From a5069fc9e182699c448d68ac1587810ba73ca03b Mon Sep 17 00:00:00 2001
From: fedoreno <fedoreno>
Date: Wed, 27 Apr 2016 13:58:55 +0000
Subject: [PATCH] SSDM-3511: reformatted
SVN: 36340
---
.../server/ServiceForDataStoreServer.java | 3387 +++++++++++++++++
.../ServiceForDataStoreServerLogger.java | 2 +-
.../generic/server/TrackingServerLogger.java | 5 +-
.../generic/server/TrackingServiceServer.java | 5 +-
.../TrustedCrossOriginDomainsProvider.java | 4 +-
.../WhiteListBasedRemoteHostValidator.java | 8 +-
...entToDataSetRelatedEntitiesTranslator.java | 6 +-
.../v1/GeneralInformationChangingService.java | 13 +-
...lInformationChangingServiceJsonServer.java | 8 +-
...neralInformationChangingServiceLogger.java | 2 +-
.../api/v1/GeneralInformationService.java | 45 +-
.../GeneralInformationServiceJsonServer.java | 7 +-
.../v1/GeneralInformationServiceServer.java | 11 +-
...pleToDataSetRelatedEntitiesTranslator.java | 6 +-
.../v1/WebInformationServiceJsonServer.java | 7 +-
.../authorization/ActiveAuthorization.java | 3 +-
.../server/authorization/Argument.java | 3 +-
.../server/authorization/CapabilityMap.java | 8 +-
.../DefaultAccessController.java | 16 +-
.../authorization/IAccessController.java | 11 +-
.../authorization/IReturnValueFilter.java | 7 +-
.../server/authorization/NoAuthorization.java | 3 +-
.../authorization/NoReturnValueFilter.java | 3 +-
.../server/authorization/SpaceOwnerKind.java | 3 +-
.../annotation/AuthorizationGuard.java | 4 +-
.../annotation/RolesAllowed.java | 4 +-
.../predicate/AbstractPredicate.java | 12 +-
.../predicate/AbstractProjectPredicate.java | 3 +-
.../predicate/AbstractTechIdPredicate.java | 3 +-
.../predicate/AtomicOperationsPredicate.java | 3 +-
.../DataSetUpdatesCollectionPredicate.java | 5 +-
.../predicate/DataSetUpdatesPredicate.java | 8 +-
.../DelegatedNullableAbstractPredicate.java | 4 +-
.../predicate/DelegatedPredicate.java | 8 +-
.../ExistingSpaceIdentifierPredicate.java | 1 -
.../predicate/ExperimentUpdatesPredicate.java | 5 +-
.../authorization/predicate/IPredicate.java | 4 +-
.../ListSamplesByPropertyPredicate.java | 8 +-
.../NewDataSetsWithTypePredicate.java | 3 +-
.../NullableGroupIdentifierPredicate.java | 3 +-
.../predicate/RevertDeletionPredicate.java | 3 +-
.../predicate/SamplePredicate.java | 5 +-
.../predicate/SampleTechIdPredicate.java | 3 +-
.../SampleUpdatesCollectionPredicate.java | 3 +-
.../predicate/SampleUpdatesPredicate.java | 5 +-
.../validator/AbstractValidator.java | 3 +-
.../authorization/validator/IValidator.java | 7 +-
.../validator/ProjectValidator.java | 2 +-
.../SearchDomainSearchResultValidator.java | 2 +
.../batch/AbstractBatchOperationDelegate.java | 3 +-
.../server/batch/BatchOperationExecutor.java | 14 +-
.../generic/server/batch/SampleUpdate.java | 9 +-
.../business/DataStoreServiceFactory.java | 7 +-
.../business/IDataStoreServiceFactory.java | 5 +-
.../business/IEntityOperationChecker.java | 10 +-
.../server/business/IRelationshipService.java | 92 +-
.../PropertiesBatchEvaluationErrors.java | 4 +-
.../bo/AbstractMaterialBusinessObject.java | 12 +-
.../bo/AbstractSampleBusinessObject.java | 6 +-
...bstractSampleIdentifierBusinessObject.java | 8 +-
.../server/business/bo/AttachmentBO.java | 4 +-
.../business/bo/AuthorizationGroupBO.java | 10 +-
.../server/business/bo/CorePluginTable.java | 4 +-
.../bo/DataAccessExceptionTranslator.java | 25 +-
.../server/business/bo/DataSetTable.java | 4 +-
.../server/business/bo/DeletionTable.java | 4 +-
.../business/bo/EntityCodeGenerator.java | 14 +-
.../server/business/bo/EntityTypeBO.java | 4 +-
.../business/bo/EntityTypePropertyTypeBO.java | 8 +-
.../server/business/bo/ExperimentBO.java | 10 +-
.../server/business/bo/ExperimentTable.java | 8 +-
.../business/bo/GridCustomColumnBO.java | 4 +-
.../business/bo/GridCustomFilterBO.java | 4 +-
.../server/business/bo/IAttachmentBO.java | 7 +-
.../business/bo/IAuthorizationGroupBO.java | 14 +-
.../server/business/bo/IBusinessObject.java | 5 +-
.../bo/ICommonBusinessObjectFactory.java | 5 +-
.../server/business/bo/ICorePluginTable.java | 3 +-
.../server/business/bo/IEntityTypeBO.java | 3 +-
.../bo/IEntityTypePropertyTypeBO.java | 3 +-
.../business/bo/IExternalDataTable.java | 18 +-
.../bo/IGridCustomFilterOrColumnBO.java | 5 +-
.../server/business/bo/IPropertyTypeBO.java | 4 +-
.../server/business/bo/ISampleTable.java | 15 +-
.../business/bo/ISearchDomainSearcher.java | 1 -
.../generic/server/business/bo/ISpaceBO.java | 8 +-
.../server/business/bo/MaterialBO.java | 4 +-
.../server/business/bo/MaterialTable.java | 10 +-
.../server/business/bo/MetaprojectBO.java | 4 +-
...tExceptionFallbackExceptionTranslator.java | 3 +-
.../generic/server/business/bo/ProjectBO.java | 6 +-
.../server/business/bo/PropertyTypeBO.java | 4 +-
.../server/business/bo/PropertyTypeTable.java | 4 +-
.../business/bo/RootEntitiesFinder.java | 4 +-
.../generic/server/business/bo/SampleBO.java | 4 +-
.../bo/SampleCodeGeneratorByType.java | 2 +-
.../generic/server/business/bo/ScriptBO.java | 8 +-
.../business/bo/SearchDomainSearcher.java | 22 +-
.../generic/server/business/bo/TrashBO.java | 120 +-
.../server/business/bo/VocabularyTermBO.java | 4 +-
.../bo/common/AbstractBatchIterator.java | 10 +-
.../server/business/bo/common/CodeRecord.java | 1 -
.../bo/common/EntityPropertiesEnricher.java | 4 +-
.../common/GenericEntityPropertyRecord.java | 1 -
.../bo/common/IEntityPropertiesEnricher.java | 4 +-
.../IEntityPropertiesHolderResolver.java | 2 +-
.../bo/common/IPropertyListingQuery.java | 5 +-
.../common/MaterialEntityPropertyRecord.java | 1 -
.../ExperimentProjectSpaceCodeRecord.java | 5 +-
.../entity/ISecondaryEntityListingQuery.java | 16 +-
.../bo/common/entity/SecondaryEntityDAO.java | 4 +-
.../bo/datasetlister/DatasetLister.java | 2 +-
.../datasetlister/IDatasetListingQuery.java | 16 +-
.../datasetlister/IDataSetLister.java | 9 +-
.../samplelister/ISampleLister.java | 3 +-
.../samplelister/ISampleListingQuery.java | 16 +-
.../DataSetTypeWithoutExperimentChecker.java | 7 +-
.../business/importer/DatabaseInstance.java | 1 -
.../importer/DatabaseInstanceImporter.java | 2 +-
.../coreplugin/JettyWebAppPluginInjector.java | 8 +-
.../server/dataaccess/IAttachmentDAO.java | 2 +-
.../dataaccess/IAuthorizationGroupDAO.java | 3 +-
.../dataaccess/IDataSourceProvider.java | 6 +-
.../server/dataaccess/IDataStoreDAO.java | 2 +-
.../server/dataaccess/IDeletionDAO.java | 15 +-
.../IDynamicPropertyEvaluationScheduler.java | 1 -
...cPropertyEvaluationSchedulerWithQueue.java | 17 +-
.../IEntityPropertiesConverter.java | 16 +-
.../dataaccess/IEntityPropertyTypeDAO.java | 14 +-
.../generic/server/dataaccess/IEventDAO.java | 3 +-
.../server/dataaccess/IFileFormatTypeDAO.java | 2 +-
.../server/dataaccess/ILocatorTypeDAO.java | 2 +-
.../server/dataaccess/IMetaprojectDAO.java | 6 +-
.../server/dataaccess/IPropertyTypeDAO.java | 3 +-
.../dataaccess/IPropertyValueValidator.java | 3 +-
.../server/dataaccess/ISampleTypeDAO.java | 5 +-
.../server/dataaccess/IVocabularyDAO.java | 12 +-
.../server/dataaccess/IVocabularyTermDAO.java | 8 +-
.../PlaceholderPropertyCreator.java | 9 +-
.../server/dataaccess/PropertyValidator.java | 3 +-
.../server/dataaccess/db/AbstractDAO.java | 12 +-
...bstractGenericEntityWithPropertiesDAO.java | 10 +-
.../server/dataaccess/db/AttachmentDAO.java | 12 +-
.../server/dataaccess/db/DAOFactory.java | 4 +-
.../generic/server/dataaccess/db/DataDAO.java | 8 +-
.../db/DatabaseAndIndexReplacer.java | 10 +-
.../db/DynamicPropertiesInterceptor.java | 3 +-
.../server/dataaccess/db/ExperimentDAO.java | 2 +-
.../server/dataaccess/db/IPermIdDAO.java | 3 +-
.../dataaccess/db/IndexCreationUtil.java | 5 +-
.../server/dataaccess/db/MaterialDAO.java | 2 +-
.../server/dataaccess/db/SampleDAO.java | 27 +-
.../db/deletion/AttachmentEntry.java | 14 +-
.../db/deletion/AttributeEntry.java | 4 +-
.../db/deletion/EntityHistoryCreator.java | 61 +-
.../db/deletion/EntityModification.java | 2 +-
.../db/deletion/PropertyHistoryEntry.java | 6 +-
.../db/deletion/RelationshipHistoryEntry.java | 6 +-
.../dataaccess/db/search/CharacterHelper.java | 2 +-
.../db/search/HibernateSearchContext.java | 3 +-
.../search/IFullTextIndexUpdateScheduler.java | 5 +-
.../db/search/IFullTextIndexUpdater.java | 5 +-
.../db/search/IFullTextIndexer.java | 9 +-
.../dataaccess/db/search/IndexMode.java | 8 +-
.../db/search/IndexingQueryOptimizer.java | 7 +-
.../db/search/LuceneQueryBuilder.java | 4 +-
.../PackageBasedIndexedEntityFinder.java | 6 +-
.../search/detailed/DetailedQueryBuilder.java | 21 +-
.../search/detailed/IndexFieldNameHelper.java | 2 +-
.../DynamicPropertyEvaluator.java | 26 +-
.../IBatchDynamicPropertyEvaluator.java | 10 +-
.../calculator/DynamicPropertyAdaptor.java | 3 +-
.../calculator/DynamicPropertyFunctions.java | 9 +-
.../ISampleAdaptorRelationsQuery.java | 4 +-
.../calculator/XmlPropertyAdaptor.java | 3 +-
.../calculator/api/ISampleAdaptor.java | 12 +-
.../AbstractEntityValidator.java | 3 +-
.../api/IEntityValidator.java | 6 +-
.../migration/MigrationStepFrom022To023.java | 6 +-
.../migration/MigrationStepFrom023To024.java | 5 +-
.../migration/MigrationStepFrom025To026.java | 3 +-
.../migration/MigrationStepFrom046To047.java | 4 +-
.../server/dataaccess/util/UpdateUtils.java | 8 +-
.../server/jython/api/v1/IDataSetType.java | 3 +-
.../server/jython/api/v1/IEntityType.java | 1 -
.../IMasterDataRegistrationTransaction.java | 58 +-
.../jython/api/v1/IPropertyAssignment.java | 7 +-
.../api/v1/IPropertyAssignmentImmutable.java | 3 +-
.../server/jython/api/v1/IPropertyType.java | 12 +-
.../jython/api/v1/IPropertyTypeImmutable.java | 8 +-
.../server/jython/api/v1/IVocabulary.java | 3 +-
.../jython/api/v1/IVocabularyImmutable.java | 3 +-
.../ExternalDataManagementSystemWrapper.java | 3 +-
...ataRegistrationScriptRunnerStandalone.java | 3 +-
.../v1/impl/PropertyAssignmentWrapper.java | 3 +-
.../server/jython/api/v1/impl/Script.java | 2 +-
.../server/plugin/AbstractPluginRegistry.java | 3 +-
.../plugin/DataSetServerPluginRegistry.java | 1 -
.../server/plugin/IDataSetServerPlugin.java | 2 +-
.../plugin/IDataSetTypeSlaveServerPlugin.java | 7 +-
.../plugin/ISampleTypeSlaveServerPlugin.java | 4 +-
.../generic/server/plugin/IServerPlugin.java | 7 +-
.../plugin/IServerPluginWithWildcards.java | 6 +-
.../plugin/SampleServerPluginRegistry.java | 3 +-
.../plugin/WildcardSupportingPluginMap.java | 3 +-
...SampleRegistrationTempCodeUpdaterTask.java | 8 +-
.../task/DataSetRegistrationSummaryTask.java | 13 +-
.../task/MaterialExternalDBSyncTask.java | 4 +-
.../task/RevokeUserAccessMaintenanceTask.java | 243 +-
.../server/util/LifeCycleListener.java | 3 +-
.../server/util/MethodInvocationUtils.java | 8 +-
.../generic/shared/AbstractServerLogger.java | 2 +-
.../DatabaseCreateOrDeleteModification.java | 4 +-
.../shared/DatabaseUpdateModification.java | 4 +-
.../openbis/generic/shared/ICommonServer.java | 4 +-
.../generic/shared/IDataStoreService.java | 4 +-
.../generic/shared/IRemoteHostValidator.java | 2 +-
.../shared/IServiceForDataStoreServer.java | 2 +-
.../generic/shared/ISessionProvider.java | 2 +-
.../openbis/generic/shared/ResourceNames.java | 5 +-
.../generic/shared/api/v1/Translator.java | 3 +-
.../generic/shared/basic/CodeConverter.java | 12 +-
.../generic/shared/basic/CodeNormalizer.java | 4 +-
.../shared/basic/DataSetUploadInfo.java | 2 -
.../EntityVisitComparatorByTimeStamp.java | 2 +-
.../generic/shared/basic/ExpressionUtil.java | 5 +-
.../shared/basic/GenericSharedConstants.java | 2 +-
.../generic/shared/basic/GridRowModel.java | 3 +-
.../shared/basic/IColumnDefinition.java | 3 +-
...EntityInformationHolderWithIdentifier.java | 3 +-
.../IEntityInformationHolderWithPermId.java | 3 +-
...EntityInformationHolderWithProperties.java | 3 +-
...anagedPropertyGridInformationProvider.java | 3 +-
.../shared/basic/MaterialCodeConverter.java | 3 +-
.../generic/shared/basic/MetaprojectName.java | 3 +-
.../shared/basic/PermlinkUtilities.java | 2 +-
.../generic/shared/basic/PrimitiveValue.java | 8 +-
.../shared/basic/SimpleImageHtmlRenderer.java | 1 -
.../generic/shared/basic/TableCellUtil.java | 9 +-
.../shared/basic/URLMethodWithParameters.java | 5 +-
.../shared/basic/ValidationUtilities.java | 2 +-
.../generic/shared/basic/ViewMode.java | 5 +-
.../shared/basic/WildcardSupportingMap.java | 6 +-
.../shared/basic/annotation/DoNotEscape.java | 6 +-
.../basic/dto/AbstractEntityProperty.java | 7 +-
.../basic/dto/AbstractExternalData.java | 6 +-
.../basic/dto/AssociatedEntityKind.java | 5 +-
.../basic/dto/AttachmentWithContent.java | 8 +-
.../basic/dto/BasicProjectIdentifier.java | 3 +-
.../basic/dto/BatchRegistrationResult.java | 4 +-
.../shared/basic/dto/CodeAndLabel.java | 5 +-
.../shared/basic/dto/ColumnSetting.java | 5 +-
.../shared/basic/dto/ContainerDataSet.java | 4 +-
.../shared/basic/dto/DateTableCell.java | 9 +-
.../generic/shared/basic/dto/Deletion.java | 3 +-
.../basic/dto/DetailedSearchCriterion.java | 6 +-
.../shared/basic/dto/DetailedSearchField.java | 3 +-
.../shared/basic/dto/DoubleTableCell.java | 10 +-
.../shared/basic/dto/EntityReference.java | 3 +-
.../generic/shared/basic/dto/EntityType.java | 2 +-
.../basic/dto/EntityTypePropertyType.java | 19 +-
.../generic/shared/basic/dto/EntityVisit.java | 3 +-
.../shared/basic/dto/ExperimentType.java | 2 +-
.../shared/basic/dto/FileFormatType.java | 1 -
.../basic/dto/GenericEntityProperty.java | 4 +-
.../basic/dto/IDatasetLocationNode.java | 3 +-
.../shared/basic/dto/IEntityProperty.java | 4 +-
.../shared/basic/dto/IExpressionUpdates.java | 3 +-
.../shared/basic/dto/IPropertiesBean.java | 3 +-
.../basic/dto/ISerializableComparable.java | 4 +-
.../shared/basic/dto/ImageTableCell.java | 24 +-
.../basic/dto/LastModificationState.java | 34 +-
.../generic/shared/basic/dto/LinkDataSet.java | 4 +-
.../generic/shared/basic/dto/LinkModel.java | 12 +-
.../basic/dto/ListMaterialCriteria.java | 7 +-
.../basic/dto/ListOrSearchSampleCriteria.java | 4 +-
.../dto/ManagedHtmlWidgetDescription.java | 5 +-
.../basic/dto/ManagedUiActionDescription.java | 3 +-
.../dto/ManagedUiTableActionDescription.java | 4 +-
.../dto/MaterialAttributeSearchFieldKind.java | 2 +-
.../basic/dto/MaterialEntityProperty.java | 3 +-
.../shared/basic/dto/MaterialIdentifier.java | 12 +-
.../shared/basic/dto/NewColumnOrFilter.java | 3 +-
.../shared/basic/dto/NewPTNewAssigment.java | 11 +-
.../generic/shared/basic/dto/NewSample.java | 10 +-
.../basic/dto/PortletConfiguration.java | 4 +-
.../shared/basic/dto/PropertyType.java | 4 +-
.../shared/basic/dto/RelationshipType.java | 4 +-
.../shared/basic/dto/ReportingPluginType.java | 11 +-
.../shared/basic/dto/RoleAssignment.java | 1 -
.../shared/basic/dto/RoleWithHierarchy.java | 14 +-
.../generic/shared/basic/dto/Sample.java | 7 +-
.../dto/SampleAttributeSearchFieldKind.java | 2 +-
.../basic/dto/SampleParentWithDerived.java | 3 +-
.../basic/dto/SampleTypePropertyType.java | 1 -
...earchDomainSearchResultWithFullEntity.java | 2 +-
.../SearchFieldBooleanCriterionFactory.java | 3 +-
.../dto/SearchFieldDateCriterionFactory.java | 3 +-
.../SerializableComparableIDDecorator.java | 17 +-
.../dto/SimpleAttributeSearchFieldKind.java | 3 +-
.../basic/dto/StandardPortletNames.java | 6 +-
.../basic/dto/TrackingDataSetCriteria.java | 8 +-
.../basic/dto/TrackingSampleCriteria.java | 7 +-
.../shared/basic/dto/TypedTableModel.java | 5 +-
.../dto/VocabularyTermEntityProperty.java | 3 +-
...IManagedInputWidgetDescriptionFactory.java | 3 +-
.../basic/dto/api/IManagedProperty.java | 9 +-
.../basic/dto/api/IManagedUiAction.java | 9 +-
.../basic/dto/api/IManagedUiDescription.java | 13 +-
.../basic/dto/api/IManagedUiTableAction.java | 8 +-
.../basic/dto/api/ValidationException.java | 1 -
.../shared/coreplugin/CorePluginsUtils.java | 8 +-
.../shared/coreplugin/IPluginType.java | 3 +-
.../dto/AbstractRegistrationHolder.java | 5 +-
.../generic/shared/dto/AttachmentPE.java | 4 +-
.../generic/shared/dto/CorePluginPE.java | 4 +-
.../openbis/generic/shared/dto/DataPE.java | 4 +-
.../generic/shared/dto/DataSetPropertyPE.java | 2 +-
.../shared/dto/DataSetRelationshipPE.java | 2 +-
.../shared/dto/DataSetTypePropertyTypePE.java | 4 +-
.../shared/dto/DataSetUploadContext.java | 6 +-
.../shared/dto/DataSourceDefinition.java | 12 +-
.../shared/dto/DataSourceWithDefinition.java | 2 +-
.../shared/dto/DataStoreServerInfo.java | 6 +-
.../generic/shared/dto/DataTypePE.java | 4 +-
.../shared/dto/DeletedExternalDataPE.java | 5 +-
.../EntityCollectionForCreationOrUpdate.java | 6 +-
.../dto/EntityOperationsLogEntryPE.java | 6 +-
.../shared/dto/EntityPropertyFiller.java | 4 +-
.../generic/shared/dto/EntityPropertyPE.java | 52 +-
.../shared/dto/ExperimentPropertyPE.java | 2 +-
.../dto/ExperimentTypePropertyTypePE.java | 4 +-
.../generic/shared/dto/ExternalDataPE.java | 2 +-
.../generic/shared/dto/ExtractableData.java | 12 +-
.../HibernateAbstractRegistrationHolder.java | 6 +-
...EntityInformationWithPropertiesHolder.java | 1 -
.../generic/shared/dto/IIdAndCodeHolder.java | 3 +-
.../generic/shared/dto/IMatchingEntity.java | 1 -
.../shared/dto/IUntypedValueSetter.java | 2 +-
.../generic/shared/dto/LimitFilter.java | 3 +-
.../generic/shared/dto/LocatorTypePE.java | 4 +-
.../generic/shared/dto/MaterialPE.java | 2 +-
.../shared/dto/MaterialPropertyPE.java | 2 +-
.../dto/MaterialTypePropertyTypePE.java | 4 +-
.../generic/shared/dto/MetaprojectPE.java | 2 +-
.../shared/dto/NewContainerDataSet.java | 3 +-
.../generic/shared/dto/NewExternalData.java | 14 +-
.../generic/shared/dto/NewLinkDataSet.java | 1 -
.../shared/dto/NewProcessingInstruction.java | 2 +-
.../generic/shared/dto/NewProperty.java | 1 -
.../shared/dto/OpenBISSessionHolder.java | 3 +-
.../shared/dto/ProcessingInstructionDTO.java | 2 +-
.../shared/dto/ProcessingParameters.java | 5 +-
.../generic/shared/dto/RoleAssignmentPE.java | 281 +-
.../dto/SampleParentWithDerivedDTO.java | 3 +-
.../generic/shared/dto/SamplePropertyPE.java | 4 +-
.../shared/dto/SampleRelationshipPE.java | 2 +-
.../generic/shared/dto/SampleSkeleton.java | 10 +-
.../shared/dto/SampleTypePropertyTypePE.java | 4 +-
.../generic/shared/dto/StorageFormat.java | 6 +-
.../generic/shared/dto/TimeInterval.java | 2 +-
.../generic/shared/dto/VocabularyTermPE.java | 4 +-
.../dto/hibernate/InternalNamespace.java | 5 +-
.../shared/dto/hibernate/Location.java | 2 +-
.../dto/hibernate/SearchFieldConstants.java | 8 +-
.../hibernate/SortableNumberBridgeUtils.java | 64 +-
.../identifier/LocalExperimentIdentifier.java | 3 +-
.../shared/dto/types/DataSetTypeCode.java | 3 +-
.../shared/dto/types/ExperimentTypeCode.java | 3 +-
.../SimpleTableModelBuilderAdaptor.java | 7 +-
.../api/EntityLinkElementKind.java | 3 +-
.../shared/managed_property/api/IElement.java | 14 +-
.../managed_property/api/IElementFactory.java | 8 +-
.../api/IEntityInformationProvider.java | 12 +-
.../api/IRowBuilderAdaptor.java | 6 +-
.../api/ISimpleTableModelBuilderAdaptor.java | 3 +-
.../api/IStructuredPropertyConverter.java | 3 +-
.../structured/ElementFactory.java | 4 +-
.../XmlOrJsonStructuredPropertyConverter.java | 4 +-
.../shared/parser/BisExcelFileLoader.java | 4 +-
.../shared/parser/BisTabFileLoader.java | 4 +-
.../shared/parser/GlobalProperties.java | 6 +-
.../shared/parser/GlobalPropertiesLoader.java | 5 +-
.../UpdatedSampleParserObjectFactory.java | 8 +-
.../translator/DeletedEntityTranslator.java | 4 +-
.../translator/PropertyTranslatorUtils.java | 3 +-
.../generic/shared/util/CacheManager.java | 54 +-
.../generic/shared/util/DataTypeUtils.java | 2 +-
.../generic/shared/util/EntityHelper.java | 8 +-
.../generic/shared/util/ICacheManager.java | 5 +-
.../generic/shared/util/IColumnGroup.java | 32 +-
.../generic/shared/util/IColumnMetaData.java | 3 +-
.../shared/util/IDataSourceFactory.java | 4 +-
.../cisd/openbis/generic/shared/util/Key.java | 6 +-
.../util/MaterialConfigurationProvider.java | 3 +-
.../shared/util/RelationshipUtils.java | 6 +-
.../generic/shared/util/RuntimeCache.java | 21 +-
.../util/RuntimeCacheEventListener.java | 2 +-
.../generic/shared/util/ServerUtils.java | 3 +-
.../generic/shared/util/SpaceCodeHelper.java | 17 +-
.../openbis/generic/shared/util/UuidUtil.java | 4 +-
.../shared/util/WebClientFilesUpdater.java | 6 +-
.../openbis/generic/shared/util/XmlUtils.java | 2 +-
.../AbstractPluginBusinessObjectFactory.java | 4 +-
.../plugin/AbstractSampleServerPlugin.java | 10 +-
.../client/web/client/IDemoClientService.java | 5 +-
.../client/web/client/application/Dict.java | 3 +-
.../application/module/StatisticsWidget.java | 2 +-
.../web/server/DemoClientServiceServlet.java | 7 +-
.../demo/server/DemoSampleServerPlugin.java | 3 +-
.../plugin/demo/shared/IDemoServer.java | 4 +-
.../plugin/demo/shared/ResourceNames.java | 5 +-
.../application/DelegatedClientPlugin.java | 3 +-
.../dataset/DataSetRelationshipBrowser.java | 4 +-
.../dataset/GenericDataSetViewer.java | 2 +-
...ractGenericExperimentRegisterEditForm.java | 3 +-
.../experiment/ExperimentPropertiesPanel.java | 20 +-
.../experiment/PropertiesEditor.java | 3 +-
.../material/GenericMaterialViewer.java | 21 +-
.../sample/EntityConnectionTypeProvider.java | 3 +-
.../sample/GenericSampleViewer.java | 22 +-
.../web/server/GenericClientService.java | 4 +-
.../server/GenericClientServiceServlet.java | 7 +-
.../UpdatedDataSetParserObjectFactory.java | 8 +-
.../server/AbstractGenericServerPlugin.java | 4 +-
.../server/GenericDataSetServerPlugin.java | 2 +-
.../plugin/generic/server/GenericServer.java | 34 +-
.../generic/server/GenericServerLogger.java | 2 +-
.../generic/server/GenericServiceServer.java | 5 +-
.../shared/IGenericServerInternal.java | 2 -
.../plugin/generic/shared/ResourceNames.java | 5 +-
.../query/client/api/v1/IQueryApiFacade.java | 16 +-
.../web/client/IQueryClientService.java | 5 +-
.../web/client/IQueryClientServiceAsync.java | 3 +-
.../client/web/client/application/Dict.java | 3 +-
.../module/QueryDatabaseSelectionWidget.java | 2 +-
.../client/dto/QueryBrowserGridColumnIDs.java | 8 +
.../web/server/QueryClientServiceServlet.java | 7 +-
.../cisd/openbis/plugin/query/server/DAO.java | 5 +-
.../server/api/v1/QueryServiceJsonServer.java | 7 +-
.../query/server/api/v1/ResourceNames.java | 2 -
.../resultfilter/QueryResultFilter.java | 6 +-
.../IQueryDatabaseDefinitionProvider.java | 3 +-
.../plugin/query/shared/ResourceNames.java | 5 +-
.../query/shared/api/v1/IQueryApiServer.java | 19 +-
.../shared/api/v1/dto/QueryDescription.java | 7 +-
.../shared/api/v1/dto/QueryTableModel.java | 6 +-
.../asapi/v3/cache/SearchCacheTest.java | 2 +-
.../AbstractSearchMethodExecutorTest.java | 8 +-
.../sample/FullSampleIdentifierTest.java | 28 +-
.../asapi/v3/AbstractDataSetTest.java | 13 +-
.../asapi/v3/CreateExperimentTest.java | 2 +-
.../asapi/v3/CreateMaterialTest.java | 7 +-
.../systemtest/asapi/v3/CreateSampleTest.java | 5 +-
.../asapi/v3/EntityDeletionTest.java | 3 +-
.../systemtest/asapi/v3/GetSampleTest.java | 10 +-
.../asapi/v3/ProjectSampleTest.java | 1572 ++------
.../asapi/v3/SearchDataSetTypeTest.java | 24 +-
.../asapi/v3/SearchExperimentTypeTest.java | 20 +-
.../asapi/v3/SearchMaterialTypeTest.java | 20 +-
.../systemtest/asapi/v3/SearchSampleTest.java | 12 +-
.../asapi/v3/SearchSampleTypeTest.java | 24 +-
.../asapi/v3/SearchServiceTest.java | 20 +-
.../asapi/v3/UpdateExperimentTest.java | 49 +-
.../openbis/systemtest/deletion/Change.java | 4 +-
.../deletion/DataSetDeletionTest.java | 4 +-
.../systemtest/deletion/DeletionTest.java | 101 +-
.../deletion/ExperimentDeletionTest.java | 18 +-
.../deletion/ProjectDeletionTest.java | 22 +-
.../deletion/SampleDeletionTest.java | 33 +-
.../openbis/generic/OpenbisClientTest.java | 5 +-
.../generic/client/console/LexerTest.java | 4 +-
.../application/DummyAuthenticationTest.java | 6 +-
.../web/client/application/SearchCommand.java | 3 +-
.../VocabularyRegistrationTest.java | 2 +-
.../application/locator/OpenViewCommand.java | 4 +-
.../application/ui/InvokeActionMenu.java | 3 +-
.../ui/amc/CheckAuthorizationGroupTable.java | 3 +-
.../application/ui/amc/CheckPersonTable.java | 3 +-
.../ui/amc/CheckRoleAssignmentTable.java | 3 +-
.../ui/amc/OpenAddPersonDialog.java | 3 +-
.../application/ui/amc/RemovePerson.java | 3 +-
.../ui/amc/ShowAuthorizationGroup.java | 3 +-
.../application/ui/data/ShowDataSet.java | 5 +-
.../ui/data/ShowDataSetEditor.java | 3 +-
.../ui/experiment/CheckExperimentTable.java | 3 +-
.../ui/experiment/ShowExperiment.java | 3 +-
.../filter/OpenFilterSettingsCommand.java | 5 +-
.../ui/material/CheckMaterialTable.java | 3 +-
.../ui/project/CheckProjectTable.java | 3 +-
.../project/FillProjectRegistrationForm.java | 3 +-
.../CheckPropertyTypeAssignmentTable.java | 3 +-
.../property_type/CheckPropertyTypeTable.java | 3 +-
.../ui/sample/ExportSamplesTestCommand.java | 12 +-
.../application/ui/sample/ShowSample.java | 3 +-
.../application/ui/util/GridTestUtils.java | 9 +-
.../AbstractDefaultTestCommand.java | 4 +-
.../testframework/AbstractGWTTestCase.java | 10 +-
.../testframework/AbstractProperty.java | 16 +-
.../testframework/CheckTableCommand.java | 7 +-
.../web/client/testframework/GWTTestUtil.java | 17 +-
.../testframework/IMessageValidator.java | 2 -
.../web/client/testframework/IProperty.java | 6 +-
.../testframework/IPropertyChecker.java | 8 +-
.../client/testframework/ITestCommand.java | 13 +-
.../PropertyCheckingManager.java | 2 +-
.../client/testframework/RemoteConsole.java | 18 +-
.../web/client/testframework/TestUtil.java | 5 +-
.../WaitForAllActiveCallbacksFinish.java | 4 +-
.../client/testframework/WidgetPicker.java | 6 +-
.../clientnonjs/HelpPageIdentifierTest.java | 18 +-
.../web/clientnonjs/URLListEncoderTest.java | 10 +-
.../ViewLocatorResolverRegistryTest.java | 6 +-
.../web/server/CommonClientServiceTest.java | 4 +-
.../WebClientConfigurationProviderTest.java | 15 +-
.../client/web/server/calculator/RowTest.java | 29 +-
.../server/resultset/ScriptProviderTest.java | 2 +-
.../web/server/util/FilterUtilsTest.java | 5 +-
.../web/server/util/TSVRendererTest.java | 22 +-
.../util/XMLPropertyTransformerTest.java | 2 +-
.../generic/server/CommonServerTest.java | 2 +-
.../DataStoreServiceRegistratorTest.java | 8 +-
.../DatabaseLastModificationAdvisorTest.java | 4 +-
.../server/ETLServiceDatabaseTest.java | 2 +-
.../server/JythonEvaluatorPoolTest.java | 36 +-
.../server/ServerInterfaceRegressionTest.java | 2 +-
.../DefaultAccessControllerTest.java | 53 +-
.../predicate/CollectionPredicateTest.java | 18 +-
.../validator/ExternalDataValidatorTest.java | 4 +-
.../validator/GroupValidatorTest.java | 9 +-
.../PropertiesBatchEvaluationErrorsTest.java | 1 -
.../server/business/bo/DataBOTest.java | 12 +-
.../server/business/bo/ExperimentBOTest.java | 3 +-
.../business/bo/PropertyValidatorTest.java | 46 +-
.../server/business/bo/SampleBOTest.java | 1 -
.../business/bo/SearchDomainSearcherTest.java | 18 +-
.../server/business/bo/TrashBOTest.java | 164 +-
.../common/EntityPropertiesEnricherTest.java | 6 +-
.../SecondaryEntityListingQueryTest.java | 6 +-
.../DatasetListingQueryTest.java | 16 +-
.../business/bo/entitygraph/DataSetNode.java | 23 +-
.../bo/entitygraph/EntityGraphGenerator.java | 82 +-
.../business/bo/entitygraph/EntityNode.java | 10 +-
.../bo/entitygraph/ExperimentNode.java | 12 +-
.../business/bo/entitygraph/SampleNode.java | 25 +-
.../server/business/bo/entitygraph/Utils.java | 8 +-
.../samplelister/SampleListerTest.java | 10 +-
.../SampleSetListingQueryTest.java | 4 +-
.../dataaccess/db/AttachmentDAOTest.java | 2 +-
.../db/AuthorizationGroupDAOTest.java | 2 +-
.../dataaccess/db/CorePluginDAOTest.java | 2 +-
.../server/dataaccess/db/DataDAOTest.java | 6 +-
.../dataaccess/db/DatabaseCreationUtil.java | 9 +-
.../server/dataaccess/db/DeletionDAOTest.java | 2 +-
.../db/EntityOperationsLogDAOTest.java | 2 +-
.../db/EntityPropertyTypeDAOTest.java | 18 +-
.../db/EntityResolverQueryTest.java | 2 +-
.../server/dataaccess/db/EventDAOTest.java | 2 +-
.../db/GridCustomColumnDAOTest.java | 2 +-
.../db/GridCustomFilterDAOTest.java | 2 +-
.../dataaccess/db/MetaprojectDAOTest.java | 2 +-
.../server/dataaccess/db/PermIdDAOTest.java | 2 +-
.../dataaccess/db/SqlDataMigrationTest.java | 2 +-
.../dataaccess/db/SqlMigrationTest.java | 2 +-
.../db/search/LuceneQueryBuilderTest.java | 4 +-
.../DataSetRegistrationSummaryTaskTest.java | 2 +-
.../task/MaterialExternalDBSyncTaskTest.java | 2 +-
.../util/AnnotationAppliedTestCase.java | 27 +-
.../server/util/SimpleDateRendererTest.java | 12 +-
.../server/util/TimeIntervalChecker.java | 13 +-
.../generic/shared/DataSetInfoHelperTest.java | 4 +-
.../openbis/generic/shared/INormalizer.java | 2 -
.../shared/ServletParamsParsingTestUtils.java | 2 +-
.../generic/shared/api/v1/TranslatorTest.java | 28 +-
.../shared/api/v1/dto/DataSetBuilder.java | 14 +-
.../shared/api/v1/dto/DataSetTest.java | 2 +-
.../shared/api/v1/dto/DataSetTypeTest.java | 2 +-
.../shared/api/v1/dto/SampleBuilder.java | 20 +-
.../generic/shared/api/v1/dto/SampleTest.java | 2 +-
.../PropertiesBasedDataSetFilterTest.java | 8 +-
.../v1/filter/TypeBasedDataSetFilterTest.java | 2 -
.../shared/basic/BasicURLEncoderTest.java | 4 +-
.../shared/basic/ExpressionUtilTest.java | 6 +-
.../openbis/generic/shared/basic/Row.java | 4 +-
.../shared/basic/WebAppsPropertiesTest.java | 6 +-
.../shared/basic/dto/PrimitiveValueTest.java | 4 +-
.../generic/shared/basic/dto/WebAppTest.java | 8 +-
.../basic/dto/builders/DataStoreBuilder.java | 8 +-
.../basic/dto/builders/PropertyBuilder.java | 3 +-
.../shared/basic/utils/GroupByMapTest.java | 2 +-
.../coreplugin/CorePluginsInjectorTest.java | 2 +-
.../builders/AbstractEntityTypePEBuilder.java | 2 +-
.../shared/dto/builders/SamplePEBuilder.java | 27 +-
.../JythonManagedPropertyEvaluatorTest.java | 2 +-
.../NewSampleParserObjectFactoryTest.java | 32 +-
.../UpdatedSampleParserObjectFactoryTest.java | 28 +-
.../generic/shared/util/CacheManagerTest.java | 58 +-
.../generic/shared/util/EntityHelperTest.java | 2 +-
.../application/dataset/CheckDataSet.java | 3 +-
.../dataset/GenericDataSetViewerTest.java | 8 +-
.../GenericExperimentRegistrationTest.java | 1 -
.../GenericExperimentViewerTest.java | 5 +-
.../sample/GenericSampleRegistrationTest.java | 3 +-
.../sample/GenericSampleViewerTest.java | 2 +-
.../client/application/sample/Property.java | 11 +-
.../remoteapitest/RemoteApiTestCase.java | 5 +-
.../AbstractDataSetAssignmentTestCase.java | 1 +
.../AbstractEntityDeletionTestCase.java | 214 +-
...ssignDataSetToExperimentAndSampleTest.java | 2 +-
...oExperimentAndSampleViaDropBoxAPITest.java | 8 +-
.../AssignExperimentToProjectTest.java | 2 +-
.../systemtest/AssignProjectToSpaceTest.java | 2 +-
.../AssignSampleToExperimentTest.java | 12 +-
...gnSampleToExperimentViaDropBoxAPITest.java | 12 +-
.../systemtest/AssignSampleToSpaceTest.java | 4 +-
.../systemtest/AttachmentUploadTest.java | 39 +-
.../systemtest/AuthenticationSystemTest.java | 4 +-
.../systemtest/EntityDeletionTest.java | 4 +-
.../systemtest/EntityOperationTest.java | 12 +-
.../openbis/systemtest/FilterSystemTest.java | 4 +-
.../systemtest/RegisterDataSetTest.java | 68 +-
.../openbis/systemtest/SystemTestCase.java | 2 +-
.../systemtest/TypedTableAssertions.java | 15 +-
.../UnassignSampleFromExperimentTest.java | 4 +-
.../UnassignSampleFromSpaceTest.java | 8 +-
.../systemtest/UpdateDataSetParentsTest.java | 8 +-
.../openbis/systemtest/UpdateDataSetTest.java | 59 +-
.../UpdateSampleContainmentTest.java | 12 +-
.../systemtest/UpdateSampleParentsTest.java | 12 +-
.../api/common/json/JsonApiClient.java | 40 +-
.../api/v1/GeneralInformationServiceTest.java | 2 +-
.../CommonServerAuthorizationTest.java | 4 +-
.../ETLServiceAuthorizationTest.java | 4 +-
.../authorization/PersonManagementTest.java | 1 +
.../openbis/systemtest/base/BaseTest.java | 2 +-
.../base/RelationshipServiceStub.java | 4 +-
.../systemtest/base/builder/Builder.java | 2 +-
.../base/builder/DataSetUpdateBuilder.java | 2 +-
.../base/builder/ExternalDataBuilder.java | 12 +-
.../base/builder/UpdateBuilder.java | 2 +-
.../entitygraph/EntityGraphManager.java | 281 +-
.../MultiThreadOptimisticLockingTestCase.java | 3 +-
...ltiThreadProjectOptimisticLockingTest.java | 8 +-
...ultiThreadSampleOptimisticLockingTest.java | 8 +-
.../optimistic_locking/ToolBox.java | 10 +-
.../plugin/generic/EntityValidationTest.java | 4 +-
.../generic/FileFormatTypeHeadlessTest.java | 1 -
.../plugin/query/QuerySystemTestCase.java | 5 +-
...ampleToSampleRelationshipsHistoryTest.java | 2 +-
.../cisd/openbis/util/LogRecordingUtils.java | 11 +-
650 files changed, 6768 insertions(+), 4540 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
index e69de29bb2d..2b06d92ab77 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
@@ -0,0 +1,3387 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+import java.util.UUID;
+
+import javax.servlet.http.HttpServletRequest;
+
+import org.apache.commons.collections.CollectionUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.Complete;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.LinkedDataCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.PhysicalDataCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.FileFormatTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.LocatorTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.StorageFormatPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgress;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgressListener;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.OperationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.dataset.ICreateDataSetExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.ListSampleTechIdByIdentifier;
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.authentication.DefaultSessionManager;
+import ch.systemsx.cisd.authentication.DummyAuthenticationService;
+import ch.systemsx.cisd.authentication.IAuthenticationService;
+import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
+import ch.systemsx.cisd.common.servlet.RequestContextProviderAdapter;
+import ch.systemsx.cisd.openbis.common.conversation.context.ServiceConversationsThreadContext;
+import ch.systemsx.cisd.openbis.common.conversation.progress.IServiceConversationProgressListener;
+import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
+import ch.systemsx.cisd.openbis.generic.server.api.v1.SearchCriteriaToDetailedSearchCriteriaTranslator;
+import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationServiceUtils;
+import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
+import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
+import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AtomicOperationsPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodePredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetUpdatesPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ExistingSampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ExistingSpaceIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ExperimentPermIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ListSampleCriteriaPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ListSamplesByPropertyPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.NewExperimentPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.NewSamplePredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.NewSamplesWithTypePredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ProjectPermIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SamplePermIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleUpdatesPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SpaceIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ProjectValidator;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleValidator;
+import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
+import ch.systemsx.cisd.openbis.generic.server.batch.DataSetBatchUpdate;
+import ch.systemsx.cisd.openbis.generic.server.batch.DataSetCheckBeforeBatchUpdate;
+import ch.systemsx.cisd.openbis.generic.server.batch.SampleBatchRegistration;
+import ch.systemsx.cisd.openbis.generic.server.batch.SampleCheckBeforeUpdate;
+import ch.systemsx.cisd.openbis.generic.server.batch.SampleUpdate;
+import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.generic.server.business.IServiceConversationClientManagerLocal;
+import ch.systemsx.cisd.openbis.generic.server.business.IServiceConversationServerManagerLocal;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityCodeGenerator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityObjectIdHelper;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IAuthorizationGroupBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IMetaprojectBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISpaceBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.experimentlister.ExperimentLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.util.DataSetRegistrationCache;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDataSourceManager;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IMetaprojectDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.IFullTextIndexUpdateScheduler;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.IndexUpdateOperation;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.IServiceForDataStoreServer;
+import ch.systemsx.cisd.openbis.generic.shared.LogMessagePrefixGenerator;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchableEntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.EntityOperationsState;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Attachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AttachmentHolderKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AttachmentWithContent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AuthorizationGroup;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentFetchOption;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentFetchOptions;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Grantee;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocationNode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MetaprojectAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MetaprojectAssignmentsFetchOption;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterialWithType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMetaproject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyTypeWithVocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleAssignment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.IObjectId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentPermIdId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.metaproject.IMetaprojectId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.metaproject.MetaprojectIdentifierId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetShareId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityCollectionForCreationOrUpdate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataManagementSystemPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationHolderDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewLinkDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewRoleAssignment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PermId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpaceRoleAssignment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
+import ch.systemsx.cisd.openbis.generic.shared.translator.AttachmentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.AuthorizationGroupTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTypePropertyTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypePropertyTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataManagementSystemTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypePropertyTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.RoleAssignmentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypePropertyTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SimpleDataSetHelper;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SpaceTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForDataStoreServer>
+ implements IServiceForDataStoreServer
+{
+
+ @Private
+ static final EnumSet<DataSetFetchOption> DATASET_FETCH_OPTIONS_FILE_DATASETS = EnumSet.of(
+ DataSetFetchOption.BASIC, DataSetFetchOption.EXPERIMENT, DataSetFetchOption.SAMPLE);
+
+ private final IDAOFactory daoFactory;
+
+ private final IDataStoreServiceFactory dssFactory;
+
+ private final TrustedCrossOriginDomainsProvider trustedOriginDomainProvider;
+
+ private final IETLEntityOperationChecker entityOperationChecker;
+
+ private final ISessionManager<Session> sessionManagerForEntityOperation;
+
+ private final IDataStoreServiceRegistrator dataStoreServiceRegistrator;
+
+ private final IDataStoreDataSourceManager dataSourceManager;
+
+ private IServiceConversationClientManagerLocal conversationClient;
+
+ private IServiceConversationServerManagerLocal conversationServer;
+
+ private IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
+
+ @Autowired
+ private ICreateDataSetExecutor createDataSetExecutor;
+
+ private long timeout = 5; // minutes
+
+ public ServiceForDataStoreServer(IAuthenticationService authenticationService,
+ IOpenBisSessionManager sessionManager, IDAOFactory daoFactory,
+ ICommonBusinessObjectFactory boFactory, IDataStoreServiceFactory dssFactory,
+ TrustedCrossOriginDomainsProvider trustedOriginDomainProvider,
+ IETLEntityOperationChecker entityOperationChecker,
+ IDataStoreServiceRegistrator dataStoreServiceRegistrator,
+ IDataStoreDataSourceManager dataSourceManager,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory)
+ {
+ this(authenticationService, sessionManager, daoFactory, null, boFactory, dssFactory,
+ trustedOriginDomainProvider, entityOperationChecker, dataStoreServiceRegistrator,
+ dataSourceManager, new DefaultSessionManager<Session>(new SessionFactory(),
+ new LogMessagePrefixGenerator(), new DummyAuthenticationService(),
+ new RequestContextProviderAdapter(new IRequestContextProvider()
+ {
+ @Override
+ public HttpServletRequest getHttpServletRequest()
+ {
+ return null;
+ }
+ }),
+ 30),
+ managedPropertyEvaluatorFactory, null);
+ }
+
+ ServiceForDataStoreServer(IAuthenticationService authenticationService,
+ IOpenBisSessionManager sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager, ICommonBusinessObjectFactory boFactory,
+ IDataStoreServiceFactory dssFactory,
+ TrustedCrossOriginDomainsProvider trustedOriginDomainProvider,
+ IETLEntityOperationChecker entityOperationChecker,
+ IDataStoreServiceRegistrator dataStoreServiceRegistrator,
+ IDataStoreDataSourceManager dataSourceManager,
+ ISessionManager<Session> sessionManagerForEntityOperation,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory, ICreateDataSetExecutor createDataSetExecutor)
+ {
+ super(authenticationService, sessionManager, daoFactory, propertiesBatchManager, boFactory);
+ this.daoFactory = daoFactory;
+ this.dssFactory = dssFactory;
+ this.trustedOriginDomainProvider = trustedOriginDomainProvider;
+ this.entityOperationChecker = entityOperationChecker;
+ this.dataStoreServiceRegistrator = dataStoreServiceRegistrator;
+ this.dataSourceManager = dataSourceManager;
+ this.sessionManagerForEntityOperation = sessionManagerForEntityOperation;
+ this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
+ this.createDataSetExecutor = createDataSetExecutor;
+ }
+
+ @Override
+ public IServiceForDataStoreServer createLogger(IInvocationLoggerContext context)
+ {
+ return new ServiceForDataStoreServerLogger(getSessionManager(), context);
+ }
+
+ @Override
+ public int getVersion()
+ {
+ return IServer.VERSION;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public DatabaseInstance getHomeDatabaseInstance(final String sessionToken)
+ {
+ final DatabaseInstance result = new DatabaseInstance();
+ result.setCode("CISD");
+ result.setHomeDatabase(true);
+ result.setId(1L);
+ String uuid = getDatabaseInstanceUUID();
+ result.setIdentifier(uuid);
+ result.setUuid(uuid);
+ return result;
+ }
+
+ private String getDatabaseInstanceUUID()
+ {
+ List<DataStorePE> stores = daoFactory.getDataStoreDAO().listDataStores();
+ if (stores.size() == 0)
+ {
+ return UUID.randomUUID().toString().toUpperCase();
+ } else
+ {
+ return stores.get(0).getDatabaseInstanceUUID();
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void registerDataStoreServer(String sessionToken, DataStoreServerInfo info)
+ {
+ Session session = getSession(sessionToken);
+
+ String dssSessionToken = info.getSessionToken();
+ String dssURL = checkVersion(info, session, dssSessionToken);
+ IDataStoreDAO dataStoreDAO = daoFactory.getDataStoreDAO();
+ DataStorePE dataStore = dataStoreDAO.tryToFindDataStoreByCode(info.getDataStoreCode());
+ if (dataStore == null)
+ {
+ dataStore = new DataStorePE();
+ dataStore.setDatabaseInstanceUUID(getDatabaseInstanceUUID());
+ }
+ dataStore.setCode(info.getDataStoreCode());
+ dataStore.setDownloadUrl(info.getDownloadUrl());
+ dataStore.setRemoteUrl(dssURL);
+ dataStore.setSessionToken(dssSessionToken);
+ dataStore.setArchiverConfigured(info.isArchiverConfigured());
+ dataStore.setServices(new HashSet<DataStoreServicePE>()); // services will be set by the
+ // dataStoreServiceRegistrator
+ // setServices(dataStore, info.getServicesDescriptions(), dataStoreDAO);
+ dataStoreDAO.createOrUpdateDataStore(dataStore);
+ dataStoreServiceRegistrator.setServiceDescriptions(dataStore,
+ info.getServicesDescriptions());
+ dataSourceManager.handle(info.getDataStoreCode(), info.getDataSourceDefinitions());
+
+ conversationClient.setDataStoreInformation(dssURL, info.getTimeoutInMinutes());
+ conversationServer.setDataStoreInformation(info.getDataStoreCode(), dssURL,
+ info.getTimeoutInMinutes());
+ }
+
+ private String checkVersion(DataStoreServerInfo info, Session session, String dssSessionToken)
+ {
+ int port = info.getPort();
+ String remoteHost = session.getRemoteHost() + ":" + port;
+ String dssURL = (info.isUseSSL() ? "https://" : "http://") + remoteHost;
+ checkVersion(dssSessionToken, dssURL);
+ return dssURL;
+ }
+
+ private void checkVersion(String dssSessionToken, final String dssURL)
+ {
+ final IDataStoreService service = dssFactory.create(dssURL, timeout * 60 * 1000);
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Obtain version of Data Store Server at " + dssURL);
+ }
+ int dssVersion = service.getVersion(dssSessionToken);
+ if (IDataStoreService.VERSION != dssVersion)
+ {
+ String msg =
+ "Data Store Server version is " + dssVersion + " instead of "
+ + IDataStoreService.VERSION;
+ notificationLog.error(msg);
+ throw new ConfigurationFailureException(msg);
+ }
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Data Store Server (version " + dssVersion + ") registered for "
+ + dssURL);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public String createPermId(final String sessionToken) throws UserFailureException
+ {
+ checkSession(sessionToken); // throws exception if invalid sessionToken
+ return daoFactory.getPermIdDAO().createPermId();
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> createPermIds(String sessionToken, int n) throws UserFailureException
+ {
+ checkSession(sessionToken);
+ return daoFactory.getPermIdDAO().createPermIds(n);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public long drawANewUniqueID(String sessionToken) throws UserFailureException
+ {
+ checkSession(sessionToken);
+ return daoFactory.getCodeSequenceDAO().getNextCodeSequenceId();
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<Experiment> listExperiments(String sessionToken,
+ @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) List<ExperimentIdentifier> experimentIdentifiers,
+ ExperimentFetchOptions experimentFetchOptions)
+ {
+ if (sessionToken == null)
+ {
+ throw new IllegalArgumentException("SessionToken was null");
+ }
+ if (experimentIdentifiers == null)
+ {
+ throw new IllegalArgumentException("ExperimentIdentifiers were null");
+ }
+ if (experimentFetchOptions == null)
+ {
+ throw new IllegalArgumentException("ExperimentFetchOptions were null");
+ }
+
+ checkSession(sessionToken);
+
+ if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC,
+ ExperimentFetchOption.METAPROJECTS))
+ {
+ ExperimentLister lister =
+ new ExperimentLister(getDAOFactory(), getSession(sessionToken)
+ .getBaseIndexURL());
+ return lister.listExperiments(experimentIdentifiers, experimentFetchOptions);
+ } else
+ {
+ List<Experiment> experiments = new ArrayList<Experiment>();
+ for (ExperimentIdentifier experimentIdentifier : experimentIdentifiers)
+ {
+ Experiment experiment = tryGetExperiment(sessionToken, experimentIdentifier);
+ if (experiment != null)
+ {
+ experiment.setFetchOptions(new ExperimentFetchOptions(ExperimentFetchOption
+ .values()));
+ experiments.add(experiment);
+ }
+ }
+ return experiments;
+ }
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<Experiment> listExperimentsForProjects(String sessionToken,
+ @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) List<ProjectIdentifier> projectIdentifiers,
+ ExperimentFetchOptions experimentFetchOptions)
+ {
+ if (sessionToken == null)
+ {
+ throw new IllegalArgumentException("SessionToken was null");
+ }
+ if (projectIdentifiers == null)
+ {
+ throw new IllegalArgumentException("ProjectIdentifiers were null");
+ }
+ if (experimentFetchOptions == null)
+ {
+ throw new IllegalArgumentException("ExperimentFetchOptions were null");
+ }
+
+ checkSession(sessionToken);
+
+ if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC,
+ ExperimentFetchOption.METAPROJECTS))
+ {
+ ExperimentLister lister =
+ new ExperimentLister(daoFactory, getSession(sessionToken).getBaseIndexURL());
+ return lister.listExperimentsForProjects(projectIdentifiers, experimentFetchOptions);
+ } else
+ {
+ List<Experiment> experiments = new ArrayList<Experiment>();
+ for (ProjectIdentifier projectIdentifier : projectIdentifiers)
+ {
+ List<Experiment> projectExperiments =
+ listExperiments(sessionToken, projectIdentifier);
+ if (projectExperiments != null)
+ {
+ for (Experiment projectExperiment : projectExperiments)
+ {
+ if (projectExperiment != null)
+ {
+ projectExperiment.setFetchOptions(new ExperimentFetchOptions(
+ ExperimentFetchOption.values()));
+ experiments.add(projectExperiment);
+ }
+ }
+
+ }
+ }
+ return experiments;
+ }
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public Experiment tryGetExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert experimentIdentifier != null : "Unspecified experiment identifier.";
+
+ final Session session = getSession(sessionToken);
+ ExperimentPE experiment = tryLoadExperimentByIdentifier(session, experimentIdentifier);
+ return translateExperimentWithMetaprojects(session, experiment);
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public Experiment tryGetExperimentByPermId(String sessionToken, @AuthorizationGuard(guardClass = ExperimentPermIdPredicate.class) PermId permId)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert permId != null : "Unspecified experiment perm id.";
+
+ final Session session = getSession(sessionToken);
+ ExperimentPE experiment = tryLoadExperimentByPermId(session, permId.getId());
+ return translateExperimentWithMetaprojects(session, experiment);
+ }
+
+ private Experiment translateExperimentWithMetaprojects(final Session session, ExperimentPE experiment)
+ {
+ if (experiment == null)
+ {
+ return null;
+ }
+ enrichWithProperties(experiment);
+
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
+
+ return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojectPEs), managedPropertyEvaluatorFactory,
+ LoadableFields.PROPERTIES);
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ @ReturnValueFilter(validatorClass = SampleValidator.class)
+ public List<Sample> listSamples(final String sessionToken,
+ @AuthorizationGuard(guardClass = ListSampleCriteriaPredicate.class)
+ final ListSampleCriteria criteria)
+ {
+ final Session session = getSession(sessionToken);
+ final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ return sampleLister.list(new ListOrSearchSampleCriteria(criteria));
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample tryGetSampleWithExperiment(final String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class)
+ final SampleIdentifier sampleIdentifier) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = getSession(sessionToken);
+ SamplePE sample = tryLoadSample(session, sampleIdentifier);
+ return translateSampleWithMetaProjects(session, sample);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample tryGetSampleByPermId(String sessionToken, @AuthorizationGuard(guardClass = SamplePermIdPredicate.class) PermId permId)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert permId != null : "Unspecified sample perm id.";
+
+ final Session session = getSession(sessionToken);
+ SamplePE sample = tryLoadSample(session, permId.getId());
+ return translateSampleWithMetaProjects(session, sample);
+ }
+
+ private Sample translateSampleWithMetaProjects(final Session session, SamplePE sample)
+ {
+ Collection<MetaprojectPE> metaprojects = Collections.emptySet();
+ if (sample != null)
+ {
+ HibernateUtils.initialize(sample.getProperties());
+ enrichWithProperties(sample.getExperiment());
+ metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), sample);
+ }
+ return SampleTranslator.translate(sample, session.getBaseIndexURL(), true, true,
+ MetaprojectTranslator.translate(metaprojects), managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public SampleIdentifier tryGetSampleIdentifier(String sessionToken, String samplePermID)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert samplePermID != null : "Unspecified sample perm ID.";
+
+ final SamplePE sample = daoFactory.getSampleDAO().tryToFindByPermID(samplePermID);
+ return (sample == null) ? null : sample.getSampleIdentifier();
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Map<String, SampleIdentifier> listSamplesByPermId(final String sessionToken,
+ List<String> samplePermIds)
+ {
+ List<SamplePE> samples =
+ daoFactory.getSampleDAO().listByPermID(new HashSet<String>(samplePermIds));
+
+ Map<String, SampleIdentifier> map = new HashMap<String, SampleIdentifier>();
+
+ for (SamplePE sample : samples)
+ {
+ map.put(sample.getPermId(), sample.getSampleIdentifier());
+ }
+
+ return map;
+ }
+
+ private ExperimentPE tryLoadExperimentByIdentifier(final Session session,
+ ExperimentIdentifier experimentIdentifier)
+ {
+ final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ return experimentBO.tryFindByExperimentIdentifier(experimentIdentifier);
+ }
+
+ private ExperimentPE tryLoadExperimentByPermId(final Session session,
+ String permId)
+ {
+ final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ return experimentBO.tryFindByExperimentId(new ExperimentPermIdId(permId));
+ }
+
+ private SamplePE tryLoadSample(final Session session, SampleIdentifier sampleIdentifier)
+ {
+ SamplePE result = null;
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ try
+ {
+ sampleBO.tryToLoadBySampleIdentifier(sampleIdentifier);
+ result = sampleBO.tryToGetSample();
+ } catch (UserFailureException ufe)
+ {
+ // sample does not exist
+ }
+ return result;
+ }
+
+ private SamplePE tryLoadSample(final Session session, String permId)
+ {
+ SamplePE result = null;
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ try
+ {
+ sampleBO.tryToLoadBySamplePermId(permId);
+ result = sampleBO.tryToGetSample();
+ } catch (UserFailureException ufe)
+ {
+ // sample does not exist
+ }
+ return result;
+ }
+
+ private void enrichWithProperties(ExperimentPE experiment)
+ {
+ if (experiment == null)
+ {
+ return;
+ }
+ HibernateUtils.initialize(experiment.getProperties());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public ExperimentType getExperimentType(String sessionToken, String experimentTypeCode)
+ throws UserFailureException
+ {
+ checkSession(sessionToken);
+
+ IEntityTypeDAO entityTypeDAO = getDAOFactory().getEntityTypeDAO(EntityKind.EXPERIMENT);
+ EntityTypePE entityType = entityTypeDAO.tryToFindEntityTypeByCode(experimentTypeCode);
+ if (entityType == null)
+ {
+ throw new UserFailureException("No Experiment type found with code '"
+ + experimentTypeCode + "'.");
+ }
+ assert entityType instanceof ExperimentTypePE : "Not an ExperimentTypePE: " + entityType;
+ ExperimentTypePE experimentType = (ExperimentTypePE) entityType;
+ HibernateUtils.initialize(experimentType.getExperimentTypePropertyTypes());
+ return ExperimentTypeTranslator.translate(experimentType, null);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public SampleType getSampleType(String sessionToken, String sampleTypeCode)
+ throws UserFailureException
+ {
+ checkSession(sessionToken);
+
+ ISampleTypeDAO sampleTypeDAO = getDAOFactory().getSampleTypeDAO();
+ SampleTypePE sampleType = sampleTypeDAO.tryFindSampleTypeByCode(sampleTypeCode);
+ if (sampleType == null)
+ {
+ throw new UserFailureException("No sample type found with code '" + sampleTypeCode
+ + "'.");
+ }
+ HibernateUtils.initialize(sampleType.getSampleTypePropertyTypes());
+ return SampleTypeTranslator.translate(sampleType, null);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public DataSetTypeWithVocabularyTerms getDataSetType(String sessionToken, String dataSetTypeCode)
+ throws UserFailureException
+ {
+ checkSession(sessionToken);
+
+ IDataSetTypeDAO dataSetTypeDAO = getDAOFactory().getDataSetTypeDAO();
+ DataSetTypePE dataSetType = dataSetTypeDAO.tryToFindDataSetTypeByCode(dataSetTypeCode);
+ if (dataSetType == null)
+ {
+ throw new UserFailureException("No data set type found with code '" + dataSetTypeCode
+ + "'.");
+ }
+ Set<DataSetTypePropertyTypePE> dataSetTypePropertyTypes =
+ dataSetType.getDataSetTypePropertyTypes();
+ HibernateUtils.initialize(dataSetTypePropertyTypes);
+ DataSetTypeWithVocabularyTerms result = new DataSetTypeWithVocabularyTerms();
+ result.setDataSetType(DataSetTypeTranslator.translate(dataSetType, null));
+ for (DataSetTypePropertyTypePE dataSetTypePropertyTypePE : dataSetTypePropertyTypes)
+ {
+ PropertyTypePE propertyTypePE = dataSetTypePropertyTypePE.getPropertyType();
+ PropertyTypeWithVocabulary propertyType = new PropertyTypeWithVocabulary();
+ propertyType.setCode(propertyTypePE.getCode());
+ VocabularyPE vocabulary = propertyTypePE.getVocabulary();
+ if (vocabulary != null)
+ {
+ Set<VocabularyTermPE> terms = vocabulary.getTerms();
+ HibernateUtils.initialize(terms);
+ propertyType.setTerms(VocabularyTermTranslator.translateTerms(terms));
+ }
+ result.addPropertyType(propertyType);
+ }
+ return result;
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<AbstractExternalData> listDataSetsByExperimentID(final String sessionToken,
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
+ final TechId experimentID) throws UserFailureException
+ {
+ Session session = getSession(sessionToken);
+ IDatasetLister datasetLister = createDatasetLister(session);
+ List<AbstractExternalData> datasets =
+ datasetLister.listByExperimentTechId(experimentID, true);
+ Collections.sort(datasets);
+ return datasets;
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<AbstractExternalData> listDataSetsBySampleID(final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
+ final TechId sampleId, final boolean showOnlyDirectlyConnected)
+ throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ final List<AbstractExternalData> datasets =
+ datasetLister.listBySampleTechId(sampleId, showOnlyDirectlyConnected);
+ Collections.sort(datasets);
+ return datasets;
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<AbstractExternalData> listDataSetsByCode(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ return datasetLister.listByDatasetCode(dataSetCodes);
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ @ReturnValueFilter(validatorClass = ProjectValidator.class)
+ public List<Project> listProjects(String sessionToken)
+ {
+ checkSession(sessionToken);
+ final List<ProjectPE> projects = getDAOFactory().getProjectDAO().listProjects();
+ Collections.sort(projects);
+ return ProjectTranslator.translate(projects);
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<Experiment> listExperiments(String sessionToken,
+ @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) ProjectIdentifier projectIdentifier)
+ {
+ final Session session = getSession(sessionToken);
+ final IExperimentTable experimentTable =
+ businessObjectFactory.createExperimentTable(session);
+ experimentTable.load(EntityType.ALL_TYPES_CODE, projectIdentifier);
+ final List<ExperimentPE> experiments = experimentTable.getExperiments();
+ return translateExperimentsWithMetaprojectAssignments(session, experiments);
+ }
+
+ private List<Experiment> translateExperimentsWithMetaprojectAssignments(final Session session, final List<ExperimentPE> experiments)
+ {
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), experiments, EntityKind.EXPERIMENT);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
+ Collections.sort(experiments);
+ return ExperimentTranslator.translate(experiments, session.getBaseIndexURL(), assignments,
+ managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public IEntityProperty[] tryGetPropertiesOfTopSample(final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
+ final SampleIdentifier sampleIdentifier) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = getSession(sessionToken);
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ SamplePE sample = sampleBO.getSample();
+ if (sample == null)
+ {
+ return null;
+ }
+ SamplePE top = sample.getTop();
+ Set<SamplePropertyPE> properties = top.getProperties();
+ HibernateUtils.initialize(properties);
+ return EntityPropertyTranslator.translate(properties.toArray(new SamplePropertyPE[0]),
+ new HashMap<PropertyTypePE, PropertyType>(), managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public IEntityProperty[] tryGetPropertiesOfSample(String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) SampleIdentifier sampleIdentifier) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = getSession(sessionToken);
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ SamplePE sample = sampleBO.getSample();
+ if (sample == null)
+ {
+ return null;
+ }
+ Set<SamplePropertyPE> properties = sample.getProperties();
+ HibernateUtils.initialize(properties);
+ return EntityPropertyTranslator.translate(properties.toArray(new SamplePropertyPE[0]),
+ new HashMap<PropertyTypePE, PropertyType>(), managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void registerEntities(String sessionToken, EntityCollectionForCreationOrUpdate collection)
+ throws UserFailureException
+ {
+ Session session = getSession(sessionToken);
+
+ for (NewExperiment experiment : collection.getNewExperiments())
+ {
+ registerExperiment(session, experiment);
+ }
+
+ DataSetRegistrationCache cache = new DataSetRegistrationCache();
+ for (NewExternalData dataSet : collection.getNewDataSets())
+ {
+ registerDataSetInternal(session, dataSet, cache);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public long registerExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = NewExperimentPredicate.class) NewExperiment experiment) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert experiment != null : "Unspecified new example.";
+
+ final Session session = getSession(sessionToken);
+ return registerExperiment(session, experiment);
+ }
+
+ private long registerExperiment(final Session session, NewExperiment experiment)
+ {
+ IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ experimentBO.define(experiment);
+ experimentBO.save();
+ return experimentBO.getExperiment().getId();
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void registerSamples(final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class)
+ final List<NewSamplesWithTypes> newSamplesWithType, String userIDOrNull)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ PersonPE registratorOrNull =
+ userIDOrNull != null ? getOrCreatePerson(sessionToken, userIDOrNull) : null;
+ for (NewSamplesWithTypes samples : newSamplesWithType)
+ {
+ registerSamples(session, samples, registratorOrNull);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public long registerSample(final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplePredicate.class)
+ final NewSample newSample, String userIDOrNull) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert newSample != null : "Unspecified new sample.";
+
+ final Session session = getSession(sessionToken);
+ SamplePE samplePE = registerSampleInternal(session, newSample, userIDOrNull);
+ return samplePE.getId();
+ }
+
+ private PersonPE getOrCreatePerson(String sessionToken, String userID)
+ {
+ PersonPE person = getDAOFactory().getPersonDAO().tryFindPersonByUserId(userID);
+ if (person != null)
+ {
+ return person;
+ }
+ List<PersonPE> persons = registerPersons(sessionToken, Collections.singletonList(userID));
+ return persons.get(0);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void updateSample(String sessionToken,
+ @AuthorizationGuard(guardClass = SampleUpdatesPredicate.class) SampleUpdatesDTO updates)
+ {
+ final Session session = getSession(sessionToken);
+ updateSampleInternal(updates, session);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void registerDataSet(final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
+ final SampleIdentifier sampleIdentifier, final NewExternalData externalData)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = getSession(sessionToken);
+ registerDataSetInternal(session, sampleIdentifier, externalData, new DataSetRegistrationCache());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void registerDataSet(final String sessionToken,
+ @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
+ final ExperimentIdentifier experimentIdentifier, final NewExternalData externalData)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert experimentIdentifier != null : "Unspecified experiment identifier.";
+
+ final Session session = getSession(sessionToken);
+ registerDataSetInternal(session, experimentIdentifier, externalData, new DataSetRegistrationCache());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void addPropertiesToDataSet(String sessionToken, List<NewProperty> properties,
+ String dataSetCode, @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
+ final SpaceIdentifier identifier) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.addPropertiesToDataSet(dataSetCode, properties);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public boolean isDataSetOnTrashCanOrDeleted(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
+ {
+ // Check if dataset is available for retrieval
+ DataPE dataSet = getDAOFactory().getDataDAO().tryToFindFullDataSetByCode(dataSetCode, false, false);
+ boolean isDataSetAvailable = dataSet != null;
+ // Check if the dataset is on the table, since can't be retrieved is on the trashcan
+ boolean isDataSetOnTrashCan = getDAOFactory().getDataDAO().exists(dataSetCode);
+ // Check if the dataset is finally deleted
+ boolean isDataSetDeleted = getDAOFactory().getEventDAO().tryFind(
+ dataSetCode,
+ ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType.DATASET,
+ ch.systemsx.cisd.openbis.generic.shared.dto.EventType.DELETION) != null;
+
+ return !isDataSetAvailable && (isDataSetOnTrashCan || isDataSetDeleted);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void updateShareIdAndSize(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode, String shareId, long size) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ IDataDAO dataSetDAO = getDAOFactory().getDataDAO();
+
+ DataPE dataSet = dataSetDAO.tryToFindFullDataSetByCode(dataSetCode, false, false);
+ if (dataSet == null) // Dataset is not available for retrieval
+ {
+ // Check if the dataset is on the table, since can't be retrieved is on the trashcan
+ boolean isDataSetOnTrashCan = getDAOFactory().getDataDAO().exists(dataSetCode);
+ // Check if the dataset is finally deleted
+ boolean isDataSetDeleted = getDAOFactory().getEventDAO().tryFind(
+ dataSetCode,
+ ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType.DATASET,
+ ch.systemsx.cisd.openbis.generic.shared.dto.EventType.DELETION) != null;
+
+ if (isDataSetOnTrashCan)
+ {
+ operationLog.info("The data set has been moved to the trashcan and the share will not be updated: " + dataSetCode);
+ return;
+ } else if (isDataSetDeleted)
+ {
+ operationLog.info("The data set has been deleted and the share will not be updated: " + dataSetCode);
+ return;
+ } else
+ {
+ throw new UserFailureException("Unknown data set, that has not been deleted, check for storage errors: " + dataSetCode);
+ }
+ }
+ ExternalDataPE externalData = dataSet.tryAsExternalData();
+ if (externalData == null)
+ {
+ throw new UserFailureException("Can't update share id and size of a virtual data set: "
+ + dataSetCode);
+ }
+ // data sets consisting out of empty folders have a size of 0,
+ // but we want the size of a data set to be strictly positive
+ long positiveSize = Math.max(1, size);
+ externalData.setShareId(shareId);
+ externalData.setSize(positiveSize);
+ dataSetDAO.updateDataSet(dataSet, session.tryGetPerson());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void updateDataSetStatuses(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes, final DataSetArchivingStatus newStatus,
+ boolean presentInArchive) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.updateStatuses(dataSetCodes, newStatus, presentInArchive);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public boolean compareAndSetDataSetStatus(String sessionToken, String dataSetCode,
+ DataSetArchivingStatus oldStatus, DataSetArchivingStatus newStatus,
+ boolean newPresentInArchive) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadByCode(dataSetCode);
+ return dataBO.compareAndSetDataSetStatus(oldStatus, newStatus, newPresentInArchive);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public int archiveDatasets(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> datasetCodes, boolean removeFromDataStore)
+ {
+ return super.archiveDatasets(sessionToken, datasetCodes, removeFromDataStore);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public int unarchiveDatasets(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> datasetCodes)
+ {
+ return super.unarchiveDatasets(sessionToken, datasetCodes);
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public IDatasetLocationNode tryGetDataSetLocation(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert dataSetCode != null : "Unspecified data set code.";
+
+ Session session = getSession(sessionToken);
+ IDatasetLister lister = businessObjectFactory.createDatasetLister(session);
+ return lister.listLocationsByDatasetCode(dataSetCode);
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public AbstractExternalData tryGetLocalDataSet(String sessionToken, String dataSetCode,
+ String dataStore) throws UserFailureException
+ {
+ AbstractExternalData dataSet = tryGetDataSet(sessionToken, dataSetCode);
+ if (dataSet != null && dataSet.getDataStore().getCode().equals(dataStore))
+ {
+ return dataSet;
+ }
+ return null;
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public AbstractExternalData tryGetDataSet(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert dataSetCode != null : "Unspecified data set code.";
+
+ Session session = getSession(sessionToken); // assert authenticated
+
+ IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadByCode(dataSetCode);
+ dataBO.enrichWithParentsAndExperiment();
+ dataBO.enrichWithChildren();
+ dataBO.enrichWithProperties();
+ dataBO.enrichWithContainedDataSets();
+ DataPE dataPE = dataBO.tryGetData();
+ if (null == dataPE)
+ {
+ return null;
+ }
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), dataPE);
+ return DataSetTranslator.translate(dataPE, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojects), managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public AbstractExternalData tryGetThinDataSet(String sessionToken, String dataSetCode) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert dataSetCode != null : "Unspecified data set code.";
+
+ Session session = getSession(sessionToken); // assert authenticated
+
+ IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadByCode(dataSetCode);
+ DataPE dataPE = dataBO.tryGetData();
+ if (null == dataPE)
+ {
+ return null;
+ }
+ return DataSetTranslator.translate(dataPE, session.getBaseIndexURL(),
+ Collections.<Metaproject> emptyList(), managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
+ public void checkInstanceAdminAuthorization(String sessionToken) throws UserFailureException
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_POWER_USER)
+ public void checkSpacePowerUserAuthorization(String sessionToken) throws UserFailureException
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public void checkDataSetAccess(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode) throws UserFailureException
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public void checkDataSetCollectionAccess(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes)
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_USER)
+ public void checkSpaceAccess(String sessionToken,
+ @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) SpaceIdentifier spaceId)
+ {
+ checkSession(sessionToken);
+ // do nothing, the access rights specified in method annotations are checked by a proxy
+ }
+
+ @Override
+ @RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<Sample> listSamplesByCriteria(final String sessionToken,
+ @AuthorizationGuard(guardClass = ListSamplesByPropertyPredicate.class)
+ final ListSamplesByPropertyCriteria criteria) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert criteria != null : "Unspecified criteria.";
+
+ Session session = getSession(sessionToken);
+ ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+ sampleTable.loadSamplesByCriteria(criteria);
+ List<SamplePE> samples = sampleTable.getSamples();
+
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), samples, EntityKind.SAMPLE);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
+
+ return SampleTranslator
+ .translate(samples, "", assignments, managedPropertyEvaluatorFactory);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<DataSetShareId> listShareIds(final String sessionToken, String dataStoreCode)
+ throws UserFailureException
+ {
+ Session session = getSession(sessionToken);
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ DataStorePE dataStore = loadDataStore(session, dataStoreCode);
+ return datasetLister.listAllDataSetShareIdsByDataStore(dataStore.getId());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<SimpleDataSetInformationDTO> listPhysicalDataSets(final String sessionToken,
+ String dataStoreCode) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final DataStorePE dataStore = loadDataStore(session, dataStoreCode);
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ final List<AbstractExternalData> dataSets =
+ datasetLister.listByDataStore(dataStore.getId(),
+ DATASET_FETCH_OPTIONS_FILE_DATASETS);
+ return SimpleDataSetHelper.filterAndTranslate(dataSets);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<SimpleDataSetInformationDTO> listOldestPhysicalDataSets(String sessionToken,
+ String dataStoreCode, int limit) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final DataStorePE dataStore = loadDataStore(session, dataStoreCode);
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ final List<AbstractExternalData> dataSets =
+ datasetLister.listByDataStore(dataStore.getId(), limit,
+ DATASET_FETCH_OPTIONS_FILE_DATASETS);
+ return SimpleDataSetHelper.filterAndTranslate(dataSets);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<SimpleDataSetInformationDTO> listOldestPhysicalDataSets(String sessionToken,
+ String dataStoreCode, Date youngerThan, int limit) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final DataStorePE dataStore = loadDataStore(session, dataStoreCode);
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ final List<AbstractExternalData> dataSets =
+ datasetLister.listByDataStore(dataStore.getId(), youngerThan, limit,
+ DATASET_FETCH_OPTIONS_FILE_DATASETS);
+ return SimpleDataSetHelper.filterAndTranslate(dataSets);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<SimpleDataSetInformationDTO> listPhysicalDataSetsWithUnknownSize(String sessionToken, String dataStoreCode, int chunkSize,
+ String dataSetCodeLowerLimit)
+ {
+ final Session session = getSession(sessionToken);
+ final DataStorePE dataStore = loadDataStore(session, dataStoreCode);
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ final List<AbstractExternalData> dataSets =
+ datasetLister.listByDataStoreWithUnknownSize(dataStore.getId(), chunkSize, dataSetCodeLowerLimit,
+ DATASET_FETCH_OPTIONS_FILE_DATASETS);
+ return SimpleDataSetHelper.filterAndTranslate(dataSets);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void updatePhysicalDataSetsSize(String sessionToken, Map<String, Long> sizeMap)
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.updateSizes(sizeMap);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AbstractExternalData> listAvailableDataSets(String sessionToken,
+ String dataStoreCode, ArchiverDataSetCriteria criteria)
+ {
+ Session session = getSession(sessionToken);
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ return datasetLister.listByArchiverCriteria(dataStoreCode, criteria);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AbstractExternalData> listDataSets(String sessionToken, String dataStoreCode,
+ TrackingDataSetCriteria criteria)
+ {
+ Session session = getSession(sessionToken);
+ DataStorePE dataStore =
+ getDAOFactory().getDataStoreDAO().tryToFindDataStoreByCode(dataStoreCode);
+ if (dataStore == null)
+ {
+ throw new UserFailureException("Unknown data store: " + dataStoreCode);
+ }
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ List<AbstractExternalData> allDataSets = datasetLister.listByTrackingCriteria(criteria);
+ List<AbstractExternalData> result = new ArrayList<AbstractExternalData>();
+ for (AbstractExternalData externalData : allDataSets)
+ {
+ if (dataStoreCode.equals(externalData.getDataStore().getCode()))
+ {
+ result.add(externalData);
+ }
+ }
+ return result;
+ }
+
+ private DataStorePE loadDataStore(Session session, String dataStoreCode)
+ {
+ DataStorePE dataStore =
+ getDAOFactory().getDataStoreDAO().tryToFindDataStoreByCode(dataStoreCode);
+ if (dataStore == null)
+ {
+ throw new UserFailureException(String.format("Unknown data store '%s'", dataStoreCode));
+ }
+ return dataStore;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<DeletedDataSet> listDeletedDataSets(String sessionToken,
+ Long lastSeenDeletionEventIdOrNull, Date maxDeletionDataOrNull)
+ {
+ checkSession(sessionToken);
+ return getDAOFactory().getEventDAO().listDeletedDataSets(lastSeenDeletionEventIdOrNull,
+ maxDeletionDataOrNull);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Collection<VocabularyTerm> listVocabularyTerms(String sessionToken, String vocabularyCode)
+ throws UserFailureException
+ {
+ checkSession(sessionToken);
+ VocabularyPE vocabularyOrNull =
+ getDAOFactory().getVocabularyDAO().tryFindVocabularyByCode(vocabularyCode);
+ if (vocabularyOrNull == null)
+ {
+ throw new UserFailureException(String.format("Vocabulary '%s' not found",
+ vocabularyCode));
+ }
+ return VocabularyTermTranslator.translateTerms(vocabularyOrNull.getTerms());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Vocabulary tryGetVocabulary(String sessionToken, String vocabularyCode)
+ {
+ checkSession(sessionToken);
+ VocabularyPE vocabularyOrNull =
+ getDAOFactory().getVocabularyDAO().tryFindVocabularyByCode(vocabularyCode);
+
+ if (vocabularyOrNull == null)
+ {
+ return null;
+ } else
+ {
+ return VocabularyTranslator.translate(vocabularyOrNull, true);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> generateCodes(String sessionToken, String prefix,
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind entityKind, int number)
+ {
+ checkSession(sessionToken);
+ return new EntityCodeGenerator(daoFactory).generateCodes(prefix, entityKind, number);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Person> listAdministrators(String sessionToken)
+ {
+ checkSession(sessionToken);
+ // Get all Persons in the DB
+ final List<PersonPE> persons = getDAOFactory().getPersonDAO().listPersons();
+
+ // Filter down to the admins
+ ArrayList<PersonPE> admins = new ArrayList<PersonPE>();
+ for (PersonPE person : persons)
+ {
+ for (final RoleAssignmentPE roleAssigment : person.getRoleAssignments())
+ {
+ if (roleAssigment.getSpace() == null
+ && roleAssigment.getRole().equals(RoleCode.ADMIN))
+ {
+ admins.add(person);
+ }
+ }
+ }
+ Collections.sort(admins);
+ return PersonTranslator.translate(admins);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Person tryPersonWithUserIdOrEmail(String sessionToken, String useridOrEmail)
+ {
+ checkSession(sessionToken);
+
+ PersonPE personPE = tryFindPersonForUserIdOrEmail(useridOrEmail);
+ return (null != personPE) ? PersonTranslator.translate(personPE) : null;
+ }
+
+ private PersonPE tryFindPersonForUserIdOrEmail(String userIdOrEmail)
+ {
+ if (userIdOrEmail == null)
+ {
+ return null;
+ }
+
+ // First search for a userId match
+ IPersonDAO personDao = getDAOFactory().getPersonDAO();
+ PersonPE person = personDao.tryFindPersonByUserId(userIdOrEmail);
+ if (null != person)
+ {
+ return person;
+ }
+ // Didn't find one -- try email
+ return personDao.tryFindPersonByEmail(userIdOrEmail);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample registerSampleAndDataSet(final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplePredicate.class)
+ final NewSample newSample, final NewExternalData externalData, String userIdOrNull)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert newSample != null : "Unspecified new sample.";
+
+ // Register the Sample
+ final Session session = getSession(sessionToken);
+ SamplePE samplePE = registerSampleInternal(session, newSample, userIdOrNull);
+
+ // Register the data set
+ registerDataSetInternal(getSession(sessionToken), samplePE, externalData, new DataSetRegistrationCache());
+ Sample result =
+ SampleTranslator.translate(samplePE, session.getBaseIndexURL(), null,
+ managedPropertyEvaluatorFactory);
+ return result;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample updateSampleAndRegisterDataSet(String sessionToken,
+ @AuthorizationGuard(guardClass = SampleUpdatesPredicate.class) SampleUpdatesDTO updates, NewExternalData externalData)
+ {
+ final Session session = getSession(sessionToken);
+
+ // Update the sample
+ final ISampleBO sampleBO = updateSampleInternal(updates, session);
+
+ // Register the data set
+ final SamplePE samplePE = sampleBO.getSample();
+ registerDataSetInternal(getSession(sessionToken), samplePE, externalData, new DataSetRegistrationCache());
+
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), samplePE);
+
+ Sample result =
+ SampleTranslator.translate(samplePE, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojectPEs),
+ managedPropertyEvaluatorFactory);
+ return result;
+ }
+
+ private ISampleBO updateSampleInternal(SampleUpdatesDTO updates, final Session session)
+ {
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.update(updates);
+ sampleBO.save();
+
+ return sampleBO;
+ }
+
+ private SamplePE registerSampleInternal(Session session, NewSample newSample,
+ String userIdOrNull)
+ {
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.define(newSample);
+ if (userIdOrNull != null)
+ {
+ sampleBO.getSample().setRegistrator(
+ getOrCreatePerson(session.getSessionToken(), userIdOrNull));
+ }
+ sampleBO.save();
+ SamplePE samplePE = sampleBO.getSample();
+ return samplePE;
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_ETL_SERVER })
+ public Space tryGetSpace(String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) SpaceIdentifier spaceIdentifier)
+ {
+
+ Session session = getSession(sessionToken);
+ ISpaceBO spaceBO = businessObjectFactory.createSpaceBO(session);
+ SpaceIdentifier identifier =
+ new SpaceIdentifier(spaceIdentifier.getSpaceCode());
+ try
+ {
+ spaceBO.load(identifier);
+ return SpaceTranslator.translate(spaceBO.getSpace());
+ } catch (UserFailureException ufe)
+ {
+ // space does not exist
+ return null;
+ }
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_ETL_SERVER })
+ public Project tryGetProject(String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ProjectIdentifier projectIdentifier)
+ {
+ final Session session = getSession(sessionToken);
+ final IProjectBO bo = businessObjectFactory.createProjectBO(session);
+ try
+ {
+ bo.loadByProjectIdentifier(projectIdentifier);
+ final ProjectPE project = bo.getProject();
+ return ProjectTranslator.translate(project);
+ } catch (UserFailureException ufe)
+ {
+ // project does not exist
+ return null;
+ }
+ }
+
+ @Override
+ @RolesAllowed(value = { RoleWithHierarchy.SPACE_ETL_SERVER })
+ public Project tryGetProjectByPermId(String sessionToken, @AuthorizationGuard(guardClass = ProjectPermIdPredicate.class) PermId permId)
+ throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ final IProjectBO bo = businessObjectFactory.createProjectBO(session);
+ try
+ {
+ bo.loadByPermId(permId.getId());
+ final ProjectPE project = bo.getProject();
+ return ProjectTranslator.translate(project);
+ } catch (UserFailureException ufe)
+ {
+ // project does not exist
+ return null;
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Material tryGetMaterial(String sessionToken, MaterialIdentifier materialIdentifier)
+ {
+ final Session session = getSession(sessionToken);
+ final IMaterialBO bo = businessObjectFactory.createMaterialBO(session);
+ try
+ {
+ bo.loadByMaterialIdentifier(materialIdentifier);
+ bo.enrichWithProperties();
+ MaterialPE materialPE = bo.getMaterial();
+ Collection<MetaprojectPE> metaprojectPEs = Collections.emptySet();
+ if (materialPE != null)
+ {
+ metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), materialPE);
+ }
+ return MaterialTranslator.translate(materialPE,
+ MetaprojectTranslator.translate(metaprojectPEs),
+ managedPropertyEvaluatorFactory);
+ } catch (UserFailureException ufe)
+ {
+ // material does not exist
+ return null;
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Metaproject tryGetMetaproject(String sessionToken, String name, String ownerId)
+ {
+ final Session session = getSession(sessionToken);
+ final IMetaprojectBO bo = businessObjectFactory.createMetaprojectBO(session);
+
+ MetaprojectPE pe = bo.tryFindByMetaprojectId(new MetaprojectIdentifierId(ownerId, name));
+
+ if (pe == null)
+ {
+ return null;
+ } else
+ {
+ return MetaprojectTranslator.translate(pe);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public AtomicEntityOperationResult performEntityOperations(String sessionToken,
+ @AuthorizationGuard(guardClass = AtomicOperationsPredicate.class) AtomicEntityOperationDetails operationDetails)
+ {
+ IServiceConversationProgressListener progressListener =
+ ServiceConversationsThreadContext.getProgressListener();
+
+ TechId registrationId = operationDetails.getRegistrationIdOrNull();
+
+ EntityOperationsInProgress.getInstance().addRegistrationPending(registrationId);
+
+ String sessionTokenForEntityOperation = null;
+ try
+ {
+ final Session session = getSession(sessionToken);
+ final String userId = operationDetails.tryUserIdOrNull();
+ boolean authorize = (userId != null);
+ Session sessionForEntityOperation = session;
+ if (authorize)
+ {
+ sessionTokenForEntityOperation =
+ sessionManagerForEntityOperation.tryToOpenSession(userId, "dummy password");
+ sessionForEntityOperation =
+ sessionManagerForEntityOperation.getSession(sessionTokenForEntityOperation);
+ injectPerson(sessionForEntityOperation, userId);
+ }
+
+ long spacesCreated =
+ createSpaces(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long materialsCreated =
+ createMaterials(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long projectsCreated =
+ createProjects(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long projectsUpdated =
+ updateProjects(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long vocabulariesUpdated =
+ updateVocabularies(sessionForEntityOperation, operationDetails,
+ progressListener, authorize);
+
+ long experimentsCreated =
+ createExperiments(sessionForEntityOperation, operationDetails,
+ progressListener, authorize);
+
+ long experimentsUpdates =
+ updateExperiments(sessionForEntityOperation, operationDetails,
+ progressListener, authorize);
+
+ long samplesCreated =
+ createSamples(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long samplesUpdated =
+ updateSamples(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long dataSetsCreated = createDataSetsV3(sessionForEntityOperation, operationDetails, progressListener, authorize);
+
+ long dataSetsUpdated =
+ updateDataSets(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long materialsUpdates =
+ updateMaterials(sessionForEntityOperation, operationDetails, progressListener,
+ authorize);
+
+ long metaprojectsCreated =
+ createMetaprojects(sessionForEntityOperation, operationDetails,
+ progressListener, authorize);
+
+ long metaprojectsUpdates =
+ updateMetaprojects(sessionForEntityOperation, operationDetails,
+ progressListener, authorize);
+
+ long spaceRolesAssigned = assignSpaceRoles(sessionForEntityOperation, operationDetails, progressListener, authorize);
+
+ long spaceRolesRevoked = revokeSpaceRoles(sessionForEntityOperation, operationDetails, progressListener, authorize);
+
+ // If the id is not null, the caller wants to persist the fact that the operation was
+ // invoked and completed;
+ // if the id is null, the caller does not care.
