 ++--
.../postgresql/PostgreSQLDAOFactory.java | 5 +-
.../postgresql/PostgreSQLMassUploader.java | 44 +++--
.../dbmigration/DBMigrationEngineTest.java | 171 +++++++++++-------
.../cisd/dbmigration/DBUtilitiesTest.java | 12 +-
.../dbmigration/SqlScriptExecutorTest.java | 36 ++--
.../dbmigration/SqlScriptProviderTest.java | 50 +++--
.../h2/H2TestStoredProcedures.java | 10 +-
.../postgresql/DumpPreparatorTest.java | 161 ++++++++---------
289 files changed, 3658 insertions(+), 2603 deletions(-)
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/DummyProjectHandler.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/DummyProjectHandler.java
index c13a5c9af9a..1c431e3bc3a 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/DummyProjectHandler.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/DummyProjectHandler.java
@@ -17,14 +17,12 @@
package ch.systemsx.cisd.ant.common;
/**
- *
- *
* @author felmer
*/
public class DummyProjectHandler implements IProjectHandler
{
public static final IProjectHandler INSTANCE = new DummyProjectHandler();
-
+
public IProjectHandler createHandler(EclipseClasspathEntry entry)
{
return INSTANCE;
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/EclipseClasspathReader.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/EclipseClasspathReader.java
index 01c2e6b649e..b38b8b3b8d3 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/EclipseClasspathReader.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/EclipseClasspathReader.java
@@ -34,7 +34,7 @@ public class EclipseClasspathReader
{
/** Name of the Eclipse classpath file. */
public static final String CLASSPATH_FILE = ".classpath";
-
+
private static final String CLASSPATH = "classpath";
private static final String PATH_ATTRIBUTE = "path";
@@ -46,14 +46,15 @@ public class EclipseClasspathReader
/**
* Reads from the specified Eclipse classpath file all classpathentry elements.
*/
- public static List<EclipseClasspathEntry> readClasspathEntries(IEclipseClasspathLocation location)
+ public static List<EclipseClasspathEntry> readClasspathEntries(
+ IEclipseClasspathLocation location)
{
String displayableLocation = location.getDisplayableLocation();
Node root = location.getDocument().getChildNodes().item(0);
if (CLASSPATH.equalsIgnoreCase(root.getNodeName()) == false)
{
- throw new IllegalArgumentException("Root element of '" + displayableLocation + "' is not '" + CLASSPATH
- + "'.");
+ throw new IllegalArgumentException("Root element of '" + displayableLocation
+ + "' is not '" + CLASSPATH + "'.");
}
NodeList children = root.getChildNodes();
List<Element> elements = new ArrayList<Element>();
@@ -85,8 +86,8 @@ public class EclipseClasspathReader
} catch (Exception e)
{
- throw new IllegalArgumentException((i + 1) + ". element of '" + displayableLocation + "': "
- + e.getMessage(), e);
+ throw new IllegalArgumentException((i + 1) + ". element of '" + displayableLocation
+ + "': " + e.getMessage(), e);
}
}
return entries;
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/FileBaseEclipseClasspathLocation.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/FileBaseEclipseClasspathLocation.java
index 2fb8db3130f..7bbf481f603 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/FileBaseEclipseClasspathLocation.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/FileBaseEclipseClasspathLocation.java
@@ -24,8 +24,6 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.w3c.dom.Document;
/**
- *
- *
* @author felmer
*/
public class FileBaseEclipseClasspathLocation implements IEclipseClasspathLocation
@@ -37,7 +35,7 @@ public class FileBaseEclipseClasspathLocation implements IEclipseClasspathLocati
assert classpathFile != null;
this.classpathFile = classpathFile;
}
-
+
public String getDisplayableLocation()
{
return classpathFile.getPath();
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IEclipseClasspathLocation.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IEclipseClasspathLocation.java
index 4fb38cbdff6..6ea219997eb 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IEclipseClasspathLocation.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IEclipseClasspathLocation.java
@@ -19,13 +19,11 @@ package ch.systemsx.cisd.ant.common;
import org.w3c.dom.Document;
/**
- *
- *
* @author felmer
*/
public interface IEclipseClasspathLocation
{
public Document getDocument();
-
+
public String getDisplayableLocation();
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IProjectHandler.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IProjectHandler.java
index 55f96e36201..591ac3044ee 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IProjectHandler.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/IProjectHandler.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.ant.common;
/**
* Call-back interface used by {@link RecursiveProjectTraverser} for traversing project dependency graphs.
- *
+ *
* @author felmer
*/
public interface IProjectHandler
@@ -27,27 +27,26 @@ public interface IProjectHandler
* Handle project when entering its graph vertex.
*/
public void handleOnEntering();
-
+
/**
* Handle project when entering its graph vertex.
*/
public void handleOnLeaving();
-
+
/**
* Returns the Eclipse classpath location for the correcponding project vertex.
*
* @return <code>null</code> if this project has no Eclipse classpath location.
*/
public IEclipseClasspathLocation createLocation();
-
+
/**
* Handles specified entry.
*/
public void handleEntry(EclipseClasspathEntry entry);
-
+
/**
- * Creates a new project handler based on the specified entry.
- * Implementations should never return <code>null</code>.
+ * Creates a new project handler based on the specified entry. Implementations should never return <code>null</code>.
*/
public IProjectHandler createHandler(EclipseClasspathEntry entry);
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/RecursiveProjectTraverser.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/RecursiveProjectTraverser.java
index 6fe0f59f868..1f21ddfb8f6 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/RecursiveProjectTraverser.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/RecursiveProjectTraverser.java
@@ -21,8 +21,6 @@ import java.util.List;
import java.util.Set;
/**
- *
- *
* @author felmer
*/
public class RecursiveProjectTraverser
@@ -31,8 +29,9 @@ public class RecursiveProjectTraverser
{
traverse(projectHandler, new HashSet<EclipseClasspathEntry>());
}
-
- private static void traverse(IProjectHandler projectHandler, Set<EclipseClasspathEntry> visitedEntries)
+
+ private static void traverse(IProjectHandler projectHandler,
+ Set<EclipseClasspathEntry> visitedEntries)
{
projectHandler.handleOnEntering();
IEclipseClasspathLocation loc = projectHandler.createLocation();
@@ -50,6 +49,6 @@ public class RecursiveProjectTraverser
}
}
projectHandler.handleOnLeaving();
-
+
}
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/TextBasedEclipseClasspathLocation.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/TextBasedEclipseClasspathLocation.java
index b496737a19d..2ec80f51fdc 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/common/TextBasedEclipseClasspathLocation.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/common/TextBasedEclipseClasspathLocation.java
@@ -24,13 +24,12 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.w3c.dom.Document;
/**
- *
- *
* @author felmer
*/
public class TextBasedEclipseClasspathLocation implements IEclipseClasspathLocation
{
private final String text;
+
private final String displayableLocation;
public TextBasedEclipseClasspathLocation(String text, String displayableLocation)
@@ -39,7 +38,7 @@ public class TextBasedEclipseClasspathLocation implements IEclipseClasspathLocat
this.text = text;
this.displayableLocation = displayableLocation == null ? "UNKNOWN" : displayableLocation;
}
-
+
public String getDisplayableLocation()
{
return displayableLocation;
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/RecursiveJar.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/RecursiveJar.java
index d9f1acfd44b..0a2ee27ef24 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/RecursiveJar.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/RecursiveJar.java
@@ -63,7 +63,8 @@ public class RecursiveJar extends Jar
throw new BuildException("Base directory of fileset has to be a relative one.");
}
String subdir = path.substring(basePath.length());
- File subprojectDir = new File(new File(baseDir.getParentFile(), subProject), subdir);
+ File subprojectDir =
+ new File(new File(baseDir.getParentFile(), subProject), subdir);
if (subprojectDir.exists())
{
log("scan " + subprojectDir, Project.MSG_DEBUG);
@@ -124,8 +125,8 @@ public class RecursiveJar extends Jar
subprojectsAlreadySeen.add(subproject);
jar.addFilesetPlain(new RelatedSubprojectFileSet(fileSet, subproject));
File subprojectDir = new File(subprojectsParent, subproject);
- new SubprojectFileSetAppender(jar, fileSet, subprojectsParent, subprojectsAlreadySeen)
- .execute(subprojectDir);
+ new SubprojectFileSetAppender(jar, fileSet, subprojectsParent,
+ subprojectsAlreadySeen).execute(subprojectDir);
}
}
}
@@ -142,7 +143,8 @@ public class RecursiveJar extends Jar
{
addFilesetPlain(set);
File subprojectsParent = getProject().getBaseDir().getParentFile();
- SubprojectFileSetAppender appender = new SubprojectFileSetAppender(this, set, subprojectsParent);
+ SubprojectFileSetAppender appender =
+ new SubprojectFileSetAppender(this, set, subprojectsParent);
appender.executeFor(this);
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTask.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTask.java
index 8f1a9a334b8..32d56c9b01e 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTask.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTask.java
@@ -64,10 +64,11 @@ public class SetEclipseClasspathTask extends Property
}
addProperty(propertyName, builder.toString());
}
-
+
private final class ProjectHandler extends DummyProjectHandler
{
private final Set<File> files;
+
private final File projectBaseDir;
ProjectHandler(Set<File> files, File projectBaseDir)
@@ -75,7 +76,7 @@ public class SetEclipseClasspathTask extends Property
this.files = files;
this.projectBaseDir = projectBaseDir;
}
-
+
@Override
public void handleEntry(EclipseClasspathEntry entry)
{
@@ -84,7 +85,7 @@ public class SetEclipseClasspathTask extends Property
if (entry.getKind().equals(EclipseClasspathEntry.LIB_KIND))
{
files.add(classpathElement);
- }
+ }
}
@Override
@@ -102,7 +103,8 @@ public class SetEclipseClasspathTask extends Property
@Override
public IEclipseClasspathLocation createLocation()
{
- File eclipseClasspathFile = new File(projectBaseDir, EclipseClasspathReader.CLASSPATH_FILE);
+ File eclipseClasspathFile =
+ new File(projectBaseDir, EclipseClasspathReader.CLASSPATH_FILE);
if (eclipseClasspathFile.exists())
{
return new FileBaseEclipseClasspathLocation(eclipseClasspathFile);
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subprojectbuilder/BuildJavaSubprojectsTask.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subprojectbuilder/BuildJavaSubprojectsTask.java
index b6eb089cfb7..147f6aea48d 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subprojectbuilder/BuildJavaSubprojectsTask.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subprojectbuilder/BuildJavaSubprojectsTask.java
@@ -38,7 +38,7 @@ public class BuildJavaSubprojectsTask extends Task
@Override
protected void handleAbsentsOfClasspathFile(File eclipseClasspathFile)
{
- log("No Eclipse " + EclipseClasspathReader.CLASSPATH_FILE + " file found in '"
+ log("No Eclipse " + EclipseClasspathReader.CLASSPATH_FILE + " file found in '"
+ eclipseClasspathFile.getParent() + "'.");
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/AntTaskSimpleLoggerAdapter.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/AntTaskSimpleLoggerAdapter.java
index 61fe425110c..51268ee2e6e 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/AntTaskSimpleLoggerAdapter.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/AntTaskSimpleLoggerAdapter.java
@@ -36,19 +36,20 @@ public class AntTaskSimpleLoggerAdapter implements ISimpleLogger
{
switch (level)
{
- case OFF:
+ case OFF:
return Project.MSG_DEBUG;
case TRACE:
return Project.MSG_VERBOSE;
- case DEBUG:
+ case DEBUG:
return Project.MSG_DEBUG;
- case INFO:
+ case INFO:
return Project.MSG_INFO;
- case WARN:
+ case WARN:
return Project.MSG_WARN;
- case ERROR:
+ case ERROR:
return Project.MSG_ERR;
- default: throw new IllegalArgumentException("Illegal log level " + level);
+ default:
+ throw new IllegalArgumentException("Illegal log level " + level);
}
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTask.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTask.java
index d78b42af0b2..bb0477f5b48 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTask.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTask.java
@@ -109,7 +109,8 @@ public class GatherRevisionAndVersionTask extends Property
}
}
}
- checkFailure(versions, projectRevisions, dirtyProjects, minRevision, maxRevision, maxLastChangedRevision);
+ checkFailure(versions, projectRevisions, dirtyProjects, minRevision, maxRevision,
+ maxLastChangedRevision);
setRevisionProperty(maxLastChangedRevision);
setVersionProperty(versions);
setCleanProperty(dirtyProjects);
@@ -145,7 +146,8 @@ public class GatherRevisionAndVersionTask extends Property
private Set<String> collectProjects(ISVNActions actions)
{
final ISVNProjectPathProvider pathProvider = createPathProvider(getProject().getBaseDir());
- return new SVNDependentProjectsCollector(pathProvider, actions).collectDependentProjectsFromClasspath();
+ return new SVNDependentProjectsCollector(pathProvider, actions)
+ .collectDependentProjectsFromClasspath();
}
private void setRevisionProperty(int maxLastChangedRevision)
@@ -176,8 +178,8 @@ public class GatherRevisionAndVersionTask extends Property
}
}
- private void checkFailure(HashSet<String> versions, StringBuilder projectRevisions, StringBuilder dirtyProjects,
- int minRevision, int maxRevision, int lastChangedRevision)
+ private void checkFailure(HashSet<String> versions, StringBuilder projectRevisions,
+ StringBuilder dirtyProjects, int minRevision, int maxRevision, int lastChangedRevision)
{
if (failOnInconsistency && maxRevision != minRevision)
{
@@ -190,12 +192,13 @@ public class GatherRevisionAndVersionTask extends Property
}
if (failOnInconsistency && versions.size() > 1)
{
- throw new BuildException("Versions of local copies of the projects are inconsistent: " + versions);
+ throw new BuildException("Versions of local copies of the projects are inconsistent: "
+ + versions);
}
if (maxRevision < lastChangedRevision)
{
- throw new BuildException("Maximum revision < last changed revision: " + maxRevision + " < "
- + lastChangedRevision);
+ throw new BuildException("Maximum revision < last changed revision: " + maxRevision
+ + " < " + lastChangedRevision);
}
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNActions.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNActions.java
index 274b3910ec9..bab27315872 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNActions.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNActions.java
@@ -21,6 +21,7 @@ package ch.systemsx.cisd.ant.task.subversion;
*
* @author Bernd Rinn
*/
-interface ISVNActions extends ISVNCat, ISVNList, ISVNMkDir, ISVNCopy, ISVNInfo, ISVNStatus, ISVNMucc
+interface ISVNActions extends ISVNCat, ISVNList, ISVNMkDir, ISVNCopy, ISVNInfo, ISVNStatus,
+ ISVNMucc
{
}
\ No newline at end of file
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCheckout.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCheckout.java
index 51b984110bf..e9847fba555 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCheckout.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCheckout.java
@@ -34,7 +34,8 @@ interface ISVNCheckout
* @param revision The revision in the repository to check out.
* @throws SVNException If there is a problem with performing the <code>checkout</code> command.
*/
- public void checkout(String repositoryUrl, String projectName, String revision) throws SVNException;
+ public void checkout(String repositoryUrl, String projectName, String revision)
+ throws SVNException;
/**
* @return The directory where working copies are created by {@link #checkout(String,String,String)}.
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCopy.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCopy.java
index 8b578cd50a0..7f9693e9605 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCopy.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNCopy.java
@@ -35,7 +35,7 @@ interface ISVNCopy
* @param logMessage The log message to set in the revision properties.
* @throws SVNException If there is a problem with performing the <code>copy</code> command.
*/
- public void copy(String sourcePathOrUrl, String sourceRevision, String destinationPathOrUrl, String logMessage)
- throws SVNException;
+ public void copy(String sourcePathOrUrl, String sourceRevision, String destinationPathOrUrl,
+ String logMessage) throws SVNException;
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNInfo.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNInfo.java
index 916002631f0..1147f34e338 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNInfo.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNInfo.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.ant.task.subversion;
/**
* A role that performs an <code>info</code> query on a subversion working copy.
* <p>
- * This query works on a subversion working copy.
- *
+ * This query works on a subversion working copy.
+ *
* @author Bernd Rinn
*/
interface ISVNInfo
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNProjectPathProvider.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNProjectPathProvider.java
index 43ea390fa30..19260f8b0cd 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNProjectPathProvider.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/ISVNProjectPathProvider.java
@@ -55,12 +55,12 @@ interface ISVNProjectPathProvider
* @return The name of the project that is path provider's context is based on.
*/
public String getProjectName();
-
+
/**
* @return The revision of the project that is path provider's context is based on.
*/
public String getRevision();
-
+
/**
* @return <code>true</code> if this provider represents a subversion repository path (rather than a working copy
* path).
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNActions.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNActions.java
index 757af77afba..4390200e883 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNActions.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNActions.java
@@ -41,36 +41,40 @@ class SVNActions implements ISVNActions
this.logger = logger;
}
-
public String cat(String pathOrUrl) throws SVNException
{
assert pathOrUrl != null;
- assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl + "' is neither a URL nor an absolute path.";
+ assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl
+ + "' is neither a URL nor an absolute path.";
- final ProcessInfo subversionProcessInfo = SVNUtilities.subversionCommand(logger, false, "cat", pathOrUrl);
+ final ProcessInfo subversionProcessInfo =
+ SVNUtilities.subversionCommand(logger, false, "cat", pathOrUrl);
return StringUtils.join(subversionProcessInfo.getLines(), OSUtilities.LINE_SEPARATOR);
}
public List<String> list(String pathOrUrl) throws SVNException
{
assert pathOrUrl != null;
- assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl + "' is neither a URL nor an absolute path.";
+ assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl
+ + "' is neither a URL nor an absolute path.";
- final ProcessInfo subversionProcessInfo = SVNUtilities.subversionCommand(logger, "list", pathOrUrl);
+ final ProcessInfo subversionProcessInfo =
+ SVNUtilities.subversionCommand(logger, "list", pathOrUrl);
return subversionProcessInfo.getLines();
}
public void mkdir(String pathOrUrl, String logMessage) throws SVNException
{
assert pathOrUrl != null;
- assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl + "' is neither a URL nor an absolute path.";
+ assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl
+ + "' is neither a URL nor an absolute path.";
SVNUtilities.subversionCommand(logger, "mkdir", "--message", logMessage, pathOrUrl);
}
- public void copy(String sourcePathOrUrl, String sourceRevision, String destinationPathOrUrl, String logMessage)
- throws SVNException
+ public void copy(String sourcePathOrUrl, String sourceRevision, String destinationPathOrUrl,
+ String logMessage) throws SVNException
{
assert sourcePathOrUrl != null;
assert checkUrlOrAbsolutePath(sourcePathOrUrl) : "'" + sourcePathOrUrl
@@ -81,32 +85,36 @@ class SVNActions implements ISVNActions
if (SVNUtilities.HEAD_REVISION.equals(sourceRevision))
{
- SVNUtilities.subversionCommand(logger, "copy", "--message", logMessage, sourcePathOrUrl,
- destinationPathOrUrl);
+ SVNUtilities.subversionCommand(logger, "copy", "--message", logMessage,
+ sourcePathOrUrl, destinationPathOrUrl);
} else
{
- SVNUtilities.subversionCommand(logger, "copy", "--message", logMessage, "--revision", sourceRevision,
- sourcePathOrUrl, destinationPathOrUrl);
+ SVNUtilities.subversionCommand(logger, "copy", "--message", logMessage, "--revision",
+ sourceRevision, sourcePathOrUrl, destinationPathOrUrl);
}
}
public SVNInfoRecord info(String pathOrUrl)
{
assert pathOrUrl != null;
- assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl + "' is neither a URL nor an absolute path.";
+ assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl
+ + "' is neither a URL nor an absolute path.";
- final ProcessInfo subversionProcessInfo = SVNUtilities.subversionCommand(logger, "info", "-R", pathOrUrl);
+ final ProcessInfo subversionProcessInfo =
+ SVNUtilities.subversionCommand(logger, "info", "-R", pathOrUrl);
final SVNInfoRecord infoRecord = new SVNInfoRecord();
new SVNInfoRecordExtractor().fillInfoRecord(infoRecord, subversionProcessInfo);
return infoRecord;
}
-
+
public List<SVNItemStatus> status(String pathOrUrl)
{
assert pathOrUrl != null;
- assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl + "' is neither a URL nor an absolute path.";
+ assert checkUrlOrAbsolutePath(pathOrUrl) : "'" + pathOrUrl
+ + "' is neither a URL nor an absolute path.";
- final ProcessInfo subversionProcessInfo = SVNUtilities.subversionCommand(logger, "status", pathOrUrl);
+ final ProcessInfo subversionProcessInfo =
+ SVNUtilities.subversionCommand(logger, "status", pathOrUrl);
final List<SVNItemStatus> status = new ArrayList<SVNItemStatus>();
for (String line : subversionProcessInfo.getLines())
{
@@ -128,18 +136,16 @@ class SVNActions implements ISVNActions
return false;
}
-
public boolean isMuccAvailable()
{
return SVNUtilities.isMuccAvailable();
}
-
public void mucc(String logMessage, String... args) throws SVNException
{
assert logMessage != null;
assert args.length > 0;
-
+
SVNUtilities.subversionMuccCommand(logger, logMessage, args);
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTask.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTask.java
index e816b74f0d7..7b317b8c1cd 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTask.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTask.java
@@ -40,7 +40,8 @@ public class SVNBranchAndTagTask extends Task
final private SVNRepositoryProjectContext sourceContext = new SVNRepositoryProjectContext();
/** The destination context of the project in the subversion repository. */
- final private SVNRepositoryProjectContext destinationContext = new SVNRepositoryProjectContext();
+ final private SVNRepositoryProjectContext destinationContext =
+ new SVNRepositoryProjectContext();
/** If set to <code>true</code>, both a branch will be created and a tag from this branch. */
private boolean branchIfNecessary = false;
@@ -60,7 +61,8 @@ public class SVNBranchAndTagTask extends Task
private final String tagRepositoryUrl;
- SVNRepositoryProjectContextAntWrapper(SVNRepositoryProjectContext context) throws BuildException
+ SVNRepositoryProjectContextAntWrapper(SVNRepositoryProjectContext context)
+ throws BuildException
{
this(context, null);
}
@@ -94,14 +96,14 @@ public class SVNBranchAndTagTask extends Task
}
}
- private static ISVNProjectPathProvider createPathProvider(SVNRepositoryProjectContext context)
- throws UserFailureException
+ private static ISVNProjectPathProvider createPathProvider(
+ SVNRepositoryProjectContext context) throws UserFailureException
{
return context.getPathProvider();
}
- private static void assign(SVNRepositoryProjectContext context, SVNRepositoryProjectContext contextToAssignFrom)
- throws UserFailureException
+ private static void assign(SVNRepositoryProjectContext context,
+ SVNRepositoryProjectContext contextToAssignFrom) throws UserFailureException
{
context.setRepositoryRoot(contextToAssignFrom.getRepositoryRoot());
context.setGroup(contextToAssignFrom.getGroup());
@@ -150,14 +152,16 @@ public class SVNBranchAndTagTask extends Task
throw new BuildException("No branch/tag name specified.");
}
final ISVNActions svn = createSVNActions();
- final SVNRepositoryProjectContextAntWrapper source = new SVNRepositoryProjectContextAntWrapper(sourceContext);
+ final SVNRepositoryProjectContextAntWrapper source =
+ new SVNRepositoryProjectContextAntWrapper(sourceContext);
final SVNRepositoryProjectContextAntWrapper destination =
new SVNRepositoryProjectContextAntWrapper(destinationContext, sourceContext);
switch (versionTypeToCreate)
{
case RELEASE_TAG:
- createTagInSvn(svn, source, createBranchContext(destinationContext), destination, branchIfNecessary);
+ createTagInSvn(svn, source, createBranchContext(destinationContext), destination,
+ branchIfNecessary);
break;
case RELEASE_BRANCH:
case FEATURE_BRANCH:
@@ -169,32 +173,38 @@ public class SVNBranchAndTagTask extends Task
}
- private static void createTagInSvn(final ISVNActions svn, final SVNRepositoryProjectContextAntWrapper source,
- final SVNRepositoryProjectContextAntWrapper branch, final SVNRepositoryProjectContextAntWrapper tag,
- boolean branchIfNecessary) throws BuildException
+ private static void createTagInSvn(final ISVNActions svn,
+ final SVNRepositoryProjectContextAntWrapper source,
+ final SVNRepositoryProjectContextAntWrapper branch,
+ final SVNRepositoryProjectContextAntWrapper tag, boolean branchIfNecessary)
+ throws BuildException
{
if (false == branchExists(svn, branch))
{
if (branchIfNecessary)
{
- if (false == tag.getVersion().equals(SVNUtilities.getFirstTagForBranch(branch.getVersion())))
+ if (false == tag.getVersion().equals(
+ SVNUtilities.getFirstTagForBranch(branch.getVersion())))
{
- throw new BuildException("Supposed to create branch for tag but tag doesn't start a branch (tag='"
- + tag.getVersion() + "').");
+ throw new BuildException(
+ "Supposed to create branch for tag but tag doesn't start a branch (tag='"
+ + tag.getVersion() + "').");
}
createBranchInSvn(svn, source, branch);
} else
{
- throw new BuildException("Branch from which to tag is not yet defined. (" + branch.getVersion() + ")");
+ throw new BuildException("Branch from which to tag is not yet defined. ("
+ + branch.getVersion() + ")");
}
}
final String tagName = tag.getVersion();
final String logMessage = "Create tag '" + tagName + "'";
- svn.copy(branch.getRepositoryUrl(), branch.getRevision(), tag.getRepositoryUrl(), logMessage);
+ svn.copy(branch.getRepositoryUrl(), branch.getRevision(), tag.getRepositoryUrl(),
+ logMessage);
}
- private static SVNRepositoryProjectContextAntWrapper createBranchContext(SVNRepositoryProjectContext tagContext)
- throws BuildException
+ private static SVNRepositoryProjectContextAntWrapper createBranchContext(
+ SVNRepositoryProjectContext tagContext) throws BuildException
{
try
{
@@ -208,7 +218,8 @@ public class SVNBranchAndTagTask extends Task
}
}
- private static void createBranchInSvn(final ISVNActions svn, final SVNRepositoryProjectContextAntWrapper source,
+ private static void createBranchInSvn(final ISVNActions svn,
+ final SVNRepositoryProjectContextAntWrapper source,
final SVNRepositoryProjectContextAntWrapper destination)
{
final ISVNProjectPathProvider sourcePathProvider = source.getPathProvider();
@@ -235,8 +246,9 @@ public class SVNBranchAndTagTask extends Task
}
for (String subProjectName : dependentProjects)
{
- commandLine.addAll(Arrays.asList("cp", sourcePathProvider.getRevision(), sourcePathProvider
- .getPath(subProjectName), destinationPathProvider.getPath(subProjectName)));
+ commandLine.addAll(Arrays.asList("cp", sourcePathProvider.getRevision(),
+ sourcePathProvider.getPath(subProjectName), destinationPathProvider
+ .getPath(subProjectName)));
}
svn.mucc(logMessage, commandLine.toArray(new String[commandLine.size()]));
} else
@@ -248,8 +260,9 @@ public class SVNBranchAndTagTask extends Task
}
for (String subProjectName : dependentProjects)
{
- svn.copy(sourcePathProvider.getPath(subProjectName), sourcePathProvider.getRevision(),
- destinationPathProvider.getPath(subProjectName), logMessage);
+ svn.copy(sourcePathProvider.getPath(subProjectName), sourcePathProvider
+ .getRevision(), destinationPathProvider.getPath(subProjectName),
+ logMessage);
}
}
} catch (SVNException ex)
@@ -258,7 +271,8 @@ public class SVNBranchAndTagTask extends Task
}
}
- private static boolean branchExists(final ISVNActions svn, final SVNRepositoryProjectContextAntWrapper branch)
+ private static boolean branchExists(final ISVNActions svn,
+ final SVNRepositoryProjectContextAntWrapper branch)
{
final String branchName = branch.getVersion();
final String branchUrl = branch.getRepositoryUrl();
@@ -300,7 +314,7 @@ public class SVNBranchAndTagTask extends Task
throw new BuildException(ex);
}
}
-
+
public void setGroup(String groupName)
{
try
@@ -332,7 +346,8 @@ public class SVNBranchAndTagTask extends Task
if (SVNProjectVersionType.TRUNK != destinationContext.getVersionType())
{
- throw new BuildException(String.format("Version type has already been set (Version: '%s', Type: '%s').",
+ throw new BuildException(String.format(
+ "Version type has already been set (Version: '%s', Type: '%s').",
destinationContext.getVersion(), destinationContext.getVersionType()));
}
@@ -354,7 +369,8 @@ public class SVNBranchAndTagTask extends Task
if (SVNProjectVersionType.TRUNK != destinationContext.getVersionType())
{
- throw new BuildException(String.format("Version type has already been set (Version: '%s', Type: '%s').",
+ throw new BuildException(String.format(
+ "Version type has already been set (Version: '%s', Type: '%s').",
destinationContext.getVersion(), destinationContext.getVersionType()));
}
@@ -376,7 +392,8 @@ public class SVNBranchAndTagTask extends Task
if (SVNProjectVersionType.TRUNK != destinationContext.getVersionType())
{
- throw new BuildException(String.format("Version type has already been set (Version: '%s', Type: '%s').",
+ throw new BuildException(String.format(
+ "Version type has already been set (Version: '%s', Type: '%s').",
destinationContext.getVersion(), destinationContext.getVersionType()));
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNCheckout.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNCheckout.java
index d247d8940c0..1d66ac648de 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNCheckout.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNCheckout.java
@@ -52,8 +52,8 @@ class SVNCheckout implements ISVNCheckout
assert SVNUtilities.HEAD_REVISION.equals(revision) || Integer.parseInt(revision) >= 0;
final String workingCopyPath = new File(directoryToCheckout, projectName).getAbsolutePath();
- SVNUtilities.subversionCommand(logger, "checkout", "--revision", revision, String.format("%s@%s", url,
- revision), workingCopyPath);
+ SVNUtilities.subversionCommand(logger, "checkout", "--revision", revision, String.format(
+ "%s@%s", url, revision), workingCopyPath);
}
public String getDirectoryToCheckout()
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectsCollector.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectsCollector.java
index a5dc0da16ac..3a6c50f880e 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectsCollector.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectsCollector.java
@@ -72,7 +72,7 @@ class SVNDependentProjectsCollector
private final Set<String> projects;
private final String projectPath;
-
+
private final Set<String> locationsAlreadyVisited;
ProjectHandler(Set<String> projects, String projectPath)
@@ -90,7 +90,8 @@ class SVNDependentProjectsCollector
@Override
public IEclipseClasspathLocation createLocation()
{
- final String displayableLocation = projectPath + "/" + EclipseClasspathReader.CLASSPATH_FILE;
+ final String displayableLocation =
+ projectPath + "/" + EclipseClasspathReader.CLASSPATH_FILE;
if (locationsAlreadyVisited.contains(displayableLocation))
{
return null;
@@ -100,7 +101,7 @@ class SVNDependentProjectsCollector
{
final String eclipseClasspath = actions.cat(displayableLocation);
// This is one of the possibilities what can happen if there is no .classpath file.
- if (eclipseClasspath.length() == 0)
+ if (eclipseClasspath.length() == 0)
{
return null;
}
@@ -125,7 +126,8 @@ class SVNDependentProjectsCollector
public IProjectHandler createHandler(EclipseClasspathEntry entry)
{
final String projectName = SVNUtilities.getTopLevelDirectory(entry.getPath());
- return new ProjectHandler(projects, pathProvider.getPath(projectName), locationsAlreadyVisited);
+ return new ProjectHandler(projects, pathProvider.getPath(projectName),
+ locationsAlreadyVisited);
}
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNException.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNException.java
index be9ee2df3c9..b89f63e400e 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNException.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNException.java
@@ -20,7 +20,7 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
* An exception indicating a problem performing a subversion command.
- *
+ *
* @author Bernd Rinn
*/
public class SVNException extends EnvironmentFailureException
@@ -32,7 +32,7 @@ public class SVNException extends EnvironmentFailureException
{
super(message);
}
-
+
public SVNException(String messageTemplate, Throwable cause)
{
super(messageTemplate, cause);
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecord.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecord.java
index f50c068777f..a040e21c598 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecord.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecord.java
@@ -28,19 +28,28 @@ class SVNInfoRecord
{
FILE, DIRECTORY
}
-
+
/** The writing part of the interface. */
interface Updater
{
public void setWorkingCopyPath(String workingCopyPath);
+
public void setRepositoryUrl(String repositoryUrl);
+
public void setRepositoryRootUrl(String repositoryRootUrl);
+
public void setRepositoryUUID(String repositoryUUID);
+
public void setRevision(int revision);
+
public void setNodeKind(NodeKind nodeKind);
+
public void setSchedule(String schedule);
+
public void setLastChangedAuthor(String lastChangedAuthor);
+
public void setLastChangedRevision(int lastChangedRevision);
+
public void setLastChangedDate(String lastChangedDate);
}
@@ -60,65 +69,65 @@ class SVNInfoRecord
private String lastChangedAuthor;
- private int lastChangedRevision;
+ private int lastChangedRevision;
private String lastChangedDate;
private Updater updater = new Updater()
- {
-
- public void setLastChangedAuthor(String lastChangedAuthor)
- {
- SVNInfoRecord.this.lastChangedAuthor = lastChangedAuthor;
- }
-
- public void setLastChangedRevision(int lastChangedRevision)
- {
- SVNInfoRecord.this.lastChangedRevision = lastChangedRevision;
- }
-
- public void setLastChangedDate(String lastChangedDate)
- {
- SVNInfoRecord.this.lastChangedDate = lastChangedDate;
- }
-
- public void setNodeKind(NodeKind nodeKind)
- {
- SVNInfoRecord.this.nodeKind = nodeKind;
- }
-
- public void setRepositoryRootUrl(String repositoryRootUrl)
- {
- SVNInfoRecord.this.repositoryRootUrl = repositoryRootUrl;
- }
-
- public void setRepositoryUUID(String repositoryUUID)
- {
- SVNInfoRecord.this.repositoryUUID = repositoryUUID;
- }
-
- public void setRepositoryUrl(String repositoryUrl)
- {
- SVNInfoRecord.this.repositoryUrl = repositoryUrl;
- }
-
- public void setRevision(int revision)
- {
- SVNInfoRecord.this.revision = revision;
- }
-
- public void setSchedule(String schedule)
- {
- SVNInfoRecord.this.schedule = schedule;
- }
-
- public void setWorkingCopyPath(String workingCopyPath)
- {
- SVNInfoRecord.this.workingCopyPath = workingCopyPath;
- }
-
- };
-
+ {
+
+ public void setLastChangedAuthor(String lastChangedAuthor)
+ {
+ SVNInfoRecord.this.lastChangedAuthor = lastChangedAuthor;
+ }
+
+ public void setLastChangedRevision(int lastChangedRevision)
+ {
+ SVNInfoRecord.this.lastChangedRevision = lastChangedRevision;
+ }
+
+ public void setLastChangedDate(String lastChangedDate)
+ {
+ SVNInfoRecord.this.lastChangedDate = lastChangedDate;
+ }
+
+ public void setNodeKind(NodeKind nodeKind)
+ {
+ SVNInfoRecord.this.nodeKind = nodeKind;
+ }
+
+ public void setRepositoryRootUrl(String repositoryRootUrl)
+ {
+ SVNInfoRecord.this.repositoryRootUrl = repositoryRootUrl;
+ }
+
+ public void setRepositoryUUID(String repositoryUUID)
+ {
+ SVNInfoRecord.this.repositoryUUID = repositoryUUID;
+ }
+
+ public void setRepositoryUrl(String repositoryUrl)
+ {
+ SVNInfoRecord.this.repositoryUrl = repositoryUrl;
+ }
+
+ public void setRevision(int revision)
+ {
+ SVNInfoRecord.this.revision = revision;
+ }
+
+ public void setSchedule(String schedule)
+ {
+ SVNInfoRecord.this.schedule = schedule;
+ }
+
+ public void setWorkingCopyPath(String workingCopyPath)
+ {
+ SVNInfoRecord.this.workingCopyPath = workingCopyPath;
+ }
+
+ };
+
public String getLastChangedAuthor()
{
return lastChangedAuthor;
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractor.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractor.java
index 69bc2a83566..68b189b5b64 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractor.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractor.java
@@ -24,8 +24,6 @@ import ch.systemsx.cisd.ant.task.subversion.SVNInfoRecord.Updater;
import ch.systemsx.cisd.ant.task.subversion.SVNUtilities.ProcessInfo;
/**
- *
- *
* @author felmer
*/
class SVNInfoRecordExtractor
@@ -34,7 +32,7 @@ class SVNInfoRecordExtractor
{
public void handle(SVNInfoRecord record, String value);
}
-
+
private static abstract class FirstValueHandler implements ValueHandler
{
private boolean first = true;
@@ -47,10 +45,10 @@ class SVNInfoRecordExtractor
first = false;
}
}
-
+
protected abstract void update(Updater updater, String value);
}
-
+
private static final class PathHandler extends FirstValueHandler
{
@Override
@@ -59,7 +57,7 @@ class SVNInfoRecordExtractor
updater.setWorkingCopyPath(value);
}
}
-
+
private static final class RepositoryUrlHandler extends FirstValueHandler
{
@Override
@@ -68,7 +66,7 @@ class SVNInfoRecordExtractor
updater.setRepositoryUrl(value);
}
}
-
+
private static final class RepositoryRootHandler extends FirstValueHandler
{
@Override
@@ -77,7 +75,7 @@ class SVNInfoRecordExtractor
updater.setRepositoryRootUrl(value);
}
}
-
+
private static final class RepositoryUUIDHandler extends FirstValueHandler
{
@Override
@@ -86,7 +84,7 @@ class SVNInfoRecordExtractor
updater.setRepositoryUUID(value);
}
}
-
+
private static final class ScheduleHandler extends FirstValueHandler
{
@Override
@@ -95,7 +93,7 @@ class SVNInfoRecordExtractor
updater.setSchedule(value);
}
}
-
+
private static final class LastChangedAuthorHandler extends FirstValueHandler
{
@Override
@@ -104,7 +102,7 @@ class SVNInfoRecordExtractor
updater.setLastChangedAuthor(value);
}
}
-
+
private static final class LastChangedDateHandler extends FirstValueHandler
{
@Override
@@ -113,7 +111,7 @@ class SVNInfoRecordExtractor
updater.setLastChangedDate(value);
}
}
-
+
private static final class NodeKindHandler extends FirstValueHandler
{
@Override
@@ -127,11 +125,12 @@ class SVNInfoRecordExtractor
updater.setNodeKind(NodeKind.FILE);
} else
{
- throw SVNException.fromTemplate("Subversion reports invalid node kind '%s'.", value);
+ throw SVNException
+ .fromTemplate("Subversion reports invalid node kind '%s'.", value);
}
}
}
-
+
private static final class RevisionHandler implements ValueHandler
{
public void handle(SVNInfoRecord record, String value)
@@ -142,7 +141,8 @@ class SVNInfoRecordExtractor
updater.setRevision(Math.max(record.getRevision(), Integer.parseInt(value)));
} catch (NumberFormatException ex)
{
- throw SVNException.fromTemplate("Subversion reports invalid revision number '%s'.", value);
+ throw SVNException.fromTemplate("Subversion reports invalid revision number '%s'.",
+ value);
}
}
}
@@ -154,10 +154,12 @@ class SVNInfoRecordExtractor
try
{
Updater updater = record.getUpdater();
- updater.setLastChangedRevision(Math.max(record.getLastChangedRevision(), Integer.parseInt(value)));
+ updater.setLastChangedRevision(Math.max(record.getLastChangedRevision(), Integer
+ .parseInt(value)));
} catch (NumberFormatException ex)
{
- throw SVNException.fromTemplate("Subversion reports invalid last changed revision number '%s'.", value);
+ throw SVNException.fromTemplate(
+ "Subversion reports invalid last changed revision number '%s'.", value);
}
}
}
@@ -178,7 +180,7 @@ class SVNInfoRecordExtractor
valueHandlerMap.put("Last Changed Rev", new LastChangedRevisionHandler());
valueHandlerMap.put("Last Changed Date", new LastChangedDateHandler());
}
-
+
void fillInfoRecord(final SVNInfoRecord record, final ProcessInfo subversionProcessInfo)
{
for (String line : subversionProcessInfo.getLines())
@@ -195,5 +197,4 @@ class SVNInfoRecordExtractor
}
}
-
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNItemStatus.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNItemStatus.java
index 4f7502c0cc7..56d76a76e60 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNItemStatus.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNItemStatus.java
@@ -26,24 +26,15 @@ import java.util.Map;
*/
class SVNItemStatus
{
-
+
/** The possible status an item can have. */
public enum StatusFlag
{
- UPTODATE(' '),
- ADDED('A'),
- DELETED('D'),
- MODIFIED('M'),
- REPLACED('R'),
- CONFLICTED('C'),
- EXTERNALSRELATED('X'),
- IGNORED('I'),
- UNVERSIONED('?'),
- MISSING('!'),
- TYPECHANGED('~');
-
+ UPTODATE(' '), ADDED('A'), DELETED('D'), MODIFIED('M'), REPLACED('R'), CONFLICTED('C'),
+ EXTERNALSRELATED('X'), IGNORED('I'), UNVERSIONED('?'), MISSING('!'), TYPECHANGED('~');
+
private final char statusCharacter;
-
+
StatusFlag(char statusCharacter)
{
this.statusCharacter = statusCharacter;
@@ -53,9 +44,9 @@ class SVNItemStatus
{
return statusCharacter;
}
-
+
}
-
+
private static Map<Character, StatusFlag> characterToStatusMap;
private static void ensureCharacterStatusMap()
@@ -69,7 +60,7 @@ class SVNItemStatus
}
}
}
-
+
private static final Map<Character, StatusFlag> getCharacterToStatusMap()
{
ensureCharacterStatusMap();
@@ -84,10 +75,10 @@ class SVNItemStatus
{
assert path != null;
ensureCharacterStatusMap();
-
+
this.flag = getCharacterToStatusMap().get(statusCharacter);
this.path = path;
-
+
assert flag != null;
}
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTask.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTask.java
index 98319c3410b..a95cf9900d1 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTask.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTask.java
@@ -108,13 +108,16 @@ public class SVNRecursiveCheckoutTask extends Task
final String projectToCheckOut = pathProvider.getPath(projectName);
try
{
- checkoutCmd.checkout(projectToCheckOut, projectName, pathProvider.getRevision());
+ checkoutCmd.checkout(projectToCheckOut, projectName, pathProvider
+ .getRevision());
} catch (SVNException ex)
{
throw new BuildException(ex.getMessage(), ex.getCause());
}
- final File projectWorkingCopyDir = new File(checkoutCmd.getDirectoryToCheckout(), projectName);
- new SVNCheckoutDependentExecutor(checkoutCmd).execute(projectWorkingCopyDir);
+ final File projectWorkingCopyDir =
+ new File(checkoutCmd.getDirectoryToCheckout(), projectName);
+ new SVNCheckoutDependentExecutor(checkoutCmd)
+ .execute(projectWorkingCopyDir);
}
}
}
@@ -148,12 +151,13 @@ public class SVNRecursiveCheckoutTask extends Task
try
{
final ISVNCheckout checkoutCmd = createSVNCheckout(repositoryUrl, workingCopyDir);
- checkoutCmd.checkout(pathProvider.getPath(), pathProvider.getProjectName(), pathProvider.getRevision());
+ checkoutCmd.checkout(pathProvider.getPath(), pathProvider.getProjectName(),
+ pathProvider.getRevision());
// Always check out "build_resources", though it is not specified as dependency in .classpath.
checkoutCmd.checkout(pathProvider.getPath(SVNUtilities.BUILD_RESOURCES_PROJECT),
SVNUtilities.BUILD_RESOURCES_PROJECT, pathProvider.getRevision());
- new SVNCheckoutDependentExecutor(checkoutCmd).execute(new File(workingCopyDir, pathProvider
- .getProjectName()));
+ new SVNCheckoutDependentExecutor(checkoutCmd).execute(new File(workingCopyDir,
+ pathProvider.getProjectName()));
} catch (SVNException ex)
{
throw new BuildException(ex.getMessage(), ex.getCause());
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContext.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContext.java
index c26e45e11b8..82fb301d7ca 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContext.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContext.java
@@ -30,10 +30,12 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
class SVNRepositoryProjectContext
{
/** A pattern that release branches must match. */
- private static final Pattern releaseBranchPattern = Pattern.compile(SVNUtilities.RELEASE_BRANCH_PATTERN_STRING);
+ private static final Pattern releaseBranchPattern =
+ Pattern.compile(SVNUtilities.RELEASE_BRANCH_PATTERN_STRING);
/** A pattern that release tags must match. */
- private static final Pattern releaseTagPattern = Pattern.compile(SVNUtilities.RELEASE_TAG_PATTERN_STRING);
+ private static final Pattern releaseTagPattern =
+ Pattern.compile(SVNUtilities.RELEASE_TAG_PATTERN_STRING);
/** The root of the repository url, including the protocol. */
private String repositoryRoot = SVNUtilities.DEFAULT_REPOSITORY_ROOT;
@@ -135,7 +137,7 @@ class SVNRepositoryProjectContext
this.versionType = SVNProjectVersionType.TRUNK;
this.version = SVNUtilities.DEFAULT_VERSION;
}
-
+
/**
* Sets the {@link SVNProjectVersionType} to {@link SVNProjectVersionType#RELEASE_BRANCH} and the version to
* <var>branchName</var>.
@@ -148,7 +150,8 @@ class SVNRepositoryProjectContext
if (false == isReleaseBranch(branchName))
{
- throw new UserFailureException("Branch name '" + branchName + "' does not match the pattern.");
+ throw new UserFailureException("Branch name '" + branchName
+ + "' does not match the pattern.");
}
this.versionType = SVNProjectVersionType.RELEASE_BRANCH;
this.version = branchName;
@@ -178,7 +181,8 @@ class SVNRepositoryProjectContext
}
if (version.indexOf('/') >= 0)
{
- throw new UserFailureException("Branch name '" + branchName + "' contains illegal charachter '/'.");
+ throw new UserFailureException("Branch name '" + branchName
+ + "' contains illegal charachter '/'.");
}
this.versionType = SVNProjectVersionType.FEATURE_BRANCH;
this.version = branchName;
@@ -265,15 +269,15 @@ class SVNRepositoryProjectContext
case TRUNK:
return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup()), "/");
case RELEASE_BRANCH:
- return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(), getProjectName(),
- "branches/release", getVersion()), "/");
+ return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(),
+ getProjectName(), "branches/release", getVersion()), "/");
case RELEASE_TAG:
final String branchName = SVNUtilities.getBranchForTag(getVersion());
- return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(), getProjectName(),
- "tags/release", branchName, getVersion()), "/");
+ return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(),
+ getProjectName(), "tags/release", branchName, getVersion()), "/");
case FEATURE_BRANCH:
- return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(), getProjectName(),
- "branches/feature", getVersion()), "/");
+ return StringUtils.join(Arrays.asList(getRepositoryRoot(), getGroup(),
+ getProjectName(), "branches/feature", getVersion()), "/");
default:
throw new AssertionError("Unknown version type '" + versionType + "'.");
}
@@ -302,17 +306,18 @@ class SVNRepositoryProjectContext
}
if (subProjectName.indexOf('/') >= 0 || subProjectName.indexOf('\\') >= 0)
{
- throw UserFailureException.fromTemplate("Sub-project '%s' contains invalid characters.",
- subProjectName);
+ throw UserFailureException.fromTemplate(
+ "Sub-project '%s' contains invalid characters.", subProjectName);
}
if (SVNProjectVersionType.TRUNK == versionType)
{
return StringUtils.join(Arrays.asList(getRepositoryUrl(), subProjectName,
- SVNUtilities.DEFAULT_VERSION), "/");
+ SVNUtilities.DEFAULT_VERSION), "/");
} else
{
- return StringUtils.join(Arrays.asList(getRepositoryUrl(), subProjectName), "/");
+ return StringUtils.join(Arrays.asList(getRepositoryUrl(), subProjectName),
+ "/");
}
}
@@ -321,7 +326,8 @@ class SVNRepositoryProjectContext
return getPath(SVNRepositoryProjectContext.this.getProjectName());
}
- public String getPath(String subProjectName, String entityPath) throws UserFailureException
+ public String getPath(String subProjectName, String entityPath)
+ throws UserFailureException
{
assert subProjectName != null;
assert entityPath != null;
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilities.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilities.java
index 238dc055e05..e7323f17320 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilities.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilities.java
@@ -108,6 +108,7 @@ class SVNUtilities
private static final class StreamReaderGobbler
{
private final Semaphore waitForReadingFinishedSemaphore = new Semaphore(1);
+
private final List<String> lines = new ArrayList<String>();
StreamReaderGobbler(final InputStream stream) throws InterruptedException
@@ -120,7 +121,8 @@ class SVNUtilities
{
try
{
- final BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
+ final BufferedReader reader =
+ new BufferedReader(new InputStreamReader(stream));
String line;
while ((line = reader.readLine()) != null)
{
@@ -128,7 +130,8 @@ class SVNUtilities
}
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't gobble stream content", ex);
+ throw new EnvironmentFailureException("Couldn't gobble stream content",
+ ex);
} finally
{
waitForReadingFinishedSemaphore.release();
@@ -247,17 +250,19 @@ class SVNUtilities
}
if (name.indexOf('/') >= 0 || name.indexOf('\\') >= 0)
{
- throw new UserFailureException(typeOfName + " name '" + name + "' contains illegal character.");
+ throw new UserFailureException(typeOfName + " name '" + name
+ + "' contains illegal character.");
}
}
- static ProcessInfo subversionCommand(ISimpleLogger logger, final String command, final String... args)
+ static ProcessInfo subversionCommand(ISimpleLogger logger, final String command,
+ final String... args)
{
return subversionCommand(logger, true, command, args);
}
- static ProcessInfo subversionCommand(ISimpleLogger logger, final boolean redirectErrorStream, final String command,
- final String... args)
+ static ProcessInfo subversionCommand(ISimpleLogger logger, final boolean redirectErrorStream,
+ final String command, final String... args)
{
final File svnExecutable = OSUtilities.findExecutable("svn");
if (svnExecutable == null)
@@ -276,8 +281,10 @@ class SVNUtilities
try
{
final Process process = builder.start();
- StreamReaderGobbler inputStreamGobbler = new StreamReaderGobbler(process.getInputStream());
- StreamReaderGobbler errorStreamGobbler = new StreamReaderGobbler(process.getErrorStream());
+ StreamReaderGobbler inputStreamGobbler =
+ new StreamReaderGobbler(process.getInputStream());
+ StreamReaderGobbler errorStreamGobbler =
+ new StreamReaderGobbler(process.getErrorStream());
final int exitValue = process.waitFor();
List<String> lines = inputStreamGobbler.getLines();
if (0 != exitValue)
@@ -287,7 +294,8 @@ class SVNUtilities
{
SVNUtilities.logSvnOutput(logger, errorStreamGobbler.getLines());
}
- throw SVNException.fromTemplate("Error while executing '%s' (exitValue=%d)", commandString, exitValue);
+ throw SVNException.fromTemplate("Error while executing '%s' (exitValue=%d)",
+ commandString, exitValue);
}
return new ProcessInfo(commandString, lines, exitValue);
} catch (IOException ex)
@@ -295,7 +303,8 @@ class SVNUtilities
throw SVNException.fromTemplate(ex, "Error while executing '%s'", commandString);
} catch (InterruptedException ex)
{
- throw SVNException.fromTemplate(ex, "Unexpectedly interrupted while executing '%s'", commandString);
+ throw SVNException.fromTemplate(ex, "Unexpectedly interrupted while executing '%s'",
+ commandString);
}
}
@@ -303,8 +312,9 @@ class SVNUtilities
{
return (null != OSUtilities.findExecutable("svnmucc"));
}
-
- static ProcessInfo subversionMuccCommand(ISimpleLogger logger, String logMessage, final String... args)
+
+ static ProcessInfo subversionMuccCommand(ISimpleLogger logger, String logMessage,
+ final String... args)
{
final File svnExecutable = OSUtilities.findExecutable("svnmucc");
if (svnExecutable == null)
@@ -323,13 +333,15 @@ class SVNUtilities
try
{
final Process process = builder.start();
- StreamReaderGobbler inputStreamGobbler = new StreamReaderGobbler(process.getInputStream());
+ StreamReaderGobbler inputStreamGobbler =
+ new StreamReaderGobbler(process.getInputStream());
final int exitValue = process.waitFor();
List<String> lines = inputStreamGobbler.getLines();
if (0 != exitValue)
{
SVNUtilities.logSvnOutput(logger, inputStreamGobbler.getLines());
- throw SVNException.fromTemplate("Error while executing '%s' (exitValue=%d)", commandString, exitValue);
+ throw SVNException.fromTemplate("Error while executing '%s' (exitValue=%d)",
+ commandString, exitValue);
}
return new ProcessInfo(commandString, lines, exitValue);
} catch (IOException ex)
@@ -337,7 +349,8 @@ class SVNUtilities
throw SVNException.fromTemplate(ex, "Error while executing '%s'", commandString);
} catch (InterruptedException ex)
{
- throw SVNException.fromTemplate(ex, "Unexpectedly interrupted while executing '%s'", commandString);
+ throw SVNException.fromTemplate(ex, "Unexpectedly interrupted while executing '%s'",
+ commandString);
}
}
@@ -362,7 +375,8 @@ class SVNUtilities
static String getFirstTagForBranch(String branchName)
{
- final Matcher branchMatcher = Pattern.compile(RELEASE_BRANCH_PATTERN_STRING).matcher(branchName);
+ final Matcher branchMatcher =
+ Pattern.compile(RELEASE_BRANCH_PATTERN_STRING).matcher(branchName);
boolean matches = branchMatcher.matches();
assert matches;
return String.format("%s.%s.0", branchMatcher.group(1), branchMatcher.group(2));
diff --git a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProvider.java b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProvider.java
index 79619cc7b52..e6ed4bdbb66 100644
--- a/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProvider.java
+++ b/ant_tasks/source/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProvider.java
@@ -22,15 +22,16 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
* A {@link ISVNProjectPathProvider} that works on a subversion working directory.
- *
+ *
* @author Bernd Rinn
*/
class SVNWCProjectPathProvider implements ISVNProjectPathProvider
{
private final String baseDirectory;
+
private final String projectName;
-
+
/**
* @param projectDirectory The directory of the working copy. Is expected to exist and to be a directory.
*/
@@ -38,7 +39,7 @@ class SVNWCProjectPathProvider implements ISVNProjectPathProvider
{
assert projectDirectory != null;
assert projectDirectory.isDirectory();
-
+
final String baseDirectoryPath = projectDirectory.getParentFile().getAbsolutePath();
final String thisProjectName = projectDirectory.getName();
if (baseDirectoryPath.endsWith("/.")) // Corresponds to baseDirectory = new File(".")
@@ -50,7 +51,7 @@ class SVNWCProjectPathProvider implements ISVNProjectPathProvider
}
this.projectName = thisProjectName;
}
-
+
public String getPath()
{
return getPath(projectName);
@@ -61,7 +62,7 @@ class SVNWCProjectPathProvider implements ISVNProjectPathProvider
assert subProjectName != null;
SVNUtilities.checkProjectName(subProjectName);
-
+
return new File(baseDirectory, subProjectName).getAbsolutePath();
}
@@ -69,7 +70,7 @@ class SVNWCProjectPathProvider implements ISVNProjectPathProvider
{
assert subProjectName != null;
assert entityPath != null;
-
+
if (entityPath.length() == 0)
{
throw new UserFailureException("Entity path must not be empty.");
@@ -107,5 +108,5 @@ class SVNWCProjectPathProvider implements ISVNProjectPathProvider
{
return false;
}
-
+
}
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTaskTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTaskTest.java
index 4a5145581f8..f3e2710b24b 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTaskTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/SetEclipseClasspathTaskTest.java
@@ -76,8 +76,8 @@ public class SetEclipseClasspathTaskTest extends AssertJUnit
printWriter.println("<classpath>");
for (EclipseClasspathEntry entry : entries)
{
- printWriter.printf(" <classpathentry kind=\"%s\" path=\"%s\"/>\n", entry.getKind(), entry
- .getPath());
+ printWriter.printf(" <classpathentry kind=\"%s\" path=\"%s\"/>\n", entry
+ .getKind(), entry.getPath());
}
printWriter.println("</classpath>");
} catch (IOException ex)
@@ -181,8 +181,10 @@ public class SetEclipseClasspathTaskTest extends AssertJUnit
task.execute();
StringBuilder builder = new StringBuilder();
- builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
+ builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
assertEquals(new String(builder), project.getProperty(PROPERTY_NAME));
}
@@ -199,10 +201,14 @@ public class SetEclipseClasspathTaskTest extends AssertJUnit
task.execute();
StringBuilder builder = new StringBuilder();
- builder.append(new File(PROJECT_B, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "b.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
+ builder.append(new File(PROJECT_B, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "b.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
assertEquals(new String(builder), project.getProperty(PROPERTY_NAME));
}
@@ -219,14 +225,22 @@ public class SetEclipseClasspathTaskTest extends AssertJUnit
task.execute();
StringBuilder builder = new StringBuilder();
- builder.append(new File(PROJECT_D, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(PROJECT_B, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "b.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(PROJECT_C, TARGET_CLASSES).getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "c.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
- builder.append(new File(TEMP_WORKSPACE, "d.jar").getAbsoluteFile()).append(File.pathSeparatorChar);
+ builder.append(new File(PROJECT_D, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(PROJECT_B, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(PROJECT_A, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "a.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "b.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(PROJECT_C, TARGET_CLASSES).getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "c.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
+ builder.append(new File(TEMP_WORKSPACE, "d.jar").getAbsoluteFile()).append(
+ File.pathSeparatorChar);
assertEquals(new String(builder), project.getProperty(PROPERTY_NAME));
}
}
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTaskTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTaskTest.java
index 116516c265f..7e67cfa1f2c 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTaskTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/GatherRevisionAndVersionTaskTest.java
@@ -56,7 +56,7 @@ public class GatherRevisionAndVersionTaskTest
//
// Mocks and helper classes
//
-
+
private static final class MockPathProvider implements ISVNProjectPathProvider
{
private final SVNProject project;
@@ -65,48 +65,49 @@ public class GatherRevisionAndVersionTaskTest
{
this.project = project;
}
-
+
public boolean isRepositoryPath()
{
throw new UnsupportedOperationException();
}
-
+
public String getRevision()
{
throw new UnsupportedOperationException();
}
-
+
public String getProjectName()
{
return project.getName();
}
-
+
public String getPath(String subProjectName, String entityPath) throws UserFailureException
{
throw new UnsupportedOperationException();
}
-
+
public String getPath(String subProjectName) throws UserFailureException
{
return subProjectName;
}
-
+
public String getPath()
{
return getProjectName();
}
}
-
+
private static final class MockSVN implements ISVNActions
{
- private final Map<String, List<SVNItemStatus>> statusMap = new HashMap<String, List<SVNItemStatus>>();
+ private final Map<String, List<SVNItemStatus>> statusMap =
+ new HashMap<String, List<SVNItemStatus>>();
private final Map<String, SVNInfoRecord> infoMap = new HashMap<String, SVNInfoRecord>();
private final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
private final Map<String, String> contentMap = new HashMap<String, String>();
-
+
SVNInfoRecord register(String path)
{
System.out.println("REGISTER - " + path);
@@ -148,8 +149,8 @@ public class GatherRevisionAndVersionTaskTest
return infoRecord;
}
- public void copy(String sourcePath, String sourceRevision, String destinationPath, String logMessage)
- throws SVNException
+ public void copy(String sourcePath, String sourceRevision, String destinationPath,
+ String logMessage) throws SVNException
{
throw new AssertionError("Unexpected call copy");
}
@@ -186,8 +187,8 @@ public class GatherRevisionAndVersionTaskTest
}
}
- private GatherRevisionAndVersionTask createTask(final MockSVN mockSvn, final SVNProject svnProject,
- final String reposURL)
+ private GatherRevisionAndVersionTask createTask(final MockSVN mockSvn,
+ final SVNProject svnProject, final String reposURL)
{
GatherRevisionAndVersionTask task = new GatherRevisionAndVersionTask()
{
@@ -259,7 +260,8 @@ public class GatherRevisionAndVersionTaskTest
registerProject(svn, projectBaseDir, revision, lastChangedRevision);
}
- private void registerProject(MockSVN svn, String projectBaseDir, int revision, int lastChangedRevision)
+ private void registerProject(MockSVN svn, String projectBaseDir, int revision,
+ int lastChangedRevision)
{
SVNInfoRecord info = svn.register(".." + File.separator + name);
Updater updater = info.getUpdater();
@@ -280,15 +282,19 @@ public class GatherRevisionAndVersionTaskTest
{
svn = new MockSVN();
project1 = new SVNProject("project1").addFiles("helloWorld.txt");
- project1.addClasspathFile("<classpath>\n" + "<classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + "<classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
- + "<classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + "<classpathentry kind=\"src\" path=\"/common\"/>\n" + "</classpath>\n");
+ project1
+ .addClasspathFile("<classpath>\n"
+ + "<classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + "<classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
+ + "<classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + "<classpathentry kind=\"src\" path=\"/common\"/>\n" + "</classpath>\n");
libraries = new SVNProject("libraries").addFiles("lib1.jar");
common = new SVNProject("common").addFiles("build.xml");
- common.addClasspathFile("<classpath>\n" + "<classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + "<classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + "</classpath>\n");
+ common
+ .addClasspathFile("<classpath>\n"
+ + "<classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + "<classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + "</classpath>\n");
buildResources = new SVNProject("build_resources");
}
@@ -314,7 +320,8 @@ public class GatherRevisionAndVersionTaskTest
libraries.registerAsTrunk(svn, 10, 6);
common.registerAsTrunk(svn, 11, 7);
buildResources.registerAsTrunk(svn, 10, 5);
- svn.register(".").getUpdater().setRepositoryUrl(BASE_REPOSITORY_URL + "/" + project1.getName() + "/trunk");
+ svn.register(".").getUpdater().setRepositoryUrl(
+ BASE_REPOSITORY_URL + "/" + project1.getName() + "/trunk");
GatherRevisionAndVersionTask task = createTask(svn, project1, BASE_REPOSITORY_URL);
task.setRevision("myRevision");
@@ -323,7 +330,8 @@ public class GatherRevisionAndVersionTaskTest
task.execute();
assertEquals("7", task.getProject().getProperty("myRevision"));
- assertEquals(GatherRevisionAndVersionTask.TRUNK_VERSION, task.getProject().getProperty("myVersion"));
+ assertEquals(GatherRevisionAndVersionTask.TRUNK_VERSION, task.getProject().getProperty(
+ "myVersion"));
}
@Test
@@ -335,9 +343,11 @@ public class GatherRevisionAndVersionTaskTest
libraries.registerVersion(svn, version, 10, 6);
common.registerVersion(svn, version, 11, 7);
buildResources.registerVersion(svn, version, 10, 5);
- svn.register(".").getUpdater().setRepositoryUrl(BASE_REPOSITORY_URL + "/" + version + "/" + project1.getName());
+ svn.register(".").getUpdater().setRepositoryUrl(
+ BASE_REPOSITORY_URL + "/" + version + "/" + project1.getName());
- GatherRevisionAndVersionTask task = createTask(svn, project1, BASE_REPOSITORY_URL + "/" + version);
+ GatherRevisionAndVersionTask task =
+ createTask(svn, project1, BASE_REPOSITORY_URL + "/" + version);
task.setRevision("myRevision");
task.setVersion("myVersion");
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTaskTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTaskTest.java
index 690f28f482d..51616c3d71a 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTaskTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNBranchAndTagTaskTest.java
@@ -72,8 +72,10 @@ public class SVNBranchAndTagTaskTest
return false;
}
CopyItem that = (CopyItem) obj;
- return this.sourcePath.equals(that.sourcePath) && this.sourceRevision.equals(that.sourceRevision)
- && this.destinationPath.equals(that.destinationPath) && this.logMessage.equals(that.logMessage);
+ return this.sourcePath.equals(that.sourcePath)
+ && this.sourceRevision.equals(that.sourceRevision)
+ && this.destinationPath.equals(that.destinationPath)
+ && this.logMessage.equals(that.logMessage);
}
@Override
@@ -87,8 +89,10 @@ public class SVNBranchAndTagTaskTest
@Override
public String toString()
{
- return String.format("CopyItem: (sourcePath=%s, sourceRevision=%s, destinationPath=%s, logMessage=%s)",
- sourcePath, sourceRevision, destinationPath, logMessage);
+ return String
+ .format(
+ "CopyItem: (sourcePath=%s, sourceRevision=%s, destinationPath=%s, logMessage=%s)",
+ sourcePath, sourceRevision, destinationPath, logMessage);
}
}
@@ -141,7 +145,8 @@ public class SVNBranchAndTagTaskTest
List<CopyItem> copyList = new ArrayList<CopyItem>();
- public MockSVNRepositoryActions(final Map<String, List<String>> listMap, final Map<String, String> catMap)
+ public MockSVNRepositoryActions(final Map<String, List<String>> listMap,
+ final Map<String, String> catMap)
{
super();
this.listMap = listMap;
@@ -168,8 +173,8 @@ public class SVNBranchAndTagTaskTest
mkdirList.add(new MkdirItem(path, logMessage));
}
- public void copy(String sourcePath, String sourceRevision, String destinationPath, String logMessage)
- throws SVNException
+ public void copy(String sourcePath, String sourceRevision, String destinationPath,
+ String logMessage) throws SVNException
{
copyList.add(new CopyItem(sourcePath, sourceRevision, destinationPath, logMessage));
}
@@ -204,9 +209,11 @@ public class SVNBranchAndTagTaskTest
final String branchName = "1.2.x";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String sourceUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"),
+ "/");
final String releaseBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release"), "/");
listMap.put(sourceUrl, Collections.<String> emptyList());
listMap.put(releaseBranchesUrl, Collections.<String> emptyList());
final Map<String, String> catMap = new HashMap<String, String>();
@@ -226,24 +233,27 @@ public class SVNBranchAndTagTaskTest
task.setReleaseBranch(branchName);
task.execute();
final String branchUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release", branchName), "/");
final String tagBaseUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "tags/release",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "tags/release", branchName), "/");
final String logMessage = "Create branch '" + branchName + "'";
final List<MkdirItem> expectedMkDirList =
- Arrays.asList(new MkdirItem(branchUrl, logMessage), new MkdirItem(tagBaseUrl, logMessage));
+ Arrays.asList(new MkdirItem(branchUrl, logMessage), new MkdirItem(tagBaseUrl,
+ logMessage));
assertEquals(expectedMkDirList, svn.mkdirList);
final String branchMainUrl = branchUrl + "/" + projectName;
- final String branchBuildResourcesUrl = branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
+ final String branchBuildResourcesUrl =
+ branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
final String sourceBuildResourcesUrl =
StringUtils.join(Arrays.asList(repositoryRoot, groupName,
- SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
+ SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
final Set<CopyItem> expectedCopySet =
- new HashSet<CopyItem>(Arrays.asList(new CopyItem(sourceBuildResourcesUrl, SVNUtilities.HEAD_REVISION,
- branchBuildResourcesUrl, logMessage), new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION,
- branchMainUrl, logMessage)));
+ new HashSet<CopyItem>(Arrays.asList(new CopyItem(sourceBuildResourcesUrl,
+ SVNUtilities.HEAD_REVISION, branchBuildResourcesUrl, logMessage),
+ new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION, branchMainUrl,
+ logMessage)));
assertEquals(expectedCopySet, new HashSet<CopyItem>(svn.copyList));
}
@@ -257,20 +267,24 @@ public class SVNBranchAndTagTaskTest
final String branchName = "someFeature";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String sourceUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"),
+ "/");
final String sourceUrlDependent =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, dependentProjectName, "trunk"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, dependentProjectName,
+ "trunk"), "/");
final String featureBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/feature"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/feature"), "/");
listMap.put(sourceUrl, Collections.singletonList(".classpath"));
listMap.put(sourceUrlDependent, Collections.<String> emptyList());
listMap.put(featureBranchesUrl, Collections.<String> emptyList());
final String classPathFileContent =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ "<classpath>\n"
- + String.format(
- " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/%s\"/>\n",
- dependentProjectName) + "</classpath>\n";
+ + String
+ .format(
+ " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/%s\"/>\n",
+ dependentProjectName) + "</classpath>\n";
final Map<String, String> catMap = new HashMap<String, String>();
catMap.put(sourceUrl + "/.classpath", classPathFileContent);
final MockSVNRepositoryActions svn = new MockSVNRepositoryActions(listMap, catMap);
@@ -289,22 +303,25 @@ public class SVNBranchAndTagTaskTest
task.setFeatureBranch(branchName);
task.execute();
final String branchUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/feature",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/feature", branchName), "/");
final String logMessage = "Create branch '" + branchName + "'";
- final List<MkdirItem> expectedMkDirList = Arrays.asList(new MkdirItem(branchUrl, logMessage));
+ final List<MkdirItem> expectedMkDirList =
+ Arrays.asList(new MkdirItem(branchUrl, logMessage));
assertEquals(expectedMkDirList, svn.mkdirList);
final String branchMainUrl = branchUrl + "/" + projectName;
- final String branchBuildResourcesUrl = branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
+ final String branchBuildResourcesUrl =
+ branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
final String branchDependendUrl = branchUrl + "/" + dependentProjectName;
final String sourceBuildResourcesUrl =
StringUtils.join(Arrays.asList(repositoryRoot, groupName,
- SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
+ SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
final Set<CopyItem> expectedCopySet =
- new HashSet<CopyItem>(Arrays.asList(new CopyItem(sourceBuildResourcesUrl, SVNUtilities.HEAD_REVISION,
- branchBuildResourcesUrl, logMessage), new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION,
- branchMainUrl, logMessage), new CopyItem(sourceUrlDependent, SVNUtilities.HEAD_REVISION,
- branchDependendUrl, logMessage)));
+ new HashSet<CopyItem>(Arrays.asList(new CopyItem(sourceBuildResourcesUrl,
+ SVNUtilities.HEAD_REVISION, branchBuildResourcesUrl, logMessage),
+ new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION, branchMainUrl,
+ logMessage), new CopyItem(sourceUrlDependent,
+ SVNUtilities.HEAD_REVISION, branchDependendUrl, logMessage)));
assertEquals(expectedCopySet, new HashSet<CopyItem>(svn.copyList));
}
@@ -318,7 +335,8 @@ public class SVNBranchAndTagTaskTest
final String branchName = "1.2.x";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String releaseBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release"), "/");
listMap.put(releaseBranchesUrl, Collections.singletonList(branchName + "/"));
final Map<String, String> catMap = new HashMap<String, String>();
final MockSVNRepositoryActions svn = new MockSVNRepositoryActions(listMap, catMap);
@@ -337,16 +355,16 @@ public class SVNBranchAndTagTaskTest
task.setReleaseTag(tagName);
task.execute();
final String tagUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "tags/release",
- branchName, tagName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "tags/release", branchName, tagName), "/");
final String branchUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release", branchName), "/");
final String logMessage = "Create tag '" + tagName + "'";
assertEquals(0, svn.mkdirList.size());
final Set<CopyItem> expectedCopySet =
- new HashSet<CopyItem>(Collections.singletonList(new CopyItem(branchUrl, SVNUtilities.HEAD_REVISION,
- tagUrl, logMessage)));
+ new HashSet<CopyItem>(Collections.singletonList(new CopyItem(branchUrl,
+ SVNUtilities.HEAD_REVISION, tagUrl, logMessage)));
assertEquals(expectedCopySet, new HashSet<CopyItem>(svn.copyList));
}
@@ -360,7 +378,8 @@ public class SVNBranchAndTagTaskTest
final String tagName = "1.2.0";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String releaseBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release"), "/");
listMap.put(releaseBranchesUrl, Collections.<String> emptyList());
final Map<String, String> catMap = new HashMap<String, String>();
final MockSVNRepositoryActions svn = new MockSVNRepositoryActions(listMap, catMap);
@@ -390,9 +409,11 @@ public class SVNBranchAndTagTaskTest
final String branchName = "1.2.x";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String sourceUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "trunk"),
+ "/");
final String releaseBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release"), "/");
listMap.put(releaseBranchesUrl, Collections.<String> emptyList());
final Map<String, String> catMap = new HashMap<String, String>();
final MockSVNRepositoryActions svn = new MockSVNRepositoryActions(listMap, catMap);
@@ -412,31 +433,34 @@ public class SVNBranchAndTagTaskTest
task.setBranchIfNecessary(true);
task.execute();
final String tagBaseUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "tags/release",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "tags/release", branchName), "/");
final String tagUrl = tagBaseUrl + "/" + tagName;
final String branchUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release",
- branchName), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release", branchName), "/");
final String logMessageBranch = "Create branch '" + branchName + "'";
final String logMessageTag = "Create tag '" + tagName + "'";
final List<MkdirItem> expectedMkDirList =
- Arrays.asList(new MkdirItem(branchUrl, logMessageBranch), new MkdirItem(tagBaseUrl, logMessageBranch));
+ Arrays.asList(new MkdirItem(branchUrl, logMessageBranch), new MkdirItem(tagBaseUrl,
+ logMessageBranch));
assertEquals(expectedMkDirList, svn.mkdirList);
final String branchMainUrl = branchUrl + "/" + projectName;
- final String branchBuildResourcesUrl = branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
+ final String branchBuildResourcesUrl =
+ branchUrl + "/" + SVNUtilities.BUILD_RESOURCES_PROJECT;
final String sourceBuildResourcesUrl =
StringUtils.join(Arrays.asList(repositoryRoot, groupName,
- SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
+ SVNUtilities.BUILD_RESOURCES_PROJECT, "trunk"), "/");
final List<CopyItem> expectedCopyList =
- Arrays.asList(new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION, branchMainUrl, logMessageBranch),
- new CopyItem(sourceBuildResourcesUrl, SVNUtilities.HEAD_REVISION, branchBuildResourcesUrl,
- logMessageBranch), new CopyItem(branchUrl, SVNUtilities.HEAD_REVISION, tagUrl,
- logMessageTag));
+ Arrays.asList(new CopyItem(sourceUrl, SVNUtilities.HEAD_REVISION, branchMainUrl,
+ logMessageBranch), new CopyItem(sourceBuildResourcesUrl,
+ SVNUtilities.HEAD_REVISION, branchBuildResourcesUrl, logMessageBranch),
+ new CopyItem(branchUrl, SVNUtilities.HEAD_REVISION, tagUrl, logMessageTag));
assertEquals(expectedCopyList, svn.copyList);
}
- @Test(expectedExceptions = { BuildException.class })
+ @Test(expectedExceptions =
+ { BuildException.class })
public void testCreateReleaseTagWithBranchCreationButIllegalTag()
{
final String repositoryRoot = "http://host/repos";
@@ -445,7 +469,8 @@ public class SVNBranchAndTagTaskTest
final String tagName = "1.2.1";
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
final String releaseBranchesUrl =
- StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName, "branches/release"), "/");
+ StringUtils.join(Arrays.asList(repositoryRoot, groupName, projectName,
+ "branches/release"), "/");
listMap.put(releaseBranchesUrl, Collections.<String> emptyList());
final Map<String, String> catMap = new HashMap<String, String>();
final MockSVNRepositoryActions svn = new MockSVNRepositoryActions(listMap, catMap);
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectCollectorTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectCollectorTest.java
index 74b9806801d..4ffab5d0629 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectCollectorTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNDependentProjectCollectorTest.java
@@ -41,9 +41,11 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
public class SVNDependentProjectCollectorTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "SVNDependentProjectCollector");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "SVNDependentProjectCollector");
@BeforeClass
public void init()
@@ -71,7 +73,8 @@ public class SVNDependentProjectCollectorTest
final Map<String, String> pathMap;
- public MockSVNRepositoryActions(final Map<String, List<String>> listMap, final Map<String, String> pathMap)
+ public MockSVNRepositoryActions(final Map<String, List<String>> listMap,
+ final Map<String, String> pathMap)
{
super();
this.listMap = listMap;
@@ -98,8 +101,8 @@ public class SVNDependentProjectCollectorTest
throw new AssertionError("Unexpected call mkdir()");
}
- public void copy(String sourcePath, String sourceRevision, String destinationPath, String logMessage)
- throws SVNException
+ public void copy(String sourcePath, String sourceRevision, String destinationPath,
+ String logMessage) throws SVNException
{
throw new AssertionError("Unexpected call copy()");
}
@@ -125,11 +128,13 @@ public class SVNDependentProjectCollectorTest
}
}
- private SVNDependentProjectsCollector createCollector(final ISVNProjectPathProvider pathProvider,
- final Map<String, List<String>> listMap, final Map<String, String> catMap)
+ private SVNDependentProjectsCollector createCollector(
+ final ISVNProjectPathProvider pathProvider, final Map<String, List<String>> listMap,
+ final Map<String, String> catMap)
{
final SVNDependentProjectsCollector collector =
- new SVNDependentProjectsCollector(pathProvider, new MockSVNRepositoryActions(listMap, catMap));
+ new SVNDependentProjectsCollector(pathProvider, new MockSVNRepositoryActions(
+ listMap, catMap));
return collector;
}
@@ -148,26 +153,39 @@ public class SVNDependentProjectCollectorTest
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
listMap.put("http://host/repos/group/libraries/trunk", Arrays.asList("something"));
listMap.put("http://host/repos/group/proj1/trunk", Arrays.asList(".classpath"));
- listMap.put("http://host/repos/group/proj2/trunk", Arrays.asList("something/", ".classpath"));
- listMap.put("http://host/repos/group/proj3/trunk", Arrays.asList("something/", "nothing there"));
+ listMap.put("http://host/repos/group/proj2/trunk", Arrays
+ .asList("something/", ".classpath"));
+ listMap.put("http://host/repos/group/proj3/trunk", Arrays.asList("something/",
+ "nothing there"));
final Map<String, String> catMap = new HashMap<String, String>();
- catMap.put("http://host/repos/group/proj1/trunk/.classpath", "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
- + "<classpath>\n" + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
- + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + " <classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
- + " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
- + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj2\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n" + "");
- catMap.put("http://host/repos/group/proj2/trunk/.classpath", "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
- + "<classpath>\n" + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
- + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj3\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n" + "");
+ catMap
+ .put(
+ "http://host/repos/group/proj1/trunk/.classpath",
+ "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ + "<classpath>\n"
+ + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
+ + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + " <classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
+ + " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
+ + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj2\"/>\n"
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n" + "");
+ catMap
+ .put(
+ "http://host/repos/group/proj2/trunk/.classpath",
+ "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ + "<classpath>\n"
+ + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
+ + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj3\"/>\n"
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n" + "");
SVNDependentProjectsCollector collector = createCollector(pathProvider, listMap, catMap);
final Set<String> projectsExpected =
- new HashSet<String>(Arrays.asList("proj1", "proj2", "proj3", "libraries", "build_resources"));
+ new HashSet<String>(Arrays.asList("proj1", "proj2", "proj3", "libraries",
+ "build_resources"));
final Set<String> projectsFound = collector.collectDependentProjectsFromClasspath();
assertEquals(projectsExpected, projectsFound);
}
@@ -182,34 +200,43 @@ public class SVNDependentProjectCollectorTest
context.setProjectName("proj1");
final ISVNProjectPathProvider pathProvider = context.getPathProvider();
final Map<String, List<String>> listMap = new HashMap<String, List<String>>();
- listMap.put("http://host/repos/group/proj1/branches/feature/branch/libraries", Arrays.asList("something"));
- listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj1", Arrays.asList(".classpath"));
- listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj2", Arrays.asList("something/",
- ".classpath"));
- listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj3", Arrays.asList("something/",
- "nothing there"));
+ listMap.put("http://host/repos/group/proj1/branches/feature/branch/libraries", Arrays
+ .asList("something"));
+ listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj1", Arrays
+ .asList(".classpath"));
+ listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj2", Arrays.asList(
+ "something/", ".classpath"));
+ listMap.put("http://host/repos/group/proj1/branches/feature/branch/proj3", Arrays.asList(
+ "something/", "nothing there"));
final Map<String, String> catMap = new HashMap<String, String>();
- catMap.put("http://host/repos/group/proj1/branches/feature/branch/proj1/.classpath",
- "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<classpath>\n"
- + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
- + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + " <classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
- + " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
- + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj2\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n"
- + "");
- catMap.put("http://host/repos/group/proj1/branches/feature/branch/proj2/.classpath",
- "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<classpath>\n"
- + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
- + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
- + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
- + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj3\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n"
- + "");
+ catMap
+ .put(
+ "http://host/repos/group/proj1/branches/feature/branch/proj1/.classpath",
+ "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ + "<classpath>\n"
+ + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
+ + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + " <classpathentry kind=\"lib\" path=\"/libraries/activation/activation.jar\"/>\n"
+ + " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
+ + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj2\"/>\n"
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n" + "");
+ catMap
+ .put(
+ "http://host/repos/group/proj1/branches/feature/branch/proj2/.classpath",
+ "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ + "<classpath>\n"
+ + " <classpathentry kind=\"src\" path=\"sourceTest/java\"/>\n"
+ + " <classpathentry kind=\"src\" path=\"source/java\"/>\n"
+ + " <classpathentry kind=\"con\" path=\"org.eclipse.jdt.launching.JRE_CONTAINER\"/>\n"
+ + " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/proj3\"/>\n"
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n" + "");
SVNDependentProjectsCollector collector = createCollector(pathProvider, listMap, catMap);
final Set<String> projectsExpected =
- new HashSet<String>(Arrays.asList("proj1", "proj2", "proj3", "build_resources", "libraries"));
+ new HashSet<String>(Arrays.asList("proj1", "proj2", "proj3", "build_resources",
+ "libraries"));
final Set<String> projectsFound = collector.collectDependentProjectsFromClasspath();
assertEquals(projectsExpected, projectsFound);
}
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractorTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractorTest.java
index 1169c438030..1dc9f02363a 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractorTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNInfoRecordExtractorTest.java
@@ -15,6 +15,7 @@
*/
package ch.systemsx.cisd.ant.task.subversion;
+
import static org.testng.AssertJUnit.assertEquals;
import java.util.ArrayList;
@@ -27,48 +28,45 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.ant.task.subversion.SVNInfoRecord.NodeKind;
/**
- *
- *
* @author felmer
*/
public class SVNInfoRecordExtractorTest
{
- private static final List<String> INFO1 = Collections.unmodifiableList(Arrays.asList("Path: .",
- "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk",
- "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
- "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1",
- "Revision: 290",
- "Node Kind: directory",
- "Schedule: add",
- "Last Changed Author: felmer",
- "Last Changed Rev: 255",
- "Last Changed Date: 2007-05-07 16:27:11 +0200 (Mon, 07 May 2007)",
- ""));
- private static final List<String> INFO2 = Collections.unmodifiableList(Arrays.asList("Path: build",
- "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build",
- "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
- "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1",
- "Revision: 290",
- "Node Kind: directory",
- "Schedule: normal",
- "Last Changed Author: felmer",
- "Last Changed Rev: 288",
- "Last Changed Date: 2007-05-07 16:21:00 +0200 (Mon, 07 May 2007)",
- ""));
- private static final List<String> INFO3 = Collections.unmodifiableList(Arrays.asList("Path: build\\build.xml",
- "Name: build.xml",
- "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build/build.xml",
- "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
- "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1",
- "Revision: 291",
- "Node Kind: file",
- "Schedule: normal",
- "Last Changed Author: fje",
- "Last Changed Rev: 287",
- "Last Changed Date: 2007-05-07 16:22:00 +0200 (Mon, 07 May 2007)",
- "Text Last Updated: 2007-05-07 16:20:04 +0200 (Mon, 07 May 2007)",
- "Checksum: 9236ea7a96fc9aa92c1b4ba8cabe1ae3",
- ""));
+ private static final List<String> INFO1 =
+ Collections.unmodifiableList(Arrays.asList("Path: .",
+ "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk",
+ "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
+ "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1", "Revision: 290",
+ "Node Kind: directory", "Schedule: add", "Last Changed Author: felmer",
+ "Last Changed Rev: 255",
+ "Last Changed Date: 2007-05-07 16:27:11 +0200 (Mon, 07 May 2007)", ""));
+
+ private static final List<String> INFO2 =
+ Collections.unmodifiableList(Arrays.asList("Path: build",
+ "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build",
+ "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
+ "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1", "Revision: 290",
+ "Node Kind: directory", "Schedule: normal", "Last Changed Author: felmer",
+ "Last Changed Rev: 288",
+ "Last Changed Date: 2007-05-07 16:21:00 +0200 (Mon, 07 May 2007)", ""));
+
+ private static final List<String> INFO3 =
+ Collections
+ .unmodifiableList(Arrays
+ .asList(
+ "Path: build\\build.xml",
+ "Name: build.xml",
+ "URL: svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build/build.xml",
+ "Repository Root: svn+ssh://cisd-hal.ethz.ch/internal",
+ "Repository UUID: e2bb8bc7-4a29-0410-9445-bbee19c747d1",
+ "Revision: 291",
+ "Node Kind: file",
+ "Schedule: normal",
+ "Last Changed Author: fje",
+ "Last Changed Rev: 287",
+ "Last Changed Date: 2007-05-07 16:22:00 +0200 (Mon, 07 May 2007)",
+ "Text Last Updated: 2007-05-07 16:20:04 +0200 (Mon, 07 May 2007)",
+ "Checksum: 9236ea7a96fc9aa92c1b4ba8cabe1ae3", ""));
@Test
public void testExtractingOfInfo3()
@@ -76,10 +74,10 @@ public class SVNInfoRecordExtractorTest
ArrayList<String> lines = new ArrayList<String>();
lines.addAll(INFO3);
SVNInfoRecord infoRecord = extract(lines);
-
+
assertEquals("build\\build.xml", infoRecord.getWorkingCopyPath());
- assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build/build.xml",
- infoRecord.getRepositoryUrl());
+ assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build/build.xml",
+ infoRecord.getRepositoryUrl());
assertEquals("svn+ssh://cisd-hal.ethz.ch/internal", infoRecord.getRepositoryRootUrl());
assertEquals("e2bb8bc7-4a29-0410-9445-bbee19c747d1", infoRecord.getRepositoryUUID());
assertEquals(291, infoRecord.getRevision());
@@ -87,9 +85,10 @@ public class SVNInfoRecordExtractorTest
assertEquals("normal", infoRecord.getSchedule());
assertEquals("fje", infoRecord.getLastChangedAuthor());
assertEquals(287, infoRecord.getLastChangedRevision());
- assertEquals("2007-05-07 16:22:00 +0200 (Mon, 07 May 2007)", infoRecord.getLastChangedDate());
+ assertEquals("2007-05-07 16:22:00 +0200 (Mon, 07 May 2007)", infoRecord
+ .getLastChangedDate());
}
-
+
@Test
public void testExtractingOfInfo2Info3()
{
@@ -97,9 +96,10 @@ public class SVNInfoRecordExtractorTest
lines.addAll(INFO2);
lines.addAll(INFO3);
SVNInfoRecord infoRecord = extract(lines);
-
+
assertEquals("build", infoRecord.getWorkingCopyPath());
- assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build", infoRecord.getRepositoryUrl());
+ assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk/build", infoRecord
+ .getRepositoryUrl());
assertEquals("svn+ssh://cisd-hal.ethz.ch/internal", infoRecord.getRepositoryRootUrl());
assertEquals("e2bb8bc7-4a29-0410-9445-bbee19c747d1", infoRecord.getRepositoryUUID());
assertEquals(291, infoRecord.getRevision());
@@ -107,10 +107,10 @@ public class SVNInfoRecordExtractorTest
assertEquals("normal", infoRecord.getSchedule());
assertEquals("felmer", infoRecord.getLastChangedAuthor());
assertEquals(288, infoRecord.getLastChangedRevision());
- assertEquals("2007-05-07 16:21:00 +0200 (Mon, 07 May 2007)", infoRecord.getLastChangedDate());
+ assertEquals("2007-05-07 16:21:00 +0200 (Mon, 07 May 2007)", infoRecord
+ .getLastChangedDate());
}
-
-
+
@Test
public void testExtractingOfInfo1Info2Info3()
{
@@ -119,9 +119,10 @@ public class SVNInfoRecordExtractorTest
lines.addAll(INFO2);
lines.addAll(INFO3);
SVNInfoRecord infoRecord = extract(lines);
-
+
assertEquals(".", infoRecord.getWorkingCopyPath());
- assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk", infoRecord.getRepositoryUrl());
+ assertEquals("svn+ssh://cisd-hal.ethz.ch/internal/cisd/ant_tasks/trunk", infoRecord
+ .getRepositoryUrl());
assertEquals("svn+ssh://cisd-hal.ethz.ch/internal", infoRecord.getRepositoryRootUrl());
assertEquals("e2bb8bc7-4a29-0410-9445-bbee19c747d1", infoRecord.getRepositoryUUID());
assertEquals(291, infoRecord.getRevision());
@@ -129,9 +130,10 @@ public class SVNInfoRecordExtractorTest
assertEquals("add", infoRecord.getSchedule());
assertEquals("felmer", infoRecord.getLastChangedAuthor());
assertEquals(288, infoRecord.getLastChangedRevision());
- assertEquals("2007-05-07 16:27:11 +0200 (Mon, 07 May 2007)", infoRecord.getLastChangedDate());
+ assertEquals("2007-05-07 16:27:11 +0200 (Mon, 07 May 2007)", infoRecord
+ .getLastChangedDate());
}
-
+
private SVNInfoRecord extract(ArrayList<String> lines)
{
SVNUtilities.ProcessInfo processInfo = new SVNUtilities.ProcessInfo("info", lines, 0);
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTaskTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTaskTest.java
index e34799c46b1..6feddc719db 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTaskTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRecursiveCheckoutTaskTest.java
@@ -43,9 +43,11 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
public class SVNRecursiveCheckoutTaskTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "SVNRecursiveCheckoutTask");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "SVNRecursiveCheckoutTask");
@BeforeClass
public void init()
@@ -72,13 +74,13 @@ public class SVNRecursiveCheckoutTaskTest
final String repositoryUrl;
final String prefix;
-
+
final String workingCopyDir;
final List<String> checkedOutPaths;
final List<String> checkedOutProjects;
-
+
final List<String> checkedOutRevision;
SVNCheckoutMock(String repositoryUrl, String workingCopyDir)
@@ -94,7 +96,7 @@ public class SVNRecursiveCheckoutTaskTest
public void checkout(String path, String projectName, String revision) throws SVNException
{
assert path.startsWith(prefix);
-
+
checkedOutPaths.add(path.substring(prefix.length()));
checkedOutProjects.add(projectName);
checkedOutRevision.add(revision);
@@ -130,7 +132,8 @@ public class SVNRecursiveCheckoutTaskTest
dir.deleteOnExit();
assert dir.mkdir();
- final SVNRecursiveCheckoutTaskCheckoutMock task = new SVNRecursiveCheckoutTaskCheckoutMock();
+ final SVNRecursiveCheckoutTaskCheckoutMock task =
+ new SVNRecursiveCheckoutTaskCheckoutMock();
task.setDir(dir.getAbsolutePath());
final String reposUrl = "http://somehost/somerepos";
final String projPath = "someproj";
@@ -173,13 +176,15 @@ public class SVNRecursiveCheckoutTaskTest
+ " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
+ " <classpathentry kind=\"lib\" path=\"/libraries/testng/testng-jdk15.jar\" sourcepath=\"/libraries/testng/src.zip\"/>\n"
+ " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/common\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n";
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n";
final File someProj = new File(workingDirectory, projPath);
someProj.delete();
someProj.deleteOnExit();
assert someProj.mkdir();
- final SVNRecursiveCheckoutTaskCheckoutMock task = new SVNRecursiveCheckoutTaskCheckoutMock();
+ final SVNRecursiveCheckoutTaskCheckoutMock task =
+ new SVNRecursiveCheckoutTaskCheckoutMock();
final File classPathFile = new File(someProj, ".classpath");
classPathFile.deleteOnExit();
CollectionIO.writeIterable(classPathFile, Collections.singleton(classPathFileContent));
@@ -196,15 +201,18 @@ public class SVNRecursiveCheckoutTaskTest
final List<String> expectedPaths =
isTrunk ? Arrays.asList(projPath + "/trunk", SVNUtilities.BUILD_RESOURCES_PROJECT
+ "/trunk", "libraries/trunk", "common/trunk") : Arrays.asList(projPath,
- SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries", "common");
+ SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries", "common");
assertEquals(expectedPaths, task.mock.checkedOutPaths);
final List<String> expectedProjects =
- Arrays.asList(projPath, SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries", "common");
+ Arrays
+ .asList(projPath, SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries",
+ "common");
assertEquals(expectedProjects, task.mock.checkedOutProjects);
assertEquals(task.mock.checkedOutProjects.size(), task.mock.checkedOutRevision.size());
for (int i = 0; i < task.mock.checkedOutRevision.size(); ++i)
{
- assertEquals("Entry " + i, SVNUtilities.HEAD_REVISION, task.mock.checkedOutRevision.get(i));
+ assertEquals("Entry " + i, SVNUtilities.HEAD_REVISION, task.mock.checkedOutRevision
+ .get(i));
}
}
@@ -223,7 +231,8 @@ public class SVNRecursiveCheckoutTaskTest
+ " <classpathentry kind=\"lib\" path=\"/libraries/mail/mail.jar\"/>\n"
+ " <classpathentry kind=\"lib\" path=\"/libraries/testng/testng-jdk15.jar\" sourcepath=\"/libraries/testng/src.zip\"/>\n"
+ " <classpathentry combineaccessrules=\"false\" kind=\"src\" path=\"/common\"/>\n"
- + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n" + "</classpath>\n";
+ + " <classpathentry kind=\"output\" path=\"targets/classes\"/>\n"
+ + "</classpath>\n";
final String classPathFileContent2 =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ "<classpath>\n"
@@ -248,7 +257,8 @@ public class SVNRecursiveCheckoutTaskTest
someDependantProj.deleteOnExit();
assert someDependantProj.mkdir();
- final SVNRecursiveCheckoutTaskCheckoutMock task = new SVNRecursiveCheckoutTaskCheckoutMock();
+ final SVNRecursiveCheckoutTaskCheckoutMock task =
+ new SVNRecursiveCheckoutTaskCheckoutMock();
final File classPathFile1 = new File(someProj, ".classpath");
classPathFile1.deleteOnExit();
CollectionIO.writeIterable(classPathFile1, Collections.singleton(classPathFileContent1));
@@ -269,12 +279,14 @@ public class SVNRecursiveCheckoutTaskTest
final List<String> expectedPaths =
isTrunk ? Arrays.asList(projPath + "/trunk", SVNUtilities.BUILD_RESOURCES_PROJECT
- + "/trunk", "libraries/trunk", "common/trunk", "common2/trunk") : Arrays.asList(projPath,
- SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries", "common", "common2");
+ + "/trunk", "libraries/trunk", "common/trunk", "common2/trunk") : Arrays
+ .asList(projPath, SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries",
+ "common", "common2");
CollectionIO.writeIterable(System.out, task.mock.checkedOutPaths);
assertEquals(expectedPaths, task.mock.checkedOutPaths);
final List<String> expectedProjects =
- Arrays.asList(projPath, SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries", "common", "common2");
+ Arrays.asList(projPath, SVNUtilities.BUILD_RESOURCES_PROJECT, "libraries",
+ "common", "common2");
assertEquals(expectedProjects, task.mock.checkedOutProjects);
assertEquals(task.mock.checkedOutProjects.size(), task.mock.checkedOutRevision.size());
for (int i = 0; i < task.mock.checkedOutRevision.size(); ++i)
@@ -282,7 +294,7 @@ public class SVNRecursiveCheckoutTaskTest
assertEquals("Entry " + i, revision, task.mock.checkedOutRevision.get(i));
}
}
-
+
@Test(expectedExceptions =
{ BuildException.class })
public void testSetInvalidRevision()
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContextTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContextTest.java
index df5b7be1d2d..02ed7acae19 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContextTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNRepositoryProjectContextTest.java
@@ -84,8 +84,9 @@ public class SVNRepositoryProjectContextTest
final String name = "someProject";
def.setProjectName(name);
final String repositoryUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
- final String projectPath = StringUtils.join(Arrays.asList(repositoryUrl, name, "trunk"), "/");
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
+ final String projectPath =
+ StringUtils.join(Arrays.asList(repositoryUrl, name, "trunk"), "/");
assertEquals(repositoryUrl, def.getRepositoryUrl());
assertEquals(projectPath, def.getPathProvider().getPath());
}
@@ -98,8 +99,9 @@ public class SVNRepositoryProjectContextTest
final String subName = "someSubProject";
def.setProjectName(name);
final String repositoryUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
- final String projectPath = StringUtils.join(Arrays.asList(repositoryUrl, subName, "trunk"), "/");
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
+ final String projectPath =
+ StringUtils.join(Arrays.asList(repositoryUrl, subName, "trunk"), "/");
assertEquals(projectPath, def.getPathProvider().getPath(subName));
}
@@ -112,7 +114,7 @@ public class SVNRepositoryProjectContextTest
final String pathEntry = ".classpath";
def.setProjectName(name);
final String repositoryUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP;
final String projectPath =
StringUtils.join(Arrays.asList(repositoryUrl, subName, "trunk", pathEntry), "/");
assertEquals(projectPath, def.getPathProvider().getPath(subName, pathEntry));
@@ -127,8 +129,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setReleaseBranch(branchName);
final String branchUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/branches/release/" + branchName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/branches/release/" + branchName;
final String projectPath = StringUtils.join(Arrays.asList(branchUrl, name), "/");
assertEquals(branchUrl, def.getRepositoryUrl());
assertEquals(projectPath, def.getPathProvider().getPath());
@@ -144,8 +146,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setReleaseBranch(branchName);
final String branchUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/branches/release/" + branchName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/branches/release/" + branchName;
final String projectPath = StringUtils.join(Arrays.asList(branchUrl, subName), "/");
assertEquals(projectPath, def.getPathProvider().getPath(subName));
}
@@ -161,9 +163,10 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setReleaseBranch(branchName);
final String branchUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/branches/release/" + branchName;
- final String projectPath = StringUtils.join(Arrays.asList(branchUrl, subName, pathEntry), "/");
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/branches/release/" + branchName;
+ final String projectPath =
+ StringUtils.join(Arrays.asList(branchUrl, subName, pathEntry), "/");
assertEquals(projectPath, def.getPathProvider().getPath(subName, pathEntry));
}
@@ -176,8 +179,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setFeatureBranch(branchName);
final String branchUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/branches/feature/" + branchName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/branches/feature/" + branchName;
final String projectPath = StringUtils.join(Arrays.asList(branchUrl, name), "/");
assertEquals(branchUrl, def.getRepositoryUrl());
assertEquals(projectPath, def.getPathProvider().getPath());
@@ -193,8 +196,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setFeatureBranch(branchName);
final String branchUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/branches/feature/" + branchName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/branches/feature/" + branchName;
final String projectPath = StringUtils.join(Arrays.asList(branchUrl, subName), "/");
assertEquals(projectPath, def.getPathProvider().getPath(subName));
}
@@ -209,8 +212,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setReleaseTag(tagName);
final String tagUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/tags/release/" + branchName + "/" + tagName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/tags/release/" + branchName + "/" + tagName;
final String projectPath = StringUtils.join(Arrays.asList(tagUrl, name), "/");
assertEquals(tagUrl, def.getRepositoryUrl());
assertEquals(projectPath, def.getPathProvider().getPath());
@@ -227,8 +230,8 @@ public class SVNRepositoryProjectContextTest
def.setProjectName(name);
def.setReleaseTag(tagName);
final String tagUrl =
- SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP
- + "/" + name + "/tags/release/" + branchName + "/" + tagName;
+ SVNUtilities.DEFAULT_REPOSITORY_ROOT + "/" + SVNUtilities.DEFAULT_GROUP + "/"
+ + name + "/tags/release/" + branchName + "/" + tagName;
final String projectPath = StringUtils.join(Arrays.asList(tagUrl, subName), "/");
assertEquals(tagUrl, def.getRepositoryUrl());
assertEquals(projectPath, def.getPathProvider().getPath(subName));
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilitiesTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilitiesTest.java
index 9b98a3ab110..45b5d71d6f0 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilitiesTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNUtilitiesTest.java
@@ -22,7 +22,7 @@ import static org.testng.AssertJUnit.*;
/**
* Test cases for {@link SVNUtilities}.
