From 3b3c1deb52b8d873466fbba9ebf147df7b79e132 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 1 Jun 2012 11:19:40 +0000
Subject: [PATCH] Run Clean-up to add @Override annotations for Java 1.6.
SVN: 25442
---
...bstractDelegatingDataSetInfoExtractor.java | 1 +
.../AbstractDelegatingStorageProcessor.java | 5 ++
...DelegatingStorageProcessorTransaction.java | 1 +
...trationDataSetHandlerForFileBasedUndo.java | 1 +
.../etlserver/AbstractStorageProcessor.java | 4 ++
.../AbstractStorageProcessorTransaction.java | 5 ++
.../AbstractTopLevelDataSetRegistrator.java | 1 +
.../cisd/etlserver/ConfigProvider.java | 3 +
.../DataSetRegistrationAlgorithm.java | 1 +
.../DataSetRegistrationAlgorithmRunner.java | 1 +
.../etlserver/DataSetRegistrationHelper.java | 1 +
.../cisd/etlserver/DataStrategyStore.java | 2 +
.../DefaultDataSetInfoExtractor.java | 1 +
.../etlserver/DefaultStorageProcessor.java | 2 +
.../etlserver/DispatcherStorageProcessor.java | 1 +
.../ch/systemsx/cisd/etlserver/ETLDaemon.java | 7 ++
.../cisd/etlserver/ETLServerPlugin.java | 4 ++
.../cisd/etlserver/FileBasedFile.java | 8 +++
.../cisd/etlserver/FileBasedFileFactory.java | 2 +
.../cisd/etlserver/FileTypeExtractor.java | 1 +
.../etlserver/IdentifiedDataStrategy.java | 3 +
.../cisd/etlserver/NamedDataStrategy.java | 3 +
.../NullStorageProcessorTransaction.java | 6 ++
.../etlserver/SampleRegisteringDropbox.java | 2 +
.../cisd/etlserver/SimpleTypeExtractor.java | 5 ++
.../cisd/etlserver/StandardProcessor.java | 2 +
.../etlserver/TransferredDataSetHandler.java | 11 +++
.../etlserver/api/v1/PutDataSetExecutor.java | 16 +++++
.../api/v1/PutDataSetServerPluginHolder.java | 7 ++
.../v1/PutDataSetTopLevelDataSetHandler.java | 1 +
.../cifex/CifexDataSetInfoExtractor.java | 1 +
.../etlserver/cifex/CifexTypeExtractor.java | 5 ++
.../RegistrationStatus.java | 6 ++
.../SampleAndDataSetRegistrationHandler.java | 2 +
.../SampleAndDataSetRegistrator.java | 1 +
.../SampleDataSetPairParserObjectFactory.java | 1 +
.../etlserver/hdf5/HDF5StorageProcessor.java | 2 +
.../DatabaseBasedDataSetPathsInfoFeeder.java | 2 +
.../cisd/etlserver/path/PathEntryDTO.java | 3 -
.../cisd/etlserver/path/PathInfo.java | 1 +
...thInfoDatabaseChecksumCalculationTask.java | 2 +
.../path/PathInfoDatabaseFeedingTask.java | 6 ++
...DeletionPostProcessingMaintenanceTask.java | 2 +
.../etlserver/plugins/AutoArchiverTask.java | 2 +
.../cisd/etlserver/plugins/DataSetMover.java | 1 +
.../plugins/DummyAutoArchiverPolicy.java | 1 +
.../plugins/ExperimentBasedArchivingTask.java | 4 ++
.../plugins/HierarchicalStorageUpdater.java | 3 +
.../plugins/SegmentedStoreShufflingTask.java | 5 ++
.../etlserver/plugins/SimpleShuffling.java | 3 +
.../TemplateBasedLinkNamingStrategy.java | 2 +
.../ArchivingPostRegistrationTask.java | 5 ++
.../DummyPostRegistrationTaskExecutor.java | 2 +
.../postregistration/EagerShufflingTask.java | 5 ++
.../Hdf5CompressingPostRegistrationTask.java | 5 ++
.../postregistration/NoCleanupTask.java | 1 +
.../postregistration/NotifyingTask.java | 4 ++
.../PostRegistrationMaintenanceTask.java | 4 ++
.../postregistration/TaskExecutor.java | 1 +
...ractDataSetRegistrationDetailsFactory.java | 2 +
...tOmniscientTopLevelDataSetRegistrator.java | 10 ++-
.../ConfiguredOnErrorActionDecision.java | 1 +
.../DataSetRegistrationDetails.java | 5 ++
.../DataSetRegistrationService.java | 5 ++
.../DataSetStorageAlgorithmRunner.java | 2 +
.../DefaultEntityOperationService.java | 1 +
.../JythonTopLevelDataSetHandler.java | 1 +
.../api/v1/impl/AbstractTransactionState.java | 1 +
.../registrator/api/v1/impl/DataSet.java | 25 +++++++
.../api/v1/impl/DataSetImmutable.java | 16 +++++
.../impl/DataSetRegistrationTransaction.java | 28 ++++++++
.../api/v1/impl/DataSetUpdatable.java | 6 ++
.../api/v1/impl/DataSourceQueryService.java | 2 +
.../registrator/api/v1/impl/Experiment.java | 2 +
.../api/v1/impl/ExperimentImmutable.java | 4 ++
.../registrator/api/v1/impl/Material.java | 1 +
.../api/v1/impl/MaterialImmutable.java | 5 ++
.../api/v1/impl/MkdirsCommand.java | 2 +
.../api/v1/impl/MoveFileCommand.java | 2 +
.../api/v1/impl/NewFileCommand.java | 2 +
.../registrator/api/v1/impl/Project.java | 1 +
.../api/v1/impl/ProjectImmutable.java | 3 +
.../api/v1/impl/RollbackStack.java | 5 ++
.../registrator/api/v1/impl/Sample.java | 4 ++
.../api/v1/impl/SampleImmutable.java | 8 +++
.../api/v1/impl/SearchService.java | 9 +++
.../registrator/api/v1/impl/Space.java | 1 +
.../api/v1/impl/SpaceImmutable.java | 3 +
.../v2/JythonTopLevelDataSetHandlerV2.java | 5 ++
.../DataSetStorageRecoveryManager.java | 15 ++++
.../AbstractDataSetInfoExtractorFor3V.java | 1 +
.../utils/PostRegistrationExecutor.java | 1 +
.../utils/PreRegistrationExecutor.java | 1 +
.../utils/PreprocessingExecutor.java | 1 +
.../utils/TabSeparatedValueTable.java | 3 +
.../validation/AbstractValidator.java | 1 +
.../validation/AnyValidatorFactory.java | 2 +
.../validation/DataSetValidator.java | 2 +
.../validation/DataSetValidatorForTSV.java | 2 +
.../DefaultValueValidatorFactory.java | 1 +
.../HeaderBasedValueValidatorFactory.java | 1 +
.../validation/NumericValidatorFactory.java | 1 +
.../validation/RegExBasedValidator.java | 1 +
.../validation/StringValidatorFactory.java | 1 +
.../UniqueGroupValidatorFactory.java | 1 +
.../validation/UniqueValidatorFactory.java | 2 +
.../dss/client/api/cli/AbstractCommand.java | 1 +
.../api/cli/AbstractCommandFactory.java | 1 +
.../dss/client/api/cli/CommandGet.java | 5 ++
.../dss/client/api/cli/CommandHelp.java | 2 +
.../openbis/dss/client/api/cli/CommandLs.java | 2 +
.../dss/client/api/cli/CommandPut.java | 2 +
.../dss/client/api/cli/CommandTestValid.java | 9 +++
.../api/cli/CompositeCommandFactory.java | 3 +
.../dss/client/api/cli/DssCommandFactory.java | 3 +
.../api/gui/AbstractEntityPickerDialog.java | 2 +
.../dss/client/api/gui/AbstractSwingGUI.java | 5 +-
.../api/gui/AddVocabularyTermDialog.java | 5 ++
.../client/api/gui/DataSetMetadataPanel.java | 24 ++++++-
.../client/api/gui/DataSetPickerDialog.java | 6 ++
.../client/api/gui/DataSetPickerPanel.java | 1 +
.../api/gui/DataSetPropertiesPanel.java | 8 ++-
.../client/api/gui/DataSetUploadClient.java | 4 ++
.../api/gui/DataSetUploadOperation.java | 3 +-
.../api/gui/DataSetUploadTableModel.java | 4 ++
.../client/api/gui/ErrorMessageDialog.java | 2 +
.../dss/client/api/gui/ErrorsPanel.java | 8 ++-
.../api/gui/ExperimentPickerDialog.java | 4 ++
.../client/api/gui/ExperimentPickerPanel.java | 1 +
.../client/api/gui/SamplePickerDialog.java | 6 ++
.../dss/client/api/gui/SamplePickerPanel.java | 1 +
.../api/gui/UploadClientSortingUtils.java | 3 +
.../api/gui/UploadStatusTableCellEditor.java | 3 +
.../gui/UploadStatusTableCellRenderer.java | 1 +
.../api/gui/VocabularyTermsComboBoxPanel.java | 3 +
.../client/api/gui/table/BevelArrowIcon.java | 3 +
.../api/gui/table/SortButtonRenderer.java | 1 +
.../table/SortableFilterableTableModel.java | 4 ++
.../gui/tree/FilterableMutableTreeNode.java | 2 +
.../client/api/v1/FileInfoDssDownloader.java | 3 +
.../dss/client/api/v1/impl/DataSetDss.java | 6 ++
.../dss/client/api/v1/impl/DssComponent.java | 15 ++++
.../api/v1/impl/DssServiceRpcFactory.java | 3 +
.../api/v1/impl/OpenbisServiceFacade.java | 34 ++++++++++
.../openbis/dss/generic/DataStoreServer.java | 1 +
...bstractDataSetDescriptionBasedCommand.java | 1 +
.../AbstractDataSetLocationBasedCommand.java | 1 +
.../AbstractDatasetDownloadServlet.java | 2 -
.../generic/server/AbstractDssServiceRpc.java | 6 --
.../dss/generic/server/AutoResolveUtils.java | 1 +
.../server/CIFEXRPCServiceFactory.java | 1 +
.../dss/generic/server/ConfigParameters.java | 2 +
.../server/DataSetCommandExecutor.java | 5 ++
.../dss/generic/server/DataStoreServer.java | 7 +-
.../dss/generic/server/DataStoreService.java | 21 ++++++
.../server/DataStoreServiceLogger.java | 12 ++++
.../DatabaseBasedDataSetPathInfoProvider.java | 10 +++
.../server/DatasetSessionAuthorizer.java | 5 ++
.../dss/generic/server/DeletionCommand.java | 3 +
.../DssServiceRpcAuthorizationAdvisor.java | 1 +
.../server/EncapsulatedOpenBISService.java | 68 +++++++++++++++++++
.../dss/generic/server/HTMLErrorRenderer.java | 2 +
.../LocalDataSetFileOperationsExcecutor.java | 9 +++
.../server/PlainTextRendererFactory.java | 11 +++
.../server/ProcessDatasetsCommand.java | 7 ++
.../RemoteDataSetFileOperationsExecutor.java | 9 +++
.../dss/generic/server/ShareIdManager.java | 8 +++
.../server/SimpleHTMLDirectoryRenderer.java | 6 ++
.../server/SimpleHTMLRendererFactory.java | 3 +
.../dss/generic/server/StreamRepository.java | 3 +
.../dss/generic/server/UploadingCommand.java | 8 +++
.../server/api/v1/DssServiceRpcGeneric.java | 33 ++++++++-
.../api/v1/DssServiceRpcGenericLogger.java | 12 ++++
.../generic/server/ftp/DSSFileSystemView.java | 7 ++
.../server/ftp/FtpPathResolverRegistry.java | 22 ++++++
.../dss/generic/server/ftp/FtpServer.java | 27 ++++++++
.../dss/generic/server/ftp/FtpUser.java | 8 +++
.../generic/server/ftp/FtpUserManager.java | 8 +++
.../server/ftp/resolver/AbstractFtpFile.java | 16 +++++
.../ftp/resolver/AbstractFtpFolder.java | 5 ++
.../resolver/ExperimentFolderResolver.java | 2 +
.../server/ftp/resolver/FtpFileImpl.java | 5 ++
.../ftp/resolver/ProjectFolderResolver.java | 2 +
.../ftp/resolver/RootFolderResolver.java | 2 +
.../ftp/resolver/SpaceFolderResolver.java | 2 +
.../TemplateBasedDataSetResourceResolver.java | 4 ++
.../graph/AbstractTabularDataGraph.java | 2 +
.../generic/server/graph/HeatmapDataset.java | 15 ++++
...bularDataGraphCollectionConfiguration.java | 4 ++
.../server/graph/TabularDataHistogram.java | 1 +
.../server/graph/TabularDataScatterplot.java | 1 +
.../graph/TabularDataTickUnitSource.java | 3 +
.../OpenBISAuthenticationAdvisor.java | 2 +
.../OpenBISAuthenticationInterceptor.java | 1 +
...asedImageAnalysisGraphReportingPlugin.java | 1 +
.../DatasetModificationReportingPlugin.java | 1 +
.../plugins/demo/DemoOverviewPlugin.java | 1 +
.../plugins/demo/DemoProcessingPlugin.java | 2 +
.../plugins/demo/DemoReportingPlugin.java | 2 +
.../server/plugins/jython/EmailSender.java | 5 ++
...asedAggregationServiceReportingPlugin.java | 2 +
.../jython/JythonBasedPluginUtils.java | 18 +++++
.../jython/JythonBasedProcessingPlugin.java | 1 +
.../jython/JythonBasedReportingPlugin.java | 2 +
.../server/plugins/jython/MailService.java | 4 ++
.../jython/PluginScriptRunnerFactory.java | 9 +++
.../ReportingBasedProcessingPlugin.java | 1 +
.../SimpleTableModelBuilderAdaptor.java | 13 ++++
...ractAggregationServiceReportingPlugin.java | 3 +
.../AbstractArchiverProcessingPlugin.java | 5 ++
.../AbstractDropboxProcessingPlugin.java | 1 +
.../AbstractDssLinkReportingPlugin.java | 3 +
.../AbstractTableModelReportingPlugin.java | 3 +
.../server/plugins/standard/Copier.java | 2 +
.../DataSetFileOperationsManager.java | 10 +++
.../DecoratingTableModelReportingPlugin.java | 1 +
.../standard/EntityLinksDecorator.java | 5 ++
.../GenericDssLinkReportingPlugin.java | 1 +
.../standard/HighWaterMarkChecker.java | 1 +
.../MergedColumnDataReportingPlugin.java | 1 +
.../MergedRowDataReportingPlugin.java | 1 +
.../standard/RsyncArchiveCopierFactory.java | 1 +
.../plugins/standard/RsyncArchiver.java | 1 +
.../plugins/standard/RsyncCopierFactory.java | 1 +
.../standard/SshCommandExecutorFactory.java | 1 +
.../standard/TSVViewReportingPlugin.java | 1 +
.../plugins/tasks/PluginTaskProvider.java | 1 +
.../generic/shared/AbstractShareFinder.java | 1 +
.../generic/shared/ArchiverTaskContext.java | 1 +
.../shared/DataSetDirectoryProvider.java | 4 ++
.../generic/shared/DataSourceProvider.java | 2 +
.../shared/DefaultDataSourceFactory.java | 1 +
.../shared/ExperimentBasedShareFinder.java | 1 +
.../shared/HierarchicalContentProvider.java | 5 ++
.../shared/PathInfoDatabaseVersionHolder.java | 1 +
.../QueueingDataSetStatusUpdaterService.java | 2 +
.../shared/SimpleDataSourceFactory.java | 1 +
.../dss/generic/shared/SpeedChecker.java | 3 +
.../shared/SpeedOptimizedShareFinder.java | 1 +
.../generic/shared/StandardShareFinder.java | 2 +
.../AbstractDataSetAccessPredicate.java | 1 +
.../DataSetCodeStringPredicate.java | 1 +
.../DataSetFileDTOPredicate.java | 1 +
.../DssSessionAuthorizationHolder.java | 5 ++
.../authorization/NewDataSetPredicate.java | 2 +
...hInfoProviderBasedHierarchicalContent.java | 15 ++++
.../utils/AbstractDatasetDropboxHandler.java | 3 +
.../shared/utils/CorePluginsInjector.java | 2 +
.../shared/utils/CsvFileReaderHelper.java | 4 ++
.../shared/utils/DatasetFileLines.java | 3 +
.../dss/generic/shared/utils/ImageUtil.java | 4 ++
...stgresPlusFileSystemFreeSpaceProvider.java | 1 +
.../shared/utils/SegmentedStoreUtils.java | 3 +
.../dss/generic/shared/utils/Share.java | 1 +
...stractStorageProcessorWithDropboxTest.java | 2 +-
.../DataSetRegistrationAlgorithmTest.java | 1 +
.../DefaultDataSetInfoExtractorTest.java | 2 +-
.../DefaultStorageProcessorTest.java | 5 ++
.../TransferredDataSetHandlerTest.java | 4 +-
.../PutDataSetTopLevelDataSetHandlerTest.java | 2 +
...mpleAndDatasetRegistrationHandlerTest.java | 1 +
.../AbstractHDF5StorageProcessorTest.java | 1 +
.../etlserver/path/IPathsInfoDAOTest.java | 8 +++
...foDatabaseChecksumCalculationTaskTest.java | 1 +
.../ExperimentBasedArchivingTaskTest.java | 1 +
.../HierarchicalStorageUpdaterTest.java | 1 +
.../SegmentedStoreShufflingTaskTest.java | 2 +
.../SimpleShufflingShareFinderTest.java | 1 +
.../plugins/SimpleShufflingTest.java | 1 +
.../EagerShufflingTaskTest.java | 1 +
.../PostRegistrationMaintenanceTaskTest.java | 3 +
.../AbstractJythonDataSetHandlerTest.java | 11 +++
.../DataSetStorageRollbackerTest.java | 1 +
.../JythonDropboxRecoveryTest.java | 2 +
...opLevelDataSetRegistratorRollbackTest.java | 1 +
.../JythonTopLevelDataSetRegistratorTest.java | 5 ++
.../registrator/TestingDataSetHandler.java | 1 +
.../registrator/TestingDataSetHandlerV2.java | 1 +
.../DataSetRegistrationTransactionTest.java | 15 ++++
.../api/v1/impl/RollbackStackTest.java | 2 +
.../utils/PreRegistrationExecutorTest.java | 1 +
.../DataSetValidatorForTSVTest.java | 2 +
.../validation/DataSetValidatorTest.java | 2 +
.../NumericValidatorFactoryTest.java | 6 +-
.../StringValidatorFactoryTest.java | 6 +-
.../systemtests/DssComponentTest.java | 2 +
.../systemtests/OpenbisServiceFacadeTest.java | 3 +
.../systemtests/RmiConversationTest.java | 8 +++
.../dss/client/api/cli/CommandPutTest.java | 2 +
.../client/api/v1/impl/DssComponentTest.java | 12 ++++
...abaseBasedDataSetPathInfoProviderTest.java | 1 +
.../server/DatasetDownloadServletTest.java | 18 ++---
.../generic/server/DssServiceRpcV1Test.java | 1 +
.../server/ProcessDatasetsCommandTest.java | 2 +
.../generic/server/ShareIdManagerTest.java | 4 ++
.../generic/server/StreamRepositoryTest.java | 2 +
.../generic/server/UploadingCommandTest.java | 14 ++++
.../dss/generic/server/ftp/CacheTest.java | 1 +
.../server/ftp/DSSFileSystemViewTest.java | 5 ++
...plateBasedDataSetResourceResolverTest.java | 5 ++
.../OpenBISAuthenticationInterceptorTest.java | 2 +
.../AbstractArchiverProcessingPluginTest.java | 5 ++
.../ExampleAggregationServicePlugin.java | 1 +
.../MockDataSetDirectoryProvider.java | 4 ++
.../plugins/standard/RsyncArchiverTest.java | 19 ++++++
.../tasks/PluginTaskParametersTest.java | 5 ++
.../shared/AbstractIShareFinderTestCase.java | 1 +
.../HierarchicalContentProviderTest.java | 7 ++
.../generic/shared/ProxyShareIdManager.java | 8 +++
.../generic/shared/SimpleShareFinderTest.java | 1 +
.../generic/shared/utils/ImageUtilTest.java | 13 ++++
.../shared/utils/SegmentedStoreUtilsTest.java | 1 +
312 files changed, 1349 insertions(+), 46 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingDataSetInfoExtractor.java
index 9f12e6570da..e4934d8798e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingDataSetInfoExtractor.java
@@ -94,6 +94,7 @@ abstract public class AbstractDelegatingDataSetInfoExtractor implements IDataSet
// delegation
//
+ @Override
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
index 9abd0315b52..8efb9e568cf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
@@ -91,27 +91,32 @@ abstract public class AbstractDelegatingStorageProcessor implements IStorageProc
// delegation
//
+ @Override
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters transactionParameters)
{
return delegate.createTransaction(transactionParameters);
}
+ @Override
public StorageFormat getStorageFormat()
{
return delegate.getStorageFormat();
}
+ @Override
public File getStoreRootDirectory()
{
return delegate.getStoreRootDirectory();
}
+ @Override
public void setStoreRootDirectory(File storeRootDirectory)
{
delegate.setStoreRootDirectory(storeRootDirectory);
}
+ @Override
public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
{
return delegate.getDefaultUnstoreDataAction(exception);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorTransaction.java
index 704560f0f22..d57f4bf3c9a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorTransaction.java
@@ -41,6 +41,7 @@ public abstract class AbstractDelegatingStorageProcessorTransaction extends
this.nestedTransaction = transaction;
}
+ @Override
public File tryGetProprietaryData()
{
return nestedTransaction.tryGetProprietaryData();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractPostRegistrationDataSetHandlerForFileBasedUndo.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractPostRegistrationDataSetHandlerForFileBasedUndo.java
index 81dd59e9236..cbd31725212 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractPostRegistrationDataSetHandlerForFileBasedUndo.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractPostRegistrationDataSetHandlerForFileBasedUndo.java
@@ -71,6 +71,7 @@ public abstract class AbstractPostRegistrationDataSetHandlerForFileBasedUndo imp
/**
* Deletes all files added by {@link #addFileForUndo(File)}.
*/
+ @Override
public void undoLastOperation()
{
if (operationLog.isInfoEnabled())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessor.java
index 66eabd25814..b4d30113def 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessor.java
@@ -72,11 +72,13 @@ public abstract class AbstractStorageProcessor implements IStorageProcessorTrans
// IStorageProcessorTransactional
//
+ @Override
public final File getStoreRootDirectory()
{
return storeRootDir;
}
+ @Override
public final void setStoreRootDirectory(final File storeRootDirectory)
{
this.storeRootDir = storeRootDirectory;
@@ -85,6 +87,7 @@ public abstract class AbstractStorageProcessor implements IStorageProcessorTrans
/**
* @see IStorageProcessorTransactional#getStorageFormat()
*/
+ @Override
public StorageFormat getStorageFormat()
{
return StorageFormat.PROPRIETARY;
@@ -107,6 +110,7 @@ public abstract class AbstractStorageProcessor implements IStorageProcessorTrans
return false;
}
+ @Override
public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
{
return moveUnregisteredDatasetsToErrorDir ? UnstoreDataAction.MOVE_TO_ERROR
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorTransaction.java
index 86ff1f9f7c0..6bee3ecf303 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorTransaction.java
@@ -71,6 +71,7 @@ public abstract class AbstractStorageProcessorTransaction implements IStoragePro
this.rootDirectory = parameters.getRootDir();
}
+ @Override
public final void storeData(final ITypeExtractor typeExtractor, final IMailClient mailClient,
final File incomingDataSetOverride)
{
@@ -80,6 +81,7 @@ public abstract class AbstractStorageProcessorTransaction implements IStoragePro
state = TransactionState.STORED;
}
+ @Override
public final void commit()
{
ensureState("commit", TransactionState.STORED);
@@ -87,6 +89,7 @@ public abstract class AbstractStorageProcessorTransaction implements IStoragePro
state = TransactionState.COMMITTED;
}
+ @Override
public final UnstoreDataAction rollback(Throwable ex)
{
ensureState("rollback", TransactionState.INITIAL, TransactionState.STORED);
@@ -98,11 +101,13 @@ public abstract class AbstractStorageProcessorTransaction implements IStoragePro
}
+ @Override
public final File getStoredDataDirectory()
{
return storedDataDirectory;
}
+ @Override
public final void setStoredDataDirectory(File dir)
{
storedDataDirectory = dir;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
index 4ffe5e28286..de622cfc999 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
@@ -30,6 +30,7 @@ public abstract class AbstractTopLevelDataSetRegistrator implements ITopLevelDat
this.globalState = globalState;
}
+ @Override
public TopLevelDataSetRegistratorGlobalState getGlobalState()
{
return globalState;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ConfigProvider.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ConfigProvider.java
index 5153a1f8559..e20631c7772 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ConfigProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ConfigProvider.java
@@ -47,16 +47,19 @@ public class ConfigProvider implements IConfigProvider
this.properties = properties;
}
+ @Override
public File getStoreRoot()
{
return DssPropertyParametersUtil.getStoreRootDir(properties);
}
+ @Override
public String getDataStoreCode()
{
return DssPropertyParametersUtil.getDataStoreCode(properties);
}
+ @Override
public String getOpenBisServerUrl()
{
return DssPropertyParametersUtil.getOpenBisServerUrl(properties);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
index a1a4d4e4058..22f39b4bae2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
@@ -370,6 +370,7 @@ public class DataSetRegistrationAlgorithm
dataSetInformation = state.dataSetInformation;
}
+ @Override
public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
openBisService.registerDataSet(dataSetInformation, data);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
index 2de77e9232d..30e3eea3ac3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmRunner.java
@@ -36,6 +36,7 @@ public class DataSetRegistrationAlgorithmRunner
public static final class NoOpDelegate implements IDataSetRegistrationAlgorithmRunnerDelegate
{
+ @Override
public void didNotIdentifyDataSet()
{
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationHelper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationHelper.java
index ba1352ca257..15f33fffb40 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationHelper.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationHelper.java
@@ -187,6 +187,7 @@ public abstract class DataSetRegistrationHelper implements
}
}
+ @Override
public void rollback(DataSetRegistrationAlgorithm algo, Throwable ex)
{
rollback(ex);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
index a1e24e5e915..27976a4215c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
@@ -105,11 +105,13 @@ public final class DataStrategyStore implements IDataStrategyStore
// IDataStrategyStore
//
+ @Override
public IDataStoreStrategy getDataStoreStrategy(DataStoreStrategyKey key)
{
return dataStoreStrategies.get(key);
}
+ @Override
public IDataStoreStrategy getDataStoreStrategy(final DataSetInformation dataSetInfo,
final File incomingDataSetPath)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
index ee4c7287ef9..57570f6502e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
@@ -308,6 +308,7 @@ public class DefaultDataSetInfoExtractor extends AbstractDataSetInfoExtractor
// ICodeExtractor
//
+ @Override
public DataSetInformation getDataSetInformation(final File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws EnvironmentFailureException,
UserFailureException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
index 29f20fc6535..05e94a5f424 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
@@ -68,6 +68,7 @@ public class DefaultStorageProcessor extends AbstractStorageProcessor
// AbstractStorageProcessor
//
+ @Override
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
@@ -157,6 +158,7 @@ public class DefaultStorageProcessor extends AbstractStorageProcessor
* returns the only file or directory which is expected to be found inside original
* directory
*/
+ @Override
public File tryGetProprietaryData()
{
File originalDir = getOriginalDirectory(storedDataDirectory);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DispatcherStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DispatcherStorageProcessor.java
index 2c5c882f277..e93364426d6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DispatcherStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DispatcherStorageProcessor.java
@@ -118,6 +118,7 @@ public class DispatcherStorageProcessor extends AbstractStorageProcessor
// --- dispatcher implementation
+ @Override
public IStorageProcessorTransaction createTransaction(final StorageProcessorTransactionParameters transactionParameters)
{
final IStorageProcessorTransactional storageProcessor =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
index 5816411ccd1..bb428d3778e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
@@ -476,6 +476,7 @@ public final class ETLDaemon
parameters.getQuietPeriodMillis(), ignoredErrorCountBeforeNotification);
return new FileFilter()
{
+ @Override
public boolean accept(File pathname)
{
assert pathname.getParentFile().getAbsolutePath()
@@ -493,6 +494,7 @@ public final class ETLDaemon
{
Runtime.getRuntime().addShutdownHook(new Thread(new Runnable()
{
+ @Override
public void run()
{
try
@@ -584,21 +586,25 @@ public final class ETLDaemon
return new IDirectoryScanningHandler()
{
+ @Override
public void init(IScannedStore scannedStore)
{
// do nothing
}
+ @Override
public void beforeHandle(IScannedStore scannedStore)
{
// do nothing
}
+ @Override
public Status finishItemHandle(IScannedStore scannedStore, StoreItem storeItem)
{
return Status.OK;
}
+ @Override
public HandleInstruction mayHandle(IScannedStore scannedStore, StoreItem storeItem)
{
return HandleInstruction.PROCESS;
@@ -745,6 +751,7 @@ public final class ETLDaemon
{
exitHandler = new IExitHandler()
{
+ @Override
public void exit(int exitCode)
{
throw new AssertionError("Unexpected exit: " + exitCode);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPlugin.java
index 48d1c30e96a..7620d1e10ae 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPlugin.java
@@ -51,21 +51,25 @@ public class ETLServerPlugin implements IETLServerPlugin
// IETLServerPlugin
//
+ @Override
public final IDataSetInfoExtractor getDataSetInfoExtractor()
{
return codeExtractor;
}
+ @Override
public final ITypeExtractor getTypeExtractor()
{
return typeExtractor;
}
+ @Override
public final IStorageProcessorTransactional getStorageProcessor()
{
return storageProcessor;
}
+ @Override
public IDataSetHandler getDataSetHandler(IDataSetHandler primaryDataSetHandler,
IEncapsulatedOpenBISService openbisService)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFile.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFile.java
index 755d153e959..11283f25cf6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFile.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFile.java
@@ -57,11 +57,13 @@ public class FileBasedFile implements IFile
this.hardLinkCopierOrNull = hardLinkCopierOrNull;
}
+ @Override
public void copyFrom(final File sourceFile)
{
copy(sourceFile, file);
}
+ @Override
public void copyTo(final File destinationFile)
{
copy(file, destinationFile);
@@ -136,6 +138,7 @@ public class FileBasedFile implements IFile
}
+ @Override
public void delete()
{
if (FileOperations.getMonitoredInstanceForCurrentThread().removeRecursivelyQueueing(file))
@@ -145,11 +148,13 @@ public class FileBasedFile implements IFile
}
}
+ @Override
public String getAbsolutePath()
{
return file.getAbsolutePath();
}
+ @Override
public byte[] read()
{
try
@@ -161,6 +166,7 @@ public class FileBasedFile implements IFile
}
}
+ @Override
public void write(final byte[] data)
{
try
@@ -172,6 +178,7 @@ public class FileBasedFile implements IFile
}
}
+ @Override
public final void check() throws EnvironmentFailureException, ConfigurationFailureException
{
final String response = FileUtilities.checkDirectoryFullyAccessible(file, "");
@@ -181,6 +188,7 @@ public class FileBasedFile implements IFile
}
}
+ @Override
public boolean isRemote()
{
return false;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFileFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFileFactory.java
index 659b123cedb..556fbd7a134 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFileFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileBasedFileFactory.java
@@ -79,6 +79,7 @@ public class FileBasedFileFactory implements IFileFactory
// IFileFactory
//
+ @Override
public final IFile create(final String path)
{
assert path != null : "Unspecified path.";
@@ -86,6 +87,7 @@ public class FileBasedFileFactory implements IFileFactory
return wrap(file);
}
+ @Override
public final IFile create(final IFile baseDir, final String relativePath)
{
assert baseDir != null : "Unspecified base directory.";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileTypeExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileTypeExtractor.java
index 6fab426a538..7b60062e1d0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileTypeExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/FileTypeExtractor.java
@@ -110,6 +110,7 @@ public class FileTypeExtractor implements IFileFormatTypeExtractor
return result;
}
+ @Override
public final FileFormatType getFileFormatType(final File incomingDataSetPath)
{
String fileType;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
index 8d6fdb752c4..35c1d45eb6a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
@@ -73,11 +73,13 @@ public final class IdentifiedDataStrategy implements IDataStoreStrategy
// IDataStoreStrategy
//
+ @Override
public final DataStoreStrategyKey getKey()
{
return DataStoreStrategyKey.IDENTIFIED;
}
+ @Override
public final File getBaseDirectory(final File storeRoot, final DataSetInformation dataSetInfo,
final DataSetType dataSetType)
{
@@ -98,6 +100,7 @@ public final class IdentifiedDataStrategy implements IDataStoreStrategy
return baseDirectory;
}
+ @Override
public final File getTargetPath(final File baseDirectory, final File incomingDataSetPath)
throws IllegalStateException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
index 3e6bc69db8d..4868743378a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
@@ -72,11 +72,13 @@ final class NamedDataStrategy implements IDataStoreStrategy
// IDataStoreStrategy
//
+ @Override
public final DataStoreStrategyKey getKey()
{
return key;
}
+ @Override
public final File getBaseDirectory(final File baseDirectory,
final DataSetInformation dataSetInfo, final DataSetType dataSetType)
{
@@ -87,6 +89,7 @@ final class NamedDataStrategy implements IDataStoreStrategy
.createDataSetTypeDirectory(dataSetType));
}
+ @Override
public final File getTargetPath(final File baseDirectory, final File incomingDataSetPath)
{
assertBaseDirectory(baseDirectory);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NullStorageProcessorTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NullStorageProcessorTransaction.java
index e924962811c..fffb9c629d7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NullStorageProcessorTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NullStorageProcessorTransaction.java
@@ -32,29 +32,35 @@ public class NullStorageProcessorTransaction implements IStorageProcessorTransac
private static final long serialVersionUID = 1L;
+ @Override
public void storeData(ITypeExtractor typeExtractor, IMailClient mailClient,
File incomingDataSetDirectory)
{
}
+ @Override
public void commit()
{
}
+ @Override
public UnstoreDataAction rollback(Throwable exception)
{
return null;
}
+ @Override
public File getStoredDataDirectory()
{
return null;
}
+ @Override
public void setStoredDataDirectory(File folder)
{
}
+ @Override
public File tryGetProprietaryData()
{
return null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java
index f0690ef2a3b..65a92880412 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java
@@ -86,6 +86,7 @@ public class SampleRegisteringDropbox implements IDataSetHandler
true);
}
+ @Override
public List<DataSetInformation> handleDataSet(File file)
{
File marker = new File(file.getParent(), createErrorMarkerFileName(file));
@@ -209,6 +210,7 @@ public class SampleRegisteringDropbox implements IDataSetHandler
return new SampleCodeGenerator()
{
+ @Override
public List<String> generateCodes(int size)
{
return service.generateCodes(samplePrefix, size);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/SimpleTypeExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SimpleTypeExtractor.java
index 706ebe9ceaa..a5f8a2b5ff7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/SimpleTypeExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SimpleTypeExtractor.java
@@ -71,26 +71,31 @@ public class SimpleTypeExtractor implements ITypeExtractor
// IProcedureAndDataTypeExtractor
//
+ @Override
public final FileFormatType getFileFormatType(final File incomingDataSetPath)
{
return fileFormatType;
}
+ @Override
public final LocatorType getLocatorType(final File incomingDataSetPath)
{
return locatorType;
}
+ @Override
public final DataSetType getDataSetType(final File incomingDataSetPath)
{
return dataSetType;
}
+ @Override
public String getProcessorType(File incomingDataSetPath)
{
return processorType;
}
+ @Override
public boolean isMeasuredData(File incomingDataSetPath)
{
return measured;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/StandardProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/StandardProcessor.java
index ac4f51dd18e..a1c92b2a331 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/StandardProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/StandardProcessor.java
@@ -130,11 +130,13 @@ final class StandardProcessor implements IProcessor
// IProcessor
//
+ @Override
public final StorageFormat getRequiredInputDataFormat()
{
return inputDataFormat;
}
+ @Override
public final void initiateProcessing(final ProcessingInstructionDTO instruction,
final DataSetInformation dataSetInformation, final File dataSet)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index a3a45ba1fb9..9231190f736 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -113,6 +113,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
{
private boolean didNotIdentifyDataSet = false;
+ @Override
public void didNotIdentifyDataSet()
{
didNotIdentifyDataSet = true;
@@ -186,6 +187,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
/**
* Returns the lock one needs to hold before one interrupts a data set registration.
*/
+ @Override
public Lock getRegistrationLock()
{
return registrationLock;
@@ -195,6 +197,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
// IPathHandler
//
+ @Override
public final void handle(final File file)
{
if (stopped)
@@ -204,6 +207,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
dataSetHandler.handleDataSet(file);
}
+ @Override
public void handle(File file, DataSetInformation callerDataSetInformation,
ITopLevelDataSetRegistratorDelegate delegate)
{
@@ -228,12 +232,14 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
}
}
+ @Override
public List<DataSetInformation> handleDataSet(final File dataSet)
{
final DataSetRegistrationHelper registrationHelper = createRegistrationHelper(dataSet);
return new DataSetRegistrationAlgorithmRunner(registrationHelper).runAlgorithm();
}
+ @Override
public List<DataSetInformation> handleDataSet(final File dataSet,
DataSetInformation dataSetInformation,
DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator registrator)
@@ -245,6 +251,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
return new DataSetRegistrationAlgorithmRunner(registrationHelper).runAlgorithm();
}
+ @Override
public boolean isStopped()
{
return stopped;
@@ -254,12 +261,14 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
// ISelfTestable
//
+ @Override
public final void check() throws ConfigurationFailureException, EnvironmentFailureException
{
new TopLevelDataSetChecker(operationLog, storeRootDirectoryHolder, fileOperations)
.runCheck();
}
+ @Override
public boolean isRemote()
{
return true;
@@ -543,6 +552,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
}
}
+ @Override
public File getStoreRootDir()
{
return getGlobalState().getStoreRootDir();
@@ -551,6 +561,7 @@ public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegi
/**
* Any path can be added to faulty paths as far as we are concerned.