+ if (null != registrationId)
+ {
+ daoFactory.getEntityOperationsLogDAO().addLogEntry(registrationId.getId());
+ }
+
+ return new AtomicEntityOperationResult(spacesCreated, projectsCreated, projectsUpdated,
+ materialsCreated, materialsUpdates, experimentsCreated, experimentsUpdates,
+ samplesCreated, samplesUpdated, dataSetsCreated, dataSetsUpdated,
+ metaprojectsCreated, metaprojectsUpdates, vocabulariesUpdated, spaceRolesAssigned, spaceRolesRevoked);
+ } catch (org.hibernate.StaleObjectStateException e)
+ {
+ throw new UserFailureException("The operation has failed due to conflict with simultanous operations.");
+ } finally
+ {
+ EntityOperationsInProgress.getInstance().removeRegistrationPending(registrationId);
+ if (sessionTokenForEntityOperation != null)
+ {
+ sessionManagerForEntityOperation.closeSession(sessionTokenForEntityOperation);
+ }
+ try
+ {
+ daoFactory.getSessionFactory().getCurrentSession().flush();
+ } catch (Exception e)
+ {
+ }
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public EntityOperationsState didEntityOperationsSucceed(String token, TechId registrationId)
+ {
+ if (registrationId == null)
+ {
+ return EntityOperationsState.NO_OPERATION;
+ }
+
+ if (EntityOperationsInProgress.getInstance().isRegistrationPending(registrationId))
+ {
+ return EntityOperationsState.IN_PROGRESS;
+ }
+
+ EntityOperationsLogEntryPE logEntry =
+ daoFactory.getEntityOperationsLogDAO().tryFindLogEntry(registrationId.getId());
+
+ if (logEntry != null)
+ {
+ return EntityOperationsState.OPERATION_SUCCEEDED;
+ } else
+ {
+ return EntityOperationsState.NO_OPERATION;
+ }
+ }
+
+ private long createSpaces(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ ArrayList<SpacePE> spacePEsCreated = new ArrayList<SpacePE>();
+ List<NewSpace> newSpaces = operationDetails.getSpaceRegistrations();
+ if (authorize)
+ {
+ checkSpaceCreationAllowed(session, newSpaces);
+ }
+
+ int index = 0;
+ for (NewSpace newSpace : newSpaces)
+ {
+ SpacePE spacePE =
+ registerSpaceInternal(session, newSpace, operationDetails.tryUserIdOrNull());
+ spacePEsCreated.add(spacePE);
+ progress.update("createSpaces", newSpaces.size(), ++index);
+ }
+ return index;
+ }
+
+ protected void checkSpaceCreationAllowed(Session session, List<NewSpace> newSpaces)
+ {
+ if (newSpaces != null && newSpaces.isEmpty() == false)
+ {
+ entityOperationChecker.assertSpaceCreationAllowed(session, newSpaces);
+ }
+ }
+
+ protected void checkSpaceRoleAssignmentAllowed(Session session, SpaceIdentifier space)
+ {
+ entityOperationChecker.assertSpaceRoleAssignmentAllowed(session, space);
+ }
+
+ private long updateVocabularies(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+
+ List<VocabularyUpdatesDTO> updates = operationDetails.getVocabularyUpdates();
+
+ for (VocabularyUpdatesDTO update : updates)
+ {
+ updateVocabulary(session, update);
+ }
+
+ return updates.size();
+ }
+
+ private void updateVocabulary(Session session, VocabularyUpdatesDTO updates)
+ {
+ final IVocabularyBO vocabularyBO = businessObjectFactory.createVocabularyBO(session);
+ vocabularyBO.update(updates);
+ }
+
+ private long createMaterials(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ MaterialHelper materialHelper =
+ new MaterialHelper(session, businessObjectFactory, getDAOFactory(),
+ getPropertiesBatchManager(), managedPropertyEvaluatorFactory);
+ Map<String, List<NewMaterial>> materialRegs = operationDetails.getMaterialRegistrations();
+ if (authorize)
+ {
+ checkMaterialCreationAllowed(session, materialRegs);
+ }
+
+ List<NewMaterialWithType> materials = materialHelper.convertMaterialRegistrationIntoMaterialsWithType(materialRegs);
+
+ Map<String, Set<String>> materialTypesWithMateiralProperties = materialHelper.getPropertyTypesOfMaterialType(materialRegs.keySet());
+
+ List<List<NewMaterialWithType>> materialGroups = MaterialGroupingDAG.groupByDepencies(materials, materialTypesWithMateiralProperties);
+ int index = 0;
+
+ for (List<NewMaterialWithType> materialsGroup : materialGroups)
+ {
+ materialHelper.registerMaterials(materialsGroup);
+ progress.update("createMaterials", materialRegs.size(), ++index);
+ }
+ return index;
+ }
+
+ private long updateMaterials(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ MaterialHelper materialHelper =
+ new MaterialHelper(session, businessObjectFactory, getDAOFactory(),
+ getPropertiesBatchManager(), managedPropertyEvaluatorFactory);
+
+ List<MaterialUpdateDTO> allMaterialUpdates = operationDetails.getMaterialUpdates();
+
+ if (authorize)
+ {
+ checkMaterialUpdateAllowed(session, allMaterialUpdates);
+ }
+
+ materialHelper.updateMaterials(allMaterialUpdates);
+
+ // in material helper call the update of materials - but this has to wait fo change of the
+ // material updates to a map
+ return allMaterialUpdates.size();
+ }
+
+ protected void checkMaterialCreationAllowed(Session session,
+ Map<String, List<NewMaterial>> materials)
+ {
+ if (materials != null && materials.isEmpty() == false)
+ {
+ entityOperationChecker.assertMaterialCreationAllowed(session, materials);
+ }
+ }
+
+ protected void checkMaterialUpdateAllowed(Session session,
+ List<MaterialUpdateDTO> materialUpdates)
+ {
+ if (materialUpdates != null && materialUpdates.isEmpty() == false)
+ {
+ entityOperationChecker.assertMaterialUpdateAllowed(session, materialUpdates);
+ }
+ }
+
+ private long updateMetaprojects(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ List<MetaprojectUpdatesDTO> updates = operationDetails.getMetaprojectUpdates();
+
+ for (MetaprojectUpdatesDTO update : updates)
+ {
+ updateMetaprojects(session, update);
+ }
+
+ return updates.size();
+ }
+
+ private void updateMetaprojects(Session session, MetaprojectUpdatesDTO update)
+ {
+ IMetaprojectBO metaprojectBO = businessObjectFactory.createMetaprojectBO(session);
+ metaprojectBO.loadDataByTechId(update.getMetaprojectId());
+
+ Metaproject updates = new Metaproject();
+ updates.setName(metaprojectBO.getMetaproject().getName());
+ updates.setDescription(update.getDescription());
+ metaprojectBO.update(updates);
+
+ metaprojectBO.addSamples(update.getAddedSamples());
+ metaprojectBO.removeSamples(update.getRemovedSamples());
+ metaprojectBO.addDataSets(update.getAddedDataSets());
+ metaprojectBO.removeDataSets(update.getRemovedDataSets());
+ metaprojectBO.addExperiments(update.getAddedExperiments());
+ metaprojectBO.removeExperiments(update.getRemovedExperiments());
+ metaprojectBO.addMaterials(update.getAddedMaterials());
+ metaprojectBO.removeMaterials(update.getRemovedMaterials());
+
+ metaprojectBO.save();
+ }
+
+ private long assignSpaceRoles(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progressListener, boolean authorize)
+ {
+ // see also ch.systemsx.cisd.openbis.generic.server.CommonServer.registerSpaceRole(String, RoleCode, SpaceIdentifier, Grantee)
+ List<SpaceRoleAssignment> spaceRoleAssignments = operationDetails.getSpaceRoleAssignments();
+ int index = 0;
+ int assignmentCount = 0;
+ for (SpaceRoleAssignment assignment : spaceRoleAssignments)
+ {
+ assignmentCount += assignment.getGrantees().size();
+ }
+
+ if (assignmentCount < 1)
+ {
+ return assignmentCount;
+ }
+
+ final IRoleAssignmentTable table = businessObjectFactory.createRoleAssignmentTable(session);
+
+ for (SpaceRoleAssignment assignment : spaceRoleAssignments)
+ {
+ RoleCode roleCode = assignment.getRoleCode();
+ SpaceIdentifier space = assignment.getSpaceIdentifier();
+ if (authorize)
+ {
+ checkSpaceRoleAssignmentAllowed(session, space);
+ }
+ for (Grantee grantee : assignment.getGrantees())
+ {
+ final NewRoleAssignment newRoleAssignment = new NewRoleAssignment();
+ newRoleAssignment.setGrantee(grantee);
+ newRoleAssignment.setSpaceIdentifier(space);
+ newRoleAssignment.setRole(roleCode);
+
+ table.add(newRoleAssignment);
+ progressListener.update("assignSpaceRole", assignmentCount, ++index);
+ }
+ }
+
+ table.save();
+ return index;
+ }
+
+ private long revokeSpaceRoles(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progressListener, boolean authorize)
+ {
+ // see also ch.systemsx.cisd.openbis.generic.server.CommonServer.deleteSpaceRole(String, RoleCode, SpaceIdentifier, Grantee)
+ // Did not refactor the above method to share code for fear of making merges to the release branch difficult
+ List<SpaceRoleAssignment> spaceRoleRevocations = operationDetails.getSpaceRoleRevocations();
+ int index = 0;
+ int assignmentCount = 0;
+ for (SpaceRoleAssignment assignment : spaceRoleRevocations)
+ {
+ assignmentCount += assignment.getGrantees().size();
+ }
+
+ if (assignmentCount < 1)
+ {
+ return assignmentCount;
+ }
+
+ for (SpaceRoleAssignment assignment : spaceRoleRevocations)
+ {
+ RoleCode roleCode = assignment.getRoleCode();
+ SpaceIdentifier space = assignment.getSpaceIdentifier();
+ for (Grantee grantee : assignment.getGrantees())
+ {
+ final RoleAssignmentPE roleAssignment =
+ getDAOFactory().getRoleAssignmentDAO().tryFindSpaceRoleAssignment(roleCode,
+ space.getSpaceCode(), grantee);
+ if (roleAssignment == null)
+ {
+ throw new UserFailureException("Given space role does not exist.");
+ }
+ final PersonPE personPE = session.tryGetPerson();
+ if (roleAssignment.getPerson() != null && roleAssignment.getPerson().equals(personPE)
+ && roleAssignment.getRole().equals(RoleCode.ADMIN))
+ {
+ boolean isInstanceAdmin = false;
+ for (final RoleAssignmentPE roleAssigment : personPE.getRoleAssignments())
+ {
+ if (roleAssigment.getSpace() == null
+ && roleAssigment.getRole().equals(RoleCode.ADMIN))
+ {
+ isInstanceAdmin = true;
+ }
+ }
+ if (isInstanceAdmin == false)
+ {
+ throw new UserFailureException(
+ "For safety reason you cannot give away your own space admin power. "
+ + "Ask instance admin to do that for you.");
+ }
+ }
+ getDAOFactory().getRoleAssignmentDAO().deleteRoleAssignment(roleAssignment);
+ progressListener.update("revokeSpaceRole", assignmentCount, ++index);
+ }
+ }
+
+ return index;
+ }
+
+ private long createMetaprojects(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ final List<NewMetaproject> metaprojectRegistrations =
+ operationDetails.getMetaprojectRegistrations();
+ int index = 0;
+ for (NewMetaproject metaproject : metaprojectRegistrations)
+ {
+ registerMetaproject(session, metaproject);
+ progress.update("createMetaProjects", metaprojectRegistrations.size(), ++index);
+ }
+ return index;
+ }
+
+ private MetaprojectPE registerMetaproject(final Session session, NewMetaproject metaproject)
+ {
+ IMetaprojectBO metaprojectBO = businessObjectFactory.createMetaprojectBO(session);
+
+ Metaproject registration = new Metaproject();
+ registration.setName(metaproject.getName());
+ registration.setDescription(metaproject.getDescription());
+ metaprojectBO.define(metaproject.getOwnerId(), registration);
+
+ metaprojectBO.addSamples(metaproject.getSamples());
+ metaprojectBO.addExperiments(metaproject.getExperiments());
+ metaprojectBO.addMaterials(metaproject.getMaterials());
+ metaprojectBO.addDataSets(metaproject.getDatasets());
+ metaprojectBO.save();
+ return metaprojectBO.getMetaproject();
+ }
+
+ private SpacePE registerSpaceInternal(Session session, NewSpace newSpace,
+ String registratorUserIdOrNull)
+ {
+ // create space
+ ISpaceBO groupBO = businessObjectFactory.createSpaceBO(session);
+ groupBO.define(newSpace.getCode(), newSpace.getDescription());
+ SpacePE space = groupBO.getSpace();
+
+ if (registratorUserIdOrNull != null)
+ {
+ space.setRegistrator(
+ getOrCreatePerson(session.getSessionToken(), registratorUserIdOrNull));
+ }
+ groupBO.save();
+
+ // create ADMIN role assignemnt
+ if (newSpace.getSpaceAdminUserId() != null)
+ {
+ IRoleAssignmentTable roleTable =
+ businessObjectFactory.createRoleAssignmentTable(session);
+ NewRoleAssignment assignment = new NewRoleAssignment();
+ SpaceIdentifier spaceIdentifier = new SpaceIdentifier(space.getCode());
+ assignment.setSpaceIdentifier(spaceIdentifier);
+ assignment.setRole(RoleCode.ADMIN);
+ Grantee grantee = Grantee.createPerson(newSpace.getSpaceAdminUserId());
+ assignment.setGrantee(grantee);
+ roleTable.add(assignment);
+ roleTable.save();
+ }
+ return space;
+
+ }
+
+ private long createProjects(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ ArrayList<ProjectPE> projectPEsCreated = new ArrayList<ProjectPE>();
+ List<NewProject> newProjects = operationDetails.getProjectRegistrations();
+ if (authorize)
+ {
+ checkProjectCreationAllowed(session, newProjects);
+ }
+ int index = 0;
+ for (NewProject newProject : newProjects)
+ {
+ ProjectPE projectPE =
+ registerProjectInternal(session, newProject, operationDetails.tryUserIdOrNull());
+ projectPEsCreated.add(projectPE);
+ progress.update("createProjects", newProjects.size(), ++index);
+ }
+ return index;
+ }
+
+ protected void checkProjectCreationAllowed(Session session, List<NewProject> newProjects)
+ {
+ if (newProjects != null && newProjects.isEmpty() == false)
+ {
+ entityOperationChecker.assertProjectCreationAllowed(session, newProjects);
+ }
+ }
+
+ private ProjectPE registerProjectInternal(Session session, NewProject newProject,
+ String registratorUserIdOrNull)
+ {
+ IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
+ ProjectIdentifier identifier =
+ new ProjectIdentifierFactory(newProject.getIdentifier()).createIdentifier();
+ projectBO
+ .define(identifier, newProject.getDescription(), newProject.getAttachments(), null);
+ if (registratorUserIdOrNull != null)
+ {
+ projectBO.getProject().setRegistrator(
+ getOrCreatePerson(session.getSessionToken(), registratorUserIdOrNull));
+ }
+ projectBO.save();
+
+ return projectBO.getProject();
+ }
+
+ private long updateProjects(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ ArrayList<ProjectPE> projectPEsUpdated = new ArrayList<ProjectPE>();
+ List<ProjectUpdatesDTO> projectsToUpdate = operationDetails.getProjectUpdates();
+ if (authorize)
+ {
+ checkProjectUpdateAllowed(session, projectsToUpdate);
+ }
+ int index = 0;
+ for (ProjectUpdatesDTO project : projectsToUpdate)
+ {
+ ProjectPE projectPE =
+ updateProjectInternal(session, project, operationDetails.tryUserIdOrNull());
+ projectPEsUpdated.add(projectPE);
+ progress.update("updateProjects", projectsToUpdate.size(), ++index);
+ }
+ return index;
+ }
+
+ protected void checkProjectUpdateAllowed(Session session,
+ List<ProjectUpdatesDTO> projectsToUpdate)
+ {
+ if (projectsToUpdate != null && projectsToUpdate.isEmpty() == false)
+ {
+ entityOperationChecker.assertProjectUpdateAllowed(session, projectsToUpdate);
+ }
+ }
+
+ private ProjectPE updateProjectInternal(Session session, ProjectUpdatesDTO projectToUpdate,
+ String registratorUserIdOrNull)
+ {
+ IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
+ if (projectToUpdate.getTechId() != null)
+ {
+ projectBO.loadDataByTechId(projectToUpdate.getTechId());
+ } else if (projectToUpdate.getPermId() != null)
+ {
+ projectBO.loadByPermId(projectToUpdate.getPermId());
+ } else
+ {
+ ProjectIdentifier identifier =
+ new ProjectIdentifierFactory(projectToUpdate.getIdentifier()).createIdentifier();
+ projectBO.loadByProjectIdentifier(identifier);
+ }
+ projectBO.update(projectToUpdate);
+ if (registratorUserIdOrNull != null)
+ {
+ projectBO.getProject().setModifier(
+ getOrCreatePerson(session.getSessionToken(), registratorUserIdOrNull));
+ }
+ projectBO.save();
+
+ return projectBO.getProject();
+ }
+
+ private long createSamples(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ List<NewSample> newSamples = operationDetails.getSampleRegistrations();
+
+ if (authorize)
+ {
+ authorizeSampleCreation(session, newSamples);
+ }
+ String userIdOrNull = operationDetails.tryUserIdOrNull();
+ PersonPE registratorOrNull = tryFindPersonForUserIdOrEmail(userIdOrNull);
+ final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+
+ List<List<NewSample>> sampleGroups = splitIntoDependencyGroups(newSamples);
+
+ for (List<NewSample> groupOfSamples : sampleGroups)
+ {
+ BatchOperationExecutor.executeInBatches(new SampleBatchRegistration(sampleTable,
+ groupOfSamples, registratorOrNull), getBatchSize(operationDetails), progress,
+ "createContainerSamples");
+ }
+ return newSamples.size();
+ }
+
+ /**
+ * Splits the samples using the grouping dag into groups, that can be executed in batches one after another, that samples in later batches depend
+ * only on the samples from earlier batches
+ */
+ private List<List<NewSample>> splitIntoDependencyGroups(List<NewSample> newSamples)
+ {
+ return SampleGroupingDAG.groupByDepencies(newSamples);
+ }
+
+ private void authorizeSampleCreation(Session session, List<NewSample> newSamples)
+ {
+ List<NewSample> instanceSamples = new ArrayList<NewSample>();
+ List<NewSample> spaceSamples = new ArrayList<NewSample>();
+
+ for (NewSample newSample : newSamples)
+ {
+ SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(newSample);
+ if (sampleIdentifier.isDatabaseInstanceLevel())
+ {
+ instanceSamples.add(newSample);
+ } else
+ {
+ spaceSamples.add(newSample);
+ }
+ }
+
+ checkInstanceSampleCreationAllowed(session, instanceSamples);
+ checkSpaceSampleCreationAllowed(session, spaceSamples);
+ }
+
+ private void checkInstanceSampleCreationAllowed(Session session, List<NewSample> instanceSamples)
+ {
+ if (instanceSamples.isEmpty() == false)
+ {
+ entityOperationChecker.assertInstanceSampleCreationAllowed(session, instanceSamples);
+ }
+ }
+
+ private void checkSpaceSampleCreationAllowed(Session session, List<NewSample> spaceSamples)
+ {
+ if (spaceSamples.isEmpty() == false)
+ {
+ entityOperationChecker.assertSpaceSampleCreationAllowed(session, spaceSamples);
+ }
+ }
+
+ private long updateSamples(final Session session,
+ AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ List<SampleUpdatesDTO> sampleUpdates = operationDetails.getSampleUpdates();
+ int sampleUpdateCount = sampleUpdates.size();
+ if (sampleUpdateCount < 1)
+ {
+ return 0;
+ }
+ progress.update("authorizingSampleUpdates", sampleUpdateCount, 0);
+ if (authorize)
+ {
+ checkSampleUpdatesAllowed(session, sampleUpdates);
+ }
+ progress.update("authorizingSampleUpdates", sampleUpdateCount, sampleUpdateCount);
+ final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+
+ BatchOperationExecutor.executeInBatches(new SampleCheckBeforeUpdate(sampleTable,
+ sampleUpdates), getBatchSize(operationDetails), progress,
+ "checkSamplesBeforeUpdate");
+
+ BatchOperationExecutor.executeInBatches(new SampleUpdate(sampleTable, sampleUpdates),
+ getBatchSize(operationDetails), progress, "updateSamples");
+
+ return sampleUpdateCount;
+ }
+
+ private void checkSampleUpdatesAllowed(final Session session,
+ List<SampleUpdatesDTO> sampleUpdates)
+ {
+ List<SampleUpdatesDTO> instanceSamples = new ArrayList<SampleUpdatesDTO>();
+ List<SampleUpdatesDTO> spaceSamples = new ArrayList<SampleUpdatesDTO>();
+ for (SampleUpdatesDTO sampleUpdate : sampleUpdates)
+ {
+ SampleIdentifier sampleIdentifier = sampleUpdate.getSampleIdentifier();
+ if (sampleIdentifier.isDatabaseInstanceLevel())
+ {
+ instanceSamples.add(sampleUpdate);
+ } else
+ {
+ spaceSamples.add(sampleUpdate);
+ }
+ }
+ checkInstanceSampleUpdateAllowed(session, instanceSamples);
+ checkSpaceSampleUpdateAllowed(session, spaceSamples);
+ }
+
+ private void checkInstanceSampleUpdateAllowed(Session session,
+ List<SampleUpdatesDTO> instanceSamples)
+ {
+ if (instanceSamples.isEmpty() == false)
+ {
+ entityOperationChecker.assertInstanceSampleUpdateAllowed(session, instanceSamples);
+ }
+ }
+
+ private void checkSpaceSampleUpdateAllowed(Session session, List<SampleUpdatesDTO> spaceSamples)
+ {
+ if (spaceSamples.isEmpty() == false)
+ {
+ entityOperationChecker.assertSpaceSampleUpdateAllowed(session, spaceSamples);
+ }
+ }
+
+ private long createDataSetsV3(Session session, AtomicEntityOperationDetails operationDetails,
+ final IServiceConversationProgressListener conversationProgress, boolean authorize)
+ {
+ if (operationDetails.getDataSetRegistrations() == null)
+ {
+ return 0;
+ }
+
+ if (authorize)
+ {
+ checkDataSetCreationAllowed(session, operationDetails.getDataSetRegistrations());
+ }
+
+ IOperationContext context = new OperationContext(session);
+ context.setAttribute(ListSampleTechIdByIdentifier.CONTAINER_SHORTCUT_ALLOWED_ATTRIBUTE, true);
+ context.addProgressListener(new IProgressListener()
+ {
+ @Override
+ public void onProgress(Stack<IProgress> progressStack)
+ {
+ if (progressStack.isEmpty() == false)
+ {
+ IProgress progress = progressStack.peek();
+ int totalItemsToProcess = progress.getTotalItemsToProcess() != null ? progress.getTotalItemsToProcess() : 0;
+ int numItemsProcessed = progress.getNumItemsProcessed() != null ? progress.getNumItemsProcessed() : 0;
+ conversationProgress.update(progress.getLabel(), totalItemsToProcess, numItemsProcessed);
+ }
+ }
+ });
+
+ List<DataSetCreation> creations = new LinkedList<DataSetCreation>();
+
+ for (NewExternalData newData : operationDetails.getDataSetRegistrations())
+ {
+ // Fields that were in V2 but are intentionally ignored in V3:
+ // - newData.getUserId() and newData.getUserEMail() fields were used in V2 to find a registrator (see in DataBO.tryToGetRegistrator()),
+ // but found registrator was anyway overwritten by RelationshipUtils.setExperimentForDataSet() call at the end of DataBO.define() method
+ // (a user from the session was used as registrator and modifier)
+ // - newData.getAssociatedSampleCode() field was never used in V2
+ // - newData.getRegistrationDate() field was never used in V2
+
+ DataSetCreation creation = new DataSetCreation();
+ creation.setCode(newData.getCode());
+ creation.setMeasured(newData.isMeasured());
+ creation.setDataProducer(newData.getDataProducerCode());
+ creation.setDataProductionDate(newData.getProductionDate());
+
+ // type
+ if (newData.getDataSetType() != null)
+ {
+ creation.setTypeId(new EntityTypePermId(newData.getDataSetType().getCode()));
+ }
+
+ // experiment
+ if (newData.getExperimentIdentifierOrNull() != null)
+ {
+ creation.setExperimentId(new ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier(newData
+ .getExperimentIdentifierOrNull().toString()));
+ }
+
+ // sample
+ injectSampleId(creation, newData);
+
+ // data store
+ if (newData.getDataStoreCode() != null)
+ {
+ creation.setDataStoreId(new DataStorePermId(newData.getDataStoreCode()));
+ }
+
+ // properties
+ if (newData.getDataSetProperties() != null)
+ {
+ for (NewProperty property : newData.getDataSetProperties())
+ {
+ creation.setProperty(property.getPropertyCode(), property.getValue());
+ }
+ }
+
+ // parents
+ if (newData.getParentDataSetCodes() != null)
+ {
+ List<IDataSetId> parentIds = new LinkedList<IDataSetId>();
+ for (String parentCode : newData.getParentDataSetCodes())
+ {
+ parentIds.add(new DataSetPermId(parentCode));
+ }
+ creation.setParentIds(parentIds);
+ }
+
+ if (newData instanceof NewContainerDataSet)
+ {
+ NewContainerDataSet newContainerData = (NewContainerDataSet) newData;
+
+ if (newContainerData.getContainedDataSetCodes() != null)
+ {
+ List<IDataSetId> componentIds = new LinkedList<IDataSetId>();
+ for (String componentCode : newContainerData.getContainedDataSetCodes())
+ {
+ componentIds.add(new DataSetPermId(componentCode));
+ }
+ creation.setComponentIds(componentIds);
+ }
+ } else if (newData instanceof NewLinkDataSet)
+ {
+ NewLinkDataSet newLinkData = (NewLinkDataSet) newData;
+
+ LinkedDataCreation linkCreation = new LinkedDataCreation();
+ linkCreation.setExternalCode(newLinkData.getExternalCode());
+ linkCreation.setExternalDmsId(new ExternalDmsPermId(newLinkData.getExternalDataManagementSystemCode()));
+
+ creation.setLinkedData(linkCreation);
+ } else
+ {
+ // newData is instance of NewExternalData or NewDataSet
+
+ PhysicalDataCreation physicalCreation = new PhysicalDataCreation();
+ physicalCreation.setLocation(newData.getLocation());
+ physicalCreation.setShareId(newData.getShareId());
+ physicalCreation.setSize(newData.getSize());
+ physicalCreation.setSpeedHint(newData.getSpeedHint());
+
+ // complete
+ if (newData.getComplete() != null)
+ {
+ Complete complete = null;
+ switch (newData.getComplete())
+ {
+ case T:
+ complete = Complete.YES;
+ break;
+ case F:
+ complete = Complete.NO;
+ break;
+ case U:
+ complete = Complete.UNKNOWN;
+ break;
+ default:
+ throw new IllegalArgumentException("Unsupported complete value: " + newData.getComplete());
+ }
+ physicalCreation.setComplete(complete);
+ }
+
+ // file format type
+ if (newData.getFileFormatType() != null)
+ {
+ physicalCreation.setFileFormatTypeId(new FileFormatTypePermId(newData.getFileFormatType().getCode()));
+ }
+
+ // locator type
+ if (newData.getLocatorType() != null)
+ {
+ physicalCreation.setLocatorTypeId(new LocatorTypePermId(newData.getLocatorType().getCode()));
+ }
+
+ // storage format
+ if (newData.getStorageFormat() != null)
+ {
+ physicalCreation.setStorageFormatId(new StorageFormatPermId(newData.getStorageFormat().getCode()));
+ }
+
+ creation.setPhysicalData(physicalCreation);
+ }
+
+ creations.add(creation);
+ }
+
+ List<DataSetPermId> ids = createDataSetExecutor.create(context, creations);
+ return ids.size();
+ }
+
+ private void injectSampleId(DataSetCreation creation, NewExternalData newData)
+ {
+ SampleIdentifier sampleIdentifier = newData.getSampleIdentifierOrNull();
+ String permId = newData.getSamplePermIdOrNull();
+ if (sampleIdentifier != null)
+ {
+ ISampleId sampleId;
+ if (permId != null)
+ {
+ sampleId = new SamplePermId(permId);
+ } else
+ {
+ sampleId = new ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier(
+ sampleIdentifier.toString());
+ }
+ creation.setSampleId(sampleId);
+ }
+ }
+
+ private void checkDataSetCreationAllowed(Session session,
+ List<? extends NewExternalData> dataSets)
+ {
+ if (dataSets != null && dataSets.isEmpty() == false)
+ {
+ entityOperationChecker.assertDataSetCreationAllowed(session, dataSets);
+ }
+ }
+
+ private long updateDataSets(final Session session,
+ AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ final List<DataSetBatchUpdatesDTO> dataSetUpdates = operationDetails.getDataSetUpdates();
+ final int dataSetUpdatesCount = dataSetUpdates.size();
+ if (dataSetUpdatesCount < 1)
+ {
+ return 0;
+ }
+
+ progress.update("authorizingDataSetUpdates", dataSetUpdatesCount, 0);
+ if (authorize)
+ {
+ checkDataSetUpdateAllowed(session, dataSetUpdates);
+ }
+ progress.update("authorizingDataSetUpdates", dataSetUpdatesCount, dataSetUpdatesCount);
+ final IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
+
+ BatchOperationExecutor.executeInBatches(new DataSetCheckBeforeBatchUpdate(dataSetTable,
+ dataSetUpdates), getBatchSize(operationDetails), progress,
+ "checkDataSetsBeforeUpdate");
+
+ BatchOperationExecutor.executeInBatches(
+ new DataSetBatchUpdate(dataSetTable, dataSetUpdates),
+ getBatchSize(operationDetails), progress, "updateDataSets");
+
+ return dataSetUpdatesCount;
+ }
+
+ private void checkDataSetUpdateAllowed(Session session, List<DataSetBatchUpdatesDTO> dataSets)
+ {
+ if (dataSets != null && dataSets.isEmpty() == false)
+ {
+ entityOperationChecker.assertDataSetUpdateAllowed(session, dataSets);
+ }
+ }
+
+ private IDataBO registerDataSetInternal(final Session session, NewExternalData dataSet, DataSetRegistrationCache cache)
+ {
+ SampleIdentifier sampleIdentifier = dataSet.getSampleIdentifierOrNull();
+ if (sampleIdentifier != null)
+ {
+ return registerDataSetInternal(session, sampleIdentifier, dataSet, cache);
+ } else
+ {
+ ExperimentIdentifier experimentIdentifier = dataSet.getExperimentIdentifierOrNull();
+ return registerDataSetInternal(session, experimentIdentifier, dataSet, cache);
+ }
+ }
+
+ private long createExperiments(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ final List<NewExperiment> experimentRegistrations =
+ operationDetails.getExperimentRegistrations();
+ if (authorize)
+ {
+ checkExperimentCreationAllowed(session, experimentRegistrations);
+ }
+ int index = 0;
+ for (NewExperiment experiment : experimentRegistrations)
+ {
+ registerExperiment(session, experiment);
+ progress.update("createExperiments", experimentRegistrations.size(), ++index);
+ }
+ return index;
+ }
+
+ protected void checkExperimentCreationAllowed(Session session,
+ List<NewExperiment> newExperiments)
+ {
+ if (newExperiments != null && newExperiments.isEmpty() == false)
+ {
+ entityOperationChecker.assertExperimentCreationAllowed(session, newExperiments);
+ }
+ }
+
+ private void updateExperiment(Session session, ExperimentUpdatesDTO updates)
+ {
+ final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ experimentBO.update(updates);
+ experimentBO.save();
+ }
+
+ private long updateExperiments(Session session, AtomicEntityOperationDetails operationDetails,
+ IServiceConversationProgressListener progress, boolean authorize)
+ {
+ List<ExperimentUpdatesDTO> updates = operationDetails.getExperimentUpdates();
+
+ if (authorize)
+ {
+ checkExperimentUpdateAllowed(session, updates);
+ }
+
+ for (ExperimentUpdatesDTO update : updates)
+ {
+ updateExperiment(session, update);
+ }
+
+ return updates.size();
+ }
+
+ protected void checkExperimentUpdateAllowed(Session session,
+ List<ExperimentUpdatesDTO> experimentUpdates)
+ {
+ if (experimentUpdates != null && experimentUpdates.isEmpty() == false)
+ {
+ entityOperationChecker.assertExperimentUpdateAllowed(session, experimentUpdates);
+ }
+ }
+
+ private IDataBO registerDataSetInternal(final Session session,
+ SampleIdentifier sampleIdentifier, NewExternalData externalData, DataSetRegistrationCache cache)
+ {
+ SamplePE sample = cache.getSamples().get(sampleIdentifier);
+
+ if (sample == null)
+ {
+ final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ sample = sampleBO.getSample();
+ cache.getSamples().put(sampleIdentifier, sample);
+ }
+
+ return registerDataSetInternal(session, sample, externalData, cache);
+ }
+
+ private IDataBO registerDataSetInternal(final Session session, SamplePE sample,
+ NewExternalData externalData, DataSetRegistrationCache cache)
+ {
+ final IDataBO dataBO = cache.getDataBO() != null ? cache.getDataBO() : businessObjectFactory.createDataBO(session);
+ cache.setDataBO(dataBO);
+
+ SourceType sourceType =
+ externalData.isMeasured() ? SourceType.MEASUREMENT : SourceType.DERIVED;
+ dataBO.setCache(cache);
+ dataBO.define(externalData, sample, sourceType);
+ dataBO.save();
+
+ boolean isContainer = externalData instanceof NewContainerDataSet;
+ if (isContainer)
+ {
+ dataBO.setContainedDataSets(sample.getExperiment(), sample, (NewContainerDataSet) externalData);
+ }
+
+ final String dataSetCode = dataBO.getData().getCode();
+ assert dataSetCode != null : "Data set code not specified.";
+
+ return dataBO;
+ }
+
+ private IDataBO registerDataSetInternal(final Session session,
+ ExperimentIdentifier experimentIdentifier, NewExternalData externalData, DataSetRegistrationCache cache)
+ {
+ if (false == cache.getExperiments().containsKey(experimentIdentifier))
+ {
+ cache.getExperiments().put(experimentIdentifier, tryLoadExperimentByIdentifier(session, experimentIdentifier));
+ }
+ ExperimentPE experiment = cache.getExperiments().get(experimentIdentifier);
+
+ if (experiment == null)
+ {
+ throw new UserFailureException("Unknown experiment '" + experimentIdentifier + "'.");
+ }
+ if (experiment.getDeletion() != null)
+ {
+ throw new UserFailureException("Data set can not be registered because experiment '"
+ + experiment.getIdentifier() + "' is in trash.");
+ }
+ final IDataBO externalDataBO = cache.getDataBO() != null ? cache.getDataBO() : businessObjectFactory.createDataBO(session);
+ cache.setDataBO(externalDataBO);
+
+ SourceType sourceType =
+ externalData.isMeasured() ? SourceType.MEASUREMENT : SourceType.DERIVED;
+ externalDataBO.setCache(cache);
+ externalDataBO.define(externalData, experiment, sourceType);
+ externalDataBO.save();
+
+ boolean isContainer = externalData instanceof NewContainerDataSet;
+ if (isContainer)
+ {
+ externalDataBO.setContainedDataSets(experiment, null, (NewContainerDataSet) externalData);
+ }
+
+ final String dataSetCode = externalDataBO.getData().getCode();
+ assert dataSetCode != null : "Data set code not specified.";
+
+ return externalDataBO;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria)
+ {
+ Session session = getSession(sessionToken);
+ DetailedSearchCriteria detailedSearchCriteria =
+ SearchCriteriaToDetailedSearchCriteriaTranslator.convert(getDAOFactory(),
+ SearchableEntityKind.SAMPLE, searchCriteria);
+ SearchHelper searchHelper =
+ new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ return searchHelper.searchForSamples(session.getUserName(), detailedSearchCriteria);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AbstractExternalData> searchForDataSets(String sessionToken,
+ SearchCriteria searchCriteria)
+ {
+ Session session = getSession(sessionToken);
+ DetailedSearchCriteria detailedSearchCriteria =
+ SearchCriteriaToDetailedSearchCriteriaTranslator.convert(getDAOFactory(),
+ SearchableEntityKind.DATA_SET, searchCriteria);
+ SearchHelper searchHelper =
+ new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ return searchHelper.searchForDataSets(session.getUserName(), detailedSearchCriteria);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Experiment> searchForExperiments(String sessionToken, SearchCriteria searchCriteria)
+ {
+ Session session = getSession(sessionToken);
+ DetailedSearchCriteria detailedSearchCriteria =
+ SearchCriteriaToDetailedSearchCriteriaTranslator.convert(getDAOFactory(), SearchableEntityKind.EXPERIMENT, searchCriteria);
+ SearchHelper searchHelper = new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ List<ExperimentPE> experiments = searchHelper.searchForExperiments(sessionToken, detailedSearchCriteria);
+ return translateExperimentsWithMetaprojectAssignments(session, experiments);
+ }
+
+ @Override
+ @RolesAllowed(value =
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<Material> listMaterials(String sessionToken, ListMaterialCriteria criteria,
+ boolean withProperties)
+ {
+ Session session = getSession(sessionToken);
+ IMaterialLister lister = businessObjectFactory.createMaterialLister(session);
+ ListMaterialCriteria criteriaWithIds = populateMissingTypeId(criteria);
+ return lister.list(criteriaWithIds, withProperties);
+ }
+
+ private ListMaterialCriteria populateMissingTypeId(ListMaterialCriteria criteria)
+ {
+ MaterialType materialTypeOrNull = criteria.tryGetMaterialType();
+ if (materialTypeOrNull != null && materialTypeOrNull.getId() == null)
+ {
+ String materialTypeCode = materialTypeOrNull.getCode();
+ EntityTypePE typeWithId =
+ daoFactory.getEntityTypeDAO(EntityKind.MATERIAL).tryToFindEntityTypeByCode(
+ materialTypeCode);
+ if (typeWithId == null)
+ {
+ throw UserFailureException.fromTemplate("Invalid material type '%s'",
+ materialTypeCode);
+ } else
+ {
+ MaterialType materialTypeWithId = new MaterialType();
+ materialTypeWithId.setId(typeWithId.getId());
+ materialTypeWithId.setCode(materialTypeCode);
+ return ListMaterialCriteria.createFromMaterialType(materialTypeWithId);
+ }
+ }
+
+ return criteria;
+
+ }
+
+ @Override
+ @SuppressWarnings("deprecation")
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void removeDataSetsPermanently(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes, String reason)
+ {
+ Session session = getSession(sessionToken);
+ IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
+ permanentlyDeleteDataSets(session, dataSetTable, dataSetCodes, reason, false);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void updateDataSet(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetUpdatesPredicate.class) DataSetUpdatesDTO dataSetUpdates)
+ {
+ final Session session = getSession(sessionToken);
+ final IDataBO dataSetBO = businessObjectFactory.createDataBO(session);
+ dataSetBO.update(dataSetUpdates);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> getTrustedCrossOriginDomains(String sessionToken)
+ {
+ return trustedOriginDomainProvider.getTrustedDomains();
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void setStorageConfirmed(String sessionToken, List<String> dataSetCodes)
+ {
+ checkSession(sessionToken);
+
+ List<Long> dataSetIds = new LinkedList<Long>();
+ for (String dataSetCode : dataSetCodes)
+ {
+
+ if (daoFactory.getDataDAO().confirmStorage(dataSetCode))
+ {
+ daoFactory.getPostRegistrationDAO().addDataSet(dataSetCode);
+ } else if (daoFactory.getDataDAO().exists(dataSetCode) == false)
+ {
+ throw new UserFailureException("Storage confirmation for a dataset: " + dataSetCode
+ + " failed because the data set has been already deleted.");
+ }
+
+ Long id = daoFactory.getDataDAO().tryToFindDataSetIdByCode(dataSetCode).getId();
+ dataSetIds.add(id);
+ }
+ IFullTextIndexUpdateScheduler indexUpdater =
+ daoFactory.getPersistencyResources().getIndexUpdateScheduler();
+ indexUpdater.scheduleUpdate(IndexUpdateOperation.reindex(DataPE.class,
+ dataSetIds));
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void markSuccessfulPostRegistration(String sessionToken, String dataSetCode)
+ {
+ checkSession(sessionToken);
+
+ daoFactory.getPostRegistrationDAO().removeDataSet(dataSetCode);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void notifyDatasetAccess(String sessionToken, String dataSetCode)
+ {
+ checkSession(sessionToken);
+
+ daoFactory.getDataDAO().updateAccessTimestamp(dataSetCode);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AbstractExternalData> listDataSetsForPostRegistration(String sessionToken,
+ String dataStoreCode)
+ {
+ Session session = getSession(sessionToken);
+
+ // find all datasets for registration
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ Collection<Long> allDataSetIds =
+ daoFactory.getPostRegistrationDAO().listDataSetsForPostRegistration();
+ List<AbstractExternalData> allDataSets = datasetLister.listByDatasetIds(allDataSetIds);
+
+ // find datastore
+ DataStorePE dataStore =
+ getDAOFactory().getDataStoreDAO().tryToFindDataStoreByCode(dataStoreCode);
+ if (dataStore == null)
+ {
+ throw new UserFailureException("Unknown data store: " + dataStoreCode);
+ }
+
+ // filter datasets by datastore
+ List<AbstractExternalData> result = new ArrayList<AbstractExternalData>();
+ for (AbstractExternalData externalData : allDataSets)
+ {
+ if (dataStoreCode.equals(externalData.getDataStore().getCode()))
+ {
+ result.add(externalData);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public void heartbeat(String token)
+ {
+ // do nothing
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public boolean doesUserHaveRole(String token, String user, String roleCode, String spaceOrNull)
+ {
+ return new AuthorizationServiceUtils(daoFactory, user).doesUserHaveRole(roleCode,
+ spaceOrNull);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> filterToVisibleDataSets(String token, String user, List<String> dataSetCodes)
+ {
+ return new AuthorizationServiceUtils(daoFactory, user).filterDataSetCodes(dataSetCodes);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> filterToVisibleExperiments(String token, String user,
+ List<String> experimentIds)
+ {
+ return new AuthorizationServiceUtils(daoFactory, user).filterExperimentIds(experimentIds);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> filterToVisibleSamples(String token, String user, List<String> sampleIds)
+ {
+ return new AuthorizationServiceUtils(daoFactory, user).filterSampleIds(sampleIds);
+ }
+
+ @Override
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ public List<? extends EntityTypePropertyType<?>> listPropertyDefinitionsForType(
+ String sessionToken, String code, EntityKind entityKind)
+ {
+ IEntityTypeDAO edao = daoFactory.getEntityTypeDAO(entityKind);
+ IEntityPropertyTypeDAO dao = daoFactory.getEntityPropertyTypeDAO(entityKind);
+
+ EntityTypePE type = edao.tryToFindEntityTypeByCode(code);
+ List<EntityTypePropertyTypePE> propertiesPE = dao.listEntityPropertyTypes(type);
+
+ if (entityKind == EntityKind.DATA_SET)
+ {
+ Collection<DataSetTypePropertyType> collection =
+ CollectionUtils.collect(propertiesPE,
+ DataSetTypePropertyTypeTranslator.TRANSFORMER);
+ return new LinkedList<DataSetTypePropertyType>(collection);
+ } else if (entityKind == EntityKind.SAMPLE)
+ {
+ Collection<SampleTypePropertyType> collection =
+ CollectionUtils.collect(propertiesPE,
+ SampleTypePropertyTypeTranslator.TRANSFORMER);
+ return new LinkedList<SampleTypePropertyType>(collection);
+ } else if (entityKind == EntityKind.EXPERIMENT)
+ {
+ Collection<ExperimentTypePropertyType> collection =
+ CollectionUtils.collect(propertiesPE,
+ ExperimentTypePropertyTypeTranslator.TRANSFORMER);
+ return new LinkedList<ExperimentTypePropertyType>(collection);
+ } else if (entityKind == EntityKind.MATERIAL)
+ {
+ Collection<MaterialTypePropertyType> collection =
+ CollectionUtils.collect(propertiesPE,
+ MaterialTypePropertyTypeTranslator.TRANSFORMER);
+ return new LinkedList<MaterialTypePropertyType>(collection);
+ } else
+ {
+ throw new IllegalArgumentException("Unsupported entity kind " + entityKind);
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public ExternalDataManagementSystem tryGetExternalDataManagementSystem(String token,
+ String externalDataManagementSystemCode)
+ {
+ checkSession(token);
+
+ ExternalDataManagementSystemPE externalSystem =
+ getDAOFactory().getExternalDataManagementSystemDAO()
+ .tryToFindExternalDataManagementSystemByCode(
+ externalDataManagementSystemCode);
+
+ if (externalSystem != null)
+ {
+ return ExternalDataManagementSystemTranslator.translate(externalSystem);
+ } else
+ {
+ return null;
+ }
+ }
+
+ private int getBatchSize(AtomicEntityOperationDetails details)
+ {
+ return details == null || details.getBatchSizeOrNull() == null ? BatchOperationExecutor
+ .getDefaultBatchSize() : details.getBatchSizeOrNull();
+ }
+
+ public void setConversationClient(IServiceConversationClientManagerLocal conversationClient)
+ {
+ this.conversationClient = conversationClient;
+ }
+
+ public void setConversationServer(IServiceConversationServerManagerLocal conversationServer)
+ {
+ this.conversationServer = conversationServer;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Metaproject> listMetaprojects(String sessionToken, String userId)
+ {
+ IMetaprojectDAO metaprojectDAO = daoFactory.getMetaprojectDAO();
+ PersonPE owner = daoFactory.getPersonDAO().tryFindPersonByUserId(userId);
+
+ if (owner == null)
+ {
+ throw new IllegalArgumentException("User with id " + userId + " doesn't exist.");
+ }
+
+ List<MetaprojectPE> metaprojectPEs = metaprojectDAO.listMetaprojects(owner);
+
+ return MetaprojectTranslator.translate(metaprojectPEs);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public MetaprojectAssignments getMetaprojectAssignments(String systemSessionToken, String name,
+ String userName, EnumSet<MetaprojectAssignmentsFetchOption> fetchOptions)
+ {
+ Metaproject metaproject = tryGetMetaproject(systemSessionToken, name, userName);
+
+ if (metaproject == null)
+ {
+ throw UserFailureException.fromTemplate("Can't find metaproject '%s/%s'", userName,
+ name);
+ }
+
+ MetaprojectAssignmentsHelper helper =
+ new MetaprojectAssignmentsHelper(daoFactory, managedPropertyEvaluatorFactory);
+ return helper.getMetaprojectAssignments(getSession(systemSessionToken), metaproject,
+ userName, fetchOptions);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Metaproject> listMetaprojectsForEntity(String systemSessionToken, String userId,
+ IObjectId entityId)
+ {
+ Map<IObjectId, List<Metaproject>> map = listMetaprojectsForEntities(systemSessionToken, userId, Collections.singletonList(entityId));
+ return map.get(entityId);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Map<IObjectId, List<Metaproject>> listMetaprojectsForEntities(String systemSessionToken, String userId,
+ Collection<? extends IObjectId> entityIds)
+ {
+ IMetaprojectDAO metaprojectDAO = daoFactory.getMetaprojectDAO();
+ PersonPE owner = daoFactory.getPersonDAO().tryFindPersonByUserId(userId);
+
+ EntityObjectIdHelper helper = new EntityObjectIdHelper(businessObjectFactory);
+ Map<IObjectId, List<Metaproject>> map = new HashMap<IObjectId, List<Metaproject>>();
+
+ if (entityIds != null)
+ {
+ for (IObjectId entityId : entityIds)
+ {
+ if (entityId != null)
+ {
+ IEntityInformationHolderDTO entity =
+ helper.getEntityById(getSession(systemSessionToken), entityId);
+
+ Collection<MetaprojectPE> metaprojectPEs =
+ metaprojectDAO.listMetaprojectsForEntity(owner, entity);
+
+ map.put(entityId, MetaprojectTranslator.translate(metaprojectPEs));
+ }
+ }
+ }
+
+ return map;
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AuthorizationGroup> listAuthorizationGroups(String sessionToken)
+ {
+ // see ch.systemsx.cisd.openbis.generic.server.CommonServer.listAuthorizationGroups(String)
+ checkSession(sessionToken);
+ final List<AuthorizationGroupPE> authorizationGroups =
+ getDAOFactory().getAuthorizationGroupDAO().list();
+ Collections.sort(authorizationGroups);
+ return AuthorizationGroupTranslator.translate(authorizationGroups);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AuthorizationGroup> listAuthorizationGroupsForUser(String sessionToken, String userId)
+ {
+ checkSession(sessionToken);
+ final List<AuthorizationGroupPE> allAuthorizationGroups =
+ getDAOFactory().getAuthorizationGroupDAO().list();
+ ArrayList<AuthorizationGroupPE> authorizationGroups = new ArrayList<AuthorizationGroupPE>();
+ for (AuthorizationGroupPE authorizationGroup : allAuthorizationGroups)
+ {
+ Set<PersonPE> persons = authorizationGroup.getPersons();
+ for (PersonPE person : persons)
+ {
+ if (userId.equals(person.getUserId()))
+ {
+ authorizationGroups.add(authorizationGroup);
+ }
+ }
+ }
+
+ Collections.sort(authorizationGroups);
+ return AuthorizationGroupTranslator.translate(authorizationGroups);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Person> listUsersForAuthorizationGroup(String sessionToken, TechId authorizationGroupId)
+ {
+ final Session session = getSession(sessionToken);
+ IAuthorizationGroupBO bo = businessObjectFactory.createAuthorizationGroupBO(session);
+ bo.loadByTechId(authorizationGroupId);
+ return PersonTranslator.translate(bo.getAuthorizationGroup().getPersons());
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<RoleAssignment> listRoleAssignments(String sessionToken)
+ {
+ checkSession(sessionToken);
+ final List<RoleAssignmentPE> roles =
+ getDAOFactory().getRoleAssignmentDAO().listRoleAssignments();
+ return RoleAssignmentTranslator.translate(roles);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Attachment> listAttachments(String sessionToken, AttachmentHolderKind attachmentHolderKind, Long attachmentHolderId)
+ {
+ Session session = getSession(sessionToken);
+
+ AttachmentHolderPE attachmentHolder = null;
+
+ switch (attachmentHolderKind)
+ {
+ case PROJECT:
+ {
+ IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
+ projectBO.loadDataByTechId(new TechId(attachmentHolderId));
+ attachmentHolder = projectBO.getProject();
+ break;
+ }
+ case EXPERIMENT:
+ {
+ IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ experimentBO.loadDataByTechId(new TechId(attachmentHolderId));
+ attachmentHolder = experimentBO.getExperiment();
+ break;
+ }
+ case SAMPLE:
+ {
+ ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ sampleBO.loadDataByTechId(new TechId(attachmentHolderId));
+ attachmentHolder = sampleBO.getSample();
+ break;
+ }
+ }
+
+ if (attachmentHolder != null)
+ {
+ List<AttachmentPE> attachments = getDAOFactory().getAttachmentDAO().listAttachments(attachmentHolder);
+ return AttachmentTranslator.translate(attachments, session.getBaseIndexURL());
+ } else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public AttachmentWithContent getAttachment(String sessionToken, AttachmentHolderKind attachmentHolderKind, Long attachmentHolderId,
+ String fileName, Integer versionOrNull)
+ {
+ Session session = getSession(sessionToken);
+
+ AttachmentPE attachment = null;
+
+ switch (attachmentHolderKind)
+ {
+ case PROJECT:
+ {
+ IProjectBO bo = businessObjectFactory.createProjectBO(session);
+ bo.loadDataByTechId(new TechId(attachmentHolderId));
+ attachment = bo.tryGetProjectFileAttachment(fileName, versionOrNull);
+ break;
+ }
+ case EXPERIMENT:
+ {
+ IExperimentBO bo = businessObjectFactory.createExperimentBO(session);
+ bo.loadDataByTechId(new TechId(attachmentHolderId));
+ attachment = bo.tryGetExperimentFileAttachment(fileName, versionOrNull);
+ break;
+ }
+ case SAMPLE:
+ {
+ ISampleBO bo = businessObjectFactory.createSampleBO(session);
+ bo.loadDataByTechId(new TechId(attachmentHolderId));
+ attachment = bo.tryGetSampleFileAttachment(fileName, versionOrNull);
+ break;
+ }
+ }
+
+ if (attachment != null)
+ {
+ return AttachmentTranslator.translateWithContent(attachment);
+ } else
+ {
+ return null;
+ }
+ }
+
+ public void setTimeout(String timeout)
+ {
+ try
+ {
+ this.timeout = Long.parseLong(timeout);
+ } catch (Exception e)
+ {
+ }
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<AbstractExternalData> listNotArchivedDatasetsWithMetaproject(String sessionToken, final IMetaprojectId metaprojectId)
+ {
+ final Session session = getSession(sessionToken);
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ final Metaproject metaproject = CommonServiceProvider.getCommonServer().getMetaprojectWithoutOwnershipChecks(sessionToken, metaprojectId);
+ return datasetLister.listByMetaprojectIdAndArchivalState(metaproject.getId(), false);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
index 19166b05b0b..9417ead5194 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
@@ -487,7 +487,7 @@ public class ServiceForDataStoreServerLogger extends AbstractServerLogger implem
logAccess(Level.DEBUG, sessionToken, "isDataSetOnTrashCanOrDeleted", "DATA_SET_CODE(%s)", dataSetCode);
return false;
}
-
+
@Override
public void updateShareIdAndSize(String sessionToken, String dataSetCode, String shareId,
long size) throws UserFailureException
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java
index c8581b2dfc8..999259c5f83 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java
@@ -36,9 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
final class TrackingServerLogger extends AbstractServerLogger implements ITrackingServer
{
/**
- * Creates an instance for the specified session manager, invocation status and elapsed time.
- * The session manager is used to retrieve user information which will be a part of the log
- * message.
+ * Creates an instance for the specified session manager, invocation status and elapsed time. The session manager is used to retrieve user
+ * information which will be a part of the log message.
*/
TrackingServerLogger(final ISessionManager<Session> sessionManager,
IInvocationLoggerContext context)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServiceServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServiceServer.java
index 67f76a4c7e3..f54dd4874cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServiceServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServiceServer.java
@@ -48,10 +48,11 @@ public class TrackingServiceServer extends WhiteAndBlackListHttpInvokerServiceEx
}
@RequestMapping(
- { "/rmi-tracking", "/openbis/rmi-tracking" })
+ { "/rmi-tracking", "/openbis/rmi-tracking" })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
- throws ServletException, IOException {
+ throws ServletException, IOException
+ {
super.handleRequest(request, response);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrustedCrossOriginDomainsProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrustedCrossOriginDomainsProvider.java
index 8ea9c44a8e9..ba08f173212 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrustedCrossOriginDomainsProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrustedCrossOriginDomainsProvider.java
@@ -43,8 +43,8 @@ public class TrustedCrossOriginDomainsProvider
}
/**
- * Returns a list of configured trusted domains which can host external shared web resources.
- * Typically these are lightweight webapps that integrate with openBIS via JSON-RPC services.
+ * Returns a list of configured trusted domains which can host external shared web resources. Typically these are lightweight webapps that
+ * integrate with openBIS via JSON-RPC services.
* <p>
* Can return empty list.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/WhiteListBasedRemoteHostValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/WhiteListBasedRemoteHostValidator.java
index 5944f9a6ba7..cd9c18e04ba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/WhiteListBasedRemoteHostValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/WhiteListBasedRemoteHostValidator.java
@@ -28,8 +28,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IRemoteHostValidator;
*/
public class WhiteListBasedRemoteHostValidator implements IRemoteHostValidator
{
-
- private final Set<String> allowedRemoteHosts;
+
+ private final Set<String> allowedRemoteHosts;
public WhiteListBasedRemoteHostValidator(String commaSeparatedListOfAllowedRemoteHosts)
{
@@ -43,12 +43,12 @@ public class WhiteListBasedRemoteHostValidator implements IRemoteHostValidator
}
}
}
-
+
public void removeRemoteHost(String remoteHost)
{
allowedRemoteHosts.remove(remoteHost);
}
-
+
public void addRemoteHost(String remoteHost)
{
allowedRemoteHosts.add(remoteHost);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ExperimentToDataSetRelatedEntitiesTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ExperimentToDataSetRelatedEntitiesTranslator.java
index dfd2066877c..00034fae63a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ExperimentToDataSetRelatedEntitiesTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/ExperimentToDataSetRelatedEntitiesTranslator.java
@@ -26,11 +26,9 @@ class ExperimentToDataSetRelatedEntitiesTranslator
private final ArrayList<BasicEntityInformationHolder> entityInformationHolders;
/**
- * Creates a translator from public {@Experiment} objects to the internal
- * {@link DataSetRelatedEntities} objects.
+ * Creates a translator from public {@Experiment} objects to the internal {@link DataSetRelatedEntities} objects.
* <p>
- * A list of experiment types known to the DB must be provided because Experiment knows only the
- * code of the ExperimentType.
+ * A list of experiment types known to the DB must be provided because Experiment knows only the code of the ExperimentType.
*
* @param experimentTypes A list of ExperimentTypes known to the DB.
* @param experiments The experiments to convert.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
index 424db69d2df..36aee99039c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
@@ -332,18 +332,19 @@ public class GeneralInformationChangingService extends
{
server.deletePermanentlyForced(sessionToken, TechId.createList(deletionIds));
}
-
+
@Override
public void registerPerson(String sessionToken, String userID)
{
server.registerPerson(sessionToken, userID);
}
-
+
@Override
- public void registerSpace(String sessionToken, String spaceCode, String spaceDescription) {
- server.registerSpace(sessionToken,spaceCode, spaceDescription);
+ public void registerSpace(String sessionToken, String spaceCode, String spaceDescription)
+ {
+ server.registerSpace(sessionToken, spaceCode, spaceDescription);
}
-
+
@Override
public void registerPersonSpaceRole(String sessionToken, String spaceCode, String userID, String roleCode)
{
@@ -351,5 +352,5 @@ public class GeneralInformationChangingService extends
SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
server.registerSpaceRole(sessionToken, RoleCode.valueOf(roleCode), spaceIdentifier, grantee);
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceJsonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceJsonServer.java
index b9ed6c36059..14800f19a87 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceJsonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceJsonServer.java
@@ -57,14 +57,14 @@ public class GeneralInformationChangingServiceJsonServer extends AbstractApiJson
}
@RequestMapping(
- { IGeneralInformationChangingService.JSON_SERVICE_URL,
- "/openbis" + IGeneralInformationChangingService.JSON_SERVICE_URL })
+ { IGeneralInformationChangingService.JSON_SERVICE_URL,
+ "/openbis" + IGeneralInformationChangingService.JSON_SERVICE_URL })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException,
- IOException {
+ IOException
+ {
super.handleRequest(request, response);
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
index 1bf5d91e8bd..7ab105f0323 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
@@ -248,5 +248,5 @@ class GeneralInformationChangingServiceLogger extends AbstractServerLogger imple
{
logAccess(sessionToken, "registerPersonSpaceRole", "spaceCode(%s), userID(%s), roleCode(%s)", spaceCode, userID, roleCode);
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index ee64f5a89de..b9a4da48b86 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -407,8 +407,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = SampleByIdentiferValidator.class)
public List<Sample> listSamplesForExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class)
- String experimentIdentifierString)
+ @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class) String experimentIdentifierString)
{
checkSession(sessionToken);
ExperimentIdentifier experimentId =
@@ -429,8 +428,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
@Capability("SEARCH_ON_BEHALF_OF_USER")
public List<Sample> listSamplesForExperimentOnBehalfOfUser(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class)
- String experimentIdentifierString, String userId)
+ @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class) String experimentIdentifierString, String userId)
{
checkSession(sessionToken);
ExperimentIdentifier experimentId =
@@ -464,8 +462,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = DataSetByExperimentOrSampleIdentifierValidator.class)
public List<DataSet> listDataSets(String sessionToken,
- @AuthorizationGuard(guardClass = SampleListPredicate.class)
- List<Sample> samples)
+ @AuthorizationGuard(guardClass = SampleListPredicate.class) List<Sample> samples)
{
return listDataSets(sessionToken, samples, EnumSet.noneOf(Connections.class));
}
@@ -475,8 +472,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ExperimentByIdentiferValidator.class)
public List<Experiment> listExperiments(String sessionToken,
- @AuthorizationGuard(guardClass = ProjectPredicate.class)
- List<Project> projects, String experimentTypeString)
+ @AuthorizationGuard(guardClass = ProjectPredicate.class) List<Project> projects, String experimentTypeString)
{
return listExperiments(sessionToken, projects, experimentTypeString, false, false);
}
@@ -486,8 +482,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ExperimentByIdentiferValidator.class)
public List<Experiment> listExperimentsHavingDataSets(String sessionToken,
- @AuthorizationGuard(guardClass = ProjectPredicate.class)
- List<Project> projects, String experimentTypeString)
+ @AuthorizationGuard(guardClass = ProjectPredicate.class) List<Project> projects, String experimentTypeString)
{
return listExperiments(sessionToken, projects, experimentTypeString, false, true);
}
@@ -497,8 +492,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ExperimentByIdentiferValidator.class)
public List<Experiment> listExperimentsHavingSamples(String sessionToken,
- @AuthorizationGuard(guardClass = ProjectPredicate.class)
- List<Project> projects, String experimentTypeString)
+ @AuthorizationGuard(guardClass = ProjectPredicate.class) List<Project> projects, String experimentTypeString)
{
return listExperiments(sessionToken, projects, experimentTypeString, true, false);
}
@@ -602,8 +596,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = DataSetByExperimentOrSampleIdentifierValidator.class)
public List<DataSet> listDataSetsForSample(String sessionToken,
- @AuthorizationGuard(guardClass = SamplePredicate.class)
- Sample sample, boolean areOnlyDirectlyConnectedIncluded)
+ @AuthorizationGuard(guardClass = SamplePredicate.class) Sample sample, boolean areOnlyDirectlyConnectedIncluded)
{
checkSession(sessionToken);
List<AbstractExternalData> externalData =
@@ -751,8 +744,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = DataSetByExperimentOrSampleIdentifierValidator.class)
public List<DataSet> listDataSets(String sessionToken,
- @AuthorizationGuard(guardClass = SampleListPredicate.class)
- List<Sample> samples, EnumSet<Connections> connections)
+ @AuthorizationGuard(guardClass = SampleListPredicate.class) List<Sample> samples, EnumSet<Connections> connections)
{
checkSession(sessionToken);
EnumSet<Connections> connectionsToGet =
@@ -810,8 +802,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = DataSetByExperimentOrSampleIdentifierValidator.class)
public List<DataSet> listDataSetsForExperiments(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentListPredicate.class)
- List<Experiment> experiments, EnumSet<Connections> connections)
+ @AuthorizationGuard(guardClass = ExperimentListPredicate.class) List<Experiment> experiments, EnumSet<Connections> connections)
{
checkSession(sessionToken);
EnumSet<Connections> connectionsToGet =
@@ -1049,8 +1040,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ExperimentByIdentiferValidator.class)
public List<Experiment> listExperiments(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class)
- List<String> experimentIdentifiers)
+ @AuthorizationGuard(guardClass = ExperimentAugmentedCodePredicate.class) List<String> experimentIdentifiers)
{
checkSession(sessionToken);
@@ -1213,8 +1203,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Attachment> listAttachmentsForProject(String sessionToken,
- @AuthorizationGuard(guardClass = ProjectIdPredicate.class)
- IProjectId projectId, boolean allVersions)
+ @AuthorizationGuard(guardClass = ProjectIdPredicate.class) IProjectId projectId, boolean allVersions)
{
Session session = getSession(sessionToken);
@@ -1231,8 +1220,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Attachment> listAttachmentsForExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentIdPredicate.class)
- IExperimentId experimentId, boolean allVersions)
+ @AuthorizationGuard(guardClass = ExperimentIdPredicate.class) IExperimentId experimentId, boolean allVersions)
{
Session session = getSession(sessionToken);
@@ -1249,8 +1237,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Attachment> listAttachmentsForSample(String sessionToken,
- @AuthorizationGuard(guardClass = SampleIdPredicate.class)
- ISampleId sampleId, boolean allVersions)
+ @AuthorizationGuard(guardClass = SampleIdPredicate.class) ISampleId sampleId, boolean allVersions)
{
Session session = getSession(sessionToken);
@@ -1358,7 +1345,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
{
return commonServer.listPersons(sessionToken);
}
-
+
@Override
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
@@ -1368,11 +1355,11 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
SQLQuery querySampleTypeId = currentSession.createSQLQuery("SELECT id from sample_types WHERE code = :sampleTypeCode");
querySampleTypeId.setParameter("sampleTypeCode", sampleTypeCode);
int sampleTypeId = ((Number) querySampleTypeId.uniqueResult()).intValue();
-
+
SQLQuery querySampleCount = currentSession.createSQLQuery("SELECT COUNT(*) FROM samples_all WHERE saty_id = :sampleTypeId");
querySampleCount.setParameter("sampleTypeId", sampleTypeId);
long sampleCount = ((Number) querySampleCount.uniqueResult()).longValue();
-
+
return sampleCount;
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceJsonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceJsonServer.java
index f80f5428440..d3fa4391796 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceJsonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceJsonServer.java
@@ -56,11 +56,12 @@ public class GeneralInformationServiceJsonServer extends AbstractApiJsonServiceE
}
@RequestMapping(
- { IGeneralInformationService.JSON_SERVICE_URL,
- "/openbis" + IGeneralInformationService.JSON_SERVICE_URL })
+ { IGeneralInformationService.JSON_SERVICE_URL,
+ "/openbis" + IGeneralInformationService.JSON_SERVICE_URL })
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException,
- IOException {
+ IOException
+ {
super.handleRequest(request, response);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceServer.java
index 7d1d59f5272..6afab5e88bf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceServer.java
@@ -30,8 +30,6 @@ import ch.systemsx.cisd.openbis.common.api.server.AbstractApiServiceExporter;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@Controller
@@ -47,14 +45,15 @@ public class GeneralInformationServiceServer extends AbstractApiServiceExporter
IGeneralInformationService.SERVICE_NAME, IGeneralInformationService.SERVICE_URL);
super.afterPropertiesSet();
}
-
@RequestMapping(
- { IGeneralInformationService.SERVICE_URL, "/openbis" + IGeneralInformationService.SERVICE_URL, "/openbis/openbis" + IGeneralInformationService.SERVICE_URL })
+ { IGeneralInformationService.SERVICE_URL, "/openbis" + IGeneralInformationService.SERVICE_URL,
+ "/openbis/openbis" + IGeneralInformationService.SERVICE_URL })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
- throws ServletException, IOException {
+ throws ServletException, IOException
+ {
super.handleRequest(request, response);
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
index 3a480ed5eb8..382e8ac8b8b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
@@ -42,11 +42,9 @@ class SampleToDataSetRelatedEntitiesTranslator
private final ArrayList<BasicEntityInformationHolder> entityInformationHolders;
/**
- * Creates a translator from public {@Sample} objects to the internal
- * {@link DataSetRelatedEntities} objects.