- *
+ *
* @author Bernd Rinn
*/
public class SVNUtilitiesTest
@@ -36,7 +36,7 @@ public class SVNUtilitiesTest
final String normalizedHTTPUrl = "http://home/cisd/repos/test/trunk";
assertEquals(normalizedHTTPUrl, SVNUtilities.normalizeUrl(normalizedHTTPUrl));
}
-
+
@Test
public void testNormalizeUrlOnNonNormalizedURls()
{
@@ -47,7 +47,7 @@ public class SVNUtilitiesTest
final String normalizedHTTPUrl = "http://home/cisd/repos/test/trunk";
assertEquals(normalizedHTTPUrl, SVNUtilities.normalizeUrl(nonNormalizedHTTPUrl));
}
-
+
@Test
public void testNormalizeUrlOnNonNormalizedProtocolUrl()
{
@@ -67,7 +67,7 @@ public class SVNUtilitiesTest
final String normalizedSVNSSHUrl = "svn+ssh://home/cisd/repos/test/trunk";
assertEquals(normalizedSVNSSHUrl, SVNUtilities.normalizeUrl(nonNormalizedSVNSSHUrl));
}
-
+
@Test
public void testGetParent()
{
@@ -75,7 +75,7 @@ public class SVNUtilitiesTest
final String url = parentUrl + "/trunk";
assertEquals(parentUrl, SVNUtilities.getParent(url));
}
-
+
@Test
public void testGetParentNonNormalized()
{
@@ -83,7 +83,7 @@ public class SVNUtilitiesTest
final String url = parentUrl + "//trunk/";
assertEquals(parentUrl, SVNUtilities.getParent(url));
}
-
+
@Test
public void testGetTopLevelDirectory()
{
@@ -91,7 +91,7 @@ public class SVNUtilitiesTest
assertEquals("one", SVNUtilities.getTopLevelDirectory("/one/"));
assertEquals("one", SVNUtilities.getTopLevelDirectory("/one"));
}
-
+
@Test
public void testGetBranchForTag()
{
diff --git a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProviderTest.java b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProviderTest.java
index 75eb8fa16ef..53516137b33 100644
--- a/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProviderTest.java
+++ b/ant_tasks/sourceTest/java/ch/systemsx/cisd/ant/task/subversion/SVNWCProjectPathProviderTest.java
@@ -37,9 +37,11 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
public class SVNWCProjectPathProviderTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "SVNWCProjectPathProvider");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "SVNWCProjectPathProvider");
@BeforeClass
public void init()
@@ -82,15 +84,17 @@ public class SVNWCProjectPathProviderTest
final ISVNProjectPathProvider provider = new SVNWCProjectPathProvider(workingCopyDirectory);
String expectedPath;
expectedPath =
- StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(), project), File.separator);
+ StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(), project),
+ File.separator);
assertEquals(expectedPath, provider.getPath());
expectedPath =
- StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(),
- subProject), File.separator);
+ StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(), subProject),
+ File.separator);
assertEquals(expectedPath, provider.getPath(subProject));
expectedPath =
- StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(),
- subProject, path), File.separator);
+ StringUtils.join(Arrays
+ .asList(workingDirectory.getAbsolutePath(), subProject, path),
+ File.separator);
assertEquals(expectedPath, provider.getPath(subProject, path));
}
@@ -106,10 +110,11 @@ public class SVNWCProjectPathProviderTest
workingCopyDirectory.mkdir();
assert workingCopyDirectory.isDirectory();
workingDirectory.deleteOnExit();
- final ISVNProjectPathProvider provider = new SVNWCProjectPathProvider(workingCopyDirectory);
+ final ISVNProjectPathProvider provider =
+ new SVNWCProjectPathProvider(workingCopyDirectory);
final String expectedPath =
StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(), subProject,
- "somePath/two"), File.separator);
+ "somePath/two"), File.separator);
assertEquals(expectedPath, provider.getPath(subProject, path));
} else
{
@@ -118,10 +123,11 @@ public class SVNWCProjectPathProviderTest
final String path = "somePath/two";
final File workingCopyDirectory = new File(workingDirectory, project);
workingCopyDirectory.mkdir();
- final ISVNProjectPathProvider provider = new SVNWCProjectPathProvider(workingCopyDirectory);
+ final ISVNProjectPathProvider provider =
+ new SVNWCProjectPathProvider(workingCopyDirectory);
final String expectedPath =
StringUtils.join(Arrays.asList(workingDirectory.getAbsolutePath(), subProject,
- "somePath\\two"), File.separator);
+ "somePath\\two"), File.separator);
assertEquals(expectedPath, provider.getPath(subProject, path));
}
}
diff --git a/authentication/source/java/ch/systemsx/cisd/authentication/NullAuthenticationService.java b/authentication/source/java/ch/systemsx/cisd/authentication/NullAuthenticationService.java
index ca92b492cc9..11a774f367e 100644
--- a/authentication/source/java/ch/systemsx/cisd/authentication/NullAuthenticationService.java
+++ b/authentication/source/java/ch/systemsx/cisd/authentication/NullAuthenticationService.java
@@ -20,8 +20,8 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
- * An implementation of {@link IAuthenticationService} which supports as a <code>null</code> object.
- *
+ * An implementation of {@link IAuthenticationService} which supports as a <code>null</code> object.
+ *
* @author Franz-Josef Elmer
*/
public class NullAuthenticationService implements IAuthenticationService
diff --git a/authentication/source/java/ch/systemsx/cisd/authentication/Principal.java b/authentication/source/java/ch/systemsx/cisd/authentication/Principal.java
index f50e3e75fbc..d1106bb025a 100644
--- a/authentication/source/java/ch/systemsx/cisd/authentication/Principal.java
+++ b/authentication/source/java/ch/systemsx/cisd/authentication/Principal.java
@@ -50,11 +50,12 @@ public class Principal
* @param lastName can not be <code>null</code>.
* @param email can not be <code>null</code>.
*/
- public Principal(final String userId, final String firstName, final String lastName, final String email)
+ public Principal(final String userId, final String firstName, final String lastName,
+ final String email)
{
- this(userId, firstName, lastName, email, Collections.<String, String>emptyMap());
+ this(userId, firstName, lastName, email, Collections.<String, String> emptyMap());
}
-
+
/**
* Standard constructor which accepts mandatory parameters and properties.
*
@@ -64,8 +65,8 @@ public class Principal
* @param email can not be <code>null</code>.
* @param properties can not be <code>null</code>.
*/
- public Principal(final String userId, final String firstName, final String lastName, final String email,
- final Map<String, String> properties)
+ public Principal(final String userId, final String firstName, final String lastName,
+ final String email, final Map<String, String> properties)
{
assert userId != null;
assert firstName != null;
@@ -112,9 +113,8 @@ public class Principal
return lastName;
}
- /**
- * Returns the property for given <var>key</var>, or <code>null</code>, if no property exists for this
- * <var>key</var>.
+ /**
+ * Returns the property for given <var>key</var>, or <code>null</code>, if no property exists for this <var>key</var>.
*/
public final String getProperty(String key)
{
diff --git a/authentication/source/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationService.java b/authentication/source/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationService.java
index b29b80f134f..bd9ea018ad8 100644
--- a/authentication/source/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationService.java
+++ b/authentication/source/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationService.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
+
/**
* This <code>IAuthenticationService</code> implementation first registers the application on the <i>Crowd</i>
* server, then authenticates the user.
@@ -63,21 +64,26 @@ public class CrowdAuthenticationService implements IAuthenticationService
LogFactory.getLogger(LogCategory.OPERATION, CrowdAuthenticationService.class);
/** The template to authenticate the application. */
- //@Private
+ // @Private
static final MessageFormat AUTHENTICATE_APPL =
- new MessageFormat("<soap:Envelope xmlns:soap=\"http://schemas.xmlsoap.org/soap/envelope/\" "
- + "xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" "
- + "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n" + " <soap:Body>\n"
- + " <authenticateApplication xmlns=\"urn:SecurityServer\">\n" + " <in0>\n"
- + " <credential xmlns=\"http://authentication.integration.crowd.atlassian.com\">\n"
- + " <credential>{1}</credential>\n" + " </credential>\n"
- + " <name xmlns=\"http://authentication.integration.crowd.atlassian.com\">{0}</name>\n"
- + " <validationFactors xmlns=\"http://authentication.integration.crowd.atlassian.com\" "
- + " xsi:nil=\"true\" />\n" + " </in0>\n"
- + " </authenticateApplication>\n" + " </soap:Body>\n" + "</soap:Envelope>\n");
+ new MessageFormat(
+ "<soap:Envelope xmlns:soap=\"http://schemas.xmlsoap.org/soap/envelope/\" "
+ + "xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" "
+ + "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
+ + " <soap:Body>\n"
+ + " <authenticateApplication xmlns=\"urn:SecurityServer\">\n"
+ + " <in0>\n"
+ + " <credential xmlns=\"http://authentication.integration.crowd.atlassian.com\">\n"
+ + " <credential>{1}</credential>\n"
+ + " </credential>\n"
+ + " <name xmlns=\"http://authentication.integration.crowd.atlassian.com\">{0}</name>\n"
+ + " <validationFactors xmlns=\"http://authentication.integration.crowd.atlassian.com\" "
+ + " xsi:nil=\"true\" />\n" + " </in0>\n"
+ + " </authenticateApplication>\n" + " </soap:Body>\n"
+ + "</soap:Envelope>\n");
/** The template to authenticate the user. */
- //@Private
+ // @Private
static final MessageFormat AUTHENTICATE_USER =
new MessageFormat(
"<soap:Envelope xmlns:soap=\"http://schemas.xmlsoap.org/soap/envelope/\" "
@@ -100,7 +106,7 @@ public class CrowdAuthenticationService implements IAuthenticationService
+ "</soap:Envelope>\n");
/** The template to find a principal by token or by name. */
- //@Private
+ // @Private
static final MessageFormat FIND_PRINCIPAL_BY_NAME =
new MessageFormat(
"<soap:Envelope xmlns:soap=\"http://schemas.xmlsoap.org/soap/envelope/\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
@@ -112,8 +118,9 @@ public class CrowdAuthenticationService implements IAuthenticationService
+ " </in0>\n"
+ " <in1>{2}</in1>\n"
+ " </findPrincipalByName>\n"
- + " </soap:Body>\n" + "</soap:Envelope>\n");
-
+ + " </soap:Body>\n"
+ + "</soap:Envelope>\n");
+
private static IRequestExecutor createExecutor()
{
return new IRequestExecutor()
@@ -129,7 +136,8 @@ public class CrowdAuthenticationService implements IAuthenticationService
{
HttpClient client = new HttpClient();
PostMethod post = new PostMethod(serviceUrl);
- StringRequestEntity entity = new StringRequestEntity(message, "application/soap+xml", "utf-8");
+ StringRequestEntity entity =
+ new StringRequestEntity(message, "application/soap+xml", "utf-8");
post.setRequestEntity(entity);
String response = null;
try
@@ -149,7 +157,7 @@ public class CrowdAuthenticationService implements IAuthenticationService
};
}
-
+
private final String url;
private final String application;
@@ -158,10 +166,11 @@ public class CrowdAuthenticationService implements IAuthenticationService
private final IRequestExecutor requestExecutor;
- public CrowdAuthenticationService(String host, int port, String application, String applicationPassword)
+ public CrowdAuthenticationService(String host, int port, String application,
+ String applicationPassword)
{
- this("https://" + host + ":" + port + "/crowd/services/SecurityServer", application, applicationPassword,
- createExecutor());
+ this("https://" + host + ":" + port + "/crowd/services/SecurityServer", application,
+ applicationPassword, createExecutor());
}
public CrowdAuthenticationService(String url, String application, String applicationPassword,
@@ -174,8 +183,8 @@ public class CrowdAuthenticationService implements IAuthenticationService
if (operationLog.isDebugEnabled())
{
final String msg =
- "A new CrowdAuthenticationService instance has been created for [" + "url=" + url
- + ", application=" + application + "]";
+ "A new CrowdAuthenticationService instance has been created for [" + "url="
+ + url + ", application=" + application + "]";
operationLog.debug(msg);
}
}
@@ -191,8 +200,8 @@ public class CrowdAuthenticationService implements IAuthenticationService
String response = execute(AUTHENTICATE_APPL, application, applicationPassword);
if (pickElementContent(response, CrowdSoapElements.TOKEN) == null)
{
- throw new EnvironmentFailureException("Application '" + application + "' couldn't be authenticated: "
- + response);
+ throw new EnvironmentFailureException("Application '" + application
+ + "' couldn't be authenticated: " + response);
}
} catch (EnvironmentFailureException ex)
{
@@ -209,8 +218,8 @@ public class CrowdAuthenticationService implements IAuthenticationService
public final String authenticateApplication()
{
final String applicationToken =
- StringEscapeUtils.unescapeXml(execute(CrowdSoapElements.TOKEN, AUTHENTICATE_APPL, application,
- applicationPassword));
+ StringEscapeUtils.unescapeXml(execute(CrowdSoapElements.TOKEN, AUTHENTICATE_APPL,
+ application, applicationPassword));
if (applicationToken == null)
{
operationLog.error("CROWD: application '" + application + "' failed to authenticate.");
@@ -218,7 +227,8 @@ public class CrowdAuthenticationService implements IAuthenticationService
{
if (operationLog.isDebugEnabled())
{
- operationLog.debug("CROWD: application '" + application + "' successfully authenticated.");
+ operationLog.debug("CROWD: application '" + application
+ + "' successfully authenticated.");
}
}
return applicationToken;
@@ -228,12 +238,15 @@ public class CrowdAuthenticationService implements IAuthenticationService
{
assert applicationToken != null;
assert user != null;
-
- final String userToken = StringEscapeUtils.unescapeXml(execute(CrowdSoapElements.OUT, AUTHENTICATE_USER,
- application, applicationToken, user, password));
+
+ final String userToken =
+ StringEscapeUtils.unescapeXml(execute(CrowdSoapElements.OUT, AUTHENTICATE_USER,
+ application, applicationToken, user, password));
if (operationLog.isInfoEnabled())
{
- final String msg = "CROWD: authentication of user '" + user + "', application '" + application + "': ";
+ final String msg =
+ "CROWD: authentication of user '" + user + "', application '" + application
+ + "': ";
operationLog.info(msg + (userToken == null ? "FAILED." : "SUCCESS."));
}
return userToken != null;
@@ -254,13 +267,14 @@ public class CrowdAuthenticationService implements IAuthenticationService
{
if (operationLog.isDebugEnabled())
{
- operationLog.debug("No SOAPAttribute element could be found in the SOAP XML response.");
+ operationLog
+ .debug("No SOAPAttribute element could be found in the SOAP XML response.");
}
}
if (principal == null)
{
- throw new EnvironmentFailureException("CROWD: Principal information for user '" + user
- + "' could not be obtained.");
+ throw new EnvironmentFailureException("CROWD: Principal information for user '"
+ + user + "' could not be obtained.");
}
return principal;
} catch (EnvironmentFailureException ex)
@@ -292,8 +306,7 @@ public class CrowdAuthenticationService implements IAuthenticationService
}
/** Creates a <code>Principal</code> with found SOAP attributes. */
- private final static Principal createPrincipal(String user,
- Map<String, String> soapAttributes)
+ private final static Principal createPrincipal(String user, Map<String, String> soapAttributes)
{
final String firstName = soapAttributes.get(FIRST_NAME_PROPERTY_KEY);
final String lastName = soapAttributes.get(LAST_NAME_PROPERTY_KEY);
@@ -335,8 +348,9 @@ public class CrowdAuthenticationService implements IAuthenticationService
{
if (xmlString == null)
{
- operationLog.error("Response of web service is invalid (null). We were looking for element '" + element
- + "'.");
+ operationLog
+ .error("Response of web service is invalid (null). We were looking for element '"
+ + element + "'.");
return null;
}
@@ -353,14 +367,16 @@ public class CrowdAuthenticationService implements IAuthenticationService
index = xmlString.indexOf(">", index);
if (index < 0)
{
- operationLog.error("Element '" + element + "' seems to be present but XML is invalid: '"
+ operationLog.error("Element '" + element
+ + "' seems to be present but XML is invalid: '"
+ StringUtils.abbreviate(xmlString, 50) + "'.");
return null;
}
int endIndex = getIndex(xmlString, "</", element + ">", index);
if (endIndex < 0)
{
- operationLog.error("Start tag of element '" + element + "' is present but end tag is missing: '"
+ operationLog.error("Start tag of element '" + element
+ + "' is present but end tag is missing: '"
+ StringUtils.abbreviate(xmlString, 50) + "'.");
return null;
}
diff --git a/authentication/source/java/ch/systemsx/cisd/authentication/crowd/IRequestExecutor.java b/authentication/source/java/ch/systemsx/cisd/authentication/crowd/IRequestExecutor.java
index 8b7648c7389..69070005d2f 100644
--- a/authentication/source/java/ch/systemsx/cisd/authentication/crowd/IRequestExecutor.java
+++ b/authentication/source/java/ch/systemsx/cisd/authentication/crowd/IRequestExecutor.java
@@ -18,11 +18,11 @@ package ch.systemsx.cisd.authentication.crowd;
/**
* Interface of classes executing requests.
- *
+ *
* @author Franz-Josef Elmer
*/
interface IRequestExecutor
-{
+{
/**
* Executes the specified message at the specified service.
*/
diff --git a/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationServiceTest.java b/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationServiceTest.java
index 4973d3c4f95..9724f008664 100644
--- a/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationServiceTest.java
+++ b/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/CrowdAuthenticationServiceTest.java
@@ -75,7 +75,8 @@ public class CrowdAuthenticationServiceTest
{
context = new Mockery();
executor = context.mock(IRequestExecutor.class);
- authenticationService = new CrowdAuthenticationService(URL, APPLICATION, APPLICATION_PASSWORD, executor);
+ authenticationService =
+ new CrowdAuthenticationService(URL, APPLICATION, APPLICATION_PASSWORD, executor);
logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
}
@@ -96,16 +97,18 @@ public class CrowdAuthenticationServiceTest
{
Object[] parameters = new Object[]
{ APPLICATION_ESCAPED, APPLICATION_PASSWORD_ESCAPED };
- String message = CrowdAuthenticationService.AUTHENTICATE_APPL.format(parameters);
+ String message =
+ CrowdAuthenticationService.AUTHENTICATE_APPL.format(parameters);
one(executor).execute(URL, message);
- will(returnValue(createXMLElement(CrowdSoapElements.TOKEN, APPLICATION_TOKEN_ESACPED)));
+ will(returnValue(createXMLElement(CrowdSoapElements.TOKEN,
+ APPLICATION_TOKEN_ESACPED)));
}
});
String result = authenticationService.authenticateApplication();
assertEquals(APPLICATION_TOKEN, result);
- assertEquals(createDebugLogEntry("CROWD: application '" + APPLICATION + "' successfully authenticated."),
- logRecorder.getLogContent());
+ assertEquals(createDebugLogEntry("CROWD: application '" + APPLICATION
+ + "' successfully authenticated."), logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -118,17 +121,19 @@ public class CrowdAuthenticationServiceTest
{
Object[] parameters = new Object[]
{ APPLICATION_ESCAPED, APPLICATION_PASSWORD_ESCAPED };
- String message = CrowdAuthenticationService.AUTHENTICATE_APPL.format(parameters);
+ String message =
+ CrowdAuthenticationService.AUTHENTICATE_APPL.format(parameters);
one(executor).execute(URL, message);
will(returnValue("error"));
}
});
String result = authenticationService.authenticateApplication();
assertEquals(null, result);
- assertEquals(createDebugLogEntry("Element '" + CrowdSoapElements.TOKEN + "' could not be found in 'error'.")
+ assertEquals(createDebugLogEntry("Element '" + CrowdSoapElements.TOKEN
+ + "' could not be found in 'error'.")
+ OSUtilities.LINE_SEPARATOR
- + createErrorLogEntry("CROWD: application '" + APPLICATION + "' failed to authenticate."), logRecorder
- .getLogContent());
+ + createErrorLogEntry("CROWD: application '" + APPLICATION
+ + "' failed to authenticate."), logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -139,17 +144,22 @@ public class CrowdAuthenticationServiceTest
context.checking(new Expectations()
{
{
- Object[] parameters = new Object[]
- { APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED, USER_PASSWORD_ESCAPED };
- String message = CrowdAuthenticationService.AUTHENTICATE_USER.format(parameters);
+ Object[] parameters =
+ new Object[]
+ { APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED,
+ USER_PASSWORD_ESCAPED };
+ String message =
+ CrowdAuthenticationService.AUTHENTICATE_USER.format(parameters);
one(executor).execute(URL, message);
- will(returnValue(createXMLElement("n:" + CrowdSoapElements.OUT, APPLICATION_TOKEN_ESACPED)));
+ will(returnValue(createXMLElement("n:" + CrowdSoapElements.OUT,
+ APPLICATION_TOKEN_ESACPED)));
}
});
- boolean result = authenticationService.authenticateUser(APPLICATION_TOKEN, USER, USER_PASSWORD);
+ boolean result =
+ authenticationService.authenticateUser(APPLICATION_TOKEN, USER, USER_PASSWORD);
assertEquals(true, result);
- assertEquals(createInfoLogEntry("CROWD: authentication of user '" + USER + "', application '" + APPLICATION
- + "': SUCCESS."), logRecorder.getLogContent());
+ assertEquals(createInfoLogEntry("CROWD: authentication of user '" + USER
+ + "', application '" + APPLICATION + "': SUCCESS."), logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -160,19 +170,24 @@ public class CrowdAuthenticationServiceTest
context.checking(new Expectations()
{
{
- Object[] parameters = new Object[]
- { APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED, USER_PASSWORD_ESCAPED };
- String message = CrowdAuthenticationService.AUTHENTICATE_USER.format(parameters);
+ Object[] parameters =
+ new Object[]
+ { APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED,
+ USER_PASSWORD_ESCAPED };
+ String message =
+ CrowdAuthenticationService.AUTHENTICATE_USER.format(parameters);
one(executor).execute(URL, message);
will(returnValue("error"));
}
});
- boolean result = authenticationService.authenticateUser(APPLICATION_TOKEN, USER, USER_PASSWORD);
+ boolean result =
+ authenticationService.authenticateUser(APPLICATION_TOKEN, USER, USER_PASSWORD);
assertEquals(false, result);
- assertEquals(createDebugLogEntry("Element '" + CrowdSoapElements.OUT + "' could not be found in 'error'.")
+ assertEquals(createDebugLogEntry("Element '" + CrowdSoapElements.OUT
+ + "' could not be found in 'error'.")
+ OSUtilities.LINE_SEPARATOR
- + createInfoLogEntry("CROWD: authentication of user '" + USER + "', application '" + APPLICATION
- + "': FAILED."), logRecorder.getLogContent());
+ + createInfoLogEntry("CROWD: authentication of user '" + USER + "', application '"
+ + APPLICATION + "': FAILED."), logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -185,7 +200,8 @@ public class CrowdAuthenticationServiceTest
{
Object[] parameters = new Object[]
{ APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED };
- String message = CrowdAuthenticationService.FIND_PRINCIPAL_BY_NAME.format(parameters);
+ String message =
+ CrowdAuthenticationService.FIND_PRINCIPAL_BY_NAME.format(parameters);
one(executor).execute(URL, message);
String element = createSOAPAttribute("sn", "Stepka");
element += createSOAPAttribute("invalidPasswordAttempts", "0");
@@ -200,8 +216,8 @@ public class CrowdAuthenticationServiceTest
private String createSOAPAttribute(String name, String value)
{
return "<SOAPAttribute><name>" + name
- + "</name><values><ns1:string xmlns:ns1=\"urn:SecurityServer\">" + value
- + "</ns1:string></values></SOAPAttribute>";
+ + "</name><values><ns1:string xmlns:ns1=\"urn:SecurityServer\">"
+ + value + "</ns1:string></values></SOAPAttribute>";
}
});
Principal result = authenticationService.getPrincipal(APPLICATION_TOKEN, USER);
@@ -224,7 +240,8 @@ public class CrowdAuthenticationServiceTest
{
Object[] parameters = new Object[]
{ APPLICATION_ESCAPED, APPLICATION_TOKEN_ESACPED, USER_ESCAPED };
- String message = CrowdAuthenticationService.FIND_PRINCIPAL_BY_NAME.format(parameters);
+ String message =
+ CrowdAuthenticationService.FIND_PRINCIPAL_BY_NAME.format(parameters);
one(executor).execute(URL, message);
will(returnValue("<a></a>"));
}
@@ -235,10 +252,12 @@ public class CrowdAuthenticationServiceTest
fail("EnvironmentFailureException expected");
} catch (EnvironmentFailureException e)
{
- assertEquals("CROWD: Principal information for user '" + USER + "' could not be obtained.", e.getMessage());
+ assertEquals("CROWD: Principal information for user '" + USER
+ + "' could not be obtained.", e.getMessage());
}
- assertEquals(createDebugLogEntry("No SOAPAttribute element could be found in the SOAP XML response."),
+ assertEquals(
+ createDebugLogEntry("No SOAPAttribute element could be found in the SOAP XML response."),
logRecorder.getLogContent());
context.assertIsSatisfied();
diff --git a/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/RealCrowdAuthenticationTest.java b/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/RealCrowdAuthenticationTest.java
index 43c643f0763..f4a15d8f222 100644
--- a/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/RealCrowdAuthenticationTest.java
+++ b/authentication/sourceTest/java/ch/systemsx/cisd/authentication/crowd/RealCrowdAuthenticationTest.java
@@ -44,18 +44,24 @@ public class RealCrowdAuthenticationTest
{
private static final int PORT_OF_AUTHENTICATION_SERVICE = 0; // FIX!
+
private static final String HOST_NAME_OF_AUTHENTICATION_SERVICE = null; // FIX!
+
private static final String NAME_OF_TEST_APPLICATION = "test";
+
private static final String PASSWORD_OF_TEST_APPLICATION = null; // FIX!
+
private static final String NAME_OF_TEST_USER = "test";
+
private static final String PASSWORD_OF_TEST_USER = null; // FIX!
@Test(groups = "broken")
public void testCrowdTestAccount()
{
final IAuthenticationService as =
- new CrowdAuthenticationService(HOST_NAME_OF_AUTHENTICATION_SERVICE, PORT_OF_AUTHENTICATION_SERVICE,
- NAME_OF_TEST_APPLICATION, PASSWORD_OF_TEST_APPLICATION);
+ new CrowdAuthenticationService(HOST_NAME_OF_AUTHENTICATION_SERVICE,
+ PORT_OF_AUTHENTICATION_SERVICE, NAME_OF_TEST_APPLICATION,
+ PASSWORD_OF_TEST_APPLICATION);
final String token = as.authenticateApplication();
assertNotNull(token);
assertTrue(as.authenticateUser(token, NAME_OF_TEST_USER, PASSWORD_OF_TEST_USER));
diff --git a/bds/source/java/ch/systemsx/cisd/bds/AbstractFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/AbstractFormattedData.java
index 92a81d3f895..d7b402de81d 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/AbstractFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/AbstractFormattedData.java
@@ -53,14 +53,15 @@ public abstract class AbstractFormattedData implements IFormattedData
final String formatCode = getFormat().getCode();
if (format.getCode().equals(formatCode) == false)
{
- throw new DataStructureException(String.format("Format codes do not match: '%s' versus '%s'.", format
- .getCode(), formatCode));
+ throw new DataStructureException(String.format(
+ "Format codes do not match: '%s' versus '%s'.", format.getCode(), formatCode));
}
final Version formatVersion = getFormat().getVersion();
if (format.getVersion().isBackwardsCompatibleWith(formatVersion) == false)
{
throw new DataStructureException(String.format(
- "Version '%s' is not backwards compatible with version '%s'.", format.getVersion(), formatVersion));
+ "Version '%s' is not backwards compatible with version '%s'.", format
+ .getVersion(), formatVersion));
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Constants.java b/bds/source/java/ch/systemsx/cisd/bds/Constants.java
index ee53e2c4934..f2b532f50d1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Constants.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Constants.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.bds;
/**
* Some constants used inside the <i>BDS</i> library
- *
+ *
* @author Christian Ribeaud
*/
public final class Constants
diff --git a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
index 764f2d26eb1..7a50e03c735 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureLoader.java
@@ -50,7 +50,8 @@ public class DataStructureLoader
final IStorage storage = createStorage(name);
storage.mount();
final Version version = Version.loadFrom(storage.getRoot());
- final IDataStructure dataStructure = DataStructureFactory.createDataStructure(storage, version);
+ final IDataStructure dataStructure =
+ DataStructureFactory.createDataStructure(storage, version);
dataStructure.open();
return dataStructure;
}
@@ -60,7 +61,8 @@ public class DataStructureLoader
final File file = new File(baseDir, name);
if (file.exists() == false)
{
- throw new DataStructureException("No container name '" + name + "' exists in " + baseDir.getAbsolutePath());
+ throw new DataStructureException("No container name '" + name + "' exists in "
+ + baseDir.getAbsolutePath());
}
if (file.isDirectory())
{
@@ -71,8 +73,8 @@ public class DataStructureLoader
{
return new HDF5Storage(hdf5File);
}
- throw new DataStructureException("Couldn't found appropriate container named '" + name + "' in "
- + baseDir.getAbsolutePath());
+ throw new DataStructureException("Couldn't found appropriate container named '" + name
+ + "' in " + baseDir.getAbsolutePath());
}
}
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 0021df7caec..dabba575cc4 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/DataStructureV1_0.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.bds.storage.IStorage;
public class DataStructureV1_0 extends AbstractDataStructure
{
public static final String DIR_METADATA = "metadata";
-
+
public static final String DIR_ANNOTATIONS = "annotations";
public static final String DIR_PARAMETERS = "parameters";
@@ -65,10 +65,11 @@ public class DataStructureV1_0 extends AbstractDataStructure
private final void registerHandlers()
{
- mappingFileHandler = new MappingFileHandler(getMetaDataDirectory(), getStandardData(), getOriginalData());
+ mappingFileHandler =
+ new MappingFileHandler(getMetaDataDirectory(), getStandardData(), getOriginalData());
registerHandler(mappingFileHandler);
- registerHandler(new ChecksumHandler(getMetaDataDirectory().makeDirectory(ChecksumHandler.CHECKSUM_DIRECTORY),
- getOriginalData()));
+ registerHandler(new ChecksumHandler(getMetaDataDirectory().makeDirectory(
+ ChecksumHandler.CHECKSUM_DIRECTORY), getOriginalData()));
}
/**
@@ -106,7 +107,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
return Utilities.getOrCreateSubDirectory(root, DIR_ANNOTATIONS);
}
-
+
private IDirectory getParametersDirectory()
{
assertOpenOrCreated();
@@ -124,10 +125,11 @@ public class DataStructureV1_0 extends AbstractDataStructure
assertOpenOrCreated();
if (format == null)
{
- throw new DataStructureException("Couldn't create formatted data because of unspecified format.");
+ throw new DataStructureException(
+ "Couldn't create formatted data because of unspecified format.");
}
- return FormattedDataFactory.createFormattedData(getDataDirectory(), format, UnknownFormatV1_0.UNKNOWN_1_0,
- formatParameters);
+ return FormattedDataFactory.createFormattedData(getDataDirectory(), format,
+ UnknownFormatV1_0.UNKNOWN_1_0, formatParameters);
}
/**
@@ -151,7 +153,7 @@ public class DataStructureV1_0 extends AbstractDataStructure
assert formatParameter != null : "Unspecified format parameter.";
formatParameters.addParameter(formatParameter);
}
-
+
public void setAnnotations(IAnnotations annotations)
{
this.annotations = annotations;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
index baa2d0bb1f0..d481a403c74 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentIdentifier.java
@@ -75,7 +75,8 @@ public class ExperimentIdentifier implements IStorable
/**
* Returns the group code;
*/
- // TODO 2007-12-03, Tomasz Pylak review: should not we use the term organization as everywhere else instead of group?
+ // TODO 2007-12-03, Tomasz Pylak review: should not we use the term organization as everywhere else instead of
+ // group?
public final String getGroupCode()
{
return groupCode;
@@ -131,13 +132,15 @@ public class ExperimentIdentifier implements IStorable
@Override
public int hashCode()
{
- return (groupCode.hashCode() * 37 + projectCode.hashCode()) * 37 + experimentCode.hashCode();
+ return (groupCode.hashCode() * 37 + projectCode.hashCode()) * 37
+ + experimentCode.hashCode();
}
@Override
public String toString()
{
- return "[group:" + groupCode + ",project:" + projectCode + ",experiment:" + experimentCode + "]";
+ return "[group:" + groupCode + ",project:" + projectCode + ",experiment:" + experimentCode
+ + "]";
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
index eb56a34449c..930ef0eee2e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/ExperimentRegistratorDate.java
@@ -32,7 +32,8 @@ public final class ExperimentRegistratorDate implements IStorable
{
static final String FILE_NAME = "experiment_registration_date";
- private static final SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
+ private static final SimpleDateFormat DATE_FORMAT =
+ new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
static ExperimentRegistratorDate loadFrom(IDirectory directory)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Factory.java b/bds/source/java/ch/systemsx/cisd/bds/Factory.java
index cf7c5cdf25f..48b845ab923 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Factory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Factory.java
@@ -26,12 +26,13 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
/**
* General purpose factory for versioned classes with one-argument constructors.
- *
+ *
* @author Franz-Josef Elmer
*/
class Factory<T>
{
- private final Map<Version, Class<? extends T>> repository = new HashMap<Version, Class<? extends T>>();
+ private final Map<Version, Class<? extends T>> repository =
+ new HashMap<Version, Class<? extends T>>();
void register(Version version, Class<? extends T> clazz)
{
@@ -40,7 +41,7 @@ class Factory<T>
Class<? extends T> getClassFor(Version version)
{
-
+
Version v = version;
while (true)
{
@@ -63,22 +64,26 @@ class Factory<T>
Constructor<? extends T> constructor;
try
{
- constructor = clazz.getConstructor(new Class[] {argumentClass});
+ constructor = clazz.getConstructor(new Class[]
+ { argumentClass });
} catch (Exception ex1)
{
- throw new EnvironmentFailureException(clazz + " has no constructor with argument of type "
+ throw new EnvironmentFailureException(clazz
+ + " has no constructor with argument of type "
+ argumentClass.getCanonicalName());
}
try
{
- return constructor.newInstance(new Object[] {argument});
+ return constructor.newInstance(new Object[]
+ { argument });
} catch (InvocationTargetException ex)
{
- throw new DataStructureException("Couldn't create instance of " + clazz + " for version " + version, ex
- .getCause());
+ throw new DataStructureException("Couldn't create instance of " + clazz
+ + " for version " + version, ex.getCause());
} catch (Exception ex)
{
- throw new DataStructureException("Couldn't create instance of " + clazz + " for version " + version, ex);
+ throw new DataStructureException("Couldn't create instance of " + clazz
+ + " for version " + version, ex);
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Format.java b/bds/source/java/ch/systemsx/cisd/bds/Format.java
index 17319d4ab01..9491c02f8a4 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Format.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Format.java
@@ -214,7 +214,8 @@ public class Format implements IStorable
@Override
public int hashCode()
{
- return (code.hashCode() * 37 + version.hashCode()) * 37 + (variant == null ? 0 : variant.hashCode());
+ return (code.hashCode() * 37 + version.hashCode()) * 37
+ + (variant == null ? 0 : variant.hashCode());
}
@Override
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
index 49b4b9e7902..3736db3c4d9 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatParameters.java
@@ -30,7 +30,8 @@ import ch.systemsx.cisd.bds.storage.INode;
*/
final class FormatParameters implements IFormatParameters, IStorable
{
- private final Map<String, FormatParameter> parameters = new LinkedHashMap<String, FormatParameter>();
+ private final Map<String, FormatParameter> parameters =
+ new LinkedHashMap<String, FormatParameter>();
/**
* The <code>IFormatParameterFactory</code> implementation used here.
@@ -38,14 +39,16 @@ final class FormatParameters implements IFormatParameters, IStorable
* Initialized with the default implementation {@link IFormatParameterFactory#DEFAULT_FORMAT_PARAMETER_FACTORY}.
* </p>
*/
- private IFormatParameterFactory formatParameterFactory = IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY;
+ private IFormatParameterFactory formatParameterFactory =
+ IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY;
final void loadFrom(final IDirectory directory)
{
parameters.clear();
for (INode node : directory)
{
- final FormatParameter formatParameter = formatParameterFactory.createFormatParameter(node);
+ final FormatParameter formatParameter =
+ formatParameterFactory.createFormatParameter(node);
if (formatParameter != null)
{
addParameter(formatParameter);
@@ -90,7 +93,8 @@ final class FormatParameters implements IFormatParameters, IStorable
final String parameterName = parameter.getName();
if (containsParameter(parameterName))
{
- throw new IllegalArgumentException("There is already a parameter named '" + parameterName + "'.");
+ throw new IllegalArgumentException("There is already a parameter named '"
+ + parameterName + "'.");
}
parameters.put(parameterName, parameter);
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
index f3d1aed1ca9..bb64856c665 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormatStore.java
@@ -52,7 +52,8 @@ public final class FormatStore
}
/** Constructs an unique key for given <var>formatCode</var>, <var>version</var> and <var>variant</var>. */
- private final static String getKey(final String formatCode, final Version version, final String variant)
+ private final static String getKey(final String formatCode, final Version version,
+ final String variant)
{
String key = formatCode + version.toString();
if (variant != null)
@@ -65,8 +66,8 @@ public final class FormatStore
/**
* Returns corresponding <code>Format</code> for given format code, version and format variant.
*/
- public final static Format getFormat(final String formatCode, final Version version, final String formatVariant)
- throws DataStructureException
+ public final static Format getFormat(final String formatCode, final Version version,
+ final String formatVariant) throws DataStructureException
{
return formats.get(getKey(formatCode, version, formatVariant));
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
index a2a22c8ac53..6907f4c9e7b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataContext.java
@@ -32,7 +32,8 @@ public final class FormattedDataContext
private final IFormatParameters formatParameters;
- FormattedDataContext(final IDirectory dataDirectory, final Format format, final IFormatParameters formatParameters)
+ FormattedDataContext(final IDirectory dataDirectory, final Format format,
+ final IFormatParameters formatParameters)
{
assert dataDirectory != null : "Unspecified data directory.";
this.dataDirectory = dataDirectory;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
index 6fb42641ad8..7bb8120d707 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/FormattedDataFactory.java
@@ -45,7 +45,8 @@ public final class FormattedDataFactory
// This class cannot be instantiated.
}
- private final static void register(final Format format, final Class<? extends IFormattedData> clazz)
+ private final static void register(final Format format,
+ final Class<? extends IFormattedData> clazz)
{
String code = format.getCode();
Factory<IFormattedData> factory = factories.get(code);
@@ -58,22 +59,25 @@ public final class FormattedDataFactory
}
/** Uses this public method to create a new instance of <code>IFormattedData</code>. */
- public final static IFormattedData createFormattedData(final IDirectory dataDirectory, final Format format,
- final Format defaultFormatOrNull, final IFormatParameters formatParameters)
+ public final static IFormattedData createFormattedData(final IDirectory dataDirectory,
+ final Format format, final Format defaultFormatOrNull,
+ final IFormatParameters formatParameters)
{
final Format supportedFormat = getSupportedFormat(format, defaultFormatOrNull);
final Factory<IFormattedData> factory = factories.get(supportedFormat.getCode());
- final FormattedDataContext context = new FormattedDataContext(dataDirectory, supportedFormat, formatParameters);
+ final FormattedDataContext context =
+ new FormattedDataContext(dataDirectory, supportedFormat, formatParameters);
return factory.create(FormattedDataContext.class, context, format.getVersion());
}
- private final static Format getSupportedFormat(final Format format, final Format defaultFormatOrNull)
+ private final static Format getSupportedFormat(final Format format,
+ final Format defaultFormatOrNull)
{
assert format != null : "Unspecified format.";
final String code = format.getCode();
assert code != null : "Unspecified format code.";
assert format.getVersion() != null : "Unspecified version.";
-
+
final Factory<IFormattedData> factory = factories.get(code);
if (factory == null)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IAnnotations.java b/bds/source/java/ch/systemsx/cisd/bds/IAnnotations.java
index cc2b7f3e98c..b1be631e61a 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IAnnotations.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IAnnotations.java
@@ -19,8 +19,6 @@ package ch.systemsx.cisd.bds;
import ch.systemsx.cisd.bds.exception.DataStructureException;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public interface IAnnotations extends IStorable
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java b/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
index 4b1972452fa..66f283851f6 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IDataStructure.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.bds;
import ch.systemsx.cisd.bds.exception.DataStructureException;
-
/**
* Common interface of all data structures. Implementations of this interface provide methods to manipulate a data
* structure. These methods are specific for the version of the data structure. For each version there is a concrete
@@ -36,7 +35,7 @@ public interface IDataStructure extends IHasVersion
* Creates a new empty data structure.
*/
public void create();
-
+
/**
* Opens an existing data structure and validates it.
*
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
index cb17797d40f..603abe155fe 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IFormatParameterFactory.java
@@ -28,28 +28,31 @@ import ch.systemsx.cisd.bds.storage.INode;
public interface IFormatParameterFactory
{
- public final static IFormatParameterFactory DEFAULT_FORMAT_PARAMETER_FACTORY = new IFormatParameterFactory()
- {
+ public final static IFormatParameterFactory DEFAULT_FORMAT_PARAMETER_FACTORY =
+ new IFormatParameterFactory()
+ {
- //
- // IFormatParameterFactory
- //
+ //
+ // IFormatParameterFactory
+ //
- public final FormatParameter createFormatParameter(final INode node)
- {
- if (node instanceof IFile)
- {
- final IFile file = (IFile) node;
- return new FormatParameter(file.getName(), file.getStringContent().trim());
- }
- return null;
- }
+ public final FormatParameter createFormatParameter(final INode node)
+ {
+ if (node instanceof IFile)
+ {
+ final IFile file = (IFile) node;
+ return new FormatParameter(file.getName(), file.getStringContent()
+ .trim());
+ }
+ return null;
+ }
- public final FormatParameter createFormatParameter(final String name, final String value)
- {
- return new FormatParameter(name, value);
- }
- };
+ public final FormatParameter createFormatParameter(final String name,
+ final String value)
+ {
+ return new FormatParameter(name, value);
+ }
+ };
/**
* Creates a <code>FormatParameter</code> from given <var>node</var>.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IFormattedData.java b/bds/source/java/ch/systemsx/cisd/bds/IFormattedData.java
index 87806c27167..6503067379b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IFormattedData.java
@@ -16,10 +16,9 @@
package ch.systemsx.cisd.bds;
-
/**
* Interface common for all classes handling formatted data.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IFormattedData
@@ -28,7 +27,7 @@ public interface IFormattedData
* Returns the format of data.
*/
public Format getFormat();
-
+
/**
* Returns the parameters of the data format.
*/
diff --git a/bds/source/java/ch/systemsx/cisd/bds/IHasVersion.java b/bds/source/java/ch/systemsx/cisd/bds/IHasVersion.java
index de266518297..e3f15a0ebc1 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/IHasVersion.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/IHasVersion.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.bds;
/**
* Role to be having a {@link Version}.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IHasVersion
diff --git a/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java b/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
index eb8faa09d15..2e6850cec6f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/MeasurementEntity.java
@@ -105,7 +105,8 @@ public final class MeasurementEntity implements IStorable
return false;
}
MeasurementEntity entity = (MeasurementEntity) obj;
- return entity.entityTypeDescription.equals(entityTypeDescription) && entity.entityCode.equals(entityCode);
+ return entity.entityTypeDescription.equals(entityTypeDescription)
+ && entity.entityCode.equals(entityCode);
}
@Override
diff --git a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
index 3f9a4e7be76..5fca7a2bc7e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/UnknownFormatV1_0.java
@@ -18,12 +18,13 @@ package ch.systemsx.cisd.bds;
/**
* Unknown Format V1.0.
- *
+ *
* @author Franz-Josef Elmer
*/
public final class UnknownFormatV1_0 extends Format
{
public static final String FORMAT_CODE = "UNKNOWN";
+
/**
* The one and only one instance.
*/
@@ -34,5 +35,4 @@ public final class UnknownFormatV1_0 extends Format
super(FORMAT_CODE, new Version(1, 0), null);
}
-
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
index beda0d1501b..cba6cc60b49 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Utilities.java
@@ -49,8 +49,8 @@ public class Utilities
{
return (IDirectory) node;
}
- throw new DataStructureException("There is already a node named '" + name + "' but which isn't a directory ("
- + node + ").");
+ throw new DataStructureException("There is already a node named '" + name
+ + "' but which isn't a directory (" + node + ").");
}
/**
@@ -66,8 +66,8 @@ public class Utilities
INode node = directory.tryGetNode(name);
if (node == null)
{
- throw new DataStructureException(String.format("No directory named '%s' found in directory '%s'.", name,
- directory));
+ throw new DataStructureException(String.format(
+ "No directory named '%s' found in directory '%s'.", name, directory));
}
if (node instanceof IDirectory == false)
{
@@ -142,14 +142,16 @@ public class Utilities
return Integer.parseInt(value);
} catch (NumberFormatException ex)
{
- throw new DataStructureException("Value of '" + name + "' version file is not a number: " + value);
+ throw new DataStructureException("Value of '" + name
+ + "' version file is not a number: " + value);
}
}
/**
* Recursively lists nodes in given <var>directory</var>.
*/
- public final static List<String> listNodes(final IDirectory diretory, final INodeFilter nodeFilterOrNull)
+ public final static List<String> listNodes(final IDirectory diretory,
+ final INodeFilter nodeFilterOrNull)
{
assert diretory != null : "Given node can not be null.";
final INodeFilter nodeFilter;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/Version.java b/bds/source/java/ch/systemsx/cisd/bds/Version.java
index 80c19700b43..93527193708 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/Version.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/Version.java
@@ -38,7 +38,8 @@ public final class Version implements IStorable
static Version loadFrom(IDirectory directory)
{
IDirectory versionFolder = Utilities.getSubDirectory(directory, VERSION);
- return new Version(Utilities.getNumber(versionFolder, MAJOR), Utilities.getNumber(versionFolder, MINOR));
+ return new Version(Utilities.getNumber(versionFolder, MAJOR), Utilities.getNumber(
+ versionFolder, MINOR));
}
/**
diff --git a/bds/source/java/ch/systemsx/cisd/bds/exception/DataStructureException.java b/bds/source/java/ch/systemsx/cisd/bds/exception/DataStructureException.java
index ee81cc3c8aa..32e8798364b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/exception/DataStructureException.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/exception/DataStructureException.java
@@ -16,18 +16,17 @@
package ch.systemsx.cisd.bds.exception;
-
/**
* Exception thrown by manipulations of BDS data structures which can not be classified as {@link StorageException}.
- *
+ *
* @author Franz-Josef Elmer
*/
public class DataStructureException extends RuntimeException
{
private static final long serialVersionUID = 1L;
-
+
/**
- * Creates an instance with the specified message.
+ * Creates an instance with the specified message.
*/
public DataStructureException(String message)
{
diff --git a/bds/source/java/ch/systemsx/cisd/bds/handler/ChecksumHandler.java b/bds/source/java/ch/systemsx/cisd/bds/handler/ChecksumHandler.java
index fc97d6c8fe6..6c2a970874c 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/handler/ChecksumHandler.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/handler/ChecksumHandler.java
@@ -55,7 +55,8 @@ public final class ChecksumHandler implements IDataStructureHandler
private final IDirectory originalDataDirectory;
- public ChecksumHandler(final IDirectory checksumDirectory, final IDirectory originalDataDirectory)
+ public ChecksumHandler(final IDirectory checksumDirectory,
+ final IDirectory originalDataDirectory)
{
this.checksumDirectory = checksumDirectory;
this.originalDataDirectory = originalDataDirectory;
@@ -70,7 +71,8 @@ public final class ChecksumHandler implements IDataStructureHandler
return checksums;
}
- private void addChecksums(final List<Checksum> checksums, final String nodePath, final IDirectory directory)
+ private void addChecksums(final List<Checksum> checksums, final String nodePath,
+ final IDirectory directory)
{
final List<INode> children = new ArrayList<INode>();
for (final INode child : directory)
@@ -84,21 +86,26 @@ public final class ChecksumHandler implements IDataStructureHandler
}
}
- private final void addChecksum(final List<Checksum> checksums, final String path, final INode node)
+ private final void addChecksum(final List<Checksum> checksums, final String path,
+ final INode node)
{
- final String nodePath = (path == null ? "" : path + Constants.PATH_SEPARATOR) + node.getName();
+ final String nodePath =
+ (path == null ? "" : path + Constants.PATH_SEPARATOR) + node.getName();
if (node instanceof IFile)
{
IFile file = (IFile) node;
final InputStream inputStream = file.getInputStream();
try
{
- final Checksum checksum = new Checksum(checksumCalculator.calculateChecksum(inputStream), nodePath);
- assert checksums.contains(checksum) == false : String.format("Checksum '%s' is not unique.", checksum);
+ final Checksum checksum =
+ new Checksum(checksumCalculator.calculateChecksum(inputStream), nodePath);
+ assert checksums.contains(checksum) == false : String.format(
+ "Checksum '%s' is not unique.", checksum);
checksums.add(checksum);
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't calculate checksum for file '" + nodePath + "'");
+ throw new EnvironmentFailureException("Couldn't calculate checksum for file '"
+ + nodePath + "'");
} finally
{
IOUtils.closeQuietly(inputStream);
@@ -123,14 +130,16 @@ public final class ChecksumHandler implements IDataStructureHandler
final Checksum checkum = CHECKSUM_CONVERTER.fromString(value);
if (actual.remove(checkum) == false)
{
- throw new DataStructureException(String.format("Given checksum '%s' not found in directory '%s'",
- checkum, originalDataDirectory));
+ throw new DataStructureException(String.format(
+ "Given checksum '%s' not found in directory '%s'", checkum,
+ originalDataDirectory));
}
}
if (actual.size() > 0)
{
throw new DataStructureException(String.format(
- "Following checksums '%s' are not present in the checksum file '%s'.", actual, checksumFile));
+ "Following checksums '%s' are not present in the checksum file '%s'.", actual,
+ checksumFile));
}
}
@@ -199,7 +208,8 @@ public final class ChecksumHandler implements IDataStructureHandler
}
}
- final static class ChecksumConverter implements IToStringConverter<Checksum>, IFromStringConverter<Checksum>
+ final static class ChecksumConverter implements IToStringConverter<Checksum>,
+ IFromStringConverter<Checksum>
{
private static final String SEPARATOR = " ";
diff --git a/bds/source/java/ch/systemsx/cisd/bds/handler/MD5ChecksumCalculator.java b/bds/source/java/ch/systemsx/cisd/bds/handler/MD5ChecksumCalculator.java
index d03f7a0687a..c0316b50675 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/handler/MD5ChecksumCalculator.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/handler/MD5ChecksumCalculator.java
@@ -22,7 +22,6 @@ import java.io.InputStream;
import com.twmacinta.util.MD5;
import com.twmacinta.util.MD5InputStream;
-
/**
* A {@link IChecksumCalculator} implementation based on <i>MD5</i>.
*
diff --git a/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java b/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
index 19fbacdb9b1..55edb31a332 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/handler/MappingFileHandler.java
@@ -89,7 +89,8 @@ public final class MappingFileHandler implements IDataStructureHandler
assert reference != null : "Unspecified reference.";
if (references.contains(reference))
{
- throw new DataStructureException("There is already a reference for file '" + reference + "'.");
+ throw new DataStructureException("There is already a reference for file '" + reference
+ + "'.");
}
references.add(reference);
}
@@ -104,17 +105,18 @@ public final class MappingFileHandler implements IDataStructureHandler
int i1 = referenceDefinition.indexOf('\t');
if (i1 < 0)
{
- throw new DataStructureException("Error in standard-original mapping line " + (i + 1)
- + ": missing first tab character: " + referenceDefinition);
+ throw new DataStructureException("Error in standard-original mapping line "
+ + (i + 1) + ": missing first tab character: " + referenceDefinition);
}
String path = referenceDefinition.substring(0, i1);
int i2 = referenceDefinition.indexOf('\t', i1 + 1);
if (i2 < 0)
{
- throw new DataStructureException("Error in standard-original mapping line " + (i + 1)
- + ": missing second tab character: " + referenceDefinition);
+ throw new DataStructureException("Error in standard-original mapping line "
+ + (i + 1) + ": missing second tab character: " + referenceDefinition);
}
- final ReferenceType type = ReferenceType.resolveByShortName(referenceDefinition.substring(i1 + 1, i2));
+ final ReferenceType type =
+ ReferenceType.resolveByShortName(referenceDefinition.substring(i1 + 1, i2));
references.add(new Reference(path, referenceDefinition.substring(i2 + 1), type));
}
}
@@ -143,7 +145,8 @@ public final class MappingFileHandler implements IDataStructureHandler
final String originalPath = reference.getOriginalPath();
if (originalPathRoot.tryGetNode(originalPath) == null)
{
- throw new DataStructureException(String.format(errMsg, originalPath, originalPathRoot));
+ throw new DataStructureException(String.format(errMsg, originalPath,
+ originalPathRoot));
}
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
index f2c619e5eae..9ac28dd7110 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Channel.java
@@ -71,7 +71,8 @@ public final class Channel implements IStorable
return Integer.parseInt(name.substring(CHANNEL.length()));
} catch (NumberFormatException ex)
{
- throw new DataStructureException(String.format("Could not parse the channel number in '%s'", name), ex);
+ throw new DataStructureException(String.format(
+ "Could not parse the channel number in '%s'", name), ex);
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
index 3028c701aa3..055086ae98f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/ChannelList.java
@@ -49,7 +49,8 @@ public final class ChannelList implements IStorable, Iterable<Channel>
assert channels != null && channels.size() > 0 : "At least one channel must be specified.";
if (new HashSet<Channel>(channels).size() != channels.size())
{
- throw new DataStructureException(String.format("Some duplicate channels in '%s'.", channels));
+ throw new DataStructureException(String.format("Some duplicate channels in '%s'.",
+ channels));
}
this.channels = channels;
}
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 66b4518da5e..d5cd23201ec 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/FormatParameterFactory.java
@@ -99,6 +99,7 @@ public final class FormatParameterFactory implements IFormatParameterFactory
{
return new FormatParameter(name, Boolean.valueOf(value));
}
- return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(name, value);
+ return IFormatParameterFactory.DEFAULT_FORMAT_PARAMETER_FACTORY.createFormatParameter(name,
+ value);
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
index 27c5c82365b..0fec2afd36d 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Geometry.java
@@ -108,7 +108,8 @@ public class Geometry implements IStorable
assert directory != null : "Given directory can not be null.";
assert directory.getName().startsWith(geometryDirectoryName) : "Given directory name must start with given '"
+ geometryDirectoryName + "'.";
- return new Geometry(Utilities.getNumber(directory, ROWS), Utilities.getNumber(directory, COLUMNS));
+ return new Geometry(Utilities.getNumber(directory, ROWS), Utilities.getNumber(directory,
+ COLUMNS));
}
//
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
index 98fb9e12798..bfa82a9f1af 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageAnnotations.java
@@ -31,19 +31,18 @@ import ch.systemsx.cisd.bds.exception.DataStructureException;
import ch.systemsx.cisd.bds.storage.IDirectory;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class HCSImageAnnotations implements IAnnotations
{
private static final Set<Format> FORMATS =
- Collections.unmodifiableSet(new HashSet<Format>(Arrays.asList(HCSImageFormatV1_0.HCS_IMAGE_1_0)));
-
+ Collections.unmodifiableSet(new HashSet<Format>(Arrays
+ .asList(HCSImageFormatV1_0.HCS_IMAGE_1_0)));
+
private String deviceID;
-
+
private List<Channel> channels = new ArrayList<Channel>();
-
+
public void addChannels(Iterable<Channel> channelIterable)
{
for (Channel channel : channelIterable)
@@ -51,12 +50,12 @@ public class HCSImageAnnotations implements IAnnotations
addChannel(channel);
}
}
-
+
public void addChannel(Channel channel)
{
channels.add(channel);
}
-
+
public List<Channel> getChannels()
{
return Collections.unmodifiableList(channels);
@@ -77,8 +76,8 @@ public class HCSImageAnnotations implements IAnnotations
Format format = formattedData.getFormat();
if (FORMATS.contains(format) == false)
{
- throw new DataStructureException("One of the following formats expected instead of '" + format + "': "
- + FORMATS);
+ throw new DataStructureException("One of the following formats expected instead of '"
+ + format + "': " + FORMATS);
}
// TODO 2008-01-15, Franz-Josef Elmer also checks number of channels
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
index c938138ad32..2449990cc8e 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormatV1_0.java
@@ -50,8 +50,8 @@ public final class HCSImageFormatV1_0 extends Format
*/
private final static String[] FORMAT_PARAMETERS =
new String[]
- { PlateGeometry.PLATE_GEOMETRY, WellGeometry.WELL_GEOMETRY, ChannelList.NUMBER_OF_CHANNELS,
- CONTAINS_ORIGINAL_DATA };
+ { PlateGeometry.PLATE_GEOMETRY, WellGeometry.WELL_GEOMETRY,
+ ChannelList.NUMBER_OF_CHANNELS, CONTAINS_ORIGINAL_DATA };
/**
* The one and only one instance.