*/
+ @Override
public boolean shouldNotAddToFaultyPathsOrNull(File storeItem)
{
return false;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index eaea293bd95..7543eb1b51d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -162,11 +162,13 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
}
+ @Override
public List<DataSetInformation> handleDataSet(File dataSet)
{
return handleDataSet(dataSet, null);
}
+ @Override
public List<DataSetInformation> handleDataSet(final File dataSet,
final DataSetInformation newOverride)
{
@@ -187,6 +189,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
new DataSetRegistrationAlgorithmRunner.IDataSetRegistrationAlgorithmRunnerDelegate()
{
+ @Override
public void didNotIdentifyDataSet()
{
throw new UserFailureException("Could not find owner:\n\t"
@@ -207,6 +210,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
return dataSetTypeCodeOrNull;
}
+ @Override
public List<DataSetInformation> linkAndHandleDataSet(File dataSetComponent,
DataSetInformation newOverride)
{
@@ -240,11 +244,13 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
}
}
+ @Override
public SessionContextDTO getSessionContext()
{
return getOpenBisService().tryGetSession(sessionToken);
}
+ @Override
public File getFileForDataSet(DataSet dataSet, String shareId)
{
File share = new File(service.getStoreRootDirectory(), shareId);
@@ -257,12 +263,14 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
return service.getDataStoreCode();
}
+ @Override
public DataSetOwner getDataSetOwner()
{
DataSetOwner owner = newDataSet.getDataSetOwner();
return owner;
}
+ @Override
public DataSetInformation getCallerDataSetInformation()
{
DataSetInformation dataSetInfo = new DataSetInformation();
@@ -491,6 +499,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
private static class PostRegistrationAction implements IPostRegistrationAction
{
+ @Override
public boolean execute(String dataSetCode, String dataSetAbsolutePathInStore)
{
return true;// do nothing
@@ -500,6 +509,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
private static class PreRegistrationAction implements IPreRegistrationAction
{
+ @Override
public boolean execute(String dataSetCode, String dataSetAbsolutePathInStore)
{
return true;// do nothing
@@ -529,6 +539,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
pluginTypeExtractor = plugin.getTypeExtractor();
}
+ @Override
public DataSetType getDataSetType(File incomingDataSetPath)
{
if (null != overrideOrNull)
@@ -542,21 +553,25 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
return pluginTypeExtractor.getDataSetType(incomingDataSetPath);
}
+ @Override
public FileFormatType getFileFormatType(File incomingDataSetPath)
{
return pluginTypeExtractor.getFileFormatType(incomingDataSetPath);
}
+ @Override
public LocatorType getLocatorType(File incomingDataSetPath)
{
return pluginTypeExtractor.getLocatorType(incomingDataSetPath);
}
+ @Override
public String getProcessorType(File incomingDataSetPath)
{
return pluginTypeExtractor.getProcessorType(incomingDataSetPath);
}
+ @Override
public boolean isMeasuredData(File incomingDataSetPath)
{
return pluginTypeExtractor.isMeasuredData(incomingDataSetPath);
@@ -700,6 +715,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
return dataSetInfo;
}
+ @Override
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetServerPluginHolder.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetServerPluginHolder.java
index 3922881f6ed..080ad62185b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetServerPluginHolder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetServerPluginHolder.java
@@ -55,37 +55,44 @@ public class PutDataSetServerPluginHolder extends AbstractTopLevelDataSetRegistr
return plugin;
}
+ @Override
public Lock getRegistrationLock()
{
throw new NotImplementedException();
}
+ @Override
public void handle(File file, DataSetInformation callerDataSetInformation,
ITopLevelDataSetRegistratorDelegate delegate)
{
throw new NotImplementedException();
}
+ @Override
public void handle(File path)
{
throw new NotImplementedException();
}
+ @Override
public boolean isStopped()
{
throw new NotImplementedException();
}
+ @Override
public boolean isRemote()
{
throw new NotImplementedException();
}
+ @Override
public void check() throws EnvironmentFailureException, ConfigurationFailureException
{
throw new NotImplementedException();
}
+ @Override
public boolean shouldNotAddToFaultyPathsOrNull(File storeItem)
{
throw new NotImplementedException();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
index c5318270239..43d41a7eec6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
@@ -64,6 +64,7 @@ class PutDataSetTopLevelDataSetHandler
private final ArrayList<DataSetInformation> registeredDataSets =
new ArrayList<DataSetInformation>();
+ @Override
public void didRegisterDataSets(List<DataSetInformation> dataSetInformations)
{
registeredDataSets.addAll(dataSetInformations);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
index 1ea4229dbdf..95a392bb0b2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
@@ -59,6 +59,7 @@ public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
dataSetPropertiesFileNameOrNull = properties.getProperty(DATA_SET_PROPERTIES_FILE_NAME_KEY);
}
+ @Override
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexTypeExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexTypeExtractor.java
index 8fb4d3a6714..1e493cb851f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexTypeExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexTypeExtractor.java
@@ -43,28 +43,33 @@ public class CifexTypeExtractor implements ITypeExtractor
simpleTypeExtractor = new SimpleTypeExtractor(properties);
}
+ @Override
public DataSetType getDataSetType(File incomingDataSetPath)
{
return new DataSetType(CifexExtractorHelper.getDataSetUploadInfo(incomingDataSetPath)
.getDataSetType());
}
+ @Override
public FileFormatType getFileFormatType(File incomingDataSetPath)
{
return new FileFormatType(CifexExtractorHelper.getDataSetUploadInfo(incomingDataSetPath)
.getFileType());
}
+ @Override
public LocatorType getLocatorType(File incomingDataSetPath)
{
return simpleTypeExtractor.getLocatorType(incomingDataSetPath);
}
+ @Override
public String getProcessorType(File incomingDataSetPath)
{
return simpleTypeExtractor.getProcessorType(incomingDataSetPath);
}
+ @Override
public boolean isMeasuredData(File incomingDataSetPath)
{
return simpleTypeExtractor.isMeasuredData(incomingDataSetPath);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java
index 0deef8150bd..e9638aff232 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/RegistrationStatus.java
@@ -35,16 +35,19 @@ class RegistrationError extends AbstractRegistrationStatus
this.error = error;
}
+ @Override
public boolean isError()
{
return true;
}
+ @Override
public Throwable getError()
{
return error;
}
+ @Override
public String getMessage()
{
return error.getMessage();
@@ -57,11 +60,13 @@ class RegistrationSuccess extends AbstractRegistrationStatus
{
}
+ @Override
public boolean isError()
{
return false;
}
+ @Override
public Throwable getError()
{
assert false : "getError() should not be called on a success object";
@@ -69,6 +74,7 @@ class RegistrationSuccess extends AbstractRegistrationStatus
return null;
}
+ @Override
public String getMessage()
{
return "Success";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
index 8a1ac98acde..513a5082742 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
@@ -168,11 +168,13 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
userFinishedMarkerFile, operationLog);
}
+ @Override
public void initializeMailClient(IMailClient mailClient)
{
globalState.initializeMailClient(mailClient);
}
+ @Override
public List<DataSetInformation> handleDataSet(File file)
{
File fileToRegister = file;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
index 1bfe32b30fb..e71839d8d1d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
@@ -215,6 +215,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
logInfo(message);
}
+ @Override
public void registerDataSetInApplicationServer(NewExternalData data) throws Throwable
{
syncDataToDataSetProperties(data);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
index d11efaac5ce..471089f79cc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
@@ -59,6 +59,7 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
IParserObjectFactoryFactory<SampleDataSetPair> factoryFactory =
new IParserObjectFactoryFactory<SampleDataSetPair>()
{
+ @Override
public final IParserObjectFactory<SampleDataSetPair> createFactory(
final IPropertyMapper propertyMapper) throws ParserException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
index 479f3cb5fd5..613b207d4ac 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/hdf5/HDF5StorageProcessor.java
@@ -54,6 +54,7 @@ public class HDF5StorageProcessor extends AbstractStorageProcessor
isDataCompressed = PropertyUtils.getBoolean(properties, COMPRESS_DATA_PROPERTY, false);
}
+ @Override
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
@@ -144,6 +145,7 @@ public class HDF5StorageProcessor extends AbstractStorageProcessor
fileBeingProcessed = null;
}
+ @Override
public File tryGetProprietaryData()
{
return null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/DatabaseBasedDataSetPathsInfoFeeder.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/DatabaseBasedDataSetPathsInfoFeeder.java
index 9364994b1e4..143c274051c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/DatabaseBasedDataSetPathsInfoFeeder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/DatabaseBasedDataSetPathsInfoFeeder.java
@@ -50,6 +50,7 @@ public class DatabaseBasedDataSetPathsInfoFeeder implements IDataSetPathsInfoFee
this.computeChecksum = computeChecksum;
}
+ @Override
public long addPaths(String dataSetCode, String location, File dataSetRoot)
{
long dataSetId = dao.createDataSet(dataSetCode, location);
@@ -100,6 +101,7 @@ public class DatabaseBasedDataSetPathsInfoFeeder implements IDataSetPathsInfoFee
}
}
+ @Override
public void commit()
{
if (filePaths.isEmpty() == false)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathEntryDTO.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathEntryDTO.java
index 6213d14bd82..8d2c94a8e14 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathEntryDTO.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathEntryDTO.java
@@ -62,9 +62,6 @@ public class PathEntryDTO
this.lastModifiedDate = lastModifiedDate;
}
- private PathEntryDTO() {
-
- }
//
// For unit tests.
//
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfo.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfo.java
index 1293bba41dd..223f66acedf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfo.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfo.java
@@ -76,6 +76,7 @@ final class PathInfo
}
Collections.sort(childInfos, new Comparator<PathInfo>()
{
+ @Override
public int compare(PathInfo p1, PathInfo p2)
{
return p1.getFileName().compareTo(p2.getFileName());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTask.java
index 12190c23668..cfcf90a8eea 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTask.java
@@ -68,6 +68,7 @@ public class PathInfoDatabaseChecksumCalculationTask implements IMaintenanceTask
this.timeProvider = timeProvider;
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
dao = QueryTool.getQuery(PathInfoDataSourceProvider.getDataSource(), IPathsInfoDAO.class);
@@ -75,6 +76,7 @@ public class PathInfoDatabaseChecksumCalculationTask implements IMaintenanceTask
timeProvider = SystemTimeProvider.SYSTEM_TIME_PROVIDER;
}
+ @Override
public void execute()
{
List<PathEntryDTO> entries = dao.listDataSetFilesWithUnkownChecksum();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
index 97aa139d6cb..3c9a20e6ac6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
@@ -103,11 +103,13 @@ public class PathInfoDatabaseFeedingTask implements IMaintenanceTask, IPostRegis
this.computeChecksum = computeChecksum;
}
+ @Override
public boolean requiresDataStoreLock()
{
return false;
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
service = ServiceProvider.getOpenBISService();
@@ -122,6 +124,7 @@ public class PathInfoDatabaseFeedingTask implements IMaintenanceTask, IPostRegis
return PropertyUtils.getBoolean(properties, COMPUTE_CHECKSUM_KEY, false);
}
+ @Override
public void execute()
{
List<SimpleDataSetInformationDTO> dataSets = service.listDataSets();
@@ -131,15 +134,18 @@ public class PathInfoDatabaseFeedingTask implements IMaintenanceTask, IPostRegis
}
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(final String dataSetCode, boolean container)
{
return new IPostRegistrationTaskExecutor()
{
+ @Override
public ICleanupTask createCleanupTask()
{
return new NoCleanupTask();
}
+ @Override
public void execute()
{
ExternalData dataSet = service.tryGetDataSet(dataSetCode);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AbstractDataSetDeletionPostProcessingMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AbstractDataSetDeletionPostProcessingMaintenanceTask.java
index 9b7860c9edb..e06de551d98 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AbstractDataSetDeletionPostProcessingMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AbstractDataSetDeletionPostProcessingMaintenanceTask.java
@@ -62,6 +62,7 @@ public abstract class AbstractDataSetDeletionPostProcessingMaintenanceTask imple
openBISService = ServiceProvider.getOpenBISService();
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
int delayInMinutes = PropertyUtils.getInt(properties, DELAY_AFTER_DELETION, 0);
@@ -69,6 +70,7 @@ public abstract class AbstractDataSetDeletionPostProcessingMaintenanceTask imple
delayAfterDeletion = delayInMinutes * DateUtils.MILLIS_PER_MINUTE;
}
+ @Override
public void execute()
{
if (operationLog.isDebugEnabled())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AutoArchiverTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AutoArchiverTask.java
index c2bd2af3a32..f803157b2f1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AutoArchiverTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/AutoArchiverTask.java
@@ -70,6 +70,7 @@ public class AutoArchiverTask implements IMaintenanceTask
private boolean removeFromDataStore;
+ @Override
public void execute()
{
operationLog.info("start");
@@ -86,6 +87,7 @@ public class AutoArchiverTask implements IMaintenanceTask
operationLog.info("end");
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
openBISService = ServiceProvider.getOpenBISService();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetMover.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetMover.java
index adaf6c85b06..3a0b5f284dc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetMover.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetMover.java
@@ -23,6 +23,7 @@ public class DataSetMover implements IDataSetMover
manager = shareIdManager;
}
+ @Override
public void moveDataSetToAnotherShare(File dataSetDirInStore, File share,
ISimpleLogger logger)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DummyAutoArchiverPolicy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DummyAutoArchiverPolicy.java
index 18e55b76de3..36dd0066def 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DummyAutoArchiverPolicy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DummyAutoArchiverPolicy.java
@@ -33,6 +33,7 @@ public class DummyAutoArchiverPolicy implements IAutoArchiverPolicy
{
}
+ @Override
public List<ExternalData> filter(List<ExternalData> dataSets)
{
return dataSets;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTask.java
index 9f50e17785f..0291c94615d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTask.java
@@ -157,11 +157,13 @@ public class ExperimentBasedArchivingTask implements IDataStoreLockingMaintenanc
this.service = service;
}
+ @Override
public boolean requiresDataStoreLock()
{
return true;
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
freeSpaceProvider = setUpFreeSpaceProvider(properties);
@@ -241,6 +243,7 @@ public class ExperimentBasedArchivingTask implements IDataStoreLockingMaintenanc
return result;
}
+ @Override
public void execute()
{
if (operationLog.isDebugEnabled())
@@ -423,6 +426,7 @@ public class ExperimentBasedArchivingTask implements IDataStoreLockingMaintenanc
private final class ExperimentDataSetsInfoComparator implements
Comparator<ExperimentDataSetsInfo>
{
+ @Override
public int compare(ExperimentDataSetsInfo i1, ExperimentDataSetsInfo i2)
{
Date d1 = i1.getLastModificationDate();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
index b49d2f19057..e535bbecf55 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
@@ -100,6 +100,7 @@ public class HierarchicalStorageUpdater implements IDataStoreLockingMaintenanceT
private Map<String /* data set type */, LinkSourceDescriptor> linkSourceDescriptors;
+ @Override
public void setUp(String pluginName, Properties pluginProperties)
{
LogInitializer.init();
@@ -122,6 +123,7 @@ public class HierarchicalStorageUpdater implements IDataStoreLockingMaintenanceT
+ ", hierarchy root = " + hierarchyRootFileName);
}
+ @Override
public void execute()
{
rebuildHierarchy();
@@ -130,6 +132,7 @@ public class HierarchicalStorageUpdater implements IDataStoreLockingMaintenanceT
/**
* @see IDataStoreLockingMaintenanceTask#requiresDataStoreLock()
*/
+ @Override
public boolean requiresDataStoreLock()
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTask.java
index b8a3ff90d5e..61efea49ebc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTask.java
@@ -64,10 +64,12 @@ public class SegmentedStoreShufflingTask implements IDataStoreLockingMaintenance
{
private static final int N = 3;
+ @Override
public void init(ISimpleLogger logger)
{
}
+ @Override
public void shuffleDataSets(List<Share> sourceShares, List<Share> targetShares,
IEncapsulatedOpenBISService service, IDataSetMover dataSetMover,
ISimpleLogger logger)
@@ -156,6 +158,7 @@ public class SegmentedStoreShufflingTask implements IDataStoreLockingMaintenance
operationLogger = logger;
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
dataStoreCode =
@@ -201,6 +204,7 @@ public class SegmentedStoreShufflingTask implements IDataStoreLockingMaintenance
}
}
+ @Override
public void execute()
{
operationLog.info("Starting segmented store shuffling.");
@@ -244,6 +248,7 @@ public class SegmentedStoreShufflingTask implements IDataStoreLockingMaintenance
/**
* @see IDataStoreLockingMaintenanceTask#requiresDataStoreLock()
*/
+ @Override
public boolean requiresDataStoreLock()
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SimpleShuffling.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SimpleShuffling.java
index 4e4aebb6e9d..0a9ae19b938 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SimpleShuffling.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/SimpleShuffling.java
@@ -95,12 +95,14 @@ public class SimpleShuffling implements ISegmentedStoreShuffling
SimpleShuffling.class));
}
+ @Override
public void init(ISimpleLogger logger)
{
taskExecutor.cleanup();
logger.log(LogLevel.INFO, "Simple shuffling strategy initialized");
}
+ @Override
public void shuffleDataSets(List<Share> sourceShares, List<Share> targetShares,
IEncapsulatedOpenBISService service, IDataSetMover dataSetMover, ISimpleLogger logger)
{
@@ -194,6 +196,7 @@ public class SimpleShuffling implements ISegmentedStoreShuffling
}
Collections.sort(shareStates, new Comparator<ShareAndFreeSpace>()
{
+ @Override
public int compare(ShareAndFreeSpace o1, ShareAndFreeSpace o2)
{
long s1 = o1.getFreeSpace();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
index 06ce34041fc..f3fc0695038 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
@@ -68,6 +68,7 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
*
* @return Instance_AAA/Group_BBB/Project_CCC...</code>
*/
+ @Override
public String createHierarchicalPath(SimpleDataSetInformationDTO data)
{
ExtendedProperties props = new ExtendedProperties();
@@ -89,6 +90,7 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
/**
* Creates a {@link Set} of data set paths located inside <code>root</code>.
*/
+ @Override
public Set<String> extractPaths(File root)
{
HashSet<String> set = new HashSet<String>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
index 33e6226bc99..b58abf62763 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
@@ -62,11 +62,13 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
/**
* do not allow concurrent maintenance tasks to run if they alter the data store contents.
*/
+ @Override
public boolean requiresDataStoreLock()
{
return true;
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(String dataSetCode, boolean container)
{
if (container)
@@ -89,6 +91,7 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
/**
* archives the dataset for the specified dataset code.
*/
+ @Override
public void execute()
{
@@ -152,6 +155,7 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
notificationLog.error(message);
}
+ @Override
public ICleanupTask createCleanupTask()
{
return new ArchivingCleanupTask(dataSetCode);
@@ -196,6 +200,7 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
this.dataSetCode = dataSetCode;
}
+ @Override
public void cleanup(ISimpleLogger logger)
{
IEncapsulatedOpenBISService openBISService = ServiceProvider.getOpenBISService();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/DummyPostRegistrationTaskExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/DummyPostRegistrationTaskExecutor.java
index 6d6814c896c..99aff6afbfa 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/DummyPostRegistrationTaskExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/DummyPostRegistrationTaskExecutor.java
@@ -25,10 +25,12 @@ public class DummyPostRegistrationTaskExecutor implements IPostRegistrationTaskE
{
public static final IPostRegistrationTaskExecutor INSTANCE = new DummyPostRegistrationTaskExecutor();
+ @Override
public void execute()
{
}
+ @Override
public ICleanupTask createCleanupTask()
{
return new NoCleanupTask();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTask.java
index f935bb58190..8c51edf17e9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTask.java
@@ -143,11 +143,13 @@ public class EagerShufflingTask extends AbstractPostRegistrationTask
stopOnNoShareFound = PropertyUtils.getBoolean(properties, STOP_ON_NO_SHARE_FOUND_KEY, false);
}
+ @Override
public boolean requiresDataStoreLock()
{
return true;
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(String dataSetCode, boolean container)
{
if (container)
@@ -169,6 +171,7 @@ public class EagerShufflingTask extends AbstractPostRegistrationTask
this.dataSetCode = dataSetCode;
}
+ @Override
public ICleanupTask createCleanupTask()
{
List<Share> shares =
@@ -190,6 +193,7 @@ public class EagerShufflingTask extends AbstractPostRegistrationTask
return new CleanupTask(dataSet, storeRoot, shareWithMostFreeOrNull.getShareId());
}
+ @Override
public void execute()
{
if (shareWithMostFreeOrNull != null)
@@ -234,6 +238,7 @@ public class EagerShufflingTask extends AbstractPostRegistrationTask
this.newShareId = newShareId;
}
+ @Override
public void cleanup(ISimpleLogger logger)
{
IShareIdManager shareIdManager = ServiceProvider.getShareIdManager();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
index 7fb433fe752..ae1f4490aa0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
@@ -100,11 +100,13 @@ public class Hdf5CompressingPostRegistrationTask extends AbstractPostRegistratio
/**
* do not allow concurrent maintenance tasks to run if they alter the data store contents.
*/
+ @Override
public boolean requiresDataStoreLock()
{
return true;
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(String dataSetCode, boolean container)
{
if (container)
@@ -134,6 +136,7 @@ public class Hdf5CompressingPostRegistrationTask extends AbstractPostRegistratio
// empty by design
}
+ @Override
public void execute()
{
@@ -336,6 +339,7 @@ public class Hdf5CompressingPostRegistrationTask extends AbstractPostRegistratio
return true;
}
+ @Override
public ICleanupTask createCleanupTask()
{
return new Hdf5CompressingCleanupTask(dataSetCode);
@@ -476,6 +480,7 @@ public class Hdf5CompressingPostRegistrationTask extends AbstractPostRegistratio
this.dataSetCode = dataSetCode;
}
+ @Override
public void cleanup(ISimpleLogger logger)
{
DataSet dataSet =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NoCleanupTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NoCleanupTask.java
index 1fc5255bc1f..18cde27d3cf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NoCleanupTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NoCleanupTask.java
@@ -27,6 +27,7 @@ public class NoCleanupTask implements ICleanupTask
{
private static final long serialVersionUID = 1L;
+ @Override
public void cleanup(ISimpleLogger logger)
{
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NotifyingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NotifyingTask.java
index 04aef94bc23..c37f8f6f0a3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NotifyingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/NotifyingTask.java
@@ -103,11 +103,13 @@ public class NotifyingTask extends AbstractPostRegistrationTask
}
}
+ @Override
public boolean requiresDataStoreLock()
{
return false;
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(String dataSetCode, boolean container)
{
ExternalData dataSet = service.tryGetDataSet(dataSetCode);
@@ -142,11 +144,13 @@ public class NotifyingTask extends AbstractPostRegistrationTask
this.logger = logger;
}
+ @Override
public ICleanupTask createCleanupTask()
{
return new NoCleanupTask();
}
+ @Override
public void execute()
{
if (typeMatches())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTask.java
index dd4e7240b7b..5dfdec6a126 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTask.java
@@ -82,11 +82,13 @@ public class PostRegistrationMaintenanceTask implements IDataStoreLockingMainten
private TaskExecutor executor;
+ @Override
public boolean requiresDataStoreLock()
{
return needsLockOnDataStore;
}
+ @Override
public void setUp(String pluginName, Properties properties)
{
//
@@ -154,6 +156,7 @@ public class PostRegistrationMaintenanceTask implements IDataStoreLockingMainten
ignoreBeforeDate = new Date(0);
}
+ @Override
public void execute()
{
executor.cleanup();
@@ -219,6 +222,7 @@ public class PostRegistrationMaintenanceTask implements IDataStoreLockingMainten
}
Collections.sort(filteredList, new Comparator<ExternalData>()
{
+ @Override
public int compare(ExternalData o1, ExternalData o2)
{
return (int) (o1.getId() - o2.getId());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
index 303690fa765..a33fddd18a2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/TaskExecutor.java
@@ -46,6 +46,7 @@ public class TaskExecutor
private static final FilenameFilter FILTER = new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return name.endsWith(FILE_TYPE);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java
index c3d0ed6af6b..5acd2d3be0f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java
@@ -50,6 +50,7 @@ public abstract class AbstractDataSetRegistrationDetailsFactory<T extends DataSe
/**
* Factory method that creates a new registration details object.
*/
+ @Override
public DataSetRegistrationDetails<T> createDataSetRegistrationDetails()
{
DataSetRegistrationDetails<T> registrationDetails = new DataSetRegistrationDetails<T>();
@@ -69,6 +70,7 @@ public abstract class AbstractDataSetRegistrationDetailsFactory<T extends DataSe
return registrationDetails;
}
+ @Override
public DataSet<T> createDataSet(DataSetRegistrationDetails<T> registrationDetails,
File stagingFile)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
index 321cb90c1f1..e7bf00b5f93 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
@@ -234,6 +234,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
public static class NoOpDelegate implements ITopLevelDataSetRegistratorDelegate
{
+ @Override
public void didRegisterDataSets(List<DataSetInformation> dataSetInformations)
{
}
@@ -285,6 +286,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
return state;
}
+ @Override
public Lock getRegistrationLock()
{
return state.registrationLock;
@@ -312,6 +314,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
* Setup necessary for data set handling is done, then the handleDataSet method (a subclass
* responsibility) is invoked.
*/
+ @Override
public final void handle(final File incomingDataSetFileOrIsFinishedFile)
{
if (stopped)
@@ -340,6 +343,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
{
markerFileCleanupAction = new IDelegatedActionWithResult<Boolean>()
{
+ @Override
public Boolean execute(boolean didOperationSucceed)
{
if (hasRecoveryMarkerFile(incomingDataSetFile))
@@ -411,6 +415,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
* <p>
* The handleDataSet method (a subclass responsibility) is invoked.
*/
+ @Override
public final void handle(File incomingDataSetFile, DataSetInformation callerDataSetInformation,
ITopLevelDataSetRegistratorDelegate delegate)
{
@@ -556,11 +561,13 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
rollbacker.doRollback(service.getDssRegistrationLog());
}
+ @Override
public boolean isStopped()
{
return stopped;
}
+ @Override
public boolean isRemote()
{
return true;
@@ -569,6 +576,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
//
// ISelfTestable
//
+ @Override
public final void check() throws ConfigurationFailureException, EnvironmentFailureException
{
new TopLevelDataSetChecker(operationLog, state.storageProcessor, state.fileOperations)
@@ -655,7 +663,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
ITopLevelDataSetRegistratorDelegate delegate)
{
@SuppressWarnings(
- { "unchecked" })
+ { "unchecked", "rawtypes" })
DataSetRegistrationService<T> service =
new DataSetRegistrationService(this, incomingDataSetFile,
new DefaultDataSetRegistrationDetailsFactory(getRegistratorState(),
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/ConfiguredOnErrorActionDecision.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/ConfiguredOnErrorActionDecision.java
index 2778b233035..06cac4932f8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/ConfiguredOnErrorActionDecision.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/ConfiguredOnErrorActionDecision.java
@@ -69,6 +69,7 @@ public class ConfiguredOnErrorActionDecision implements IDataSetOnErrorActionDec
preRegistrationError = getAction(ErrorType.PRE_REGISTRATION_ERROR, properties);
}
+ @Override
public UnstoreDataAction computeUndoAction(ErrorType errorType, Throwable failureOrNull)
{
UnstoreDataAction action = null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationDetails.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationDetails.java
index 4b0ab782301..941d4e214ec 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationDetails.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationDetails.java
@@ -47,26 +47,31 @@ public class DataSetRegistrationDetails<T extends DataSetInformation> implements
measuredData = true;
}
+ @Override
public FileFormatType getFileFormatType(File incomingDataSetPath)
{
return fileFormatType;
}
+ @Override
public boolean isMeasuredData(File incomingDataSetPath)
{
return measuredData;
}
+ @Override
public String getProcessorType(File incomingDataSetPath)
{
return processorType;
}
+ @Override
public DataSetType getDataSetType(File incomingDataSetPath)
{
return getDataSetType();
}
+ @Override
public LocatorType getLocatorType(File incomingDataSetPath)
{
return getLocatorType();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
index 12e3d818b3d..d418a8765d8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
@@ -129,6 +129,7 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
/**
* Create a new transaction that atomically performs file operations and registers entities.
*/
+ @Override
public IDataSetRegistrationTransaction transaction()
{
return transaction(incomingDataSetFile.getLogicalIncomingFile(),
@@ -138,6 +139,7 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
/**
* Create a new transaction that atomically performs file operations and registers entities.
*/
+ @Override
public IDataSetRegistrationTransaction transaction(File dataSetFile)
{
return transaction(dataSetFile, getDataSetRegistrationDetailsFactory());
@@ -232,6 +234,7 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
}
}
+ @Override
public File moveIncomingToError(String dataSetTypeCodeOrNull)
{
DataSetStorageRollbacker rollbacker =
@@ -265,11 +268,13 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
registrator.didCommitTransaction(this, transaction);
}
+ @Override
public void executePreRegistration(DataSetRegistrationPersistentMap.IHolder persistentMapHolder)
{
registrator.didPreRegistration(this, persistentMapHolder);
}
+ @Override
public void executePostRegistration(DataSetRegistrationPersistentMap.IHolder persistentMapHolder)
{
registrator.didPostRegistration(this, persistentMapHolder);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
index 3d4f1a198bc..93cf420f4fd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
@@ -207,11 +207,13 @@ public class DataSetStorageAlgorithmRunner<T extends DataSetInformation>
this.transaction = transaction;
}
+ @Override
public void execute()
{
}
+ @Override
public void rollback()
{
transaction.rollback(null);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
index 727ca9f7b0d..4fab5b33328 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
@@ -50,6 +50,7 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
this.delegate = delegate;
}
+ @Override
public AtomicEntityOperationResult performOperationsInApplcationServer(
AtomicEntityOperationDetails<T> registrationDetails)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
index fca31a2d052..976dc0918e7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
@@ -609,6 +609,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
/**
* V1 registration framework -- any file can go into faulty paths.
*/
+ @Override
public boolean shouldNotAddToFaultyPathsOrNull(File storeItem)
{
return false;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index 4ecbcb84e58..b4142a3b2b5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -876,6 +876,7 @@ public abstract class AbstractTransactionState<T extends DataSetInformation>
LiveTransactionState.fileSystemAvailablityPollingWaitTimeMs;
}
+ @Override
public void willContinueRollbackAll(RollbackStack stack)
{
// Stop rolling back if the thread was interrupted
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
index fbfc76fdd65..1b41d0094bd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
@@ -104,16 +104,19 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
}
+ @Override
public String getDataSetCode()
{
return registrationDetails.getDataSetInformation().getDataSetCode();
}
+ @Override
public IExperimentImmutable getExperiment()
{
return experiment;
}
+ @Override
public void setExperiment(IExperimentImmutable experiment)
{
this.experiment = experiment;
@@ -122,11 +125,13 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
setExperiment(experimentToSet);
}
+ @Override
public ISampleImmutable getSample()
{
return sampleOrNull;
}
+ @Override
public void setSample(ISampleImmutable sampleOrNull)
{
this.sampleOrNull = sampleOrNull;
@@ -156,41 +161,49 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
}
}
+ @Override
public String getFileFormatType()
{
return registrationDetails.getFileFormatType().getCode();
}
+ @Override
public void setFileFormatType(String fileFormatTypeCode)
{
registrationDetails.setFileFormatType(new FileFormatType(fileFormatTypeCode));
}
+ @Override
public boolean isMeasuredData()
{
return registrationDetails.isMeasuredData();
}
+ @Override
public void setMeasuredData(boolean measuredData)
{
registrationDetails.setMeasuredData(measuredData);
}
+ @Override
public int getSpeedHint()
{
return registrationDetails.getDataSetInformation().getSpeedHint();
}
+ @Override
public void setSpeedHint(int speedHint)
{
registrationDetails.getDataSetInformation().setSpeedHint(speedHint);
}
+ @Override
public String getDataSetType()
{
return registrationDetails.getDataSetType().getCode();
}
+ @Override
public DataSetType getDataSetTypeWithPropertyTypes()
{
String dataSetTypeCode = getDataSetType();
@@ -203,6 +216,7 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
return getDataSetTypeWithPropertyTypes(dataSetTypeCode);
}
+ @Override
public void setDataSetType(String dataSetTypeCode)
{
registrationDetails.setDataSetType(dataSetTypeCode);
@@ -217,11 +231,13 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
registrationDetails.getDataSetInformation().setExperimentIdentifier(experimentId);
}
+ @Override
public String getPropertyValue(String propertyCode)
{
return registrationDetails.getPropertyValue(propertyCode);
}
+ @Override
public List<String> getAllPropertyCodes()
{
List<NewProperty> properties =
@@ -235,33 +251,39 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
return codes;
}
+ @Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
registrationDetails.setPropertyValue(propertyCode, propertyValue);
}
+ @Override
public void setParentDatasets(List<String> parentDatasetCodes)
{
DataSetInformation dataSetInformation = registrationDetails.getDataSetInformation();
dataSetInformation.setParentDataSetCodes(parentDatasetCodes);
}
+ @Override
public List<String> getParentDatasets()
{
return registrationDetails.getDataSetInformation().getParentDataSetCodes();
}
+ @Override
public boolean isContainerDataSet()
{
return registrationDetails.getDataSetInformation().isContainerDataSet();
}
+ @Override
public List<String> getContainedDataSetCodes()
{
return Collections.unmodifiableList(registrationDetails.getDataSetInformation()
.getContainedDataSetCodes());
}
+ @Override
public void setContainedDataSetCodes(List<String> containedDataSetCodes)
{
ArrayList<String> newContainedDataSetCodes =
@@ -272,6 +294,7 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
}
+ @Override
public List<IDataSetImmutable> getChildrenDataSets()
{
throw new UnsupportedOperationException("The operation is not supported for data "
@@ -279,11 +302,13 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
}
//the dataset cannot be contained before it is created
+ @Override
public boolean isContainedDataSet()
{
return false;
}
+ @Override
public String getContainerDataSet()
{
return null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
index 4802830aa8a..b6fdf509986 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
@@ -46,16 +46,19 @@ public class DataSetImmutable extends AbstractDataSetImmutable
this.dataSet = dataSet;
}
+ @Override
public String getDataSetCode()
{
return dataSet.getCode();
}
+ @Override
public IExperimentImmutable getExperiment()
{
return new ExperimentImmutable(dataSet.getExperiment());
}
+ @Override
public ISampleImmutable getSample()
{
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample = dataSet.getSample();
@@ -68,6 +71,7 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
}
+ @Override
public String getFileFormatType()
{
if (isContainerDataSet())
@@ -79,11 +83,13 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
}
+ @Override
public boolean isMeasuredData()
{
return dataSet.isDerived() == false;
}
+ @Override
public int getSpeedHint()
{
if (isContainerDataSet())
@@ -95,21 +101,25 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
}
+ @Override
public String getDataSetType()
{
return dataSet.getDataSetType().getCode();
}
+ @Override
public DataSetType getDataSetTypeWithPropertyTypes()
{
return getDataSetTypeWithPropertyTypes(getDataSetType());
}
+ @Override
public String getPropertyValue(String propertyCode)
{
return EntityHelper.tryFindPropertyValue(dataSet, propertyCode);
}
+ @Override
public List<String> getAllPropertyCodes()
{
List<IEntityProperty> properties = dataSet.getProperties();
@@ -121,21 +131,25 @@ public class DataSetImmutable extends AbstractDataSetImmutable
return codes;
}
+ @Override
public List<String> getParentDatasets()
{
return Code.extractCodes(dataSet.getParents());
}
+ @Override
public boolean isContainerDataSet()
{
return dataSet.isContainer();
}
+ @Override
public boolean isContainedDataSet()
{
return dataSet.tryGetContainer() != null;
}
+ @Override
public String getContainerDataSet()
{
ContainerDataSet container = dataSet.tryGetContainer();
@@ -148,6 +162,7 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
}
+ @Override
public List<String> getContainedDataSetCodes()
{
if (isContainerDataSet())
@@ -159,6 +174,7 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
}
+ @Override
public List<IDataSetImmutable> getChildrenDataSets()
{
List<IDataSetImmutable> result = new ArrayList<IDataSetImmutable>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index 1dadc843b45..00489bb7553 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -104,6 +104,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
File[] rollbackQueue1Files = rollBackStackParentFolder.listFiles(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return name.endsWith(ROLLBACK_QUEUE1_FILE_NAME_SUFFIX);
@@ -231,16 +232,19 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
getStateAsLiveState().setUserId(userIdOrNull);
}
+ @Override
public IDataSet createNewDataSet()
{
return getStateAsLiveState().createNewDataSet();
}
+ @Override
public IDataSet createNewDataSet(String dataSetType)
{
return getStateAsLiveState().createNewDataSet(dataSetType);
}
+ @Override
public IDataSet createNewDataSet(String dataSetType, String dataSetCode)
{
return getStateAsLiveState().createNewDataSet(dataSetType, dataSetCode);
@@ -257,16 +261,19 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return getStateAsLiveState().createNewDataSet(factory, dataSetType, null);
}
+ @Override
public IDataSetImmutable getDataSet(String dataSetCode)
{
return getStateAsLiveState().getDataSet(dataSetCode);
}
+ @Override
public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
{
return getStateAsLiveState().getDataSetForUpdate(dataSetCode);
}
+ @Override
public ISampleImmutable getSample(String sampleIdentifierString)
{
SampleIdentifier sampleIdentifier =
@@ -276,21 +283,25 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == sampleOrNull) ? null : new SampleImmutable(sampleOrNull);
}
+ @Override
public ISample getSampleForUpdate(String sampleIdentifierString)
{
return getStateAsLiveState().getSampleForUpdate(sampleIdentifierString);
}
+ @Override
public IExperiment getExperimentForUpdate(String experimentIdentifierString)
{
return getStateAsLiveState().getExperimentForUpdate(experimentIdentifierString);
}
+ @Override
public ISample createNewSample(String sampleIdentifierString, String sampleTypeCode)
{
return getStateAsLiveState().createNewSample(sampleIdentifierString, sampleTypeCode);
}
+ @Override
public IExperimentImmutable getExperiment(String experimentIdentifierString)
{
ExperimentIdentifier experimentIdentifier =
@@ -300,6 +311,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == experimentOrNull) ? null : new ExperimentImmutable(experimentOrNull);
}
+ @Override
public IExperiment createNewExperiment(String experimentIdentifierString,
String experimentTypeCode)
{
@@ -307,11 +319,13 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
experimentTypeCode);
}
+ @Override
public IProject createNewProject(String projectIdentifier)
{
return getStateAsLiveState().createNewProject(projectIdentifier);
}
+ @Override
public IProjectImmutable getProject(String projectIdentifierString)
{
ProjectIdentifier projectIdentifier =
@@ -321,11 +335,13 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == projectOrNull) ? null : new ProjectImmutable(projectOrNull);
}
+ @Override
public ISpace createNewSpace(String spaceCode, String spaceAdminUserIdOrNull)
{
return getStateAsLiveState().createNewSpace(spaceCode, spaceAdminUserIdOrNull);
}
+ @Override
public ISpaceImmutable getSpace(String spaceCode)
{
SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
@@ -334,6 +350,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == spaceOrNull) ? null : new SpaceImmutable(spaceOrNull);
}
+ @Override
public IMaterialImmutable getMaterial(String materialCode, String materialType)
{
MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, materialType);
@@ -342,31 +359,37 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == materialOrNull) ? null : new MaterialImmutable(materialOrNull);
}
+ @Override
public IMaterial createNewMaterial(String materialCode, String materialType)
{
return getStateAsLiveState().createNewMaterial(materialCode, materialType);
}
+ @Override
public String moveFile(String src, IDataSet dst)
{
return getStateAsLiveState().moveFile(src, dst);
}
+ @Override
public String moveFile(String src, IDataSet dst, String dstInDataset)
{
return getStateAsLiveState().moveFile(src, dst, dstInDataset);
}
+ @Override
public String createNewDirectory(IDataSet dst, String dirName)
{
return getStateAsLiveState().createNewDirectory(dst, dirName);
}
+ @Override
public String createNewFile(IDataSet dst, String fileName)
{
return getStateAsLiveState().createNewFile(dst, fileName);
}
+ @Override
public String createNewFile(IDataSet dst, String dstInDataset, String fileName)
{
return getStateAsLiveState().createNewFile(dst, dstInDataset, fileName);
@@ -381,6 +404,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
* Marked as deprecated, to prevent using this method directly. Instead it should only be used
* implicitly as an implementation of the persistent map holder interface.