+ * Creates a translator from public {@Sample} objects to the internal {@link DataSetRelatedEntities} objects.
* <p>
- * A list of sample types known to the DB must be provided because Sample knows only the code of
- * the SampleType.
+ * A list of sample types known to the DB must be provided because Sample knows only the code of the SampleType.
*
* @param sampleTypes A list of SampleTypes known to the DB.
* @param samples The samples to convert.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/WebInformationServiceJsonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/WebInformationServiceJsonServer.java
index 736de594016..e2f5dff6987 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/WebInformationServiceJsonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/WebInformationServiceJsonServer.java
@@ -55,11 +55,12 @@ public class WebInformationServiceJsonServer extends AbstractApiJsonServiceExpor
}
@RequestMapping(
- { IWebInformationService.JSON_SERVICE_URL, "/openbis" + IWebInformationService.JSON_SERVICE_URL })
+ { IWebInformationService.JSON_SERVICE_URL, "/openbis" + IWebInformationService.JSON_SERVICE_URL })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException,
- IOException {
+ IOException
+ {
super.handleRequest(request, response);
- }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/ActiveAuthorization.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/ActiveAuthorization.java
index 2f53ebe55e1..e326c588bee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/ActiveAuthorization.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/ActiveAuthorization.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.authorization;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
/**
- * A {@link IAuthorizationComponentFactory} implementation which provides components for an active
- * authorization.
+ * A {@link IAuthorizationComponentFactory} implementation which provides components for an active authorization.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Argument.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Argument.java
index 9f78a080076..f7dabde51a7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Argument.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Argument.java
@@ -6,8 +6,7 @@ import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
/**
- * Small class encapsulating a method argument which could have been annotated with
- * {@link AuthorizationGuard}.
+ * Small class encapsulating a method argument which could have been annotated with {@link AuthorizationGuard}.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/CapabilityMap.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/CapabilityMap.java
index e6a29a98fb9..952c2cfa85e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/CapabilityMap.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/CapabilityMap.java
@@ -89,7 +89,7 @@ class CapabilityMap
}
String[] terms = StringUtils.split(trimmed, ';');
String firstTerm = terms[0].trim();
-
+
final String[] firstTermSplitted = StringUtils.split(firstTerm, " \t:", 2);
if (firstTermSplitted.length != 2)
{
@@ -111,7 +111,7 @@ class CapabilityMap
}
}
}
-
+
private void addRolesForParameter(String capabilityName, String parameterTerm, String line, String filePath)
{
int indexOfEqual = parameterTerm.indexOf('=');
@@ -129,7 +129,7 @@ class CapabilityMap
String roleNames = parameterTerm.substring(indexOfEqual + 1).trim();
addRoles(capabilityName + ":" + parameterName, roleNames, line, filePath);
}
-
+
private void addRoles(String capabilityName, String roleNames, String line, String filePath)
{
Collection<RoleWithHierarchy> roles = capMap.get(capabilityName);
@@ -157,7 +157,7 @@ class CapabilityMap
}
}
}
-
+
private void logWarning(String line, String filePath, String messageOrNull)
{
String msg = String.format(
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessController.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessController.java
index 7c513392552..18224192b48 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessController.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessController.java
@@ -76,7 +76,7 @@ public final class DefaultAccessController implements IAccessController
new HashMap<Method, Set<RoleWithHierarchy>>();
private final Map<Method, Map<String, Set<RoleWithHierarchy>>> argumentRolesCache = new HashMap<>();
-
+
private final CapabilityMap capabilities = new CapabilityMap(new File("etc/capabilities"));
private PredicateExecutor predicateExecutor;
@@ -203,7 +203,7 @@ public final class DefaultAccessController implements IAccessController
return rootRoles;
}
- private Set<RoleWithHierarchy> getArgumentRoles(Method method, Argument<?> argument,
+ private Set<RoleWithHierarchy> getArgumentRoles(Method method, Argument<?> argument,
Set<RoleWithHierarchy> defaultRoles)
{
synchronized (argumentRolesCache)
@@ -233,8 +233,8 @@ public final class DefaultAccessController implements IAccessController
return roles;
}
}
-
- private Collection<RoleWithHierarchy> getRootRoles(Method method, AuthorizationGuard predicateCandidate,
+
+ private Collection<RoleWithHierarchy> getRootRoles(Method method, AuthorizationGuard predicateCandidate,
Set<RoleWithHierarchy> defaultRoles)
{
Collection<RoleWithHierarchy> roles = capabilities.tryGetRoles(method, predicateCandidate.name());
@@ -252,8 +252,7 @@ public final class DefaultAccessController implements IAccessController
return roles;
}
-
- private Status checkNotEmpty(List<RoleWithIdentifier> relevantRoles, Set<RoleWithHierarchy> argumentRoles,
+ private Status checkNotEmpty(List<RoleWithIdentifier> relevantRoles, Set<RoleWithHierarchy> argumentRoles,
IAuthSession session)
{
if (relevantRoles.isEmpty() == false)
@@ -263,7 +262,7 @@ public final class DefaultAccessController implements IAccessController
final String msg = String.format(MATCHING_ROLE_NOT_FOUND_TEMPLATE, argumentRoles, session.getUserName());
return Status.createError(msg);
}
-
+
private List<RoleWithIdentifier> getRelevantRoles(
final List<RoleWithIdentifier> userRoles, final Set<RoleWithHierarchy> methodOrParameterRoles)
{
@@ -279,8 +278,7 @@ public final class DefaultAccessController implements IAccessController
}
/**
- * Retains {@link RoleWithIdentifier}s with {@link RoleWithIdentifier#getRole()} included in the
- * set of {@link RoleWithHierarchy}s.
+ * Retains {@link RoleWithIdentifier}s with {@link RoleWithIdentifier#getRole()} included in the set of {@link RoleWithHierarchy}s.
*
* @return retained user roles
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAccessController.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAccessController.java
index c80d6f60e8d..8357bb153cb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAccessController.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAccessController.java
@@ -33,15 +33,12 @@ public interface IAccessController
/**
* Whether given <code>Session</code> has enough rights to access the calling <var>method</var>.
*
- * @param arguments the method arguments (minus the first one which is expected to be a
- * {@link IAuthSession} object).
+ * @param arguments the method arguments (minus the first one which is expected to be a {@link IAuthSession} object).
* @throws UserFailureException if the authorization could not be checked for some reason.
- * @return a {@link Status} with {@link StatusFlag#OK} if given <var>session</var> is
- * authorized to access the given <code>Method</code>. In case of
- * {@link StatusFlag#ERROR} you might find more information by calling
- * {@link Status#tryGetErrorMessage()}.
+ * @return a {@link Status} with {@link StatusFlag#OK} if given <var>session</var> is authorized to access the given <code>Method</code>. In case
+ * of {@link StatusFlag#ERROR} you might find more information by calling {@link Status#tryGetErrorMessage()}.
*/
public Status isAuthorized(final IAuthSession session, final Method method,
final Argument<?>[] arguments) throws UserFailureException;
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IReturnValueFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IReturnValueFilter.java
index 4e756475c42..2d32763c39a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IReturnValueFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IReturnValueFilter.java
@@ -23,8 +23,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
/**
* A return value filter.
* <p>
- * A <code>IReturnValueFilter</code> should never throw an exception but should only take care of
- * filtering.
+ * A <code>IReturnValueFilter</code> should never throw an exception but should only take care of filtering.
* </p>
*
* @author Christian Ribeaud
@@ -35,8 +34,8 @@ public interface IReturnValueFilter
/**
* Applies filtering on given <var>returnValue</var>.
*
- * @param returnValueOrNull the return value that should be filtered. If the method has a return
- * value of type <code>void</code>, this would be <code>null</code>.
+ * @param returnValueOrNull the return value that should be filtered. If the method has a return value of type <code>void</code>, this would be
+ * <code>null</code>.
*/
public Object applyFilter(final IAuthSession session, final Method method,
final Object returnValueOrNull);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoAuthorization.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoAuthorization.java
index 14da5d05023..4d1c40286ce 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoAuthorization.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoAuthorization.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
/**
- * A {@link IAuthorizationComponentFactory} implementation which provides components in case we do
- * not want any authorization.
+ * A {@link IAuthorizationComponentFactory} implementation which provides components in case we do not want any authorization.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoReturnValueFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoReturnValueFilter.java
index 6281b6e4415..d7eeb2b4f06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoReturnValueFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/NoReturnValueFilter.java
@@ -21,8 +21,7 @@ import java.lang.reflect.Method;
import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
/**
- * A dummy <code>IReturnValueFilter</code> implementation which does not apply any filter to given
- * return value.
+ * A dummy <code>IReturnValueFilter</code> implementation which does not apply any filter to given return value.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/SpaceOwnerKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/SpaceOwnerKind.java
index d58b6935374..cb1dc6176a2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/SpaceOwnerKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/SpaceOwnerKind.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.authorization;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
/**
- * Enumeration of the various ways to get the space of an entity knowing its
- * {@link TechId}.
+ * Enumeration of the various ways to get the space of an entity knowing its {@link TechId}.
*
* @author Piotr Buczek
* @author Franz-Josef Elmer
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/AuthorizationGuard.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/AuthorizationGuard.java
index cd6da3a93b9..ee80ff3a663 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/AuthorizationGuard.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/AuthorizationGuard.java
@@ -39,12 +39,12 @@ public @interface AuthorizationGuard
* Class responsible for evaluating the method parameter.
*/
Class<? extends IPredicate<?>> guardClass();
-
+
/**
* List of roles replacing corresponding list of @RolesAllowed annotation.
*/
RoleWithHierarchy[] rolesAllowed() default {};
-
+
/**
* Name of the guard. Needed for the capabilities file to override allowed roles list.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RolesAllowed.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RolesAllowed.java
index dd4efbec566..788bfc0dab5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RolesAllowed.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RolesAllowed.java
@@ -35,8 +35,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
public @interface RolesAllowed
{
/**
- * The set of roles that are allowed to execute a method. The method will be accessible by all
- * users with a role defined in any of {@link RoleWithHierarchy#getRoles()}.
+ * The set of roles that are allowed to execute a method. The method will be accessible by all users with a role defined in any of
+ * {@link RoleWithHierarchy#getRoles()}.
*/
RoleWithHierarchy[] value() default {};
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractPredicate.java
index cbe5a4651b7..d177444f587 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractPredicate.java
@@ -28,8 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleL
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <i>abstract</i> <code>IPredicate</code> implementation which mainly checks method parameters
- * before doing the real work.
+ * An <i>abstract</i> <code>IPredicate</code> implementation which mainly checks method parameters before doing the real work.
*
* @author Christian Ribeaud
*/
@@ -50,8 +49,7 @@ public abstract class AbstractPredicate<T> implements IPredicate<T>
final List<RoleWithIdentifier> allowedRoles, final T value);
/**
- * Is the checked value allowed to be <code>null</code>, <code>false</code> by default.
- * Can be overridden in sub-classes.
+ * Is the checked value allowed to be <code>null</code>, <code>false</code> by default. Can be overridden in sub-classes.
*/
protected boolean isNullValueAllowed()
{
@@ -59,8 +57,7 @@ public abstract class AbstractPredicate<T> implements IPredicate<T>
}
/**
- * Returns <code>true</code> if <var>allowedRoles</var> contains a role that allows writing to
- * all entities.
+ * Returns <code>true</code> if <var>allowedRoles</var> contains a role that allows writing to all entities.
*/
public static Status hasInstanceWritePermissions(PersonPE aPerson,
List<RoleWithIdentifier> allowedRoles)
@@ -82,8 +79,7 @@ public abstract class AbstractPredicate<T> implements IPredicate<T>
}
/**
- * Returns <code>true</code> if <var>allowedRoles</var> contains a role that allows reading all
- * entities.
+ * Returns <code>true</code> if <var>allowedRoles</var> contains a role that allows reading all entities.
*/
public static Status hasInstanceReadPermissions(PersonPE aPerson,
List<RoleWithIdentifier> allowedRoles)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractProjectPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractProjectPredicate.java
index b26d73e5295..555184f4215 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractProjectPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractProjectPredicate.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.IAuthorizationDataP
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ProjectTechIdPredicate;
/**
- * An <code>IPredicate</code> implementation that has the tools for authenticating projects based on
- * any kind of identifier.
+ * An <code>IPredicate</code> implementation that has the tools for authenticating projects based on any kind of identifier.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractTechIdPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractTechIdPredicate.java
index 859ad685800..7dfd3dc746a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractTechIdPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractTechIdPredicate.java
@@ -26,8 +26,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
- * An <code>IPredicate</code> abstract implementation based on {@link TechId} and
- * {@link SpaceOwnerKind}
+ * An <code>IPredicate</code> abstract implementation based on {@link TechId} and {@link SpaceOwnerKind}
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AtomicOperationsPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AtomicOperationsPredicate.java
index e49b7ff5709..9e84daed0ea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AtomicOperationsPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AtomicOperationsPredicate.java
@@ -35,8 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- * The predicate for the {@link AtomicEntityOperationDetails}. This check is always being performed
- * as the user
+ * The predicate for the {@link AtomicEntityOperationDetails}. This check is always being performed as the user
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesCollectionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesCollectionPredicate.java
index 30e12af3dbf..64358a73edc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesCollectionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesCollectionPredicate.java
@@ -34,9 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
- * Predicate for lists of {@link DataSetUpdatesDTO} instances. Checks that the user has update
- * rights for all data sets. In addition for all data sets with changed samples or experiments it is
- * check that the user has access rights for those samples and experiments.
+ * Predicate for lists of {@link DataSetUpdatesDTO} instances. Checks that the user has update rights for all data sets. In addition for all data sets
+ * with changed samples or experiments it is check that the user has access rights for those samples and experiments.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesPredicate.java
index 52832ad7cb5..e9d08753619 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DataSetUpdatesPredicate.java
@@ -27,9 +27,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- * An <code>IPredicate</code> implementation based on {@link DataSetUpdatesDTO}. Checks that: 1) the
- * user has rights to update the data set 2) if data set is moved to a different sample the user has
- * access to this sample.
+ * An <code>IPredicate</code> implementation based on {@link DataSetUpdatesDTO}. Checks that: 1) the user has rights to update the data set 2) if data
+ * set is moved to a different sample the user has access to this sample.
*
* @author Piotr Buczek
*/
@@ -59,8 +58,7 @@ public class DataSetUpdatesPredicate extends AbstractPredicate<DataSetUpdatesDTO
}
@Override
- protected
- Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
+ protected Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
final DataSetUpdatesDTO updates)
{
assert dataSetTechIdPredicate.initialized : "Predicate has not been initialized";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedNullableAbstractPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedNullableAbstractPredicate.java
index 45440e112d2..e9b417336d7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedNullableAbstractPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedNullableAbstractPredicate.java
@@ -24,8 +24,8 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <code>AbstractPredicate</code> extension which delegates its method calls to the encapsulated
- * {@link AbstractPredicate} allowing the value to be null.
+ * An <code>AbstractPredicate</code> extension which delegates its method calls to the encapsulated {@link AbstractPredicate} allowing the value to be
+ * null.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedPredicate.java
index 58d795dfee1..8ad534db890 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DelegatedPredicate.java
@@ -24,12 +24,10 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <code>AbstractPredicate</code> extension which delegates its method calls to the encapsulated
- * {@link IPredicate}.
+ * An <code>AbstractPredicate</code> extension which delegates its method calls to the encapsulated {@link IPredicate}.
* <p>
- * Each implementation should know how to convert <code>T</code> to <code>P</code> by implementing
- * {@link #tryConvert(Object)} method. Note that {@link #doEvaluation(PersonPE, List, Object)}
- * delegates its call to {@link IPredicate#evaluate(PersonPE, List, Object)} of the specified
+ * Each implementation should know how to convert <code>T</code> to <code>P</code> by implementing {@link #tryConvert(Object)} method. Note that
+ * {@link #doEvaluation(PersonPE, List, Object)} delegates its call to {@link IPredicate#evaluate(PersonPE, List, Object)} of the specified
* <code>delegate</code>.
* </p>
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExistingSpaceIdentifierPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExistingSpaceIdentifierPredicate.java
index ccdc0e4ddf3..f65d7158210 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExistingSpaceIdentifierPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExistingSpaceIdentifierPredicate.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
-
/**
* A {@link SpaceIdentifierPredicate} which evaluates to OK if the space does not exist.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentUpdatesPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentUpdatesPredicate.java
index 7d1cf715f16..8572f787536 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentUpdatesPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentUpdatesPredicate.java
@@ -24,9 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <code>IPredicate</code> implementation based on {@link ExperimentUpdatesDTO}. Checks that: 1)
- * the user has rights to update the experiment 2) if experiment is moved to a different projects
- * the user has access to this project.
+ * An <code>IPredicate</code> implementation based on {@link ExperimentUpdatesDTO}. Checks that: 1) the user has rights to update the experiment 2) if
+ * experiment is moved to a different projects the user has access to this project.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/IPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/IPredicate.java
index 62851ab331f..af22024b16a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/IPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/IPredicate.java
@@ -28,8 +28,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* Performs some predicate which returns a {@link Status} based on the input objects.
* <p>
- * Each implementation is expected to have an empty <code>public</code> constructor and might be
- * statefull. So do not try to reuse it. Use a {@link IPredicateFactory} to get an implementation.
+ * Each implementation is expected to have an empty <code>public</code> constructor and might be statefull. So do not try to reuse it. Use a
+ * {@link IPredicateFactory} to get an implementation.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ListSamplesByPropertyPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ListSamplesByPropertyPredicate.java
index fab5175ce71..a2218b2ea61 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ListSamplesByPropertyPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ListSamplesByPropertyPredicate.java
@@ -25,9 +25,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <code>IPredicate</code> implementation based on {@link ListSamplesByPropertyCriteria}. Checks
- * that the user has the right to access the group from which samples are referenced. Note that we
- * can ignore the experiment, since it belongs to the same group.
+ * An <code>IPredicate</code> implementation based on {@link ListSamplesByPropertyCriteria}. Checks that the user has the right to access the group
+ * from which samples are referenced. Note that we can ignore the experiment, since it belongs to the same group.
*
* @author Tomasz Pylak
*/
@@ -54,8 +53,7 @@ public class ListSamplesByPropertyPredicate extends
}
@Override
- protected
- Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
+ protected Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
final ListSamplesByPropertyCriteria criteria)
{
assert spacePredicate.initialized : "Predicate has not been initialized";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewDataSetsWithTypePredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewDataSetsWithTypePredicate.java
index 9dd927ac5c7..eb605b83c80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewDataSetsWithTypePredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewDataSetsWithTypePredicate.java
@@ -49,8 +49,7 @@ public class NewDataSetsWithTypePredicate extends AbstractPredicate<NewDataSetsW
}
@Override
- protected
- Status doEvaluation(PersonPE person, List<RoleWithIdentifier> allowedRoles,
+ protected Status doEvaluation(PersonPE person, List<RoleWithIdentifier> allowedRoles,
NewDataSetsWithTypes dataSets)
{
List<String> codes = new ArrayList<String>();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NullableGroupIdentifierPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NullableGroupIdentifierPredicate.java
index 8fd15faff82..ff4de6715c5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NullableGroupIdentifierPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NullableGroupIdentifierPredicate.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
- * An <code>IPredicate</code> implementation based on {@link SpaceIdentifierPredicate} which allows
- * the identifier to be null.
+ * An <code>IPredicate</code> implementation based on {@link SpaceIdentifierPredicate} which allows the identifier to be null.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/RevertDeletionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/RevertDeletionPredicate.java
index 006d3f2bb22..5cb787fea80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/RevertDeletionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/RevertDeletionPredicate.java
@@ -46,8 +46,7 @@ public class RevertDeletionPredicate extends AbstractPredicate<List<TechId>>
}
@Override
- public void init(@SuppressWarnings("hiding")
- IAuthorizationDataProvider provider)
+ public void init(@SuppressWarnings("hiding") IAuthorizationDataProvider provider)
{
this.provider = provider;
deletionTechIdCollectionPredicate.init(provider);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SamplePredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SamplePredicate.java
index 088c03afd8a..222bbaf2b58 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SamplePredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SamplePredicate.java
@@ -22,9 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
/**
- * Predicate based on {@link ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample}. This
- * predicate authorizes for read-only access, i.e. it will allow access to shared samples for all
- * users.
+ * Predicate based on {@link ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample}. This predicate authorizes for read-only access, i.e. it will
+ * allow access to shared samples for all users.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleTechIdPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleTechIdPredicate.java
index d961fb39841..6c42f2a30f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleTechIdPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleTechIdPredicate.java
@@ -63,8 +63,7 @@ public class SampleTechIdPredicate extends AbstractDatabaseInstancePredicate<Tec
}
@Override
- protected
- final Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
+ protected final Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
final TechId techId)
{
SamplePE sample = authorizationDataProvider.getSample(techId);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesCollectionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesCollectionPredicate.java
index ddfc654ce3a..9a79f31e0fe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesCollectionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesCollectionPredicate.java
@@ -33,8 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
- * Predicate for a list of {@link SampleUpdatesDTO} instances. The logical is similar to
- * {@link SampleUpdatesPredicate}.
+ * Predicate for a list of {@link SampleUpdatesDTO} instances. The logical is similar to {@link SampleUpdatesPredicate}.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesPredicate.java
index 3f73b47f444..861696a6d2e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleUpdatesPredicate.java
@@ -24,9 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
/**
- * An <code>IPredicate</code> implementation based on {@link SampleUpdatesDTO}. Checks that: 1) the
- * user has rights to update the sample 2) if sample is moved to a different group the user has
- * access to this group 3) if sample is attached to experiment, user has access to this experiment.
+ * An <code>IPredicate</code> implementation based on {@link SampleUpdatesDTO}. Checks that: 1) the user has rights to update the sample 2) if sample
+ * is moved to a different group the user has access to this group 3) if sample is attached to experiment, user has access to this experiment.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/AbstractValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/AbstractValidator.java
index 3819e810b54..5c5ee7a10a1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/AbstractValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/AbstractValidator.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.IAuthorizationDataP
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * An <i>abstract</i> <code>IValidator</code> implementation which mainly checks method parameters
- * before doing the real work.
+ * An <i>abstract</i> <code>IValidator</code> implementation which mainly checks method parameters before doing the real work.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/IValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/IValidator.java
index 0730e1f5df3..1929e02d3d6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/IValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/IValidator.java
@@ -21,11 +21,10 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.ValidatorStore;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- * Performs some validation which returns <code>true</code> or <code>false</code> based on the input
- * objects.
+ * Performs some validation which returns <code>true</code> or <code>false</code> based on the input objects.
* <p>
- * Each implementation is expected to have an empty <code>public</code> constructor and is expected
- * to be stateless. Use {@link ValidatorStore} to get an implementation.
+ * Each implementation is expected to have an empty <code>public</code> constructor and is expected to be stateless. Use {@link ValidatorStore} to get
+ * an implementation.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ProjectValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ProjectValidator.java
index 0cb71cba4b1..7ba9a737a59 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ProjectValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ProjectValidator.java
@@ -44,5 +44,5 @@ public final class ProjectValidator extends AbstractValidator<Project>
final Space space = value.getSpace();
return groupValidator.isValid(person, space);
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
index 9e35e7c1eb9..b5ef1159b91 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SearchDomainSearchResultValidator.java
@@ -31,7 +31,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
public class SearchDomainSearchResultValidator extends AbstractValidator<SearchDomainSearchResultWithFullEntity>
{
private final ExternalDataValidator dataSetValidator = new ExternalDataValidator();
+
private final SampleValidator sampleValidator = new SampleValidator();
+
private final ExperimentValidator experimentValidator = new ExperimentValidator();
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/AbstractBatchOperationDelegate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/AbstractBatchOperationDelegate.java
index 0f5f0193f8e..f6c18553887 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/AbstractBatchOperationDelegate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/AbstractBatchOperationDelegate.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server.batch;
/**
- * A shell superclass for batch operation delegates. Subclasses only need to override those methods
- * they actually use.
+ * A shell superclass for batch operation delegates. Subclasses only need to override those methods they actually use.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
index 21e37048135..7bc393f25ea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
@@ -29,10 +29,9 @@ public class BatchOperationExecutor
* Executes an operation in batches using the default batch size.
*
* @param strategy The operation to execute
- * @param progressListenerOrNull The progress listener to notify of progress. If this is
- * non-null, the progressPhaseOrNull must be non-null as well.
- * @param progressPhaseOrNull The phase used in updating the progressListenerOrNull. Must be
- * non-null if the progressListenerOrNull is
+ * @param progressListenerOrNull The progress listener to notify of progress. If this is non-null, the progressPhaseOrNull must be non-null as
+ * well.
+ * @param progressPhaseOrNull The phase used in updating the progressListenerOrNull. Must be non-null if the progressListenerOrNull is
*/
public static <S> void executeInBatches(IBatchOperation<S> strategy,
IServiceConversationProgressListener progressListenerOrNull, String progressPhaseOrNull)
@@ -50,10 +49,9 @@ public class BatchOperationExecutor
*
* @param strategy The operation to execute
* @param batchSize The size of the batches
- * @param progressListenerOrNull The progress listener to notify of progress. If this is
- * non-null, the progressPhaseOrNull must be non-null as well.
- * @param progressPhaseOrNull The phase used in updating the progressListenerOrNull. Must be
- * non-null if the progressListenerOrNull is
+ * @param progressListenerOrNull The progress listener to notify of progress. If this is non-null, the progressPhaseOrNull must be non-null as
+ * well.
+ * @param progressPhaseOrNull The phase used in updating the progressListenerOrNull. Must be non-null if the progressListenerOrNull is
*/
public static <S> void executeInBatches(IBatchOperation<S> strategy, int batchSize,
IServiceConversationProgressListener progressListenerOrNull, String progressPhaseOrNull)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleUpdate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleUpdate.java
index eba771887b2..a17a9b15bc7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleUpdate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleUpdate.java
@@ -22,12 +22,11 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
/**
- * {@link IBatchOperation} updating samples. It is like {@link SampleBatchUpdate}, but uses
- * {@link SampleUpdatesDTO} to specify the updates instead of {@link SampleBatchUpdate} and thus has
- * slightly different semantics.
+ * {@link IBatchOperation} updating samples. It is like {@link SampleBatchUpdate}, but uses {@link SampleUpdatesDTO} to specify the updates instead of
+ * {@link SampleBatchUpdate} and thus has slightly different semantics.
* <p>
- * Whereas SampleBatchUpdate only makes changes to the sample that are explicitly specified in it
- * the details object of its DTO, SampleUpdate changes the sample to match the DTO.
+ * Whereas SampleBatchUpdate only makes changes to the sample that are explicitly specified in it the details object of its DTO, SampleUpdate changes
+ * the sample to match the DTO.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServiceFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServiceFactory.java
index 704445259ee..4e3d2f2136b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServiceFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServiceFactory.java
@@ -56,10 +56,11 @@ public class DataStoreServiceFactory implements IDataStoreServiceFactory
"Monitoring Proxy").corePoolSize(NUMBER_OF_CORE_THREADS).daemonize();
@Override
- public IDataStoreService create(String serverURL) {
+ public IDataStoreService create(String serverURL)
+ {
return create(serverURL, 5 * DateUtils.MILLIS_PER_MINUTE);
}
-
+
@Override
public IDataStoreService create(String serverURL, long timeout)
{
@@ -89,7 +90,7 @@ public class DataStoreServiceFactory implements IDataStoreServiceFactory
.executorService(executorService)
.callAsynchronously(
IDataStoreService.class.getMethod("cleanupSession", new Class<?>[]
- { String.class })).get();
+ { String.class })).get();
} catch (SecurityException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IDataStoreServiceFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IDataStoreServiceFactory.java
index ef9cf77610d..900d8cfcadd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IDataStoreServiceFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IDataStoreServiceFactory.java
@@ -27,10 +27,9 @@ public interface IDataStoreServiceFactory
public IDataStoreService create(String serverURL);
public IDataStoreService create(String serverURL, long timeout);
-
+
/**
- * Creates a monitored version of the service where
- * {@link IDataStoreService#cleanupSession(String)} is run asynchronously.
+ * Creates a monitored version of the service where {@link IDataStoreService#cleanupSession(String)} is run asynchronously.
*/
public IDataStoreService createMonitored(String serverURL, LogLevel logLevelForNotSuccessfulCalls);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IEntityOperationChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IEntityOperationChecker.java
index 0b0f75063c9..85c0fc2d75e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IEntityOperationChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IEntityOperationChecker.java
@@ -34,15 +34,13 @@ public interface IEntityOperationChecker
{
@RolesAllowed(
- { RoleWithHierarchy.INSTANCE_ADMIN, RoleWithHierarchy.INSTANCE_ETL_SERVER })
+ { RoleWithHierarchy.INSTANCE_ADMIN, RoleWithHierarchy.INSTANCE_ETL_SERVER })
public void assertInstanceSampleCreationAllowed(IAuthSession session,
- @AuthorizationGuard(guardClass = NewSamplePredicate.class)
- List<? extends NewSample> instanceSamples);
+ @AuthorizationGuard(guardClass = NewSamplePredicate.class) List<? extends NewSample> instanceSamples);
@RolesAllowed(
- { RoleWithHierarchy.INSTANCE_ADMIN, RoleWithHierarchy.INSTANCE_ETL_SERVER })
+ { RoleWithHierarchy.INSTANCE_ADMIN, RoleWithHierarchy.INSTANCE_ETL_SERVER })
public void assertInstanceSampleUpdateAllowed(IAuthSession session,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- List<? extends SampleOwnerIdentifier> instanceSamples);
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) List<? extends SampleOwnerIdentifier> instanceSamples);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IRelationshipService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IRelationshipService.java
index cc028262fc7..00af457ed65 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IRelationshipService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/IRelationshipService.java
@@ -50,27 +50,24 @@ public interface IRelationshipService
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_EXPERIMENT_TO_PROJECT")
public void assignExperimentToProject(IAuthSession session,
- @AuthorizationGuard(guardClass = ExperimentPEPredicate.class)
- ExperimentPE experiment, @AuthorizationGuard(guardClass = ProjectPEPredicate.class)
- ProjectPE project);
+ @AuthorizationGuard(guardClass = ExperimentPEPredicate.class) ExperimentPE experiment,
+ @AuthorizationGuard(guardClass = ProjectPEPredicate.class) ProjectPE project);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_SAMPLE_TO_PROJECT")
public void assignSampleToProject(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(guardClass = ProjectPEPredicate.class)
- ProjectPE project);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(guardClass = ProjectPEPredicate.class) ProjectPE project);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_PROJECT_TO_SPACE")
public void assignProjectToSpace(IAuthSession session,
- @AuthorizationGuard(guardClass = ProjectPEPredicate.class)
- ProjectPE project, @AuthorizationGuard(guardClass = SpacePEPredicate.class)
- SpacePE space);
+ @AuthorizationGuard(guardClass = ProjectPEPredicate.class) ProjectPE project,
+ @AuthorizationGuard(guardClass = SpacePEPredicate.class) SpacePE space);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
@@ -78,149 +75,130 @@ public interface IRelationshipService
RoleWithHierarchy.SPACE_USER })
@Capability("ASSIGN_SAMPLE_TO_EXPERIMENT")
public void assignSampleToExperiment(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(guardClass = ExperimentPEPredicate.class)
- ExperimentPE experiment);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(guardClass = ExperimentPEPredicate.class) ExperimentPE experiment);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("UNASSIGN_SAMPLE_FROM_EXPERIMENT")
public void checkCanUnassignSampleFromExperiment(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("UNASSIGN_SAMPLE_FROM_EXPERIMENT")
public void unassignSampleFromExperiment(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("UNASSIGN_SAMPLE_FROM_PROJECT")
public void unassignSampleFromProject(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.INSTANCE_ETL_SERVER, RoleWithHierarchy.INSTANCE_ADMIN })
@Capability("UNSHARE_SAMPLE")
public void unshareSample(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(guardClass = SpacePEPredicate.class)
- SpacePE space);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(guardClass = SpacePEPredicate.class) SpacePE space);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_SAMPLE_TO_SPACE")
public void assignSampleToSpace(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(guardClass = SpacePEPredicate.class)
- SpacePE space);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(guardClass = SpacePEPredicate.class) SpacePE space);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.INSTANCE_ETL_SERVER, RoleWithHierarchy.INSTANCE_ADMIN })
@Capability("SHARE_SAMPLE")
public void shareSample(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_DATASET_TO_EXPERIMENT")
public void assignDataSetToExperiment(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE dataSet, @AuthorizationGuard(guardClass = ExperimentPEOrNullPredicate.class)
- ExperimentPE experimentOrNull);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE dataSet,
+ @AuthorizationGuard(guardClass = ExperimentPEOrNullPredicate.class) ExperimentPE experimentOrNull);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ASSIGN_DATASET_TO_SAMPLE")
public void assignDataSetToSample(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE dataSet, @AuthorizationGuard(guardClass = SamplePEOrNullPredicate.class)
- SamplePE sampleOrNull);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE dataSet,
+ @AuthorizationGuard(guardClass = SamplePEOrNullPredicate.class) SamplePE sampleOrNull);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_USER })
@Capability("ADD_PARENT_TO_SAMPLE")
public void addParentToSample(IAuthSession session,
- @AuthorizationGuard(name = "SAMPLE", guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(name = "PARENT", guardClass = SamplePEPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_USER })
- SamplePE parent);
+ @AuthorizationGuard(name = "SAMPLE", guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(name = "PARENT", guardClass = SamplePEPredicate.class,
+ rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_USER }) SamplePE parent);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("REMOVE_PARENT_FROM_SAMPLE")
public void removeParentFromSample(IAuthSession session,
- @AuthorizationGuard(name = "SAMPLE", guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(name = "PARENT", guardClass = SamplePEPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_USER })
- SamplePE parent);
+ @AuthorizationGuard(name = "SAMPLE", guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(name = "PARENT", guardClass = SamplePEPredicate.class,
+ rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_USER }) SamplePE parent);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ADD_CONTAINER_TO_SAMPLE")
public void assignSampleToContainer(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample, @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE container);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample,
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE container);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("REMOVE_CONTAINER_FROM_SAMPLE")
public void removeSampleFromContainer(IAuthSession session,
- @AuthorizationGuard(guardClass = SamplePEPredicate.class)
- SamplePE sample);
+ @AuthorizationGuard(guardClass = SamplePEPredicate.class) SamplePE sample);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ADD_PARENT_TO_DATASET")
public void addParentToDataSet(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE parent);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE parent);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("REMOVE_PARENT_FROM_DATASET")
public void removeParentFromDataSet(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE parent);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE parent);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("ADD_CONTAINER_TO_DATASET")
public void assignDataSetToContainer(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE container);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE data,
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE container);
@Transactional(propagation = Propagation.MANDATORY)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER, RoleWithHierarchy.SPACE_POWER_USER })
@Capability("REMOVE_CONTAINER_FROM_DATASET")
public void removeDataSetFromContainer(IAuthSession session,
- @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE data, @AuthorizationGuard(guardClass = DataPEPredicate.class)
- DataPE container);
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE data,
+ @AuthorizationGuard(guardClass = DataPEPredicate.class) DataPE container);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrors.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrors.java
index 750ab4ead3c..817cb261ba7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrors.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrors.java
@@ -35,8 +35,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ScriptPE;
class PropertiesBatchEvaluationErrors
{
/**
- * limitation on the number of ErrorDetails objects kept in memory. This guards us from scripts
- * generating unique error messages for excessively large batches.
+ * limitation on the number of ErrorDetails objects kept in memory. This guards us from scripts generating unique error messages for excessively
+ * large batches.
*/
static final int MAX_ERROR_DETAILS_KEPT = 10;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
index 0279bbee17f..3a088d4a228 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
@@ -35,8 +35,8 @@ import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedProperty
public class AbstractMaterialBusinessObject extends AbstractBusinessObject
{
protected AbstractMaterialBusinessObject(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, EntityKind.MATERIAL, managedPropertyEvaluatorFactory, dataSetTypeChecker,
@@ -45,11 +45,11 @@ public class AbstractMaterialBusinessObject extends AbstractBusinessObject
protected AbstractMaterialBusinessObject(final IDAOFactory daoFactory, final Session session,
final IEntityPropertiesConverter entityPropertiesConverter,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
- super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
}
@@ -59,7 +59,7 @@ public class AbstractMaterialBusinessObject extends AbstractBusinessObject
{
assert materialId != null : "Material technical id unspecified.";
String[] connections =
- { PROPERTY_TYPES };
+ { PROPERTY_TYPES };
final MaterialPE result = getMaterialDAO().tryGetByTechId(materialId, connections);
if (result == null)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index 23379bfe8b5..ec1bec10939 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -80,7 +80,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
AbstractSampleBusinessObject(final IDAOFactory daoFactory, final Session session,
IRelationshipService relationshipService,
IEntityOperationChecker entityOperationChecker,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
super(daoFactory, session, EntityKind.SAMPLE, managedPropertyEvaluatorFactory, dataSetTypeChecker,
@@ -92,10 +92,10 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
final IEntityPropertiesConverter entityPropertiesConverter,
IRelationshipService relationshipService,
IEntityOperationChecker entityOperationChecker,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
- super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
this.entityOperationChecker = entityOperationChecker;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
index d44a978c181..9b9b7183fc4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
@@ -48,8 +48,8 @@ abstract class AbstractSampleIdentifierBusinessObject extends AbstractBusinessOb
private final SampleOwnerFinder sampleOwnerFinder;
AbstractSampleIdentifierBusinessObject(final IDAOFactory daoFactory, final Session session,
- EntityKind entityKind, IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ EntityKind entityKind, IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, entityKind, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -58,8 +58,8 @@ abstract class AbstractSampleIdentifierBusinessObject extends AbstractBusinessOb
public AbstractSampleIdentifierBusinessObject(IDAOFactory daoFactory, Session session,
IEntityPropertiesConverter converter,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, converter, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
index 47f309101dd..b945eb5bc08 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AttachmentBO.java
@@ -43,8 +43,8 @@ public final class AttachmentBO extends AbstractBusinessObject implements IAttac
private boolean dataChanged;
public AttachmentBO(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AuthorizationGroupBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AuthorizationGroupBO.java
index d4b506f2c72..c4619477454 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AuthorizationGroupBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AuthorizationGroupBO.java
@@ -57,8 +57,8 @@ public class AuthorizationGroupBO extends AbstractBusinessObject implements IAut
@Private
AuthorizationGroupBO(IDAOFactory daoFactory, Session session,
IAuthorizationGroupFactory factory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -66,11 +66,11 @@ public class AuthorizationGroupBO extends AbstractBusinessObject implements IAut
}
public AuthorizationGroupBO(IDAOFactory daoFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
- this(daoFactory, session, new AuthorizationGroupFactory(), managedPropertyEvaluatorFactory,
+ this(daoFactory, session, new AuthorizationGroupFactory(), managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/CorePluginTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/CorePluginTable.java
index ac1ef379b56..90f98997e63 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/CorePluginTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/CorePluginTable.java
@@ -52,8 +52,8 @@ public final class CorePluginTable extends AbstractBusinessObject implements ICo
public CorePluginTable(IDAOFactory daoFactory, Session session,
IMasterDataScriptRegistrationRunner masterDataScriptRunner,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataAccessExceptionTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataAccessExceptionTranslator.java
index 035eff2b4e8..09190c75d14 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataAccessExceptionTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataAccessExceptionTranslator.java
@@ -26,16 +26,14 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
- * This class converts the low-level {@link DataAccessException} into a high-level exception
- * {@link UserFailureException}.
+ * This class converts the low-level {@link DataAccessException} into a high-level exception {@link UserFailureException}.
* <p>
- * This class can only be used on the business layer side as, only there, we dispose of enough
- * information to decide whether or not a <code>DataAccessException</code> should be translated into
- * an high-level exception.
+ * This class can only be used on the business layer side as, only there, we dispose of enough information to decide whether or not a
+ * <code>DataAccessException</code> should be translated into an high-level exception.
* </p>
* <p>
- * Do not try to put this logic on the <i>DAO</i> level or do not try to automate this conversion as
- * we want full control on this translation and we prefer to call it manually.
+ * Do not try to put this logic on the <i>DAO</i> level or do not try to automate this conversion as we want full control on this translation and we
+ * prefer to call it manually.
* </p>
*
* @author Tomasz Pylak
@@ -61,17 +59,14 @@ public final class DataAccessExceptionTranslator
}
/**
- * Analyzes given <code>DataAccessException</code> and converts it into a
- * <code>UserFailureException</code>.
+ * Analyzes given <code>DataAccessException</code> and converts it into a <code>UserFailureException</code>.
* <p>
- * This method is typically used by <i>creator</i> methods (methods which inserts a new object
- * into the database) and <i>deletion</i> methods.
+ * This method is typically used by <i>creator</i> methods (methods which inserts a new object into the database) and <i>deletion</i> methods.
* </p>
*
- * @param subject short description of the object that got blessed by the unique/foreign key
- * violation constraint.
- * @param entityKindOrNull entity kind of the subject object (if specified can make the error
- * message more detailed especially for foreign key violation upon deletion)
+ * @param subject short description of the object that got blessed by the unique/foreign key violation constraint.
+ * @param entityKindOrNull entity kind of the subject object (if specified can make the error message more detailed especially for foreign key
+ * violation upon deletion)
*/
public final static void throwException(final DataAccessException exception,
final String subject, final EntityKind entityKindOrNull) throws UserFailureException
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index d7a8f5569a0..ee90b77299d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -1128,11 +1128,11 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
updateSample(dataSet, sampleIdentifierOrNull);
} else
{
- updateExperiment(dataSet,dataSetUpdates.getExperimentIdentifierOrNull());
+ updateExperiment(dataSet, dataSetUpdates.getExperimentIdentifierOrNull());
}
} else if (details.isExperimentUpdateRequested() && dataSetUpdates.getExperimentIdentifierOrNull() != null)
{
- updateExperiment(dataSet,dataSetUpdates.getExperimentIdentifierOrNull());
+ updateExperiment(dataSet, dataSetUpdates.getExperimentIdentifierOrNull());
}
if (details.isContainerUpdateRequested())
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DeletionTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DeletionTable.java
index 21241e86d28..1ec091f47f2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DeletionTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DeletionTable.java
@@ -44,8 +44,8 @@ public class DeletionTable extends AbstractBusinessObject implements IDeletionTa
private List<Deletion> deletions;
public DeletionTable(IDAOFactory daoFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
index a1922fffe93..9a206c8ad57 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
@@ -27,11 +27,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
/**
- * Generates unique codes for openBIS entities. It uses database sequences as a base for the code
- * generation. Moreover it verifies that the generated codes are in fact unique (i.e. entities with
- * such codes do not exist yet). If it finds that the new generated code is already used by an
- * existing entity (e.g. the entity code was manually entered by a user) then it regenerates the
- * code until it is unique.
+ * Generates unique codes for openBIS entities. It uses database sequences as a base for the code generation. Moreover it verifies that the generated
+ * codes are in fact unique (i.e. entities with such codes do not exist yet). If it finds that the new generated code is already used by an existing
+ * entity (e.g. the entity code was manually entered by a user) then it regenerates the code until it is unique.
*
* @author pkupczyk
*/
@@ -74,10 +72,8 @@ public class EntityCodeGenerator
/**
* Generate unique codes for openBIS entities.
*
- * @param codePrefix Prefix for the generated codes (e.g. when "ABC-" then codes will be
- * "ABC-1", "ABC-2", ...)
- * @param entityKind Kind of an entity the codes should be generated for (different kinds of
- * entities use different database sequences).
+ * @param codePrefix Prefix for the generated codes (e.g. when "ABC-" then codes will be "ABC-1", "ABC-2", ...)
+ * @param entityKind Kind of an entity the codes should be generated for (different kinds of entities use different database sequences).
* @param numberOfCodes Number of codes to be generated.
*/
public List<String> generateCodes(String codePrefix, EntityKind entityKind, int numberOfCodes)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypeBO.java
index 46f6920bb1f..8cf51ac30e1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypeBO.java
@@ -69,8 +69,8 @@ public final class EntityTypeBO extends AbstractBusinessObject implements IEntit
private EntityKind entityKind;
public EntityTypeBO(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypePropertyTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypePropertyTypeBO.java
index f7f6c9b826d..bf9d8b1c03d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypePropertyTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityTypePropertyTypeBO.java
@@ -65,8 +65,8 @@ public class EntityTypePropertyTypeBO extends AbstractBusinessObject implements
@Private
EntityTypePropertyTypeBO(IDAOFactory daoFactory, Session session, EntityKind entityKind,
IEntityPropertiesConverter converter,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -75,8 +75,8 @@ public class EntityTypePropertyTypeBO extends AbstractBusinessObject implements
}
public EntityTypePropertyTypeBO(IDAOFactory daoFactory, Session session, EntityKind entityKind,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index fdf638d1d3d..1b2e59b213b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -89,20 +89,20 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
public ExperimentBO(final IDAOFactory daoFactory, final Session session,
IRelationshipService relationshipService,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
- super(daoFactory, session, EntityKind.EXPERIMENT, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, EntityKind.EXPERIMENT, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
}
ExperimentBO(final IDAOFactory daoFactory, final Session session,
final IEntityPropertiesConverter entityPropertiesConverter,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
- super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
index c279e73cb21..2b13d09a881 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentTable.java
@@ -70,8 +70,8 @@ public final class ExperimentTable extends AbstractBusinessObject implements IEx
ExperimentTable(final IDAOFactory daoFactory, final Session session,
IEntityPropertiesConverter converter,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, converter, managedPropertyEvaluatorFactory, dataSetTypeChecker,
@@ -80,10 +80,10 @@ public final class ExperimentTable extends AbstractBusinessObject implements IEx
public ExperimentTable(final IDAOFactory daoFactory, final Session session,
IRelationshipService relationshipService,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
- super(daoFactory, session, EntityKind.EXPERIMENT, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, EntityKind.EXPERIMENT, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomColumnBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomColumnBO.java
index 6a6a7fff63a..efb3b99650a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomColumnBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomColumnBO.java
@@ -47,8 +47,8 @@ public class GridCustomColumnBO extends AbstractBusinessObject implements
private GridCustomColumnPE column;
public GridCustomColumnBO(IDAOFactory daoFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomFilterBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomFilterBO.java
index c33dc966d9b..9198cd8b55c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomFilterBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/GridCustomFilterBO.java
@@ -41,8 +41,8 @@ public class GridCustomFilterBO extends AbstractBusinessObject implements
private GridCustomFilterPE filter;
public GridCustomFilterBO(IDAOFactory daoFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAttachmentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAttachmentBO.java
index bd076e0d624..a9e3fd0c8dd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAttachmentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAttachmentBO.java
@@ -30,11 +30,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
public interface IAttachmentBO
{
/**
- * Deletes specified {@link AttachmentHolderPE} attachments (all versions with given file names)
- * for specified reason.
+ * Deletes specified {@link AttachmentHolderPE} attachments (all versions with given file names) for specified reason.
*
- * @param fileNames list of file names of attachments to be deleted (there will be no error if
- * there are no attachments with these file names attached to specified holder)
+ * @param fileNames list of file names of attachments to be deleted (there will be no error if there are no attachments with these file names
+ * attached to specified holder)
* @throws UserFailureException if holder with given technical identifier is not found.
*/
void deleteHolderAttachments(final AttachmentHolderPE holder, final List<String> fileNames,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAuthorizationGroupBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAuthorizationGroupBO.java
index 1a857e8b319..a36e6818820 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAuthorizationGroupBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAuthorizationGroupBO.java
@@ -32,17 +32,15 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
public interface IAuthorizationGroupBO extends IBusinessObject
{
/**
- * Defines a authorization group. After invocation of this method
- * {@link IAuthorizationGroupBO#save()} should be invoked to store the new authorization group
- * in the Data Access Layer.
+ * Defines a authorization group. After invocation of this method {@link IAuthorizationGroupBO#save()} should be invoked to store the new
+ * authorization group in the Data Access Layer.
*/
void define(final NewAuthorizationGroup newAuthorizationGroup) throws UserFailureException;
/**
* Deletes the authorization group.
*
- * @throws UserFailureException if authorization group with given technical identifier is not
- * found.
+ * @throws UserFailureException if authorization group with given technical identifier is not found.
*/
public void deleteByTechId(TechId authGroupId, String reason);
@@ -57,14 +55,12 @@ public interface IAuthorizationGroupBO extends IBusinessObject
public AuthorizationGroupPE getAuthorizationGroup();
/**
- * Loads authorization group with given technical id or throws exception if no such group
- * exists.
+ * Loads authorization group with given technical id or throws exception if no such group exists.
*/
public void loadByTechId(TechId authorizatonGroupId);
/**
- * Adds persons with given codes to the loaded authorization group. Returns a list of users
- * codes not registered in the system.
+ * Adds persons with given codes to the loaded authorization group. Returns a list of users codes not registered in the system.
*/
public List<String> addPersons(List<String> personsCodes);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IBusinessObject.java
index 4f891dd32ea..d5978062ffa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IBusinessObject.java
@@ -21,15 +21,14 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
* Common method(s) all Business Objects and Tables have to implement.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IBusinessObject
{
/**
* Writes changed or added data to the Data Access Layers.
*
- * @throws UnsupportedOperationException if saving isn't supported because it is a read-only
- * object.
+ * @throws UnsupportedOperationException if saving isn't supported because it is a read-only object.
*/
public void save() throws UserFailureException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
index 5d15adaa6fa..d092f65a723 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
- * The <i>generic</i> specific <i>Business Object</i> factory. Each method creates one kind of a
- * business object.
+ * The <i>generic</i> specific <i>Business Object</i> factory. Each method creates one kind of a business object.
*
* @author Tomasz Pylak
*/
@@ -46,7 +45,7 @@ public interface ICommonBusinessObjectFactory extends IAbstractBussinessObjectFa
public IDataBO createDataBO(Session session);
public IDataSetTable createDataSetTable(final Session session);
-
+
public ISearchDomainSearcher createSearchDomainSearcher(Session session);
public IDeletedDataSetTable createDeletedDataSetTable(final Session session);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICorePluginTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICorePluginTable.java
index 7f617539d4d..311e72eb78d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICorePluginTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICorePluginTable.java
@@ -32,8 +32,7 @@ public interface ICorePluginTable
List<CorePlugin> listCorePluginsByName(String name);
/**
- * Registers a core plugin. The operation has no effect if the plugin has already been deployed
- * on the openBIS AS.
+ * Registers a core plugin. The operation has no effect if the plugin has already been deployed on the openBIS AS.
*/
public void registerPlugin(CorePlugin plugin, ICorePluginResourceLoader resourceLoader);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypeBO.java
index 4d3896e8da5..3830cd17404 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypeBO.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
- * Operations on {@link EntityTypePE} extensions. Note that you can use only one <em>define</em>
- * method at a time.
+ * Operations on {@link EntityTypePE} extensions. Note that you can use only one <em>define</em> method at a time.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypePropertyTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypePropertyTypeBO.java
index 4be23daee68..2628662fbbc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypePropertyTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityTypePropertyTypeBO.java
@@ -38,8 +38,7 @@ public interface IEntityTypePropertyTypeBO
void loadAssignment(String propertyTypeCode, String entityTypeCode);
/**
- * Returns number of property values used by entities for assignment between specified property
- * type and entity type.
+ * Returns number of property values used by entities for assignment between specified property type and entity type.
*/
int countAssignmentValues(String propertyTypeCode, String entityTypeCode);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
index 75f948aa917..9b6884a6062 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
@@ -36,11 +36,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
public interface IExternalDataTable
{
/**
- * Loads data sets specified by their codes. Data set codes will be ignored if no
- * {@link ExternalDataPE} could be found. Properties will be loaded too depending on
- * <var>withProperties</var> value. Optionally if <var>lockForUpdate</var> is <var>true</var>
- * all updates to loaded data sets from other transactions will be blocked until current
- * transaction is finished.
+ * Loads data sets specified by their codes. Data set codes will be ignored if no {@link ExternalDataPE} could be found. Properties will be loaded
+ * too depending on <var>withProperties</var> value. Optionally if <var>lockForUpdate</var> is <var>true</var> all updates to loaded data sets
+ * from other transactions will be blocked until current transaction is finished.
*/
void loadByDataSetCodes(List<String> dataSetCodes, boolean withProperties, boolean lockForUpdate);
@@ -77,11 +75,10 @@ public interface IExternalDataTable
String uploadLoadedDataSetsToCIFEX(DataSetUploadContext uploadContext);
/**
- * Schedules archiving of loaded data sets. Only available data sets that are not locked will be
- * archived.
+ * Schedules archiving of loaded data sets. Only available data sets that are not locked will be archived.
*
- * @param removeFromDataStore when set to <code>true</code> the data sets will be removed from
- * the data store after a successful archiving operation.
+ * @param removeFromDataStore when set to <code>true</code> the data sets will be removed from the data store after a successful archiving
+ * operation.
* @return number of data sets scheduled for archiving.
*/
int archiveDatasets(boolean removeFromDataStore);
@@ -112,8 +109,7 @@ public interface IExternalDataTable
List<String> datasetCodes);
/**
- * Schedules processing of specified datasets with specified parameter bindings using the
- * specified datastore service.
+ * Schedules processing of specified datasets with specified parameter bindings using the specified datastore service.
*
* @param parameterBindings Should be a map where additional entries can be added.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IGridCustomFilterOrColumnBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IGridCustomFilterOrColumnBO.java
index e88c28b9a5c..e1be193dd8e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IGridCustomFilterOrColumnBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IGridCustomFilterOrColumnBO.java
@@ -31,9 +31,8 @@ public interface IGridCustomFilterOrColumnBO extends IEntityBusinessObject
{
/**
- * Defines a new grid custom filter or column. After invocation of this method
- * {@link IBusinessObject#save()} should be invoked to store the new group in the <i>Data Access
- * Layer</i>.
+ * Defines a new grid custom filter or column. After invocation of this method {@link IBusinessObject#save()} should be invoked to store the new
+ * group in the <i>Data Access Layer</i>.
*/
public void define(NewColumnOrFilter filterOrColumn) throws UserFailureException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IPropertyTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IPropertyTypeBO.java
index 70459793e51..702b1906929 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IPropertyTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IPropertyTypeBO.java
@@ -33,8 +33,8 @@ public interface IPropertyTypeBO extends IBusinessObject
/**
* Defines a new property type.
* <p>
- * After invocation of this method {@link IBusinessObject#save()} should be invoked to store the
- * new property type in the <i>Data Access Layer</i>.
+ * After invocation of this method {@link IBusinessObject#save()} should be invoked to store the new property type in the <i>Data Access
+ * Layer</i>.
* </p>
*
* @throws UserFailureException if <var>propertyType</var> does already exist.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
index dc09b130df0..b3ca6abbebe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
@@ -36,8 +36,7 @@ public interface ISampleTable
{
/**
- * Lists samples filtered by specified criteria, see {@link ListSamplesByPropertyCriteria} to
- * see the details.
+ * Lists samples filtered by specified criteria, see {@link ListSamplesByPropertyCriteria} to see the details.
*/
void loadSamplesByCriteria(final ListSamplesByPropertyCriteria criteria);
@@ -53,9 +52,8 @@ public interface ISampleTable
throws UserFailureException;
/**
- * This method should be invoked before a series of prepareForUpdateXXX() method calls. It
- * checks the data before the update can be started. For instance, it verifies versions of
- * objects for Optimistic Locking.
+ * This method should be invoked before a series of prepareForUpdateXXX() method calls. It checks the data before the update can be started. For
+ * instance, it verifies versions of objects for Optimistic Locking.
*/
public void checkBeforeUpdate(List<SampleUpdatesDTO> updates) throws UserFailureException;
@@ -67,10 +65,9 @@ public interface ISampleTable
public void prepareForUpdate(List<SampleBatchUpdatesDTO> updates) throws UserFailureException;
/**
- * Comparable to {@link #prepareForUpdate(List)} but takes a {@link SampleUpdatesDTO} object
- * instead of a {@link SampleBatchUpdatesDTO} object. Whereas prepareForUpdate only changes the
- * fields requested in the updates' details object, this method changes the samples to match the
- * updates object.
+ * Comparable to {@link #prepareForUpdate(List)} but takes a {@link SampleUpdatesDTO} object instead of a {@link SampleBatchUpdatesDTO} object.
+ * Whereas prepareForUpdate only changes the fields requested in the updates' details object, this method changes the samples to match the updates
+ * object.
*/
void prepareForUpdateWithSampleUpdates(List<SampleUpdatesDTO> updates)
throws UserFailureException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
index d880533b630..fd43a14b9a5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
@@ -39,6 +39,5 @@ public interface ISearchDomainSearcher
*/
List<SearchDomainSearchResultWithFullEntity> searchForEntitiesWithSequences(String preferredSearchDomainOrNull,
String sequenceSnippet, Map<String, String> optionalParametersOrNull);
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISpaceBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISpaceBO.java
index e7c3957fe0d..a39a4974804 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISpaceBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISpaceBO.java
@@ -31,9 +31,8 @@ public interface ISpaceBO extends IEntityBusinessObject
{
/**
- * Defines a new space of specified code for the home database instance. After invocation of
- * this method {@link IBusinessObject#save()} should be invoked to store the new group in the
- * <i>Data Access Layer</i>.
+ * Defines a new space of specified code for the home database instance. After invocation of this method {@link IBusinessObject#save()} should be
+ * invoked to store the new group in the <i>Data Access Layer</i>.
*
* @throws UserFailureException if <code>group</code> does already exist.
*/
@@ -42,8 +41,7 @@ public interface ISpaceBO extends IEntityBusinessObject
/**
* Loads a space described by identifier from Database Layer.
*
- * @throws UserFailureException if <code>groupIdentifier</code> does not describe existing
- * group.
+ * @throws UserFailureException if <code>groupIdentifier</code> does not describe existing group.
*/
public void load(SpaceIdentifier spaceIdentifier) throws UserFailureException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
index d36803d002b..a08e55b94ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
@@ -178,8 +178,8 @@ public final class MaterialBO extends AbstractMaterialBusinessObject implements
{
List<Long> idsToDelete = Collections.singletonList(material.getId());
String content = historyCreator.apply(getSessionFactory().getCurrentSession(), idsToDelete,
- MaterialDAO.sqlPropertyHistory, null, MaterialDAO.sqlAttributesHistory, null,
- null, session.tryGetPerson());
+ MaterialDAO.sqlPropertyHistory, null, MaterialDAO.sqlAttributesHistory, null,
+ null, session.tryGetPerson());
getMaterialDAO().delete(material);
getEventDAO().persist(createDeletionEvent(material, session.tryGetPerson(), reason, content));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
index 4dd9f49fd23..966616efb50 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
@@ -59,8 +59,8 @@ public final class MaterialTable extends AbstractMaterialBusinessObject implemen
private boolean dataChanged;
public MaterialTable(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -70,11 +70,11 @@ public final class MaterialTable extends AbstractMaterialBusinessObject implemen
// for tests only
MaterialTable(final IDAOFactory daoFactory, final Session session,
final IEntityPropertiesConverter entityPropertiesConverter, List<MaterialPE> materials,
- boolean dataChanged, IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ boolean dataChanged, IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
- super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
+ super(daoFactory, session, entityPropertiesConverter, managedPropertyEvaluatorFactory,
dataSetTypeChecker, relationshipService);
this.materials = materials;
this.dataChanged = dataChanged;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MetaprojectBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MetaprojectBO.java
index a7da2747e5e..24ef0a5e106 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MetaprojectBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MetaprojectBO.java
@@ -83,8 +83,8 @@ public class MetaprojectBO extends AbstractBusinessObject implements IMetaprojec
public MetaprojectBO(final IDAOFactory daoFactory, IExperimentBO experimentBO,
ISampleBO sampleBO, IDataBO dataBO, IMaterialBO materialBO, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/NextExceptionFallbackExceptionTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/NextExceptionFallbackExceptionTranslator.java
index 55cad85849f..e4eff0faedf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/NextExceptionFallbackExceptionTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/NextExceptionFallbackExceptionTranslator.java
@@ -21,8 +21,7 @@ import java.sql.SQLException;
import org.springframework.jdbc.support.SQLStateSQLExceptionTranslator;
/**
- * A translator that takes into includes the message from the next exception in the chain as this
- * often has the real cause.
+ * A translator that takes into includes the message from the next exception in the chain as this often has the real cause.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ProjectBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ProjectBO.java
index d8cb2b41e91..183c65a95c9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ProjectBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ProjectBO.java
@@ -350,7 +350,7 @@ public final class ProjectBO extends AbstractBusinessObject implements IProjectB
private static final String propertyHistoryQuery =
"SELECT 1 as a, 1 as b, 1 as c, 1 as d, 1 as e, 1 as f, 1 as g, 1 as h, 1 as i FROM materials WHERE id = -1 and id IN (:entityIds)";
-
+
private static final String ENTITY_TYPE = "case "
+ "when h.space_id is not null then 'SPACE' "
+ "when h.expe_id is not null then 'EXPERIMENT' "
@@ -408,8 +408,8 @@ public final class ProjectBO extends AbstractBusinessObject implements IProjectB
{
List<Long> idsToDelete = Collections.singletonList(projectId.getId());
String content = historyCreator.apply(getSessionFactory().getCurrentSession(), idsToDelete,
- propertyHistoryQuery, relationshipHistoryQuery, sqlAttributesHistory,
- Arrays.asList(project), null, session.tryGetPerson());
+ propertyHistoryQuery, relationshipHistoryQuery, sqlAttributesHistory,
+ Arrays.asList(project), null, session.tryGetPerson());
getProjectDAO().delete(project);
getEventDAO().persist(createDeletionEvent(project, session.tryGetPerson(), reason, content));
} else
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeBO.java
index 3ff528e66d8..2aa6d30377c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeBO.java
@@ -63,8 +63,8 @@ public final class PropertyTypeBO extends VocabularyBO implements IPropertyTypeB
private PropertyTypePE propertyTypePE;
public PropertyTypeBO(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeTable.java
index 09116c3ead3..1626d9d4369 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyTypeTable.java
@@ -36,8 +36,8 @@ public final class PropertyTypeTable extends AbstractBusinessObject implements I
private List<PropertyTypePE> propertyTypes;
public PropertyTypeTable(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/RootEntitiesFinder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/RootEntitiesFinder.java
index 3ca8ace59cf..cd14721dc50 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/RootEntitiesFinder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/RootEntitiesFinder.java
@@ -32,8 +32,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.IDeletablePE;
import ch.systemsx.cisd.openbis.generic.shared.translator.DeletedEntityTranslator;
/**
- * Helper class for finding the root entities of entities belonging to the same deletion event. It
- * is assumed that experiments are added before samples which are added before data sets.
+ * Helper class for finding the root entities of entities belonging to the same deletion event. It is assumed that experiments are added before
+ * samples which are added before data sets.
*
* @author Franz-Josef Elmer
* @author Kaloyan Enimanev
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 812c5889ec2..c008c9b0a64 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -69,7 +69,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
public SampleBO(final IDAOFactory daoFactory, final Session session,
final IRelationshipService relationshipService,
final IEntityOperationChecker entityOperationChecker,
- final IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ final IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
super(daoFactory, session, relationshipService, entityOperationChecker,
@@ -80,7 +80,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
final IEntityPropertiesConverter entityPropertiesConverter,
IRelationshipService relationshipService,
final IEntityOperationChecker entityOperationChecker,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
DataSetTypeWithoutExperimentChecker dataSetTypeChecker)
{
super(daoFactory, session, entityPropertiesConverter, relationshipService,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleCodeGeneratorByType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleCodeGeneratorByType.java
index 5e4b2333b99..405afeae627 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleCodeGeneratorByType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleCodeGeneratorByType.java
@@ -42,7 +42,7 @@ public class SampleCodeGeneratorByType extends EntityCodeGenerator
super(daoFactory);
this.maxQuery = QueryTool.getManagedQuery(MaxQuery.class);
}
-
+
@Override
public List<String> generateCodes(String codePrefix, EntityKind entityKind, int numberOfCodes)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBO.java
index 673240c8689..dc638865bf8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ScriptBO.java
@@ -55,8 +55,8 @@ public final class ScriptBO extends AbstractBusinessObject implements IScriptBO
private final IJythonEvaluatorPool jythonEvaluatorPool;
public ScriptBO(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService,
IJythonEvaluatorPool jythonEvaluationPool)
{
@@ -67,8 +67,8 @@ public final class ScriptBO extends AbstractBusinessObject implements IScriptBO
@Private
// for testing
ScriptBO(final IDAOFactory daoFactory, final Session session, IScriptFactory scriptFactory,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService,
IJythonEvaluatorPool jythonEvaluationPool)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
index 407d048098e..a3713888f06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
@@ -52,13 +52,11 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SearchDomainSearcher extends AbstractBusinessObject implements ISearchDomainSearcher
{
- private static final Map<Long, Set<Metaproject>> EMPTY_METAPROJECTS = Collections.<Long, Set<Metaproject>>emptyMap();
+ private static final Map<Long, Set<Metaproject>> EMPTY_METAPROJECTS = Collections.<Long, Set<Metaproject>> emptyMap();
private static final IKeyExtractor<String, IEntityInformationHolderWithPermId> PERM_ID_EXTRACTOR =
new IKeyExtractor<String, IEntityInformationHolderWithPermId>()
@@ -72,9 +70,9 @@ public class SearchDomainSearcher extends AbstractBusinessObject implements ISea
private final IDataStoreServiceFactory dssFactory;
- public SearchDomainSearcher(IDAOFactory daoFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker, IRelationshipService relationshipService,
+ public SearchDomainSearcher(IDAOFactory daoFactory, Session session,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker, IRelationshipService relationshipService,
IDataStoreServiceFactory dssFactory)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -98,11 +96,10 @@ public class SearchDomainSearcher extends AbstractBusinessObject implements ISea
}
@Override
- public List<SearchDomainSearchResultWithFullEntity> searchForEntitiesWithSequences(String preferredSearchDomainOrNull,
+ public List<SearchDomainSearchResultWithFullEntity> searchForEntitiesWithSequences(String preferredSearchDomainOrNull,
String sequenceSnippet, Map<String, String> optionalParametersOrNull)
{
- List<SearchDomainSearchResult> searchResults
- = askAllDataStoreServers(preferredSearchDomainOrNull, sequenceSnippet, optionalParametersOrNull);
+ List<SearchDomainSearchResult> searchResults = askAllDataStoreServers(preferredSearchDomainOrNull, sequenceSnippet, optionalParametersOrNull);
return enrichWithEntities(searchResults);
}
@@ -179,8 +176,7 @@ public class SearchDomainSearcher extends AbstractBusinessObject implements ISea
{
EntityLoader loader = entry.getKey();
List<String> permIds = entry.getValue();
- List<IEntityInformationHolderWithPermId> entities
- = loader.loadEntities(this, managedPropertyEvaluatorFactory, permIds);
+ List<IEntityInformationHolderWithPermId> entities = loader.loadEntities(this, managedPropertyEvaluatorFactory, permIds);
result.put(loader, new TableMap<String, IEntityInformationHolderWithPermId>(entities, PERM_ID_EXTRACTOR));
}
return result;
@@ -273,7 +269,7 @@ public class SearchDomainSearcher extends AbstractBusinessObject implements ISea
{
return permId;
}
-
+
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
index fd7ee1c61e9..7e3a0d357d8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
@@ -79,8 +79,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
*/
public class TrashBO extends AbstractBusinessObject implements ITrashBO
{
- static final EnumSet<DataSetFetchOption> DATA_SET_FETCH_OPTIONS
- = EnumSet.of(DataSetFetchOption.EXPERIMENT, DataSetFetchOption.SAMPLE);
+ static final EnumSet<DataSetFetchOption> DATA_SET_FETCH_OPTIONS = EnumSet.of(DataSetFetchOption.EXPERIMENT, DataSetFetchOption.SAMPLE);
private enum CascadeSampleDependentComponents
{
@@ -92,8 +91,8 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
private DeletionPE deletion;
public TrashBO(IDAOFactory daoFactory, ICommonBusinessObjectFactory boFactory, Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
@@ -125,7 +124,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
public void trashDataSets(List<TechId> dataSetIds)
{
assert deletion != null;
-
+
IDatasetLister datasetLister = boFactory.createDatasetLister(session);
final Set<TechId> experimentIds = new HashSet<TechId>();
final Set<TechId> sampleIds = new HashSet<TechId>();
@@ -135,7 +134,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
if (sample != null)
{
sampleIds.add(new TechId(sample));
- }
+ }
if (dataSet.getExperiment() != null)
{
experimentIds.add(new TechId(dataSet.getExperiment()));
@@ -160,7 +159,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
return filtered;
}
-
+
private boolean contains(Set<TechId> ids, IIdAndCodeHolder entity)
{
return entity != null && ids.contains(new TechId(HibernateUtils.getId(entity)));
@@ -187,8 +186,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
assert deletion != null;
TrashOperationsManager trashManager = new TrashOperationsManager(session, deletion, this, getTransactionTimeStamp());
- Set<TechId> allSampleIds
- = trashSamples(trashManager, sampleIds, CascadeSampleDependentComponents.TRUE, true);
+ Set<TechId> allSampleIds = trashSamples(trashManager, sampleIds, CascadeSampleDependentComponents.TRUE, true);
Set<TechId> experimentsOfSamples = getExperimentsOfSamples(sampleIds);
trashSampleDependentDataSets(trashManager, experimentsOfSamples, allSampleIds);
trashManager.trash();
@@ -209,8 +207,8 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
return experimentIds;
}
-
- private Set<TechId> trashSamples(TrashOperationsManager trashManager,
+
+ private Set<TechId> trashSamples(TrashOperationsManager trashManager,
final List<TechId> sampleIds, final CascadeSampleDependentComponents cascadeType, boolean isOriginalDeletion)
{
assert deletion != null;
@@ -229,22 +227,25 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
{
public List<TechId> filter(List<AbstractExternalData> dataSets);
}
-
+
private static interface IIdHolderProvider
{
public IIdHolder getIdHolder(AbstractExternalData dataSet);
}
-
+
private static final class DataSetFilter implements IDataSetFilter
{
private Set<Long> ids;
+
private IIdHolderProvider idHolderProvider;
+
DataSetFilter(Collection<TechId> ids, IIdHolderProvider idHolderProvider)
{
this.ids = new LinkedHashSet<Long>(TechId.asLongs(ids));
this.idHolderProvider = idHolderProvider;
-
+
}
+
@Override
public List<TechId> filter(List<AbstractExternalData> dataSets)
{
@@ -261,7 +262,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
}
- private void trashDataSets(TrashOperationsManager trashManager, final List<TechId> dataSetIds,
+ private void trashDataSets(TrashOperationsManager trashManager, final List<TechId> dataSetIds,
boolean isOriginalDeletion, IDataSetFilter filterOrNull)
{
assert deletion != null;
@@ -328,7 +329,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
}
- private Set<TechId> trashSampleDependentComponents(TrashOperationsManager trashManager,
+ private Set<TechId> trashSampleDependentComponents(TrashOperationsManager trashManager,
List<TechId> sampleIds)
{
final ISampleDAO sampleDAO = getSampleDAO();
@@ -349,7 +350,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
return trashSamples(trashManager, batchOperation.getResults(), CascadeSampleDependentComponents.FALSE, false);
}
- private void trashSampleDependentDataSets(TrashOperationsManager trashManager,
+ private void trashSampleDependentDataSets(TrashOperationsManager trashManager,
Set<TechId> experimentsOfSamples, Set<TechId> sampleIds)
{
AbstractQueryBatchOperation batchOperation =
@@ -367,14 +368,14 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
List<TechId> dataSetIds = batchOperation.getResults();
assertDataSetDeletionBusinessRules(experimentsOfSamples, sampleIds, dataSetIds);
trashDataSets(trashManager, dataSetIds, false, new DataSetFilter(sampleIds,
- new IIdHolderProvider()
- {
- @Override
- public IIdHolder getIdHolder(AbstractExternalData dataSet)
- {
- return dataSet.getSample();
- }
- }));
+ new IIdHolderProvider()
+ {
+ @Override
+ public IIdHolder getIdHolder(AbstractExternalData dataSet)
+ {
+ return dataSet.getSample();
+ }
+ }));
}
private Set<TechId> trashExperimentDependentSamples(TrashOperationsManager trashManager, Set<TechId> experimentIds)
@@ -394,7 +395,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
return trashSamples(trashManager, sampleIds, CascadeSampleDependentComponents.TRUE, false);
}
- private void trashExperimentDependentDataSets(TrashOperationsManager trashManager, Set<TechId> experimentIds,
+ private void trashExperimentDependentDataSets(TrashOperationsManager trashManager, Set<TechId> experimentIds,
Set<TechId> dependentSampleIds)
{
AbstractQueryBatchOperation batchOperation =
@@ -411,17 +412,17 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
List<TechId> dataSetIds = batchOperation.getResults();
assertDataSetDeletionBusinessRules(experimentIds, dependentSampleIds, dataSetIds);
trashDataSets(trashManager, dataSetIds, false, new DataSetFilter(experimentIds,
- new IIdHolderProvider()
- {
- @Override
- public IIdHolder getIdHolder(AbstractExternalData dataSet)
- {
- return dataSet.getExperiment();
- }
- }));
+ new IIdHolderProvider()
+ {
+ @Override
+ public IIdHolder getIdHolder(AbstractExternalData dataSet)
+ {
+ return dataSet.getExperiment();
+ }
+ }));
}
-
- private void assertDataSetDeletionBusinessRules(Set<TechId> experimentIds, Set<TechId> sampleIdes,
+
+ private void assertDataSetDeletionBusinessRules(Set<TechId> experimentIds, Set<TechId> sampleIdes,
List<TechId> dataSetIds)
{
IDatasetLister datasetLister = boFactory.createDatasetLister(session);
@@ -469,15 +470,15 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
throw new UserFailureException(builder.toString().trim());
}
}
-
- private void addTo(StringBuilder builder, String entityDescription, AbstractExternalData dataSet,
+
+ private void addTo(StringBuilder builder, String entityDescription, AbstractExternalData dataSet,
Map<Long, Set<Long>> containerIds)
{
String findOriginalDataSet = findOriginalDataSet(containerIds, dataSet);
- builder.append("The data set " + findOriginalDataSet + " is a component of the data set "
+ builder.append("The data set " + findOriginalDataSet + " is a component of the data set "
+ dataSet.getCode() + " which belongs to the " + entityDescription + " which is outside the deletion set.\n");
}
-
+
private String findOriginalDataSet(Map<Long, Set<Long>> relations, AbstractExternalData dataSet)
{
Set<Entry<Long, Set<Long>>> entrySet = relations.entrySet();
@@ -503,7 +504,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
{
return datasetLister.listByDatasetIds(TechId.asLongs(dataSetIds), DATA_SET_FETCH_OPTIONS);
}
-
+
@Override
public void revertDeletion(TechId deletionId)
{
@@ -516,22 +517,31 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
throwException(ex, "Deletion");
}
}
-
+
private static final class TrashOperationsManager
{
private final Session session;
+
private final DeletionPE deletion;
+
private final IDAOFactory daoFactory;
-
+
private final Map<EntityKind, Set<TechId>> entityIdsByKind = new HashMap<EntityKind, Set<TechId>>();
+
private final List<TrashBatchOperation> operations = new ArrayList<TrashBatchOperation>();
+
private final PersonPE person;
+
private final List<RoleWithIdentifier> allowedRoles;
+
private final ExperimentPEPredicate experimentPredicate;
+
private final SamplePEPredicate samplesPredicate;
+
private final DataPEPredicate dataSetPredicate;
+
private final Date modificationTimestamp;
-
+
TrashOperationsManager(Session session, DeletionPE deletion, IDAOFactory daoFactory, Date modificationTimestamp)
{
this.session = session;
@@ -549,7 +559,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
samplesPredicate = new SamplePEPredicate();
dataSetPredicate = new DataPEPredicate();
}
-
+
void addTrashOperation(EntityKind entityKind, List<TechId> entityIds, boolean isOriginalDeletion)
{
if (entityIds.isEmpty() == false)
@@ -575,7 +585,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
@SuppressWarnings({ "unchecked", "rawtypes" })
- private void assertAuthorization(PersistentEntityPredicate entityPredicate,
+ private void assertAuthorization(PersistentEntityPredicate entityPredicate,
List<? extends IIdentifierHolder> entities, String entityKindName)
{
List<String> identifiers = new ArrayList<String>();
@@ -591,12 +601,12 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
}
if (identifiers.isEmpty() == false)
{
- throw new AuthorizationFailureException("Can not delete " + entityKindName + " "
- + CollectionUtils.abbreviate(identifiers, 10) + " because user "
+ throw new AuthorizationFailureException("Can not delete " + entityKindName + " "
+ + CollectionUtils.abbreviate(identifiers, 10) + " because user "
+ errorMessage);
}
}
-
+
void trash()
{
updateModificationDateAndModifierOfRelatedProjectsOfExperiments();
@@ -607,7 +617,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
BatchOperationExecutor.executeInBatches(operation);
}
}
-
+
private void updateModificationDateAndModifierOfRelatedProjectsOfExperiments()
{
List<Long> ids = TechId.asLongs(entityIdsByKind.get(EntityKind.EXPERIMENT));
@@ -618,7 +628,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
experiments, session, modificationTimestamp);
}
}
-
+
private void updateModificationDateAndModifierOfRelatedEntitiesOfSamples()
{
List<Long> ids = TechId.asLongs(entityIdsByKind.get(EntityKind.SAMPLE));
@@ -629,7 +639,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
samples, session, modificationTimestamp);
}
}
-
+
private void updateModificationDateAndModifierOfRelatedEntitiesOfDataSets()
{
List<Long> ids = TechId.asLongs(entityIdsByKind.get(EntityKind.DATA_SET));
@@ -640,7 +650,7 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
dataSets, session, modificationTimestamp);
}
}
-
+
}
private static class TrashBatchOperation implements IBatchOperation<TechId>
@@ -692,10 +702,10 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
@Override
public String toString()
{
- return getOperationName() + (isOriginalDeletion ? " original " : " dependent ") + entityKind
+ return getOperationName() + (isOriginalDeletion ? " original " : " dependent ") + entityKind
+ " " + getEntityName() + " " + entityIds;
}
-
+
}
private abstract static class AbstractQueryBatchOperation implements IBatchOperation<TechId>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyTermBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyTermBO.java
index 99ad08e2ead..d09f673d3b6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyTermBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyTermBO.java
@@ -41,8 +41,8 @@ public final class VocabularyTermBO extends AbstractBusinessObject implements IV
private VocabularyTermPE vocabularyTermPE;
public VocabularyTermBO(final IDAOFactory daoFactory, final Session session,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
- DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory,
+ DataSetTypeWithoutExperimentChecker dataSetTypeChecker,
IRelationshipService relationshipService)
{
super(daoFactory, session, managedPropertyEvaluatorFactory, dataSetTypeChecker, relationshipService);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/AbstractBatchIterator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/AbstractBatchIterator.java
index 0bbcb4a45f0..f90e99a5863 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/AbstractBatchIterator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/AbstractBatchIterator.java
@@ -24,18 +24,16 @@ import java.util.Iterator;
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
/**
- * Allows to convert an memory-inefficient iterator into a one which has lower memory consumption.