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 d15d52437c1..ac48fa1058f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedData.java
@@ -39,7 +39,8 @@ import ch.systemsx.cisd.bds.storage.INode;
*
* @author Christian Ribeaud
*/
-public final class HCSImageFormattedData extends AbstractFormattedData implements IHCSImageFormattedData
+public final class HCSImageFormattedData extends AbstractFormattedData implements
+ IHCSImageFormattedData
{
/** The <i>column</i> (or <i>x</i>) coordinate. */
@@ -82,8 +83,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
{
if (geometry.contains(location) == false)
{
- throw new IllegalArgumentException(String.format("Given geometry '%s' does not contain location '%s'",
- geometry, location));
+ throw new IllegalArgumentException(String.format(
+ "Given geometry '%s' does not contain location '%s'", geometry, location));
}
}
@@ -92,12 +93,14 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
{
if (channel < 1)
{
- throw new IndexOutOfBoundsException(String.format("Channel index must start at 1 (given value is %d).", channel));
+ throw new IndexOutOfBoundsException(String.format(
+ "Channel index must start at 1 (given value is %d).", channel));
}
final int channelCount = getChannelCount();
if (channel > channelCount)
{
- throw new IndexOutOfBoundsException(String.format("Channel index %d exceeds the number of channels %d", channel, channelCount));
+ throw new IndexOutOfBoundsException(String.format(
+ "Channel index %d exceeds the number of channels %d", channel, channelCount));
}
}
@@ -133,7 +136,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
return Channel.CHANNEL + channel;
}
- private void checkCoordinates(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.";
@@ -155,7 +159,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
if (imageRootNode == null)
{
throw new DataStructureException(String.format(
- "No image root directory named '%s' could be found in the original directory.", imageRootDirName));
+ "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;
@@ -165,15 +170,19 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
// IHCSFormattedData
//
- public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation)
+ public final INode tryGetStandardNodeAt(final int channel, final Location plateLocation,
+ final Location wellLocation)
{
checkCoordinates(channel, plateLocation, wellLocation);
try
{
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));
+ 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)
{
@@ -181,21 +190,26 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
}
}
- public final NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath,
- final 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)
{
- throw new DataStructureException(String.format(
- "A node already exists at channel %d, plate location '%s' and well location '%s'.", channel,
- plateLocation, wellLocation));
+ throw new DataStructureException(
+ String
+ .format(
+ "A node already exists at channel %d, plate location '%s' and well location '%s'.",
+ channel, plateLocation, wellLocation));
}
final IDirectory standardDir = getStandardDataDirectory();
- final IDirectory channelDir = Utilities.getOrCreateSubDirectory(standardDir, getChannelName(channel));
- final IDirectory plateRowDir = Utilities.getOrCreateSubDirectory(channelDir, getPlateRowDirName(plateLocation));
+ 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);
@@ -206,13 +220,16 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
if (imageNode == null)
{
throw new DataStructureException(String.format(
- "No image node with path '%s' could be found in the original directory.", imageRelativePath));
+ "No image node with path '%s' could be found in the original directory.",
+ imageRelativePath));
}
node = plateColumnDir.tryAddLink(wellFileName, imageNode);
} else
{
// Copies the file. So we are able to undo the operation.
- node = plateColumnDir.addFile(new File(imageRootDirectory, imageRelativePath), wellFileName, false);
+ node =
+ plateColumnDir.addFile(new File(imageRootDirectory, imageRelativePath),
+ wellFileName, false);
}
if (node == null)
{
@@ -224,8 +241,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
}
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);
}
@@ -254,7 +271,8 @@ public final class HCSImageFormattedData extends AbstractFormattedData implement
if (notPresent.isEmpty() == false)
{
throw new DataStructureException(String.format(
- "Following format parameters '%s' could not be found in the structure.", notPresent));
+ "Following format parameters '%s' could not be found in the structure.",
+ notPresent));
}
}
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 3af684d35e5..398d5216dc5 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/IHCSImageFormattedData.java
@@ -39,7 +39,8 @@ public interface IHCSImageFormattedData extends IFormattedData
* @return this could be, for instance, a {@link ILink} pointing to the <code>data/original</code> directory or a
* {@link IFile} that can be extracted somewhere. Might return <code>null</code>.
*/
- public INode tryGetStandardNodeAt(final int channel, final Location plateLocation, final Location wellLocation);
+ public INode tryGetStandardNodeAt(final int channel, final Location plateLocation,
+ final Location wellLocation);
/**
* Adds a new image file at given coordinates.
@@ -52,8 +53,9 @@ public interface IHCSImageFormattedData extends IFormattedData
* in the <code>standard</code> directory. Never returns <code>null</code>.
* @throws DataStructureException if a node already exists at given coordinates.
*/
- public NodePath addStandardNode(final File imageRootDirectory, final String imageRelativePath, 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/source/java/ch/systemsx/cisd/bds/hcs/Location.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
index 648248d1593..564ac25ea18 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
@@ -51,7 +51,8 @@ public final class Location
*
* @return <code>null</code> if position is out of range.
*/
- public static final Location tryCreateLocationFromPosition(final int position, final Geometry geometry)
+ public static final Location tryCreateLocationFromPosition(final int position,
+ final Geometry geometry)
{
assert geometry != null : "Given geometry can not be null.";
final int columns = geometry.getColumns();
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 e9eaa7fae97..4deac1f415b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IDirectory.java
@@ -44,7 +44,8 @@ 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 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.
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java b/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java
index ee0f5074e9a..9ff767dbe8c 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/ILink.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.bds.storage;
/**
* Node representing a symbolic link.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface ILink extends INode
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
index 841eae10582..249bf935f22 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/IStorage.java
@@ -18,10 +18,9 @@ package ch.systemsx.cisd.bds.storage;
import ch.systemsx.cisd.bds.exception.StorageException;
-
/**
* Abstraction of a hierarchical storage.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IStorage
@@ -30,14 +29,14 @@ public interface IStorage
* Mounts this storage. May perform some initializations. Should be called before calling {@link #getRoot()}.
*/
public void mount();
-
+
/**
- * Returns root directory of this storage.
+ * Returns root directory of this storage.
*
* @throws StorageException if invoked before {@link #mount()} or after {@link #unmount()}.
*/
public IDirectory getRoot();
-
+
/**
* Unmounts this storage. May perform some finalization (e.g. make cached data persistent).
*/
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java b/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
index 966673912ec..4232d9e3f5f 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/NodeFilters.java
@@ -46,7 +46,8 @@ public final class NodeFilters
/**
* Creates filter nodes based on the extension (what the filename ends with).
*/
- public final static INodeFilter createExtensionNodeFilter(final boolean ignoreCase, final String... extensions)
+ public final static INodeFilter createExtensionNodeFilter(final boolean ignoreCase,
+ final String... extensions)
{
assert extensions != null : "Given extensions can not be null.";
return new SuffixNodeFilter(ignoreCase, toSuffixes(extensions));
@@ -103,12 +104,12 @@ public final class NodeFilters
{
if (ignoreCase)
{
- return s.toLowerCase();
+ return s.toLowerCase();
} else
{
return s;
}
}
}
-
+
}
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 87091b93a08..c79cf19f0ec 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
@@ -30,8 +30,8 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
*/
abstract class AbstractNode implements INode
{
- protected final static File moveFileToDirectory(final File source, final File directory, final String nameOrNull)
- throws EnvironmentFailureException
+ protected final static File moveFileToDirectory(final File source, final File directory,
+ final String nameOrNull) throws EnvironmentFailureException
{
assert source != null;
assert directory != null && directory.isDirectory();
@@ -49,8 +49,9 @@ 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());
}
}
return destination;
@@ -72,7 +73,8 @@ abstract class AbstractNode implements INode
}
if (file.exists() == false)
{
- throw new StorageException(String.format("Non existing file '%s'.", file.getAbsolutePath()));
+ throw new StorageException(String.format("Non existing file '%s'.", file
+ .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 791543b517d..50fb5acf7fc 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
@@ -43,7 +43,8 @@ final class Directory extends AbstractNode implements IDirectory
super(directory);
if (directory.isDirectory() == false)
{
- throw new StorageException(String.format("Not a directory '%s'.", directory.getAbsolutePath()));
+ throw new StorageException(String.format("Not a directory '%s'.", directory
+ .getAbsolutePath()));
}
}
@@ -90,15 +91,16 @@ final class Directory extends AbstractNode implements IDirectory
{
if (dir.isDirectory() == false)
{
- throw new StorageException("There already exists a file named '" + name + "' in directory " + this);
+ throw new StorageException("There already exists a file named '" + name
+ + "' in directory " + this);
}
return new Directory(dir);
}
boolean successful = dir.mkdir();
if (successful == false)
{
- throw new EnvironmentFailureException("Couldn't create directory " + dir.getAbsolutePath()
- + " for some unknown reason.");
+ throw new EnvironmentFailureException("Couldn't create directory "
+ + dir.getAbsolutePath() + " for some unknown reason.");
}
return new Directory(dir);
}
@@ -140,8 +142,9 @@ final class Directory extends AbstractNode implements IDirectory
}
} catch (IOException ex)
{
- throw EnvironmentFailureException.fromTemplate(ex, "Couldn't not copy file '%s' to directory '%s'.",
- file, nodeFile.getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate(ex,
+ "Couldn't not copy file '%s' to directory '%s'.", file, nodeFile
+ .getAbsolutePath());
}
}
return NodeFactory.createNode(newFile);
@@ -152,7 +155,8 @@ final class Directory extends AbstractNode implements IDirectory
assert node != null : "Node can not be null.";
assert name != null : "Name can not be null.";
final java.io.File file = getNodeFile(node);
- final java.io.File fileLink = LinkMakerProvider.getLinkMaker().tryCopy(file, nodeFile, name);
+ final java.io.File fileLink =
+ LinkMakerProvider.getLinkMaker().tryCopy(file, nodeFile, name);
if (fileLink != null)
{
final Link link = (Link) NodeFactory.createLinkNode(name, file);
@@ -200,8 +204,9 @@ final class Directory extends AbstractNode implements IDirectory
FileUtils.copyDirectoryToDirectory(nodeFile, directory);
} catch (IOException ex)
{
- throw EnvironmentFailureException.fromTemplate(ex, "Couldn't copy directory '%s' to directory '%s'.",
- nodeFile.getAbsolutePath(), directory.getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate(ex,
+ "Couldn't copy directory '%s' to directory '%s'.", nodeFile.getAbsolutePath(),
+ directory.getAbsolutePath());
}
}
@@ -213,14 +218,15 @@ final class Directory extends AbstractNode implements IDirectory
{
if (FileUtilities.deleteRecursively(file, null) == false)
{
- throw EnvironmentFailureException.fromTemplate("Couldn't remove directory '%s'.", file
- .getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate("Couldn't remove directory '%s'.",
+ file.getAbsolutePath());
}
} else if (file.isFile())
{
if (file.delete() == false)
{
- throw EnvironmentFailureException.fromTemplate("Couldn't remove file '%s'.", file.getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate("Couldn't remove file '%s'.", file
+ .getAbsolutePath());
}
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
index 7f9b7aa7601..8bde99e3f57 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/File.java
@@ -54,7 +54,8 @@ final class File extends AbstractNode implements IFile
return IOUtils.toByteArray(inputStream);
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't get data from file " + nodeFile.getAbsolutePath(), ex);
+ throw new EnvironmentFailureException("Couldn't get data from file "
+ + nodeFile.getAbsolutePath(), ex);
} finally
{
IOUtils.closeQuietly(inputStream);
@@ -68,7 +69,8 @@ final class File extends AbstractNode implements IFile
return new FileInputStream(nodeFile);
} catch (FileNotFoundException ex)
{
- throw new EnvironmentFailureException("Couldn't open input stream for file " + nodeFile.getAbsolutePath());
+ throw new EnvironmentFailureException("Couldn't open input stream for file "
+ + nodeFile.getAbsolutePath());
}
}
@@ -90,8 +92,9 @@ final class File extends AbstractNode implements IFile
FileUtils.copyFileToDirectory(nodeFile, directory);
} catch (IOException ex)
{
- throw EnvironmentFailureException.fromTemplate(ex, "Couldn't not copy file '%s' to directory '%s'.",
- nodeFile.getAbsolutePath(), directory.getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate(ex,
+ "Couldn't not copy file '%s' to directory '%s'.", nodeFile.getAbsolutePath(),
+ directory.getAbsolutePath());
}
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
index 52c97f329e3..09ff0a5e842 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/FileStorage.java
@@ -24,13 +24,13 @@ import ch.systemsx.cisd.bds.storage.IStorage;
/**
* Implementation of {@link IStorage} based on the file system.
- *
+ *
* @author Franz-Josef Elmer
*/
public class FileStorage implements IStorage
{
private final Directory root;
-
+
private boolean mounted;
/**
@@ -42,7 +42,7 @@ public class FileStorage implements IStorage
{
root = new Directory(folder);
}
-
+
public IDirectory getRoot()
{
if (mounted == false)
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
index e44ee8283c0..b632c04ae7b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/Link.java
@@ -40,7 +40,8 @@ final class Link implements ILink
{
assert name != null : "A name must be specified.";
assert reference != null : "Reference can not be null.";
- assert reference instanceof IFile : "Given reference must be of type IFile: " + reference.getClass().getName();
+ assert reference instanceof IFile : "Given reference must be of type IFile: "
+ + reference.getClass().getName();
assert reference.isValid() : "Given reference must be valid: " + reference;
this.name = name;
this.reference = reference;
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
index cac88fa1ff0..293fabd241b 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactory.java
@@ -67,8 +67,8 @@ public final class NodeFactory
return file.getCanonicalPath();
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't get canonical path of file '" + file.getAbsolutePath()
- + "'", ex);
+ throw new EnvironmentFailureException("Couldn't get canonical path of file '"
+ + file.getAbsolutePath() + "'", ex);
}
}
@@ -89,12 +89,14 @@ public final class NodeFactory
* This only works for <i>symbolic</i> links and not for <i>hard</i> links.
* </p>
*/
- public final static ILink createLinkNode(final java.io.File file) throws EnvironmentFailureException
+ public final static ILink createLinkNode(final java.io.File file)
+ throws EnvironmentFailureException
{
final String canonicalPath = getCanonicalPath(file);
final String absolutePath = file.getAbsolutePath();
assert absolutePath.equals(canonicalPath) == false : String.format(
- "Given file must be a link [absolute=%s,canonical=%s].", absolutePath, canonicalPath);
+ "Given file must be a link [absolute=%s,canonical=%s].", absolutePath,
+ canonicalPath);
return new Link(file.getName(), createNode(new java.io.File(canonicalPath)));
}
diff --git a/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java b/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java
index 6a2a29b8444..d560cc27357 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/storage/hdf5/HDF5Storage.java
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.common.exceptions.NotImplementedException;
/**
* Storage based on HDF5.
- *
+ *
* @author Franz-Josef Elmer
*/
public class HDF5Storage implements IStorage
@@ -33,7 +33,7 @@ public class HDF5Storage implements IStorage
{
assert hdf5File != null : "Unspecified HDF5 file.";
}
-
+
public IDirectory getRoot()
{
throw new NotImplementedException();
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
index 84890cef0b9..3a1d488ac42 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureFactoryTest.java
@@ -48,8 +48,10 @@ public class DataStructureFactoryTest
@Test
public void testGetDataStructureClassFor()
{
- assertEquals(DataStructureV1_0.class, DataStructureFactory.getDataStructureClassFor(new Version(1, 0)));
- assertEquals(DataStructureV1_0.class, DataStructureFactory.getDataStructureClassFor(new Version(1, 1)));
+ assertEquals(DataStructureV1_0.class, DataStructureFactory
+ .getDataStructureClassFor(new Version(1, 0)));
+ assertEquals(DataStructureV1_0.class, DataStructureFactory
+ .getDataStructureClassFor(new Version(1, 1)));
}
@Test
@@ -76,7 +78,8 @@ public class DataStructureFactoryTest
}
});
- IDataStructure dataStructure = DataStructureFactory.createDataStructure(storage, new Version(1, 0));
+ IDataStructure dataStructure =
+ DataStructureFactory.createDataStructure(storage, new Version(1, 0));
assertEquals(DataStructureV1_0.class, dataStructure.getClass());
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
index 5212ea8a796..d22ac7c21b1 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureLoaderTest.java
@@ -45,7 +45,8 @@ public final class DataStructureLoaderTest extends AbstractFileSystemTestCase
dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(experimentIdentifier);
- ExperimentRegistrator experimentRegistrator = new ExperimentRegistrator("john", "doe", "j@doe");
+ ExperimentRegistrator experimentRegistrator =
+ new ExperimentRegistrator("john", "doe", "j@doe");
dataStructure.setExperimentRegistrator(experimentRegistrator);
dataStructure.setExperimentRegistrationDate(new ExperimentRegistratorDate(new Date(0)));
dataStructure.setMeasurementEntity(new MeasurementEntity("a", "b"));
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
index 9f347c32fec..87a0b7916b1 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/DataStructureTestV1_0.java
@@ -97,7 +97,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
- assertEquals("Couldn't create formatted data because of unspecified format.", e.getMessage());
+ assertEquals("Couldn't create formatted data because of unspecified format.", e
+ .getMessage());
}
}
@@ -108,7 +109,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- assertEquals("COMPUTED_DATA\n", Utilities.getString(metaData, ProcessingType.PROCESSING_TYPE));
+ assertEquals("COMPUTED_DATA\n", Utilities.getString(metaData,
+ ProcessingType.PROCESSING_TYPE));
}
@Test
@@ -119,7 +121,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
dataStructure.setProcessingType(ProcessingType.COMPUTED_DATA);
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- assertEquals("COMPUTED_DATA\n", Utilities.getString(metaData, ProcessingType.PROCESSING_TYPE));
+ assertEquals("COMPUTED_DATA\n", Utilities.getString(metaData,
+ ProcessingType.PROCESSING_TYPE));
}
@Test
@@ -355,10 +358,12 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
dataStructure.setFormat(UnknownFormatV1_0.UNKNOWN_1_0);
ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier("g", "p", "e");
dataStructure.setExperimentIdentifier(experimentIdentifier);
- ExperimentRegistratorDate experimentRegistratorDate = new ExperimentRegistratorDate(new Date(4711L * 4711000L));
+ ExperimentRegistratorDate experimentRegistratorDate =
+ new ExperimentRegistratorDate(new Date(4711L * 4711000L));
System.out.println(experimentRegistratorDate);
dataStructure.setExperimentRegistrationDate(experimentRegistratorDate);
- ExperimentRegistrator experimentRegistrator = new ExperimentRegistrator("john", "doe", "j@doe");
+ ExperimentRegistrator experimentRegistrator =
+ new ExperimentRegistrator("john", "doe", "j@doe");
dataStructure.setExperimentRegistrator(experimentRegistrator);
MeasurementEntity measurementEntity = new MeasurementEntity("cp001", "plate");
dataStructure.setMeasurementEntity(measurementEntity);
@@ -384,7 +389,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
reloadedDataStructure.open();
assertEquals("42\n", Utilities.getString(reloadedDataStructure.getOriginalData(), "answer"));
assertEquals(experimentIdentifier, reloadedDataStructure.getExperimentIdentifier());
- assertEquals(experimentRegistratorDate, reloadedDataStructure.getExperimentRegistratorDate());
+ assertEquals(experimentRegistratorDate, reloadedDataStructure
+ .getExperimentRegistratorDate());
assertEquals(experimentRegistrator, reloadedDataStructure.getExperimentRegistrator());
assertEquals(measurementEntity, reloadedDataStructure.getMeasurementEntity());
assertEquals(ProcessingType.RAW_DATA, reloadedDataStructure.getProcessingType());
@@ -393,8 +399,10 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
checkFormattedData(reloadedDataStructure.getFormattedData());
IDirectory metaDataDir = Utilities.getSubDirectory(root, DIR_METADATA);
- IDirectory checksumDir = Utilities.getSubDirectory(metaDataDir, ChecksumHandler.CHECKSUM_DIRECTORY);
- assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n" + "d41d8cd98f00b204e9800998ecf8427e origFile1\n"
+ IDirectory checksumDir =
+ Utilities.getSubDirectory(metaDataDir, ChecksumHandler.CHECKSUM_DIRECTORY);
+ assertEquals("a1d0c6e83f027327d8461063f4ac58a6 answer\n"
+ + "d41d8cd98f00b204e9800998ecf8427e origFile1\n"
+ "d41d8cd98f00b204e9800998ecf8427e origFile2\n", Utilities.getString(checksumDir,
DataStructureV1_0.DIR_ORIGINAL));
}
@@ -468,8 +476,9 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
fail("DataStructureException expected.");
} catch (DataStructureException e)
{
- assertEquals("Version of loaded data structure is V2.0 which is not backward compatible with V1.0", e
- .getMessage());
+ assertEquals(
+ "Version of loaded data structure is V2.0 which is not backward compatible with V1.0",
+ e.getMessage());
}
}
@@ -480,7 +489,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
storage.mount();
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(1, 1), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(1, 1), null)
+ .saveTo(metaData);
storage.unmount();
dataStructure.open();
assertEquals(UnknownFormatV1_0.UNKNOWN_1_0, dataStructure.getFormattedData().getFormat());
@@ -493,7 +503,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
storage.mount();
IDirectory root = storage.getRoot();
IDirectory metaData = Utilities.getSubDirectory(root, DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null)
+ .saveTo(metaData);
storage.unmount();
dataStructure.open();
try
@@ -533,7 +544,8 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
IDirectory originalDataDir = data.makeDirectory(DataStructureV1_0.DIR_ORIGINAL);
originalDataDir.addKeyValuePair("file1", "This is my first file.");
IDirectory metaData = root.makeDirectory(DataStructureV1_0.DIR_METADATA);
- new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null).saveTo(metaData);
+ new Format(UnknownFormatV1_0.UNKNOWN_1_0.getCode(), new Version(2, 0), null)
+ .saveTo(metaData);
new ExperimentIdentifier("g", "p", "e").saveTo(metaData);
new ExperimentRegistratorDate(new Date(0)).saveTo(metaData);
new ExperimentRegistrator("john", "doe", "j@doe").saveTo(metaData);
@@ -547,6 +559,7 @@ public final class DataStructureTestV1_0 extends AbstractFileSystemTestCase
private final static void createExampleChecksum(final IDirectory metaData)
{
final IDirectory checksumDir = metaData.makeDirectory(ChecksumHandler.CHECKSUM_DIRECTORY);
- checksumDir.addKeyValuePair(DataStructureV1_0.DIR_ORIGINAL, "23b447be20a6ddfe875a8b59ceae83ff file1");
+ checksumDir.addKeyValuePair(DataStructureV1_0.DIR_ORIGINAL,
+ "23b447be20a6ddfe875a8b59ceae83ff file1");
}
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
index 8dd0c018f28..8f9c0bfb726 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/UtilitiesTest.java
@@ -97,7 +97,8 @@ public class UtilitiesTest extends AbstractFileSystemTestCase
dir2.mkdir();
createFile(dir1, "file2");
createFile(dir2, "file3");
- final List<String> nodes = Utilities.listNodes(NodeFactory.createDirectoryNode(workingDirectory), null);
+ final List<String> nodes =
+ Utilities.listNodes(NodeFactory.createDirectoryNode(workingDirectory), null);
assertEquals(3, nodes.size());
Collections.sort(nodes);
assertEquals("dir1/file2", nodes.get(0));
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/handler/MappingFileHandlerTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/handler/MappingFileHandlerTest.java
index 56e092ff44a..d43a3bf36e6 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/handler/MappingFileHandlerTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/handler/MappingFileHandlerTest.java
@@ -43,7 +43,8 @@ public final class MappingFileHandlerTest extends AbstractFileSystemTestCase
{
private final static String MAPPING_FILE_CONTENT =
- "row1/row2_column1.tiff\tI\toriginal1.tiff\n" + "row2/row3_column2.tiff\tI\toriginal2.tiff\n";
+ "row1/row2_column1.tiff\tI\toriginal1.tiff\n"
+ + "row2/row3_column2.tiff\tI\toriginal2.tiff\n";
private MappingFileHandler handler;
@@ -85,9 +86,9 @@ public final class MappingFileHandlerTest extends AbstractFileSystemTestCase
@Override
@BeforeMethod
- public void setup() throws IOException
+ public void setUp() throws IOException
{
- super.setup();
+ super.setUp();
prepareMappingFileHandler();
}
@@ -124,8 +125,10 @@ public final class MappingFileHandlerTest extends AbstractFileSystemTestCase
@Test
public final void testPerformClosing() throws IOException
{
- handler.addReference(new Reference("row1/row2_column1.tiff", "original1.tiff", ReferenceType.IDENTICAL));
- handler.addReference(new Reference("row2/row3_column2.tiff", "original2.tiff", ReferenceType.IDENTICAL));
+ handler.addReference(new Reference("row1/row2_column1.tiff", "original1.tiff",
+ ReferenceType.IDENTICAL));
+ handler.addReference(new Reference("row2/row3_column2.tiff", "original2.tiff",
+ ReferenceType.IDENTICAL));
handler.performClosing();
final File mappingFile = new File(workingDirectory, MappingFileHandler.MAPPING_FILE);
assertTrue(mappingFile.exists());
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
index d0b8b6bc044..b08b007999a 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSDataStructureTestV1_0.java
@@ -62,10 +62,14 @@ public final class HCSDataStructureTestV1_0 extends AbstractFileSystemTestCase
{
dataStructure.setFormat(HCSImageFormatV1_0.HCS_IMAGE_1_0);
dataStructure.addFormatParameter(new FormatParameter(HCSImageFormatV1_0.DEVICE_ID, "M1"));
- dataStructure.addFormatParameter(new FormatParameter(HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA, Boolean.TRUE));
- dataStructure.addFormatParameter(new FormatParameter(ChannelList.NUMBER_OF_CHANNELS, createChannelList()));
- dataStructure.addFormatParameter(new FormatParameter(PlateGeometry.PLATE_GEOMETRY, new PlateGeometry(2, 3)));
- dataStructure.addFormatParameter(new FormatParameter(WellGeometry.WELL_GEOMETRY, new WellGeometry(7, 5)));
+ dataStructure.addFormatParameter(new FormatParameter(
+ HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA, Boolean.TRUE));
+ dataStructure.addFormatParameter(new FormatParameter(ChannelList.NUMBER_OF_CHANNELS,
+ createChannelList()));
+ dataStructure.addFormatParameter(new FormatParameter(PlateGeometry.PLATE_GEOMETRY,
+ new PlateGeometry(2, 3)));
+ dataStructure.addFormatParameter(new FormatParameter(WellGeometry.WELL_GEOMETRY,
+ new WellGeometry(7, 5)));
}
//
@@ -109,7 +113,9 @@ public final class HCSDataStructureTestV1_0 extends AbstractFileSystemTestCase
setFormatAndFormatParameters();
dataStructure.close();
// And loading...
- final IDataStructure ds = new DataStructureLoader(workingDirectory.getParentFile()).load(getClass().getName());
+ final IDataStructure ds =
+ new DataStructureLoader(workingDirectory.getParentFile())
+ .load(getClass().getName());
assertNotNull(ds);
}
}
\ No newline at end of file
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 e868022dd46..2d3c376f9e2 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/HCSImageFormattedDataTest.java
@@ -94,8 +94,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
formattedData =
- (HCSImageFormattedData) FormattedDataFactory.createFormattedData(directory, format, null,
- formatParameters);
+ (HCSImageFormattedData) FormattedDataFactory.createFormattedData(directory, format,
+ null, formatParameters);
}
private final void prepareStandardNode()
@@ -213,8 +213,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
final NodePath nodePath =
- formattedData.addStandardNode(imageRootDirectory, ORIGINAL_TIFF, 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.getNode() instanceof ILink);
@@ -225,7 +225,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
assertTrue(standardFile instanceof IFile);
assertEquals(standardFileName, standardFile.getName());
// Node should still be in the 'original' directory.
- assertNotNull(((IDirectory) originalNode.tryGetNode(IMAGE_ROOT_DIRECTORY_NAME)).tryGetNode(ORIGINAL_TIFF));
+ assertNotNull(((IDirectory) originalNode.tryGetNode(IMAGE_ROOT_DIRECTORY_NAME))
+ .tryGetNode(ORIGINAL_TIFF));
context.assertIsSatisfied();
}
@@ -247,8 +248,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
}
});
final NodePath nodePath =
- formattedData.addStandardNode(imageRootDirectory, ORIGINAL_TIFF, 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.getNode() instanceof IFile);
@@ -277,7 +278,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
will(returnValue(standardNode));
}
});
- final INode node = formattedData.tryGetStandardNodeAt(channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ final INode node =
+ formattedData.tryGetStandardNodeAt(channelIndex, PLATE_LOCATION, WELL_LOCATION);
assertNull(node);
context.assertIsSatisfied();
}
@@ -298,7 +300,8 @@ public class HCSImageFormattedDataTest extends AbstractFileSystemTestCase
will(returnValue(standardNode));
}
});
- final INode node = formattedData.tryGetStandardNodeAt(channelIndex, PLATE_LOCATION, WELL_LOCATION);
+ final INode node =
+ formattedData.tryGetStandardNodeAt(channelIndex, PLATE_LOCATION, WELL_LOCATION);
assertNotNull(node);
context.assertIsSatisfied();
}
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
index 9485681f345..4bd1ee2702e 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/PlateGeometryTest.java
@@ -84,7 +84,8 @@ public final class PlateGeometryTest extends AbstractFileSystemTestCase
{
testSaveTo();
final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
- final IDirectory geoDir = Utilities.getOrCreateSubDirectory(dir, PlateGeometry.PLATE_GEOMETRY);
+ final IDirectory geoDir =
+ Utilities.getOrCreateSubDirectory(dir, PlateGeometry.PLATE_GEOMETRY);
final Geometry loaded = PlateGeometry.loadFrom(geoDir);
assertNotNull(loaded);
assertTrue(loaded.getRows() == 2);
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
index 179ef192b9b..34331fd9b5e 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/WellGeometryTest.java
@@ -84,7 +84,8 @@ public final class WellGeometryTest extends AbstractFileSystemTestCase
{
testSaveTo();
final IDirectory dir = NodeFactory.createDirectoryNode(workingDirectory);
- final IDirectory geoDir = Utilities.getOrCreateSubDirectory(dir, WellGeometry.WELL_GEOMETRY);
+ final IDirectory geoDir =
+ Utilities.getOrCreateSubDirectory(dir, WellGeometry.WELL_GEOMETRY);
final Geometry loaded = WellGeometry.loadFrom(geoDir);
assertNotNull(loaded);
assertTrue(loaded.getRows() == 2);
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
index e834a0f16b9..c948f34ab3b 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/FileTest.java
@@ -59,7 +59,8 @@ public final class FileTest extends AbstractFileSystemTestCase
java.io.File subdir = new java.io.File(workingDirectory, "subdir");
subdir.mkdir();
stringFile.extractTo(subdir);
- assertEquals("Hello\nworld!\n", FileUtilities.loadToString(new java.io.File(subdir, stringFile.getName())));
+ assertEquals("Hello\nworld!\n", FileUtilities.loadToString(new java.io.File(subdir,
+ stringFile.getName())));
}
@Test
@@ -73,7 +74,8 @@ public final class FileTest extends AbstractFileSystemTestCase
file.moveTo(workingDirectory);
assertEquals(false, directory.iterator().hasNext());
- assertEquals("property 1", FileUtilities.loadToString(new java.io.File(workingDirectory, "p1")).trim());
+ assertEquals("property 1", FileUtilities.loadToString(
+ new java.io.File(workingDirectory, "p1")).trim());
}
@Test
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
index 330335e396a..e5bed9cffe9 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/storage/filesystem/NodeFactoryTest.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
* Test cases for corresponding {@link NodeFactory} class.
- *
+ *
* @author Franz-Josef Elmer
*/
public class NodeFactoryTest extends AbstractFileSystemTestCase
@@ -43,7 +43,7 @@ public class NodeFactoryTest extends AbstractFileSystemTestCase
assertTrue(node instanceof IFile);
assertEquals("text.txt", node.getName());
}
-
+
@Test
public void testCreateDirectoryNode()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/Constants.java b/common/source/java/ch/systemsx/cisd/common/Constants.java
index 1306a277a0d..7b2e82f670e 100644
--- a/common/source/java/ch/systemsx/cisd/common/Constants.java
+++ b/common/source/java/ch/systemsx/cisd/common/Constants.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common;
/**
* Constants common to more than one CISD project.
- *
+ *
* @author Bernd Rinn
*/
public class Constants
@@ -26,11 +26,12 @@ public class Constants
/** String that indicates a marker file */
public static final String MARKER_PREFIX = ".MARKER_";
-
+
/** The prefix of marker files that indicate that the processing of some path is finished. */
public static final String IS_FINISHED_PREFIX = MARKER_PREFIX + "is_finished_";
/** The prefix of marker files that indicate that the processing of some path is finished. */
- public static final String DELETION_IN_PROGRESS_PREFIX = MARKER_PREFIX + "deletion_in_progress_";
+ public static final String DELETION_IN_PROGRESS_PREFIX =
+ MARKER_PREFIX + "deletion_in_progress_";
}
diff --git a/common/source/java/ch/systemsx/cisd/common/Script.java b/common/source/java/ch/systemsx/cisd/common/Script.java
index a15ecd91584..734bfccdfb9 100644
--- a/common/source/java/ch/systemsx/cisd/common/Script.java
+++ b/common/source/java/ch/systemsx/cisd/common/Script.java
@@ -20,14 +20,16 @@ import org.apache.commons.lang.builder.EqualsBuilder;
import org.apache.commons.lang.builder.HashCodeBuilder;
/**
- * Bean class for a script. Holds script name and code.
- *
+ * Bean class for a script. Holds script name and code.
+ *
* @author Franz-Josef Elmer
*/
public class Script
{
private final String name;
+
private final String code;
+
private final String version;
/**
@@ -37,7 +39,7 @@ public class Script
{
this(name, code, "-");
}
-
+
/**
* Creates an instance for the specified script name, code and version.
*/
@@ -86,5 +88,5 @@ public class Script
{
return HashCodeBuilder.reflectionHashCode(this);
}
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java b/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
index 85094d8e048..24bf50f28c4 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
@@ -124,7 +124,7 @@ public abstract class AbstractCollectionDecorator<E> implements Collection<E>
{
return collection.retainAll(coll);
}
-
+
//
// Object
//
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java b/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
index 7bd8d4a76d3..222eeb502e9 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
@@ -49,7 +49,8 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
public class CollectionIO
{
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, FileUtilities.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, FileUtilities.class);
/**
* Reads a collection of {@link String}s from a <var>resource</var>. One line in the resource corresponds to one
@@ -61,7 +62,8 @@ public class CollectionIO
*/
public static boolean readCollectionFromResource(String resource, Collection<String> collection)
{
- return readCollectionFromResource(resource, collection, FromStringIdentityConverter.getInstance());
+ return readCollectionFromResource(resource, collection, FromStringIdentityConverter
+ .getInstance());
}
/**
@@ -82,7 +84,8 @@ public class CollectionIO
machineLog.error(String.format("Resource '%s' not found.", resource));
return false;
}
- return readCollection(resourceStream, collection, converter, String.format("<resource '%s'>", resource));
+ return readCollection(resourceStream, collection, converter, String.format(
+ "<resource '%s'>", resource));
}
/**
@@ -106,12 +109,13 @@ public class CollectionIO
* @param converter The converter to use in order to convert each line in the file.
* @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
*/
- public static <T> boolean readCollection(File file, Collection<T> collection, IFromStringConverter<T> converter)
+ public static <T> boolean readCollection(File file, Collection<T> collection,
+ IFromStringConverter<T> converter)
{
try
{
- return readCollection(new FileInputStream(file), collection, converter, String.format("<file '%s'>", file
- .getPath()));
+ return readCollection(new FileInputStream(file), collection, converter, String.format(
+ "<file '%s'>", file.getPath()));
} catch (FileNotFoundException e)
{
machineLog.error(String.format("File '%s' is not accessible.", file.getPath()), e);
@@ -205,7 +209,7 @@ public class CollectionIO
}
return true;
}
-
+
/**
* Reads a list of {@link String}s from a <var>resource</var>. One line in the resource corresponds to one entry
* in the list.
@@ -227,7 +231,8 @@ public class CollectionIO
* @return A new {@link ArrayList} containing the entries from the <var>file</var>, or <code>null</code> if there
* is an error when reading the <var>file</var>.
*/
- public static <T> List<T> readListFromResource(String resource, IFromStringConverter<T> converter)
+ public static <T> List<T> readListFromResource(String resource,
+ IFromStringConverter<T> converter)
{
assert resource != null;
assert converter != null;
@@ -370,7 +375,8 @@ public class CollectionIO
* @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into a {@link String}.
* @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
*/
- public static <T> boolean writeIterable(File file, Iterable<T> iterable, IToStringConverter<? super T> converter)
+ public static <T> boolean writeIterable(File file, Iterable<T> iterable,
+ IToStringConverter<? super T> converter)
{
FileOutputStream fos = null;
try
@@ -486,8 +492,8 @@ public class CollectionIO
* @param iterable The iterable to write to the writer.
* @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
*/
- public final static <T> boolean writeIterable(final PrintWriter writer, final Iterable<T> iterable,
- final IToStringConverter<? super T> converterOrNull)
+ public final static <T> boolean writeIterable(final PrintWriter writer,
+ final Iterable<T> iterable, final IToStringConverter<? super T> converterOrNull)
{
assert writer != null : "Given PrintWriter can not be null";
assert iterable != null : "Given Iterable can not be null";
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/CollectionStyle.java b/common/source/java/ch/systemsx/cisd/common/collections/CollectionStyle.java
index 5155e4792f2..35783b9113a 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/CollectionStyle.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/CollectionStyle.java
@@ -24,8 +24,8 @@ package ch.systemsx.cisd.common.collections;
public enum CollectionStyle
{
/** Default <code>CollectionStyle</code>. */
- DEFAULT_COLLECTION_STYLE("[", "]", ", "), NO_BOUNDARY_COLLECTION_STYLE("", "", ", "), NICE_COLLECTION_STYLE("'",
- "'", "', '");
+ DEFAULT_COLLECTION_STYLE("[", "]", ", "), NO_BOUNDARY_COLLECTION_STYLE("", "", ", "),
+ NICE_COLLECTION_STYLE("'", "'", "', '");
private final String collectionStart;
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java b/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
index 78586100752..f0f326bd62f 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
@@ -71,7 +71,8 @@ public final class CollectionUtils
* @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
* displayed.
*/
- public final static <T> String abbreviate(final T[] objects, final int maxLength, final CollectionStyle style)
+ public final static <T> String abbreviate(final T[] objects, final int maxLength,
+ final CollectionStyle style)
{
return abbreviate(objects, maxLength, true, ToStringDefaultConverter.getInstance(), style);
}
@@ -103,7 +104,8 @@ public final class CollectionUtils
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final IToStringConverter<? super T> converter)
{
- return abbreviate(collection, maxLength, converter, CollectionStyle.DEFAULT_COLLECTION_STYLE);
+ return abbreviate(collection, maxLength, converter,
+ CollectionStyle.DEFAULT_COLLECTION_STYLE);
}
/**
@@ -130,7 +132,8 @@ public final class CollectionUtils
* @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
* displayed.
*/
- public final static <T> String abbreviate(final T[] objects, final int maxLength, final boolean showLeft)
+ public final static <T> String abbreviate(final T[] objects, final int maxLength,
+ final boolean showLeft)
{
return abbreviate(objects, maxLength, showLeft, ToStringDefaultConverter.getInstance());
}
@@ -159,10 +162,11 @@ public final class CollectionUtils
* @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
* displayed.
*/
- public final static <T> String abbreviate(final T[] objects, final int maxLength, final boolean showLeft,
- final IToStringConverter<? super T> converter)
+ public final static <T> String abbreviate(final T[] objects, final int maxLength,
+ final boolean showLeft, final IToStringConverter<? super T> converter)
{
- return abbreviate(objects, maxLength, showLeft, converter, CollectionStyle.DEFAULT_COLLECTION_STYLE);
+ return abbreviate(objects, maxLength, showLeft, converter,
+ CollectionStyle.DEFAULT_COLLECTION_STYLE);
}
/**
@@ -171,7 +175,8 @@ public final class CollectionUtils
* {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} is used and all items is displayed.
* </p>
*/
- public final static <T> String abbreviate(final T[] objects, final IToStringConverter<? super T> converter)
+ public final static <T> String abbreviate(final T[] objects,
+ final IToStringConverter<? super T> converter)
{
return abbreviate(objects, -1, false, converter, CollectionStyle.DEFAULT_COLLECTION_STYLE);
}
@@ -188,7 +193,8 @@ public final class CollectionUtils
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final boolean showLeft, final IToStringConverter<? super T> converter)
{
- return abbreviate(collection, maxLength, showLeft, converter, CollectionStyle.DEFAULT_COLLECTION_STYLE);
+ return abbreviate(collection, maxLength, showLeft, converter,
+ CollectionStyle.DEFAULT_COLLECTION_STYLE);
}
/**
@@ -205,8 +211,9 @@ public final class CollectionUtils
* relevant if you limit the number of items displayed.
* @param style the style that should be applied to the output.
*/
- public final static <T> String abbreviate(final T[] objects, final int maxLength, final boolean showLeft,
- final IToStringConverter<? super T> converter, final CollectionStyle style)
+ public final static <T> String abbreviate(final T[] objects, final int maxLength,
+ final boolean showLeft, final IToStringConverter<? super T> converter,
+ final CollectionStyle style)
{
assert objects != null : "Given objects can not be null.";
return abbreviate(Arrays.asList(objects), maxLength, showLeft, converter, style);
@@ -222,7 +229,8 @@ public final class CollectionUtils
* @param style the style that should be applied to the output.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
- final boolean showLeft, final IToStringConverter<? super T> converter, final CollectionStyle style)
+ final boolean showLeft, final IToStringConverter<? super T> converter,
+ final CollectionStyle style)
{
assert collection != null : "Given collection can not be null.";
assert converter != null : "Given converter can not be null.";
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java b/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
index 804f7b97b8a..b8a18e7c13e 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
@@ -70,7 +70,8 @@ public class FilteredCollection<E> extends AbstractCollectionDecorator<E>
* </p>
*/
@SuppressWarnings("unchecked")
- protected final static <E> Collection<E> filterCollection(Collection<? extends E> collection, Validator<E> validator)
+ protected final static <E> Collection<E> filterCollection(Collection<? extends E> collection,
+ Validator<E> validator)
{
if (collection == null)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/IKeyExtractor.java b/common/source/java/ch/systemsx/cisd/common/collections/IKeyExtractor.java
index ce880e12d94..83fa9fdff8b 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/IKeyExtractor.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/IKeyExtractor.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.collections;
/**
* Interface defining the role of a key extractor.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IKeyExtractor<K, E>
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java b/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
index 18ffe8b79bf..32303c63d3d 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
@@ -109,12 +109,14 @@ public class TableMap<K, E> implements Iterable<E>
public final void add(final E row) throws UniqueKeyViolationException
{
final K key = extractor.getKey(row);
- if (uniqueKeyViolationStrategy == UniqueKeyViolationStrategy.KEEP_LAST || map.get(key) == null)
+ if (uniqueKeyViolationStrategy == UniqueKeyViolationStrategy.KEEP_LAST
+ || map.get(key) == null)
{
map.put(key, row);
} else if (uniqueKeyViolationStrategy == UniqueKeyViolationStrategy.ERROR)
{
- throw new UniqueKeyViolationException("Key '" + key.toString() + "' already in the map.");
+ throw new UniqueKeyViolationException("Key '" + key.toString()
+ + "' already in the map.");
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java b/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
index 4ca38e698c9..a82efcc2128 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
@@ -125,13 +125,14 @@ public class TableMapNonUniqueKey<K, E> implements Iterable<E>
set.add(row);
} else if (uniqueValueViolationStrategy == UniqueValueViolationStrategy.ERROR)
{
- throw new UniqueValueViolationException("Row '" + row.toString() + "' already stored in the map.");
+ throw new UniqueValueViolationException("Row '" + row.toString()
+ + "' already stored in the map.");
}
}
/**
* Gets the row set for the specified <var>key</var>.
- *
+ *
* @return The set, given in the order of addition, or <code>null</code> if the <var>key</var> is not found.
*/
public final Set<E> tryGet(final K key)
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/CompressionWorker.java b/common/source/java/ch/systemsx/cisd/common/compression/file/CompressionWorker.java
index f341dbc15ab..47481b7c0f6 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/CompressionWorker.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/CompressionWorker.java
@@ -43,23 +43,26 @@ class CompressionWorker implements Runnable
static final String COMPRESSING_MSG_TEMPLATE = "Compressing '%s'.";
// @Private
- static final String EXCEPTION_COMPRESSING_MSG_TEMPLATE = "Exceptional condition when trying to compress '%s'.";
-
+ static final String EXCEPTION_COMPRESSING_MSG_TEMPLATE =
+ "Exceptional condition when trying to compress '%s'.";
+
// @Private
static final String INTERRPTED_MSG = "Thread has been interrupted - exiting worker.";
// @Private
static final String EXITING_MSG = "No more files to compress - exiting worker.";
- private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, CompressionWorker.class);
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, CompressionWorker.class);
private final Queue<File> workerQueue;
-
+
private final Collection<FailureRecord> failures;
private final ICompressionMethod compressor;
- CompressionWorker(Queue<File> incommingQueue, Collection<FailureRecord> failures, ICompressionMethod compressor)
+ CompressionWorker(Queue<File> incommingQueue, Collection<FailureRecord> failures,
+ ICompressionMethod compressor)
{
assert incommingQueue != null;
assert failures != null;
@@ -101,12 +104,14 @@ class CompressionWorker implements Runnable
status = compressor.compress(fileToCompressOrNull);
} catch (Throwable th)
{
- operationLog.error(String.format(EXCEPTION_COMPRESSING_MSG_TEMPLATE, fileToCompressOrNull), th);
+ operationLog.error(String.format(EXCEPTION_COMPRESSING_MSG_TEMPLATE,
+ fileToCompressOrNull), th);
failures.add(new FailureRecord(fileToCompressOrNull, th));
status = null;
break;
}
- } while (StatusFlag.RETRIABLE_ERROR.equals(status.getFlag()) && ++count < MAX_RETRY_OF_FAILED_COMPRESSIONS);
+ } while (StatusFlag.RETRIABLE_ERROR.equals(status.getFlag())
+ && ++count < MAX_RETRY_OF_FAILED_COMPRESSIONS);
if (status != null && Status.OK.equals(status) == false)
{
failures.add(new FailureRecord(fileToCompressOrNull, status));
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/Compressor.java b/common/source/java/ch/systemsx/cisd/common/compression/file/Compressor.java
index 59293c83a54..7ba9948c196 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/Compressor.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/Compressor.java
@@ -47,9 +47,11 @@ public class Compressor
LogInitializer.init();
}
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, Compressor.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, Compressor.class);
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, Compressor.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, Compressor.class);
private static final int NUMBER_OF_WORKERS = Runtime.getRuntime().availableProcessors();
@@ -70,17 +72,20 @@ public class Compressor
}
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("Found %d files to compress.", filesToCompressOrNull.length));
+ operationLog.info(String.format("Found %d files to compress.",
+ filesToCompressOrNull.length));
}
- return new ArrayBlockingQueue<File>(filesToCompressOrNull.length, false, Arrays.asList(filesToCompressOrNull));
+ return new ArrayBlockingQueue<File>(filesToCompressOrNull.length, false, Arrays
+ .asList(filesToCompressOrNull));
}
- private static void startUpWorkerThreads(Queue<File> workerQueue, Collection<FailureRecord> failed,
- ICompressionMethod compressor)
+ private static void startUpWorkerThreads(Queue<File> workerQueue,
+ Collection<FailureRecord> failed, ICompressionMethod compressor)
{
for (int i = 0; i < NUMBER_OF_WORKERS; ++i)
{
- new Thread(new CompressionWorker(workerQueue, failed, compressor), "Compressor " + i).start();
+ new Thread(new CompressionWorker(workerQueue, failed, compressor), "Compressor " + i)
+ .start();
}
if (operationLog.isInfoEnabled())
{
@@ -88,14 +93,17 @@ public class Compressor
}
}
- public static Collection<FailureRecord> start(String directoryName, ICompressionMethod compressionMethod)
+ public static Collection<FailureRecord> start(String directoryName,
+ ICompressionMethod compressionMethod)
{
if (compressionMethod instanceof ISelfTestable)
{
((ISelfTestable) compressionMethod).check();
}
- final Queue<File> workerQueue = fillWorkerQueueOrExit(new File(directoryName), compressionMethod);
- final Collection<FailureRecord> failed = Collections.synchronizedCollection(new ArrayList<FailureRecord>());
+ final Queue<File> workerQueue =
+ fillWorkerQueueOrExit(new File(directoryName), compressionMethod);
+ final Collection<FailureRecord> failed =
+ Collections.synchronizedCollection(new ArrayList<FailureRecord>());
startUpWorkerThreads(workerQueue, failed, compressionMethod);
return failed;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
index fb4b1a12125..7bc8b3c36a0 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
@@ -32,7 +32,7 @@ public interface ICompressionMethod extends FileFilter
/**
* Compress the <var>fileToCompress</var>
- *
+ *
* @return {@link Status#OK} if the operation was successful, a status indicating the kind of problem otherwise.
*/
public Status compress(File fileToCompress);
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
index a3a8ac385e2..b8da33aab31 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
@@ -142,13 +142,13 @@ public abstract class InPlaceCompressionMethod implements ICompressionMethod, IS
final boolean ok = fileToCompress.delete();
if (ok)
{
- operationLog.warn(String.format("Clean up: deleting left-over file '%s'", fileToCompress
- .getAbsolutePath()));
+ operationLog.warn(String.format("Clean up: deleting left-over file '%s'",
+ fileToCompress.getAbsolutePath()));
return Status.OK;
} else
{
- return createStatusAndLog("Clean up: Unable to delete left-over file '%s'", fileToCompress
- .getAbsolutePath());
+ return createStatusAndLog("Clean up: Unable to delete left-over file '%s'",
+ fileToCompress.getAbsolutePath());
}
}
if (isCompressedFile(fileToCompress))
@@ -160,7 +160,8 @@ public abstract class InPlaceCompressionMethod implements ICompressionMethod, IS
final boolean ok = originalFile.delete();
if (ok == false)
{
- return createStatusAndLog("Clean up: Unable to delete uncompressed file '%s'", originalFile);
+ return createStatusAndLog("Clean up: Unable to delete uncompressed file '%s'",
+ originalFile);
}
}
if (fileToCompress.renameTo(originalFile))
@@ -168,15 +169,16 @@ public abstract class InPlaceCompressionMethod implements ICompressionMethod, IS
return Status.OK;
} else
{
- return createStatusAndLog("Renaming compressed file '%s' to original name '%s' failed.",
+ return createStatusAndLog(
+ "Renaming compressed file '%s' to original name '%s' failed.",
fileToCompress, originalFile);
}
}
final File inProgressFile = prefixInProgress(fileToCompress);
final File compressionFinishedFile = prefixCompressed(fileToCompress);
final boolean runOK =
- ProcessExecutionHelper.runAndLog(createCommandLine(fileToCompress, inProgressFile), operationLog,
- machineLog);
+ ProcessExecutionHelper.runAndLog(createCommandLine(fileToCompress, inProgressFile),
+ operationLog, machineLog);
if (runOK == false)
{
return createStatusAndLog("Unable to compress '%s'.", fileToCompress.getAbsolutePath());
@@ -184,19 +186,20 @@ public abstract class InPlaceCompressionMethod implements ICompressionMethod, IS
final boolean firstRenameOK = inProgressFile.renameTo(compressionFinishedFile);
if (firstRenameOK == false)
{
- return createStatusAndLog("Unable to rename '%s' to '%s'.", inProgressFile.getAbsolutePath(),
- compressionFinishedFile.getAbsolutePath());
+ return createStatusAndLog("Unable to rename '%s' to '%s'.", inProgressFile
+ .getAbsolutePath(), compressionFinishedFile.getAbsolutePath());
}
final boolean removalOfOriginalOK = fileToCompress.delete();
if (removalOfOriginalOK == false)
{
- return createStatusAndLog("Unable to delete original file '%s'", fileToCompress.getAbsolutePath());
+ return createStatusAndLog("Unable to delete original file '%s'", fileToCompress
+ .getAbsolutePath());
}
final boolean secondRenameOK = compressionFinishedFile.renameTo(fileToCompress);
if (secondRenameOK == false)
{
- return createStatusAndLog("Unable to rename '%s' to '%s'.", compressionFinishedFile.getAbsolutePath(),
- fileToCompress.getAbsolutePath());
+ return createStatusAndLog("Unable to rename '%s' to '%s'.", compressionFinishedFile
+ .getAbsolutePath(), fileToCompress.getAbsolutePath());
}
return Status.OK;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java
index b6cb1f7f24e..ad6e60609ed 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffCompressor.java
@@ -43,7 +43,8 @@ public class TiffCompressor extends Compressor
}
for (FailureRecord r : failed)
{
- System.err.printf("%s (%s)\n", r.getFailedFile().getName(), r.getFailureStatus().getMessage());
+ System.err.printf("%s (%s)\n", r.getFailedFile().getName(), r.getFailureStatus()
+ .getMessage());
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
index 90271e47f2e..0f32b9d2238 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
@@ -20,7 +20,6 @@ import java.io.File;
import java.util.Arrays;
import java.util.List;
-
import ch.systemsx.cisd.common.compression.file.InPlaceCompressionMethod;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -75,10 +74,11 @@ public class TiffZipCompressionMethod extends InPlaceCompressionMethod
assert fileToCompress.isFile();
assert inProgressFile != null;
assert inProgressFile.exists() == false;
-
+
final List<String> parameters =
- Arrays.asList(convertExecutable.getAbsolutePath(), fileToCompress.getAbsolutePath(), "-compress",
- "Zip", inProgressFile.getAbsolutePath());
+ Arrays.asList(convertExecutable.getAbsolutePath(),
+ fileToCompress.getAbsolutePath(), "-compress", "Zip", inProgressFile
+ .getAbsolutePath());
return parameters;
}
@@ -87,15 +87,17 @@ public class TiffZipCompressionMethod extends InPlaceCompressionMethod
{
return Arrays.asList(".tif", ".tiff");
}
-
+
@Override
public void check() throws EnvironmentFailureException, ConfigurationFailureException
{
if (convertExecutable == null)
{
- throw new ConfigurationFailureException("Cannot find executable of the convert utility.");
+ throw new ConfigurationFailureException(
+ "Cannot find executable of the convert utility.");
}
- final String imageMagickVersionOrNull = getImageMagickVersion(convertExecutable.getAbsolutePath());
+ final String imageMagickVersionOrNull =
+ getImageMagickVersion(convertExecutable.getAbsolutePath());
if (imageMagickVersionOrNull == null)
{
throw new ConfigurationFailureException("Invalid convert utility");
@@ -110,12 +112,13 @@ public class TiffZipCompressionMethod extends InPlaceCompressionMethod
if (imageMagickMajorVersion < 6 || imageMagickMinorVersion < 2)
{
throw ConfigurationFailureException.fromTemplate(
- "Convert utility is too old (expected: v6.2 or newer, found: v%s)", imageMagickVersionOrNull);
+ "Convert utility is too old (expected: v6.2 or newer, found: v%s)",
+ imageMagickVersionOrNull);
}
if (machineLog.isInfoEnabled())
{
- machineLog.info(String.format("Using convert executable '%s', ImageMagick version %s", convertExecutable,
- imageMagickVersionOrNull));
+ machineLog.info(String.format("Using convert executable '%s', ImageMagick version %s",
+ convertExecutable, imageMagickVersionOrNull));
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java b/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
index 82188978dee..5bfb9170c19 100644
--- a/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
@@ -44,7 +44,8 @@ public final class ConcurrencyUtilities
* @param corePoolSize The number of threads that should be kept running even if less theads are needed.
* @param maximumPoolSize The number of threads that this executor service is maximally allowed to spawn.
*/
- public static ExecutorService newNamedPool(final String name, int corePoolSize, int maximumPoolSize)
+ public static ExecutorService newNamedPool(final String name, int corePoolSize,
+ int maximumPoolSize)
{
return new ThreadPoolExecutor(corePoolSize, maximumPoolSize, 0L, TimeUnit.MILLISECONDS,
new LinkedBlockingQueue<Runnable>(), new ThreadFactory()
@@ -79,8 +80,8 @@ public final class ConcurrencyUtilities
* @return The result of the future, or <code>null</code>, if the result does not become available within
* <var>timeoutMillis</var> ms or if the waiting thread gets interrupted.
*/
- public static <T> T tryGetResult(Future<T> future, long timeoutMillis, ISimpleLogger loggerOrNull,
- String operationNameOrNull)
+ public static <T> T tryGetResult(Future<T> future, long timeoutMillis,
+ ISimpleLogger loggerOrNull, String operationNameOrNull)
{
try
{
@@ -90,10 +91,10 @@ public final class ConcurrencyUtilities
future.cancel(true);
if (loggerOrNull != null)
{
- loggerOrNull
- .log(LogLevel.DEBUG, String.format("%s took longer than %f s, cancelled.",
- operationNameOrNull == null ? "UNKNOWN OPERATION" : operationNameOrNull,
- timeoutMillis / 1000f));
+ loggerOrNull.log(LogLevel.DEBUG, String.format(
+ "%s took longer than %f s, cancelled.",
+ operationNameOrNull == null ? "UNKNOWN OPERATION" : operationNameOrNull,
+ timeoutMillis / 1000f));
}
return null;
} catch (InterruptedException ex)
@@ -111,8 +112,9 @@ public final class ConcurrencyUtilities
if (loggerOrNull != null)
{
loggerOrNull.log(LogLevel.ERROR, String.format("%s has caused an exception: %s",
- operationNameOrNull == null ? "UNKNOWN OPERATION" : operationNameOrNull, cause.getClass()
- .getSimpleName(), cause.getMessage() != null ? cause.getMessage() : "<no message>"));
+ operationNameOrNull == null ? "UNKNOWN OPERATION" : operationNameOrNull,
+ cause.getClass().getSimpleName(), cause.getMessage() != null ? cause
+ .getMessage() : "<no message>"));
}
if (cause instanceof Error)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java b/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
index 0b63d2a97ca..b815ae834c4 100644
--- a/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
+++ b/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
@@ -95,7 +95,8 @@ public final class ConverterPool
{
return (T) Boolean.valueOf(value);
}
- throw new IllegalArgumentException("No converter for type '" + type.getCanonicalName() + "'.");
+ throw new IllegalArgumentException("No converter for type '" + type.getCanonicalName()
+ + "'.");
}
/**
diff --git a/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java b/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
index f30b28fdbeb..7bdfc67c389 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
@@ -40,7 +40,8 @@ public class DBRestrictionParser
{
private static final String CREATE_DOMAIN_PREFIX = "create domain ";
- private static final Pattern VARCHAR_PATTERN = Pattern.compile("(varchar|character varying)\\(([0-9]+)\\).*");
+ private static final Pattern VARCHAR_PATTERN =
+ Pattern.compile("(varchar|character varying)\\(([0-9]+)\\).*");
/** The prefix each <code>create table</code> statement starts with. */
private static final String CREATE_TABLE_PREFIX = "create table ";
@@ -50,18 +51,21 @@ public class DBRestrictionParser
private static final Pattern NOT_NULL_TABLE_PATTERN =
Pattern.compile("\\w+ ((default .+ not null)|(not null)|(not null .+ default.+))");
-
+
/** The prefix each <code>alter table</code> statement starts with (to add a constraint). */
private static final String ALTER_TABLE_PREFIX = "alter table ";
private static final Pattern CHECK_CONSTRAINT_PATTERN =
- Pattern.compile(ALTER_TABLE_PREFIX
- + "([a-z,0-9,_]+) add constraint [a-z,0-9,_]+ check \\(([a-z,0-9,_]+) in \\((.+)\\)\\)");
+ Pattern
+ .compile(ALTER_TABLE_PREFIX
+ + "([a-z,0-9,_]+) add constraint [a-z,0-9,_]+ check \\(([a-z,0-9,_]+) in \\((.+)\\)\\)");
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, DBRestrictionParser.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DBRestrictionParser.class);
// @Private
- final Map<String, DBTableRestrictions> tableRestrictionMap = new HashMap<String, DBTableRestrictions>();
+ final Map<String, DBTableRestrictions> tableRestrictionMap =
+ new HashMap<String, DBTableRestrictions>();
public DBRestrictionParser(String ddlScript)
{
@@ -135,8 +139,8 @@ public class DBRestrictionParser
}
}
- private void parseColumnDefinition(String columnDefinition, final String tableName, Map<String, Integer> domains)
- throws NumberFormatException
+ private void parseColumnDefinition(String columnDefinition, final String tableName,
+ Map<String, Integer> domains) throws NumberFormatException
{
if (columnDefinition.startsWith("constraint "))
{
@@ -145,7 +149,8 @@ public class DBRestrictionParser
int indexOfFirstSpace = columnDefinition.indexOf(' ');
if (indexOfFirstSpace < 0)
{
- operationLog.warn("Invalid column definition \"" + columnDefinition + "\" for table " + tableName);
+ operationLog.warn("Invalid column definition \"" + columnDefinition + "\" for table "
+ + tableName);
return;
}
String columnName = columnDefinition.substring(0, indexOfFirstSpace).trim();
@@ -157,8 +162,8 @@ public class DBRestrictionParser
final Matcher varCharMatcher = VARCHAR_PATTERN.matcher(typeDefinition);
if (varCharMatcher.matches())
{
- getTableRestrictions(tableName).columnLengthMap.put(columnName, Integer.parseInt(varCharMatcher
- .group(2)));
+ getTableRestrictions(tableName).columnLengthMap.put(columnName, Integer
+ .parseInt(varCharMatcher.group(2)));
} else
{
final Integer domainLength = domains.get(StringUtils.split(typeDefinition, ' ')[0]);
@@ -167,7 +172,7 @@ public class DBRestrictionParser
getTableRestrictions(tableName).columnLengthMap.put(columnName, domainLength);
}
}
-
+
if (NOT_NULL_TABLE_PATTERN.matcher(typeDefinition).matches())
{
getTableRestrictions(tableName).notNullSet.add(columnName);
@@ -188,15 +193,17 @@ public class DBRestrictionParser
final Set<String> alternativeSet = new HashSet<String>();
for (String alternative : alternatives)
{
- if (alternative.charAt(0) != '\'' || alternative.charAt(alternative.length() - 1) != '\'')
+ if (alternative.charAt(0) != '\''
+ || alternative.charAt(alternative.length() - 1) != '\'')
{
- operationLog.warn("Invalid alternatives definition \"" + alternative + "\" for column "
- + columnName + " of table " + tableName);
+ operationLog.warn("Invalid alternatives definition \"" + alternative
+ + "\" for column " + columnName + " of table " + tableName);
continue;
}
alternativeSet.add(alternative.substring(1, alternative.length() - 1));
}
- getTableRestrictions(tableName).checkedConstraintsMap.put(columnName, alternativeSet);
+ getTableRestrictions(tableName).checkedConstraintsMap.put(columnName,
+ alternativeSet);
}
}
}
@@ -220,5 +227,5 @@ public class DBRestrictionParser
{
return Collections.unmodifiableMap(tableRestrictionMap);
}
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/db/ISequenceNameMapper.java b/common/source/java/ch/systemsx/cisd/common/db/ISequenceNameMapper.java
index b9c7cc2909b..4ced91124b7 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/ISequenceNameMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/ISequenceNameMapper.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.db;
/**
* Interface for mapping a table to its corresponding sequence.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface ISequenceNameMapper
diff --git a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutionLogger.java b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutionLogger.java
index ca84e1b7688..6d5f0f5c052 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutionLogger.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutionLogger.java
@@ -20,16 +20,16 @@ import ch.systemsx.cisd.common.Script;
/**
* Interface for logging of SQL script executions.
- *
+ *
* @author Bernd Rinn
*/
public interface ISqlScriptExecutionLogger
{
public void logStart(final Script moduleScript);
-
+
public void logSuccess(final Script moduleScript);
-
+
public void logFailure(final Script moduleScript, Throwable runException);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
index 862d080edd5..c697f5f905e 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
@@ -34,5 +34,6 @@ public interface ISqlScriptExecutor
* @param loggerOrNull A logger to log the execution of the <var>sqlScript</var>, or <code>null</code>, if no
* logging should be performed.
*/
- public void execute(Script sqlScript, boolean honorSingleStepMode, ISqlScriptExecutionLogger loggerOrNull);
+ public void execute(Script sqlScript, boolean honorSingleStepMode,
+ ISqlScriptExecutionLogger loggerOrNull);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/db/OracleSequencerHandler.java b/common/source/java/ch/systemsx/cisd/common/db/OracleSequencerHandler.java
index 5f9514442ed..7cf53ca3ca8 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/OracleSequencerHandler.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/OracleSequencerHandler.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.db;
/**
* Implementation of {@link ISequencerHandler} for Oracle.
- *
+ *
* @author Franz-Josef Elmer
*/
public class OracleSequencerHandler implements ISequencerHandler
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java b/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
index 65ad21c3fe0..c974ab12783 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
@@ -32,15 +32,15 @@ public final class SQLCommandTokenizer
private final String sqlScript;
private int index = 0;
-
+
private Mode mode = Mode.SCANNING;
private boolean newLine = true;
-
+
private boolean newWord = false;
-
+
private Character previous = '\0';
-
+
private Character current;
public SQLCommandTokenizer(String sqlScript)
@@ -154,7 +154,7 @@ public final class SQLCommandTokenizer
return;
}
}
-
+
private void scanConstant(StringBuilder builder)
{
do
@@ -168,10 +168,10 @@ public final class SQLCommandTokenizer
} while (current != '\'' || previous == '\\');
mode = Mode.SCANNING;
}
-
+
private void scanWhitespaces()
{
- while (Character.isWhitespace(next()))
+ while (Character.isWhitespace(next()))
{
if (current == '\n')
{
@@ -184,7 +184,7 @@ public final class SQLCommandTokenizer
}
mode = Mode.SCANNING;
}
-
+
private void skipLine()
{
do
@@ -196,5 +196,5 @@ public final class SQLCommandTokenizer
--index;
}
}
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java b/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
index 5e327f7f130..bba78cb4104 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
@@ -41,7 +41,7 @@ public final class SQLStateUtils
/** SQL State. */
public static final String DUPLICATE_OBJECT = "42710";
-
+
/** SQL State. */
public static final String DUPLICATE_DATABASE = "42P04";
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java b/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
index f53dd2252ea..b6094ce5776 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
@@ -32,34 +32,37 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
import ch.systemsx.cisd.common.utilities.OSUtilities;
/**
- * Runner of SQL Unit tests. Needs an implementation of {@link ISqlScriptExecutor} to do the actual tests.
- * The runner executes all test scripts found in the specified test scripts folder. The folder should have the
- * following structure
+ * Runner of SQL Unit tests. Needs an implementation of {@link ISqlScriptExecutor} to do the actual tests. The runner
+ * executes all test scripts found in the specified test scripts folder. The folder should have the following structure
+ *
* <pre>
- * <<i>test script folder</i>>
- * <<i>1. test case</i>>
+ * <<i>test script folder</i>>
+ * <<i>1. test case</i>>
* buildup.sql
- * 1=<<i>first test</i>>.sql
- * 2=<<i>second test</i>>.sql
+ * 1=<<i>first test</i>>.sql
+ * 2=<<i>second test</i>>.sql
* ...
* teardown.sql
- * <<i>2. test case</i>>
+ * <<i>2. test case</i>>
* ...
* ...
* </pre>
- * Folder starting with '.' or <code>migration</code> are ignored.
- * The test cases are executed in lexicographical order of their name. For each test case <code>buildup.sql</code>
- * will be executed first. The test scripts follow the naming schema
+ *
+ * Folder starting with '.' or <code>migration</code> are ignored. The test cases are executed in lexicographical
+ * order of their name. For each test case <code>buildup.sql</code> will be executed first. The test scripts follow
+ * the naming schema
+ *
* <pre>
- * <<i>decimal number</i>>=<<i>test name</i>>.sql
+ * <<i>decimal number</i>>=<<i>test name</i>>.sql
* </pre>
- * They are executed in ascending order of their numbers. Finally <code>teardown.sql</code> is executed.
- * If execution of <code>buildup.sql</code> failed all test scripts and the tear down script are skipped.
- * Note that <code>buildup.sql</code> and <code>teardown.sql</code> are optional.
+ *
+ * They are executed in ascending order of their numbers. Finally <code>teardown.sql</code> is executed. If execution
+ * of <code>buildup.sql</code> failed all test scripts and the tear down script are skipped. Note that
+ * <code>buildup.sql</code> and <code>teardown.sql</code> are optional.
+ * <p>
+ * A script fails if its execution throws an exception. Its innermost cause (usually a {@link SQLException}) will be
+ * recorded together with the name of the test case and the script. All failed scripts will be recorded.
* <p>
- * A script fails if its execution throws an exception. Its innermost cause (usually a {@link SQLException}) will
- * be recorded together with the name of the test case and the script. All failed scripts will be recorded.
- * <p>
* The runner throws an {@link AssertionError} if at least one script failed.
*
* @author Franz-Josef Elmer
@@ -72,14 +75,16 @@ public class SqlUnitTestRunner
private static final class TestResult
{
private final boolean ok;
+
private final Throwable throwable;
+
private final File testScript;
-
+
public TestResult(File testScript)
{
this(testScript, true, null);
}
-
+
public TestResult(File testScript, Throwable throwable)
{
this(testScript, false, throwable);
@@ -91,7 +96,7 @@ public class SqlUnitTestRunner
this.ok = ok;
this.throwable = throwable;
}
-
+
public final File getTestScript()
{
return testScript;
@@ -107,13 +112,14 @@ public class SqlUnitTestRunner
return throwable;
}
}
-
+
private final ISqlScriptExecutor executor;
+
private final PrintWriter writer;
-
+
/**
* Creates an instance for the specified SQL script executor and writer.
- *
+ *
* @param executor SQL script executor.
* @param writer Writer used to monitor running progress by printing test and test case names.
*/
@@ -121,7 +127,7 @@ public class SqlUnitTestRunner
{
assert executor != null : "Undefined SQL script executor.";
assert writer != null : "Undefined writer.";
-
+
this.executor = executor;
this.writer = writer;
}
@@ -172,7 +178,7 @@ public class SqlUnitTestRunner
{
throw new AssertionError(builder.toString());
}
-
+
}
private void runTestCase(File testCaseFolder, List<TestResult> results)
@@ -219,13 +225,14 @@ public class SqlUnitTestRunner
});
return testScripts;
}
-
+
private TestResult runScript(File scriptFile)
{
writer.println(" execute script " + scriptFile.getName());
try
{
- executor.execute(new Script(scriptFile.getName(), FileUtilities.loadToString(scriptFile)), true, null);
+ executor.execute(new Script(scriptFile.getName(), FileUtilities
+ .loadToString(scriptFile)), true, null);
return new TestResult(scriptFile);
} catch (Throwable t)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java b/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
index 2ac63d0a628..a2521bfd9f4 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
@@ -64,7 +64,9 @@ public class StandardSequenceNameMapper implements ISequenceNameMapper
String sequenceName = nonstandardMapping.get(tableNameInLowerCase);
if (sequenceName == null)
{
- sequenceName = tableNameInLowerCase.substring(0, tableNameInLowerCase.length() - 1) + "_id_seq";
+ sequenceName =
+ tableNameInLowerCase.substring(0, tableNameInLowerCase.length() - 1)
+ + "_id_seq";
}
return sequenceName;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
index 2fd4b6e64b4..52ffd5e0c73 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
@@ -48,7 +48,8 @@ public class ConfigurationFailureException extends HighLevelException
/**
* Creates an {@link ConfigurationFailureException} using a {@link java.util.Formatter}.
*/
- public static ConfigurationFailureException fromTemplate(Throwable cause, String messageTemplate, Object... args)
+ public static ConfigurationFailureException fromTemplate(Throwable cause,
+ String messageTemplate, Object... args)
{
return new ConfigurationFailureException(String.format(messageTemplate, args), cause);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
index 3264dd973c1..002a2c251a7 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
@@ -49,7 +49,8 @@ public class EnvironmentFailureException extends HighLevelException
/**
* Creates an {@link EnvironmentFailureException} using a {@link java.util.Formatter}.
*/
- public static EnvironmentFailureException fromTemplate(Throwable cause, String messageTemplate, Object... args)
+ public static EnvironmentFailureException fromTemplate(Throwable cause, String messageTemplate,
+ Object... args)
{
return new EnvironmentFailureException(String.format(messageTemplate, args), cause);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
index b6763c6196b..a35cfd9d357 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * An exception that is "high-level" in the sense that we have a pretty good understanding what the failure
- * means in the context where the exception has been thrown.
+ * An exception that is "high-level" in the sense that we have a pretty good understanding what the failure means in the
+ * context where the exception has been thrown.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/InvalidSessionException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/InvalidSessionException.java
index c3602ceb77d..cb8a72104de 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/InvalidSessionException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/InvalidSessionException.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.common.exceptions;
-
/**
* This <code>UserFailureException</code> extension signals that a session has expired.
*
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
index f7252b3359c..2b79c591012 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
@@ -43,7 +43,9 @@ public final class NotImplementedException extends RuntimeException
{
super();
final StackTraceExtractor extractor = new StackTraceExtractor(this);
- this.message = String.format(MESSAGE_TEMPLATE, extractor.getMethodName(), extractor.getSimpleClassName());
+ this.message =
+ String.format(MESSAGE_TEMPLATE, extractor.getMethodName(), extractor
+ .getSimpleClassName());
}
public NotImplementedException(final String message)
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
index 280f02f0dc1..cbf0253ccf9 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
@@ -45,7 +45,8 @@ public class RetriableEnvironmentFailureException extends EnvironmentFailureExce
/**
* Creates a {@link RetriableEnvironmentFailureException} using a {@link java.util.Formatter}.
*/
- public static RetriableEnvironmentFailureException fromTemplate(String messageTemplate, Object... args)
+ public static RetriableEnvironmentFailureException fromTemplate(String messageTemplate,
+ Object... args)
{
return new RetriableEnvironmentFailureException(String.format(messageTemplate, args));
}
@@ -53,8 +54,8 @@ public class RetriableEnvironmentFailureException extends EnvironmentFailureExce
/**
* Creates a {@link RetriableEnvironmentFailureException} using a {@link java.util.Formatter}.
*/
- public static RetriableEnvironmentFailureException fromTemplate(Throwable cause, String messageTemplate,
- Object... args)
+ public static RetriableEnvironmentFailureException fromTemplate(Throwable cause,
+ String messageTemplate, Object... args)
{
return new RetriableEnvironmentFailureException(String.format(messageTemplate, args), cause);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java b/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
index 194ef4e7adb..e7a239e14cf 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * A class that holds the information about the status of an operation. To be used whenever a failure of an
- * operation is signalled back via a return value rather than an exception.
+ * A class that holds the information about the status of an operation. To be used whenever a failure of an operation is
+ * signalled back via a return value rather than an exception.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java b/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
index c92a4d2ae24..50555756b8b 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The status of an operation. To be used whenever a failure of an operation is signalled back via a return value
- * rather than an exception.
+ * The status of an operation. To be used whenever a failure of an operation is signalled back via a return value rather
+ * than an exception.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
index 64e5be4e6af..c17919cf5c2 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
@@ -49,7 +49,8 @@ public class UserFailureException extends HighLevelException
/**
* Creates an {@link UserFailureException} using a {@link java.util.Formatter}.
*/
- public static UserFailureException fromTemplate(Throwable cause, String messageTemplate, Object... args)
+ public static UserFailureException fromTemplate(Throwable cause, String messageTemplate,
+ Object... args)
{
return new UserFailureException(String.format(messageTemplate, args), cause);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/io/ILinePrinter.java b/common/source/java/ch/systemsx/cisd/common/io/ILinePrinter.java
index cf8ca729cb1..c3827aa173c 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/ILinePrinter.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/ILinePrinter.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.io;
/**
* Interface for classes able to print some text line by line.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface ILinePrinter
diff --git a/common/source/java/ch/systemsx/cisd/common/io/SimpleLinePrinter.java b/common/source/java/ch/systemsx/cisd/common/io/SimpleLinePrinter.java
index febb1f2073a..da3c990dd7e 100644
--- a/common/source/java/ch/systemsx/cisd/common/io/SimpleLinePrinter.java
+++ b/common/source/java/ch/systemsx/cisd/common/io/SimpleLinePrinter.java
@@ -20,8 +20,8 @@ import java.io.PrintWriter;
import java.io.Writer;
/**
- * Line printer based on a {@link Writer} instance.
- *
+ * Line printer based on a {@link Writer} instance.
+ *
* @author Franz-Josef Elmer
*/
public class SimpleLinePrinter implements ILinePrinter
@@ -29,12 +29,12 @@ public class SimpleLinePrinter implements ILinePrinter
private final PrintWriter printWriter;
/**
- * Creates an instance for the specified writer.
+ * Creates an instance for the specified writer.
*/
public SimpleLinePrinter(Writer writer)
{
assert writer != null : "Unspecified writer.";
-
+
printWriter = new PrintWriter(writer, true);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/ConsoleLogger.java b/common/source/java/ch/systemsx/cisd/common/logging/ConsoleLogger.java
index 15705b96b78..032f65ab58f 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/ConsoleLogger.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/ConsoleLogger.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.logging;
/**
* A {@link ISimpleLogger} that logs to {@link System#out} (for debugging purposes).
- *
+ *
* @author Bernd Rinn
*/
public class ConsoleLogger implements ISimpleLogger
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/ISimpleLogger.java b/common/source/java/ch/systemsx/cisd/common/logging/ISimpleLogger.java
index 800e1977810..b536c5eb042 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/ISimpleLogger.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/ISimpleLogger.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.logging;
/**
* A role that represents a simple logger (may be an ant task or a log4j logger}.