*/
+ @Override
@Deprecated
public DataSetRegistrationPersistentMap getPersistentMap()
{
@@ -481,6 +505,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
* the DataSetRegistrationService to register not just the data sets, but perform any creation
* or updates of Experiments and Samples as well.
*/
+ @Override
public void registerDataSetsInApplicationServer(TechId registrationId,
List<DataSetRegistrationInformation<T>> dataSetRegistrations) throws Throwable
{
@@ -544,11 +569,13 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
}
}
+ @Override
public ISearchService getSearchService()
{
return new SearchService(openBisService);
}
+ @Override
public DynamicTransactionQuery getDatabaseQuery(String dataSourceName)
throws IllegalArgumentException
{
@@ -568,6 +595,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
}
}
+ @Override
public OmniscientTopLevelDataSetRegistratorState getRegistratorContext()
{
return registrationService.getRegistratorContext();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
index d926ed801dc..504acee9965 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
@@ -46,6 +46,7 @@ public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdata
}
}
+ @Override
public void setExperiment(IExperimentImmutable experiment)
{
if (experiment == null)
@@ -58,6 +59,7 @@ public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdata
}
}
+ @Override
public void setSample(ISampleImmutable sampleOrNull)
{
if (sampleOrNull == null)
@@ -71,6 +73,7 @@ public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdata
}
}
+ @Override
public void setFileFormatType(String fileFormatTypeCode)
{
if (isContainerDataSet())
@@ -84,17 +87,20 @@ public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdata
}
}
+ @Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
EntityHelper.createOrUpdateProperty(dataSet, propertyCode, propertyValue);
}
+ @Override
public void setParentDatasets(List<String> parentDatasetCodes)
{
List<ExternalData> dummyParents = createDummyDataSetsFromCodes(parentDatasetCodes);
dataSet.setParents(dummyParents);
}
+ @Override
public void setContainedDataSetCodes(List<String> containedDataSetCodes)
{
if (isContainerDataSet())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSourceQueryService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSourceQueryService.java
index 5939d362365..41b54d842bc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSourceQueryService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSourceQueryService.java
@@ -45,6 +45,7 @@ public class DataSourceQueryService implements IDataSourceQueryService
return ServiceProvider.getDataSourceProvider();
}
+ @Override
public DataSet<Map<String, Object>> select(String dataSourceName, String query,
Object... parameters)
{
@@ -59,6 +60,7 @@ public class DataSourceQueryService implements IDataSourceQueryService
}
}
+ @Override
public DataSet<Map<String, Object>> select(String dataSourceName, String query)
throws IllegalArgumentException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
index c58141e4332..24e4c50e33a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
@@ -48,11 +48,13 @@ class Experiment extends ExperimentImmutable implements IExperiment
return false;
}
+ @Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
EntityHelper.createOrUpdateProperty(getExperiment(), propertyCode, propertyValue);
}
+ @Override
public void setExperimentType(String experimentType)
{
ExperimentType type = new ExperimentType();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
index 0739b51f29d..8140ed5c5a7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
@@ -33,12 +33,14 @@ public class ExperimentImmutable implements IExperimentImmutable
this.experiment = experiment;
}
+ @Override
public String getExperimentIdentifier()
{
String identifier = experiment.getIdentifier();
return identifier == null ? null : identifier.toUpperCase();
}
+ @Override
public boolean isExistingExperiment()
{
return true;
@@ -60,11 +62,13 @@ public class ExperimentImmutable implements IExperimentImmutable
return experiment;
}
+ @Override
public String getPropertyValue(String propertyCode)
{
return EntityHelper.tryFindPropertyValue(experiment, propertyCode);
}
+ @Override
public String getExperimentType()
{
if (experiment.getExperimentType() != null)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
index 8d583bf15ac..7e945657812 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
@@ -53,6 +53,7 @@ public class Material extends MaterialImmutable implements IMaterial
super(buildMaterialWithCodeAndType(code, type), false);
}
+ @Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
EntityHelper.createOrUpdateProperty(getMaterial(), propertyCode, propertyValue);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
index 8d0c4f283d0..20d16b5e0ac 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
@@ -41,16 +41,19 @@ public class MaterialImmutable implements IMaterialImmutable
this.existingMaterial = existingMaterial;
}
+ @Override
public String getMaterialIdentifier()
{
return material.getIdentifier();
}
+ @Override
public String getCode()
{
return material.getCode();
}
+ @Override
public String getMaterialType()
{
if (material.getMaterialType() != null)
@@ -60,6 +63,7 @@ public class MaterialImmutable implements IMaterialImmutable
return null;
}
+ @Override
public boolean isExistingMaterial()
{
return existingMaterial;
@@ -81,6 +85,7 @@ public class MaterialImmutable implements IMaterialImmutable
}
}
+ @Override
public String getPropertyValue(String propertyCode)
{
return EntityHelper.tryFindPropertyValue(material, propertyCode);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MkdirsCommand.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MkdirsCommand.java
index d8cd065e002..10edb924ef7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MkdirsCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MkdirsCommand.java
@@ -38,6 +38,7 @@ public class MkdirsCommand extends AbstractTransactionalCommand
}
+ @Override
public void execute()
{
File src = new File(directoryAbsoutePath);
@@ -46,6 +47,7 @@ public class MkdirsCommand extends AbstractTransactionalCommand
fileOperations.mkdirs(src);
}
+ @Override
public void rollback()
{
File src = new File(directoryAbsoutePath);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MoveFileCommand.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MoveFileCommand.java
index ce66ecf05c4..b5c11fca56c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MoveFileCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MoveFileCommand.java
@@ -52,6 +52,7 @@ public class MoveFileCommand extends AbstractTransactionalCommand
this.dstFileName = dstFileName;
}
+ @Override
public void execute()
{
File src = getSrc();
@@ -76,6 +77,7 @@ public class MoveFileCommand extends AbstractTransactionalCommand
return new File(srcParentDirAbsolutePath, srcFileName);
}
+ @Override
public void rollback()
{
// The src is the original location, dst is the location we moved it to. We want to undo the
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/NewFileCommand.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/NewFileCommand.java
index 78c120cc561..62d073110a2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/NewFileCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/NewFileCommand.java
@@ -38,6 +38,7 @@ public class NewFileCommand extends AbstractTransactionalCommand
}
+ @Override
public void execute()
{
File src = new File(fileAbsolutePath);
@@ -46,6 +47,7 @@ public class NewFileCommand extends AbstractTransactionalCommand
fileOperations.createNewFile(src);
}
+ @Override
public void rollback()
{
File src = new File(fileAbsolutePath);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Project.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Project.java
index f115a3cb0dd..0f9a7c396c6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Project.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Project.java
@@ -29,6 +29,7 @@ class Project extends ProjectImmutable implements IProject
getProject().setIdentifier(projectIdentifier);
}
+ @Override
public void setDescription(String description)
{
getProject().setDescription(description);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ProjectImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ProjectImmutable.java
index b0339878929..ffe36ea8134 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ProjectImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ProjectImmutable.java
@@ -40,11 +40,13 @@ public class ProjectImmutable implements IProjectImmutable
this.isExistingProject = isExistingProject;
}
+ @Override
public String getProjectIdentifier()
{
return project.getIdentifier();
}
+ @Override
public boolean isExistingProject()
{
return isExistingProject;
@@ -66,6 +68,7 @@ public class ProjectImmutable implements IProjectImmutable
return project;
}
+ @Override
public String getDescription()
{
return project.getDescription();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStack.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStack.java
index e633626329a..9b3bc966f0b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStack.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStack.java
@@ -146,6 +146,7 @@ public class RollbackStack implements IRollbackStack
/**
* Push the command onto the stack and execute it.
*/
+ @Override
public void pushAndExecuteCommand(ITransactionalCommand cmd)
{
// Push is simple -- just put the new command onto the live stack
@@ -232,6 +233,7 @@ public class RollbackStack implements IRollbackStack
{
rollbackAll(new IRollbackStackDelegate()
{
+ @Override
public void willContinueRollbackAll(RollbackStack stack)
{
// Don't do anything
@@ -291,6 +293,7 @@ public class RollbackStack implements IRollbackStack
{ queue1File, queue2File };
}
+ @Override
public void setLockedState(boolean lockedState)
{
if (!lockedState && isLockedState())
@@ -302,6 +305,7 @@ public class RollbackStack implements IRollbackStack
}
}
+ @Override
public boolean isLockedState()
{
return lockedMarkerFile.exists();
@@ -349,6 +353,7 @@ public class RollbackStack implements IRollbackStack
this.order = order;
}
+ @Override
public int compareTo(StackElement o)
{
// The order should be the reverse of the step order (later steps should come first in
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
index fd27f855acf..c4719c07667 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
@@ -84,17 +84,20 @@ public class Sample extends SampleImmutable implements ISample
getSample().setPermId(permId);
}
+ @Override
public void setExperiment(IExperimentImmutable experiment)
{
ExperimentImmutable exp = (ExperimentImmutable) experiment;
getSample().setExperiment(exp.getExperiment());
}
+ @Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
EntityHelper.createOrUpdateProperty(getSample(), propertyCode, propertyValue);
}
+ @Override
public void setSampleType(String type)
{
SampleType sampleType = new SampleType();
@@ -103,6 +106,7 @@ public class Sample extends SampleImmutable implements ISample
getSample().setSampleType(sampleType);
}
+ @Override
public void setContainer(ISampleImmutable container)
{
SampleImmutable containerImpl = (SampleImmutable) container;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
index d62a3b76a2f..9bf77a28e3a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
@@ -45,6 +45,7 @@ public class SampleImmutable implements ISampleImmutable
this.existingSample = existingSample;
}
+ @Override
public IExperimentImmutable getExperiment()
{
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
@@ -52,6 +53,7 @@ public class SampleImmutable implements ISampleImmutable
return (null != experiment) ? new ExperimentImmutable(experiment) : null;
}
+ @Override
public String getSampleIdentifier()
{
String identifier = sample.getIdentifier();
@@ -63,6 +65,7 @@ public class SampleImmutable implements ISampleImmutable
return sample;
}
+ @Override
public boolean isExistingSample()
{
return existingSample;
@@ -79,11 +82,13 @@ public class SampleImmutable implements ISampleImmutable
}
}
+ @Override
public String getPropertyValue(String propertyCode)
{
return EntityHelper.tryFindPropertyValue(sample, propertyCode);
}
+ @Override
public String getSampleType()
{
if (sample.getSampleType() != null)
@@ -93,16 +98,19 @@ public class SampleImmutable implements ISampleImmutable
return null;
}
+ @Override
public String getSpace()
{
return sample.getSpace().getCode();
}
+ @Override
public String getCode()
{
return sample.getCode();
}
+ @Override
public List<ISampleImmutable> getContainedSamples()
{
List<ISampleImmutable> result = new ArrayList<ISampleImmutable>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
index fedc1ec2a70..e3819323d1c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
@@ -55,6 +55,7 @@ class SearchService implements ISearchService
this.openBisService = openBisService;
}
+ @Override
public List<IExperimentImmutable> listExperiments(String projectIdentifierString)
{
ProjectIdentifier projectIdentifier =
@@ -70,12 +71,14 @@ class SearchService implements ISearchService
return experiments;
}
+ @Override
public List<IDataSetImmutable> searchForDataSets(String property, String value,
String typeOrNull)
{
return searchForDataSets(property, value, typeOrNull, false);
}
+ @Override
public List<IDataSetImmutable> searchForDataSets(String property, String value,
String typeOrNull, boolean escape)
{
@@ -90,11 +93,13 @@ class SearchService implements ISearchService
return searchForDataSets(sc);
}
+ @Override
public List<ISampleImmutable> searchForSamples(String property, String value, String typeOrNull)
{
return searchForSamples(property, value, typeOrNull, false);
}
+ @Override
public List<ISampleImmutable> searchForSamples(String property, String value,
String typeOrNull, boolean escape)
{
@@ -109,6 +114,7 @@ class SearchService implements ISearchService
return searchForSamples(sc);
}
+ @Override
public List<IDataSetImmutable> searchForDataSets(SearchCriteria searchCriteria)
{
List<ExternalData> serverDataSets = openBisService.searchForDataSets(searchCriteria);
@@ -121,6 +127,7 @@ class SearchService implements ISearchService
return dataSets;
}
+ @Override
public List<ISampleImmutable> searchForSamples(SearchCriteria searchCriteria)
{
List<Sample> serverSamples = openBisService.searchForSamples(searchCriteria);
@@ -132,6 +139,7 @@ class SearchService implements ISearchService
return samples;
}
+ @Override
public List<IMaterialImmutable> listMaterials(MaterialIdentifierCollection identifierCollection)
{
final Set<String> identifiers = new HashSet<String>(identifierCollection.getIdentifiers());
@@ -146,6 +154,7 @@ class SearchService implements ISearchService
new ICollectionFilter<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material>()
{
+ @Override
public boolean isPresent(Material element)
{
return identifiers.contains(element.getIdentifier());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Space.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Space.java
index 162ee13f36a..982117f5884 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Space.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Space.java
@@ -32,6 +32,7 @@ public class Space extends SpaceImmutable implements ISpace
getSpace().getRegistrator().setUserId(spaceAdminUserIdOrNull);
}
+ @Override
public void setDescription(String description)
{
getSpace().setDescription(description);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SpaceImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SpaceImmutable.java
index 757bb6d71e2..b4e2ebb2381 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SpaceImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SpaceImmutable.java
@@ -41,16 +41,19 @@ public class SpaceImmutable implements ISpaceImmutable
}
+ @Override
public String getSpaceCode()
{
return space.getCode();
}
+ @Override
public String getDescription()
{
return space.getDescription();
}
+ @Override
public boolean isExistingSpace()
{
return isExistingSpace;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
index eda4b013aa5..1dc810d763b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/JythonTopLevelDataSetHandlerV2.java
@@ -201,6 +201,7 @@ public class JythonTopLevelDataSetHandlerV2<T extends DataSetInformation> extend
IDelegatedActionWithResult<Boolean> recoveryMarkerFileCleanupAction =
new IDelegatedActionWithResult<Boolean>()
{
+ @Override
public Boolean execute(boolean didOperationSucceed)
{
if (!didOperationSucceed
@@ -296,6 +297,7 @@ public class JythonTopLevelDataSetHandlerV2<T extends DataSetInformation> extend
IRollbackDelegate<T> rollbackDelegate = new IRollbackDelegate<T>()
{
+ @Override
public void didRollbackStorageAlgorithmRunner(
DataSetStorageAlgorithmRunner<T> algorithm, Throwable ex,
ErrorType errorType)
@@ -320,6 +322,7 @@ public class JythonTopLevelDataSetHandlerV2<T extends DataSetInformation> extend
new DataSetRegistrationPersistentMap.IHolder()
{
+ @Override
public DataSetRegistrationPersistentMap getPersistentMap()
{
return recoveryState.getPersistentMap();
@@ -480,12 +483,14 @@ public class JythonTopLevelDataSetHandlerV2<T extends DataSetInformation> extend
return internalInterpreter;
}
+ @Override
public void executePreRegistration(
DataSetRegistrationPersistentMap.IHolder persistentMapHolder)
{
throw new NotImplementedException("Recovery cannot execute pre-registration hook.");
}
+ @Override
public void executePostRegistration(
DataSetRegistrationPersistentMap.IHolder persistentMapHolder)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/recovery/DataSetStorageRecoveryManager.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/recovery/DataSetStorageRecoveryManager.java
index 2f80bf6f284..a47d8a2300c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/recovery/DataSetStorageRecoveryManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/recovery/DataSetStorageRecoveryManager.java
@@ -57,6 +57,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
/**
* Serializes data for recovery information
*/
+ @Override
public <T extends DataSetInformation> void checkpointPrecommittedState(TechId registrationId,
DataSetStorageAlgorithmRunner<T> runner)
{
@@ -70,6 +71,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
checkpointState(runner, recoveryState, RecoveryStage.PRECOMMIT);
}
+ @Override
public <T extends DataSetInformation> void checkpointPrecommittedStateAfterPostRegistrationHook(
DataSetStorageAlgorithmRunner<T> runner)
{
@@ -83,6 +85,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
checkpointState(runner, recoveryState, RecoveryStage.POST_REGISTRATION_HOOK_EXECUTED);
}
+ @Override
public <T extends DataSetInformation> void checkpointStoredStateBeforeStorageConfirmation(
DataSetStorageAlgorithmRunner<T> runner)
{
@@ -115,6 +118,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
operationLog.info("Store recovery checkpoint with markerfile " + processingMarkerFile);
}
+ @Override
public <T extends DataSetInformation> void removeCheckpoint(
DataSetStorageAlgorithmRunner<T> runner)
{
@@ -130,6 +134,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
/**
* @return processing marker file for a given incoming file.
*/
+ @Override
public File getProcessingMarkerFile(File incoming)
{
return new File(recoveryMarkerFilesDir, incoming.getName() + PROCESSING_MARKER);
@@ -144,11 +149,13 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
return new File(dropboxRecoveryStateDir, incomingFileName + PRECOMMIT_SERIALIZED);
}
+ @Override
public DataSetStorageRecoveryInfo getRecoveryFileFromMarker(File markerFile)
{
return DataSetStorageRecoveryInfo.loadFromFile(markerFile);
}
+ @Override
@SuppressWarnings("unchecked")
public <T extends DataSetInformation> AbstractRecoveryState<T> extractRecoveryCheckpoint(
File markerFile)
@@ -158,6 +165,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
DataSetStoragePrecommitRecoveryState.class);
}
+ @Override
public <T extends DataSetInformation> void registrationCompleted(
DataSetStorageAlgorithmRunner<T> runner)
{
@@ -177,6 +185,7 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
FileUtilities.delete(recoveryState);
}
+ @Override
public boolean canRecoverFromError(Throwable ex)
{
if (ex instanceof UserFailureException)
@@ -186,31 +195,37 @@ public class DataSetStorageRecoveryManager implements IDataSetStorageRecoveryMan
return true;
}
+ @Override
public void setDropboxRecoveryStateDir(File dropboxRecoveryStateDir)
{
this.dropboxRecoveryStateDir = dropboxRecoveryStateDir;
}
+ @Override
public void setRecoveryMarkerFilesDir(File recoveryMarkerFileDir)
{
this.recoveryMarkerFilesDir = recoveryMarkerFileDir;
}
+ @Override
public void setMaximumRertyCount(int maxRetryCount)
{
this.maxRetryCount = maxRetryCount;
}
+ @Override
public int getMaximumRertyCount()
{
return this.maxRetryCount;
}
+ @Override
public int getRetryPeriodInSeconds()
{
return retryPeriodInSeconds;
}
+ @Override
public void setRetryPeriodInSeconds(int retryPeriodInSeconds)
{
this.retryPeriodInSeconds = retryPeriodInSeconds;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/threev/AbstractDataSetInfoExtractorFor3V.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/threev/AbstractDataSetInfoExtractorFor3V.java
index 3d3edad2f37..c75d2cf2a7d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/threev/AbstractDataSetInfoExtractorFor3V.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/threev/AbstractDataSetInfoExtractorFor3V.java
@@ -82,6 +82,7 @@ abstract class AbstractDataSetInfoExtractorFor3V extends AbstractDataSetInfoExtr
// AbstractCodeExtractor
//
+ @Override
public DataSetInformation getDataSetInformation(final File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java
index 30f8cbda308..0a2b2dbdf4e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PostRegistrationExecutor.java
@@ -61,6 +61,7 @@ public class PostRegistrationExecutor extends AbstractPreOrPostRegistrationExecu
operationLog.info(getExecutorAdjectivalDescription() + " script: " + script);
}
+ @Override
public boolean execute(final String dataSetCode, final String dataSetAbsolutePathInStore)
{
return callScript(operationLog, machineLog, scriptPath, dataSetCode,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutor.java
index 8e132070be3..634f6471e1b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutor.java
@@ -61,6 +61,7 @@ public class PreRegistrationExecutor extends AbstractPreOrPostRegistrationExecut
operationLog.info(getExecutorAdjectivalDescription() + " script: " + script);
}
+ @Override
public boolean execute(final String dataSetCode, final String dataSetAbsolutePathInDropbox)
{
return callScript(operationLog, machineLog, scriptPath, dataSetCode,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreprocessingExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreprocessingExecutor.java
index 3fca2f8dcf6..482d294117b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreprocessingExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/PreprocessingExecutor.java
@@ -129,6 +129,7 @@ public class PreprocessingExecutor
.executeCallable(new Callable<Object>()
{
// returns null on error, non-null on success
+ @Override
public Object call() throws Exception
{
boolean ok = executeOnce(filePath);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/TabSeparatedValueTable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/TabSeparatedValueTable.java
index 9b097b0453f..7c2c48bfe41 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/TabSeparatedValueTable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/utils/TabSeparatedValueTable.java
@@ -51,6 +51,7 @@ public class TabSeparatedValueTable
this.ignoreHashedLines = ignoreHashedLines;
}
+ @Override
public boolean hasNext()
{
if (currentLine == null)
@@ -60,6 +61,7 @@ public class TabSeparatedValueTable
return currentLine != null;
}
+ @Override
public String next()
{
if (currentLine == null)
@@ -80,6 +82,7 @@ public class TabSeparatedValueTable
return currentLineNumber;
}
+ @Override
public void remove()
{
throw new UnsupportedOperationException();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
index 1c87958daaf..839eef07590 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AbstractValidator.java
@@ -38,6 +38,7 @@ abstract class AbstractValidator implements IValidator
this.emptyValueSynonyms = emptyValueSynonyms;
}
+ @Override
public final void assertValid(String value)
{
if (allowEmptyValues)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AnyValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AnyValidatorFactory.java
index 7c68dc191b4..e9187e60d68 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AnyValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/AnyValidatorFactory.java
@@ -23,6 +23,7 @@ final class AnyValidatorFactory implements IValidatorFactory
IValidator VALIDATOR = new IValidator()
{
+ @Override
public void assertValid(String value)
{
}
@@ -32,6 +33,7 @@ final class AnyValidatorFactory implements IValidatorFactory
{
}
+ @Override
public IValidator createValidator(String header)
{
return VALIDATOR;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
index 63346c68a7e..d4f1ed6d11a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidator.java
@@ -105,6 +105,7 @@ public class DataSetValidator implements IDataSetValidator
return ClassUtils.create(IDataSetValidator.class, validatorClass, validatorProperties);
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, File incomingDataSetFileOrFolder)
{
IDataSetValidator validator = validators.get(dataSetType.getCode());
@@ -126,6 +127,7 @@ public class DataSetValidator implements IDataSetValidator
}
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, Reader reader, String dataSourceName)
{
IDataSetValidator validator = validators.get(dataSetType.getCode());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
index 49915307da5..2ddc1605434 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSV.java
@@ -134,6 +134,7 @@ public class DataSetValidatorForTSV implements IDataSetValidator
}
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, File incomingDataSetFileOrFolder)
{
Set<File> excludedFiles = new HashSet<File>();
@@ -179,6 +180,7 @@ public class DataSetValidatorForTSV implements IDataSetValidator
}
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, Reader reader, String dataSourceName)
{
TabSeparatedValueTable table =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
index 5fbbb8b01b5..ac048282b7a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/DefaultValueValidatorFactory.java
@@ -97,6 +97,7 @@ public class DefaultValueValidatorFactory implements IValidatorFactory
factory = valueType.createFactory(properties);
}
+ @Override
public IValidator createValidator(String header)
{
return factory.createValidator(header);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/HeaderBasedValueValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/HeaderBasedValueValidatorFactory.java
index f6774f0d71c..25252197472 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/HeaderBasedValueValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/HeaderBasedValueValidatorFactory.java
@@ -84,6 +84,7 @@ public class HeaderBasedValueValidatorFactory implements IValidatorFactory
headerMessage = builder.toString();
}
+ @Override
public IValidator createValidator(String columnHeader)
{
for (HeaderPatternAndFactory factory : factories)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactory.java
index 904f1b98a65..c8549987a7f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactory.java
@@ -152,6 +152,7 @@ class NumericValidatorFactory extends AbstractValidatorFactory
validator = new NumericValidator(allowEmptyValues, emptyValueSynonyms, rangeOrNull);
}
+ @Override
public IValidator createValidator(String header)
{
return validator;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/RegExBasedValidator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/RegExBasedValidator.java
index 7b22151a170..777f9f7270c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/RegExBasedValidator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/RegExBasedValidator.java
@@ -54,6 +54,7 @@ class RegExBasedValidator extends AbstractValidator implements IColumnHeaderVali
}
}
+ @Override
public Result validateHeader(String header)
{
if (pattern.matcher(header).matches())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactory.java
index 0ae8424e943..dbb9241a268 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactory.java
@@ -38,6 +38,7 @@ class StringValidatorFactory extends AbstractValidatorFactory
validator = new RegExBasedValidator(allowEmptyValues, emptyValueSynonyms, regex);
}
+ @Override
public IValidator createValidator(String header)
{
return validator;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueGroupValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueGroupValidatorFactory.java
index 9562b1d34b2..f7d54c519ab 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueGroupValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueGroupValidatorFactory.java
@@ -68,6 +68,7 @@ class UniqueGroupValidatorFactory implements IValidatorFactory
return "Illegal group: " + g;
}
+ @Override
public IValidator createValidator(String header)
{
return new UniqueGroupValidator(regex, groups);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueValidatorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueValidatorFactory.java
index 9dc1cb5160e..1db62c31b1c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueValidatorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/validation/UniqueValidatorFactory.java
@@ -43,12 +43,14 @@ class UniqueValidatorFactory implements IValidatorFactory
}
}
+ @Override
public IValidator createValidator(String header)
{
return new IValidator()
{
private final Set<String> values = new HashSet<String>();
+ @Override
public void assertValid(String value)
{
validator.assertValid(value);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommand.java
index 20d321b7832..df17a0de1a9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommand.java
@@ -43,6 +43,7 @@ abstract public class AbstractCommand<T extends GlobalArguments> implements ICom
/**
* Print usage information about the command.
*/
+ @Override
public void printUsage(PrintStream out)
{
out.println(getUsagePrefixString() + " [options] " + getRequiredArgumentsString());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommandFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommandFactory.java
index 02191c0314c..d0dc14d0593 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommandFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/AbstractCommandFactory.java
@@ -59,6 +59,7 @@ abstract public class AbstractCommandFactory implements ICommandFactory
*
* @param parentCommandFactoryOrNull A command factory, or null if this one has no parent.