- * Divides the items used to produce iterated elements into batches and calls the original iterator
- * on each batch. The outside interface make the division into batches invisible, but the
- * inefficient iterator is never used with a big number of items.
+ * Allows to convert an memory-inefficient iterator into a one which has lower memory consumption. Divides the items used to produce iterated elements
+ * into batches and calls the original iterator on each batch. The outside interface make the division into batches invisible, but the inefficient
+ * iterator is never used with a big number of items.
*
* @author Tomasz Pylak
*/
abstract public class AbstractBatchIterator<T> implements Iterable<T>
{
/**
- * Creates an iterator which is not very memory efficient and should not be called with too many
- * items at the same time.
+ * Creates an iterator which is not very memory efficient and should not be called with too many items at the same time.
*/
abstract protected Iterable<T> createUnefficientIterator(LongSet itemsBatch);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/CodeRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/CodeRecord.java
index 59925bc47aa..5bf540328bc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/CodeRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/CodeRecord.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-
/**
* A record object for id and code.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
index 9c5fada9dda..6fd38ebfd6e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
@@ -109,8 +109,8 @@ public final class EntityPropertiesEnricher implements IEntityPropertiesEnricher
}
/**
- * Enriches the entities with given <var>entityIDs</var> with its properties. The entities will
- * be resolved by the {@link IEntityPropertiesHolderResolver} and will be enriched in place.
+ * Enriches the entities with given <var>entityIDs</var> with its properties. The entities will be resolved by the
+ * {@link IEntityPropertiesHolderResolver} and will be enriched in place.
*/
@Override
public void enrich(final LongSet entityIDs, final IEntityPropertiesHolderResolver entities)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
index d1c843d931b..9a0f6973442 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-
/**
* A record object for a generic entity property.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesEnricher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesEnricher.java
index d8870fbee1e..cd17994c5d6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesEnricher.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesEnricher.java
@@ -26,8 +26,8 @@ import it.unimi.dsi.fastutil.longs.LongSet;
public interface IEntityPropertiesEnricher
{
/**
- * Enriches the entities specified by its IDs its properties. The entities will be retrieved
- * by the {@link IEntityPropertiesHolderResolver} and will be enriched "in place".
+ * Enriches the entities specified by its IDs its properties. The entities will be retrieved by the {@link IEntityPropertiesHolderResolver} and
+ * will be enriched "in place".
*/
public void enrich(final LongSet entityIDs, final IEntityPropertiesHolderResolver entities);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesHolderResolver.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesHolderResolver.java
index 19697c0f2ae..8938e555906 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesHolderResolver.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertiesHolderResolver.java
@@ -21,7 +21,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder
/**
* Resolver of objects holding entity properties.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IEntityPropertiesHolderResolver
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
index caaf001e6e2..cfbb6643586 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
@@ -28,9 +28,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
public interface IPropertyListingQuery
{
/**
- * Returns all property types. Fills only <code>id</code>, <code>code</code>,
- * <code>label</var> and <code>DataType</code>. Note that code and label are already HTML
- * escaped.
+ * Returns all property types. Fills only <code>id</code>, <code>code</code>, <code>label</var> and <code>DataType</code>. Note that code and
+ * label are already HTML escaped.
*/
@Select(sql = "select pt.id as pt_id, pt.code as pt_code, dt.code as dt_code,"
+ " pt.label as pt_label, pt.is_internal_namespace, pt.schema, pt.transformation"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/MaterialEntityPropertyRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/MaterialEntityPropertyRecord.java
index 76b8e94e339..cdc45e5ae3a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/MaterialEntityPropertyRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/MaterialEntityPropertyRecord.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-
/**
* A record object for an entity property of type MATERIAL.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectSpaceCodeRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectSpaceCodeRecord.java
index 581f0c90f69..1a71d998fc5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectSpaceCodeRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectSpaceCodeRecord.java
@@ -3,14 +3,13 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity;
import ch.rinn.restrictions.Private;
/**
- * A class representing an experiment, project and space code. It contains also deletion id, code of
- * experiment type and database instance id.
+ * A class representing an experiment, project and space code. It contains also deletion id, code of experiment type and database instance id.
*/
@Private
public class ExperimentProjectSpaceCodeRecord
{
public long id;
-
+
public String e_code;
public String e_permid;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
index 79bd2678f48..42a7e398cc5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
@@ -37,12 +37,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
{ SampleReferenceRecord.class })
public interface ISecondaryEntityListingQuery extends BaseQuery
{
- public static final String SELECT_FROM_EXPERIMENTS
- = "select e.id as id, e.code as e_code, e.perm_id as e_permid, e.del_id as del_id, et.code as et_code, "
- + "p.code as p_code, p.id as p_id, p.perm_id as p_perm_id, g.code as spc_code from experiments e "
- + "join experiment_types et on e.exty_id=et.id join projects p on e.proj_id=p.id "
- + "join spaces g on p.space_id=g.id";
-
+ public static final String SELECT_FROM_EXPERIMENTS =
+ "select e.id as id, e.code as e_code, e.perm_id as e_permid, e.del_id as del_id, et.code as et_code, "
+ + "p.code as p_code, p.id as p_id, p.perm_id as p_perm_id, g.code as spc_code from experiments e "
+ + "join experiment_types et on e.exty_id=et.id join projects p on e.proj_id=p.id "
+ + "join spaces g on p.space_id=g.id";
+
public static final int FETCH_SIZE = 1000;
//
@@ -57,9 +57,9 @@ public interface ISecondaryEntityListingQuery extends BaseQuery
@Select(SELECT_FROM_EXPERIMENTS + " where e.id=?{1}")
public ExperimentProjectSpaceCodeRecord getExperimentAndProjectAndGroupCodeForId(
long experimentId);
-
+
@Select(sql = SELECT_FROM_EXPERIMENTS + " where e.id = any(?{1})", parameterBindings =
- { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<ExperimentProjectSpaceCodeRecord> getExperiments(LongSet experimentIds);
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
index 944c8d443f8..a6969d3d4a9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
@@ -164,7 +164,7 @@ public class SecondaryEntityDAO
}
return result;
}
-
+
public Long2ObjectMap<Experiment> getExperiments(LongSet experimentIds)
{
Iterable<ExperimentProjectSpaceCodeRecord> experimentRecords = query.getExperiments(experimentIds);
@@ -175,7 +175,7 @@ public class SecondaryEntityDAO
}
return result;
}
-
+
public LongSet getSampleDescendantIdsAndSelf(Long sampleId)
{
LongSet results = new LongOpenHashSet();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index cda4425eff6..1e7aecf647b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -839,7 +839,7 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
}
return ids;
}
-
+
// assumes that the connection to experiment has been already established and experiment has the
// id set.
private void enrichWithExperiments(Long2ObjectMap<AbstractExternalData> datasetMap)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index a8d95d7e268..a79251823a9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -54,16 +54,16 @@ public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
public final static String SELECT_ALL =
"select data.*, external_data.*, link_data.*, "
- + "prdq.id IS NULL as is_post_registered "
- + "from data left outer join external_data on data.id = external_data.data_id "
- + "left outer join link_data on data.id = link_data.data_id "
- + "left outer join post_registration_dataset_queue prdq on data.id = prdq.ds_id ";
+ + "prdq.id IS NULL as is_post_registered "
+ + "from data left outer join external_data on data.id = external_data.data_id "
+ + "left outer join link_data on data.id = link_data.data_id "
+ + "left outer join post_registration_dataset_queue prdq on data.id = prdq.ds_id ";
public final static String SELECT_ALL_EXTERNAL_DATAS =
"select data.*, external_data.*, prdq.id IS NULL as is_post_registered "
- + "from data "
- + "join external_data on data.id = external_data.data_id "
- + "left outer join post_registration_dataset_queue prdq on data.id = prdq.ds_id ";
+ + "from data "
+ + "join external_data on data.id = external_data.data_id "
+ + "left outer join post_registration_dataset_queue prdq on data.id = prdq.ds_id ";
/**
* Returns the datasets for the given experiment id.
@@ -91,7 +91,7 @@ public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
+ "left outer join external_data as ed on d.id = ed.data_id "
+ "left outer join link_data as ld on d.id = ld.data_id "
+ "left outer join post_registration_dataset_queue prdq on d.id = prdq.ds_id "
- + "where expe_id = ?{1} "
+ + "where expe_id = ?{1} "
+ " or samp_id in (with recursive connected_samples as "
+ " (select id from samples where expe_id = ?{1} "
+ " union select s.id from connected_samples as cs "
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetLister.java
index 9857dd37a77..cab3dc4d91a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/IDataSetLister.java
@@ -29,8 +29,7 @@ public interface IDataSetLister
{
/**
- * Returns the data set meta data for the given <var>dataSetCodes</var> with the given
- * <var>dataSetFetchOptions</var>.
+ * Returns the data set meta data for the given <var>dataSetCodes</var> with the given <var>dataSetFetchOptions</var>.
*
* @return One data set meta data object for each entry in <var>dataSetCodes</var>.
*/
@@ -40,16 +39,14 @@ public interface IDataSetLister
/**
* Returns the download URLs for a set of <var>dataSetCodes</var>.
*
- * @return The list of data store download URLs, each with the list of data set codes it has
- * stored.
+ * @return The list of data store download URLs, each with the list of data set codes it has stored.
*/
public List<DataStoreURLForDataSets> getDataStoreDownloadURLs(List<String> dataSetCodes);
/**
* Returns the remote URLs for a set of <var>dataSetCodes</var>.
*
- * @return The list of data store remote URLs, each with the list of data set codes it has
- * stored.
+ * @return The list of data store remote URLs, each with the list of data set codes it has stored.
*/
public List<DataStoreURLForDataSets> getDataStoreRemoteURLs(List<String> dataSetCodes);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleLister.java
index d0fa0d3d445..50bd4a8ca36 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleLister.java
@@ -33,8 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifierHolder;
public interface ISampleLister
{
/**
- * Returns all samples of specified technical ids. Properties and related samples are added in
- * accordance to the fetch options.
+ * Returns all samples of specified technical ids. Properties and related samples are added in accordance to the fetch options.
*
* @param filter A filter which returns only samples and related samples which pass the filter.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
index fe0d1b14baf..9e2631aa756 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
@@ -55,17 +55,17 @@ public interface ISampleListingQuery extends BaseQuery
+ "left join spaces as ps on p.space_id = ps.id "
+ "left join persons as mod on s.pers_id_modifier = mod.id "
+ "join persons as pe on s.pers_id_registerer = pe.id where s.id = any(?{1}) ", parameterBindings =
- { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRecord> listSamplesByIds(LongSet sampleIDs);
@Select(sql = "Select * from sample_relationships "
+ "where relationship_id = ?{1} and sample_id_parent = any(?{2})", parameterBindings =
- { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRelationshipRecord> getChildren(Long relationshipID, LongSet sampleIDs);
@Select(sql = "Select * from sample_relationships "
+ "where relationship_id = ?{1} and sample_id_child = any(?{2})", parameterBindings =
- { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRelationshipRecord> getParents(Long relationshipID, LongSet sampleIDs);
@Select(sql = "with recursive connected_relationships as (select * from sample_relationships "
@@ -73,7 +73,7 @@ public interface ISampleListingQuery extends BaseQuery
+ "union select sr.* from connected_relationships as cr "
+ "join sample_relationships as sr on cr.sample_id_child = sr.sample_id_parent) "
+ "select * from connected_relationships", parameterBindings =
- { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRelationshipRecord> getDescendants(Long relationshipID, LongSet sampleIDs);
@Select(sql = "with recursive connected_relationships as (select * from sample_relationships "
@@ -81,7 +81,7 @@ public interface ISampleListingQuery extends BaseQuery
+ "union select sr.* from connected_relationships as cr "
+ "join sample_relationships as sr on cr.sample_id_parent = sr.sample_id_child) "
+ "select * from connected_relationships", parameterBindings =
- { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<SampleRelationshipRecord> getAncestors(Long relationshipID, LongSet sampleIDs);
@Select(sql = "select p.samp_id as entity_id, pt.code as code, dt.code as data_type, p.value, "
@@ -94,20 +94,20 @@ public interface ISampleListingQuery extends BaseQuery
+ "left join material_types as mt on m.maty_id = mt.id "
+ "left join controlled_vocabulary_terms as vt on p.cvte_id = vt.id "
+ "where p.samp_id = any(?{1})", parameterBindings =
- { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<PropertyRecord> getProperties(LongSet entityIDs);
@Select(sql = "select ma.mepr_id as metaproject_id, ma.samp_id as entity_id "
+ " from metaproject_assignments as ma "
+ " join metaprojects as m on ma.mepr_id = m.id "
+ "where ma.samp_id = any(?{1}) and m.owner = ?{2}", parameterBindings =
- { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<EntityMetaprojectRelationRecord> getMetaprojectAssignments(LongSet sampleIDs,
Long ownerId);
@Select(sql = "select id as id, name as name, description as description, "
+ " private as is_private, creation_date as creation_date " + " from metaprojects"
+ " where id = any(?{1})", parameterBindings =
- { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<MetaprojectRecord> getMetaprojects(LongSet metaprojectIDs);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
index a104cd35731..301b888b528 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/DataSetTypeWithoutExperimentChecker.java
@@ -34,9 +34,9 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
public class DataSetTypeWithoutExperimentChecker
{
public static final String PROPERTY_KEY = "data-set-types-with-no-experiment-needed";
-
+
private final String regularExpressions;
-
+
private List<Pattern> patternsForDataSetTypesWithoutExperiment = new ArrayList<Pattern>();
public DataSetTypeWithoutExperimentChecker(Properties properties)
@@ -63,7 +63,7 @@ public class DataSetTypeWithoutExperimentChecker
}
}
}
-
+
public String getRegularExpressions()
{
return regularExpressions;
@@ -81,5 +81,4 @@ public class DataSetTypeWithoutExperimentChecker
return false;
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstance.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstance.java
index 5ff095ca980..120bee3bddc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstance.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstance.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.business.importer;
-
/**
* The database instance for the importer.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstanceImporter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstanceImporter.java
index a63f0d063ca..070f276f9e8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstanceImporter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/importer/DatabaseInstanceImporter.java
@@ -54,7 +54,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
/**
* Class which allows to import another database instance.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class DatabaseInstanceImporter
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/coreplugin/JettyWebAppPluginInjector.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/coreplugin/JettyWebAppPluginInjector.java
index bfcb2220b5d..a1a9a26c2ef 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/coreplugin/JettyWebAppPluginInjector.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/coreplugin/JettyWebAppPluginInjector.java
@@ -48,7 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.coreplugin.CorePluginsUtils;
public class JettyWebAppPluginInjector
{
private static final String WEBAPP_FOLDER = "webapp";
-
+
private static final String START_PAGE = "start-page";
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
@@ -112,7 +112,7 @@ public class JettyWebAppPluginInjector
}
}
}
-
+
public void injectWebApps()
{
List<String> remainingWebapps = replaceDefaultStartPageByWebApp();
@@ -140,7 +140,7 @@ public class JettyWebAppPluginInjector
{
try
{
- if (!folder.getCanonicalPath().equals(link.getCanonicalPath())) //Verifies they are pointing to the same version
+ if (!folder.getCanonicalPath().equals(link.getCanonicalPath())) // Verifies they are pointing to the same version
{
link.delete();
}
@@ -159,7 +159,7 @@ public class JettyWebAppPluginInjector
}
return;
}
-
+
private List<String> replaceDefaultStartPageByWebApp()
{
List<String> remainingWebApps = new ArrayList<String>(webapps);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAttachmentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAttachmentDAO.java
index d6d5d7593b3..89e0e20f331 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAttachmentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAttachmentDAO.java
@@ -87,7 +87,7 @@ public interface IAttachmentDAO extends IGenericDAO<AttachmentPE>
*/
public int deleteByOwnerAndFileName(final AttachmentHolderPE owner, final String fileName)
throws DataAccessException;
-
+
public Map<String, AttachmentEntry> deleteAttachments(final AttachmentHolderPE holder, final String reason,
final List<String> fileNames, PersonPE registrator);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationGroupDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationGroupDAO.java
index 5ed7880d66d..c60437b8fe5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationGroupDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationGroupDAO.java
@@ -38,8 +38,7 @@ public interface IAuthorizationGroupDAO extends IGenericDAO<AuthorizationGroupPE
public void create(AuthorizationGroupPE authorizationGroup);
/**
- * Returns the authorization group with given code located in home database or null if no such
- * group exists.
+ * Returns the authorization group with given code located in home database or null if no such group exists.
*/
public AuthorizationGroupPE tryFindByCode(String code);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSourceProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSourceProvider.java
index 3113ab225ba..c0ce9d888a1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSourceProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSourceProvider.java
@@ -21,8 +21,7 @@ import javax.sql.DataSource;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- * Interface for providing a {@link DataSource} for a technology specific database based on data set
- * code or data store server code
+ * Interface for providing a {@link DataSource} for a technology specific database based on data set code or data store server code
*
* @author Franz-Josef Elmer
*/
@@ -31,8 +30,7 @@ public interface IDataSourceProvider
/**
* Returns an appropriated data source for specified data store server code and technology.
*
- * @throws IllegalArgumentException if getting data source by data store server code isn't
- * supported for the specified technology.
+ * @throws IllegalArgumentException if getting data source by data store server code isn't supported for the specified technology.
* @throws UserFailureException if the specified data store server doesn't exist.
*/
public DataSource getDataSourceByDataStoreServerCode(String dssCode, String technology);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java
index a64072db9e1..69ef07c787d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
/**
* <i>Data Access Object</i> for {@link DataStorePE}.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IDataStoreDAO
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDeletionDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDeletionDAO.java
index 0f9e65818bc..d6c364291a6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDeletionDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDeletionDAO.java
@@ -37,19 +37,16 @@ public interface IDeletionDAO extends IGenericDAO<DeletionPE>
void create(final DeletionPE deletion) throws DataAccessException;
/**
- * Moves entities with given ids to trash using specified deletion. Ignores ids of entities that
- * don't exist or are already in the trash.
+ * Moves entities with given ids to trash using specified deletion. Ignores ids of entities that don't exist or are already in the trash.
*
- * @param isOriginalDeletion if true than the specified entities are considered originally
- * deleted entities
+ * @param isOriginalDeletion if true than the specified entities are considered originally deleted entities
* @return number of trashed entities
*/
int trash(EntityKind entityKind, List<TechId> entityIds, DeletionPE deletion,
boolean isOriginalDeletion) throws DataAccessException;
/**
- * Moves entities with given ids to trash using specified deletion. Ignores ids of entities that
- * don't exist or are already in the trash.
+ * Moves entities with given ids to trash using specified deletion. Ignores ids of entities that don't exist or are already in the trash.
* <p>
* The entites are considered to be originally deleted
*
@@ -70,14 +67,12 @@ public interface IDeletionDAO extends IGenericDAO<DeletionPE>
List<TechId> findTrashedSampleIds(List<TechId> deletionIds);
/**
- * Returns list of ids of non-comonent samples (having no container) moved to trash in specified
- * deletions.
+ * Returns list of ids of non-comonent samples (having no container) moved to trash in specified deletions.
*/
List<TechId> findTrashedNonComponentSampleIds(List<TechId> deletionIds);
/**
- * Returns list of ids of component samples (samples with container) moved to trash in specified
- * deletions.
+ * Returns list of ids of component samples (samples with container) moved to trash in specified deletions.
*/
List<TechId> findTrashedComponentSampleIds(List<TechId> deletionIds);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationScheduler.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationScheduler.java
index eb7bcdfb386..48908b2e7f5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationScheduler.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationScheduler.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
-
/**
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationSchedulerWithQueue.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationSchedulerWithQueue.java
index 013b9ae1846..567c2c32857 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationSchedulerWithQueue.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDynamicPropertyEvaluationSchedulerWithQueue.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
/**
- * {@link IDynamicPropertyEvaluationScheduler} extension with methods for dealing with persistent
- * blocking queue.
+ * {@link IDynamicPropertyEvaluationScheduler} extension with methods for dealing with persistent blocking queue.
*
* @author Piotr Buczek
*/
@@ -26,8 +25,7 @@ public interface IDynamicPropertyEvaluationSchedulerWithQueue extends
IDynamicPropertyEvaluationScheduler
{
/**
- * Retrieves, but does not remove, an operation from the head of this queue, waiting if no
- * elements are present on this queue.
+ * Retrieves, but does not remove, an operation from the head of this queue, waiting if no elements are present on this queue.
*
* @return an operation from the head of this queue
* @throws InterruptedException if interrupted while waiting.
@@ -35,8 +33,7 @@ public interface IDynamicPropertyEvaluationSchedulerWithQueue extends
DynamicPropertyEvaluationOperation peekWait() throws InterruptedException;
/**
- * Retrieves and removes an operation from the head of this queue, waiting if no elements are
- * present on this queue.
+ * Retrieves and removes an operation from the head of this queue, waiting if no elements are present on this queue.
*
* @return an operation from the head of this queue
* @throws InterruptedException if interrupted while waiting.
@@ -44,15 +41,13 @@ public interface IDynamicPropertyEvaluationSchedulerWithQueue extends
DynamicPropertyEvaluationOperation take() throws InterruptedException;
/**
- * Synchronizes all operations scheduled in a transaction handled by current thread with this
- * queue. Should be called after transaction is successfuly commited (otherwise evaluator can
- * work on stale data).
+ * Synchronizes all operations scheduled in a transaction handled by current thread with this queue. Should be called after transaction is
+ * successfuly commited (otherwise evaluator can work on stale data).
*/
void synchronizeThreadQueue();
/**
- * Remove all operations scheduled in a transaction handled by current thread with this queue.
- * Should be called after transaction is rolled back.
+ * Remove all operations scheduled in a transaction handled by current thread with this queue. Should be called after transaction is rolled back.
*/
void clearThreadQueue();
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertiesConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertiesConverter.java
index 1e10d96b5a1..dcb2c5f7f0d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertiesConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertiesConverter.java
@@ -38,8 +38,7 @@ public interface IEntityPropertiesConverter
{
/**
- * Converts the set of {@link IEntityProperty} objects obtained from the specified entity to an
- * array of {@link EntityPropertyPE} objects.
+ * Converts the set of {@link IEntityProperty} objects obtained from the specified entity to an array of {@link EntityPropertyPE} objects.
*
* @param registrator Will appear in the objects of the output.
*/
@@ -48,8 +47,7 @@ public interface IEntityPropertiesConverter
final PersonPE registrator);
/**
- * Returns given value validated and converted for given property type and entity type. Result
- * may be null if given value is null.
+ * Returns given value validated and converted for given property type and entity type. Result may be null if given value is null.
*/
public String tryCreateValidatedPropertyValue(PropertyTypePE propertyType,
EntityTypePropertyTypePE entityTypPropertyType, String value);
@@ -72,8 +70,7 @@ public interface IEntityPropertiesConverter
EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE author);
/**
- * Updates Set<T> of properties but preserve those old properties which codes are not among
- * <var>propertiesToUpdate</var>.
+ * Updates Set<T> of properties but preserve those old properties which codes are not among <var>propertiesToUpdate</var>.
*/
public <T extends EntityPropertyPE> Set<T> updateProperties(Collection<T> oldProperties,
EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE author,
@@ -86,15 +83,14 @@ public interface IEntityPropertiesConverter
EntityTypePE entityTypePE);
/**
- * Checks whether all mandatory properties are provided. It uses (and fills) the
- * <var>cache</var> in order to avoid looking up the assigned properties time and again.
+ * Checks whether all mandatory properties are provided. It uses (and fills) the <var>cache</var> in order to avoid looking up the assigned
+ * properties time and again.
*/
public <T extends EntityPropertyPE> void checkMandatoryProperties(Collection<T> properties,
EntityTypePE entityTypePE, Map<EntityTypePE, List<EntityTypePropertyTypePE>> cache);
/**
- * Update the value of a managed property, assuming the managedProperty already has the updated
- * value.
+ * Update the value of a managed property, assuming the managedProperty already has the updated value.
*/
public <T extends EntityPropertyPE> Set<T> updateManagedProperty(Collection<T> oldProperties,
EntityTypePE entityType, IManagedProperty managedProperty, PersonPE author);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertyTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertyTypeDAO.java
index 416f614581f..76e9fdb9b5e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertyTypeDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityPropertyTypeDAO.java
@@ -38,8 +38,7 @@ public interface IEntityPropertyTypeDAO
{
/**
- * Returns a list of all entity type - property type assignments connected to given
- * {@link EntityTypePE}.
+ * Returns a list of all entity type - property type assignments connected to given {@link EntityTypePE}.
*/
public List<EntityTypePropertyTypePE> listEntityPropertyTypes(final EntityTypePE entityType)
throws DataAccessException;
@@ -50,8 +49,8 @@ public interface IEntityPropertyTypeDAO
public List<String> listPropertyTypeCodes() throws DataAccessException;
/**
- * Returns {@link EntityTypePropertyTypePE} assignment connecting given {@link EntityTypePE} and
- * {@link PropertyTypePE} if it exists and null otherwise.
+ * Returns {@link EntityTypePropertyTypePE} assignment connecting given {@link EntityTypePE} and {@link PropertyTypePE} if it exists and null
+ * otherwise.
*/
public EntityTypePropertyTypePE tryFindAssignment(EntityTypePE entityType,
PropertyTypePE propertyType);
@@ -71,8 +70,8 @@ public interface IEntityPropertyTypeDAO
public List<Long> listEntityIds(final EntityTypePE entityType) throws DataAccessException;
/**
- * Returns a list of ids of all entities of type from specified assignment with that don't have
- * any value for property assigned with the assignment.
+ * Returns a list of ids of all entities of type from specified assignment with that don't have any value for property assigned with the
+ * assignment.
*/
public List<Long> listIdsOfEntitiesWithoutPropertyValue(
final EntityTypePropertyTypePE assignment) throws DataAccessException;
@@ -102,8 +101,7 @@ public interface IEntityPropertyTypeDAO
/**
* Updates given persistent (already saved) <var>entity</var> after successful validation.<br>
* <br>
- * Useful especially instead of a save() method (used for making entity persistent) after BO
- * update that does not flush.
+ * Useful especially instead of a save() method (used for making entity persistent) after BO update that does not flush.
*
* @param entity the entity to be validated and updated
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEventDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEventDAO.java
index 8b46374ab61..1d55cce7532 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEventDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEventDAO.java
@@ -33,8 +33,7 @@ public interface IEventDAO extends IGenericDAO<EventPE>
{
/**
- * Tries to find <var>eventType</var> event concerning an object of given <var>entityType</var>
- * and <code>identifier</code>.
+ * Tries to find <var>eventType</var> event concerning an object of given <var>entityType</var> and <code>identifier</code>.
*/
public EventPE tryFind(final String identifier, final EntityType entityType,
final EventType eventType);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
index 6a57c93aaef..fe48f2f0e33 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
/**
* Interface to the data access layer for retrieving instances of {@link FileFormatTypePE}.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IFileFormatTypeDAO extends IGenericDAO<FileFormatTypePE>
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
index 31109e6abef..badd415758f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
@@ -21,7 +21,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
/**
* Interface to the data access layer for retrieving instances of {@link LocatorTypePE}.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface ILocatorTypeDAO extends IGenericDAO<LocatorTypePE>
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
index b7cb69c6d77..40eb1c4f6e1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
@@ -32,8 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
public interface IMetaprojectDAO extends IGenericDAO<MetaprojectPE>
{
/**
- * Finds a metaproject by the specified owner id and metaproject name. Returns null if no
- * metaproject is found.
+ * Finds a metaproject by the specified owner id and metaproject name. Returns null if no metaproject is found.
*/
public MetaprojectPE tryFindByOwnerAndName(String ownerId, String metaprojectName);
@@ -72,8 +71,7 @@ public interface IMetaprojectDAO extends IGenericDAO<MetaprojectPE>
EntityKind entityKind);
/**
- * Returns a map with counts of assignments for different entity kinds for the given
- * metaproject.
+ * Returns a map with counts of assignments for different entity kinds for the given metaproject.
*/
public int getMetaprojectAssignmentsCount(Long metaprojectId, EntityKind entityKind);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyTypeDAO.java
index 2b04dc33e90..02f562aa638 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyTypeDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyTypeDAO.java
@@ -58,8 +58,7 @@ public interface IPropertyTypeDAO extends IGenericDAO<PropertyTypePE>
public List<DataTypePE> listDataTypes() throws DataAccessException;
/**
- * Returns the {@link DataTypePE} for specified <var>code</var> or <code>null</code> if none
- * could be found.
+ * Returns the {@link DataTypePE} for specified <var>code</var> or <code>null</code> if none could be found.
*/
public DataTypePE getDataTypeByCode(final DataTypeCode code) throws DataAccessException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyValueValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyValueValidator.java
index d1161f6c268..81fba56ee86 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyValueValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPropertyValueValidator.java
@@ -27,8 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
public interface IPropertyValueValidator
{
/**
- * Validates given <var>value</var> against given {@link PropertyTypePE} and returns the
- * validated value as <code>String</code>.
+ * Validates given <var>value</var> against given {@link PropertyTypePE} and returns the validated value as <code>String</code>.
*
* @return the validated value. It does not implicitly equal given <var>value</var>
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleTypeDAO.java
index 082719dee43..af51e5e125f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleTypeDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleTypeDAO.java
@@ -30,9 +30,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
public interface ISampleTypeDAO extends IGenericDAO<SampleTypePE>
{
/**
- * Returns a list of {@link SampleTypePE} which have their property types and corresponding
- * vocabulary terms eagerly fetched (overriding default behavior which lazily loads the property
- * types).
+ * Returns a list of {@link SampleTypePE} which have their property types and corresponding vocabulary terms eagerly fetched (overriding default
+ * behavior which lazily loads the property types).
*
* @return The list of {@link SampleTypePE}s registered in the database.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyDAO.java
index 73a04854311..0e580887d17 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyDAO.java
@@ -22,8 +22,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
/**
- * An interface that contains all data access operations on {@link VocabularyTermPE} and
- * {@link VocabularyPE}.
+ * An interface that contains all data access operations on {@link VocabularyTermPE} and {@link VocabularyPE}.
*
* @author Christian Ribeaud
*/
@@ -36,11 +35,9 @@ public interface IVocabularyDAO extends IGenericDAO<VocabularyPE>
void createOrUpdateVocabulary(final VocabularyPE vocabularyPE);
/**
- * Returns the {@link VocabularyPE} object for the given <var>vocabularyCode</var>, or
- * <code>null</code>, if it doesn't exist.<br>
+ * Returns the {@link VocabularyPE} object for the given <var>vocabularyCode</var>, or <code>null</code>, if it doesn't exist.<br>
* <br>
- * NOTE: Only internally managed vocabularies have codes that can be used as business
- * identifiers (cannot be edited).
+ * NOTE: Only internally managed vocabularies have codes that can be used as business identifiers (cannot be edited).
*/
VocabularyPE tryFindVocabularyByCode(final String vocabularyCode);
@@ -50,8 +47,7 @@ public interface IVocabularyDAO extends IGenericDAO<VocabularyPE>
List<VocabularyPE> listVocabularies(boolean excludeInternal);
/**
- * @return {@link VocabularyTermPE} with given <var>code</var> for given {@link VocabularyPE} or
- * null if it does not exist.
+ * @return {@link VocabularyTermPE} with given <var>code</var> for given {@link VocabularyPE} or null if it does not exist.
*/
VocabularyTermPE tryFindVocabularyTermByCode(VocabularyPE vocabulary, String code);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyTermDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyTermDAO.java
index 33ca358f6b7..f516bacfc6b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyTermDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IVocabularyTermDAO.java
@@ -31,12 +31,10 @@ public interface IVocabularyTermDAO extends IGenericDAO<VocabularyTermPE>
void validate(final VocabularyTermPE term);
/**
- * All terms in specified vocabulary starting from specified ordinal will have the ordinal
- * increased by specified increment.
+ * All terms in specified vocabulary starting from specified ordinal will have the ordinal increased by specified increment.
* <p>
- * After this change a collection of terms with size equal to <var>increment</var> can be put
- * consecutively starting from <var>fromOrdinal</var> and ordinals in the vocabulary will stay
- * unique.
+ * After this change a collection of terms with size equal to <var>increment</var> can be put consecutively starting from <var>fromOrdinal</var>
+ * and ordinals in the vocabulary will stay unique.
*/
void increaseVocabularyTermOrdinals(final VocabularyPE vocabulary, final Long fromOrdinal,
final int increment);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PlaceholderPropertyCreator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PlaceholderPropertyCreator.java
index 36b8cc66805..b17997ff1f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PlaceholderPropertyCreator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PlaceholderPropertyCreator.java
@@ -26,8 +26,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
class PlaceholderPropertyCreator implements IPropertyPlaceholderCreator
{
/**
- * Adds placeholders for <var>dynamicProperties</var> to <var>definedProperties</var> if they
- * don't exist yet.
+ * Adds placeholders for <var>dynamicProperties</var> to <var>definedProperties</var> if they don't exist yet.
*/
@Override
public void addDynamicPropertiesPlaceholders(Set<IEntityProperty> definedProperties,
@@ -38,8 +37,7 @@ class PlaceholderPropertyCreator implements IPropertyPlaceholderCreator
}
/**
- * Adds placeholders for <var>managedProperties</var> to <var>definedProperties</var> if they
- * don't exist yet.
+ * Adds placeholders for <var>managedProperties</var> to <var>definedProperties</var> if they don't exist yet.
*/
@Override
public void addManagedPropertiesPlaceholders(Set<IEntityProperty> definedProperties,
@@ -50,8 +48,7 @@ class PlaceholderPropertyCreator implements IPropertyPlaceholderCreator
}
/**
- * Adds <var>placeholderProperties</var> with specified <var>placeholderValue</var>to
- * <var>definedProperties</var> if they don't exist yet.
+ * Adds <var>placeholderProperties</var> with specified <var>placeholderValue</var>to <var>definedProperties</var> if they don't exist yet.
*/
private void addPlaceholders(Set<IEntityProperty> definedProperties,
Set<String> placeholderProperties, String placeholderValue)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PropertyValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PropertyValidator.java
index 32808f02ce8..5355dfa64e7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PropertyValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/PropertyValidator.java
@@ -144,8 +144,7 @@ public final class PropertyValidator implements IPropertyValueValidator
}
/**
- * @return Details about vocabulary dependent on {@link VocabularyPE#isChosenFromList()}
- * value:
+ * @return Details about vocabulary dependent on {@link VocabularyPE#isChosenFromList()} value:
* <ul>
* <li>for <var>true</var> - returns a list of first few vocabulary terms from it.
* <li>for <var>false</var> - returns a vocabulary description
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAO.java
index 7e0d324cb15..160f1d82904 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAO.java
@@ -70,8 +70,9 @@ public abstract class AbstractDAO extends HibernateDaoSupport
{
private static ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
+
private static final int MAX_STRING_ERROR_LENGTH = 500;
-
+
protected AbstractDAO(final SessionFactory sessionFactory)
{
assert sessionFactory != null : "Unspecified session factory";
@@ -99,8 +100,11 @@ public abstract class AbstractDAO extends HibernateDaoSupport
for (ConstraintViolation v : violations)
{
Object invalidValue = v.getInvalidValue();
- if(invalidValue instanceof String && (((String) invalidValue).length() > MAX_STRING_ERROR_LENGTH)) {
- invalidValue = String.format("%s... (complete value was %d characters)", ((String) invalidValue).substring(0, MAX_STRING_ERROR_LENGTH), ((String) invalidValue).length());
+ if (invalidValue instanceof String && (((String) invalidValue).length() > MAX_STRING_ERROR_LENGTH))
+ {
+ invalidValue =
+ String.format("%s... (complete value was %d characters)", ((String) invalidValue).substring(0, MAX_STRING_ERROR_LENGTH),
+ ((String) invalidValue).length());
}
msg += ", " + String.format(v.getMessage(), invalidValue);
}
@@ -179,7 +183,7 @@ public abstract class AbstractDAO extends HibernateDaoSupport
size);
}
}
-
+
protected Date getTransactionTimeStamp()
{
return UpdateUtils.getTransactionTimeStamp(getSessionFactory());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
index b713d4d02db..2278e300d46 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
@@ -125,7 +125,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
final List<TechId> entityTechIds, final PersonPE registrator, final String reason,
final String sqlSelectPermIds, final String sqlDeleteProperties,
final String sqlDeleteAttachments, final String sqlDeleteEntities,
- final String sqlInsertEvent, final String sqlSelectPropertyHistory,
+ final String sqlInsertEvent, final String sqlSelectPropertyHistory,
final String sqlSelectRelationshipHistory, final String sqlSelectAttributes,
List<? extends AttachmentHolderPE> attachmentHolders,
AttachmentHolderKind attachmentHolderKind)
@@ -133,7 +133,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
List<Long> entityIds = TechId.asLongs(entityTechIds);
DeletePermanentlyBatchOperation deleteOperation =
new DeletePermanentlyBatchOperation(entityType, entityIds, registrator, reason,
- sqlSelectPermIds, sqlDeleteProperties,
+ sqlSelectPermIds, sqlDeleteProperties,
sqlDeleteAttachments, sqlDeleteEntities,
sqlInsertEvent, sqlSelectPropertyHistory, sqlSelectRelationshipHistory,
sqlSelectAttributes, attachmentHolders, attachmentHolderKind);
@@ -179,7 +179,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
DeletePermanentlyBatchOperation(EntityType entityType, List<Long> allEntityIds,
PersonPE registrator, String reason, String sqlSelectPermIds,
String sqlDeleteProperties, String sqlDeleteAttachments,
- String sqlDeleteEntities, String sqlInsertEvent, String selectPropertyHistory,
+ String sqlDeleteEntities, String sqlInsertEvent, String selectPropertyHistory,
String selectRelationshipHistory, String sqlSelectAttributes,
List<? extends AttachmentHolderPE> attachmentHolders,
AttachmentHolderKind attachmentHolderKind)
@@ -257,8 +257,8 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
return null;
}
- String content = historyCreator.apply(session, entityIdsToDelete, sqlSelectPropertyHistory,
- sqlSelectRelationshipHistory, sqlSelectAttributes, attachmentHolders,
+ String content = historyCreator.apply(session, entityIdsToDelete, sqlSelectPropertyHistory,
+ sqlSelectRelationshipHistory, sqlSelectAttributes, attachmentHolders,
attachmentHolderKind, registrator);
deleteProperties(sqlQueryDeleteProperties, entityIdsToDelete);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAO.java
index 03133291f2c..ea4027fcda5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAO.java
@@ -67,10 +67,9 @@ final class AttachmentDAO extends AbstractGenericEntityDAO<AttachmentPE> impleme
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
AttachmentDAO.class);
-
private final IEventDAO eventDAO;
- AttachmentDAO(final PersistencyResources persistencyResources,
+ AttachmentDAO(final PersistencyResources persistencyResources,
IEventDAO eventDAO, EntityHistoryCreator historyCreator)
{
super(persistencyResources.getSessionFactory(), ATTACHMENT_CLASS, historyCreator);
@@ -101,7 +100,7 @@ final class AttachmentDAO extends AbstractGenericEntityDAO<AttachmentPE> impleme
//
@Override
- public Map<String, AttachmentEntry> deleteAttachments(final AttachmentHolderPE holder, final String reason,
+ public Map<String, AttachmentEntry> deleteAttachments(final AttachmentHolderPE holder, final String reason,
final List<String> fileNames, PersonPE registrator)
{
Map<String, AttachmentEntry> attachmentEntries = new TreeMap<>();
@@ -121,7 +120,7 @@ final class AttachmentDAO extends AbstractGenericEntityDAO<AttachmentPE> impleme
return attachmentEntries;
}
- private Map<String, AttachmentEntry> createDeletionEvents(List<AttachmentPE> attachmentsToBeDeleted,
+ private Map<String, AttachmentEntry> createDeletionEvents(List<AttachmentPE> attachmentsToBeDeleted,
PersonPE registrator, String reason)
{
Map<String, AttachmentEntry> attachmentEntries = new TreeMap<>();
@@ -141,8 +140,7 @@ final class AttachmentDAO extends AbstractGenericEntityDAO<AttachmentPE> impleme
event.setReason(reason);
event.setRegistrator(registrator);
event.setAttachmentContent(attachmentToBeDeleted.getAttachmentContent());
- Map<String, List<? extends EntityModification>> modifications
- = new HashMap<String, List<? extends EntityModification>>();
+ Map<String, List<? extends EntityModification>> modifications = new HashMap<String, List<? extends EntityModification>>();
AttachmentEntry attachmentEntry = new AttachmentEntry();
attachmentEntry.fileName = fileName;
attachmentEntry.version = version;
@@ -167,7 +165,7 @@ final class AttachmentDAO extends AbstractGenericEntityDAO<AttachmentPE> impleme
{
AttachmentHolderPE result = internalCreateAttachment(attachment, ownerParam);
getHibernateTemplate().flush();
-
+
scheduleDynamicPropertiesEvaluation(ownerParam);
return result;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
index caa3ae78c84..2988dc0cc23 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
@@ -355,8 +355,8 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
public void afterPropertiesSet() throws Exception
{
// TODO: project samples
-// Properties serviceProperties = configurer.getResolvedProps();
-// boolean projectSamplesEnabled = PropertyUtils.getBoolean(serviceProperties, Constants.PROJECT_SAMPLES_ENABLED_KEY, false);
+ // Properties serviceProperties = configurer.getResolvedProps();
+ // boolean projectSamplesEnabled = PropertyUtils.getBoolean(serviceProperties, Constants.PROJECT_SAMPLES_ENABLED_KEY, false);
boolean projectSamplesEnabled = false;
Connection connection = null;
try
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
index 71cf4536991..a041cb66d4e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
@@ -937,12 +937,12 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
private static String createQueryRelationshipHistorySQL()
{
- return " SELECT d.code, relation_type,entity_perm_id, " + ENTITY_TYPE + ", "
+ return " SELECT d.code, relation_type,entity_perm_id, " + ENTITY_TYPE + ", "
+ "p.user_id, valid_from_timestamp, valid_until_timestamp "
+ "FROM " + TableNames.DATA_ALL_TABLE + " d, " + TableNames.DATA_SET_RELATIONSHIPS_HISTORY_TABLE + " h, "
+ TableNames.PERSONS_TABLE + " p "
- + "WHERE d.id = main_data_id and main_data_id " + SQLBuilder.inEntityIds()
- + " and h.pers_id_author = p.id"
+ + "WHERE d.id = main_data_id and main_data_id " + SQLBuilder.inEntityIds()
+ + " and h.pers_id_author = p.id"
+ " order by 1, valid_from_timestamp";
}
@@ -1058,7 +1058,7 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
final List<DeletedDataSetLocation> locations =
selectLocations(selectLocations, entityIdsToDelete);
- String content = historyCreator.apply(session, entityIdsToDelete, sqls.selectPropertyHistory,
+ String content = historyCreator.apply(session, entityIdsToDelete, sqls.selectPropertyHistory,
sqls.selectRelationshipHistory, sqls.selectAttributes, null, null, registrator);
executeUpdate(deleteProperties, entityIdsToDelete);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseAndIndexReplacer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseAndIndexReplacer.java
index 3994a56fc4f..6c2ae1fbb83 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseAndIndexReplacer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseAndIndexReplacer.java
@@ -28,16 +28,14 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.logging.LogInitializer;
/**
- * Helper application which replaces a database and its Lucene index by another existing database and
- * its index.
+ * Helper application which replaces a database and its Lucene index by another existing database and its index.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class DatabaseAndIndexReplacer
{
private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, DatabaseAndIndexReplacer.class);
-
+ LogFactory.getLogger(LogCategory.OPERATION, DatabaseAndIndexReplacer.class);
public static void main(String[] args)
{
@@ -53,7 +51,7 @@ public class DatabaseAndIndexReplacer
File destinationFolder = new File(args[1]);
String sourceDatabase = IndexCreationUtil.DATABASE_NAME_PREFIX + args[2];
File sourceFolder = new File(args[3]);
-
+
boolean ok = IndexCreationUtil.duplicateDatabase(destinationDatabase, sourceDatabase);
if (ok == false)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DynamicPropertiesInterceptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DynamicPropertiesInterceptor.java
index 313ab2d3687..cff239c2791 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DynamicPropertiesInterceptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DynamicPropertiesInterceptor.java
@@ -23,8 +23,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDynamicPropertyEvalua
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
- * Synchronizes all dynamic property evaluations scheduled in a transaction with persistent queue
- * after transaction is successfully committed.
+ * Synchronizes all dynamic property evaluations scheduled in a transaction with persistent queue after transaction is successfully committed.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
index 91e84c5d734..ad10c25309c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
@@ -492,7 +492,7 @@ public class ExperimentDAO extends AbstractGenericEntityWithPropertiesDAO<Experi
executePermanentDeleteAction(EntityType.EXPERIMENT, experimentIds, registrator, reason,
sqlSelectPermIds, sqlDeleteProperties, sqlDeleteAttachments, sqlDeleteExperiments,
- sqlInsertEvent, sqlSelectPropertyHistory, sqlSelectRelationshipHistory, sqlSelectAttributes,
+ sqlInsertEvent, sqlSelectPropertyHistory, sqlSelectRelationshipHistory, sqlSelectAttributes,
null, AttachmentHolderKind.EXPERIMENT);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IPermIdDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IPermIdDAO.java
index ee9fc390069..96363f25a79 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IPermIdDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IPermIdDAO.java
@@ -39,8 +39,7 @@ public interface IPermIdDAO
public List<String> createPermIds(int n);
/**
- * Returns {@link IEntityInformationHolderDTO} for given permId and entityKind or null if
- * nothing found;
+ * Returns {@link IEntityInformationHolderDTO} for given permId and entityKind or null if nothing found;
*/
public IEntityInformationHolderDTO tryToFindByPermId(String permId, EntityKind entityKind);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IndexCreationUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IndexCreationUtil.java
index 588f5f4a8a8..134b443194d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IndexCreationUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/IndexCreationUtil.java
@@ -73,7 +73,7 @@ public final class IndexCreationUtil
if (applicationContext == null)
{
final AbstractApplicationContext appC = new ClassPathXmlApplicationContext(new String[]
- { "applicationContext.xml" }, true);
+ { "applicationContext.xml" }, true);
IndexCreationUtil.applicationContext = appC;
}
return applicationContext;
@@ -119,8 +119,7 @@ public final class IndexCreationUtil
}
/**
- * Creates a freshly new {@link HibernateSearchContext} overriding the one loaded by
- * <i>Spring</i>.
+ * Creates a freshly new {@link HibernateSearchContext} overriding the one loaded by <i>Spring</i>.
*/
private final static HibernateSearchContext createHibernateSearchContext(String indexFolder)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MaterialDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MaterialDAO.java
index f60d67499ab..65014315e16 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MaterialDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MaterialDAO.java
@@ -308,7 +308,7 @@ public class MaterialDAO extends AbstractGenericEntityWithPropertiesDAO<Material
String materialTypeCode = (String) codeAndType[1];
String permId = MaterialPE.createPermId(materialCode, materialTypeCode);
- String content = historyCreator.apply(session, Collections.singletonList(techId.getId()),
+ String content = historyCreator.apply(session, Collections.singletonList(techId.getId()),
sqlPropertyHistory, null, sqlAttributesHistory, null, null, registrator);
try
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
index 437c006d62e..172437d7cc1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
@@ -72,8 +72,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
/**
* This logger does not output any SQL statement. If you want to do so, you had better set an appropriate debugging level for class
- * {@link JdbcAccessor}.
- * </p>
+ * {@link JdbcAccessor}. </p>
*/
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
SampleDAO.class);
@@ -353,7 +352,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
@Override
public final void createOrUpdateSamples(final List<SamplePE> samples, final PersonPE modifier,
boolean clearCache)
- throws DataAccessException
+ throws DataAccessException
{
assert samples != null && samples.size() > 0 : "Unspecified or empty samples.";
@@ -457,7 +456,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
final String sqlSelectAttributes = createQueryAttributesSQL();
executePermanentDeleteAction(EntityType.SAMPLE, sampleIds, registrator, reason,
- sqlSelectPermIds, sqlDeleteProperties,
+ sqlSelectPermIds, sqlDeleteProperties,
sqlDeleteAttachments, sqlDeleteSamples, sqlInsertEvent, sqlSelectPropertyHistory,
sqlSelectRelationshipHistory, sqlSelectAttributes, null, AttachmentHolderKind.SAMPLE);
}
@@ -491,7 +490,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
+ ") "
+ " ORDER BY 1, valid_from_timestamp";
}
-
+
private static String createQueryRelationshipHistorySQL()
{
return "SELECT s.perm_id, h.relation_type, h.entity_perm_id, " + ENTITY_TYPE + ", "
@@ -570,7 +569,7 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
String permIds = permIdList.substring(2);
String content = historyCreator.apply(session, entityIdsToDelete, createQueryPropertyHistorySQL(),
- createQueryRelationshipHistorySQL(), createQueryAttributesSQL(), null,
+ createQueryRelationshipHistorySQL(), createQueryAttributesSQL(), null,
AttachmentHolderKind.SAMPLE, registrator);
SQLQuery deleteProperties = session.createSQLQuery(properties);
@@ -586,14 +585,14 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
deleteAttachments.setParameter("id", deletion.getId());
deleteAttachments.executeUpdate();
-// if (attachmentContentIdList.size() > 0)
-// {
-// SQLQuery deleteAttachmentContents =
-// session.createSQLQuery(attachmentContents);
-// deleteAttachmentContents.setParameterList("ids", attachmentContentIdList);
-// deleteAttachmentContents.executeUpdate();
-// }
-//
+ // if (attachmentContentIdList.size() > 0)
+ // {
+ // SQLQuery deleteAttachmentContents =
+ // session.createSQLQuery(attachmentContents);
+ // deleteAttachmentContents.setParameterList("ids", attachmentContentIdList);
+ // deleteAttachmentContents.executeUpdate();
+ // }
+ //
SQLQuery deleteSamples = session.createSQLQuery(samples);
deleteSamples.setParameter("id", deletion.getId());
deleteSamples.executeUpdate();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttachmentEntry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttachmentEntry.java
index fae3b327558..4b76b8cc8fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttachmentEntry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttachmentEntry.java
@@ -21,8 +21,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class AttachmentEntry extends EntityModification
@@ -30,22 +28,22 @@ public class AttachmentEntry extends EntityModification
public static final String ATTACHMENT = "ATTACHMENT";
public final String type = ATTACHMENT;
-
+
@JsonProperty("key")
public String relationType;
-
+
@JsonProperty("value")
public String relatedEntity;
public String entityType;
-
+
public String fileName;
-
+
public int version;
-
+
@JsonInclude(Include.NON_EMPTY)
public String description;
-
+
@JsonInclude(Include.NON_EMPTY)
public String title;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttributeEntry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttributeEntry.java
index 7d425b61745..3d65dc72722 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttributeEntry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/AttributeEntry.java
@@ -19,8 +19,6 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.deletion;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class AttributeEntry extends EntityModification
@@ -33,7 +31,7 @@ public class AttributeEntry extends EntityModification
public String attributeName;
public String value;
-
+
@Override
public String toString()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityHistoryCreator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityHistoryCreator.java
index 5118e9ebae2..d63f9f002a1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityHistoryCreator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityHistoryCreator.java
@@ -57,7 +57,7 @@ public class EntityHistoryCreator
}
public String apply(SharedSessionContract session, List<Long> entityIdsToDelete,
- String propertyHistoryQuery, String relationshipHistoryQuery, String attributesQuery,
+ String propertyHistoryQuery, String relationshipHistoryQuery, String attributesQuery,
List<? extends AttachmentHolderPE> attachmentHolders, AttachmentHolderKind attachmentHolderKind,
PersonPE registrator)
{
@@ -73,7 +73,7 @@ public class EntityHistoryCreator
selectAttributeEntries(session.createSQLQuery(attributesQuery), entityIdsToDelete);
addToHistories(histories, attributeEntries);
}
-
+
List<PropertyHistoryEntry> propertyHistory =
selectHistoryPropertyEntries(session.createSQLQuery(propertyHistoryQuery), entityIdsToDelete);
addToHistories(histories, propertyHistory);
@@ -85,17 +85,15 @@ public class EntityHistoryCreator
entityIdsToDelete);
addToHistories(histories, relationshipHistory);
}
-
+
if (attachmentHolders != null)
{
- List<RelationshipHistoryEntry> deletedAttachments
- = deleteAttachments(session, registrator, attachmentHolders);
+ List<RelationshipHistoryEntry> deletedAttachments = deleteAttachments(session, registrator, attachmentHolders);
addToHistories(histories, deletedAttachments);
}
if (attachmentHolderKind != null)
{
- List<RelationshipHistoryEntry> deletedAttachments
- = deleteAttachments(session, registrator, attachmentHolderKind, entityIdsToDelete);
+ List<RelationshipHistoryEntry> deletedAttachments = deleteAttachments(session, registrator, attachmentHolderKind, entityIdsToDelete);
addToHistories(histories, deletedAttachments);
}
@@ -116,7 +114,7 @@ public class EntityHistoryCreator
}
return content;
}
-
+
private List<RelationshipHistoryEntry> deleteAttachments(SharedSessionContract session,
PersonPE registrator, AttachmentHolderKind attachmentHolderKind, List<Long> holderIds)
{
@@ -150,8 +148,7 @@ public class EntityHistoryCreator
insertQuery.setParameter("registerer", registrator.getId());
insertQuery.setParameter("identifiers", identifier);
insertQuery.setParameter("attachment", ((Number) row.get("EXAC_ID")).longValue());
- Map<String, List<? extends EntityModification>> modifications
- = new HashMap<String, List<? extends EntityModification>>();
+ Map<String, List<? extends EntityModification>> modifications = new HashMap<String, List<? extends EntityModification>>();
AttachmentEntry attachmentEntry = new AttachmentEntry();
attachmentEntry.fileName = fileName;
attachmentEntry.version = version;
@@ -183,35 +180,47 @@ public class EntityHistoryCreator
}
return result;
}
-
+
private String createSelectHolderStatement(AttachmentHolderKind holderKind)
{
String tableName = "";
switch (holderKind)
{
- case PROJECT: tableName = "projects"; break;
- case EXPERIMENT: tableName = "experiments_all"; break;
- case SAMPLE: tableName = "samples_all"; break;
+ case PROJECT:
+ tableName = "projects";
+ break;
+ case EXPERIMENT:
+ tableName = "experiments_all";
+ break;
+ case SAMPLE:
+ tableName = "samples_all";
+ break;
}
return "SELECT id, perm_id from " + tableName + " WHERE id in (:" + ENTITY_IDS + ")";
}
-
+
private String createSelectAttachmentsStatement(AttachmentHolderKind attachmentHolderKind)
{
String holderColumn = "";
switch (attachmentHolderKind)
{
- case PROJECT: holderColumn = "proj_id"; break;
- case EXPERIMENT: holderColumn = "expe_id"; break;
- case SAMPLE: holderColumn = "samp_id"; break;
+ case PROJECT:
+ holderColumn = "proj_id";
+ break;
+ case EXPERIMENT:
+ holderColumn = "expe_id";
+ break;
+ case SAMPLE:
+ holderColumn = "samp_id";
+ break;
}
return "SELECT " + holderColumn + " as holder_id, file_name, "
+ "version, title, description, a.registration_timestamp, r.user_id, exac_id "
+ "FROM attachments a join persons r on a.pers_id_registerer = r.id "
+ "WHERE " + holderColumn + " in (:" + ENTITY_IDS + ")";
}
-
- private List<RelationshipHistoryEntry> deleteAttachments(SharedSessionContract session,
+
+ private List<RelationshipHistoryEntry> deleteAttachments(SharedSessionContract session,
PersonPE registrator, List<? extends AttachmentHolderPE> attachmentHolders)
{
List<RelationshipHistoryEntry> relationshipHistoryEntries = new ArrayList<>();
@@ -224,15 +233,14 @@ public class EntityHistoryCreator
{
fileNames.add(attachment.getFileName());
}
- Map<String, AttachmentEntry> deletedAttachments
- = attachmentDAO.deleteAttachments(holder, "", fileNames, registrator);
+ Map<String, AttachmentEntry> deletedAttachments = attachmentDAO.deleteAttachments(holder, "", fileNames, registrator);
Set<Entry<String, AttachmentEntry>> entrySet = deletedAttachments.entrySet();
for (Entry<String, AttachmentEntry> entry : entrySet)
{
RelationshipHistoryEntry relationshipHistoryEntry = new RelationshipHistoryEntry();
relationshipHistoryEntry.userId = entry.getValue().userId;
relationshipHistoryEntry.entityType = "ATTACHMENT";
- relationshipHistoryEntry.permId = holder.getPermId() ;
+ relationshipHistoryEntry.permId = holder.getPermId();
relationshipHistoryEntry.relatedEntity = entry.getKey();
relationshipHistoryEntry.relationType = "OWNER";
relationshipHistoryEntry.validFrom = entry.getValue().validFrom;
@@ -241,7 +249,7 @@ public class EntityHistoryCreator
}
return relationshipHistoryEntries;
}
-
+
private List<AttributeEntry> selectAttributeEntries(SQLQuery sqlQuery, List<Long> entityIdsToDelete)
{
List<Map<String, Object>> rows = getRows(sqlQuery, entityIdsToDelete);
@@ -446,11 +454,12 @@ public class EntityHistoryCreator
}
}
-
+
private static class AttachmentHolder
{
long id;
+
String permId;
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityModification.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityModification.java
index 60d7d36cecd..b3f457e439f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityModification.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/EntityModification.java
@@ -10,7 +10,7 @@ public class EntityModification
{
@JsonInclude(Include.NON_EMPTY)
public String userId;
-
+
@JsonIgnore
public String permId;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/PropertyHistoryEntry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/PropertyHistoryEntry.java
index 49546304a56..189de5d88a5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/PropertyHistoryEntry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/PropertyHistoryEntry.java
@@ -2,12 +2,10 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.deletion;
import com.fasterxml.jackson.annotation.JsonProperty;
-
-
public class PropertyHistoryEntry extends EntityModification
{
public final String type = "PROPERTY";
-
+
@JsonProperty("key")
public String propertyCode;
@@ -17,7 +15,7 @@ public class PropertyHistoryEntry extends EntityModification
public String toString()
{
return "HistoryPropertyEntry [permId=" + permId + ", propertyCode=" + propertyCode + ", value=" + value
- + ", user_id=" + userId
+ + ", user_id=" + userId
+ ", valid_from_timestamp=" + validFrom + ", valid_until_timestamp=" + validUntil + "]";
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/RelationshipHistoryEntry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/RelationshipHistoryEntry.java
index 4dfa99e5762..3f3b1438240 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/RelationshipHistoryEntry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/deletion/RelationshipHistoryEntry.java
@@ -2,12 +2,10 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.deletion;
import com.fasterxml.jackson.annotation.JsonProperty;
-
-
public class RelationshipHistoryEntry extends EntityModification
{
public final String type = "RELATIONSHIP";
-
+
@JsonProperty("key")
public String relationType;
@@ -20,7 +18,7 @@ public class RelationshipHistoryEntry extends EntityModification
public String toString()
{
return "RelationshipHistoryEntry [permId=" + permId + ", relationType=" + relationType + ", relatedEntity="
- + relatedEntity + ", entityType=" + entityType + ", userId=" + userId + ", validFromTimestamp="
+ + relatedEntity + ", entityType=" + entityType + ", userId=" + userId + ", validFromTimestamp="
+ validFrom + ", validUntilTimestamp=" + validUntil + "]";
}
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/CharacterHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/CharacterHelper.java
index 0c8d82d702a..9a31f8d4619 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/CharacterHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/CharacterHelper.java
@@ -31,7 +31,7 @@ public class CharacterHelper
private static final char ESCAPE_CHARACTER = '\\';
public final static Set<Character> SPECIAL_CHARACTERS = new HashSet<Character>(Arrays.asList(
- // Special code characters
+ // Special code characters
'.', ':', '-', '_',
// Special word characters
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/HibernateSearchContext.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/HibernateSearchContext.java
index cd9408794b5..3aa88581c31 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/HibernateSearchContext.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/HibernateSearchContext.java
@@ -33,8 +33,7 @@ import ch.systemsx.cisd.common.reflection.ModifiedShortPrefixToStringStyle;
/**
* A bean class that contains properties related to <i>Hibernate Search</i>.
* <p>
- * This bean must be initialized before <code>hibernate-session-factory</code> bean as it will
- * remove the <code>indexBase</code> directory.
+ * This bean must be initialized before <code>hibernate-session-factory</code> bean as it will remove the <code>indexBase</code> directory.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdateScheduler.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdateScheduler.java
index 81ca1bb53ae..fbd5de16b69 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdateScheduler.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdateScheduler.java
@@ -17,9 +17,8 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search;
/**
- * Each implementation is able to schedule a <i>full-text</i> index update. Updates are expected to
- * be executed asynchronously in the order they had been scheduled. The thread executing updates
- * will run with low priority.
+ * Each implementation is able to schedule a <i>full-text</i> index update. Updates are expected to be executed asynchronously in the order they had
+ * been scheduled. The thread executing updates will run with low priority.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdater.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdater.java
index a158dea6f89..ea7cc234cda 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdater.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexUpdater.java
@@ -17,9 +17,8 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search;
/**
- * Each implementation is able to perform a <i>full-text</i> index update. Updates are expected to
- * be executed asynchronously in the order they had been scheduled. The thread executing updates
- * will run with low priority.
+ * Each implementation is able to perform a <i>full-text</i> index update. Updates are expected to be executed asynchronously in the order they had
+ * been scheduled. The thread executing updates will run with low priority.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexer.java
index a0e484f72aa..c065a8a5dd8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IFullTextIndexer.java
@@ -31,22 +31,19 @@ public interface IFullTextIndexer
{
/**
- * Performs a <i>full-text</i> index on entities of given <var>clazz</var> using given
- * <i>Hibernate</i> session.
+ * Performs a <i>full-text</i> index on entities of given <var>clazz</var> using given <i>Hibernate</i> session.
*/
public <T> void doFullTextIndex(final Session hibernateSession, final Class<T> clazz)
throws DataAccessException;
/**
- * Performs a <i>full-text</i> index update on entities of given <var>clazz</var> with given
- * <var>ids</var> using given <i>Hibernate</i> session.
+ * Performs a <i>full-text</i> index update on entities of given <var>clazz</var> with given <var>ids</var> using given <i>Hibernate</i> session.
*/
public <T> void doFullTextIndexUpdate(final Session hibernateSession, final Class<T> clazz,
final List<Long> ids) throws DataAccessException;
/**
- * Removes entities of given <var>clazz</var> with given <var>ids</var> from the
- * <i>full-text</i> index using given <i>Hibernate</i> session.
+ * Removes entities of given <var>clazz</var> with given <var>ids</var> from the <i>full-text</i> index using given <i>Hibernate</i> session.
*/
public <T> void removeFromIndex(final Session hibernateSession, final Class<T> clazz,
final List<Long> ids) throws DataAccessException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexMode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexMode.java
index 36cbae20f5f..872396de1fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexMode.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexMode.java
@@ -20,11 +20,9 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search;
* The mode in which the indexing is working:
* <ul>
* <li><b>NO_INDEX</b>: no manual index will be performed.</li>
- * <li><b>SKIP_IF_MARKER_FOUND</b>: skips the indexing if
- * {@link FullTextIndexerRunnable#FULL_TEXT_INDEX_MARKER_FILENAME} marker file is found (meaning
- * that a manual index has already been performed).</li>
- * <li><b>INDEX_FROM_SCRATCH</b>: performs a manual index from the scratch, deleting the whole
- * <code>index-base</code> directory.</li>
+ * <li><b>SKIP_IF_MARKER_FOUND</b>: skips the indexing if {@link FullTextIndexerRunnable#FULL_TEXT_INDEX_MARKER_FILENAME} marker file is found
+ * (meaning that a manual index has already been performed).</li>
+ * <li><b>INDEX_FROM_SCRATCH</b>: performs a manual index from the scratch, deleting the whole <code>index-base</code> directory.</li>
* </ul>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexingQueryOptimizer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexingQueryOptimizer.java
index 6162d4f3ddb..b6e9af68505 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexingQueryOptimizer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/IndexingQueryOptimizer.java
@@ -44,10 +44,9 @@ public class IndexingQueryOptimizer
}
/**
- * Modifies a Criteria instance to optimize database queries that are used to do full text
- * indexing. Sets fetch mode to FetchMode.JOIN for all properties of an entity class that are
- * either annotated with IndexedEmbedded or they are eagerly fetched associations annotated with
- * OneToOne, ManyToOne, OneToMany or ManyToMany.
+ * Modifies a Criteria instance to optimize database queries that are used to do full text indexing. Sets fetch mode to FetchMode.JOIN for all
+ * properties of an entity class that are either annotated with IndexedEmbedded or they are eagerly fetched associations annotated with OneToOne,
+ * ManyToOne, OneToMany or ManyToMany.
*
* @param clazz Entity class whose instances are to be queried
* @param criteria Criteria query to be optimized
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilder.java
index 795d9787f71..b68b9faf815 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilder.java
@@ -207,7 +207,7 @@ public class LuceneQueryBuilder
String fieldName = fieldNames.get(i);
String searchPattern = searchPatterns.get(i);
Analyzer analyzer = analyzers.get(i);
-
+
Query query = parseQuery(fieldName, searchPattern, analyzer);
Occur occur = occurs.get(i);
if (Occur.MUST_NOT.equals(occur))
@@ -244,7 +244,7 @@ public class LuceneQueryBuilder
{
parser.setAllowLeadingWildcard(true);
BooleanQuery.setMaxClauseCount(Integer.MAX_VALUE);
-
+
try
{
return parser.parse(wholeQuery);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/PackageBasedIndexedEntityFinder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/PackageBasedIndexedEntityFinder.java
index f14b2c4056b..369348686de 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/PackageBasedIndexedEntityFinder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/PackageBasedIndexedEntityFinder.java
@@ -26,11 +26,9 @@ import ch.systemsx.cisd.common.reflection.ClassUtils;
import ch.systemsx.cisd.common.reflection.IClassFilter;
/**
- * A {@link IIndexedEntityFinder} based on a package name specified in the constructor. Classes
- * ending with <code>Test</code> will be ignored.
+ * A {@link IIndexedEntityFinder} based on a package name specified in the constructor. Classes ending with <code>Test</code> will be ignored.
* <p>
- * This does not work recursively and expects to find all the correctly annotated classes in the
- * given package.
+ * This does not work recursively and expects to find all the correctly annotated classes in the given package.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/DetailedQueryBuilder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/DetailedQueryBuilder.java
index 5271725b369..66072f122a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/DetailedQueryBuilder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/DetailedQueryBuilder.java
@@ -88,7 +88,7 @@ public class DetailedQueryBuilder
{
this.entityKind = entityKind;
}
-
+
private Query createQuery(String userId, DetailedSearchCriteria searchCriteria,
List<IAssociationCriteria> associations, Map<String, DocValuesType> fieldTypes)
{
@@ -121,11 +121,12 @@ public class DetailedQueryBuilder
fieldPattern = LuceneQueryBuilder.adaptQuery(fieldUserQuery,
useWildcardSearchMode, false);
fieldAnalyzer = new IgnoreCaseAnalyzer();
- } else if(isNumeric && criterion.getType() != null)
+ } else if (isNumeric && criterion.getType() != null)
{
fieldPattern = getRangeNumberQuery(criterion, fieldPattern);
fieldAnalyzer = PassThroughAnalyzer.INSTANCE;
- } else {
+ } else
+ {
fieldPattern = LuceneQueryBuilder.adaptQuery(value, useWildcardSearchMode);
fieldAnalyzer = searchAnalyzer;
}
@@ -135,7 +136,7 @@ public class DetailedQueryBuilder
fieldOccur.add(criterion.isNegated() ? Occur.MUST_NOT : Occur.SHOULD);
}
- Query luceneQuery = LuceneQueryBuilder.parseQuery(criterion.getType(), fieldNames,
+ Query luceneQuery = LuceneQueryBuilder.parseQuery(criterion.getType(), fieldNames,
fieldPatterns, fieldAnalyzers, fieldOccur);
resultQuery.add(luceneQuery, occureCondition);
} else
@@ -164,7 +165,8 @@ public class DetailedQueryBuilder
private String getRangeNumberQuery(DetailedSearchCriterion criterion, String fieldPattern)
{
String parsedNumberValue = SortableNumberBridgeUtils.getNumberForLucene(criterion.getValue());
- switch(criterion.getType()) {
+ switch (criterion.getType())
+ {
case LESS_THAN:
return "{* TO " + parsedNumberValue + "}";
case LESS_THAN_OR_EQUAL:
@@ -178,7 +180,7 @@ public class DetailedQueryBuilder
}
return fieldPattern;
}
-
+
private Occur createOccureCondition(SearchCriteriaConnection connection)
{
switch (connection)
@@ -191,8 +193,9 @@ public class DetailedQueryBuilder
throw InternalErr.error("unknown enum " + connection);
}
}
-
- public static List<String> getIndexFieldNames(List<DetailedSearchCriterion> criteria, EntityKind entityKind) {
+
+ public static List<String> getIndexFieldNames(List<DetailedSearchCriterion> criteria, EntityKind entityKind)
+ {
List<String> fieldNames = new ArrayList<String>();
for (DetailedSearchCriterion criterion : criteria)
{
@@ -200,7 +203,7 @@ public class DetailedQueryBuilder
}
return fieldNames;
}
-
+
private static List<String> getIndexFieldNames(DetailedSearchField searchField, EntityKind entityKind)
{
DetailedSearchFieldKind fieldKind = searchField.getKind();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/IndexFieldNameHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/IndexFieldNameHelper.java
index d9a2195afc4..6dac8cd7a6f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/IndexFieldNameHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/detailed/IndexFieldNameHelper.java
@@ -49,7 +49,7 @@ class IndexFieldNameHelper
return SearchFieldConstants.EXPERIMENT_ID;
}
throw createAssociationNotHandledException(entityKind, associationKind);
-
+
case SAMPLE:
if (entityKind == EntityKind.DATA_SET)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
index c3ff30ec57e..e4584b2fe06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
@@ -113,14 +113,16 @@ public class DynamicPropertyEvaluator implements IDynamicPropertyEvaluator
.setParameter("sample", entity);
allPropertyTypes = propertyTypeQuery.list();
- if (allPropertyTypes.size() > 0) {
+ if (allPropertyTypes.size() > 0)
+ {
propertyQuery =
session.createQuery(
"SELECT property FROM SamplePropertyPE property WHERE " +
"property.entity = :sample AND property.entityTypePropertyType IN (:types)")
.setParameter("sample", entity).setParameterList("types", allPropertyTypes);
existingProperties = propertyQuery.list();
- } else {
+ } else
+ {
existingProperties = new ArrayList<EntityPropertyPE>();
}
break;
@@ -131,14 +133,16 @@ public class DynamicPropertyEvaluator implements IDynamicPropertyEvaluator
.setParameter("data", entity);
allPropertyTypes = propertyTypeQuery.list();
- if (allPropertyTypes.size() > 0) {
+ if (allPropertyTypes.size() > 0)
+ {
propertyQuery =
session.createQuery(
"SELECT property FROM DataSetPropertyPE property WHERE " +
"property.entity = :data AND property.entityTypePropertyType IN (:types)")
.setParameter("data", entity).setParameterList("types", allPropertyTypes);
existingProperties = propertyQuery.list();
- } else {
+ } else
+ {
existingProperties = new ArrayList<EntityPropertyPE>();
}
break;
@@ -149,17 +153,19 @@ public class DynamicPropertyEvaluator implements IDynamicPropertyEvaluator
.setParameter("experiment", entity);
allPropertyTypes = propertyTypeQuery.list();
- if (allPropertyTypes.size() > 0) {
+ if (allPropertyTypes.size() > 0)
+ {
propertyQuery =
session.createQuery(
"SELECT property FROM ExperimentPropertyPE property WHERE " +
"property.entity = :experiment AND property.entityTypePropertyType IN (:types)")
.setParameter("experiment", entity).setParameterList("types", allPropertyTypes);
existingProperties = propertyQuery.list();
- } else {
+ } else
+ {
existingProperties = new ArrayList<EntityPropertyPE>();
}
-
+
break;
case MATERIAL:
propertyTypeQuery =
@@ -168,14 +174,16 @@ public class DynamicPropertyEvaluator implements IDynamicPropertyEvaluator
.setParameter("material", entity);
allPropertyTypes = propertyTypeQuery.list();
- if (allPropertyTypes.size() > 0) {
+ if (allPropertyTypes.size() > 0)
+ {
propertyQuery =
session.createQuery(
"SELECT property FROM MaterialPropertyPE property WHERE " +
"property.entity = :material AND property.entityTypePropertyType IN (:types)")
.setParameter("material", entity).setParameterList("types", allPropertyTypes);
existingProperties = propertyQuery.list();
- } else {
+ } else
+ {
existingProperties = new ArrayList<EntityPropertyPE>();
}
break;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IBatchDynamicPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IBatchDynamicPropertyEvaluator.java
index 5569bd95d69..6b73cb15dce 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IBatchDynamicPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IBatchDynamicPropertyEvaluator.java
@@ -24,8 +24,8 @@ import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
/**
- * Each implementation is able to evaluate dynamic properties of specified entities in batches.