- *
+ *
* @author Bernd Rinn
*/
public interface ISimpleLogger
@@ -26,5 +26,5 @@ public interface ISimpleLogger
/** Log <var>message</var> at log <var>level</var> out to some log file or display. */
public void log(LogLevel level, String message);
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java b/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
index fd51ae77c70..ad2f343e46d 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
@@ -49,7 +49,8 @@ public final class LogFactory
{
if (category.isAdminLog() == false)
{
- throw new IllegalArgumentException("Only admin logs are allowed here, but we got " + category + ".");
+ throw new IllegalArgumentException("Only admin logs are allowed here, but we got "
+ + category + ".");
}
return category.name();
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java b/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
index 4d60f86bb3b..6939d005ba3 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
@@ -59,7 +59,8 @@ public class LogInitializer
assert logFile != null && logFile.exists() : "Given log file must be not null and must exist.";
// For non-XML files, you will use <code>PropertyConfigurator.configureAndWatch(String)</code>
DOMConfigurator.configureAndWatch(logFile.getPath());
- LogLog.debug(String.format("Log configured from file '%s' (watching).", logFile.getAbsolutePath()));
+ LogLog.debug(String.format("Log configured from file '%s' (watching).", logFile
+ .getAbsolutePath()));
}
private final static void configureFromURL(final URL url)
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java b/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java
index d228981dc02..fb3a8cc0a90 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java
@@ -47,7 +47,8 @@ public final class LogInvocationHandler implements InvocationHandler
* @param logLevel The log level to use for normal (successful) events.
* @param classUsedToNameLogger Class used to specify the name of the logger.
*/
- public LogInvocationHandler(Object object, String name, Level logLevel, Class<?> classUsedToNameLogger)
+ public LogInvocationHandler(Object object, String name, Level logLevel,
+ Class<?> classUsedToNameLogger)
{
this.object = object;
this.name = name;
@@ -80,7 +81,8 @@ public final class LogInvocationHandler implements InvocationHandler
final Logger logger = createLogger(method);
if (throwable != null || logger.isEnabledFor(logLevel))
{
- final StringBuilder builder = new StringBuilder(throwable == null ? "Successful" : "Failed");
+ final StringBuilder builder =
+ new StringBuilder(throwable == null ? "Successful" : "Failed");
builder.append(" invocation of ");
builder.append(name).append('.').append(method.getName()).append('(');
if (args != null)
@@ -124,7 +126,8 @@ public final class LogInvocationHandler implements InvocationHandler
private Logger createLogger(Method method)
{
final LogAnnotation annotation = method.getAnnotation(LogAnnotation.class);
- final LogCategory logCategory = (annotation == null) ? LogCategory.OPERATION : annotation.logCategory();
+ final LogCategory logCategory =
+ (annotation == null) ? LogCategory.OPERATION : annotation.logCategory();
return LogFactory.getLogger(logCategory, classUsedToNameLogger);
}
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LoggingContextHandler.java b/common/source/java/ch/systemsx/cisd/common/logging/LoggingContextHandler.java
index 1fd2a7acd57..2dd2d415f2e 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LoggingContextHandler.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LoggingContextHandler.java
@@ -23,8 +23,6 @@ import org.apache.log4j.MDC;
import ch.systemsx.cisd.common.server.IRemoteHostProvider;
-
-
/**
* A class that handles the log4j context information.
*
diff --git a/common/source/java/ch/systemsx/cisd/common/mail/IMailClient.java b/common/source/java/ch/systemsx/cisd/common/mail/IMailClient.java
index 168036d093b..dadda7f16fc 100644
--- a/common/source/java/ch/systemsx/cisd/common/mail/IMailClient.java
+++ b/common/source/java/ch/systemsx/cisd/common/mail/IMailClient.java
@@ -31,6 +31,7 @@ public interface IMailClient
*
* @param recipients list of recipients (of type <code>Message.RecipientType.TO</code>)
*/
- public void sendMessage(String subject, String content, String... recipients) throws EnvironmentFailureException;
+ public void sendMessage(String subject, String content, String... recipients)
+ throws EnvironmentFailureException;
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java b/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
index 7db4a402c7f..28711540136 100644
--- a/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
+++ b/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
@@ -45,8 +45,8 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
* <p>
* Just instantiate this class and use {@link #sendMessage(String, String, String[])} to send the email via SMTP.
* </p>
- * If the SMTP host starts with <code>file://</code> the mail is not send to a real SMTP server but it is
- * stored in a file in the directory specified by the relative path following this prefix.
+ * If the SMTP host starts with <code>file://</code> the mail is not send to a real SMTP server but it is stored in a
+ * file in the directory specified by the relative path following this prefix.
*
* @author Christian Ribeaud
*/
@@ -58,7 +58,8 @@ public final class MailClient extends Authenticator implements IMailClient
/** This system property is not supported by the <i>JavaMail API</i> */
public final static String MAIL_SMTP_PASSWORD = "mail.smtp.password";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, MailClient.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, MailClient.class);
private final String smtpUsername;
@@ -77,10 +78,12 @@ public final class MailClient extends Authenticator implements IMailClient
{
this(properties.getProperty(JavaMailProperties.MAIL_FROM), properties
.getProperty(JavaMailProperties.MAIL_SMTP_HOST), properties
- .getProperty(JavaMailProperties.MAIL_SMTP_USER), properties.getProperty(MAIL_SMTP_PASSWORD));
+ .getProperty(JavaMailProperties.MAIL_SMTP_USER), properties
+ .getProperty(MAIL_SMTP_PASSWORD));
}
- public MailClient(final String from, final String smtpHost, final String smtpUsername, final String smtpPassword)
+ public MailClient(final String from, final String smtpHost, final String smtpUsername,
+ final String smtpPassword)
{
assert from != null;
assert smtpHost != null;
@@ -113,8 +116,8 @@ public final class MailClient extends Authenticator implements IMailClient
{
properties.put(JavaMailProperties.MAIL_SMTP_AUTH, Boolean.TRUE.toString());
}
- properties.put(JavaMailProperties.MAIL_DEBUG, operationLog.isDebugEnabled() ? Boolean.TRUE.toString()
- : Boolean.FALSE.toString());
+ properties.put(JavaMailProperties.MAIL_DEBUG, operationLog.isDebugEnabled() ? Boolean.TRUE
+ .toString() : Boolean.FALSE.toString());
properties.put(JavaMailProperties.MAIL_TRANSPORT_PROTOCOL, "smtp");
return properties;
}
@@ -124,9 +127,11 @@ public final class MailClient extends Authenticator implements IMailClient
Properties properties = createProperties();
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Creating mail session with following properties '" + properties + "'.");
+ operationLog.debug("Creating mail session with following properties '" + properties
+ + "'.");
}
- boolean mailSmtpAuth = Boolean.parseBoolean(properties.getProperty(JavaMailProperties.MAIL_SMTP_AUTH));
+ boolean mailSmtpAuth =
+ Boolean.parseBoolean(properties.getProperty(JavaMailProperties.MAIL_SMTP_AUTH));
Session session = Session.getInstance(properties, mailSmtpAuth ? this : null);
session.setDebug(operationLog.isDebugEnabled());
return session;
@@ -154,7 +159,8 @@ public final class MailClient extends Authenticator implements IMailClient
{
if (operationLog.isInfoEnabled())
{
- operationLog.info("Sending message from '" + from + "' to recipients '" + Arrays.asList(recipients) + "'");
+ operationLog.info("Sending message from '" + from + "' to recipients '"
+ + Arrays.asList(recipients) + "'");
}
int len = recipients.length;
InternetAddress[] internetAddresses = new InternetAddress[len];
@@ -172,8 +178,8 @@ public final class MailClient extends Authenticator implements IMailClient
send(msg);
} catch (MessagingException ex)
{
- throw new EnvironmentFailureException("Sending e-mail with subject '" + subject + "' to recipients "
- + Arrays.asList(recipients) + " failed. Reason: " + ex, ex);
+ throw new EnvironmentFailureException("Sending e-mail with subject '" + subject
+ + "' to recipients " + Arrays.asList(recipients) + " failed. Reason: " + ex, ex);
}
}
@@ -186,8 +192,9 @@ public final class MailClient extends Authenticator implements IMailClient
{
if (emailFolder.isDirectory() == false)
{
- throw new EnvironmentFailureException("There exists already a file but not a folder with path '"
- + emailFolder.getAbsolutePath() + "'.");
+ throw new EnvironmentFailureException(
+ "There exists already a file but not a folder with path '"
+ + emailFolder.getAbsolutePath() + "'.");
}
} else
{
@@ -217,7 +224,7 @@ public final class MailClient extends Authenticator implements IMailClient
Transport.send(msg);
}
}
-
+
private String renderAddresses(Address[] addresses)
{
StringBuilder builder = new StringBuilder();
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java b/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
index e54f7f29cfc..c5c630ca951 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
@@ -46,7 +46,8 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
/** Analyzes specified <code>beanClass</code> for its mandatory resp. optional properties. */
private final BeanAnalyzer<E> beanAnalyzer;
- protected AbstractParserObjectFactory(final Class<E> beanClass, final IAliasPropertyMapper propertyMapper)
+ protected AbstractParserObjectFactory(final Class<E> beanClass,
+ final IAliasPropertyMapper propertyMapper)
{
assert beanClass != null : "Given bean class can not be null.";
assert propertyMapper != null : "Given property mapper can not be null.";
@@ -102,8 +103,8 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
* not be found in the same annotated write methods (throws a <code>MandatoryPropertyMissingException</code>).
* </p>
*/
- private final void checkPropertyMapper(final Class<E> clazz, final IAliasPropertyMapper propMapper)
- throws ParserException
+ private final void checkPropertyMapper(final Class<E> clazz,
+ final IAliasPropertyMapper propMapper) throws ParserException
{
final Set<String> allPropertyNames = propMapper.getAllPropertyNames();
final Set<String> propertyNames = new LinkedHashSet<String>(allPropertyNames);
@@ -120,17 +121,18 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
missingProperties.add(fieldName);
}
}
- final Set<String> mandatoryPropertyNames = getPropertyNames(beanAnalyzer.getMandatoryProperties(), propMapper);
+ final Set<String> mandatoryPropertyNames =
+ getPropertyNames(beanAnalyzer.getMandatoryProperties(), propMapper);
if (missingProperties.size() > 0)
{
- throw new MandatoryPropertyMissingException(mandatoryPropertyNames, getPropertyNames(missingProperties,
- propMapper));
+ throw new MandatoryPropertyMissingException(mandatoryPropertyNames, getPropertyNames(
+ missingProperties, propMapper));
}
if (propertyNames.size() > 0)
{
Set<String> names = getPropertyNames(beanAnalyzer.getOptionalProperties(), propMapper);
- throw new UnmatchedPropertiesException(clazz, allPropertyNames, mandatoryPropertyNames, names,
- propertyNames);
+ throw new UnmatchedPropertiesException(clazz, allPropertyNames, mandatoryPropertyNames,
+ names, propertyNames);
}
}
@@ -152,7 +154,8 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
return propertyNames;
}
- private final String getPropertyValue(final String[] lineTokens, final IPropertyModel propertyModel)
+ private final String getPropertyValue(final String[] lineTokens,
+ final IPropertyModel propertyModel)
{
final int column = propertyModel.getColumn();
if (column >= lineTokens.length)
@@ -169,7 +172,8 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
public E createObject(final String[] lineTokens) throws ParserException
{
final E object = ClassUtils.createInstance(beanClass);
- for (final Map.Entry<String, Method> entry : beanAnalyzer.getLabelToWriteMethods().entrySet())
+ for (final Map.Entry<String, Method> entry : beanAnalyzer.getLabelToWriteMethods()
+ .entrySet())
{
final Method writeMethod = entry.getValue();
final IPropertyModel propertyModel = tryGetPropertyModel(entry.getKey());
@@ -178,8 +182,8 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
if (propertyModel != null)
{
final String propertyValue = getPropertyValue(lineTokens, propertyModel);
- ClassUtils
- .invokeMethod(writeMethod, object, convert(propertyValue, writeMethod.getParameterTypes()[0]));
+ ClassUtils.invokeMethod(writeMethod, object, convert(propertyValue, writeMethod
+ .getParameterTypes()[0]));
}
}
return object;
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java b/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
index ad4a0ff238d..428e927173e 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
@@ -56,14 +56,16 @@ final class BeanAnalyzer<T>
private final void fillProperties()
{
- final List<Method> annotatedMethods = AnnotationUtils.getAnnotatedMethodList(beanClass, BeanProperty.class);
+ final List<Method> annotatedMethods =
+ AnnotationUtils.getAnnotatedMethodList(beanClass, BeanProperty.class);
for (final Method method : annotatedMethods)
{
checkMethod(method);
final BeanProperty annotation = method.getAnnotation(BeanProperty.class);
final String label = annotation.label();
assert StringUtils.isNotEmpty(label) : String.format(
- "BeanProperty annotation's label is not specified for method '%s'", method.getName());
+ "BeanProperty annotation's label is not specified for method '%s'", method
+ .getName());
labelToWriteMethods.put(label, method);
final boolean optional = annotation.optional();
checkUnique(label, optional);
@@ -80,18 +82,19 @@ final class BeanAnalyzer<T>
private final static void checkMethod(final Method method)
{
final Class<?> returnType = method.getReturnType();
- assert returnType.equals(Void.TYPE) : String.format("Return value of method '%s' must be void.", method
- .getName());
+ assert returnType.equals(Void.TYPE) : String.format(
+ "Return value of method '%s' must be void.", method.getName());
final Class<?>[] parameterTypes = method.getParameterTypes();
- assert parameterTypes.length == 1 : String.format("Annotated method '%s' must only accept one parameter.",
- method.getName());
+ assert parameterTypes.length == 1 : String.format(
+ "Annotated method '%s' must only accept one parameter.", method.getName());
}
private final void checkUnique(final String fieldName, final boolean optional)
{
- assert optionalProperties.contains(fieldName) == false && mandatoryProperties.contains(fieldName) == false : String
- .format("%s bean property '%s' already found and must be unique.", optional ? "Optional" : "Mandatory",
- fieldName);
+ assert optionalProperties.contains(fieldName) == false
+ && mandatoryProperties.contains(fieldName) == false : String.format(
+ "%s bean property '%s' already found and must be unique.", optional ? "Optional"
+ : "Mandatory", fieldName);
}
/** Whether given <code>property</code> is mandatory. */
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java b/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
index 89a6bb55b3f..5f5c0dae934 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
@@ -30,7 +30,8 @@ public final class ColumnSizeMismatchException extends ParsingException
private final String message;
- public ColumnSizeMismatchException(final String[] tokens, final int lineNumber, final int headerLength)
+ public ColumnSizeMismatchException(final String[] tokens, final int lineNumber,
+ final int headerLength)
{
super(tokens, lineNumber);
assert tokens.length != headerLength : "Tokens length and header length must be different (otherwise no reason to throw this exception).";
@@ -52,8 +53,9 @@ public final class ColumnSizeMismatchException extends ParsingException
}
}
lineStructure.append(" <END_OF_LINE>");
- return String.format("Line <%s> has %s columns (%s) than the header (%s):\n %s", getLineNumber(), moreLessStr,
- String.valueOf(tokens.length), String.valueOf(headerLength), lineStructure.toString());
+ return String.format("Line <%s> has %s columns (%s) than the header (%s):\n %s",
+ getLineNumber(), moreLessStr, String.valueOf(tokens.length), String
+ .valueOf(headerLength), lineStructure.toString());
}
private final static String getMoreOrLessString(final String[] tokens, final int headerLength)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
index 47b2900358a..0b574df4742 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
@@ -27,7 +27,8 @@ import java.util.TreeSet;
* @author Christian Ribeaud
*/
// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field aliases)
-public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements IAliasPropertyMapper
+public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements
+ IAliasPropertyMapper
{
private final Map<String, String> aliasToPropertyMappings;
@@ -44,15 +45,15 @@ public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements
final String alias = tryGetAliasForProperty(propertyName);
if (alias != null)
{
- throw new IllegalArgumentException("Following property name '" + propertyName + "' has already alias '"
- + alias + "' registered.");
+ throw new IllegalArgumentException("Following property name '" + propertyName
+ + "' has already alias '" + alias + "' registered.");
}
// No alias for two different properties.
final String property = aliasToPropertyMappings.get(aliasName);
if (aliasToPropertyMappings.containsKey(aliasName))
{
- throw new IllegalArgumentException("Alias name '" + aliasName + "' already specified for property '"
- + property + "'.");
+ throw new IllegalArgumentException("Alias name '" + aliasName
+ + "' already specified for property '" + property + "'.");
}
}
@@ -147,7 +148,8 @@ public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements
}
@Override
- public final IPropertyModel getPropertyModel(final String propertyName) throws IllegalArgumentException
+ public final IPropertyModel getPropertyModel(final String propertyName)
+ throws IllegalArgumentException
{
return super.getPropertyModel(getRealPropertyName(propertyName));
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
index 4ceb0c5a59e..9ec9d01d3a3 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
@@ -52,7 +52,8 @@ public class DefaultLineTokenizer implements ILineTokenizer
private final Map<PropertyKey, String> properties;
/** The default <code>StrMatcher</code> for each <code>PropertyKey</code>. */
- private final static Map<PropertyKey, StrMatcher> defaultStrMatchers = createDefaultStrMatchers();
+ private final static Map<PropertyKey, StrMatcher> defaultStrMatchers =
+ createDefaultStrMatchers();
/**
* Original value is <code>null</code>.
@@ -69,7 +70,8 @@ public class DefaultLineTokenizer implements ILineTokenizer
private static final Map<PropertyKey, StrMatcher> createDefaultStrMatchers()
{
- EnumMap<PropertyKey, StrMatcher> map = new EnumMap<PropertyKey, StrMatcher>(PropertyKey.class);
+ EnumMap<PropertyKey, StrMatcher> map =
+ new EnumMap<PropertyKey, StrMatcher>(PropertyKey.class);
map.put(PropertyKey.SEPARATOR_CHARS, StrMatcher.tabMatcher());
map.put(PropertyKey.QUOTE_CHARS, StrMatcher.noneMatcher());
map.put(PropertyKey.TRIMMER_CHARS, StrMatcher.trimMatcher());
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
index 4fc09f6d007..346e117cb2a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
@@ -75,8 +75,8 @@ public class DefaultParser<E> implements IParser<E>
// Parser
//
- public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter, final int headerLength)
- throws ParsingException
+ public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter,
+ final int headerLength) throws ParsingException
{
final List<E> elements = new ArrayList<E>();
synchronized (lineTokenizer)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultPropertyMapper.java
index e092e2d318e..703b0abb81f 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultPropertyMapper.java
@@ -51,8 +51,8 @@ public class DefaultPropertyMapper implements IPropertyMapper
final String token = properties[i];
if (StringUtils.isBlank(token))
{
- throw new IllegalArgumentException(String.format("%s token of %s is blank.", StringUtilities
- .getOrdinal(i), Arrays.asList(properties)));
+ throw new IllegalArgumentException(String.format("%s token of %s is blank.",
+ StringUtilities.getOrdinal(i), Arrays.asList(properties)));
}
String tokenInLowerCase = token.toLowerCase();
propertyModels.put(tokenInLowerCase, new MappedProperty(i, tokenInLowerCase));
@@ -73,11 +73,13 @@ public class DefaultPropertyMapper implements IPropertyMapper
return new TreeSet<String>(propertyModels.keySet());
}
- public IPropertyModel getPropertyModel(final String propertyName) throws IllegalArgumentException
+ public IPropertyModel getPropertyModel(final String propertyName)
+ throws IllegalArgumentException
{
if (containsPropertyName(propertyName) == false)
{
- throw new IllegalArgumentException(String.format("Given property name '%s' does not exist.", propertyName));
+ throw new IllegalArgumentException(String.format(
+ "Given property name '%s' does not exist.", propertyName));
}
return propertyModels.get(propertyName.toLowerCase());
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
index 77fdb325a74..a5fee8a621f 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
@@ -20,8 +20,8 @@ import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
- * A <code>ILineFilter</code> implementation that extends {@link ExcludeEmptyAndCommentLineFilter} by
- * excluding the header line (if <code>> 1</code>) as well.
+ * A <code>ILineFilter</code> implementation that extends {@link ExcludeEmptyAndCommentLineFilter} by excluding the
+ * header line (if <code>> 1</code>) as well.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
index a47a6b7c519..3604b5c8d2b 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
@@ -23,7 +23,7 @@ import java.util.Set;
*
* @author Christian Ribeaud
*/
-//TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field aliases)
+// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field aliases)
public interface IAliasPropertyMapper extends IPropertyMapper
{
/**
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
index c906e5975c0..71bc73639c7 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
@@ -32,7 +32,7 @@ public interface ILineTokenizer
* </p>
*/
public void init();
-
+
/** Splits given <code>line</code> into an array of tokens. */
public String[] tokenize(String line);
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
index 28a1f135573..6c48a000a33 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
@@ -37,8 +37,8 @@ public interface IParser<E>
* @param headerLength number of columns in the header
* @return a <code>List</code> of elements.
*/
- public List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter, final int headerLength)
- throws ParsingException;
+ public List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter,
+ final int headerLength) throws ParsingException;
/**
* Sets the <code>IParserObjectFactory</code>.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
index 107c438e41c..83fdbaa52af 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
@@ -45,7 +45,8 @@ public interface IParserObjectFactory<E>
// IParserObjectFactory
//
- public final String[] createObject(final String[] lineTokens) throws ParserException
+ public final String[] createObject(final String[] lineTokens)
+ throws ParserException
{
return lineTokens;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactoryFactory.java b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactoryFactory.java
index 1a37e2db980..f53c590f954 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactoryFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactoryFactory.java
@@ -26,5 +26,6 @@ public interface IParserObjectFactoryFactory<T>
/**
* Creates a new factory for the specified property mapper.
*/
- public IParserObjectFactory<T> createFactory(final IAliasPropertyMapper propertyMapper) throws ParserException;
+ public IParserObjectFactory<T> createFactory(final IAliasPropertyMapper propertyMapper)
+ throws ParserException;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
index e4296aa2b07..a64cc458734 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
@@ -31,7 +31,8 @@ public interface IPropertyMapper
*
* @throws IllegalArgumentException if given <var>propertyName</var> does not exist.
*/
- public IPropertyModel getPropertyModel(final String propertyName) throws IllegalArgumentException;
+ public IPropertyModel getPropertyModel(final String propertyName)
+ throws IllegalArgumentException;
/**
* Returns a set of all property names.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java b/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
index ea0c295e7e4..74303463b39 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
@@ -24,7 +24,8 @@ package ch.systemsx.cisd.common.parser;
public final class IndexOutOfBoundsException extends ParserException
{
- static final String MESSAGE_FORMAT = "Not enough tokens are available (index: %d, available: %d)";
+ static final String MESSAGE_FORMAT =
+ "Not enough tokens are available (index: %d, available: %d)";
private static final long serialVersionUID = 1L;
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/Line.java b/common/source/java/ch/systemsx/cisd/common/parser/Line.java
index 8dc1066ac95..dfcd0d41157 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/Line.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/Line.java
@@ -43,6 +43,5 @@ public final class Line
{
return number;
}
-
-
+
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
index f07f180a40e..c9c953c4167 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
@@ -36,7 +36,8 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
public final class ParserUtilities
{
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, ParserUtilities.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, ParserUtilities.class);
private ParserUtilities()
{
@@ -57,7 +58,8 @@ public final class ParserUtilities
public final static Line getFirstAcceptedLine(final File file, final ILineFilter lineFilter)
{
assert file != null && file.exists() : "Given file must not be null and must exist.";
- final ILineFilter filter = lineFilter == null ? AlwaysAcceptLineFilter.INSTANCE : lineFilter;
+ final ILineFilter filter =
+ lineFilter == null ? AlwaysAcceptLineFilter.INSTANCE : lineFilter;
LineIterator lineIterator = null;
try
@@ -74,7 +76,8 @@ public final class ParserUtilities
}
} catch (IOException ex)
{
- machineLog.error("An I/O exception has occurred while reading file '" + file + "'.", ex);
+ machineLog
+ .error("An I/O exception has occurred while reading file '" + file + "'.", ex);
} finally
{
LineIterator.closeQuietly(lineIterator);
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ParsingException.java b/common/source/java/ch/systemsx/cisd/common/parser/ParsingException.java
index f59791e9725..c320fa4609a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ParsingException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ParsingException.java
@@ -41,7 +41,8 @@ public class ParsingException extends HighLevelException
this(null, tokens, lineNumber);
}
- public ParsingException(final RuntimeException cause, final String[] tokens, final int lineNumber)
+ public ParsingException(final RuntimeException cause, final String[] tokens,
+ final int lineNumber)
{
super(createMessage(tokens), cause);
this.lineNumber = lineNumber;
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index 694959fbb45..a228461fe9f 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
@@ -128,7 +128,8 @@ public class TabFileLoader<T>
boolean previousLineHasColumnHeaders = false;
while (lineIterator.hasNext())
{
- previousLineHasColumnHeaders = (previousLine != null) && PREFIX.equals(previousLine.getText());
+ previousLineHasColumnHeaders =
+ (previousLine != null) && PREFIX.equals(previousLine.getText());
previousLine = line;
line = lineIterator.next();
if (line.getText().startsWith(PREFIX) == false)
@@ -137,7 +138,8 @@ public class TabFileLoader<T>
}
}
@SuppressWarnings("null")
- final String headerLine = previousLineHasColumnHeaders ? previousLine.getText().substring(1) : line.getText();
+ final String headerLine =
+ previousLineHasColumnHeaders ? previousLine.getText().substring(1) : line.getText();
final DefaultParser<T> parser = new DefaultParser<T>();
final String[] tokens = StringUtils.split(headerLine, "\t");
@@ -209,7 +211,8 @@ public class TabFileLoader<T>
{
if (unique.add(token.toLowerCase()) == false)
{
- throw new IllegalArgumentException(String.format("Duplicated column name '%s'.", token));
+ throw new IllegalArgumentException(String.format("Duplicated column name '%s'.",
+ token));
}
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java b/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
index dbd09511271..c0ff42beb03 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
@@ -49,8 +49,9 @@ public final class UnmatchedPropertiesException extends ParserException
*/
private final Set<String> propertyNames;
- public UnmatchedPropertiesException(final Class<?> beanClass, final Set<String> allPropertyNames,
- final Set<String> mandatoryNames, final Set<String> optionalNames, final Set<String> propertyNames)
+ public UnmatchedPropertiesException(final Class<?> beanClass,
+ final Set<String> allPropertyNames, final Set<String> mandatoryNames,
+ final Set<String> optionalNames, final Set<String> propertyNames)
{
super(createMessage(beanClass, propertyNames));
assert allPropertyNames != null : "All property names can not be null.";
@@ -63,13 +64,14 @@ public final class UnmatchedPropertiesException extends ParserException
this.propertyNames = propertyNames;
}
- private final static String createMessage(final Class<?> beanClass, final Set<String> propertyNames)
+ private final static String createMessage(final Class<?> beanClass,
+ final Set<String> propertyNames)
{
assert beanClass != null : "Bean class can not be null.";
assert propertyNames != null : "Property names can not be null.";
assert propertyNames.size() > 0 : "There is no reason to throw this exception.";
- return String.format(MESSAGE_FORMAT, beanClass.getSimpleName(), MandatoryPropertyMissingException
- .toString((propertyNames)));
+ return String.format(MESSAGE_FORMAT, beanClass.getSimpleName(),
+ MandatoryPropertyMissingException.toString((propertyNames)));
}
public final Class<?> getBeanClass()
diff --git a/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java b/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
index d0a57d7e04c..0879a73c306 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.common.process;
-
/**
* A class that implements the logic of cleaning up a resource even in case of an exception but re-throws an exception
* of the clean up procedure only when the main procedure didn't throw one. <code>CleanUpRunner</code>s can be
diff --git a/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java b/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
index afc7e5c76a0..fb4b57e5ee2 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
@@ -19,10 +19,9 @@ package ch.systemsx.cisd.common.process;
import java.util.ArrayList;
import java.util.List;
-
/**
* A class that allows registering items for clean up and that allows to perform the clean up later.
- *
+ *
* @author Bernd Rinn
*/
public final class CleanUpRegistry implements ICleanUpRegistry
diff --git a/common/source/java/ch/systemsx/cisd/common/process/FileRenamingProcess.java b/common/source/java/ch/systemsx/cisd/common/process/FileRenamingProcess.java
index 97dd5f2fa09..ec7aae1b0cf 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/FileRenamingProcess.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/FileRenamingProcess.java
@@ -30,7 +30,8 @@ import ch.systemsx.cisd.common.logging.LogFactory;
*/
public final class FileRenamingProcess implements IProcess
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, FileRenamingProcess.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, FileRenamingProcess.class);
public static final long DEFAULT_MILLIS_TO_SLEEP = 5000L;
@@ -53,8 +54,8 @@ public final class FileRenamingProcess implements IProcess
this(DEFAULT_MAX_RETRIES, DEFAULT_MILLIS_TO_SLEEP, sourceFile, destinationFile);
}
- public FileRenamingProcess(final int maxRetries, final long millisToSleep, final File sourceFile,
- final File destinationFile)
+ public FileRenamingProcess(final int maxRetries, final long millisToSleep,
+ final File sourceFile, final File destinationFile)
{
this.sourceFile = sourceFile;
this.maxRetries = maxRetries;
@@ -98,12 +99,14 @@ public final class FileRenamingProcess implements IProcess
{
if (sourceFile.exists() == false)
{
- operationLog.error(String.format("Path '%s' doesn't exist, so it can't be moved to '%s'.", sourceFile,
+ operationLog.error(String.format(
+ "Path '%s' doesn't exist, so it can't be moved to '%s'.", sourceFile,
destinationFile));
// Nothing to do here. So exit the looping by returning true.
return true;
}
- operationLog.warn(String.format("Moving path '%s' to directory '%s' failed (attempt %d).", sourceFile,
+ operationLog.warn(String.format(
+ "Moving path '%s' to directory '%s' failed (attempt %d).", sourceFile,
destinationFile, ++failures));
}
return true;
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java b/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
index d78a39be4b0..d0a5b098c56 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
@@ -18,7 +18,7 @@ package ch.systemsx.cisd.common.process;
/**
* A role that allows to register a clean-up method that is called regardless of whether an exception occurs or not.
- *
+ *
* @author Bernd Rinn
*/
public interface ICleanUpRegistry
@@ -28,5 +28,5 @@ public interface ICleanUpRegistry
* Register a clean-up to run when the main {@link Runnable} has been executed.
*/
public void registerCleanUp(Runnable cleanUp);
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java b/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
index ef192bf08a6..66366724fa2 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
@@ -100,10 +100,11 @@ public class ProcessExecutionHelper
* @param machineLog The {@link Logger} to use for all message on the lower (machine) level.
* @return <code>true</code>, if the process did complete successfully, <code>false</code> otherwise.
*/
- public static boolean runAndLog(List<String> cmd, long millisToWaitForCompletion, Logger operationLog,
- Logger machineLog)
+ public static boolean runAndLog(List<String> cmd, long millisToWaitForCompletion,
+ Logger operationLog, Logger machineLog)
{
- return new ProcessExecutionHelper(operationLog, machineLog).runAndLog(cmd, millisToWaitForCompletion);
+ return new ProcessExecutionHelper(operationLog, machineLog).runAndLog(cmd,
+ millisToWaitForCompletion);
}
/**
@@ -116,10 +117,11 @@ public class ProcessExecutionHelper
* @param machineLog The {@link Logger} to use for all message on the lower (machine) level.
* @return The process result.
*/
- public static ProcessResult run(List<String> cmd, long millisToWaitForCompletion, Logger operationLog,
- Logger machineLog)
+ public static ProcessResult run(List<String> cmd, long millisToWaitForCompletion,
+ Logger operationLog, Logger machineLog)
{
- return new ProcessExecutionHelper(operationLog, machineLog).run(cmd, millisToWaitForCompletion);
+ return new ProcessExecutionHelper(operationLog, machineLog).run(cmd,
+ millisToWaitForCompletion);
}
/**
@@ -148,7 +150,8 @@ public class ProcessExecutionHelper
{
return processOutput;
}
- final BufferedReader reader = new BufferedReader(new InputStreamReader(processOrNull.getInputStream()));
+ final BufferedReader reader =
+ new BufferedReader(new InputStreamReader(processOrNull.getInputStream()));
try
{
String ln;
@@ -158,7 +161,8 @@ public class ProcessExecutionHelper
}
} catch (IOException e)
{
- machineLog.warn(String.format("IOException when reading stdout, msg='%s'.", e.getMessage()));
+ machineLog.warn(String.format("IOException when reading stdout, msg='%s'.", e
+ .getMessage()));
} finally
{
IOUtils.closeQuietly(reader);
@@ -231,7 +235,8 @@ public class ProcessExecutionHelper
boolean isInterrupted = false;
try
{
- watchDogOrNull = tryCreateWatchDog(processStatus, millisoWaitForCompletion, commandLine.get(0));
+ watchDogOrNull =
+ tryCreateWatchDog(processStatus, millisoWaitForCompletion, commandLine.get(0));
final Process process;
try
{
@@ -279,7 +284,8 @@ public class ProcessExecutionHelper
return ProcessResult.createNotStarted(commandLine, operationLog, machineLog);
}
- private ProcessResult createResult(List<String> commandLine, final Process processOrNull, boolean isInterrupted)
+ private ProcessResult createResult(List<String> commandLine, final Process processOrNull,
+ boolean isInterrupted)
{
if (processOrNull == null)
{
@@ -288,7 +294,8 @@ public class ProcessExecutionHelper
{
if (isInterrupted)
{
- return ProcessResult.createWaitingInterrupted(processOrNull, commandLine, operationLog, machineLog);
+ return ProcessResult.createWaitingInterrupted(processOrNull, commandLine,
+ operationLog, machineLog);
} else
{
return ProcessResult.create(processOrNull, commandLine, operationLog, machineLog);
@@ -296,22 +303,24 @@ public class ProcessExecutionHelper
}
}
- private void logInterruption(final String commandLine, ProcessStatus terminationStatus, InterruptedException ex)
+ private void logInterruption(final String commandLine, ProcessStatus terminationStatus,
+ InterruptedException ex)
{
if (terminationStatus.isInterruptedAfterTimeout() == false) // have NOT been stopped by the watchDog
{
machineLog.error(String.format("Execution of %s interrupted", commandLine), ex);
} else
{
- operationLog.warn(String.format("Execution of %s interrupted after timeout", commandLine));
+ operationLog.warn(String.format("Execution of %s interrupted after timeout",
+ commandLine));
}
}
/*
* isTerminated is passed by reference. Access to it should be synchronized on process variable
*/
- private Timer tryCreateWatchDog(final ProcessStatus processStatus, final long millisToWaitForCompletion,
- final String commandForLog)
+ private Timer tryCreateWatchDog(final ProcessStatus processStatus,
+ final long millisToWaitForCompletion, final String commandForLog)
{
final Timer watchDogOrNull;
if (millisToWaitForCompletion > 0L)
@@ -323,7 +332,8 @@ public class ProcessExecutionHelper
@Override
public void run()
{
- operationLog.warn(String.format("Destroy process since it didn't finish in %d milli seconds",
+ operationLog.warn(String.format(
+ "Destroy process since it didn't finish in %d milli seconds",
millisToWaitForCompletion));
Process process = processStatus.tryGetProcess();
if (process != null)
@@ -338,7 +348,8 @@ public class ProcessExecutionHelper
{
processStatus.setInterruptedAfterTimeout();
operationLog.info(String.format(
- "Interrupting waiting for the process %s by the watchDog", commandForLog));
+ "Interrupting waiting for the process %s by the watchDog",
+ commandForLog));
// stop waiting for the process. We want to prevent situations when the child process,
// which is an external program, gets stuck during the start or cannot be destroyed. It
// would cause the whole system to hang and we do not want that.
@@ -373,8 +384,8 @@ public class ProcessExecutionHelper
return result.isOK();
}
- public static void logProcessExecution(String commandName, int exitValue, List<String> processOutput,
- Logger operationLog, Logger machineLog)
+ public static void logProcessExecution(String commandName, int exitValue,
+ List<String> processOutput, Logger operationLog, Logger machineLog)
{
if (exitValue != EXIT_VALUE_OK)
{
@@ -387,7 +398,8 @@ public class ProcessExecutionHelper
}
}
- private static void logProcessExitValue(final Level logLevel, Logger operationLog, String commandName, int exitValue)
+ private static void logProcessExitValue(final Level logLevel, Logger operationLog,
+ String commandName, int exitValue)
{
assert logLevel != null;
assert operationLog != null;
@@ -398,13 +410,13 @@ public class ProcessExecutionHelper
operationLog.log(logLevel, String.format("[%s] process was destroyed.", commandName));
} else
{
- operationLog.log(logLevel, String.format("[%s] process returned with exit value %d.", commandName,
- exitValue));
+ operationLog.log(logLevel, String.format("[%s] process returned with exit value %d.",
+ commandName, exitValue));
}
}
- private static void logProcessOutput(final Level logLevel, Logger machineLog, String commandName,
- List<String> processOutputLines)
+ private static void logProcessOutput(final Level logLevel, Logger machineLog,
+ String commandName, List<String> processOutputLines)
{
assert logLevel != null;
assert machineLog != null;
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java b/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
index 06cf63111cc..8272c38bc20 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
@@ -46,13 +46,15 @@ public final class ProcessResult
private List<String> outputLines;
// process finished or was terminated after timeout
- public static ProcessResult create(Process process, List<String> commandLine, Logger operationLog, Logger machineLog)
+ public static ProcessResult create(Process process, List<String> commandLine,
+ Logger operationLog, Logger machineLog)
{
return new ProcessResult(process, false, commandLine, operationLog, machineLog);
}
// process could not start at all
- public static ProcessResult createNotStarted(List<String> commandLine, Logger operationLog, Logger machineLog)
+ public static ProcessResult createNotStarted(List<String> commandLine, Logger operationLog,
+ Logger machineLog)
{
return new ProcessResult(null, false, commandLine, operationLog, machineLog);
}
@@ -64,8 +66,8 @@ public final class ProcessResult
return new ProcessResult(process, true, commandLine, operationLog, machineLog);
}
- private ProcessResult(Process processOrNull, boolean hasBlocked, List<String> commandLine, Logger operationLog,
- Logger machineLog)
+ private ProcessResult(Process processOrNull, boolean hasBlocked, List<String> commandLine,
+ Logger operationLog, Logger machineLog)
{
this.commandLine = commandLine;
this.commandName = new File(commandLine.get(0)).getName();
@@ -180,18 +182,19 @@ public final class ProcessResult
{
if (isRun() == false)
{
- operationLog.log(logLevel, String.format("[%s] process could not be run.", commandName));
+ operationLog
+ .log(logLevel, String.format("[%s] process could not be run.", commandName));
} else if (isTerminated())
{
operationLog.log(logLevel, String.format("[%s] process was destroyed.", commandName));
} else if (hasBlocked())
{
- operationLog.log(logLevel, String.format("[%s] process has blocked and could not be destroyed.",
- commandName));
+ operationLog.log(logLevel, String.format(
+ "[%s] process has blocked and could not be destroyed.", commandName));
} else
{
- operationLog.log(logLevel, String.format("[%s] process returned with exit value %d.", commandName,
- exitValue()));
+ operationLog.log(logLevel, String.format("[%s] process returned with exit value %d.",
+ commandName, exitValue()));
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java b/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
index 73d0465f5e8..939a000fc2c 100644
--- a/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
+++ b/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
@@ -26,24 +26,24 @@ import java.util.HashSet;
import java.util.Set;
/**
- * Helper class for checking an interface or a class to be ready for RMI.
- *
+ * Helper class for checking an interface or a class to be ready for RMI.
+ *
* @author Franz-Josef Elmer
*/
public class InterfaceForRMIChecker
{
/**
- * Asserts that the specified interface is ready for RMI. That is, for all methods
- * the parameter types and the return type is {@link Serializable}.
+ * Asserts that the specified interface is ready for RMI. That is, for all methods the parameter types and the
+ * return type is {@link Serializable}.
*
- * @throws AssertionError if <code>interfaze</code> is not an interface or a parameter type or
- * a return value is not serializable.
+ * @throws AssertionError if <code>interfaze</code> is not an interface or a parameter type or a return value is
+ * not serializable.
*/
public static void assertInterfaceForRMI(Class<?> interfaze)
{
assert interfaze != null : "Unspecified interface.";
assert interfaze.isInterface() : "Not an interface " + interfaze;
-
+
Set<Class<?>> visitedClasses = new HashSet<Class<?>>();
Method[] methods = interfaze.getMethods();
for (Method method : methods)
@@ -51,7 +51,7 @@ public class InterfaceForRMIChecker
assertMethodForRMI(method, visitedClasses);
}
}
-
+
private static void assertMethodForRMI(Method method, Set<Class<?>> visitedClasses)
{
Class<?>[] parameterTypes = method.getParameterTypes();
@@ -65,19 +65,20 @@ public class InterfaceForRMIChecker
assertSerializable(returnType, visitedClasses, true);
}
}
-
+
/**
* Asserts that the specified class is serializable.
*
- * @throws AssertionError if <code>clazz</code> is not serializable or a non-transient non-static
- * attribute isn't serializable.
+ * @throws AssertionError if <code>clazz</code> is not serializable or a non-transient non-static attribute isn't
+ * serializable.
*/
public static void assertSerializable(Class<?> clazz)
{
assertSerializable(clazz, new HashSet<Class<?>>(), true);
}
- private static void assertSerializable(Class<?> clazz, Set<Class<?>> visitedClasses, boolean checkImplementsSerializable)
+ private static void assertSerializable(Class<?> clazz, Set<Class<?>> visitedClasses,
+ boolean checkImplementsSerializable)
{
assert clazz != null : "Unspecified class.";
if (clazz.isPrimitive() || visitedClasses.contains(clazz))
@@ -92,7 +93,8 @@ public class InterfaceForRMIChecker
{
if (checkImplementsSerializable)
{
- assert Serializable.class.isAssignableFrom(clazz) : clazz + " does not implements java.io.Serializable";
+ assert Serializable.class.isAssignableFrom(clazz) : clazz
+ + " does not implements java.io.Serializable";
}
Field[] fields = clazz.getDeclaredFields();
for (Field field : fields)
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java b/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
index 15dc6ab3683..65a3808055f 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
@@ -23,7 +23,6 @@ import org.apache.commons.lang.builder.EqualsBuilder;
import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang.builder.ToStringBuilder;
-
/**
* If you want your class to behave correctly when used in {@link Map}s or {@link Set}s, you can do this by:
* <ol>
@@ -55,6 +54,7 @@ public abstract class AbstractHashable
@Override
public final String toString()
{
- return ToStringBuilder.reflectionToString(this, ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
index a90fe315a14..848ba013c38 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
@@ -151,9 +151,10 @@ public final class BeanUtils
@SuppressWarnings("unchecked")
private static final Set<Class> immutableTypes =
- new LinkedHashSet<Class>(Arrays.asList(boolean.class, Boolean.class, byte.class, Byte.class, short.class,
- Short.class, int.class, Integer.class, long.class, Long.class, float.class, Float.class,
- double.class, Double.class, String.class, Date.class));
+ new LinkedHashSet<Class>(Arrays.asList(boolean.class, Boolean.class, byte.class,
+ Byte.class, short.class, Short.class, int.class, Integer.class, long.class,
+ Long.class, float.class, Float.class, double.class, Double.class, String.class,
+ Date.class));
/**
* Creates a new list of Beans of type <var>clazz</var>.
@@ -173,7 +174,8 @@ public final class BeanUtils
* Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code> for parameter
* specification.
*/
- public static <T, S> T[] createBeanArray(Class<T> clazz, Collection<S> source, Converter converter)
+ public static <T, S> T[] createBeanArray(Class<T> clazz, Collection<S> source,
+ Converter converter)
{
assert clazz != null;
@@ -214,7 +216,8 @@ public final class BeanUtils
* @return The new list filled from <var>sourceList</var> or <code>null</code>, if <var>sourceList</var> is
* <code>null</code>.
*/
- public final static <T, S> List<T> createBeanList(Class<T> clazz, Iterable<S> source, Converter converter)
+ public final static <T, S> List<T> createBeanList(Class<T> clazz, Iterable<S> source,
+ Converter converter)
{
assert clazz != null;
@@ -260,7 +263,8 @@ public final class BeanUtils
* <code>null</code>, in which case only standard conversions are allowed.
* @return The new bean or <code>null</code> if <var>sourceBean</var> is <code>null</code>.
*/
- public static <T> T fillBean(Class<T> beanClass, T beanInstance, Object sourceBean, Converter converter)
+ public static <T> T fillBean(Class<T> beanClass, T beanInstance, Object sourceBean,
+ Converter converter)
{
Converter c = converter;
if (c == null)
@@ -319,7 +323,8 @@ public final class BeanUtils
try
{
T destinationBean =
- (beanInstance != null) ? beanInstance : instantiateBean(beanClass, sourceBean, setterAnnotations);
+ (beanInstance != null) ? beanInstance : instantiateBean(beanClass, sourceBean,
+ setterAnnotations);
if (isArray(destinationBean))
{
if (isArray(sourceBean))
@@ -327,17 +332,20 @@ public final class BeanUtils
destinationBean = copyArrayToArray(destinationBean, sourceBean, converter);
} else if (isCollection(sourceBean))
{
- destinationBean = (T) copyCollectionToArray(destinationBean, (Collection<?>) sourceBean, converter);
+ destinationBean =
+ (T) copyCollectionToArray(destinationBean, (Collection<?>) sourceBean,
+ converter);
}
} else if (isCollection(destinationBean))
{
if (isArray(sourceBean))
{
- copyArrayToCollection((Collection<?>) destinationBean, sourceBean, setterAnnotations, converter);
+ copyArrayToCollection((Collection<?>) destinationBean, sourceBean,
+ setterAnnotations, converter);
} else if (isCollection(sourceBean))
{
- copyCollectionToCollection((Collection<?>) destinationBean, (Collection<?>) sourceBean,
- setterAnnotations, converter);
+ copyCollectionToCollection((Collection<?>) destinationBean,
+ (Collection<?>) sourceBean, setterAnnotations, converter);
}
} else
{
@@ -378,8 +386,9 @@ public final class BeanUtils
return clazz.isArray();
}
- private static <T> T instantiateBean(Class<T> beanClass, Object sourceBean, AnnotationMap setterAnnotations)
- throws InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException
+ private static <T> T instantiateBean(Class<T> beanClass, Object sourceBean,
+ AnnotationMap setterAnnotations) throws InstantiationException, IllegalAccessException,
+ InvocationTargetException, NoSuchMethodException
{
if (sourceBean == null)
{
@@ -421,21 +430,24 @@ public final class BeanUtils
}
@SuppressWarnings("unchecked")
- private static <T> T createArray(Class<T> beanClass, int length) throws NegativeArraySizeException
+ private static <T> T createArray(Class<T> beanClass, int length)
+ throws NegativeArraySizeException
{
return (T) Array.newInstance(beanClass.getComponentType(), length);
}
@SuppressWarnings("unchecked")
- private static <E> E[] createArrayOfType(Class<E> elemClass, int length) throws NegativeArraySizeException
+ private static <E> E[] createArrayOfType(Class<E> elemClass, int length)
+ throws NegativeArraySizeException
{
return (E[]) Array.newInstance(elemClass, length);
}
@SuppressWarnings("unchecked")
// No way to avoid the warning since the compiler doesn't accept something like ArrayList<String>.class
- private final static <T> T createCollection(final int size, final AnnotationMap setterAnnotations)
- throws InstantiationException, IllegalAccessException, SecurityException, NoSuchMethodException,
+ private final static <T> T createCollection(final int size,
+ final AnnotationMap setterAnnotations) throws InstantiationException,
+ IllegalAccessException, SecurityException, NoSuchMethodException,
IllegalArgumentException, InvocationTargetException
{
final CollectionMapping mapping = getCollectionMapping(setterAnnotations);
@@ -452,8 +464,10 @@ public final class BeanUtils
}
@SuppressWarnings("unchecked")
- private static <T> T constructCollection(final Constructor<? extends Collection> constructorWithSize, int size)
- throws InstantiationException, IllegalAccessException, IllegalArgumentException, InvocationTargetException
+ private static <T> T constructCollection(
+ final Constructor<? extends Collection> constructorWithSize, int size)
+ throws InstantiationException, IllegalAccessException, IllegalArgumentException,
+ InvocationTargetException
{
// This conversion _can_ go wrong if the concrete collection class doesn't implement the right sub-interface of
// collection, e.g. when using a HashSet as concrete collection class where a List is required.
@@ -506,7 +520,8 @@ public final class BeanUtils
for (int index = 0; index < length; ++index)
{
final Object sourceElement = Array.get(source, index);
- final Object destinationElement = createBean(componentType, sourceElement, converter);
+ final Object destinationElement =
+ createBean(componentType, sourceElement, converter);
Array.set(returned, index, destinationElement);
}
}
@@ -514,8 +529,8 @@ public final class BeanUtils
}
@SuppressWarnings("unchecked")
- private final static <T> T[] copyCollectionToArray(Object destination, Collection<T> source, Converter converter)
- throws IllegalAccessException, InvocationTargetException
+ private final static <T> T[] copyCollectionToArray(Object destination, Collection<T> source,
+ Converter converter) throws IllegalAccessException, InvocationTargetException
{
if (destination == null)
{
@@ -543,7 +558,8 @@ public final class BeanUtils
int index = 0;
for (Object sourceElement : source)
{
- final Object destinationElement = createBean(componentType, sourceElement, converter);
+ final Object destinationElement =
+ createBean(componentType, sourceElement, converter);
Array.set(returned, index++, destinationElement);
}
}
@@ -571,7 +587,8 @@ public final class BeanUtils
for (int index = 0; index < length; ++index)
{
final Object sourceElement = Array.get(source, index);
- final Object destinationElement = createBean(componentType, sourceElement, converter);
+ final Object destinationElement =
+ createBean(componentType, sourceElement, converter);
addToUntypedCollection(destination, destinationElement);
}
}
@@ -595,7 +612,8 @@ public final class BeanUtils
{
for (Object sourceElement : source)
{
- final Object destinationElement = createBean(componentType, sourceElement, converter);
+ final Object destinationElement =
+ createBean(componentType, sourceElement, converter);
addToUntypedCollection(destination, destinationElement);
}
}
@@ -623,20 +641,25 @@ public final class BeanUtils
return mapping;
}
- private static <T> void copyBean(T destination, Object source, Converter converter) throws IllegalAccessException,
- InvocationTargetException
+ private static <T> void copyBean(T destination, Object source, Converter converter)
+ throws IllegalAccessException, InvocationTargetException
{
if (destination == null)
{
return;
}
- final Collection<Method> destinationSetters = scanForPublicMethods(destination, SETTER_PREFIX, 1).values();
- final Map<String, Method> destinationGetters = scanForPublicMethods(destination, GETTER_PREFIX, 0);
+ final Collection<Method> destinationSetters =
+ scanForPublicMethods(destination, SETTER_PREFIX, 1).values();
+ final Map<String, Method> destinationGetters =
+ scanForPublicMethods(destination, GETTER_PREFIX, 0);
final Map<String, Method> sourceGetters = scanForPublicMethods(source, GETTER_PREFIX, 0);
- scanForPublicMethods(source, sourceGetters, BOOLEAN_GETTER_PREFIX, 0, boolean.class, Boolean.class);
+ scanForPublicMethods(source, sourceGetters, BOOLEAN_GETTER_PREFIX, 0, boolean.class,
+ Boolean.class);
for (Method setter : destinationSetters)
{
- final T newBean = emergeNewBean(setter, source, destination, sourceGetters, destinationGetters, converter);
+ final T newBean =
+ emergeNewBean(setter, source, destination, sourceGetters, destinationGetters,
+ converter);
if (newBean != null)
{
try
@@ -648,9 +671,10 @@ public final class BeanUtils
final String defaultJavaArgumentTypeMismatchMessage = "argument type mismatch";
if (defaultJavaArgumentTypeMismatchMessage.equals(ex.getMessage()))
{
- throw new IllegalArgumentException(defaultJavaArgumentTypeMismatchMessage + ": method '"
- + setter.toGenericString() + "': cannot assign from '"
- + newBean.getClass().getCanonicalName() + "'.");
+ throw new IllegalArgumentException(defaultJavaArgumentTypeMismatchMessage
+ + ": method '" + setter.toGenericString()
+ + "': cannot assign from '" + newBean.getClass().getCanonicalName()
+ + "'.");
} else
{
throw ex;
@@ -674,9 +698,10 @@ public final class BeanUtils
* </p>
*/
@SuppressWarnings("unchecked")
- private static <T> T emergeNewBean(Method setter, Object source, T destination, Map<String, Method> sourceGetters,
- Map<String, Method> destinationGetters, Converter converter) throws IllegalArgumentException,
- IllegalAccessException, InvocationTargetException
+ private static <T> T emergeNewBean(Method setter, Object source, T destination,
+ Map<String, Method> sourceGetters, Map<String, Method> destinationGetters,
+ Converter converter) throws IllegalArgumentException, IllegalAccessException,
+ InvocationTargetException
{
final AnnotationMap annotationMap = new SetterAnnotationMap(setter);
final Method converterMethod = getConverterMethod(setter, source, converter);
@@ -739,12 +764,15 @@ public final class BeanUtils
{
String methodName = "convertTo" + setter.getName().substring(SETTER_PREFIX.length());
Class<? extends Converter> converterClasss = converter.getClass();
- Collection<Class<?>> classes = ClassUtils.gatherAllCastableClassesAndInterfacesFor(sourceBean);
+ Collection<Class<?>> classes =
+ ClassUtils.gatherAllCastableClassesAndInterfacesFor(sourceBean);
for (Class<?> clazz : classes)
{
try
{
- final Method converterMethod = converterClasss.getMethod(methodName, new Class[] { clazz });
+ final Method converterMethod =
+ converterClasss.getMethod(methodName, new Class[]
+ { clazz });
if (converterMethod.isAccessible() == false)
{
converterMethod.setAccessible(true);
@@ -778,27 +806,30 @@ public final class BeanUtils
return null;
}
- private static Map<String, Method> scanForPublicMethods(Object bean, String prefix, int numberOfParameters)
+ private static Map<String, Method> scanForPublicMethods(Object bean, String prefix,
+ int numberOfParameters)
{
final Map<String, Method> methodMap = new LinkedHashMap<String, Method>();
scanForPublicMethods(bean, methodMap, prefix, numberOfParameters, (Set<Class<?>>) null);
return methodMap;
}
- private static void scanForPublicMethods(Object bean, Map<String, Method> methodMap, String prefix,
- int numberOfParameters, Class<?>... returnValueTypes)
+ private static void scanForPublicMethods(Object bean, Map<String, Method> methodMap,
+ String prefix, int numberOfParameters, Class<?>... returnValueTypes)
{
List<Class<?>> list = Arrays.asList(returnValueTypes);
- scanForPublicMethods(bean, methodMap, prefix, numberOfParameters, new LinkedHashSet<Class<?>>(list));
+ scanForPublicMethods(bean, methodMap, prefix, numberOfParameters,
+ new LinkedHashSet<Class<?>>(list));
}
- private static void scanForPublicMethods(Object bean, Map<String, Method> methodMap, String prefix,
- int numberOfParameters, Set<Class<?>> returnValueTypes)
+ private static void scanForPublicMethods(Object bean, Map<String, Method> methodMap,
+ String prefix, int numberOfParameters, Set<Class<?>> returnValueTypes)
{
for (Method method : bean.getClass().getMethods())
{
final String methodName = method.getName();
- if (methodName.startsWith(prefix) && method.getParameterTypes().length == numberOfParameters
+ if (methodName.startsWith(prefix)
+ && method.getParameterTypes().length == numberOfParameters
&& Modifier.isPublic(method.getModifiers()))
{
if (returnValueTypes == null || returnValueTypes.contains(method.getReturnType()))
@@ -820,7 +851,8 @@ public final class BeanUtils
{
try
{
- final Map<String, PropertyDescriptor> map = new LinkedHashMap<String, PropertyDescriptor>();
+ final Map<String, PropertyDescriptor> map =
+ new LinkedHashMap<String, PropertyDescriptor>();
final List<PropertyDescriptor> descriptors =
new ArrayList<PropertyDescriptor>(Arrays.asList(Introspector.getBeanInfo(clazz)
.getPropertyDescriptors()));
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
index 29dba01ad90..9e0149c1968 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
@@ -45,7 +45,8 @@ public final class ClassUtils
/**
* Gathers all classes and interfaces the specified object can be casted to.
*/
- public final static Collection<Class<?>> gatherAllCastableClassesAndInterfacesFor(final Object object)
+ public final static Collection<Class<?>> gatherAllCastableClassesAndInterfacesFor(
+ final Object object)
{
assert object != null : "Unspecified object";
@@ -134,7 +135,8 @@ public final class ClassUtils
* <code>null</code> arguments but rather as <code>new Object[]{null}</code>.
* @return an instance of type <code>interface</code>.
*/
- public static <T> T create(final Class<T> superClazz, final String className, final Object... argumentsOrNull)
+ public static <T> T create(final Class<T> superClazz, final String className,
+ final Object... argumentsOrNull)
{
assert superClazz != null : "Missing super class";
assert className != null : "Missing class name";
@@ -144,8 +146,8 @@ public final class ClassUtils
final Class<?> clazz = Class.forName(className);
assert clazz.isInterface() == false : "Interface '" + clazz.getName()
+ "' can not be instanciated as it is an interface.";
- assert superClazz.isAssignableFrom(clazz) : "Class '" + clazz.getName() + "' does not implements/extends '"
- + superClazz.getName() + "'.";
+ assert superClazz.isAssignableFrom(clazz) : "Class '" + clazz.getName()
+ + "' does not implements/extends '" + superClazz.getName() + "'.";
if (argumentsOrNull == null)
{
return cast(clazz.newInstance());
@@ -154,8 +156,8 @@ public final class ClassUtils
final Constructor<T> constructor = getConstructor(clazz, classes);
if (constructor == null)
{
- throw new IllegalArgumentException(String.format("No constructor could be found for classes '%s'.",
- Arrays.asList(classes)));
+ throw new IllegalArgumentException(String.format(
+ "No constructor could be found for classes '%s'.", Arrays.asList(classes)));
}
return constructor.newInstance(argumentsOrNull);
} catch (final ClassNotFoundException e)
@@ -169,8 +171,9 @@ public final class ClassUtils
} catch (final NoSuchMethodException ex)
{
}
- throw new IllegalArgumentException(String.format("Cannot instantiate class '%s' with given arguments '%s'.",
- className, Arrays.asList(argumentsOrNull)));
+ throw new IllegalArgumentException(String.format(
+ "Cannot instantiate class '%s' with given arguments '%s'.", className, Arrays
+ .asList(argumentsOrNull)));
}
@SuppressWarnings("unchecked")
@@ -190,8 +193,8 @@ public final class ClassUtils
return classes;
}
- private final static <T> Constructor<T> getConstructor(final Class<?> clazz, final Class<?>[] classes)
- throws NoSuchMethodException
+ private final static <T> Constructor<T> getConstructor(final Class<?> clazz,
+ final Class<?>[] classes) throws NoSuchMethodException
{
final Constructor<?>[] constructors = clazz.getConstructors();
Constructor<?> returned = null;
@@ -250,7 +253,8 @@ public final class ClassUtils
* Wraps any checked exception in a {@link CheckedExceptionTunnel}.
* </p>
*/
- public final static void invokeMethod(final Method method, final Object obj, final Object... args)
+ public final static void invokeMethod(final Method method, final Object obj,
+ final Object... args)
{
try
{
@@ -274,7 +278,8 @@ public final class ClassUtils
*
* @return a <code>true</code> if <code>fieldName</code> has been modified.
*/
- public final static boolean setFieldValue(final Object object, final String fieldName, final Object newValue)
+ public final static boolean setFieldValue(final Object object, final String fieldName,
+ final Object newValue)
{
assert object != null : "Unspecified object.";
final Class<?> clazz = object.getClass();
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
index 4479526ac02..bf43a88d806 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
@@ -105,11 +105,11 @@ public final class DirectoryScanningTimerTask extends TimerTask
* next error is logged (can be used to suppress error when the directory is on a remote share and the
* server is flaky sometimes)
*/
- public DirectoryScanningTimerTask(File sourceDirectory, FileFilter filter, IPathHandler handler,
- int ignoredErrorCount)
+ public DirectoryScanningTimerTask(File sourceDirectory, FileFilter filter,
+ IPathHandler handler, int ignoredErrorCount)
{
- this(asScannedStore(sourceDirectory, filter), sourceDirectory, asScanningHandler(sourceDirectory, handler),
- ignoredErrorCount);
+ this(asScannedStore(sourceDirectory, filter), sourceDirectory, asScanningHandler(
+ sourceDirectory, handler), ignoredErrorCount);
}
/**
@@ -122,8 +122,8 @@ public final class DirectoryScanningTimerTask extends TimerTask
* next error is logged (can be used to suppress error when the directory is on a remote share and the
* server is flaky sometimes)
*/
- public DirectoryScanningTimerTask(IScannedStore scannedStore, File faultyPathDirectory, IStoreHandler handler,
- int ignoredErrorCount)
+ public DirectoryScanningTimerTask(IScannedStore scannedStore, File faultyPathDirectory,
+ IStoreHandler handler, int ignoredErrorCount)
{
assert scannedStore != null;
assert handler != null;
@@ -265,7 +265,8 @@ public final class DirectoryScanningTimerTask extends TimerTask
faultyPathsLastChanged = faultyPathsFile.lastModified();
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("Reread faulty paths file (%s), new set contains %d entries",
+ operationLog.info(String.format(
+ "Reread faulty paths file (%s), new set contains %d entries",
getLocationDescription(faultyPathsFile), faultyPaths.size()));
}
}
@@ -282,14 +283,16 @@ public final class DirectoryScanningTimerTask extends TimerTask
final boolean logOperationError = (errorCountReadingDirectory < ignoredErrorCount);
final ISimpleLogger errorLogger =
logNotifyError ? createSimpleErrorLogger(LogCategory.NOTIFY)
- : (logOperationError ? createSimpleErrorLogger(LogCategory.OPERATION) : null);
+ : (logOperationError ? createSimpleErrorLogger(LogCategory.OPERATION)
+ : null);
final StoreItem[] paths = sourceDirectory.tryListSortedReadyToProcess(errorLogger);
if (errorCountReadingDirectory > ignoredErrorCount && paths != null)
{
if (notificationLog.isInfoEnabled())
{
- notificationLog.info(String.format("Directory '%s' is available again.", sourceDirectory));
+ notificationLog.info(String.format("Directory '%s' is available again.",
+ sourceDirectory));
}
}
if (paths == null)
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
index 8b8206377e1..6417aa3989e 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
@@ -54,12 +54,14 @@ public final class ExceptionUtils
}
/** Recursively copies cause exception from <var>fromException</var> to <var>toException</var>. */
- private final static void copyCauseException(final Exception fromException, final Exception toException)
+ private final static void copyCauseException(final Exception fromException,
+ final Exception toException)
{
assert fromException != null : "Unspecified 'from' Exception.";
assert toException != null : "Unspecified 'to' Exception.";
final Exception fromCauseException =
- (Exception) org.apache.commons.lang.exception.ExceptionUtils.getCause(fromException);
+ (Exception) org.apache.commons.lang.exception.ExceptionUtils
+ .getCause(fromException);
if (fromCauseException != null && fromCauseException != fromException)
{
final Exception toCauseException = createMasqueradingException(fromCauseException);
@@ -67,7 +69,8 @@ public final class ExceptionUtils
{
if (ClassUtils.setFieldValue(toException, "cause", toCauseException) == false)
{
- org.apache.commons.lang.exception.ExceptionUtils.setCause(toException, toCauseException);
+ org.apache.commons.lang.exception.ExceptionUtils.setCause(toException,
+ toCauseException);
}
}
copyCauseException(fromCauseException, toCauseException);
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ExtendedProperties.java b/common/source/java/ch/systemsx/cisd/common/utilities/ExtendedProperties.java
index a811bd2bac5..9af049459f5 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ExtendedProperties.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ExtendedProperties.java
@@ -76,7 +76,8 @@ public final class ExtendedProperties extends Properties
* @param prefix string, each property key should start with.
* @param dropPrefix If <code>true</code> the prefix will be removed from the key.
*/
- public static ExtendedProperties getSubset(Properties properties, String prefix, boolean dropPrefix)
+ public static ExtendedProperties getSubset(Properties properties, String prefix,
+ boolean dropPrefix)
{
return ExtendedProperties.createWith(properties).getSubset(prefix, dropPrefix);
}
@@ -205,6 +206,7 @@ public final class ExtendedProperties extends Properties
@Override
public final String toString()
{
- return StringUtils.replace(super.toString(), PROPERTY_SEPARATOR, SystemUtils.LINE_SEPARATOR);
+ return StringUtils
+ .replace(super.toString(), PROPERTY_SEPARATOR, SystemUtils.LINE_SEPARATOR);
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
index bc115557a4a..6ce02a6c347 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileUtilities.java
@@ -91,8 +91,8 @@ public final class FileUtilities
* be transfered to <code>destinationFile</code>.
* @throws EnvironmentFailureException if a {@link IOException} occured.
*/
- public static void copyFileTo(File sourceFile, File destinationFile, boolean preservesLastModifiedDate)
- throws CheckedExceptionTunnel
+ public static void copyFileTo(File sourceFile, File destinationFile,
+ boolean preservesLastModifiedDate) throws CheckedExceptionTunnel
{
FileInputStream inputStream = null;
FileOutputStream outputStream = null;
@@ -103,8 +103,8 @@ public final class FileUtilities
IOUtils.copy(inputStream, outputStream);
} catch (IOException ex)
{
- throw new EnvironmentFailureException("Couldn't copy file '" + sourceFile + "' to '" + destinationFile
- + "'.", ex);
+ throw new EnvironmentFailureException("Couldn't copy file '" + sourceFile + "' to '"
+ + destinationFile + "'.", ex);
} finally
{
IOUtils.closeQuietly(inputStream);
@@ -116,8 +116,8 @@ public final class FileUtilities
boolean successful = destinationFile.setLastModified(sourceFile.lastModified());
if (successful == false)
{
- throw new EnvironmentFailureException("Couldn't copy last modified date of file '" + sourceFile
- + "' to '" + destinationFile + "' for some unknown reason.");
+ throw new EnvironmentFailureException("Couldn't copy last modified date of file '"
+ + sourceFile + "' to '" + destinationFile + "' for some unknown reason.");
}
}
}
@@ -180,7 +180,8 @@ public final class FileUtilities
* @return The content of the file line by line.
* @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
*/
- public final static List<String> loadToStringList(final File file) throws CheckedExceptionTunnel
+ public final static List<String> loadToStringList(final File file)
+ throws CheckedExceptionTunnel
{
return loadToStringList(file, null);
}
@@ -194,8 +195,8 @@ public final class FileUtilities
* @return The content of the file line by line.
* @throws CheckedExceptionTunnel for wrapping an {@link IOException}, e.g. if the file does not exist.
*/
- public final static List<String> loadToStringList(final File file, final ILineFilter lineFilterOrNull)
- throws CheckedExceptionTunnel
+ public final static List<String> loadToStringList(final File file,
+ final ILineFilter lineFilterOrNull) throws CheckedExceptionTunnel
{
assert file != null : "Unspecified file.";
@@ -224,7 +225,8 @@ public final class FileUtilities
* @return The content of the resource, or <code>null</code> if the specified resource does not exist.
* @throws CheckedExceptionTunnel for wrapping an {@link IOException}
*/
- public static String loadToString(final Class<?> clazz, final String resource) throws CheckedExceptionTunnel
+ public static String loadToString(final Class<?> clazz, final String resource)
+ throws CheckedExceptionTunnel
{
assert clazz != null : "Given class can not be null.";
assert resource != null && resource.length() > 0 : "Given resource can not be null.";
@@ -293,8 +295,8 @@ public final class FileUtilities
}
}
- private final static BufferedReader tryGetBufferedReader(final Class<?> clazz, final String resource)
- throws FileNotFoundException
+ private final static BufferedReader tryGetBufferedReader(final Class<?> clazz,
+ final String resource) throws FileNotFoundException
{
final URL url = clazz.getResource(resource);
if (url == null)
@@ -322,8 +324,8 @@ public final class FileUtilities
return builder.toString();
}
- private final static List<String> readStringList(final BufferedReader reader, final ILineFilter lineFilterOrNull)
- throws IOException
+ private final static List<String> readStringList(final BufferedReader reader,
+ final ILineFilter lineFilterOrNull) throws IOException
{
assert reader != null : "Unspecified BufferedReader.";
final ILineFilter lineFilter;
@@ -375,13 +377,14 @@ public final class FileUtilities
final String msg = checkPathFullyAccessible(directory, kindOfDirectory, "directory");
if (msg == null && directory.isDirectory() == false)
{
- return String.format("Path '%s' is supposed to be a %s directory, but is a file.", directory.getPath(),
- kindOfDirectory);
+ return String.format("Path '%s' is supposed to be a %s directory, but is a file.",
+ directory.getPath(), kindOfDirectory);
}
return msg;
}
- private static String checkPathFullyAccessible(File path, String kindOfPath, String directoryOrFile)
+ private static String checkPathFullyAccessible(File path, String kindOfPath,
+ String directoryOrFile)
{
assert path != null;
assert kindOfPath != null;
@@ -391,18 +394,18 @@ public final class FileUtilities
{
if (path.exists() == false)
{
- return String.format("%s %s '%s' does not exist.", StringUtilities.capitalize(kindOfPath),
- directoryOrFile, path.getPath());
+ return String.format("%s %s '%s' does not exist.", StringUtilities
+ .capitalize(kindOfPath), directoryOrFile, path.getPath());
} else
{
- return String.format("%s %s '%s' is not readable.", StringUtilities.capitalize(kindOfPath),
- directoryOrFile, path.getPath());
+ return String.format("%s %s '%s' is not readable.", StringUtilities
+ .capitalize(kindOfPath), directoryOrFile, path.getPath());
}
}
if (path.canWrite() == false)
{
- return String.format("%s directory '%s' is not writable.", StringUtilities.capitalize(kindOfPath), path
- .getPath());
+ return String.format("%s directory '%s' is not writable.", StringUtilities
+ .capitalize(kindOfPath), path.getPath());
}
return null;
}
@@ -447,7 +450,8 @@ public final class FileUtilities
{
if (loggerOrNull != null)
{
- loggerOrNull.log(LogLevel.INFO, String.format("Deleting file '%s'", file.getPath()));
+ loggerOrNull.log(LogLevel.INFO, String.format("Deleting file '%s'", file
+ .getPath()));
}
file.delete();
}
@@ -455,7 +459,8 @@ public final class FileUtilities
}
if (loggerOrNull != null)
{
- loggerOrNull.log(LogLevel.INFO, String.format("Deleting directory '%s'", path.getPath()));
+ loggerOrNull.log(LogLevel.INFO, String
+ .format("Deleting directory '%s'", path.getPath()));
}
return path.delete();
}
@@ -504,7 +509,8 @@ public final class FileUtilities
private boolean terminated;
- LastChangedWorker(File root, boolean subDirectoriesOnly, long reference, boolean referenceIsRelative)
+ LastChangedWorker(File root, boolean subDirectoriesOnly, long reference,
+ boolean referenceIsRelative)
{
assert root != null;
@@ -526,8 +532,8 @@ public final class FileUtilities
if (path.canRead() == false)
{
- throw new CheckedExceptionTunnel(new IOException(String.format("Path '%s' cannot be read.", path
- .getPath())));
+ throw new CheckedExceptionTunnel(new IOException(String.format(
+ "Path '%s' cannot be read.", path.getPath())));
}
final long lastModified = path.lastModified();
lastChanged = Math.max(lastModified, lastChanged);
@@ -565,7 +571,8 @@ public final class FileUtilities
}
if (Thread.interrupted())
{
- throw new CheckedExceptionTunnel(new InterruptedException("lastChanged() interrupted"));
+ throw new CheckedExceptionTunnel(new InterruptedException(
+ "lastChanged() interrupted"));
}
traverse(entry);
}
@@ -620,7 +627,8 @@ public final class FileUtilities
*/
public static long lastChanged(File path, boolean subDirectoriesOnly, long stopWhenFindYounger)
{
- return (new LastChangedWorker(path, subDirectoriesOnly, stopWhenFindYounger, false)).getLastChanged();
+ return (new LastChangedWorker(path, subDirectoriesOnly, stopWhenFindYounger, false))
+ .getLastChanged();
}
/**
@@ -643,9 +651,11 @@ public final class FileUtilities
* @throws CheckedExceptionTunnel of a {@link InterruptedException} if the thread that the method runs in gets
* interrupted.
*/
- public static long lastChangedRelative(File path, boolean subDirectoriesOnly, long stopWhenFindYoungerRelative)
+ public static long lastChangedRelative(File path, boolean subDirectoriesOnly,
+ long stopWhenFindYoungerRelative)
{
- return (new LastChangedWorker(path, subDirectoriesOnly, stopWhenFindYoungerRelative, true)).getLastChanged();
+ return (new LastChangedWorker(path, subDirectoriesOnly, stopWhenFindYoungerRelative, true))
+ .getLastChanged();
}
/**
@@ -703,7 +713,8 @@ public final class FileUtilities
* @param regexOrNull pattern to find out the counter. If <code>null</code> then a default (<code>(\\d+)</code>)
* will be used. The given <var>regex</var> must contain <code>(\\d+)</code> or <code>([0-9]+)</code>.
*/
- public final static File createNextNumberedFile(File path, Pattern regexOrNull, String defaultFileNameOrNull)
+ public final static File createNextNumberedFile(File path, Pattern regexOrNull,
+ String defaultFileNameOrNull)
{
assert path != null;
if (path.exists() == false)
@@ -716,7 +727,8 @@ public final class FileUtilities
pattern = ONE_OR_MORE_DIGITS;
} else
{
- assert regexOrNull.pattern().indexOf("(\\d+)") > -1 || regexOrNull.pattern().indexOf("([0-9]+)") > -1;
+ assert regexOrNull.pattern().indexOf("(\\d+)") > -1
+ || regexOrNull.pattern().indexOf("([0-9]+)") > -1;
pattern = regexOrNull;
}
@@ -733,7 +745,8 @@ public final class FileUtilities
{
fileName = pathName + "1";
}
- return createNextNumberedFile(new File(path.getParent(), fileName), pattern, defaultFileNameOrNull);
+ return createNextNumberedFile(new File(path.getParent(), fileName), pattern,
+ defaultFileNameOrNull);
}
StringBuilder builder = new StringBuilder();
int nextStart = 0;
@@ -823,25 +836,32 @@ public final class FileUtilities
Arrays.sort(files, FileComparator.BY_LAST_MODIFIED);
}
- private static void logFailureInDirectoryListing(RuntimeException exOrNull, File directory, ISimpleLogger logger)
+ private static void logFailureInDirectoryListing(RuntimeException exOrNull, File directory,
+ ISimpleLogger logger)
{
if (exOrNull == null)
{
if (directory.isFile())
{
- logger.log(LogLevel.ERROR, String.format(
- "Failed to get listing of directory '%s' (path is file instead of directory).", directory));
+ logger
+ .log(
+ LogLevel.ERROR,
+ String
+ .format(
+ "Failed to get listing of directory '%s' (path is file instead of directory).",
+ directory));
} else
{
- logger.log(LogLevel.ERROR, String.format("Failed to get listing of directory '%s' (path not found).",
- directory));
+ logger.log(LogLevel.ERROR, String.format(
+ "Failed to get listing of directory '%s' (path not found).", directory));
}
} else
{
StringWriter exStackWriter = new StringWriter();
exOrNull.printStackTrace(new PrintWriter(exStackWriter));
- logger.log(LogLevel.ERROR, String.format("Failed to get listing of directory '%s'. Exception: %s",
- directory, exStackWriter.toString()));
+ logger.log(LogLevel.ERROR, String.format(
+ "Failed to get listing of directory '%s'. Exception: %s", directory,
+ exStackWriter.toString()));
}
}
@@ -892,7 +912,8 @@ public final class FileUtilities
* @param postfix The postfix to use for the temporary name.
* @return The name of the temporary file, or <code>null</code>, if the resource could not be copied.
*/
- public final static String tryCopyResourceToTempFile(String resource, String prefix, String postfix)
+ public final static String tryCopyResourceToTempFile(String resource, String prefix,
+ String postfix)
{
try
{
@@ -916,8 +937,8 @@ public final class FileUtilities
final File[] fileList = directory.listFiles();
if (fileList == null)
{
- throw EnvironmentFailureException.fromTemplate("Failed to get listing of directory '%s'", directory
- .getAbsolutePath());
+ throw EnvironmentFailureException.fromTemplate(
+ "Failed to get listing of directory '%s'", directory.getAbsolutePath());
}
return fileList;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
index 65b709d6fe3..2aa0ba20dfc 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
@@ -38,9 +38,11 @@ public abstract class FileWatcher extends TimerTask
static final String HAS_CHANGED_FORMAT = "Watched file '%s' has changed.";
- static final String PERMISSION_EXCEPTION_FORMAT = "Was not allowed to check existence of file '%s'.";
+ static final String PERMISSION_EXCEPTION_FORMAT =
+ "Was not allowed to check existence of file '%s'.";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, FileWatcher.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, FileWatcher.class);
/** The default <code>FileWatcherState</code> implementation used. */
private static final IFileWatcherState DEFAULT_FILE_WATCHER_STATE = new LastModifiedState();
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
index 6cdc01f992c..25b45c7c7bd 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
@@ -81,7 +81,8 @@ public class FileWatcherSynchronizer extends TimerTask
}
}
- public final synchronized void addChangeListener(final File file, final ChangeListener changeListener)
+ public final synchronized void addChangeListener(final File file,
+ final ChangeListener changeListener)
{
FileWatcher fileWatcher = fileWatchers.get(file);
if (fileWatcher == null)
@@ -101,7 +102,8 @@ public class FileWatcherSynchronizer extends TimerTask
};
if (operationLog.isDebugEnabled())
{
- operationLog.debug(String.format("A new watcher has been created for file '%s'", file));
+ operationLog.debug(String.format("A new watcher has been created for file '%s'",
+ file));
}
fileWatchers.put(file, fileWatcher);
}
@@ -114,13 +116,16 @@ public class FileWatcherSynchronizer extends TimerTask
listeners.add(changeListener);
if (operationLog.isDebugEnabled())
{
- operationLog.debug(String.format(
- "A new listener has been registered for file '%s'. Currently %d listener(s) registered.", file,
- listeners.size()));
+ operationLog
+ .debug(String
+ .format(
+ "A new listener has been registered for file '%s'. Currently %d listener(s) registered.",
+ file, listeners.size()));
}
}
- public final synchronized void removeChangeListener(final File file, final ChangeListener changeListener)
+ public final synchronized void removeChangeListener(final File file,
+ final ChangeListener changeListener)
{
final FileWatcher fileWatcher = fileWatchers.get(file);
if (fileWatcher == null)
@@ -136,8 +141,11 @@ public class FileWatcherSynchronizer extends TimerTask
final int size = listeners.size();
if (operationLog.isDebugEnabled())
{
- operationLog.debug(String.format(
- "A listener for file '%s' has been removed. Currently %d listener(s) registered.", file, size));
+ operationLog
+ .debug(String
+ .format(
+ "A listener for file '%s' has been removed. Currently %d listener(s) registered.",
+ file, size));
}
if (size == 0)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/IExitHandler.java b/common/source/java/ch/systemsx/cisd/common/utilities/IExitHandler.java
index 582d3d39948..50558a7306e 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/IExitHandler.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/IExitHandler.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.utilities;
/**
- * Interface which capsulates the behaviour of a system exit.