*/
+ @Override
public void setParentCommandFactory(ICommandFactory parentCommandFactoryOrNull)
{
this.parentCommandFactoryOrNull = parentCommandFactoryOrNull;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandGet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandGet.java
index 6077f8b15d4..7d794fc9e6d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandGet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandGet.java
@@ -69,16 +69,19 @@ class CommandGet extends AbstractDssCommand<CommandGet.CommandGetArguments>
this.targetDir = targetDir;
}
+ @Override
public void willDownload(FileInfoDssDTO fileInfo)
{
System.out.println("downloading " + getPathForFileInfo(fileInfo));
}
+ @Override
public void willCreateDirectory(FileInfoDssDTO fileInfo)
{
System.out.println("mkdir " + getPathForFileInfo(fileInfo));
}
+ @Override
public void didFinish()
{
System.out.println("Finished.");
@@ -161,12 +164,14 @@ class CommandGet extends AbstractDssCommand<CommandGet.CommandGetArguments>
super(new CommandGetArguments());
}
+ @Override
public ResultCode execute(String[] args) throws UserFailureException,
EnvironmentFailureException
{
return new CommandGetExecutor(arguments, this).execute(args);
}
+ @Override
public String getName()
{
return "get";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandHelp.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandHelp.java
index bffda17932f..dc8d39708d6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandHelp.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandHelp.java
@@ -45,6 +45,7 @@ public class CommandHelp extends AbstractCommand<CommandHelp.CommandHelpArgument
this.programCallString = programCallString;
}
+ @Override
public ResultCode execute(String[] args) throws UserFailureException,
EnvironmentFailureException
{
@@ -66,6 +67,7 @@ public class CommandHelp extends AbstractCommand<CommandHelp.CommandHelpArgument
return ResultCode.OK;
}
+ @Override
public String getName()
{
return "help";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandLs.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandLs.java
index b27409a39bd..76315197c5f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandLs.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandLs.java
@@ -61,12 +61,14 @@ class CommandLs extends AbstractDssCommand<DataSetArguments>
super(new DataSetArguments());
}
+ @Override
public ResultCode execute(String[] args) throws UserFailureException,
EnvironmentFailureException
{
return new CommandLsExecutor(arguments, this).execute(args);
}
+ @Override
public String getName()
{
return "ls";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPut.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPut.java
index 5ccde812032..f7383215162 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPut.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPut.java
@@ -239,12 +239,14 @@ class CommandPut extends AbstractDssCommand<CommandPut.CommandPutArguments>
super(new CommandPutArguments());
}
+ @Override
public ResultCode execute(String[] args) throws UserFailureException,
EnvironmentFailureException
{
return new CommandPutExecutor(arguments, this).execute(args);
}
+ @Override
public String getName()
{
return "put";
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
index 81763a8366e..98667a2f324 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandTestValid.java
@@ -223,12 +223,14 @@ class CommandTestValid extends AbstractDssCommand<CommandTestValid.CommandTestVa
super(new CommandTestValidArguments());
}
+ @Override
public ResultCode execute(String[] args) throws UserFailureException,
EnvironmentFailureException
{
return new CommandTestValidExecutor(arguments, this).execute(args);
}
+ @Override
public String getName()
{
return "testvalid";
@@ -273,39 +275,46 @@ class CommandTestValid extends AbstractDssCommand<CommandTestValid.CommandTestVa
IDssComponent component = new IDssComponent()
{
+ @Override
public void checkSession() throws InvalidSessionException
{
}
+ @Override
public String getSessionToken() throws IllegalStateException
{
return null;
}
+ @Override
public IDataSetDss getDataSet(String code) throws IllegalStateException,
EnvironmentFailureException
{
return null;
}
+ @Override
public IDataSetDss putDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
return null;
}
+ @Override
public void logout()
{
}
+ @Override
public List<ValidationError> validateDataSet(NewDataSetDTO newDataset,
File dataSetFile) throws IllegalStateException, EnvironmentFailureException
{
return new ArrayList<ValidationError>();
}
+ @Override
public Map<String, String> extractMetadata(NewDataSetDTO newDataset,
File dataSetFile) throws IllegalStateException, EnvironmentFailureException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CompositeCommandFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CompositeCommandFactory.java
index 70834ba3c72..64beabd463d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CompositeCommandFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CompositeCommandFactory.java
@@ -47,6 +47,7 @@ public class CompositeCommandFactory extends AbstractCommandFactory
}
}
+ @Override
public List<String> getKnownCommands()
{
ArrayList<String> commands = new ArrayList<String>();
@@ -57,11 +58,13 @@ public class CompositeCommandFactory extends AbstractCommandFactory
return commands;
}
+ @Override
public ICommand getHelpCommand()
{
return new CommandHelp(this, programCallString);
}
+ @Override
public ICommand tryCommandForName(String name)
{
for (ICommandFactory factory : factories)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/DssCommandFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/DssCommandFactory.java
index 5fd296ec5b7..ed3d038b21c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/DssCommandFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/cli/DssCommandFactory.java
@@ -31,6 +31,7 @@ public class DssCommandFactory extends AbstractCommandFactory
LS, GET, HELP, PUT, TESTVALID, TESTEXTRACT,
}
+ @Override
public ICommand tryCommandForName(String name)
{
ICommand helpCommandOrNull = tryHelpCommandForName(name);
@@ -77,11 +78,13 @@ public class DssCommandFactory extends AbstractCommandFactory
return result;
}
+ @Override
public ICommand getHelpCommand()
{
return getHelpCommand(PROGRAM_CALL_STRING);
}
+ @Override
public List<String> getKnownCommands()
{
String[] commands =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractEntityPickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractEntityPickerDialog.java
index 39617de26e8..9ba4a504b14 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractEntityPickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractEntityPickerDialog.java
@@ -80,6 +80,7 @@ public abstract class AbstractEntityPickerDialog extends JDialog
button.setText("Refresh");
button.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
button.setEnabled(false);
@@ -102,6 +103,7 @@ public abstract class AbstractEntityPickerDialog extends JDialog
// update UI
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
setDialogData();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
index 7656d081067..b4b61750fce 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
@@ -27,6 +27,7 @@ import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
+import javax.swing.WindowConstants;
import org.apache.commons.lang.WordUtils;
import org.apache.commons.lang.time.DateUtils;
@@ -71,7 +72,7 @@ public abstract class AbstractSwingGUI
// create the window frame
windowFrame = new JFrame(getTitle());
- windowFrame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+ windowFrame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
// add callbacks to close the app properly
shutdownHook = new Thread()
@@ -96,6 +97,7 @@ public abstract class AbstractSwingGUI
addWindowCloseHook();
Thread.setDefaultUncaughtExceptionHandler(new Thread.UncaughtExceptionHandler()
{
+ @Override
public void uncaughtException(Thread thread, Throwable throwable)
{
final String message =
@@ -236,6 +238,7 @@ public abstract class AbstractSwingGUI
{
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showMessageDialog(parentFrame,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
index 3cebcd0e563..8874930cd30 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
@@ -95,6 +95,7 @@ public class AddVocabularyTermDialog extends JDialog
JButton addButton = new JButton("Add");
addButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clientModel.addUnofficialVocabularyTerm(vocabulary, codeField.getText(),
@@ -108,6 +109,7 @@ public class AddVocabularyTermDialog extends JDialog
JButton cancelButton = new JButton("Cancel");
cancelButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AddVocabularyTermDialog.this.dispose();
@@ -135,16 +137,19 @@ public class AddVocabularyTermDialog extends JDialog
labelField.requestFocus();
labelField.addKeyListener(new KeyListener()
{
+ @Override
public void keyPressed(KeyEvent arg0)
{
handleEvent();
}
+ @Override
public void keyReleased(KeyEvent arg0)
{
handleEvent();
}
+ @Override
public void keyTyped(KeyEvent arg0)
{
handleEvent();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetMetadataPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetMetadataPanel.java
index a265daa6eee..68f56ee6808 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetMetadataPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetMetadataPanel.java
@@ -47,6 +47,7 @@ import javax.swing.JComponent;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.SwingConstants;
import ch.systemsx.cisd.openbis.dss.client.api.gui.DataSetPropertiesPanel.Observer;
import ch.systemsx.cisd.openbis.dss.client.api.gui.DataSetUploadClientModel.NewDataSetInfo;
@@ -62,6 +63,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
{
private class AsynchronousValidator implements Runnable
{
+ @Override
public void run()
{
while (true)
@@ -88,6 +90,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
{
private ValidatedFile file = null;
+ @Override
public void run()
{
while (true)
@@ -183,7 +186,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
this.mainWindow = mainWindow;
// Initialize the fields in the gui
- ownerIdLabel = new JLabel("Owner:", JLabel.TRAILING);
+ ownerIdLabel = new JLabel("Owner:", SwingConstants.TRAILING);
samplePanel = new SamplePickerPanel(mainWindow, clientModel);
dataSetPanel = new DataSetPickerPanel(mainWindow, clientModel);
experimentPicker = new ExperimentPickerPanel(mainWindow, clientModel);
@@ -203,7 +206,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetFileComboBox = new JComboBox(initialOptions);
dataSetFileButton = new JButton("Browse...");
dataSetFileValidateButton = new JButton("Validate");
- dataSetFileLabel = new JLabel("File:", JLabel.TRAILING);
+ dataSetFileLabel = new JLabel("File:", SwingConstants.TRAILING);
validationErrors = new ErrorsPanel(mainWindow);
@@ -310,6 +313,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetFileComboBox.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
if (null == newDataSetInfo)
@@ -340,6 +344,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetFileButton.setToolTipText("The file to upload.");
dataSetFileButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (null == newDataSetInfo)
@@ -364,6 +369,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetFileValidateButton.setToolTipText("File will be refreshed and revalidated");
dataSetFileValidateButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
if (null == newDataSetInfo
@@ -385,6 +391,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
samplePanel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
setOwnerId(samplePanel.getText());
@@ -394,11 +401,13 @@ public class DataSetMetadataPanel extends JPanel implements Observer
samplePanel.addFocusListener(new FocusListener()
{
+ @Override
public void focusLost(FocusEvent e)
{
setOwnerId(samplePanel.getText());
}
+ @Override
public void focusGained(FocusEvent e)
{
// Do nothing
@@ -409,6 +418,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
experimentPicker.setToolTipText("Experiment identifier");
experimentPicker.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
setOwnerId(experimentPicker.getText());
@@ -417,11 +427,13 @@ public class DataSetMetadataPanel extends JPanel implements Observer
});
experimentPicker.addFocusListener(new FocusListener()
{
+ @Override
public void focusLost(FocusEvent e)
{
setOwnerId(experimentPicker.getText());
}
+ @Override
public void focusGained(FocusEvent e)
{
// Do nothing
@@ -433,6 +445,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetPanel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
setOwnerId(dataSetPanel.getText());
@@ -442,11 +455,13 @@ public class DataSetMetadataPanel extends JPanel implements Observer
dataSetPanel.addFocusListener(new FocusListener()
{
+ @Override
public void focusLost(FocusEvent e)
{
setOwnerId(dataSetPanel.getText());
}
+ @Override
public void focusGained(FocusEvent e)
{
// Do nothing
@@ -456,6 +471,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
ownerComboBox.setPreferredSize(new Dimension(BUTTON_WIDTH, BUTTON_HEIGHT));
ownerComboBox.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
DataSetOwnerType type = (DataSetOwnerType) ownerComboBox.getSelectedItem();
@@ -472,7 +488,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
addRow(2, ownerIdLabel, ownerIdPanel, ownerComboBox);
// The data set type row
- JLabel label = new JLabel("Data Set Type:", JLabel.TRAILING);
+ JLabel label = new JLabel("Data Set Type:", SwingConstants.TRAILING);
label.setPreferredSize(new Dimension(LABEL_WIDTH, BUTTON_HEIGHT));
dataSetTypeComboBox.setPreferredSize(new Dimension(BUTTON_WIDTH, BUTTON_HEIGHT));
@@ -483,6 +499,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
}
dataSetTypeComboBox.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
setDataSetType((String) e.getItem());
@@ -764,6 +781,7 @@ public class DataSetMetadataPanel extends JPanel implements Observer
component.setToolTipText(label.getToolTipText());
}
+ @Override
public void update()
{
validationQueue.add(Boolean.TRUE);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
index 9183b4d1aee..db6d7ba75c6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
@@ -126,6 +126,7 @@ public class DataSetPickerDialog extends AbstractEntityPickerDialog implements
new JOptionPane(objects, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
optionPane.addPropertyChangeListener(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals(JOptionPane.VALUE_PROPERTY)
@@ -173,16 +174,19 @@ public class DataSetPickerDialog extends AbstractEntityPickerDialog implements
textField.setEditable(true);
textField.getDocument().addDocumentListener(new DocumentListener()
{
+ @Override
public void removeUpdate(DocumentEvent e)
{
updateTreeSelection();
}
+ @Override
public void insertUpdate(DocumentEvent e)
{
updateTreeSelection();
}
+ @Override
public void changedUpdate(DocumentEvent e)
{
updateTreeSelection();
@@ -241,6 +245,7 @@ public class DataSetPickerDialog extends AbstractEntityPickerDialog implements
return true;
}
+ @Override
public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException
{
final DefaultMutableTreeNode node =
@@ -331,6 +336,7 @@ public class DataSetPickerDialog extends AbstractEntityPickerDialog implements
return dataSets;
}
+ @Override
public void treeWillCollapse(TreeExpansionEvent event) throws ExpandVetoException
{
DefaultMutableTreeNode node =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerPanel.java
index 89aa0db1460..88d39b32dd7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerPanel.java
@@ -36,6 +36,7 @@ public class DataSetPickerPanel extends AbstractEntityPickerPanel
dialog = new DataSetPickerDialog(mainWindow, clientModel);
}
+ @Override
public void actionPerformed(ActionEvent e)
{
String dataSetId = dialog.pickDataSet();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
index 7d1270cc8d6..40fff89b1f3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
@@ -43,6 +43,7 @@ import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;
+import javax.swing.SwingConstants;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
@@ -135,7 +136,7 @@ public class DataSetPropertiesPanel extends JPanel
private void addFormFieldForPropertyType(int row, int col, final PropertyType propertyType)
{
String labelString = getLabelStringForPropertyType(propertyType);
- JLabel label = new JLabel(labelString + ":", JLabel.TRAILING);
+ JLabel label = new JLabel(labelString + ":", SwingConstants.TRAILING);
label.setPreferredSize(new Dimension(LABEL_WIDTH, BUTTON_HEIGHT));
label.setToolTipText(propertyType.getDescription());
if (propertyType.isMandatory())
@@ -168,15 +169,18 @@ public class DataSetPropertiesPanel extends JPanel
class FieldListener implements ActionListener, FocusListener
{
+ @Override
public void focusGained(FocusEvent e)
{
}
+ @Override
public void focusLost(FocusEvent e)
{
handleEvent();
}
+ @Override
public void actionPerformed(ActionEvent e)
{
handleEvent();
@@ -211,6 +215,7 @@ public class DataSetPropertiesPanel extends JPanel
comboBox.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
setPropertyValue(propertyType, ((VocabularyTerm) e.getItem()).getCode());
@@ -227,6 +232,7 @@ public class DataSetPropertiesPanel extends JPanel
checkBox.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
setPropertyValue(propertyType,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
index ce6c7feb85e..5e9ac8e6de1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
@@ -209,6 +209,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
addButton.setToolTipText("Add a new data set");
addButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
tableModel.addNewDataSet();
@@ -220,6 +221,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
removeButton.setToolTipText("Remove the selected data set");
removeButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
tableModel.removeSelectedDataSet();
@@ -231,6 +233,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
uploadAllButton.setToolTipText("Attach the data set to a sample.");
uploadAllButton.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clientModel.queueUploadOfDataSet(clientModel.getNewDataSetInfos());
@@ -265,6 +268,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
fileTable.getSelectionModel().addListSelectionListener(new ListSelectionListener()
{
+ @Override
public void valueChanged(ListSelectionEvent e)
{
// Notify the table model
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadOperation.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadOperation.java
index 007bd0240d8..33755669944 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadOperation.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadOperation.java
@@ -59,6 +59,7 @@ final class DataSetUploadOperation implements Runnable
this.newDataSetInfo = newDataSetInfo;
}
+ @Override
public void run()
{
try
@@ -94,7 +95,7 @@ final class DataSetUploadOperation implements Runnable
}
if (actualTh instanceof FileExistsException == false)
{
- DataSetUploadClient.notifyUserOfThrowable(tableModel.getMainWindow(),
+ AbstractSwingGUI.notifyUserOfThrowable(tableModel.getMainWindow(),
newDataSetInfo.getNewDataSetBuilder().getFile().getAbsolutePath(),
"Uploading", actualTh, null);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadTableModel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadTableModel.java
index bf078000653..de3885c0e82 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadTableModel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadTableModel.java
@@ -124,6 +124,7 @@ public class DataSetUploadTableModel extends AbstractTableModel
*/
private class NewDataSetInfoComparator implements Comparator<NewDataSetInfo>
{
+ @Override
public int compare(NewDataSetInfo info1, NewDataSetInfo info2)
{
int result = 0;
@@ -197,11 +198,13 @@ public class DataSetUploadTableModel extends AbstractTableModel
selectNewDataSetInfo(selectedDataSet);
}
+ @Override
public int getColumnCount()
{
return 5;
}
+ @Override
public int getRowCount()
{
return newDataSetInfos.size();
@@ -236,6 +239,7 @@ public class DataSetUploadTableModel extends AbstractTableModel
return name;
}
+ @Override
public Object getValueAt(int rowIndex, int columnIndex)
{
NewDataSetInfo newDataSetInfo = newDataSetInfos.get(rowIndex);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorMessageDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorMessageDialog.java
index 59073ab15df..067210a9d9d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorMessageDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorMessageDialog.java
@@ -97,6 +97,7 @@ public class ErrorMessageDialog extends JDialog
popup.add(menuItem);
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
errorArea.copy();
@@ -105,6 +106,7 @@ public class ErrorMessageDialog extends JDialog
optionPane.addPropertyChangeListener(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorsPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorsPanel.java
index 7ab00087cce..55208abf351 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorsPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ErrorsPanel.java
@@ -33,6 +33,7 @@ import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.ScrollPaneConstants;
+import javax.swing.SwingConstants;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
@@ -80,9 +81,9 @@ public class ErrorsPanel extends JPanel
.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
this.add(errorsAreaScroll, VALIDATION_ERRORS_CARD);
- this.add(new JLabel("Validating, please wait...", WAIT_ICON, JLabel.LEFT),
+ this.add(new JLabel("Validating, please wait...", WAIT_ICON, SwingConstants.LEFT),
VALIDATION_WAIT_CARD);
- this.add(new JLabel("Validated successfully.", OK_ICON, JLabel.LEFT),
+ this.add(new JLabel("Validated successfully.", OK_ICON, SwingConstants.LEFT),
VALIDATION_SUCCESS_CARD);
}
@@ -111,7 +112,7 @@ public class ErrorsPanel extends JPanel
{
JPanel line = new JPanel(new FlowLayout(FlowLayout.LEFT));
String truncateErrorMessage = truncateErrorMessage(error);
- JLabel label = new JLabel(truncateErrorMessage, WRONG_ICON, JLabel.LEFT);
+ JLabel label = new JLabel(truncateErrorMessage, WRONG_ICON, SwingConstants.LEFT);
line.add(label);
if (truncateErrorMessage.length() < error.length())
{
@@ -119,6 +120,7 @@ public class ErrorsPanel extends JPanel
button.setPreferredSize(new Dimension(25, label.getPreferredSize().height));
button.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
errorMessageDialog.showErrorMessage(error);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerDialog.java
index 5c237150486..1e3e9e6d516 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerDialog.java
@@ -86,6 +86,7 @@ public class ExperimentPickerDialog extends AbstractEntityPickerDialog
new JOptionPane(objects, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
optionPane.addPropertyChangeListener(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals(JOptionPane.VALUE_PROPERTY)
@@ -164,6 +165,7 @@ public class ExperimentPickerDialog extends AbstractEntityPickerDialog
filterField.setEditable(true);
filterField.getDocument().addDocumentListener(new DocumentListener()
{
+ @Override
public void removeUpdate(DocumentEvent e)
{
SortableFilterableTableModel model =
@@ -171,6 +173,7 @@ public class ExperimentPickerDialog extends AbstractEntityPickerDialog
model.filter(filterField.getText());
}
+ @Override
public void insertUpdate(DocumentEvent e)
{
SortableFilterableTableModel model =
@@ -178,6 +181,7 @@ public class ExperimentPickerDialog extends AbstractEntityPickerDialog
model.filter(filterField.getText());
}
+ @Override
public void changedUpdate(DocumentEvent e)
{
SortableFilterableTableModel model =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerPanel.java
index c60103ed2c7..7824506a9eb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/ExperimentPickerPanel.java
@@ -36,6 +36,7 @@ public class ExperimentPickerPanel extends AbstractEntityPickerPanel
dialog = new ExperimentPickerDialog(mainWindow, clientModel);
}
+ @Override
public void actionPerformed(ActionEvent e)
{
String experimentId = dialog.pickExperiment();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
index c6b2d4143d0..7a6ec885988 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
@@ -127,6 +127,7 @@ public class SamplePickerDialog extends AbstractEntityPickerDialog implements
theOptionPane.addPropertyChangeListener(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (false == evt.getPropertyName().equals(JOptionPane.VALUE_PROPERTY)
@@ -198,16 +199,19 @@ public class SamplePickerDialog extends AbstractEntityPickerDialog implements
textField.setEditable(true);
textField.getDocument().addDocumentListener(new DocumentListener()
{
+ @Override
public void removeUpdate(DocumentEvent e)
{
updateTreeSelection();
}
+ @Override
public void insertUpdate(DocumentEvent e)
{
updateTreeSelection();
}
+ @Override
public void changedUpdate(DocumentEvent e)
{
updateTreeSelection();
@@ -261,6 +265,7 @@ public class SamplePickerDialog extends AbstractEntityPickerDialog implements
}
}
+ @Override
public void treeWillExpand(TreeExpansionEvent event) throws ExpandVetoException
{
// if top level, then finish
@@ -303,6 +308,7 @@ public class SamplePickerDialog extends AbstractEntityPickerDialog implements
return samples;
}
+ @Override
public void treeWillCollapse(TreeExpansionEvent event) throws ExpandVetoException
{
DefaultMutableTreeNode node =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerPanel.java
index 5336ac80b86..b6eca79426f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerPanel.java
@@ -36,6 +36,7 @@ public class SamplePickerPanel extends AbstractEntityPickerPanel
dialog = new SamplePickerDialog(mainWindow, clientModel);
}
+ @Override
public void actionPerformed(ActionEvent e)
{
String sampleId = dialog.pickSample();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadClientSortingUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadClientSortingUtils.java
index c405471b3f6..d2787498232 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadClientSortingUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadClientSortingUtils.java
@@ -35,6 +35,7 @@ public class UploadClientSortingUtils
{
CollectionUtils.sort(samples, new IKeyExtractor<String, Sample>()
{
+ @Override
public String getKey(Sample sample)
{
return sample.getIdentifier();
@@ -46,6 +47,7 @@ public class UploadClientSortingUtils
{
CollectionUtils.sort(samples, new IKeyExtractor<String, Experiment>()
{
+ @Override
public String getKey(Experiment experiment)
{
return experiment.getIdentifier();
@@ -57,6 +59,7 @@ public class UploadClientSortingUtils
{
CollectionUtils.sort(dataSets, new IKeyExtractor<String, DataSet>()
{
+ @Override
public String getKey(DataSet dataSet)
{
return dataSet.getCode();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellEditor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellEditor.java
index 625e89602ae..b395c57c725 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellEditor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellEditor.java
@@ -47,6 +47,7 @@ public class UploadStatusTableCellEditor extends AbstractCellEditor implements T
button.setOpaque(true);
button.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fireEditingStopped();
@@ -54,6 +55,7 @@ public class UploadStatusTableCellEditor extends AbstractCellEditor implements T
});
}
+ @Override
public Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected,
int row, int column)
{
@@ -69,6 +71,7 @@ public class UploadStatusTableCellEditor extends AbstractCellEditor implements T
return button;
}
+ @Override
public Object getCellEditorValue()
{
return tableModel.getSelectedNewDataSetOrNull();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellRenderer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellRenderer.java
index 28f5c07deab..97839526490 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellRenderer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UploadStatusTableCellRenderer.java
@@ -116,6 +116,7 @@ public class UploadStatusTableCellRenderer implements TableCellRenderer
uploadPanel.setOpaque(true);
}
+ @Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
boolean hasFocus, int row, int column)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
index 53c0b10e890..4e3248b5f51 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
@@ -134,6 +134,7 @@ public class VocabularyTermsComboBoxPanel extends JPanel implements Observer
button.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AddVocabularyTermDialog dialog =
@@ -179,6 +180,7 @@ public class VocabularyTermsComboBoxPanel extends JPanel implements Observer
{
comboBox.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
itemListener.itemStateChanged(new ItemEvent(e.getItemSelectable(), e.getID(),
@@ -193,6 +195,7 @@ public class VocabularyTermsComboBoxPanel extends JPanel implements Observer
comboBox.setToolTipText(text);
}
+ @Override
public void update(@SuppressWarnings("hiding") Vocabulary vocabulary, String code)
{
String selectedCode =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/BevelArrowIcon.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/BevelArrowIcon.java
index 2cf524f5057..623fb96828a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/BevelArrowIcon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/BevelArrowIcon.java
@@ -113,6 +113,7 @@ public class BevelArrowIcon implements Icon
* @param x .
* @param y .
*/
+ @Override
public void paintIcon(final Component c, final Graphics g, final int x, final int y)
{
switch (this.direction)
@@ -131,6 +132,7 @@ public class BevelArrowIcon implements Icon
*
* @return the icon width.
*/
+ @Override
public int getIconWidth()
{
return this.size;
@@ -141,6 +143,7 @@ public class BevelArrowIcon implements Icon
*
* @return the icon height.
*/
+ @Override
public int getIconHeight()
{
return this.size;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortButtonRenderer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortButtonRenderer.java
index 4b22a969654..51ef2e6d2f0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortButtonRenderer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortButtonRenderer.java
@@ -165,6 +165,7 @@ public class SortButtonRenderer implements TableCellRenderer
* @param column the column.
* @return the renderer.
*/
+ @Override
public Component getTableCellRendererComponent(final JTable table, final Object value,
final boolean isSelected, final boolean hasFocus, final int row, final int column)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortableFilterableTableModel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortableFilterableTableModel.java
index daaaa9bd9bd..38ca3283069 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortableFilterableTableModel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/table/SortableFilterableTableModel.java
@@ -48,6 +48,7 @@ public class SortableFilterableTableModel extends AbstractTableModel
this.reverse = reverse;
}
+ @Override
public int compare(String[] o1, String[] o2)
{
if (reverse)
@@ -85,6 +86,7 @@ public class SortableFilterableTableModel extends AbstractTableModel
return headers[col];
}
+ @Override
public int getRowCount()
{
if (viewData != null)
@@ -96,6 +98,7 @@ public class SortableFilterableTableModel extends AbstractTableModel
}
}
+ @Override
public int getColumnCount()
{
return headers.length;
@@ -137,6 +140,7 @@ public class SortableFilterableTableModel extends AbstractTableModel
fireTableDataChanged();
}
+ @Override
public Object getValueAt(int rowIndex, int columnIndex)
{
if (viewData != null)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
index 16308fad99f..5d4219b7510 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
@@ -46,11 +46,13 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
this.pattern = pattern;
}
+ @Override
public boolean hasMoreElements()
{
return next != null;
}
+ @Override
public Object nextElement()
{
if (next == null)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/FileInfoDssDownloader.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/FileInfoDssDownloader.java
index 9a13204b6e8..ccdbdbd9610 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/FileInfoDssDownloader.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/FileInfoDssDownloader.java
@@ -61,16 +61,19 @@ public final class FileInfoDssDownloader
this(dataSetDss, fileInfos, outputDir, new FileInfoDssDownloaderListener()
{
+ @Override
public void willCreateDirectory(FileInfoDssDTO fileInfo)
{
}
+ @Override
public void willDownload(FileInfoDssDTO fileInfo)
{
}
+ @Override
public void didFinish()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
index d9603fa4ad9..93acd76dc28 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DataSetDss.java
@@ -45,35 +45,41 @@ public class DataSetDss implements IDataSetDss
this.parent = parent;
}
+ @Override
public String getCode()
{
return code;
}
+ @Override
public InputStream getFile(String path) throws IllegalArgumentException,
InvalidSessionException
{
return parent.getFile(this, path);
}
+ @Override
public FileInfoDssDTO[] listFiles(String startPath, boolean isRecursive)
throws IllegalArgumentException, InvalidSessionException
{
return parent.listFiles(this, startPath, isRecursive);
}
+ @Override
public File tryLinkToContents(String overrideStoreRootPathOrNull)
throws IllegalArgumentException, InvalidSessionException
{
return parent.tryLinkToContents(this, overrideStoreRootPathOrNull);
}
+ @Override
public File getLinkOrCopyOfContents(String overrideStoreRootPathOrNull, File downloadDir)
throws IllegalArgumentException, InvalidSessionException
{
return parent.getLinkOrCopyOfContents(this, overrideStoreRootPathOrNull, downloadDir, null);
}
+ @Override
public File getLinkOrCopyOfContent(String overrideStoreRootPathOrNull, File downloadDir,
String pathInDataSet) throws IllegalArgumentException, InvalidSessionException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
index 8898e6caef2..53cd41c7f25 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponent.java
@@ -169,22 +169,26 @@ public class DssComponent implements IDssComponent
}
}
+ @Override
public String getSessionToken()
{
return state.getSessionToken();
}
+ @Override
public void checkSession() throws InvalidSessionException
{
state.checkSession();
}
+ @Override
public IDataSetDss getDataSet(String code) throws EnvironmentFailureException,
IllegalStateException
{
return state.getDataSet(code);
}
+ @Override
public void logout()
{
// logout and transition to the unauthenticated state
@@ -209,18 +213,21 @@ public class DssComponent implements IDssComponent
state.getSessionToken());
}
+ @Override
public IDataSetDss putDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
return state.putDataSet(newDataset, dataSetFile);
}
+ @Override
public List<ValidationError> validateDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
return state.validateDataSet(newDataset, dataSetFile);
}
+ @Override
public Map<String, String> extractMetadata(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
@@ -245,28 +252,33 @@ abstract class AbstractDssComponentState implements IDssComponent
this.service = service;
}
+ @Override
public void checkSession() throws IllegalStateException
{
throw new IllegalStateException("Please log in");
}
+ @Override
public IDataSetDss getDataSet(String code) throws IllegalStateException
{
throw new IllegalStateException("Please log in");
}
+ @Override
public IDataSetDss putDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
throw new IllegalStateException("Please log in");
}
+ @Override
public List<ValidationError> validateDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
throw new IllegalStateException("Please log in");
}
+ @Override
public Map<String, String> extractMetadata(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
@@ -286,6 +298,7 @@ abstract class AbstractDssComponentState implements IDssComponent
/**
* Package visible method used to transfer context information between states.
*/
+ @Override
public abstract String getSessionToken();
}
@@ -327,6 +340,7 @@ class UnauthenticatedState extends AbstractDssComponentState
throw new AuthorizationFailureException("Login or Password invalid");
}
+ @Override
public void logout()
{
return;
@@ -371,6 +385,7 @@ class AuthenticatedState extends AbstractDssComponentState
}
}
+ @Override
public void logout()
{
service.logout(getSessionToken());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssServiceRpcFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssServiceRpcFactory.java
index d7cff59cf7d..37b51c0e506 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssServiceRpcFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssServiceRpcFactory.java
@@ -61,6 +61,7 @@ public class DssServiceRpcFactory implements IRpcServiceFactory
this.timeoutInMillis = timeoutInMillis;
}
+ @Override
public Collection<RpcServiceInterfaceDTO> getSupportedInterfaces(String serverURL,
boolean getServerCertificateFromServer) throws IncompatibleAPIVersionsException
{
@@ -78,6 +79,7 @@ public class DssServiceRpcFactory implements IRpcServiceFactory
return nameServer.getSupportedInterfaces();
}
+ @Override
public <T extends IRpcService> T getService(RpcServiceInterfaceVersionDTO ifaceVersion,
Class<T> ifaceClazz, String serverURL, boolean getServerCertificateFromServer)
throws IncompatibleAPIVersionsException
@@ -181,6 +183,7 @@ class ServiceProxyBuilder<T extends IRpcService>
this.service = service;
}
+ @Override
public Object invoke(Object proxy, Method method, Object[] args) throws Throwable
{
try
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
index 63e79dcef61..9741a72b96f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/OpenbisServiceFacade.java
@@ -189,29 +189,34 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
// ISimpleOpenbisServiceFacade
//
+ @Override
public List<Project> listProjects()
{
return service.listProjects(sessionToken);
}
+ @Override
public List<SpaceWithProjectsAndRoleAssignments> getSpacesWithProjects()
throws EnvironmentFailureException
{
return service.listSpacesWithProjectsAndRoleAssignments(sessionToken, null);
}
+ @Override
public List<Experiment> getExperiments(List<String> experimentIdentifiers)
throws EnvironmentFailureException
{
return service.listExperiments(sessionToken, experimentIdentifiers);
}
+ @Override
public List<Experiment> listExperimentsForProjects(List<String> projectIdentifiers)
throws EnvironmentFailureException
{
return service.listExperiments(sessionToken, getProjects(projectIdentifiers), null);
}
+ @Override
public List<Experiment> listExperimentsHavingSamplesForProjects(List<String> projectIdentifiers)
throws EnvironmentFailureException
{
@@ -219,6 +224,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
null);
}
+ @Override
public List<Experiment> listExperimentsHavingDataSetsForProjects(List<String> projectIdentifiers)
throws EnvironmentFailureException
{
@@ -238,12 +244,14 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return projects;
}
+ @Override
public List<Sample> getSamples(final List<String> sampleIdentifiers)
throws EnvironmentFailureException
{
return getSamples(sampleIdentifiers, null);
}
+ @Override
public List<Sample> getSamples(final List<String> sampleIdentifiers,
final EnumSet<SampleFetchOption> fetchOptions)
{
@@ -260,6 +268,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
List<Sample> filteredSamples =
CollectionUtils.filter(samples, new CollectionUtils.ICollectionFilter<Sample>()
{
+ @Override
public boolean isPresent(Sample element)
{
String identifier = element.getIdentifier();
@@ -269,12 +278,14 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return filteredSamples;
}
+ @Override
public List<Sample> listSamplesForExperiments(final List<String> experimentIdentifiers)
throws EnvironmentFailureException
{
return listSamplesForExperiments(experimentIdentifiers, null);
}
+ @Override
public List<Sample> listSamplesForExperiments(final List<String> experimentIdentifiers,
final EnumSet<SampleFetchOption> fetchOptions)
{
@@ -286,6 +297,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
List<Sample> filteredSamples =
CollectionUtils.filter(samples, new CollectionUtils.ICollectionFilter<Sample>()
{
+ @Override
public boolean isPresent(Sample element)
{
String identifier = element.getExperimentIdentifierOrNull();
@@ -295,11 +307,13 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return filteredSamples;
}
+ @Override
public List<Sample> listSamplesForProjects(List<String> projectIdentifiers)
{
return listSamplesForProjects(projectIdentifiers, null);
}
+ @Override
public List<Sample> listSamplesForProjects(List<String> projectIdentifiers,
EnumSet<SampleFetchOption> fetchOptions)
{
@@ -316,12 +330,14 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return samples;
}
+ @Override
public DataSet getDataSet(String dataSetCode) throws EnvironmentFailureException
{
List<DataSet> dataSets = getDataSets(Collections.singletonList(dataSetCode));
return (dataSets.size() > 0) ? dataSets.get(0) : null;
}
+ @Override
public List<DataSet> getDataSets(List<String> dataSetCodes) throws EnvironmentFailureException
{
enforceNotEmpty("Dataset codes", dataSetCodes);
@@ -336,6 +352,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return convertDataSets(service.searchForDataSets(sessionToken, searchCriteria));
}
+ @Override
public List<DataSet> listDataSetsForExperiments(final List<String> experimentIdentifiers)
throws EnvironmentFailureException
{
@@ -349,6 +366,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
.filter(dataSets,
new CollectionUtils.ICollectionFilter<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>()
{
+ @Override
public boolean isPresent(
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet dataSet)
{
@@ -360,6 +378,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return convertDataSets(filteredDataSets);
}
+ @Override
public List<DataSet> listDataSetsForSamples(final List<String> sampleIdentifiers)
throws EnvironmentFailureException
{
@@ -371,6 +390,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
.filter(dataSets,
new CollectionUtils.ICollectionFilter<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet>()
{
+ @Override
public boolean isPresent(
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet dataSet)
{
@@ -382,6 +402,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return convertDataSets(filteredDataSets);
}
+ @Override
public List<DataSetType> listDataSetTypes()
{
return service.listDataSetTypes(sessionToken);
@@ -392,6 +413,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return RetryProxyFactory.createProxy(dssComponent.getDataSet(code));
}
+ @Override
public DataSet putDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws EnvironmentFailureException
{
@@ -399,23 +421,27 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return new DataSet(this, dssComponent, null, dataSetDss);
}
+ @Override
public List<ValidationError> validateDataSet(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
return dssComponent.validateDataSet(newDataset, dataSetFile);
}
+ @Override
public Map<String, String> extractMetadata(NewDataSetDTO newDataset, File dataSetFile)
throws IllegalStateException, EnvironmentFailureException
{
return dssComponent.extractMetadata(newDataset, dataSetFile);
}
+ @Override
public void checkSession() throws InvalidSessionException
{
dssComponent.checkSession();
}
+ @Override
public synchronized void logout()
{
service.logout(sessionToken);
@@ -495,22 +521,26 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
//
// IOpenbisServiceFacade
//
+ @Override
public List<Sample> searchForSamples(SearchCriteria searchCriteria)
{
return service.searchForSamples(sessionToken, searchCriteria);
}
+ @Override
public List<Sample> searchForSamples(SearchCriteria searchCriteria,
EnumSet<SampleFetchOption> fetchOptions)
{
return service.searchForSamples(sessionToken, searchCriteria, fetchOptions);
}
+ @Override
public List<DataSet> searchForDataSets(SearchCriteria searchCriteria)
{
return convertDataSets(service.searchForDataSets(sessionToken, searchCriteria));
}
+ @Override
public List<DataSet> listDataSets(List<Sample> samples, EnumSet<Connections> connectionsToGet)
{
return convertDataSets(service.listDataSets(sessionToken, samples, connectionsToGet));
@@ -529,6 +559,7 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
return convertedDataSets;
}
+ @Override
@SuppressWarnings("deprecation")
public void addAdHocVocabularyTerm(TechId vocabularyId, String code, String label,
String description, Long previousTermOrdinal)
@@ -537,17 +568,20 @@ public class OpenbisServiceFacade implements IOpenbisServiceFacade
description, previousTermOrdinal);
}
+ @Override
public void addAdHocVocabularyTerm(Long vocabularyId, NewVocabularyTerm term)
{
changingService.addUnofficialVocabularyTerm(sessionToken, vocabularyId, term);
}
+ @Override
@SuppressWarnings("deprecation")
public HashMap<Vocabulary, List<VocabularyTerm>> getVocabularyTermsMap()
{
return service.getVocabularyTermsMap(sessionToken);
}
+ @Override
public List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary> listVocabularies()
{
return service.listVocabularies(sessionToken);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java
index 720d72d2ed0..2b7921da9eb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java
@@ -57,6 +57,7 @@ public class DataStoreServer
// UncaughtExceptionHandler
//
+ @Override
public final void uncaughtException(final Thread t, final Throwable e)
{
notificationLog.error("An exception has occurred [thread: '" + t.getName()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetDescriptionBasedCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetDescriptionBasedCommand.java
index 3e5b649f178..ef25cf42602 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetDescriptionBasedCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetDescriptionBasedCommand.java
@@ -38,6 +38,7 @@ abstract class AbstractDataSetDescriptionBasedCommand implements IDataSetCommand
this.dataSets = dataSets;
}
+ @Override
public List<String> getDataSetCodes()
{
List<String> result = new ArrayList<String>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetLocationBasedCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetLocationBasedCommand.java
index 92c8c6c0d04..4fa013f2a48 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetLocationBasedCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDataSetLocationBasedCommand.java
@@ -38,6 +38,7 @@ abstract class AbstractDataSetLocationBasedCommand implements IDataSetCommand
this.dataSets = dataSets;
}
+ @Override
public List<String> getDataSetCodes()
{
List<String> result = new ArrayList<String>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
index 045fae0479c..4d094e8ec8f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
@@ -43,9 +43,7 @@ import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentN
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
index 5647ea49849..5eaeed073db 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
@@ -19,12 +19,9 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
import java.io.InputStream;
-import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.spring.AbstractServiceWithLogger;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
@@ -43,9 +40,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
*/
public abstract class AbstractDssServiceRpc<T> extends AbstractServiceWithLogger<T>
{
- static protected final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- AbstractDssServiceRpc.class);
-
private final IEncapsulatedOpenBISService openBISService;
@Autowired
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
index 79bdbed92be..01521a71d61 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AutoResolveUtils.java
@@ -162,6 +162,7 @@ public class AutoResolveUtils
{
FileFilter filter = new FileFilter()
{
+ @Override
public boolean accept(File pathname)
{
return acceptFile(pattern, pathname);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CIFEXRPCServiceFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CIFEXRPCServiceFactory.java
index 3b546490804..180a1e316a0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CIFEXRPCServiceFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/CIFEXRPCServiceFactory.java
@@ -34,6 +34,7 @@ final class CIFEXRPCServiceFactory implements ICIFEXRPCServiceFactory
this.cifexURL = cifexURL;
}
+ @Override
public ICIFEXComponent createCIFEXComponent()
{
if (cifexComponent == null)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
index c79e82c2075..7c1170cb2c8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ConfigParameters.java
@@ -187,6 +187,7 @@ public final class ConfigParameters implements IServletPropertiesManager
return DssPropertyParametersUtil.getDssInternalTempDir(properties);
}
+ @Override
public void addServletsProperties(String keyPrefix, SectionProperties[] servletsProperties)
{
for (SectionProperties sectionProperties : servletsProperties)
@@ -197,6 +198,7 @@ public final class ConfigParameters implements IServletPropertiesManager
}
}
+ @Override
public void addServletProperties(String propertiesName, Properties servletProperties)
{
String servletClass =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
index 0514aa521d0..61a896f7d38 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
@@ -77,10 +77,12 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
return new File(store, "commandQueue");
}
+ @Override
public void start()
{
Thread thread = new Thread(new Runnable()
{
+ @Override
public void run()
{
String description = "?";
@@ -131,11 +133,13 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
thread.start();
}
+ @Override
public void scheduleDeletionOfDataSets(List<? extends IDatasetLocation> dataSets)
{
scheduleCommand(new DeletionCommand(dataSets));
}
+ @Override
public void scheduleUploadingDataSetsToCIFEX(ICIFEXRPCServiceFactory cifexServiceFactory,
MailClientParameters mailClientParameters, List<ExternalData> dataSets,
DataSetUploadContext uploadContext, String cifexAdminUserOrNull,
@@ -145,6 +149,7 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
uploadContext, cifexAdminUserOrNull, cifexAdminPasswordOrNull));
}
+ @Override
public void scheduleProcessDatasets(IProcessingPluginTask task,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull, String sessionTokenOrNull,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
index a0b683abeee..322af245b87 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServer.java
@@ -65,7 +65,6 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.IInitializable;
-import ch.systemsx.cisd.openbis.dss.generic.server.api.v1.DssServiceRpcGeneric;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.DssSessionAuthorizationHolder;
@@ -309,10 +308,10 @@ public class DataStoreServer
IRpcServiceNameServer.PREFFERED_URL_SUFFIX,
rpcNameServer.getMajorVersion(), rpcNameServer.getMinorVersion());
RpcServiceInterfaceVersionDTO v1Interface =
- new RpcServiceInterfaceVersionDTO(DssServiceRpcGeneric.DSS_SERVICE_NAME,
+ new RpcServiceInterfaceVersionDTO(IDssServiceRpcGeneric.DSS_SERVICE_NAME,
rpcV1Suffix, service.getMajorVersion(), service.getMinorVersion());
RpcServiceInterfaceVersionDTO jsonV1Interface =
- new RpcServiceInterfaceVersionDTO(DssServiceRpcGeneric.DSS_SERVICE_NAME,
+ new RpcServiceInterfaceVersionDTO(IDssServiceRpcGeneric.DSS_SERVICE_NAME,
jsonRpcV1Suffix, service.getMajorVersion(), service.getMinorVersion());
rpcNameServer.addSupportedInterfaceVersion(nameServerVersion);
@@ -390,7 +389,7 @@ public class DataStoreServer
if (configParams.isUseSSL())
{
final SslContextFactory sslContextFactory = new SslContextFactory();
- sslContextFactory.setKeyStore(configParams.getKeystorePath());
+ sslContextFactory.setKeyStorePath(configParams.getKeystorePath());
sslContextFactory.setKeyStorePassword(configParams.getKeystorePassword());
sslContextFactory.setKeyManagerPassword(configParams.getKeystoreKeyPassword());
final SslConnector socketConnector =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index 71782a1ee78..aefa2480124 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -103,6 +103,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
{
this(sessionTokenManager, new IDataSetCommandExecutorFactory()
{
+ @Override
public IDataSetCommandExecutor create(File store, File queueDir)
{
return new DataSetCommandExecutor(store, queueDir);
@@ -147,6 +148,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
this.cifexAdminPasswordOrNull = cifexAdminPasswordOrNull;
}
+ @Override
public void afterPropertiesSet()
{
String prefix = "Property 'storeRoot' ";
@@ -180,6 +182,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
migrateStore();
}
+ @Override
public void initialize()
{
commandExecutor.start();
@@ -208,6 +211,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
File[] stores = storeRoot.listFiles(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return UuidUtil.isValidUUID(name);
@@ -225,11 +229,13 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
}
+ @Override
public IDataStoreService createLogger(IInvocationLoggerContext context)
{
return new DataStoreServiceLogger(operationLog, context);
}
+ @Override
public int getVersion(String sessionToken)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
@@ -237,12 +243,14 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return IDataStoreService.VERSION;
}
+ @Override
public List<String> getKnownDataSets(String sessionToken,
List<? extends IDatasetLocation> dataSets) throws InvalidAuthenticationException
{
return getKnownDataSets(sessionToken, dataSets, false);
}
+ @Override
public List<String> getKnownDataSets(String sessionToken,
List<? extends IDatasetLocation> dataSets, boolean ignoreNonExistingLocation)
throws InvalidAuthenticationException
@@ -272,6 +280,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return knownLocations;
}
+ @Override
public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException
{
@@ -301,6 +310,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return new CIFEXRPCServiceFactory(cifexURL);
}
+ @Override
public TableModel createReportFromDatasets(String sessionToken, String userSessionToken,
String serviceKey, List<DatasetDescription> datasets)
{
@@ -326,6 +336,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
}
+ @Override
public void processDatasets(String sessionToken, String userSessionToken, String serviceKey,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull)
@@ -341,6 +352,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
userSessionToken, pluginDescription, mailClientParameters);
}
+ @Override
public void unarchiveDatasets(String sessionToken, List<DatasetDescription> datasets,
String userEmailOrNull)
{
@@ -350,6 +362,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
scheduleTask(sessionToken, description, task, datasets, userEmailOrNull);
}
+ @Override
public void archiveDatasets(String sessionToken, List<DatasetDescription> datasets,
String userEmailOrNull, boolean removeFromDataStore)
{
@@ -360,17 +373,20 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
scheduleTask(sessionToken, description, task, datasets, userEmailOrNull);
}
+ @Override
public IArchiverPlugin getArchiverPlugin()
{
ArchiverPluginFactory factory = pluginTaskParameters.getArchiverPluginFactory();
return factory.createInstance(storeRoot);
}
+ @Override
public IDataSetDirectoryProvider getDataSetDirectoryProvider()
{
return new DataSetDirectoryProvider(storeRoot, getShareIdManager());
}
+ @Override
public TableModel createReportFromAggregationService(String sessionToken,
String userSessionToken, String serviceKey, Map<String, Object> parameters)
{
@@ -419,6 +435,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
this.removeFromDataStore = removeFromDataStore;
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
@@ -440,6 +457,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
this.archiverTask = archiverTask;
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
@@ -454,6 +472,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
context.getHierarchicalContentProvider());
}
+ @Override
public LinkModel retrieveLinkFromDataSet(String sessionToken, String serviceKey,
DatasetDescription dataSet)
{
@@ -465,11 +484,13 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return task.createLink(dataSet);
}
+ @Override
public IDataSetDeleter getDataSetDeleter()
{
return commandExecutor;
}
+ @Override
public String putDataSet(String sessionToken, String dropboxName,
CustomImportFile customImportFile)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 155833b6f6f..694ac583613 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -76,11 +76,13 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
invocationStatusMessage, loggerContext.getElapsedTime()));
}
+ @Override
public void initialize()
{
log("initialize", "");
}
+ @Override
public int getVersion(String sessionToken)
{
log("getVersion", "SESSION(%s)", sessionToken);
@@ -92,6 +94,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
log("send", "", message);
}
+ @Override
public List<String> getKnownDataSets(String sessionToken,
List<? extends IDatasetLocation> dataSetLocations)
throws InvalidAuthenticationException
@@ -100,6 +103,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
return null;
}
+ @Override
public List<String> getKnownDataSets(String sessionToken,
List<? extends IDatasetLocation> dataSetLocations, boolean ignoreNonExistingLocation)
throws InvalidAuthenticationException
@@ -115,6 +119,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
log("deleteDataSets", "DATA_SETS(%s)", dataSets);
}
+ @Override
public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException
{
@@ -127,6 +132,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
.toString().trim());
}
+ @Override
public TableModel createReportFromDatasets(String sessionToken, String userSessionToken,
String serviceKey, List<DatasetDescription> datasets)
{
@@ -135,6 +141,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
return null;
}
+ @Override
public void processDatasets(String sessionToken, String userSessionToken, String serviceKey,
List<DatasetDescription> datasets, Map<String, String> parameterBindings,
String userEmailOrNull)
@@ -144,6 +151,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
userSessionToken, serviceKey, datasets.size(), parameterBindings, userEmailOrNull);
}
+ @Override
public void unarchiveDatasets(String sessionToken, List<DatasetDescription> datasets,
String userEmailOrNull)
{
@@ -151,6 +159,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
userEmailOrNull);
}
+ @Override
public void archiveDatasets(String sessionToken, List<DatasetDescription> datasets,
String userEmailOrNull, boolean removeFromDataStore)
{
@@ -158,6 +167,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
datasets.size(), userEmailOrNull, removeFromDataStore);
}
+ @Override
public LinkModel retrieveLinkFromDataSet(String sessionToken, String serviceKey,
DatasetDescription dataSet)
{
@@ -165,6 +175,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
return null;
}
+ @Override
public TableModel createReportFromAggregationService(String sessionToken,
String userSessionToken, String serviceKey, Map<String, Object> parameters)
{
@@ -173,6 +184,7 @@ class DataStoreServiceLogger implements IDataStoreService, IInitializable
return null;
}
+ @Override
public String putDataSet(String sessionToken, String dropboxName,
CustomImportFile customImportFile)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProvider.java
index 9cf9dc173ef..adc32e011bf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProvider.java
@@ -118,11 +118,13 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
this.dao = dao;
}
+ @Override
public List<DataSetPathInfo> listPathInfosByRegularExpression(String dataSetCode,
final String regularExpression)
{
return new Loader(dataSetCode, new ILoader()
{
+ @Override
public List<DataSetFileRecord> listDataSetFiles(long dataSetId)
{
String likeExpressionOrNull =
@@ -141,10 +143,12 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
}).getInfos();
}
+ @Override
public DataSetPathInfo tryGetFullDataSetRootPathInfo(String dataSetCode)
{
return new Loader(dataSetCode, new ILoader()
{
+ @Override
public List<DataSetFileRecord> listDataSetFiles(long dataSetId)
{
return getDao().listDataSetFiles(dataSetId);
@@ -152,6 +156,7 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
}).getRoot();
}
+ @Override
public ISingleDataSetPathInfoProvider tryGetSingleDataSetPathInfoProvider(String dataSetCode)
{
final Long dataSetId = getDao().tryToGetDataSetId(dataSetCode);
@@ -174,6 +179,7 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
this.dao = dao;
}
+ @Override
public DataSetPathInfo getRootPathInfo()
{
DataSetFileRecord record = dao.getDataSetRootFile(dataSetId);
@@ -186,6 +192,7 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
}
}
+ @Override
public DataSetPathInfo tryGetPathInfoByRelativePath(String relativePath)
{
final String normalizedRelativePath = relativePath.replaceAll("/+", "/");
@@ -200,12 +207,14 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
}
}
+ @Override
public List<DataSetPathInfo> listChildrenPathInfos(DataSetPathInfo parent)
{
List<DataSetFileRecord> records = dao.listChildrenByParentId(dataSetId, parent.getId());
return asPathInfos(records);
}
+ @Override
public List<DataSetPathInfo> listMatchingPathInfos(String relativePathPattern)
{
String likeExpressionOrNull =
@@ -225,6 +234,7 @@ public class DatabaseBasedDataSetPathInfoProvider implements IDataSetPathInfoPro
return asPathInfos(records);
}
+ @Override
public List<DataSetPathInfo> listMatchingPathInfos(String startingPath,
String fileNamePattern)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetSessionAuthorizer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetSessionAuthorizer.java
index 421343d503f..00e17095f85 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetSessionAuthorizer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetSessionAuthorizer.java
@@ -69,6 +69,7 @@ public class DatasetSessionAuthorizer implements IDssSessionAuthorizer
* MILLIS_PER_MINUTE);
}
+ @Override
public Status checkDatasetAccess(String sessionToken, List<String> datasetCodes)
{
final Status cachedStatus = tryGetCached(sessionToken, datasetCodes);
@@ -105,6 +106,7 @@ public class DatasetSessionAuthorizer implements IDssSessionAuthorizer
}
}
+ @Override
public Status checkDatasetAccess(String sessionToken, String datasetCode)
{
final Status cachedStatus = tryGetCached(sessionToken, datasetCode);
@@ -138,6 +140,7 @@ public class DatasetSessionAuthorizer implements IDssSessionAuthorizer
}
}
+ @Override
public Status checkSpaceWriteable(String sessionToken, SpaceIdentifier spaceId)
{
if (operationLog.isInfoEnabled())
@@ -158,6 +161,7 @@ public class DatasetSessionAuthorizer implements IDssSessionAuthorizer
}
}
+ @Override
public Status checkInstanceAdminAuthorization(String sessionToken)
{
if (operationLog.isInfoEnabled())
@@ -178,6 +182,7 @@ public class DatasetSessionAuthorizer implements IDssSessionAuthorizer
}
}
+ @Override
public Status checkSpacePowerUserAuthorization(String sessionToken)
{
if (operationLog.isInfoEnabled())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
index fd8429469cc..13b97ce21c4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
@@ -52,6 +52,7 @@ class DeletionCommand extends AbstractDataSetLocationBasedCommand
super(dataSets);
}
+ @Override
public void execute(final IHierarchicalContentProvider contentProvider,
final IDataSetDirectoryProvider dataSetDirectoryProvider)
{
@@ -64,6 +65,7 @@ class DeletionCommand extends AbstractDataSetLocationBasedCommand
{
executor.submit(new Runnable()
{
+ @Override
public void run()
{
try
@@ -86,6 +88,7 @@ class DeletionCommand extends AbstractDataSetLocationBasedCommand
return new Log4jSimpleLogger(operationLog);
}
+ @Override
public String getDescription()
{
final StringBuilder b = new StringBuilder();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcAuthorizationAdvisor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcAuthorizationAdvisor.java
index c85bd837c7e..26631556f87 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcAuthorizationAdvisor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcAuthorizationAdvisor.java
@@ -198,6 +198,7 @@ public class DssServiceRpcAuthorizationAdvisor extends DefaultPointcutAdvisor
* Get the session token and any guarded parameters and invoke the guards on those
* parameters.