- * After evaluation of properties the entities will be reindexed.
+ * Each implementation is able to evaluate dynamic properties of specified entities in batches. After evaluation of properties the entities will be
+ * reindexed.
*
* @author Piotr Buczek
*/
@@ -33,8 +33,7 @@ public interface IBatchDynamicPropertyEvaluator
{
/**
- * Evaluates dynamic properties of all entities of given <var>clazz</var> using given
- * <i>Hibernate</i> session.
+ * Evaluates dynamic properties of all entities of given <var>clazz</var> using given <i>Hibernate</i> session.
*
* @return list of ids of entities with dynamic properties that have been evaluated
*/
@@ -42,8 +41,7 @@ public interface IBatchDynamicPropertyEvaluator
final Session hibernateSession, final Class<T> clazz) throws DataAccessException;
/**
- * Evaluates dynamic properties of entities of given <var>clazz</var> with given <var>ids</var>
- * using given <i>Hibernate</i> session.
+ * Evaluates dynamic properties of entities of given <var>clazz</var> with given <var>ids</var> using given <i>Hibernate</i> session.
*
* @return list of ids of entities with dynamic properties that have been evaluated
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyAdaptor.java
index 04d136d4ca5..d2c0d8262ed 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyAdaptor.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.hotdeploy_plugins.api.IEntityAdap
import ch.systemsx.cisd.openbis.generic.shared.hotdeploy_plugins.api.IEntityPropertyAdaptor;
/**
- * {@link IEntityPropertyAdaptor} for dynamic property with lazy evaluation and cyclic dependencies
- * detection.
+ * {@link IEntityPropertyAdaptor} for dynamic property with lazy evaluation and cyclic dependencies detection.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyFunctions.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyFunctions.java
index 298cb7a2fb2..2456b03c5cf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyFunctions.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/DynamicPropertyFunctions.java
@@ -28,8 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
public final class DynamicPropertyFunctions
{
/**
- * @return String representation of material identifier for given material code and material
- * type code.
+ * @return String representation of material identifier for given material code and material type code.
*/
public static String material(String code, String typeCode)
{
@@ -37,8 +36,7 @@ public final class DynamicPropertyFunctions
}
/**
- * @return code of material with given identifier or null if the identifier is not a valid
- * material identifier
+ * @return code of material with given identifier or null if the identifier is not a valid material identifier
*/
public static String materialCode(String materialIdentifier)
{
@@ -48,8 +46,7 @@ public final class DynamicPropertyFunctions
}
/**
- * @return type of material with given identifier or null if the identifier is not a valid
- * material identifier
+ * @return type of material with given identifier or null if the identifier is not a valid material identifier
*/
public static String materialTypeCode(String materialIdentifier)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ISampleAdaptorRelationsQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ISampleAdaptorRelationsQuery.java
index 1630b8ccca9..e098f5fc6bc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ISampleAdaptorRelationsQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ISampleAdaptorRelationsQuery.java
@@ -43,7 +43,7 @@ public interface ISampleAdaptorRelationsQuery extends BaseQuery
+ " sr.relationship_id = rt.id AND sr.sample_id_parent = s.id AND "
+ " s.saty_id = st.id AND sr.sample_id_child = ?{1} AND " + " rt.code = '"
+ BasicConstant.PARENT_CHILD_DB_RELATIONSHIP + "' AND st.id = any(?{2})", parameterBindings =
- { TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<Long> getParentIdsOfTypes(Long childId, LongSet parentTypeIds);
@Select(sql = "SELECT sr.sample_id_child FROM sample_relationships sr, "
@@ -51,7 +51,7 @@ public interface ISampleAdaptorRelationsQuery extends BaseQuery
+ " sr.relationship_id = rt.id AND sr.sample_id_child = s.id AND "
+ " s.saty_id = st.id AND sr.sample_id_parent = ?{1} AND " + " rt.code = '"
+ BasicConstant.PARENT_CHILD_DB_RELATIONSHIP + "' AND st.id = any(?{2})", parameterBindings =
- { TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ { TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<Long> getChildIdsOfTypes(Long parentId, LongSet childTypeIds);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/XmlPropertyAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/XmlPropertyAdaptor.java
index 0d308cc207a..fb81cf717b0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/XmlPropertyAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/XmlPropertyAdaptor.java
@@ -21,8 +21,7 @@ import ch.systemsx.cisd.openbis.generic.shared.hotdeploy_plugins.api.IEntityProp
import ch.systemsx.cisd.openbis.generic.shared.util.XmlUtils;
/**
- * {@link IEntityPropertyAdaptor} implementation for xml property with lazy evaluation of rendered
- * value using XSLT script.
+ * {@link IEntityPropertyAdaptor} implementation for xml property with lazy evaluation of rendered value using XSLT script.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/ISampleAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/ISampleAdaptor.java
index f83cc94c5c2..0d1332c1436 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/ISampleAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/ISampleAdaptor.java
@@ -34,8 +34,7 @@ public interface ISampleAdaptor extends IEntityAdaptor
public Iterable<ISampleAdaptor> parents();
/**
- * Returns parent samples of this sample. Types of the returned parent samples must match the
- * specified regular expression.
+ * Returns parent samples of this sample. Types of the returned parent samples must match the specified regular expression.
*/
public Iterable<ISampleAdaptor> parentsOfType(String typeCodeRegexp);
@@ -45,8 +44,7 @@ public interface ISampleAdaptor extends IEntityAdaptor
public Iterable<ISampleAdaptor> children();
/**
- * Returns child samples of this sample. Types of the returned child samples must match the
- * specified regular expression.
+ * Returns child samples of this sample. Types of the returned child samples must match the specified regular expression.
*/
public Iterable<ISampleAdaptor> childrenOfType(String typeCodeRegexp);
@@ -61,8 +59,7 @@ public interface ISampleAdaptor extends IEntityAdaptor
public Iterable<ISampleAdaptor> contained();
/**
- * Returns contained samples of this sample. Types of the returned contained samples must match
- * the specified regular expression.
+ * Returns contained samples of this sample. Types of the returned contained samples must match the specified regular expression.
*/
public Iterable<ISampleAdaptor> containedOfType(String typeCodeRegexp);
@@ -72,8 +69,7 @@ public interface ISampleAdaptor extends IEntityAdaptor
public Iterable<IDataAdaptor> dataSets();
/**
- * Returns data sets of this sample. Types of the returned data sets must match the specified
- * regular expression.
+ * Returns data sets of this sample. Types of the returned data sets must match the specified regular expression.
*/
public Iterable<IDataAdaptor> dataSetsOfType(String typeCodeRegexp);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/AbstractEntityValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/AbstractEntityValidator.java
index 26697ef95b4..426f5b98f20 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/AbstractEntityValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/AbstractEntityValidator.java
@@ -28,8 +28,7 @@ public abstract class AbstractEntityValidator implements IEntityValidator
protected IValidationRequestDelegate<INonAbstractEntityAdapter> validationRequestedDelegate;
@Override
- public final void init(@SuppressWarnings("hiding")
- IValidationRequestDelegate<INonAbstractEntityAdapter> validationRequestedDelegate)
+ public final void init(@SuppressWarnings("hiding") IValidationRequestDelegate<INonAbstractEntityAdapter> validationRequestedDelegate)
{
this.validationRequestedDelegate = validationRequestedDelegate;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/api/IEntityValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/api/IEntityValidator.java
index c0bd826fea0..ac1526b5f5e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/api/IEntityValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/entity_validation/api/IEntityValidator.java
@@ -30,8 +30,7 @@ public interface IEntityValidator
/**
* Before the validation is triggered, the validator is initialized by calling this method.
*
- * @param validationRequestedDelegate object responsible for handling requests for entity
- * validation
+ * @param validationRequestedDelegate object responsible for handling requests for entity validation
*/
public void init(
IValidationRequestDelegate<INonAbstractEntityAdapter> validationRequestedDelegate);
@@ -40,8 +39,7 @@ public interface IEntityValidator
* Main method, that performs actual validation
*
* @param entity entity that needs to be validated
- * @param isNew <code>true</code> if the entity is freshly created, <code>false</code> if the
- * entity was only updated.
+ * @param isNew <code>true</code> if the entity is freshly created, <code>false</code> if the entity was only updated.
*/
public String validate(IEntityAdaptor entity, boolean isNew);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom022To023.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom022To023.java
index 26eb0eb15dc..7b909eb5f48 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom022To023.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom022To023.java
@@ -27,11 +27,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
import ch.systemsx.cisd.openbis.generic.shared.util.UuidUtil;
/**
- * Finishes migration of the database version 22 to version 23 by setting the <i>UUID</i> code of
- * the database instance.
+ * Finishes migration of the database version 22 to version 23 by setting the <i>UUID</i> code of the database instance.
* <p>
- * Note that, at that time, the <i>UUID</i> column label was <code>GLOBAL_CODE</code> and not
- * <code>UUID</code>.
+ * Note that, at that time, the <i>UUID</i> column label was <code>GLOBAL_CODE</code> and not <code>UUID</code>.
* </p>
*
* @author Tomasz Pylak
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom023To024.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom023To024.java
index e75fd08eb01..625895e71b1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom023To024.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom023To024.java
@@ -38,9 +38,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
/**
* A migration step from database version <code>v23</code> to version <code>v24</code>.
* <p>
- * This migration step does the following: it migrate the dataset locations in the database (
- * <code>Instance_<instance code></code> renamed Instance_<UUID> when <instance
- * code> is the original source).
+ * This migration step does the following: it migrate the dataset locations in the database ( <code>Instance_<instance code></code> renamed
+ * Instance_<UUID> when <instance code> is the original source).
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom025To026.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom025To026.java
index 1d0cba3311c..ef298c42d2b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom025To026.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom025To026.java
@@ -40,8 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
/**
* A migration step from database version <code>v25</code> to version <code>v26</code>.
* <p>
- * Adapts the data set locations in database after OBSERVABLE_TYPE has been renamed to
- * DATA_SET_TYPE.
+ * Adapts the data set locations in database after OBSERVABLE_TYPE has been renamed to DATA_SET_TYPE.
* </p>
*
* @author Izabela Adamczyk
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom046To047.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom046To047.java
index 513587e7f67..c7e70032685 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom046To047.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom046To047.java
@@ -41,8 +41,8 @@ import ch.systemsx.cisd.openbis.generic.shared.util.DisplaySettingsSerialization
/**
* A migration step from database version <code>v46</code> to version <code>v47</code>.
* <p>
- * Sets wildcard search mode for old users apart from system user. After this migration all users
- * will have a serialized display settings object in the DB (before it could be null).
+ * Sets wildcard search mode for old users apart from system user. After this migration all users will have a serialized display settings object in
+ * the DB (before it could be null).
* </p>
*
* @author Piotr Buczek
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java
index dba3e3781d3..5a9ee160369 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/util/UpdateUtils.java
@@ -32,8 +32,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.DynamicPropertyEvaluat
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.FullTextIndexUpdater;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class UpdateUtils
@@ -45,14 +43,14 @@ public class UpdateUtils
FullTextIndexUpdater indexUpdater = (FullTextIndexUpdater) applicationContext.getBean("full-text-index-updater");
DynamicPropertyEvaluationScheduler dynamicPropertyScheduler =
(DynamicPropertyEvaluationScheduler) applicationContext.getBean("dynamic-property-scheduler");
-
+
if (indexUpdater != null)
{
while (true)
{
IExtendedBlockingQueue<DynamicPropertyEvaluationOperation> dynamicPropertiesQueue = dynamicPropertyScheduler.getEvaluatorQueue();
int indexingQueueSize = indexUpdater.getQueueSize();
-
+
try
{
if (dynamicPropertiesQueue != null && dynamicPropertiesQueue.size() > 0)
@@ -76,7 +74,7 @@ public class UpdateUtils
}
}
}
-
+
public static Date getTransactionTimeStamp(SessionFactory sessionFactory)
{
Session currentSession = sessionFactory.getCurrentSession();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IDataSetType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IDataSetType.java
index d66c54d2d05..5b515c656fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IDataSetType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IDataSetType.java
@@ -23,8 +23,7 @@ public interface IDataSetType extends IDataSetTypeImmutable, IEntityTypeMutable
{
/**
- * @deprecated use {@link #setDataSetKind(String)} instead Set to <code>true</code> if the type
- * is a container type.
+ * @deprecated use {@link #setDataSetKind(String)} instead Set to <code>true</code> if the type is a container type.
*/
@Deprecated
public void setContainerType(boolean isContainerType);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IEntityType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IEntityType.java
index 89771146cda..bcd3486e420 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IEntityType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IEntityType.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.jython.api.v1;
-
/**
* The superinterface for all entity types (as opposed to property types).
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
index 3b0900916bb..ecbe663e4ad 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IMasterDataRegistrationTransaction.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.jython.api.v1;
import java.util.List;
/**
- * API for master data registration. Offers methods for creation and retrieval of openBIS types,
- * property assignments, vocabularies etc.
+ * API for master data registration. Offers methods for creation and retrieval of openBIS types, property assignments, vocabularies etc.
*
* @author Kaloyan Enimanev
*/
@@ -35,8 +34,7 @@ public interface IMasterDataRegistrationTransaction
IExperimentType createNewExperimentType(String code);
/**
- * Get an experiment type from the openBIS AS. Returns null if the experiment type does not
- * exist.
+ * Get an experiment type from the openBIS AS. Returns null if the experiment type does not exist.
*
* @return An experiment type or null
*/
@@ -45,8 +43,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates experiment type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IExperimentType getOrCreateNewExperimentType(String code);
@@ -72,8 +70,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates sample type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
ISampleType getOrCreateNewSampleType(String code);
@@ -99,8 +97,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates data set type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IDataSetType getOrCreateNewDataSetType(String code);
@@ -119,8 +117,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates a script from the openBIS AS.
*
- * @return the already existing script or a freshly created one if it doesn't exist. Setter
- * methods on the returned script are ignored if the script already exists.
+ * @return the already existing script or a freshly created one if it doesn't exist. Setter methods on the returned script are ignored if the
+ * script already exists.
*/
IScript getOrCreateNewScript(String code);
@@ -146,8 +144,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates material type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IMaterialType getOrCreateNewMaterialType(String code);
@@ -175,8 +173,8 @@ public interface IMasterDataRegistrationTransaction
* Gets or creates property type from the openBIS AS.
*
* @param dataType the data type of the property in case it has to be created.
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IPropertyType getOrCreateNewPropertyType(String code, DataType dataType);
@@ -186,11 +184,10 @@ public interface IMasterDataRegistrationTransaction
List<IPropertyTypeImmutable> listPropertyTypes();
/**
- * Assigns a property type to an entity type. If the assignment is already established an object
- * is returned where all setter method invocations are silently be ignored.
+ * Assigns a property type to an entity type. If the assignment is already established an object is returned where all setter method invocations
+ * are silently be ignored.
*
- * @param entityType One of IExperimentTypeImmutable, ISampleTypeImmutable,
- * IDataSetTypeImmutable, or IMaterialTypeImmutable.
+ * @param entityType One of IExperimentTypeImmutable, ISampleTypeImmutable, IDataSetTypeImmutable, or IMaterialTypeImmutable.
* @param propertyType The property type to assign to the entity type.
* @return An object representing the assignment.
*/
@@ -210,8 +207,7 @@ public interface IMasterDataRegistrationTransaction
IFileFormatType createNewFileFormatType(String code);
/**
- * Get a file format type from the openBIS AS. Returns null if the file format type does not
- * exist.
+ * Get a file format type from the openBIS AS. Returns null if the file format type does not exist.
*
* @return A file format type or null
*/
@@ -220,8 +216,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates file format type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IFileFormatType getOrCreateNewFileFormatType(String code);
@@ -247,8 +243,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates vocabulary type from the openBIS AS.
*
- * @return the already existing type or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IVocabulary getOrCreateNewVocabulary(String code);
@@ -258,8 +254,7 @@ public interface IMasterDataRegistrationTransaction
List<IVocabularyImmutable> listVocabularies();
/**
- * Create a new vocabulary term. The resulting object can be added to a vocabulary via the
- * {@link IVocabulary#addTerm(IVocabularyTerm)} method.
+ * Create a new vocabulary term. The resulting object can be added to a vocabulary via the {@link IVocabulary#addTerm(IVocabularyTerm)} method.
*
* @param code the vocabulary term's code
*/
@@ -285,8 +280,7 @@ public interface IMasterDataRegistrationTransaction
IExternalDataManagementSystem createNewExternalDataManagementSystem(String code);
/**
- * Get an external data management system from the openBIS AS. Returns null if the external data
- * management system does not exist.
+ * Get an external data management system from the openBIS AS. Returns null if the external data management system does not exist.
*
* @return An external data management system or null
*/
@@ -295,8 +289,8 @@ public interface IMasterDataRegistrationTransaction
/**
* Gets or creates external data management system from the openBIS AS.
*
- * @return the already existing system or a freshly created one if it doesn't exist. Setter
- * methods on the returned type are ignored if the type already exists.
+ * @return the already existing system or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type
+ * already exists.
*/
IExternalDataManagementSystem getOrCreateNewExternalDataManagementSystem(String code);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignment.java
index eb24f608707..e881d335d10 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignment.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignment.java
@@ -28,8 +28,8 @@ public interface IPropertyAssignment extends IPropertyAssignmentImmutable
void setMandatory(boolean mandatory);
/**
- * Set the name of the form section. It will appear when editing objects of the specified entity
- * in openBIS. Specifying a section name is optional.
+ * Set the name of the form section. It will appear when editing objects of the specified entity in openBIS. Specifying a section name is
+ * optional.
*/
void setSection(String section);
@@ -39,8 +39,7 @@ public interface IPropertyAssignment extends IPropertyAssignmentImmutable
void setDefaultValue(String defaultValue);
/**
- * Sets the position where the property will appear in forms. If not specified the property will
- * be displayed at the bottom of the form.
+ * Sets the position where the property will appear in forms. If not specified the property will be displayed at the bottom of the form.
*/
void setPositionInForms(Long position);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignmentImmutable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignmentImmutable.java
index 08bb02d3c12..468f9401606 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignmentImmutable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyAssignmentImmutable.java
@@ -49,8 +49,7 @@ public interface IPropertyAssignmentImmutable
String getSection();
/**
- * Return the position at which the property will be rendered when editing/registering objects
- * of the specified entity type.
+ * Return the position at which the property will be rendered when editing/registering objects of the specified entity type.
*/
Long getPositionInForms();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyType.java
index bfb637124b5..6939b15c884 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyType.java
@@ -22,14 +22,12 @@ package ch.systemsx.cisd.openbis.generic.server.jython.api.v1;
public interface IPropertyType extends IPropertyTypeImmutable
{
/**
- * Set the description for this property type. This is a mandatory parameter and must not be
- * left emtpy when creating new {@link IPropertyType}-s.
+ * Set the description for this property type. This is a mandatory parameter and must not be left emtpy when creating new {@link IPropertyType}-s.
*/
void setDescription(String description);
/**
- * Set the label for this property type. This is a mandatory parameter and must not be left
- * emtpy when creating new {@link IPropertyType}-s.
+ * Set the label for this property type. This is a mandatory parameter and must not be left emtpy when creating new {@link IPropertyType}-s.
*/
void setLabel(String label);
@@ -49,16 +47,14 @@ public interface IPropertyType extends IPropertyTypeImmutable
void setXmlSchema(String schema);
/**
- * Set an XSLT transformation to be applied to properties of XML {@link DataType} before
- * rendering in the UI.
+ * Set an XSLT transformation to be applied to properties of XML {@link DataType} before rendering in the UI.
*/
void setTransformation(String xsltTransformation);
void setManagedInternally(boolean isManagedInternally);
/**
- * Property of internal names receive a special prefix to avoid naming conflicts with
- * user-defined property types.
+ * Property of internal names receive a special prefix to avoid naming conflicts with user-defined property types.
*/
void setInternalNamespace(boolean isInternalNamespace);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyTypeImmutable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyTypeImmutable.java
index ba733829f29..5fe5d099f71 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyTypeImmutable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IPropertyTypeImmutable.java
@@ -44,14 +44,14 @@ public interface IPropertyTypeImmutable extends IAbstractType
IVocabularyImmutable getVocabulary();
/**
- * Return an XSD used to verify the validity of properties with XML {@link DataType}. Return
- * <code>null</code> if the DataType is not XML or there is no schema set.
+ * Return an XSD used to verify the validity of properties with XML {@link DataType}. Return <code>null</code> if the DataType is not XML or there
+ * is no schema set.
*/
String getXmlSchema();
/**
- * Return an XSLT transformation applied to properties with XML {@link DataType}. Return
- * <code>null</code> if the DataType is not XML or there is no transformation set.
+ * Return an XSLT transformation applied to properties with XML {@link DataType}. Return <code>null</code> if the DataType is not XML or there is
+ * no transformation set.
*/
String getTransformation();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabulary.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabulary.java
index d1341032895..09a9b0eb2c1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabulary.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabulary.java
@@ -40,8 +40,7 @@ public interface IVocabulary extends IVocabularyImmutable
void setChosenFromList(boolean isChosenFromList);
/**
- * Sets a URL template (e.g a search query) that can display additional information for the
- * concrete vocabulary terms.
+ * Sets a URL template (e.g a search query) that can display additional information for the concrete vocabulary terms.
*/
void setUrlTemplate(String urlTemplate);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabularyImmutable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabularyImmutable.java
index 619183a337d..d72f1951e85 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabularyImmutable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/IVocabularyImmutable.java
@@ -49,8 +49,7 @@ public interface IVocabularyImmutable
boolean isChosenFromList();
/**
- * Returns a URL template (e.g a search query) that can display additional information for the
- * concrete vocabulary terms. Can return null.
+ * Returns a URL template (e.g a search query) that can display additional information for the concrete vocabulary terms. Can return null.
*/
String getUrlTemplate();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/ExternalDataManagementSystemWrapper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/ExternalDataManagementSystemWrapper.java
index e9137d86883..27f1d98f75b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/ExternalDataManagementSystemWrapper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/ExternalDataManagementSystemWrapper.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IExternalDataManagementSystem;
/**
- * Wrapper of {@link ExternalDataManagementSystemImmutable} as {@link IExternalDataManagementSystem}
- * where setters do nothing.
+ * Wrapper of {@link ExternalDataManagementSystemImmutable} as {@link IExternalDataManagementSystem} where setters do nothing.
*
* @author Pawel Glyzewski
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunnerStandalone.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunnerStandalone.java
index 2a573e80de7..ab7cc01004c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunnerStandalone.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/MasterDataRegistrationScriptRunnerStandalone.java
@@ -28,8 +28,7 @@ import ch.systemsx.cisd.common.logging.LogLevel;
import ch.systemsx.cisd.openbis.generic.shared.cli.OpenBisConsoleClientArguments;
/**
- * A standalone command line tool allowing the execution of Jython scripts to initialize the master
- * data on an openBIS AS.
+ * A standalone command line tool allowing the execution of Jython scripts to initialize the master data on an openBIS AS.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/PropertyAssignmentWrapper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/PropertyAssignmentWrapper.java
index d2589dd5dbd..522e43ddca9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/PropertyAssignmentWrapper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/PropertyAssignmentWrapper.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IPropertyAssignment;
/**
- * Wrapper of {@link PropertyAssignmentImmutable} as {@link IPropertyAssignment} where setters do
- * nothing.
+ * Wrapper of {@link PropertyAssignmentImmutable} as {@link IPropertyAssignment} where setters do nothing.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/Script.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/Script.java
index e248896cba1..2604ae60d18 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/Script.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/jython/api/v1/impl/Script.java
@@ -63,7 +63,7 @@ public class Script extends ScriptImmutable implements IScript
} else
{
script.setEntityKind(new EntityKind[]
- { EntityKind.valueOf(entityKind) });
+ { EntityKind.valueOf(entityKind) });
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/AbstractPluginRegistry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/AbstractPluginRegistry.java
index 84fdd3cf188..8515ff75a89 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/AbstractPluginRegistry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/AbstractPluginRegistry.java
@@ -113,8 +113,7 @@ abstract class AbstractPluginRegistry<P extends IServerPlugin> implements BeanFa
/**
* Returns the appropriate plug-in for the specified entity kind and entity type.
*
- * @return never <code>null</code> but could return the <i>generic</i> implementation if none
- * has been found.
+ * @return never <code>null</code> but could return the <i>generic</i> implementation if none has been found.
*/
public final synchronized P getPlugin(EntityKind entityKind, EntityTypePE entityType)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/DataSetServerPluginRegistry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/DataSetServerPluginRegistry.java
index ef4fd18f7a1..f86a5968fcf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/DataSetServerPluginRegistry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/DataSetServerPluginRegistry.java
@@ -20,7 +20,6 @@ import org.springframework.stereotype.Component;
import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
-
/**
* A registry for data set server plug-ins.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetServerPlugin.java
index 8c588cdd9cc..dc11dffdc3b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetServerPlugin.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.plugin;
/**
* Plug-in interface for data sets.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IDataSetServerPlugin extends IServerPlugin
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
index 37a6ba7a630..42017e86dd2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
* The slave server plug-in for a Data set type
* <p>
- * The implementation will give access to {@link DAOFactory} and appropriate business object
- * factory. Each method specified here must start with {@link Session} parameter.
+ * The implementation will give access to {@link DAOFactory} and appropriate business object factory. Each method specified here must start with
+ * {@link Session} parameter.
* </p>
*
* @author Christian Ribeaud
@@ -38,8 +38,7 @@ public interface IDataSetTypeSlaveServerPlugin
/**
* Permanently deletes the specified data sets for the specified reason.
*
- * @deprecated this is legacy code and should be removed when we remove the option of disabled
- * trash
+ * @deprecated this is legacy code and should be removed when we remove the option of disabled trash
*/
@Deprecated
public void permanentlyDeleteDataSets(Session session, List<DataPE> dataSets, String reason,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
index 5f6f870cc51..e0aa031fa29 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
@@ -30,8 +30,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
* The slave server plug-in for a <i>Sample Type</i>.
* <p>
- * The implementation will give access to {@link DAOFactory} and appropriate business object
- * factory. Each method specified here must start with {@link Session} parameter.
+ * The implementation will give access to {@link DAOFactory} and appropriate business object factory. Each method specified here must start with
+ * {@link Session} parameter.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPlugin.java
index 336b9f10936..5a553de0e9f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPlugin.java
@@ -21,15 +21,12 @@ import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
/**
- *
- *
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IServerPlugin
{
/**
- * Returns all the entity type codes for specified entity kind which are supported by this
- * server plugin.
+ * Returns all the entity type codes for specified entity kind which are supported by this server plugin.
*/
public Set<String> getEntityTypeCodes(final EntityKind entityKind);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPluginWithWildcards.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPluginWithWildcards.java
index 091e3f51e80..017d7969262 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPluginWithWildcards.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IServerPluginWithWildcards.java
@@ -21,16 +21,14 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
/**
- * An extension of the @{link IServerPlugin} that supports using regular expression wildcards in the
- * codes.
+ * An extension of the @{link IServerPlugin} that supports using regular expression wildcards in the codes.
*
* @author Chandrasekhar Ramakrishnan
*/
public interface IServerPluginWithWildcards extends IServerPlugin
{
/**
- * Returns all the entity type codes for given <var>entityKind</var> supported by this
- * implementation.
+ * Returns all the entity type codes for given <var>entityKind</var> supported by this implementation.
*/
public List<String> getOrderedEntityTypeCodes(final EntityKind entityKind);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/SampleServerPluginRegistry.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/SampleServerPluginRegistry.java
index 44c68f4b21c..bbfab1bb9aa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/SampleServerPluginRegistry.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/SampleServerPluginRegistry.java
@@ -20,14 +20,13 @@ import org.springframework.stereotype.Component;
import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
-
/**
* A registry for sample server plug-ins.
*/
@Component(ResourceNames.SAMPLE_PLUGIN_REGISTRY)
public final class SampleServerPluginRegistry extends AbstractPluginRegistry<ISampleServerPlugin>
{
-
+
@Override
protected String getBeanNameOfGenericPlugin()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/WildcardSupportingPluginMap.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/WildcardSupportingPluginMap.java
index 8c2808f25da..6dd92412736 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/WildcardSupportingPluginMap.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/WildcardSupportingPluginMap.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.WildcardSupportingMap;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKindAndTypeCode;
/**
- * Utility class that manages mappings from entity types/codes (possibly including wildcards) to
- * IServerPlugin objects.
+ * Utility class that manages mappings from entity types/codes (possibly including wildcards) to IServerPlugin objects.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/BatchSampleRegistrationTempCodeUpdaterTask.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/BatchSampleRegistrationTempCodeUpdaterTask.java
index 3e5b3c5af60..0e9bccdff5d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/BatchSampleRegistrationTempCodeUpdaterTask.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/BatchSampleRegistrationTempCodeUpdaterTask.java
@@ -39,16 +39,16 @@ public class BatchSampleRegistrationTempCodeUpdaterTask implements IMaintenanceT
{
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, BatchSampleRegistrationTempCodeUpdaterTask.class);
-
+
private BatchSampleRegistrationTempCodeUpdaterBean bean;
@Override
public void setUp(String pluginName, Properties properties)
{
}
- // TODO FJE: Do the update in single queue which is also fed by the
- // GenericClientService.updateTemporaryCodes()
+ // TODO FJE: Do the update in single queue which is also fed by the
+ // GenericClientService.updateTemporaryCodes()
// this bean is programmatically created so that we can use spring managed transactions
// in this maintenance task. Otherwise QueryTool needs to set the datasource/connection
@@ -143,7 +143,7 @@ public class BatchSampleRegistrationTempCodeUpdaterTask implements IMaintenanceT
sampleDAO.createOrUpdateSamples(samplePEs, personPE, true);
}
}
-
+
@Override
public void execute()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTask.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTask.java
index dd656cbec21..5ebb267eb67 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTask.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTask.java
@@ -57,13 +57,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
/**
* Maintenance task send e-mails with reports on recently registered data sets.
* <p>
- * The maintenance task may be run in one of two modes, the normal mode is to report on data sets
- * registered in the period specified by the days-of-month or days-of-week. The period goes from the
- * current day to the last day the maintenance task was run.
+ * The maintenance task may be run in one of two modes, the normal mode is to report on data sets registered in the period specified by the
+ * days-of-month or days-of-week. The period goes from the current day to the last day the maintenance task was run.
* <p>
- * Sometimes, however, for the first run, the user may want to explicitly specify the date range for
- * the maintenance task. This can be done, but the maintenance task should then only be run once,
- * because it will always report on the specified date range.
+ * Sometimes, however, for the first run, the user may want to explicitly specify the date range for the maintenance task. This can be done, but the
+ * maintenance task should then only be run once, because it will always report on the specified date range.
*
* @author Franz-Josef Elmer
*/
@@ -297,8 +295,7 @@ public class DataSetRegistrationSummaryTask implements IMaintenanceTask
}
/**
- * @return True if the data set type should <b>not</b> be included in the report; return false
- * if it should be included in the report.
+ * @return True if the data set type should <b>not</b> be included in the report; return false if it should be included in the report.
*/
private boolean excludeDataSetType(DataSetType dataSetType)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTask.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTask.java
index 29e7bc45126..d36d852718c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTask.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTask.java
@@ -672,8 +672,8 @@ public class MaterialExternalDBSyncTask implements IMaintenanceTask
{
String sql = tryToReadTimestamp() == null ? insertTimestampSql : updateTimestampSql;
jdbcTemplate.update(sql, new Object[]
- { newTimestamp }, new int[]
- { Types.TIMESTAMP });
+ { newTimestamp }, new int[]
+ { Types.TIMESTAMP });
}
@Private
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RevokeUserAccessMaintenanceTask.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RevokeUserAccessMaintenanceTask.java
index 2386a8b77c8..f6d839aa173 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RevokeUserAccessMaintenanceTask.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RevokeUserAccessMaintenanceTask.java
@@ -46,123 +46,130 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
*
* @author Juan Fuentes
*/
-public class RevokeUserAccessMaintenanceTask implements IMaintenanceTask {
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RevokeUserAccessMaintenanceTask.class);
- private static final String AUTH_SERVICE_BEAN = "authentication-service";
- private static final IAuthenticationService authService;
-
- static {
- IAuthenticationService authServiceAux = (IAuthenticationService) CommonServiceProvider.tryToGetBean(AUTH_SERVICE_BEAN);
-
- if (authServiceAux instanceof StackedAuthenticationService && ((StackedAuthenticationService) authServiceAux).allServicesSupportListingByUserId())
- {
- authService = authServiceAux;
- } else if(authServiceAux.supportsListingByUserId())
- {
- authService = authServiceAux;
- }
- else
- {
- authService = null;
- }
- }
-
- @Override
- public void setUp(String pluginName, Properties properties) {
- operationLog.info("Task " + pluginName + " initialized.");
- }
-
- @Override
- public void execute()
- {
- operationLog.info("execution started");
- //0. Initial Check
- if(authService == null)
- {
- operationLog.info("This plugin doesn't work with authentication services that don't support listing by user idt.");
- return;
- }
- // 1. Grab all users, user roles and user authorization groups
- IPersonDAO personDAO = CommonServiceProvider.getDAOFactory().getPersonDAO();
- IRoleAssignmentDAO rolesDAO = CommonServiceProvider.getDAOFactory().getRoleAssignmentDAO();
-
- // Used to manage the authorization groups since the IPersonDAO throw a session exception when accessing this information.
- ICommonServerForInternalUse server = CommonServiceProvider.getCommonServer();
- SessionContextDTO contextOrNull = server.tryToAuthenticateAsSystem();
-
- List<PersonPE> people = personDAO.listActivePersons();
-
- // 2. Users to Revoke
- List<PersonPE> peopleToRevoke = new ArrayList<PersonPE>();
-
- // 3. Check if the users exists on LDAP currently
- personCheck:
- for (PersonPE person : people)
- {
- if (false == person.isSystemUser() && person.isActive() && false == isUserValid(person.getUserId()))
- {
- List<RoleAssignmentPE> roles = rolesDAO.listRoleAssignmentsByPerson(person);
- for (RoleAssignmentPE role : roles)
- {
- if (role.getRole().name().equals("ETL_SERVER"))
- {
- continue personCheck;
- }
- }
- peopleToRevoke.add(person);
- }
- }
-
- // 4. If is not found on the authentication service, revoke access
- for (PersonPE person : peopleToRevoke)
- {
- String userIdToRevoke = person.getUserId();
- operationLog.info("person " + userIdToRevoke + " is going to be revoked.");
-
- // Delete person roles
- for (RoleAssignmentPE role : rolesDAO.listRoleAssignmentsByPerson(person))
- {
- rolesDAO.delete(role);
- }
-
- // Delete person from groups
- List<AuthorizationGroup> groups = server.listAuthorizationGroups(contextOrNull.getSessionToken());
-
- for (AuthorizationGroup group : groups)
- {
- List<Person> peopleInGroup = server.listPersonInAuthorizationGroup(contextOrNull.getSessionToken(), new TechId(group.getId()));
- for (Person personInGroup : peopleInGroup)
- {
- if (personInGroup.getUserId().equals(userIdToRevoke))
- {
- List<String> toRemoveFromGroup = new ArrayList<String>();
- toRemoveFromGroup.add(person.getUserId());
- server.removePersonsFromAuthorizationGroup(contextOrNull.getSessionToken(), new TechId(group.getId()), toRemoveFromGroup);
- }
- }
- }
-
- // Change userId and disable
- person.setUserId(person.getUserId() + "-" + getTimeStamp());
- person.setActive(false);
- personDAO.updatePerson(person);
-
- operationLog.info("person " + userIdToRevoke + " has been revoked.");
- }
-
- operationLog.info("task executed");
- }
-
- /*
- * We can only delete the users if, the Principals are listable and they are not available.
- */
- private boolean isUserValid(String userId) {
- return authService.supportsListingByUserId() && false == authService.listPrincipalsByUserId(userId).isEmpty();
- }
-
- private String getTimeStamp() {
- DateFormat dateFormat = new SimpleDateFormat("yyyy.MM.dd");
- return dateFormat.format(new Date());
- }
+public class RevokeUserAccessMaintenanceTask implements IMaintenanceTask
+{
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, RevokeUserAccessMaintenanceTask.class);
+
+ private static final String AUTH_SERVICE_BEAN = "authentication-service";
+
+ private static final IAuthenticationService authService;
+
+ static
+ {
+ IAuthenticationService authServiceAux = (IAuthenticationService) CommonServiceProvider.tryToGetBean(AUTH_SERVICE_BEAN);
+
+ if (authServiceAux instanceof StackedAuthenticationService
+ && ((StackedAuthenticationService) authServiceAux).allServicesSupportListingByUserId())
+ {
+ authService = authServiceAux;
+ } else if (authServiceAux.supportsListingByUserId())
+ {
+ authService = authServiceAux;
+ }
+ else
+ {
+ authService = null;
+ }
+ }
+
+ @Override
+ public void setUp(String pluginName, Properties properties)
+ {
+ operationLog.info("Task " + pluginName + " initialized.");
+ }
+
+ @Override
+ public void execute()
+ {
+ operationLog.info("execution started");
+ // 0. Initial Check
+ if (authService == null)
+ {
+ operationLog.info("This plugin doesn't work with authentication services that don't support listing by user idt.");
+ return;
+ }
+ // 1. Grab all users, user roles and user authorization groups
+ IPersonDAO personDAO = CommonServiceProvider.getDAOFactory().getPersonDAO();
+ IRoleAssignmentDAO rolesDAO = CommonServiceProvider.getDAOFactory().getRoleAssignmentDAO();
+
+ // Used to manage the authorization groups since the IPersonDAO throw a session exception when accessing this information.
+ ICommonServerForInternalUse server = CommonServiceProvider.getCommonServer();
+ SessionContextDTO contextOrNull = server.tryToAuthenticateAsSystem();
+
+ List<PersonPE> people = personDAO.listActivePersons();
+
+ // 2. Users to Revoke
+ List<PersonPE> peopleToRevoke = new ArrayList<PersonPE>();
+
+ // 3. Check if the users exists on LDAP currently
+ personCheck: for (PersonPE person : people)
+ {
+ if (false == person.isSystemUser() && person.isActive() && false == isUserValid(person.getUserId()))
+ {
+ List<RoleAssignmentPE> roles = rolesDAO.listRoleAssignmentsByPerson(person);
+ for (RoleAssignmentPE role : roles)
+ {
+ if (role.getRole().name().equals("ETL_SERVER"))
+ {
+ continue personCheck;
+ }
+ }
+ peopleToRevoke.add(person);
+ }
+ }
+
+ // 4. If is not found on the authentication service, revoke access
+ for (PersonPE person : peopleToRevoke)
+ {
+ String userIdToRevoke = person.getUserId();
+ operationLog.info("person " + userIdToRevoke + " is going to be revoked.");
+
+ // Delete person roles
+ for (RoleAssignmentPE role : rolesDAO.listRoleAssignmentsByPerson(person))
+ {
+ rolesDAO.delete(role);
+ }
+
+ // Delete person from groups
+ List<AuthorizationGroup> groups = server.listAuthorizationGroups(contextOrNull.getSessionToken());
+
+ for (AuthorizationGroup group : groups)
+ {
+ List<Person> peopleInGroup = server.listPersonInAuthorizationGroup(contextOrNull.getSessionToken(), new TechId(group.getId()));
+ for (Person personInGroup : peopleInGroup)
+ {
+ if (personInGroup.getUserId().equals(userIdToRevoke))
+ {
+ List<String> toRemoveFromGroup = new ArrayList<String>();
+ toRemoveFromGroup.add(person.getUserId());
+ server.removePersonsFromAuthorizationGroup(contextOrNull.getSessionToken(), new TechId(group.getId()), toRemoveFromGroup);
+ }
+ }
+ }
+
+ // Change userId and disable
+ person.setUserId(person.getUserId() + "-" + getTimeStamp());
+ person.setActive(false);
+ personDAO.updatePerson(person);
+
+ operationLog.info("person " + userIdToRevoke + " has been revoked.");
+ }
+
+ operationLog.info("task executed");
+ }
+
+ /*
+ * We can only delete the users if, the Principals are listable and they are not available.
+ */
+ private boolean isUserValid(String userId)
+ {
+ return authService.supportsListingByUserId() && false == authService.listPrincipalsByUserId(userId).isEmpty();
+ }
+
+ private String getTimeStamp()
+ {
+ DateFormat dateFormat = new SimpleDateFormat("yyyy.MM.dd");
+ return dateFormat.format(new Date());
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/LifeCycleListener.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/LifeCycleListener.java
index 749f47e28a6..6a1ab8115cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/LifeCycleListener.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/LifeCycleListener.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.util;
import org.eclipse.jetty.util.component.LifeCycle;
/**
- * Stops a component (e.g. Web Server) if it goes into state "Failure". Prints messages
- * on console in case of success and failure.
+ * Stops a component (e.g. Web Server) if it goes into state "Failure". Prints messages on console in case of success and failure.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/MethodInvocationUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/MethodInvocationUtils.java
index b21c54b3e7f..19542c1d692 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/MethodInvocationUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/MethodInvocationUtils.java
@@ -43,12 +43,10 @@ public class MethodInvocationUtils
}
/**
- * Returns either the method of the specified {@link MethodInvocation} object or the method of
- * the target object. The later is returned if <code>methodInvocation.getMethod()</code> has
- * none the specified annotations and the target object class isn't a synthetic proxy class.
+ * Returns either the method of the specified {@link MethodInvocation} object or the method of the target object. The later is returned if
+ * <code>methodInvocation.getMethod()</code> has none the specified annotations and the target object class isn't a synthetic proxy class.
* <p>
- * This function should be used if it isn't known whether the interface of a proxy or the real
- * target has the annotation.
+ * This function should be used if it isn't known whether the interface of a proxy or the real target has the annotation.
*/
public static Method getMethod(final MethodInvocation methodInvocation,
List<Class<? extends Annotation>> annotationClasses) throws NoSuchMethodException
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerLogger.java
index 3a8464b2711..b37bc9ba85a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerLogger.java
@@ -198,7 +198,7 @@ public abstract class AbstractServerLogger implements IServer
if (parameter instanceof Collection)
{
unquotedParameter = CollectionUtils.abbreviate((Collection<?>) unquotedParameter, 20);
- }
+ }
parameters[i] = "'" + unquotedParameter + "'";
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseCreateOrDeleteModification.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseCreateOrDeleteModification.java
index a449dbab6f8..98815ed8172 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseCreateOrDeleteModification.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseCreateOrDeleteModification.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKin
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LastModificationState;
/**
- * Annotation used to mark methods which create or delete specified database objects. It can be used
- * by a (GUI) client to trigger view updates. For more details see {@link LastModificationState}.
+ * Annotation used to mark methods which create or delete specified database objects. It can be used by a (GUI) client to trigger view updates. For
+ * more details see {@link LastModificationState}.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseUpdateModification.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseUpdateModification.java
index acdc68fbdaa..271759554fb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseUpdateModification.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/DatabaseUpdateModification.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKin
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LastModificationState;
/**
- * Annotation used to mark methods which update specified database objects. It can be used by a
- * (GUI) client to trigger view updates. For more details see {@link LastModificationState}.
+ * Annotation used to mark methods which update specified database objects. It can be used by a (GUI) client to trigger view updates. For more details
+ * see {@link LastModificationState}.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index d391dc59d45..ed4a20cf23d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -663,7 +663,7 @@ public interface ICommonServer extends IServer
* Searches on a search domain. The result is sorted by score in descending order.
*/
@Transactional(readOnly = true)
- public List<SearchDomainSearchResultWithFullEntity> searchOnSearchDomain(String sessionToken,
+ public List<SearchDomainSearchResultWithFullEntity> searchOnSearchDomain(String sessionToken,
String preferredSearchDomainOrNull, String searchString, Map<String, String> optionalParametersOrNull);
/**
@@ -1600,7 +1600,7 @@ public interface ICommonServer extends IServer
*/
@Transactional(readOnly = true)
public List<String> listPredeployedPlugins(String sessionToken, ScriptType scriptType);
-
+
/**
* Gets text for front page if the AS is disabled, null otherwise.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index fc42bc011b2..0f8aa36a024 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -174,8 +174,8 @@ public interface IDataStoreService
public void cleanupSession(String userSessionToken);
/**
- * Searches for the specified sequence snippet. If no preferred search domain is specified the first available one will be used. If the
- * preferred search domain doesn't exist or isn't available also the first one will be used.
+ * Searches for the specified sequence snippet. If no preferred search domain is specified the first available one will be used. If the preferred
+ * search domain doesn't exist or isn't available also the first one will be used.
*
* @param preferredSearchDomainOrNull The key of the preferred search domain or <code>null</code>.
* @param sequenceSnippet Snippet of nucleotid or aminoacid sequence.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IRemoteHostValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IRemoteHostValidator.java
index c6a007b6f04..fbe6e4b252a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IRemoteHostValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IRemoteHostValidator.java
@@ -26,5 +26,5 @@ public interface IRemoteHostValidator
/**
* Returns <code>true</code> if the specified remote host is allowed.
*/
- public boolean isValidRemoteHost(String remoteHost);
+ public boolean isValidRemoteHost(String remoteHost);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
index e4b4e6a1b49..3b244034282 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
@@ -521,7 +521,7 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
public boolean isDataSetOnTrashCanOrDeleted(String sessionToken, String dataSetCode);
-
+
/**
* Updates share id and size of specified data set.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionProvider.java
index c38e9a0ed13..382067dbae6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ISessionProvider.java
@@ -22,7 +22,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
/**
* Provider of {@link IAuthSession}.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface ISessionProvider
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
index 0b7d5e1967e..03492b31207 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.generic.shared;
/**
* Resource name used in <i>generic</i>.
* <p>
- * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here
- * should not conflict with already existing bean names. Look for other <code>ResourceNames</code>
- * classes.
+ * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here should not conflict with already existing bean names.
+ * Look for other <code>ResourceNames</code> classes.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
index 266e51e07a2..ddec8c194a2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
@@ -535,7 +535,8 @@ public class Translator
}
initializer.setStorageConfirmed(externalDatum.isStorageConfirmation());
initializer.setStub(externalDatum.isStub());
- if(externalDatum.isContainer() == false) {
+ if (externalDatum.isContainer() == false)
+ {
initializer.setPostRegistered(externalDatum.isPostRegistered());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeConverter.java
index a09e06214ef..a0f04275425 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeConverter.java
@@ -35,9 +35,8 @@ public final class CodeConverter
/**
* Converts a code from database form to business layer form.
* <p>
- * If <var>internalNamespace</var> is <code>true</code>, the prefix '$' will be used, because
- * internal properties will be represented as 'NAME' in the database and as $NAME in the
- * business layer.
+ * If <var>internalNamespace</var> is <code>true</code>, the prefix '$' will be used, because internal properties will be represented as 'NAME' in
+ * the database and as $NAME in the business layer.
*
* @return The code appropriate for the business layer.
*/
@@ -56,8 +55,8 @@ public final class CodeConverter
/**
* Converts a property type code from business layer form to database form.
* <p>
- * The code will be translated to upper case. Internal properties will be represented as 'NAME'
- * in the database and as $NAME in the business layer.
+ * The code will be translated to upper case. Internal properties will be represented as 'NAME' in the database and as $NAME in the business
+ * layer.
*
* @return The code appropriate for the database.
*/
@@ -78,8 +77,7 @@ public final class CodeConverter
}
/**
- * Returns <code>true</code>, if the <var>codeFromBusinessLayerOrNull</var> represents a
- * internal property code.
+ * Returns <code>true</code>, if the <var>codeFromBusinessLayerOrNull</var> represents a internal property code.
*/
public static boolean isInternalNamespace(final String codeFromBusinessLayerOrNull)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
index c8823dda016..f85979a7d0f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
@@ -29,8 +29,8 @@ public class CodeNormalizer
}
/**
- * Normalizes the specified code. That is lower-case characters are turned to upper case and any
- * symbol which isn't from A-Z, 0-9 or '-' is replaced by an underscore character.
+ * Normalizes the specified code. That is lower-case characters are turned to upper case and any symbol which isn't from A-Z, 0-9 or '-' is
+ * replaced by an underscore character.
*/
public static String normalize(String code)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
index 935c19a90e4..66659a214e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/DataSetUploadInfo.java
@@ -101,7 +101,6 @@ public class DataSetUploadInfo
{
this.parents = parents;
}
-
@Override
public String toString()
@@ -124,7 +123,6 @@ public class DataSetUploadInfo
return builder.toString();
}
-
public static class DataSetUploadInfoHelper
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/EntityVisitComparatorByTimeStamp.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/EntityVisitComparatorByTimeStamp.java
index dc60c0a532f..ff5d5b6d45c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/EntityVisitComparatorByTimeStamp.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/EntityVisitComparatorByTimeStamp.java
@@ -5,7 +5,7 @@ import java.util.Comparator;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityVisit;
/**
- * Comparator between {@link EntityVisit} instances. Newer visit comes before older visit.
+ * Comparator between {@link EntityVisit} instances. Newer visit comes before older visit.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtil.java
index f59e4c72992..5e829809d8c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtil.java
@@ -27,8 +27,9 @@ import java.util.List;
public class ExpressionUtil
{
public static final String START = "${";
+
public static final String END = "}";
-
+
private static final int START_LENGTH = START.length();
/**
@@ -72,7 +73,7 @@ public class ExpressionUtil
}
return result;
}
-
+
private ExpressionUtil()
{
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GenericSharedConstants.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GenericSharedConstants.java
index d3eba6e3abe..e7c85654cef 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GenericSharedConstants.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GenericSharedConstants.java
@@ -37,7 +37,7 @@ public final class GenericSharedConstants
/** Part of the URL of the DSS service. */
public static final String DATA_STORE_SERVER_SERVICE_NAME =
DATA_STORE_SERVER_WEB_APPLICATION_NAME + "/dss";
-
+
public static final String SESSION_ID_PARAMETER = "sessionID";
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GridRowModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GridRowModel.java
index c962f2fbeab..7a97e35bc8b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GridRowModel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/GridRowModel.java
@@ -23,8 +23,7 @@ import java.util.Map;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
- * Stores the original object which will be a basis to calculate a grid row together with calculated
- * all custom columns values.
+ * Stores the original object which will be a basis to calculate a grid row together with calculated all custom columns values.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IColumnDefinition.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IColumnDefinition.java
index efde92ff914..16809f5f8db 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IColumnDefinition.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IColumnDefinition.java
@@ -21,8 +21,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
/**
- * Describes table column's metadata. Has the ability to render cell values for the column given the
- * row model.
+ * Describes table column's metadata. Has the ability to render cell values for the column given the row model.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithIdentifier.java
index 9f9821ae453..4201df39220 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithIdentifier.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic;
/**
- * Contains the information stored in both {@link IIdentifierHolder} and
- * {@link IEntityInformationHolderWithPermId}.
+ * Contains the information stored in both {@link IIdentifierHolder} and {@link IEntityInformationHolderWithPermId}.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithPermId.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithPermId.java
index ed4d798e90f..170736074c2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithPermId.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithPermId.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic;
/**
- * Contains the information stored in both {@link IPermIdHolder} and
- * {@link IEntityInformationHolder}.
+ * Contains the information stored in both {@link IPermIdHolder} and {@link IEntityInformationHolder}.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithProperties.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithProperties.java
index 2b4ed00a3bf..80f5835ada4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithProperties.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IEntityInformationHolderWithProperties.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
/**
- * Contains the information stored in both {@link IEntityInformationHolderWithIdentifier} and
- * {@link IEntityPropertiesHolder}.
+ * Contains the information stored in both {@link IEntityInformationHolderWithIdentifier} and {@link IEntityPropertiesHolder}.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IManagedPropertyGridInformationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IManagedPropertyGridInformationProvider.java
index 5e4db7d1ced..ed999373ca4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IManagedPropertyGridInformationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IManagedPropertyGridInformationProvider.java
@@ -22,8 +22,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic;
public interface IManagedPropertyGridInformationProvider
{
/**
- * the key of a grid that can be used when creating ids (unique in the context of an entity,
- * doesn't contain spaces)
+ * the key of a grid that can be used when creating ids (unique in the context of an entity, doesn't contain spaces)
*/
public String getKey();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MaterialCodeConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MaterialCodeConverter.java
index 83f3f3060e4..184f94fc355 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MaterialCodeConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MaterialCodeConverter.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic;
import ch.systemsx.cisd.openbis.generic.shared.util.MaterialConfigurationProvider;
/**
- * Methods to convert material codes from business layer to database and from database to business
- * layer.
+ * Methods to convert material codes from business layer to database and from database to business layer.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MetaprojectName.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MetaprojectName.java
index 2cc5ea70658..551172fd6a3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MetaprojectName.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/MetaprojectName.java
@@ -21,8 +21,7 @@ import java.util.regex.Pattern;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- * Metaproject name representation. The name cannot be null, empty or contain white spaces, commas,
- * slashes or backslashes.
+ * Metaproject name representation. The name cannot be null, empty or contain white spaces, commas, slashes or backslashes.
*
* @author pkupczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermlinkUtilities.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermlinkUtilities.java
index bdfa260d117..e15a64f85b3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermlinkUtilities.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermlinkUtilities.java
@@ -34,7 +34,7 @@ public class PermlinkUtilities
/** The HTTP URL parameter used to specify the entity kind. */
public static final String ENTITY_KIND_PARAMETER_KEY = "entity";
- /** The optional HTTP URL parameter used to specify the subtab that should be opened. */
+ /** The optional HTTP URL parameter used to specify the subtab that should be opened. */
public static final String SUBTAB_PARAMETER_KEY = "ui-subtab";
public final static String createPermlinkURL(final String baseIndexURL,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PrimitiveValue.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PrimitiveValue.java
index aafabd47fb1..96c24b87b81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PrimitiveValue.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PrimitiveValue.java
@@ -23,11 +23,9 @@ import com.google.gwt.user.client.rpc.IsSerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
/**
- * Stores one primitive value: Double, Long or String (null is represented as "" -
- * {@link PrimitiveValue#NULL}).
+ * Stores one primitive value: Double, Long or String (null is represented as "" - {@link PrimitiveValue#NULL}).
* <p>
- * Such a type is needed because GWT does not support serialization fields of Object or Serializable
- * type.
+ * Such a type is needed because GWT does not support serialization fields of Object or Serializable type.
* </p>
*
* @author Tomasz Pylak
@@ -89,7 +87,7 @@ public class PrimitiveValue implements IsSerializable, Serializable, Comparable<
@Override
@SuppressWarnings(
- { "unchecked", "rawtypes" })
+ { "unchecked", "rawtypes" })
public int compareTo(PrimitiveValue o)
{
Integer thisTypeOrdinal = getComparableDataTypeOrdinal();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/SimpleImageHtmlRenderer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/SimpleImageHtmlRenderer.java
index 6b5ce220694..0fb58d8d0e9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/SimpleImageHtmlRenderer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/SimpleImageHtmlRenderer.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic;
-
/**
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TableCellUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TableCellUtil.java
index 653b0ec033a..780c9cb1ba5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TableCellUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TableCellUtil.java
@@ -35,9 +35,8 @@ public class TableCellUtil
public static final String INTERN_PREFIX = "INTERN-";
/**
- * Returns an appropriate table cell for the specified string token. If it can be parsed as an
- * integer number a {@link IntegerTableCell} is returned. If it can be parsed as a floating
- * point number a {@link DoubleTableCell} is returned. Otherwise a {@link StringTableCell} is
+ * Returns an appropriate table cell for the specified string token. If it can be parsed as an integer number a {@link IntegerTableCell} is
+ * returned. If it can be parsed as a floating point number a {@link DoubleTableCell} is returned. Otherwise a {@link StringTableCell} is
* returned.
*/
public static ISerializableComparable createTableCell(String token)
@@ -63,8 +62,8 @@ public class TableCellUtil
}
/**
- * Returns the code of specified property type with prefix <code>INTERN-</code> or
- * <code>USER-</code> depending on whether it is internal name space or not.
+ * Returns the code of specified property type with prefix <code>INTERN-</code> or <code>USER-</code> depending on whether it is internal name
+ * space or not.
*/
public static String getPropertyTypeCode(PropertyType propertyType)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/URLMethodWithParameters.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/URLMethodWithParameters.java
index 6a5ae4f0a55..6868194fed5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/URLMethodWithParameters.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/URLMethodWithParameters.java
@@ -21,9 +21,8 @@ import com.google.gwt.user.client.rpc.IsSerializable;
import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
/**
- * Helper class to create URL's with parameters. Characters in path, parameter names and values are
- * URL encoded except '0'-'9', 'a'-'z', 'A'-'Z', ':', '/', '.', '*', '-', and '_'. Space character
- * is replaced by '+'.
+ * Helper class to create URL's with parameters. Characters in path, parameter names and values are URL encoded except '0'-'9', 'a'-'z', 'A'-'Z', ':',
+ * '/', '.', '*', '-', and '_'. Space character is replaced by '+'.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ValidationUtilities.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ValidationUtilities.java
index 61e0d6c4f39..78c16bdb349 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ValidationUtilities.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ValidationUtilities.java
@@ -36,7 +36,7 @@ public class ValidationUtilities
private static final String HYPERLINK_REGEXP = "[^<>()\\[\\]]*";
private static final String[] HYPERLINK_VALID_PROTOCOLS =
- { "http://", "https://", "ftp://" };
+ { "http://", "https://", "ftp://" };
/** @return does given <var>string</var> start with a valid external hyperlink protocol */
public static final boolean isProtocolValid(String string)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ViewMode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ViewMode.java
index 2acc4442c9c..7f9982e34a2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ViewMode.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/ViewMode.java
@@ -26,9 +26,8 @@ public enum ViewMode implements IsSerializable
SIMPLE,
/**
- * Embedded mode inherits most of the SIMPLE mode behaviors. But it has less widgets (e.g. top
- * toolbar and footer are invisible, grids have only "Export" button) to allow embedding the
- * application on other web sites.
+ * Embedded mode inherits most of the SIMPLE mode behaviors. But it has less widgets (e.g. top toolbar and footer are invisible, grids have only
+ * "Export" button) to allow embedding the application on other web sites.
*/
EMBEDDED,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/WildcardSupportingMap.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/WildcardSupportingMap.java
index 1937db13803..727fc5652e8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/WildcardSupportingMap.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/WildcardSupportingMap.java
@@ -21,8 +21,7 @@ import java.util.ArrayList;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKindAndTypeCode;
/**
- * Utility class that manages mappings from entity types/codes (possibly including wildcards) to
- * IServerPlugin objects.
+ * Utility class that manages mappings from entity types/codes (possibly including wildcards) to IServerPlugin objects.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -30,8 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKindAndTypeCode;
public class WildcardSupportingMap<T>
{
/**
- * Internal class for keeping mappings from entityKind/codes (which may include wildcards) to
- * factories.
+ * Internal class for keeping mappings from entityKind/codes (which may include wildcards) to factories.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/annotation/DoNotEscape.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/annotation/DoNotEscape.java
index 84573cd7236..3f0cdeec127 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/annotation/DoNotEscape.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/annotation/DoNotEscape.java
@@ -23,12 +23,10 @@ import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
/**
- * An annotation for marking an object that should not be escaped when returned to the client from
- * server. There may be two reasons for this:
+ * An annotation for marking an object that should not be escaped when returned to the client from server. There may be two reasons for this:
* <p>
* <ol>
- * <li>object contains important information used internally by application that are not shown to
- * the user and shouldn't be escaped (like session id)
+ * <li>object contains important information used internally by application that are not shown to the user and shouldn't be escaped (like session id)
* <li>object is escaped in a different place (e.g. in ResultSetTranslator)
* </ol>
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractEntityProperty.java
index fe2d078ffa0..a8b5ee7d895 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractEntityProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractEntityProperty.java
@@ -17,11 +17,10 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * The abstract base implementation of {@link IEntityProperty}, only featuring a
- * {@link PropertyType}.
+ * The abstract base implementation of {@link IEntityProperty}, only featuring a {@link PropertyType}.
* <p>
- * All getters (except {@link #getPropertyType()} will return <code>null</code>, all setters (except
- * {@link #setPropertyType(PropertyType)} will throw an {@link UnsupportedOperationException}.
+ * All getters (except {@link #getPropertyType()} will return <code>null</code>, all setters (except {@link #setPropertyType(PropertyType)} will throw
+ * an {@link UnsupportedOperationException}.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractExternalData.java
index 29867311fb4..1fbe2a7d9d3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AbstractExternalData.java
@@ -117,7 +117,7 @@ public abstract class AbstractExternalData extends
private boolean storageConfirmation;
private boolean isStub;
-
+
private boolean isPostRegistered;
private Collection<Metaproject> metaprojects;
@@ -475,7 +475,7 @@ public abstract class AbstractExternalData extends
{
return this.isStub;
}
-
+
public boolean isPostRegistered()
{
return isPostRegistered;
@@ -495,7 +495,7 @@ public abstract class AbstractExternalData extends
{
this.accessTimestamp = accessTimestamp;
}
-
+
public Space getSpace()
{
if (experiment != null)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
index 51462e3c04d..91fee5efe1a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
@@ -23,8 +23,7 @@ import java.util.List;
import java.util.Set;
/**
- * The <i>GWT</i> counterpart to
- * ch.systemsx.cisd.openbis.generic.shared.api.v1.SearchableEntityKind.
+ * The <i>GWT</i> counterpart to ch.systemsx.cisd.openbis.generic.shared.api.v1.SearchableEntityKind.
*
* @author Piotr Buczek
*/
@@ -34,7 +33,7 @@ public enum AssociatedEntityKind implements Serializable
EXPERIMENT("Experiment", EntityKind.EXPERIMENT, EnumSet.of(EntityKind.SAMPLE,
EntityKind.DATA_SET)),
-
+
DATA_SET("Data Set", EntityKind.DATA_SET, EnumSet.noneOf(EntityKind.class)),
DATA_SET_PARENT("Parent", EntityKind.DATA_SET, EnumSet.of(EntityKind.DATA_SET)),
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AttachmentWithContent.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AttachmentWithContent.java
index 53b248a46bc..652ffaf764f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AttachmentWithContent.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AttachmentWithContent.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * An {@link Attachment} which has the actual content.
+ * An {@link Attachment} which has the actual content.
*
* @author Bernd Rinn
*/
@@ -25,9 +25,9 @@ public class AttachmentWithContent extends Attachment
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private byte[] content;
-
+
public AttachmentWithContent()
{
}
@@ -42,6 +42,4 @@ public class AttachmentWithContent extends Attachment
this.content = content;
}
-
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicProjectIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicProjectIdentifier.java
index fbf86cffd96..5f716b679fb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicProjectIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicProjectIdentifier.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * The <i>GWT</i> counterpart to
- * {@link ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier}.
+ * The <i>GWT</i> counterpart to {@link ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier}.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
index 86b9da34ede..ccefc091aca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * Batch registration is based on file input. This class returns to the client a small message after
- * each file has been uploaded and handled on the server side.
+ * Batch registration is based on file input. This class returns to the client a small message after each file has been uploaded and handled on the
+ * server side.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/CodeAndLabel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/CodeAndLabel.java
index 8bc977b9e5d..ed299178d84 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/CodeAndLabel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/CodeAndLabel.java
@@ -21,9 +21,8 @@ import java.util.ArrayList;
import java.util.List;
/**
- * Value object which has a label and a normalized code. Normalized means that the original code
- * arguments turn to upper case and any symbol which isn't from A-Z or 0-9 is replaced by an
- * underscore character.
+ * Value object which has a label and a normalized code. Normalized means that the original code arguments turn to upper case and any symbol which
+ * isn't from A-Z or 0-9 is replaced by an underscore character.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ColumnSetting.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ColumnSetting.java
index 61a1ca3fde5..386532bb246 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ColumnSetting.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ColumnSetting.java
@@ -21,9 +21,8 @@ import java.io.Serializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SortInfo.SortDir;
/**
- * Class storing personalised display settings for a table column. This class implements
- * {@link Serializable} not only for transferring it's content remotely but also to store it in the
- * database. Thus, CHANGES IN THIS CLASS MIGHT LEAD TO A LOST OF PERSONAL SETTINGS.
+ * Class storing personalised display settings for a table column. This class implements {@link Serializable} not only for transferring it's content
+ * remotely but also to store it in the database. Thus, CHANGES IN THIS CLASS MIGHT LEAD TO A LOST OF PERSONAL SETTINGS.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ContainerDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ContainerDataSet.java
index 2b4ac718064..98f17f4298c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ContainerDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ContainerDataSet.java
@@ -20,8 +20,8 @@ import java.util.ArrayList;
import java.util.List;
/**
- * A virtual data set "containing" other data sets. Container data sets have no physical
- * representation. Their sole purpose is to provide a merged view of their contents.
+ * A virtual data set "containing" other data sets. Container data sets have no physical representation. Their sole purpose is to provide a merged
+ * view of their contents.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DateTableCell.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DateTableCell.java
index 57ec6454be6..95dcb099f29 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DateTableCell.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DateTableCell.java
@@ -26,19 +26,19 @@ import java.util.Date;
public class DateTableCell implements ISerializableComparable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private long dateTime;
-
+
public DateTableCell(long dateTime)
{
this.dateTime = dateTime;
}
-
+
public DateTableCell(Date date)
{
dateTime = date.getTime();
}
-
+
public Date getDateTime()
{
return new Date(dateTime);
@@ -73,6 +73,7 @@ public class DateTableCell implements ISerializableComparable
{
return new Date(dateTime).toString();
}
+
// ---------------------------
// GWT only
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Deletion.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Deletion.java
index 04be5dce282..c8e4b0d736d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Deletion.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Deletion.java
@@ -77,8 +77,7 @@ public final class Deletion extends AbstractRegistrationHolder implements IIdHol
}
/*
- * The deletion counts are supposed to be used in situations when not all deleted entities are
- * fetched into the <code>deletedEntities<?code>
+ * The deletion counts are supposed to be used in situations when not all deleted entities are fetched into the <code>deletedEntities<?code>
*/
public int getTotalSamplesCount()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchCriterion.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchCriterion.java
index 76e7d1b6b58..1292e005937 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchCriterion.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchCriterion.java
@@ -36,7 +36,7 @@ public class DetailedSearchCriterion implements Serializable
private String value;
private String timezone;
-
+
private boolean negated;
public DetailedSearchCriterion()
@@ -55,14 +55,14 @@ public class DetailedSearchCriterion implements Serializable
{
this(field, type, date, SERVER_TIMEZONE);
}
-
+
public DetailedSearchCriterion(DetailedSearchField field, CompareType type, Number value)
{
this.field = field;
this.value = value.toString();
this.type = type;
}
-
+
public DetailedSearchCriterion(DetailedSearchField field, CompareType type, String value, String timezoneOrNull)
{
this.field = field;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
index 342085c9f26..95371a3b231 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
@@ -20,8 +20,7 @@ import java.io.Serializable;
import java.util.List;
/**
- * Full specification of the field connected with an entity which can be used in detailed text
- * queries.
+ * Full specification of the field connected with an entity which can be used in detailed text queries.
*
* @author Tomasz Pylak
* @author Piotr Buczek
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DoubleTableCell.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DoubleTableCell.java
index 44c2b7d2f99..f71986f9748 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DoubleTableCell.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DoubleTableCell.java
@@ -24,19 +24,19 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public class DoubleTableCell implements ISerializableComparable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private double number;
-
+
public DoubleTableCell(double doubleValue)
{
this.number = doubleValue;
}
-
+
public double getNumber()
{
return number;
}
-
+
@Override
public int compareTo(ISerializableComparable o)
{
@@ -68,7 +68,7 @@ public class DoubleTableCell implements ISerializableComparable
{
return Double.toString(number);
}
-
+
// ---------------------------
// GWT only
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityReference.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityReference.java
index 24896499ae1..3ae7c37ae63 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityReference.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityReference.java
@@ -21,8 +21,7 @@ import java.io.Serializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
/**
- * Reference to an entity with minimal information to uniquely identify it in the database and to
- * choose the right plugin to handle it.
+ * Reference to an entity with minimal information to uniquely identify it in the database and to choose the right plugin to handle it.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityType.java
index 11be668e3e7..bdb666a8d27 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityType.java
@@ -73,6 +73,6 @@ abstract public class EntityType extends BasicEntityType
* return true if this entity type is of given kind, or if the kind is null
*/
public abstract boolean isEntityKind(EntityKind kind);
-
+
public abstract EntityKind getEntityKind();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityTypePropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityTypePropertyType.java
index 907b083eda6..914b42a7c3f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityTypePropertyType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityTypePropertyType.java
@@ -106,12 +106,10 @@ public abstract class EntityTypePropertyType<T extends EntityType> implements Se
}
/**
- * Some properties, managed properties in particular, may or may not need to be available in
- * edit and update views.
+ * Some properties, managed properties in particular, may or may not need to be available in edit and update views.
* <p>
- * The current behavior is to always return true for non-script-based properties and always
- * return false for dynamically computed properties. Only dynamically managed properties take
- * this value into account.
+ * The current behavior is to always return true for non-script-based properties and always return false for dynamically computed properties. Only
+ * dynamically managed properties take this value into account.
*
* @return True if the property should be shown in edit and update views.
*/
@@ -120,18 +118,17 @@ public abstract class EntityTypePropertyType<T extends EntityType> implements Se
if (isDynamic())
{
return false;
- } else {
+ } else
+ {
return showInEditView;
}
}
/**
- * Some properties, managed properties in particular, may or may not need to be available in
- * edit and update views.
+ * Some properties, managed properties in particular, may or may not need to be available in edit and update views.
* <p>
- * The current behavior is to always use the value true for non-script-based properties and
- * always use false for dynamically computed properties. Only dynamically managed properties
- * take this value into account.
+ * The current behavior is to always use the value true for non-script-based properties and always use false for dynamically computed properties.
+ * Only dynamically managed properties take this value into account.
*
* @param showInEditView Pass in true if this property should be shown in edit and update views.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityVisit.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityVisit.java
index bd1fcdfc270..143c2d1d7e4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityVisit.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/EntityVisit.java
@@ -22,8 +22,7 @@ import java.util.Date;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
/**
- * Visit of an entity. Objects of this class are created when the detail view of an entity is opened
- * in the GUI.
+ * Visit of an entity. Objects of this class are created when the detail view of an entity is opened in the GUI.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentType.java
index 6c58ac1390f..bf62425ba5b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentType.java
@@ -46,7 +46,7 @@ public class ExperimentType extends EntityType
{
return kind == null || kind == EntityKind.EXPERIMENT;
}
-
+
@Override
public EntityKind getEntityKind()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/FileFormatType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/FileFormatType.java
index 1097c0d488c..c2d6dc22762 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/FileFormatType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/FileFormatType.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
-
/**
* The <i>GWT</i> equivalent to FileFormatTypePE.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/GenericEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/GenericEntityProperty.java
index 1eec8e21294..39c1ebe5338 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/GenericEntityProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/GenericEntityProperty.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * A {@link IEntityProperty} class that only stores the generic value, but not a vocabulary term
- * value or a material value.
+ * A {@link IEntityProperty} class that only stores the generic value, but not a vocabulary term value or a material value.
*
* @author Bernd Rinn
*/
@@ -28,6 +27,7 @@ public class GenericEntityProperty extends AbstractEntityProperty
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private String originalValue;
+
private String value;
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IDatasetLocationNode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IDatasetLocationNode.java
index dfe3c184f44..a24524cfeee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IDatasetLocationNode.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IDatasetLocationNode.java
@@ -37,8 +37,7 @@ public interface IDatasetLocationNode
boolean isContainer();
/**
- * Returns a collection of component locations. For a data set that is not a container always
- * returns an empty collection. Never returns null.
+ * Returns a collection of component locations. For a data set that is not a container always returns an empty collection. Never returns null.
*/
Collection<IDatasetLocationNode> getComponents();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IEntityProperty.java
index 1e202f4a3e5..a82021c0941 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IEntityProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IEntityProperty.java
@@ -28,8 +28,8 @@ public interface IEntityProperty extends Serializable, Comparable<IEntityPropert
public static final IEntityProperty[] EMPTY_ARRAY = new IEntityProperty[0];
/**
- * Returns a string representation of whatever value this property represents. Vocabulary terms
- * will be represented as their CODE, material values will be represented as "CODE (TYPE_CODE)".
+ * Returns a string representation of whatever value this property represents. Vocabulary terms will be represented as their CODE, material values
+ * will be represented as "CODE (TYPE_CODE)".
*/
public String tryGetAsString();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IExpressionUpdates.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IExpressionUpdates.java
index b6c7917352b..aad406108a6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IExpressionUpdates.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IExpressionUpdates.java
@@ -22,8 +22,7 @@ import java.util.Date;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
/**
- * Description of the updates which should be performed on a stored expression (e.g. grid custom
- * filter or column expression).
+ * Description of the updates which should be performed on a stored expression (e.g. grid custom filter or column expression).
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java
index 8dfb9110404..ee86bc3619b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
-
/**
* Interface implemented by beans with properties attribute.
*
@@ -25,6 +24,6 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public interface IPropertiesBean
{
public IEntityProperty[] getProperties();
-
+
public void setProperties(IEntityProperty[] properties);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ISerializableComparable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ISerializableComparable.java
index b489934cb6e..7d6286e1406 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ISerializableComparable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ISerializableComparable.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * Interface for objects which are comparable, java.io.Serializable and GWT serializable.
- * Implementations should override {@link Object#equals(Object)} and {@link Object#hashCode()}.
+ * Interface for objects which are comparable, java.io.Serializable and GWT serializable. Implementations should override
+ * {@link Object#equals(Object)} and {@link Object#hashCode()}.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
index 609aede0eb0..c7c8fd20c01 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ImageTableCell.java
@@ -22,7 +22,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public class ImageTableCell implements ISerializableComparable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private static final String SLASH = "/";
private static String getPath(String dataSetCode, String dataSetLocation, String originalPath)
@@ -36,7 +36,7 @@ public class ImageTableCell implements ISerializableComparable
String relativePath = originalPath.substring(indexOfLocation + dataSetLocation.length());
return getPath(dataSetCode, relativePath);
}
-
+
private static String getPath(String dataSetCode, String relativePath)
{
String delimiter = "";
@@ -52,16 +52,15 @@ public class ImageTableCell implements ISerializableComparable
private int maxThumbnailWidth;
private int maxThumbnailHeight;
-
+
public ImageTableCell(String dataSetCode, String dataSetLocation, String originalPath,
int maxThumbnailWidth, int maxThumbnailHeight)
{
this(getPath(dataSetCode, dataSetLocation, originalPath), maxThumbnailWidth, maxThumbnailHeight);
}
-
+
/**
- * @param relativePathFromDataSetRoot the relative path to this image file starting from the
- * data set root.
+ * @param relativePathFromDataSetRoot the relative path to this image file starting from the data set root.
*/
public ImageTableCell(String dataSetCode, String relativePathFromDataSetRoot,
int maxThumbnailWidth,
@@ -77,17 +76,17 @@ public class ImageTableCell implements ISerializableComparable
this.maxThumbnailWidth = maxThumbnailWidth;
this.maxThumbnailHeight = maxThumbnailHeight;
}
-
+
public String getPath()
{
return path;
}
-
+
public int getMaxThumbnailWidth()
{
return maxThumbnailWidth;
}
-
+
public int getMaxThumbnailHeight()
{
return maxThumbnailHeight;
@@ -104,19 +103,19 @@ public class ImageTableCell implements ISerializableComparable
{
return this == obj || (obj instanceof ImageTableCell && ((ImageTableCell) obj).path.equals(path));
}
-
+
@Override
public int hashCode()
{
return path.hashCode();
}
-
+
@Override
public String toString()
{
return path;
}
-
+
// ---------------------------
// GWT only
@@ -125,4 +124,3 @@ public class ImageTableCell implements ISerializableComparable
{
}
}
-
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LastModificationState.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LastModificationState.java
index 653e6c3acae..3f3522680a2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LastModificationState.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LastModificationState.java
@@ -28,31 +28,24 @@ import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.annotation.DoNotEscape;
/**
- * Stores information about the time and {@link DatabaseModificationKind} of the last modification,
- * separately for each kind of database object.