- *
+ * Interface which capsulates the behaviour of a system exit.
+ *
* @author Franz-Josef Elmer
*/
public interface IExitHandler
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ITriggerable.java b/common/source/java/ch/systemsx/cisd/common/utilities/ITriggerable.java
index 7742bff2535..77550c71300 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ITriggerable.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ITriggerable.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.utilities;
/**
- * A role that allows to trigger some operation.
- *
+ * A role that allows to trigger some operation.
+ *
* @author Bernd Rinn
*/
public interface ITriggerable
@@ -28,5 +28,5 @@ public interface ITriggerable
* The trigger.
*/
public void trigger();
-
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java b/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
index d23f0a9cfcb..b4806772d39 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
@@ -18,20 +18,20 @@ package ch.systemsx.cisd.common.utilities;
import org.apache.commons.lang.builder.ToStringStyle;
-
/**
- * A modified short prefix {@link ToStringStyle} which allows to work together with jmock and
- * cruisecontrol. The problem was that in jmock exception messages <code>]]></code> appeared which is the
- * end of a <code><![CDATA[</code> section in the XML test report. This yields a hiccup in cruisecontrol.
- *
+ * A modified short prefix {@link ToStringStyle} which allows to work together with jmock and cruisecontrol. The problem
+ * was that in jmock exception messages <code>]]></code> appeared which is the end of a <code><![CDATA[</code>
+ * section in the XML test report. This yields a hiccup in cruisecontrol.
+ *
* @author Franz-Josef Elmer
*/
public class ModifiedShortPrefixToStringStyle extends ToStringStyle
{
private static final long serialVersionUID = 1L;
-
+
/** The one and only one instance. */
- public static final ToStringStyle MODIFIED_SHORT_PREFIX_STYLE = new ModifiedShortPrefixToStringStyle();
+ public static final ToStringStyle MODIFIED_SHORT_PREFIX_STYLE =
+ new ModifiedShortPrefixToStringStyle();
private ModifiedShortPrefixToStringStyle()
{
@@ -42,7 +42,8 @@ public class ModifiedShortPrefixToStringStyle extends ToStringStyle
}
/**
- * <p>Ensure <code>Singleton</ode> after serialization.</p>
+ * <p>
+ * Ensure <code>Singleton</ode> after serialization.</p>
* @return the singleton
*/
private Object readResolve()
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java b/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
index f7ee6291719..0d184a6ba91 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
@@ -35,7 +35,7 @@ public class NamePrefixFileFilter implements FileFilter
public NamePrefixFileFilter(String prefix, boolean shouldStartWithPrefix)
{
assert prefix != null;
-
+
this.prefix = prefix;
this.shouldStartWithPrefix = shouldStartWithPrefix;
}
@@ -43,7 +43,7 @@ public class NamePrefixFileFilter implements FileFilter
public boolean accept(File pathname)
{
assert pathname != null;
-
+
final boolean startsWithPrefix = pathname.getName().startsWith(prefix);
return startsWithPrefix == shouldStartWithPrefix;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
index fbb92686ea1..fedbc80aedd 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
@@ -69,7 +69,7 @@ public class OSUtilities
{
return System.getProperty("os.arch") + "-" + System.getProperty("os.name");
}
-
+
/**
* @return The name of user that runs this program.
*/
@@ -98,7 +98,8 @@ public class OSUtilities
*/
public static Set<String> getOSPath()
{
- final String[] pathEntries = System.getenv("PATH").split(Pattern.quote(System.getProperty("path.separator")));
+ final String[] pathEntries =
+ System.getenv("PATH").split(Pattern.quote(System.getProperty("path.separator")));
return new LinkedHashSet<String>(Arrays.asList(pathEntries));
}
@@ -172,7 +173,8 @@ public class OSUtilities
*/
public static File findExecutable(String executableName, Set<String> pathSet)
{
- final String executableNameWithExtension = addWindowsExecutableExtensionIfNecessary(executableName);
+ final String executableNameWithExtension =
+ addWindowsExecutableExtensionIfNecessary(executableName);
for (String dir : pathSet)
{
final File fileToCheck = new File(dir, executableNameWithExtension);
@@ -189,7 +191,8 @@ public class OSUtilities
*/
public static boolean executableExists(String executableName)
{
- return (new File(OSUtilities.addWindowsExecutableExtensionIfNecessary(executableName))).exists();
+ return (new File(OSUtilities.addWindowsExecutableExtensionIfNecessary(executableName)))
+ .exists();
}
/**
@@ -197,7 +200,8 @@ public class OSUtilities
*/
public static boolean executableExists(File executable)
{
- return (new File(OSUtilities.addWindowsExecutableExtensionIfNecessary(executable.getPath()))).exists();
+ return (new File(OSUtilities.addWindowsExecutableExtensionIfNecessary(executable.getPath())))
+ .exists();
}
private static String addWindowsExecutableExtensionIfNecessary(String executableName)
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/PasswordGenerator.java b/common/source/java/ch/systemsx/cisd/common/utilities/PasswordGenerator.java
index 77c36ac8026..14d8e66ae2f 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/PasswordGenerator.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/PasswordGenerator.java
@@ -20,7 +20,7 @@ import java.util.Random;
/**
* Generator for human pronounceable passwords
- *
+ *
* @author Franz-Josef Elmer
*/
public class PasswordGenerator
@@ -41,7 +41,7 @@ public class PasswordGenerator
return "0123456789";
}
},
-
+
CONSONANT()
{
@Override
@@ -55,9 +55,9 @@ public class PasswordGenerator
{
return "bdcfghjklmnpqrstvwxzBCDFGHJKLMNPQRSTVWXZ";
}
-
+
},
-
+
VOWEL()
{
@Override
@@ -72,23 +72,23 @@ public class PasswordGenerator
return "aeiouyAEIOUY";
}
};
-
+
State nextState(Random random)
{
return this;
}
-
+
void appendCharacterTo(StringBuilder builder, Random random)
{
String characters = getCharacters();
builder.append(characters.charAt(random.nextInt(characters.length())));
}
-
+
abstract String getCharacters();
}
-
+
private final Random random;
-
+
/**
* Creates an instance based on the default constructor of {@link Random}.
*/
@@ -105,7 +105,7 @@ public class PasswordGenerator
assert random != null : "Unspecified random number generator.";
this.random = random;
}
-
+
/**
* Creates a password of specified length.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java b/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
index b4b1c299972..6eb8cc20243 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
@@ -38,8 +38,8 @@ public final class PathPrefixPrepender
/**
* Creates an instances for the specified prefixes. <code>null</code> arguments are handled as empty strings.
*/
- public PathPrefixPrepender(final String prefixForAbsolutePathsOrNull, final String prefixForRelativePathsOrNull)
- throws ConfigurationFailureException
+ public PathPrefixPrepender(final String prefixForAbsolutePathsOrNull,
+ final String prefixForRelativePathsOrNull) throws ConfigurationFailureException
{
this.prefixForAbsolutePaths = StringUtils.defaultString(prefixForAbsolutePathsOrNull);
assertValid(this.prefixForAbsolutePaths, "absolute");
@@ -60,7 +60,8 @@ public final class PathPrefixPrepender
return pathPrefix + "/";
}
- private void assertValid(final String prefix, final String type) throws ConfigurationFailureException
+ private void assertValid(final String prefix, final String type)
+ throws ConfigurationFailureException
{
if (prefix.length() != 0)
{
@@ -68,7 +69,8 @@ public final class PathPrefixPrepender
if (file.exists() == false)
{
throw ConfigurationFailureException.fromTemplate(
- "Invalid prefix for %s paths: given file '%s' does not exist.", type, file.getAbsolutePath());
+ "Invalid prefix for %s paths: given file '%s' does not exist.", type, file
+ .getAbsolutePath());
}
}
}
@@ -79,6 +81,8 @@ public final class PathPrefixPrepender
public String addPrefixTo(final String path)
{
assert path != null : "Undefined path.";
- return (FilenameUtils.getPrefixLength(path) > 0 ? prefixForAbsolutePaths : prefixForRelativePaths) + path;
+ return (FilenameUtils.getPrefixLength(path) > 0 ? prefixForAbsolutePaths
+ : prefixForRelativePaths)
+ + path;
}
}
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java b/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
index ac8eba0e301..81ac30951e6 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
@@ -41,17 +41,20 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, RecursiveHardLinkMaker.class);
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, RecursiveHardLinkMaker.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, RecursiveHardLinkMaker.class);
private final String linkExecPath;
private final RetryingOperationTimeout singleFileLinkTimeout;
- private RecursiveHardLinkMaker(final String linkExecPath, RetryingOperationTimeout singleFileLinkTimeoutOrNull)
+ private RecursiveHardLinkMaker(final String linkExecPath,
+ RetryingOperationTimeout singleFileLinkTimeoutOrNull)
{
this.linkExecPath = linkExecPath;
this.singleFileLinkTimeout =
- singleFileLinkTimeoutOrNull != null ? singleFileLinkTimeoutOrNull : createNoTimeout();
+ singleFileLinkTimeoutOrNull != null ? singleFileLinkTimeoutOrNull
+ : createNoTimeout();
}
private RetryingOperationTimeout createNoTimeout()
@@ -106,11 +109,13 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
* @param millisToSleepOnFailure The number of milliseconds we should wait before re-executing the copy of a single
* file. Specify 0 to wait till the first operation completes.
*/
- public static final IPathImmutableCopier tryCreateRetrying(final long millisToWaitForCompletion,
- final int maxRetryOnFailure, final long millisToSleepOnFailure)
+ public static final IPathImmutableCopier tryCreateRetrying(
+ final long millisToWaitForCompletion, final int maxRetryOnFailure,
+ final long millisToSleepOnFailure)
{
RetryingOperationTimeout timeout =
- new RetryingOperationTimeout(millisToWaitForCompletion, maxRetryOnFailure, millisToSleepOnFailure);
+ new RetryingOperationTimeout(millisToWaitForCompletion, maxRetryOnFailure,
+ millisToSleepOnFailure);
return tryCreate(timeout);
}
@@ -120,7 +125,8 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
return tryCreate(null);
}
- private static final IPathImmutableCopier tryCreate(RetryingOperationTimeout singleFileLinkTimeoutOrNull)
+ private static final IPathImmutableCopier tryCreate(
+ RetryingOperationTimeout singleFileLinkTimeoutOrNull)
{
final File lnExec = OSUtilities.findExecutable(HARD_LINK_EXEC);
if (lnExec == null)
@@ -137,7 +143,8 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
* <i>Note that <var>nameOrNull</var> cannot already exist in given <var>destinationDirectory</var>.</i>
* </p>
*/
- public final File tryCopy(final File path, final File destinationDirectory, final String nameOrNull)
+ public final File tryCopy(final File path, final File destinationDirectory,
+ final String nameOrNull)
{
assert path != null : "Given path can not be null.";
assert destinationDirectory != null && destinationDirectory.isDirectory() : "Given destination directory can not be null and must be a directory.";
@@ -145,19 +152,21 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
final File destFile = new File(destinationDirectory, destName);
if (destFile.exists())
{
- operationLog.error(String.format("File '%s' already exists in given destination directory '%s'", destName,
+ operationLog.error(String.format(
+ "File '%s' already exists in given destination directory '%s'", destName,
destinationDirectory));
return null;
}
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("Creating a hard link copy of '%s' in '%s'.", path.getPath(),
- destinationDirectory.getPath()));
+ operationLog.info(String.format("Creating a hard link copy of '%s' in '%s'.", path
+ .getPath(), destinationDirectory.getPath()));
}
return tryMakeCopy(path, destinationDirectory, nameOrNull);
}
- private final File tryMakeCopy(final File resource, final File destinationDirectory, final String nameOrNull)
+ private final File tryMakeCopy(final File resource, final File destinationDirectory,
+ final String nameOrNull)
{
if (resource.isFile())
{
@@ -185,11 +194,12 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
{
if (resource.exists() == false)
{
- operationLog.error(String.format("Path '%s' vanished during processing.", resource));
+ operationLog.error(String.format("Path '%s' vanished during processing.",
+ resource));
} else
{
- operationLog.error(String.format("Found path '%s' that is neither a file nor a directory.",
- resource));
+ operationLog.error(String.format(
+ "Found path '%s' that is neither a file nor a directory.", resource));
}
}
return dir;
@@ -204,12 +214,13 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
{
if (dir.isDirectory())
{
- machineLog.error(String.format("Directory %s already exists in %s", name, destDir.getAbsolutePath()));
+ machineLog.error(String.format("Directory %s already exists in %s", name, destDir
+ .getAbsolutePath()));
ok = true;
} else
{
- machineLog.error(String.format("Could not create directory %s inside %s.", name, destDir
- .getAbsolutePath()));
+ machineLog.error(String.format("Could not create directory %s inside %s.", name,
+ destDir.getAbsolutePath()));
if (dir.isFile())
{
machineLog.error("There is a file with a same name.");
@@ -219,7 +230,8 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
return ok ? dir : null;
}
- private final File tryCreateHardLinkIn(final File file, final File destDir, final String nameOrNull)
+ private final File tryCreateHardLinkIn(final File file, final File destDir,
+ final String nameOrNull)
{
assert file.isFile() : String.format("Given file '%s' must be a file and is not.", file);
final File destFile = new File(destDir, nameOrNull == null ? file.getName() : nameOrNull);
@@ -228,13 +240,13 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
{
public boolean run()
{
- return ProcessExecutionHelper.runAndLog(cmd, singleFileLinkTimeout.getMillisToWaitForCompletion(),
- operationLog, machineLog);
+ return ProcessExecutionHelper.runAndLog(cmd, singleFileLinkTimeout
+ .getMillisToWaitForCompletion(), operationLog, machineLog);
}
};
boolean ok =
- runRepeatableProcess(processTask, singleFileLinkTimeout.getMaxRetryOnFailure(), singleFileLinkTimeout
- .getMillisToSleepOnFailure());
+ runRepeatableProcess(processTask, singleFileLinkTimeout.getMaxRetryOnFailure(),
+ singleFileLinkTimeout.getMillisToSleepOnFailure());
return ok ? destFile : null;
}
@@ -252,8 +264,8 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
boolean run(); // returns true if operation succeeded
}
- private static boolean runRepeatableProcess(final IProcessTask task, final int maxRetryOnFailure,
- final long millisToSleepOnFailure)
+ private static boolean runRepeatableProcess(final IProcessTask task,
+ final int maxRetryOnFailure, final long millisToSleepOnFailure)
{
IProcess process = new IProcess()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java b/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
index 151bef30956..530ee22e72d 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
@@ -96,7 +96,8 @@ public class RegexFileFilter implements FileFilter
return false;
}
final PathPattern that = (PathPattern) obj;
- return this.type.equals(that.type) && this.pattern.pattern().equals(that.pattern.pattern());
+ return this.type.equals(that.type)
+ && this.pattern.pattern().equals(that.pattern.pattern());
}
@Override
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
index abef1b0b831..18e5451489c 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
@@ -39,31 +39,38 @@ public final class StringUtilities
private static final String[] STRINGS =
new String[]
- { "phalanx", "nightmare", "concierge", "asbestos", "cody", "hermit", "nbc", "couplet", "dice",
- "thumbnail", "finley", "figure", "exclamation", "whoosh", "punish", "servitor", "portend",
- "boulevard", "bacterial", "dilate", "emboss", "birmingham", "illustrate", "pomona", "truk",
- "bursitis", "trustworthy", "harriman", "schenectady", "obligate", "oceania", "knew",
- "quickstep", "woo", "strickland", "sadie", "malabar", "posit", "breadfruit", "grandfather",
- "vishnu", "vacuous", "melpomene", "assam", "blaine", "taskmaster", "polymeric", "hector",
- "counterrevolution", "compassionate", "linkage", "distant", "vet", "shako", "eagan",
- "neutronium", "stony", "lie", "hoydenish", "dial", "hecate", "pinch", "olin", "piglet",
- "basswood", "yawn", "ouzo", "scrupulosity", "bestiary", "subpoena", "nudge", "baton", "thing",
- "hallmark", "bossy", "preferential", "bambi", "narwhal", "brighten", "omnipotent", "forsake",
- "flapping", "orthodoxy", "upcome", "teaspoonful", "wabash", "lipid", "enjoin", "shoshone",
- "wartime", "gatekeeper", "litigate", "siderite", "sadden", "visage", "boogie", "scald",
- "equate", "tragic", "ordinary", "wick", "gigawatt", "desultory", "bambi", "aureomycin", "car",
- "especial", "rescue", "protector", "burnett", "constant", "heroes", "filmstrip", "homeown",
- "verdant", "governor", "cornwall", "predisposition", "sedan", "resemblant", "satellite",
- "committeemen", "given", "narragansett", "switzer", "clockwatcher", "sweeten", "monologist",
- "execrate", "gila", "lad", "mahayanist", "solicitation", "linemen", "reading", "hoard",
- "phyla", "carcinoma", "glycol", "polymer", "hangmen", "dualism", "betrayal", "corpsman",
- "stint", "hannah", "balsam", "granola", "charitable", "osborn", "party", "laboratory",
- "norwich", "laxative", "collude", "rockefeller", "crack", "lamarck", "purposeful",
- "neuroanotomy", "araby", "crucible", "oratorical", "dramaturgy", "kitty", "pit", "ephesus",
- "bum", "amuse", "clogging", "joker", "fobbing", "extent", "colossal", "macromolecule",
- "choppy", "tennessee", "primrose", "glassine", "vampire", "chap", "precursor", "incorrigible",
- "slither", "interrogate", "spectral", "debut", "creche", "pyrolysis", "homicidal", "sonnet",
- "gin", "science", "magma", "metaphor", "cobble", "dyer", "narrate", "goody", "optometric" };
+ { "phalanx", "nightmare", "concierge", "asbestos", "cody", "hermit", "nbc",
+ "couplet", "dice", "thumbnail", "finley", "figure", "exclamation",
+ "whoosh", "punish", "servitor", "portend", "boulevard", "bacterial",
+ "dilate", "emboss", "birmingham", "illustrate", "pomona", "truk",
+ "bursitis", "trustworthy", "harriman", "schenectady", "obligate",
+ "oceania", "knew", "quickstep", "woo", "strickland", "sadie", "malabar",
+ "posit", "breadfruit", "grandfather", "vishnu", "vacuous", "melpomene",
+ "assam", "blaine", "taskmaster", "polymeric", "hector",
+ "counterrevolution", "compassionate", "linkage", "distant", "vet", "shako",
+ "eagan", "neutronium", "stony", "lie", "hoydenish", "dial", "hecate",
+ "pinch", "olin", "piglet", "basswood", "yawn", "ouzo", "scrupulosity",
+ "bestiary", "subpoena", "nudge", "baton", "thing", "hallmark", "bossy",
+ "preferential", "bambi", "narwhal", "brighten", "omnipotent", "forsake",
+ "flapping", "orthodoxy", "upcome", "teaspoonful", "wabash", "lipid",
+ "enjoin", "shoshone", "wartime", "gatekeeper", "litigate", "siderite",
+ "sadden", "visage", "boogie", "scald", "equate", "tragic", "ordinary",
+ "wick", "gigawatt", "desultory", "bambi", "aureomycin", "car", "especial",
+ "rescue", "protector", "burnett", "constant", "heroes", "filmstrip",
+ "homeown", "verdant", "governor", "cornwall", "predisposition", "sedan",
+ "resemblant", "satellite", "committeemen", "given", "narragansett",
+ "switzer", "clockwatcher", "sweeten", "monologist", "execrate", "gila",
+ "lad", "mahayanist", "solicitation", "linemen", "reading", "hoard",
+ "phyla", "carcinoma", "glycol", "polymer", "hangmen", "dualism",
+ "betrayal", "corpsman", "stint", "hannah", "balsam", "granola",
+ "charitable", "osborn", "party", "laboratory", "norwich", "laxative",
+ "collude", "rockefeller", "crack", "lamarck", "purposeful", "neuroanotomy",
+ "araby", "crucible", "oratorical", "dramaturgy", "kitty", "pit", "ephesus",
+ "bum", "amuse", "clogging", "joker", "fobbing", "extent", "colossal",
+ "macromolecule", "choppy", "tennessee", "primrose", "glassine", "vampire",
+ "chap", "precursor", "incorrigible", "slither", "interrogate", "spectral",
+ "debut", "creche", "pyrolysis", "homicidal", "sonnet", "gin", "science",
+ "magma", "metaphor", "cobble", "dyer", "narrate", "goody", "optometric" };
private final static Pattern pattern = Pattern.compile("([a-zA-Z]+)([0-9]+)");
@@ -71,7 +78,7 @@ public final class StringUtilities
{
// This class can not be instantiated.
}
-
+
/**
* Computes the MD5 hash value of <var>string</var>.
*
@@ -80,14 +87,14 @@ public final class StringUtilities
public static String computeMD5Hash(String string)
{
assert string != null : "Unspecified string.";
-
+
try
{
MessageDigest algorithm = MessageDigest.getInstance("MD5");
algorithm.reset();
algorithm.update(string.getBytes("utf8"));
byte messageDigest[] = algorithm.digest();
-
+
StringBuilder builder = new StringBuilder();
for (int i = 0; i < messageDigest.length; i++)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/SynchronizationMonitor.java b/common/source/java/ch/systemsx/cisd/common/utilities/SynchronizationMonitor.java
index 42718ce9891..0223f167946 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/SynchronizationMonitor.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/SynchronizationMonitor.java
@@ -18,17 +18,17 @@ package ch.systemsx.cisd.common.utilities;
/**
* A pure monitor for us in <code>synchronized()</code> clauses.
- *
+ *
* @author Bernd Rinn
*/
public final class SynchronizationMonitor
{
-
+
private SynchronizationMonitor()
{
// Use create() to call this.
}
-
+
/**
* Creates a new {@link SynchronizationMonitor}.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/Template.java b/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
index 50191c811ef..0e492528a3d 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
@@ -23,25 +23,28 @@ import java.util.Map;
/**
* A little template engine. Usage example:
+ *
* <pre>
- * Template template = new Template("Hello ${name}!");
- * template.bind("name", "world");
+ * Template template = new Template("Hello ${name}!");
+ * template.bind("name", "world");
* String text = template.createText();
* </pre>
- * The method {@link #bind(String, String)} throws an exception if the placeholder name is unknown.
- * The method {@link #attemptToBind(String, String)} returns <code>false</code> if the placeholder name is unknown.
- * The method {@link #createText()} throws an exception if not all placeholders have been bound.
+ *
+ * The method {@link #bind(String, String)} throws an exception if the placeholder name is unknown. The method
+ * {@link #attemptToBind(String, String)} returns <code>false</code> if the placeholder name is unknown. The method
+ * {@link #createText()} throws an exception if not all placeholders have been bound.
* <p>
* Since placeholder bindings change the state of an instance of this class there is method {@link #createFreshCopy()}
* which creates a copy without reparsing the template. Usage example:
+ *
* <pre>
- * static final Template TEMPLATE = new Template("Hello ${name}!");
+ * static final Template TEMPLATE = new Template("Hello ${name}!");
*
* void doSomething()
* {
- * Template template = TEMPLATE.createFreshCopy();
- * template.bind("name", "world");
- * String text = template.createText();
+ * Template template = TEMPLATE.createFreshCopy();
+ * template.bind("name", "world");
+ * String text = template.createText();
* }
* </pre>
*
@@ -50,41 +53,44 @@ import java.util.Map;
public class Template
{
private static final char PLACEHOLDER_ESCAPE_CHARACTER = '$';
+
private static final char PLACEHOLDER_START_CHARACTER = '{';
+
private static final char PLACEHOLDER_END_CHARACTER = '}';
-
+
private static final String createPlaceholder(String variableName)
{
- return PLACEHOLDER_ESCAPE_CHARACTER + (PLACEHOLDER_START_CHARACTER + variableName) + PLACEHOLDER_END_CHARACTER;
+ return PLACEHOLDER_ESCAPE_CHARACTER + (PLACEHOLDER_START_CHARACTER + variableName)
+ + PLACEHOLDER_END_CHARACTER;
}
-
+
private static interface IToken
{
public void appendTo(StringBuilder builder);
}
-
+
private static final class PlainToken implements IToken
{
private final String plainText;
-
+
PlainToken(String plainText)
{
assert plainText != null : "Unspecified plain text.";
this.plainText = plainText;
}
-
+
public void appendTo(StringBuilder builder)
{
builder.append(plainText);
}
}
-
+
private static final class VariableToken implements IToken
{
private final String variableName;
-
+
private String value;
-
+
VariableToken(String variablePlaceHolder)
{
assert variablePlaceHolder != null : "Unspecified variable place holder.";
@@ -95,7 +101,7 @@ public class Template
{
builder.append(isBound() ? value : createPlaceholder(variableName));
}
-
+
String getVariableName()
{
return variableName;
@@ -105,13 +111,13 @@ public class Template
{
return value != null;
}
-
+
void bind(String v)
{
this.value = v;
}
}
-
+
private static enum State
{
PLAIN()
@@ -127,7 +133,7 @@ public class Template
return PLAIN;
}
},
-
+
STARTING_PLACEHOLDER()
{
@Override
@@ -135,7 +141,7 @@ public class Template
{
switch (character)
{
- case PLACEHOLDER_ESCAPE_CHARACTER:
+ case PLACEHOLDER_ESCAPE_CHARACTER:
tokenBuilder.addCharacter(PLACEHOLDER_ESCAPE_CHARACTER);
return PLAIN;
case PLACEHOLDER_START_CHARACTER:
@@ -148,7 +154,7 @@ public class Template
}
}
},
-
+
PLACEHOLDER()
{
@Override
@@ -163,14 +169,16 @@ public class Template
return PLACEHOLDER;
}
};
-
+
abstract State next(char character, TokenBuilder tokenBuilder);
}
-
+
private static final class TokenBuilder
{
private final Map<String, VariableToken> variableTokens;
+
private final List<IToken> tokens;
+
private final StringBuilder builder;
TokenBuilder(Map<String, VariableToken> variableTokens, List<IToken> tokens)
@@ -184,7 +192,7 @@ public class Template
{
builder.append(character);
}
-
+
public void finishPlainToken()
{
if (builder.length() > 0)
@@ -199,7 +207,8 @@ public class Template
String variableName = builder.toString();
if (variableName.length() == 0)
{
- throw new IllegalArgumentException("Nameless placeholder " + createPlaceholder("") + " found.");
+ throw new IllegalArgumentException("Nameless placeholder " + createPlaceholder("")
+ + " found.");
}
VariableToken token = variableTokens.get(variableName);
if (token == null)
@@ -213,18 +222,19 @@ public class Template
}
private final Map<String, VariableToken> variableTokens;
+
private final List<IToken> tokens;
-
+
/**
* Creates a new instance for the specified template.
- *
+ *
* @throws IllegalArgumentException if some error occurred during parsing.
*/
public Template(String template)
{
this(new LinkedHashMap<String, VariableToken>(), new ArrayList<IToken>());
assert template != null : "Unspecified template.";
-
+
TokenBuilder tokenBuilder = new TokenBuilder(variableTokens, tokens);
State state = State.PLAIN;
final int n = template.length();
@@ -238,13 +248,13 @@ public class Template
}
tokenBuilder.finishPlainToken();
}
-
+
private Template(Map<String, VariableToken> variableTokens, List<IToken> tokens)
{
this.variableTokens = variableTokens;
this.tokens = tokens;
}
-
+
/**
* Creates a copy of this template with no variable bindings.
*/
@@ -269,7 +279,6 @@ public class Template
}
return new Template(map, list);
}
-
/**
* Binds the specified value to the specified placeholder name.
@@ -281,7 +290,7 @@ public class Template
boolean successful = attemptToBind(placeholderName, value);
if (successful == false)
{
- throw new IllegalArgumentException("Unknown variable '" + placeholderName + "'.");
+ throw new IllegalArgumentException("Unknown variable '" + placeholderName + "'.");
}
}
@@ -294,7 +303,7 @@ public class Template
{
assert placeholderName != null : "Unspecified placeholder name.";
assert value != null : "Unspecified value for '" + placeholderName + "'";
-
+
VariableToken variableToken = variableTokens.get(placeholderName);
if (variableToken == null)
{
@@ -303,7 +312,7 @@ public class Template
variableToken.bind(value);
return true;
}
-
+
/**
* Creates the text by using all placeholder bindings.
*
@@ -313,12 +322,12 @@ public class Template
{
return createText(true);
}
-
+
/**
* Creates the text by using placeholder bindings.
*
- * @param complete If <code>true</code> an {@link IllegalStateException} will be thrown if not all
- * bindings are set.
+ * @param complete If <code>true</code> an {@link IllegalStateException} will be thrown if not all bindings are
+ * set.
*/
public String createText(boolean complete)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/TimerHelper.java b/common/source/java/ch/systemsx/cisd/common/utilities/TimerHelper.java
index e671cd4f0d6..606e1a9fecf 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/TimerHelper.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/TimerHelper.java
@@ -20,14 +20,14 @@ import java.util.Timer;
/**
* Helper methods for timer operations.
- *
+ *
* @author Bernd Rinn
*/
public class TimerHelper
{
/**
- * Returns an {@link ITerminable} for the <var>timer</var>.
+ * Returns an {@link ITerminable} for the <var>timer</var>.
*/
public static ITerminable asTerminable(final Timer timer)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java b/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
index 459f69952bc..9e4a9644e39 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
@@ -32,9 +32,11 @@ import ch.systemsx.cisd.common.logging.LogFactory;
public class TriggeringTimerTask extends TimerTask
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, TriggeringTimerTask.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, TriggeringTimerTask.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, TriggeringTimerTask.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, TriggeringTimerTask.class);
private final ITriggerable triggerable;
@@ -62,7 +64,8 @@ public class TriggeringTimerTask extends TimerTask
* action available.
* @param monitor The monitor to synchronize on.
*/
- public TriggeringTimerTask(File triggerFile, ITriggerable triggerable, SynchronizationMonitor monitor)
+ public TriggeringTimerTask(File triggerFile, ITriggerable triggerable,
+ SynchronizationMonitor monitor)
{
assert triggerFile != null;
assert triggerable != null;
@@ -79,7 +82,7 @@ public class TriggeringTimerTask extends TimerTask
@Override
public synchronized void run()
{
- synchronized(monitor)
+ synchronized (monitor)
{
try
{
@@ -101,7 +104,8 @@ public class TriggeringTimerTask extends TimerTask
{
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("File '%s' found - triggering.", triggerFile.getAbsolutePath()));
+ operationLog.info(String.format("File '%s' found - triggering.", triggerFile
+ .getAbsolutePath()));
}
triggerable.trigger();
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionIOTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionIOTest.java
index 0dbbad3203d..1cd14b997b8 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionIOTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionIOTest.java
@@ -47,7 +47,8 @@ import ch.systemsx.cisd.common.logging.LogInitializer;
public class CollectionIOTest
{
- private static final File workingDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File workingDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
@BeforeSuite
public void init()
@@ -129,13 +130,14 @@ public class CollectionIOTest
assert ps.checkError() == false;
final String resultingString = new String(os.toByteArray());
final String lineSeparator = System.getProperty("line.separator");
- assert resultingString.equals(String.format("One%1$sTwo%1$sThree%1$sStill open%1$s", lineSeparator));
+ assert resultingString.equals(String.format("One%1$sTwo%1$sThree%1$sStill open%1$s",
+ lineSeparator));
assert CollectionIO.writeIterable(ps, Arrays.asList("yellow"));
assert ps.checkError() == false;
ps.println("Still open");
final String resultingString2 = new String(os.toByteArray());
- assert resultingString2.equals(String.format("One%1$sTwo%1$sThree%1$sStill open%1$syellow%1$sStill open%1$s",
- lineSeparator));
+ assert resultingString2.equals(String.format(
+ "One%1$sTwo%1$sThree%1$sStill open%1$syellow%1$sStill open%1$s", lineSeparator));
}
@Test
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionUtilsTest.java
index c99f4634f1d..2507007ae71 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/CollectionUtilsTest.java
@@ -61,7 +61,8 @@ public final class CollectionUtilsTest
final String[] s = StringUtilities.getStrings(5);
final CollectionStyle collectionStyle = CollectionStyle.DEFAULT_COLLECTION_STYLE;
String string =
- collectionStyle.getCollectionStart() + StringUtils.join(s, collectionStyle.getCollectionSeparator())
+ collectionStyle.getCollectionStart()
+ + StringUtils.join(s, collectionStyle.getCollectionSeparator())
+ collectionStyle.getCollectionEnd();
assertEquals(string, CollectionUtils.abbreviate(s, -1, false));
assertEquals(string, CollectionUtils.abbreviate(s, -10, false));
@@ -83,7 +84,8 @@ public final class CollectionUtilsTest
}
try
{
- CollectionUtils.abbreviate(objects, 0, false, ToStringDefaultConverter.getInstance(), null);
+ CollectionUtils.abbreviate(objects, 0, false, ToStringDefaultConverter.getInstance(),
+ null);
fail("Given CollectionStyle can not be null.");
} catch (AssertionError e)
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/FilteredListTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/FilteredListTest.java
index f5359f63553..0e4b1f72fc2 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/FilteredListTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/FilteredListTest.java
@@ -134,7 +134,7 @@ public final class FilteredListTest
assertEquals(5, list.size());
assertEquals("renew", list.get(4));
}
-
+
@Test
public final void testSubList()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKeyTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKeyTest.java
index 25bd8aa9df0..0a6f190d19b 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKeyTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKeyTest.java
@@ -52,7 +52,8 @@ public class TableMapNonUniqueKeyTest
public void testIterationUniqueKey()
{
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0"), integerExtractor);
+ new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0"),
+ integerExtractor);
Iterator<String> it = tableMap.iterator();
assertEquals("1", it.next());
assertEquals("7", it.next());
@@ -63,7 +64,8 @@ public class TableMapNonUniqueKeyTest
@Test(expectedExceptions = TableMapNonUniqueKey.UniqueValueViolationException.class)
public void testIterationDuplicateValuesStrategyError()
{
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0", "0", "1"), integerExtractor);
+ new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0", "0", "1"),
+ integerExtractor);
}
@Test
@@ -72,14 +74,15 @@ public class TableMapNonUniqueKeyTest
final String null1 = new String(Integer.toString(0));
final String null2 = new String(Integer.toString(0));
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", null1, null2, "1"), integerExtractor,
+ new TableMapNonUniqueKey<Integer, String>(Arrays
+ .asList("1", "7", null1, null2, "1"), integerExtractor,
TableMapNonUniqueKey.UniqueValueViolationStrategy.KEEP_LAST);
Iterator<String> it = tableMap.iterator();
assertEquals("1", it.next());
assertEquals("7", it.next());
final String null3 = it.next();
- System.out.println(System.identityHashCode(null1) + ":" + System.identityHashCode(null2) + ":"
- + System.identityHashCode(null3));
+ System.out.println(System.identityHashCode(null1) + ":" + System.identityHashCode(null2)
+ + ":" + System.identityHashCode(null3));
assertEquals(System.identityHashCode(null2), System.identityHashCode(null3));
assertFalse(it.hasNext());
}
@@ -90,14 +93,15 @@ public class TableMapNonUniqueKeyTest
final String null1 = new String(Integer.toString(0));
final String null2 = new String(Integer.toString(0));
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", null1, null2, "1"), integerExtractor,
+ new TableMapNonUniqueKey<Integer, String>(Arrays
+ .asList("1", "7", null1, null2, "1"), integerExtractor,
TableMapNonUniqueKey.UniqueValueViolationStrategy.KEEP_FIRST);
Iterator<String> it = tableMap.iterator();
assertEquals("1", it.next());
assertEquals("7", it.next());
final String null3 = it.next();
- System.out.println(System.identityHashCode(null1) + ":" + System.identityHashCode(null2) + ":"
- + System.identityHashCode(null3));
+ System.out.println(System.identityHashCode(null1) + ":" + System.identityHashCode(null2)
+ + ":" + System.identityHashCode(null3));
assertEquals(System.identityHashCode(null1), System.identityHashCode(null3));
assertFalse(it.hasNext());
}
@@ -106,7 +110,8 @@ public class TableMapNonUniqueKeyTest
public void testIterationDuplicateKey()
{
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0", "x:0", "x:1"), integerExtractor);
+ new TableMapNonUniqueKey<Integer, String>(Arrays
+ .asList("1", "7", "0", "x:0", "x:1"), integerExtractor);
Iterator<String> it = tableMap.iterator();
assertEquals("1", it.next());
assertEquals("x:1", it.next());
@@ -120,7 +125,8 @@ public class TableMapNonUniqueKeyTest
public void testTryGet()
{
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0"), integerExtractor);
+ new TableMapNonUniqueKey<Integer, String>(Arrays.asList("1", "7", "0"),
+ integerExtractor);
assertNull(tableMap.tryGet(10));
assertEquals(Collections.singleton("0"), tableMap.tryGet(0));
assertEquals(Collections.singleton("1"), tableMap.tryGet(1));
@@ -131,12 +137,13 @@ public class TableMapNonUniqueKeyTest
public void testTryGetNonUnique()
{
final TableMapNonUniqueKey<Integer, String> tableMap =
- new TableMapNonUniqueKey<Integer, String>(Arrays.asList("a:42", "7", "b:42", "0", "b:7", "c:42"),
- integerExtractor);
+ new TableMapNonUniqueKey<Integer, String>(Arrays.asList("a:42", "7", "b:42", "0",
+ "b:7", "c:42"), integerExtractor);
assertNull(tableMap.tryGet(10));
assertEquals(Collections.singleton("0"), tableMap.tryGet(0));
assertEquals(new HashSet<String>(Arrays.asList("7", "b:7")), tableMap.tryGet(7));
- assertEquals(new HashSet<String>(Arrays.asList("a:42", "b:42", "c:42")), tableMap.tryGet(42));
+ assertEquals(new HashSet<String>(Arrays.asList("a:42", "b:42", "c:42")), tableMap
+ .tryGet(42));
}
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapTest.java
index 28a2f3e10ae..905ca1d7302 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/TableMapTest.java
@@ -86,8 +86,8 @@ public class TableMapTest
public void testUniqueKeyViolationKeepFirst()
{
final TableMap<Integer, String> tableMap =
- new TableMap<Integer, String>(Arrays.asList("a:1", "7", "0", "b:1"), integerExtractor,
- UniqueKeyViolationStrategy.KEEP_FIRST);
+ new TableMap<Integer, String>(Arrays.asList("a:1", "7", "0", "b:1"),
+ integerExtractor, UniqueKeyViolationStrategy.KEEP_FIRST);
assertNull(tableMap.tryGet(10));
assertEquals("0", tableMap.tryGet(0));
assertEquals("a:1", tableMap.tryGet(1));
@@ -98,8 +98,8 @@ public class TableMapTest
public void testUniqueKeyViolationKeepLast()
{
final TableMap<Integer, String> tableMap =
- new TableMap<Integer, String>(Arrays.asList("a:1", "7", "0", "b:1"), integerExtractor,
- UniqueKeyViolationStrategy.KEEP_LAST);
+ new TableMap<Integer, String>(Arrays.asList("a:1", "7", "0", "b:1"),
+ integerExtractor, UniqueKeyViolationStrategy.KEEP_LAST);
assertNull(tableMap.tryGet(10));
assertEquals("0", tableMap.tryGet(0));
assertEquals("b:1", tableMap.tryGet(1));
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/ValidatorUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/ValidatorUtilsTest.java
index b694e275072..37778d646b7 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/collections/ValidatorUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/ValidatorUtilsTest.java
@@ -41,14 +41,14 @@ public final class ValidatorUtilsTest
{
// Nothing to do here.
}
-
+
s = "hello";
String regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("hello", regEx);
Pattern pattern = Pattern.compile(regEx);
assertEquals(false, pattern.matcher("heelo").matches());
assertEquals(true, pattern.matcher("hello").matches());
-
+
s = "he?lo";
regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("he.lo", regEx);
@@ -56,7 +56,7 @@ public final class ValidatorUtilsTest
assertEquals(true, pattern.matcher("heelo").matches());
assertEquals(false, pattern.matcher("helllo").matches());
assertEquals(false, pattern.matcher("xhello").matches());
-
+
s = "he?l";
regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("he.l", regEx);
@@ -65,7 +65,7 @@ public final class ValidatorUtilsTest
assertEquals(true, pattern.matcher("heul").matches());
assertEquals(false, pattern.matcher("hello").matches());
assertEquals(false, pattern.matcher("helloo").matches());
-
+
s = "he*o";
regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("he.*o", regEx);
@@ -74,11 +74,11 @@ public final class ValidatorUtilsTest
assertEquals(true, pattern.matcher("helllllllllllllllo").matches());
assertEquals(true, pattern.matcher("helloo").matches());
assertEquals(false, pattern.matcher("chelloo").matches());
-
+
s = "h?l*o";
regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("h.l.*o", regEx);
-
+
s = "h\\*ll*o";
regEx = ValidatorUtils.convertToRegEx(s);
assertEquals("h\\*ll.*o", regEx);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/compression/file/CompressionWorkerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/compression/file/CompressionWorkerTest.java
index 87e70d3ccab..39ad51041ae 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/compression/file/CompressionWorkerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/compression/file/CompressionWorkerTest.java
@@ -309,8 +309,8 @@ public class CompressionWorkerTest
final FailureRecord record = failed.iterator().next();
assertEquals(faultyFile, record.getFailedFile().getName());
assertEquals(StatusFlag.FATAL_ERROR, record.getFailureStatus().getFlag());
- assertEquals("Exceptional condition: " + FakedException.class.getSimpleName(), record.getFailureStatus()
- .getMessage());
+ assertEquals("Exceptional condition: " + FakedException.class.getSimpleName(), record
+ .getFailureStatus().getMessage());
assertEquals(ex, record.tryGetThrowable());
assertTrue(logRecorder.getLogContent().indexOf(
String.format(CompressionWorker.EXCEPTION_COMPRESSING_MSG_TEMPLATE, faultyFile)) >= 0);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilitiesTest.java
index b630996e30b..bfa5c0bcce4 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilitiesTest.java
@@ -33,14 +33,15 @@ import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.logging.LogInitializer;
/**
- * Test cases for {@link ConcurrencyUtilities}.
- *
+ * Test cases for {@link ConcurrencyUtilities}.
+ *
* @author Bernd Rinn
*/
public class ConcurrencyUtilitiesTest
{
private final static String name = "This is the pool name";
+
private ThreadPoolExecutor eservice;
@BeforeClass
@@ -49,19 +50,19 @@ public class ConcurrencyUtilitiesTest
LogInitializer.init();
eservice = (ThreadPoolExecutor) ConcurrencyUtilities.newNamedPool(name, 1, 2);
}
-
+
@Test
public void testNewNamedPool() throws Throwable
{
assertEquals(1, eservice.getCorePoolSize());
assertEquals(2, eservice.getMaximumPoolSize());
final Future<?> future = eservice.submit(new Runnable()
- {
- public void run()
{
- assertEquals(name + " 1", Thread.currentThread().getName());
- }
- });
+ public void run()
+ {
+ assertEquals(name + " 1", Thread.currentThread().getName());
+ }
+ });
try
{
future.get(200L, TimeUnit.MILLISECONDS);
@@ -70,25 +71,24 @@ public class ConcurrencyUtilitiesTest
throw ex.getCause();
}
}
-
-
+
@Test
public void testTryGetFutureTimeout()
{
final Future<String> future = eservice.submit(new Callable<String>()
+ {
+ public String call() throws Exception
{
- public String call() throws Exception
+ try
+ {
+ Thread.sleep(200L);
+ } catch (InterruptedException ex)
{
- try
- {
- Thread.sleep(200L);
- } catch (InterruptedException ex)
- {
- throw new CheckedExceptionTunnel(ex);
- }
- return null;
+ throw new CheckedExceptionTunnel(ex);
}
- });
+ return null;
+ }
+ });
final String shouldBeNull = ConcurrencyUtilities.tryGetResult(future, 20L);
assertNull(shouldBeNull);
assertTrue(future.isDone());
@@ -99,27 +99,28 @@ public class ConcurrencyUtilitiesTest
{
final Thread thread = Thread.currentThread();
final Future<String> future = eservice.submit(new Callable<String>()
+ {
+ public String call() throws Exception
{
- public String call() throws Exception
+ try
+ {
+ Thread.sleep(200L);
+ } catch (InterruptedException ex)
{
- try
- {
- Thread.sleep(200L);
- } catch (InterruptedException ex)
- {
- throw new CheckedExceptionTunnel(ex);
- }
- return null;
+ throw new CheckedExceptionTunnel(ex);
}
- });
+ return null;
+ }
+ });
final Timer t = new Timer();
- t.schedule(new TimerTask() {
- @Override
- public void run()
+ t.schedule(new TimerTask()
{
- thread.interrupt();
- }
- }, 20L);
+ @Override
+ public void run()
+ {
+ thread.interrupt();
+ }
+ }, 20L);
final String shouldBeNull = ConcurrencyUtilities.tryGetResult(future, 200L);
t.cancel();
assertNull(shouldBeNull);
@@ -131,17 +132,17 @@ public class ConcurrencyUtilitiesTest
{
private static final long serialVersionUID = 1L;
}
-
+
@Test
public void testTryGetFutureException()
{
final Future<String> future = eservice.submit(new Callable<String>()
+ {
+ public String call() throws Exception
{
- public String call() throws Exception
- {
- throw new TaggedException();
- }
- });
+ throw new TaggedException();
+ }
+ });
try
{
ConcurrencyUtilities.tryGetResult(future, 100L);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java
index 721b5b75ce0..9330c22c360 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java
@@ -51,15 +51,17 @@ public class DBRestrictionParserTest
{
LogInitializer.init();
sqlScript =
- FileUtilities.loadToString(new File(
- "../common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionsTest.sql"));
+ FileUtilities
+ .loadToString(new File(
+ "../common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionsTest.sql"));
assert sqlScript != null;
}
@Test
public void testNormalize()
{
- final List<String> normalizedList = DBRestrictionParser.normalize(" a 1 ;; B\t2;\n\nC; \n--D\n E ");
+ final List<String> normalizedList =
+ DBRestrictionParser.normalize(" a 1 ;; B\t2;\n\nC; \n--D\n E ");
assertEquals(Arrays.asList("a 1", "b 2", "c", "e"), normalizedList);
}
@@ -68,10 +70,12 @@ public class DBRestrictionParserTest
{
String invalidDomainStatement = "create domain bla for varchar(0)";
final List<String> domainScript =
- Arrays.asList("create table sometable", "create domain user_id as varchar(15)", invalidDomainStatement,
- "create domain code as varchar(8)", "create domain description_80 as varchar(81)");
+ Arrays.asList("create table sometable", "create domain user_id as varchar(15)",
+ invalidDomainStatement, "create domain code as varchar(8)",
+ "create domain description_80 as varchar(81)");
final LogMonitoringAppender appender =
- LogMonitoringAppender.addAppender(LogCategory.OPERATION, "line \"" + invalidDomainStatement
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION, "line \""
+ + invalidDomainStatement
+ "\" starts like a domain definition, but key word 'AS' is missing.");
try
{
@@ -91,9 +95,11 @@ public class DBRestrictionParserTest
@Test
public void testDefaultKeywordInDomain()
{
- final List<String> domainScript = Arrays.asList("create domain vc22 as varchar(22) default 'nothing special'");
+ final List<String> domainScript =
+ Arrays.asList("create domain vc22 as varchar(22) default 'nothing special'");
- final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
+ final LogMonitoringAppender appender =
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
try
{
final Map<String, Integer> domains = DBRestrictionParser.parseDomains(domainScript);
@@ -111,7 +117,8 @@ public class DBRestrictionParserTest
{
final List<String> domainScript = Arrays.asList("create domain dp as double precision");
- final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
+ final LogMonitoringAppender appender =
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
try
{
final Map<String, Integer> domains = DBRestrictionParser.parseDomains(domainScript);
@@ -126,9 +133,11 @@ public class DBRestrictionParserTest
@Test
public void testDoublePrecisionAndDefaultInDomain()
{
- final List<String> domainScript = Arrays.asList("create domain dp as double precision default 3.14159");
+ final List<String> domainScript =
+ Arrays.asList("create domain dp as double precision default 3.14159");
- final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
+ final LogMonitoringAppender appender =
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
try
{
final Map<String, Integer> domains = DBRestrictionParser.parseDomains(domainScript);
@@ -163,14 +172,17 @@ public class DBRestrictionParserTest
public void testInvalidTable()
{
final DBRestrictionParser parser = new DBRestrictionParser("");
- assertEquals(Integer.MAX_VALUE, parser.getTableRestrictions("doesnotexit").getLength("doesnotexist"));
+ assertEquals(Integer.MAX_VALUE, parser.getTableRestrictions("doesnotexit").getLength(
+ "doesnotexist"));
}
@Test(expectedExceptions = AssertionError.class)
public void testInvalidColumn()
{
- final DBRestrictionParser parser = new DBRestrictionParser("create table tab (a integer, b varchar(1))");
- assertEquals(Integer.MAX_VALUE, parser.getTableRestrictions("tab").getLength("doesnotexist"));
+ final DBRestrictionParser parser =
+ new DBRestrictionParser("create table tab (a integer, b varchar(1))");
+ assertEquals(Integer.MAX_VALUE, parser.getTableRestrictions("tab")
+ .getLength("doesnotexist"));
}
@Test
@@ -178,10 +190,10 @@ public class DBRestrictionParserTest
{
final DBRestrictionParser parser = new DBRestrictionParser(sqlScript);
- assertEquals(new HashSet<String>(Arrays.asList("PERS", "ORGA")), parser.getTableRestrictions("contacts")
- .tryGetCheckedConstaint("cnta_type"));
- assertEquals(new HashSet<String>(Arrays.asList("STOB", "MATE")), parser.getTableRestrictions("materials")
- .tryGetCheckedConstaint("mate_sub_type"));
+ assertEquals(new HashSet<String>(Arrays.asList("PERS", "ORGA")), parser
+ .getTableRestrictions("contacts").tryGetCheckedConstaint("cnta_type"));
+ assertEquals(new HashSet<String>(Arrays.asList("STOB", "MATE")), parser
+ .getTableRestrictions("materials").tryGetCheckedConstaint("mate_sub_type"));
}
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/db/SQLCommandTokenizerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/db/SQLCommandTokenizerTest.java
index a771314becd..04e63defd5d 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/db/SQLCommandTokenizerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/db/SQLCommandTokenizerTest.java
@@ -69,7 +69,8 @@ public class SQLCommandTokenizerTest
@Test
public void testWhitespaces()
{
- final SQLCommandTokenizer cmdTokenizer = new SQLCommandTokenizer(" A ; \n b B;\t c\tC\n ");
+ final SQLCommandTokenizer cmdTokenizer =
+ new SQLCommandTokenizer(" A ; \n b B;\t c\tC\n ");
assertEquals("a", cmdTokenizer.getNextCommand());
assertEquals("b b", cmdTokenizer.getNextCommand());
assertEquals("c c", cmdTokenizer.getNextCommand());
@@ -101,7 +102,8 @@ public class SQLCommandTokenizerTest
@Test
public void testConstants()
{
- final SQLCommandTokenizer cmdTokenizer = new SQLCommandTokenizer("A 'A \\'B\tc';\nb;\ncC;");
+ final SQLCommandTokenizer cmdTokenizer =
+ new SQLCommandTokenizer("A 'A \\'B\tc';\nb;\ncC;");
assertEquals("a 'A \\'B\tc'", cmdTokenizer.getNextCommand());
assertEquals("b", cmdTokenizer.getNextCommand());
assertEquals("cc", cmdTokenizer.getNextCommand());
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/db/SqlUnitTestRunnerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/db/SqlUnitTestRunnerTest.java
index 27468c27213..ea68f6e4904 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/db/SqlUnitTestRunnerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/db/SqlUnitTestRunnerTest.java
@@ -41,19 +41,20 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
import ch.systemsx.cisd.common.utilities.OSUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SqlUnitTestRunnerTest
{
private static final File TEST_SCRIPTS_FOLDER = new File("temporary_test_scripts_folder");
-
+
private Mockery context;
+
private ISqlScriptExecutor executor;
+
private StringWriter monitor;
+
private SqlUnitTestRunner testRunner;
-
+
@BeforeMethod
public void setup()
{
@@ -63,7 +64,7 @@ public class SqlUnitTestRunnerTest
monitor = new StringWriter();
testRunner = new SqlUnitTestRunner(executor, new PrintWriter(monitor));
}
-
+
@AfterMethod
public void teardown()
{
@@ -72,57 +73,58 @@ public class SqlUnitTestRunnerTest
// Otherwise one do not known which test failed.
context.assertIsSatisfied();
}
-
+
@Test
public void testNullFolder()
{
testRunner.run(null);
assertEquals("", monitor.toString());
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testNotExistingFolder()
{
testRunner.run(new File("blabla"));
assertEquals("", monitor.toString());
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testEmptyFolder()
{
testRunner.run(TEST_SCRIPTS_FOLDER);
assertEquals("", monitor.toString());
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testNonEmptyFolderButNoTestCases() throws IOException
{
assert new File(TEST_SCRIPTS_FOLDER, "some file").createNewFile();
assert new File(TEST_SCRIPTS_FOLDER, ".folder").mkdir();
-
+
testRunner.run(TEST_SCRIPTS_FOLDER);
assertEquals("", monitor.toString());
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testEmptyTestCase()
{
assert new File(TEST_SCRIPTS_FOLDER, "my test case").mkdir();
-
+
testRunner.run(TEST_SCRIPTS_FOLDER);
- assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR, monitor.toString());
-
+ assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR, monitor
+ .toString());
+
context.assertIsSatisfied();
}
-
+
@Test
public void testNonEmptyTestCaseButNoScripts() throws IOException
{
@@ -130,35 +132,38 @@ public class SqlUnitTestRunnerTest
assert testCaseFolder.mkdir();
assert new File(testCaseFolder, "blabla.sql").createNewFile();
assert new File(testCaseFolder, "folder").mkdir();
-
+
testRunner.run(TEST_SCRIPTS_FOLDER);
- assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR, monitor.toString());
-
+ assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR, monitor
+ .toString());
+
context.assertIsSatisfied();
}
-
+
@Test
- public void testTestCaseWithNoTestsButBuildupScript() throws IOException
+ public void testTestCaseWithNoTestsButBuildupScript() throws IOException
{
File testCaseFolder = new File(TEST_SCRIPTS_FOLDER, "my test case");
assert testCaseFolder.mkdir();
createScriptPrepareExecutor(new File(testCaseFolder, "buildup.sql"), "-- build up\n", null);
-
+
testRunner.run(TEST_SCRIPTS_FOLDER);
assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR
- + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR, monitor.toString());
-
+ + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR, monitor
+ .toString());
+
context.assertIsSatisfied();
}
@Test
- public void testTestCaseWithFailingBuildupScript() throws IOException
+ public void testTestCaseWithFailingBuildupScript() throws IOException
{
File testCaseFolder = new File(TEST_SCRIPTS_FOLDER, "my test case");
assert testCaseFolder.mkdir();
RuntimeException runtimeException = new RuntimeException("42");
- createScriptPrepareExecutor(new File(testCaseFolder, "buildup.sql"), "-- build up\n", runtimeException);
-
+ createScriptPrepareExecutor(new File(testCaseFolder, "buildup.sql"), "-- build up\n",
+ runtimeException);
+
try
{
testRunner.run(TEST_SCRIPTS_FOLDER);
@@ -167,27 +172,28 @@ public class SqlUnitTestRunnerTest
{
final String message = StringUtils.split(e.getMessage(), "\n")[0];
assertEquals("Script 'buildup.sql' of test case 'my test case' failed because of "
- + runtimeException, message.trim());
+ + runtimeException, message.trim());
}
assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR
- + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR
- + " script failed: skip test scripts and teardown script." + OSUtilities.LINE_SEPARATOR,
- monitor.toString());
-
+ + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR
+ + " script failed: skip test scripts and teardown script."
+ + OSUtilities.LINE_SEPARATOR, monitor.toString());
+
context.assertIsSatisfied();
}
-
+
@Test
- public void testOrderOfExecutingTestScripts() throws IOException
+ public void testOrderOfExecutingTestScripts() throws IOException
{
File testCaseFolder = new File(TEST_SCRIPTS_FOLDER, "my test case");
assert testCaseFolder.mkdir();
RuntimeException runtimeException = new RuntimeException("42");
- createScriptPrepareExecutor(new File(testCaseFolder, "9=b.sql"), "Select 9\n", runtimeException);
+ createScriptPrepareExecutor(new File(testCaseFolder, "9=b.sql"), "Select 9\n",
+ runtimeException);
FileUtils.writeStringToFile(new File(testCaseFolder, "abc=abc.sql"), "Select abc\n");
createScriptPrepareExecutor(new File(testCaseFolder, "10=c.sql"), "Select 10\n", null);
createScriptPrepareExecutor(new File(testCaseFolder, "1=a.sql"), "Select 1\n", null);
-
+
try
{
testRunner.run(TEST_SCRIPTS_FOLDER);
@@ -197,41 +203,41 @@ public class SqlUnitTestRunnerTest
// Strip away stack trace
final String message = StringUtils.split(e.getMessage(), "\n")[0];
assertEquals("Script '9=b.sql' of test case 'my test case' failed because of "
- + runtimeException, message.trim());
+ + runtimeException, message.trim());
}
assertEquals("====== Test case: my test case ======" + OSUtilities.LINE_SEPARATOR
- + " execute script 1=a.sql" + OSUtilities.LINE_SEPARATOR
- + " execute script 9=b.sql" + OSUtilities.LINE_SEPARATOR
- + " execute script 10=c.sql" + OSUtilities.LINE_SEPARATOR,
- monitor.toString());
-
+ + " execute script 1=a.sql" + OSUtilities.LINE_SEPARATOR
+ + " execute script 9=b.sql" + OSUtilities.LINE_SEPARATOR
+ + " execute script 10=c.sql" + OSUtilities.LINE_SEPARATOR, monitor.toString());
+
context.assertIsSatisfied();
}
-
+
@Test
- public void testOrderOfExecutingTestCases() throws IOException
+ public void testOrderOfExecutingTestCases() throws IOException
{
assert new File(TEST_SCRIPTS_FOLDER, "TC002").mkdir();
File testCaseFolder1 = new File(TEST_SCRIPTS_FOLDER, "TC001");
assert testCaseFolder1.mkdir();
- createScriptPrepareExecutor(new File(testCaseFolder1, "buildup.sql"), "create table\n", null);
+ createScriptPrepareExecutor(new File(testCaseFolder1, "buildup.sql"), "create table\n",
+ null);
createScriptPrepareExecutor(new File(testCaseFolder1, "1=a.sql"), "Select 1\n", null);
createScriptPrepareExecutor(new File(testCaseFolder1, "2=b.sql"), "Select 2\n", null);
createScriptPrepareExecutor(new File(testCaseFolder1, "teardown.sql"), "drop table\n", null);
-
+
testRunner.run(TEST_SCRIPTS_FOLDER);
assertEquals("====== Test case: TC001 ======" + OSUtilities.LINE_SEPARATOR
- + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR
- + " execute script 1=a.sql" + OSUtilities.LINE_SEPARATOR
- + " execute script 2=b.sql" + OSUtilities.LINE_SEPARATOR
- + " execute script teardown.sql" + OSUtilities.LINE_SEPARATOR
- + "====== Test case: TC002 ======" + OSUtilities.LINE_SEPARATOR,
- monitor.toString());
-
- context.assertIsSatisfied();
+ + " execute script buildup.sql" + OSUtilities.LINE_SEPARATOR
+ + " execute script 1=a.sql" + OSUtilities.LINE_SEPARATOR
+ + " execute script 2=b.sql" + OSUtilities.LINE_SEPARATOR
+ + " execute script teardown.sql" + OSUtilities.LINE_SEPARATOR
+ + "====== Test case: TC002 ======" + OSUtilities.LINE_SEPARATOR, monitor.toString());
+
+ context.assertIsSatisfied();
}
-
- private void createScriptPrepareExecutor(File scriptFile, String script, Throwable throwable) throws IOException
+
+ private void createScriptPrepareExecutor(File scriptFile, String script, Throwable throwable)
+ throws IOException
{
FileUtils.writeStringToFile(scriptFile, script);
InvocationExpectationBuilder builder = new InvocationExpectationBuilder();
@@ -240,5 +246,5 @@ public class SqlUnitTestRunnerTest
Action action = throwable == null ? new VoidAction() : new ThrowAction(throwable);
context.addExpectation(builder.toExpectation(action));
}
-
+
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/exceptions/UserFailureExceptionTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/exceptions/UserFailureExceptionTest.java
index 6c43b4dac71..4584b62c977 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/exceptions/UserFailureExceptionTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/exceptions/UserFailureExceptionTest.java
@@ -37,19 +37,25 @@ public final class UserFailureExceptionTest
@Test
public final void testFromTemplateStringObjectArray()
{
- UserFailureException exception = UserFailureException.fromTemplate("This is a %s exception to see how it works.", "dummy");
+ UserFailureException exception =
+ UserFailureException.fromTemplate("This is a %s exception to see how it works.",
+ "dummy");
assertEquals("This is a dummy exception to see how it works.", exception.getMessage());
// With not enough arguments.
try
{
- exception = UserFailureException.fromTemplate("This is a %s exception to see how it works.");
+ exception =
+ UserFailureException
+ .fromTemplate("This is a %s exception to see how it works.");
fail("MissingFormatArgumentException must be thrown.");
} catch (MissingFormatArgumentException e)
{
// Does nothing here.
}
// With more arguments than needed.
- exception = UserFailureException.fromTemplate("This is a %s exception to see how it works.", "dummy", "more dummy");
+ exception =
+ UserFailureException.fromTemplate("This is a %s exception to see how it works.",
+ "dummy", "more dummy");
assertEquals("This is a dummy exception to see how it works.", exception.getMessage());
exception = UserFailureException.fromTemplate("This is an exception to see how it works.");
// No format needed.
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/logging/LogMonitoringAppender.java b/common/sourceTest/java/ch/systemsx/cisd/common/logging/LogMonitoringAppender.java
index 5e16109a171..1fa2ef8be1f 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/logging/LogMonitoringAppender.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/logging/LogMonitoringAppender.java
@@ -35,7 +35,8 @@ import ch.systemsx.cisd.common.logging.LogCategory;
public final class LogMonitoringAppender extends AppenderSkeleton
{
- private static Map<LogMonitoringAppender, String> appenderMap = new HashMap<LogMonitoringAppender, String>();
+ private static Map<LogMonitoringAppender, String> appenderMap =
+ new HashMap<LogMonitoringAppender, String>();
private final StringBuilder eventRecorder = new StringBuilder();
@@ -54,7 +55,8 @@ public final class LogMonitoringAppender extends AppenderSkeleton
*
* @return The created appender.