*/
+ @Override
public Object invoke(MethodInvocation methodInvocation) throws Throwable
{
final Object[] args = methodInvocation.getArguments();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 86981338c55..9c06c2823c7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -166,17 +166,20 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return shareIdManager;
}
+ @Override
public Object getObject() throws Exception
{
return this;
}
+ @Override
@SuppressWarnings("rawtypes")
public Class getObjectType()
{
return IEncapsulatedOpenBISService.class;
}
+ @Override
public boolean isSingleton()
{
return true;
@@ -186,63 +189,74 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
// IEncapsulatedOpenBISService
//
+ @Override
public Experiment tryToGetExperiment(ExperimentIdentifier experimentIdentifier)
{
assert experimentIdentifier != null : " Unspecified experiment identifier.";
return service.tryToGetExperiment(session.getToken(), experimentIdentifier);
}
+ @Override
public Space tryGetSpace(SpaceIdentifier spaceIdentifier) throws UserFailureException
{
assert spaceIdentifier != null : "Unspecified space identifier";
return service.tryGetSpace(session.getToken(), spaceIdentifier);
}
+ @Override
public Project tryGetProject(ProjectIdentifier projectIdentifier) throws UserFailureException
{
assert projectIdentifier != null : "Unspecified project identifier";
return service.tryGetProject(session.getToken(), projectIdentifier);
}
+ @Override
public List<Sample> listSamples(ListSampleCriteria criteria)
{
assert criteria != null : "Unspecifed criteria.";
return service.listSamples(session.getToken(), criteria);
}
+ @Override
public final Sample tryGetSampleWithExperiment(final SampleIdentifier sampleIdentifier)
{
assert sampleIdentifier != null : "Given sample identifier can not be null.";
return service.tryGetSampleWithExperiment(session.getToken(), sampleIdentifier);
}
+ @Override
public SampleIdentifier tryToGetSampleIdentifier(String samplePermID)
throws UserFailureException
{
return service.tryToGetSampleIdentifier(session.getToken(), samplePermID);
}
+ @Override
public ExperimentType getExperimentType(String experimentTypeCode) throws UserFailureException
{
return service.getExperimentType(session.getToken(), experimentTypeCode);
}
+ @Override
public Collection<VocabularyTerm> listVocabularyTerms(String vocabularyCode)
throws UserFailureException
{
return service.listVocabularyTerms(session.getToken(), vocabularyCode);
}
+ @Override
public SampleType getSampleType(String sampleTypeCode) throws UserFailureException
{
return service.getSampleType(session.getToken(), sampleTypeCode);
}
+ @Override
public DataSetTypeWithVocabularyTerms getDataSetType(String dataSetTypeCode)
{
return service.getDataSetType(session.getToken(), dataSetTypeCode);
}
+ @Override
public List<ExternalData> listDataSetsByExperimentID(long experimentID)
throws UserFailureException
{
@@ -250,6 +264,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.listDataSetsByExperimentID(session.getToken(), id);
}
+ @Override
public List<ExternalData> listDataSetsBySampleID(long sampleID,
boolean showOnlyDirectlyConnected)
{
@@ -257,18 +272,21 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.listDataSetsBySampleID(session.getToken(), id, showOnlyDirectlyConnected);
}
+ @Override
public List<ExternalData> listDataSetsByCode(List<String> dataSetCodes)
throws UserFailureException
{
return service.listDataSetsByCode(session.getToken(), dataSetCodes);
}
+ @Override
public long registerExperiment(NewExperiment experiment) throws UserFailureException
{
assert experiment != null : "Unspecified experiment.";
return service.registerExperiment(session.getToken(), experiment);
}
+ @Override
public void registerSamples(List<NewSamplesWithTypes> newSamples, String userIDOrNull)
throws UserFailureException
{
@@ -277,6 +295,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
service.registerSamples(session.getToken(), newSamples, userIDOrNull);
}
+ @Override
public long registerSample(NewSample newSample, String userIDOrNull)
throws UserFailureException
{
@@ -285,6 +304,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.registerSample(session.getToken(), newSample, userIDOrNull);
}
+ @Override
public void updateSample(SampleUpdatesDTO sampleUpdate) throws UserFailureException
{
assert sampleUpdate != null : "Unspecified sample.";
@@ -292,6 +312,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
service.updateSample(session.getToken(), sampleUpdate);
}
+ @Override
public final void registerDataSet(final DataSetInformation dataSetInformation,
final NewExternalData data)
{
@@ -317,6 +338,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
+ @Override
public final void updateDataSet(String code, List<NewProperty> properties, SpaceIdentifier space)
throws UserFailureException
@@ -333,6 +355,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
+ @Override
public void updateShareIdAndSize(String dataSetCode, String shareId, long size)
throws UserFailureException
{
@@ -345,6 +368,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
+ @Override
public final void updateDataSetStatuses(List<String> codes, DataSetArchivingStatus newStatus,
boolean presentInArchive) throws UserFailureException
@@ -359,6 +383,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
+ @Override
public boolean compareAndSetDataSetStatus(String dataSetCode, DataSetArchivingStatus oldStatus,
DataSetArchivingStatus newStatus, boolean newPresentInArchive)
throws UserFailureException
@@ -370,6 +395,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
newStatus, newPresentInArchive);
}
+ @Override
public final IEntityProperty[] getPropertiesOfTopSampleRegisteredFor(
final SampleIdentifier sampleIdentifier) throws UserFailureException
{
@@ -378,12 +404,14 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
sampleIdentifier);
}
+ @Override
public final List<Sample> listSamplesByCriteria(final ListSamplesByPropertyCriteria criteria)
throws UserFailureException
{
return service.listSamplesByCriteria(session.getToken(), criteria);
}
+ @Override
public final int getVersion()
{
if (version == null)
@@ -393,6 +421,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return version;
}
+ @Override
public final DatabaseInstance getHomeDatabaseInstance()
{
if (homeDatabaseInstance == null)
@@ -402,58 +431,69 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return homeDatabaseInstance;
}
+ @Override
public final String createDataSetCode()
{
return service.createDataSetCode(session.getToken());
}
+ @Override
public final String createPermId()
{
return service.createPermId(session.getToken());
}
+ @Override
public long drawANewUniqueID()
{
return service.drawANewUniqueID(session.getToken());
}
+ @Override
public ExternalData tryGetDataSet(String dataSetCode) throws UserFailureException
{
return service.tryGetDataSet(session.getToken(), dataSetCode);
}
+ @Override
public ExternalData tryGetDataSet(String sToken, String dataSetCode)
throws UserFailureException
{
return service.tryGetDataSet(sToken, dataSetCode);
}
+ @Override
public void checkInstanceAdminAuthorization(String sToken) throws UserFailureException
{
service.checkInstanceAdminAuthorization(sToken);
}
+ @Override
public void checkSpacePowerUserAuthorization(String sessionToken) throws UserFailureException
{
service.checkSpacePowerUserAuthorization(sessionToken);
}
+ @Override
public void checkDataSetAccess(String sToken, String dataSetCode) throws UserFailureException
{
service.checkDataSetAccess(sToken, dataSetCode);
}
+ @Override
public void checkDataSetCollectionAccess(String sToken, List<String> dataSetCodes)
throws UserFailureException
{
service.checkDataSetCollectionAccess(sToken, dataSetCodes);
}
+ @Override
public void checkSpaceAccess(String sToken, SpaceIdentifier spaceId)
{
service.checkSpaceAccess(sToken, spaceId);
}
+ @Override
public List<DataSetShareId> listDataSetShareIds() throws UserFailureException
{
List<DataSetShareId> shareIds =
@@ -469,6 +509,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return shareIds;
}
+ @Override
public List<SimpleDataSetInformationDTO> listDataSets() throws UserFailureException
{
List<SimpleDataSetInformationDTO> dataSets =
@@ -483,12 +524,14 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return dataSets;
}
+ @Override
public List<ExternalData> listNewerDataSets(TrackingDataSetCriteria criteria)
throws UserFailureException
{
return service.listDataSets(session.getToken(), session.getDataStoreCode(), criteria);
}
+ @Override
public List<ExternalData> listAvailableDataSets(ArchiverDataSetCriteria criteria)
throws UserFailureException
{
@@ -496,6 +539,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
criteria);
}
+ @Override
public List<DeletedDataSet> listDeletedDataSets(Long lastSeenDeletionEventIdOrNull,
Date maxDeletionDataOrNull)
{
@@ -503,42 +547,50 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
maxDeletionDataOrNull);
}
+ @Override
public void archiveDataSets(List<String> dataSetCodes, boolean removeFromDataStore)
throws UserFailureException
{
service.archiveDatasets(session.getToken(), dataSetCodes, removeFromDataStore);
}
+ @Override
public void unarchiveDataSets(List<String> dataSetCodes) throws UserFailureException
{
service.unarchiveDatasets(session.getToken(), dataSetCodes);
}
+ @Override
public SessionContextDTO tryGetSession(String sToken)
{
return service.tryGetSession(sToken);
}
+ @Override
public ExternalData tryGetDataSetForServer(String dataSetCode) throws UserFailureException
{
return service.tryGetDataSetForServer(session.getToken(), dataSetCode);
}
+ @Override
public List<String> generateCodes(String prefix, int size)
{
return service.generateCodes(session.getToken(), prefix, size);
}
+ @Override
public List<Person> listAdministrators()
{
return service.listAdministrators(session.getToken());
}
+ @Override
public Person tryPersonWithUserIdOrEmail(String useridOrEmail)
{
return service.tryPersonWithUserIdOrEmail(session.getToken(), useridOrEmail);
}
+ @Override
public Sample registerSampleAndDataSet(NewSample newSample, NewExternalData externalData,
String userIdOrNull) throws UserFailureException
{
@@ -549,6 +601,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return sample;
}
+ @Override
public Sample updateSampleAndRegisterDataSet(SampleUpdatesDTO newSample,
NewExternalData externalData)
{
@@ -558,6 +611,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return sample;
}
+ @Override
public AtomicEntityOperationResult performEntityOperations(
AtomicEntityOperationDetails operationDetails)
{
@@ -575,6 +629,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return operations;
}
+ @Override
public void send(ServiceMessage message)
{
this.conversationController.process(message);
@@ -585,67 +640,80 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
getShareIdManager().setShareId(data.getCode(), data.getShareId());
}
+ @Override
public List<Sample> searchForSamples(SearchCriteria searchCriteria)
{
return service.searchForSamples(session.getToken(), searchCriteria);
}
+ @Override
public List<ExternalData> searchForDataSets(SearchCriteria searchCriteria)
{
return service.searchForDataSets(session.getToken(), searchCriteria);
}
+ @Override
public List<Project> listProjects()
{
return service.listProjects(session.getToken());
}
+ @Override
public List<Experiment> listExperiments(ProjectIdentifier projectIdentifier)
{
return service.listExperiments(session.getToken(), projectIdentifier);
}
+ @Override
public Material tryGetMaterial(MaterialIdentifier materialIdentifier)
{
return service.tryGetMaterial(session.getToken(), materialIdentifier);
}
+ @Override
public List<Material> listMaterials(ListMaterialCriteria criteria, boolean withProperties)
{
return service.listMaterials(session.getToken(), criteria, withProperties);
}
+ @Override
public void removeDataSetsPermanently(List<String> dataSetCodes, String reason)
{
service.removeDataSetsPermanently(session.getToken(), dataSetCodes, reason);
}
+ @Override
public void updateDataSet(DataSetUpdatesDTO dataSetUpdates)
{
service.updateDataSet(session.getToken(), dataSetUpdates);
}
+ @Override
public List<String> getTrustedCrossOriginDomains()
{
return service.getTrustedCrossOriginDomains(session.getToken());
}
+ @Override
public void setStorageConfirmed(String dataSetCode)
{
service.setStorageConfirmed(session.getToken(), dataSetCode);
}
+ @Override
public void markSuccessfulPostRegistration(String dataSetCode)
{
service.markSuccessfulPostRegistration(session.getToken(), dataSetCode);
}
+ @Override
public List<ExternalData> listDataSetsForPostRegistration()
{
return service.listDataSetsForPostRegistration(session.getToken(),
session.getDataStoreCode());
}
+ @Override
public Boolean didEntityOperationsSucceed(TechId registrationId)
{
return service.didEntityOperationsSucceed(session.getToken(), registrationId);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/HTMLErrorRenderer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/HTMLErrorRenderer.java
index 71aa3e8d01a..41fc11622ae 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/HTMLErrorRenderer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/HTMLErrorRenderer.java
@@ -27,11 +27,13 @@ public class HTMLErrorRenderer implements IErrorRenderer
{
private PrintWriter writer;
+ @Override
public void setWriter(PrintWriter writer)
{
this.writer = writer;
}
+ @Override
public void printErrorMessage(String errorMessage)
{
writer.println("<html><body><h1>Error</h1>");
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
index 71a18be2e98..5d16c442e52 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/LocalDataSetFileOperationsExcecutor.java
@@ -60,6 +60,7 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
this.rsyncPasswordFileOrNull = rsyncPasswordFileOrNull;
}
+ @Override
public BooleanStatus checkSame(File dataSet, File destination)
{
if (false == fileOperations.exists(dataSet))
@@ -118,11 +119,13 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public BooleanStatus exists(File file)
{
return BooleanStatus.createFromBoolean(fileOperations.exists(file));
}
+ @Override
public void createFolder(File folder)
{
try
@@ -135,6 +138,7 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public void deleteFolder(File folder)
{
try
@@ -147,11 +151,13 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public void copyDataSetToDestination(File dataSet, File destination)
{
syncDataSetWithDestination(dataSet, destination);
}
+ @Override
public void syncDataSetWithDestination(File dataSet, File destination)
{
// rsync --delete is more effective then deletion of destination directory & copy all
@@ -165,6 +171,7 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public void retrieveDataSetFromDestination(File dataSet, File destination)
{
try
@@ -184,6 +191,7 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public void renameTo(File newFile, File oldFile)
{
boolean result = oldFile.renameTo(newFile);
@@ -194,6 +202,7 @@ public final class LocalDataSetFileOperationsExcecutor implements IDataSetFileOp
}
}
+ @Override
public void createMarkerFile(File markerFile)
{
try
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/PlainTextRendererFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/PlainTextRendererFactory.java
index b23a7c4761f..b3433189321 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/PlainTextRendererFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/PlainTextRendererFactory.java
@@ -28,23 +28,27 @@ import org.apache.commons.io.FileUtils;
public class PlainTextRendererFactory implements IRendererFactory
{
+ @Override
public IDirectoryRenderer createDirectoryRenderer(RenderingContext context)
{
return new PlainTextDirectoryRenderer();
}
+ @Override
public IErrorRenderer createErrorRenderer()
{
return new IErrorRenderer()
{
private PrintWriter writer;
+ @Override
public void printErrorMessage(String errorMessage)
{
writer.println("Error:");
writer.println(errorMessage);
}
+ @Override
public void setWriter(PrintWriter writer)
{
this.writer = writer;
@@ -52,6 +56,7 @@ public class PlainTextRendererFactory implements IRendererFactory
};
}
+ @Override
public String getContentType()
{
return "text";
@@ -61,29 +66,35 @@ public class PlainTextRendererFactory implements IRendererFactory
{
private PrintWriter writer;
+ @Override
public void printDirectory(String name, String relativePath)
{
writer.print(name + "\n");
}
+ @Override
public void printFile(String name, String relativePath, long size)
{
writer.format("%s\t%s\n", name, FileUtils.byteCountToDisplaySize(size));
}
+ @Override
public void printFooter()
{
}
+ @Override
public void printHeader()
{
writer.println("Directory content:");
}
+ @Override
public void printLinkToParentDirectory(String relativePath)
{
}
+ @Override
public void setWriter(PrintWriter writer)
{
this.writer = writer;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
index 0ef4f6db4e0..0011c6aad38 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommand.java
@@ -108,6 +108,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
return mailSent;
}
+ @Override
public void sendMessage(String subject, String content, String replyToOrNull,
From fromOrNull, String... recipients) throws EnvironmentFailureException
{
@@ -115,6 +116,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
mailSent = true;
}
+ @Override
public void sendEmailMessage(String subject, String content, EMailAddress replyToOrNull,
EMailAddress fromOrNull, EMailAddress... recipients)
throws EnvironmentFailureException
@@ -123,6 +125,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
mailSent = true;
}
+ @Override
@SuppressWarnings("deprecation")
public void sendMessageWithAttachment(String subject, String content, String filename,
DataHandler attachmentContent, String replyToOrNull, From fromOrNull,
@@ -133,6 +136,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
mailSent = true;
}
+ @Override
public void sendEmailMessageWithAttachment(String subject, String content, String filename,
DataHandler attachmentContent, EMailAddress replyToOrNull, EMailAddress fromOrNull,
EMailAddress... recipients) throws EnvironmentFailureException
@@ -142,6 +146,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
mailSent = true;
}
+ @Override
public void sendTestEmail()
{
mailClient.sendTestEmail();
@@ -149,6 +154,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
}
+ @Override
public void execute(IHierarchicalContentProvider contentProvider,
IDataSetDirectoryProvider dataSetDirectoryProvider)
{
@@ -232,6 +238,7 @@ public class ProcessDatasetsCommand extends AbstractDataSetDescriptionBasedComma
getDataSetCodes(getDataSetCodes()));
}
+ @Override
public String getDescription()
{
return getDescription(getShortDescription(""));
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/RemoteDataSetFileOperationsExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/RemoteDataSetFileOperationsExecutor.java
index 098f9801640..7bb77589fce 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/RemoteDataSetFileOperationsExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/RemoteDataSetFileOperationsExecutor.java
@@ -70,11 +70,13 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
this.timeoutInMillis = timeoutInMillis;
}
+ @Override
public BooleanStatus exists(File file)
{
return executor.exists(file.getPath(), timeoutInMillis);
}
+ @Override
public void deleteFolder(File folder)
{
ProcessResult result =
@@ -95,6 +97,7 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public void createFolder(File folder)
{
ProcessResult result =
@@ -117,6 +120,7 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public void copyDataSetToDestination(File dataSet, File destination)
{
Status result =
@@ -128,11 +132,13 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public void syncDataSetWithDestination(File dataSet, File destination)
{
copyDataSetToDestination(dataSet, destination);
}
+ @Override
public void retrieveDataSetFromDestination(File dataSet, File destination)
{
Status result =
@@ -144,6 +150,7 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public void renameTo(File newFile, File oldFile)
{
ProcessResult result =
@@ -165,6 +172,7 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public void createMarkerFile(File markerFile)
{
ProcessResult result =
@@ -186,6 +194,7 @@ public final class RemoteDataSetFileOperationsExecutor implements IDataSetFileOp
}
}
+ @Override
public BooleanStatus checkSame(File dataSet, File destination)
{
if (false == dataSet.exists())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManager.java
index 70dea78483f..8cbf5850d12 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManager.java
@@ -129,16 +129,19 @@ public class ShareIdManager implements IShareIdManager
map.put(dataSetCode, guardedShareId);
}
+ @Override
public boolean isKnown(String dataSetCode)
{
return getDataSetCodeToShareIdMap().containsKey(dataSetCode);
}
+ @Override
public String getShareId(String dataSetCode)
{
return getGuardedShareId(dataSetCode).getShareId();
}
+ @Override
public void setShareId(String dataSetCode, String shareId)
{
Map<String, GuardedShareID> map = getDataSetCodeToShareIdMap();
@@ -154,6 +157,7 @@ public class ShareIdManager implements IShareIdManager
}
}
+ @Override
public void lock(String dataSetCode)
{
synchronized (lockedDataSets)
@@ -177,6 +181,7 @@ public class ShareIdManager implements IShareIdManager
}
}
+ @Override
public void lock(List<String> dataSetCodes)
{
synchronized (lockedDataSets)
@@ -215,6 +220,7 @@ public class ShareIdManager implements IShareIdManager
}
}
+ @Override
public void await(String dataSetCode)
{
Map<String, GuardedShareID> map = getDataSetCodeToShareIdMap();
@@ -251,6 +257,7 @@ public class ShareIdManager implements IShareIdManager
}
}
+ @Override
public void releaseLock(String dataSetCode)
{
synchronized (lockedDataSets)
@@ -274,6 +281,7 @@ public class ShareIdManager implements IShareIdManager
}
}
+ @Override
public void releaseLocks()
{
synchronized (lockedDataSets)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLDirectoryRenderer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLDirectoryRenderer.java
index 44cac34d26d..42a9e437274 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLDirectoryRenderer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLDirectoryRenderer.java
@@ -73,11 +73,13 @@ final class SimpleHTMLDirectoryRenderer implements IDirectoryRenderer
this.urlPrefix = prefix.endsWith("/") ? prefix : prefix + "/";
}
+ @Override
public void setWriter(final PrintWriter writer)
{
this.writer = writer;
}
+ @Override
public void printHeader()
{
final Template template = HEADER_TEMPLATE.createFreshCopy();
@@ -92,16 +94,19 @@ final class SimpleHTMLDirectoryRenderer implements IDirectoryRenderer
writer.println(template.createText());
}
+ @Override
public void printLinkToParentDirectory(final String aRelativePath)
{
printRow("..", aRelativePath, "");
}
+ @Override
public void printDirectory(final String name, final String aRelativePath)
{
printRow(name, aRelativePath, "");
}
+ @Override
public void printFile(final String name, final String aRelativePath, final long size)
{
printRow(name, aRelativePath, renderFileSize(size));
@@ -133,6 +138,7 @@ final class SimpleHTMLDirectoryRenderer implements IDirectoryRenderer
return FileUtils.byteCountToDisplaySize(size);
}
+ @Override
public void printFooter()
{
final Template template = FOOTER_TEMPLATE.createFreshCopy();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLRendererFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLRendererFactory.java
index 1fcd7121b33..916ec84cbac 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLRendererFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/SimpleHTMLRendererFactory.java
@@ -24,16 +24,19 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
*/
public class SimpleHTMLRendererFactory implements IRendererFactory
{
+ @Override
public String getContentType()
{
return "text/html";
}
+ @Override
public IDirectoryRenderer createDirectoryRenderer(RenderingContext context)
{
return new SimpleHTMLDirectoryRenderer(context);
}
+ @Override
public IErrorRenderer createErrorRenderer()
{
return new HTMLErrorRenderer();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepository.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepository.java
index c4ca988e04c..897fc5534a0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepository.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepository.java
@@ -55,6 +55,7 @@ public class StreamRepository implements IStreamRepository
{
private final TokenGenerator tokenGenerator = new TokenGenerator();
+ @Override
public String createUniqueID()
{
return tokenGenerator.getNewToken(System.currentTimeMillis());
@@ -85,6 +86,7 @@ public class StreamRepository implements IStreamRepository
this.timeProvider = timeProvider;
}
+ @Override
public synchronized String addStream(InputStream inputStream, String path)
{
removeStaleInputStreams();
@@ -94,6 +96,7 @@ public class StreamRepository implements IStreamRepository
return id;
}
+ @Override
public synchronized InputStreamWithPath getStream(String inputStreamID)
{
removeStaleInputStreams();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
index 3a4d6eb4315..f9be2b49837 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
@@ -87,6 +87,7 @@ class UploadingCommand implements IDataSetCommand
this.zipFile = zipFile;
}
+ @Override
public void start(File file, long fileSize, Long fileIdOrNull)
{
if (operationLog.isInfoEnabled())
@@ -95,10 +96,12 @@ class UploadingCommand implements IDataSetCommand
}
}
+ @Override
public void reportProgress(int percentage, long numberOfBytes)
{
}
+ @Override
public void finished(boolean successful)
{
if (successful)
@@ -116,12 +119,14 @@ class UploadingCommand implements IDataSetCommand
}
}
+ @Override
public void exceptionOccured(Throwable throwable)
{
notificationLog.error("An error occured during uploading of zip file " + zipFile + ".",
throwable);
}
+ @Override
public void warningOccured(String warningMessage)
{
operationLog.warn(warningMessage);
@@ -307,6 +312,7 @@ class UploadingCommand implements IDataSetCommand
tokenGenerator = new TokenGenerator();
}
+ @Override
public List<String> getDataSetCodes()
{
List<String> result = new ArrayList<String>();
@@ -317,6 +323,7 @@ class UploadingCommand implements IDataSetCommand
return result;
}
+ @Override
public void execute(IHierarchicalContentProvider contentProvider,
IDataSetDirectoryProvider dataSetDirectoryProvider)
{
@@ -592,6 +599,7 @@ class UploadingCommand implements IDataSetCommand
.sendMessage("[Data Set Server] Uploading failed", message, null, null, userEMail);
}
+ @Override
public String getDescription()
{
final StringBuilder b = new StringBuilder();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
index 47dc981d18b..d3a7f9e458e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGeneric.java
@@ -21,9 +21,13 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
+import org.apache.log4j.Logger;
+
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.common.utilities.HierarchicalContentUtils;
import ch.systemsx.cisd.etlserver.api.v1.PutDataSetService;
@@ -47,6 +51,14 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGenericInternal>
implements IDssServiceRpcGenericInternal
{
+ /**
+ * Logger with {@link LogCategory#OPERATION} with name of the concrete class, needs to be static
+ * for our purpose.
+ */
+ @SuppressWarnings("hiding")
+ protected static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ DssServiceRpcGeneric.class);
+
private final PutDataSetService putService;
/**
@@ -61,14 +73,16 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
DssServiceRpcGeneric(IEncapsulatedOpenBISService openBISService,
IShareIdManager shareIdManager, IHierarchicalContentProvider contentProvider)
{
- this(openBISService, null, shareIdManager, contentProvider, new PutDataSetService(openBISService,
+ this(openBISService, null, shareIdManager, contentProvider, new PutDataSetService(
+ openBISService,
operationLog));
}
/**
* A constructor for testing.