+ * Stores information about the time and {@link DatabaseModificationKind} of the last modification, separately for each kind of database object.
* <p>
* A {@link DatabaseModificationKind} has two bits of information:
* <ul>
- * <li>The kind of database object (e.g. Sample, Experiment etc. see
- * {@link DatabaseModificationKind.ObjectKind}).
- * <li>The kind of operation either update or creation/deletion (see
- * {@link DatabaseModificationKind.OperationKind}).
+ * <li>The kind of database object (e.g. Sample, Experiment etc. see {@link DatabaseModificationKind.ObjectKind}).
+ * <li>The kind of operation either update or creation/deletion (see {@link DatabaseModificationKind.OperationKind}).
* </ul>
- * Instances of {@link LastModificationState} store for each combination of object kind and
- * operation kind the time stamp of last invocation of a service method annotated with either
- * {@link DatabaseCreateOrDeleteModification} or {@link DatabaseUpdateModification}.
+ * Instances of {@link LastModificationState} store for each combination of object kind and operation kind the time stamp of last invocation of a
+ * service method annotated with either {@link DatabaseCreateOrDeleteModification} or {@link DatabaseUpdateModification}.
* <p>
- * The method {@link #getLastModificationTime(DatabaseModificationKind)} allows to retrieve this
- * time stamp.
+ * The method {@link #getLastModificationTime(DatabaseModificationKind)} allows to retrieve this time stamp.
* <p>
- * The service method {@link ICommonServer#getLastModificationState(String)} provides an instance of
- * this class with the latest time stamps. It can be used by a client to update views (see for
- * example ch.systemsx
+ * The service method {@link ICommonServer#getLastModificationState(String)} provides an instance of this class with the latest time stamps. It can be
+ * used by a client to update views (see for example ch.systemsx
* .cisd.openbis.generic.client.web.client.application.framework.LastModificationStateUpdater).
* <p>
- * Note, that only the kind of object not the actual type or even instance is stored. That means for
- * example that the creation of a new sample will lead to an update of any sample detailed view in
- * the Web GUI.
+ * Note, that only the kind of object not the actual type or even instance is stored. That means for example that the creation of a new sample will
+ * lead to an update of any sample detailed view in the Web GUI.
*
* @author Tomasz Pylak
*/
@@ -84,10 +77,9 @@ public class LastModificationState implements Serializable
}
/**
- * To avoid expensive computation of the last modification time at the beginning (which would
- * require browsing the whole database) at the beginning we assume that it's equal to the
- * initialization time of the whole state. We can do this since all the future modifications
- * will happen after this moment.
+ * To avoid expensive computation of the last modification time at the beginning (which would require browsing the whole database) at the
+ * beginning we assume that it's equal to the initialization time of the whole state. We can do this since all the future modifications will
+ * happen after this moment.
*
* @return The last registered time of the specified kind of database modification.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkDataSet.java
index fdb8d700c2a..730b5bf489a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkDataSet.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * A virtual data set storing the reference to the data set in external data management system. Link
- * data sets have no physical representation in local dss.
+ * A virtual data set storing the reference to the data set in external data management system. Link data sets have no physical representation in
+ * local dss.
*
* @author Pawel Glyzewski
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkModel.java
index 37ed54a57c1..47eecfdf4e1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkModel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/LinkModel.java
@@ -23,8 +23,8 @@ import java.util.List;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
- * A model for reporting plug-ins of type DSS_LINK. It keeps the different parts of the URL separate
- * so that users can easily use only the parts they need.
+ * A model for reporting plug-ins of type DSS_LINK. It keeps the different parts of the URL separate so that users can easily use only the parts they
+ * need.
* <p>
* The url is broken into schemAndDomain, path, and query parameters. An example: <br>
* https://openbis.ethz.ch/datastore_server/2010093083732894?param1=482745¶m2=something
@@ -34,8 +34,8 @@ import com.google.gwt.user.client.rpc.IsSerializable;
* <li>param1=482745¶m2=something <b>[parameters]</b></li>
* </ul>
* <p>
- * LinkModels returned by the server do not (necessarily) contain a sessionID. The client should
- * provide the session Id to the LinkModel before using it.
+ * LinkModels returned by the server do not (necessarily) contain a sessionID. The client should provide the session Id to the LinkModel before using
+ * it.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -167,8 +167,8 @@ public class LinkModel implements Serializable
}
/**
- * The session token is a special parameter. It is returned as one of the parameters by
- * {@link #getParameters()}, but it can be retrieved directly this way.
+ * The session token is a special parameter. It is returned as one of the parameters by {@link #getParameters()}, but it can be retrieved directly
+ * this way.
*/
public String trySessionId()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListMaterialCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListMaterialCriteria.java
index 3e9d0a2b2ca..0b9dafeeca8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListMaterialCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListMaterialCriteria.java
@@ -86,13 +86,14 @@ public final class ListMaterialCriteria implements Serializable
{
return materialIdentifiersOrNull;
}
-
+
@Override
- public String toString() {
+ public String toString()
+ {
return "ListMaterialCriteria [materialTypeOrNull=" + materialTypeOrNull
+ ", materialIdsOrNull=" + materialIdsOrNull
+ ", materialIdentifiersOrNull=" + materialIdentifiersOrNull
+ "]";
- }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
index e13126f3232..677f52ec2bb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
@@ -27,8 +27,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
* <li>detailed sample search
* <li>tracking new samples of particular type
* </ul>
- * Additionally one can decide if dependent samples that are loaded (parents and containers) should
- * be enriched with properties. By default only 'primary' samples are enriched.<br>
+ * Additionally one can decide if dependent samples that are loaded (parents and containers) should be enriched with properties. By default only
+ * 'primary' samples are enriched.<br>
* <br>
* NOTE: This bean is not serializable.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedHtmlWidgetDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedHtmlWidgetDescription.java
index fb74439e51a..576d5a2298a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedHtmlWidgetDescription.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedHtmlWidgetDescription.java
@@ -20,9 +20,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedOutputWidge
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ManagedOutputWidgetType;
/**
- * {@link IManagedOutputWidgetDescription} implementation for multi-line text fields. This class
- * functions as a simple marker that the UI should use an HTML widget to display the result, and
- * offers no configuration options or behavior.
+ * {@link IManagedOutputWidgetDescription} implementation for multi-line text fields. This class functions as a simple marker that the UI should use
+ * an HTML widget to display the result, and offers no configuration options or behavior.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiActionDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiActionDescription.java
index c1a4582f2ff..d11cb5d040e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiActionDescription.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiActionDescription.java
@@ -25,8 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedUiAction;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IPerson;
/**
- * Object that declaratively describes a UI for an action (e.g. describing UI of a dialog that
- * should be shown after clicking on a button).
+ * Object that declaratively describes a UI for an action (e.g. describing UI of a dialog that should be shown after clicking on a button).
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiTableActionDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiTableActionDescription.java
index 7581366c903..e5e98ad9835 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiTableActionDescription.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ManagedUiTableActionDescription.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedUiTableActi
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ManagedTableActionRowSelectionType;
/**
- * Object that declaratively describes a UI for an action related to a table (e.g. describing UI of
- * a dialog that should be shown after clicking on a button when some table rows are selected).
+ * Object that declaratively describes a UI for an action related to a table (e.g. describing UI of a dialog that should be shown after clicking on a
+ * button when some table rows are selected).
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialAttributeSearchFieldKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialAttributeSearchFieldKind.java
index 96fb5a2b50f..ee2a14b26ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialAttributeSearchFieldKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialAttributeSearchFieldKind.java
@@ -28,7 +28,7 @@ public enum MaterialAttributeSearchFieldKind implements Serializable, IAttribute
ID("Id"),
CODE("Code"),
-
+
PERM_ID("Perm Id"),
MATERIAL_TYPE("Material Type"),
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialEntityProperty.java
index cf37bd85cc4..86ff90f2a62 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialEntityProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialEntityProperty.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * A {@link IEntityProperty} class that only stores the material value, but not a generic value or a
- * vocabulary term value.
+ * A {@link IEntityProperty} class that only stores the material value, but not a generic value or a vocabulary term value.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialIdentifier.java
index 1bf36e93fa3..372efb5e22f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialIdentifier.java
@@ -44,8 +44,7 @@ public final class MaterialIdentifier implements Serializable
private String code;
/**
- * The code of material type of this material: together with code uniquely identifies the
- * material.
+ * The code of material type of this material: together with code uniquely identifies the material.
* <p>
* Could not be <code>null</code>.
* </p>
@@ -89,12 +88,10 @@ public final class MaterialIdentifier implements Serializable
// -----------
/**
- * Creates material identifier from specified identifier or code and material type code if no
- * full identifier is specified.
+ * Creates material identifier from specified identifier or code and material type code if no full identifier is specified.
*
* @return <code>null</code> if no full identifier specified and material type is unknown.
- * @throw {@link IllegalArgumentException} if material type of full identifier doesn't match
- * specified material type.
+ * @throw {@link IllegalArgumentException} if material type of full identifier doesn't match specified material type.
*/
public static MaterialIdentifier tryCreate(String codeOrIdentifierOrNull,
ICodeHolder materialTypeCodeHolderOrNull)
@@ -125,8 +122,7 @@ public final class MaterialIdentifier implements Serializable
}
/**
- * Parses the material code and type. Assumes the syntax: "code (type)". Returns the chosen
- * material if parsing went ok, null otherwise.
+ * Parses the material code and type. Assumes the syntax: "code (type)". Returns the chosen material if parsing went ok, null otherwise.
*/
public static MaterialIdentifier tryParseIdentifier(String value)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewColumnOrFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewColumnOrFilter.java
index 1b6c2b9fb36..e84e4ee6078 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewColumnOrFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewColumnOrFilter.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
-
/**
* A custom grid filter or column to register.
*
@@ -25,7 +24,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public class NewColumnOrFilter extends NewExpression
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private String gridId;
public String getGridId()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewPTNewAssigment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewPTNewAssigment.java
index 485b37b809f..e39f248f499 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewPTNewAssigment.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewPTNewAssigment.java
@@ -5,32 +5,39 @@ import java.io.Serializable;
public class NewPTNewAssigment implements Serializable
{
private boolean existingPropertyType;
+
private PropertyType propertyType;
+
private NewETPTAssignment assignment;
-
+
public boolean isExistingPropertyType()
{
return existingPropertyType;
}
+
public void setExistingPropertyType(boolean existingPropertyType)
{
this.existingPropertyType = existingPropertyType;
}
+
public PropertyType getPropertyType()
{
return propertyType;
}
+
public void setPropertyType(PropertyType propertyType)
{
this.propertyType = propertyType;
}
+
public NewETPTAssignment getAssignment()
{
return assignment;
}
+
public void setAssignment(NewETPTAssignment assignment)
{
this.assignment = assignment;
}
-
+
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
index 679fd72d6a8..a982ec05d7b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
@@ -59,8 +59,7 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
private SampleType sampleType;
/**
- * Set of parent sample codes or identifiers. It will be assumed that all the samples belong to
- * the same group as the child sample.
+ * Set of parent sample codes or identifiers. It will be assumed that all the samples belong to the same group as the child sample.
*/
private String[] parentsOrNull;
@@ -70,8 +69,8 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
private String containerIdentifier;
/**
- * The current container identifier. Used only if the sample identifier does not have the
- * container specified. In such a case it will be assumed that the sample is in that container.
+ * The current container identifier. Used only if the sample identifier does not have the container specified. In such a case it will be assumed
+ * that the sample is in that container.
*/
private String currentContainerIdentifier;
@@ -194,8 +193,7 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
}
/**
- * @deprecated kept for backward compatibility and used as a convenience method for tests - use
- * {@link #setParents(String)} instead
+ * @deprecated kept for backward compatibility and used as a convenience method for tests - use {@link #setParents(String)} instead
*/
@Deprecated
@BeanProperty(label = PARENT, optional = true)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PortletConfiguration.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PortletConfiguration.java
index 42552d62f48..4412c2dadcc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PortletConfiguration.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PortletConfiguration.java
@@ -21,8 +21,8 @@ import java.io.Serializable;
/**
* Configuration parameters of a portlet.
* <p>
- * Instances of this class are serialized in the personal {@link DisplaySettings} of a user. Thus,
- * CHANGES IN THIS CLASS MIGHT LEAD TO A LOST OF PERSONAL SETTINGS
+ * Instances of this class are serialized in the personal {@link DisplaySettings} of a user. Thus, CHANGES IN THIS CLASS MIGHT LEAD TO A LOST OF
+ * PERSONAL SETTINGS
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PropertyType.java
index ecee128b259..9632d69a740 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PropertyType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PropertyType.java
@@ -31,8 +31,8 @@ public class PropertyType extends Code<PropertyType> implements IPropertyTypeUpd
private Long id;
/**
- * Only used for displaying/viewing. With <code>managedInternally</code> is unambiguous (meaning
- * that <code>simpleCode</code> alone could be not unique).
+ * Only used for displaying/viewing. With <code>managedInternally</code> is unambiguous (meaning that <code>simpleCode</code> alone could be not
+ * unique).
* <p>
* We have to use it, partly because <i>Javascript</i> handle '.' in an object-oriented way.
* </p>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java
index 940cf75a3f9..eae92967a96 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java
@@ -30,8 +30,8 @@ public class RelationshipType extends Code<PropertyType> implements Serializable
private Long id;
/**
- * Only used for displaying/viewing. With <code>managedInternally</code> is unambiguous (meaning
- * that <code>simpleCode</code> alone could be not unique).
+ * Only used for displaying/viewing. With <code>managedInternally</code> is unambiguous (meaning that <code>simpleCode</code> alone could be not
+ * unique).
* <p>
* We have to use it, partly because <i>Javascript</i> handle '.' in an object-oriented way.
* </p>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ReportingPluginType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ReportingPluginType.java
index 9702dfe2b4c..1368a60829f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ReportingPluginType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ReportingPluginType.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * Different kinds of reporting plug-ins that are supported. Also keeps track of which
- * IReportingPluginTask methods can be invoked on the different types of plugin types.
+ * Different kinds of reporting plug-ins that are supported. Also keeps track of which IReportingPluginTask methods can be invoked on the different
+ * types of plugin types.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -30,13 +30,12 @@ public enum ReportingPluginType implements Serializable
TABLE_MODEL(ImplementedPluginMethods.CREATE_REPORT),
DSS_LINK(new ImplementedPluginMethods[]
- { ImplementedPluginMethods.CREATE_REPORT, ImplementedPluginMethods.CREATE_LINK }),
+ { ImplementedPluginMethods.CREATE_REPORT, ImplementedPluginMethods.CREATE_LINK }),
AGGREGATION_TABLE_MODEL(ImplementedPluginMethods.CREATE_AGGREGATION_REPORT);
/**
- * An enum representing the methods implemented by the
- * ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask interface.
+ * An enum representing the methods implemented by the ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask interface.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -50,7 +49,7 @@ public enum ReportingPluginType implements Serializable
private ReportingPluginType(ImplementedPluginMethods implementedMethods)
{
this(new ImplementedPluginMethods[]
- { implementedMethods });
+ { implementedMethods });
}
private ReportingPluginType(ImplementedPluginMethods[] implementedMethods)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleAssignment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleAssignment.java
index fd4cbb0cefc..f10dbd86da8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleAssignment.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleAssignment.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
-
/**
* The DTO for authorization role assignments.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleWithHierarchy.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleWithHierarchy.java
index 5acdb31460b..dc2db87f2ae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleWithHierarchy.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RoleWithHierarchy.java
@@ -23,25 +23,23 @@ import java.util.Set;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
- * Hierarchical role. Combines {@link RoleCode} with {@link RoleLevel} and a set of
- * {@link RoleWithHierarchy}s that are stronger.
+ * Hierarchical role. Combines {@link RoleCode} with {@link RoleLevel} and a set of {@link RoleWithHierarchy}s that are stronger.
* <p>
* Available roles can:
* <ol>
* <li>be presented to the user
* <li>be easily mapped to database structure
* <li>be used to restrict access to server methods
- * <li>define the role hierarchy by specifying which roles are stronger (users that have only the
- * "stronger" role will also be able to access given server method)
+ * <li>define the role hierarchy by specifying which roles are stronger (users that have only the "stronger" role will also be able to access given
+ * server method)
* </ol>
* </p>
* <h4>Example:</h4>To annotate an interface method with a new role e.g. <code>SECRET_AGENT</code>:
* <ol>
* <li>Add <code>SECRET_AGENT</code> to {@link RoleCode} enumerator.
- * <li>Add <code>SECRET_AGENT</code> to <code>authorization_role</code> domain in the database (and
- * prepare migration).
- * <li>Add <code>INSTANCE_SECRET_AGENT</code> (or <code>SPACE_SECRET_AGENT</code>) to
- * {@link RoleWithHierarchy} enumerator and define the "stronger" roles.
+ * <li>Add <code>SECRET_AGENT</code> to <code>authorization_role</code> domain in the database (and prepare migration).
+ * <li>Add <code>INSTANCE_SECRET_AGENT</code> (or <code>SPACE_SECRET_AGENT</code>) to {@link RoleWithHierarchy} enumerator and define the "stronger"
+ * roles.
* <li>Use the new {@link RoleWithHierarchy} to annotate the interface method.
* </ol>
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
index 6b4120ee802..c5e3967b4ea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
@@ -275,9 +275,10 @@ public final class Sample extends CodeWithRegistrationAndModificationDate<Sample
@Override
public final int compareTo(final Sample o)
{
- if (getIdentifier() == null) {
- return o.getIdentifier() == null ? 0 : 1;
- }
+ if (getIdentifier() == null)
+ {
+ return o.getIdentifier() == null ? 0 : 1;
+ }
return getIdentifier().compareTo(o.getIdentifier());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleAttributeSearchFieldKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleAttributeSearchFieldKind.java
index 9cdf9d33d03..1d9f7f7878c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleAttributeSearchFieldKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleAttributeSearchFieldKind.java
@@ -38,7 +38,7 @@ public enum SampleAttributeSearchFieldKind implements Serializable, IAttributeSe
PROJECT_PERM_ID("Project Perm Id"),
PROJECT_SPACE("Project Space"),
-
+
METAPROJECT("Metaproject"),
REGISTRATION_DATE(CommonAttributeSearchFieldKindDecsriptions.REGISTRATION_DATE_DESCRIPTION,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleParentWithDerived.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleParentWithDerived.java
index 3a1c17267fc..65a603b2b95 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleParentWithDerived.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleParentWithDerived.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * A <code>SampleParentWithDerived</code> encapsulates a <code>Sample</code> (the parent) and its
- * derived <code>Sample</code>s.
+ * A <code>SampleParentWithDerived</code> encapsulates a <code>Sample</code> (the parent) and its derived <code>Sample</code>s.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleTypePropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleTypePropertyType.java
index 09d18dcd8cf..c6ca092718d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleTypePropertyType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleTypePropertyType.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
-
/**
* The {@link EntityTypePropertyType} extension for <i>Sample Type</i>.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullEntity.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullEntity.java
index 4d307809314..603f08be8f7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullEntity.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchDomainSearchResultWithFullEntity.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWit
public class SearchDomainSearchResultWithFullEntity implements Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private IEntityInformationHolderWithPermId entity;
private SearchDomainSearchResult searchResult;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldBooleanCriterionFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldBooleanCriterionFactory.java
index 146f8946d34..427b43be5af 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldBooleanCriterionFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldBooleanCriterionFactory.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * Creates a criterion for a boolean field. Accepts following values: "true", "yes", "false", "no".
- * For other values is returns "*".
+ * Creates a criterion for a boolean field. Accepts following values: "true", "yes", "false", "no". For other values is returns "*".
*
* @author pkupczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldDateCriterionFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldDateCriterionFactory.java
index 44281809a4e..cfaf10b5315 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldDateCriterionFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SearchFieldDateCriterionFactory.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * Creates a criterion for a date field. Supports registration and modification dates with equals,
- * from and until versions.
+ * Creates a criterion for a date field. Supports registration and modification dates with equals, from and until versions.
*
* @author pkupczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SerializableComparableIDDecorator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SerializableComparableIDDecorator.java
index 2620f59df3d..d85b7200337 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SerializableComparableIDDecorator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SerializableComparableIDDecorator.java
@@ -26,22 +26,23 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
public class SerializableComparableIDDecorator implements ISerializableComparable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
private ISerializableComparable serializableComparable;
+
private Long id;
-
+
public SerializableComparableIDDecorator(ISerializableComparable serializableComparable, Long idOrNull)
{
assert serializableComparable != null : "Unspecified ISerializableComparable";
this.serializableComparable = serializableComparable;
this.id = idOrNull;
}
-
+
public Long getID()
{
return id;
}
-
+
@Override
public int compareTo(ISerializableComparable o)
{
@@ -66,20 +67,20 @@ public class SerializableComparableIDDecorator implements ISerializableComparabl
}
SerializableComparableIDDecorator decorator = (SerializableComparableIDDecorator) obj;
return serializableComparable.equals(decorator.serializableComparable);
- }
-
+ }
+
@Override
public int hashCode()
{
return serializableComparable.hashCode();
}
-
+
@Override
public String toString()
{
return serializableComparable.toString();
}
-
+
// ---------------------------
// GWT only
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SimpleAttributeSearchFieldKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SimpleAttributeSearchFieldKind.java
index ff1d172c4b3..7069f5eb620 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SimpleAttributeSearchFieldKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SimpleAttributeSearchFieldKind.java
@@ -24,6 +24,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public class SimpleAttributeSearchFieldKind implements IAttributeSearchFieldKind
{
private String code;
+
private String description;
public SimpleAttributeSearchFieldKind(String code, String description)
@@ -31,7 +32,7 @@ public class SimpleAttributeSearchFieldKind implements IAttributeSearchFieldKind
this.code = code;
this.description = description;
}
-
+
@Override
public ISearchFieldAvailability getAvailability()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/StandardPortletNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/StandardPortletNames.java
index 3bca556e674..93628e8b8da 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/StandardPortletNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/StandardPortletNames.java
@@ -19,14 +19,14 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
* Names of standard portlets.
* <p>
- * Portlet names are part of a {@link PortletConfiguration} instance. Because a portlet
- * configuration is stored in the personal {@link DisplaySettings} of a user a CHANGE OF PORTLET
- * NAMES MIGHT LEAD TO A LOST OF PERSONAL SETTINGS
+ * Portlet names are part of a {@link PortletConfiguration} instance. Because a portlet configuration is stored in the personal
+ * {@link DisplaySettings} of a user a CHANGE OF PORTLET NAMES MIGHT LEAD TO A LOST OF PERSONAL SETTINGS
*
* @author Franz-Josef Elmer
*/
public class StandardPortletNames
{
public static final String WELCOME = "Welcome";
+
public static final String HISTORY = "History";
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
index 23ac5831b70..975a771020b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
@@ -19,11 +19,11 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
/**
- * Criteria for tracking <i>data sets</i> with technical id bigger than the specified one. Optional,
- * the search is restricted to data sets connected to samples of a certain type.
+ * Criteria for tracking <i>data sets</i> with technical id bigger than the specified one. Optional, the search is restricted to data sets connected
+ * to samples of a certain type.
* <p>
- * Connected samples should be loaded as well as their parent and container samples according to
- * {@link SampleType} hierarchy depths. All referenced samples should have all properties loaded.
+ * Connected samples should be loaded as well as their parent and container samples according to {@link SampleType} hierarchy depths. All referenced
+ * samples should have all properties loaded.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
index 67ad6dbf6f5..7d693f6a58e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
@@ -20,11 +20,10 @@ import java.io.Serializable;
import java.util.Collection;
/**
- * Criteria for tracking <i>samples</i> of particular type with certain property set to specified
- * value.
+ * Criteria for tracking <i>samples</i> of particular type with certain property set to specified value.
* <p>
- * Parent and Container samples should be loaded according to {@link SampleType} hierarchy depths.
- * All referenced samples should have all properties loaded.
+ * Parent and Container samples should be loaded according to {@link SampleType} hierarchy depths. All referenced samples should have all properties
+ * loaded.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TypedTableModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TypedTableModel.java
index e83ad98cf6a..23dbb507ad0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TypedTableModel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TypedTableModel.java
@@ -22,9 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
/**
- * Table model for {@link TypedTableGrid} classes. It contains column meta-data as a list of
- * {@link TableModelColumnHeader} instances and the row data as a list of
- * {@link TableModelRowWithObject} instances for row objects of type <code>T</code>.
+ * Table model for {@link TypedTableGrid} classes. It contains column meta-data as a list of {@link TableModelColumnHeader} instances and the row data
+ * as a list of {@link TableModelRowWithObject} instances for row objects of type <code>T</code>.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/VocabularyTermEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/VocabularyTermEntityProperty.java
index b691553545a..9cb2a03aaab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/VocabularyTermEntityProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/VocabularyTermEntityProperty.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
/**
- * A {@link IEntityProperty} class that only stores the vocabulary term value, but not a generic
- * value or a material value.
+ * A {@link IEntityProperty} class that only stores the vocabulary term value, but not a generic value or a material value.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedInputWidgetDescriptionFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedInputWidgetDescriptionFactory.java
index 3d450480752..bd310f57e94 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedInputWidgetDescriptionFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedInputWidgetDescriptionFactory.java
@@ -38,8 +38,7 @@ public interface IManagedInputWidgetDescriptionFactory extends Serializable
IManagedInputWidgetDescription createMultilineTextInputField(String label);
/**
- * @return a combo box input field with given <var>label</var> and specified list of selectable
- * <var>values</var>.
+ * @return a combo box input field with given <var>label</var> and specified list of selectable <var>values</var>.
*/
IManagedInputWidgetDescription createComboBoxInputField(String labels, String[] values);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedProperty.java
index 901985422ef..cf71d73d712 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedProperty.java
@@ -31,8 +31,7 @@ public interface IManagedProperty extends Serializable
String getPropertyTypeCode();
/**
- * Returns <var>true</var> if the detailed view of the entity owning the property will show the
- * managed property in an extra tab.
+ * Returns <var>true</var> if the detailed view of the entity owning the property will show the managed property in an extra tab.
*/
boolean isOwnTab();
@@ -40,8 +39,7 @@ public interface IManagedProperty extends Serializable
void setOwnTab(boolean ownTab);
/**
- * Returns <code>true</code> if the value is special, that is either a place-holder value or an
- * error message.
+ * Returns <code>true</code> if the value is special, that is either a place-holder value or an error message.
*/
boolean isSpecialValue();
@@ -52,8 +50,7 @@ public interface IManagedProperty extends Serializable
void setValue(String value);
/**
- * Return an object which allows to manage data for the user interface (input as well as
- * output).
+ * Return an object which allows to manage data for the user interface (input as well as output).
*/
IManagedUiDescription getUiDescription();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiAction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiAction.java
index 0ba850ca044..95cb1952e04 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiAction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiAction.java
@@ -41,20 +41,17 @@ public interface IManagedUiAction extends Serializable
public IManagedUiAction setDescription(String description);
/**
- * Adds specified input widget descriptions that will be used in user interface for modifcation
- * of a managed property.
+ * Adds specified input widget descriptions that will be used in user interface for modifcation of a managed property.
*/
public void addInputWidgets(IManagedInputWidgetDescription... widgets);
/**
- * Returns list of objects describing input widgets that will be used in user interface for
- * modification of the managed property.
+ * Returns list of objects describing input widgets that will be used in user interface for modification of the managed property.
*/
public List<IManagedInputWidgetDescription> getInputWidgetDescriptions();
/**
- * Convenience method returning value of input widget with given label or null if such widget
- * doesn't exist.
+ * Convenience method returning value of input widget with given label or null if such widget doesn't exist.
*/
public String getInputValue(String inputLabel);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiDescription.java
index 024e9000cbf..7421b5a050c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiDescription.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiDescription.java
@@ -28,8 +28,8 @@ import java.util.List;
public interface IManagedUiDescription extends Serializable
{
/**
- * Sets the given table model to define an output that will be shown in detail view of the
- * entity owning the property. The table will be shown in an extra tab.
+ * Sets the given table model to define an output that will be shown in detail view of the entity owning the property. The table will be shown in
+ * an extra tab.
*/
void useTableOutput(ITableModel tableModel);
@@ -39,14 +39,12 @@ public interface IManagedUiDescription extends Serializable
void useHtmlOutput(String htmlString);
/**
- * Adds a table action with given name to actions that can be performed in the user interface
- * for modification of the managed property.
+ * Adds a table action with given name to actions that can be performed in the user interface for modification of the managed property.
*/
IManagedUiTableAction addTableAction(String name);
/**
- * Adds an action with given <var>name</var> to actions that can be performed in the user
- * interface for modification of the managed property.
+ * Adds an action with given <var>name</var> to actions that can be performed in the user interface for modification of the managed property.
* <p>
* NOTE: currently there is only support for table actions
*/
@@ -58,8 +56,7 @@ public interface IManagedUiDescription extends Serializable
List<IManagedUiAction> getActions();
/**
- * Returns description of the widget that will be shown in detail view of the entity owning the
- * property.
+ * Returns description of the widget that will be shown in detail view of the entity owning the property.
*/
IManagedOutputWidgetDescription getOutputWidgetDescription();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiTableAction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiTableAction.java
index e63839c5da8..55270a876c3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiTableAction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/IManagedUiTableAction.java
@@ -22,11 +22,11 @@ import java.util.Map;
/**
* Extension of {@link IManagedUiAction} for actions assigned with a table output.
* <p>
- * Every table action can specify table selection mode required for the action to be enabled. If an
- * action requires table rows to be selected than it will contain list of indices of selected rows.
+ * Every table action can specify table selection mode required for the action to be enabled. If an action requires table rows to be selected than it
+ * will contain list of indices of selected rows.
* <p>
- * For actions that require single row to be selected it is possible to bind values of selected
- * row's columns with input fields (e.g. useful in edit actions).
+ * For actions that require single row to be selected it is possible to bind values of selected row's columns with input fields (e.g. useful in edit
+ * actions).
*
* @see ManagedTableActionRowSelectionType
* @author Piotr Buczek
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java
index 967c204a21d..c339cb3c569 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto.api;
-
/**
* Exception thrown by jython scripts in case of invalid input.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsUtils.java
index 6cd59375a4c..407e03181df 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsUtils.java
@@ -38,11 +38,9 @@ public class CorePluginsUtils
public static final String CORE_PLUGINS_PROPERTIES_FILE = "core-plugins.properties";
/**
- * Adds the content of <code>core-plugins.properties</code> file to the specified properties.
- * The folder with the core plugins properties file is specified by the property
- * <code>core-plugins-folder</code> of the specified properties. If undefined a default value is
- * used. Note, that the core plugin properties might overwrite value in the specified properties
- * object.
+ * Adds the content of <code>core-plugins.properties</code> file to the specified properties. The folder with the core plugins properties file is
+ * specified by the property <code>core-plugins-folder</code> of the specified properties. If undefined a default value is used. Note, that the
+ * core plugin properties might overwrite value in the specified properties object.
*/
public static void addCorePluginsProperties(Properties properties, ScannerType scannerType)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/IPluginType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/IPluginType.java
index 70365c4de32..99215b2121b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/IPluginType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/IPluginType.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.coreplugin;
import java.util.Properties;
/**
- * A core plugin type is defined by a name which is used as a folder and an optional property which
- * lists all keys of the plugins of this type.
+ * A core plugin type is defined by a name which is used as a folder and an optional property which lists all keys of the plugins of this type.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistrationHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistrationHolder.java
index 9db40ae3d16..375363c3e9e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistrationHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistrationHolder.java
@@ -21,7 +21,7 @@ import java.util.Date;
/**
* Super class of DTOs which hold registration data.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public abstract class AbstractRegistrationHolder extends Id
{
@@ -63,8 +63,7 @@ public abstract class AbstractRegistrationHolder extends Id
/**
* Sets the person who has registered the experiment.
*
- * @throws AssertionError if <code>registratorID</code> is defined but unequal
- * <code>registrator.getId()</code>.
+ * @throws AssertionError if <code>registratorID</code> is defined but unequal <code>registrator.getId()</code>.
*/
public final void setRegistrator(final PersonPE registrator)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java
index 68b9a4c1c9f..d82aafe7b32 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java
@@ -102,8 +102,8 @@ public class AttachmentPE extends HibernateAbstractRegistrationHolder implements
public static class AttachmentSearchBridge implements FieldBridge
{
@Override
- public void set(String name, Object/* AttachmentPE */ value,
- Document/* Lucene document */ document, LuceneOptions luceneOptions)
+ public void set(String name, Object/* AttachmentPE */value,
+ Document/* Lucene document */document, LuceneOptions luceneOptions)
{
AttachmentPE attachment = (AttachmentPE) value;
String attachmentName = attachment.getFileName();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CorePluginPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CorePluginPE.java
index ad064d88b36..1ac165a6327 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CorePluginPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CorePluginPE.java
@@ -38,8 +38,8 @@ import org.hibernate.annotations.GenerationTime;
*/
@Entity
@Table(name = TableNames.CORE_PLUGINS_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.NAME_COLUMN, ColumnNames.VERSION_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.NAME_COLUMN, ColumnNames.VERSION_COLUMN }) })
public final class CorePluginPE implements Comparable<CorePluginPE>
{
transient private Long id;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
index e6bca2894f8..98a264e9161 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -84,11 +84,11 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
* @author Bernd Rinn
*/
@Entity
-@Table(name = TableNames.DATA_VIEW, uniqueConstraints = @UniqueConstraint(columnNames = ColumnNames.CODE_COLUMN) )
+@Table(name = TableNames.DATA_VIEW, uniqueConstraints = @UniqueConstraint(columnNames = ColumnNames.CODE_COLUMN))
@Inheritance(strategy = InheritanceType.JOINED)
@Indexed(index = "DataPE")
@ClassBridge(impl = DataGlobalSearchBridge.class)
-public class DataPE extends AbstractIdAndCodeHolder<DataPE>implements
+public class DataPE extends AbstractIdAndCodeHolder<DataPE> implements
IEntityInformationWithPropertiesHolder, IMatchingEntity, IIdentifierHolder, IDeletablePE,
IEntityWithMetaprojects, IModifierAndModificationDateBean
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java
index b7af5aa6a46..07a83ac8b3f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetPropertyPE.java
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.DATA_SET_PROPERTIES_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
- { ColumnNames.DATA_SET_COLUMN, ColumnNames.DATA_SET_TYPE_PROPERTY_TYPE_COLUMN }))
+{ ColumnNames.DATA_SET_COLUMN, ColumnNames.DATA_SET_TYPE_PROPERTY_TYPE_COLUMN }))
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
public class DataSetPropertyPE extends EntityPropertyPE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
index d5e52cdd323..ded922095ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
@@ -49,7 +49,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
@Table(name = TableNames.DATA_SET_RELATIONSHIPS_VIEW, uniqueConstraints = @UniqueConstraint(columnNames =
{ ColumnNames.DATA_PARENT_COLUMN, ColumnNames.DATA_CHILD_COLUMN, ColumnNames.RELATIONSHIP_COLUMN }))
@IdClass(DataSetRelationshipId.class)
-@TypeDefs({@TypeDef(name="transactiontimestamp", typeClass=DbTimestampType.class)})
+@TypeDefs({ @TypeDef(name = "transactiontimestamp", typeClass = DbTimestampType.class) })
public class DataSetRelationshipPE implements Serializable
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java
index 11c8ec100ae..1ff7161582d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePropertyTypePE.java
@@ -42,8 +42,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.DATA_SET_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.DATA_SET_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.DATA_SET_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
public class DataSetTypePropertyTypePE extends EntityTypePropertyTypePE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java
index 21d988e9151..aff96c4e50a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
* Context data needed for uploading data sets to a CIFEX server.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class DataSetUploadContext implements Serializable
{
@@ -46,9 +46,9 @@ public class DataSetUploadContext implements Serializable
private String comment;
private String email;
-
+
private String sessionUserID;
-
+
public final String getFileName()
{
return fileName;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceDefinition.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceDefinition.java
index 23444811ea8..d453cb547f6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceDefinition.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceDefinition.java
@@ -55,8 +55,7 @@ public class DataSourceDefinition implements Serializable, Cloneable
}
/**
- * Creates a list of definitions from specified string which could be the output of
- * {@link #toString(List)}.
+ * Creates a list of definitions from specified string which could be the output of {@link #toString(List)}.
*/
public static List<DataSourceDefinition> listFromString(String serializedDefinitions)
{
@@ -73,8 +72,7 @@ public class DataSourceDefinition implements Serializable, Cloneable
}
/**
- * Creates a string representation of specified definition. It can be used as an input of
- * {@link #listFromString(String)}.
+ * Creates a string representation of specified definition. It can be used as an input of {@link #listFromString(String)}.
*/
public static String toString(List<DataSourceDefinition> definitions)
{
@@ -87,8 +85,7 @@ public class DataSourceDefinition implements Serializable, Cloneable
}
/**
- * Creates an instance from the specified string. The input could be the output of
- * {@link #toString()}.
+ * Creates an instance from the specified string. The input could be the output of {@link #toString()}.
*/
public static DataSourceDefinition fromString(String serializedDefinition)
{
@@ -241,8 +238,7 @@ public class DataSourceDefinition implements Serializable, Cloneable
}
/**
- * Returns this instance as a string which allows reconstruction by applying
- * {@link #fromString(String)}.
+ * Returns this instance as a string which allows reconstruction by applying {@link #fromString(String)}.
*/
@Override
public String toString()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceWithDefinition.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceWithDefinition.java
index 5cc522d6897..64f70bc62ee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceWithDefinition.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSourceWithDefinition.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
import javax.sql.DataSource;
-
/**
* Bean for a {@link DataSource} together with its {@link DataSourceDefinition}.
*
@@ -27,6 +26,7 @@ import javax.sql.DataSource;
public class DataSourceWithDefinition
{
private final DataSource dataSource;
+
private final DataSourceDefinition definition;
public DataSourceWithDefinition(DataSource dataSource, DataSourceDefinition definitionOrNull)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java
index 5f858101c4e..38c1a1135bb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java
@@ -28,11 +28,9 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
* <p>
* It contains
* <ul>
- * <li>the port on which the DSS is reachable. Note, that the host can be inferred by the asking
- * {@link HttpServletRequest}.
+ * <li>the port on which the DSS is reachable. Note, that the host can be inferred by the asking {@link HttpServletRequest}.
* <li>the DSS session token which has to used when invoking methods on the DSS.
- * <li>the download URL which is the URL at which the DSS Web server can be accessed from a Web
- * browser.
+ * <li>the download URL which is the URL at which the DSS Web server can be accessed from a Web browser.
* <li>the unique code of the DSS,
* <li>information about available services.
* </ul>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java
index d3451d075dc..84b63111a8a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java
@@ -50,8 +50,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
*/
@Entity
@Table(name = TableNames.DATA_TYPES_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.CODE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.CODE_COLUMN }) })
public final class DataTypePE implements IIdHolder, Serializable, Comparable<DataTypePE>
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedExternalDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedExternalDataPE.java
index 5f9777595bd..82f949bfb64 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedExternalDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedExternalDataPE.java
@@ -33,14 +33,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.Location;
/**
- * {@link ExternalDataPE} counterpart for deleted data sets mapping only those attributes that are
- * needed for permanent deletion of data sets.
+ * {@link ExternalDataPE} counterpart for deleted data sets mapping only those attributes that are needed for permanent deletion of data sets.
*
* @author Piotr Buczek
*/
@Entity
@Table(name = TableNames.EXTERNAL_DATA_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
- { ColumnNames.LOCATION_COLUMN, ColumnNames.LOCATOR_TYPE_COLUMN }))
+{ ColumnNames.LOCATION_COLUMN, ColumnNames.LOCATOR_TYPE_COLUMN }))
@PrimaryKeyJoinColumn(name = ColumnNames.DATA_ID_COLUMN)
public final class DeletedExternalDataPE extends DeletedDataPE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityCollectionForCreationOrUpdate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityCollectionForCreationOrUpdate.java
index 03117d8287c..70fae40719a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityCollectionForCreationOrUpdate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityCollectionForCreationOrUpdate.java
@@ -24,16 +24,16 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
/**
- * Collections of {@link NewExternalData}, {@link NewExperiment}.
+ * Collections of {@link NewExternalData}, {@link NewExperiment}.
*
* @author Franz-Josef Elmer
*/
public class EntityCollectionForCreationOrUpdate implements Serializable
{
private static final long serialVersionUID = IServer.VERSION;
-
+
private final List<NewExperiment> newExperiments = new ArrayList<NewExperiment>();
-
+
private final List<NewExternalData> newDataSets = new ArrayList<NewExternalData>();
public List<NewExperiment> getNewExperiments()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
index da7f5638e64..53d06506ef8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
@@ -11,14 +11,12 @@ import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.validation.constraints.NotNull;
-import ch.systemsx.cisd.openbis.generic.server.ServiceForDataStoreServer;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
/**
- * Persistent entity representing an invocation of the
- * {@link ServiceForDataStoreServer#performEntityOperations(String, AtomicEntityOperationDetails)} method. This
- * table is used to check if the results of an invocation of this method made it into the database.
+ * Persistent entity representing an invocation of the {@link ServiceForDataStoreServer#performEntityOperations(String, AtomicEntityOperationDetails)}
+ * method. This table is used to check if the results of an invocation of this method made it into the database.
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java
index 86a1ecc8b28..5deb384f89a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java
@@ -23,8 +23,8 @@ import ch.systemsx.cisd.common.reflection.AbstractHashable;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
- * Used when assigning mandatory property to an entity, which has some instances or when mandatory
- * flag is change from optional and properties for some entities are unset.
+ * Used when assigning mandatory property to an entity, which has some instances or when mandatory flag is change from optional and properties for
+ * some entities are unset.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java
index e0a4d11a95a..cadebaa63f7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java
@@ -71,7 +71,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.SimplePropertyValidator.Supp
*/
@MappedSuperclass
@ClassBridge(index = Index.YES, store = Store.YES, impl = EntityPropertyPE.EntityPropertySearchBridge.class)
-@TypeDefs({@TypeDef(name="transactiontimestamp", typeClass=DbTimestampType.class)})
+@TypeDefs({ @TypeDef(name = "transactiontimestamp", typeClass = DbTimestampType.class) })
public abstract class EntityPropertyPE extends HibernateAbstractRegistrationHolder implements
IUntypedValueSetter, IEntityPropertyHolder
{
@@ -114,7 +114,7 @@ public abstract class EntityPropertyPE extends HibernateAbstractRegistrationHold
private PersonPE author;
private Date modificationDate;
-
+
/**
* This bridge allows to save in the search index not only the value of property, but also the corresponding property code.
*/
@@ -130,9 +130,9 @@ public abstract class EntityPropertyPE extends HibernateAbstractRegistrationHold
@Override
public void set(
- String name,
+ String name,
Object/* EntityPropertyPE */value,
- Document/* Lucene document */document,
+ Document/* Lucene document */document,
LuceneOptions luceneOptions)
{
EntityPropertyPE entityProperty = (EntityPropertyPE) value;
@@ -154,29 +154,48 @@ public abstract class EntityPropertyPE extends HibernateAbstractRegistrationHold
{
// leave the original value
}
- field = new Field(fieldFullName, fieldValue, luceneOptions.getStore(), indexingStrategy);
+ field = new Field(fieldFullName, fieldValue, luceneOptions.getStore(), indexingStrategy);
}
- else if(DataTypeCode.INTEGER.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode())) {
+ else if (DataTypeCode.INTEGER.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode()))
+ {
try
{
String numericTextValue = SortableNumberBridgeUtils.getNumberForLucene(fieldValue);
field = new Field(fieldFullName, numericTextValue, luceneOptions.getStore(), Field.Index.NOT_ANALYZED_NO_NORMS);
- fieldIsdocTypeSortedNumeric = new SortedNumericDocValuesField(fieldFullName, Long.parseLong(fieldValue)); //Needed to identify the field as number, if not type is not stored
+ fieldIsdocTypeSortedNumeric = new SortedNumericDocValuesField(fieldFullName, Long.parseLong(fieldValue)); // Needed to identify
+ // the field as number,
+ // if not type is not
+ // stored
} catch (Exception e)
{
// leave the original value
}
- } else if(DataTypeCode.REAL.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode())) {
+ } else if (DataTypeCode.REAL.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode()))
+ {
try
{
String numericTextValue = SortableNumberBridgeUtils.getNumberForLucene(fieldValue);
field = new Field(fieldFullName, numericTextValue, luceneOptions.getStore(), Field.Index.NOT_ANALYZED_NO_NORMS);
- fieldIsdocTypeSortedNumeric = new SortedNumericDocValuesField(fieldFullName, NumericUtils.doubleToSortableLong(Double.parseDouble(fieldValue))); //Needed to identify the field as number, if not type is not stored
+ fieldIsdocTypeSortedNumeric =
+ new SortedNumericDocValuesField(fieldFullName, NumericUtils.doubleToSortableLong(Double.parseDouble(fieldValue))); // Needed
+ // to
+ // identify
+ // the
+ // field
+ // as
+ // number,
+ // if
+ // not
+ // type
+ // is
+ // not
+ // stored
} catch (Exception e)
{
// leave the original value
}
- } else if(DataTypeCode.MULTILINE_VARCHAR.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode())) {
+ } else if (DataTypeCode.MULTILINE_VARCHAR.equals(entityProperty.getEntityTypePropertyType().getPropertyType().getType().getCode()))
+ {
try
{
XMLInputFactory xif = XMLInputFactory.newFactory();
@@ -197,16 +216,19 @@ public abstract class EntityPropertyPE extends HibernateAbstractRegistrationHold
fieldValue = valueBuff.toString();
} catch (Exception e)
{
- //Do Nothing
+ // Do Nothing
}
- field = new Field(fieldFullName, fieldValue, luceneOptions.getStore(), indexingStrategy); //Strips out XML tags from text that can be rich text using HTML format
- } else {
+ field = new Field(fieldFullName, fieldValue, luceneOptions.getStore(), indexingStrategy); // Strips out XML tags from text that can be
+ // rich text using HTML format
+ } else
+ {
field = new Field(fieldFullName, fieldValue, luceneOptions.getStore(), indexingStrategy);
}
-
+
field.setBoost(luceneOptions.getBoost());
document.add(field);
- if(fieldIsdocTypeSortedNumeric != null) {
+ if (fieldIsdocTypeSortedNumeric != null)
+ {
document.add(fieldIsdocTypeSortedNumeric);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java
index b2d47b9cdd3..938de7362ae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.EXPERIMENT_PROPERTIES_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
- { ColumnNames.EXPERIMENT_COLUMN, ColumnNames.EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN }))
+{ ColumnNames.EXPERIMENT_COLUMN, ColumnNames.EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN }))
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
public class ExperimentPropertyPE extends EntityPropertyPE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java
index 8a4b41637ba..268921ba76f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java
@@ -42,8 +42,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.EXPERIMENT_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.EXPERIMENT_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.EXPERIMENT_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
public class ExperimentTypePropertyTypePE extends EntityTypePropertyTypePE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
index 304a0e9af10..2ca29505aa8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
@@ -54,7 +54,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.SearchFieldConstant
*/
@Entity
@Table(name = TableNames.EXTERNAL_DATA_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = { ColumnNames.LOCATION_COLUMN,
- ColumnNames.LOCATOR_TYPE_COLUMN }) )
+ ColumnNames.LOCATOR_TYPE_COLUMN }))
@PrimaryKeyJoinColumn(name = ColumnNames.DATA_ID_COLUMN)
@Indexed(index = "DataPE")
@ClassBridge(impl = ExternalDataGlobalSearchBridge.class)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java
index 37c78adae8b..838eacbfec0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java
@@ -45,8 +45,7 @@ public class ExtractableData extends Code<ExtractableData>
private List<NewProperty> dataSetProperties = new ArrayList<NewProperty>();
/**
- * Returns the date when the measurement / calculation that produced this external data set has
- * been performed.
+ * Returns the date when the measurement / calculation that produced this external data set has been performed.
* <p>
* This may not be known in which case this method will return <code>null</code>.
*/
@@ -56,8 +55,7 @@ public class ExtractableData extends Code<ExtractableData>
}
/**
- * Sets the date when the measurement / calculation that produced this external data set has
- * been performed.
+ * Sets the date when the measurement / calculation that produced this external data set has been performed.
*/
public void setProductionDate(final Date productionDate)
{
@@ -65,8 +63,7 @@ public class ExtractableData extends Code<ExtractableData>
}
/**
- * Returns the code identifying the data source (i.e. measurement device or software pipeline)
- * that produced this external data set.
+ * Returns the code identifying the data source (i.e. measurement device or software pipeline) that produced this external data set.
* <p>
* This may not be known in which case this method will return <code>null</code>.
*/
@@ -76,8 +73,7 @@ public class ExtractableData extends Code<ExtractableData>
}
/**
- * Sets the code identifying the data source (i.e. measurement device or software pipeline) that
- * produced this external data set.
+ * Sets the code identifying the data source (i.e. measurement device or software pipeline) that produced this external data set.
*/
public void setDataProducerCode(final String dataProducerCode)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistrationHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistrationHolder.java
index 601ff90a1bd..3266db2b79e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistrationHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistrationHolder.java
@@ -33,8 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
* Super class of <i>Persistent Entities</i> which hold registration data.
* <p>
- * <b>Note:</b> there is no <i>NOT-NULL</i> constraint applied to registrator (by comparison with
- * the database where there almost one).
+ * <b>Note:</b> there is no <i>NOT-NULL</i> constraint applied to registrator (by comparison with the database where there almost one).
* </p>
*
* @author Christian Ribeaud
@@ -61,8 +60,7 @@ public abstract class HibernateAbstractRegistrationHolder implements Serializabl
private Date registrationDate;
/**
- * Ensures that given <var>date</var> is a real one (<code>java.util.Date</code>) and not a
- * <i>SQL</i> one.
+ * Ensures that given <var>date</var> is a real one (<code>java.util.Date</code>) and not a <i>SQL</i> one.
*/
public final static Date getDate(final Date date)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityInformationWithPropertiesHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityInformationWithPropertiesHolder.java
index 0494c6a7a2c..74cdba9ea52 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityInformationWithPropertiesHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityInformationWithPropertiesHolder.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.dto;
-
/**
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java
index 4c01667c26d..d4ff71b103f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.ICodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
/**
- * Read-only interface for beans with a (unique) business code as a string and a unique technical
- * ID.
+ * Read-only interface for beans with a (unique) business code as a string and a unique technical ID.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IMatchingEntity.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IMatchingEntity.java
index 2c5257652e0..5dd8f95c268 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IMatchingEntity.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IMatchingEntity.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.dto;
-
/**
* A entity that matches the <i>Hibernate Search</i> request.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java
index 9b6f071eb42..716ac9270c6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
/**
* Holds the untyped property value.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IUntypedValueSetter
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
index f486545c389..71f99308818 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
* A <i>Java Bean</i> that filters a list of results.
* <p>
- * Typically this filter is applied to results returned by the database before sending them to the
- * client.
+ * Typically this filter is applied to results returned by the database before sending them to the client.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java
index 8d6a0086c01..f6d512fb8ca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java
@@ -34,8 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.LOCATOR_TYPES_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.CODE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.CODE_COLUMN }) })
public final class LocatorTypePE extends AbstractTypePE
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java
index f6bbda01ef9..0b25fd44f29 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java
@@ -75,7 +75,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*/
@Entity
@Table(name = TableNames.MATERIALS_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = { ColumnNames.CODE_COLUMN,
- ColumnNames.MATERIAL_TYPE_COLUMN }) )
+ ColumnNames.MATERIAL_TYPE_COLUMN }))
@Indexed(index = "MaterialPE")
@ClassBridge(impl = MaterialGlobalSearchBridge.class)
public class MaterialPE implements IIdAndCodeHolder, Comparable<MaterialPE>,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java
index 7a3d932098a..1caed7ac6fe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java
@@ -41,7 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.MATERIAL_PROPERTIES_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
- { ColumnNames.MATERIAL_COLUMN, ColumnNames.MATERIAL_TYPE_PROPERTY_TYPE_COLUMN }))
+{ ColumnNames.MATERIAL_COLUMN, ColumnNames.MATERIAL_TYPE_PROPERTY_TYPE_COLUMN }))
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
public class MaterialPropertyPE extends EntityPropertyPE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java
index d5396161714..bc0a71ec568 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.MATERIAL_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.MATERIAL_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.MATERIAL_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
public class MaterialTypePropertyTypePE extends EntityTypePropertyTypePE
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MetaprojectPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MetaprojectPE.java
index dccc0642dd2..ffb9ecead71 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MetaprojectPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MetaprojectPE.java
@@ -62,7 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EqualsHashUtils;
* @author Pawel Glyzewski
*/
@Entity
-@Table(name = TableNames.METAPROJECTS_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = { ColumnNames.NAME_COLUMN, ColumnNames.OWNER }) )
+@Table(name = TableNames.METAPROJECTS_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = { ColumnNames.NAME_COLUMN, ColumnNames.OWNER }))
public class MetaprojectPE implements Serializable, IIdHolder, ICodeHolder
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewContainerDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewContainerDataSet.java
index 716f7da383c..e869a1e72d5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewContainerDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewContainerDataSet.java
@@ -37,6 +37,5 @@ public class NewContainerDataSet extends NewExternalData
{
this.containedDataSetCodes = containedDataSetCodes;
}
-
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
index 9f3fd67b3c8..c133c9119e0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
@@ -77,7 +77,7 @@ public class NewExternalData implements Serializable
private ExperimentIdentifier experimentIdentifierOrNull;
private SampleIdentifier sampleIdentifierOrNull;
-
+
private String samplePermIdOrNull;
public ExperimentIdentifier getExperimentIdentifierOrNull()
@@ -237,10 +237,9 @@ public class NewExternalData implements Serializable
}
/**
- * Returns {@link BooleanOrUnknown#T}, if the data set is complete in the data store and
- * {@link BooleanOrUnknown#F}, if some parts of the data are missing. If the completeness is not
- * known (e.g. because the data set is stored in a format that does not allow to assess the
- * completeness, {@link BooleanOrUnknown#U} is returned.
+ * Returns {@link BooleanOrUnknown#T}, if the data set is complete in the data store and {@link BooleanOrUnknown#F}, if some parts of the data are
+ * missing. If the completeness is not known (e.g. because the data set is stored in a format that does not allow to assess the completeness,
+ * {@link BooleanOrUnknown#U} is returned.
*/
public final BooleanOrUnknown getComplete()
{
@@ -248,9 +247,8 @@ public class NewExternalData implements Serializable
}
/**
- * Sets whether this data set is complete in the data store or not. The default is
- * {@link BooleanOrUnknown#U}, which corresponds to the case where the data are stored in a
- * format that does not allow to assess completeness.
+ * Sets whether this data set is complete in the data store or not. The default is {@link BooleanOrUnknown#U}, which corresponds to the case where
+ * the data are stored in a format that does not allow to assess completeness.
*/
public final void setComplete(final BooleanOrUnknown complete)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewLinkDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewLinkDataSet.java
index a39104f066d..d0cbdcfe88f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewLinkDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewLinkDataSet.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared.dto;
-
/**
* @author Jakub Straszewski
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java
index d83ba0c6f04..c2835d11bee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java
@@ -25,7 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
* Processing instruction is a specific experiment attachment.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public final class NewProcessingInstruction extends AbstractHashable implements Serializable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProperty.java
index 4141127fb1d..420f90e4ed6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProperty.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProperty.java
@@ -99,5 +99,4 @@ public class NewProperty implements Serializable
return false;
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/OpenBISSessionHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/OpenBISSessionHolder.java
index d858357f611..2b3cf73750f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/OpenBISSessionHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/OpenBISSessionHolder.java
@@ -21,8 +21,7 @@ import java.io.Serializable;
import ch.systemsx.cisd.common.server.ISessionTokenProvider;
/**
- * A class that holds information about the openBIS session. It has the information necessary to
- * connect to any of the openBIS APIs.
+ * A class that holds information about the openBIS session. It has the information necessary to connect to any of the openBIS APIs.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java
index 3939f00a31e..3aa2f001c7d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
/**
* Processing instruction needed to process raw data.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class ProcessingInstructionDTO extends AbstractRegistrationHolder
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java
index cc50c7ba12e..24ecca2459c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java
@@ -21,10 +21,9 @@ import java.io.Serializable;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
- * Processing parameters are a binary byte sequence from a file. It is stored BASE64 encoded in
- * order to be marshalling and unmarshalling for SOAP.
+ * Processing parameters are a binary byte sequence from a file. It is stored BASE64 encoded in order to be marshalling and unmarshalling for SOAP.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public class ProcessingParameters implements Serializable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
index c23baf199ba..f26512388b7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
@@ -55,136 +55,155 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EqualsHashUtils;
@Check(constraints = "((AG_ID_GRANTEE IS NOT NULL AND PERS_ID_GRANTEE IS NULL) OR (AG_ID_GRANTEE IS NULL AND PERS_ID_GRANTEE IS NOT NULL))")
@Table(name = TableNames.ROLE_ASSIGNMENTS_TABLE)
public final class RoleAssignmentPE extends HibernateAbstractRegistrationHolder
- implements IIdHolder, Serializable {
-
- private static final long serialVersionUID = IServer.VERSION;
-
- public static final RoleAssignmentPE[] EMPTY_ARRAY = new RoleAssignmentPE[0];
-
- private transient Long id;
-
- // private DatabaseInstancePE databaseInstance;
-
- private SpacePE space;
-
- private PersonPE person;
-
- private AuthorizationGroupPE authorizationGroup;
-
- private RoleCode role;
-
- @NotNull(message = ValidationMessages.ROLE_NOT_NULL_MESSAGE)
- @Column(name = ColumnNames.ROLE_COLUMN)
- @Enumerated(EnumType.STRING)
- public final RoleCode getRole() {
- return role;
- }
-
- public final void setRole(final RoleCode role) {
- this.role = role;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.PERSON_GRANTEE_COLUMN, updatable = false)
- @Private
- public final PersonPE getPersonInternal() {
- return person;
- }
-
- @Private
- public final void setPersonInternal(final PersonPE person) {
- this.person = person;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.AUTHORIZATION_GROUP_ID_GRANTEE_COLUMN, updatable = false)
- @Private
- public final AuthorizationGroupPE getAuthorizationGroupInternal() {
- return authorizationGroup;
- }
-
- @Private
- public final void setAuthorizationGroupInternal(
- final AuthorizationGroupPE authorizationGroup) {
- this.authorizationGroup = authorizationGroup;
- }
-
- @Transient
- public final PersonPE getPerson() {
- return getPersonInternal();
- }
-
- @Transient
- public final AuthorizationGroupPE getAuthorizationGroup() {
- return getAuthorizationGroupInternal();
- }
-
- public final void setId(final Long id) {
- this.id = id;
- }
-
- @ManyToOne(fetch = FetchType.EAGER)
- @JoinColumn(name = ColumnNames.SPACE_COLUMN, updatable = false)
- public final SpacePE getSpace() {
- return space;
- }
-
- public final void setSpace(final SpacePE space) {
- this.space = space;
- }
-
- //
- // IIdHolder
- //
-
- @Override
- @SequenceGenerator(name = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE, sequenceName = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE, allocationSize = 1)
- @Id
- @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE)
- public final Long getId() {
- return id;
- }
-
- //
- // Object
- //
-
- @Override
- public final boolean equals(final Object obj) {
- EqualsHashUtils.assertDefined(getRole(), "role");
- if (getPerson() == null) {
- EqualsHashUtils.assertDefined(getAuthorizationGroupInternal(),
- "authorization group");
- }
-
- if (obj == this) {
- return true;
- }
- if (obj instanceof RoleAssignmentPE == false) {
- return false;
- }
- final RoleAssignmentPE that = (RoleAssignmentPE) obj;
- final EqualsBuilder builder = new EqualsBuilder();
- builder.append(getRole(), that.getRole());
- builder.append(getPerson(), that.getPerson());
- builder.append(getAuthorizationGroup(), that.getAuthorizationGroup());
- builder.append(getSpace(), that.getSpace());
- return builder.isEquals();
- }
-
- @Override
- public final int hashCode() {
- final HashCodeBuilder builder = new HashCodeBuilder();
- builder.append(getRole());
- builder.append(getPerson());
- builder.append(getSpace());
- return builder.toHashCode();
- }
-
- @Override
- public final String toString() {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
+ implements IIdHolder, Serializable
+{
+
+ private static final long serialVersionUID = IServer.VERSION;
+
+ public static final RoleAssignmentPE[] EMPTY_ARRAY = new RoleAssignmentPE[0];
+
+ private transient Long id;
+
+ // private DatabaseInstancePE databaseInstance;
+
+ private SpacePE space;
+
+ private PersonPE person;
+
+ private AuthorizationGroupPE authorizationGroup;
+
+ private RoleCode role;
+
+ @NotNull(message = ValidationMessages.ROLE_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.ROLE_COLUMN)
+ @Enumerated(EnumType.STRING)
+ public final RoleCode getRole()
+ {
+ return role;
+ }
+
+ public final void setRole(final RoleCode role)
+ {
+ this.role = role;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PERSON_GRANTEE_COLUMN, updatable = false)
+ @Private
+ public final PersonPE getPersonInternal()
+ {
+ return person;
+ }
+
+ @Private
+ public final void setPersonInternal(final PersonPE person)
+ {
+ this.person = person;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.AUTHORIZATION_GROUP_ID_GRANTEE_COLUMN, updatable = false)
+ @Private
+ public final AuthorizationGroupPE getAuthorizationGroupInternal()
+ {
+ return authorizationGroup;
+ }
+
+ @Private
+ public final void setAuthorizationGroupInternal(
+ final AuthorizationGroupPE authorizationGroup)
+ {
+ this.authorizationGroup = authorizationGroup;
+ }
+
+ @Transient
+ public final PersonPE getPerson()
+ {
+ return getPersonInternal();
+ }
+
+ @Transient
+ public final AuthorizationGroupPE getAuthorizationGroup()
+ {
+ return getAuthorizationGroupInternal();
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.SPACE_COLUMN, updatable = false)
+ public final SpacePE getSpace()
+ {
+ return space;
+ }
+
+ public final void setSpace(final SpacePE space)
+ {
+ this.space = space;
+ }
+
+ //
+ // IIdHolder
+ //
+
+ @Override
+ @SequenceGenerator(name = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE, sequenceName = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.ROLE_ASSIGNMENT_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ EqualsHashUtils.assertDefined(getRole(), "role");
+ if (getPerson() == null)
+ {
+ EqualsHashUtils.assertDefined(getAuthorizationGroupInternal(),
+ "authorization group");
+ }
+
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof RoleAssignmentPE == false)
+ {
+ return false;
+ }
+ final RoleAssignmentPE that = (RoleAssignmentPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getRole(), that.getRole());
+ builder.append(getPerson(), that.getPerson());
+ builder.append(getAuthorizationGroup(), that.getAuthorizationGroup());
+ builder.append(getSpace(), that.getSpace());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getRole());
+ builder.append(getPerson());
+ builder.append(getSpace());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleParentWithDerivedDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleParentWithDerivedDTO.java
index ecc88027db6..798f1dcd00d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleParentWithDerivedDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleParentWithDerivedDTO.java
@@ -22,8 +22,7 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
- * A <code>SampleParentWithDerivedDTO</code> encapsulates a <code>SamplePE</code> (the parent) and
- * its derived <code>SamplePE</code>s.
+ * A <code>SampleParentWithDerivedDTO</code> encapsulates a <code>SamplePE</code> (the parent) and its derived <code>SamplePE</code>s.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
index 31ba368dcbb..59c55b21ffa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
@@ -41,8 +41,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.SAMPLE_PROPERTIES_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.SAMPLE_COLUMN, ColumnNames.SAMPLE_TYPE_PROPERTY_TYPE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.SAMPLE_COLUMN, ColumnNames.SAMPLE_TYPE_PROPERTY_TYPE_COLUMN }) })
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
public class SamplePropertyPE extends EntityPropertyPE
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
index b8fd693e010..de6a5792736 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
@@ -53,7 +53,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
@Table(name = TableNames.SAMPLE_RELATIONSHIPS_VIEW, uniqueConstraints = @UniqueConstraint(columnNames =
{ ColumnNames.PARENT_SAMPLE_COLUMN, ColumnNames.CHILD_SAMPLE_COLUMN,
ColumnNames.RELATIONSHIP_COLUMN }))
-@TypeDefs({@TypeDef(name="transactiontimestamp", typeClass=DbTimestampType.class)})
+@TypeDefs({ @TypeDef(name = "transactiontimestamp", typeClass = DbTimestampType.class) })
public class SampleRelationshipPE implements Serializable
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
index 79265eac888..16a57c23052 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
@@ -24,13 +24,13 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
public class SampleSkeleton
{
private long id;
-
+
private Long databaseInstanceID;
-
+
private Long spaceID;
-
+
private long typeID;
-
+
private Long experimentID;
public final long getId()
@@ -82,5 +82,5 @@ public class SampleSkeleton
{
this.experimentID = experimentID;
}
-
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
index 40878e679f1..b0ce1a8ef02 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
@Entity
@Table(name = TableNames.SAMPLE_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.SAMPLE_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.SAMPLE_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
public class SampleTypePropertyTypePE extends EntityTypePropertyTypePE
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java
index ffc0cec5efd..8109a009890 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java
@@ -31,8 +31,7 @@ public enum StorageFormat
/** The proprietary data format as acquired from the measurement device. */
PROPRIETARY("PROPRIETARY"),
/**
- * The standardized data according to the Biological Data Standard format, using a directory
- * container.
+ * The standardized data according to the Biological Data Standard format, using a directory container.
*/
BDS_DIRECTORY("BDS_DIRECTORY");
@@ -67,8 +66,7 @@ public enum StorageFormat
}
/**
- * Returns the appropriate format for the given <var>code</var>, or <code>null</code>, if there
- * is no format for this <var>code</var>.
+ * Returns the appropriate format for the given <var>code</var>, or <code>null</code>, if there is no format for this <var>code</var>.
*/
public final static StorageFormat tryGetFromCode(final String code)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java
index 872261eb900..baa52962c55 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
* Note that both dates can be <code>null</code>.
* </p>
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public final class TimeInterval implements Serializable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java
index 74b31aad53c..9ed2801e11e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java
@@ -55,8 +55,8 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EqualsHashUtils;
*/
@Entity
@Table(name = TableNames.CONTROLLED_VOCABULARY_TERM_TABLE, uniqueConstraints =
- { @UniqueConstraint(columnNames =
- { ColumnNames.CODE_COLUMN, ColumnNames.CONTROLLED_VOCABULARY_COLUMN }) })
+{ @UniqueConstraint(columnNames =
+{ ColumnNames.CODE_COLUMN, ColumnNames.CONTROLLED_VOCABULARY_COLUMN }) })
public class VocabularyTermPE extends HibernateAbstractRegistrationHolder implements
IIdAndCodeHolder, Comparable<VocabularyTermPE>, Serializable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/InternalNamespace.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/InternalNamespace.java
index 7d59e99a298..38eb95e3a54 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/InternalNamespace.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/InternalNamespace.java
@@ -28,13 +28,12 @@ import javax.validation.Constraint;
import javax.validation.Payload;
/**
- * <code>boolean</code> value has to be <code>false</code> for entities that must not be in the
- * internal namespace.
+ * <code>boolean</code> value has to be <code>false</code> for entities that must not be in the internal namespace.
*
* @author Christian Ribeaud
*/
@Target(
- { METHOD, FIELD })
+{ METHOD, FIELD })
@Retention(RetentionPolicy.RUNTIME)
@Documented
@Constraint(validatedBy = InternalNamespaceValidator.class)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java
index 4e6897cc382..23bf12b0e80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java
@@ -33,7 +33,7 @@ import javax.validation.Payload;
* @author Christian Ribeaud
*/
@Target(
- { METHOD, FIELD })
+{ METHOD, FIELD })
@Retention(RetentionPolicy.RUNTIME)
@Documented
@Constraint(validatedBy = LocationValidator.class)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SearchFieldConstants.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SearchFieldConstants.java
index b1c5d38a57d..cc113acfe29 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SearchFieldConstants.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SearchFieldConstants.java
@@ -56,10 +56,10 @@ public final class SearchFieldConstants
public static final String PREFIX_METAPROJECT = "metaproject" + SEPARATOR;
public static final String[] PREFIXES =
- { PREFIX_PROPERTIES, PREFIX_EXPERIMENT, PREFIX_SAMPLE, PREFIX_ENTITY_TYPE,
- PREFIX_FILE_FORMAT_TYPE, PREFIX_FILE_FORMAT_TYPE, PREFIX_PROJECT, PREFIX_SPACE,
- PREFIX_REGISTRATOR, PREFIX_ATTACHMENT, PREFIX_PROPERTIES + PREFIX_VOCABULARY_TERM,
- PREFIX_METAPROJECT };
+ { PREFIX_PROPERTIES, PREFIX_EXPERIMENT, PREFIX_SAMPLE, PREFIX_ENTITY_TYPE,
+ PREFIX_FILE_FORMAT_TYPE, PREFIX_FILE_FORMAT_TYPE, PREFIX_PROJECT, PREFIX_SPACE,
+ PREFIX_REGISTRATOR, PREFIX_ATTACHMENT, PREFIX_PROPERTIES + PREFIX_VOCABULARY_TERM,
+ PREFIX_METAPROJECT };
public static final String ID = "id";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SortableNumberBridgeUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SortableNumberBridgeUtils.java
index 27b081c1ac0..7ebe53b2e5c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SortableNumberBridgeUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/SortableNumberBridgeUtils.java
@@ -5,52 +5,68 @@ public class SortableNumberBridgeUtils
//
// Util Methods
//
- private static int LUCENE_INTEGER_PADDING = 19; //On the UI a integer field can't have more than 18 characters, a long can have 19 taking out the minus sign
-
- public static String getNumberForLucene(String number) {
- try {
+ private static int LUCENE_INTEGER_PADDING = 19; // On the UI a integer field can't have more than 18 characters, a long can have 19 taking out the
+ // minus sign
+
+ public static String getNumberForLucene(String number)
+ {
+ try
+ {
return getNumberForLucene(Long.parseLong(number));
- } catch(Exception ex) {
- try {
+ } catch (Exception ex)
+ {
+ try
+ {
return getNumberForLucene(Double.parseDouble(number));
- } catch(Exception ex2) {
+ } catch (Exception ex2)
+ {
return number;
}
}
}
-
- private static String getNumberForLucene(Number number) {
- if(number instanceof Integer || number instanceof Long) {
+
+ private static String getNumberForLucene(Number number)
+ {
+ if (number instanceof Integer || number instanceof Long)
+ {
return getIntegerAsStringForLucene(number) + ".0";
- } if(number instanceof Float || number instanceof Double) {
+ }
+ if (number instanceof Float || number instanceof Double)
+ {
String rawReal = number.toString();
int indexOfDot = rawReal.indexOf('.');
return getIntegerAsStringForLucene(Long.parseLong(rawReal.substring(0, indexOfDot))) + rawReal.substring(indexOfDot, rawReal.length());
- } else {
+ } else
+ {
return number.toString();
}
}
-
- private static String getIntegerAsStringForLucene(Number number) {
+
+ private static String getIntegerAsStringForLucene(Number number)
+ {
String rawInteger = number.toString();
-
+
StringBuilder paddedInteger = new StringBuilder();
-
- if(rawInteger.startsWith("-")) {
+
+ if (rawInteger.startsWith("-"))
+ {
rawInteger = rawInteger.substring(1, rawInteger.length());
paddedInteger.append('-');
- } else {
+ } else
+ {
paddedInteger.append('+');
}
-
- if (rawInteger.length() > LUCENE_INTEGER_PADDING) {
- throw new IllegalArgumentException( "Try to pad on a number too big" );
+
+ if (rawInteger.length() > LUCENE_INTEGER_PADDING)
+ {
+ throw new IllegalArgumentException("Try to pad on a number too big");
}
-
- for ( int padIndex = rawInteger.length() ; padIndex < LUCENE_INTEGER_PADDING ; padIndex++ ) {
+
+ for (int padIndex = rawInteger.length(); padIndex < LUCENE_INTEGER_PADDING; padIndex++)
+ {
paddedInteger.append('0');
}
-
+
paddedInteger.append(rawInteger);
return paddedInteger.toString();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/LocalExperimentIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/LocalExperimentIdentifier.java
index 2429394a21b..6190df5f620 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/LocalExperimentIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/LocalExperimentIdentifier.java
@@ -21,8 +21,7 @@ import java.io.Serializable;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
- * Identifies the experiment. This identifier points to an experiment if a group and database
- * instance is provided in addition.
+ * Identifies the experiment. This identifier points to an experiment if a group and database instance is provided in addition.
*
* @author Tomasz Pylak
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java
index a2cbcc93449..5cb4314baf0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.dto.types;
/**
* The current <code>DataSetType</code> codes.
* <p>
- * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure
- * this point.
+ * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure this point.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java
index 1bd6015c4b4..4486b132661 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.dto.types;
/**
* The current <code>ExperimentType</code> codes.
* <p>
- * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure
- * this point.
+ * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure this point.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/SimpleTableModelBuilderAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/SimpleTableModelBuilderAdaptor.java
index 2e70fd56fa5..d058fb07638 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/SimpleTableModelBuilderAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/SimpleTableModelBuilderAdaptor.java
@@ -29,11 +29,10 @@ import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
/**
- * An {@link ISimpleTableModelBuilderAdaptor} implementation adapting
- * {@link SimpleTableModelBuilder}.
+ * An {@link ISimpleTableModelBuilderAdaptor} implementation adapting {@link SimpleTableModelBuilder}.
* <p>
- * The intent of the interface and adaptor is not to expose {@link SimpleTableModelBuilder}
- * interface in Managed Property API and optionally add convenience methods for scripts.
+ * The intent of the interface and adaptor is not to expose {@link SimpleTableModelBuilder} interface in Managed Property API and optionally add
+ * convenience methods for scripts.
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/EntityLinkElementKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/EntityLinkElementKind.java
index 1cc88d3e6d7..7aa03d27b32 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/EntityLinkElementKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/EntityLinkElementKind.java
@@ -60,8 +60,7 @@ public enum EntityLinkElementKind
}
/**
- * @return the {@link EntityLinkElementKind} for a given element name or <code>null</code> if no
- * matching kind exists.
+ * @return the {@link EntityLinkElementKind} for a given element name or <code>null</code> if no matching kind exists.
*/
public static EntityLinkElementKind tryGetForElementName(String elementName)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElement.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElement.java
index 3fb13c82324..091b1b1d2dc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElement.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElement.java
@@ -20,12 +20,10 @@ import java.util.List;
import java.util.Map;
/**
- * An {@link IElement} is an object that can be transparently converted to {@link String} (see
- * {@link IStructuredPropertyConverter}) e.g. when we want to save the value of a structured
- * (managed) property.
+ * An {@link IElement} is an object that can be transparently converted to {@link String} (see {@link IStructuredPropertyConverter}) e.g. when we want
+ * to save the value of a structured (managed) property.
* <p>
- * {@link IElement}-s are meant to be used as a convenient, hierarchical property-value persistence
- * technique for managed properties.
+ * {@link IElement}-s are meant to be used as a convenient, hierarchical property-value persistence technique for managed properties.
*
* @author Piotr Buczek
* @author Kaloyan Enimanev
@@ -46,14 +44,12 @@ public interface IElement
String getAttribute(String key);
/**
- * @return the value of an attribute or <code>defaultValue</code> if the attribute is not
- * defined for this {@link IElement}
+ * @return the value of an attribute or <code>defaultValue</code> if the attribute is not defined for this {@link IElement}
*/
String getAttribute(String key, String defaultValue);
/**
- * The "Data" field is intended for a chunk raw data that can be attached to an element
- * instance. This might be useful in scenarios where
+ * The "Data" field is intended for a chunk raw data that can be attached to an element instance. This might be useful in scenarios where
*/
String getData();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElementFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElementFactory.java
index ca1ea3bb521..207e56b7876 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElementFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IElementFactory.java
@@ -46,15 +46,13 @@ public interface IElementFactory
IEntityLinkElement createDataSetLink(String permId);
/**
- * @return creates an link element pointing towards a material with given code and typeCode
- * parameters.
+ * @return creates an link element pointing towards a material with given code and typeCode parameters.
*/
IEntityLinkElement createMaterialLink(String code, String typeCode);
/**
- * @return <code>true</code> if the specified element is a link element, <code>false</code>
- * otherwise. This method might come handy in Jython scripts, where it is undesirable to
- * hard-code class names or invoke "instanceof".
+ * @return <code>true</code> if the specified element is a link element, <code>false</code> otherwise. This method might come handy in Jython
+ * scripts, where it is undesirable to hard-code class names or invoke "instanceof".