*/
- public static synchronized LogMonitoringAppender addAppender(LogCategory category, String messagePart)
+ public static synchronized LogMonitoringAppender addAppender(LogCategory category,
+ String messagePart)
{
return addAppender(category, Pattern.compile(Pattern.quote(messagePart)));
}
@@ -112,7 +114,8 @@ public final class LogMonitoringAppender extends AppenderSkeleton
{
eventRecorder.append("event throwable: ").append(throwableStr).append('\n');
}
- if (regex.matcher(event.getMessage().toString()).find() || regex.matcher(getThrowableStr(event)).find())
+ if (regex.matcher(event.getMessage().toString()).find()
+ || regex.matcher(getThrowableStr(event)).find())
{
++logCount;
}
@@ -144,8 +147,8 @@ public final class LogMonitoringAppender extends AppenderSkeleton
public void verifyLogHappendNTimes(int n)
{
assert logCount == n : String.format(
- "Log snippet '%s' should have found %d times, but has been found %d times.", regex, n,
- logCount);
+ "Log snippet '%s' should have found %d times, but has been found %d times.", regex,
+ n, logCount);
}
public void reset()
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/mail/MailClientTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/mail/MailClientTest.java
index ce87483bc43..929355bb1d8 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/mail/MailClientTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/mail/MailClientTest.java
@@ -27,8 +27,6 @@ import ch.systemsx.cisd.common.utilities.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class MailClientTest extends AbstractFileSystemTestCase
@@ -39,18 +37,19 @@ public class MailClientTest extends AbstractFileSystemTestCase
String path = workingDirectory.getPath() + "/emails";
File emailFolder = new File(path);
assert emailFolder.exists() == false;
-
+
MailClient mailClient = new MailClient("sender", "file://" + path);
mailClient.sendMessage("some message", "Hello world\nHow are you today?", "a@b.c", "d@e.f");
-
+
assert emailFolder.exists();
assert emailFolder.isDirectory();
File[] files = emailFolder.listFiles();
assertEquals(1, files.length);
assertEquals("email", files[0].getName());
- assertEquals("Subj: some message\n" + "From: sender\n" + "To: a@b.c, d@e.f\n" + "Content:\n"
- + "Hello world\nHow are you today?\n", FileUtilities.loadToString(files[0]));
-
+ assertEquals("Subj: some message\n" + "From: sender\n" + "To: a@b.c, d@e.f\n"
+ + "Content:\n" + "Hello world\nHow are you today?\n", FileUtilities
+ .loadToString(files[0]));
+
// second mail
mailClient.sendMessage("Greetings", "Hello world!");
files = emailFolder.listFiles();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactoryTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactoryTest.java
index f9300089494..c9ca6c087f0 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactoryTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactoryTest.java
@@ -68,15 +68,17 @@ public final class AbstractParserObjectFactoryTest
fail("Following properties '[isnotin]' are not part of 'Bean'.");
} catch (final UnmatchedPropertiesException ex)
{
- assertEquals("Following header columns are not part of 'Bean': isnotin", ex.getMessage());
+ assertEquals("Following header columns are not part of 'Bean': isnotin", ex
+ .getMessage());
}
}
@Test
public final void testMandatoryFields()
{
- final DefaultAliasPropertyMapper propertyMapper = new DefaultAliasPropertyMapper(new String[]
- { "description" });
+ final DefaultAliasPropertyMapper propertyMapper =
+ new DefaultAliasPropertyMapper(new String[]
+ { "description" });
try
{
final BeanFactory beanFactory = new BeanFactory(Bean.class, propertyMapper);
@@ -86,7 +88,8 @@ public final class AbstractParserObjectFactoryTest
fail("Field/Property name 'name' is mandatory.");
} catch (final MandatoryPropertyMissingException ex)
{
- assertEquals(String.format(MandatoryPropertyMissingException.MESSAGE_FORMAT, "name"), ex.getMessage());
+ assertEquals(String.format(MandatoryPropertyMissingException.MESSAGE_FORMAT, "name"),
+ ex.getMessage());
}
}
@@ -106,8 +109,10 @@ public final class AbstractParserObjectFactoryTest
final IAliasPropertyMapper propertyMapper = createPropertyMapper();
final BeanFactory beanFactory = new BeanFactory(Bean.class, propertyMapper);
final String[] defaultTokens = createDefaultLineTokens();
- final String[] lineTokens = (String[]) ArrayUtils.remove(defaultTokens, defaultTokens.length - 1);
- final String msg = String.format(IndexOutOfBoundsException.MESSAGE_FORMAT, 2, lineTokens.length);
+ final String[] lineTokens =
+ (String[]) ArrayUtils.remove(defaultTokens, defaultTokens.length - 1);
+ final String msg =
+ String.format(IndexOutOfBoundsException.MESSAGE_FORMAT, 2, lineTokens.length);
try
{
beanFactory.createObject(lineTokens);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
index 7655ffbca14..a487f15ae8c 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
@@ -49,7 +49,8 @@ public final class DefaultParserTest
public final void testParseWithoutFactoryAndHeader()
{
final IParser<String[]> parser = createParser();
- final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter(), HEADER_LENGTH);
+ final List<String[]> result =
+ parser.parse(createLineIterator(), new HeaderLineFilter(), HEADER_LENGTH);
assertEquals(3, result.size());
assertEquals(result.get(0)[0], "firstName");
assertEquals(result.get(1)[1], "Darwin");
@@ -61,7 +62,8 @@ public final class DefaultParserTest
public final void testParseWithoutFactoryWithLineFilter()
{
final IParser<String[]> parser = createParser();
- final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH);
+ final List<String[]> result =
+ parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH);
assertEquals(2, result.size());
assertEquals(result.get(0)[0], "Charles");
assertEquals(result.get(1)[1], "Einstein");
@@ -76,9 +78,10 @@ public final class DefaultParserTest
parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH + 1);
} catch (final ColumnSizeMismatchException ex)
{
- assertEquals("Line <4> has less columns (4) than the header (5):\n "
- + "Charles <TAB> Darwin <TAB> Humboldt Ave. 1865 <TAB> 4242 Somewhere <END_OF_LINE>", ex
- .getMessage());
+ assertEquals(
+ "Line <4> has less columns (4) than the header (5):\n "
+ + "Charles <TAB> Darwin <TAB> Humboldt Ave. 1865 <TAB> 4242 Somewhere <END_OF_LINE>",
+ ex.getMessage());
}
}
@@ -103,8 +106,9 @@ public final class DefaultParserTest
parser.parse(createLineIterator(), new HeaderLineFilter(2), HEADER_LENGTH);
} catch (final ParsingException ex)
{
- assertEquals("Creating an object with following tokens '[firstName, lastName, address, city]' failed.", ex
- .getMessage());
+ assertEquals(
+ "Creating an object with following tokens '[firstName, lastName, address, city]' failed.",
+ ex.getMessage());
assertEquals(3, ex.getLineNumber());
}
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
index 48960489187..dd5103f7b36 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
@@ -20,8 +20,8 @@ import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
/**
- * Test cases for the {@link HeaderLineFilter}
- *
+ * Test cases for the {@link HeaderLineFilter}
+ *
* @author Bernd Rinn
*/
public class HeaderLineFilterTest
@@ -36,13 +36,18 @@ public class HeaderLineFilterTest
assert filter.acceptLine("text", i) : "Line " + i;
}
}
-
+
@DataProvider(name = "headerNumbers")
public Object[][] headerNumbers()
{
- return new Object[][] { { 0 }, { 1 }, { 2 }, { 3 } };
+ return new Object[][]
+ {
+ { 0 },
+ { 1 },
+ { 2 },
+ { 3 } };
}
-
+
@Test(dataProvider = "headerNumbers")
public void testHeaderLine(int headerLine)
{
@@ -51,10 +56,12 @@ public class HeaderLineFilterTest
{
if (headerLine == i)
{
- assert filter.acceptLine("text", i) == false : "Line " + i + " (header line: " + headerLine + ")";
+ assert filter.acceptLine("text", i) == false : "Line " + i + " (header line: "
+ + headerLine + ")";
} else
{
- assert filter.acceptLine("text", i) : "Line " + i + " (header line: " + headerLine + ")";
+ assert filter.acceptLine("text", i) : "Line " + i + " (header line: " + headerLine
+ + ")";
}
}
}
@@ -66,33 +73,33 @@ public class HeaderLineFilterTest
assert filter.acceptLine("", 0) == false;
assert filter.acceptLine("something", 1);
}
-
+
@Test
public void testSkipEmptyLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
assert filter.acceptLine("", 0) == false;
}
-
+
@Test
public void testSkipBlankLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
assert filter.acceptLine(" ", 0) == false;
}
-
+
@Test
public void testSkipCommentLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
assert filter.acceptLine("# Some comment", 0) == false;
}
-
+
@Test
public void testSkipCommentLineWithLeadingWhiteSpace()
{
final HeaderLineFilter filter = new HeaderLineFilter();
assert filter.acceptLine("\t# Some comment", 0) == false;
}
-
+
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
index f2af1aa96ec..845faba0f00 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
@@ -40,9 +40,11 @@ import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
public final class ParserUtilitiesTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "ParserUtilitiesTest");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "ParserUtilitiesTest");
@BeforeClass
public final void setUp()
@@ -102,7 +104,9 @@ public final class ParserUtilitiesTest
{ StringUtils.EMPTY, "# comment line", StringUtils.EMPTY, "hello" };
File file = new File(workingDirectory, "test.txt");
FileUtils.writeLines(file, Arrays.asList(lines));
- Line line = ParserUtilities.getFirstAcceptedLine(file, ExcludeEmptyAndCommentLineFilter.INSTANCE);
+ Line line =
+ ParserUtilities.getFirstAcceptedLine(file,
+ ExcludeEmptyAndCommentLineFilter.INSTANCE);
assertEquals("hello", line.getText());
assertEquals(3, line.getNumber());
assert file.delete();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/TabFileLoaderTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/TabFileLoaderTest.java
index 0e8cdd13512..01c3a570da4 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/TabFileLoaderTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/TabFileLoaderTest.java
@@ -87,8 +87,8 @@ public final class TabFileLoaderTest
// IParserObjectFactoryFactory
//
- public final IParserObjectFactory<ABC> createFactory(final IAliasPropertyMapper propertyMapper)
- throws ParserException
+ public final IParserObjectFactory<ABC> createFactory(
+ final IAliasPropertyMapper propertyMapper) throws ParserException
{
return new IParserObjectFactory<ABC>()
{
@@ -160,7 +160,9 @@ public final class TabFileLoaderTest
private void loadAndCheck(String preamble)
{
TabFileLoader<ABC> loader = new TabFileLoader<ABC>(new ABCFactoryFactory());
- List<ABC> list = loader.load(new StringReader(preamble + "A\tB\tC\n" + "a1\tb1\tc1\n" + "a2\tb2\tc2\n"));
+ List<ABC> list =
+ loader.load(new StringReader(preamble + "A\tB\tC\n" + "a1\tb1\tc1\n"
+ + "a2\tb2\tc2\n"));
assertEquals(list.toString(), 2, list.size());
assertEquals("a1b1c1", list.get(0).toString());
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/process/ProcessExecutionHelperTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/process/ProcessExecutionHelperTest.java
index d539bf06e0d..30a9de40e0c 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/process/ProcessExecutionHelperTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/process/ProcessExecutionHelperTest.java
@@ -50,26 +50,32 @@ public class ProcessExecutionHelperTest
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, ProcessExecutionHelperTest.class);
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "ProcessExecutionHelperTest");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "ProcessExecutionHelperTest");
- private File createExecutable(String name, String... lines) throws IOException, InterruptedException
+ private File createExecutable(String name, String... lines) throws IOException,
+ InterruptedException
{
final File executable = new File(workingDirectory, name);
executable.delete();
CollectionIO.writeIterable(executable, Arrays.asList(lines));
- Runtime.getRuntime().exec(String.format("/bin/chmod +x %s", executable.getPath())).waitFor();
+ Runtime.getRuntime().exec(String.format("/bin/chmod +x %s", executable.getPath()))
+ .waitFor();
executable.deleteOnExit();
return executable;
}
- private File createExecutable(String name, int exitValue) throws IOException, InterruptedException
+ private File createExecutable(String name, int exitValue) throws IOException,
+ InterruptedException
{
return createExecutable(name, "#! /bin/sh", "exit " + exitValue);
}
- private File createSleepingExecutable(String name, long millisToSleep) throws IOException, InterruptedException
+ private File createSleepingExecutable(String name, long millisToSleep) throws IOException,
+ InterruptedException
{
return createExecutable(name, "#! /bin/sh", "sleep " + (millisToSleep / 1000.0f), "exit 0");
}
@@ -96,7 +102,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createExecutable("dummy.sh", 0);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ operationLog, machineLog);
assertTrue(ok);
}
@@ -106,7 +113,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createExecutable("dummy.sh", 1);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ operationLog, machineLog);
assertFalse(ok);
}
@@ -116,8 +124,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createExecutable("dummy.sh", 0);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), WATCHDOG_WAIT_MILLIS,
- operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ WATCHDOG_WAIT_MILLIS, operationLog, machineLog);
assertTrue(ok);
}
@@ -127,8 +135,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createExecutable("dummy.sh", 1);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), WATCHDOG_WAIT_MILLIS,
- operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ WATCHDOG_WAIT_MILLIS, operationLog, machineLog);
assertFalse(ok);
}
@@ -138,8 +146,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createSleepingExecutable("dummy.sh", WATCHDOG_WAIT_MILLIS / 2);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), WATCHDOG_WAIT_MILLIS,
- operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ WATCHDOG_WAIT_MILLIS, operationLog, machineLog);
assertTrue(ok);
}
@@ -149,8 +157,8 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createSleepingExecutable("dummy.sh", 2 * WATCHDOG_WAIT_MILLIS);
final boolean ok =
- ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()), WATCHDOG_WAIT_MILLIS,
- operationLog, machineLog);
+ ProcessExecutionHelper.runAndLog(Arrays.asList(dummyExec.getAbsolutePath()),
+ WATCHDOG_WAIT_MILLIS, operationLog, machineLog);
assertFalse(ok);
}
@@ -160,9 +168,10 @@ public class ProcessExecutionHelperTest
{
final File dummyExec = createSleepingExecutable("dummy.sh", 2 * WATCHDOG_WAIT_MILLIS);
final ProcessResult result =
- ProcessExecutionHelper.run(Arrays.asList(dummyExec.getAbsolutePath()), WATCHDOG_WAIT_MILLIS,
- operationLog, machineLog);
- assertTrue(result.hasBlocked() || ProcessExecutionHelper.isProcessTerminated(result.exitValue()));
+ ProcessExecutionHelper.run(Arrays.asList(dummyExec.getAbsolutePath()),
+ WATCHDOG_WAIT_MILLIS, operationLog, machineLog);
+ assertTrue(result.hasBlocked()
+ || ProcessExecutionHelper.isProcessTerminated(result.exitValue()));
}
@Test(groups =
@@ -174,9 +183,11 @@ public class ProcessExecutionHelperTest
final String stderr1 = "This goes to stderr, 1";
final String stderr2 = "This goes to stderr, 2";
final File dummyExec =
- createExecutable("dummy.sh", "echo " + stdout1, "echo " + stderr1, "echo " + stdout2, "echo " + stderr2);
+ createExecutable("dummy.sh", "echo " + stdout1, "echo " + stderr1, "echo "
+ + stdout2, "echo " + stderr2);
final ProcessResult result =
- ProcessExecutionHelper.run(Arrays.asList(dummyExec.getAbsolutePath()), operationLog, machineLog);
+ ProcessExecutionHelper.run(Arrays.asList(dummyExec.getAbsolutePath()),
+ operationLog, machineLog);
final int exitValue = result.exitValue();
assertEquals(0, exitValue);
result.log();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/test/InterfaceForRMICheckerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/test/InterfaceForRMICheckerTest.java
index 4f369039090..d2c8d93d018 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/test/InterfaceForRMICheckerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/test/InterfaceForRMICheckerTest.java
@@ -25,8 +25,6 @@ import java.util.List;
import org.testng.annotations.Test;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class InterfaceForRMICheckerTest
@@ -34,32 +32,35 @@ public class InterfaceForRMICheckerTest
public static class NonSerializableClass
{
}
-
+
@Test
public void testRMIReadyInterface()
{
InterfaceForRMIChecker.assertInterfaceForRMI(RMIReadyInterface.class);
}
-
+
public interface RMIReadyInterface
{
public int get();
+
public void set(int a);
+
public Void set2(String s);
+
public Number get2();
}
-
+
@Test
public void testRMIReadyInterfaceWhichRefersToItself()
{
InterfaceForRMIChecker.assertInterfaceForRMI(RMIReadyInterfaceWhichRefersToItself.class);
}
-
+
public interface RMIReadyInterfaceWhichRefersToItself extends Serializable
{
public void set(RMIReadyInterfaceWhichRefersToItself interfaze);
}
-
+
@Test
public void testInterfaceWithNonSerializableParameter()
{
@@ -70,43 +71,48 @@ public class InterfaceForRMICheckerTest
{
public void set(NonSerializableClass a);
}
-
+
@Test
public void testInterfaceWithNonSerializableReturnValue()
{
checkNonRMIReadyInterface(InterfaceWithNonSerializableParameter.class);
}
-
+
public interface InterfaceWithNonSerializableReturnValue
{
public NonSerializableClass get();
}
-
+
@Test
public void testInterfaceExtendsNonRMIReadyInterface()
{
checkNonRMIReadyInterface(InterfaceExtendsNonRMIReadyInterface.class);
}
-
- public interface InterfaceExtendsNonRMIReadyInterface extends InterfaceWithNonSerializableParameter
+
+ public interface InterfaceExtendsNonRMIReadyInterface extends
+ InterfaceWithNonSerializableParameter
{
public int get();
}
-
+
@Test
public void testSerializablityOfSerializableClass()
{
InterfaceForRMIChecker.assertSerializable(SerializableClass.class);
}
-
+
public static class SerializableClass implements Serializable
{
private static final long serialVersionUID = 1L;
+
private static NonSerializableClass non;
+
private int n;
+
private transient NonSerializableClass transientNon;
+
private List<String> list;
-
+
@Override
public String toString()
{
@@ -118,21 +124,27 @@ public class InterfaceForRMICheckerTest
return list;
}
}
-
+
@Test
public void testSerializablityOfSerializableClassExtendsNonSerializableClass()
{
- InterfaceForRMIChecker.assertSerializable(SerializableClassExtendsNonSerializableClass.class);
+ InterfaceForRMIChecker
+ .assertSerializable(SerializableClassExtendsNonSerializableClass.class);
}
-
- public static class SerializableClassExtendsNonSerializableClass extends NonSerializableClass implements Serializable
+
+ public static class SerializableClassExtendsNonSerializableClass extends NonSerializableClass
+ implements Serializable
{
private static final long serialVersionUID = 1L;
+
private static NonSerializableClass non;
+
private int n;
+
private transient NonSerializableClass transientNon;
+
private List<String> list;
-
+
@Override
public String toString()
{
@@ -144,22 +156,23 @@ public class InterfaceForRMICheckerTest
return list;
}
}
-
+
@Test
public void testSerializablityOfNonSerializableClass()
{
checkNonSerializableClass(NonSerializableClass.class);
}
-
+
@Test
public void testSerializablityOfClassWithNonSerializableAttribute()
{
checkNonSerializableClass(ClassWithNonSerializableAttribute.class);
}
-
+
public static class ClassWithNonSerializableAttribute implements Serializable
{
private static final long serialVersionUID = 1L;
+
private NonSerializableClass nonSerializable;
@Override
@@ -168,56 +181,57 @@ public class InterfaceForRMICheckerTest
return nonSerializable.toString();
}
}
-
+
@Test
public void testSerializablityOfClassWithAnArrayOfNonSerializables()
{
checkNonSerializableClass(ClassWithAnArrayOfNonSerializables.class);
}
-
+
public static class ClassWithAnArrayOfNonSerializables implements Serializable
{
private static final long serialVersionUID = 1L;
+
private NonSerializableClass[] nonSerializables;
-
+
@Override
public String toString()
{
return nonSerializables.toString();
}
}
-
+
@Test
public void testSerializablityOfClassWithAListOfNonSerializables()
{
checkNonSerializableClass(ClassWithAListOfNonSerializables.class);
}
-
+
public static class ClassWithAListOfNonSerializables implements Serializable
{
private static final long serialVersionUID = 1L;
+
private List<NonSerializableClass> nonSerializables;
-
+
@Override
public String toString()
{
return nonSerializables.toString();
}
}
-
+
@Test
public void testClassWithExtendingClassWithNonSerializableAttribute()
{
checkNonSerializableClass(ClassWithExtendingClassWithNonSerializableAttribute.class);
}
-
- public static class ClassWithExtendingClassWithNonSerializableAttribute extends ClassWithNonSerializableAttribute
+
+ public static class ClassWithExtendingClassWithNonSerializableAttribute extends
+ ClassWithNonSerializableAttribute
{
private static final long serialVersionUID = 1L;
}
-
-
-
+
private void checkNonRMIReadyInterface(Class<?> interfaze)
{
boolean failed = false;
@@ -253,11 +267,11 @@ public class InterfaceForRMICheckerTest
fail("AssertionError expected");
}
}
-
private void checkErrorMessage(AssertionError e)
{
- assertEquals(NonSerializableClass.class + " does not implements java.io.Serializable", e.getMessage());
+ assertEquals(NonSerializableClass.class + " does not implements java.io.Serializable", e
+ .getMessage());
}
-
+
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java b/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
index 604cf248f15..2091bfac24f 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
@@ -83,8 +83,8 @@ public final class StoringUncaughtExceptionHandler implements UncaughtExceptionH
{
if (hasExceptionOccurred())
{
- throw new RuntimeException(String.format("An exception occurred in thread %s.", getThreadName()),
- getThrowable());
+ throw new RuntimeException(String.format("An exception occurred in thread %s.",
+ getThreadName()), getThrowable());
}
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/BeanUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/BeanUtilsTest.java
index 459f8b32641..402dc6dcf88 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/BeanUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/BeanUtilsTest.java
@@ -48,11 +48,12 @@ public final class BeanUtilsTest
@SuppressWarnings("null")
@Test
- public final void testGetPropertyDescriptors() throws IllegalArgumentException, IllegalAccessException,
- InvocationTargetException
+ public final void testGetPropertyDescriptors() throws IllegalArgumentException,
+ IllegalAccessException, InvocationTargetException
{
List<PropertyDescriptor> descriptors =
- new ArrayList<PropertyDescriptor>(BeanUtils.getPropertyDescriptors(FooBean.class).values());
+ new ArrayList<PropertyDescriptor>(BeanUtils.getPropertyDescriptors(FooBean.class)
+ .values());
assertEquals(1, descriptors.size());
PropertyDescriptor outerDescriptor = null;
// Play with property 'description'
@@ -587,7 +588,8 @@ public final class BeanUtilsTest
final String[] array = new String[]
{ "hot", "warm", "cool", "icy" };
aWrapper.setArray(array);
- final CollectionWrapper1 colWrapper = BeanUtils.createBean(CollectionWrapper1.class, aWrapper);
+ final CollectionWrapper1 colWrapper =
+ BeanUtils.createBean(CollectionWrapper1.class, aWrapper);
List<String> list = colWrapper.getArray();
assertNotNull(list);
assertEquals(array.length, list.size());
@@ -604,7 +606,8 @@ public final class BeanUtilsTest
final List<String> list = new ArrayList<String>(Arrays.asList(new String[]
{ "hot", "warm", "cool", "icy" }));
colWrapper.setArray(list);
- final CollectionWrapper1 colWrapper2 = BeanUtils.createBean(CollectionWrapper1.class, colWrapper);
+ final CollectionWrapper1 colWrapper2 =
+ BeanUtils.createBean(CollectionWrapper1.class, colWrapper);
List<String> list2 = colWrapper2.getArray();
assertNotNull(list2);
assertEquals(list.size(), list2.size());
@@ -768,7 +771,8 @@ public final class BeanUtilsTest
final Bean1a[] arrayb1 = new Bean1a[]
{ b1a, b1b };
b1Array.setBeanArray(arrayb1);
- final BeanWithBeanCollection2 b2Collection = BeanUtils.createBean(BeanWithBeanCollection2.class, b1Array);
+ final BeanWithBeanCollection2 b2Collection =
+ BeanUtils.createBean(BeanWithBeanCollection2.class, b1Array);
final Collection<Bean2a> colb2 = b2Collection.getBeanArray();
assertNotNull(colb2);
assertEquals(arrayb1.length, colb2.size());
@@ -792,7 +796,8 @@ public final class BeanUtilsTest
final Bean2a[] arrayb2 = new Bean2a[]
{ b2a, b2b };
b2Array.setBeanArray(arrayb2);
- final BeanWithBeanCollection1 b1Collection = BeanUtils.createBean(BeanWithBeanCollection1.class, b2Array);
+ final BeanWithBeanCollection1 b1Collection =
+ BeanUtils.createBean(BeanWithBeanCollection1.class, b2Array);
final Collection<Bean1a> colb1 = b1Collection.getBeanArray();
assertNotNull(colb1);
assertEquals(arrayb2.length, colb1.size());
@@ -822,7 +827,8 @@ public final class BeanUtilsTest
final Collection<Bean1a> colb1 = new LinkedHashSet<Bean1a>(Arrays.asList(new Bean1a[]
{ b1a, b1b }));
b1Collection.setBeanArray(colb1);
- final BeanWithBeanArray2 b2Array = BeanUtils.createBean(BeanWithBeanArray2.class, b1Collection);
+ final BeanWithBeanArray2 b2Array =
+ BeanUtils.createBean(BeanWithBeanArray2.class, b1Collection);
final Bean2a[] arrayb2 = b2Array.getBeanArray();
assertNotNull(arrayb2);
assertEquals(colb1.size(), arrayb2.length);
@@ -859,7 +865,8 @@ public final class BeanUtilsTest
assertBeanArraysAreEqual(arrayb1, arrayb2);
}
- private final static void assertBeanArraysAreEqual(final Bean1a[] arrayb1, final Bean2a[] arrayb2)
+ private final static void assertBeanArraysAreEqual(final Bean1a[] arrayb1,
+ final Bean2a[] arrayb2)
{
assertEquals(arrayb1.length, arrayb2.length);
for (int i = 0; i < arrayb1.length; ++i)
@@ -877,7 +884,8 @@ public final class BeanUtilsTest
final Collection<Bean1a> colb1 = new LinkedHashSet<Bean1a>(Arrays.asList(new Bean1a[]
{ b1a, b1b }));
b1Collection.setBeanArray(colb1);
- final BeanWithBeanCollection2 b2Collection = BeanUtils.createBean(BeanWithBeanCollection2.class, b1Collection);
+ final BeanWithBeanCollection2 b2Collection =
+ BeanUtils.createBean(BeanWithBeanCollection2.class, b1Collection);
final Collection<Bean2a> colb2 = b2Collection.getBeanArray();
assertNotNull(colb2);
assertBeanCollectionsAreEqual(colb1, colb2);
@@ -955,7 +963,7 @@ public final class BeanUtilsTest
assertEquals(msg, b2.getI(), b1.getI());
assertEquals(msg, b2.getS(), b1.getS());
}
-
+
private static interface IFoo
{
public String getFoo();
@@ -996,30 +1004,32 @@ public final class BeanUtilsTest
{
final FooBean tofuBean = new FooBean();
tofuBean.setFoo("some tofu");
- final BarBean toFooBean = BeanUtils.createBean(BarBean.class, tofuBean, new BeanUtils.Converter()
- {
- @SuppressWarnings("unused")
- public String convertToBar(FooBean foo)
- {
- return StringUtils.replace(foo.getFoo(), "tofu", "to Foo");
- }
- });
+ final BarBean toFooBean =
+ BeanUtils.createBean(BarBean.class, tofuBean, new BeanUtils.Converter()
+ {
+ @SuppressWarnings("unused")
+ public String convertToBar(FooBean foo)
+ {
+ return StringUtils.replace(foo.getFoo(), "tofu", "to Foo");
+ }
+ });
assertEquals("some to Foo", toFooBean.getBar());
}
-
+
@Test
public void testConverterWithArgumentOfInterfaceType()
{
final FooBean tofuBean = new FooBean();
tofuBean.setFoo("some tofu");
- final BarBean toFooBean = BeanUtils.createBean(BarBean.class, tofuBean, new BeanUtils.Converter()
- {
- @SuppressWarnings("unused")
- public String convertToBar(IFoo foo)
- {
- return StringUtils.replace(foo.getFoo(), "tofu", "to Foo");
- }
- });
+ final BarBean toFooBean =
+ BeanUtils.createBean(BarBean.class, tofuBean, new BeanUtils.Converter()
+ {
+ @SuppressWarnings("unused")
+ public String convertToBar(IFoo foo)
+ {
+ return StringUtils.replace(foo.getFoo(), "tofu", "to Foo");
+ }
+ });
assertEquals("some to Foo", toFooBean.getBar());
}
}
\ No newline at end of file
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
index edb37833088..4c92f4f0c11 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
@@ -89,8 +89,8 @@ public final class ClassUtilsTest
{
assertEquals("testGetCurrentMethod", ClassUtils.getCurrentMethod().getName());
// Border cases
- assertEquals(new SameMethodName().getMethodName(), new SameMethodName().getMethodName(new Object(),
- new Object()));
+ assertEquals(new SameMethodName().getMethodName(), new SameMethodName().getMethodName(
+ new Object(), new Object()));
}
private final static class SameMethodName
@@ -128,7 +128,9 @@ public final class ClassUtilsTest
@Test
public void testCreateWithDefaultConstructor()
{
- final CharSequence cs = ClassUtils.create(CharSequence.class, StringBuffer.class.getName(), (Object[]) null);
+ final CharSequence cs =
+ ClassUtils
+ .create(CharSequence.class, StringBuffer.class.getName(), (Object[]) null);
assertTrue(cs instanceof StringBuffer);
assertEquals(0, cs.length());
}
@@ -137,7 +139,8 @@ public final class ClassUtilsTest
public void testCreateWithPropertiesConstructor()
{
final Properties properties = new Properties();
- final Appendable appendable = ClassUtils.create(Appendable.class, MyClass.class.getName(), properties);
+ final Appendable appendable =
+ ClassUtils.create(Appendable.class, MyClass.class.getName(), properties);
assertTrue(appendable instanceof MyClass);
assertSame(properties, ((MyClass) appendable).properties);
}
@@ -151,7 +154,9 @@ public final class ClassUtilsTest
fail("AssertionError expected.");
} catch (final AssertionError e)
{
- assertEquals("Class 'java.lang.Integer' does not implements/extends 'java.lang.Float'.", e.getMessage());
+ assertEquals(
+ "Class 'java.lang.Integer' does not implements/extends 'java.lang.Float'.", e
+ .getMessage());
}
}
@@ -164,8 +169,9 @@ public final class ClassUtilsTest
fail("AssertionError expected.");
} catch (final AssertionError e)
{
- assertEquals("Interface 'java.lang.CharSequence' can not be instanciated as it is an interface.", e
- .getMessage());
+ assertEquals(
+ "Interface 'java.lang.CharSequence' can not be instanciated as it is an interface.",
+ e.getMessage());
}
}
@@ -174,7 +180,8 @@ public final class ClassUtilsTest
{
final List<String> list = new ArrayList<String>();
list.add("Hello");
- final Appendable appendable = ClassUtils.create(Appendable.class, MyClass.class.getName(), list);
+ final Appendable appendable =
+ ClassUtils.create(Appendable.class, MyClass.class.getName(), list);
assertSame(list, ((MyClass) appendable).iterable);
}
@@ -248,7 +255,8 @@ public final class ClassUtilsTest
return null;
}
- public Appendable append(final CharSequence csq, final int start, final int end) throws IOException
+ public Appendable append(final CharSequence csq, final int start, final int end)
+ throws IOException
{
return null;
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
index e987e4851d2..620fbfc9a85 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
@@ -43,9 +43,11 @@ import ch.systemsx.cisd.common.logging.LogMonitoringAppender;
public class DirectoryScanningTimerTaskTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "DirectoryScanningTimerTaskTest");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "DirectoryScanningTimerTaskTest");
private final static FileFilter ALWAYS_FALSE_FILE_FILTER = new FileFilter()
{
@@ -55,7 +57,8 @@ public class DirectoryScanningTimerTaskTest
}
};
- private final static String EXCEPTION_THROWING_FILE_FILTER_MESSAGE = "Exception throwing file filter does its job.";
+ private final static String EXCEPTION_THROWING_FILE_FILTER_MESSAGE =
+ "Exception throwing file filter does its job.";
private final static FileFilter EXCEPTION_THROWING_FILE_FILTER = new FileFilter()
{
@@ -108,7 +111,8 @@ public class DirectoryScanningTimerTaskTest
@Test
public void testFaultyPathsDeletion()
{
- final File faultyPaths = new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
+ final File faultyPaths =
+ new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
CollectionIO.writeIterable(faultyPaths, Collections.singleton("some_path"));
new DirectoryScanningTimerTask(workingDirectory, ACCEPT_ALL_FILTER, mockPathHandler);
assertEquals(0, faultyPaths.length());
@@ -135,7 +139,8 @@ public class DirectoryScanningTimerTaskTest
someFile.createNewFile();
someFile.deleteOnExit();
final DirectoryScanningTimerTask scanner =
- new DirectoryScanningTimerTask(workingDirectory, ALWAYS_FALSE_FILE_FILTER, mockPathHandler);
+ new DirectoryScanningTimerTask(workingDirectory, ALWAYS_FALSE_FILE_FILTER,
+ mockPathHandler);
assertEquals(0, mockPathHandler.handledPaths.size());
scanner.run();
assertEquals(0, mockPathHandler.handledPaths.size());
@@ -144,7 +149,8 @@ public class DirectoryScanningTimerTaskTest
@Test
public void testManipulateFaultyPaths() throws IOException
{
- final File faultyPaths = new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
+ final File faultyPaths =
+ new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
final File someFile = new File(workingDirectory, "some_file");
someFile.createNewFile();
someFile.deleteOnExit();
@@ -160,7 +166,8 @@ public class DirectoryScanningTimerTaskTest
@Test
public void testFaultyPaths() throws IOException
{
- final File faultyPaths = new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
+ final File faultyPaths =
+ new File(workingDirectory, DirectoryScanningTimerTask.FAULTY_PATH_FILENAME);
final File someFile = new File(workingDirectory, "some_file");
final MockPathHandler myPathHandler = new MockPathHandler()
{
@@ -238,7 +245,8 @@ public class DirectoryScanningTimerTaskTest
final File dir = new File(workingDirectory, "testMissingDirectory");
dir.mkdir();
final LogMonitoringAppender appender =
- LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "Failed to get listing of directory");
+ LogMonitoringAppender.addAppender(LogCategory.NOTIFY,
+ "Failed to get listing of directory");
try
{
// The directory needs to exist when the scanner is created, otherwise the self-test will fail.
@@ -260,7 +268,8 @@ public class DirectoryScanningTimerTaskTest
final File dir = new File(workingDirectory, "testMissingDirectory");
dir.mkdir();
final LogMonitoringAppender appender =
- LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "Failed to get listing of directory");
+ LogMonitoringAppender.addAppender(LogCategory.NOTIFY,
+ "Failed to get listing of directory");
try
{
// The directory needs to exist when the scanner is created, otherwise the self-test will fail.
@@ -289,14 +298,17 @@ public class DirectoryScanningTimerTaskTest
file.createNewFile();
file.deleteOnExit();
final LogMonitoringAppender appender1 =
- LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "Failed to get listing of directory");
+ LogMonitoringAppender.addAppender(LogCategory.NOTIFY,
+ "Failed to get listing of directory");
final LogMonitoringAppender appender2 =
- LogMonitoringAppender.addAppender(LogCategory.NOTIFY, EXCEPTION_THROWING_FILE_FILTER_MESSAGE);
+ LogMonitoringAppender.addAppender(LogCategory.NOTIFY,
+ EXCEPTION_THROWING_FILE_FILTER_MESSAGE);
try
{
// The directory needs to exist when the scanner is created, otherwise the self-test will fail.
final DirectoryScanningTimerTask scanner =
- new DirectoryScanningTimerTask(dir, EXCEPTION_THROWING_FILE_FILTER, mockPathHandler);
+ new DirectoryScanningTimerTask(dir, EXCEPTION_THROWING_FILE_FILTER,
+ mockPathHandler);
scanner.run();
appender1.verifyLogHasHappened();
appender2.verifyLogHasHappened();
@@ -315,9 +327,11 @@ public class DirectoryScanningTimerTaskTest
final File dir = new File(workingDirectory, "testSuppressLogging");
dir.mkdir();
final LogMonitoringAppender appenderNotifyError =
- LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "Failed to get listing of directory");
+ LogMonitoringAppender.addAppender(LogCategory.NOTIFY,
+ "Failed to get listing of directory");
final LogMonitoringAppender appenderOperationError =
- LogMonitoringAppender.addAppender(LogCategory.OPERATION, "Failed to get listing of directory");
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION,
+ "Failed to get listing of directory");
final LogMonitoringAppender appenderOK =
LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "' is available again");
try
@@ -325,7 +339,8 @@ public class DirectoryScanningTimerTaskTest
final int numberOfErrorsToIgnore = 2;
// The directory needs to exist when the scanner is created, otherwise the self-test will fail.
final DirectoryScanningTimerTask scanner =
- new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler, numberOfErrorsToIgnore);
+ new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler,
+ numberOfErrorsToIgnore);
dir.delete();
assert dir.exists() == false;
// First error -> ignored
@@ -358,7 +373,8 @@ public class DirectoryScanningTimerTaskTest
@Test
public void testDoNotLogDirectoryAvailableWhenNoErrorWasLogged() throws IOException
{
- final File dir = new File(workingDirectory, "testDoNotLogDirectoryAvailableWhenNoErrorWasLogged");
+ final File dir =
+ new File(workingDirectory, "testDoNotLogDirectoryAvailableWhenNoErrorWasLogged");
dir.mkdir();
final LogMonitoringAppender appender =
LogMonitoringAppender.addAppender(LogCategory.NOTIFY, "' is available again.");
@@ -367,7 +383,8 @@ public class DirectoryScanningTimerTaskTest
final int numberOfErrorsToIgnore = 2;
// The directory needs to exist when the scanner is created, otherwise the self-test will fail.
final DirectoryScanningTimerTask scanner =
- new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler, numberOfErrorsToIgnore);
+ new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler,
+ numberOfErrorsToIgnore);
dir.delete();
assert dir.exists() == false;
// First error -> ignored
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ExceptionUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ExceptionUtilsTest.java
index de5fe663a0f..e24581d8f77 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ExceptionUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ExceptionUtilsTest.java
@@ -41,8 +41,9 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
public final class ExceptionUtilsTest
{
- private final void checkReturnedClientSafeException(final String message, final Exception rootException,
- final Exception clientSafeException, final boolean clientSafe)
+ private final void checkReturnedClientSafeException(final String message,
+ final Exception rootException, final Exception clientSafeException,
+ final boolean clientSafe)
{
if (clientSafe)
{
@@ -53,7 +54,8 @@ public final class ExceptionUtilsTest
assertTrue(clientSafeException instanceof MasqueradingException);
}
assertEquals(message, clientSafeException.getMessage());
- assertTrue(Arrays.equals(rootException.getStackTrace(), clientSafeException.getStackTrace()));
+ assertTrue(Arrays
+ .equals(rootException.getStackTrace(), clientSafeException.getStackTrace()));
if (rootException.getCause() != null)
{
assertTrue(clientSafeException.getCause() != null);
@@ -78,7 +80,8 @@ public final class ExceptionUtilsTest
{
final String message = "Oooops!";
final UserFailureException exception = new UserFailureException(message);
- final Exception clientSafeException = ExceptionUtils.createMasqueradingExceptionIfNeeded(exception);
+ final Exception clientSafeException =
+ ExceptionUtils.createMasqueradingExceptionIfNeeded(exception);
checkReturnedClientSafeException(message, exception, clientSafeException, true);
}
@@ -87,7 +90,8 @@ public final class ExceptionUtilsTest
{
final String message = "Oooops!";
final Exception exception = new SAXException(message);
- final Exception clientSafeException = ExceptionUtils.createMasqueradingExceptionIfNeeded(exception);
+ final Exception clientSafeException =
+ ExceptionUtils.createMasqueradingExceptionIfNeeded(exception);
checkReturnedClientSafeException(message, exception, clientSafeException, false);
}
@@ -97,18 +101,19 @@ public final class ExceptionUtilsTest
final String userFailureText = "Oooops!";
final UserFailureException userFailureException = new UserFailureException(userFailureText);
final String runtimeText = "Oooops! I did it again...";
- final RuntimeException runtimeException = new RuntimeException(runtimeText, userFailureException);
+ final RuntimeException runtimeException =
+ new RuntimeException(runtimeText, userFailureException);
final String unsupportedOperationText = "Wishiiiii!";
final UnsupportedOperationException unsupportedOperationException =
new UnsupportedOperationException(unsupportedOperationText, runtimeException);
final Exception clientSafeException =
ExceptionUtils.createMasqueradingExceptionIfNeeded(unsupportedOperationException);
- checkReturnedClientSafeException(unsupportedOperationText, unsupportedOperationException, clientSafeException,
- true);
- checkReturnedClientSafeException(runtimeText, runtimeException, (Exception) clientSafeException.getCause(),
- true);
- checkReturnedClientSafeException(userFailureText, userFailureException, (Exception) clientSafeException
- .getCause().getCause(), true);
+ checkReturnedClientSafeException(unsupportedOperationText, unsupportedOperationException,
+ clientSafeException, true);
+ checkReturnedClientSafeException(runtimeText, runtimeException,
+ (Exception) clientSafeException.getCause(), true);
+ checkReturnedClientSafeException(userFailureText, userFailureException,
+ (Exception) clientSafeException.getCause().getCause(), true);
}
@Test
@@ -119,13 +124,16 @@ public final class ExceptionUtilsTest
final String runtimeText = "Oooops! I did it again...";
final RuntimeException runtimeException = new RuntimeException(runtimeText, saxException);
final String digestExceptionText = "Wishiiiii!";
- final DigestException digestException = new DigestException(digestExceptionText, runtimeException);
- final Exception clientSafeException = ExceptionUtils.createMasqueradingExceptionIfNeeded(digestException);
- checkReturnedClientSafeException(digestExceptionText, digestException, clientSafeException, false);
- checkReturnedClientSafeException(runtimeText, runtimeException, (Exception) clientSafeException.getCause(),
- true);
- checkReturnedClientSafeException(saxExceptionText, saxException, (Exception) clientSafeException.getCause()
- .getCause(), false);
+ final DigestException digestException =
+ new DigestException(digestExceptionText, runtimeException);
+ final Exception clientSafeException =
+ ExceptionUtils.createMasqueradingExceptionIfNeeded(digestException);
+ checkReturnedClientSafeException(digestExceptionText, digestException, clientSafeException,
+ false);
+ checkReturnedClientSafeException(runtimeText, runtimeException,
+ (Exception) clientSafeException.getCause(), true);
+ checkReturnedClientSafeException(saxExceptionText, saxException,
+ (Exception) clientSafeException.getCause().getCause(), false);
}
@Test
@@ -133,8 +141,10 @@ public final class ExceptionUtilsTest
{
final String text = "Oooops!";
final IOException ioException = new IOException(text);
- final RuntimeException checkedExceptionTunnel = CheckedExceptionTunnel.wrapIfNecessary(ioException);
- final Exception clientSafeException = ExceptionUtils.createMasqueradingExceptionIfNeeded(checkedExceptionTunnel);
+ final RuntimeException checkedExceptionTunnel =
+ CheckedExceptionTunnel.wrapIfNecessary(ioException);
+ final Exception clientSafeException =
+ ExceptionUtils.createMasqueradingExceptionIfNeeded(checkedExceptionTunnel);
assertNotSame(clientSafeException, checkedExceptionTunnel);
assertNotSame(clientSafeException, ioException);
assertTrue(clientSafeException instanceof MasqueradingException);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesDeleteRecursivelyTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesDeleteRecursivelyTest.java
index d66650a69d2..1571f733af0 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesDeleteRecursivelyTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesDeleteRecursivelyTest.java
@@ -180,7 +180,8 @@ public final class FileUtilitiesDeleteRecursivelyTest extends AbstractFileSystem
{
public boolean accept(File pathname)
{
- return pathname.getName().equals("file1a") || pathname.getName().equals("file3");
+ return pathname.getName().equals("file1a")
+ || pathname.getName().equals("file3");
}
}, null);
checkDirectories(true);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
index ac0742c593c..5cff1cfc264 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
@@ -38,22 +38,26 @@ import static org.testng.AssertJUnit.*;
public class FileUtilitiesLastChangedTest
{
- private static final File workingDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File workingDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
@DataProvider(name = "testLastChanged")
public Object[][] getDirectories()
{
return new Object[][]
{
- { ".fsLastChangedCheckerTestDirectory", ".fsLastChangedCheckerTestDirectory" },
{ ".fsLastChangedCheckerTestDirectory",
- ".fsLastChangedCheckerTestDirectory" + File.separator + "1" },
+ ".fsLastChangedCheckerTestDirectory" },
{ ".fsLastChangedCheckerTestDirectory",
- ".fsLastChangedCheckerTestDirectory" + File.separator + "1" + File.separator + 2 },
+ ".fsLastChangedCheckerTestDirectory" + File.separator + "1" },
{
".fsLastChangedCheckerTestDirectory",
- ".fsLastChangedCheckerTestDirectory" + File.separator + "1" + File.separator + 2
- + File.separator + 3 } };
+ ".fsLastChangedCheckerTestDirectory" + File.separator + "1"
+ + File.separator + 2 },
+ {
+ ".fsLastChangedCheckerTestDirectory",
+ ".fsLastChangedCheckerTestDirectory" + File.separator + "1"
+ + File.separator + 2 + File.separator + 3 } };
}
private void restALittleBit()
@@ -83,20 +87,21 @@ public class FileUtilitiesLastChangedTest
testDir.deleteOnExit();
if (testDir.exists() && testDir.isDirectory() == false)
{
- throw EnvironmentFailureException.fromTemplate("Directory '%s' exists and is not a directory.", testDir
- .getPath());
+ throw EnvironmentFailureException.fromTemplate(
+ "Directory '%s' exists and is not a directory.", testDir.getPath());
}
final File createDir = new File(workingDirectory, dirToCreate);
if (createDir.exists() && FileUtilities.deleteRecursively(createDir) == false)
{
- throw EnvironmentFailureException.fromTemplate("Directory '%s' exists and cannot be deleted.", createDir
- .getPath());
+ throw EnvironmentFailureException.fromTemplate(
+ "Directory '%s' exists and cannot be deleted.", createDir.getPath());
}
createDir.deleteOnExit();
final long now = System.currentTimeMillis();
if (createDir.mkdir() == false)
{
- throw new EnvironmentFailureException("Can't make directory " + createDir.getPath() + ".");
+ throw new EnvironmentFailureException("Can't make directory " + createDir.getPath()
+ + ".");
}
final long lastChanged = FileUtilities.lastChanged(testDir);
final long diff = Math.abs(lastChanged - now);
@@ -127,7 +132,7 @@ public class FileUtilitiesLastChangedTest
assertEquals(1000L, FileUtilities.lastChanged(dirA, false, 999L));
assertEquals(1000L, FileUtilities.lastChanged(dirA, true, 999L));
}
-
+
@Test
public void testLastChangedRelative() throws IOException
{
@@ -142,9 +147,11 @@ public class FileUtilitiesLastChangedTest
final long fakedModTime2 = now - 30000L;
fileB.setLastModified(fakedModTime1);
dirA.setLastModified(fakedModTime2);
- final long diff1 = Math.abs(fakedModTime2 - FileUtilities.lastChangedRelative(dirA, false, 31000L));
+ final long diff1 =
+ Math.abs(fakedModTime2 - FileUtilities.lastChangedRelative(dirA, false, 31000L));
assertTrue("Difference to big: " + diff1 + " ms", diff1 < 1000L);
- final long diff2 = Math.abs(fakedModTime1 - FileUtilities.lastChangedRelative(dirA, false, 11000L));
+ final long diff2 =
+ Math.abs(fakedModTime1 - FileUtilities.lastChangedRelative(dirA, false, 11000L));
assertTrue("Difference to big: " + diff2 + " ms", diff2 < 1000L);
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
index 68e3079d203..68bf4da94de 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
@@ -85,7 +85,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
// --- clean before checking results
// Unfortunately, with JDK 5 there is no portable way to set a file or directory read/write, once
// it has been set read-only, thus this test 'requires_unix' for the time being.
- Runtime.getRuntime().exec(String.format("/bin/chmod u+w %s", readOnlyDirectory.getPath())).waitFor();
+ Runtime.getRuntime().exec(String.format("/bin/chmod u+w %s", readOnlyDirectory.getPath()))
+ .waitFor();
if (readOnlyDirectory.canWrite() == false)
{
// Can't use assert here since we expect an AssertationError
@@ -103,7 +104,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
assertEquals(47110000, sourceFile.lastModified());
File destinationFile = new File(workingDirectory, "destination.txt");
FileUtilities.copyFileTo(sourceFile, destinationFile, true);
- assertEquals(FileUtilities.loadToString(sourceFile), FileUtilities.loadToString(destinationFile));
+ assertEquals(FileUtilities.loadToString(sourceFile), FileUtilities
+ .loadToString(destinationFile));
assertEquals(47110000, destinationFile.lastModified());
}
@@ -138,7 +140,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
Throwable cause = e.getCause();
assertTrue(cause instanceof IOException);
String message = cause.getMessage();
- assertTrue("Exception message not as expected: " + message, cause.getMessage().startsWith(dir.toString()));
+ assertTrue("Exception message not as expected: " + message, cause.getMessage()
+ .startsWith(dir.toString()));
}
}
@@ -157,7 +160,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
Throwable cause = e.getCause();
assertTrue(cause instanceof IOException);
String message = cause.getMessage();
- assertTrue("Exception message not as expected: " + message, cause.getMessage().startsWith(file.toString()));
+ assertTrue("Exception message not as expected: " + message, cause.getMessage()
+ .startsWith(file.toString()));
} finally
{
assert file.delete();
@@ -186,7 +190,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
public void testLoadToStringResource() throws Exception
{
final String thisFile =
- FileUtilities.loadToString(getClass(), "/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.class");
+ FileUtilities.loadToString(getClass(),
+ "/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.class");
assert thisFile != null;
assert thisFile.indexOf("FileUtilitiesTest") >= 0;
}
@@ -255,10 +260,11 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
// Nothing to do here
}
assertEquals(file, FileUtilities.removePrefixFromFileName(file, null));
- assertEquals(file, FileUtilities.removePrefixFromFileName(file, Constants.IS_FINISHED_PREFIX));
+ assertEquals(file, FileUtilities.removePrefixFromFileName(file,
+ Constants.IS_FINISHED_PREFIX));
file = new File("/tmp/dir/" + Constants.IS_FINISHED_PREFIX + "x.txt");
- assertEquals("/tmp/dir/x.txt", FileUtilities.removePrefixFromFileName(file, Constants.IS_FINISHED_PREFIX)
- .getPath());
+ assertEquals("/tmp/dir/x.txt", FileUtilities.removePrefixFromFileName(file,
+ Constants.IS_FINISHED_PREFIX).getPath());
}
@Test
@@ -295,7 +301,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
String defaultFileName = "abc_[1]";
try
{
- FileUtilities.createNextNumberedFile(file, Pattern.compile("dummyPattern"), defaultFileName);
+ FileUtilities.createNextNumberedFile(file, Pattern.compile("dummyPattern"),
+ defaultFileName);
fail("Must contain either '(\\d+)' or ([0-9]+).");
} catch (AssertionError e)
{
@@ -325,7 +332,9 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
FileUtils.touch(file);
newFile = FileUtilities.createNextNumberedFile(file, pattern, "12abc_[1]");
assertEquals(new File(workingDirectory, "12abc_[13]"), newFile);
- newFile = FileUtilities.createNextNumberedFile(file, Pattern.compile("xxx(\\d+)xxx"), "12abc_[1]");
+ newFile =
+ FileUtilities.createNextNumberedFile(file, Pattern.compile("xxx(\\d+)xxx"),
+ "12abc_[1]");
assertEquals(new File(workingDirectory, "12abc_[1]"), newFile);
}
@@ -341,11 +350,13 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
// Nothing to do here
}
File file = new File(workingDirectory, "hello");
- assertEquals(workingDirectory.getAbsolutePath() + File.separator + "hello", file.getAbsolutePath());
+ assertEquals(workingDirectory.getAbsolutePath() + File.separator + "hello", file
+ .getAbsolutePath());
// If the given string is the empty string, then the result is the empty abstract pathname.
final File rootFile = new File("");
- assertEquals(TARGETS_DIRECTORY + File.separator + UNIT_TEST_WORKING_DIRECTORY + File.separator
- + workingDirectory.getName() + File.separator + "hello", FileUtilities.getRelativeFile(rootFile, file));
+ assertEquals(TARGETS_DIRECTORY + File.separator + UNIT_TEST_WORKING_DIRECTORY
+ + File.separator + workingDirectory.getName() + File.separator + "hello",
+ FileUtilities.getRelativeFile(rootFile, file));
String root = "/temp";
String relativeFile = FileUtilities.getRelativeFile(new File(root), file);
assertNull(relativeFile);
@@ -364,7 +375,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
public final void testCopyResourceToTempFile()
{
final String resourceName = "/ch/systemsx/cisd/common/utilities/FileUtilities.class";
- final String absoluteTempFileName = FileUtilities.copyResourceToTempFile(resourceName, "pre", "post");
+ final String absoluteTempFileName =
+ FileUtilities.copyResourceToTempFile(resourceName, "pre", "post");
assertNotNull(absoluteTempFileName);
final File tempFile = new File(absoluteTempFileName);
final String tempFileName = tempFile.getName();
@@ -372,7 +384,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
assertTrue(tempFile.length() > 0);
assertTrue(tempFileName.startsWith("pre"));
assertTrue(tempFileName.endsWith("post"));
- assertTrue(Arrays.equals(resourceToByteArray(resourceName), fileToByteArray(absoluteTempFileName)));
+ assertTrue(Arrays.equals(resourceToByteArray(resourceName),
+ fileToByteArray(absoluteTempFileName)));
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileWatcherTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileWatcherTest.java
index c655fe2ce93..7f1a6603cef 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileWatcherTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileWatcherTest.java
@@ -42,7 +42,8 @@ import ch.systemsx.cisd.common.logging.BufferedAppender;
*/
public class FileWatcherTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
private static final File workingDirectory = new File(unitTestRootDirectory, "FileWatcherTest");
@@ -87,14 +88,16 @@ public class FileWatcherTest
File file = new File(workingDirectory, "doesNotExist");
assert file.exists() == false;
new TestFileWatcher(file).run();
- assertEquals(String.format(FileWatcher.DOES_NOT_EXIST_FORMAT, file), testAppender.getLogContent());
+ assertEquals(String.format(FileWatcher.DOES_NOT_EXIST_FORMAT, file), testAppender
+ .getLogContent());
}
@Test
public final void testNonChangingFile()
{
new TestFileWatcher(tmpFile1).run();
- assertEquals(String.format(FileWatcher.HAS_NOT_CHANGED_FORMAT, tmpFile1), testAppender.getLogContent());
+ assertEquals(String.format(FileWatcher.HAS_NOT_CHANGED_FORMAT, tmpFile1), testAppender
+ .getLogContent());
}
@Test
@@ -104,7 +107,8 @@ public class FileWatcherTest
FileWatcher fileWatcher = new TestFileWatcher(tmpFile1);
FileUtils.touch(tmpFile1);
fileWatcher.run();
- assertEquals(String.format(FileWatcher.HAS_CHANGED_FORMAT, tmpFile1), testAppender.getLogContent());
+ assertEquals(String.format(FileWatcher.HAS_CHANGED_FORMAT, tmpFile1), testAppender
+ .getLogContent());
assertEquals(true, onChangeCalled);
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilterTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilterTest.java
index 453d5e3a2b6..690c687c477 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilterTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilterTest.java
@@ -23,14 +23,14 @@ import org.testng.annotations.Test;
/**
* Test cases for {@link NamePrefixFileFilter}.
- *
+ *
* @author Bernd Rinn
*/
public class NamePrefixFileFilterTest
{
-
+
private static final String PREFIX = "PReFiX";
-
+
@Test
public void testNamePrefixShouldOccurAndFound()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/OSUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/OSUtilitiesTest.java
index e5ebcfa4ed1..07625aa284c 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/OSUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/OSUtilitiesTest.java
@@ -36,7 +36,8 @@ import ch.systemsx.cisd.common.logging.LogInitializer;
public class OSUtilitiesTest
{
- private static final File workingDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File workingDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
@BeforeSuite
public void init()
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/PathPrefixPrependerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/PathPrefixPrependerTest.java
index e2bc77e16b2..3730af1b69b 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/PathPrefixPrependerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/PathPrefixPrependerTest.java
@@ -62,9 +62,8 @@ public final class PathPrefixPrependerTest extends AbstractFileSystemTestCase
{
try
{
- new PathPrefixPrepender((workingDirectory.getAbsolutePath() + "/absolute"), workingDirectory
- .getAbsolutePath()
- + "/relative");
+ new PathPrefixPrepender((workingDirectory.getAbsolutePath() + "/absolute"),
+ workingDirectory.getAbsolutePath() + "/relative");
fail("Given prefixes are not valid.");
} catch (final ConfigurationFailureException ex)
{
@@ -102,8 +101,10 @@ public final class PathPrefixPrependerTest extends AbstractFileSystemTestCase
// Nothing to do here.
}
assertEquals(prefixForRelativePathsOrNull + "/", prepender.addPrefixTo(""));
- assertEquals(prefixForRelativePathsOrNull + "/choubidou", prepender.addPrefixTo("choubidou"));
- assertEquals(prefixForAbsolutePathsOrNull + "/choubidou", prepender.addPrefixTo("/choubidou"));
+ assertEquals(prefixForRelativePathsOrNull + "/choubidou", prepender
+ .addPrefixTo("choubidou"));
+ assertEquals(prefixForAbsolutePathsOrNull + "/choubidou", prepender
+ .addPrefixTo("/choubidou"));
assertEquals(prefixForAbsolutePathsOrNull + "/", prepender.addPrefixTo("/"));
}
}
\ No newline at end of file
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMakerTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMakerTest.java
index 066d59af09b..06d1ff15aca 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMakerTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMakerTest.java
@@ -41,7 +41,8 @@ import ch.systemsx.cisd.common.utilities.RecursiveHardLinkMaker;
*/
public class RecursiveHardLinkMakerTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
private static final File workingDirectory =
new File(unitTestRootDirectory, RecursiveHardLinkMakerTest.class.getSimpleName());
@@ -74,7 +75,8 @@ public class RecursiveHardLinkMakerTest
final File file = new File(directory, name);
file.createNewFile();
assert file.isFile();
- CollectionIO.writeIterable(file, Arrays.asList("test line 1", "test line 2", "test line 3"));
+ CollectionIO
+ .writeIterable(file, Arrays.asList("test line 1", "test line 2", "test line 3"));
file.deleteOnExit();
return file;
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RegexFileFilterTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RegexFileFilterTest.java
index 7be34f36462..1639ec63f7f 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RegexFileFilterTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/RegexFileFilterTest.java
@@ -41,9 +41,11 @@ import ch.systemsx.cisd.common.utilities.RegexFileFilter.PathType;
public class RegexFileFilterTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "RegexFileFilterTestTest");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "RegexFileFilterTestTest");
@BeforeClass
public void init()
@@ -69,7 +71,8 @@ public class RegexFileFilterTest
createFile("baa");
createFile("bba");
createDirectory("bab");
- Set<File> actual = new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter())));
+ Set<File> actual =
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter())));
assert actual.isEmpty();
}
@@ -82,17 +85,20 @@ public class RegexFileFilterTest
final File f4 = createFile("bba");
createDirectory("bab");
Set<File> actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.FILE, "a.+"))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.FILE, "a.+"))));
Set<File> expected = new HashSet<File>(Arrays.asList(f1, f2));
assertEquals(expected, actual);
actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.FILE, ".a."))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.FILE, ".a."))));
expected = new HashSet<File>(Arrays.asList(f1, f3));
assertEquals(expected, actual);
actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.FILE, ".+a"))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.FILE, ".+a"))));
expected = new HashSet<File>(Arrays.asList(f1, f2, f3, f4));
assertEquals(expected, actual);
}
@@ -106,20 +112,20 @@ public class RegexFileFilterTest
final File d4 = createDirectory("bba");
createFile("bab");
Set<File> actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.DIRECTORY,
- "a.+"))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.DIRECTORY, "a.+"))));
Set<File> expected = new HashSet<File>(Arrays.asList(d1, d2));
assertEquals(expected, actual);
actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.DIRECTORY,
- ".a."))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.DIRECTORY, ".a."))));
expected = new HashSet<File>(Arrays.asList(d1, d3));
assertEquals(expected, actual);
actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.DIRECTORY,
- ".+a"))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.DIRECTORY, ".+a"))));
expected = new HashSet<File>(Arrays.asList(d1, d2, d3, d4));
assertEquals(expected, actual);
}
@@ -133,15 +139,20 @@ public class RegexFileFilterTest
final File d4 = createDirectory("bba");
final File f5 = createFile("bab");
Set<File> actual =
- new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.ALL, "a.+"))));
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.ALL, "a.+"))));
Set<File> expected = new HashSet<File>(Arrays.asList(f1, d2));
assertEquals(expected, actual);
- actual = new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.ALL, ".a."))));
+ actual =
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.ALL, ".a."))));
expected = new HashSet<File>(Arrays.asList(f1, f3, f5));
assertEquals(expected, actual);
- actual = new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(PathType.ALL, ".+a"))));
+ actual =
+ new HashSet<File>(Arrays.asList(workingDirectory.listFiles(new RegexFileFilter(
+ PathType.ALL, ".+a"))));
expected = new HashSet<File>(Arrays.asList(f1, d2, f3, d4));
assertEquals(expected, actual);
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/StringUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/StringUtilitiesTest.java
index aa93ae098b2..6d0788df83d 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/StringUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/StringUtilitiesTest.java
@@ -54,10 +54,11 @@ public class StringUtilitiesTest
{
final List<String> list = Arrays.asList("one", "two", "three");
assertEquals("one two three", StringUtilities.concatenateWithSpace(list));
- final String brokenDownInLines = String.format("one%1$stwo%1$sthree", System.getProperty("line.separator"));
+ final String brokenDownInLines =
+ String.format("one%1$stwo%1$sthree", System.getProperty("line.separator"));
assertEquals(brokenDownInLines, StringUtilities.concatenateWithNewLine(list));
}
-
+
@Test
public void testComputeMD5Hash()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/TemplateTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/TemplateTest.java
index 96beb89adfa..0dc21fa4718 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/TemplateTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/TemplateTest.java
@@ -22,8 +22,6 @@ import static org.testng.AssertJUnit.fail;
import org.testng.annotations.Test;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class TemplateTest
@@ -33,13 +31,13 @@ public class TemplateTest
{
assertEquals("", new Template("").createText());
}
-
+
@Test
public void testWithoutPlaceholders()
{
assertEquals("hello", new Template("hello").createText());
}
-
+
@Test
public void testWithOnePlaceholder()
{
@@ -47,7 +45,7 @@ public class TemplateTest
template.bind("name", "world");
assertEquals("hello world!", template.createText());
}
-
+
@Test
public void testWithTwiceTheSamePlaceholder()
{
@@ -55,7 +53,7 @@ public class TemplateTest
template.bind("name", "world");
assertEquals("hello worldworld", template.createText());
}
-
+
@Test
public void testWithTwoPlaceholders()
{
@@ -64,14 +62,14 @@ public class TemplateTest
template.bind("name2", "Albert Einstein");
assertEquals("hello world, do you know Albert Einstein?", template.createText());
}
-
+
@Test
public void testWithEscaping()
{
Template template = new Template("hello $${name}. I have 25$.");
assertEquals("hello ${name}. I have 25$.", template.createText());
}
-
+
@Test
public void testNamelessPlaceholderInTemplate()
{
@@ -84,7 +82,7 @@ public class TemplateTest
assertEquals("Nameless placeholder ${} found.", e.getMessage());
}
}
-
+
@Test
public void testUnfinishedPlaceholderInTemplate()
{
@@ -113,7 +111,7 @@ public class TemplateTest
assertEquals("Incomplete placeholder detected at the end.", e.getMessage());
}
}
-
+
@Test
public void testBindUnknownPlaceholder()
{
@@ -127,7 +125,7 @@ public class TemplateTest
assertEquals("Unknown variable 'blabla'.", e.getMessage());
}
}
-
+
@Test
public void testAttemptToBind()
{
@@ -136,7 +134,7 @@ public class TemplateTest
assertEquals(false, template.attemptToBind("blabla", "blub"));
assertEquals("Hi ${name}!", template.createText(false));
}
-
+
@Test
public void testIncompleteBinding()
{
@@ -149,7 +147,7 @@ public class TemplateTest
{
assertEquals("The following variables are not bound: greeting name ", e.getMessage());
}
-
+
template.bind("greeting", "hello");
assertEquals("hello ${name}!", template.createText(false));
try
@@ -161,7 +159,7 @@ public class TemplateTest
assertEquals("The following variables are not bound: name ", e.getMessage());
}
}
-
+
@Test
public void testCreateFreshCopy()
{
@@ -178,7 +176,7 @@ public class TemplateTest
template1.bind("name", "world");
assertEquals("hello world.world!", template1.createText());
assertEquals("hello ${name}.${name}!", template.createText(false));
-
+
Template template2 = template.createFreshCopy();
template2.bind("name", "universe");
assertEquals("hello universe.universe!", template2.createText());
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/DataMover.java b/datamover/source/java/ch/systemsx/cisd/datamover/DataMover.java
index 3cc78667e50..2b58fdd32e3 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/DataMover.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/DataMover.java
@@ -84,7 +84,8 @@ public class DataMover
return new DataMover(parameters, factory, localBufferDirs).start();
}
- private DataMover(Parameters parameters, IFileSysOperationsFactory factory, LocalBufferDirs bufferDirs)
+ private DataMover(Parameters parameters, IFileSysOperationsFactory factory,
+ LocalBufferDirs bufferDirs)
{
this.parameters = parameters;
this.factory = factory;
@@ -101,7 +102,8 @@ public class DataMover
localProcessor.startup(parameters.getCheckIntervalInternalMillis() / 2L, parameters
.getCheckIntervalInternalMillis());
incomingProcess.startup(0L, parameters.getCheckIntervalMillis());
- return createCompoundTerminable(recoveryProcess, outgoingMovingProcess, localProcessor, incomingProcess);
+ return createCompoundTerminable(recoveryProcess, outgoingMovingProcess, localProcessor,
+ incomingProcess);
}
private ITerminable startupRecoveryProcess(final DataMoverProcess localProcessor,
@@ -120,7 +122,8 @@ public class DataMover
final TriggeringTimerTask recoveryingTimerTask =
new TriggeringTimerTask(new File(RECOVERY_MARKER_FIILENAME), recoverable);
final Timer recoveryTimer = new Timer("Recovery");
- recoveryTimer.schedule(recoveryingTimerTask, 0, parameters.getCheckIntervalInternalMillis());
+ recoveryTimer
+ .schedule(recoveryingTimerTask, 0, parameters.getCheckIntervalInternalMillis());
return TimerHelper.asTerminable(recoveryTimer);
}
@@ -132,11 +135,11 @@ public class DataMover
private DataMoverProcess createLocalProcessor()
{
final LocalProcessor localProcessor =
- LocalProcessor.create(parameters, bufferDirs.getCopyCompleteDir(), bufferDirs.getReadyToMoveDir(),
- bufferDirs.getTempDir(), factory);
+ LocalProcessor.create(parameters, bufferDirs.getCopyCompleteDir(), bufferDirs
+ .getReadyToMoveDir(), bufferDirs.getTempDir(), factory);
final DirectoryScanningTimerTask localProcessingTask =
- new DirectoryScanningTimerTask(bufferDirs.getCopyCompleteDir(), FileUtilities.ACCEPT_ALL_FILTER,
- localProcessor);
+ new DirectoryScanningTimerTask(bufferDirs.getCopyCompleteDir(),
+ FileUtilities.ACCEPT_ALL_FILTER, localProcessor);
return new DataMoverProcess(localProcessingTask, "Local Processor", localProcessor);
}
@@ -144,8 +147,10 @@ public class DataMover
{
final FileStore outgoingStore = parameters.getOutgoingStore(factory);
final File readyToMoveDir = bufferDirs.getReadyToMoveDir();
- final IFileStore readyToMoveStore = FileStoreFactory.createLocal(readyToMoveDir, "ready-to-move", factory);
- final IStoreHandler remoteStoreMover = createRemotePathMover(readyToMoveStore, outgoingStore);
+ final IFileStore readyToMoveStore =
+ FileStoreFactory.createLocal(readyToMoveDir, "ready-to-move", factory);
+ final IStoreHandler remoteStoreMover =
+ createRemotePathMover(readyToMoveStore, outgoingStore);
final DirectoryScanningTimerTask outgoingMovingTask =
new DirectoryScanningTimerTask(readyToMoveDir, FileUtilities.ACCEPT_ALL_FILTER,
@@ -153,7 +158,8 @@ public class DataMover
return new DataMoverProcess(outgoingMovingTask, "Final Destination Mover");
}
- // TODO 2007-10-10, Tomasz Pylak: remove this when DirectoryScanningTimerTask will work with IStoreHandler. This is a
+ // TODO 2007-10-10, Tomasz Pylak: remove this when DirectoryScanningTimerTask will work with IStoreHandler. This is
+ // a
// quick hack.
private static IPathHandler asPathHandler(final IStoreHandler storeHandler)
{
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/IncomingProcessor.java b/datamover/source/java/ch/systemsx/cisd/datamover/IncomingProcessor.java
index 0471e04fc30..482cd6177a3 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/IncomingProcessor.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/IncomingProcessor.java
@@ -55,7 +55,8 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
*/
private final static int NUMBER_OF_ERRORS_IN_LISTING_IGNORED = 2;
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, IncomingProcessor.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, IncomingProcessor.class);
private static final ISimpleLogger simpleOperationLog = new Log4jSimpleLogger(operationLog);
@@ -73,15 +74,16 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
private final QuietPeriodFileFilter quietPeriodFileFilter;
- public static final DataMoverProcess createMovingProcess(Parameters parameters, IFileSysOperationsFactory factory,
- LocalBufferDirs bufferDirs)
+ public static final DataMoverProcess createMovingProcess(Parameters parameters,
+ IFileSysOperationsFactory factory, LocalBufferDirs bufferDirs)
{
final IncomingProcessor processor = new IncomingProcessor(parameters, factory, bufferDirs);
return processor.create();
}
- private IncomingProcessor(Parameters parameters, IFileSysOperationsFactory factory, LocalBufferDirs bufferDirs)
+ private IncomingProcessor(Parameters parameters, IFileSysOperationsFactory factory,
+ LocalBufferDirs bufferDirs)
{
this.parameters = parameters;
this.prefixForIncoming = parameters.getPrefixForIncoming();
@@ -102,8 +104,8 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
final IStoreHandler pathHandler = createIncomingMovingPathHandler();
final DirectoryScanningTimerTask movingTask =
- new DirectoryScanningTimerTask(createIncomingStoreScanner(), bufferDirs.getCopyInProgressDir(),
- pathHandler, NUMBER_OF_ERRORS_IN_LISTING_IGNORED);
+ new DirectoryScanningTimerTask(createIncomingStoreScanner(), bufferDirs
+ .getCopyInProgressDir(), pathHandler, NUMBER_OF_ERRORS_IN_LISTING_IGNORED);
return new DataMoverProcess(movingTask, "Mover of Incoming Data", this);
}
@@ -177,7 +179,8 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
private void moveFromLocalIncoming(IExtendedFileStore sourceStore, StoreItem sourceItem)
{
- sourceStore.tryMoveLocal(sourceItem, bufferDirs.getCopyCompleteDir(), parameters.getPrefixForIncoming());
+ sourceStore.tryMoveLocal(sourceItem, bufferDirs.getCopyCompleteDir(), parameters
+ .getPrefixForIncoming());
}
private void moveFromRemoteIncoming(StoreItem sourceItem)
@@ -196,7 +199,8 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
tryMoveFromInProgressToFinished(copiedFile, markerFile, bufferDirs.getCopyCompleteDir());
}
- private File tryMoveFromInProgressToFinished(File copiedFile, File markerFileOrNull, File copyCompleteDir)
+ private File tryMoveFromInProgressToFinished(File copiedFile, File markerFileOrNull,
+ File copyCompleteDir)
{
final File finalFile = tryMoveLocal(copiedFile, copyCompleteDir, prefixForIncoming);
if (finalFile != null)
@@ -219,15 +223,18 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
}
}
- private void moveFromRemoteToLocal(StoreItem sourceItem, IFileStore sourceStore, File localDestDir)
+ private void moveFromRemoteToLocal(StoreItem sourceItem, IFileStore sourceStore,
+ File localDestDir)
{
- createRemotePathMover(sourceStore, FileStoreFactory.createLocal(localDestDir, "local", factory)).handle(
- sourceItem);
+ createRemotePathMover(sourceStore,
+ FileStoreFactory.createLocal(localDestDir, "local", factory)).handle(sourceItem);
}
- private IStoreHandler createRemotePathMover(IFileStore sourceDirectory, FileStore destinationDirectory)
+ private IStoreHandler createRemotePathMover(IFileStore sourceDirectory,
+ FileStore destinationDirectory)
{
- return RemoteMonitoredMoverFactory.create(sourceDirectory, destinationDirectory, parameters);
+ return RemoteMonitoredMoverFactory
+ .create(sourceDirectory, destinationDirectory, parameters);
}
private File tryMoveLocal(File sourceFile, File destinationDir, String prefixTemplate)
@@ -248,7 +255,8 @@ public class IncomingProcessor implements IRecoverableTimerTaskFactory
}
if (incomingStore.isRemote())
{
- recoverIncomingInProgress(bufferDirs.getCopyInProgressDir(), bufferDirs.getCopyCompleteDir());
+ recoverIncomingInProgress(bufferDirs.getCopyInProgressDir(), bufferDirs
+ .getCopyCompleteDir());
}
if (operationLog.isDebugEnabled())
{
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/LocalProcessor.java b/datamover/source/java/ch/systemsx/cisd/datamover/LocalProcessor.java
index 29bdb4d7cbf..41136d7962f 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/LocalProcessor.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/LocalProcessor.java
@@ -44,13 +44,15 @@ import ch.systemsx.cisd.datamover.filesystem.intf.IRecoverableTimerTaskFactory;
*/
public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactory
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, LocalProcessor.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, LocalProcessor.class);
private static final Logger manualInterventionLog = Logger.getLogger("MANUAL_INTERVENTION");
private static final ISimpleLogger simpleOperationLog = new Log4jSimpleLogger(operationLog);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, LocalProcessor.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, LocalProcessor.class);
private final Parameters parameters;
@@ -84,8 +86,8 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
this.mover = factory.getMover();
}
- public static final LocalProcessor create(Parameters parameters, File inputDir, File outputDir, File bufferDir,
- IFileSysOperationsFactory factory)
+ public static final LocalProcessor create(Parameters parameters, File inputDir, File outputDir,
+ File bufferDir, IFileSysOperationsFactory factory)
{
final LocalProcessor handlerAndRecoverable =
new LocalProcessor(parameters, inputDir, outputDir, bufferDir, factory);
@@ -167,11 +169,13 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
extraTmpCopy = new File(tempDir, path.getName());
if (extraTmpCopy.exists())
{
- operationLog.warn(String.format("Half-finished extra copy directory '%s' exists - removing it.",
+ operationLog.warn(String.format(
+ "Half-finished extra copy directory '%s' exists - removing it.",
extraTmpCopy.getAbsolutePath()));
if (FileUtilities.deleteRecursively(extraTmpCopy) == false)
{
- notificationLog.error(String.format("Removal of half-finished extra copy directory '%s' failed.",
+ notificationLog.error(String.format(
+ "Removal of half-finished extra copy directory '%s' failed.",
extraTmpCopy.getAbsolutePath()));
return;
}
@@ -187,8 +191,8 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
final File movedFile = mover.tryMove(path, outputDir);
if (movedFile == null)
{
- notificationLog.error(String
- .format("Moving '%s' to '%s' for final moving process failed.", path, outputDir));
+ notificationLog.error(String.format(
+ "Moving '%s' to '%s' for final moving process failed.", path, outputDir));
return;
}
@@ -198,7 +202,8 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
File extraCopy = mover.tryMove(extraTmpCopy, extraCopyDirOrNull);
if (extraCopy == null)
{
- notificationLog.error(String.format("Moving temporary extra copy '%s' to destination '%s' failed.",
+ notificationLog.error(String.format(
+ "Moving temporary extra copy '%s' to destination '%s' failed.",
extraTmpCopy, extraCopyDirOrNull));
}
}
@@ -238,8 +243,10 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
cleansingFilter.add(PathType.FILE, cleansingRegex);
}
final ISimpleLogger logger =
- operationLog.isDebugEnabled() ? new Log4jSimpleLogger(operationLog, Level.DEBUG) : null;
- final boolean pathDeleted = FileUtilities.deleteRecursively(resource, cleansingFilter, logger);
+ operationLog.isDebugEnabled() ? new Log4jSimpleLogger(operationLog, Level.DEBUG)
+ : null;
+ final boolean pathDeleted =
+ FileUtilities.deleteRecursively(resource, cleansingFilter, logger);
return pathDeleted;
}
@@ -282,13 +289,15 @@ public class LocalProcessor implements IPathHandler, IRecoverableTimerTaskFactor
operationLog.info(String.format("%s on %s", description, path.getPath()));
}
}
-
+
private static void logManualIntervention(File path, boolean needsManualIntervention)
{
if (manualInterventionLog.isInfoEnabled())
{
- manualInterventionLog.info(String.format("%s %s [created: %3$tY-%3$tm-%3$td %3$tH:%3$tM:%3$tS]",
- needsManualIntervention ? "ATTENTION" : "DEFAULT", path.getAbsolutePath(), path.lastModified()));
+ manualInterventionLog.info(String.format(
+ "%s %s [created: %3$tY-%3$tm-%3$td %3$tH:%3$tM:%3$tS]",
+ needsManualIntervention ? "ATTENTION" : "DEFAULT", path.getAbsolutePath(), path
+ .lastModified()));
}
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/Main.java b/datamover/source/java/ch/systemsx/cisd/datamover/Main.java
index 29904733617..d3605bddbb3 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/Main.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/Main.java
@@ -42,17 +42,21 @@ import ch.systemsx.cisd.datamover.utils.LocalBufferDirs;
public class Main
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, Main.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, Main.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, Main.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, Main.class);
- private static final UncaughtExceptionHandler loggingExceptionHandler = new UncaughtExceptionHandler()
- {
- public void uncaughtException(Thread t, Throwable e)
- {
- notificationLog.error("An exception has occurred [thread: '" + t.getName() + "'].", e);
- }
- };
+ private static final UncaughtExceptionHandler loggingExceptionHandler =
+ new UncaughtExceptionHandler()
+ {
+ public void uncaughtException(Thread t, Throwable e)
+ {
+ notificationLog.error("An exception has occurred [thread: '" + t.getName()
+ + "'].", e);
+ }
+ };
private static final Runnable loggingShutdownHook = new Runnable()
{
@@ -97,28 +101,30 @@ public class Main
FileSysOperationsFactory factory = new FileSysOperationsFactory(parameters);
stores.add(parameters.getIncomingStore(factory));
FileStore buferStore =
- FileStoreFactory.createLocal(parameters.getBufferDirectoryPath(), Parameters.BUFFER_KIND_DESC,
- factory);
+ FileStoreFactory.createLocal(parameters.getBufferDirectoryPath(),
+ Parameters.BUFFER_KIND_DESC, factory);
stores.add(buferStore);
stores.add(parameters.getOutgoingStore(factory));
if (parameters.tryGetManualInterventionDir() != null)
{
FileStore dummyStore =
- FileStoreFactory.createLocal(parameters.tryGetManualInterventionDir(), "manual intervention",
- factory);
+ FileStoreFactory.createLocal(parameters.tryGetManualInterventionDir(),
+ "manual intervention", factory);
stores.add(dummyStore);
}
if (parameters.tryGetExtraCopyDir() != null)
{
FileStore dummyStore =
- FileStoreFactory.createLocal(parameters.tryGetExtraCopyDir(), "extra-copy", factory);
+ FileStoreFactory.createLocal(parameters.tryGetExtraCopyDir(), "extra-copy",
+ factory);
stores.add(dummyStore);
}
IPathCopier copyProcess = factory.getCopier(false);
SelfTest.check(copyProcess, stores.toArray(new FileStore[] {}));
} catch (HighLevelException e)
{
- System.err.printf(msgStart + " [%s: %s]\n", e.getClass().getSimpleName(), e.getMessage());
+ System.err.printf(msgStart + " [%s: %s]\n", e.getClass().getSimpleName(), e
+ .getMessage());
System.exit(1);
} catch (RuntimeException e)
{
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/Parameters.java b/datamover/source/java/ch/systemsx/cisd/datamover/Parameters.java
index 7333ba8bc4d..d39d702ab3c 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/Parameters.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/Parameters.java
@@ -53,9 +53,11 @@ public class Parameters implements ITimingParameters, IFileSysParameters
{
private static final String SERVICE_PROPERTIES_FILE = "etc/service.properties";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, Parameters.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, Parameters.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, Parameters.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, Parameters.class);
/**
* The name of the <code>rsync</code> executable to use for copy operations.
@@ -266,7 +268,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
@Option(longName = "version", skipForExample = true, usage = "Prints out the version information.")
void printVersion(boolean exit)
{
- System.err.println("Datamover version " + BuildAndEnvironmentInfo.INSTANCE.getFullVersion());
+ System.err
+ .println("Datamover version " + BuildAndEnvironmentInfo.INSTANCE.getFullVersion());
if (exit)
{
System.exit(0);
@@ -277,7 +280,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
+ "sent out).")
void sendTestNotification(boolean exit)
{
- notificationLog.info("This is a test notification given due to specifying the --test-notify option.");
+ notificationLog
+ .info("This is a test notification given due to specifying the --test-notify option.");
if (exit)
{
System.exit(0);
@@ -347,8 +351,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
}
}
- private static FileStore createStore(File directory, String kind, String hostOrNull, boolean isRemote,
- IFileSysOperationsFactory factory)
+ private static FileStore createStore(File directory, String kind, String hostOrNull,
+ boolean isRemote, IFileSysOperationsFactory factory)
{
if (hostOrNull != null)
{
@@ -413,7 +417,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
Integer.parseInt(serviceProperties.getProperty("inactivity-period", Integer
.toString(DEFAULT_INACTIVITY_PERIOD))) * 1000;
quietPeriodMillis =
- Integer.parseInt(serviceProperties.getProperty("quiet-period", Integer.toString(DEFAULT_QUIET_PERIOD))) * 1000;
+ Integer.parseInt(serviceProperties.getProperty("quiet-period", Integer
+ .toString(DEFAULT_QUIET_PERIOD))) * 1000;
intervalToWaitAfterFailureMillis =
Integer.parseInt(serviceProperties.getProperty("failure-interval", Integer
.toString(DEFAULT_INTERVAL_TO_WAIT_AFTER_FAILURES))) * 1000;
@@ -421,8 +426,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
Integer.parseInt(serviceProperties.getProperty("max-retries", Integer
.toString(DEFAULT_MAXIMAL_NUMBER_OF_RETRIES)));
treatIncomingAsRemote =
- Boolean.parseBoolean(serviceProperties.getProperty("treat-incoming-as-remote", Boolean
- .toString(DEFAULT_TREAT_INCOMING_AS_REMOTE)).trim());
+ Boolean.parseBoolean(serviceProperties.getProperty("treat-incoming-as-remote",
+ Boolean.toString(DEFAULT_TREAT_INCOMING_AS_REMOTE)).trim());
prefixForIncoming = serviceProperties.getProperty("prefix-for-incoming", "").trim();
if (serviceProperties.getProperty("incoming-dir") != null)
{
@@ -435,7 +440,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
}
if (serviceProperties.getProperty("manual-intervention-dir") != null)
{
- manualInterventionDirectoryOrNull = new File(serviceProperties.getProperty("manual-intervention-dir").trim());
+ manualInterventionDirectoryOrNull =
+ new File(serviceProperties.getProperty("manual-intervention-dir").trim());
}
if (serviceProperties.getProperty("outgoing-dir") != null)
{
@@ -452,7 +458,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
}
if (serviceProperties.getProperty("manual-intervention-regex") != null)
{
- manualInterventionRegex = Pattern.compile(serviceProperties.getProperty("manual-intervention-regex"));
+ manualInterventionRegex =
+ Pattern.compile(serviceProperties.getProperty("manual-intervention-regex"));
}
}
@@ -477,7 +484,9 @@ public class Parameters implements ITimingParameters, IFileSysParameters
}
} catch (Exception ex)
{
- final String msg = "Could not load the service properties from resource '" + SERVICE_PROPERTIES_FILE + "'.";
+ final String msg =
+ "Could not load the service properties from resource '"
+ + SERVICE_PROPERTIES_FILE + "'.";
operationLog.warn(msg, ex);
throw new ConfigurationFailureException(msg, ex);
}
@@ -573,7 +582,8 @@ public class Parameters implements ITimingParameters, IFileSysParameters
*/
public FileStore getIncomingStore(IFileSysOperationsFactory factory)
{
- return createStore(incomingDirectory, INCOMING_KIND_DESC, incomingHost, treatIncomingAsRemote, factory);
+ return createStore(incomingDirectory, INCOMING_KIND_DESC, incomingHost,
+ treatIncomingAsRemote, factory);
}
/**
@@ -647,45 +657,56 @@ public class Parameters implements ITimingParameters, IFileSysParameters
{
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("Incoming directory: '%s'.", incomingDirectory.getAbsolutePath()));
+ operationLog.info(String.format("Incoming directory: '%s'.", incomingDirectory
+ .getAbsolutePath()));
if (null != incomingHost)
{
operationLog.info(String.format("Incoming host: '%s'.", incomingHost));
}
- operationLog.info(String.format("Is incoming directory remote: %b.", treatIncomingAsRemote));
- operationLog.info(String.format("Buffer directory: '%s'.", bufferDirectory.getAbsolutePath()));
- operationLog.info(String.format("Outgoing directory: '%s'.", outgoingDirectory.getAbsolutePath()));
+ operationLog.info(String.format("Is incoming directory remote: %b.",
+ treatIncomingAsRemote));
+ operationLog.info(String.format("Buffer directory: '%s'.", bufferDirectory
+ .getAbsolutePath()));
+ operationLog.info(String.format("Outgoing directory: '%s'.", outgoingDirectory
+ .getAbsolutePath()));
if (null != outgoingHost)
{
operationLog.info(String.format("Outgoing host: '%s'.", outgoingHost));
}
if (null != tryGetManualInterventionDir())
{
- operationLog.info(String.format("Manual interventions directory: '%s'.", tryGetManualInterventionDir()
- .getAbsolutePath()));
+ operationLog.info(String.format("Manual interventions directory: '%s'.",
+ tryGetManualInterventionDir().getAbsolutePath()));
}
if (null != extraCopyDirectory)
{
- operationLog.info(String.format("Extra copy directory: '%s'.", extraCopyDirectory.getAbsolutePath()));
+ operationLog.info(String.format("Extra copy directory: '%s'.", extraCopyDirectory
+ .getAbsolutePath()));
}
- operationLog.info(String.format("Check intervall (external): %d s.", getCheckIntervalMillis() / 1000));
+ operationLog.info(String.format("Check intervall (external): %d s.",
+ getCheckIntervalMillis() / 1000));
operationLog.info(String.format("Check intervall (internal): %d s.",
getCheckIntervalInternalMillis() / 1000));
operationLog.info(String.format("Quiet period: %d s.", getQuietPeriodMillis() / 1000));
- operationLog.info(String.format("Inactivity (stall) period: %d s.", getInactivityPeriodMillis() / 1000));
+ operationLog.info(String.format("Inactivity (stall) period: %d s.",
+ getInactivityPeriodMillis() / 1000));
operationLog.info(String.format("Intervall to wait after failure: %d s.",
getIntervalToWaitAfterFailure() / 1000));
- operationLog.info(String.format("Maximum number of retries: %d.", getMaximalNumberOfRetries()));
+ operationLog.info(String.format("Maximum number of retries: %d.",
+ getMaximalNumberOfRetries()));
if (tryGetCleansingRegex() != null)
{
- operationLog.info(String.format("Regular expression used for cleansing before moving: '%s'",
+ operationLog.info(String.format(
+ "Regular expression used for cleansing before moving: '%s'",
tryGetCleansingRegex().pattern()));
}
if (tryGetManualInterventionRegex() != null)
{
- operationLog.info(String.format(
- "Regular expression used for deciding whether a path needs manual intervention: '%s'",
- tryGetManualInterventionRegex().pattern()));
+ operationLog
+ .info(String
+ .format(
+ "Regular expression used for deciding whether a path needs manual intervention: '%s'",
+ tryGetManualInterventionRegex().pattern()));
}
}
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/SelfTest.java b/datamover/source/java/ch/systemsx/cisd/datamover/SelfTest.java
index c6a8739a89c..8b42f3df7de 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/SelfTest.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/SelfTest.java
@@ -36,7 +36,8 @@ public class SelfTest
{
private static final long TIMEOUT_MILLIS = 3000L;
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, SelfTest.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, SelfTest.class);
static
{
@@ -58,7 +59,8 @@ public class SelfTest
}
}
- private static void checkPathRecordsContainEachOther(IFileStore[] store) throws ConfigurationFailureException
+ private static void checkPathRecordsContainEachOther(IFileStore[] store)
+ throws ConfigurationFailureException
{
for (int i = 1; i < store.length; ++i)
{
@@ -66,8 +68,8 @@ public class SelfTest
{
if (store[i].isParentDirectory(store[j]) || store[j].isParentDirectory(store[i]))
{
- throw ConfigurationFailureException.fromTemplate("Directory '%s' and '%s' contain each other",
- store[i], store[j]);
+ throw ConfigurationFailureException.fromTemplate(
+ "Directory '%s' and '%s' contain each other", store[i], store[j]);
}
}
}
@@ -91,13 +93,13 @@ public class SelfTest
}
} catch (HighLevelException e)
{
- operationLog.error(String.format("Self test failed: [%s: %s]\n", e.getClass().getSimpleName(), e
- .getMessage()));
+ operationLog.error(String.format("Self test failed: [%s: %s]\n", e.getClass()
+ .getSimpleName(), e.getMessage()));
throw e;
} catch (RuntimeException e)
{
- operationLog.error(String.format("Self test failed: [%s: %s]\n", e.getClass().getSimpleName(), e
- .getMessage()), e);
+ operationLog.error(String.format("Self test failed: [%s: %s]\n", e.getClass()
+ .getSimpleName(), e.getMessage()), e);
throw e;
}
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileStoreFactory.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileStoreFactory.java
index 1e608bb5465..6ec4c3a9caf 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileStoreFactory.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileStoreFactory.java
@@ -30,13 +30,15 @@ import ch.systemsx.cisd.datamover.filesystem.store.FileStoreRemoteMounted;
public class FileStoreFactory
{
/** use when file store is on a local host */
- public static final FileStore createLocal(File path, String kind, IFileSysOperationsFactory factory)
+ public static final FileStore createLocal(File path, String kind,
+ IFileSysOperationsFactory factory)
{
return new FileStoreLocal(path, kind, factory);
}
/** use when file store is on a remote share mounted on local host */
- public static final FileStore createRemoteShare(File path, String kind, IFileSysOperationsFactory factory)
+ public static final FileStore createRemoteShare(File path, String kind,
+ IFileSysOperationsFactory factory)
{
return new FileStoreRemoteMounted(path, kind, factory);
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileSysOperationsFactory.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileSysOperationsFactory.java
index a856e41ee80..c3b2bf8ebdf 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileSysOperationsFactory.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/FileSysOperationsFactory.java
@@ -92,7 +92,8 @@ public class FileSysOperationsFactory implements IFileSysOperationsFactory
// IPathImmutableCopier
//
- public final File tryCopy(final File file, final File destinationDirectory, final String nameOrNull)
+ public final File tryCopy(final File file, final File destinationDirectory,
+ final String nameOrNull)
{
final Status status = normalCopier.copy(file, destinationDirectory);
if (StatusFlag.OK.equals(status.getFlag()))
@@ -100,8 +101,8 @@ public class FileSysOperationsFactory implements IFileSysOperationsFactory
return new File(destinationDirectory, file.getName());
} else
{
- notificationLog.error(String.format("Copy of '%s' to '%s' failed: %s.", file.getPath(),
- destinationDirectory.getPath(), status));
+ notificationLog.error(String.format("Copy of '%s' to '%s' failed: %s.",
+ file.getPath(), destinationDirectory.getPath(), status));
return null;
}
}
@@ -114,8 +115,8 @@ public class FileSysOperationsFactory implements IFileSysOperationsFactory
final File sshExecutable = findSshExecutable(parameters.getSshExecutable());
if (rsyncExecutable != null)
{
- return new RsyncCopier(rsyncExecutable, sshExecutable, requiresDeletionBeforeCreation, parameters
- .isRsyncOverwrite());
+ return new RsyncCopier(rsyncExecutable, sshExecutable, requiresDeletionBeforeCreation,
+ parameters.isRsyncOverwrite());
} else
{
throw new ConfigurationFailureException("Unable to find a copy engine.");
@@ -137,8 +138,8 @@ public class FileSysOperationsFactory implements IFileSysOperationsFactory
}
if (rsyncExecutable != null && OSUtilities.executableExists(rsyncExecutable) == false)
{
- throw ConfigurationFailureException.fromTemplate("Cannot find rsync executable '%s'.", rsyncExecutable
- .getAbsoluteFile());
+ throw ConfigurationFailureException.fromTemplate("Cannot find rsync executable '%s'.",
+ rsyncExecutable.getAbsoluteFile());
}
return rsyncExecutable;
}
@@ -162,8 +163,8 @@ public class FileSysOperationsFactory implements IFileSysOperationsFactory
}
if (sshExecutable != null && OSUtilities.executableExists(sshExecutable) == false)
{
- throw ConfigurationFailureException.fromTemplate("Cannot find ssh executable '%s'.", sshExecutable
- .getAbsoluteFile());
+ throw ConfigurationFailureException.fromTemplate("Cannot find ssh executable '%s'.",
+ sshExecutable.getAbsoluteFile());
}
return sshExecutable;
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RemoteMonitoredMoverFactory.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RemoteMonitoredMoverFactory.java
index 62a77853dc1..3da68cb365f 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RemoteMonitoredMoverFactory.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RemoteMonitoredMoverFactory.java
@@ -36,11 +36,13 @@ public class RemoteMonitoredMoverFactory
* @param destinationDirectory The directory to move paths to.