*/
- public DssServiceRpcGeneric(IEncapsulatedOpenBISService openBISService, IStreamRepository streamRepository,
+ public DssServiceRpcGeneric(IEncapsulatedOpenBISService openBISService,
+ IStreamRepository streamRepository,
IShareIdManager shareIdManager, IHierarchicalContentProvider contentProvider,
PutDataSetService service)
{
@@ -77,11 +91,13 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
operationLog.info("[rpc] Started DSS API V1 service.");
}
+ @Override
public IDssServiceRpcGenericInternal createLogger(IInvocationLoggerContext context)
{
return new DssServiceRpcGenericLogger(context);
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, String dataSetCode,
String startPath, boolean isRecursive) throws IllegalArgumentException
{
@@ -118,6 +134,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
}
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, String dataSetCode, String path)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -139,7 +156,9 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
}
}
- public String getDownloadUrlForFileForDataSet(String sessionToken, String dataSetCode, String path)
+ @Override
+ public String getDownloadUrlForFileForDataSet(String sessionToken, String dataSetCode,
+ String path)
throws IOExceptionUnchecked, IllegalArgumentException
{
InputStream stream = getFileForDataSet(sessionToken, dataSetCode, path);
@@ -152,17 +171,20 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
return content.getNode(startPath.startsWith("/") ? startPath.substring(1) : startPath);
}
+ @Override
public String putDataSet(String sessionToken, NewDataSetDTO newDataSet, InputStream inputStream)
throws IOExceptionUnchecked, IllegalArgumentException
{
return putService.putDataSet(sessionToken, newDataSet, inputStream);
}
+ @Override
public int getMajorVersion()
{
return 1;
}
+ @Override
public int getMinorVersion()
{
return 4;
@@ -188,6 +210,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
factory.appendFileInfos(list, isRecursive);
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -195,6 +218,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
fileOrFolder.getPath());
}
+ @Override
public String getDownloadUrlForFileForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -202,6 +226,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
return addToRepositoryAndReturnDownloadUrl(stream, fileOrFolder.getPath());
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -216,6 +241,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
putService.setStoreDirectory(aFile);
}
+ @Override
public String getPathToDataSet(String sessionToken, String dataSetCode,
String overrideStoreRootPathOrNull) throws IOExceptionUnchecked,
IllegalArgumentException
@@ -253,6 +279,7 @@ public class DssServiceRpcGeneric extends AbstractDssServiceRpc<IDssServiceRpcGe
return usersPath.getPath();
}
+ @Override
public String getValidationScript(String sessionToken, String dataSetTypeOrNull)
throws IOExceptionUnchecked, IllegalArgumentException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericLogger.java
index 567b43f0ca9..28f33791f59 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericLogger.java
@@ -38,16 +38,19 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
super(null, context);
}
+ @Override
public int getMajorVersion()
{
return 0;
}
+ @Override
public int getMinorVersion()
{
return 0;
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -55,6 +58,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -62,6 +66,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public String getDownloadUrlForFileForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -69,6 +74,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, String dataSetCode,
String path, boolean isRecursive) throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -77,6 +83,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, String dataSetCode, String path)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -85,6 +92,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
}
+ @Override
public String getDownloadUrlForFileForDataSet(String sessionToken, String dataSetCode, String path)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -92,6 +100,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public String putDataSet(String sessionToken, NewDataSetDTO newDataset, InputStream inputStream)
throws IOExceptionUnchecked, IllegalArgumentException
{
@@ -99,6 +108,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public String getPathToDataSet(String sessionToken, String dataSetCode,
String overrideStoreRootPathOrNull) throws IOExceptionUnchecked,
IllegalArgumentException
@@ -108,6 +118,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
return null;
}
+ @Override
public void setStoreDirectory(File aFile)
{
}
@@ -116,6 +127,7 @@ public class DssServiceRpcGenericLogger extends AbstractServerLogger implements
{
}
+ @Override
public String getValidationScript(String sessionToken, String dataSetTypeOrNull)
throws IOExceptionUnchecked, IllegalArgumentException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemView.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemView.java
index d847a891424..f5f2c28e1a5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemView.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemView.java
@@ -64,6 +64,7 @@ public class DSSFileSystemView implements FileSystemView
this.openbisService = service;
}
+ @Override
public Object invoke(Object proxy, Method method, Object[] args)
throws Throwable
{
@@ -116,6 +117,7 @@ public class DSSFileSystemView implements FileSystemView
this.workingDirectory = getHomeDirectory();
}
+ @Override
public boolean changeWorkingDirectory(String path) throws FtpException
{
FtpFile ftpFile = getFile(path);
@@ -127,10 +129,12 @@ public class DSSFileSystemView implements FileSystemView
return false;
}
+ @Override
public void dispose()
{
}
+ @Override
public FtpFile getFile(String path) throws FtpException
{
return getFile(path, new Cache(SystemTimeProvider.SYSTEM_TIME_PROVIDER));
@@ -196,16 +200,19 @@ public class DSSFileSystemView implements FileSystemView
}
}
+ @Override
public FtpFile getHomeDirectory() throws FtpException
{
return getFile(FtpConstants.ROOT_DIRECTORY);
}
+ @Override
public FtpFile getWorkingDirectory() throws FtpException
{
return workingDirectory;
}
+ @Override
public boolean isRandomAccessible() throws FtpException
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpPathResolverRegistry.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpPathResolverRegistry.java
index cee9ed0f854..3af5bb4360c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpPathResolverRegistry.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpPathResolverRegistry.java
@@ -77,6 +77,7 @@ public class FtpPathResolverRegistry implements IFtpPathResolverRegistry
return null;
}
+ @Override
public FtpFile resolve(String path, FtpPathResolverContext resolverContext)
{
IFtpPathResolver resolver = tryFindResolver(path);
@@ -100,101 +101,121 @@ public class FtpPathResolverRegistry implements IFtpPathResolverRegistry
{
return new FtpFile()
{
+ @Override
public String getAbsolutePath()
{
return path;
}
+ @Override
public String getName()
{
return FilenameUtils.getName(path);
}
+ @Override
public boolean isHidden()
{
return false;
}
+ @Override
public boolean isDirectory()
{
return false;
}
+ @Override
public boolean isFile()
{
return false;
}
+ @Override
public boolean doesExist()
{
return false;
}
+ @Override
public boolean isReadable()
{
return false;
}
+ @Override
public boolean isWritable()
{
return false;
}
+ @Override
public boolean isRemovable()
{
return false;
}
+ @Override
public String getOwnerName()
{
return "UNKNOWN";
}
+ @Override
public String getGroupName()
{
return "UNKNOWN";
}
+ @Override
public int getLinkCount()
{
return 0;
}
+ @Override
public long getLastModified()
{
return 0;
}
+ @Override
public boolean setLastModified(long time)
{
return false;
}
+ @Override
public long getSize()
{
return 0;
}
+ @Override
public boolean mkdir()
{
return false;
}
+ @Override
public boolean delete()
{
return false;
}
+ @Override
public boolean move(FtpFile destination)
{
return false;
}
+ @Override
public List<FtpFile> listFiles()
{
return Collections.emptyList();
}
+ @Override
public OutputStream createOutputStream(long offset) throws IOException
{
if (errorMsgOrNull != null)
@@ -207,6 +228,7 @@ public class FtpPathResolverRegistry implements IFtpPathResolverRegistry
}
}
+ @Override
public InputStream createInputStream(long offset) throws IOException
{
if (errorMsgOrNull != null)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpServer.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpServer.java
index eb6dc0e33ea..ec15d93bd27 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpServer.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpServer.java
@@ -205,6 +205,7 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
s.setFileSystemFactory(this);
s.setPasswordAuthenticator(new PasswordAuthenticator()
{
+ @Override
public boolean authenticate(String username, String password, ServerSession session)
{
try
@@ -250,6 +251,7 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
}
}
+ @Override
public DSSFileSystemView createFileSystemView(User user) throws FtpException
{
if (user instanceof FtpUser)
@@ -263,6 +265,7 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
}
}
+ @Override
public org.apache.sshd.server.FileSystemView createFileSystemView(Session session)
throws IOException
{
@@ -274,11 +277,13 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
{
private Cache cache = new Cache(SystemTimeProvider.SYSTEM_TIME_PROVIDER);
+ @Override
public SshFile getFile(SshFile baseDir, String file)
{
throw new UnsupportedOperationException();
}
+ @Override
public SshFile getFile(String file)
{
return new FileView(view, file, cache);
@@ -320,96 +325,115 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
return file;
}
+ @Override
public String getAbsolutePath()
{
return getFile().getAbsolutePath();
}
+ @Override
public String getName()
{
return FileUtilities.getFileNameFromRelativePath(path);
}
+ @Override
public boolean isDirectory()
{
return getFile().isDirectory();
}
+ @Override
public boolean isFile()
{
return getFile().isFile();
}
+ @Override
public boolean doesExist()
{
return getFile().doesExist();
}
+ @Override
public boolean isReadable()
{
return getFile().isReadable();
}
+ @Override
public boolean isWritable()
{
return false;
}
+ @Override
public boolean isExecutable()
{
return false;
}
+ @Override
public boolean isRemovable()
{
return getFile().isRemovable();
}
+ @Override
public SshFile getParentFile()
{
return null;
}
+ @Override
public long getLastModified()
{
return getFile().getLastModified();
}
+ @Override
public boolean setLastModified(long time)
{
return false;
}
+ @Override
public long getSize()
{
return getFile().getSize();
}
+ @Override
public boolean mkdir()
{
return false;
}
+ @Override
public boolean delete()
{
return false;
}
+ @Override
public boolean create() throws IOException
{
return false;
}
+ @Override
public void truncate() throws IOException
{
throw new UnsupportedOperationException();
}
+ @Override
public boolean move(SshFile destination)
{
return false;
}
+ @Override
public List<SshFile> listSshFiles()
{
List<FtpFile> files = getFile().listFiles();
@@ -421,11 +445,13 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
return result;
}
+ @Override
public OutputStream createOutputStream(long offset) throws IOException
{
throw new UnsupportedOperationException();
}
+ @Override
public InputStream createInputStream(long offset) throws IOException
{
InputStream inputStream = getFile().createInputStream(offset);
@@ -433,6 +459,7 @@ public class FtpServer implements FileSystemFactory, org.apache.sshd.server.File
return inputStream;
}
+ @Override
public void handleClose() throws IOException
{
for (InputStream inputStream : inputStreams)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUser.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUser.java
index d3fe821cf75..855aa0446a6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUser.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUser.java
@@ -43,26 +43,31 @@ public class FtpUser implements User
this.sessionToken = sessionToken;
}
+ @Override
public boolean getEnabled()
{
return true;
}
+ @Override
public String getHomeDirectory()
{
return "/";
}
+ @Override
public int getMaxIdleTime()
{
return SECONDS_PER_HOUR;
}
+ @Override
public String getName()
{
return name;
}
+ @Override
public String getPassword()
{
throw new UnsupportedOperationException();
@@ -73,17 +78,20 @@ public class FtpUser implements User
return sessionToken;
}
+ @Override
public AuthorizationRequest authorize(AuthorizationRequest request)
{
// authorization is implemented by not showing the users datasets they cannot see.
return request;
}
+ @Override
public List<Authority> getAuthorities()
{
return Collections.emptyList();
}
+ @Override
public List<Authority> getAuthorities(Class<? extends Authority> arg0)
{
return Collections.emptyList();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUserManager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUserManager.java
index 40671c09966..04b8f40e3ec 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUserManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/FtpUserManager.java
@@ -49,6 +49,7 @@ public class FtpUserManager implements UserManager
this.service = service;
}
+ @Override
public User authenticate(Authentication authentication) throws AuthenticationFailedException
{
if (authentication instanceof UsernamePasswordAuthentication)
@@ -68,36 +69,43 @@ public class FtpUserManager implements UserManager
throw new AuthenticationFailedException();
}
+ @Override
public void delete(String arg0) throws FtpException
{
throw new UnsupportedOperationException();
}
+ @Override
public boolean doesExist(String arg0) throws FtpException
{
return false;
}
+ @Override
public String getAdminName() throws FtpException
{
throw new UnsupportedOperationException();
}
+ @Override
public String[] getAllUserNames() throws FtpException
{
throw new UnsupportedOperationException();
}
+ @Override
public User getUserByName(String userName) throws FtpException
{
return new FtpUser(userName, null);
}
+ @Override
public boolean isAdmin(String arg0) throws FtpException
{
return false;
}
+ @Override
public void save(User arg0) throws FtpException
{
throw new UnsupportedOperationException();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFile.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFile.java
index 2987e797d93..960e34202a4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFile.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFile.java
@@ -51,6 +51,7 @@ public abstract class AbstractFtpFile implements FtpFile
* exceptions are being propagated to the surrounding Apache FTP classes. Apache FTP swallows
* exceptions without logging and thereby hinders error analysis.
*/
+ @Override
public final List<FtpFile> listFiles()
{
try
@@ -68,46 +69,55 @@ public abstract class AbstractFtpFile implements FtpFile
*/
public abstract List<FtpFile> unsafeListFiles() throws RuntimeException;
+ @Override
public boolean doesExist()
{
return true;
}
+ @Override
public String getAbsolutePath()
{
return absolutePath;
}
+ @Override
public String getName()
{
return new File(absolutePath).getName();
}
+ @Override
public String getOwnerName()
{
return FtpConstants.FTP_USER_NAME;
}
+ @Override
public String getGroupName()
{
return FtpConstants.FTP_USER_GROUP_NAME;
}
+ @Override
public boolean isHidden()
{
return false;
}
+ @Override
public boolean isReadable()
{
return true;
}
+ @Override
public boolean isRemovable()
{
return false;
}
+ @Override
public boolean isWritable()
{
return false;
@@ -117,31 +127,37 @@ public abstract class AbstractFtpFile implements FtpFile
// Unsupported operations
// =================================
+ @Override
public OutputStream createOutputStream(long arg0) throws IOException
{
return null;
}
+ @Override
public boolean delete()
{
return false;
}
+ @Override
public boolean mkdir()
{
return false;
}
+ @Override
public boolean move(FtpFile arg0)
{
return false;
}
+ @Override
public boolean setLastModified(long arg0)
{
return false;
}
+ @Override
public int getLinkCount()
{
return 0;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFolder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFolder.java
index 3b567621009..79a3c6cf722 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFolder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/AbstractFtpFolder.java
@@ -32,26 +32,31 @@ public abstract class AbstractFtpFolder extends AbstractFtpFile
super(absolutePath);
}
+ @Override
public boolean isDirectory()
{
return true;
}
+ @Override
public boolean isFile()
{
return false;
}
+ @Override
public InputStream createInputStream(long arg0) throws IOException
{
return null;
}
+ @Override
public long getSize()
{
return 0;
}
+ @Override
public long getLastModified()
{
return System.currentTimeMillis();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ExperimentFolderResolver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ExperimentFolderResolver.java
index 06bc78fee48..7a75d1fb423 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ExperimentFolderResolver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ExperimentFolderResolver.java
@@ -50,12 +50,14 @@ public class ExperimentFolderResolver implements IFtpPathResolver
* @return <code>true</code> for all paths containing 3 levels of nested folders,
* <code>false</code> for all other paths.
*/
+ @Override
public boolean canResolve(String path)
{
int nestedLevels = StringUtils.countMatches(path, FtpConstants.FILE_SEPARATOR);
return nestedLevels == 3;
}
+ @Override
public FtpFile resolve(final String path, final FtpPathResolverContext resolverContext)
{
return new AbstractFtpFolder(path)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/FtpFileImpl.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/FtpFileImpl.java
index e76d6ffe535..39275899f20 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/FtpFileImpl.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/FtpFileImpl.java
@@ -68,6 +68,7 @@ public class FtpFileImpl extends AbstractFtpFile
this.childrenFilter = childrenFilter;
}
+ @Override
public InputStream createInputStream(long offset) throws IOException
{
try
@@ -92,11 +93,13 @@ public class FtpFileImpl extends AbstractFtpFile
}
}
+ @Override
public long getLastModified()
{
return lastModified;
}
+ @Override
public long getSize()
{
if (isFile())
@@ -106,11 +109,13 @@ public class FtpFileImpl extends AbstractFtpFile
return 0;
}
+ @Override
public boolean isDirectory()
{
return isDirectory;
}
+ @Override
public boolean isFile()
{
return isDirectory() == false;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ProjectFolderResolver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ProjectFolderResolver.java
index 4d820ccf472..b914aee44bf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ProjectFolderResolver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/ProjectFolderResolver.java
@@ -44,12 +44,14 @@ public class ProjectFolderResolver implements IFtpPathResolver
* @return <code>true</code> for all paths containing 2 levels of nested folders,
* <code>false</code> for all other paths.
*/
+ @Override
public boolean canResolve(String path)
{
int nestedLevels = StringUtils.countMatches(path, FtpConstants.FILE_SEPARATOR);
return nestedLevels == 2;
}
+ @Override
public FtpFile resolve(final String path, final FtpPathResolverContext resolverContext)
{
return new AbstractFtpFolder(path)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/RootFolderResolver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/RootFolderResolver.java
index c4140e267b2..5614a0f4d64 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/RootFolderResolver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/RootFolderResolver.java
@@ -37,11 +37,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
public class RootFolderResolver implements IFtpPathResolver
{
+ @Override
public boolean canResolve(String path)
{
return FtpConstants.ROOT_DIRECTORY.equals(path);
}
+ @Override
public FtpFile resolve(String path, final FtpPathResolverContext resolverContext)
{
return new AbstractFtpFolder(path)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/SpaceFolderResolver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/SpaceFolderResolver.java
index d143eb18023..aa810736e9b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/SpaceFolderResolver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/SpaceFolderResolver.java
@@ -39,11 +39,13 @@ public class SpaceFolderResolver implements IFtpPathResolver
* @return <code>true</code> for all paths containing single folder, <code>false</code> for all
* other paths.
*/
+ @Override
public boolean canResolve(String path)
{
return false == removeStartingSlash(path).contains(FtpConstants.FILE_SEPARATOR);
}
+ @Override
public FtpFile resolve(final String path, final FtpPathResolverContext resolverContext)
{
return new AbstractFtpFolder(path)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolver.java
index 7dea42bfc1f..4b311afdc72 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolver.java
@@ -222,12 +222,14 @@ public class TemplateBasedDataSetResourceResolver implements IFtpPathResolver,
/**
* @return <code>true</code> for paths containing at least 4 nested directory levels.
*/
+ @Override
public boolean canResolve(String path)
{
int nestedLevels = StringUtils.countMatches(path, FtpConstants.FILE_SEPARATOR);
return nestedLevels >= 4;
}
+ @Override
public FtpFile resolve(final String path, final FtpPathResolverContext resolverContext)
{
String experimentId = extractExperimentIdFromPath(path);
@@ -413,6 +415,7 @@ public class TemplateBasedDataSetResourceResolver implements IFtpPathResolver,
/**
* @see IExperimentChildrenLister
*/
+ @Override
public List<FtpFile> listExperimentChildrenPaths(Experiment experiment,
final String parentPath, FtpPathResolverContext context)
{
@@ -624,6 +627,7 @@ public class TemplateBasedDataSetResourceResolver implements IFtpPathResolver,
{
private final Pattern compiledPattern = Pattern.compile(fileFilterPattern);
+ @Override
public boolean accept(IHierarchicalContentNode node)
{
if (node.isDirectory())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
index d84963cf85d..51a820d790c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/AbstractTabularDataGraph.java
@@ -106,6 +106,7 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
*
* @throws IOException
*/
+ @Override
public void generateImage() throws IOException
{
generateImage(configuration.getImageWidth(), configuration.getImageHeight());
@@ -119,6 +120,7 @@ abstract class AbstractTabularDataGraph<T extends TabularDataGraphConfiguration>
* @param imageHeight The desired height of the image
* @throws IOException
*/
+ @Override
public void generateImage(int imageWidth, int imageHeight) throws IOException
{
JFreeChart chart = createChart(imageWidth, imageHeight);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java
index a504e534ec1..58ebde8fa4f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/HeatmapDataset.java
@@ -54,77 +54,92 @@ public class HeatmapDataset implements XYZDataset
}
// XYZDataset
+ @Override
public Number getZ(int series, int item)
{
return wrappedDataset.getZ(series, item);
}
+ @Override
public double getZValue(int series, int item)
{
return wrappedDataset.getZValue(series, item);
}
+ @Override
public DomainOrder getDomainOrder()
{
return wrappedDataset.getDomainOrder();
}
+ @Override
public int getItemCount(int series)
{
return wrappedDataset.getItemCount(series);
}
+ @Override
public Number getX(int series, int item)
{
return wrappedDataset.getX(series, item);
}
+ @Override
public double getXValue(int series, int item)
{
return wrappedDataset.getXValue(series, item);
}
+ @Override
public Number getY(int series, int item)
{
return wrappedDataset.getY(series, item);
}
+ @Override
public double getYValue(int series, int item)
{
return wrappedDataset.getYValue(series, item);
}
+ @Override
public int getSeriesCount()
{
return wrappedDataset.getSeriesCount();
}
// The JFreeChart interface does not use generics
+ @Override
public Comparable<?> getSeriesKey(int series)
{
return wrappedDataset.getSeriesKey(series);
}
+ @Override
public int indexOf(@SuppressWarnings("rawtypes") Comparable seriesKey)
{
return wrappedDataset.indexOf(seriesKey);
}
+ @Override
public void addChangeListener(DatasetChangeListener arg0)
{
wrappedDataset.addChangeListener(arg0);
}
+ @Override
public DatasetGroup getGroup()
{
return wrappedDataset.getGroup();
}
+ @Override
public void removeChangeListener(DatasetChangeListener arg0)
{
wrappedDataset.removeChangeListener(arg0);
}
+ @Override
public void setGroup(DatasetGroup arg0)
{
wrappedDataset.setGroup(arg0);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index 1a14af3891c..efac61d8c59 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -304,21 +304,25 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
return null;
}
+ @Override
public char getColumnDelimiter()
{
return columnDelimiter;
}
+ @Override
public boolean isIgnoreComments()
{
return ignoreComments;
}
+ @Override
public char getCommentDelimiter()
{
return comment;
}
+ @Override
public boolean isSkipEmptyRecords()
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
index 573209fe7f1..bd0b4bd02cd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogram.java
@@ -55,6 +55,7 @@ public class TabularDataHistogram extends
boolean success = tryIterateOverFileLinesUsing(new ILineProcessor()
{
+ @Override
public void processLine(String xString, String yString, int index)
{
// The x and y should have the same value, since a histogram requires only one
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
index c7c7a1d19f2..0c5b0d7a7bd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplot.java
@@ -54,6 +54,7 @@ public class TabularDataScatterplot extends
boolean success = tryIterateOverFileLinesUsing(new ILineProcessor()
{
+ @Override
public void processLine(String xString, String yString, int index)
{
double x = parseDouble(xString);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
index 9ca9e7bcae4..80c9f0ed016 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
@@ -43,6 +43,7 @@ public class TabularDataTickUnitSource implements TickUnitSource, Serializable
* @param unit the unit (<code>null</code> not permitted).
* @return A tick unit that is larger than the supplied unit.
*/
+ @Override
public TickUnit getLargerTickUnit(TickUnit unit)
{
double x = unit.getSize();
@@ -56,6 +57,7 @@ public class TabularDataTickUnitSource implements TickUnitSource, Serializable
* @param unit the unit (<code>null</code> not permitted).
* @return A unit from the collection.
*/
+ @Override
public TickUnit getCeilingTickUnit(TickUnit unit)
{
return getLargerTickUnit(unit);
@@ -67,6 +69,7 @@ public class TabularDataTickUnitSource implements TickUnitSource, Serializable
* @param size the size.
* @return A unit from the collection.
*/
+ @Override
public TickUnit getCeilingTickUnit(double size)
{
final double numberOfDigits = Math.log(size) / LOG_10_VALUE;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationAdvisor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationAdvisor.java
index 6301c183448..c91f254493a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationAdvisor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationAdvisor.java
@@ -46,11 +46,13 @@ public class OpenBISAuthenticationAdvisor extends DefaultPointcutAdvisor
return new Pointcut()
{
+ @Override
public MethodMatcher getMethodMatcher()
{
return new AnnotationMethodMatcher(ManagedAuthentication.class);
}
+ @Override
public ClassFilter getClassFilter()
{
return new RootClassFilter(IEncapsulatedOpenBISService.class);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptor.java
index 1df41c35a68..302590a3704 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptor.java
@@ -103,6 +103,7 @@ public class OpenBISAuthenticationInterceptor implements MethodInterceptor
/**
* authenticate when the session has expired.
*/
+ @Override
public synchronized Object invoke(MethodInvocation invocation) throws Throwable
{
checkSessionToken();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
index 6b1de00c4db..d02b5396a24 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FileBasedImageAnalysisGraphReportingPlugin.java
@@ -72,6 +72,7 @@ public class FileBasedImageAnalysisGraphReportingPlugin extends AbstractDataMerg
TabularDataGraphCollectionConfiguration.getConfiguration(propertiesFilePath);
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
index 535d78fd040..813a8f45330 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
@@ -45,6 +45,7 @@ public class DatasetModificationReportingPlugin extends AbstractTableModelReport
super(properties, storeRoot);
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoOverviewPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoOverviewPlugin.java
index cd69c751319..22535786148 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoOverviewPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoOverviewPlugin.java
@@ -54,6 +54,7 @@ public class DemoOverviewPlugin implements IDatasetImageOverviewPlugin
label = PropertyUtils.getProperty(properties, LABEL_PROPERTY_KEY, "(no label)");
}
+ @Override
public ResponseContentStream createImageOverview(String datasetCode, String datasetTypeCode,
IHierarchicalContent datasetRoot, ImageResolutionKind resolution)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
index 6820984199d..104ce5081a8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoProcessingPlugin.java
@@ -50,6 +50,7 @@ public class DemoProcessingPlugin implements IProcessingPluginTask
{
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
@@ -71,6 +72,7 @@ public class DemoProcessingPlugin implements IProcessingPluginTask
{
return new IHierarchicalContentNodeVisitor()
{
+ @Override
public void visit(IHierarchicalContentNode node)
{
String relativePath = node.getRelativePath();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
index c91cc2bb4fa..fe5d781a614 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
@@ -53,6 +53,7 @@ public class DemoReportingPlugin extends AbstractTableModelReportingPlugin
super(properties, storeRoot);
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
@@ -84,6 +85,7 @@ public class DemoReportingPlugin extends AbstractTableModelReportingPlugin
return new IHierarchicalContentNodeVisitor()
{
+ @Override
public void visit(IHierarchicalContentNode node)
{
if (false == node.isDirectory())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/EmailSender.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/EmailSender.java
index db4945abfa9..4fad16c0dbc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/EmailSender.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/EmailSender.java
@@ -50,18 +50,21 @@ public class EmailSender implements IEmailSender
// builder
+ @Override
public IEmailSender withSubject(String aSubject)
{
this.subject = aSubject;
return this;
}
+ @Override
public IEmailSender withBody(String aBodyText)
{
this.bodyText = aBodyText;
return this;
}
+ @Override
public IEmailSender withAttachedFile(String filePath, String attachmentName)
{
if (attachmentName == null)
@@ -77,6 +80,7 @@ public class EmailSender implements IEmailSender
return this;
}
+ @Override
public IEmailSender withAttachedText(String text, String attachmentName)
{
if (attachmentName == null)
@@ -102,6 +106,7 @@ public class EmailSender implements IEmailSender
// sender
+ @Override
public void send()
{
try
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPlugin.java
index 3acd4ff27fe..c83402c2a16 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPlugin.java
@@ -62,11 +62,13 @@ public class JythonBasedAggregationServiceReportingPlugin extends
this.scriptRunnerFactory = scriptRunnerFactory;
}
+ @Override
public TableModel createAggregationReport(final Map<String, Object> parameters,
final DataSetProcessingContext context)
{
ITableModelCreator generator = new ITableModelCreator()
{
+ @Override
public void create(ISimpleTableModelBuilderAdaptor builder)
{
operationLog.info("Aggregation report for the following parameters "
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
index f3c8f9dabb2..ac452ae6fb8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedPluginUtils.java
@@ -40,6 +40,7 @@ public class JythonBasedPluginUtils
{
return new IDataSet()
{
+ @Override
public IHierarchicalContent getContent()
{
return content;
@@ -47,86 +48,103 @@ public class JythonBasedPluginUtils
// delegator to description
+ @Override
public int getSpeedHint()
{
return description.getSpeedHint();
}
+ @Override
public String getSpaceCode()
{
return description.getSpaceCode();
}
+ @Override
public String getSampleTypeCode()
{
return description.getSampleTypeCode();
}
+ @Override
public String getSampleIdentifier()
{
return description.getSampleIdentifier();
}
+ @Override
public String getSampleCode()
{
return description.getSampleCode();
}
+ @Override
public String getProjectCode()
{
return description.getProjectCode();
}
+ @Override
public String getMainDataSetPattern()
{
return description.getMainDataSetPattern();
}
+ @Override
public String getMainDataSetPath()
{
return description.getMainDataSetPath();
}
+ @Override
public String getInstanceCode()
{
return description.getInstanceCode();
}
+ @Override
public String getExperimentTypeCode()
{
return description.getExperimentTypeCode();
}
+ @Override
public String getExperimentIdentifier()
{
return description.getExperimentIdentifier();
}
+ @Override
public String getExperimentCode()
{
return description.getExperimentCode();
}
+ @Override
public String getDataSetTypeCode()
{
return description.getDataSetTypeCode();
}
+ @Override
public String getDatabaseInstanceCode()
{
return description.getDatabaseInstanceCode();
}
+ @Override
public Long getDataSetSize()
{
return description.getDataSetSize();
}
+ @Override
public String getDataSetLocation()
{
return description.getDataSetLocation();
}
+ @Override
public String getDataSetCode()
{
return description.getDataSetCode();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
index 19f22fe7cab..f3288ecf66d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedProcessingPlugin.java
@@ -79,6 +79,7 @@ public class JythonBasedProcessingPlugin implements IProcessingPluginTask
return hierarchicalContentProvider;
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> dataSets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
index 94d0a794edb..a8c9ef5c105 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedReportingPlugin.java
@@ -70,6 +70,7 @@ public class JythonBasedReportingPlugin extends AbstractTableModelReportingPlugi
this.hierarchicalContentProvider = contentProvider;
}
+ @Override
public TableModel createReport(List<DatasetDescription> dataSets,
DataSetProcessingContext context)
{
@@ -92,6 +93,7 @@ public class JythonBasedReportingPlugin extends AbstractTableModelReportingPlugi
{
ITableModelCreator generator = new ITableModelCreator()
{
+ @Override
public void create(ISimpleTableModelBuilderAdaptor builder)
{
operationLog.info("Report for the following datasets has been requested: "
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/MailService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/MailService.java
index d4f9ebbaba7..d02a59e7208 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/MailService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/MailService.java
@@ -58,6 +58,7 @@ public class MailService implements IMailService
this.defaultBodyText = defaultBodyText;
}
+ @Override
public IEmailSender createEmailSender()
{
return new EmailSender(senderService, defaultSubject, defaultBodyText);
@@ -70,11 +71,13 @@ public class MailService implements IMailService
return new IEmailSenderService()
{
+ @Override
public void trySendEmail(String subject, String bodyText)
{
mailClient.sendEmailMessage(subject, bodyText, null, null, recipient);
}
+ @Override
public void trySendEmailWithTextAttachment(String subject, String bodyText,
String attachmentFileName, String attachmentText) throws IOException
{
@@ -83,6 +86,7 @@ public class MailService implements IMailService
attachmentFileName, new DataHandler(dataSource), null, null, recipient);
}
+ @Override
public void trySendEmailWithFileAttachment(String subject, String bodyText,
String attachmentFileName, String attachmentFilePath)
throws FileNotFoundException, IOException
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
index 17d480069e9..8d2fd2fd352 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
@@ -73,6 +73,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
* Factory method for creating an IAggregationServiceReportingPluginScriptRunner for a given
* processing context.
*/
+ @Override
public IAggregationServiceReportingPluginScriptRunner createAggregationServiceReportingPluginRunner(
DataSetProcessingContext context)
{
@@ -93,6 +94,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
/**
* Factory method for creating an IReportingPluginScriptRunner for a given processing context.
*/
+ @Override
public IReportingPluginScriptRunner createReportingPluginRunner(DataSetProcessingContext context)
{
String scriptString = extractScriptFromPath(scriptPath);
@@ -108,6 +110,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
/**
* Factory method for creating an IProcessingPluginScriptRunner for a given processing context.
*/
+ @Override
public IProcessingPluginScriptRunner createProcessingPluginRunner(
DataSetProcessingContext context)
{
@@ -186,6 +189,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
this.contentProvider = contentProvider;
}
+ @Override
public IHierarchicalContent getContent(String dataSetCode)
{
IHierarchicalContent content = contents.get(dataSetCode);
@@ -225,12 +229,14 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
}
}
+ @Override
public void aggregate(Map<String, Object> parameters,
ISimpleTableModelBuilderAdaptor tableBuilder) throws EvaluatorException
{
evaluator.evalFunction(FUNCTION_NAME, parameters, tableBuilder);
}
+ @Override
public void closeContentResources()
{
contentProvider.closeContents();
@@ -253,6 +259,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
}
}
+ @Override
public void describe(List<IDataSet> dataSets, ISimpleTableModelBuilderAdaptor tableBuilder)
{
evaluator.evalFunction(DESCRIBE_FUNCTION_NAME, dataSets, tableBuilder);
@@ -275,6 +282,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
}
}
+ @Override
public Status process(IDataSet dataSet)
{
try
@@ -290,6 +298,7 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
}
+ @Override
public String getScriptPath()
{
return scriptPath;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
index 8d2febc5808..7b077050a3a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/ReportingBasedProcessingPlugin.java
@@ -107,6 +107,7 @@ public class ReportingBasedProcessingPlugin implements IProcessingPluginTask
PropertyUtils.getProperty(properties, ATTACHMENT_NAME, DEFAULT_ATTACHMENT_NAME);
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> dataSets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/SimpleTableModelBuilderAdaptor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/SimpleTableModelBuilderAdaptor.java
index 158434912dd..03541dfe650 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/SimpleTableModelBuilderAdaptor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/SimpleTableModelBuilderAdaptor.java
@@ -57,57 +57,68 @@ class SimpleTableModelBuilderAdaptor implements ISimpleTableModelBuilderAdaptor
//
// NOTE: TableModel is exposed to keep dependencies simple
+ @Override
public TableModel getTableModel()
{
return builder.getTableModel();
}
+ @Override
public void addHeader(String title)
{
builder.addHeader(title);
}
+ @Override
public void addHeader(String title, String code)
{
builder.addHeader(title, code);
}
+ @Override
public void addHeader(String title, int defaultColumnWidth)
{
builder.addHeader(title, defaultColumnWidth);
}
+ @Override
public IRowBuilderAdaptor addRow()
{
final IRowBuilder row = builder.addRow();
return new IRowBuilderAdaptor()
{
+ @Override
public void setCell(String headerTitle, String value)
{
row.setCell(headerTitle, value);
}
+ @Override
public void setCell(String headerTitle, long value)
{
row.setCell(headerTitle, value);
}
+ @Override
public void setCell(String headerTitle, double value)
{
row.setCell(headerTitle, value);
}
+ @Override
public void setCell(String headerTitle, Date value)
{
row.setCell(headerTitle, value);
}
+ @Override
public void setCell(String headerTitle, IEntityLinkElement value)
{
row.setCell(headerTitle, asTableCell(value, null));
}
+ @Override
public void setCell(String headerTitle, IEntityLinkElement value, String linkText)
{
row.setCell(headerTitle, asTableCell(value, linkText));
@@ -128,11 +139,13 @@ class SimpleTableModelBuilderAdaptor implements ISimpleTableModelBuilderAdaptor
};
}
+ @Override
public void addFullHeader(String... titles)
{
builder.addFullHeader(titles);
}
+ @Override
public void addFullRow(String... values)
{
builder.addFullRow(values);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
index 1480bc984aa..cab7817037b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
@@ -42,16 +42,19 @@ public abstract class AbstractAggregationServiceReportingPlugin extends Abstract
super(properties, storeRoot);
}
+ @Override
public ReportingPluginType getReportingPluginType()
{
return ReportingPluginType.AGGREGATION_TABLE_MODEL;
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
throw createException();
}
+ @Override
public LinkModel createLink(DatasetDescription dataset)
{
throw createException();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPlugin.java
index b6655741fc4..8d2104ae3be 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPlugin.java
@@ -138,6 +138,7 @@ public abstract class AbstractArchiverProcessingPlugin extends AbstractDatastore
*/
abstract protected BooleanStatus isDataSetPresentInArchive(DatasetDescription dataset);
+ @Override
public ProcessingStatus archive(List<DatasetDescription> datasets,
final ArchiverTaskContext context, boolean removeFromDataStore)
{
@@ -273,6 +274,7 @@ public abstract class AbstractArchiverProcessingPlugin extends AbstractDatastore
dataSetDeleter.scheduleDeletionOfDataSets(datasets);
}
+ @Override
public ProcessingStatus unarchive(List<DatasetDescription> datasets, ArchiverTaskContext context)
{
operationLog.info("Unarchiving of the following datasets has been requested: "
@@ -325,6 +327,7 @@ public abstract class AbstractArchiverProcessingPlugin extends AbstractDatastore
return statuses;
}
+ @Override
public ProcessingStatus deleteFromArchive(List<DatasetLocation> datasets)
{
DatasetProcessingStatuses status = doDeleteFromArchive(datasets);
@@ -473,6 +476,7 @@ public abstract class AbstractArchiverProcessingPlugin extends AbstractDatastore
{
statusUpdater = new IDataSetStatusUpdater()
{
+ @Override
public void update(List<String> codes, DataSetArchivingStatus status,
boolean present)
{
@@ -571,6 +575,7 @@ public abstract class AbstractArchiverProcessingPlugin extends AbstractDatastore
this.shares = shares;
}
+ @Override
public void prepareForUnarchiving(DatasetDescription dataSet)
{
SimpleDataSetInformationDTO translatedDataSet = SimpleDataSetHelper.translate(dataSet);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
index 61e02a8085b..37b20b2122e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
@@ -86,6 +86,7 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
sendingDetailedEMail = PropertyUtils.getBoolean(properties, SEND_DETAILED_EMAIL_KEY, false);
}
+ @Override
public ProcessingStatus process(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDssLinkReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDssLinkReportingPlugin.java
index f3e0d82e243..bc160210971 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDssLinkReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDssLinkReportingPlugin.java
@@ -48,6 +48,7 @@ public abstract class AbstractDssLinkReportingPlugin extends AbstractDatastorePl
super(properties, storeRoot);
}
+ @Override
public ReportingPluginType getReportingPluginType()
{
return ReportingPluginType.DSS_LINK;
@@ -56,6 +57,7 @@ public abstract class AbstractDssLinkReportingPlugin extends AbstractDatastorePl
/**
* Generate a report using containing links to each of the data sets.
*/
+ @Override
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
@@ -71,6 +73,7 @@ public abstract class AbstractDssLinkReportingPlugin extends AbstractDatastorePl
return builder.getTableModel();
}
+ @Override
public TableModel createAggregationReport(Map<String, Object> parameters, DataSetProcessingContext context)
{
throw new IllegalArgumentException(
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractTableModelReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractTableModelReportingPlugin.java
index 57181a886ef..c0330eba5fc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractTableModelReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractTableModelReportingPlugin.java
@@ -57,17 +57,20 @@ public abstract class AbstractTableModelReportingPlugin extends AbstractDatastor
super(properties, storeRoot);
}
+ @Override
public ReportingPluginType getReportingPluginType()
{
return ReportingPluginType.TABLE_MODEL;
}
+ @Override
public LinkModel createLink(DatasetDescription dataset)
{
throw new IllegalArgumentException(
"The method createLink is not supported by TABLE_MODEL tasks");
}
+ @Override
public TableModel createAggregationReport(Map<String, Object> parameters, DataSetProcessingContext context)
{
throw new IllegalArgumentException(
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/Copier.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/Copier.java
index dca6c8f3c81..402dd6fb041 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/Copier.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/Copier.java
@@ -78,6 +78,7 @@ public class Copier implements Serializable, IPostRegistrationDatasetHandler
return originalHostFile;
}
+ @Override
public Status handle(File originalData, DataSetInformation dataSetInformation,
Map<String, String> parameterBindings)
{
@@ -169,6 +170,7 @@ public class Copier implements Serializable, IPostRegistrationDatasetHandler
}
}
+ @Override
public void undoLastOperation()
{
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManager.java
index 08868caf784..c4c1068ab57 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DataSetFileOperationsManager.java
@@ -147,6 +147,7 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
* Copies specified dataset's data to destination specified in constructor. The path at the
* destination is defined by the original location of the data set.
*/
+ @Override
public Status copyToDestination(File originalData, DatasetDescription dataset)
{
try
@@ -175,6 +176,7 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
* Retrieves specified datases's data from the destination specified in constructor. The path at
* the destination is defined by original location of the data set.