*/
boolean isEntityLink(IElement element);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
index 829d4b47ca1..161f675ac98 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
@@ -27,20 +27,17 @@ import java.util.List;
public interface IEntityInformationProvider
{
/**
- * @return identifier of entity specified by given link, <code>null</code> if such an entity
- * doesn't exist
+ * @return identifier of entity specified by given link, <code>null</code> if such an entity doesn't exist
*/
String getIdentifier(IEntityLinkElement entityLink);
/**
- * @return permId of sample specified by given space and code, <code>null</code> if such a
- * sample doesn't exist
+ * @return permId of sample specified by given space and code, <code>null</code> if such a sample doesn't exist
*/
String getSamplePermId(String spaceCode, String sampleCode);
/**
- * @return permId of sample specified by given identifier, <code>null</code> if such a sample
- * doesn't exist
+ * @return permId of sample specified by given identifier, <code>null</code> if such a sample doesn't exist
*/
String getSamplePermId(String sampleIdentifier);
@@ -55,8 +52,7 @@ public interface IEntityInformationProvider
List<String> getSampleParentPermIds(String permId);
/**
- * @return value of a property with given code of a sample with given permIds, empty string if
- * the property doesn't exist
+ * @return value of a property with given code of a sample with given permIds, empty string if the property doesn't exist
*/
String getSamplePropertyValue(String permId, String propertyCode);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IRowBuilderAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IRowBuilderAdaptor.java
index 19a7d8d3dde..a72f4d0d731 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IRowBuilderAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IRowBuilderAdaptor.java
@@ -49,14 +49,12 @@ public interface IRowBuilderAdaptor
public void setCell(String headerTitle, Date value);
/**
- * Sets the value of the column specified by the header title to the specified entity link
- * rendered using identifier.
+ * Sets the value of the column specified by the header title to the specified entity link rendered using identifier.
*/
public void setCell(String headerTitle, IEntityLinkElement value);
/**
- * Sets the value of the column specified by the header title to the specified entity link
- * rendered using given text.
+ * Sets the value of the column specified by the header title to the specified entity link rendered using given text.
*/
public void setCell(String headerTitle, IEntityLinkElement value, String linkText);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ISimpleTableModelBuilderAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ISimpleTableModelBuilderAdaptor.java
index 540fe223c71..a706c58bba8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ISimpleTableModelBuilderAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ISimpleTableModelBuilderAdaptor.java
@@ -60,8 +60,7 @@ public interface ISimpleTableModelBuilderAdaptor
void addHeader(String title, String code);
/**
- * A convenience method for adding complete header with columns with specified titles and
- * default column width 150.
+ * A convenience method for adding complete header with columns with specified titles and default column width 150.
*
* @throws UserFailureException if header titles are not unique.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IStructuredPropertyConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IStructuredPropertyConverter.java
index 76ef98deebb..227d83a422b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IStructuredPropertyConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IStructuredPropertyConverter.java
@@ -44,8 +44,7 @@ public interface IStructuredPropertyConverter
List<IElement> convertStringToElements(String propertyValue);
/**
- * @return a {@link String} representation of the specified elements that can be persisted in
- * the database.
+ * @return a {@link String} representation of the specified elements that can be persisted in the database.
*/
String convertToString(List<IElement> elements);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/ElementFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/ElementFactory.java
index 120103d700e..9152f11a2e0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/ElementFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/ElementFactory.java
@@ -23,8 +23,8 @@ import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IElementFact
import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IEntityLinkElement;
/**
- * For now we only expose methods for creation of Sample and Material links, but it is quite easy to
- * add support for experiment and datasets links in the future.
+ * For now we only expose methods for creation of Sample and Material links, but it is quite easy to add support for experiment and datasets links in
+ * the future.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/XmlOrJsonStructuredPropertyConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/XmlOrJsonStructuredPropertyConverter.java
index 8b1680908c9..cdc8bd8a825 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/XmlOrJsonStructuredPropertyConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/structured/XmlOrJsonStructuredPropertyConverter.java
@@ -24,8 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IElement;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IStructuredPropertyConverter;
/**
- * An implementation of {@link IStructuredPropertyConverter}, that translates elements either to XML
- * or to JSON and that can translate back both formats.
+ * An implementation of {@link IStructuredPropertyConverter}, that translates elements either to XML or to JSON and that can translate back both
+ * formats.
*
* @author Bernd Rinn
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
index 56556fce0f7..f0159c65f3b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
@@ -30,8 +30,8 @@ import ch.systemsx.cisd.common.parser.ParsingException;
import ch.systemsx.cisd.common.parser.TabFileLoader;
/**
- * A <i>openBIS</i> {@link TabFileLoader} extension which translates a {@link ParsingException} into
- * a more user friendly {@link UserFailureException}.
+ * A <i>openBIS</i> {@link TabFileLoader} extension which translates a {@link ParsingException} into a more user friendly {@link UserFailureException}
+ * .
* <p>
* Note that this extension prefers to work with {@link NamedReader}.
* </p>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
index 5f80d90cb4f..d67b040411f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
@@ -28,8 +28,8 @@ import ch.systemsx.cisd.common.parser.ParsingException;
import ch.systemsx.cisd.common.parser.TabFileLoader;
/**
- * A <i>openBIS</i> {@link TabFileLoader} extension which translates a {@link ParsingException} into
- * a more user friendly {@link UserFailureException}.
+ * A <i>openBIS</i> {@link TabFileLoader} extension which translates a {@link ParsingException} into a more user friendly {@link UserFailureException}
+ * .
* <p>
* Note that this extension prefers to work with {@link NamedReader}.
* </p>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java
index c35035444ab..36e14c0f72f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java
@@ -32,8 +32,7 @@ public class GlobalProperties
}
/**
- * Adds property with given key and value.Throws {@link IllegalArgumentException} if property
- * already defined.
+ * Adds property with given key and value.Throws {@link IllegalArgumentException} if property already defined.
*/
public void add(String key, String value)
{
@@ -45,8 +44,7 @@ public class GlobalProperties
}
/**
- * Returns value of given property. Throws {@link IllegalArgumentException} if property not
- * defined.
+ * Returns value of given property. Throws {@link IllegalArgumentException} if property not defined.
*/
public String get(String key)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java
index 32497f1cbf5..1648b99ec91 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java
@@ -28,9 +28,8 @@ import org.apache.commons.lang.StringUtils;
/**
* Loads global properties.
* <p>
- * Global properties are defined as comments and start with a line
- * <code>#! GLOBAL_PROPERTIES:</code> (followed by a new line character.) Each property is defined
- * in a separate line and has the following format:
+ * Global properties are defined as comments and start with a line <code>#! GLOBAL_PROPERTIES:</code> (followed by a new line character.) Each
+ * property is defined in a separate line and has the following format:
* <p>
* #! key = value
* </p>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
index 553e1857646..8210dca8d28 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
@@ -47,8 +47,8 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
}
/**
- * Prepares details about which values should be updated in general taking into account only the
- * information about availability of columns in the file.
+ * Prepares details about which values should be updated in general taking into account only the information about availability of columns in the
+ * file.
*/
private SampleBatchUpdateDetails createBasicBatchUpdateDetails()
{
@@ -85,8 +85,8 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
//
/**
- * Returns details about which values should be updated for the specified sample. If a cell was
- * left empty in the file the corresponding value will not be modified.
+ * Returns details about which values should be updated for the specified sample. If a cell was left empty in the file the corresponding value
+ * will not be modified.
*/
private SampleBatchUpdateDetails createBatchUpdateDetails(NewSample newSample)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DeletedEntityTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DeletedEntityTranslator.java
index bcadfbd6cf8..d6042791c0b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DeletedEntityTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DeletedEntityTranslator.java
@@ -31,8 +31,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
/**
- * A generic translator for deleted entities. In the future, if we need to access specific fields of
- * a deleted entity in the UI we'll have to create a DTO layer of deleted object.
+ * A generic translator for deleted entities. In the future, if we need to access specific fields of a deleted entity in the UI we'll have to create a
+ * DTO layer of deleted object.
* <p>
* For now, a single DeletedEntity covers all required uses cases of the trash can.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/PropertyTranslatorUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/PropertyTranslatorUtils.java
index 88358f6ae0f..1cdf9509e8b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/PropertyTranslatorUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/PropertyTranslatorUtils.java
@@ -59,8 +59,7 @@ final class PropertyTranslatorUtils
}
/**
- * Creates an appropriate {@link IEntityProperty} for the given <var>propertyPE</var> based on
- * its type.
+ * Creates an appropriate {@link IEntityProperty} for the given <var>propertyPE</var> based on its type.
*/
static IEntityProperty createEntityProperty(EntityPropertyPE propertyPE)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManager.java
index 8c9f00f26fc..ec689118618 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManager.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManager.java
@@ -111,9 +111,9 @@ public class CacheManager implements ICacheManager
{
timeStamp = new Date(timeProvider.getTimeInMilliseconds());
fileName = new MessageFormat(FILE_NAME_FORMAT).format(new Object[]
- { timeStamp, counter++ });
+ { timeStamp, counter++ });
}
-
+
@Override
public String toString()
{
@@ -122,28 +122,46 @@ public class CacheManager implements ICacheManager
}
private static final int DAY = 24 * 60 * 60 * 1000;
- @Private public static final String CACHE_FOLDER_KEY = "cache-folder";
+
+ @Private
+ public static final String CACHE_FOLDER_KEY = "cache-folder";
+
private static final String CACHE_FOLDER_DEFAULT_VALUE = "cache";
- @Private static final String MINIMUM_FREE_DISK_SPACE_KEY = "minimum-free-disk-space-in-MB";
+
+ @Private
+ static final String MINIMUM_FREE_DISK_SPACE_KEY = "minimum-free-disk-space-in-MB";
+
private static final int MINIMUM_FREE_DISK_SPACE_DEFAULT_VALUE = 1024;
- @Private static final String MAXIMUM_RETENTION_TIME_KEY = "maximum-retention-time-in-days";
+
+ @Private
+ static final String MAXIMUM_RETENTION_TIME_KEY = "maximum-retention-time-in-days";
+
private static final int MAXIMUM_RETENTION_TIME_DEFAULT_VALUE = 7;
-
- @Private static final String CACHE_VERSION_FILE_NAME = ".cache-version";
- @Private static final String KEY_FILE_TYPE = ".key";
- @Private static final String DATA_FILE_TYPE = ".data";
-
+
+ @Private
+ static final String CACHE_VERSION_FILE_NAME = ".cache-version";
+
+ @Private
+ static final String KEY_FILE_TYPE = ".key";
+
+ @Private
+ static final String DATA_FILE_TYPE = ".data";
+
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
CacheManager.class);
-
+
private final ITimeProvider timeProvider;
+
private final Map<Key, FileName> keyToFileNameMap;
+
private final IFreeSpaceProvider freeSpaceProvider;
+
private final File cacheFolder;
+
private final long minimumFreeDiskSpaceInKB;
+
private final long maximumRetentionTimeInMillis;
-
-
+
public CacheManager(WebClientConfiguration configuration, String technologyName,
ITimeProvider timeProvider, IFreeSpaceProvider freeSpaceProvider, String cacheVersion)
{
@@ -208,7 +226,7 @@ public class CacheManager implements ICacheManager
}
return key;
}
-
+
private int getIntegerProperty(WebClientConfiguration configuration, String technologyName, String key, int defaultValue)
{
String value = configuration.getPropertyOrNull(technologyName, key);
@@ -232,7 +250,7 @@ public class CacheManager implements ICacheManager
String value = configuration.getPropertyOrNull(technologyName, key);
return value == null ? defaultValue : value;
}
-
+
@Override
public Object tryToGetData(Key key)
{
@@ -299,7 +317,7 @@ public class CacheManager implements ICacheManager
}
}
}
-
+
private void cleanUp()
{
long currentTime = timeProvider.getTimeInMilliseconds();
@@ -335,7 +353,7 @@ public class CacheManager implements ICacheManager
operationLog.warn("Can not obtain available free disk space.", ex);
}
}
-
+
private void removeFromCache(Key key)
{
FileName fileName = keyToFileNameMap.remove(key);
@@ -361,7 +379,7 @@ public class CacheManager implements ICacheManager
operationLog.warn("For key " + key + " removing from cache caused some unknown error: " + file);
}
}
-
+
private void assertFreeSpaceAvailableFor(int numberOfBytes) throws IOException
{
long freeSpace = 1024 * freeSpaceProvider.freeSpaceKb(new HostAwareFile(cacheFolder));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/DataTypeUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/DataTypeUtils.java
index 51216a6b996..50587180458 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/DataTypeUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/DataTypeUtils.java
@@ -102,7 +102,7 @@ public class DataTypeUtils
{
String pattern = SupportedDatePattern.CANONICAL_DATE_PATTERN.getPattern();
return DateUtils.parseDate(value, new String[]
- { pattern });
+ { pattern });
} catch (ParseException ex)
{
throw new IllegalArgumentException("Is not a date in canonical format: "
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
index 0df7488d769..fff63b2ac78 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
@@ -57,7 +57,7 @@ public class EntityHelper
/**
* Returns <code>true</code> if both entities are <code>null</code> or have the same id (which could be <code>null</code>).
*/
- public static <T extends IIdHolder >boolean equalEntities(T entity1OrNull, T entity2OrNull)
+ public static <T extends IIdHolder> boolean equalEntities(T entity1OrNull, T entity2OrNull)
{
if (entity1OrNull == null || entity2OrNull == null)
{
@@ -100,8 +100,7 @@ public class EntityHelper
}
/**
- * @return finds and returns an {@link IEntityProperty} for a specified code. Returns
- * <code>null</code> if no matching property is found.
+ * @return finds and returns an {@link IEntityProperty} for a specified code. Returns <code>null</code> if no matching property is found.
*/
public static IEntityProperty tryFindProperty(Iterable<IEntityProperty> properties,
final String propertyCode)
@@ -237,8 +236,7 @@ public class EntityHelper
}
/**
- * Creates a property with specified code and value. An already existing property with same code
- * will be removed.
+ * Creates a property with specified code and value. An already existing property with same code will be removed.
*/
public static void createOrUpdateProperty(IEntityPropertiesHolder holder, String propertyCode,
String propertyValue)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ICacheManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ICacheManager.java
index c62204ed00c..365d47a8adb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ICacheManager.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ICacheManager.java
@@ -19,20 +19,19 @@ package ch.systemsx.cisd.openbis.generic.shared.util;
/**
* Interface of a manager of objects which are stored in a cache using a unique {@link Key}.
*
- *
* @author Franz-Josef Elmer
*/
public interface ICacheManager
{
/**
- * Tries to retrieve object for specified key.
+ * Tries to retrieve object for specified key.
*
* @return <code>null</code> if not found in cache.
*/
public Object tryToGetData(Key key);
/**
- * Stores specified object for specified key.
+ * Stores specified object for specified key.
*/
public void storeData(Key key, Object object);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnGroup.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnGroup.java
index ed70a747de5..19a84397e4f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnGroup.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnGroup.java
@@ -37,22 +37,19 @@ public interface IColumnGroup
public IColumn column(String id);
/**
- * Intends uneditable property columns for all property columns added by one of the add methods
- * after this method has been invoked.
+ * Intends uneditable property columns for all property columns added by one of the add methods after this method has been invoked.
*/
public IColumnGroup uneditablePropertyColumns();
/**
- * Adds for all assigned property types of the specified entity type a column. The group name is
- * used as a prefix which combined with the property type code to determine the column id. The
- * property type label is used as column title.
+ * Adds for all assigned property types of the specified entity type a column. The group name is used as a prefix which combined with the property
+ * type code to determine the column id. The property type label is used as column title.
*/
public void addColumnsForAssignedProperties(EntityType entityType);
/**
- * Adds for all assigned property types of the specified entity type a column. The specified
- * identifier prefix is used as a prefix which combined with the property type code to determine
- * the column id. The property type label is used as column title.
+ * Adds for all assigned property types of the specified entity type a column. The specified identifier prefix is used as a prefix which combined
+ * with the property type code to determine the column id. The property type label is used as column title.
*/
public void addColumnsForAssignedProperties(String idPrefix, EntityType entityType);
@@ -67,30 +64,27 @@ public interface IColumnGroup
public void addColumnsForPropertyTypesForUpdate(List<PropertyType> propertyTypes);
/**
- * Adds a column for all given property types. The specified identifier prefix is used as a
- * prefix which combined with the property type code to determine the column id. The property
- * type label is used as column title.
+ * Adds a column for all given property types. The specified identifier prefix is used as a prefix which combined with the property type code to
+ * determine the column id. The property type label is used as column title.
*/
public void addColumnsForPropertyTypes(String idPrefix, List<PropertyType> propertyTypes,
boolean forUpdate);
/**
- * Adds all specified properties. The group name is used as a prefix which is combined with the
- * property type code to determine the column id. The property type label is used as column
- * title.
+ * Adds all specified properties. The group name is used as a prefix which is combined with the property type code to determine the column id. The
+ * property type label is used as column title.
*/
public void addProperties(Collection<IEntityProperty> properties);
/**
- * Adds all specified properties. The specified identifier prefix is combined with the property
- * type code to determine the column id. The property type label is used as column title.
+ * Adds all specified properties. The specified identifier prefix is combined with the property type code to determine the column id. The property
+ * type label is used as column title.
*/
public void addProperties(String idPrefix, Collection<IEntityProperty> properties);
/**
- * Adds all specified properties such that the table can be used for batch update. The original
- * property type code determines the column id. For vocabulary terms only the code is added as
- * value.
+ * Adds all specified properties such that the table can be used for batch update. The original property type code determines the column id. For
+ * vocabulary terms only the code is added as value.
*/
public void addPropertiesForUpdate(Collection<IEntityProperty> properties);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnMetaData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnMetaData.java
index cbdea36525b..b6525994f06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnMetaData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IColumnMetaData.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.util;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
/**
- * Interface for setting meta data of columns defined by
- * {@link TypedTableModelBuilder#addColumn(String)}.
+ * Interface for setting meta data of columns defined by {@link TypedTableModelBuilder#addColumn(String)}.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IDataSourceFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IDataSourceFactory.java
index 10037320e3e..aaadf5d8b71 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IDataSourceFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/IDataSourceFactory.java
@@ -27,8 +27,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataSourceWithDefinition;
public interface IDataSourceFactory
{
/**
- * Creates a data source optional definition from specified properties. Note, that if the
- * definition is provided its code attribute might be undefined.
+ * Creates a data source optional definition from specified properties. Note, that if the definition is provided its code attribute might be
+ * undefined.
*/
public DataSourceWithDefinition create(Properties dbProps);
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/Key.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/Key.java
index 02dbe560299..14fbd6c6714 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/Key.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/Key.java
@@ -26,9 +26,9 @@ import java.io.Serializable;
public final class Key implements Serializable
{
private static final long serialVersionUID = 1L;
-
+
private final Object[] objects;
-
+
public Key(Object... objects)
{
this.objects = objects;
@@ -61,7 +61,7 @@ public final class Key implements Serializable
}
return true;
}
-
+
@Override
public int hashCode()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/MaterialConfigurationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/MaterialConfigurationProvider.java
index f6bb1bda68e..66da13ffdd3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/MaterialConfigurationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/MaterialConfigurationProvider.java
@@ -78,8 +78,7 @@ public class MaterialConfigurationProvider
}
/**
- * Return <code>true</code> if the material codes can contain only alphanumeric characters and
- * underscores.
+ * Return <code>true</code> if the material codes can contain only alphanumeric characters and underscores.
*/
public boolean isStrictCodeConstraints()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RelationshipUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RelationshipUtils.java
index c1a2f29dec6..a6f1b86f24b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RelationshipUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RelationshipUtils.java
@@ -49,7 +49,7 @@ public class RelationshipUtils
}
}
- public static void updateModificationDateAndModifierOfRelatedEntitiesOfSamples(List<SamplePE> samples,
+ public static void updateModificationDateAndModifierOfRelatedEntitiesOfSamples(List<SamplePE> samples,
IAuthSession session, Date modificationTimestamp)
{
for (SamplePE sample : samples)
@@ -84,7 +84,7 @@ public class RelationshipUtils
}
}
- public static void updateModificationDateAndModifierOfRelatedEntitiesOfDataSets(List<DataPE> dataSets,
+ public static void updateModificationDateAndModifierOfRelatedEntitiesOfDataSets(List<DataPE> dataSets,
IAuthSession session, Date modificationTimestamp)
{
for (DataPE dataSet : dataSets)
@@ -106,7 +106,7 @@ public class RelationshipUtils
}
}
- private static void updateModificationDateAndModifierOfDataSets(List<DataPE> dataSets,
+ private static void updateModificationDateAndModifierOfDataSets(List<DataPE> dataSets,
IAuthSession session, Date modificationTimestamp)
{
if (dataSets != null)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCache.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCache.java
index 9d5df52ada8..141bbea600c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCache.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCache.java
@@ -36,8 +36,6 @@ import ch.systemsx.cisd.common.parser.MemorySizeFormatter;
import ch.systemsx.cisd.common.parser.PercentFormatter;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class RuntimeCache<K, V>
@@ -56,14 +54,14 @@ public class RuntimeCache<K, V>
this.name = name;
this.cacheSizePropertyName = cacheSizePropertyName;
}
-
+
@SuppressWarnings("unchecked")
public V get(K key)
{
Element element = getCache().get(key);
return element == null ? null : ((ValueWrapper<V>) element.getObjectValue()).getValue();
}
-
+
public void put(K key, V value)
{
Element element = getCache().get(key);
@@ -82,12 +80,12 @@ public class RuntimeCache<K, V>
getCache().recalculateSize(key);
}
}
-
+
public boolean remove(K key)
{
return getCache().remove(key);
}
-
+
public void initCache()
{
Cache cache = cacheManager.getCache(name);
@@ -115,7 +113,7 @@ public class RuntimeCache<K, V>
operationLog.info("The cache " + name + " already exists. It must have been configured in ehcache.xml file.");
}
}
-
+
protected long getCacheSize()
{
String propertyValue = getSystemProperty(cacheSizePropertyName);
@@ -159,7 +157,7 @@ public class RuntimeCache<K, V>
{
return System.getProperty(propertyName);
}
-
+
private Cache getCache()
{
return cacheManager.getCache(name);
@@ -175,7 +173,7 @@ public class RuntimeCache<K, V>
+ cacheSizePropertyName + "' system property in openbis.conf file.");
return cacheSize;
}
-
+
private static final class ValueWrapper<V>
{
private V value;
@@ -200,5 +198,6 @@ public class RuntimeCache<K, V>
{
return String.valueOf(value);
}
-
- }}
+
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCacheEventListener.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCacheEventListener.java
index 05d26a2511d..5c5a033de4c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCacheEventListener.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/RuntimeCacheEventListener.java
@@ -86,7 +86,7 @@ public class RuntimeCacheEventListener implements CacheEventListener
{
StringBuilder sb = new StringBuilder();
sb.append("Cache entry " + entry.hashCode() + " that contains search result with " + entry + " " + operation + ".");
-
+
int cacheSize = cache.getSize();
if (cacheSize == 1)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java
index b878cf0f625..bc2512dc442 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java
@@ -64,8 +64,7 @@ public class ServerUtils
/**
* Extracts from the comma-separated list of strings all distinct strings.
*
- * @return an empty list if the argument is <code>null</code>, an empty string or starts with
- * '$'.
+ * @return an empty list if the argument is <code>null</code>, an empty string or starts with '$'.
*/
public static Set<String> extractSet(String commaSeparatedList)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SpaceCodeHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SpaceCodeHelper.java
index 35086c17f3e..8c234210f23 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SpaceCodeHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/SpaceCodeHelper.java
@@ -40,8 +40,7 @@ public class SpaceCodeHelper
/**
* Tries to find out the space.
* <p>
- * If not specified in given {@link SpaceIdentifier} the real space must be specified as home
- * space in given {@link PersonPE}.
+ * If not specified in given {@link SpaceIdentifier} the real space must be specified as home space in given {@link PersonPE}.
* </p>
*
* @throws UndefinedSpaceException if no space could be found.
@@ -55,8 +54,7 @@ public class SpaceCodeHelper
/**
* Tries to find out the space.
* <p>
- * If not specified in given {@link SpacePE} the real space must be specified as home space in
- * given {@link PersonPE}.
+ * If not specified in given {@link SpacePE} the real space must be specified as home space in given {@link PersonPE}.
* </p>
*
* @throws UndefinedSpaceException if no space could be found.
@@ -70,9 +68,8 @@ public class SpaceCodeHelper
/**
* Tries to find out the space.
* <p>
- * If given <var>spaceCode</var> specifies the home space, the home space of the
- * {@link PersonPE} is returned. May return <code>null</code>, if no home space is defined for
- * the user.
+ * If given <var>spaceCode</var> specifies the home space, the home space of the {@link PersonPE} is returned. May return <code>null</code>, if no
+ * home space is defined for the user.
* </p>
*/
public final static String tryGetSpaceCode(final PersonPE person, final String spaceCode)
@@ -95,8 +92,7 @@ public class SpaceCodeHelper
/**
* Tries to find out the space.
* <p>
- * If given <var>spaceCode</var> is a home space, the real space must be specified as home space
- * in given {@link PersonPE}.
+ * If given <var>spaceCode</var> is a home space, the real space must be specified as home space in given {@link PersonPE}.
* </p>
*
* @throws UndefinedSpaceException if no space could be found.
@@ -115,8 +111,7 @@ public class SpaceCodeHelper
/**
* Tries to find out the space.
* <p>
- * If given <var>spaceCode</var> is a home space, the real space must be specified as
- * <var>homeSpaceCode</var>.
+ * If given <var>spaceCode</var> is a home space, the real space must be specified as <var>homeSpaceCode</var>.
* </p>
*
* @throws UndefinedSpaceException if no space could be found.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/UuidUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/UuidUtil.java
index 78a3f511159..005024e9b0c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/UuidUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/UuidUtil.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
/**
* Some utility methods based on {@link UUID}.
* <p>
- * In its canonical form, a <i>UUID</i> consists of 32 hexadecimal digits, displayed in 5 groups
- * separated by hyphens, in the form 8-4-4-4-12 for a total of 36 characters.<br>
+ * In its canonical form, a <i>UUID</i> consists of 32 hexadecimal digits, displayed in 5 groups separated by hyphens, in the form 8-4-4-4-12 for a
+ * total of 36 characters.<br>
* For example:
*
* <pre>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/WebClientFilesUpdater.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/WebClientFilesUpdater.java
index 86a59e8a1f1..38c9f5618bf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/WebClientFilesUpdater.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/WebClientFilesUpdater.java
@@ -32,10 +32,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.Def
/**
* Class which updates <code>OpenBIS.gwt.xml</code> and {@link DefaultClientPluginFactoryProvider}.
* <p>
- * Usage:
- * <tt>java {@link WebClientFilesUpdater} [<working directory> [<technology 1> <technology 2> ...]]</tt>
- * Without technology arguments all technologies found in the code base are available. If at least
- * one technology is specified only the specified technologies will be available.
+ * Usage: <tt>java {@link WebClientFilesUpdater} [<working directory> [<technology 1> <technology 2> ...]]</tt> Without technology arguments all
+ * technologies found in the code base are available. If at least one technology is specified only the specified technologies will be available.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/XmlUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/XmlUtils.java
index 3388155555c..6afa1649118 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/XmlUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/XmlUtils.java
@@ -62,7 +62,7 @@ public class XmlUtils
/** indentation to be used when serializing to xml. */
public static final Integer INDENTATION = 2;
-
+
/**
* Parse given string as XML {@link Document}.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractPluginBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractPluginBusinessObjectFactory.java
index 5d2cddf3f5e..ad8d343de94 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractPluginBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractPluginBusinessObjectFactory.java
@@ -23,8 +23,8 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.AbstractBusinessObjec
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
/**
- * An <i>abstract</i> {@link AbstractBusinessObjectFactory} extension which is able to delegate
- * calls to the encapsulated {@link ICommonBusinessObjectFactory}.
+ * An <i>abstract</i> {@link AbstractBusinessObjectFactory} extension which is able to delegate calls to the encapsulated
+ * {@link ICommonBusinessObjectFactory}.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractSampleServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractSampleServerPlugin.java
index 9326f2d7eb9..31df2e3f656 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractSampleServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractSampleServerPlugin.java
@@ -27,12 +27,10 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.SampleServerPluginRegistry
import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
/**
- * An abstract {@link ISampleServerPlugin} which registers itself to
- * {@link SampleServerPluginRegistry}.
+ * An abstract {@link ISampleServerPlugin} which registers itself to {@link SampleServerPluginRegistry}.
* <p>
- * Each subclass should be annotated with {@link Component} so that it automatically gets registered
- * to {@link SampleServerPluginRegistry} by <i>Spring</i>. It is a good idea as well to make the
- * empty constructor <i>private</i>.
+ * Each subclass should be annotated with {@link Component} so that it automatically gets registered to {@link SampleServerPluginRegistry} by
+ * <i>Spring</i>. It is a good idea as well to make the empty constructor <i>private</i>.
* </p>
*
* @author Christian Ribeaud
@@ -41,7 +39,7 @@ public abstract class AbstractSampleServerPlugin implements ISampleServerPlugin,
{
@Resource(name = ResourceNames.SAMPLE_PLUGIN_REGISTRY)
private SampleServerPluginRegistry sampleServerPluginRegistry;
-
+
@Resource(name = ResourceNames.GENERIC_SAMPLE_TYPE_SLAVE_SERVER_PLUGIN)
private ISampleTypeSlaveServerPlugin genericSampleTypeSlaveServerPlugin;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/IDemoClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/IDemoClientService.java
index 46678255a0d..9755c1e350e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/IDemoClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/IDemoClientService.java
@@ -25,9 +25,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived
/**
* Service interface for the <i>demo</i> <i>GWT</i> client.
* <p>
- * Each method should declare throwing {@link UserFailureException}. The authorization framework can
- * throw it when the user has insufficient privileges. If it is not marked, the GWT client will
- * report unexpected exception.
+ * Each method should declare throwing {@link UserFailureException}. The authorization framework can throw it when the user has insufficient
+ * privileges. If it is not marked, the GWT client will report unexpected exception.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/Dict.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/Dict.java
index b6fdfc1df84..304ed432c8d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/Dict.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/Dict.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.demo.client.web.client.application;
/**
- * An {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict} extension for
- * <i>demo</i> specific message keys.
+ * An {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict} extension for <i>demo</i> specific message keys.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/module/StatisticsWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/module/StatisticsWidget.java
index 53c98f70956..2480265dcba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/module/StatisticsWidget.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/client/application/module/StatisticsWidget.java
@@ -94,7 +94,7 @@ public class StatisticsWidget extends ContentPanel implements IDatabaseModificat
public DatabaseModificationKind[] getRelevantModifications()
{
return new DatabaseModificationKind[]
- { DatabaseModificationKind.createOrDelete(ObjectKind.EXPERIMENT) };
+ { DatabaseModificationKind.createOrDelete(ObjectKind.EXPERIMENT) };
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/server/DemoClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/server/DemoClientServiceServlet.java
index 3b7b912e7c9..e943c4ec48c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/server/DemoClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/client/web/server/DemoClientServiceServlet.java
@@ -29,16 +29,15 @@ import ch.systemsx.cisd.openbis.plugin.demo.shared.ResourceNames;
/**
* The {@link GWTRPCServiceExporter} for the <i>demo</i> service.
* <p>
- * <i>URL</i> mappings are: <code>/demo</code> and <code>/openbis/demo</code>. The encapsulated
- * {@link ICommonClientService} service implementation is expected to be defined as bean with name
- * <code>demo-service</code>.
+ * <i>URL</i> mappings are: <code>/demo</code> and <code>/openbis/demo</code>. The encapsulated {@link ICommonClientService} service implementation is
+ * expected to be defined as bean with name <code>demo-service</code>.
* </p>
*
* @author Christian Ribeaud
*/
@Controller
@RequestMapping(
- { "/demo", "/openbis/demo" })
+{ "/demo", "/openbis/demo" })
public final class DemoClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoSampleServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoSampleServerPlugin.java
index 89cc5663d3d..083cb72b73d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoSampleServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoSampleServerPlugin.java
@@ -31,8 +31,7 @@ import ch.systemsx.cisd.openbis.plugin.demo.shared.ResourceNames;
/**
* The {@link ISampleServerPlugin} implementation for plates of type <code>DEMO_PLUGIN</code>.
* <p>
- * This class is annotated with {@link Component} so that it automatically gets registered to
- * {@link SampleServerPluginRegistry} by <i>Spring</i>.
+ * This class is annotated with {@link Component} so that it automatically gets registered to {@link SampleServerPluginRegistry} by <i>Spring</i>.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/IDemoServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/IDemoServer.java
index c50ee03544a..d4bf8c7ba5a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/IDemoServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/IDemoServer.java
@@ -47,8 +47,8 @@ public interface IDemoServer extends IServer
* For given {@link TechId} returns the {@link Sample} and its derived (child) samples.
*
* @return never <code>null</code>.
- * @throws UserFailureException if given <var>sessionToken</var> is invalid or whether sample
- * uniquely identified by given <var>sampleId</var> does not exist.
+ * @throws UserFailureException if given <var>sessionToken</var> is invalid or whether sample uniquely identified by given <var>sampleId</var>
+ * does not exist.
*/
@Transactional(readOnly = true)
public SampleParentWithDerived getSampleInfo(final String sessionToken, final TechId sampleId)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/ResourceNames.java
index c98f88e0157..9c050fd6205 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/shared/ResourceNames.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.plugin.demo.shared;
/**
* Resource name used in <i>demo</i> plug-in.
* <p>
- * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here
- * should not conflict with already existing bean names. Look for other <code>ResourceNames</code>
- * classes.
+ * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here should not conflict with already existing bean names.
+ * Look for other <code>ResourceNames</code> classes.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/DelegatedClientPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/DelegatedClientPlugin.java
index ad865252e5c..051ba0bec79 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/DelegatedClientPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/DelegatedClientPlugin.java
@@ -33,8 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedInputWidgetDescription;
/**
- * delegates all operations to generic plugin, should be subclasssed and the needed functionality
- * can override the default behaviour
+ * delegates all operations to generic plugin, should be subclasssed and the needed functionality can override the default behaviour
*/
public class DelegatedClientPlugin<T extends BasicEntityType> implements
IClientPlugin<T, IIdAndCodeHolder>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetRelationshipBrowser.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetRelationshipBrowser.java
index 9beea2bbf30..1e25cd40b6f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetRelationshipBrowser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/DataSetRelationshipBrowser.java
@@ -32,8 +32,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
/**
- * {@link AbstractExternalDataGrid} containing data sets directly connected with a specified data
- * set being in a specified relationship role (parent/child).
+ * {@link AbstractExternalDataGrid} containing data sets directly connected with a specified data set being in a specified relationship role
+ * (parent/child).
*
* @author Piotr Buczek
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewer.java
index 2451756fcbe..28f2552ef69 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewer.java
@@ -133,7 +133,7 @@ abstract public class GenericDataSetViewer extends AbstractViewerWithVerticalSpl
{
Widget spaceBreadcrumb = createSpaceLink(originalData.getSpace());
widgets.add(spaceBreadcrumb);
-
+
Experiment experiment = originalData.getExperiment();
if (experiment != null)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
index 0650a729d45..0721f1ed2ca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
@@ -65,8 +65,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientS
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.AbstractGenericEntityRegistrationForm;
/**
- * A {@link AbstractGenericEntityRegistrationForm} extension for registering and editing
- * experiments.
+ * A {@link AbstractGenericEntityRegistrationForm} extension for registering and editing experiments.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/ExperimentPropertiesPanel.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/ExperimentPropertiesPanel.java
index dbd06b0a23d..30611d60617 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/ExperimentPropertiesPanel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/ExperimentPropertiesPanel.java
@@ -157,16 +157,16 @@ public class ExperimentPropertiesPanel extends ContentPanel
public DatabaseModificationKind[] getRelevantModifications()
{
return new DatabaseModificationKind[]
- {
- DatabaseModificationKind.edit(ObjectKind.EXPERIMENT),
- DatabaseModificationKind.createOrDelete(ObjectKind.EXPERIMENT),
- DatabaseModificationKind
- .createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
- DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM),
- DatabaseModificationKind.createOrDelete(ObjectKind.METAPROJECT),
- DatabaseModificationKind.edit(ObjectKind.METAPROJECT) };
+ {
+ DatabaseModificationKind.edit(ObjectKind.EXPERIMENT),
+ DatabaseModificationKind.createOrDelete(ObjectKind.EXPERIMENT),
+ DatabaseModificationKind
+ .createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
+ DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM),
+ DatabaseModificationKind.createOrDelete(ObjectKind.METAPROJECT),
+ DatabaseModificationKind.edit(ObjectKind.METAPROJECT) };
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
index 0f6e4afd89e..23211a8ef3c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
@@ -227,8 +227,7 @@ abstract public class PropertiesEditor<T extends EntityType, S extends EntityTyp
}
/**
- * Returns a list of fields appropriate for entity type - property type assignments specific to
- * given {@link PropertiesEditor}.
+ * Returns a list of fields appropriate for entity type - property type assignments specific to given {@link PropertiesEditor}.
*/
public final List<DatabaseModificationAwareField<?>> getPropertyFields()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
index 93d238683d0..6872e36e1f5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
@@ -147,8 +147,7 @@ abstract public class GenericMaterialViewer extends AbstractViewerWithVerticalSp
}
/**
- * To be subclassed. Creates additional panels of the viewer in the right side section besides
- * components, datasets and attachments
+ * To be subclassed. Creates additional panels of the viewer in the right side section besides components, datasets and attachments
*/
protected List<TabContent> createAdditionalSectionPanels(Material material)
{
@@ -262,15 +261,15 @@ abstract public class GenericMaterialViewer extends AbstractViewerWithVerticalSp
public DatabaseModificationKind[] getRelevantModifications()
{
return new DatabaseModificationKind[]
- {
- DatabaseModificationKind.edit(ObjectKind.MATERIAL),
- DatabaseModificationKind
- .createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
- DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM),
- DatabaseModificationKind.createOrDelete(ObjectKind.METAPROJECT),
- DatabaseModificationKind.edit(ObjectKind.METAPROJECT) };
+ {
+ DatabaseModificationKind.edit(ObjectKind.MATERIAL),
+ DatabaseModificationKind
+ .createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
+ DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM),
+ DatabaseModificationKind.createOrDelete(ObjectKind.METAPROJECT),
+ DatabaseModificationKind.edit(ObjectKind.METAPROJECT) };
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/EntityConnectionTypeProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/EntityConnectionTypeProvider.java
index 123c3509e41..f2f674715f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/EntityConnectionTypeProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/EntityConnectionTypeProvider.java
@@ -25,8 +25,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDele
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDirectlyConnectedController;
/**
- * Class capsulating a {@link CheckBox} and delegating check box changes to an associated
- * {@link IDelegatedAction}.
+ * Class capsulating a {@link CheckBox} and delegating check box changes to an associated {@link IDelegatedAction}.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
index 107d6891d91..106b47a9d87 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
@@ -184,19 +184,19 @@ abstract public class GenericSampleViewer extends AbstractViewerWithVerticalSpli
List<TechId> sampleIds = new ArrayList<TechId>(Arrays.asList(TechId.create(getOriginalData())));
viewContext.getCommonService().getSampleChildrenInfo(sampleIds, true,
new AbstractAsyncCallback<List<SampleChildrenInfo>>(viewContext)
- {
- @Override
- protected void process(List<SampleChildrenInfo> info)
- {
- SampleChildrenInfo sampleInfo = info.get(0);
+ {
+ @Override
+ protected void process(List<SampleChildrenInfo> info)
+ {
+ SampleChildrenInfo sampleInfo = info.get(0);
- additionalMessage.append(EntityDeletionConfirmationUtils.getMessageForSingleSample(sampleInfo));
+ additionalMessage.append(EntityDeletionConfirmationUtils.getMessageForSingleSample(sampleInfo));
- new SampleListDeletionConfirmationDialog(getViewContext()
- .getCommonViewContext(), getOriginalDataAsSingleton(), callback,
- getOriginalData(), additionalMessage.toString()).show();
- }
- });
+ new SampleListDeletionConfirmationDialog(getViewContext()
+ .getCommonViewContext(), getOriginalDataAsSingleton(), callback,
+ getOriginalData(), additionalMessage.toString()).show();
+ }
+ });
}
}));
addToolBarButton(createRevertDeletionButton(new IDelegatedAction()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index e6501d40010..8ccd75f054a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -294,7 +294,7 @@ public class GenericClientService extends AbstractClientService implements IGene
private void updateTemporaryCodes(final String sessionToken, BatchSamplesOperation info)
{
- // TODO FJE: Do the update in single queue which is also fed by the
+ // TODO FJE: Do the update in single queue which is also fed by the
// BatchSampleRegistrationTempCodeUpdaterTask
// 1. Fill Structure
Map<String, List<String>> sampleTypeCodeToTemporaryIdentifiers = new HashMap<String, List<String>>();
@@ -546,7 +546,7 @@ public class GenericClientService extends AbstractClientService implements IGene
{
files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
-
+
BatchSamplesOperation batchSamplesOperation =
SampleUploadSectionsParser.prepareSamples(sampleType, files,
defaultGroupIdentifier, sampleCodeGeneratorOrNull, allowExperiments,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
index 33610c755e0..0ed383b19bc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
@@ -29,16 +29,15 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
/**
* The {@link GWTRPCServiceExporter} for the <i>generic</i> service.
* <p>
- * <i>URL</i> mappings are: <code>/generic</code> and <code>/openbis/generic</code>. The
- * encapsulated {@link ICommonClientService} service implementation is expected to be defined as
- * bean with name <code>generic-service</code>.
+ * <i>URL</i> mappings are: <code>/generic</code> and <code>/openbis/generic</code>. The encapsulated {@link ICommonClientService} service
+ * implementation is expected to be defined as bean with name <code>generic-service</code>.
* </p>
*
* @author Christian Ribeaud
*/
@Controller
@RequestMapping(
- { "/generic", "/openbis/generic" })
+{ "/generic", "/openbis/generic" })
public final class GenericClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedDataSetParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedDataSetParserObjectFactory.java
index 85c024e16f8..27a5bada53b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedDataSetParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedDataSetParserObjectFactory.java
@@ -89,8 +89,8 @@ public final class UpdatedDataSetParserObjectFactory extends
}
/**
- * Prepares details about which values should be updated in general taking into account only the
- * information about availability of columns in the file.
+ * Prepares details about which values should be updated in general taking into account only the information about availability of columns in the
+ * file.
*/
private DataSetBatchUpdateDetails createBasicBatchUpdateDetails()
{
@@ -104,8 +104,8 @@ public final class UpdatedDataSetParserObjectFactory extends
}
/**
- * Returns details about which values should be updated for the specified data set. If a cell
- * was left empty in the file the corresponding value will not be modified.
+ * Returns details about which values should be updated for the specified data set. If a cell was left empty in the file the corresponding value
+ * will not be modified.
*/
private DataSetBatchUpdateDetails createBatchUpdateDetails(NewDataSet dataSet)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/AbstractGenericServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/AbstractGenericServerPlugin.java
index c0613108bdd..9e234ad1547 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/AbstractGenericServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/AbstractGenericServerPlugin.java
@@ -22,9 +22,7 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.IServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
/**
- *
- *
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
abstract class AbstractGenericServerPlugin implements IServerPlugin
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetServerPlugin.java
index e80f3025366..e5a8147729e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetServerPlugin.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlu
/**
* The default {@link IDataSetServerPlugin} implementation for the <i>generic</i> technology.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
@Component(ch.systemsx.cisd.openbis.generic.shared.ResourceNames.GENERIC_DATA_SET_SERVER_PLUGIN)
public class GenericDataSetServerPlugin extends AbstractGenericServerPlugin implements
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index f6810591560..2713cccc6b4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -293,8 +293,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AbstractExternalData getDataSetInfo(String sessionToken,
- @AuthorizationGuard(guardClass = DataSetTechIdPredicate.class)
- TechId datasetId)
+ @AuthorizationGuard(guardClass = DataSetTechIdPredicate.class) TechId datasetId)
{
return commonServer.getDataSetInfo(sessionToken, datasetId);
}
@@ -302,8 +301,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AttachmentWithContent getExperimentFileAttachment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
- TechId experimentId, String filename, Integer versionOrNull)
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId, String filename, Integer versionOrNull)
throws UserFailureException
{
final Session session = getSession(sessionToken);
@@ -734,8 +732,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AttachmentWithContent getProjectFileAttachment(String sessionToken,
- @AuthorizationGuard(guardClass = ProjectTechIdPredicate.class)
- TechId projectId, String fileName, Integer versionOrNull)
+ @AuthorizationGuard(guardClass = ProjectTechIdPredicate.class) TechId projectId, String fileName, Integer versionOrNull)
{
final Session session = getSession(sessionToken);
final IProjectBO bo = businessObjectFactory.createProjectBO(session);
@@ -747,8 +744,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AttachmentWithContent getSampleFileAttachment(String sessionToken,
- @AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
- TechId sampleId, String fileName, Integer versionOrNull)
+ @AuthorizationGuard(guardClass = SampleTechIdPredicate.class) TechId sampleId, String fileName, Integer versionOrNull)
{
final Session session = getSession(sessionToken);
final ISampleBO bo = businessObjectFactory.createSampleBO(session);
@@ -779,8 +775,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
@Capability("WRITE_EXPERIMENT_SAMPLE")
public ExperimentUpdateResult updateExperiment(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentUpdatesPredicate.class)
- ExperimentUpdatesDTO updates)
+ @AuthorizationGuard(guardClass = ExperimentUpdatesPredicate.class) ExperimentUpdatesDTO updates)
{
final Session session = getSession(sessionToken);
if (updates.isRegisterSamples())
@@ -810,8 +805,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
public SampleUpdateResult updateSample(String sessionToken,
- @AuthorizationGuard(guardClass = SampleUpdatesPredicate.class)
- SampleUpdatesDTO updates)
+ @AuthorizationGuard(guardClass = SampleUpdatesPredicate.class) SampleUpdatesDTO updates)
{
return commonServer.updateSample(sessionToken, updates);
}
@@ -820,8 +814,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
@RolesAllowed(RoleWithHierarchy.SPACE_POWER_USER)
@Capability("WRITE_DATASET")
public DataSetUpdateResult updateDataSet(String sessionToken,
- @AuthorizationGuard(guardClass = DataSetUpdatesPredicate.class)
- DataSetUpdatesDTO updates)
+ @AuthorizationGuard(guardClass = DataSetUpdatesPredicate.class) DataSetUpdatesDTO updates)
{
return commonServer.updateDataSet(sessionToken, updates);
}
@@ -1020,14 +1013,17 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
Map<String, SpacePE> spaceCache = new HashMap<String, SpacePE>();
Map<String, List<String>> spaceToOldSampleCodes = new HashMap<String, List<String>>();
Map<String, String> identifiersToNewSampleCodes = new HashMap<String, String>();
-
+
// Generate Updates for each space and build helper maps
- for(String sampleTypeCode : sampleTypeCodeToTemporaryIdentifiers.keySet()) {
+ for (String sampleTypeCode : sampleTypeCodeToTemporaryIdentifiers.keySet())
+ {
String codePrefix = getGeneratedCodePrefix(sessionToken, sampleTypeCode);
List<String> temporaryIdentifiers = sampleTypeCodeToTemporaryIdentifiers.get(sampleTypeCode);
int numberOfCodesToGenerate = temporaryIdentifiers.size();
- List<String> newCodes = new SampleCodeGeneratorByType(getDAOFactory()).generateCodes(codePrefix, ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind.SAMPLE, numberOfCodesToGenerate);
- for(int tIdx = 0; tIdx < numberOfCodesToGenerate; tIdx++)
+ List<String> newCodes =
+ new SampleCodeGeneratorByType(getDAOFactory()).generateCodes(codePrefix,
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind.SAMPLE, numberOfCodesToGenerate);
+ for (int tIdx = 0; tIdx < numberOfCodesToGenerate; tIdx++)
{
String tempIdentifier = temporaryIdentifiers.get(tIdx);
String spaceCode = tempIdentifier.split("/")[1];
@@ -1048,7 +1044,7 @@ public final class GenericServer extends AbstractServer<IGenericServerInternal>
identifiersToNewSampleCodes.put(tempIdentifier, newCodes.get(tIdx));
}
}
-
+
// Retrieve all sample PE objects
List<SamplePE> allSamplesPE = new ArrayList<SamplePE>();
for (String spaceCode : spaceToOldSampleCodes.keySet())
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
index c736c6567b4..91cad13420e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
@@ -268,7 +268,7 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
logTracking(sessionToken, "update_experiments", "TYPE(%s) EXPERIMENTS(%s)", experiments
.getExperimentType().getCode(), experiments.getUpdatedExperiments().size());
}
-
+
@Override
public void registerOrUpdateSamplesAndMaterials(final String sessionToken,
final List<NewSamplesWithTypes> newSamplesWithType,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServiceServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServiceServer.java
index 491e68ad6c2..03e496ba5db 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServiceServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServiceServer.java
@@ -48,10 +48,11 @@ public class GenericServiceServer extends WhiteAndBlackListHttpInvokerServiceExp
}
@RequestMapping(
- { "/rmi-plugin-generic", "/openbis/rmi-plugin-generic" })
+ { "/rmi-plugin-generic", "/openbis/rmi-plugin-generic" })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
- throws ServletException, IOException {
+ throws ServletException, IOException
+ {
super.handleRequest(request, response);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServerInternal.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServerInternal.java
index e7b9d5fb822..28627563be0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServerInternal.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServerInternal.java
@@ -25,8 +25,6 @@ import ch.systemsx.cisd.openbis.generic.shared.DatabaseUpdateModification;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public interface IGenericServerInternal extends IGenericServer
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/ResourceNames.java
index 51c93e0716e..66a443fc534 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/ResourceNames.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.plugin.generic.shared;
/**
* Resource name used in <i>generic</i> plug-in.
* <p>
- * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here
- * should not conflict with already existing bean names. Look for other <code>ResourceNames</code>
- * classes.
+ * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here should not conflict with already existing bean names.
+ * Look for other <code>ResourceNames</code> classes.
* </p>
*
* @author Christian Ribeaud
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/api/v1/IQueryApiFacade.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/api/v1/IQueryApiFacade.java
index 079dd9726c4..79c6d5eab87 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/api/v1/IQueryApiFacade.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/api/v1/IQueryApiFacade.java
@@ -58,18 +58,17 @@ public interface IQueryApiFacade
public List<ReportDescription> listTableReportDescriptions();
/**
- * Creates for the specified data sets and specified report description a report. Available
- * report descriptions can be obtained by {@link #listTableReportDescriptions()}.
+ * Creates for the specified data sets and specified report description a report. Available report descriptions can be obtained by
+ * {@link #listTableReportDescriptions()}.
*/
@Retry
public QueryTableModel createReportFromDataSets(ReportDescription reportDescription,
List<String> dataSetCodes);
/**
- * Creates for the specified data sets and specified report key a report. It groups the data
- * sets by a data store and creates a report for each group of objects on appropriate data store
- * server. Results from the data stores are combined and returned as a result of this method.
- * Available report keys can be obtained by {@link #listTableReportDescriptions()}.
+ * Creates for the specified data sets and specified report key a report. It groups the data sets by a data store and creates a report for each
+ * group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method. Available
+ * report keys can be obtained by {@link #listTableReportDescriptions()}.
*/
@Retry
public QueryTableModel createReportFromDataSets(String reportKey, List<String> dataSetCodes);
@@ -87,9 +86,8 @@ public interface IQueryApiFacade
public List<AggregationServiceDescription> listAggregationServices();
/**
- * Executes the specified aggregation or ingestion service for the specified parameters and
- * creates a report. Available service descriptions can be obtained by
- * {@link #listAggregationServices()}.
+ * Executes the specified aggregation or ingestion service for the specified parameters and creates a report. Available service descriptions can
+ * be obtained by {@link #listAggregationServices()}.
*/
@Retry
public QueryTableModel createReportFromAggregationService(
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientService.java
index f3c5b547b08..8b2f904cfe3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientService.java
@@ -38,9 +38,8 @@ import ch.systemsx.cisd.openbis.plugin.query.shared.basic.dto.QueryParameterBind
/**
* Service interface for the query module GWT client.
* <p>
- * Each method should declare throwing {@link UserFailureException}. The authorization framework can
- * throw it when the user has insufficient privileges. If it is not marked, the GWT client will
- * report unexpected exception.
+ * Each method should declare throwing {@link UserFailureException}. The authorization framework can throw it when the user has insufficient
+ * privileges. If it is not marked, the GWT client will report unexpected exception.
* </p>
*
* @author Piotr Buczek
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientServiceAsync.java
index 2d6aea7ea64..4817369641a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/IQueryClientServiceAsync.java
@@ -54,8 +54,7 @@ public interface IQueryClientServiceAsync extends IClientServiceAsync
AsyncCallback<TableModelReference> callback);
/**
- * @see IQueryClientService#createQueryResultsReport(QueryDatabase, String,
- * QueryParameterBindings)
+ * @see IQueryClientService#createQueryResultsReport(QueryDatabase, String, QueryParameterBindings)
*/
public void createQueryResultsReport(QueryDatabase queryDatabase, String sqlQuery,
QueryParameterBindings bindingsOrNull, AsyncCallback<TableModelReference> callback);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/Dict.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/Dict.java
index 3e5f277debd..a51620ee10b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/Dict.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/Dict.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.query.client.web.client.application;
/**
- * An {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict} extension for
- * <i>query</i> specific message keys.
+ * An {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict} extension for <i>query</i> specific message keys.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/module/QueryDatabaseSelectionWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/module/QueryDatabaseSelectionWidget.java
index 3db3d9db74b..d2e35a2cef1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/module/QueryDatabaseSelectionWidget.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/application/module/QueryDatabaseSelectionWidget.java
@@ -85,7 +85,7 @@ public final class QueryDatabaseSelectionWidget extends
return DatabaseModificationKind.any(ObjectKind.QUERY);
}
- //
+ //
// initial value support
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/dto/QueryBrowserGridColumnIDs.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/dto/QueryBrowserGridColumnIDs.java
index 9500051c736..c430925f3c6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/dto/QueryBrowserGridColumnIDs.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/client/dto/QueryBrowserGridColumnIDs.java
@@ -26,12 +26,20 @@ import ch.systemsx.cisd.openbis.plugin.query.client.web.client.application.modul
public class QueryBrowserGridColumnIDs
{
public static final String NAME = "NAME";
+
public static final String DESCRIPTION = "DESCRIPTION";
+
public static final String SQL_QUERY = "SQL_QUERY";
+
public static final String IS_PUBLIC = "IS_PUBLIC";
+
public static final String QUERY_TYPE = "QUERY_TYPE";
+
public static final String ENTITY_TYPE = "ENTITY_TYPE";
+
public static final String QUERY_DATABASE = "QUERY_DATABASE";
+
public static final String REGISTRATOR = "REGISTRATOR";
+
public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/server/QueryClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/server/QueryClientServiceServlet.java
index 935833b48da..377ee0f755b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/server/QueryClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/client/web/server/QueryClientServiceServlet.java
@@ -29,16 +29,15 @@ import ch.systemsx.cisd.openbis.plugin.query.shared.ResourceNames;
/**
* The {@link GWTRPCServiceExporter} for the <i>query</i> service.
* <p>
- * <i>URL</i> mappings are: <code>/query</code> and <code>/openbis/query</code>. The encapsulated
- * {@link ICommonClientService} service implementation is expected to be defined as bean with name
- * <code>query-plugin-service</code>.
+ * <i>URL</i> mappings are: <code>/query</code> and <code>/openbis/query</code>. The encapsulated {@link ICommonClientService} service implementation
+ * is expected to be defined as bean with name <code>query-plugin-service</code>.
* </p>
*
* @author Christian Ribeaud
*/
@Controller
@RequestMapping(
- { "/query", "/openbis/query" })
+{ "/query", "/openbis/query" })
public final class QueryClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/DAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/DAO.java
index e537f82a4dc..f2609258191 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/DAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/DAO.java
@@ -264,9 +264,8 @@ class DAO extends SimpleJdbcDaoSupport implements IDAO
/**
* A class for figuring out the parameter type.
* <p>
- * Note that some JDBC drivers (like the one from Oracle) have
- * {@link ParameterMetaData#getParameterType(int)} not implemented and thus requires setting it
- * explicitly in the variable metadata.
+ * Note that some JDBC drivers (like the one from Oracle) have {@link ParameterMetaData#getParameterType(int)} not implemented and thus requires
+ * setting it explicitly in the variable metadata.
*/
private static class ParameterTypeProvider
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/QueryServiceJsonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/QueryServiceJsonServer.java
index 222e3fdba2c..b4c79fc81fb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/QueryServiceJsonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/QueryServiceJsonServer.java
@@ -56,11 +56,12 @@ public class QueryServiceJsonServer extends AbstractApiJsonServiceExporter
}
@RequestMapping(
- { IQueryApiServer.JSON_SERVICE_URL, "/openbis" + IQueryApiServer.JSON_SERVICE_URL })
+ { IQueryApiServer.JSON_SERVICE_URL, "/openbis" + IQueryApiServer.JSON_SERVICE_URL })
@Override
public void handleRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException,
- IOException {
+ IOException
+ {
super.handleRequest(request, response);
- }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/ResourceNames.java
index aa4c659946a..d41255c5add 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/api/v1/ResourceNames.java
@@ -17,8 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.query.server.api.v1;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ResourceNames
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/authorization/resultfilter/QueryResultFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/authorization/resultfilter/QueryResultFilter.java
index 964d38b364f..be4ebf4f9e5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/authorization/resultfilter/QueryResultFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/authorization/resultfilter/QueryResultFilter.java
@@ -37,8 +37,8 @@ import ch.systemsx.cisd.openbis.plugin.query.server.authorization.AuthorizationC
import ch.systemsx.cisd.openbis.plugin.query.server.authorization.IAuthorizationChecker;
/**
- * Filters the rows of {@link TableModel} on magic columns (experiment, sample or data set
- * referenced by 'experiment_key', 'sample_key', 'data_set_key').
+ * Filters the rows of {@link TableModel} on magic columns (experiment, sample or data set referenced by 'experiment_key', 'sample_key',
+ * 'data_set_key').
*
* @author Izabela Adamczyk
*/
@@ -49,7 +49,7 @@ public class QueryResultFilter
private final IAuthorizationChecker authorizationChecker;
private static final EntityKind[] FILTRABLE_ENTITY_KINDS =
- { EntityKind.EXPERIMENT, EntityKind.SAMPLE, EntityKind.DATA_SET };
+ { EntityKind.EXPERIMENT, EntityKind.SAMPLE, EntityKind.DATA_SET };
public QueryResultFilter(IDAOFactory daoFactory)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/IQueryDatabaseDefinitionProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/IQueryDatabaseDefinitionProvider.java
index 2e01a350053..0720c922eae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/IQueryDatabaseDefinitionProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/IQueryDatabaseDefinitionProvider.java
@@ -33,8 +33,7 @@ public interface IQueryDatabaseDefinitionProvider
void initDatabaseDefinitions();
/**
- * Returns {@link DatabaseDefinition} configured for given <var>dbKey</var> or null if such a
- * definition doesn't exist.
+ * Returns {@link DatabaseDefinition} configured for given <var>dbKey</var> or null if such a definition doesn't exist.
*
* @throws UserFailureException if this provider wasn't initialized before
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/ResourceNames.java
index a622d2f8da8..3177410c720 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/ResourceNames.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.plugin.query.shared;
/**
* Resource name used in <i>query</i> plug-in.
* <p>
- * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here
- * should not conflict with already existing bean names. Look for other <code>ResourceNames</code>
- * classes.
+ * Be aware about the uniqueness of the bean names loaded by <i>Spring</i>. Names defined here should not conflict with already existing bean names.
+ * Look for other <code>ResourceNames</code> classes.
* </p>
*
* @author Franz-Josef Elmer
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/IQueryApiServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/IQueryApiServer.java
index d4b3a367532..f2442a13895 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/IQueryApiServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/IQueryApiServer.java
@@ -48,8 +48,7 @@ public interface IQueryApiServer extends IRpcService
public static final String JSON_SERVICE_URL = QUERY_PLUGIN_SERVER_URL + ".json";
/**
- * Tries to authenticate specified user with specified password. Returns session token if
- * succeeded otherwise <code>null</code> is returned.
+ * Tries to authenticate specified user with specified password. Returns session token if succeeded otherwise <code>null</code> is returned.
*/
@Transactional
// this is not a readOnly transaction - it can create new users
@@ -83,8 +82,7 @@ public interface IQueryApiServer extends IRpcService
public List<ReportDescription> listTableReportDescriptions(String sessionToken);
/**
- * Creates for the specified data sets a report. Available reports can be obtained by
- * {@link #listTableReportDescriptions(String)}.
+ * Creates for the specified data sets a report. Available reports can be obtained by {@link #listTableReportDescriptions(String)}.
*
* @param dataStoreCode Code of the data store.
* @param serviceKey Key of the data store service.
@@ -95,10 +93,9 @@ public interface IQueryApiServer extends IRpcService
String serviceKey, List<String> dataSetCodes);
/**
- * Creates for the specified data sets a report. It groups the data sets by a data store and
- * creates a report for each group of objects on appropriate data store server. Results from the
- * data stores are combined and returned as a result of this method. Available report keys can
- * be obtained by {@link #listTableReportDescriptions(String)}.
+ * Creates for the specified data sets a report. It groups the data sets by a data store and creates a report for each group of objects on
+ * appropriate data store server. Results from the data stores are combined and returned as a result of this method. Available report keys can be
+ * obtained by {@link #listTableReportDescriptions(String)}.
*
* @param serviceKey Key of the data store service.
* @since 1.6
@@ -116,10 +113,8 @@ public interface IQueryApiServer extends IRpcService
public List<AggregationServiceDescription> listAggregationServices(String sessionToken);
/**
- * Executes the specified aggregation or ingestion service for the specified parameters and
- * creates a report. Available service descriptions can be obtained by
- * {@link #listAggregationServices(String)}. The service resolved to by the serviceKey must be a
- * service of type REPORT.
+ * Executes the specified aggregation or ingestion service for the specified parameters and creates a report. Available service descriptions can
+ * be obtained by {@link #listAggregationServices(String)}. The service resolved to by the serviceKey must be a service of type REPORT.
*
* @param sessionToken A valid session token.
* @param dataStoreCode Code of the data store.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryDescription.java
index bac747fbfe4..3346a88fbfa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryDescription.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryDescription.java
@@ -26,8 +26,8 @@ import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.util.JsonPropertyUtil;
/**
- * Description of a query. Contains everything needed on client side to show to the user what
- * queries are available, to specify parameter bindings, and to identify a query uniquely.
+ * Description of a query. Contains everything needed on client side to show to the user what queries are available, to specify parameter bindings,
+ * and to identify a query uniquely.
*
* @author Franz-Josef Elmer
*/
@@ -102,8 +102,7 @@ public class QueryDescription implements Serializable
}
/**
- * Returns <code>true</code> if and only if the specified object is of type
- * {@link QueryDescription} and has the same ID as this.
+ * Returns <code>true</code> if and only if the specified object is of type {@link QueryDescription} and has the same ID as this.
*/
@Override
public boolean equals(Object obj)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryTableModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryTableModel.java
index 077b258f3dc..1876c4f48a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryTableModel.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/api/v1/dto/QueryTableModel.java
@@ -60,8 +60,7 @@ public class QueryTableModel implements Serializable
/**
* Adds a row of values.
*
- * @throws IllegalArgumentException if the number of values is not the same as the number of
- * columns.
+ * @throws IllegalArgumentException if the number of values is not the same as the number of columns.
*/
public void addRow(Serializable[] values)
{
@@ -99,8 +98,7 @@ public class QueryTableModel implements Serializable
}
/**
- * Jackson cannot deserialize things typed as Serializable because it has no idea what the
- * correct type might be.
+ * Jackson cannot deserialize things typed as Serializable because it has no idea what the correct type might be.
* <p>
* Thus we convert the values to strings and add type information.
*/
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/cache/SearchCacheTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/cache/SearchCacheTest.java
index fd64a8caffb..eeb7bd655b3 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/cache/SearchCacheTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/cache/SearchCacheTest.java
@@ -208,7 +208,7 @@ public class SearchCacheTest
final CacheManager manager = new CacheManager(new ByteArrayInputStream(managerConfig.getBytes()));
SearchCache cache = new SearchCache(
- new RuntimeCache<Serializable, Serializable>(manager, SearchCache.CACHE_NAME,
+ new RuntimeCache<Serializable, Serializable>(manager, SearchCache.CACHE_NAME,
SearchCache.CACHE_SIZE_PROPERTY_NAME)
{
@Override
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/method/AbstractSearchMethodExecutorTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/method/AbstractSearchMethodExecutorTest.java
index 7707b9be848..7945d0996f9 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/method/AbstractSearchMethodExecutorTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/method/AbstractSearchMethodExecutorTest.java
@@ -58,7 +58,7 @@ public class AbstractSearchMethodExecutorTest
private static final String SESSION_TOKEN2 = "sessionToken2";
private MessageChannel channel;
-
+
private MessageChannel channel2;
private TestSearchMethodExecutor executor;
@@ -240,7 +240,7 @@ public class AbstractSearchMethodExecutorTest
private Map<Thread, SearchCacheEntry<Object>> entries = new HashMap<>();
private IDelegatedAction getAction;
-
+
private IDelegatedAction putAction;
private SearchCacheEntry<Object> defaultEntry;
@@ -280,7 +280,7 @@ public class AbstractSearchMethodExecutorTest
}
@Override
- protected Collection doSearchAndTranslate(IOperationContext context, AbstractSearchCriteria criteria,
+ protected Collection doSearchAndTranslate(IOperationContext context, AbstractSearchCriteria criteria,
FetchOptions fetchOptions)
{
return Collections.emptySet();
@@ -300,7 +300,7 @@ public class AbstractSearchMethodExecutorTest
{
this.getAction = getAction;
}
-
+
void setPutAction(IDelegatedAction putAction)
{
this.putAction = putAction;
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/FullSampleIdentifierTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/FullSampleIdentifierTest.java
index 1706cce1642..c0b0fae72ef 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/FullSampleIdentifierTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/FullSampleIdentifierTest.java
@@ -24,8 +24,6 @@ import org.testng.annotations.Test;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample.FullSampleIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class FullSampleIdentifierTest
@@ -39,15 +37,15 @@ public class FullSampleIdentifierTest
assertSampId("/SPACE1/S2");
assertSampId("/SPACE1/S2:A02");
// TODO: project samples
-// assertSampId("/SPACE1/PROJECT1/S1");
-// assertSampId("/SPACE1/PROJECT1/S1:A02");
+ // assertSampId("/SPACE1/PROJECT1/S1");
+ // assertSampId("/SPACE1/PROJECT1/S1:A02");
assertSampIdWithHomeSpace("/HS/S1", "//s1", "HS");
assertSampIdWithHomeSpace("/HS/C1:S1", "//c1:s1", "HS");
-// assertSampIdWithHomeSpace("/HS/PROJECT1/S1", "//Project1/s1", "HS");
-// assertSampIdWithHomeSpace("/HS/PROJECT1/C1:S1", "//project1/c1:s1", "HS");
-// assertSampIdWithHomeSpace("/SP1/PROJECT1/C1:S1", "/sp1/project1/c1:s1", "HS");
+ // assertSampIdWithHomeSpace("/HS/PROJECT1/S1", "//Project1/s1", "HS");
+ // assertSampIdWithHomeSpace("/HS/PROJECT1/C1:S1", "//project1/c1:s1", "HS");
+ // assertSampIdWithHomeSpace("/SP1/PROJECT1/C1:S1", "/sp1/project1/c1:s1", "HS");
}
-
+
@Test
public void testFailingCases()
{
@@ -56,17 +54,17 @@ public class FullSampleIdentifierTest
assertInvalidSampId("Sample identifier has to start with a '/': A/BC", "A/BC");
assertInvalidSampId("Sample identifier can not contain more than three '/': /A/B/C/D", "/A/B/C/D");
assertInvalidSampId("Sample code can not contain more than one ':': /A/B:C:D", "/A/B:C:D");
-
+
assertInvalidSampId("Sample identifier don't contain any codes: ///", "///");
assertInvalidSampId("Sample identifier don't contain any codes: //", "//");
assertInvalidSampId("Sample identifier don't contain any codes: /", "/");
-
+
assertInvalidSampId("Space code can not be an empty string.", "//S1");
assertInvalidSampId("Project code can not be an empty string.", "/S//S1");
assertInvalidSampId("Sample code starts or ends with ':': /S/:S1", "/S/:S1");
assertInvalidSampId("Sample code starts or ends with ':': /S/C1:", "/S/C1:");
assertInvalidSampId("Sample code can not contain more than one ':': /S/C1:S1:", "/S/C1:S1:");
-
+
String prefix = " containing other characters than letters, numbers, '_', '-' and '.': ";
assertInvalidSampId("Sample code" + prefix + "S1&*", "/S1&*");
assertInvalidSampId("Space code" + prefix + "SPA&CE1", "/SPA&CE1/S2");
@@ -74,12 +72,12 @@ public class FullSampleIdentifierTest
assertInvalidSampId("Project code" + prefix + "PRO<>JECT1", "/SPACE1/PRO<>JECT1/S1");
assertInvalidSampId("Sample subcode" + prefix + "A0(2", "/SPACE1/PROJECT1/S1:A0(2");
}
-
+
private void assertInvalidSampId(String expectedErrorMsg, String identifier)
{
assertInvalidSampId(expectedErrorMsg, identifier, null);
}
-
+
private void assertInvalidSampId(String expectedErrorMsg, String identifier, String homeSpaceOrNull)
{
try
@@ -91,12 +89,12 @@ public class FullSampleIdentifierTest
assertEquals(expectedErrorMsg, ex.getMessage());
}
}
-
+
private void assertSampId(String identifier)
{
assertEquals(new FullSampleIdentifier(identifier, null).toString(), identifier);
}
-
+
private void assertSampIdWithHomeSpace(String expectedIdentifier, String identifier, String homeSpace)
{
assertEquals(new FullSampleIdentifier(identifier, homeSpace).toString(), expectedIdentifier);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractDataSetTest.java
index 82ee7a75e69..85878b3c574 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractDataSetTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractDataSetTest.java
@@ -12,14 +12,13 @@ import ch.systemsx.cisd.common.collection.SimpleComparator;
public class AbstractDataSetTest extends AbstractTest
{
protected static final SimpleComparator<DataSet, String> DATA_SET_COMPARATOR = new SimpleComparator<DataSet, String>()
+ {
+ @Override
+ public String evaluate(DataSet item)
{
- @Override
- public String evaluate(DataSet item)
- {
- return item.getCode();
- }
- };
-
+ return item.getCode();
+ }
+ };
protected static void assertIdentifiers(Collection<DataSet> dataSets, String... expectedCodesIdentifiers)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExperimentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExperimentTest.java
index 605d5c75d8a..54a5cc23eda 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExperimentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExperimentTest.java
@@ -258,7 +258,7 @@ public class CreateExperimentTest extends AbstractExperimentTest
public void testCreateWithSystemProperty()
{
final String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
+
NewETPTAssignment assignment = new NewETPTAssignment();
assignment.setPropertyTypeCode("$PLATE_GEOMETRY");
assignment.setEntityTypeCode("SIRNA_HCS");
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateMaterialTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateMaterialTest.java
index fbfc7abe00b..2248b25283f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateMaterialTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateMaterialTest.java
@@ -74,7 +74,7 @@ public class CreateMaterialTest extends AbstractSampleTest
public void testMaterialCreationWithSystemProperty()
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
-
+
NewETPTAssignment assignment = new NewETPTAssignment();
assignment.setPropertyTypeCode("$PLATE_GEOMETRY");
assignment.setEntityTypeCode("GENE");
@@ -95,7 +95,7 @@ public class CreateMaterialTest extends AbstractSampleTest
Material material = map.get(new MaterialPermId("1982", "GENE"));
assertEquals(material.getCode(), "1982");
assertEquals(material.getPermId().getTypeCode(), "GENE");
-
+
assertEquals(material.getProperty("$PLATE_GEOMETRY"), "384_WELLS_16X24");
}
@@ -109,7 +109,7 @@ public class CreateMaterialTest extends AbstractSampleTest
TagCode test123 = new TagCode("TEST_123");
TagCode testMetaprojects = new TagCode("TEST_METAPROJECTS");
m1.setTagIds(Arrays.asList(test123, testMetaprojects));
-
+
List<MaterialPermId> materialIds = v3api.createMaterials(sessionToken, Arrays.asList(m1));
MaterialFetchOptions fetchOptions = new MaterialFetchOptions();
@@ -236,6 +236,7 @@ public class CreateMaterialTest extends AbstractSampleTest
}
}, "Property type with code 'CODE_THAT_DOESNT_EXIST' does not exist");
}
+
private MaterialCreation materialCreation(MaterialPermId permId)
{
String code = permId.getCode();
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateSampleTest.java
index d74c97a9f5f..cf51c1d2d0f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateSampleTest.java
@@ -84,7 +84,7 @@ public class CreateSampleTest extends AbstractSampleTest
final String sessionToken = v3api.login(TEST_USER, PASSWORD);
final SampleCreation sample = sampleCreation("SAMPLE_WITH_USER_GIVEN_CODE");
sample.setAutoGeneratedCode(true);
-
+
assertUserFailureException(new IDelegatedAction()
{
@Override
@@ -103,12 +103,11 @@ public class CreateSampleTest extends AbstractSampleTest
sample1.setAutoGeneratedCode(true);
final SampleCreation sample2 = sampleCreation(null);
sample2.setAutoGeneratedCode(true);
-
+
List<SamplePermId> sampleWithAutogeneratedCode = v3api.createSamples(sessionToken, Arrays.asList(sample1, sample2));
AssertionUtil.assertCollectionSize(sampleWithAutogeneratedCode, 2);
}
-
@Test
public void testCreateWithCodeExisting()
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/EntityDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/EntityDeletionTest.java
index 6ff28dc476b..d52c6bd5057 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/EntityDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/EntityDeletionTest.java
@@ -33,7 +33,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.EntityNod
import ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph.SampleNode;
import ch.systemsx.cisd.openbis.systemtest.AbstractEntityDeletionTestCase;
-
/**
* Implementation of {@link AbstractEntityDeletionTestCase} based on V3 API.