* @param parameters The timing parameters used for monitoring and reporting stall situations.
*/
- public static final IStoreHandler create(IFileStore sourceDirectory, FileStore destinationDirectory,
- ITimingParameters parameters)
+ public static final IStoreHandler create(IFileStore sourceDirectory,
+ FileStore destinationDirectory, ITimingParameters parameters)
{
final IStoreCopier copier = sourceDirectory.getCopier(destinationDirectory);
- final CopyActivityMonitor monitor = new CopyActivityMonitor(destinationDirectory, copier, parameters);
- return new RemotePathMover(sourceDirectory, destinationDirectory, copier, monitor, parameters);
+ final CopyActivityMonitor monitor =
+ new CopyActivityMonitor(destinationDirectory, copier, parameters);
+ return new RemotePathMover(sourceDirectory, destinationDirectory, copier, monitor,
+ parameters);
}
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathMover.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathMover.java
index 6d192cf2421..cd0bed08beb 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathMover.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathMover.java
@@ -36,9 +36,11 @@ import ch.systemsx.cisd.datamover.filesystem.intf.IPathMover;
*/
class RetryingPathMover implements IPathMover
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RetryingPathMover.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, RetryingPathMover.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, RetryingPathMover.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, RetryingPathMover.class);
private final int maxRetriesOnFailure;
@@ -63,18 +65,22 @@ class RetryingPathMover implements IPathMover
assert prefixTemplate != null;
assert sourcePath != null;
- final String destinationPath = createDestinationPath(sourcePath, null, destinationDirectory, prefixTemplate);
+ final String destinationPath =
+ createDestinationPath(sourcePath, null, destinationDirectory, prefixTemplate);
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format("Moving path '%s' to '%s'", sourcePath.getPath(), destinationPath));
+ operationLog.info(String.format("Moving path '%s' to '%s'", sourcePath.getPath(),
+ destinationPath));
}
File destFile = new File(destinationPath);
final FileRenamingProcess process =
- new FileRenamingProcess(maxRetriesOnFailure, millisToSleepOnFailure, sourcePath, destFile);
+ new FileRenamingProcess(maxRetriesOnFailure, millisToSleepOnFailure, sourcePath,
+ destFile);
new ProcessRunner(process);
if (process.isRenamed() == false)
{
- notificationLog.error(String.format("Moving path '%s' to directory '%s' failed, giving up.", sourcePath,
+ notificationLog.error(String.format(
+ "Moving path '%s' to directory '%s' failed, giving up.", sourcePath,
destinationDirectory));
return null;
} else
@@ -102,14 +108,14 @@ class RetryingPathMover implements IPathMover
} else
{
- return destinationDirectory.getAbsolutePath() + File.separator + createPrefix(prefixTemplate)
- + sourcePath.getName();
+ return destinationDirectory.getAbsolutePath() + File.separator
+ + createPrefix(prefixTemplate) + sourcePath.getName();
}
}
private static String createPrefix(String prefixTemplate)
{
- return StringUtils.replace(prefixTemplate, "%t", DateFormatUtils.format(System.currentTimeMillis(),
- "yyyyMMddHHmmss"));
+ return StringUtils.replace(prefixTemplate, "%t", DateFormatUtils.format(System
+ .currentTimeMillis(), "yyyyMMddHHmmss"));
}
}
\ No newline at end of file
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathRemover.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathRemover.java
index 8ee9658fc90..e3ae9b46dea 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathRemover.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/RetryingPathRemover.java
@@ -36,9 +36,11 @@ import ch.systemsx.cisd.datamover.filesystem.intf.IPathRemover;
*/
final class RetryingPathRemover implements IPathRemover
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RetryingPathMover.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, RetryingPathMover.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, RetryingPathMover.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, RetryingPathMover.class);
private final int maxRetriesOnFailure;
@@ -50,7 +52,8 @@ final class RetryingPathRemover implements IPathRemover
this.millisToSleepOnFailure = millisToSleepOnFailure;
}
- private final static Status STATUS_FAILED_DELETION = new Status(StatusFlag.FATAL_ERROR, "Failed to remove path.");
+ private final static Status STATUS_FAILED_DELETION =
+ new Status(StatusFlag.FATAL_ERROR, "Failed to remove path.");
public Status remove(File path)
{
@@ -72,11 +75,13 @@ final class RetryingPathRemover implements IPathRemover
{
if (path.exists() == false)
{
- operationLog.warn(String.format("Path '%s' doesn't exist, so it can't be removed.", path));
+ operationLog.warn(String.format(
+ "Path '%s' doesn't exist, so it can't be removed.", path));
break;
}
++failures;
- operationLog.warn(String.format("Removing path '%s' failed (attempt %d).", path, failures));
+ operationLog.warn(String.format("Removing path '%s' failed (attempt %d).", path,
+ failures));
if (failures >= maxRetriesOnFailure)
{
break;
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/FileStore.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/FileStore.java
index 37a38bee507..caeda2847de 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/FileStore.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/FileStore.java
@@ -44,7 +44,8 @@ public abstract class FileStore implements IFileStore
protected final IFileSysOperationsFactory factory;
- protected FileStore(File path, String hostOrNull, boolean remote, String kind, IFileSysOperationsFactory factory)
+ protected FileStore(File path, String hostOrNull, boolean remote, String kind,
+ IFileSysOperationsFactory factory)
{
assert path != null;
assert kind != null;
@@ -144,8 +145,8 @@ public abstract class FileStore implements IFileStore
return file.getCanonicalPath() + File.separator;
} catch (IOException e)
{
- throw EnvironmentFailureException.fromTemplate(e, "Cannot determine canonical form of path '%s'", file
- .getPath());
+ throw EnvironmentFailureException.fromTemplate(e,
+ "Cannot determine canonical form of path '%s'", file.getPath());
}
}
@@ -156,8 +157,9 @@ public abstract class FileStore implements IFileStore
{
FileStore fileStore = (FileStore) obj;
boolean sameHost =
- (hostOrNull == null ? fileStore.hostOrNull == null : fileStore.hostOrNull != null
- && hostOrNull.equals(fileStore.hostOrNull));
+ (hostOrNull == null ? fileStore.hostOrNull == null
+ : fileStore.hostOrNull != null
+ && hostOrNull.equals(fileStore.hostOrNull));
return sameHost && kind.equals(fileStore.kind) && path.equals(fileStore.path);
} else
{
@@ -232,6 +234,7 @@ public abstract class FileStore implements IFileStore
public abstract boolean createNewFile(StoreItem item);
- public abstract File tryMoveLocal(StoreItem sourceItem, File destinationDir, String newFilePrefix);
+ public abstract File tryMoveLocal(StoreItem sourceItem, File destinationDir,
+ String newFilePrefix);
}
}
\ No newline at end of file
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IExtendedFileStore.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IExtendedFileStore.java
index 2d8d199156f..09f4b34daf5 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IExtendedFileStore.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IExtendedFileStore.java
@@ -22,7 +22,7 @@ import ch.systemsx.cisd.common.utilities.StoreItem;
/**
* An {@link IFileStore} with additional capabilites.
- *
+ *
* @author Bernd Rinn
*/
public interface IExtendedFileStore extends IFileStore
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileStore.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileStore.java
index 3a22ec57191..89495158338 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileStore.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileStore.java
@@ -22,7 +22,7 @@ import ch.systemsx.cisd.common.utilities.StoreItem;
/**
* An abstraction for a file store.
- *
+ *
* @author Bernd Rinn
*/
public interface IFileStore
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileSysOperationsFactory.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileSysOperationsFactory.java
index 71d7c436a69..e7fe4bb220a 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileSysOperationsFactory.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IFileSysOperationsFactory.java
@@ -17,7 +17,6 @@ package ch.systemsx.cisd.datamover.filesystem.intf;
import ch.systemsx.cisd.common.utilities.IPathImmutableCopier;
-
/**
* A role that provides access to the roles which perform file system operations.
*
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IPathMover.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IPathMover.java
index 3f01f5e5944..79717330f27 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IPathMover.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IPathMover.java
@@ -25,7 +25,7 @@ import java.io.File;
*/
public interface IPathMover
{
-
+
/**
* Moves source path (file or directory) to destination directory, putting <var>prefixTemplate</var> in front of
* its name, where any occurrence of '%t' in the template is replaced with the current time stamp.
@@ -36,6 +36,5 @@ public interface IPathMover
* Moves source path (file or directory) to destination directory.
*/
public File tryMove(File sourcePath, File destinationDir);
-
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IRecoverableTimerTaskFactory.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IRecoverableTimerTaskFactory.java
index bbdbaa1441f..69dac2d2ef1 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IRecoverableTimerTaskFactory.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/intf/IRecoverableTimerTaskFactory.java
@@ -20,7 +20,7 @@ import java.util.TimerTask;
/**
* A factory for creating {@link TimerTask}s that, when run, perform a recovery operation on the data mover.
- *
+ *
* @author Bernd Rinn
*/
public interface IRecoverableTimerTaskFactory
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitor.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitor.java
index e9c1b9db1e8..6a34d041eb6 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitor.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitor.java
@@ -43,9 +43,11 @@ import ch.systemsx.cisd.datamover.intf.ITimingParameters;
public class CopyActivityMonitor
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, CopyActivityMonitor.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, CopyActivityMonitor.class);
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, CopyActivityMonitor.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, CopyActivityMonitor.class);
private final IFileStore destinationStore;
@@ -77,7 +79,8 @@ public class CopyActivityMonitor
* process gets stuck.
* @param timingParameters The {@link ITimingParameters} to get the check interval and the inactivity period from.
*/
- public CopyActivityMonitor(IFileStore destinationStore, ITerminable copyProcess, ITimingParameters timingParameters)
+ public CopyActivityMonitor(IFileStore destinationStore, ITerminable copyProcess,
+ ITimingParameters timingParameters)
{
assert destinationStore != null;
assert copyProcess != null;
@@ -129,7 +132,8 @@ public class CopyActivityMonitor
private final class ActivityMonitoringTimerTask extends TimerTask
{
- private static final String TERMINATION_LOG_TEMPLATE = "Terminating %s due to a lack of activity.";
+ private static final String TERMINATION_LOG_TEMPLATE =
+ "Terminating %s due to a lack of activity.";
private static final String INACTIVITY_REPORT_TEMPLATE =
"No progress on copying '%s' to '%s' for %f seconds - network connection might be stalled.";
@@ -164,12 +168,14 @@ public class CopyActivityMonitor
{
if (operationLog.isTraceEnabled())
{
- operationLog.trace(String.format("Asking for last change time of '%s' inside '%s'.",
- itemToBeCopied, destinationStore));
+ operationLog.trace(String.format(
+ "Asking for last change time of '%s' inside '%s'.", itemToBeCopied,
+ destinationStore));
}
if (destinationStore.exists(itemToBeCopied) == false)
{
- operationLog.warn(String.format("File or directory '%s' inside '%s' does not (yet?) exist.",
+ operationLog.warn(String.format(
+ "File or directory '%s' inside '%s' does not (yet?) exist.",
itemToBeCopied, destinationStore));
return;
}
@@ -177,27 +183,33 @@ public class CopyActivityMonitor
lastChanged(destinationStore, itemToBeCopied, monitoredItemLastChanged);
if (operationLog.isTraceEnabled())
{
- operationLog.trace(String.format(
- "Checker reported last changed time of '%s' inside '%s' to be %3$tF %3$tT.",
- itemToBeCopied, destinationStore, lastChangedAsFoundByPathChecker));
+ operationLog
+ .trace(String
+ .format(
+ "Checker reported last changed time of '%s' inside '%s' to be %3$tF %3$tT.",
+ itemToBeCopied, destinationStore,
+ lastChangedAsFoundByPathChecker));
}
// This catches the case where since the last check copying a files has been finished (and consequently
// the "last changed" time has been set to that of the source file), but copying of the next file has
// not yet been started.
- final long lastChanged = Math.max(lastChangedAsFoundByPathChecker, monitoredItemLastChanged);
+ final long lastChanged =
+ Math.max(lastChangedAsFoundByPathChecker, monitoredItemLastChanged);
final long now = System.currentTimeMillis();
if (lastChanged > now) // That can happen if the system clock of the data producer is screwed up.
{
- machineLog.error(String.format("Found \"last changed time\" in the future (%1$tF %1$tT), "
- + "check system clock of data producer.", lastChanged));
+ machineLog.error(String.format(
+ "Found \"last changed time\" in the future (%1$tF %1$tT), "
+ + "check system clock of data producer.", lastChanged));
}
monitoredItemLastChanged = lastChanged;
final long noProgressSinceMillis = now - lastChanged;
if (noProgressSinceMillis > inactivityPeriodMillis)
{
- machineLog.error(String.format(INACTIVITY_REPORT_TEMPLATE, itemToBeCopied, destinationStore,
- noProgressSinceMillis / 1000.0f));
- operationLog.warn(String.format(TERMINATION_LOG_TEMPLATE, terminable.getClass().getName()));
+ machineLog.error(String.format(INACTIVITY_REPORT_TEMPLATE, itemToBeCopied,
+ destinationStore, noProgressSinceMillis / 1000.0f));
+ operationLog.warn(String.format(TERMINATION_LOG_TEMPLATE, terminable.getClass()
+ .getName()));
terminable.terminate();
stop();
}
@@ -227,11 +239,12 @@ public class CopyActivityMonitor
minusSafetyMargin(inactivityPeriodMillis)));
final long timeoutMillis = Math.min(checkIntervallMillis * 3, inactivityPeriodMillis);
final Long lastChanged =
- ConcurrencyUtilities.tryGetResult(lastChangedFuture, timeoutMillis, simpleMachineLog,
- "Check for recent paths");
+ ConcurrencyUtilities.tryGetResult(lastChangedFuture, timeoutMillis,
+ simpleMachineLog, "Check for recent paths");
if (lastChanged == null)
{
- operationLog.error(String.format("Could not determine \"last changed time\" of %s: time out.", item));
+ operationLog.error(String.format(
+ "Could not determine \"last changed time\" of %s: time out.", item));
return lastLastChanged;
}
return lastChanged;
@@ -251,24 +264,30 @@ public class CopyActivityMonitor
{
if (machineLog.isTraceEnabled())
{
- machineLog.trace("Starting quick check for recent paths on '" + item + "'.");
+ machineLog.trace("Starting quick check for recent paths on '" + item
+ + "'.");
}
try
{
- final long lastChanged = store.lastChangedRelative(item, stopWhenYoungerThan);
+ final long lastChanged =
+ store.lastChangedRelative(item, stopWhenYoungerThan);
if (machineLog.isTraceEnabled())
{
- machineLog.trace(String.format(
- "Finishing quick check for recent paths on '%s', found to be %2$tF %2$tT.",
- item, lastChanged));
+ machineLog
+ .trace(String
+ .format(
+ "Finishing quick check for recent paths on '%s', found to be %2$tF %2$tT.",
+ item, lastChanged));
}
return lastChanged;
} catch (RuntimeException ex)
{
if (machineLog.isTraceEnabled())
{
- final Throwable th = (ex instanceof CheckedExceptionTunnel) ? ex.getCause() : ex;
- machineLog.trace("Failed on quick check for recent paths on '" + item + "'.", th);
+ final Throwable th =
+ (ex instanceof CheckedExceptionTunnel) ? ex.getCause() : ex;
+ machineLog.trace("Failed on quick check for recent paths on '"
+ + item + "'.", th);
}
throw ex;
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/RemotePathMover.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/RemotePathMover.java
index cdf3814952e..aa7e6defedc 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/RemotePathMover.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/RemotePathMover.java
@@ -45,29 +45,37 @@ public final class RemotePathMover implements IStoreHandler
private static final String START_COPYING_PATH_TEMPLATE = "Start copying path '%s' to '%s'.";
- private static final String START_COPYING_PATH_RETRY_TEMPLATE = "Start copying path '%s' to '%s' [retry: %d].";
+ private static final String START_COPYING_PATH_RETRY_TEMPLATE =
+ "Start copying path '%s' to '%s' [retry: %d].";
- private static final String FINISH_COPYING_PATH_TEMPLATE = "Finish copying path '%s' to '%s' [time: %.2f s].";
+ private static final String FINISH_COPYING_PATH_TEMPLATE =
+ "Finish copying path '%s' to '%s' [time: %.2f s].";
private static final String REMOVED_PATH_TEMPLATE = "Removed path '%s'.";
- private static final String COPYING_PATH_TO_REMOTE_FAILED = "Copying path '%s' to remote directory '%s' failed: %s";
+ private static final String COPYING_PATH_TO_REMOTE_FAILED =
+ "Copying path '%s' to remote directory '%s' failed: %s";
private static final String MOVING_PATH_TO_REMOTE_FAILED_TEMPLATE =
"Moving path '%s' to remote directory '%s' failed.";
- private static final String REMOVING_LOCAL_PATH_FAILED_TEMPLATE = "Removing local path '%s' failed (%s).";
+ private static final String REMOVING_LOCAL_PATH_FAILED_TEMPLATE =
+ "Removing local path '%s' failed (%s).";
- private static final String FAILED_TO_CREATE_FILE_TEMPLATE = "Failed to create file '%s' in '%s'";
+ private static final String FAILED_TO_CREATE_FILE_TEMPLATE =
+ "Failed to create file '%s' in '%s'";
private static final String FAILED_TO_COPY_FILE_TO_REMOTE_TEMPLATE =
"Failed to copy file '%s' from '%s' to remote (%s)";
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, RemotePathMover.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, RemotePathMover.class);
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RemotePathMover.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, RemotePathMover.class);
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY, RemotePathMover.class);
+ private static final Logger notificationLog =
+ LogFactory.getLogger(LogCategory.NOTIFY, RemotePathMover.class);
private final IFileStore sourceDirectory;
@@ -89,19 +97,21 @@ public final class RemotePathMover implements IStoreHandler
* @param copier Copies items from source to destination
* @param monitor The activity monitor to inform about actions.
* @param timingParameters The timing parameters used for monitoring and reporting stall situations.
- *
* @throws ConfigurationFailureException If the destination directory is not fully accessible.
*/
- public RemotePathMover(IFileStore sourceDirectory, IFileStore destinationDirectory, IStoreCopier copier,
- CopyActivityMonitor monitor, ITimingParameters timingParameters) throws ConfigurationFailureException
+ public RemotePathMover(IFileStore sourceDirectory, IFileStore destinationDirectory,
+ IStoreCopier copier, CopyActivityMonitor monitor, ITimingParameters timingParameters)
+ throws ConfigurationFailureException
{
assert sourceDirectory != null;
assert destinationDirectory != null;
assert monitor != null;
assert timingParameters != null;
- assert sourceDirectory.tryAsExtended() != null || destinationDirectory.tryAsExtended() != null;
+ assert sourceDirectory.tryAsExtended() != null
+ || destinationDirectory.tryAsExtended() != null;
- final String errorMsg = destinationDirectory.tryCheckDirectoryFullyAccessible(TIMEOUT_DESTINATION_MILLIS);
+ final String errorMsg =
+ destinationDirectory.tryCheckDirectoryFullyAccessible(TIMEOUT_DESTINATION_MILLIS);
if (StringUtils.isNotBlank(errorMsg))
{
throw new ConfigurationFailureException(errorMsg);
@@ -124,9 +134,11 @@ public final class RemotePathMover implements IStoreHandler
// This is a recovery situation: we have been interrupted removing the path and now finish the job.
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format(
- "Detected recovery situation: '%s' has been interrupted in deletion phase, finishing up.",
- getSrcPath(item)));
+ operationLog
+ .info(String
+ .format(
+ "Detected recovery situation: '%s' has been interrupted in deletion phase, finishing up.",
+ getSrcPath(item)));
}
removeAndMark(item);
return;
@@ -138,12 +150,12 @@ public final class RemotePathMover implements IStoreHandler
{
if (tryCount > 0) // This is a retry
{
- operationLog.info(String.format(START_COPYING_PATH_RETRY_TEMPLATE, getSrcPath(item),
- destinationDirectory, tryCount));
+ operationLog.info(String.format(START_COPYING_PATH_RETRY_TEMPLATE,
+ getSrcPath(item), destinationDirectory, tryCount));
} else
{
- operationLog.info(String
- .format(START_COPYING_PATH_TEMPLATE, getSrcPath(item), destinationDirectory));
+ operationLog.info(String.format(START_COPYING_PATH_TEMPLATE, getSrcPath(item),
+ destinationDirectory));
}
}
// TODO 2008-03-17, Bernd Rinn: There needs to be a limit for how often we take this exit without sending
@@ -166,8 +178,8 @@ public final class RemotePathMover implements IStoreHandler
return;
} else
{
- operationLog.warn(String.format(COPYING_PATH_TO_REMOTE_FAILED, getSrcPath(item), destinationDirectory,
- copyStatus));
+ operationLog.warn(String.format(COPYING_PATH_TO_REMOTE_FAILED, getSrcPath(item),
+ destinationDirectory, copyStatus));
if (StatusFlag.FATAL_ERROR.equals(copyStatus.getFlag()))
{
break;
@@ -188,8 +200,8 @@ public final class RemotePathMover implements IStoreHandler
}
} while (true);
- notificationLog.error(String.format(MOVING_PATH_TO_REMOTE_FAILED_TEMPLATE, getSrcPath(item),
- destinationDirectory));
+ notificationLog.error(String.format(MOVING_PATH_TO_REMOTE_FAILED_TEMPLATE,
+ getSrcPath(item), destinationDirectory));
}
private Status copyAndMonitor(StoreItem item)
@@ -208,7 +220,8 @@ public final class RemotePathMover implements IStoreHandler
private boolean checkTargetAvailable()
{
- final String msg = destinationDirectory.tryCheckDirectoryFullyAccessible(TIMEOUT_DESTINATION_MILLIS);
+ final String msg =
+ destinationDirectory.tryCheckDirectoryFullyAccessible(TIMEOUT_DESTINATION_MILLIS);
if (msg != null)
{
machineLog.error(msg);
@@ -225,8 +238,8 @@ public final class RemotePathMover implements IStoreHandler
if (Status.OK.equals(removalStatus) == false)
{
- notificationLog.error(String.format(REMOVING_LOCAL_PATH_FAILED_TEMPLATE, getSrcPath(sourceItem),
- removalStatus));
+ notificationLog.error(String.format(REMOVING_LOCAL_PATH_FAILED_TEMPLATE,
+ getSrcPath(sourceItem), removalStatus));
} else if (operationLog.isInfoEnabled())
{
operationLog.info(String.format(REMOVED_PATH_TEMPLATE, getSrcPath(sourceItem)));
@@ -235,19 +248,22 @@ public final class RemotePathMover implements IStoreHandler
private boolean isDeletionInProgress(StoreItem item)
{
- StoreItem markDeletionInProgressMarkerFile = MarkerFile.createDeletionInProgressMarker(item);
+ StoreItem markDeletionInProgressMarkerFile =
+ MarkerFile.createDeletionInProgressMarker(item);
return getDeletionMarkerStore().exists(markDeletionInProgressMarkerFile);
}
private StoreItem tryMarkAsDeletionInProgress(StoreItem item)
{
- final StoreItem markDeletionInProgressMarkerFile = MarkerFile.createDeletionInProgressMarker(item);
+ final StoreItem markDeletionInProgressMarkerFile =
+ MarkerFile.createDeletionInProgressMarker(item);
if (createFileInside(getDeletionMarkerStore(), markDeletionInProgressMarkerFile))
{
return markDeletionInProgressMarkerFile;
} else
{
- machineLog.error(String.format("Cannot create deletion-in-progress marker file for path '%s' [%s]", item,
+ machineLog.error(String.format(
+ "Cannot create deletion-in-progress marker file for path '%s' [%s]", item,
markDeletionInProgressMarkerFile));
return null;
}
@@ -260,8 +276,8 @@ public final class RemotePathMover implements IStoreHandler
final Status status = getDeletionMarkerStore().delete(markerOrNull);
if (status.equals(Status.OK) == false)
{
- machineLog.error(String.format("Cannot remove marker file '%s'", getPath(destinationDirectory,
- markerOrNull)));
+ machineLog.error(String.format("Cannot remove marker file '%s'", getPath(
+ destinationDirectory, markerOrNull)));
}
}
}
@@ -295,7 +311,8 @@ public final class RemotePathMover implements IStoreHandler
}
}
- private boolean markOnSourceLocalAndCopyToRemoteDestination(IExtendedFileStore sourceFileStore, StoreItem markerFile)
+ private boolean markOnSourceLocalAndCopyToRemoteDestination(IExtendedFileStore sourceFileStore,
+ StoreItem markerFile)
{
try
{
@@ -309,8 +326,8 @@ public final class RemotePathMover implements IStoreHandler
return true;
} else
{
- machineLog.error(String.format(FAILED_TO_COPY_FILE_TO_REMOTE_TEMPLATE, markerFile, sourceFileStore,
- copyStatus.toString()));
+ machineLog.error(String.format(FAILED_TO_COPY_FILE_TO_REMOTE_TEMPLATE, markerFile,
+ sourceFileStore, copyStatus.toString()));
return false;
}
} finally
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopier.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopier.java
index 72e107ce370..b6b274de944 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopier.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopier.java
@@ -51,22 +51,26 @@ public class RsyncCopier implements IPathCopier
/**
* The {@link Status} returned if the process was terminated by {@link Process#destroy()}.
*/
- protected static final Status TERMINATED_STATUS = new Status(StatusFlag.RETRIABLE_ERROR, "Process was terminated.");
+ protected static final Status TERMINATED_STATUS =
+ new Status(StatusFlag.RETRIABLE_ERROR, "Process was terminated.");
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, RsyncCopier.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, RsyncCopier.class);
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RsyncCopier.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, RsyncCopier.class);
- private static final Status INTERRUPTED_STATUS = new Status(StatusFlag.RETRIABLE_ERROR, "Process was interrupted.");
+ private static final Status INTERRUPTED_STATUS =
+ new Status(StatusFlag.RETRIABLE_ERROR, "Process was interrupted.");
private final String rsyncExecutable;
private final RsyncVersion rsyncVersion;
-
+
private final String sshExecutable;
private final List<String> additionalCmdLineFlags;
-
+
private final boolean overwrite;
/**
@@ -91,8 +95,9 @@ public class RsyncCopier implements IPathCopier
* directories on the remote side will be deleted before starting the copy process (no overwriting of
* paths).
*/
- public RsyncCopier(File rsyncExecutable, File sshExecutableOrNull,
- boolean destinationDirectoryRequiresDeletionBeforeCreation, boolean overwrite, String... cmdLineFlags)
+ public RsyncCopier(File rsyncExecutable, File sshExecutableOrNull,
+ boolean destinationDirectoryRequiresDeletionBeforeCreation, boolean overwrite,
+ String... cmdLineFlags)
{
assert rsyncExecutable != null && rsyncExecutable.exists();
assert sshExecutableOrNull == null || rsyncExecutable.exists();
@@ -100,7 +105,8 @@ public class RsyncCopier implements IPathCopier
this.rsyncExecutable = rsyncExecutable.getAbsolutePath();
this.rsyncVersion = RsyncVersionChecker.getVersion(rsyncExecutable.getAbsolutePath());
this.sshExecutable = (sshExecutableOrNull != null) ? sshExecutableOrNull.getPath() : null;
- this.destinationDirectoryRequiresDeletionBeforeCreation = destinationDirectoryRequiresDeletionBeforeCreation;
+ this.destinationDirectoryRequiresDeletionBeforeCreation =
+ destinationDirectoryRequiresDeletionBeforeCreation;
this.copyProcessReference = new AtomicReference<Process>(null);
this.overwrite = overwrite;
if (cmdLineFlags.length > 0)
@@ -111,17 +117,18 @@ public class RsyncCopier implements IPathCopier
this.additionalCmdLineFlags = null;
}
}
-
+
private boolean rsyncSupportsAppend()
{
assert rsyncVersion != null;
-
+
return rsyncVersion.isNewerOrEqual(2, 6, 7);
}
-
+
private boolean isOverwriteMode()
{
- return overwrite || destinationDirectoryRequiresDeletionBeforeCreation || (rsyncSupportsAppend() == false);
+ return overwrite || destinationDirectoryRequiresDeletionBeforeCreation
+ || (rsyncSupportsAppend() == false);
}
public Status copy(File sourcePath, File destinationDirectory)
@@ -151,8 +158,8 @@ public class RsyncCopier implements IPathCopier
try
{
final ProcessBuilder copyProcessBuilder =
- new ProcessBuilder(createCommandLine(sourcePath, sourceHostOrNull, destinationDirectory,
- destinationHostOrNull));
+ new ProcessBuilder(createCommandLine(sourcePath, sourceHostOrNull,
+ destinationDirectory, destinationHostOrNull));
copyProcessBuilder.redirectErrorStream(true);
if (operationLog.isDebugEnabled())
{
@@ -167,7 +174,8 @@ public class RsyncCopier implements IPathCopier
} catch (IOException e)
{
machineLog.error(String.format("Cannot execute rsync binary %s", rsyncExecutable), e);
- return new Status(StatusFlag.FATAL_ERROR, String.format("ProcessBuilder: %s", e.getMessage()));
+ return new Status(StatusFlag.FATAL_ERROR, String.format("ProcessBuilder: %s", e
+ .getMessage()));
} catch (InterruptedException e)
{
// Shouldn't happen because this is called in a timer, anyway, it's just another error condition.
@@ -189,11 +197,12 @@ public class RsyncCopier implements IPathCopier
}
}
- private List<String> createCommandLine(File sourcePath, String sourceHost, File destinationDirectory,
- String destinationHost)
+ private List<String> createCommandLine(File sourcePath, String sourceHost,
+ File destinationDirectory, String destinationHost)
{
assert sourcePath != null && (sourceHost != null || sourcePath.exists());
- assert destinationDirectory != null && (destinationHost != null || destinationDirectory.isDirectory());
+ assert destinationDirectory != null
+ && (destinationHost != null || destinationDirectory.isDirectory());
assert (destinationHost != null && sshExecutable != null) || (destinationHost == null);
assert (sourceHost != null && sshExecutable != null) || (sourceHost == null);
@@ -286,8 +295,10 @@ public class RsyncCopier implements IPathCopier
private static void logRsyncExitValue(final Process copyProcess)
{
final int exitValue = copyProcess.exitValue();
- final List<String> processOutput = ProcessExecutionHelper.readProcessOutputLines(copyProcess, machineLog);
- ProcessExecutionHelper.logProcessExecution("rsync", exitValue, processOutput, operationLog, machineLog);
+ final List<String> processOutput =
+ ProcessExecutionHelper.readProcessOutputLines(copyProcess, machineLog);
+ ProcessExecutionHelper.logProcessExecution("rsync", exitValue, processOutput, operationLog,
+ machineLog);
}
/**
@@ -322,29 +333,33 @@ public class RsyncCopier implements IPathCopier
{
if (OSUtilities.executableExists(rsyncExecutable))
{
- throw new ConfigurationFailureException(String.format("Rsync executable '%s' is invalid.",
- rsyncExecutable));
+ throw new ConfigurationFailureException(String.format(
+ "Rsync executable '%s' is invalid.", rsyncExecutable));
} else
{
- throw new ConfigurationFailureException(String.format("Rsync executable '%s' does not exist.",
- rsyncExecutable));
+ throw new ConfigurationFailureException(String.format(
+ "Rsync executable '%s' does not exist.", rsyncExecutable));
}
}
if (rsyncVersion.isNewerOrEqual(2, 6, 0) == false)
{
throw new ConfigurationFailureException(String.format(
- "Rsync executable '%s' is too old (required: 2.6.0, found: %s)", rsyncExecutable, rsyncVersion
- .getVersionString()));
+ "Rsync executable '%s' is too old (required: 2.6.0, found: %s)",
+ rsyncExecutable, rsyncVersion.getVersionString()));
}
if (machineLog.isInfoEnabled())
{
- machineLog.info(String.format("Using rsync executable '%s', version %s, mode: %s", rsyncExecutable,
- rsyncVersion.getVersionString(), (isOverwriteMode() ? "overwrite" : "append")));
+ machineLog.info(String.format("Using rsync executable '%s', version %s, mode: %s",
+ rsyncExecutable, rsyncVersion.getVersionString(),
+ (isOverwriteMode() ? "overwrite" : "append")));
}
if (rsyncVersion.isRsyncPreReleaseVersion())
{
- machineLog.warn(String.format("The rsync executable '%s' is a pre-release version. It is not recommended "
- + "to use such a version in a production environment.", rsyncExecutable));
+ machineLog.warn(String
+ .format(
+ "The rsync executable '%s' is a pre-release version. It is not recommended "
+ + "to use such a version in a production environment.",
+ rsyncExecutable));
}
}
@@ -355,7 +370,8 @@ public class RsyncCopier implements IPathCopier
final String destination = buildPath(destinationHost, destinationDirectory, true);
final ProcessBuilder listProcessBuilder =
- new ProcessBuilder(rsyncExecutable, "--rsh", getSshExecutableArgument(sshExecutable), destination)
+ new ProcessBuilder(rsyncExecutable, "--rsh",
+ getSshExecutableArgument(sshExecutable), destination)
.redirectErrorStream(true);
if (operationLog.isDebugEnabled())
{
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncVersionChecker.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncVersionChecker.java
index ea829269ab0..8ab9621ba03 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncVersionChecker.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncVersionChecker.java
@@ -34,9 +34,11 @@ import ch.systemsx.cisd.common.process.ProcessResult;
final class RsyncVersionChecker
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RsyncVersionChecker.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, RsyncVersionChecker.class);
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, RsyncVersionChecker.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, RsyncVersionChecker.class);
/**
* The class holding the version information about an <code>rsync</code> binary.
@@ -69,8 +71,8 @@ final class RsyncVersionChecker
*/
private final boolean rsyncPreReleaseVersion;
- private RsyncVersion(String rsyncVersion, int rsyncMajorVersion, int rsyncMinorVersion, int rsyncPatchVersion,
- boolean rsyncPreReleaseVersion)
+ private RsyncVersion(String rsyncVersion, int rsyncMajorVersion, int rsyncMinorVersion,
+ int rsyncPatchVersion, boolean rsyncPreReleaseVersion)
{
this.rsyncVersion = rsyncVersion;
this.rsyncMajorVersion = rsyncMajorVersion;
@@ -110,7 +112,7 @@ final class RsyncVersionChecker
{
return rsyncPatchVersion;
}
-
+
/**
* @return <code>true</code>, if this version is a pre-release version.
*/
@@ -120,7 +122,7 @@ final class RsyncVersionChecker
}
/**
- * @return <code>true</code>, if this version is newer or as new the minimal version specified.
+ * @return <code>true</code>, if this version is newer or as new the minimal version specified.
*/
public boolean isNewerOrEqual(int minMajorVerson, int minMinorVersion, int minPatchLevel)
{
@@ -188,8 +190,8 @@ final class RsyncVersionChecker
}
}
- return new RsyncVersion(rsyncVersion, rsyncMajorVersion, rsyncMinorVersion, rsyncPatchVersion,
- preReleaseVersion);
+ return new RsyncVersion(rsyncVersion, rsyncMajorVersion, rsyncMinorVersion,
+ rsyncPatchVersion, preReleaseVersion);
}
private static String tryGetRsyncVersion(String rsyncExecutableToCheck)
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/store/FileStoreLocal.java b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/store/FileStoreLocal.java
index dedb0ab2512..b2ae61feab8 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/store/FileStoreLocal.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/filesystem/store/FileStoreLocal.java
@@ -42,7 +42,8 @@ import ch.systemsx.cisd.datamover.filesystem.intf.FileStore.ExtendedFileStore;
*/
public class FileStoreLocal extends ExtendedFileStore
{
- private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, FileStoreLocal.class);
+ private static final Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, FileStoreLocal.class);
private final IPathMover mover;
@@ -72,11 +73,12 @@ public class FileStoreLocal extends ExtendedFileStore
{
return FileUtilities.lastChanged(getChildFile(item), true, stopWhenFindYounger);
}
-
+
@Override
public long lastChangedRelative(StoreItem item, long stopWhenFindYoungerRelative)
{
- return FileUtilities.lastChangedRelative(getChildFile(item), true, stopWhenFindYoungerRelative);
+ return FileUtilities.lastChangedRelative(getChildFile(item), true,
+ stopWhenFindYoungerRelative);
}
@Override
@@ -85,8 +87,9 @@ public class FileStoreLocal extends ExtendedFileStore
final boolean available = FileUtilities.isAvailable(getPath(), timeOutMillis);
if (available == false)
{
- return String.format("Path '%s' which is supposed to be a %s directory is not available.", getPath(),
- getDescription());
+ return String.format(
+ "Path '%s' which is supposed to be a %s directory is not available.",
+ getPath(), getDescription());
}
return FileUtilities.checkDirectoryFullyAccessible(getPath(), getDescription());
}
@@ -95,7 +98,8 @@ public class FileStoreLocal extends ExtendedFileStore
public IStoreCopier getCopier(FileStore destinationDirectory)
{
boolean requiresDeletion = false;
- final IStoreCopier simpleCopier = constructStoreCopier(destinationDirectory, requiresDeletion);
+ final IStoreCopier simpleCopier =
+ constructStoreCopier(destinationDirectory, requiresDeletion);
if (requiresDeletionBeforeCreation(destinationDirectory, simpleCopier))
{
requiresDeletion = true;
@@ -176,7 +180,8 @@ public class FileStoreLocal extends ExtendedFileStore
* @return <code>true</code> if the <var>simpleCopier</var> on the file system where the
* <var>destinationDirectory</var> resides requires deleting an existing file before it can be overwritten.
*/
- protected boolean requiresDeletionBeforeCreation(IFileStore destinationDirectory, final IStoreCopier simpleCopier)
+ protected boolean requiresDeletionBeforeCreation(IFileStore destinationDirectory,
+ final IStoreCopier simpleCopier)
{
StoreItem item = MarkerFile.createRequiresDeletionBeforeCreationMarker();
createNewFile(item);
@@ -210,18 +215,22 @@ public class FileStoreLocal extends ExtendedFileStore
}
}
- private static void logCopierOverwriteState(IFileStore destinationDirectory, boolean requiresDeletion)
+ private static void logCopierOverwriteState(IFileStore destinationDirectory,
+ boolean requiresDeletion)
{
if (machineLog.isInfoEnabled())
{
if (requiresDeletion)
{
- machineLog.info(String.format(
- "Copier on directory '%s' requires deletion before creation of existing files.",
- destinationDirectory));
+ machineLog
+ .info(String
+ .format(
+ "Copier on directory '%s' requires deletion before creation of existing files.",
+ destinationDirectory));
} else
{
- machineLog.info(String.format("Copier on directory '%s' works with overwriting existing files.",
+ machineLog.info(String.format(
+ "Copier on directory '%s' works with overwriting existing files.",
destinationDirectory));
}
}
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/utils/LocalBufferDirs.java b/datamover/source/java/ch/systemsx/cisd/datamover/utils/LocalBufferDirs.java
index 36cca1ee348..204429aa5f7 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/utils/LocalBufferDirs.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/utils/LocalBufferDirs.java
@@ -35,8 +35,8 @@ public class LocalBufferDirs
private final File tempDir;
- public LocalBufferDirs(File bufferDir, String copyInProgressDirName, String copyCompleteDirName,
- String readyToMoveDirName, String tempDirName)
+ public LocalBufferDirs(File bufferDir, String copyInProgressDirName,
+ String copyCompleteDirName, String readyToMoveDirName, String tempDirName)
{
this.copyInProgressDir = ensureDirectoryExists(bufferDir, copyInProgressDirName);
this.copyCompleteDir = ensureDirectoryExists(bufferDir, copyCompleteDirName);
diff --git a/datamover/source/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilter.java b/datamover/source/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilter.java
index a978d026c18..34bc833fe3c 100644
--- a/datamover/source/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilter.java
+++ b/datamover/source/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilter.java
@@ -51,9 +51,11 @@ public class QuietPeriodFileFilter
private static final String TIME_FORMAT_TEMPLATE = "%#$tY-%#$tm-%#$td %#$tH:%#$tM:%#$tS";
- private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, QuietPeriodFileFilter.class);
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, QuietPeriodFileFilter.class);
- private final static Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE, QuietPeriodFileFilter.class);
+ private final static Logger machineLog =
+ LogFactory.getLogger(LogCategory.MACHINE, QuietPeriodFileFilter.class);
private final long quietPeriodMillis;
@@ -205,12 +207,13 @@ public class QuietPeriodFileFilter
}
// @Private
- static String getClockProblemLogMessage(final String pathname, final long oldCheck, final long oldLastChanged,
- final long newCheck, final long newLastChanged)
+ static String getClockProblemLogMessage(final String pathname, final long oldCheck,
+ final long oldLastChanged, final long newCheck, final long newLastChanged)
{
- return String.format("Last modification time of path '%1$s' jumped back: check at " + getTimeFormat(2)
- + " -> last modification time " + getTimeFormat(3) + ", check at later time " + getTimeFormat(4)
- + " -> last modification time " + getTimeFormat(5) + " (which is %6$d ms younger)", pathname, oldCheck,
+ return String.format("Last modification time of path '%1$s' jumped back: check at "
+ + getTimeFormat(2) + " -> last modification time " + getTimeFormat(3)
+ + ", check at later time " + getTimeFormat(4) + " -> last modification time "
+ + getTimeFormat(5) + " (which is %6$d ms younger)", pathname, oldCheck,
oldLastChanged, newCheck, newLastChanged, (oldLastChanged - newLastChanged));
}
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/MainTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/MainTest.java
index c84356861fe..edd44429965 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/MainTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/MainTest.java
@@ -60,9 +60,11 @@ public class MainTest
private static final int QUIET_PERIOD = 2;
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, MainTest.class.getSimpleName());
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, MainTest.class.getSimpleName());
@BeforeClass(alwaysRun = true)
public void init()
@@ -121,8 +123,8 @@ public class MainTest
// ----------------- higher level assertions
- private static void assertSampleStructMovedWithCopy(ExternalDirs dirs, LocalBufferDirs bufferDirs,
- FileStructEngine structEngine) throws IOException
+ private static void assertSampleStructMovedWithCopy(ExternalDirs dirs,
+ LocalBufferDirs bufferDirs, FileStructEngine structEngine) throws IOException
{
assertSampleStructMoved(dirs, bufferDirs, structEngine);
structEngine.assertSampleStructureExists(dirs.extraCopy);
@@ -135,15 +137,15 @@ public class MainTest
assertSampleStructInOutgoing(dirs, structEngine);
}
- private static void assertSampleStructInOutgoing(ExternalDirs dirs, FileStructEngine structEngine)
- throws IOException
+ private static void assertSampleStructInOutgoing(ExternalDirs dirs,
+ FileStructEngine structEngine) throws IOException
{
structEngine.assertSampleStructureExists(dirs.outgoing);
structEngine.assertSampleStructFinishMarkerExists(dirs.outgoing);
}
- private static void assertSampleStructMovedWithCopy(ExternalDirs dirs, LocalBufferDirs bufferDirs)
- throws IOException
+ private static void assertSampleStructMovedWithCopy(ExternalDirs dirs,
+ LocalBufferDirs bufferDirs) throws IOException
{
assertEmptyIncomingAndBufferDir(dirs, bufferDirs);
assertSampleStructInOutgoing(dirs);
@@ -158,7 +160,8 @@ public class MainTest
assertEquals(2, dirs.outgoing.list().length);
}
- private static void assertEmptyIncomingAndBufferDir(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ private static void assertEmptyIncomingAndBufferDir(ExternalDirs dirs,
+ LocalBufferDirs bufferDirs)
{
assertEmptyDir(dirs.incoming);
assertEmptyBufferDirs(bufferDirs);
@@ -206,16 +209,18 @@ public class MainTest
private static ArrayList<String> getDefaultParameters(ExternalDirs dirs)
{
- return createList("--incoming-dir", dirs.incoming.getPath(), "--buffer-dir", dirs.buffer.getPath(),
- "--outgoing-dir", dirs.outgoing.getPath(), "--check-interval", Integer.toString(CHECK_INTERVAL),
- "--check-interval-internal", Integer.toString(CHECK_INTERVAL_INTERNAL), "--quiet-period", Integer
- .toString(QUIET_PERIOD), "--treat-incoming-as-remote");
+ return createList("--incoming-dir", dirs.incoming.getPath(), "--buffer-dir", dirs.buffer
+ .getPath(), "--outgoing-dir", dirs.outgoing.getPath(), "--check-interval", Integer
+ .toString(CHECK_INTERVAL), "--check-interval-internal", Integer
+ .toString(CHECK_INTERVAL_INTERNAL), "--quiet-period", Integer
+ .toString(QUIET_PERIOD), "--treat-incoming-as-remote");
}
- private static ArrayList<String> getManualInterventionParameters(ExternalDirs dirs, String filteredName)
+ private static ArrayList<String> getManualInterventionParameters(ExternalDirs dirs,
+ String filteredName)
{
- return createList("--manual-intervention-dir", dirs.manualIntervDir.getPath(), "--manual-intervention-regex",
- filteredName);
+ return createList("--manual-intervention-dir", dirs.manualIntervDir.getPath(),
+ "--manual-intervention-regex", filteredName);
}
private static ArrayList<String> getCleansingParameters(String cleansingStruct)
@@ -257,8 +262,8 @@ public class MainTest
return createParameters(list);
}
- private static Parameters createParametersWithFilter(ExternalDirs dirs, String manualIntervName,
- String cleansingStruct)
+ private static Parameters createParametersWithFilter(ExternalDirs dirs,
+ String manualIntervName, String cleansingStruct)
{
ArrayList<String> list = getDefaultParameters(dirs);
list.addAll(getExtraCopyParameters(dirs));
@@ -269,8 +274,8 @@ public class MainTest
private static LocalBufferDirs createBufferDirs(Parameters parameters)
{
- return new LocalBufferDirs(parameters.getBufferDirectoryPath(), "test-copy-in-progress", "test-copy-complete",
- "test-ready-to-move", "test-temp");
+ return new LocalBufferDirs(parameters.getBufferDirectoryPath(), "test-copy-in-progress",
+ "test-copy-complete", "test-ready-to-move", "test-temp");
}
private static interface IFSPreparator
@@ -279,7 +284,8 @@ public class MainTest
void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception;
}
- private static void performGenericTest(IFSPreparator preparator, long millisToWaitForPrep) throws Exception
+ private static void performGenericTest(IFSPreparator preparator, long millisToWaitForPrep)
+ throws Exception
{
ExternalDirs dirs = new ExternalDirs(workingDirectory);
Parameters parameters = createDefaultParametersWithExtraCopy(dirs);
@@ -297,21 +303,23 @@ public class MainTest
assertSampleStructMovedWithCopy(dirs, bufferDirs);
}
- private static void runDataMover(Parameters parameters, LocalBufferDirs bufferDirs) throws InterruptedException
+ private static void runDataMover(Parameters parameters, LocalBufferDirs bufferDirs)
+ throws InterruptedException
{
runDataMover(parameters, bufferDirs, DATA_MOVER_COMPLETION_TIME);
}
- private static void runDataMover(Parameters parameters, LocalBufferDirs bufferDirs, long dataMoverCompleteionTime)
- throws InterruptedException
+ private static void runDataMover(Parameters parameters, LocalBufferDirs bufferDirs,
+ long dataMoverCompleteionTime) throws InterruptedException
{
ITerminable terminable = Main.startupServer(parameters, bufferDirs);
Thread.sleep(dataMoverCompleteionTime);
assertTrue(terminable.terminate());
}
- private static void runDataMover(ExternalDirs dirs, Parameters parameters, LocalBufferDirs bufferDirs,
- IFSPreparator preparator, long millisToWaitForPrep) throws Exception
+ private static void runDataMover(ExternalDirs dirs, Parameters parameters,
+ LocalBufferDirs bufferDirs, IFSPreparator preparator, long millisToWaitForPrep)
+ throws Exception
{
ITerminable terminable = Main.startupServer(parameters, bufferDirs);
Thread.sleep(millisToWaitForPrep);
@@ -342,7 +350,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(dirs.incoming);
createSampleStructure(bufferDirs.getCopyInProgressDir());
@@ -357,7 +366,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(dirs.incoming);
createPartialSampleStructure(bufferDirs.getCopyInProgressDir());
@@ -372,7 +382,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyInProgressDir());
}
@@ -386,7 +397,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyInProgressDir());
createSampleFinishedMarkerFile(bufferDirs.getCopyInProgressDir());
@@ -401,7 +413,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyCompleteDir());
createSampleFinishedMarkerFile(bufferDirs.getCopyInProgressDir());
@@ -416,7 +429,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyInProgressDir());
createPartialSampleStructure(dirs.incoming);
@@ -432,7 +446,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyCompleteDir());
}
@@ -446,7 +461,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getCopyCompleteDir());
createPartialSampleStructure(bufferDirs.getTempDir());
@@ -461,7 +477,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getTempDir());
createSampleStructure(bufferDirs.getReadyToMoveDir());
@@ -473,11 +490,13 @@ public class MainTest
{ "slow" }, dataProvider = "delays")
// recovery after failure during local processing, extra copy created in temp-dir, data moved to read-to-move,
// outgoing processing has not started. It tests also outgoing process recovery.
- public void testRecoveryLocalProcessingExtraCopyInTmpAndReadyToMove(long delay) throws Exception
+ public void testRecoveryLocalProcessingExtraCopyInTmpAndReadyToMove(long delay)
+ throws Exception
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(bufferDirs.getTempDir());
createSampleStructure(bufferDirs.getReadyToMoveDir());
@@ -492,7 +511,8 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(dirs.extraCopy);
createSampleStructure(bufferDirs.getReadyToMoveDir());
@@ -508,15 +528,16 @@ public class MainTest
{
performGenericTest(new IFSPreparator()
{
- public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs) throws Exception
+ public void prepareState(ExternalDirs dirs, LocalBufferDirs bufferDirs)
+ throws Exception
{
createSampleStructure(dirs.incoming);
}
}, delay);
}
- private FileStructEngine[] createAllThreadsPartialStruct(ExternalDirs dirs, LocalBufferDirs bufferDirs)
- throws Exception
+ private FileStructEngine[] createAllThreadsPartialStruct(ExternalDirs dirs,
+ LocalBufferDirs bufferDirs) throws Exception
{
FileStructEngine[] structs = new FileStructEngine[6];
int c = 0;
@@ -567,7 +588,8 @@ public class MainTest
}
// checks recovery mode when all threads need recovery, but no restart is made
- public void testRecoveryAllThreadsPartial(Parameters parameters, ExternalDirs dirs) throws Exception
+ public void testRecoveryAllThreadsPartial(Parameters parameters, ExternalDirs dirs)
+ throws Exception
{
LocalBufferDirs bufferDirs = createBufferDirs(parameters);
@@ -697,8 +719,8 @@ public class MainTest
FileStructEngine cleansinStruct = new FileStructEngine("test2");
Parameters parameters =
- createParametersWithFilter(dirs, manualIntervStruct.getMainStructName(), cleansinStruct
- .getSampleCleansingRegExp());
+ createParametersWithFilter(dirs, manualIntervStruct.getMainStructName(),
+ cleansinStruct.getSampleCleansingRegExp());
LocalBufferDirs bufferDirs = createBufferDirs(parameters);
manualIntervStruct.createSampleStructure(dirs.incoming);
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/ParametersTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/ParametersTest.java
index 20f46e25594..8524dfd8036 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/ParametersTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/ParametersTest.java
@@ -103,7 +103,8 @@ public class ParametersTest
{
final String localDataDir = ".." + File.separator + "test_it_data";
final Parameters parameters = parse("--incoming-dir", localDataDir);
- assertEquals(createIncomingStore(localDataDir, null, parameters), getIncomingStore(parameters));
+ assertEquals(createIncomingStore(localDataDir, null, parameters),
+ getIncomingStore(parameters));
}
@Test
@@ -125,7 +126,8 @@ public class ParametersTest
public void testDefaultCheckIntervalInternal() throws Exception
{
final Parameters parameters = parse();
- assertEquals(1000 * Parameters.DEFAULT_CHECK_INTERVAL_INTERNAL, parameters.getCheckIntervalInternalMillis());
+ assertEquals(1000 * Parameters.DEFAULT_CHECK_INTERVAL_INTERNAL, parameters
+ .getCheckIntervalInternalMillis());
}
@Test
@@ -147,14 +149,16 @@ public class ParametersTest
public void testDefaultMaximalNumberOfRetries() throws Exception
{
final Parameters parameters = parse();
- assertEquals(Parameters.DEFAULT_MAXIMAL_NUMBER_OF_RETRIES, parameters.getMaximalNumberOfRetries());
+ assertEquals(Parameters.DEFAULT_MAXIMAL_NUMBER_OF_RETRIES, parameters
+ .getMaximalNumberOfRetries());
}
@Test
public void testDefaultInactivityPeriod() throws Exception
{
final Parameters parameters = parse();
- assertEquals(1000 * Parameters.DEFAULT_INACTIVITY_PERIOD, parameters.getInactivityPeriodMillis());
+ assertEquals(1000 * Parameters.DEFAULT_INACTIVITY_PERIOD, parameters
+ .getInactivityPeriodMillis());
}
@Test
@@ -183,7 +187,8 @@ public class ParametersTest
public void testSetCheckIntervalInternalLong() throws Exception
{
final int checkInterval = 1;
- final Parameters parameters = parse("--check-interval-internal", Integer.toString(checkInterval));
+ final Parameters parameters =
+ parse("--check-interval-internal", Integer.toString(checkInterval));
assertEquals(1000 * checkInterval, parameters.getCheckIntervalInternalMillis());
}
@@ -231,10 +236,13 @@ public class ParametersTest
final String localTempDir = "l" + File.separator + "tmp";
final String remoteDataDir = "rrr";
final Parameters parameters =
- parse("--incoming-dir", localDataDir, "--buffer-dir", localTempDir, "--outgoing-dir", remoteDataDir);
- assertEquals(createIncomingStore(localDataDir, null, parameters), getIncomingStore(parameters));
+ parse("--incoming-dir", localDataDir, "--buffer-dir", localTempDir,
+ "--outgoing-dir", remoteDataDir);
+ assertEquals(createIncomingStore(localDataDir, null, parameters),
+ getIncomingStore(parameters));
assertEquals(localTempDir, parameters.getBufferDirectoryPath().getPath());
- assertEquals(createOutgoingStore(remoteDataDir, null, parameters), getOutgoingStore(parameters));
+ assertEquals(createOutgoingStore(remoteDataDir, null, parameters),
+ getOutgoingStore(parameters));
}
@Test
@@ -250,14 +258,17 @@ public class ParametersTest
final String extraCopyDir = "xxx";
final Parameters parameters =
- parse("--incoming-dir", localDataDir, "--buffer-dir", localTempDir, "--outgoing-dir", remoteDataDir,
- "--outgoing-host", remoteHost, "--check-interval", Integer.toString(checkIntervall),
- "--quiet-period", Integer.toString(quietPeriod), "--treat-incoming-as-remote",
+ parse("--incoming-dir", localDataDir, "--buffer-dir", localTempDir,
+ "--outgoing-dir", remoteDataDir, "--outgoing-host", remoteHost,
+ "--check-interval", Integer.toString(checkIntervall), "--quiet-period",
+ Integer.toString(quietPeriod), "--treat-incoming-as-remote",
"--incoming-host", remoteIncomingHost, "--extra-copy-dir", extraCopyDir,
"--rsync-overwrite");
- IFileStore incomingStoreExpected = createIncomingStore(localDataDir, remoteIncomingHost, parameters);
+ IFileStore incomingStoreExpected =
+ createIncomingStore(localDataDir, remoteIncomingHost, parameters);
IFileStore incomingStore = getIncomingStore(parameters);
- IFileStore outgoingStoreExpected = createOutgoingStore(remoteDataDir, remoteHost, parameters);
+ IFileStore outgoingStoreExpected =
+ createOutgoingStore(remoteDataDir, remoteHost, parameters);
IFileStore outgoingStore = getOutgoingStore(parameters);
assertEquals(incomingStoreExpected, incomingStore);
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/SelfTestTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/SelfTestTest.java
index 28041f8d94f..246c795d07e 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/SelfTestTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/SelfTestTest.java
@@ -41,7 +41,8 @@ import ch.systemsx.cisd.datamover.testhelper.FileOperationsUtil;
public class SelfTestTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
private static final File workingDirectory = new File(unitTestRootDirectory, "SelfTestTest");
@@ -98,12 +99,14 @@ public class SelfTestTest
throw new AssertionError();
}
- public Status copyFromRemote(File sourcePath, String sourceHost, File destinationDirectory)
+ public Status copyFromRemote(File sourcePath, String sourceHost,
+ File destinationDirectory)
{
throw new AssertionError();
}
- public Status copyToRemote(File sourcePath, File destinationDirectory, String destinationHost)
+ public Status copyToRemote(File sourcePath, File destinationDirectory,
+ String destinationHost)
{
throw new AssertionError();
}
@@ -118,7 +121,8 @@ public class SelfTestTest
return true;
}
- public void check() throws EnvironmentFailureException, ConfigurationFailureException
+ public void check() throws EnvironmentFailureException,
+ ConfigurationFailureException
{
}
@@ -133,7 +137,8 @@ public class SelfTestTest
public void testHappyCaseWithRemoteHost()
{
final String outgoingHost = "some_remote_host";
- final FileStore remoteHostOutgoingStore = createRemoteStore(outgoingDirectory, outgoingHost, "outgoing");
+ final FileStore remoteHostOutgoingStore =
+ createRemoteStore(outgoingDirectory, outgoingHost, "outgoing");
SelfTest.check(mockCopier, remoteHostOutgoingStore);
}
@@ -155,18 +160,21 @@ public class SelfTestTest
public void testNonExistentPaths()
{
final File nonExistentIncomingDirectory = new File(workingDirectory, "data");
- final FileStore nonExistentIncomingStore = createLocalStore(nonExistentIncomingDirectory, "incoming");
+ final FileStore nonExistentIncomingStore =
+ createLocalStore(nonExistentIncomingDirectory, "incoming");
SelfTest.check(mockCopier, nonExistentIncomingStore, bufferStore, outgoingStore);
}
private FileStore createRemoteStore(File path, String host, String description)
{
- return FileStoreFactory.createRemoteHost(path, host, description, FileOperationsUtil.createTestFatory());
+ return FileStoreFactory.createRemoteHost(path, host, description, FileOperationsUtil
+ .createTestFatory());
}
private static FileStore createLocalStore(File path, String description)
{
- return FileStoreFactory.createLocal(path, description, FileOperationsUtil.createTestFatory());
+ return FileStoreFactory.createLocal(path, description, FileOperationsUtil
+ .createTestFatory());
}
}
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitorTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitorTest.java
index 28734f0f15c..f047b4cf5bc 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitorTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/CopyActivityMonitorTest.java
@@ -51,13 +51,16 @@ import static org.testng.AssertJUnit.*;
public class CopyActivityMonitorTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
- private static final File workingDirectory = new File(unitTestRootDirectory, "CopyActivityMonitorTest");
+ private static final File workingDirectory =
+ new File(unitTestRootDirectory, "CopyActivityMonitorTest");
private static final int INACTIVITY_PERIOD_MILLIS = 50;
- private final StoringUncaughtExceptionHandler exceptionHandler = new StoringUncaughtExceptionHandler();
+ private final StoringUncaughtExceptionHandler exceptionHandler =
+ new StoringUncaughtExceptionHandler();
// ////////////////////////////////////////
// Some mock and dummy implementations.
@@ -98,12 +101,12 @@ public class CopyActivityMonitorTest
private final class HappyPathLastChangedChecker implements ILastChangedChecker
{
private final long stopWhenFindYoungerRelativeExpected;
-
+
public HappyPathLastChangedChecker(long stopWhenFindYoungerRelativeExpected)
{
this.stopWhenFindYoungerRelativeExpected = stopWhenFindYoungerRelativeExpected;
}
-
+
public long lastChangedRelative(StoreItem item, long stopWhenFindYoungerRelative)
{
assertEquals(stopWhenFindYoungerRelativeExpected, stopWhenFindYoungerRelative);
@@ -161,7 +164,8 @@ public class CopyActivityMonitorTest
return asFileStore(directory, checker, factory);
}
- private IFileStore asFileStore(File directory, final ILastChangedChecker checker, IFileSysOperationsFactory factory)
+ private IFileStore asFileStore(File directory, final ILastChangedChecker checker,
+ IFileSysOperationsFactory factory)
{
final FileStoreLocal localImpl = new FileStoreLocal(directory, "input-test", factory);
return new FileStore(directory, null, false, "input-test", factory)
@@ -261,9 +265,11 @@ public class CopyActivityMonitorTest
final ITerminable dummyTerminable = new DummyTerminable();
final long inactivityPeriodMillis = 5000L;
final ITimingParameters parameters = new MyTimingParameters(0, inactivityPeriodMillis);
- final ILastChangedChecker checker = new HappyPathLastChangedChecker(inactivityPeriodMillis - 1000L);
+ final ILastChangedChecker checker =
+ new HappyPathLastChangedChecker(inactivityPeriodMillis - 1000L);
final CopyActivityMonitor monitor =
- new CopyActivityMonitor(asFileStore(workingDirectory, checker), dummyTerminable, parameters);
+ new CopyActivityMonitor(asFileStore(workingDirectory, checker), dummyTerminable,
+ parameters);
StoreItem item = createDirectoryInside(workingDirectory);
monitor.start(item);
Thread.sleep(INACTIVITY_PERIOD_MILLIS * 15);
@@ -278,7 +284,8 @@ public class CopyActivityMonitorTest
final MockTerminable copyProcess = new MockTerminable();
final ITimingParameters parameters = new MyTimingParameters(0);
final CopyActivityMonitor monitor =
- new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess, parameters);
+ new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess,
+ parameters);
StoreItem item = createDirectoryInside(workingDirectory);
monitor.start(item);
Thread.sleep(INACTIVITY_PERIOD_MILLIS * 15);
@@ -322,7 +329,8 @@ public class CopyActivityMonitorTest
final MockTerminable copyProcess = new MockTerminable();
final ITimingParameters parameters = new MyTimingParameters(0);
final CopyActivityMonitor monitor =
- new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess, parameters);
+ new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess,
+ parameters);
StoreItem item = createDirectoryInside(workingDirectory);
monitor.start(item);
Thread.sleep(INACTIVITY_PERIOD_MILLIS * 15);
@@ -342,15 +350,17 @@ public class CopyActivityMonitorTest
{ "slow" })
public void testActivityMonitorTimedOut() throws Throwable
{
- final PathLastChangedCheckerDelayed checker = new PathLastChangedCheckerDelayed(INACTIVITY_PERIOD_MILLIS);
+ final PathLastChangedCheckerDelayed checker =
+ new PathLastChangedCheckerDelayed(INACTIVITY_PERIOD_MILLIS);
final MockTerminable copyProcess = new MockTerminable();
final ITimingParameters parameters = new MyTimingParameters(0);
final CopyActivityMonitor monitor =
- new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess, parameters);
+ new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess,
+ parameters);
final StoreItem item = createDirectoryInside(workingDirectory);
final LogMonitoringAppender appender =
- LogMonitoringAppender.addAppender(LogCategory.OPERATION,
- String.format("Could not determine \"last changed time\" of %s: time out.", item));
+ LogMonitoringAppender.addAppender(LogCategory.OPERATION, String.format(
+ "Could not determine \"last changed time\" of %s: time out.", item));
monitor.start(item);
Thread.sleep(INACTIVITY_PERIOD_MILLIS * 15);
monitor.stop();
@@ -364,11 +374,13 @@ public class CopyActivityMonitorTest
{ "slow" })
public void testActivityMonitorOnceTimedOutTheOK() throws Throwable
{
- final PathLastChangedCheckerDelayed checker = new PathLastChangedCheckerDelayed(INACTIVITY_PERIOD_MILLIS, 0L);
+ final PathLastChangedCheckerDelayed checker =
+ new PathLastChangedCheckerDelayed(INACTIVITY_PERIOD_MILLIS, 0L);
final MockTerminable copyProcess = new MockTerminable();
final ITimingParameters parameters = new MyTimingParameters(0);
final CopyActivityMonitor monitor =
- new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess, parameters);
+ new CopyActivityMonitor(asFileStore(workingDirectory, checker), copyProcess,
+ parameters);
final StoreItem item = createDirectoryInside(workingDirectory);
monitor.start(item);
Thread.sleep(INACTIVITY_PERIOD_MILLIS * 15);
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopierTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopierTest.java
index 07a7b5589b9..545ce6d1f91 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopierTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/filesystem/remote/rsync/RsyncCopierTest.java
@@ -45,7 +45,8 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
public class RsyncCopierTest
{
- private static final File unitTestRootDirectory = new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory =
+ new File("targets" + File.separator + "unit-test-wd");
private static final File workingDirectory = new File(unitTestRootDirectory, "RsyncCopierTest");
@@ -53,7 +54,8 @@ public class RsyncCopierTest
private final File destinationDirectory = new File(workingDirectory, "b");
- private final StoringUncaughtExceptionHandler exceptionHandler = new StoringUncaughtExceptionHandler();
+ private final StoringUncaughtExceptionHandler exceptionHandler =
+ new StoringUncaughtExceptionHandler();
@BeforeClass
public void init()
@@ -79,16 +81,18 @@ public class RsyncCopierTest
destinationDirectory.deleteOnExit();
}
- private File createRsync(String rsyncVersion, String... additionalLines) throws IOException, InterruptedException
+ private File createRsync(String rsyncVersion, String... additionalLines) throws IOException,
+ InterruptedException
{
final File rsyncBinary = new File(workingDirectory, "rsync");
rsyncBinary.delete();
final List<String> lines = new ArrayList<String>();
- lines.addAll(Arrays.asList("#! /bin/sh", "if [ \"$1\" = \"--version\" ]; then ", String.format(
- " echo \"rsync version %s\"", rsyncVersion), "exit 0", "fi"));
+ lines.addAll(Arrays.asList("#! /bin/sh", "if [ \"$1\" = \"--version\" ]; then ", String
+ .format(" echo \"rsync version %s\"", rsyncVersion), "exit 0", "fi"));
lines.addAll(Arrays.asList(additionalLines));
CollectionIO.writeIterable(rsyncBinary, lines);
- Runtime.getRuntime().exec(String.format("/bin/chmod +x %s", rsyncBinary.getPath())).waitFor();
+ Runtime.getRuntime().exec(String.format("/bin/chmod +x %s", rsyncBinary.getPath()))
+ .waitFor();
rsyncBinary.deleteOnExit();
return rsyncBinary;
}
@@ -138,7 +142,8 @@ public class RsyncCopierTest
{
final File parametersLogFile = new File(workingDirectory, "parameters.log");
final File loggingRsyncBinary =
- createRsync("2.6.7", String.format("echo \"$@\" > %s", parametersLogFile.getAbsolutePath()));
+ createRsync("2.6.7", String.format("echo \"$@\" > %s", parametersLogFile
+ .getAbsolutePath()));
final RsyncCopier copier = new RsyncCopier(loggingRsyncBinary, null, false, false);
copier.copy(sourceFile, destinationDirectory);
String rsyncParameters = FileUtilities.loadToString(parametersLogFile);
@@ -152,7 +157,8 @@ public class RsyncCopierTest
{
final File parametersLogFile = new File(workingDirectory, "parameters.log");
final File loggingRsyncBinary =
- createRsync("2.6.6", String.format("echo \"$@\" > %s", parametersLogFile.getAbsolutePath()));
+ createRsync("2.6.6", String.format("echo \"$@\" > %s", parametersLogFile
+ .getAbsolutePath()));
final RsyncCopier copier = new RsyncCopier(loggingRsyncBinary, null, false, false);
copier.copy(sourceFile, destinationDirectory);
String rsyncParameters = FileUtilities.loadToString(parametersLogFile);
@@ -166,7 +172,8 @@ public class RsyncCopierTest
{
final File parametersLogFile = new File(workingDirectory, "parameters.log");
final File loggingRsyncBinary =
- createRsync("2.6.7", String.format("echo \"$@\" > %s", parametersLogFile.getAbsolutePath()));
+ createRsync("2.6.7", String.format("echo \"$@\" > %s", parametersLogFile
+ .getAbsolutePath()));
final RsyncCopier copier = new RsyncCopier(loggingRsyncBinary, null, false, true);
copier.copy(sourceFile, destinationDirectory);
String rsyncParameters = FileUtilities.loadToString(parametersLogFile);
diff --git a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilterTest.java b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilterTest.java
index 20889472a08..c6f5a748009 100644
--- a/datamover/sourceTest/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilterTest.java
+++ b/datamover/sourceTest/java/ch/systemsx/cisd/datamover/utils/QuietPeriodFileFilterTest.java
@@ -86,7 +86,8 @@ public class QuietPeriodFileFilterTest
public void testGetTimeFormat()
{
assertEquals("%0$tY-%0$tm-%0$td %0$tH:%0$tM:%0$tS", QuietPeriodFileFilter.getTimeFormat(0));
- assertEquals("%17$tY-%17$tm-%17$td %17$tH:%17$tM:%17$tS", QuietPeriodFileFilter.getTimeFormat(17));
+ assertEquals("%17$tY-%17$tm-%17$td %17$tH:%17$tM:%17$tS", QuietPeriodFileFilter
+ .getTimeFormat(17));
}
@Test
@@ -96,7 +97,8 @@ public class QuietPeriodFileFilterTest
"Last modification time of path 'bla' jumped back: check at 1970-01-01 01:00:01 -> "
+ "last modification time 1970-01-01 01:00:50, check at later time 1970-01-01 01:00:10 -> "
+ "last modification time 1970-01-01 01:00:30 (which is 20000 ms younger)";
- assertEquals(expected, QuietPeriodFileFilter.getClockProblemLogMessage("bla", 1000L, 50000L, 10000L, 30000L));
+ assertEquals(expected, QuietPeriodFileFilter.getClockProblemLogMessage("bla", 1000L,
+ 50000L, 10000L, 30000L));
}
@Test
@@ -268,7 +270,8 @@ public class QuietPeriodFileFilterTest
// calls to get the required number of calls for clean up
allowing(timeProvider).getCurrentTimeMillis();
will(returnValue(nowMillis2));
- allowing(fileStore).lastChanged(with(same(ITEM)), with(greaterThanOrEqualTo(0L)));
+ allowing(fileStore).lastChanged(with(same(ITEM)),
+ with(greaterThanOrEqualTo(0L)));
will(returnValue(pathLastChangedMillis2));
}
});
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBMigrationEngine.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBMigrationEngine.java
index 255dbaf6f49..fa1d63856ec 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBMigrationEngine.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBMigrationEngine.java
@@ -33,25 +33,29 @@ import ch.systemsx.cisd.common.logging.LogFactory;
*/
public class DBMigrationEngine
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, DBMigrationEngine.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DBMigrationEngine.class);
/**
* Creates or migrates a database specified in the context for/to the specified version.
*
* @return the SQL script provider.
*/
- public static ISqlScriptProvider createOrMigrateDatabaseAndGetScriptProvider(DatabaseConfigurationContext context,
- String databaseVersion)
+ public static ISqlScriptProvider createOrMigrateDatabaseAndGetScriptProvider(
+ DatabaseConfigurationContext context, String databaseVersion)
{
assert context != null : "Unspecified database configuration context.";
assert StringUtils.isNotBlank(databaseVersion) : "Unspecified database version.";
- final ch.systemsx.cisd.dbmigration.IDAOFactory migrationDAOFactory = context.createDAOFactory();
+ final ch.systemsx.cisd.dbmigration.IDAOFactory migrationDAOFactory =
+ context.createDAOFactory();
final String scriptFolder = context.getScriptFolder();
String databaseEngineCode = context.getDatabaseEngineCode();
- final ISqlScriptProvider sqlScriptProvider = new SqlScriptProvider(scriptFolder, databaseEngineCode);
+ final ISqlScriptProvider sqlScriptProvider =
+ new SqlScriptProvider(scriptFolder, databaseEngineCode);
final DBMigrationEngine migrationEngine =
- new DBMigrationEngine(migrationDAOFactory, sqlScriptProvider, context.isCreateFromScratch());
+ new DBMigrationEngine(migrationDAOFactory, sqlScriptProvider, context
+ .isCreateFromScratch());
migrationEngine.migrateTo(databaseVersion);
return sqlScriptProvider;
}
@@ -71,7 +75,8 @@ public class DBMigrationEngine
*
* @param shouldCreateFromScratch If <code>true</code> the database should be dropped and created from scratch.
*/
- public DBMigrationEngine(IDAOFactory daoFactory, ISqlScriptProvider scriptProvider, boolean shouldCreateFromScratch)
+ public DBMigrationEngine(IDAOFactory daoFactory, ISqlScriptProvider scriptProvider,
+ boolean shouldCreateFromScratch)
{
adminDAO = daoFactory.getDatabaseDAO();
logDAO = daoFactory.getDatabaseVersionLogDAO();
@@ -121,8 +126,8 @@ public class DBMigrationEngine
final String databaseName = adminDAO.getDatabaseName();
if (operationLog.isInfoEnabled())
{
- operationLog.info("Trying to migrate database '" + databaseName + "' from version "
- + databaseVersion + " to " + version + ".");
+ operationLog.info("Trying to migrate database '" + databaseName
+ + "' from version " + databaseVersion + " to " + version + ".");
}
}
migrate(databaseVersion, version);
@@ -131,8 +136,9 @@ public class DBMigrationEngine
final String databaseName = adminDAO.getDatabaseName();
if (operationLog.isInfoEnabled())
{
- operationLog.info("Database '" + databaseName + "' successfully migrated from version "
- + databaseVersion + " to " + version + ".");
+ operationLog.info("Database '" + databaseName
+ + "' successfully migrated from version " + databaseVersion + " to "
+ + version + ".");
}
}
} else
@@ -161,7 +167,9 @@ public class DBMigrationEngine
}
if (entry.getRunStatus() != LogEntry.RunStatus.SUCCESS)
{
- String message = "Inconsistent database: Last creation/migration didn't succeed. Last log entry: " + entry;
+ String message =
+ "Inconsistent database: Last creation/migration didn't succeed. Last log entry: "
+ + entry;
operationLog.error(message);
throw new EnvironmentFailureException(message);
}
@@ -182,7 +190,8 @@ public class DBMigrationEngine
if (operationLog.isInfoEnabled())
{
String databaseName = adminDAO.getDatabaseName();
- operationLog.info("Database '" + databaseName + "' version " + version + " has been successfully created.");
+ operationLog.info("Database '" + databaseName + "' version " + version
+ + " has been successfully created.");
}
}
@@ -232,8 +241,8 @@ public class DBMigrationEngine
{
final String databaseName = adminDAO.getDatabaseName();
final String message =
- "Cannot migrate database '" + databaseName + "' from version " + version + " to " + nextVersion
- + " because of missing migration script.";
+ "Cannot migrate database '" + databaseName + "' from version " + version
+ + " to " + nextVersion + " because of missing migration script.";
operationLog.error(message);
throw new EnvironmentFailureException(message);
}
@@ -241,8 +250,8 @@ public class DBMigrationEngine
scriptExecutor.execute(migrationScript, true, logDAO);
if (operationLog.isInfoEnabled())
{
- operationLog.info("Successfully migrated from version " + version + " to " + nextVersion + " in "
- + (System.currentTimeMillis() - time) + " msec");
+ operationLog.info("Successfully migrated from version " + version + " to "
+ + nextVersion + " in " + (System.currentTimeMillis() - time) + " msec");
}
version = nextVersion;
} while (version.equals(toVersion) == false);
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBScriptFormatter.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBScriptFormatter.java
index 87042be954f..1478f1a08f5 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBScriptFormatter.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBScriptFormatter.java
@@ -50,52 +50,49 @@ public class DBScriptFormatter
private static enum StatementClass
{
- CREATE_DOMAIN("Creating domains", "CREATE DOMAIN "),
- CREATE_TABLE("Creating tables", "CREATE TABLE "),
- CREATE_SEQUENCE("Creating sequences", "CREATE SEQUENCE ",
+ CREATE_DOMAIN("Creating domains", "CREATE DOMAIN "), CREATE_TABLE("Creating tables",
+ "CREATE TABLE "), CREATE_SEQUENCE("Creating sequences", "CREATE SEQUENCE ",
new ILineProcessor()
{
public String process(String line)
{
- return StringUtils.replace(line, " NO MAXVALUE NO MINVALUE NO CYCLE", "");
+ return StringUtils.replace(line, " NO MAXVALUE NO MINVALUE NO CYCLE",
+ "");
}
- }),
- PRIMARY_KEY_CONSTRAINTS("Creating primary key constraints", new ILineMatcher()
- {
- public boolean match(String line)
- {
- return Pattern.matches("ALTER TABLE .+ PRIMARY KEY.+", line);
- }
- }, null),
- UNIQUE_CONSTRAINTS("Creating unique constraints", new ILineMatcher()
- {
- public boolean match(String line)
- {
- return Pattern.matches("ALTER TABLE .+ UNIQUE.+", line);
- }
- }, null),
- FOREIGN_KEY_CONSTRAINTS("Creating foreign key constraints", new ILineMatcher()
- {
- public boolean match(String line)
- {
- return Pattern.matches("ALTER TABLE .+ FOREIGN KEY.+", line);
- }
- }, null),
- CHECK_CONSTRAINTS("Creating check constraints", new ILineMatcher()
- {
- public boolean match(String line)
+ }), PRIMARY_KEY_CONSTRAINTS("Creating primary key constraints",
+ new ILineMatcher()
+ {
+ public boolean match(String line)
+ {
+ return Pattern.matches("ALTER TABLE .+ PRIMARY KEY.+", line);
+ }
+ }, null), UNIQUE_CONSTRAINTS("Creating unique constraints", new ILineMatcher()
{
- return Pattern.matches("ALTER TABLE .+ CHECK.+", line);
- }
- }, null),
- CREATE_INDEX("Creating indices", "CREATE INDEX "),
- MISC("Miscellaneous", new ILineMatcher()
+ public boolean match(String line)
+ {
+ return Pattern.matches("ALTER TABLE .+ UNIQUE.+", line);
+ }
+ }, null), FOREIGN_KEY_CONSTRAINTS("Creating foreign key constraints",
+ new ILineMatcher()
+ {
+ public boolean match(String line)
+ {
+ return Pattern.matches("ALTER TABLE .+ FOREIGN KEY.+", line);
+ }
+ }, null), CHECK_CONSTRAINTS("Creating check constraints", new ILineMatcher()
{
public boolean match(String line)
{
- return true;
+ return Pattern.matches("ALTER TABLE .+ CHECK.+", line);
}
- }, null);
+ }, null), CREATE_INDEX("Creating indices", "CREATE INDEX "), MISC("Miscellaneous",
+ new ILineMatcher()
+ {
+ public boolean match(String line)
+ {
+ return true;
+ }
+ }, null);
private ILineMatcher matcher;
@@ -108,7 +105,8 @@ public class DBScriptFormatter
this(comment, prefix, null);
}
- StatementClass(final String comment, final String prefix, final ILineProcessor processorOrNull)
+ StatementClass(final String comment, final String prefix,
+ final ILineProcessor processorOrNull)
{
this(comment, new ILineMatcher()
{
@@ -116,11 +114,11 @@ public class DBScriptFormatter
{
return line.startsWith(prefix);
}
- },
- processorOrNull);
+ }, processorOrNull);
}
- StatementClass(final String comment, final ILineMatcher matcher, final ILineProcessor processorOrNull)
+ StatementClass(final String comment, final ILineMatcher matcher,
+ final ILineProcessor processorOrNull)
{
this.comment = comment;
this.matcher = matcher;
@@ -131,7 +129,7 @@ public class DBScriptFormatter
{
return comment;
}
-
+
public boolean matches(String statement)
{
return matcher.match(statement);
@@ -154,7 +152,8 @@ public class DBScriptFormatter
{
break;
}
- if (trimmedScriptLine.substring(COMMENT.length()).trim().toUpperCase().startsWith("CREATING"))
+ if (trimmedScriptLine.substring(COMMENT.length()).trim().toUpperCase().startsWith(
+ "CREATING"))
{
continue;
}
@@ -162,7 +161,8 @@ public class DBScriptFormatter
}
}
- private static List<String> getOrCreateList(Map<StatementClass, List<String>> map, StatementClass key)
+ private static List<String> getOrCreateList(Map<StatementClass, List<String>> map,
+ StatementClass key)
{
List<String> list = map.get(key);
if (list == null)
@@ -216,7 +216,8 @@ public class DBScriptFormatter
System.exit(1);
}
- final PrintWriter out = new PrintWriter(new FileOutputStream(new File(args[0] + ".formatted")));
+ final PrintWriter out =
+ new PrintWriter(new FileOutputStream(new File(args[0] + ".formatted")));
final String sqlScript = FileUtilities.loadToString(new File(args[0]));
final List<String> sqlStatements = DBUtilities.splitSqlStatements(sqlScript);
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBUtilities.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBUtilities.java
index 876372b3470..98eb23e2d23 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBUtilities.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DBUtilities.java
@@ -102,11 +102,12 @@ public final class DBUtilities
return statements;
}
- private final static void addToStatements(final List<String> statements, final StringBuilder statement)
+ private final static void addToStatements(final List<String> statements,
+ final StringBuilder statement)
{
final String statementStr =
- statement.toString().trim().replaceAll("\\s+", " ").replaceAll("\\)(\\w)", ") $1").replaceAll("\\s+;",
- ";");
+ statement.toString().trim().replaceAll("\\s+", " ").replaceAll("\\)(\\w)", ") $1")
+ .replaceAll("\\s+;", ";");
statements.add(statementStr);
statement.setLength(0);
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseConfigurationContext.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseConfigurationContext.java
index d97a2e2d88a..be5b60aebde 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseConfigurationContext.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseConfigurationContext.java
@@ -236,7 +236,8 @@ public class DatabaseConfigurationContext implements DisposableBean
if (adminDataSource == null)
{
adminDataSource =
- dataSourceFactory.createDataSource(getDriver(), getAdminURL(), getAdminUser(), getAdminPassword());
+ dataSourceFactory.createDataSource(getDriver(), getAdminURL(), getAdminUser(),
+ getAdminPassword());
}
return adminDataSource;
}
@@ -471,7 +472,8 @@ public class DatabaseConfigurationContext implements DisposableBean
* @param databaseEngineCode New value.