*/
+ @Override
public Status retrieveFromDestination(File originalData, DatasetDescription dataset)
{
try
@@ -197,15 +199,18 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
* Deletes specified datases's data from the destination specified in constructor. The path at
* the destination is defined by original location of the data set.
*/
+ @Override
public Status deleteFromDestination(IDatasetLocation dataset)
{
return delete(dataset, new IDeleteAction()
{
+ @Override
public String getName()
{
return "delete";
}
+ @Override
public void delete(File dataSetFolder, String dataSetCode)
{
executor.deleteFolder(dataSetFolder);
@@ -213,15 +218,18 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
});
}
+ @Override
public Status markAsDeleted(IDatasetLocation dataset)
{
return delete(dataset, new IDeleteAction()
{
+ @Override
public String getName()
{
return "mark as deleted";
}
+ @Override
public void delete(File dataSetFolder, String dataSetCode)
{
File deletedFolder =
@@ -259,6 +267,7 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
* Checks if specified dataset's data are present and synchronized in the destination specified
* in constructor. The path at the destination is defined by original location of the data set.
*/
+ @Override
public BooleanStatus isSynchronizedWithDestination(File originalData, DatasetDescription dataset)
{
try
@@ -281,6 +290,7 @@ public class DataSetFileOperationsManager implements IDataSetFileOperationsManag
* Checks if specified dataset's data are present in the destination specified in constructor.
* The path at the destination is defined by original location of the data set.
*/
+ @Override
public BooleanStatus isPresentInDestination(DatasetDescription dataset)
{
try
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DecoratingTableModelReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DecoratingTableModelReportingPlugin.java
index 0193d42fb5a..721efe91484 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DecoratingTableModelReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/DecoratingTableModelReportingPlugin.java
@@ -99,6 +99,7 @@ public class DecoratingTableModelReportingPlugin extends AbstractTableModelRepor
}
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/EntityLinksDecorator.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/EntityLinksDecorator.java
index 8937a4d4e60..5110315851f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/EntityLinksDecorator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/EntityLinksDecorator.java
@@ -69,6 +69,7 @@ public class EntityLinksDecorator implements ITableModelTransformation
final String materialType = getMaterialType(properties);
return new IEntityTableCellTranslation()
{
+ @Override
public ISerializableComparable translation(ISerializableComparable value)
{
String materialCode = value.toString();
@@ -79,6 +80,7 @@ public class EntityLinksDecorator implements ITableModelTransformation
return entityTableCell;
}
+ @Override
public EntityKind getEntityKind()
{
return EntityKind.MATERIAL;
@@ -110,6 +112,7 @@ public class EntityLinksDecorator implements ITableModelTransformation
return new IEntityTableCellTranslation()
{
+ @Override
public ISerializableComparable translation(ISerializableComparable value)
{
String identifier =
@@ -121,6 +124,7 @@ public class EntityLinksDecorator implements ITableModelTransformation
return entityTableCell;
}
+ @Override
public EntityKind getEntityKind()
{
return EntityKind.SAMPLE;
@@ -174,6 +178,7 @@ public class EntityLinksDecorator implements ITableModelTransformation
return factory;
}
+ @Override
public TableModel transform(TableModel tableModel)
{
class TranslationAndIndex
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/GenericDssLinkReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/GenericDssLinkReportingPlugin.java
index 37f10a985eb..8219524f9d1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/GenericDssLinkReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/GenericDssLinkReportingPlugin.java
@@ -105,6 +105,7 @@ public class GenericDssLinkReportingPlugin extends AbstractDssLinkReportingPlugi
return linkModel;
}
+ @Override
public LinkModel createLink(DatasetDescription dataSet)
{
return getDataSetLinkModel(dataSet);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/HighWaterMarkChecker.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/HighWaterMarkChecker.java
index 28eb5d6547c..2e19b9f2f22 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/HighWaterMarkChecker.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/HighWaterMarkChecker.java
@@ -27,6 +27,7 @@ public class HighWaterMarkChecker implements IStatusChecker, Serializable
this.highWaterMarkPath = archiveHighWaterMarkPath;
}
+ @Override
public Status check(int numberOfItems)
{
HighwaterMarkWatcher w = new HighwaterMarkWatcher(highWaterMark * numberOfItems);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedColumnDataReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedColumnDataReportingPlugin.java
index d566ab492c1..fb45a4c09c6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedColumnDataReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedColumnDataReportingPlugin.java
@@ -61,6 +61,7 @@ public class MergedColumnDataReportingPlugin extends AbstractDataMergingReportin
(rowIdColumnHeaderOrNull == null) ? "id" : rowIdColumnHeaderOrNull;
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets,
DataSetProcessingContext context)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedRowDataReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedRowDataReportingPlugin.java
index 82f1aca351d..636a26801a9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedRowDataReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MergedRowDataReportingPlugin.java
@@ -48,6 +48,7 @@ public class MergedRowDataReportingPlugin extends AbstractDataMergingReportingPl
super(properties, storeRoot);
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiveCopierFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiveCopierFactory.java
index e7d8236706f..ffef651b5ad 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiveCopierFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiveCopierFactory.java
@@ -39,6 +39,7 @@ public final class RsyncArchiveCopierFactory implements Serializable, IPathCopie
{
private static final long serialVersionUID = 1L;
+ @Override
public IPathCopier create(File rsyncExecutable, File sshExecutableOrNull, long timeoutInMillis)
{
return new RsyncCopier(rsyncExecutable, sshExecutableOrNull, "--archive", "--delete",
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiver.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiver.java
index d2120532d82..55206730796 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiver.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiver.java
@@ -59,6 +59,7 @@ public class RsyncArchiver extends AbstractArchiverProcessingPlugin
private static final Comparator<IHierarchicalContentNode> NODE_COMPARATOR =
new Comparator<IHierarchicalContentNode>()
{
+ @Override
public int compare(IHierarchicalContentNode n1, IHierarchicalContentNode n2)
{
return n1.getName().compareTo(n2.getName());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncCopierFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncCopierFactory.java
index 39cd73cb094..3e92d913e73 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncCopierFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncCopierFactory.java
@@ -26,6 +26,7 @@ public final class RsyncCopierFactory implements Serializable, IPathCopierFactor
{
private static final long serialVersionUID = 1L;
+ @Override
public IPathCopier create(File rsyncExecutable, File sshExecutableOrNull, long timeoutInMillis)
{
return new RsyncCopier(rsyncExecutable, sshExecutableOrNull, false, false);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/SshCommandExecutorFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/SshCommandExecutorFactory.java
index 166253b1b6e..96c13ecbb76 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/SshCommandExecutorFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/SshCommandExecutorFactory.java
@@ -27,6 +27,7 @@ public final class SshCommandExecutorFactory implements Serializable,
{
private static final long serialVersionUID = 1L;
+ @Override
public ISshCommandExecutor create(File sshExecutableOrNull, String host)
{
return new SshCommandExecutor(sshExecutableOrNull, host);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPlugin.java
index 77b61079315..e554a015ae7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/TSVViewReportingPlugin.java
@@ -48,6 +48,7 @@ public class TSVViewReportingPlugin extends AbstractFileTableReportingPlugin
this.transpose = PropertyUtils.getBoolean(properties, TRANSPOSE_KEY, false);
}
+ @Override
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
assureOnlyOneDataSetSelected(datasets);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
index 0d80c7d6a62..cbda8fb6b51 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
@@ -39,6 +39,7 @@ public class PluginTaskProvider<P>
new TableMap<String, AbstractPluginTaskFactory<P>>(Arrays.asList(factories),
new IKeyExtractor<String, AbstractPluginTaskFactory<P>>()
{
+ @Override
public String getKey(AbstractPluginTaskFactory<P> factory)
{
return factory.getPluginDescription().getKey();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractShareFinder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractShareFinder.java
index d3aa2f187b0..f266a1ccbca 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractShareFinder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractShareFinder.java
@@ -32,6 +32,7 @@ public abstract class AbstractShareFinder implements IShareFinder
/**
* Tries to find a share fulfilling speed hint contract.
*/
+ @Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
SpeedChecker[] values = SpeedChecker.values();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ArchiverTaskContext.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ArchiverTaskContext.java
index af8fd6904cc..f8022b16f7d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ArchiverTaskContext.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ArchiverTaskContext.java
@@ -29,6 +29,7 @@ public class ArchiverTaskContext
private final IDataSetDirectoryProvider directoryProvider;
private IUnarchivingPreparation unarchivingPreparation = new IUnarchivingPreparation()
{
+ @Override
public void prepareForUnarchiving(DatasetDescription dataSet)
{
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetDirectoryProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetDirectoryProvider.java
index 0b178d670fb..be63d174451 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetDirectoryProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSetDirectoryProvider.java
@@ -38,11 +38,13 @@ public class DataSetDirectoryProvider implements IDataSetDirectoryProvider
}
+ @Override
public File getStoreRoot()
{
return storeRoot;
}
+ @Override
public File getDataSetDirectory(IDatasetLocation dataSet)
{
String shareId = shareIdManager.getShareId(dataSet.getDataSetCode());
@@ -50,6 +52,7 @@ public class DataSetDirectoryProvider implements IDataSetDirectoryProvider
return getDataSetDirectory(shareId, location);
}
+ @Override
public File getDataSetDirectory(String shareId, String location)
{
String loc = location.replace("\\", File.separator);
@@ -57,6 +60,7 @@ public class DataSetDirectoryProvider implements IDataSetDirectoryProvider
return new File(share, loc);
}
+ @Override
public IShareIdManager getShareIdManager()
{
return shareIdManager;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSourceProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSourceProvider.java
index ffad43d6145..286aebf6f63 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSourceProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DataSourceProvider.java
@@ -121,6 +121,7 @@ public class DataSourceProvider implements IDataSourceProvider
* Returns data source configured with given name or throws {@link IllegalArgumentException} if
* not configured.
*/
+ @Override
public DataSource getDataSource(String name) throws IllegalArgumentException
{
DataSource result = dataSources.get(name);
@@ -138,6 +139,7 @@ public class DataSourceProvider implements IDataSourceProvider
* Extracts data source name ({@link #DATA_SOURCE_KEY}) from properties and returns requested
* data source. See also {@link #getDataSource(String)}.
*/
+ @Override
public DataSource getDataSource(Properties properties)
{
return getDataSource(extractDataSourceName(properties));
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DefaultDataSourceFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DefaultDataSourceFactory.java
index 057bb492c5d..5d1cb495046 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DefaultDataSourceFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/DefaultDataSourceFactory.java
@@ -38,6 +38,7 @@ public class DefaultDataSourceFactory implements IDataSourceFactory
public static final String VERSION_HOLDER_CLASS_KEY = "version-holder-class";
+ @Override
public DataSource create(Properties dbProps)
{
DatabaseConfigurationContext context =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
index 21f8bc08cce..e2beda075b0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
@@ -39,6 +39,7 @@ public class ExperimentBasedShareFinder implements IShareFinder
{
}
+ @Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
String experimentIdentifier =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProvider.java
index dda907c836d..ad22e1d4bc1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProvider.java
@@ -74,6 +74,7 @@ public class HierarchicalContentProvider implements IHierarchicalContentProvider
this.hierarchicalContentFactory = hierarchicalContentFactory;
}
+ @Override
public IHierarchicalContent asContent(String dataSetCode)
{
ExternalData externalData = openbisService.tryGetDataSet(dataSetCode);
@@ -86,6 +87,7 @@ public class HierarchicalContentProvider implements IHierarchicalContentProvider
return asContent(externalData);
}
+ @Override
public IHierarchicalContent asContent(ExternalData externalData)
{
if (externalData.isContainer())
@@ -126,6 +128,7 @@ public class HierarchicalContentProvider implements IHierarchicalContentProvider
}
}
+ @Override
public IHierarchicalContent asContent(final IDatasetLocation datasetLocation)
{
// NOTE: remember to call IHierarchicalContent.close() to unlock the data set when finished
@@ -134,6 +137,7 @@ public class HierarchicalContentProvider implements IHierarchicalContentProvider
File dataSetDirectory = directoryProvider.getDataSetDirectory(datasetLocation);
IDelegatedAction onCloseAction = new IDelegatedAction()
{
+ @Override
public void execute()
{
directoryProvider.getShareIdManager().releaseLock(
@@ -143,6 +147,7 @@ public class HierarchicalContentProvider implements IHierarchicalContentProvider
return asContent(dataSetDirectory, onCloseAction);
}
+ @Override
public IHierarchicalContent asContent(File dataSetDirectory)
{
return getHierarchicalContentFactory().asHierarchicalContent(dataSetDirectory,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/PathInfoDatabaseVersionHolder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/PathInfoDatabaseVersionHolder.java
index 6d9d5215d65..4011ddbe706 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/PathInfoDatabaseVersionHolder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/PathInfoDatabaseVersionHolder.java
@@ -23,6 +23,7 @@ package ch.systemsx.cisd.openbis.dss.generic.shared;
*/
public class PathInfoDatabaseVersionHolder implements IDatabaseVersionHolder
{
+ @Override
public String getDatabaseVersion()
{
return "005"; // S131
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/QueueingDataSetStatusUpdaterService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/QueueingDataSetStatusUpdaterService.java
index 0e066b69c7e..7de162e80e5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/QueueingDataSetStatusUpdaterService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/QueueingDataSetStatusUpdaterService.java
@@ -93,6 +93,7 @@ public class QueueingDataSetStatusUpdaterService
updater = createDataSetStatusUpdater();
thread = new Thread(new Runnable()
{
+ @Override
public void run()
{
try
@@ -155,6 +156,7 @@ public class QueueingDataSetStatusUpdaterService
{
return new IDataSetStatusUpdater()
{
+ @Override
public void updateDataSetStatuses(List<String> dataSetCodes,
DataSetArchivingStatus newStatus, boolean presentInArchive)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleDataSourceFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleDataSourceFactory.java
index bf3dd1d4684..dce0fa8d6af 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleDataSourceFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleDataSourceFactory.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.dbmigration.SimpleDatabaseConfigurationContext;
public class SimpleDataSourceFactory implements IDataSourceFactory
{
+ @Override
public DataSource create(Properties dbProps)
{
SimpleDatabaseConfigurationContext context =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedChecker.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedChecker.java
index 9f1149ef40a..c9a7efb9f57 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedChecker.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedChecker.java
@@ -29,6 +29,7 @@ public enum SpeedChecker implements ISpeedChecker
{
MATCHING_CHECKER()
{
+ @Override
public boolean check(SimpleDataSetInformationDTO dataSet, Share share)
{
return Math.abs(dataSet.getSpeedHint()) == share.getSpeed();
@@ -37,6 +38,7 @@ public enum SpeedChecker implements ISpeedChecker
RESPECTING_SPEED_HINT_CHECKER()
{
+ @Override
public boolean check(SimpleDataSetInformationDTO dataSet, Share share)
{
int speedHint = dataSet.getSpeedHint();
@@ -47,6 +49,7 @@ public enum SpeedChecker implements ISpeedChecker
IGNORING_SPEED_HINT_CHECKER()
{
+ @Override
public boolean check(SimpleDataSetInformationDTO dataSet, Share share)
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedOptimizedShareFinder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedOptimizedShareFinder.java
index 3d2efb64387..17a30911ecd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedOptimizedShareFinder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/SpeedOptimizedShareFinder.java
@@ -39,6 +39,7 @@ public class SpeedOptimizedShareFinder implements IShareFinder
simpleFinder = new SimpleShareFinder(properties);
}
+ @Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
Share share = tryToFindExtensionShare(dataSet, shares, SpeedChecker.MATCHING_CHECKER);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/StandardShareFinder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/StandardShareFinder.java
index 18f72b154c7..7f83621e02c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/StandardShareFinder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/StandardShareFinder.java
@@ -68,6 +68,7 @@ public class StandardShareFinder implements IShareFinder
FileUtils.ONE_MB * PropertyUtils.getLong(properties, MINIMUM_FREE_SPACE_KEY, 1024);
}
+ @Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
List<CandidateShare> candidates = new ArrayList<CandidateShare>();
@@ -177,6 +178,7 @@ public class StandardShareFinder implements IShareFinder
}
+ @Override
public int compareTo(CandidateShare otherCandidate)
{
int incomingToExtensionComparison = compareIncomingToExtension(otherCandidate);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/AbstractDataSetAccessPredicate.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/AbstractDataSetAccessPredicate.java
index 400bad2c02b..0e233beecf0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/AbstractDataSetAccessPredicate.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/AbstractDataSetAccessPredicate.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
public abstract class AbstractDataSetAccessPredicate<T, D> implements IAuthorizationGuardPredicate<T, D>
{
+ @Override
public Status evaluate(T receiver, String sessionToken, D argument) throws UserFailureException
{
List<String> dataSetCodes = getDataSetCodes(argument);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetCodeStringPredicate.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetCodeStringPredicate.java
index bf0faebb830..8c881fc83c3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetCodeStringPredicate.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetCodeStringPredicate.java
@@ -28,6 +28,7 @@ import java.util.List;
*/
public class DataSetCodeStringPredicate extends AbstractDataSetAccessPredicate<IDssServiceRpcGenericInternal, String>
{
+ @Override
public List<String> getDataSetCodes(String argument)
{
return Arrays.asList(argument);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetFileDTOPredicate.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetFileDTOPredicate.java
index 1d72ab2001d..e74c0909f49 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetFileDTOPredicate.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DataSetFileDTOPredicate.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric;
public class DataSetFileDTOPredicate extends
AbstractDataSetAccessPredicate<IDssServiceRpcGeneric, DataSetFileDTO>
{
+ @Override
public List<String> getDataSetCodes(DataSetFileDTO argument)
{
return Arrays.asList(argument.getDataSetCode());
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DssSessionAuthorizationHolder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DssSessionAuthorizationHolder.java
index de0a967d1b9..d5c81e08d34 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DssSessionAuthorizationHolder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/DssSessionAuthorizationHolder.java
@@ -33,27 +33,32 @@ public class DssSessionAuthorizationHolder
private static IDssSessionAuthorizer authorizer = new IDssSessionAuthorizer()
{
+ @Override
public Status checkDatasetAccess(String sessionToken,
List<String> datasetCodes)
{
return Status.createError("Data set authorizer not set.");
}
+ @Override
public Status checkDatasetAccess(String sessionToken, String datasetCode)
{
return Status.createError("Data set authorizer not set.");
}
+ @Override
public Status checkSpaceWriteable(String sessionToken, SpaceIdentifier spaceId)
{
return Status.createError("Data set authorizer not set.");
}
+ @Override
public Status checkInstanceAdminAuthorization(String sessionToken)
{
return Status.createError("Data set authorizer not set.");
}
+ @Override
public Status checkSpacePowerUserAuthorization(String sessionToken)
{
return Status.createError("Data set authorizer not set.");
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/NewDataSetPredicate.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/NewDataSetPredicate.java
index 351adbb05b2..5db377bab0c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/NewDataSetPredicate.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/authorization/NewDataSetPredicate.java
@@ -42,11 +42,13 @@ public class NewDataSetPredicate implements
IAuthorizationGuardPredicate<IDssServiceRpcGeneric, NewDataSetDTO>
{
+ @Override
public List<String> getDataSetCodes(NewDataSetDTO argument)
{
return Arrays.asList();
}
+ @Override
public Status evaluate(IDssServiceRpcGeneric receiver, String sessionToken,
NewDataSetDTO newDataSet) throws UserFailureException
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
index 1b8e94e043d..6de430654f3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/content/PathInfoProviderBasedHierarchicalContent.java
@@ -64,6 +64,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
this.root = dataSetDir;
}
+ @Override
public IHierarchicalContentNode getRootNode()
{
if (rootNode == null)
@@ -74,6 +75,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return rootNode;
}
+ @Override
public IHierarchicalContentNode getNode(String relativePath)
{
if (StringUtils.isBlank(relativePath))
@@ -103,6 +105,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
}
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(final String relativePathPattern)
{
List<IHierarchicalContentNode> result = new ArrayList<IHierarchicalContentNode>();
@@ -115,6 +118,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return result;
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(final String startingPath,
final String fileNamePattern)
{
@@ -128,6 +132,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return result;
}
+ @Override
public void close()
{
onCloseAction.execute();
@@ -193,21 +198,25 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
this.pathInfo = pathInfo;
}
+ @Override
public String getName()
{
return pathInfo.getFileName();
}
+ @Override
public boolean exists()
{
return true;
}
+ @Override
public boolean isDirectory()
{
return pathInfo.isDirectory();
}
+ @Override
public long getLastModified()
{
return pathInfo.getLastModified().getTime();
@@ -249,6 +258,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return IOUtilities.getChecksumCRC32(getInputStream());
}
+ @Override
public File getFile() throws UnsupportedOperationException
{
File result = doGetFile();
@@ -261,6 +271,7 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
}
}
+ @Override
public File tryGetFile()
{
File result = doGetFile();
@@ -351,11 +362,13 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return new IFileContentProvider()
{
+ @Override
public IRandomAccessFile getReadOnlyRandomAccessFile()
{
return new RandomAccessFileImpl(existingFile, "r");
}
+ @Override
public InputStream getInputStream()
{
try
@@ -375,11 +388,13 @@ class PathInfoProviderBasedHierarchicalContent implements IHierarchicalContent
return new IFileContentProvider()
{
+ @Override
public IRandomAccessFile getReadOnlyRandomAccessFile()
{
return node.getFileContent();
}
+ @Override
public InputStream getInputStream()
{
return node.getInputStream();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/AbstractDatasetDropboxHandler.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/AbstractDatasetDropboxHandler.java
index d9880f77813..9a25658ed47 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/AbstractDatasetDropboxHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/AbstractDatasetDropboxHandler.java
@@ -126,6 +126,7 @@ abstract public class AbstractDatasetDropboxHandler implements Serializable,
return file;
}
+ @Override
public final Status handle(File originalData, final DataSetInformation dataSetInformation, Map<String, String> parameterBindings)
{
File dropboxDir = tryGetDropboxDir(originalData, dataSetInformation);
@@ -152,6 +153,7 @@ abstract public class AbstractDatasetDropboxHandler implements Serializable,
.executeCallable(new Callable<Object>()
{
// returns null on error, non-null on success
+ @Override
public Object call() throws Exception
{
try
@@ -181,6 +183,7 @@ abstract public class AbstractDatasetDropboxHandler implements Serializable,
.getPath(), newName);
}
+ @Override
public void undoLastOperation()
{
if (recentlyStoredDropboxDataset != null && recentlyStoredDropboxDataset.exists())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CorePluginsInjector.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CorePluginsInjector.java
index 67ed109aa44..95675a3fa97 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CorePluginsInjector.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CorePluginsInjector.java
@@ -238,6 +238,7 @@ public class CorePluginsInjector
{
File[] pluginFolders = file.listFiles(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return name.startsWith(".") == false;
@@ -315,6 +316,7 @@ public class CorePluginsInjector
}
File[] scripts = definingFolder.listFiles(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return name.equals(PLUGIN_PROPERTIES_FILE_NAME) == false;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CsvFileReaderHelper.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CsvFileReaderHelper.java
index 47ed1b0d726..ee44ebe9ef3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CsvFileReaderHelper.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CsvFileReaderHelper.java
@@ -129,21 +129,25 @@ public class CsvFileReaderHelper
public static final ICsvFileReaderConfiguration INSTANCE =
new DefaultCsvFileReaderConfiguration();
+ @Override
public char getColumnDelimiter()
{
return ';';
}
+ @Override
public char getCommentDelimiter()
{
return '#';
}
+ @Override
public boolean isIgnoreComments()
{
return true;
}
+ @Override
public boolean isSkipEmptyRecords()
{
return true;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
index 5f57f581282..2b6f599e09d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
@@ -107,6 +107,7 @@ public class DatasetFileLines implements ITabularData
/**
* Returns the headers as defined in the file.
*/
+ @Override
public String[] getHeaderLabels()
{
return headerTokens;
@@ -116,11 +117,13 @@ public class DatasetFileLines implements ITabularData
* Returns the normalized headers. Normalization is done by
* {@link CodeNormalizer#normalize(String)}.
*/
+ @Override
public String[] getHeaderCodes()
{
return headerCodes;
}
+ @Override
public List<String[]> getDataLines()
{
return dataLines;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
index e19bf663f87..dae33dbcdaf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
@@ -94,6 +94,7 @@ public class ImageUtil
{
private final static int MAX_READ_AHEAD = 30000000;
+ @Override
public BufferedImage load(IRandomAccessFile handle, ImageID imageID)
{
handle.mark(MAX_READ_AHEAD);
@@ -121,6 +122,7 @@ public class ImageUtil
}
}
+ @Override
public Dimension readDimension(IRandomAccessFile handle, ImageID imageID)
{
handle.mark(MAX_READ_AHEAD);
@@ -237,6 +239,7 @@ public class ImageUtil
this.fileType = fileType;
}
+ @Override
public BufferedImage load(IRandomAccessFile handle, ImageID imageID)
{
if (imageID.equals(ImageID.NULL))
@@ -256,6 +259,7 @@ public class ImageUtil
}
}
+ @Override
public Dimension readDimension(IRandomAccessFile handle, ImageID imageID)
{
if (imageID.equals(ImageID.NULL))
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PostgresPlusFileSystemFreeSpaceProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PostgresPlusFileSystemFreeSpaceProvider.java
index f17f8606856..9e33cde6c19 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PostgresPlusFileSystemFreeSpaceProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PostgresPlusFileSystemFreeSpaceProvider.java
@@ -92,6 +92,7 @@ public class PostgresPlusFileSystemFreeSpaceProvider implements IFreeSpaceProvid
this.fileSystemFreeSpaceProvider = fileSystemFreeSpaceProvider;
}
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
long dataSourceFreeSpace = calculateDataSourceFreeSpace() / 1024L;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
index bc2a7e3b1d7..e040a2c66ae 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtils.java
@@ -60,6 +60,7 @@ public class SegmentedStoreUtils
{
private static final IFreeSpaceProvider DUMMY_FREE_SPACE_PROVIDER = new IFreeSpaceProvider()
{
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
return Long.MAX_VALUE;
@@ -72,6 +73,7 @@ public class SegmentedStoreUtils
private static final Comparator<Share> SHARE_COMPARATOR = new Comparator<Share>()
{
+ @Override
public int compare(Share o1, Share o2)
{
return o1.getShareId().compareTo(o2.getShareId());
@@ -80,6 +82,7 @@ public class SegmentedStoreUtils
private static final FileFilter FILTER_ON_SHARES = new FileFilter()
{
+ @Override
public boolean accept(File pathname)
{
if (pathname.isDirectory() == false)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/Share.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/Share.java
index 096206c676a..8385076d7cf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/Share.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/Share.java
@@ -40,6 +40,7 @@ public final class Share
public static final Comparator<SimpleDataSetInformationDTO> DATA_SET_SIZE_COMPARATOR =
new Comparator<SimpleDataSetInformationDTO>()
{
+ @Override
public int compare(SimpleDataSetInformationDTO o1,
SimpleDataSetInformationDTO o2)
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
index 0b54fb29761..4037b0ef9ec 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
@@ -172,7 +172,7 @@ public class AbstractStorageProcessorWithDropboxTest extends AbstractFileSystemT
String expectedErrorMsg = "Given key 'processor' not found in properties '[]'";
try
{
- DelegatingStorageProcessorWithDropbox.createDelegateStorageProcessor(new Properties());
+ AbstractDelegatingStorageProcessor.createDelegateStorageProcessor(new Properties());
} catch (ConfigurationFailureException e)
{
assertEquals(expectedErrorMsg, e.getMessage());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
index c6feed46e0b..007b13c266a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
@@ -331,6 +331,7 @@ public class DataSetRegistrationAlgorithmTest extends AbstractFileSystemTestCase
final Action storeDataAction = new CustomAction("StoreData")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
fileOperations.move(incomingDataSetFile, storedDataSetFile);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
index 976bb9b4770..59e4317c8d8 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
@@ -168,7 +168,7 @@ public final class DefaultDataSetInfoExtractorTest extends CodeExtractortTestCas
String localGroupCode = "localGroup";
String fileName =
- localGroupCode + DefaultDataSetInfoExtractor.DEFAULT_ENTITY_SEPARATOR
+ localGroupCode + AbstractDataSetInfoExtractor.DEFAULT_ENTITY_SEPARATOR
+ "sampleCode";
final DataSetInformation dsInfo = extractDatasetInfo(properties, fileName);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
index 0967090d7a2..0f42ec1515f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
@@ -154,26 +154,31 @@ public final class DefaultStorageProcessorTest extends AbstractFileSystemTestCas
// IProcedureAndDataTypeExtractor
//
+ @Override
public final FileFormatType getFileFormatType(final File incomingDataSetPath)
{
return new FileFormatType(FILE_FORMAT_TYPE);
}
+ @Override
public final LocatorType getLocatorType(final File incomingDataSetPath)
{
return new LocatorType(LOCATOR_TYPE);
}
+ @Override
public final DataSetType getDataSetType(final File incomingDataSetPath)
{
return new DataSetType(DATA_SET_TYPE);
}
+ @Override
public String getProcessorType(File incomingDataSetPath)
{
return "da";
}
+ @Override
public boolean isMeasuredData(File incomingDataSetPath)
{
return true;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
index b90f31b32ed..4727cf8e76f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -62,7 +62,6 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
-import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -128,11 +127,13 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
this.expectedData = externalData;
}
+ @Override
public void describeTo(final Description description)
{
description.appendValue(expectedData);
}
+ @Override
public boolean matches(final Object item)
{
if (item instanceof NewExternalData == false)
@@ -177,6 +178,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
this.codeExtractor = codeExtractor;
}
+ @Override
public DataSetInformation getDataSetInformation(final File incomingDataSetPath,
IEncapsulatedOpenBISService openbisService) throws UserFailureException,
EnvironmentFailureException
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandlerTest.java
index 68860042c05..e4cfb935f64 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandlerTest.java
@@ -259,6 +259,7 @@ public class PutDataSetTopLevelDataSetHandlerTest extends AbstractFileSystemTest
one(registrator).handle(with(dataSet), with(dataSetInfoMatcher),
with(new BaseMatcher<ITopLevelDataSetRegistratorDelegate>()
{
+ @Override
public boolean matches(Object item)
{
// We can check file content only here because after
@@ -272,6 +273,7 @@ public class PutDataSetTopLevelDataSetHandlerTest extends AbstractFileSystemTest
return true;
}
+ @Override
public void describeTo(Description description)
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index 7a6ba51f9de..a1a84b781b4 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -598,6 +598,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
with(dataSetInfoMatcher), with(registratorMatcher));
will(new CustomAction("Call registrator")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
List<DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator> recordedObjects =
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHDF5StorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHDF5StorageProcessorTest.java
index 1f26f54db21..6c6be735e45 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHDF5StorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/hdf5/AbstractHDF5StorageProcessorTest.java
@@ -72,6 +72,7 @@ abstract class AbstractHDF5StorageProcessorTest extends AbstractFileSystemTestCa
container.runReaderClient(new IHDF5ReaderClient()
{
+ @Override
public void runWithSimpleReader(IHDF5ContainerReader reader)
{
FileToHDF5DuplicationVerifier verifier =
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/IPathsInfoDAOTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/IPathsInfoDAOTest.java
index 7a0bf069b97..fcea6f6d9fd 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/IPathsInfoDAOTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/IPathsInfoDAOTest.java
@@ -37,39 +37,47 @@ public class IPathsInfoDAOTest
private final DataSource DUMMY_DATA_SOURCE = new DataSource()
{
+ @Override
public Connection getConnection() throws SQLException
{
return null;
}
+ @Override
public Connection getConnection(String username, String password) throws SQLException
{
return null;
}
+ @Override
public PrintWriter getLogWriter() throws SQLException
{
return null;
}
+ @Override
public void setLogWriter(PrintWriter out) throws SQLException
{
}
+ @Override
public void setLoginTimeout(int seconds) throws SQLException
{
}
+ @Override
public int getLoginTimeout() throws SQLException
{
return 0;
}
+ @Override
public <T> T unwrap(java.lang.Class<T> iface) throws java.sql.SQLException
{
return null;
}
+ @Override
public boolean isWrapperFor(java.lang.Class<?> iface) throws java.sql.SQLException
{
return false;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTaskTest.java
index 21c1c945137..db3fd557e88 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseChecksumCalculationTaskTest.java
@@ -58,6 +58,7 @@ public class PathInfoDatabaseChecksumCalculationTaskTest extends AbstractFileSys
private long previousTime;
private long currentTime = 1000;
+ @Override
public long getTimeInMilliseconds()
{
long nextTime = previousTime + currentTime;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTaskTest.java
index 96fd3c362e3..102726a8156 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/ExperimentBasedArchivingTaskTest.java
@@ -58,6 +58,7 @@ public class ExperimentBasedArchivingTaskTest extends AbstractFileSystemTestCase
static IFreeSpaceProvider mock;
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
return mock.freeSpaceKb(path);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdaterTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdaterTest.java
index c5977ebb571..dac65fc982a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdaterTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdaterTest.java
@@ -53,6 +53,7 @@ public class HierarchicalStorageUpdaterTest extends AbstractFileSystemTestCase
private final static FileFilter ignoreSVNFiles = new FileFilter()
{
+ @Override
public boolean accept(File pathname)
{
return pathname.getName().equals(".svn") == false;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTaskTest.java
index 7eb335f827b..86f938cabf1 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SegmentedStoreShufflingTaskTest.java
@@ -86,11 +86,13 @@ public class SegmentedStoreShufflingTaskTest extends AbstractFileSystemTestCase
this.properties = properties;
}
+ @Override
public void init(ISimpleLogger l)
{
initialized = true;
}
+ @Override
public void shuffleDataSets(List<Share> sources, List<Share> targets,
IEncapsulatedOpenBISService openBisService, IDataSetMover mover,
ISimpleLogger simpleLogger)
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingShareFinderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingShareFinderTest.java
index ebc73e2ba77..898c745c27a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingShareFinderTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingShareFinderTest.java
@@ -63,6 +63,7 @@ public class SimpleShufflingShareFinderTest extends AssertJUnit
this.checkingResults = checkingResults;
}
+ @Override
public boolean check(SimpleDataSetInformationDTO dataSet, Share share)
{
recordedDataSet = dataSet;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingTest.java
index 688a0a43130..55ef886ac3e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/SimpleShufflingTest.java
@@ -78,6 +78,7 @@ public class SimpleShufflingTest extends AbstractFileSystemTestCase
list.add(valueInKb);
}
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
File file = path.getFile();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTaskTest.java
index e16bc37be39..bfca0ac9e37 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/EagerShufflingTaskTest.java
@@ -69,6 +69,7 @@ public class EagerShufflingTaskTest extends AbstractFileSystemTestCase
this.freeSpaceValues = freeSpaceValues;
}
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
shares.add(path.getFile().getName());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTaskTest.java
index d90bc1f9046..69992696fe2 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/postregistration/PostRegistrationMaintenanceTaskTest.java
@@ -78,6 +78,7 @@ public class PostRegistrationMaintenanceTaskTest extends AbstractFileSystemTestC
this.name = name;
}
+ @Override
public void cleanup(ISimpleLogger logger)
{
cleanupInvocations.add(name);
@@ -97,11 +98,13 @@ public class PostRegistrationMaintenanceTaskTest extends AbstractFileSystemTestC
assertNotNull("No task found for '" + taskName + "'.", task);
}
+ @Override
public boolean requiresDataStoreLock()
{
return task.requiresDataStoreLock();
}
+ @Override
public IPostRegistrationTaskExecutor createExecutor(String dataSetCode, boolean container)
{
return task.createExecutor(dataSetCode, container);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
index ef6dc9258f2..9bda0f3ab35 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
@@ -328,27 +328,32 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
instance = this;
}
+ @Override
public File getStoreRootDirectory()
{
calledGetStoreRootDirectoryCount++;
return storeRootDirectory;
}
+ @Override
public void setStoreRootDirectory(File storeRootDirectory)
{
this.storeRootDirectory = storeRootDirectory;
}
+ @Override
public StorageFormat getStorageFormat()
{
return StorageFormat.PROPRIETARY;
}
+ @Override
public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
{
return UnstoreDataAction.LEAVE_UNTOUCHED;
}
+ @Override
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
@@ -361,6 +366,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
private File storedFolder = rootDir;
+ @Override
public void storeData(ITypeExtractor typeExtractor, IMailClient mailClient,
File incomingDataSetFile)
{
@@ -383,27 +389,32 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
storedFolder = rootDir;
}
+ @Override
public UnstoreDataAction rollback(Throwable exception)
{
FileOperations.getInstance().deleteRecursively(storedFolder);
return null;
}
+ @Override
public File getStoredDataDirectory()
{
return storedFolder;
}
+ @Override
public void setStoredDataDirectory(File folder)
{
storedFolder = folder;
}
+ @Override
public void commit()
{
calledCommitCount++;
}
+ @Override
public File tryGetProprietaryData()
{
return null;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
index dd5b8019fcb..2741f2d4c3f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
@@ -155,6 +155,7 @@ public class DataSetStorageRollbackerTest extends AbstractFileSystemTestCase
/**
* V1 Rollbacker test -- any file can go into faulty paths.