* @throws ConfigurationFailureException If there is no such database engine.
*/
- public final void setDatabaseEngineCode(String databaseEngineCode) throws ConfigurationFailureException
+ public final void setDatabaseEngineCode(String databaseEngineCode)
+ throws ConfigurationFailureException
{
this.databaseEngine = DatabaseEngine.getEngineForCode(databaseEngineCode);
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseEngine.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseEngine.java
index 2bca8602b8a..0ff7a5bbfca 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseEngine.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseEngine.java
@@ -38,9 +38,9 @@ import ch.systemsx.cisd.dbmigration.postgresql.PostgreSQLDAOFactory;
*/
public enum DatabaseEngine
{
- POSTGRESQL("postgresql", "org.postgresql.Driver", PostgreSQLDAOFactory.class, new DefaultLobHandler(),
- new PostgreSQLSequencerHandler(), "jdbc:postgresql:{0}", "jdbc:postgresql:{0}{1}", "//localhost/",
- "postgres"),
+ POSTGRESQL("postgresql", "org.postgresql.Driver", PostgreSQLDAOFactory.class,
+ new DefaultLobHandler(), new PostgreSQLSequencerHandler(), "jdbc:postgresql:{0}",
+ "jdbc:postgresql:{0}{1}", "//localhost/", "postgres"),
H2("h2", "org.h2.Driver", H2DAOFactory.class, new DefaultLobHandler(),
new PostgreSQLSequencerHandler(), "jdbc:h2:{0}{1};DB_CLOSE_DELAY=-1",
@@ -70,8 +70,8 @@ public enum DatabaseEngine
@SuppressWarnings("unchecked")
DatabaseEngine(String code, String driver, Class<?> daoFactoryClass, LobHandler lobHandler,
- ISequencerHandler sequenceHandler, String adminUrlTemplate, String urlTemplate, String defaultURLHostPart,
- String defaultAdminUser)
+ ISequencerHandler sequenceHandler, String adminUrlTemplate, String urlTemplate,
+ String defaultURLHostPart, String defaultAdminUser)
{
assert code != null;
assert driver != null;
@@ -94,7 +94,8 @@ public enum DatabaseEngine
this.daoFactoryClass = (Class<ch.systemsx.cisd.dbmigration.IDAOFactory>) daoFactoryClass;
try
{
- this.daoFactoryConstructor = this.daoFactoryClass.getConstructor(DatabaseConfigurationContext.class);
+ this.daoFactoryConstructor =
+ this.daoFactoryClass.getConstructor(DatabaseConfigurationContext.class);
} catch (NoSuchMethodException ex)
{
throw new Error("No constructor", ex);
@@ -149,7 +150,8 @@ public enum DatabaseEngine
*/
public final String getAdminURL(String urlHostPartOrNull, String databaseName)
{
- final String hostPartUrl = (urlHostPartOrNull == null) ? defaultURLHostPart : urlHostPartOrNull;
+ final String hostPartUrl =
+ (urlHostPartOrNull == null) ? defaultURLHostPart : urlHostPartOrNull;
final String url = MessageFormat.format(adminUrlTemplate, hostPartUrl, databaseName);
return url;
}
@@ -167,7 +169,8 @@ public enum DatabaseEngine
*/
public final String getURL(String urlHostPartOrNull, String databaseName)
{
- final String hostPartUrl = (urlHostPartOrNull == null) ? defaultURLHostPart : urlHostPartOrNull;
+ final String hostPartUrl =
+ (urlHostPartOrNull == null) ? defaultURLHostPart : urlHostPartOrNull;
final String url = MessageFormat.format(urlTemplate, hostPartUrl, databaseName);
return url;
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseVersionLogDAO.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseVersionLogDAO.java
index d52e6ab9942..79f86a65e99 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseVersionLogDAO.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/DatabaseVersionLogDAO.java
@@ -66,8 +66,8 @@ public class DatabaseVersionLogDAO extends SimpleJdbcDaoSupport implements IData
private static final String DB_VERSION = "db_version";
private static final String SELECT_LAST_ENTRY =
- "select * from " + DB_VERSION_LOG + " where " + RUN_STATUS_TIMESTAMP + " in (select max("
- + RUN_STATUS_TIMESTAMP + ") from " + DB_VERSION_LOG + ")";
+ "select * from " + DB_VERSION_LOG + " where " + RUN_STATUS_TIMESTAMP
+ + " in (select max(" + RUN_STATUS_TIMESTAMP + ") from " + DB_VERSION_LOG + ")";
private static final class LogEntryRowMapper implements ParameterizedRowMapper<LogEntry>
{
@@ -87,7 +87,8 @@ public class DatabaseVersionLogDAO extends SimpleJdbcDaoSupport implements IData
logEntry.setRunStatusTimestamp(rs.getDate(RUN_STATUS_TIMESTAMP));
try
{
- logEntry.setModuleCode(new String(lobHandler.getBlobAsBytes(rs, MODULE_CODE), ENCODING));
+ logEntry.setModuleCode(new String(lobHandler.getBlobAsBytes(rs, MODULE_CODE),
+ ENCODING));
} catch (UnsupportedEncodingException ex)
{
throw new CheckedExceptionTunnel(ex);
@@ -140,73 +141,83 @@ public class DatabaseVersionLogDAO extends SimpleJdbcDaoSupport implements IData
public LogEntry getLastEntry()
{
SimpleJdbcTemplate template = getSimpleJdbcTemplate();
- List<LogEntry> entries = template.query(SELECT_LAST_ENTRY, new LogEntryRowMapper(lobHandler));
+ List<LogEntry> entries =
+ template.query(SELECT_LAST_ENTRY, new LogEntryRowMapper(lobHandler));
return entries.size() == 0 ? null : entries.get(entries.size() - 1);
}
/**
- * Inserts a new entry into the version log with {@link LogEntry.RunStatus#START}.
+ * Inserts a new entry into the version log with {@link LogEntry.RunStatus#START}.
*
* @param moduleScript The script of the module to be logged.
*/
public void logStart(final Script moduleScript)
{
JdbcTemplate template = getJdbcTemplate();
- PreparedStatementCallback callback = new AbstractLobCreatingPreparedStatementCallback(this.lobHandler)
- {
- @Override
- protected void setValues(PreparedStatement ps, LobCreator lobCreator) throws SQLException
- {
- ps.setString(1, moduleScript.getVersion());
- ps.setString(2, moduleScript.getName());
- ps.setString(3, LogEntry.RunStatus.START.toString());
- ps.setTimestamp(4, new Timestamp(System.currentTimeMillis()));
- lobCreator.setBlobAsBytes(ps, 5, getAsByteArray(moduleScript.getCode()));
- }
- };
- template.execute("insert into " + DB_VERSION_LOG + " (" + DB_VERSION + "," + MODULE_NAME + "," + RUN_STATUS
- + "," + RUN_STATUS_TIMESTAMP + "," + MODULE_CODE + ") values (?,?,?,?,?)", callback);
+ PreparedStatementCallback callback =
+ new AbstractLobCreatingPreparedStatementCallback(this.lobHandler)
+ {
+ @Override
+ protected void setValues(PreparedStatement ps, LobCreator lobCreator)
+ throws SQLException
+ {
+ ps.setString(1, moduleScript.getVersion());
+ ps.setString(2, moduleScript.getName());
+ ps.setString(3, LogEntry.RunStatus.START.toString());
+ ps.setTimestamp(4, new Timestamp(System.currentTimeMillis()));
+ lobCreator
+ .setBlobAsBytes(ps, 5, getAsByteArray(moduleScript.getCode()));
+ }
+ };
+ template.execute("insert into " + DB_VERSION_LOG + " (" + DB_VERSION + "," + MODULE_NAME
+ + "," + RUN_STATUS + "," + RUN_STATUS_TIMESTAMP + "," + MODULE_CODE
+ + ") values (?,?,?,?,?)", callback);
}
/**
- * Update log entry specified by version and module name to {@link LogEntry.RunStatus#SUCCESS}.
+ * Update log entry specified by version and module name to {@link LogEntry.RunStatus#SUCCESS}.
*
* @param moduleScript The script of the successfully applied module.
*/
public void logSuccess(final Script moduleScript)
{
SimpleJdbcTemplate template = getSimpleJdbcTemplate();
- template.update("update " + DB_VERSION_LOG + " SET " + RUN_STATUS + " = ? , " + RUN_STATUS_TIMESTAMP + " = ? "
- + "where " + DB_VERSION + " = ? and " + MODULE_NAME + " = ?", LogEntry.RunStatus.SUCCESS.toString(),
- new Date(System.currentTimeMillis()), moduleScript.getVersion(), moduleScript.getName());
+ template.update("update " + DB_VERSION_LOG + " SET " + RUN_STATUS + " = ? , "
+ + RUN_STATUS_TIMESTAMP + " = ? " + "where " + DB_VERSION + " = ? and "
+ + MODULE_NAME + " = ?", LogEntry.RunStatus.SUCCESS.toString(), new Date(System
+ .currentTimeMillis()), moduleScript.getVersion(), moduleScript.getName());
}
/**
- * Update log entry specified by version and module name to {@link LogEntry.RunStatus#FAILED}.
+ * Update log entry specified by version and module name to {@link LogEntry.RunStatus#FAILED}.
*
* @param moduleScript Script of the failed module.
- * @param runException Exception causing the failure.
+ * @param runException Exception causing the failure.
*/
public void logFailure(final Script moduleScript, Throwable runException)
{
final StringWriter stringWriter = new StringWriter();
runException.printStackTrace(new PrintWriter(stringWriter));
JdbcTemplate template = getJdbcTemplate();
- PreparedStatementCallback callback = new AbstractLobCreatingPreparedStatementCallback(this.lobHandler)
- {
- @Override
- protected void setValues(PreparedStatement ps, LobCreator lobCreator) throws SQLException
- {
- ps.setString(1, LogEntry.RunStatus.FAILED.toString());
- ps.setTimestamp(2, new Timestamp(System.currentTimeMillis()));
- lobCreator.setBlobAsBytes(ps, 3, getAsByteArray(stringWriter.toString()));
- ps.setString(4, moduleScript.getVersion());
- ps.setString(5, moduleScript.getName());
- }
- };
- template.execute("update " + DB_VERSION_LOG + " SET " + RUN_STATUS + " = ?, " + RUN_STATUS_TIMESTAMP + " = ?, "
- + RUN_EXCEPTION + " = ? where " + DB_VERSION + " = ? and " + MODULE_NAME + " = ?", callback);
+ PreparedStatementCallback callback =
+ new AbstractLobCreatingPreparedStatementCallback(this.lobHandler)
+ {
+ @Override
+ protected void setValues(PreparedStatement ps, LobCreator lobCreator)
+ throws SQLException
+ {
+ ps.setString(1, LogEntry.RunStatus.FAILED.toString());
+ ps.setTimestamp(2, new Timestamp(System.currentTimeMillis()));
+ lobCreator.setBlobAsBytes(ps, 3,
+ getAsByteArray(stringWriter.toString()));
+ ps.setString(4, moduleScript.getVersion());
+ ps.setString(5, moduleScript.getName());
+ }
+ };
+ template.execute("update " + DB_VERSION_LOG + " SET " + RUN_STATUS + " = ?, "
+ + RUN_STATUS_TIMESTAMP + " = ?, " + RUN_EXCEPTION + " = ? where " + DB_VERSION
+ + " = ? and " + MODULE_NAME + " = ?", callback);
}
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDataSourceFactory.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDataSourceFactory.java
index 6ffd2c0057d..70d4c850bd4 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDataSourceFactory.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDataSourceFactory.java
@@ -20,7 +20,7 @@ import javax.sql.DataSource;
/**
* Factory for a {@link DataSource}.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IDataSourceFactory
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseAdminDAO.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseAdminDAO.java
index 71b4df96b92..8b90956d0ae 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseAdminDAO.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseAdminDAO.java
@@ -20,7 +20,7 @@ import java.io.File;
/**
* Interface for administration of a database.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IDatabaseAdminDAO
@@ -29,28 +29,28 @@ public interface IDatabaseAdminDAO
* Returns the name of the database to be created / dropped.
*/
public String getDatabaseName();
-
+
/**
* Returns the complete URL of the database to be created / dropped.
*/
public String getDatabaseURL();
-
+
/**
- * Creates the owner/user of the database. Implementation should handle the case of already existing owner/user
+ * Creates the owner/user of the database. Implementation should handle the case of already existing owner/user
* gracefully.
*/
public void createOwner();
-
+
/**
* Creates the database and the 'database_version_logs' table.
*/
public void createDatabase();
-
+
/**
* Restores the database from previously created dump.
*/
public void restoreDatabaseFromDump(File dumpFolder, String version);
-
+
/**
* Drops the database.
*/
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseVersionLogDAO.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseVersionLogDAO.java
index c624460c137..b7fa568c305 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseVersionLogDAO.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/IDatabaseVersionLogDAO.java
@@ -19,10 +19,9 @@ package ch.systemsx.cisd.dbmigration;
import ch.systemsx.cisd.common.Script;
import ch.systemsx.cisd.common.db.ISqlScriptExecutionLogger;
-
/**
* Interface for a Data Access Object for the database version log.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IDatabaseVersionLogDAO extends ISqlScriptExecutionLogger
@@ -31,17 +30,17 @@ public interface IDatabaseVersionLogDAO extends ISqlScriptExecutionLogger
* Returns <code>true</code> if the database instance with database version log can be connected.
*/
public boolean canConnectToDatabase();
-
+
/**
* Creates the table DATABASE_VERSION_LOG by using the specified script.
*/
public void createTable(Script script);
-
+
/**
* Returns the last log entry found.
*
* @return <code>null</code> if log is empty.
*/
public LogEntry getLastEntry();
-
+
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/LogEntry.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/LogEntry.java
index cc587f9f0c5..db7702b1baf 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/LogEntry.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/LogEntry.java
@@ -20,7 +20,7 @@ import java.util.Date;
/**
* Log entry of DATABASE_VERSION_LOG.
- *
+ *
* @author Franz-Josef Elmer
*/
public class LogEntry
@@ -30,14 +30,19 @@ public class LogEntry
{
START, SUCCESS, FAILED, UNKNOWN
}
-
+
private String version;
+
private String moduleName;
+
private RunStatus runStatus;
+
private Date runStatusTimestamp;
+
private String moduleCode;
+
private String runException;
-
+
/**
* Returns moduleCode.
*
@@ -47,7 +52,7 @@ public class LogEntry
{
return moduleCode;
}
-
+
/**
* Sets moduleCode.
*
@@ -57,7 +62,7 @@ public class LogEntry
{
this.moduleCode = moduleCode;
}
-
+
/**
* Returns moduleName.
*
@@ -67,7 +72,7 @@ public class LogEntry
{
return moduleName;
}
-
+
/**
* Sets moduleName.
*
@@ -77,7 +82,7 @@ public class LogEntry
{
this.moduleName = moduleName;
}
-
+
/**
* Returns runException.
*
@@ -87,7 +92,7 @@ public class LogEntry
{
return runException;
}
-
+
/**
* Sets runException.
*
@@ -97,7 +102,7 @@ public class LogEntry
{
this.runException = runException;
}
-
+
/**
* Returns runStatus.
*
@@ -107,7 +112,7 @@ public class LogEntry
{
return runStatus;
}
-
+
/**
* Sets runStatus based its string representation. If the argument does not match one of the valid constants.
* {@link RunStatus#UNKNOWN} will be used.
@@ -120,7 +125,7 @@ public class LogEntry
runStatus = RunStatus.UNKNOWN;
}
}
-
+
/**
* Sets runStatus.
*
@@ -130,7 +135,7 @@ public class LogEntry
{
this.runStatus = runStatus;
}
-
+
/**
* Returns runStatusTimestamp.
*
@@ -140,7 +145,7 @@ public class LogEntry
{
return runStatusTimestamp;
}
-
+
/**
* Sets runStatusTimestamp.
*
@@ -150,7 +155,7 @@ public class LogEntry
{
this.runStatusTimestamp = runStatusTimestamp;
}
-
+
/**
* Returns version.
*
@@ -160,7 +165,7 @@ public class LogEntry
{
return version;
}
-
+
/**
* Sets version.
*
@@ -176,13 +181,13 @@ public class LogEntry
{
StringBuilder builder = new StringBuilder();
builder.append("Version:").append(version).append(", Module:").append(moduleName);
- builder.append(", Run status:").append(runStatus).append(", Time stamp:").append(runStatusTimestamp);
+ builder.append(", Run status:").append(runStatus).append(", Time stamp:").append(
+ runStatusTimestamp);
if (runStatus == RunStatus.FAILED && runException != null)
{
builder.append(", Exception:").append(runException);
}
return builder.toString();
}
-
-
+
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/MassUploadFileType.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/MassUploadFileType.java
index 61a8bb26e15..719537ccde6 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/MassUploadFileType.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/MassUploadFileType.java
@@ -17,21 +17,21 @@
package ch.systemsx.cisd.dbmigration;
/**
- * File type enumeration.
- *
+ * File type enumeration.
+ *
* @author Franz-Josef Elmer
*/
public enum MassUploadFileType
{
CSV(".csv"), TSV(".tsv");
-
+
private final String fileType;
private MassUploadFileType(String fileType)
{
this.fileType = fileType;
}
-
+
/**
* Returns the file type string including the '.'.
*/
@@ -41,7 +41,7 @@ public enum MassUploadFileType
}
/**
- * Returns <code>true</code> if the specify file is of this type.
+ * Returns <code>true</code> if the specify file is of this type.
*/
public boolean isOfType(String fileName)
{
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutor.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutor.java
index 146000dc98e..f080d13f2a0 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutor.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutor.java
@@ -40,7 +40,8 @@ import ch.systemsx.cisd.common.logging.LogFactory;
*/
public class SqlScriptExecutor extends JdbcDaoSupport implements ISqlScriptExecutor
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, SqlScriptExecutor.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, SqlScriptExecutor.class);
/** Gives better error messages, but is a lot slower. */
private final boolean singleStepMode;
@@ -51,7 +52,8 @@ public class SqlScriptExecutor extends JdbcDaoSupport implements ISqlScriptExecu
this.singleStepMode = singleStepMode;
}
- public void execute(Script sqlScript, boolean honorSingleStepMode, ISqlScriptExecutionLogger loggerOrNull)
+ public void execute(Script sqlScript, boolean honorSingleStepMode,
+ ISqlScriptExecutionLogger loggerOrNull)
{
if (loggerOrNull != null)
{
@@ -70,12 +72,12 @@ public class SqlScriptExecutor extends JdbcDaoSupport implements ISqlScriptExecu
execute(sqlStatement);
} catch (BadSqlGrammarException ex2)
{
- throw new BadSqlGrammarException(getTask(ex2), lastSqlStatement + ">-->" + sqlStatement
- + "<--<", getCause(ex2));
+ throw new BadSqlGrammarException(getTask(ex2), lastSqlStatement + ">-->"
+ + sqlStatement + "<--<", getCause(ex2));
} catch (UncategorizedSQLException ex2)
{
- throw new UncategorizedSQLException(getTask(ex2), lastSqlStatement + ">-->" + sqlStatement
- + "<--<", getCause(ex2));
+ throw new UncategorizedSQLException(getTask(ex2), lastSqlStatement + ">-->"
+ + sqlStatement + "<--<", getCause(ex2));
}
lastSqlStatement = sqlStatement;
}
@@ -89,8 +91,8 @@ public class SqlScriptExecutor extends JdbcDaoSupport implements ISqlScriptExecu
}
} catch (Throwable t)
{
- operationLog.error("Executing script '" + sqlScript.getName() + "', version " + sqlScript.getVersion()
- + " failed.", t);
+ operationLog.error("Executing script '" + sqlScript.getName() + "', version "
+ + sqlScript.getVersion() + " failed.", t);
if (loggerOrNull != null)
{
loggerOrNull.logFailure(sqlScript, t);
@@ -109,7 +111,7 @@ public class SqlScriptExecutor extends JdbcDaoSupport implements ISqlScriptExecu
{
getJdbcTemplate().execute(script);
}
-
+
private String getTask(BadSqlGrammarException ex)
{
final String marker = "; bad SQL grammar [";
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptProvider.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptProvider.java
index 99cd7224b83..dee4b81952c 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptProvider.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/SqlScriptProvider.java
@@ -40,7 +40,8 @@ public class SqlScriptProvider implements ISqlScriptProvider
private static final String SQL_FILE_TYPE = ".sql";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, SqlScriptProvider.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, SqlScriptProvider.class);
private final String genericScriptFolder;
@@ -142,10 +143,12 @@ public class SqlScriptProvider implements ISqlScriptProvider
private Script tryLoadScript(String scriptName, String scriptVersion, String prefix)
{
- Script script = tryPrimLoadScript(specificScriptFolder + "/" + prefix, scriptName, scriptVersion);
+ Script script =
+ tryPrimLoadScript(specificScriptFolder + "/" + prefix, scriptName, scriptVersion);
if (script == null)
{
- script = tryPrimLoadScript(genericScriptFolder + "/" + prefix, scriptName, scriptVersion);
+ script =
+ tryPrimLoadScript(genericScriptFolder + "/" + prefix, scriptName, scriptVersion);
}
return script;
}
@@ -160,7 +163,8 @@ public class SqlScriptProvider implements ISqlScriptProvider
File file = new File(scriptFolder, scriptName);
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Resource '" + resource + "' could not be found. Trying '" + file.getPath() + "'.");
+ operationLog.debug("Resource '" + resource + "' could not be found. Trying '"
+ + file.getPath() + "'.");
}
if (file.exists() == false)
{
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2AdminDAO.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2AdminDAO.java
index 2a460040380..ae42f4e8d38 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2AdminDAO.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2AdminDAO.java
@@ -51,20 +51,23 @@ public class H2AdminDAO extends SimpleJdbcDaoSupport implements IDatabaseAdminDA
private static final String DROP_ALL_OBJECTS_SQL = "drop all objects;";
private static final String SQL_FILE_TYPE = ".sql";
-
+
private static final Pattern dbDirPartPattern = Pattern.compile(".*:file:(.*?)/.*");
private static final String CREATE_TABLE_DATABASE_VERSION_LOGS_SQL =
- "create table " + DatabaseVersionLogDAO.DB_VERSION_LOG + " (db_version varchar(4) not null, "
+ "create table "
+ + DatabaseVersionLogDAO.DB_VERSION_LOG
+ + " (db_version varchar(4) not null, "
+ "module_name varchar(250), run_status varchar(10), run_status_timestamp timestamp, "
+ "module_code bytea, run_exception bytea);";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, H2AdminDAO.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, H2AdminDAO.class);
private final String databaseName;
-
+
private final String databaseDir;
-
+
private final String databaseURL;
private final ISqlScriptExecutor scriptExecutor;
@@ -80,8 +83,8 @@ public class H2AdminDAO extends SimpleJdbcDaoSupport implements IDatabaseAdminDA
* @param databaseName Name of the database.
* @param databaseURL URL of the database.
*/
- public H2AdminDAO(DataSource dataSource, ISqlScriptExecutor scriptExecutor, IMassUploader massUploader,
- String databaseName, String databaseURL)
+ public H2AdminDAO(DataSource dataSource, ISqlScriptExecutor scriptExecutor,
+ IMassUploader massUploader, String databaseName, String databaseURL)
{
this.scriptExecutor = scriptExecutor;
this.massUploader = massUploader;
@@ -165,7 +168,8 @@ public class H2AdminDAO extends SimpleJdbcDaoSupport implements IDatabaseAdminDA
operationLog.error(message);
throw new ConfigurationFailureException(message);
}
- final Script script = new Script(scriptFile.getPath(), FileUtilities.loadToString(scriptFile), version);
+ final Script script =
+ new Script(scriptFile.getPath(), FileUtilities.loadToString(scriptFile), version);
return script;
}
@@ -176,13 +180,15 @@ public class H2AdminDAO extends SimpleJdbcDaoSupport implements IDatabaseAdminDA
{
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Searching for mass upload files in directory '" + dumpFolder.getAbsolutePath() + "'.");
+ operationLog.debug("Searching for mass upload files in directory '"
+ + dumpFolder.getAbsolutePath() + "'.");
}
String[] csvFiles = dumpFolder.list(new FilenameFilter()
{
public boolean accept(File dir, String name)
{
- return MassUploadFileType.CSV.isOfType(name) || MassUploadFileType.TSV.isOfType(name);
+ return MassUploadFileType.CSV.isOfType(name)
+ || MassUploadFileType.TSV.isOfType(name);
}
});
if (csvFiles == null)
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2MassUploader.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2MassUploader.java
index 41a49c57ccc..0cf45133bd2 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2MassUploader.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2MassUploader.java
@@ -55,7 +55,8 @@ import ch.systemsx.cisd.dbmigration.IMassUploader;
*/
public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploader
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, H2MassUploader.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, H2MassUploader.class);
private final ISequenceNameMapper sequenceNameMapper;
@@ -77,7 +78,8 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
final BitSet isBinaryColumn;
- MassUploadRecord(final File massUploadFile, final String tableName, final BitSet isBinaryColumn)
+ MassUploadRecord(final File massUploadFile, final String tableName,
+ final BitSet isBinaryColumn)
{
this.massUploadFile = massUploadFile;
this.tableName = tableName;
@@ -90,21 +92,26 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
String task = "Get database metadata";
try
{
- final List<MassUploadRecord> massUploadRecords = new ArrayList<MassUploadRecord>(massUploadFiles.length);
+ final List<MassUploadRecord> massUploadRecords =
+ new ArrayList<MassUploadRecord>(massUploadFiles.length);
final DatabaseMetaData dbMetaData = getConnection().getMetaData();
try
{
for (final File massUploadFile : massUploadFiles)
{
final String[] splitName = StringUtils.split(massUploadFile.getName(), "=");
- assert splitName.length == 2 : "Missing '=' in name of file '" + massUploadFile.getName() + "'.";
+ assert splitName.length == 2 : "Missing '=' in name of file '"
+ + massUploadFile.getName() + "'.";
final String tableNameWithExtension = splitName[1];
final boolean tsvFileType = TSV.isOfType(tableNameWithExtension);
- assert tsvFileType : "Not a " + TSV.getFileType() + " file: " + massUploadFile.getName();
+ assert tsvFileType : "Not a " + TSV.getFileType() + " file: "
+ + massUploadFile.getName();
final String tableName =
- tableNameWithExtension.substring(0, tableNameWithExtension.lastIndexOf('.'));
+ tableNameWithExtension.substring(0, tableNameWithExtension
+ .lastIndexOf('.'));
final BitSet isBinaryColumn = findBinaryColumns(dbMetaData, tableName);
- massUploadRecords.add(new MassUploadRecord(massUploadFile, tableName, isBinaryColumn));
+ massUploadRecords.add(new MassUploadRecord(massUploadFile, tableName,
+ isBinaryColumn));
}
} finally
{
@@ -131,8 +138,8 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
{
if (operationLog.isInfoEnabled())
{
- operationLog.info("Perform mass upload of file '" + record.massUploadFile + "' to table '"
- + record.tableName + "'.");
+ operationLog.info("Perform mass upload of file '" + record.massUploadFile
+ + "' to table '" + record.tableName + "'.");
}
final List<String[]> rows = readTSVFile(record.massUploadFile);
final int numberOfRows = rows.size();
@@ -154,7 +161,8 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
return numberOfRows;
}
- public void setValues(final PreparedStatement ps, final int rowNo) throws SQLException
+ public void setValues(final PreparedStatement ps, final int rowNo)
+ throws SQLException
{
for (int colNo = 0; colNo < numberOfColumns; ++colNo)
{
@@ -203,7 +211,8 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
private final List<String[]> readTSVFile(final File tsvFile) throws IOException
{
final List<String[]> result = new ArrayList<String[]>();
- final BufferedReader reader = new BufferedReader(new InputStreamReader(FileUtils.openInputStream(tsvFile)));
+ final BufferedReader reader =
+ new BufferedReader(new InputStreamReader(FileUtils.openInputStream(tsvFile)));
try
{
String line = reader.readLine();
@@ -219,8 +228,8 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
}
if (numberOfColumns != cols.length)
{
- throw new IllegalArgumentException("line '" + line + "', cols found: " + cols.length
- + ", cols expected: " + numberOfColumns);
+ throw new IllegalArgumentException("line '" + line + "', cols found: "
+ + cols.length + ", cols expected: " + numberOfColumns);
}
for (int i = 0; i < cols.length; ++i)
{
@@ -251,19 +260,22 @@ public class H2MassUploader extends SimpleJdbcDaoSupport implements IMassUploade
}
try
{
- final long maxId = getSimpleJdbcTemplate().queryForLong(String.format("select max(id) from %s", tableName));
+ final long maxId =
+ getSimpleJdbcTemplate().queryForLong(
+ String.format("select max(id) from %s", tableName));
final long newSequenceValue = maxId + 1;
if (operationLog.isInfoEnabled())
{
- operationLog.info("Updating sequence " + sequenceName + " for table " + tableName + " to value "
- + newSequenceValue);
+ operationLog.info("Updating sequence " + sequenceName + " for table " + tableName
+ + " to value " + newSequenceValue);
}
getJdbcTemplate().execute(
- String.format("alter sequence %s restart with %d", sequenceName, newSequenceValue));
+ String.format("alter sequence %s restart with %d", sequenceName,
+ newSequenceValue));
} catch (final DataAccessException ex)
{
- operationLog.error("Failed to set new value for sequence '" + sequenceName + "' of table '" + tableName
- + "'.", ex);
+ operationLog.error("Failed to set new value for sequence '" + sequenceName
+ + "' of table '" + tableName + "'.", ex);
}
}
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2StoredProcedures.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2StoredProcedures.java
index ef9beab1906..1d8e022aa4f 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2StoredProcedures.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/h2/H2StoredProcedures.java
@@ -32,18 +32,20 @@ public class H2StoredProcedures
* Renames the sequence <var>oldName</var> into <var>newName</var> ensuring the <code>NEXTVAL()</code> will
* return the right value.
*
- * @return The next value the sequence will deliver.
+ * @return The next value the sequence will deliver.
*/
- public static int renameSequence(Connection conn, String oldName, String newName) throws SQLException
+ public static int renameSequence(Connection conn, String oldName, String newName)
+ throws SQLException
{
- final ResultSet rs = conn.createStatement().executeQuery(String.format("SELECT NEXTVAL('%s')", oldName));
+ final ResultSet rs =
+ conn.createStatement().executeQuery(String.format("SELECT NEXTVAL('%s')", oldName));
if (rs.first() == false)
{
throw new SQLException("Cannot get next value of sequence '" + oldName + "'");
}
final int currSeqVal = rs.getInt(1);
rs.close();
- conn.createStatement().execute("CREATE SEQUENCE " + newName + " START WITH " + currSeqVal);
+ conn.createStatement().execute("CREATE SEQUENCE " + newName + " START WITH " + currSeqVal);
conn.createStatement().execute("DROP SEQUENCE " + oldName);
return currSeqVal;
}
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparator.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparator.java
index c7bba5b658f..580c761ab81 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparator.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparator.java
@@ -50,14 +50,16 @@ public class DumpPreparator
{
private static final Set<String> FILTERED_SCHEMA_LINES =
new LinkedHashSet<String>(Arrays.asList("SET client_encoding = 'UTF8';",
- "COMMENT ON SCHEMA public IS 'Standard public schema';", "CREATE PROCEDURAL LANGUAGE plpgsql;"));
+ "COMMENT ON SCHEMA public IS 'Standard public schema';",
+ "CREATE PROCEDURAL LANGUAGE plpgsql;"));
public static void main(String[] args) throws IOException
{
if (args.length < 1)
{
- System.out.println("Usage: java ch.systemsx.cisd.dbmigration.postgresql.DumpPreparator "
- + "<main folder> [<dump file>]");
+ System.out
+ .println("Usage: java ch.systemsx.cisd.dbmigration.postgresql.DumpPreparator "
+ + "<main folder> [<dump file>]");
System.exit(1);
}
File destination = new File(args[0]);
@@ -104,7 +106,8 @@ public class DumpPreparator
BufferedReader reader = new BufferedReader(dumpReader);
String line;
State state = State.SCHEMA;
- UploadFileManager uploadFileManager = new UploadFileManager(destinationFolder, FILTERED_SCHEMA_LINES);
+ UploadFileManager uploadFileManager =
+ new UploadFileManager(destinationFolder, FILTERED_SCHEMA_LINES);
while ((line = reader.readLine()) != null)
{
if (line.length() != 0 && line.startsWith("--") == false)
@@ -141,7 +144,8 @@ public class DumpPreparator
manager.createUploadFile(matcher.group(1));
} else
{
- throw new IllegalArgumentException("Couldn't extract table name from the following line: " + line);
+ throw new IllegalArgumentException(
+ "Couldn't extract table name from the following line: " + line);
}
return IN_COPY;
}
@@ -236,7 +240,8 @@ public class DumpPreparator
{
if (currentTable == null)
{
- throw new IllegalStateException("No table created to add the following line: " + line);
+ throw new IllegalStateException("No table created to add the following line: "
+ + line);
}
if (line.startsWith("\\."))
{
@@ -250,7 +255,8 @@ public class DumpPreparator
{
String databaseVersion = getDatabaseVersion();
File folder = createDestinationFolder();
- writeTo(folder, "schema-" + databaseVersion + ".sql", Arrays.asList(schemaScript.toString()));
+ writeTo(folder, "schema-" + databaseVersion + ".sql", Arrays.asList(schemaScript
+ .toString()));
for (Table table : tables.values())
{
List<String> rows = table.getRows();
@@ -259,7 +265,8 @@ public class DumpPreparator
writeTo(folder, table.getUploadFileName(), rows);
}
}
- writeTo(folder, "finish-" + databaseVersion + ".sql", Arrays.asList(finishScript.toString()));
+ writeTo(folder, "finish-" + databaseVersion + ".sql", Arrays.asList(finishScript
+ .toString()));
}
private void writeTo(File folder, String fileName, List<String> lines) throws IOException
@@ -307,20 +314,21 @@ public class DumpPreparator
{
if (file.delete() == false)
{
- throw new IllegalStateException("Couldn't delete file '" + file.getAbsolutePath()
- + "' for some unknown reasons.");
+ throw new IllegalStateException("Couldn't delete file '"
+ + file.getAbsolutePath() + "' for some unknown reasons.");
}
}
} else
{
- throw new IllegalStateException("Is not a directory: " + folder.getAbsolutePath());
+ throw new IllegalStateException("Is not a directory: "
+ + folder.getAbsolutePath());
}
} else
{
if (folder.mkdirs() == false)
{
- throw new IllegalStateException("Couldn't create folder '" + folder.getAbsolutePath()
- + "' for some unknown reason.");
+ throw new IllegalStateException("Couldn't create folder '"
+ + folder.getAbsolutePath() + "' for some unknown reason.");
}
}
return folder;
@@ -340,7 +348,8 @@ public class DumpPreparator
Matcher matcher = VERSION_PATTERN.matcher(row);
if (matcher.matches() == false)
{
- throw new IllegalArgumentException("Row does not start with a version number: " + row);
+ throw new IllegalArgumentException("Row does not start with a version number: "
+ + row);
}
String v = matcher.group(1);
if (v.compareTo(result) > 0)
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLAdminDAO.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLAdminDAO.java
index 89ca545f736..9cb1948abcc 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLAdminDAO.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLAdminDAO.java
@@ -52,11 +52,14 @@ public class PostgreSQLAdminDAO extends SimpleJdbcDaoSupport implements IDatabas
+ "alter database %1$s set default_with_oids = off;";
private static final String CREATE_TABLE_DATABASE_VERSION_LOGS_SQL =
- "create table " + DatabaseVersionLogDAO.DB_VERSION_LOG + " (db_version varchar(4) not null, "
- + "module_name varchar(250), run_status varchar(10), run_status_timestamp timestamp, "
- + "module_code bytea, run_exception bytea);";
+ "create table "
+ + DatabaseVersionLogDAO.DB_VERSION_LOG
+ + " (db_version varchar(4) not null, "
+ + "module_name varchar(250), run_status varchar(10), run_status_timestamp timestamp, "
+ + "module_code bytea, run_exception bytea);";
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, PostgreSQLAdminDAO.class);
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, PostgreSQLAdminDAO.class);
private final ISqlScriptExecutor scriptExecutor;
@@ -78,8 +81,8 @@ public class PostgreSQLAdminDAO extends SimpleJdbcDaoSupport implements IDatabas
* @param databaseName Name of the database.
* @param databaseURL URL of the database.
*/
- public PostgreSQLAdminDAO(DataSource dataSource, ISqlScriptExecutor scriptExecutor, IMassUploader massUploader,
- String owner, String databaseName, String databaseURL)
+ public PostgreSQLAdminDAO(DataSource dataSource, ISqlScriptExecutor scriptExecutor,
+ IMassUploader massUploader, String owner, String databaseName, String databaseURL)
{
this.scriptExecutor = scriptExecutor;
this.massUploader = massUploader;
@@ -145,15 +148,19 @@ public class PostgreSQLAdminDAO extends SimpleJdbcDaoSupport implements IDatabas
private void createEmptyDatabase()
{
- operationLog.info("Try to create empty database '" + databaseName + "' with owner '" + owner + "'.");
+ operationLog.info("Try to create empty database '" + databaseName + "' with owner '"
+ + owner + "'.");
try
{
- getJdbcTemplate().execute(String.format(CREATE_DATABASE_SQL_TEMPLATE, databaseName, owner));
+ getJdbcTemplate().execute(
+ String.format(CREATE_DATABASE_SQL_TEMPLATE, databaseName, owner));
} catch (RuntimeException ex)
{
- if (ex instanceof DataAccessException && DBUtilities.isDuplicateDatabaseException((DataAccessException) ex))
+ if (ex instanceof DataAccessException
+ && DBUtilities.isDuplicateDatabaseException((DataAccessException) ex))
{
- operationLog.warn("Cannot create database '" + databaseName + "' since it already exists.");
+ operationLog.warn("Cannot create database '" + databaseName
+ + "' since it already exists.");
} else
{
operationLog.error("Failed to create database '" + databaseName + "'.", ex);
@@ -198,7 +205,8 @@ public class PostgreSQLAdminDAO extends SimpleJdbcDaoSupport implements IDatabas
operationLog.error(message);
throw new ConfigurationFailureException(message);
}
- final Script script = new Script(scriptFile.getPath(), FileUtilities.loadToString(scriptFile), version);
+ final Script script =
+ new Script(scriptFile.getPath(), FileUtilities.loadToString(scriptFile), version);
return script;
}
@@ -209,13 +217,15 @@ public class PostgreSQLAdminDAO extends SimpleJdbcDaoSupport implements IDatabas
{
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Searching for mass upload files in directory '" + dumpFolder.getAbsolutePath() + "'.");
+ operationLog.debug("Searching for mass upload files in directory '"
+ + dumpFolder.getAbsolutePath() + "'.");
}
String[] csvFiles = dumpFolder.list(new FilenameFilter()
{
public boolean accept(File dir, String name)
{
- return MassUploadFileType.CSV.isOfType(name) || MassUploadFileType.TSV.isOfType(name);
+ return MassUploadFileType.CSV.isOfType(name)
+ || MassUploadFileType.TSV.isOfType(name);
}
});
if (csvFiles == null)
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLDAOFactory.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLDAOFactory.java
index 143cda3b204..98b73de749f 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLDAOFactory.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLDAOFactory.java
@@ -61,8 +61,9 @@ public class PostgreSQLDAOFactory implements IDAOFactory
throw new CheckedExceptionTunnel(ex);
}
databaseDAO =
- new PostgreSQLAdminDAO(context.getAdminDataSource(), sqlScriptExecutor, massUploader, context
- .getOwner(), context.getDatabaseName(), context.getDatabaseURL());
+ new PostgreSQLAdminDAO(context.getAdminDataSource(), sqlScriptExecutor,
+ massUploader, context.getOwner(), context.getDatabaseName(), context
+ .getDatabaseURL());
}
public IDatabaseAdminDAO getDatabaseDAO()
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLMassUploader.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLMassUploader.java
index 39232c520f0..223996c646b 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLMassUploader.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/postgresql/PostgreSQLMassUploader.java
@@ -63,15 +63,16 @@ public class PostgreSQLMassUploader extends SimpleJdbcDaoSupport implements IMas
/**
* Creates an instance for the specified data source and sequence mapper.
*/
- public PostgreSQLMassUploader(final DataSource dataSource, final ISequenceNameMapper sequenceNameMapper)
- throws SQLException
+ public PostgreSQLMassUploader(final DataSource dataSource,
+ final ISequenceNameMapper sequenceNameMapper) throws SQLException
{
this.dataSource = dataSource;
this.sequenceNameMapper = sequenceNameMapper;
setDataSource(dataSource);
}
- private final CopyManager getCopyManager() throws SQLException, NoSuchFieldException, IllegalAccessException
+ private final CopyManager getCopyManager() throws SQLException, NoSuchFieldException,
+ IllegalAccessException
{
if (copyManager == null)
{
@@ -98,16 +99,19 @@ public class PostgreSQLMassUploader extends SimpleJdbcDaoSupport implements IMas
try
{
final String[] splitName = StringUtils.split(massUploadFile.getName(), "=");
- assert splitName.length == 2 : "Missing '=' in name of file '" + massUploadFile.getName() + "'.";
+ assert splitName.length == 2 : "Missing '=' in name of file '"
+ + massUploadFile.getName() + "'.";
final String tableNameWithExtension = splitName[1];
final boolean csvFileType = CSV.isOfType(tableNameWithExtension);
final boolean tsvFileType = TSV.isOfType(tableNameWithExtension);
- assert tsvFileType || csvFileType : "Non of expected file types [" + TSV.getFileType() + ", "
- + CSV.getFileType() + "]: " + massUploadFile.getName();
- final String tableName = tableNameWithExtension.substring(0, tableNameWithExtension.lastIndexOf('.'));
+ assert tsvFileType || csvFileType : "Non of expected file types [" + TSV.getFileType()
+ + ", " + CSV.getFileType() + "]: " + massUploadFile.getName();
+ final String tableName =
+ tableNameWithExtension.substring(0, tableNameWithExtension.lastIndexOf('.'));
if (operationLog.isInfoEnabled())
{
- operationLog.info("Perform mass upload of file '" + massUploadFile + "' to table '" + tableName + "'.");
+ operationLog.info("Perform mass upload of file '" + massUploadFile + "' to table '"
+ + tableName + "'.");
}
final InputStream is = new FileInputStream(massUploadFile);
try
@@ -117,7 +121,8 @@ public class PostgreSQLMassUploader extends SimpleJdbcDaoSupport implements IMas
getCopyManager().copyIn(tableName, is);
} else
{
- getCopyManager().copyInQuery("COPY " + tableName + " FROM STDIN WITH CSV HEADER", is);
+ getCopyManager().copyInQuery(
+ "COPY " + tableName + " FROM STDIN WITH CSV HEADER", is);
tables.add(tableName);
}
} finally
@@ -142,26 +147,28 @@ public class PostgreSQLMassUploader extends SimpleJdbcDaoSupport implements IMas
// The result returned by setval is just the value of its second argument.
final long newSequenceValue =
getSimpleJdbcTemplate().queryForLong(
- String.format("select setval('%s', max(id)) from %s", sequenceName, tableName));
+ String.format("select setval('%s', max(id)) from %s", sequenceName,
+ tableName));
if (operationLog.isInfoEnabled())
{
- operationLog.info("Updating sequence " + sequenceName + " for table " + tableName + " to value "
- + newSequenceValue);
+ operationLog.info("Updating sequence " + sequenceName + " for table " + tableName
+ + " to value " + newSequenceValue);
}
} catch (final DataAccessException ex)
{
- operationLog.error("Failed to set new value for sequence '" + sequenceName + "' of table '" + tableName
- + "'.", ex);
+ operationLog.error("Failed to set new value for sequence '" + sequenceName
+ + "' of table '" + tableName + "'.", ex);
}
}
- private final PGConnection getPGConnection() throws SQLException, NoSuchFieldException, IllegalAccessException
+ private final PGConnection getPGConnection() throws SQLException, NoSuchFieldException,
+ IllegalAccessException
{
return getPGConnection(dataSource.getConnection());
}
- private final PGConnection getPGConnection(final Connection conn) throws SQLException, NoSuchFieldException,
- IllegalAccessException
+ private final PGConnection getPGConnection(final Connection conn) throws SQLException,
+ NoSuchFieldException, IllegalAccessException
{
if (conn instanceof PGConnection)
{
@@ -169,7 +176,8 @@ public class PostgreSQLMassUploader extends SimpleJdbcDaoSupport implements IMas
}
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Found connection of type '" + conn.getClass().getCanonicalName() + "'.");
+ operationLog.debug("Found connection of type '" + conn.getClass().getCanonicalName()
+ + "'.");
}
final Field delegateField = getField(conn.getClass(), "_conn");
if (delegateField == null)
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBMigrationEngineTest.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBMigrationEngineTest.java
index 5c747cc32e0..7d0affa9424 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBMigrationEngineTest.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBMigrationEngineTest.java
@@ -126,20 +126,25 @@ public class DBMigrationEngineTest
one(scriptProvider).tryGetSchemaScript(version);
expectSuccessfulExecution(new Script("schema", "schema code", version), true);
one(scriptProvider).tryGetFunctionScript(version);
- expectSuccessfulExecution(new Script("function", "db function code", version), false);
+ expectSuccessfulExecution(new Script("function", "db function code", version),
+ false);
one(scriptProvider).tryGetDataScript(version);
expectSuccessfulExecution(new Script("data", "data code", version), true);
one(adminDAO).getDatabaseName();
will(returnValue("my 2. database"));
}
});
- final DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, true);
+ final DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, true);
migrationEngine.migrateTo(version);
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 2. database' version 042 has been successfully created.", logRecorder.getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 2. database' version 042 has been successfully created.",
+ logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -175,13 +180,17 @@ public class DBMigrationEngineTest
will(returnValue("my 2. database"));
}
});
- final DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, true);
+ final DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, true);
migrationEngine.migrateTo(version);
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 2. database' version 042 has been successfully created.", logRecorder.getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 2. database' version 042 has been successfully created.",
+ logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -190,7 +199,8 @@ public class DBMigrationEngineTest
public void testCreateFromScratchButCouldNotCreateOwner()
{
final String version = "042";
- final BadSqlGrammarException exception = new BadSqlGrammarException("", "", new SQLException("owner"));
+ final BadSqlGrammarException exception =
+ new BadSqlGrammarException("", "", new SQLException("owner"));
context.checking(new MyExpectations()
{
{
@@ -219,9 +229,11 @@ public class DBMigrationEngineTest
{
assertSame(exception, e);
}
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 1. database' does not exist.", logRecorder.getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 1. database' does not exist.", logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -258,12 +270,14 @@ public class DBMigrationEngineTest
will(returnValue("my 2. database"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
migrationEngine.migrateTo(version);
assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 2. database' version 042 has been successfully created.", logRecorder.getLogContent());
+ + "Database 'my 2. database' version 042 has been successfully created.",
+ logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -294,19 +308,22 @@ public class DBMigrationEngineTest
one(scriptProvider).tryGetSchemaScript(version);
expectSuccessfulExecution(new Script("schema", "schema code", version), true);
one(scriptProvider).tryGetFunctionScript(version);
- expectSuccessfulExecution(new Script("function", "db function code", version), false);
+ expectSuccessfulExecution(new Script("function", "db function code", version),
+ false);
one(scriptProvider).tryGetDataScript(version);
will(returnValue(null));
one(adminDAO).getDatabaseName();
will(returnValue("my 2. database"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
migrationEngine.migrateTo(version);
assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 2. database' version 042 has been successfully created.", logRecorder.getLogContent());
+ + "Database 'my 2. database' version 042 has been successfully created.",
+ logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -337,7 +354,8 @@ public class DBMigrationEngineTest
will(returnValue(null));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
String message = "No schema script found for version 042";
try
{
@@ -349,8 +367,8 @@ public class DBMigrationEngineTest
}
assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ "Database 'my 1. database' does not exist." + OSUtilities.LINE_SEPARATOR
- + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + message, logRecorder
- .getLogContent());
+ + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + message,
+ logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -382,13 +400,15 @@ public class DBMigrationEngineTest
will(returnValue("my database URL"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
migrationEngine.migrateTo(version);
- assertEquals("DEBUG OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "No migration needed for database 'my database'. It has the right version (042)."
- + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Using database 'my database URL'",
+ assertEquals(
+ "DEBUG OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "No migration needed for database 'my database'. It has the right version (042)."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Using database 'my database URL'",
logRecorder.getLogContent());
context.assertIsSatisfied();
@@ -421,28 +441,35 @@ public class DBMigrationEngineTest
one(adminDAO).getDatabaseURL();
will(returnValue("my database URL"));
one(scriptProvider).tryGetMigrationScript(fromVersion, "100");
- expectSuccessfulExecution(new Script("m-099-100", "code 099 100", toVersion), true);
+ expectSuccessfulExecution(new Script("m-099-100", "code 099 100", toVersion),
+ true);
one(scriptProvider).tryGetMigrationScript("100", toVersion);
- expectSuccessfulExecution(new Script("m-100-101", "code 100 101", toVersion), true);
+ expectSuccessfulExecution(new Script("m-100-101", "code 100 101", toVersion),
+ true);
one(adminDAO).getDatabaseName();
will(returnValue("my 2. database"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
migrationEngine.migrateTo(toVersion);
String logContent = logRecorder.getLogContent();
logContent = logContent.replaceAll("\\d+ msec", "0 msec");
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Trying to migrate database 'my 1. database' from version 099 to 101." + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Successfully migrated from version 099 to 100 in 0 msec" + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Successfully migrated from version 100 to 101 in 0 msec" + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Database 'my 2. database' successfully migrated from version 099 to 101."
- + OSUtilities.LINE_SEPARATOR
- + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Using database 'my database URL'",
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Trying to migrate database 'my 1. database' from version 099 to 101."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Successfully migrated from version 099 to 100 in 0 msec"
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Successfully migrated from version 100 to 101 in 0 msec"
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + "Database 'my 2. database' successfully migrated from version 099 to 101."
+ + OSUtilities.LINE_SEPARATOR
+ + "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Using database 'my database URL'",
logContent);
context.assertIsSatisfied();
@@ -477,7 +504,8 @@ public class DBMigrationEngineTest
will(returnValue("my 2. database"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
String errorMessage =
"Cannot migrate database 'my 2. database' from version 099 to 100 because of "
@@ -491,9 +519,10 @@ public class DBMigrationEngineTest
assertEquals(errorMessage, e.getMessage());
}
assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Trying to migrate database 'my 1. database' from version 099 to 101." + OSUtilities.LINE_SEPARATOR
- + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + errorMessage, logRecorder
- .getLogContent());
+ + "Trying to migrate database 'my 1. database' from version 099 to 101."
+ + OSUtilities.LINE_SEPARATOR
+ + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + errorMessage, logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -524,9 +553,11 @@ public class DBMigrationEngineTest
will(returnValue("my database"));
}
});
- DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
- String errorMessage = "Cannot revert database 'my database' from version 101 to earlier version 099.";
+ String errorMessage =
+ "Cannot revert database 'my database' from version 101 to earlier version 099.";
try
{
migrationEngine.migrateTo(toVersion);
@@ -535,8 +566,8 @@ public class DBMigrationEngineTest
{
assertEquals(errorMessage, e.getMessage());
}
- assertEquals("ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + errorMessage, logRecorder
- .getLogContent());
+ assertEquals("ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + errorMessage, logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -571,9 +602,11 @@ public class DBMigrationEngineTest
{
assertEquals(message, e.getMessage());
}
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + message, logRecorder
- .getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + message, logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -605,7 +638,9 @@ public class DBMigrationEngineTest
});
DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, true);
- String message = "Inconsistent database: Last creation/migration didn't succeed. Last log entry: " + logEntry;
+ String message =
+ "Inconsistent database: Last creation/migration didn't succeed. Last log entry: "
+ + logEntry;
try
{
migrationEngine.migrateTo("001");
@@ -614,9 +649,11 @@ public class DBMigrationEngineTest
{
assertEquals(message, e.getMessage());
}
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + message, logRecorder
- .getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + message, logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -649,7 +686,9 @@ public class DBMigrationEngineTest
});
DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, true);
- String message = "Inconsistent database: Last creation/migration didn't succeed. Last log entry: " + logEntry;
+ String message =
+ "Inconsistent database: Last creation/migration didn't succeed. Last log entry: "
+ + logEntry;
try
{
migrationEngine.migrateTo("001");
@@ -658,9 +697,11 @@ public class DBMigrationEngineTest
{
assertEquals(message, e.getMessage());
}
- assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
- + OSUtilities.LINE_SEPARATOR + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - " + message, logRecorder
- .getLogContent());
+ assertEquals(
+ "INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - Dropping database."
+ + OSUtilities.LINE_SEPARATOR
+ + "ERROR OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
+ + message, logRecorder.getLogContent());
context.assertIsSatisfied();
}
@@ -697,7 +738,8 @@ public class DBMigrationEngineTest
will(throwException(exception));
}
});
- final DBMigrationEngine migrationEngine = new DBMigrationEngine(daoFactory, scriptProvider, false);
+ final DBMigrationEngine migrationEngine =
+ new DBMigrationEngine(daoFactory, scriptProvider, false);
try
{
@@ -708,7 +750,8 @@ public class DBMigrationEngineTest
assertSame(exception, e);
}
assertEquals("INFO OPERATION.ch.systemsx.cisd.dbmigration.DBMigrationEngine - "
- + "Trying to migrate database 'my database' from version 001 to 002.", logRecorder.getLogContent());
+ + "Trying to migrate database 'my database' from version 001 to 002.", logRecorder
+ .getLogContent());
context.assertIsSatisfied();
}
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBUtilitiesTest.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBUtilitiesTest.java
index bdc5057696b..4d4bb05ea61 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBUtilitiesTest.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/DBUtilitiesTest.java
@@ -61,15 +61,19 @@ public class DBUtilitiesTest
@Test
public void testSplitSqlStatementsOneStatementOnMultipleLines()
{
- assertEquals(Arrays.asList("statement part1 statement part2;", "statement2.1 statement2.2;"), DBUtilities
- .splitSqlStatements("statement part1 \n statement part2 ;\n statement2.1\nstatement2.2 ; "));
+ assertEquals(
+ Arrays.asList("statement part1 statement part2;", "statement2.1 statement2.2;"),
+ DBUtilities
+ .splitSqlStatements("statement part1 \n statement part2 ;\n statement2.1\nstatement2.2 ; "));
}
@Test
public void testSplitSqlStatementsComments()
{
- assertEquals(Arrays.asList("statement1 statement2;"), DBUtilities
- .splitSqlStatements("statement1 -- comment\n -- just comments; bla\n statement2; -- another comment"));
+ assertEquals(
+ Arrays.asList("statement1 statement2;"),
+ DBUtilities
+ .splitSqlStatements("statement1 -- comment\n -- just comments; bla\n statement2; -- another comment"));
}
}
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutorTest.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutorTest.java
index 5f5a3815bfc..9ab0004bc75 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutorTest.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptExecutorTest.java
@@ -43,13 +43,14 @@ public class SqlScriptExecutorTest
private class TestSqlScriptExecutor extends SqlScriptExecutor
{
private final List<String> executions;
-
+
private final Error th;
public TestSqlScriptExecutor(boolean singleStepMode)
{
this(null, singleStepMode);
}
+
public TestSqlScriptExecutor(Error th, boolean singleStepMode)
{
super(new DelegatingDataSource(), singleStepMode);
@@ -90,7 +91,8 @@ public class SqlScriptExecutorTest
scriptExecutor.execute(simpleScript1, true, null);
scriptExecutor.execute(simpleScript2, true, null);
assertEquals(2, scriptExecutor.getExecutions().size());
- assertEquals(Arrays.asList(simpleScriptContent1, simpleScriptContent2), scriptExecutor.getExecutions());
+ assertEquals(Arrays.asList(simpleScriptContent1, simpleScriptContent2), scriptExecutor
+ .getExecutions());
}
@Test
@@ -104,8 +106,8 @@ public class SqlScriptExecutorTest
scriptExecutor.execute(simpleScript1, true, null);
scriptExecutor.execute(simpleScript2, true, null);
assertEquals(3, scriptExecutor.getExecutions().size());
- assertEquals(Arrays.asList("statement1;", "statement2;", "statement3.1 statement3.2;"), scriptExecutor
- .getExecutions());
+ assertEquals(Arrays.asList("statement1;", "statement2;", "statement3.1 statement3.2;"),
+ scriptExecutor.getExecutions());
}
@Test
@@ -119,13 +121,13 @@ public class SqlScriptExecutorTest
final Script simpleScript = new Script("script1", simpleScriptContent, "VERSION");
final ISqlScriptExecutionLogger logger = context.mock(ISqlScriptExecutionLogger.class);
context.checking(new Expectations()
- {
{
- one(logger).logStart(simpleScript);
- one(logger).logSuccess(simpleScript);
- }
-
- });
+ {
+ one(logger).logStart(simpleScript);
+ one(logger).logSuccess(simpleScript);
+ }
+
+ });
scriptExecutor.execute(simpleScript, true, logger);
} finally
{
@@ -137,7 +139,7 @@ public class SqlScriptExecutorTest
{
private static final long serialVersionUID = 1L;
}
-
+
@Test(expectedExceptions = MyError.class)
public void testLoggingScriptThrowsException()
{
@@ -150,13 +152,13 @@ public class SqlScriptExecutorTest
final Script simpleScript = new Script("script1", simpleScriptContent, "VERSION");
final ISqlScriptExecutionLogger logger = context.mock(ISqlScriptExecutionLogger.class);
context.checking(new Expectations()
- {
{
- one(logger).logStart(simpleScript);
- one(logger).logFailure(simpleScript, error);
- }
-
- });
+ {
+ one(logger).logStart(simpleScript);
+ one(logger).logFailure(simpleScript, error);
+ }
+
+ });
scriptExecutor.execute(simpleScript, true, logger);
} finally
{
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptProviderTest.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptProviderTest.java
index d3509490e2f..243b58e0c80 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptProviderTest.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/SqlScriptProviderTest.java
@@ -48,9 +48,11 @@ public class SqlScriptProviderTest
private static final String DB_ENGINE_CODE = "dbengine";
- private static final File TEMP_SCHEMA_SCRIPT_ROOT_FOLDER = new File(TEMPORARY_SCHEMA_SCRIPT_FOLDER_NAME);
+ private static final File TEMP_SCHEMA_SCRIPT_ROOT_FOLDER =
+ new File(TEMPORARY_SCHEMA_SCRIPT_FOLDER_NAME);
- private static final File TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER = new File(TEMP_SCHEMA_SCRIPT_ROOT_FOLDER, "generic");
+ private static final File TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER =
+ new File(TEMP_SCHEMA_SCRIPT_ROOT_FOLDER, "generic");
private static final File TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER =
new File(TEMP_SCHEMA_SCRIPT_ROOT_FOLDER, DB_ENGINE_CODE);
@@ -73,24 +75,29 @@ public class SqlScriptProviderTest
genericSchemaVersionFolder.mkdirs();
specificSchemaVersionFolder.mkdirs();
write(new File(specificSchemaVersionFolder, "schema-" + VERSION + ".sql"), "code: schema");
- write(new File(specificSchemaVersionFolder, "function-" + VERSION + ".sql"), "code: function");
+ write(new File(specificSchemaVersionFolder, "function-" + VERSION + ".sql"),
+ "code: function");
final File migrationFolder = new File(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER, MIGRATION);
migrationFolder.mkdir();
- write(new File(migrationFolder, "migration-" + VERSION + "-" + VERSION2 + ".sql"), "code: migration");
+ write(new File(migrationFolder, "migration-" + VERSION + "-" + VERSION2 + ".sql"),
+ "code: migration");
write(new File(specificSchemaVersionFolder, "data-" + VERSION + ".sql"), "code: data");
- sqlScriptProvider = new SqlScriptProvider(TEMPORARY_SCHEMA_SCRIPT_FOLDER_NAME, DB_ENGINE_CODE);
+ sqlScriptProvider =
+ new SqlScriptProvider(TEMPORARY_SCHEMA_SCRIPT_FOLDER_NAME, DB_ENGINE_CODE);
dumpFile = new File(sqlScriptProvider.getDumpFolder(VERSION), ".DUMP");
}
private File createSpecificSchemaFolder()
{
- final File specificSchemaVersionFolder = new File(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER, VERSION);
+ final File specificSchemaVersionFolder =
+ new File(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER, VERSION);
return specificSchemaVersionFolder;
}
private File createGenericSchemaFolder()
{
- final File specificSchemaVersionFolder = new File(TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER, VERSION);
+ final File specificSchemaVersionFolder =
+ new File(TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER, VERSION);
return specificSchemaVersionFolder;
}
@@ -137,28 +144,30 @@ public class SqlScriptProviderTest
{
final Script script = sqlScriptProvider.tryGetSchemaScript(VERSION);
assertNotNull(script);
- assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/schema-" + VERSION + ".sql",
- script.getName());
+ assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/schema-"
+ + VERSION + ".sql", script.getName());
assertEquals("code: schema", script.getCode().trim());
}
- // Note: we make it dependent on testGetSchemaScript(), because we delete the specific schema script
+ // Note: we make it dependent on testGetSchemaScript(), because we delete the specific schema script
// in this test case and thus testGetSchemaScript() would fail if run after this test case.
@Test(dependsOnMethods = "testGetSchemaScript")
public void testGetGenericSchemaScript()
{
- final File specificSchemaScript = new File(createSpecificSchemaFolder(), "schema-" + VERSION + ".sql");
+ final File specificSchemaScript =
+ new File(createSpecificSchemaFolder(), "schema-" + VERSION + ".sql");
specificSchemaScript.delete();
- final File genericSchemaScript = new File(createGenericSchemaFolder(), "schema-" + VERSION + ".sql");
+ final File genericSchemaScript =
+ new File(createGenericSchemaFolder(), "schema-" + VERSION + ".sql");
final String genericSchemaScriptContent = "code: generic schema";
write(genericSchemaScript, genericSchemaScriptContent);
final Script script = sqlScriptProvider.tryGetSchemaScript(VERSION);
assertNotNull(script);
- assertEquals(TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/schema-" + VERSION + ".sql",
- script.getName());
+ assertEquals(TEMP_SCHEMA_GENERIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/schema-"
+ + VERSION + ".sql", script.getName());
assertEquals(genericSchemaScriptContent, script.getCode().trim());
}
-
+
@Test
public void testGetNonExistingSchemaScript()
{
@@ -170,8 +179,8 @@ public class SqlScriptProviderTest
{
final Script script = sqlScriptProvider.tryGetFunctionScript(VERSION);
assertNotNull(script);
- assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/function-" + VERSION + ".sql",
- script.getName());
+ assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + VERSION + "/function-"
+ + VERSION + ".sql", script.getName());
assertEquals("code: function", script.getCode().trim());
}
@@ -185,7 +194,8 @@ public class SqlScriptProviderTest
public void testGetDataScript()
{
Script script = sqlScriptProvider.tryGetDataScript(VERSION);
- assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER + "/" + VERSION + "/data-" + VERSION + ".sql", script.getName());
+ assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER + "/" + VERSION + "/data-" + VERSION
+ + ".sql", script.getName());
assertEquals("code: data", script.getCode().trim());
}
@@ -199,8 +209,8 @@ public class SqlScriptProviderTest
public void testGetMigrationScript()
{
Script script = sqlScriptProvider.tryGetMigrationScript(VERSION, VERSION2);
- assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + MIGRATION + "/migration-" + VERSION + "-"
- + VERSION2 + ".sql", script.getName());
+ assertEquals(TEMP_SCHEMA_SPECIFIC_SCRIPT_FOLDER.getPath() + "/" + MIGRATION + "/migration-"
+ + VERSION + "-" + VERSION2 + ".sql", script.getName());
assertEquals("code: migration", script.getCode().trim());
}
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/h2/H2TestStoredProcedures.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/h2/H2TestStoredProcedures.java
index f61903f811d..8bda7836748 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/h2/H2TestStoredProcedures.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/h2/H2TestStoredProcedures.java
@@ -35,7 +35,8 @@ public class H2TestStoredProcedures
{
if (actual != expected)
{
- throw new SQLException(String.format("%s: expected:%d, but actual: %d", message, expected, actual));
+ throw new SQLException(String.format("%s: expected:%d, but actual: %d", message,
+ expected, actual));
}
return 0;
}
@@ -46,12 +47,13 @@ public class H2TestStoredProcedures
*
* @return 0.
*/
- public static int assertMinimum(String message, long minExpected, long actual) throws SQLException
+ public static int assertMinimum(String message, long minExpected, long actual)
+ throws SQLException
{
if (actual < minExpected)
{
- throw new SQLException(String.format("%s: Minimum expected:%d, but actual: %d", message, minExpected,
- actual));
+ throw new SQLException(String.format("%s: Minimum expected:%d, but actual: %d",
+ message, minExpected, actual));
}
return 0;
}
diff --git a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparatorTest.java b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparatorTest.java
index 9d45b40a3ea..5fa18308984 100644
--- a/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparatorTest.java
+++ b/dbmigration/sourceTest/java/ch/systemsx/cisd/dbmigration/postgresql/DumpPreparatorTest.java
@@ -27,85 +27,78 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class DumpPreparatorTest
{
private static final File TEST_FOLDER = new File("targets/unit-test-wd/dump-preparator");
-
- private static final String EXAMPLE = "--\n" +
- "-- PostgreSQL database dump\n" +
- "--\n" +
- "\n" +
- "-- Started on 2007-11-28 13:36:10\n" +
- "\n" +
- "SET client_encoding = \'UTF8\';\n" +
- "SET standard_conforming_strings = off;\n" +
- "COMMENT ON SCHEMA public IS 'Standard public schema';\n" +
- "CREATE PROCEDURAL LANGUAGE plpgsql;\n" +
- "--\n" +
- "-- TOC entry 1908 (class 0 OID 326942)\n" +
- "-- Dependencies: 1374\n" +
- "-- Data for Name: data; Type: TABLE DATA; Schema: public; Owner: felmer\n" +
- "--\n" +
- "\n" +
- "COPY data (id, registration_timestamp, obty_id) FROM stdin;\n" +
- "\\.\n" +
- "\n" +
- "\n" +
- "--\n" +
- "-- TOC entry 1890 (class 0 OID 326868)\n" +
- "-- Dependencies: 1356\n" +
- "-- Data for Name: data_types; Type: TABLE DATA; Schema: public; Owner: felmer\n" +
- "--\n" +
- "\n" +
- "COPY data_types (id, code, description) FROM stdin;\n" +
- "1\tVARCHAR\tVariable length character\n" +
- "2\tINTEGER\tInteger\n" +
- "3\tREAL\tReal number, i.e. an inexact, variable-precision numeric type\n" +
- "\\.\n" +
- "\n" +
- "\n" +
- "--\n" +
- "-- TOC entry 1891 (class 0 OID 326873)\n" +
- "-- Dependencies: 1357\n" +
- "-- Data for Name: data_values; Type: TABLE DATA; Schema: public; Owner: felmer\n" +
- "--\n" +
- "\n" +
- "COPY data_values (id, data_id, saco_id, value) FROM stdin;\n" +
- "\\.\n" +
- "\n" +
- "\n" +
- "--\n" +
- "-- TOC entry 1887 (class 0 OID 326837)\n" +
- "-- Dependencies: 1353\n" +
- "-- Data for Name: database_version_logs; Type: TABLE DATA; Schema: public; Owner: felmer\n" +
- "--\n" +
- "\n" +
- "COPY database_version_logs (db_version, module_name, run_status) FROM stdin;\n" +
- "011\tsource/sql/postgresql/010/schema-010.sql\tSUCCESS 2007-11-22 08:46:04.25\n" +
- "010\tsource/sql/postgresql/010/data-010.sql\tSUCCESS 2007-11-22 08:46:04.53\n" +
- "\\.\n" +
- "\n" +
- "\n" +
- "\n" +
- "--\n" +
- "-- TOC entry 1823 (class 2606 OID 327015)\n" +
- "-- Dependencies: 1374 1374\n" +
- "-- Name: data_pk; Type: CONSTRAINT; Schema: public; Owner: felmer; Tablespace: \n" +
- "--\n" +
- "\n" +
- "ALTER TABLE ONLY data\n" +
- " ADD CONSTRAINT data_pk PRIMARY KEY (id);\n" +
- "\n" +
- "-- Completed on 2007-11-28 13:36:13\n" +
- "\n" +
- "--\n" +
- "-- PostgreSQL database dump complete\n" +
- "--\n";
-
+
+ private static final String EXAMPLE =
+ "--\n"
+ + "-- PostgreSQL database dump\n"
+ + "--\n"
+ + "\n"
+ + "-- Started on 2007-11-28 13:36:10\n"
+ + "\n"
+ + "SET client_encoding = \'UTF8\';\n"
+ + "SET standard_conforming_strings = off;\n"
+ + "COMMENT ON SCHEMA public IS 'Standard public schema';\n"
+ + "CREATE PROCEDURAL LANGUAGE plpgsql;\n"
+ + "--\n"
+ + "-- TOC entry 1908 (class 0 OID 326942)\n"
+ + "-- Dependencies: 1374\n"
+ + "-- Data for Name: data; Type: TABLE DATA; Schema: public; Owner: felmer\n"
+ + "--\n"
+ + "\n"
+ + "COPY data (id, registration_timestamp, obty_id) FROM stdin;\n"
+ + "\\.\n"
+ + "\n"
+ + "\n"
+ + "--\n"
+ + "-- TOC entry 1890 (class 0 OID 326868)\n"
+ + "-- Dependencies: 1356\n"
+ + "-- Data for Name: data_types; Type: TABLE DATA; Schema: public; Owner: felmer\n"
+ + "--\n"
+ + "\n"
+ + "COPY data_types (id, code, description) FROM stdin;\n"
+ + "1\tVARCHAR\tVariable length character\n"
+ + "2\tINTEGER\tInteger\n"
+ + "3\tREAL\tReal number, i.e. an inexact, variable-precision numeric type\n"
+ + "\\.\n"
+ + "\n"
+ + "\n"
+ + "--\n"
+ + "-- TOC entry 1891 (class 0 OID 326873)\n"
+ + "-- Dependencies: 1357\n"
+ + "-- Data for Name: data_values; Type: TABLE DATA; Schema: public; Owner: felmer\n"
+ + "--\n"
+ + "\n"
+ + "COPY data_values (id, data_id, saco_id, value) FROM stdin;\n"
+ + "\\.\n"
+ + "\n"
+ + "\n"
+ + "--\n"
+ + "-- TOC entry 1887 (class 0 OID 326837)\n"
+ + "-- Dependencies: 1353\n"
+ + "-- Data for Name: database_version_logs; Type: TABLE DATA; Schema: public; Owner: felmer\n"
+ + "--\n"
+ + "\n"
+ + "COPY database_version_logs (db_version, module_name, run_status) FROM stdin;\n"
+ + "011\tsource/sql/postgresql/010/schema-010.sql\tSUCCESS 2007-11-22 08:46:04.25\n"
+ + "010\tsource/sql/postgresql/010/data-010.sql\tSUCCESS 2007-11-22 08:46:04.53\n"
+ + "\\.\n"
+ + "\n"
+ + "\n"
+ + "\n"
+ + "--\n"
+ + "-- TOC entry 1823 (class 2606 OID 327015)\n"
+ + "-- Dependencies: 1374 1374\n"
+ + "-- Name: data_pk; Type: CONSTRAINT; Schema: public; Owner: felmer; Tablespace: \n"
+ + "--\n" + "\n" + "ALTER TABLE ONLY data\n"
+ + " ADD CONSTRAINT data_pk PRIMARY KEY (id);\n" + "\n"
+ + "-- Completed on 2007-11-28 13:36:13\n" + "\n" + "--\n"
+ + "-- PostgreSQL database dump complete\n" + "--\n";
+
@Test
public void test() throws IOException
{
@@ -117,16 +110,18 @@ public class DumpPreparatorTest
DumpPreparator.createUploadFiles(reader, folder);
assertEquals(true, folder.isDirectory());
- assertEquals("SET standard_conforming_strings = off;\n\n", FileUtilities.loadToString(new File(folder,
- "schema-011.sql")));
+ assertEquals("SET standard_conforming_strings = off;\n\n", FileUtilities
+ .loadToString(new File(folder, "schema-011.sql")));
assertEquals("1\tVARCHAR\tVariable length character\n" + "2\tINTEGER\tInteger\n"
- + "3\tREAL\tReal number, i.e. an inexact, variable-precision numeric type\n", FileUtilities
- .loadToString(new File(folder, "002=data_types.tsv")));
- assertEquals("011\tsource/sql/postgresql/010/schema-010.sql\tSUCCESS 2007-11-22 08:46:04.25\n"
- + "010\tsource/sql/postgresql/010/data-010.sql\tSUCCESS 2007-11-22 08:46:04.53\n", FileUtilities
- .loadToString(new File(folder, "004=database_version_logs.tsv")));
- assertEquals("ALTER TABLE ONLY data\n" + " ADD CONSTRAINT data_pk PRIMARY KEY (id);\n\n", FileUtilities
- .loadToString(new File(folder, "finish-011.sql")));
+ + "3\tREAL\tReal number, i.e. an inexact, variable-precision numeric type\n",
+ FileUtilities.loadToString(new File(folder, "002=data_types.tsv")));
+ assertEquals(
+ "011\tsource/sql/postgresql/010/schema-010.sql\tSUCCESS 2007-11-22 08:46:04.25\n"
+ + "010\tsource/sql/postgresql/010/data-010.sql\tSUCCESS 2007-11-22 08:46:04.53\n",
+ FileUtilities.loadToString(new File(folder, "004=database_version_logs.tsv")));
+ assertEquals(
+ "ALTER TABLE ONLY data\n" + " ADD CONSTRAINT data_pk PRIMARY KEY (id);\n\n",
+ FileUtilities.loadToString(new File(folder, "finish-011.sql")));
assertEquals(4, folder.listFiles().length);
}
}
--
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