*/
+ @Override
public boolean shouldNotAddToFaultyPathsOrNull(File storeItem)
{
return false;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonDropboxRecoveryTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonDropboxRecoveryTest.java
index b9f37da6f34..05c7a1bb5f6 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonDropboxRecoveryTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonDropboxRecoveryTest.java
@@ -852,6 +852,7 @@ public class JythonDropboxRecoveryTest extends AbstractJythonDataSetHandlerTest
{
return new CustomAction("makeSystemUnavailable")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
makeFileSystemUnavailable(workingDirectory);
@@ -864,6 +865,7 @@ public class JythonDropboxRecoveryTest extends AbstractJythonDataSetHandlerTest
{
return new CustomAction("makeSystemAvailable")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
makeFileSystemAvailable(workingDirectory);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java
index f17affd6d48..6415abf03ae 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorRollbackTest.java
@@ -89,6 +89,7 @@ public class JythonTopLevelDataSetRegistratorRollbackTest extends AbstractJython
CustomAction makeFileSystemUnavailable = new CustomAction("foo")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
makeFileSystemUnavailable(workingDirectory);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index ce4555d404d..658c1e6b4d7 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -121,6 +121,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
// creates data with more than only one dataset
IDelegatedAction createTwoDataSetsDelegate = new IDelegatedAction()
{
+ @Override
public void execute()
{
createData();
@@ -224,6 +225,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
testCase.failurePoint = TestCaseParameters.FailurePoint.AFTER_CREATE_DATA_SET_CODE;
testCase.exceptionAcceptor = new IPredicate<Exception>()
{
+ @Override
public boolean execute(Exception arg)
{
PyException pyException = (PyException) arg;
@@ -257,6 +259,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
testCase.shouldThrowExceptionDuringRegistration = true;
testCase.exceptionAcceptor = new IPredicate<Exception>()
{
+ @Override
public boolean execute(Exception arg)
{
System.out.println(arg);
@@ -1583,6 +1586,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
{
return new CustomAction("foo")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
assertEquals("[]",
@@ -1597,6 +1601,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
{
return new CustomAction("foo")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
assertNotSame(0, handler.getGlobalState().getPreCommitDir().list().length);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandler.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandler.java
index 267e062c5e1..2fad00a1b3a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandler.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandler.java
@@ -54,6 +54,7 @@ public class TestingDataSetHandler extends JythonTopLevelDataSetHandler<DataSetI
expectations.handleRollbackException(throwable);
}
+ @Override
public TestingDataSetHandlerExpectations getExpectations()
{
return expectations;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandlerV2.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandlerV2.java
index caa9e1a5e71..3499ef2ace8 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandlerV2.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/TestingDataSetHandlerV2.java
@@ -54,6 +54,7 @@ public class TestingDataSetHandlerV2 extends JythonTopLevelDataSetHandlerV2<Data
expectations.handleRollbackException(throwable);
}
+ @Override
public TestingDataSetHandlerExpectations getExpectations()
{
return expectations;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
index fe9a3a76d87..2bcaa84f74d 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
@@ -399,6 +399,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
{
File[] rollbackQueueFiles = workingDirectory.listFiles(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
final String ROLLBACK_QUEUE1_FILE_NAME_SUFFIX = "rollBackQueue1";
@@ -576,27 +577,32 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
instance = this;
}
+ @Override
public File getStoreRootDirectory()
{
calledGetStoreRootDirectoryCount++;
return storeRootDirectory;
}
+ @Override
public void setStoreRootDirectory(File storeRootDirectory)
{
this.storeRootDirectory = storeRootDirectory;
}
+ @Override
public StorageFormat getStorageFormat()
{
return StorageFormat.PROPRIETARY;
}
+ @Override
public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
{
return UnstoreDataAction.LEAVE_UNTOUCHED;
}
+ @Override
public IStorageProcessorTransaction createTransaction(
StorageProcessorTransactionParameters parameters)
{
@@ -609,6 +615,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
private File storedFolder;
+ @Override
public void storeData(ITypeExtractor typeExtractor, IMailClient mailClient,
File incomingDataSetDirectory)
{
@@ -630,26 +637,31 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
storedFolder = rootDir;
}
+ @Override
public UnstoreDataAction rollback(Throwable exception)
{
return null;
}
+ @Override
public File getStoredDataDirectory()
{
return storedFolder;
}
+ @Override
public void setStoredDataDirectory(File folder)
{
storedFolder = folder;
}
+ @Override
public void commit()
{
calledCommitCount++;
}
+ @Override
public File tryGetProprietaryData()
{
return null;
@@ -688,6 +700,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
/**
* Factory method that creates a new registration details object.
*/
+ @Override
public DataSetRegistrationDetails<DataSetInformation> createDataSetRegistrationDetails()
{
DataSetRegistrationDetails<DataSetInformation> registrationDetails =
@@ -708,6 +721,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
return dataSetInfo;
}
+ @Override
public DataSet<DataSetInformation> createDataSet(
DataSetRegistrationDetails<DataSetInformation> registrationDetails, File stagingFile)
{
@@ -717,6 +731,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
/**
* V1 test -- any file can go into faulty paths.
*/
+ @Override
public boolean shouldNotAddToFaultyPathsOrNull(File storeItem)
{
return false;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStackTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStackTest.java
index cb5692c0a9f..ae8db13f4c7 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStackTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/RollbackStackTest.java
@@ -293,11 +293,13 @@ public class RollbackStackTest extends AbstractTestWithRollbackStack
this.predecessor = predecessor;
}
+ @Override
public void execute()
{
status = TrackingCommandStatus.EXECUTED;
}
+ @Override
public void rollback()
{
status = TrackingCommandStatus.ROLLEDBACK;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutorTest.java
index d964937ef29..573480d6fe6 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/utils/PreRegistrationExecutorTest.java
@@ -54,6 +54,7 @@ public class PreRegistrationExecutorTest extends AbstractFileSystemTestCase
String[] contents = workingDirectory.list(new FilenameFilter()
{
+ @Override
public boolean accept(File dir, String name)
{
return "data-set-code".equals(name);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
index 852561f5acc..d6efb51c195 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorForTSVTest.java
@@ -72,6 +72,7 @@ public class DataSetValidatorForTSVTest extends AbstractFileSystemTestCase
validators.add(this);
}
+ @Override
public void assertValid(String value)
{
assertTrue((index + 1) + ". value for validator '" + name + "' unexpected: "
@@ -93,6 +94,7 @@ public class DataSetValidatorForTSVTest extends AbstractFileSystemTestCase
validator = new MockValidator(properties);
}
+ @Override
public IValidator createValidator(String header)
{
return validator;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorTest.java
index 5b27b3270da..82c254732f6 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/DataSetValidatorTest.java
@@ -50,12 +50,14 @@ public class DataSetValidatorTest extends AbstractFileSystemTestCase
expectedFile = properties.getProperty(EXPECTED_FILE_KEY);
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, File incomingDataSetFileOrFolder)
{
assertEquals(expectedDataSetType, dataSetType.getCode());
assertEquals(expectedFile, incomingDataSetFileOrFolder.toString());
}
+ @Override
public void assertValidDataSet(DataSetType dataSetType, Reader reader, String dataSourceName)
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactoryTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactoryTest.java
index 5898fb3c593..8a7d7a88b4e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactoryTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/NumericValidatorFactoryTest.java
@@ -148,7 +148,7 @@ public class NumericValidatorFactoryTest extends AssertJUnit
public void testAllowEmptyValues()
{
Properties properties = new Properties();
- properties.setProperty(NumericValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "true");
+ properties.setProperty(AbstractValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "true");
properties.setProperty(NumericValidatorFactory.VALUE_RANGE_KEY, "(0,1]");
NumericValidatorFactory validatorFactory = new NumericValidatorFactory(properties);
IValidator validator = validatorFactory.createValidator("blabla");
@@ -165,8 +165,8 @@ public class NumericValidatorFactoryTest extends AssertJUnit
public void testAllowEmptyValueSynonyms()
{
Properties properties = new Properties();
- properties.setProperty(NumericValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "true");
- properties.setProperty(NumericValidatorFactory.EMPTY_VALUE_SYNONYMS_KEY, "-, N/A");
+ properties.setProperty(AbstractValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "true");
+ properties.setProperty(AbstractValidatorFactory.EMPTY_VALUE_SYNONYMS_KEY, "-, N/A");
properties.setProperty(NumericValidatorFactory.VALUE_RANGE_KEY, "(0,1]");
NumericValidatorFactory validatorFactory = new NumericValidatorFactory(properties);
IValidator validator = validatorFactory.createValidator("blabla");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactoryTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactoryTest.java
index deef95c8184..4886fd4ebff 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactoryTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/validation/StringValidatorFactoryTest.java
@@ -80,7 +80,7 @@ public class StringValidatorFactoryTest extends AssertJUnit
{
Properties properties = new Properties();
properties.setProperty(StringValidatorFactory.VALUE_PATTERN_KEY, "a.*");
- properties.setProperty(StringValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "yes");
+ properties.setProperty(AbstractValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "yes");
StringValidatorFactory factory = new StringValidatorFactory(properties);
IValidator validator = factory.createValidator("blabla");
@@ -106,8 +106,8 @@ public class StringValidatorFactoryTest extends AssertJUnit
{
Properties properties = new Properties();
properties.setProperty(StringValidatorFactory.VALUE_PATTERN_KEY, "a.*");
- properties.setProperty(StringValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "yes");
- properties.setProperty(StringValidatorFactory.EMPTY_VALUE_SYNONYMS_KEY, "-");
+ properties.setProperty(AbstractValidatorFactory.ALLOW_EMPTY_VALUES_KEY, "yes");
+ properties.setProperty(AbstractValidatorFactory.EMPTY_VALUE_SYNONYMS_KEY, "-");
StringValidatorFactory factory = new StringValidatorFactory(properties);
IValidator validator = factory.createValidator("blabla");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
index e3f41709a02..ce8bfa65d9c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
@@ -57,6 +57,7 @@ public class DssComponentTest extends SystemTestCase
private static final Comparator<FileInfoDssDTO> FILE_INFO_COMPARATOR =
new Comparator<FileInfoDssDTO>()
{
+ @Override
public int compare(FileInfoDssDTO f1, FileInfoDssDTO f2)
{
return f1.getPathInDataSet().compareTo(f2.getPathInDataSet());
@@ -335,6 +336,7 @@ public class DssComponentTest extends SystemTestCase
List<SimpleDataSetInformationDTO> dataSets = openBISService.listDataSets();
Collections.sort(dataSets, new Comparator<SimpleDataSetInformationDTO>()
{
+ @Override
public int compare(SimpleDataSetInformationDTO d1, SimpleDataSetInformationDTO d2)
{
return d2.getDataSetCode().compareTo(d1.getDataSetCode());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/OpenbisServiceFacadeTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/OpenbisServiceFacadeTest.java
index 152ad7c7335..17a03674cae 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/OpenbisServiceFacadeTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/OpenbisServiceFacadeTest.java
@@ -58,6 +58,7 @@ public class OpenbisServiceFacadeTest extends SystemTestCase
private static final Comparator<FileInfoDssDTO> FILE_INFO_COMPARATOR =
new Comparator<FileInfoDssDTO>()
{
+ @Override
public int compare(FileInfoDssDTO f1, FileInfoDssDTO f2)
{
return f1.getPathInDataSet().compareTo(f2.getPathInDataSet());
@@ -253,6 +254,7 @@ public class OpenbisServiceFacadeTest extends SystemTestCase
List<SimpleDataSetInformationDTO> dataSets = openBISService.listDataSets();
Collections.sort(dataSets, new Comparator<SimpleDataSetInformationDTO>()
{
+ @Override
public int compare(SimpleDataSetInformationDTO d1, SimpleDataSetInformationDTO d2)
{
return d2.getDataSetCode().compareTo(d1.getDataSetCode());
@@ -267,6 +269,7 @@ public class OpenbisServiceFacadeTest extends SystemTestCase
List<DataSet> dataSets = serviceFacade.searchForDataSets(sc);
Collections.sort(dataSets, new Comparator<DataSet>()
{
+ @Override
public int compare(DataSet o1, DataSet o2)
{
// sort decreasing
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/RmiConversationTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/RmiConversationTest.java
index ff8210bef15..52543d5714e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/RmiConversationTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/RmiConversationTest.java
@@ -165,6 +165,7 @@ public class RmiConversationTest extends SystemTestCase
this.server = new ServiceConversationServer();
}
+ @Override
public ServiceConversationDTO startConversation(String sessionToken, String clientUrl,
String typeId)
{
@@ -173,11 +174,13 @@ public class RmiConversationTest extends SystemTestCase
return this.server.startConversation(typeId, "test-client-id");
}
+ @Override
public void send(ServiceMessage message)
{
server.getIncomingMessageTransport().send(message);
}
+ @Override
public String echo(String input, Integer delayInMillis)
{
return echo(input, delayInMillis);
@@ -201,6 +204,7 @@ public class RmiConversationTest extends SystemTestCase
return input;
}
+ @Override
public String echoWithoutProgress(String input, Integer delayInMillis)
{
return echoWithoutProgress(input, delayInMillis, null);
@@ -217,6 +221,7 @@ public class RmiConversationTest extends SystemTestCase
return input;
}
+ @Override
public String echoWithStore(String input)
{
return echoWithStore(input, null);
@@ -233,6 +238,7 @@ public class RmiConversationTest extends SystemTestCase
return input;
}
+ @Override
public String echoWithStoreAndProcessingException(String input)
{
return echoWithStoreAndProcessingException(input, null);
@@ -250,6 +256,7 @@ public class RmiConversationTest extends SystemTestCase
throw new NullPointerException("Exception");
}
+ @Override
public boolean exists(String code) {
return exists(code, null);
}
@@ -277,6 +284,7 @@ public class RmiConversationTest extends SystemTestCase
public static class ClientBean implements ConversationalRmiClient {
+ @Override
public void send(ServiceMessage message)
{
cont.process(message);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPutTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPutTest.java
index f23160467b3..72e63a0e93a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPutTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/cli/CommandPutTest.java
@@ -94,12 +94,14 @@ public class CommandPutTest extends AbstractFileSystemTestCase
new BaseMatcher<NewDataSetDTO>()
{
+ @Override
public boolean matches(Object item)
{
assertEquals(newDataSetDTO.toString(), item.toString());
return true;
}
+ @Override
public void describeTo(Description description)
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
index ddc6052ed99..e20e6592234 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/client/api/v1/impl/DssComponentTest.java
@@ -576,36 +576,42 @@ public class DssComponentTest extends AbstractFileSystemTestCase
}
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
return fileInputStream;
}
+ @Override
public String getDownloadUrlForFileForDataSet(String sessionToken,
DataSetFileDTO fileOrFolder) throws IOExceptionUnchecked, IllegalArgumentException
{
return url.toString();
}
+ @Override
public InputStream getFileForDataSet(String sessionToken, String dataSetCode, String path)
throws IOExceptionUnchecked, IllegalArgumentException
{
return fileInputStream;
}
+ @Override
public String getDownloadUrlForFileForDataSet(String sessionToken, String dataSetCode,
String path) throws IOExceptionUnchecked, IllegalArgumentException
{
return url.toString();
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, DataSetFileDTO fileOrFolder)
throws IOExceptionUnchecked, IllegalArgumentException
{
return fileInfos;
}
+ @Override
public FileInfoDssDTO[] listFilesForDataSet(String sessionToken, String dataSetCode,
String path, boolean isRecursive) throws IOExceptionUnchecked,
IllegalArgumentException
@@ -613,22 +619,26 @@ public class DssComponentTest extends AbstractFileSystemTestCase
return fileInfos;
}
+ @Override
public String putDataSet(String sessionToken, NewDataSetDTO newDataset,
InputStream inputStream) throws IOExceptionUnchecked, IllegalArgumentException
{
return null;
}
+ @Override
public int getMajorVersion()
{
return 1;
}
+ @Override
public int getMinorVersion()
{
return 0;
}
+ @Override
public String getPathToDataSet(String sessionToken, String dataSetCode,
String overrideStoreRootPathOrNull) throws IOExceptionUnchecked,
IllegalArgumentException
@@ -636,11 +646,13 @@ public class DssComponentTest extends AbstractFileSystemTestCase
throw new IllegalArgumentException("Unimplemented in v1.0");
}
+ @Override
public IDssServiceRpcGeneric createLogger(IInvocationLoggerContext context)
{
return null;
}
+ @Override
public String getValidationScript(String sessionToken, String dataSetTypeOrNull)
throws IOExceptionUnchecked, IllegalArgumentException
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
index 4cb55dc5d78..c30424707a8 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatabaseBasedDataSetPathInfoProviderTest.java
@@ -436,6 +436,7 @@ public class DatabaseBasedDataSetPathInfoProviderTest extends AssertJUnit
{
Collections.sort(list, new Comparator<DataSetPathInfo>()
{
+ @Override
public int compare(DataSetPathInfo i1, DataSetPathInfo i2)
{
return i1.getRelativePath().compareTo(i2.getRelativePath());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
index 11149e67ec8..c9aabbc31c1 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
@@ -255,7 +255,7 @@ public class DatasetDownloadServletTest
one(request).getParameter(Utils.SESSION_ID_PARAM);
will(returnValue(EXAMPLE_SESSION_ID));
- one(request).getParameter(DatasetDownloadServlet.DISPLAY_MODE_PARAM);
+ one(request).getParameter(AbstractDatasetDownloadServlet.DISPLAY_MODE_PARAM);
will(returnValue(null));
one(request).getParameter(DatasetDownloadServlet.AUTO_RESOLVE_KEY);
@@ -595,10 +595,10 @@ public class DatasetDownloadServletTest
{
{
Map<String, Boolean> accessMap = new HashMap<String, Boolean>();
- checkAndSetAttribute(this, DatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
+ checkAndSetAttribute(this, AbstractDatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
accessMap);
- one(httpSession).getAttribute(DatasetDownloadServlet.DATA_SET_SESSION_KEY);
+ one(httpSession).getAttribute(AbstractDatasetDownloadServlet.DATA_SET_SESSION_KEY);
Map<String, ExternalData> map = new HashMap<String, ExternalData>();
map.put(externalData.getCode(), externalData);
will(Expectations.returnValue(map));
@@ -631,7 +631,7 @@ public class DatasetDownloadServletTest
exp.one(request).getParameter(Utils.SESSION_ID_PARAM);
exp.will(Expectations.returnValue(null));
- exp.allowing(request).getParameter(DatasetDownloadServlet.DISPLAY_MODE_PARAM);
+ exp.allowing(request).getParameter(AbstractDatasetDownloadServlet.DISPLAY_MODE_PARAM);
exp.will(Expectations.returnValue("html"));
exp.one(request).getParameter(DatasetDownloadServlet.AUTO_RESOLVE_KEY);
@@ -645,7 +645,7 @@ public class DatasetDownloadServletTest
// For the logging of problem requests
Vector<String> parameterNames = new Vector<String>();
- parameterNames.add(DatasetDownloadServlet.DISPLAY_MODE_PARAM);
+ parameterNames.add(AbstractDatasetDownloadServlet.DISPLAY_MODE_PARAM);
exp.allowing(request).getParameterNames();
exp.will(Expectations.returnValue(parameterNames.elements()));
}
@@ -658,7 +658,7 @@ public class DatasetDownloadServletTest
one(request).getParameter(Utils.SESSION_ID_PARAM);
will(returnValue(EXAMPLE_SESSION_ID));
- one(request).getParameter(DatasetDownloadServlet.DISPLAY_MODE_PARAM);
+ one(request).getParameter(AbstractDatasetDownloadServlet.DISPLAY_MODE_PARAM);
will(returnValue("thumbnail" + width + "x" + height));
one(request).getParameter(DatasetDownloadServlet.AUTO_RESOLVE_KEY);
@@ -733,17 +733,17 @@ public class DatasetDownloadServletTest
context.checking(new Expectations()
{
{
- getSessionAttribute(this, DatasetDownloadServlet.DATA_SET_SESSION_KEY,
+ getSessionAttribute(this, AbstractDatasetDownloadServlet.DATA_SET_SESSION_KEY,
new HashMap<String, ExternalDataPE>());
Map<String, Boolean> map = new HashMap<String, Boolean>();
- checkAndSetAttribute(this, DatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
+ checkAndSetAttribute(this, AbstractDatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
map);
one(openbisService).checkDataSetAccess(EXAMPLE_SESSION_ID,
EXAMPLE_DATA_SET_CODE);
- getSessionAttribute(this, DatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
+ getSessionAttribute(this, AbstractDatasetDownloadServlet.DATA_SET_ACCESS_SESSION_KEY,
map);
}
});
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
index 6350b760ba1..97423e9eb25 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
@@ -292,6 +292,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
with(delegateMatcher));
will(new CustomAction("Notify the delegate")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
List<DataSetInformation> dataSetInfos =
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
index 8cc761fa453..0a10aa824f7 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ProcessDatasetsCommandTest.java
@@ -211,6 +211,7 @@ public class ProcessDatasetsCommandTest extends AssertJUnit
{
return new BaseMatcher<DataSetProcessingContext>()
{
+ @Override
public boolean matches(Object item)
{
DataSetProcessingContext processingContext = (DataSetProcessingContext) item;
@@ -224,6 +225,7 @@ public class ProcessDatasetsCommandTest extends AssertJUnit
return true;
}
+ @Override
public void describeTo(Description description)
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManagerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManagerTest.java
index f43c52126d8..31d562f244a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManagerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ShareIdManagerTest.java
@@ -146,6 +146,7 @@ public class ShareIdManagerTest extends AssertJUnit
final MessageChannel ch = new MessageChannel(2000);
new Thread(new Runnable()
{
+ @Override
public void run()
{
manager.lock(DS1);
@@ -183,6 +184,7 @@ public class ShareIdManagerTest extends AssertJUnit
final MessageChannel ch1 = new MessageChannel();
new Thread(new Runnable()
{
+ @Override
public void run()
{
manager.lock(DS1);
@@ -223,6 +225,7 @@ public class ShareIdManagerTest extends AssertJUnit
final MessageChannel ch4 = new MessageChannel();
new Thread(new Runnable()
{
+ @Override
public void run()
{
manager.lock(DS1);
@@ -235,6 +238,7 @@ public class ShareIdManagerTest extends AssertJUnit
final MessageChannel ch2 = new MessageChannel();
new Thread(new Runnable()
{
+ @Override
public void run()
{
ch3.assertNextMessage("locked");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepositoryTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepositoryTest.java
index bbaa6f110fe..8bf1cd7ae5b 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepositoryTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/StreamRepositoryTest.java
@@ -41,6 +41,7 @@ public class StreamRepositoryTest extends AssertJUnit
{
private int id;
+ @Override
public String createUniqueID()
{
return Integer.toString(id++);
@@ -50,6 +51,7 @@ public class StreamRepositoryTest extends AssertJUnit
{
private long time;
+ @Override
public long getTimeInMilliseconds()
{
long result = time;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index 1484274b7fa..06a7466ce2a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -94,12 +94,14 @@ public class UploadingCommandTest extends AssertJUnit
private DefaultFileBasedHierarchicalContentFactory hierarchicalContentFactory =
new DefaultFileBasedHierarchicalContentFactory();
+ @Override
public IHierarchicalContent asContent(File datasetDirectory)
{
return hierarchicalContentFactory.asHierarchicalContent(datasetDirectory,
IDelegatedAction.DO_NOTHING);
}
+ @Override
public IHierarchicalContent asContent(IDatasetLocation datasetLocation)
{
return getContent(datasetLocation.getDataSetLocation());
@@ -110,11 +112,13 @@ public class UploadingCommandTest extends AssertJUnit
return asContent(new File(new File(STORE, SHARE_ID), location));
}
+ @Override
public IHierarchicalContent asContent(ExternalData dataSet)
{
return getContent(dataSet.getCode());
}
+ @Override
public IHierarchicalContent asContent(String dataSetCode)
throws IllegalArgumentException
{
@@ -124,21 +128,25 @@ public class UploadingCommandTest extends AssertJUnit
private static final class MockDataSetDirectoryProvider implements IDataSetDirectoryProvider
{
+ @Override
public File getStoreRoot()
{
return STORE;
}
+ @Override
public File getDataSetDirectory(IDatasetLocation dataSet)
{
return new File(new File(getStoreRoot(), SHARE_ID), dataSet.getDataSetLocation());
}
+ @Override
public File getDataSetDirectory(String shareId, String location)
{
return new File(new File(getStoreRoot(), SHARE_ID), location);
}
+ @Override
public IShareIdManager getShareIdManager()
{
return null;
@@ -367,6 +375,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).addProgressListener(with(any(IProgressListener.class)));
will(new CustomAction("store listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0] = (IProgressListener) invocation.getParameter(0);
@@ -379,6 +388,7 @@ public class UploadingCommandTest extends AssertJUnit
"id:user", null);
will(new CustomAction("report 'finish' to listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0].finished(true);
@@ -423,6 +433,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).addProgressListener(with(any(IProgressListener.class)));
will(new CustomAction("store listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0] = (IProgressListener) invocation.getParameter(0);
@@ -435,6 +446,7 @@ public class UploadingCommandTest extends AssertJUnit
"id:user", null);
will(new CustomAction("report 'finish' to listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0].finished(true);
@@ -519,6 +531,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).addProgressListener(with(any(IProgressListener.class)));
will(new CustomAction("store listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0] = (IProgressListener) invocation.getParameter(0);
@@ -531,6 +544,7 @@ public class UploadingCommandTest extends AssertJUnit
"id:user", null);
will(new CustomAction("report 'abort' to listener")
{
+ @Override
public Object invoke(Invocation invocation) throws Throwable
{
listener[0].finished(false);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/CacheTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/CacheTest.java
index 618e77786f9..8352127bc8a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/CacheTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/CacheTest.java
@@ -85,6 +85,7 @@ public class CacheTest extends AssertJUnit
{
private int index;
+ @Override
public long getTimeInMilliseconds()
{
return timestamps[Math.min(index++, timestamps.length - 1)];
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemViewTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemViewTest.java
index b797e04849a..70da3e50427 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemViewTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/DSSFileSystemViewTest.java
@@ -114,26 +114,31 @@ public class DSSFileSystemViewTest extends AssertJUnit
will(returnValue(new AbstractFtpFile(normalizedPath)
{
+ @Override
public boolean isFile()
{
return false;
}
+ @Override
public boolean isDirectory()
{
return true;
}
+ @Override
public long getSize()
{
return 0;
}
+ @Override
public long getLastModified()
{
return 0;
}
+ @Override
public InputStream createInputStream(long offset) throws IOException
{
return null;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolverTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolverTest.java
index f4d49d41c41..1066eaab902 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolverTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ftp/resolver/TemplateBasedDataSetResourceResolverTest.java
@@ -81,22 +81,26 @@ public class TemplateBasedDataSetResourceResolverTest extends AbstractFileSystem
this.root = root;
}
+ @Override
public IHierarchicalContent asContent(ExternalData dataSet)
{
return asContent((IDatasetLocation) dataSet.tryGetAsDataSet());
}
+ @Override
public IHierarchicalContent asContent(IDatasetLocation datasetLocation)
{
String dataSetCode = datasetLocation.getDataSetCode();
return asContent(dataSetCode);
}
+ @Override
public IHierarchicalContent asContent(String dataSetCode)
{
return asContent(new File(root, dataSetCode));
}
+ @Override
public IHierarchicalContent asContent(File datasetDirectory)
{
return new DefaultFileBasedHierarchicalContentFactory().asHierarchicalContent(
@@ -153,6 +157,7 @@ public class TemplateBasedDataSetResourceResolverTest extends AbstractFileSystem
private ITimeProvider timeProvider = new ITimeProvider()
{
+ @Override
public long getTimeInMilliseconds()
{
return 0;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptorTest.java
index 99c26dff871..0972fe5761c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/openbisauth/OpenBISAuthenticationInterceptorTest.java
@@ -158,6 +158,7 @@ public class OpenBISAuthenticationInterceptorTest
return new BaseMatcher<DataStoreServerInfo>()
{
+ @Override
public boolean matches(Object o)
{
if (o instanceof DataStoreServerInfo)
@@ -174,6 +175,7 @@ public class OpenBISAuthenticationInterceptorTest
return false;
}
+ @Override
public void describeTo(Description description)
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPluginTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPluginTest.java
index 63015878d85..918aaa571d2 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPluginTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractArchiverProcessingPluginTest.java
@@ -141,6 +141,7 @@ public class AbstractArchiverProcessingPluginTest extends AbstractFileSystemTest
return dataSetsToBeDeletedFromArchive;
}
+ @Override
public DatasetProcessingStatuses doArchive(List<DatasetDescription> datasets,
ArchiverTaskContext context)
{
@@ -166,6 +167,7 @@ public class AbstractArchiverProcessingPluginTest extends AbstractFileSystemTest
return result;
}
+ @Override
public DatasetProcessingStatuses doUnarchive(List<DatasetDescription> datasets,
ArchiverTaskContext context)
{
@@ -190,6 +192,7 @@ public class AbstractArchiverProcessingPluginTest extends AbstractFileSystemTest
return result;
}
+ @Override
public DatasetProcessingStatuses doDeleteFromArchive(List<? extends IDatasetLocation> datasets)
{
for (IDatasetLocation datasetLocation : datasets)
@@ -199,12 +202,14 @@ public class AbstractArchiverProcessingPluginTest extends AbstractFileSystemTest
return null;
}
+ @Override
public BooleanStatus isDataSetSynchronizedWithArchive(DatasetDescription dataset,
ArchiverTaskContext context)
{
return isInSet(dataSetsSynchronizedWithArchive, dataset);
}
+ @Override
public BooleanStatus isDataSetPresentInArchive(DatasetDescription dataset)
{
return isInSet(dataSetsInArchive, dataset);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/ExampleAggregationServicePlugin.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/ExampleAggregationServicePlugin.java
index 57db5ed00b9..ade2237e418 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/ExampleAggregationServicePlugin.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/ExampleAggregationServicePlugin.java
@@ -43,6 +43,7 @@ public class ExampleAggregationServicePlugin extends AbstractAggregationServiceR
super(properties, storeRoot);
}
+ @Override
public TableModel createAggregationReport(Map<String, Object> parameters, DataSetProcessingContext context)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MockDataSetDirectoryProvider.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MockDataSetDirectoryProvider.java
index 73e1d04d684..50a77d00951 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MockDataSetDirectoryProvider.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/MockDataSetDirectoryProvider.java
@@ -42,21 +42,25 @@ public final class MockDataSetDirectoryProvider implements IDataSetDirectoryProv
this.shareIdManager = shareIdManager;
}
+ @Override
public File getStoreRoot()
{
return store;
}
+ @Override
public File getDataSetDirectory(IDatasetLocation dataSet)
{
return new File(new File(getStoreRoot(), shareID), dataSet.getDataSetLocation());
}
+ @Override
public File getDataSetDirectory(String shareId, String location)
{
return new File(new File(getStoreRoot(), shareID), location);
}
+ @Override
public IShareIdManager getShareIdManager()
{
return shareIdManager;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiverTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiverTest.java
index 17ccf593822..e8487048e00 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiverTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/RsyncArchiverTest.java
@@ -100,6 +100,7 @@ public class RsyncArchiverTest extends AbstractFileSystemTestCase
}
}
+ @Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
ShareFinder.recordedDataSet = dataSet;
@@ -581,67 +582,80 @@ public class RsyncArchiverTest extends AbstractFileSystemTestCase
children.add(node);
}
+ @Override
public String getName()
{
return name;
}
+ @Override
public String getRelativePath()
{
return relativePath;
}
+ @Override
public String getParentRelativePath()
{
return parent == null ? null : parent.getRelativePath();
}
+ @Override
public boolean exists()
{
return true;
}
+ @Override
public boolean isDirectory()
{
return directory;
}
+ @Override
public long getLastModified()
{
return 0;
}
+ @Override
public List<IHierarchicalContentNode> getChildNodes() throws UnsupportedOperationException
{
return children;
}
+ @Override
public File getFile() throws UnsupportedOperationException
{
throw new UnsupportedOperationException();
}
+ @Override
public File tryGetFile()
{
return null;
}
+ @Override
public long getFileLength() throws UnsupportedOperationException
{
return size;
}
+ @Override
public long getChecksumCRC32() throws UnsupportedOperationException
{
return checksum;
}
+ @Override
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
throw new UnsupportedOperationException();
}
+ @Override
public InputStream getInputStream() throws UnsupportedOperationException,
IOExceptionUnchecked
{
@@ -695,28 +709,33 @@ public class RsyncArchiverTest extends AbstractFileSystemTestCase
}
}
+ @Override
public IHierarchicalContentNode getRootNode()
{
return root;
}
+ @Override
public IHierarchicalContentNode getNode(String relativePath)
throws IllegalArgumentException
{
return nodes.get(relativePath);
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(String relativePathPattern)
{
throw new UnsupportedOperationException();
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(String startingPath,
String fileNamePattern)
{
throw new UnsupportedOperationException();
}
+ @Override
public void close()
{
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
index d7ad12c1fbb..305f996943e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
@@ -80,6 +80,7 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
contentProvider = new IHierarchicalContentProvider()
{
+ @Override
public IHierarchicalContent asContent(String dataSetCode)
{
File dataSetFolder = new File(STORE_ROOT, dataSetCode);
@@ -87,16 +88,19 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
dataSetFolder, IDelegatedAction.DO_NOTHING);
}
+ @Override
public IHierarchicalContent asContent(File datasetDirectory)
{
return null;
}
+ @Override
public IHierarchicalContent asContent(IDatasetLocation datasetLocation)
{
return null;
}
+ @Override
public IHierarchicalContent asContent(ExternalData dataSet)
{
return null;
@@ -162,6 +166,7 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
SectionProperties[] sectionProperties = sectionPropertiesMatcher.recordedObject();
Arrays.sort(sectionProperties, new Comparator<SectionProperties>()
{
+ @Override
public int compare(SectionProperties sp1, SectionProperties sp2)
{
return sp1.getKey().compareTo(sp2.getKey());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractIShareFinderTestCase.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractIShareFinderTestCase.java
index a54f709e374..c61fb6ce80b 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractIShareFinderTestCase.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/AbstractIShareFinderTestCase.java
@@ -59,6 +59,7 @@ public class AbstractIShareFinderTestCase extends AssertJUnit
Share share = new Share(file, speed, new IFreeSpaceProvider()
{
+ @Override
public long freeSpaceKb(HostAwareFile path) throws IOException
{
assertSame(file, path.getFile());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProviderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProviderTest.java
index e031d5612fc..83803716de9 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProviderTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/HierarchicalContentProviderTest.java
@@ -253,11 +253,13 @@ public class HierarchicalContentProviderTest extends AssertJUnit
final IDatasetLocation dataSetLocation = new IDatasetLocation()
{
+ @Override
public String getDataSetCode()
{
return code;
}
+ @Override
public String getDataSetLocation()
{
return location;
@@ -315,28 +317,33 @@ public class HierarchicalContentProviderTest extends AssertJUnit
private static class DummyHierarchicalContent implements IHierarchicalContent
{
+ @Override
public IHierarchicalContentNode getRootNode()
{
return null;
}
+ @Override
public IHierarchicalContentNode getNode(String relativePath)
throws IllegalArgumentException
{
return null;
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(String relativePathPattern)
{
return null;
}
+ @Override
public List<IHierarchicalContentNode> listMatchingNodes(String startingPath,
String fileNamePattern)
{
return null;
}
+ @Override
public void close()
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/ProxyShareIdManager.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/ProxyShareIdManager.java
index 3cdfe2774e5..39b7619a157 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/ProxyShareIdManager.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/ProxyShareIdManager.java
@@ -34,41 +34,49 @@ public class ProxyShareIdManager implements IShareIdManager
this.shareIdManager = shareIdManager;
}
+ @Override
public boolean isKnown(String dataSetCode)
{
return shareIdManager.isKnown(dataSetCode);
}
+ @Override
public String getShareId(String dataSetCode)
{
return shareIdManager.getShareId(dataSetCode);
}
+ @Override
public void setShareId(String dataSetCode, String shareId)
{
shareIdManager.setShareId(dataSetCode, shareId);
}
+ @Override
public void lock(String dataSetCode)
{
shareIdManager.lock(dataSetCode);
}
+ @Override
public void lock(List<String> dataSetCodes)
{
shareIdManager.lock(dataSetCodes);
}
+ @Override
public void await(String dataSetCode)
{
shareIdManager.await(dataSetCode);
}
+ @Override
public void releaseLock(String dataSetCode)
{
shareIdManager.releaseLock(dataSetCode);
}
+ @Override
public void releaseLocks()
{
shareIdManager.releaseLocks();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleShareFinderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleShareFinderTest.java
index d6310bc54ec..84593308acb 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleShareFinderTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/SimpleShareFinderTest.java
@@ -48,6 +48,7 @@ public class SimpleShareFinderTest extends AbstractIShareFinderTestCase
this.checkingResults = checkingResults;
}
+ @Override
public boolean check(SimpleDataSetInformationDTO dataSet, Share share)
{
recordedDataSet = dataSet;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index e5c728592c4..791a259d662 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -44,67 +44,80 @@ public class ImageUtilTest extends AssertJUnit
{
final MockRandomAccessFile is = new MockRandomAccessFile();
+ @Override
public boolean exists()
{
throw new UnsupportedOperationException();
}
+ @Override
public InputStream getInputStream()
{
throw new UnsupportedOperationException();
}
+ @Override
public String getName()
{
throw new UnsupportedOperationException();
}
+ @Override
public String getRelativePath()
{
throw new UnsupportedOperationException();
}
+ @Override
public String getParentRelativePath()
{
throw new UnsupportedOperationException();
}
+ @Override
public boolean isDirectory()
{
throw new UnsupportedOperationException();
}
+ @Override
public long getLastModified()
{
throw new UnsupportedOperationException();
}
+ @Override
public List<IHierarchicalContentNode> getChildNodes() throws UnsupportedOperationException
{
throw new UnsupportedOperationException();
}
+ @Override
public File getFile() throws UnsupportedOperationException
{
throw new UnsupportedOperationException();
}
+ @Override
public long getFileLength() throws UnsupportedOperationException
{
throw new UnsupportedOperationException();
}
+ @Override
public long getChecksumCRC32() throws UnsupportedOperationException
{
throw new UnsupportedOperationException();
}
+ @Override
public IRandomAccessFile getFileContent() throws UnsupportedOperationException,
IOExceptionUnchecked
{
return is;
}
+ @Override
public File tryGetFile()
{
return null;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtilsTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtilsTest.java
index 53b8660e3cd..eeca7ee9207 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtilsTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/SegmentedStoreUtilsTest.java
@@ -239,6 +239,7 @@ public class SegmentedStoreUtilsTest extends AbstractFileSystemTestCase
new Thread(new Runnable()
{
+ @Override
public void run()
{
SegmentedStoreUtils.moveDataSetToAnotherShare(dataSetDirInStore, share2,
--
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