*
@@ -44,7 +43,7 @@ public class EntityDeletionTest extends AbstractEntityDeletionTestCase
{
private static final String CONTEXT_DESCRIPTION = " (Context: [])";
-
+
@Autowired
protected IApplicationServerApi v3api;
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTest.java
index f92321d6a6f..401b9a9fff2 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetSampleTest.java
@@ -1065,23 +1065,23 @@ public class GetSampleTest extends AbstractSampleTest
assertSpaceNotFetched(sample);
v3api.logout(sessionToken);
}
-
+
@Test
public void testGetWithTypeAndPropertyAssignments()
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
SampleFetchOptions fetchOptions = new SampleFetchOptions();
fetchOptions.withType().withPropertyAssignments().sortBy().label().desc();
-
+
List<SamplePermId> sampleIds = Collections.singletonList(new SamplePermId("200811050917877-331"));
Map<ISampleId, Sample> map = v3api.getSamples(sessionToken, sampleIds, fetchOptions);
List<Sample> samples = new ArrayList<Sample>(map.values());
-
+
assertEquals(samples.size(), 1);
-
+
Sample sample = samples.get(0);
assertEquals(sample.getIdentifier().toString(), "/CISD/MP002-1");
-
+
SampleType type = sample.getType();
assertEquals(type.getCode(), "MASTER_PLATE");
assertEquals(type.getFetchOptions().hasPropertyAssignments(), true);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
index b891fb6468a..94db197b491 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/ProjectSampleTest.java
@@ -22,1165 +22,427 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.systemtest.base.BaseTest;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@TransactionConfiguration(transactionManager = "transaction-manager", defaultRollback = false)
@Test(groups = "project-samples")
public class ProjectSampleTest extends BaseTest
{
- /*
- private static final String SYSTEM_USER = "system";
- private static final SpacePermId HOME_SPACE_ID = new SpacePermId("DEFAULT");
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, ProjectSampleTest.class);
- private static final EntityTypePermId ENTITY_TYPE_UNKNOWN = new EntityTypePermId("UNKNOWN");
-
- @Autowired
- protected IApplicationServerApi v3api;
-
- private ISpaceId space1;
- private ISpaceId space2;
- private ProjectPermId project1inSpace1;
- private ProjectPermId project2inSpace1;
- private ProjectPermId project1inSpace2;
- private ProjectPermId project2inSpace2;
- private ProjectPermId project1inHomeSpace;
- private String adminSessionToken;
- private String adminUser;
- @BeforeClass
- public void createData()
- {
- List<SpacePermId> spaces = createSpaces(systemSessionToken, "SPACE1", "SPACE2");
- space1 = spaces.get(0);
- space2 = spaces.get(1);
- List<ProjectPermId> projects = createProjects(systemSessionToken, space1, "PROJECT1", "PROJECT2");
- project1inSpace1 = projects.get(0);
- project2inSpace1 = projects.get(1);
- project1inSpace2 = createProjects(systemSessionToken, space2, "PROJECT1").get(0);
- project2inSpace2 = createProjects(systemSessionToken, space2, "PROJECT2").get(0);
- project1inHomeSpace = createProjects(systemSessionToken, HOME_SPACE_ID, "PROJECT1").get(0);
- createSamples(systemSessionToken, null, null, null, "SHARED1", "SHARED2");
- createSamples(systemSessionToken, space1, null, null, "SAMPLE1", "SAMPLE2");
- createSamples(systemSessionToken, space1, project1inSpace1, null, "SAMPLE3", "SAMPLE4");
- createSamples(systemSessionToken, space2, project2inSpace2, null, "SAMPLE5", "SAMPLE6");
- waitAtLeastASecond(); // to allow checks on modification time stamps
- UpdateUtils.waitUntilIndexUpdaterIsIdle(applicationContext, operationLog);
- SessionBuilder session = aSession().withInstanceRole(RoleCode.ADMIN);
- adminUser = session.getUserID();
- adminSessionToken = create(session);
- commonServer.changeUserHomeSpace(adminSessionToken, new TechId(1)); // home space = DEFAULT
- }
-
- @Override
- @AfterTransaction
- @Test(enabled = false)
- public void cleanDatabase()
- {
- // super method deletes samples, experiments and data sets from the database
- }
-
- @Test
- public void testCreateASharedSampleWithASharedSampleAsComponent()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
-
- List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
-
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
- assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/" + sampleCode + ":A01");
- }
-
- @Test
- public void testCreateASharedSampleWithASpaceSampleAsComponent()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
-
- List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
-
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
- assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode + ":A01");
- }
-
- @Test
- public void testCreateASharedSampleWithAProjectSampleAsComponent()
- {
- String projectCode = createUniqueCode("P");
- createProjects(systemSessionToken, space1, projectCode);
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setProjectId(new ProjectIdentifier("SPACE1", projectCode));
- s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
-
- List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
-
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
- assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode + ":A01");
- }
-
- @Test
- public void testCreateASharedSampleWithAProjectExperimentSampleAsComponent()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String experimentCode = createUniqueCode("E");
- createExperiments(systemSessionToken, project, experimentCode);
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setProjectId(new ProjectIdentifier("SPACE1", projectCode));
- s2.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode));
- s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
-
- List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
-
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
- assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode + ":A01");
- }
-
- @Test
- public void testCreateASharedSampleWithAnExperimentSampleAsComponent()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String experimentCode = createUniqueCode("E");
- createExperiments(systemSessionToken, project, experimentCode);
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode));
- s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
-
- List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
-
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
- assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode + ":A01");
- }
-
- @Test
- public void testCreateSampleAndMapSamplesByPermId()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation sampleCreation = new SampleCreation();
- sampleCreation.setCode(sampleCode);
- sampleCreation.setTypeId(ENTITY_TYPE_UNKNOWN);
- sampleCreation.setSpaceId(space1);
- sampleCreation.setProjectId(project1inSpace1);
-
- List<SamplePermId> ids = v3api.createSamples(systemSessionToken, Arrays.asList(sampleCreation));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
- Sample sample = samples.get(ids.get(0));
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/" + sampleCode);
- assertEquals(sample.getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- }
-
- @Test
- public void testCreateThreeSamplesWithSameCodeInDifferentProjectOfSameSpaceAndMapSamplesByIdentifier()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- s1.setSpaceId(space1);
- s1.setProjectId(project1inSpace1);
- SampleCreation s2 = new SampleCreation();
- s2.setCode(sampleCode);
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setProjectId(project2inSpace1);
- SampleCreation s3 = new SampleCreation();
- s3.setCode(sampleCode);
- s3.setTypeId(ENTITY_TYPE_UNKNOWN);
- s3.setSpaceId(space1);
-
- v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2, s3));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
- List<ISampleId> ids = new ArrayList<>();
- ids.add(new SampleIdentifier("/SPACE1/PROJECT1/" + sampleCode));
- ids.add(new SampleIdentifier("/SPACE1/PROJECT2/" + sampleCode));
- ids.add(new SampleIdentifier("/SPACE1/" + sampleCode));
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
- assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT1");
- assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT2");
- assertEquals(samples.get(ids.get(2)).getProject(), null);
- }
-
- @Test
- public void testCreateProjectSampleWithAProjectSampleComponentFromAnotherSpace()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- s1.setSpaceId(space1);
- s1.setProjectId(project1inSpace1);
- SamplePermId s1PermId = v3api.createSamples(systemSessionToken, Arrays.asList(s1)).get(0);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space2);
- s2.setProjectId(project1inSpace2);
- s2.setContainerId(s1PermId);
-
- v3api.createSamples(systemSessionToken, Arrays.asList(s2));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
- fetchOptions.withContainer();
- List<ISampleId> ids = new ArrayList<>();
- ids.add(new SampleIdentifier("/SPACE1/PROJECT1/" + sampleCode));
- ids.add(new SampleIdentifier("/SPACE2/PROJECT1/" + sampleCode + ":A01"));
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
- assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT1");
- assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/SPACE2/PROJECT1");
- }
-
- @Test
- public void testCreateProjectSampleWithComponentInHomeSpace()
- {
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- s1.setSpaceId(HOME_SPACE_ID);
- s1.setProjectId(project1inHomeSpace);
- SamplePermId s1PermId = v3api.createSamples(systemSessionToken, Arrays.asList(s1)).get(0);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(HOME_SPACE_ID);
- s2.setProjectId(project1inHomeSpace);
- s2.setContainerId(s1PermId);
-
- v3api.createSamples(systemSessionToken, Arrays.asList(s2));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
- fetchOptions.withContainer();
- List<ISampleId> ids = new ArrayList<>();
- ids.add(new SampleIdentifier("//PROJECT1/" + sampleCode));
- ids.add(new SampleIdentifier("//PROJECT1/" + sampleCode + ":A01"));
- Map<ISampleId, Sample> samples = v3api.mapSamples(adminSessionToken, ids, fetchOptions);
- assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/DEFAULT/PROJECT1");
- assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/DEFAULT/PROJECT1");
- }
-
- @Test
- public void testAssignSpaceSampleToAProject()
- {
- String sampleCode = createUniqueCode("S");
- createSamples(systemSessionToken, space1, null, null, sampleCode);
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + sampleCode));
- sampleUpdate.setProjectId(project);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- SampleIdentifier newSampleIdentifier = new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode);
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(newSampleIdentifier), fetchOptions);
- Sample sample = samples.get(newSampleIdentifier);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
- Project sampleProject = sample.getProject();
- assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode);
- assertModification(sampleProject, sampleProject, now, adminUser);
- }
-
- @Test
- public void testAssignHomeSpaceSampleToAProjectInHomeSpace()
- {
- String sampleCode = createUniqueCode("S");
- createSamples(systemSessionToken, HOME_SPACE_ID, null, null, sampleCode);
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, HOME_SPACE_ID, projectCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(new SampleIdentifier("//" + sampleCode));
- sampleUpdate.setProjectId(project);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- SampleIdentifier newSampleIdentifier = new SampleIdentifier("//" + projectCode + "/" + sampleCode);
- Map<ISampleId, Sample> samples = v3api.mapSamples(adminSessionToken, Arrays.asList(newSampleIdentifier), fetchOptions);
- Sample sample = samples.get(newSampleIdentifier);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/DEFAULT/" + projectCode + "/" + sampleCode);
- Project sampleProject = sample.getProject();
- assertEquals(sampleProject.getIdentifier().getIdentifier(), "/DEFAULT/" + projectCode);
- assertModification(sampleProject, sampleProject, now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleToADifferentProjectInTheSameSpace()
- {
- String projectCode1 = createUniqueCode("P");
- ProjectPermId project1 = createProjects(systemSessionToken, space1, projectCode1).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId spaceSample = createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0);
- String projectCode2 = createUniqueCode("P");
- ProjectPermId project2 = createProjects(systemSessionToken, space1, projectCode2).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + projectCode1 + "/" + sampleCode));
- sampleUpdate.setProjectId(project2);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
- Sample sample = samples.get(spaceSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" + sampleCode);
- Project sampleProject = sample.getProject();
- assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2);
- assertModification(sampleProject, sampleProject, now, adminUser);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(project1), projectFetchOptions);
- assertModification(projects.get(project1), projects.get(project1), now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleWithComponentToAProjectInADifferentSpace()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project1 = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SampleCreation s1 = new SampleCreation();
- s1.setCode(sampleCode);
- s1.setTypeId(ENTITY_TYPE_UNKNOWN);
- s1.setSpaceId(space1);
- s1.setProjectId(project1);
- SampleCreation s2 = new SampleCreation();
- s2.setCode("A01");
- s2.setTypeId(ENTITY_TYPE_UNKNOWN);
- s2.setSpaceId(space1);
- s2.setProjectId(project1);
- s2.setContainerId(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode));
- v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
- ProjectPermId project2 = createProjects(systemSessionToken, space2, projectCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode));
- sampleUpdate.setSpaceId(space2);
- sampleUpdate.setProjectId(project2);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- SampleIdentifier containerID = new SampleIdentifier("/SPACE2/" + projectCode + "/" + sampleCode);
- SampleIdentifier componentID = new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode + ":A01");
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(containerID, componentID), fetchOptions);
- Sample sample = samples.get(containerID);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode + "/" + sampleCode);
- Project project = sample.getProject();
- assertEquals(project.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode);
- assertModification(project, project, now, adminUser);
- Sample component = samples.get(componentID);
- assertEquals(component.getModifier().getUserId(), SYSTEM_USER);
- assertEquals(component.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode + ":A01");
- Project componentProject = component.getProject();
- assertEquals(componentProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode);
- assertModification(componentProject, componentProject, now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleToAProjectInADifferentSpace()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project1 = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId spaceSample = createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0);
- ProjectPermId project2 = createProjects(systemSessionToken, space2, projectCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(spaceSample);
- sampleUpdate.setSpaceId(space2);
- sampleUpdate.setProjectId(project2);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions);
- Sample sample = samples.get(spaceSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode + "/" + sampleCode);
- Project project = sample.getProject();
- assertEquals(project.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode);
- assertModification(project, project, now, adminUser);
- }
-
- @Test
- public void testAssignExperimentWithProjectSamplesToADifferentProject()
- {
- String projectCode1 = createUniqueCode("P");
- String projectCode2 = projectCode1 + "A";
- createProjects(systemSessionToken, space1, projectCode1, projectCode2);
- String experimentCode = createUniqueCode("E");
- ProjectIdentifier project1 = new ProjectIdentifier("SPACE1", projectCode1);
- ExperimentPermId experiment = createExperiments(systemSessionToken, project1, experimentCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId sample = createSamples(systemSessionToken, space1, project1, experiment, sampleCode).get(0);
- ExperimentUpdate experimentUpdate = new ExperimentUpdate();
- experimentUpdate.setExperimentId(experiment);
- experimentUpdate.setProjectId(new ProjectIdentifier("SPACE1", projectCode2));
- Date now = sleep();
-
- v3api.updateExperiments(adminSessionToken, Arrays.asList(experimentUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Sample experimentSample = v3api.mapSamples(systemSessionToken, Arrays.asList(sample), fetchOptions).values().iterator().next();
- assertModification(experimentSample, experimentSample, now, adminUser);
- assertEquals(experimentSample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" + sampleCode);
- Project project = experimentSample.getProject();
- assertEquals(project.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2);
- assertModification(project, project, now, adminUser);
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
- experimentFetchOptions.withModifier();
- Experiment sampleExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
- experimentFetchOptions).values().iterator().next();
- assertModification(sampleExperiment, sampleExperiment, now, adminUser);
- }
-
- @Test
- public void testDeleteExperimentWithProjectSamples()
- {
- String projectCode = createUniqueCode("P");
- createProjects(systemSessionToken, space1, projectCode);
- String experimentCode = createUniqueCode("E");
- ProjectIdentifier project = new ProjectIdentifier("SPACE1", projectCode);
- ExperimentPermId experiment = createExperiments(systemSessionToken, project, experimentCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId sample = createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0);
- ExperimentDeletionOptions deletionOptions = new ExperimentDeletionOptions();
- deletionOptions.setReason("a test");
-
- v3api.deleteExperiments(adminSessionToken, Arrays.asList(experiment), deletionOptions);
-
- assertEquals(v3api.mapSamples(systemSessionToken, Arrays.asList(sample), new SampleFetchOptions()).size(), 0);
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
- experimentFetchOptions.withModifier();
- assertEquals(v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
- experimentFetchOptions).size(), 0);
- }
-
- @Test
- public void testUnassignProjectSampleFromProject()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project, null, sampleCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setProjectId(null);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode);
- assertEquals(sample.getProject(), null);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(project), projectFetchOptions);
- Project previousProject = projects.values().iterator().next();
- assertModification(previousProject, previousProject, now, adminUser);
- }
-
- @Test
- public void testUnassignProjectSampleFromProjectAndSpace()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project, null, sampleCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setProjectId(null);
- sampleUpdate.setSpaceId(null);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/" + sampleCode);
- assertEquals(sample.getProject(), null);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(project), projectFetchOptions);
- Project previousProject = projects.values().iterator().next();
- assertModification(previousProject, previousProject, now, adminUser);
- }
-
- @Test
- public void testUnassignProjectExperimentSampleFromExperiment()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String experimentCode = createUniqueCode("E");
- ExperimentPermId experiment = createExperiments(systemSessionToken, project, experimentCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setExperimentId(null);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
- Project sampleProject = sample.getProject();
- assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode);
- assertEquals(sampleProject.getModifier().getUserId(), SYSTEM_USER);
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
- experimentFetchOptions.withModifier();
- Experiment previousExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
- experimentFetchOptions).values().iterator().next();
- assertModification(previousExperiment, previousExperiment, now, adminUser);
- }
-
- @Test
- public void testUpdateProjectSample()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project, null, sampleCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
- assertEquals(sample.getProject().getIdentifier().getIdentifier(), "/SPACE1/" + projectCode);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
- Arrays.asList(project), projectFetchOptions);
- Project sampleProject = projects.values().iterator().next();
- assertEquals(sampleProject.getModifier().getUserId(), SYSTEM_USER);
- }
-
- @Test
- public void testAssignSpaceSampleToAnExperimentInTheSameSpace()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, null, null, sampleCode).get(0);
- String experimentCode = createUniqueCode("E");
- createExperiments(systemSessionToken, project, experimentCode);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode));
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- fetchOptions.withExperiment().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getProject(), null);
- Experiment experiment = sample.getExperiment();
- assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + experimentCode);
- assertModification(experiment, experiment, now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleToAnExperimentInTheSameProject()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project, null, sampleCode).get(0);
- String experimentCode = createUniqueCode("E");
- createExperiments(systemSessionToken, project, experimentCode);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode));
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- fetchOptions.withExperiment().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getProject().getModifier().getUserId(), SYSTEM_USER);
- Experiment experiment = sample.getExperiment();
- assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + experimentCode);
- assertModification(experiment, experiment, now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleWithExperimentToAnotherExperimentInTheSameProject()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String experimentCode1 = createUniqueCode("E");
- String experimentCode2 = experimentCode1 + "A";
- createExperiments(systemSessionToken, project, experimentCode1, experimentCode2);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project,
- new ExperimentIdentifier("SPACE1", projectCode, experimentCode1), sampleCode).get(0);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode2));
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- fetchOptions.withExperiment().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
- assertModification(sample, sample, now, adminUser);
- assertEquals(sample.getProject().getModifier().getUserId(), SYSTEM_USER);
- Experiment experiment = sample.getExperiment();
- assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + experimentCode2);
- assertModification(experiment, experiment, now, adminUser);
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
- experimentFetchOptions.withModifier();
- Experiment previousExperiment = v3api.mapExperiments(systemSessionToken,
- Arrays.asList(new ExperimentIdentifier("SPACE1", projectCode, experimentCode1)),
- experimentFetchOptions).values().iterator().next();
- assertModification(previousExperiment, previousExperiment, now, adminUser);
- }
-
- @Test
- public void testAssignProjectSampleToAnExperimentInADifferentProjectOfTheSameSpace()
- {
- String projectCode1 = createUniqueCode("P");
- ProjectPermId project1 = createProjects(systemSessionToken, space1, projectCode1).get(0);
- String sampleCode = createUniqueCode("S");
- SamplePermId projectSample = createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0);
- String experimentCode = createUniqueCode("E");
- String projectCode2 = createUniqueCode("P");
- ProjectPermId project2 = createProjects(systemSessionToken, space1, projectCode2).get(0);
- createExperiments(systemSessionToken, project2, experimentCode);
- SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(projectSample);
- sampleUpdate.setProjectId(new ProjectIdentifier("SPACE1", projectCode2));
- sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode2, experimentCode));
- Date now = sleep();
-
- v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
-
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withModifier();
- fetchOptions.withSpace();
- fetchOptions.withProject().withModifier();
- fetchOptions.withExperiment().withModifier();
- Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions);
- Sample sample = samples.get(projectSample);
- assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" + sampleCode);
- assertModification(sample, sample, now, adminUser);
- assertModification(sample.getProject(), sample.getProject(), now, adminUser);
- Experiment experiment = sample.getExperiment();
- assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" + experimentCode);
- assertModification(experiment, experiment, now, adminUser);
- }
-
- @Test
- public void testDeleteProjectSample()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- createSamples(systemSessionToken, space1, project, null, sampleCode);
- SampleDeletionOptions deletionOptions = new SampleDeletionOptions();
- deletionOptions.setReason("test");
- List<SampleIdentifier> sampleIds = Arrays.asList(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode));
- Date now = sleep();
-
- v3api.deleteSamples(adminSessionToken, sampleIds, deletionOptions);
-
- assertEquals(v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions()).size(), 0);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Project sampleProject = v3api.mapProjects(systemSessionToken, Arrays.asList(project),
- projectFetchOptions).values().iterator().next();
- assertModification(sampleProject, sampleProject, now, adminUser);
- }
-
- @Test
- public void testDeleteProjectExperimentSample()
- {
- String projectCode = createUniqueCode("P");
- ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0);
- String sampleCode = createUniqueCode("S");
- String experimentCode = createUniqueCode("E");
- ExperimentPermId experiment = createExperiments(systemSessionToken, project, experimentCode).get(0);
- SamplePermId sample = createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0);
- SampleDeletionOptions deletionOptions = new SampleDeletionOptions();
- deletionOptions.setReason("test");
- List<SamplePermId> sampleIds = Arrays.asList(sample);
- Date now = sleep();
-
- v3api.deleteSamples(adminSessionToken, sampleIds, deletionOptions);
-
- assertEquals(v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions()).size(), 0);
- ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
- projectFetchOptions.withModifier();
- Project sampleProject = v3api.mapProjects(systemSessionToken, Arrays.asList(project),
- projectFetchOptions).values().iterator().next();
- assertModification(sampleProject, sampleProject, now, adminUser);
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
- experimentFetchOptions.withModifier();
- Experiment sampleExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
- experimentFetchOptions).values().iterator().next();
- assertModification(sampleExperiment, sampleExperiment, now, adminUser);
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testCreateWithProjectAndSpaceInconsistent()
- {
- final SampleCreation creation = new SampleCreation();
- creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE");
- creation.setTypeId(ENTITY_TYPE_UNKNOWN);
- creation.setSpaceId(space1);
- creation.setProjectId(project1inSpace2);
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
- }
- }, "Sample space must be the same as project space. "
- + "Sample: /SPACE1/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE, "
- + "Project: /SPACE2/PROJECT1 "
- + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE])");
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testCreateWithProjectAndNoSpaceInconsistent()
- {
- final SampleCreation creation = new SampleCreation();
- creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE");
- creation.setTypeId(ENTITY_TYPE_UNKNOWN);
- creation.setProjectId(project1inSpace1);
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
- }
- }, "Shared samples cannot be attached to projects. "
- + "Sample: /SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE, "
- + "Project: /SPACE1/PROJECT1 "
- + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE])");
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testCreateWithProjectAndExperimentInconsistent()
- {
- final SampleCreation creation = new SampleCreation();
- creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT");
- creation.setTypeId(ENTITY_TYPE_UNKNOWN);
- creation.setSpaceId(space1);
- creation.setProjectId(project2inSpace1);
- String expCode = createUniqueCode("E");
- creation.setExperimentId(createExperiments(systemSessionToken, project1inSpace1, expCode).get(0));
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(systemSessionToken, Collections.singletonList(creation));
- }
- }, "Sample project must be the same as experiment project. "
- + "Sample: /SPACE1/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT, "
- + "Project: /SPACE1/PROJECT2, "
- + "Experiment: /SPACE1/PROJECT1/" + expCode + " "
- + "(Context: [verify experiment for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT])");
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testAssignSpaceSampleToProjectInDifferentSpace()
- {
- String code = createUniqueCode("S");
- ISampleId sampleId = createSamples(systemSessionToken, space1, null, null, code).get(0);
- final SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(sampleId);
- sampleUpdate.setProjectId(project2inSpace2);
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate));
- }
- }, "Sample space must be the same as project space. "
- + "Sample: /SPACE1/" + code + ", "
- + "Project: /SPACE2/PROJECT2 "
- + "(Context: [verify project for sample " + code + "])");
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testAssignSampleOfAnExperimentToProjectDifferentToTheExperimentProject()
- {
- String sampleCode = createUniqueCode("S");
- String expCode = createUniqueCode("E");
- IExperimentId experiment = createExperiments(systemSessionToken, project1inSpace1, expCode).get(0);
- SamplePermId sample = createSamples(systemSessionToken, space1, null, experiment, sampleCode).get(0);
- final SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(sample);
- sampleUpdate.setProjectId(project2inSpace1);
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate));
- }
- }, "Sample project must be the same as experiment project. "
- + "Sample: /SPACE1/" + sampleCode + ", "
- + "Project: /SPACE1/PROJECT2, "
- + "Experiment: /SPACE1/PROJECT1/" + expCode + " "
- + "(Context: [verify experiment for sample " + sampleCode + "])");
-
- }
-
- @Test
- @Transactional(propagation = Propagation.NEVER)
- public void testAssignSharedSampleToProject()
- {
- String code = createUniqueCode("S");
- ISampleId sharedSample = createSamples(systemSessionToken, null, null, null, code).get(0);
- final SampleUpdate sampleUpdate = new SampleUpdate();
- sampleUpdate.setSampleId(sharedSample);
- sampleUpdate.setProjectId(project1inSpace1);
-
- assertUserFailureException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate));
- }
- }, "Shared samples cannot be attached to projects. "
- + "Sample: /" + code + ", "
- + "Project: /SPACE1/PROJECT1 "
- + "(Context: [verify project for sample " + code + "])");
- }
-
- @Test(priority = -1)
- public void testSearchForSamplesWithProject() throws InterruptedException
- {
-
- SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
- searchCriteria.withProject();
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
-
- SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
-
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
- assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE4");
- assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- assertEquals(result.getObjects().get(2).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE5");
- assertEquals(result.getObjects().get(2).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
- assertEquals(result.getObjects().get(3).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE6");
- assertEquals(result.getObjects().get(3).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
- assertEquals(result.getTotalCount(), 4);
- }
-
- @Test(priority = -1)
- public void testSearchForSamplesWithCodeAndWithProject()
- {
- SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
- searchCriteria.withCode().thatEndsWith("3");
- searchCriteria.withProject();
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
-
- SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
-
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
- assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- assertEquals(result.getTotalCount(), 1);
- }
-
- @Test(priority = -1)
- public void testSearchForSamplesWithProjectWithSpaceWithCode()
- {
- SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
- searchCriteria.withProject().withSpace().withCode().thatEquals("SPACE1");
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
-
- SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
-
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
- assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE4");
- assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
- assertEquals(result.getTotalCount(), 2);
- }
-
- @Test(priority = -1)
- public void testSearchForSamplesWithProjectWithPermId()
- {
- SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
- searchCriteria.withProject().withPermId().thatEquals(project2inSpace2.getPermId());
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
-
- SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
-
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE5");
- assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
- assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE6");
- assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
- assertEquals(result.getTotalCount(), 2);
- }
-
- @Test(priority = -1)
- public void testSearchForSamplesWithoutProjects()
- {
- SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
- searchCriteria.withCode().thatStartsWith("SAMP");
- searchCriteria.withoutProject();
- SampleFetchOptions fetchOptions = new SampleFetchOptions();
- fetchOptions.withProject();
-
- SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
-
- assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/SAMPLE1");
- assertEquals(result.getObjects().get(0).getProject(), null);
- assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE1/SAMPLE2");
- assertEquals(result.getObjects().get(1).getProject(), null);
- assertEquals(result.getTotalCount(), 2);
- }
-
- private void assertUserFailureException(IDelegatedAction action, String expectedExceptionMessage)
- {
- try
- {
- action.execute();
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals(ex.getMessage(), expectedExceptionMessage);
- }
- }
-
- private void assertModification(IModificationDateHolder modificationDateHolder, IModifierHolder modifierHolder,
- Date date, String modifier)
- {
- assertNotOlder(modificationDateHolder.getModificationDate(), date);
- assertEquals(modifierHolder.getModifier().getUserId(), modifier);
- }
-
- private void assertNotOlder(Date actualDate, Date referenceDate)
- {
- SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
- String renderedReferenceDate = format.format(referenceDate.getTime());
- String renderedActualDate = format.format(actualDate);
- assertEquals(renderedReferenceDate.compareTo(renderedActualDate) <= 0, true,
- renderedActualDate + " > " + renderedReferenceDate);
- }
-
- private Date sleep()
- {
- Date now = daoFactory.getTransactionTimestamp();
- return now;
- }
-
- private List<SpacePermId> createSpaces(String sessionToken, String...spaceCodes)
- {
- List<SpaceCreation> newSpaces = new ArrayList<SpaceCreation>();
- for (String spaceCode : spaceCodes)
- {
- SpaceCreation space = new SpaceCreation();
- space.setCode(spaceCode);
- newSpaces.add(space);
- }
- return v3api.createSpaces(sessionToken, newSpaces);
- }
-
- private List<ProjectPermId> createProjects(String sessionToken, ISpaceId spaceId, String...projectCodes)
- {
- List<ProjectCreation> newProjects = new ArrayList<ProjectCreation>();
- for (String projectCode : projectCodes)
- {
- ProjectCreation project = new ProjectCreation();
- project.setSpaceId(spaceId);
- project.setCode(projectCode);
- newProjects.add(project);
- }
- return v3api.createProjects(sessionToken, newProjects);
- }
-
- private List<SamplePermId> createSamples(String sessionToken, ISpaceId spaceOrNull,
- IProjectId projectOrNull, IExperimentId experimentOrNull, String...codes)
- {
- List<SampleCreation> newSamples = new ArrayList<SampleCreation>();
- for (String code : codes)
- {
- SampleCreation sample = new SampleCreation();
- sample.setTypeId(ENTITY_TYPE_UNKNOWN);
- sample.setSpaceId(spaceOrNull);
- sample.setProjectId(projectOrNull);
- sample.setExperimentId(experimentOrNull);
- sample.setCode(code);
- newSamples.add(sample);
- }
- return v3api.createSamples(sessionToken, newSamples);
- }
-
- private List<ExperimentPermId> createExperiments(String sessionToken, IProjectId project, String...codes)
- {
- List<ExperimentCreation> newExperiments = new ArrayList<ExperimentCreation>();
- for (String code : codes)
- {
- ExperimentCreation experiment = new ExperimentCreation();
- experiment.setCode(code);
- experiment.setTypeId(ENTITY_TYPE_UNKNOWN);
- experiment.setProjectId(project);
- newExperiments.add(experiment);
- }
- return v3api.createExperiments(sessionToken, newExperiments);
- }
-
- private String createUniqueCode(String prefix)
- {
- return prefix + "-" + System.currentTimeMillis();
- }
-
- private void waitAtLeastASecond()
- {
- try
- {
- Thread.sleep(1100);
- } catch (InterruptedException ex)
- {
- // silently ignored
- }
- }
-*/
+ /*
+ * private static final String SYSTEM_USER = "system"; private static final SpacePermId HOME_SPACE_ID = new SpacePermId("DEFAULT"); private static
+ * final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, ProjectSampleTest.class); private static final EntityTypePermId
+ * ENTITY_TYPE_UNKNOWN = new EntityTypePermId("UNKNOWN");
+ * @Autowired protected IApplicationServerApi v3api; private ISpaceId space1; private ISpaceId space2; private ProjectPermId project1inSpace1;
+ * private ProjectPermId project2inSpace1; private ProjectPermId project1inSpace2; private ProjectPermId project2inSpace2; private ProjectPermId
+ * project1inHomeSpace; private String adminSessionToken; private String adminUser;
+ * @BeforeClass public void createData() { List<SpacePermId> spaces = createSpaces(systemSessionToken, "SPACE1", "SPACE2"); space1 =
+ * spaces.get(0); space2 = spaces.get(1); List<ProjectPermId> projects = createProjects(systemSessionToken, space1, "PROJECT1", "PROJECT2");
+ * project1inSpace1 = projects.get(0); project2inSpace1 = projects.get(1); project1inSpace2 = createProjects(systemSessionToken, space2,
+ * "PROJECT1").get(0); project2inSpace2 = createProjects(systemSessionToken, space2, "PROJECT2").get(0); project1inHomeSpace =
+ * createProjects(systemSessionToken, HOME_SPACE_ID, "PROJECT1").get(0); createSamples(systemSessionToken, null, null, null, "SHARED1",
+ * "SHARED2"); createSamples(systemSessionToken, space1, null, null, "SAMPLE1", "SAMPLE2"); createSamples(systemSessionToken, space1,
+ * project1inSpace1, null, "SAMPLE3", "SAMPLE4"); createSamples(systemSessionToken, space2, project2inSpace2, null, "SAMPLE5", "SAMPLE6");
+ * waitAtLeastASecond(); // to allow checks on modification time stamps UpdateUtils.waitUntilIndexUpdaterIsIdle(applicationContext, operationLog);
+ * SessionBuilder session = aSession().withInstanceRole(RoleCode.ADMIN); adminUser = session.getUserID(); adminSessionToken = create(session);
+ * commonServer.changeUserHomeSpace(adminSessionToken, new TechId(1)); // home space = DEFAULT }
+ * @Override
+ * @AfterTransaction
+ * @Test(enabled = false) public void cleanDatabase() { // super method deletes samples, experiments and data sets from the database }
+ * @Test public void testCreateASharedSampleWithASharedSampleAsComponent() { String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); SampleCreation s2 = new SampleCreation(); s2.setCode("A01");
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setContainerId(new SampleIdentifier(null, null, sampleCode)); List<SamplePermId> sampleIds =
+ * v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2)); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
+ * sampleIds, new SampleFetchOptions()); assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/" + sampleCode + ":A01"); }
+ * @Test public void testCreateASharedSampleWithASpaceSampleAsComponent() { String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); SampleCreation s2 = new SampleCreation(); s2.setCode("A01");
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setContainerId(new SampleIdentifier(null, null, sampleCode)); List<SamplePermId>
+ * sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2)); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
+ * assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode + ":A01"); }
+ * @Test public void testCreateASharedSampleWithAProjectSampleAsComponent() { String projectCode = createUniqueCode("P");
+ * createProjects(systemSessionToken, space1, projectCode); String sampleCode = createUniqueCode("S"); SampleCreation s1 = new SampleCreation();
+ * s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); SampleCreation s2 = new SampleCreation(); s2.setCode("A01");
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setProjectId(new ProjectIdentifier("SPACE1", projectCode)); s2.setContainerId(new
+ * SampleIdentifier(null, null, sampleCode)); List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2));
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
+ * assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode + ":A01"); }
+ * @Test public void testCreateASharedSampleWithAProjectExperimentSampleAsComponent() { String projectCode = createUniqueCode("P"); ProjectPermId
+ * project = createProjects(systemSessionToken, space1, projectCode).get(0); String experimentCode = createUniqueCode("E");
+ * createExperiments(systemSessionToken, project, experimentCode); String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); SampleCreation s2 = new SampleCreation(); s2.setCode("A01");
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setProjectId(new ProjectIdentifier("SPACE1", projectCode)); s2.setExperimentId(new
+ * ExperimentIdentifier("SPACE1", projectCode, experimentCode)); s2.setContainerId(new SampleIdentifier(null, null, sampleCode));
+ * List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2)); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
+ * assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode + ":A01"); }
+ * @Test public void testCreateASharedSampleWithAnExperimentSampleAsComponent() { String projectCode = createUniqueCode("P"); ProjectPermId
+ * project = createProjects(systemSessionToken, space1, projectCode).get(0); String experimentCode = createUniqueCode("E");
+ * createExperiments(systemSessionToken, project, experimentCode); String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); SampleCreation s2 = new SampleCreation(); s2.setCode("A01");
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode));
+ * s2.setContainerId(new SampleIdentifier(null, null, sampleCode)); List<SamplePermId> sampleIds = v3api.createSamples(systemSessionToken,
+ * Arrays.asList(s1, s2)); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, sampleIds, new SampleFetchOptions());
+ * assertEquals(samples.get(sampleIds.get(0)).getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(samples.get(sampleIds.get(1)).getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode + ":A01"); }
+ * @Test public void testCreateSampleAndMapSamplesByPermId() { String sampleCode = createUniqueCode("S"); SampleCreation sampleCreation = new
+ * SampleCreation(); sampleCreation.setCode(sampleCode); sampleCreation.setTypeId(ENTITY_TYPE_UNKNOWN); sampleCreation.setSpaceId(space1);
+ * sampleCreation.setProjectId(project1inSpace1); List<SamplePermId> ids = v3api.createSamples(systemSessionToken, Arrays.asList(sampleCreation));
+ * SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withProject(); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, ids, fetchOptions); Sample sample = samples.get(ids.get(0));
+ * assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/" + sampleCode);
+ * assertEquals(sample.getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1"); }
+ * @Test public void testCreateThreeSamplesWithSameCodeInDifferentProjectOfSameSpaceAndMapSamplesByIdentifier() { String sampleCode =
+ * createUniqueCode("S"); SampleCreation s1 = new SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN);
+ * s1.setSpaceId(space1); s1.setProjectId(project1inSpace1); SampleCreation s2 = new SampleCreation(); s2.setCode(sampleCode);
+ * s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setProjectId(project2inSpace1); SampleCreation s3 = new SampleCreation();
+ * s3.setCode(sampleCode); s3.setTypeId(ENTITY_TYPE_UNKNOWN); s3.setSpaceId(space1); v3api.createSamples(systemSessionToken, Arrays.asList(s1, s2,
+ * s3)); SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withProject(); List<ISampleId> ids = new ArrayList<>();
+ * ids.add(new SampleIdentifier("/SPACE1/PROJECT1/" + sampleCode)); ids.add(new SampleIdentifier("/SPACE1/PROJECT2/" + sampleCode)); ids.add(new
+ * SampleIdentifier("/SPACE1/" + sampleCode)); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
+ * assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT1");
+ * assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT2");
+ * assertEquals(samples.get(ids.get(2)).getProject(), null); }
+ * @Test public void testCreateProjectSampleWithAProjectSampleComponentFromAnotherSpace() { String sampleCode = createUniqueCode("S");
+ * SampleCreation s1 = new SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); s1.setSpaceId(space1);
+ * s1.setProjectId(project1inSpace1); SamplePermId s1PermId = v3api.createSamples(systemSessionToken, Arrays.asList(s1)).get(0); SampleCreation s2
+ * = new SampleCreation(); s2.setCode("A01"); s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space2); s2.setProjectId(project1inSpace2);
+ * s2.setContainerId(s1PermId); v3api.createSamples(systemSessionToken, Arrays.asList(s2)); SampleFetchOptions fetchOptions = new
+ * SampleFetchOptions(); fetchOptions.withProject(); fetchOptions.withContainer(); List<ISampleId> ids = new ArrayList<>(); ids.add(new
+ * SampleIdentifier("/SPACE1/PROJECT1/" + sampleCode)); ids.add(new SampleIdentifier("/SPACE2/PROJECT1/" + sampleCode + ":A01")); Map<ISampleId,
+ * Sample> samples = v3api.mapSamples(systemSessionToken, ids, fetchOptions);
+ * assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/SPACE1/PROJECT1");
+ * assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/SPACE2/PROJECT1"); }
+ * @Test public void testCreateProjectSampleWithComponentInHomeSpace() { String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); s1.setSpaceId(HOME_SPACE_ID);
+ * s1.setProjectId(project1inHomeSpace); SamplePermId s1PermId = v3api.createSamples(systemSessionToken, Arrays.asList(s1)).get(0); SampleCreation
+ * s2 = new SampleCreation(); s2.setCode("A01"); s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(HOME_SPACE_ID);
+ * s2.setProjectId(project1inHomeSpace); s2.setContainerId(s1PermId); v3api.createSamples(systemSessionToken, Arrays.asList(s2));
+ * SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withProject(); fetchOptions.withContainer(); List<ISampleId> ids = new
+ * ArrayList<>(); ids.add(new SampleIdentifier("//PROJECT1/" + sampleCode)); ids.add(new SampleIdentifier("//PROJECT1/" + sampleCode + ":A01"));
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(adminSessionToken, ids, fetchOptions);
+ * assertEquals(samples.get(ids.get(0)).getProject().getIdentifier().toString(), "/DEFAULT/PROJECT1");
+ * assertEquals(samples.get(ids.get(1)).getProject().getIdentifier().toString(), "/DEFAULT/PROJECT1"); }
+ * @Test public void testAssignSpaceSampleToAProject() { String sampleCode = createUniqueCode("S"); createSamples(systemSessionToken, space1,
+ * null, null, sampleCode); String projectCode = createUniqueCode("P"); ProjectPermId project = createProjects(systemSessionToken, space1,
+ * projectCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate(); sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + sampleCode));
+ * sampleUpdate.setProjectId(project); Date now = sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions
+ * fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier();
+ * SampleIdentifier newSampleIdentifier = new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, Arrays.asList(newSampleIdentifier), fetchOptions); Sample sample = samples.get(newSampleIdentifier);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" +
+ * sampleCode); Project sampleProject = sample.getProject(); assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" +
+ * projectCode); assertModification(sampleProject, sampleProject, now, adminUser); }
+ * @Test public void testAssignHomeSpaceSampleToAProjectInHomeSpace() { String sampleCode = createUniqueCode("S");
+ * createSamples(systemSessionToken, HOME_SPACE_ID, null, null, sampleCode); String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, HOME_SPACE_ID, projectCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(new SampleIdentifier("//" + sampleCode)); sampleUpdate.setProjectId(project); Date now = sleep();
+ * v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); SampleIdentifier newSampleIdentifier = new
+ * SampleIdentifier("//" + projectCode + "/" + sampleCode); Map<ISampleId, Sample> samples = v3api.mapSamples(adminSessionToken,
+ * Arrays.asList(newSampleIdentifier), fetchOptions); Sample sample = samples.get(newSampleIdentifier); assertModification(sample, sample, now,
+ * adminUser); assertEquals(sample.getIdentifier().getIdentifier(), "/DEFAULT/" + projectCode + "/" + sampleCode); Project sampleProject =
+ * sample.getProject(); assertEquals(sampleProject.getIdentifier().getIdentifier(), "/DEFAULT/" + projectCode); assertModification(sampleProject,
+ * sampleProject, now, adminUser); }
+ * @Test public void testAssignProjectSampleToADifferentProjectInTheSameSpace() { String projectCode1 = createUniqueCode("P"); ProjectPermId
+ * project1 = createProjects(systemSessionToken, space1, projectCode1).get(0); String sampleCode = createUniqueCode("S"); SamplePermId spaceSample
+ * = createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0); String projectCode2 = createUniqueCode("P"); ProjectPermId
+ * project2 = createProjects(systemSessionToken, space1, projectCode2).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + projectCode1 + "/" + sampleCode)); sampleUpdate.setProjectId(project2); Date now =
+ * sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, Arrays.asList(spaceSample), fetchOptions); Sample sample = samples.get(spaceSample);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" +
+ * sampleCode); Project sampleProject = sample.getProject(); assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" +
+ * projectCode2); assertModification(sampleProject, sampleProject, now, adminUser); ProjectFetchOptions projectFetchOptions = new
+ * ProjectFetchOptions(); projectFetchOptions.withModifier(); Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
+ * Arrays.asList(project1), projectFetchOptions); assertModification(projects.get(project1), projects.get(project1), now, adminUser); }
+ * @Test public void testAssignProjectSampleWithComponentToAProjectInADifferentSpace() { String projectCode = createUniqueCode("P"); ProjectPermId
+ * project1 = createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SampleCreation s1 = new
+ * SampleCreation(); s1.setCode(sampleCode); s1.setTypeId(ENTITY_TYPE_UNKNOWN); s1.setSpaceId(space1); s1.setProjectId(project1); SampleCreation
+ * s2 = new SampleCreation(); s2.setCode("A01"); s2.setTypeId(ENTITY_TYPE_UNKNOWN); s2.setSpaceId(space1); s2.setProjectId(project1);
+ * s2.setContainerId(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode)); v3api.createSamples(systemSessionToken, Arrays.asList(s1,
+ * s2)); ProjectPermId project2 = createProjects(systemSessionToken, space2, projectCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode)); sampleUpdate.setSpaceId(space2);
+ * sampleUpdate.setProjectId(project2); Date now = sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
+ * SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier(); fetchOptions.withSpace();
+ * fetchOptions.withProject().withModifier(); SampleIdentifier containerID = new SampleIdentifier("/SPACE2/" + projectCode + "/" + sampleCode);
+ * SampleIdentifier componentID = new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode + ":A01"); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, Arrays.asList(containerID, componentID), fetchOptions); Sample sample = samples.get(containerID);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode + "/" +
+ * sampleCode); Project project = sample.getProject(); assertEquals(project.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode);
+ * assertModification(project, project, now, adminUser); Sample component = samples.get(componentID);
+ * assertEquals(component.getModifier().getUserId(), SYSTEM_USER); assertEquals(component.getIdentifier().getIdentifier(), "/SPACE1/" +
+ * projectCode + "/" + sampleCode + ":A01"); Project componentProject = component.getProject();
+ * assertEquals(componentProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode); assertModification(componentProject,
+ * componentProject, now, adminUser); }
+ * @Test public void testAssignProjectSampleToAProjectInADifferentSpace() { String projectCode = createUniqueCode("P"); ProjectPermId project1 =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId spaceSample =
+ * createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0); ProjectPermId project2 = createProjects(systemSessionToken,
+ * space2, projectCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate(); sampleUpdate.setSampleId(spaceSample);
+ * sampleUpdate.setSpaceId(space2); sampleUpdate.setProjectId(project2); Date now = sleep(); v3api.updateSamples(adminSessionToken,
+ * Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier();
+ * fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
+ * Arrays.asList(spaceSample), fetchOptions); Sample sample = samples.get(spaceSample); assertModification(sample, sample, now, adminUser);
+ * assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode + "/" + sampleCode); Project project = sample.getProject();
+ * assertEquals(project.getIdentifier().getIdentifier(), "/SPACE2/" + projectCode); assertModification(project, project, now, adminUser); }
+ * @Test public void testAssignExperimentWithProjectSamplesToADifferentProject() { String projectCode1 = createUniqueCode("P"); String
+ * projectCode2 = projectCode1 + "A"; createProjects(systemSessionToken, space1, projectCode1, projectCode2); String experimentCode =
+ * createUniqueCode("E"); ProjectIdentifier project1 = new ProjectIdentifier("SPACE1", projectCode1); ExperimentPermId experiment =
+ * createExperiments(systemSessionToken, project1, experimentCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId sample =
+ * createSamples(systemSessionToken, space1, project1, experiment, sampleCode).get(0); ExperimentUpdate experimentUpdate = new ExperimentUpdate();
+ * experimentUpdate.setExperimentId(experiment); experimentUpdate.setProjectId(new ProjectIdentifier("SPACE1", projectCode2)); Date now = sleep();
+ * v3api.updateExperiments(adminSessionToken, Arrays.asList(experimentUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Sample experimentSample =
+ * v3api.mapSamples(systemSessionToken, Arrays.asList(sample), fetchOptions).values().iterator().next(); assertModification(experimentSample,
+ * experimentSample, now, adminUser); assertEquals(experimentSample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" +
+ * sampleCode); Project project = experimentSample.getProject(); assertEquals(project.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2);
+ * assertModification(project, project, now, adminUser); ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
+ * experimentFetchOptions.withModifier(); Experiment sampleExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
+ * experimentFetchOptions).values().iterator().next(); assertModification(sampleExperiment, sampleExperiment, now, adminUser); }
+ * @Test public void testDeleteExperimentWithProjectSamples() { String projectCode = createUniqueCode("P"); createProjects(systemSessionToken,
+ * space1, projectCode); String experimentCode = createUniqueCode("E"); ProjectIdentifier project = new ProjectIdentifier("SPACE1", projectCode);
+ * ExperimentPermId experiment = createExperiments(systemSessionToken, project, experimentCode).get(0); String sampleCode = createUniqueCode("S");
+ * SamplePermId sample = createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0); ExperimentDeletionOptions
+ * deletionOptions = new ExperimentDeletionOptions(); deletionOptions.setReason("a test"); v3api.deleteExperiments(adminSessionToken,
+ * Arrays.asList(experiment), deletionOptions); assertEquals(v3api.mapSamples(systemSessionToken, Arrays.asList(sample), new
+ * SampleFetchOptions()).size(), 0); ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
+ * experimentFetchOptions.withModifier(); assertEquals(v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
+ * experimentFetchOptions).size(), 0); }
+ * @Test public void testUnassignProjectSampleFromProject() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, project, null, sampleCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setProjectId(null); Date now = sleep(); v3api.updateSamples(adminSessionToken,
+ * Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier();
+ * fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
+ * Arrays.asList(projectSample), fetchOptions); Sample sample = samples.get(projectSample); assertModification(sample, sample, now, adminUser);
+ * assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode); assertEquals(sample.getProject(), null); ProjectFetchOptions
+ * projectFetchOptions = new ProjectFetchOptions(); projectFetchOptions.withModifier(); Map<IProjectId, Project> projects =
+ * v3api.mapProjects(systemSessionToken, Arrays.asList(project), projectFetchOptions); Project previousProject =
+ * projects.values().iterator().next(); assertModification(previousProject, previousProject, now, adminUser); }
+ * @Test public void testUnassignProjectSampleFromProjectAndSpace() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, project, null, sampleCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setProjectId(null); sampleUpdate.setSpaceId(null); Date now = sleep();
+ * v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples =
+ * v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions); Sample sample = samples.get(projectSample);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getIdentifier().getIdentifier(), "/" + sampleCode);
+ * assertEquals(sample.getProject(), null); ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions();
+ * projectFetchOptions.withModifier(); Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken, Arrays.asList(project),
+ * projectFetchOptions); Project previousProject = projects.values().iterator().next(); assertModification(previousProject, previousProject, now,
+ * adminUser); }
+ * @Test public void testUnassignProjectExperimentSampleFromExperiment() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String experimentCode = createUniqueCode("E"); ExperimentPermId experiment =
+ * createExperiments(systemSessionToken, project, experimentCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setExperimentId(null); Date now = sleep(); v3api.updateSamples(adminSessionToken,
+ * Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier();
+ * fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken,
+ * Arrays.asList(projectSample), fetchOptions); Sample sample = samples.get(projectSample); assertModification(sample, sample, now, adminUser);
+ * assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode); Project sampleProject = sample.getProject();
+ * assertEquals(sampleProject.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode); assertEquals(sampleProject.getModifier().getUserId(),
+ * SYSTEM_USER); ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions(); experimentFetchOptions.withModifier(); Experiment
+ * previousExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment), experimentFetchOptions).values().iterator().next();
+ * assertModification(previousExperiment, previousExperiment, now, adminUser); }
+ * @Test public void testUpdateProjectSample() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, project, null, sampleCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); Date now = sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate));
+ * SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withModifier(); fetchOptions.withSpace();
+ * fetchOptions.withProject().withModifier(); Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample),
+ * fetchOptions); Sample sample = samples.get(projectSample); assertModification(sample, sample, now, adminUser);
+ * assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
+ * assertEquals(sample.getProject().getIdentifier().getIdentifier(), "/SPACE1/" + projectCode); ProjectFetchOptions projectFetchOptions = new
+ * ProjectFetchOptions(); projectFetchOptions.withModifier(); Map<IProjectId, Project> projects = v3api.mapProjects(systemSessionToken,
+ * Arrays.asList(project), projectFetchOptions); Project sampleProject = projects.values().iterator().next();
+ * assertEquals(sampleProject.getModifier().getUserId(), SYSTEM_USER); }
+ * @Test public void testAssignSpaceSampleToAnExperimentInTheSameSpace() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, null, null, sampleCode).get(0); String experimentCode = createUniqueCode("E");
+ * createExperiments(systemSessionToken, project, experimentCode); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode)); Date
+ * now = sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); fetchOptions.withExperiment().withModifier();
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions); Sample sample =
+ * samples.get(projectSample); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + sampleCode); assertModification(sample, sample,
+ * now, adminUser); assertEquals(sample.getProject(), null); Experiment experiment = sample.getExperiment();
+ * assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + experimentCode); assertModification(experiment,
+ * experiment, now, adminUser); }
+ * @Test public void testAssignProjectSampleToAnExperimentInTheSameProject() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); SamplePermId projectSample =
+ * createSamples(systemSessionToken, space1, project, null, sampleCode).get(0); String experimentCode = createUniqueCode("E");
+ * createExperiments(systemSessionToken, project, experimentCode); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode)); Date
+ * now = sleep(); v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); fetchOptions.withExperiment().withModifier();
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions); Sample sample =
+ * samples.get(projectSample); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getProject().getModifier().getUserId(), SYSTEM_USER); Experiment
+ * experiment = sample.getExperiment(); assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + experimentCode);
+ * assertModification(experiment, experiment, now, adminUser); }
+ * @Test public void testAssignProjectSampleWithExperimentToAnotherExperimentInTheSameProject() { String projectCode = createUniqueCode("P");
+ * ProjectPermId project = createProjects(systemSessionToken, space1, projectCode).get(0); String experimentCode1 = createUniqueCode("E"); String
+ * experimentCode2 = experimentCode1 + "A"; createExperiments(systemSessionToken, project, experimentCode1, experimentCode2); String sampleCode =
+ * createUniqueCode("S"); SamplePermId projectSample = createSamples(systemSessionToken, space1, project, new ExperimentIdentifier("SPACE1",
+ * projectCode, experimentCode1), sampleCode).get(0); SampleUpdate sampleUpdate = new SampleUpdate(); sampleUpdate.setSampleId(projectSample);
+ * sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode, experimentCode2)); Date now = sleep();
+ * v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); fetchOptions.withExperiment().withModifier();
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions); Sample sample =
+ * samples.get(projectSample); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" + sampleCode);
+ * assertModification(sample, sample, now, adminUser); assertEquals(sample.getProject().getModifier().getUserId(), SYSTEM_USER); Experiment
+ * experiment = sample.getExperiment(); assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode + "/" +
+ * experimentCode2); assertModification(experiment, experiment, now, adminUser); ExperimentFetchOptions experimentFetchOptions = new
+ * ExperimentFetchOptions(); experimentFetchOptions.withModifier(); Experiment previousExperiment = v3api.mapExperiments(systemSessionToken,
+ * Arrays.asList(new ExperimentIdentifier("SPACE1", projectCode, experimentCode1)), experimentFetchOptions).values().iterator().next();
+ * assertModification(previousExperiment, previousExperiment, now, adminUser); }
+ * @Test public void testAssignProjectSampleToAnExperimentInADifferentProjectOfTheSameSpace() { String projectCode1 = createUniqueCode("P");
+ * ProjectPermId project1 = createProjects(systemSessionToken, space1, projectCode1).get(0); String sampleCode = createUniqueCode("S");
+ * SamplePermId projectSample = createSamples(systemSessionToken, space1, project1, null, sampleCode).get(0); String experimentCode =
+ * createUniqueCode("E"); String projectCode2 = createUniqueCode("P"); ProjectPermId project2 = createProjects(systemSessionToken, space1,
+ * projectCode2).get(0); createExperiments(systemSessionToken, project2, experimentCode); SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(projectSample); sampleUpdate.setProjectId(new ProjectIdentifier("SPACE1", projectCode2));
+ * sampleUpdate.setExperimentId(new ExperimentIdentifier("SPACE1", projectCode2, experimentCode)); Date now = sleep();
+ * v3api.updateSamples(adminSessionToken, Arrays.asList(sampleUpdate)); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withModifier(); fetchOptions.withSpace(); fetchOptions.withProject().withModifier(); fetchOptions.withExperiment().withModifier();
+ * Map<ISampleId, Sample> samples = v3api.mapSamples(systemSessionToken, Arrays.asList(projectSample), fetchOptions); Sample sample =
+ * samples.get(projectSample); assertEquals(sample.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" + sampleCode);
+ * assertModification(sample, sample, now, adminUser); assertModification(sample.getProject(), sample.getProject(), now, adminUser); Experiment
+ * experiment = sample.getExperiment(); assertEquals(experiment.getIdentifier().getIdentifier(), "/SPACE1/" + projectCode2 + "/" +
+ * experimentCode); assertModification(experiment, experiment, now, adminUser); }
+ * @Test public void testDeleteProjectSample() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); createSamples(systemSessionToken,
+ * space1, project, null, sampleCode); SampleDeletionOptions deletionOptions = new SampleDeletionOptions(); deletionOptions.setReason("test");
+ * List<SampleIdentifier> sampleIds = Arrays.asList(new SampleIdentifier("/SPACE1/" + projectCode + "/" + sampleCode)); Date now = sleep();
+ * v3api.deleteSamples(adminSessionToken, sampleIds, deletionOptions); assertEquals(v3api.mapSamples(systemSessionToken, sampleIds, new
+ * SampleFetchOptions()).size(), 0); ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions(); projectFetchOptions.withModifier();
+ * Project sampleProject = v3api.mapProjects(systemSessionToken, Arrays.asList(project), projectFetchOptions).values().iterator().next();
+ * assertModification(sampleProject, sampleProject, now, adminUser); }
+ * @Test public void testDeleteProjectExperimentSample() { String projectCode = createUniqueCode("P"); ProjectPermId project =
+ * createProjects(systemSessionToken, space1, projectCode).get(0); String sampleCode = createUniqueCode("S"); String experimentCode =
+ * createUniqueCode("E"); ExperimentPermId experiment = createExperiments(systemSessionToken, project, experimentCode).get(0); SamplePermId sample
+ * = createSamples(systemSessionToken, space1, project, experiment, sampleCode).get(0); SampleDeletionOptions deletionOptions = new
+ * SampleDeletionOptions(); deletionOptions.setReason("test"); List<SamplePermId> sampleIds = Arrays.asList(sample); Date now = sleep();
+ * v3api.deleteSamples(adminSessionToken, sampleIds, deletionOptions); assertEquals(v3api.mapSamples(systemSessionToken, sampleIds, new
+ * SampleFetchOptions()).size(), 0); ProjectFetchOptions projectFetchOptions = new ProjectFetchOptions(); projectFetchOptions.withModifier();
+ * Project sampleProject = v3api.mapProjects(systemSessionToken, Arrays.asList(project), projectFetchOptions).values().iterator().next();
+ * assertModification(sampleProject, sampleProject, now, adminUser); ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
+ * experimentFetchOptions.withModifier(); Experiment sampleExperiment = v3api.mapExperiments(systemSessionToken, Arrays.asList(experiment),
+ * experimentFetchOptions).values().iterator().next(); assertModification(sampleExperiment, sampleExperiment, now, adminUser); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testCreateWithProjectAndSpaceInconsistent() { final SampleCreation creation = new
+ * SampleCreation(); creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE"); creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ * creation.setSpaceId(space1); creation.setProjectId(project1inSpace2); assertUserFailureException(new IDelegatedAction() {
+ * @Override public void execute() { v3api.createSamples(systemSessionToken, Collections.singletonList(creation)); } },
+ * "Sample space must be the same as project space. " + "Sample: /SPACE1/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE, " +
+ * "Project: /SPACE2/PROJECT1 " + "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_SPACE])"); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testCreateWithProjectAndNoSpaceInconsistent() { final SampleCreation creation = new
+ * SampleCreation(); creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE"); creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ * creation.setProjectId(project1inSpace1); assertUserFailureException(new IDelegatedAction() {
+ * @Override public void execute() { v3api.createSamples(systemSessionToken, Collections.singletonList(creation)); } },
+ * "Shared samples cannot be attached to projects. " + "Sample: /SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE, " + "Project: /SPACE1/PROJECT1 " +
+ * "(Context: [verify project for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_NOSPACE])"); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testCreateWithProjectAndExperimentInconsistent() { final SampleCreation creation =
+ * new SampleCreation(); creation.setCode("SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT"); creation.setTypeId(ENTITY_TYPE_UNKNOWN);
+ * creation.setSpaceId(space1); creation.setProjectId(project2inSpace1); String expCode = createUniqueCode("E");
+ * creation.setExperimentId(createExperiments(systemSessionToken, project1inSpace1, expCode).get(0)); assertUserFailureException(new
+ * IDelegatedAction() {
+ * @Override public void execute() { v3api.createSamples(systemSessionToken, Collections.singletonList(creation)); } },
+ * "Sample project must be the same as experiment project. " + "Sample: /SPACE1/SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT, " +
+ * "Project: /SPACE1/PROJECT2, " + "Experiment: /SPACE1/PROJECT1/" + expCode + " " +
+ * "(Context: [verify experiment for sample SAMPLE_WITH_INCONSISTENT_PROJECT_AND_EXPERIMENT])"); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testAssignSpaceSampleToProjectInDifferentSpace() { String code =
+ * createUniqueCode("S"); ISampleId sampleId = createSamples(systemSessionToken, space1, null, null, code).get(0); final SampleUpdate sampleUpdate
+ * = new SampleUpdate(); sampleUpdate.setSampleId(sampleId); sampleUpdate.setProjectId(project2inSpace2); assertUserFailureException(new
+ * IDelegatedAction() {
+ * @Override public void execute() { v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate)); } },
+ * "Sample space must be the same as project space. " + "Sample: /SPACE1/" + code + ", " + "Project: /SPACE2/PROJECT2 " +
+ * "(Context: [verify project for sample " + code + "])"); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testAssignSampleOfAnExperimentToProjectDifferentToTheExperimentProject() { String
+ * sampleCode = createUniqueCode("S"); String expCode = createUniqueCode("E"); IExperimentId experiment = createExperiments(systemSessionToken,
+ * project1inSpace1, expCode).get(0); SamplePermId sample = createSamples(systemSessionToken, space1, null, experiment, sampleCode).get(0); final
+ * SampleUpdate sampleUpdate = new SampleUpdate(); sampleUpdate.setSampleId(sample); sampleUpdate.setProjectId(project2inSpace1);
+ * assertUserFailureException(new IDelegatedAction() {
+ * @Override public void execute() { v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate)); } },
+ * "Sample project must be the same as experiment project. " + "Sample: /SPACE1/" + sampleCode + ", " + "Project: /SPACE1/PROJECT2, " +
+ * "Experiment: /SPACE1/PROJECT1/" + expCode + " " + "(Context: [verify experiment for sample " + sampleCode + "])"); }
+ * @Test
+ * @Transactional(propagation = Propagation.NEVER) public void testAssignSharedSampleToProject() { String code = createUniqueCode("S"); ISampleId
+ * sharedSample = createSamples(systemSessionToken, null, null, null, code).get(0); final SampleUpdate sampleUpdate = new SampleUpdate();
+ * sampleUpdate.setSampleId(sharedSample); sampleUpdate.setProjectId(project1inSpace1); assertUserFailureException(new IDelegatedAction() {
+ * @Override public void execute() { v3api.updateSamples(systemSessionToken, Collections.singletonList(sampleUpdate)); } },
+ * "Shared samples cannot be attached to projects. " + "Sample: /" + code + ", " + "Project: /SPACE1/PROJECT1 " +
+ * "(Context: [verify project for sample " + code + "])"); }
+ * @Test(priority = -1) public void testSearchForSamplesWithProject() throws InterruptedException { SampleSearchCriteria searchCriteria = new
+ * SampleSearchCriteria(); searchCriteria.withProject(); SampleFetchOptions fetchOptions = new SampleFetchOptions(); fetchOptions.withProject();
+ * SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
+ * assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
+ * assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
+ * assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE4");
+ * assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
+ * assertEquals(result.getObjects().get(2).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE5");
+ * assertEquals(result.getObjects().get(2).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
+ * assertEquals(result.getObjects().get(3).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE6");
+ * assertEquals(result.getObjects().get(3).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2"); assertEquals(result.getTotalCount(),
+ * 4); }
+ * @Test(priority = -1) public void testSearchForSamplesWithCodeAndWithProject() { SampleSearchCriteria searchCriteria = new
+ * SampleSearchCriteria(); searchCriteria.withCode().thatEndsWith("3"); searchCriteria.withProject(); SampleFetchOptions fetchOptions = new
+ * SampleFetchOptions(); fetchOptions.withProject(); SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria,
+ * fetchOptions); assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
+ * assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1"); assertEquals(result.getTotalCount(),
+ * 1); }
+ * @Test(priority = -1) public void testSearchForSamplesWithProjectWithSpaceWithCode() { SampleSearchCriteria searchCriteria = new
+ * SampleSearchCriteria(); searchCriteria.withProject().withSpace().withCode().thatEquals("SPACE1"); SampleFetchOptions fetchOptions = new
+ * SampleFetchOptions(); fetchOptions.withProject(); SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria,
+ * fetchOptions); assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE3");
+ * assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1");
+ * assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE1/PROJECT1/SAMPLE4");
+ * assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE1/PROJECT1"); assertEquals(result.getTotalCount(),
+ * 2); }
+ * @Test(priority = -1) public void testSearchForSamplesWithProjectWithPermId() { SampleSearchCriteria searchCriteria = new
+ * SampleSearchCriteria(); searchCriteria.withProject().withPermId().thatEquals(project2inSpace2.getPermId()); SampleFetchOptions fetchOptions =
+ * new SampleFetchOptions(); fetchOptions.withProject(); SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria,
+ * fetchOptions); assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE5");
+ * assertEquals(result.getObjects().get(0).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2");
+ * assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(), "/SPACE2/PROJECT2/SAMPLE6");
+ * assertEquals(result.getObjects().get(1).getProject().getIdentifier().getIdentifier(), "/SPACE2/PROJECT2"); assertEquals(result.getTotalCount(),
+ * 2); }
+ * @Test(priority = -1) public void testSearchForSamplesWithoutProjects() { SampleSearchCriteria searchCriteria = new SampleSearchCriteria();
+ * searchCriteria.withCode().thatStartsWith("SAMP"); searchCriteria.withoutProject(); SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ * fetchOptions.withProject(); SearchResult<Sample> result = v3api.searchSamples(systemSessionToken, searchCriteria, fetchOptions);
+ * assertEquals(result.getObjects().get(0).getIdentifier().getIdentifier(), "/SPACE1/SAMPLE1");
+ * assertEquals(result.getObjects().get(0).getProject(), null); assertEquals(result.getObjects().get(1).getIdentifier().getIdentifier(),
+ * "/SPACE1/SAMPLE2"); assertEquals(result.getObjects().get(1).getProject(), null); assertEquals(result.getTotalCount(), 2); } private void
+ * assertUserFailureException(IDelegatedAction action, String expectedExceptionMessage) { try { action.execute();
+ * fail("UserFailureException expected"); } catch (UserFailureException ex) { assertEquals(ex.getMessage(), expectedExceptionMessage); } } private
+ * void assertModification(IModificationDateHolder modificationDateHolder, IModifierHolder modifierHolder, Date date, String modifier) {
+ * assertNotOlder(modificationDateHolder.getModificationDate(), date); assertEquals(modifierHolder.getModifier().getUserId(), modifier); } private
+ * void assertNotOlder(Date actualDate, Date referenceDate) { SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS"); String
+ * renderedReferenceDate = format.format(referenceDate.getTime()); String renderedActualDate = format.format(actualDate);
+ * assertEquals(renderedReferenceDate.compareTo(renderedActualDate) <= 0, true, renderedActualDate + " > " + renderedReferenceDate); } private
+ * Date sleep() { Date now = daoFactory.getTransactionTimestamp(); return now; } private List<SpacePermId> createSpaces(String sessionToken,
+ * String...spaceCodes) { List<SpaceCreation> newSpaces = new ArrayList<SpaceCreation>(); for (String spaceCode : spaceCodes) { SpaceCreation
+ * space = new SpaceCreation(); space.setCode(spaceCode); newSpaces.add(space); } return v3api.createSpaces(sessionToken, newSpaces); } private
+ * List<ProjectPermId> createProjects(String sessionToken, ISpaceId spaceId, String...projectCodes) { List<ProjectCreation> newProjects = new
+ * ArrayList<ProjectCreation>(); for (String projectCode : projectCodes) { ProjectCreation project = new ProjectCreation();
+ * project.setSpaceId(spaceId); project.setCode(projectCode); newProjects.add(project); } return v3api.createProjects(sessionToken, newProjects);
+ * } private List<SamplePermId> createSamples(String sessionToken, ISpaceId spaceOrNull, IProjectId projectOrNull, IExperimentId experimentOrNull,
+ * String...codes) { List<SampleCreation> newSamples = new ArrayList<SampleCreation>(); for (String code : codes) { SampleCreation sample = new
+ * SampleCreation(); sample.setTypeId(ENTITY_TYPE_UNKNOWN); sample.setSpaceId(spaceOrNull); sample.setProjectId(projectOrNull);
+ * sample.setExperimentId(experimentOrNull); sample.setCode(code); newSamples.add(sample); } return v3api.createSamples(sessionToken, newSamples);
+ * } private List<ExperimentPermId> createExperiments(String sessionToken, IProjectId project, String...codes) { List<ExperimentCreation>
+ * newExperiments = new ArrayList<ExperimentCreation>(); for (String code : codes) { ExperimentCreation experiment = new ExperimentCreation();
+ * experiment.setCode(code); experiment.setTypeId(ENTITY_TYPE_UNKNOWN); experiment.setProjectId(project); newExperiments.add(experiment); } return
+ * v3api.createExperiments(sessionToken, newExperiments); } private String createUniqueCode(String prefix) { return prefix + "-" +
+ * System.currentTimeMillis(); } private void waitAtLeastASecond() { try { Thread.sleep(1100); } catch (InterruptedException ex) { // silently
+ * ignored } }
+ */
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchDataSetTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchDataSetTypeTest.java
index aed5fe80f7f..cb526708b2d 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchDataSetTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchDataSetTypeTest.java
@@ -31,8 +31,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.sort.CodeComparator;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SearchDataSetTypeTest extends AbstractTest
@@ -45,15 +43,17 @@ public class SearchDataSetTypeTest extends AbstractTest
DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<DataSetType> searchResult = v3api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<DataSetType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
- assertEquals(codes.toString(), "[CONTAINER_TYPE, DELETION_TEST, DELETION_TEST_CONTAINER, HCS_IMAGE, HCS_IMAGE_ANALYSIS_DATA, LINK_TYPE, REQUIRES_EXPERIMENT, UNKNOWN, VALIDATED_CONTAINER_TYPE, VALIDATED_IMPOSSIBLE_TO_UPDATE_TYPE, VALIDATED_NORMAL_TYPE]");
+ assertEquals(
+ codes.toString(),
+ "[CONTAINER_TYPE, DELETION_TEST, DELETION_TEST_CONTAINER, HCS_IMAGE, HCS_IMAGE_ANALYSIS_DATA, LINK_TYPE, REQUIRES_EXPERIMENT, UNKNOWN, VALIDATED_CONTAINER_TYPE, VALIDATED_IMPOSSIBLE_TO_UPDATE_TYPE, VALIDATED_NORMAL_TYPE]");
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchExactCode()
{
@@ -63,7 +63,7 @@ public class SearchDataSetTypeTest extends AbstractTest
DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<DataSetType> searchResult = v3api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<DataSetType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -71,7 +71,7 @@ public class SearchDataSetTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchWithCodeThatStartsWithD()
{
@@ -79,9 +79,9 @@ public class SearchDataSetTypeTest extends AbstractTest
EntityTypeSearchCriteria searchCriteria = new EntityTypeSearchCriteria();
searchCriteria.withCode().thatStartsWith("D");
DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
-
+
SearchResult<DataSetType> searchResult = v3api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<DataSetType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -98,9 +98,9 @@ public class SearchDataSetTypeTest extends AbstractTest
searchCriteria.withCode().thatStartsWith("D");
DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
fetchOptions.withPropertyAssignments().sortBy().code().desc();
-
+
SearchResult<DataSetType> searchResult = v3api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<DataSetType> types = searchResult.getObjects();
Collections.sort(types, new CodeComparator<DataSetType>());
List<String> codes = extractCodes(types);
@@ -110,5 +110,5 @@ public class SearchDataSetTypeTest extends AbstractTest
assertOrder(propertyAssignments, "ORGANISM", "DESCRIPTION", "BACTERIUM");
v3api.logout(sessionToken);
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchExperimentTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchExperimentTypeTest.java
index 6d2fe244a1f..9891d122583 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchExperimentTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchExperimentTypeTest.java
@@ -31,8 +31,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.sort.CodeComparator;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SearchExperimentTypeTest extends AbstractTest
@@ -45,7 +43,7 @@ public class SearchExperimentTypeTest extends AbstractTest
ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<ExperimentType> searchResult = v3api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<ExperimentType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -53,7 +51,7 @@ public class SearchExperimentTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchExactCode()
{
@@ -63,7 +61,7 @@ public class SearchExperimentTypeTest extends AbstractTest
ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<ExperimentType> searchResult = v3api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<ExperimentType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -71,7 +69,7 @@ public class SearchExperimentTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchWithCodeThatStartsWithD()
{
@@ -79,9 +77,9 @@ public class SearchExperimentTypeTest extends AbstractTest
EntityTypeSearchCriteria searchCriteria = new EntityTypeSearchCriteria();
searchCriteria.withCode().thatStartsWith("D");
ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
-
+
SearchResult<ExperimentType> searchResult = v3api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<ExperimentType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -98,9 +96,9 @@ public class SearchExperimentTypeTest extends AbstractTest
searchCriteria.withCode().thatStartsWith("D");
ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
fetchOptions.withPropertyAssignments().sortBy().code().desc();
-
+
SearchResult<ExperimentType> searchResult = v3api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<ExperimentType> types = searchResult.getObjects();
Collections.sort(types, new CodeComparator<ExperimentType>());
List<String> codes = extractCodes(types);
@@ -110,5 +108,5 @@ public class SearchExperimentTypeTest extends AbstractTest
assertOrder(propertyAssignments, "ORGANISM", "DESCRIPTION", "BACTERIUM");
v3api.logout(sessionToken);
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchMaterialTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchMaterialTypeTest.java
index 1124a4e54d6..1a47898e493 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchMaterialTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchMaterialTypeTest.java
@@ -31,8 +31,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.sort.CodeComparator;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SearchMaterialTypeTest extends AbstractTest
@@ -45,7 +43,7 @@ public class SearchMaterialTypeTest extends AbstractTest
MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<MaterialType> searchResult = v3api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<MaterialType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -53,7 +51,7 @@ public class SearchMaterialTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchExactCode()
{
@@ -63,7 +61,7 @@ public class SearchMaterialTypeTest extends AbstractTest
MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<MaterialType> searchResult = v3api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<MaterialType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -71,7 +69,7 @@ public class SearchMaterialTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchWithCodeThatStartsWithB()
{
@@ -79,9 +77,9 @@ public class SearchMaterialTypeTest extends AbstractTest
EntityTypeSearchCriteria searchCriteria = new EntityTypeSearchCriteria();
searchCriteria.withCode().thatStartsWith("B");
MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
-
+
SearchResult<MaterialType> searchResult = v3api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<MaterialType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -98,9 +96,9 @@ public class SearchMaterialTypeTest extends AbstractTest
searchCriteria.withCode().thatStartsWith("B");
MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
fetchOptions.withPropertyAssignments().sortBy().label().desc();
-
+
SearchResult<MaterialType> searchResult = v3api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<MaterialType> types = searchResult.getObjects();
Collections.sort(types, new CodeComparator<MaterialType>());
List<String> codes = extractCodes(types);
@@ -110,5 +108,5 @@ public class SearchMaterialTypeTest extends AbstractTest
assertOrder(propertyAssignments, "ORGANISM", "DESCRIPTION");
v3api.logout(sessionToken);
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTest.java
index ab5655e9d31..293b4ed9996 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTest.java
@@ -969,6 +969,7 @@ public class SearchSampleTest extends AbstractSampleTest
}
final String LISTED_ID = "/CISD/C1";
+
final String UNLISTED_ID = "/CISD/CL1:A01";
@Test
@@ -980,12 +981,11 @@ public class SearchSampleTest extends AbstractSampleTest
SampleSearchCriteria criteria = new SampleSearchCriteria();
criteria.withId().thatEquals(new SampleIdentifier(UNLISTED_ID));
-
-
+
List<Sample> samples = search(sessionToken, criteria, fo);
-
+
assertEquals(samples.size(), 1);
-
+
assertSampleIdentifiersInOrder(samples, UNLISTED_ID);
final SampleTypeSearchCriteria withType = criteria.withType();
@@ -1008,9 +1008,9 @@ public class SearchSampleTest extends AbstractSampleTest
final SampleTypeSearchCriteria withType = criteria.withType();
List<Sample> samples = search(sessionToken, criteria, fo);
-
+
assertEquals(samples.size(), 1);
-
+
assertEquals(samples.get(0).getIdentifier().getIdentifier(), LISTED_ID);
withType.withListable().thatEquals(true);
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTypeTest.java
index 80c1276e5c2..e41d7f5307c 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchSampleTypeTest.java
@@ -31,8 +31,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFe
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.sort.CodeComparator;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SearchSampleTypeTest extends AbstractTest
@@ -45,15 +43,17 @@ public class SearchSampleTypeTest extends AbstractTest
SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<SampleType> searchResult = v3api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<SampleType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
- assertEquals(codes.toString(), "[CELL_PLATE, CONTROL_LAYOUT, DELETION_TEST, DILUTION_PLATE, DYNAMIC_PLATE, IMPOSSIBLE, IMPOSSIBLE_TO_UPDATE, MASTER_PLATE, NORMAL, REINFECT_PLATE, VALIDATE_CHILDREN, WELL]");
+ assertEquals(
+ codes.toString(),
+ "[CELL_PLATE, CONTROL_LAYOUT, DELETION_TEST, DILUTION_PLATE, DYNAMIC_PLATE, IMPOSSIBLE, IMPOSSIBLE_TO_UPDATE, MASTER_PLATE, NORMAL, REINFECT_PLATE, VALIDATE_CHILDREN, WELL]");
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchExactCode()
{
@@ -63,7 +63,7 @@ public class SearchSampleTypeTest extends AbstractTest
SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
fetchOptions.withPropertyAssignments();
SearchResult<SampleType> searchResult = v3api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<SampleType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -71,7 +71,7 @@ public class SearchSampleTypeTest extends AbstractTest
assertEquals(types.get(0).getFetchOptions().hasPropertyAssignments(), true);
v3api.logout(sessionToken);
}
-
+
@Test
public void testSearchWithCodeThatStartsWithD()
{
@@ -79,9 +79,9 @@ public class SearchSampleTypeTest extends AbstractTest
EntityTypeSearchCriteria searchCriteria = new EntityTypeSearchCriteria();
searchCriteria.withCode().thatStartsWith("D");
SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
-
+
SearchResult<SampleType> searchResult = v3api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<SampleType> types = searchResult.getObjects();
List<String> codes = extractCodes(types);
Collections.sort(codes);
@@ -98,9 +98,9 @@ public class SearchSampleTypeTest extends AbstractTest
searchCriteria.withCode().thatStartsWith("D");
SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
fetchOptions.withPropertyAssignments().sortBy().label().desc();
-
+
SearchResult<SampleType> searchResult = v3api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
-
+
List<SampleType> types = searchResult.getObjects();
Collections.sort(types, new CodeComparator<SampleType>());
List<String> codes = extractCodes(types);
@@ -110,5 +110,5 @@ public class SearchSampleTypeTest extends AbstractTest
assertOrder(propertyAssignments, "BACTERIUM", "ORGANISM", "DESCRIPTION");
v3api.logout(sessionToken);
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchServiceTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchServiceTest.java
index c35e60fec7a..846778e5ad0 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchServiceTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/SearchServiceTest.java
@@ -38,37 +38,37 @@ public class SearchServiceTest extends AbstractTest
CustomASServiceSearchCriteria searchCriteria = new CustomASServiceSearchCriteria();
searchCriteria.withCode().thatEquals("simple-service");
- SearchResult<CustomASService> result = v3api.searchCustomASServices(sessionToken, searchCriteria,
+ SearchResult<CustomASService> result = v3api.searchCustomASServices(sessionToken, searchCriteria,
new CustomASServiceFetchOptions());
assertEquals(result.getTotalCount(), 1);
}
-
+
@Test
public void testSearchAllServicesSortedPage2()
{
CustomASServiceFetchOptions fetchOptions = new CustomASServiceFetchOptions();
fetchOptions.from(2).count(1).sortBy();
- SearchResult<CustomASService> result = v3api.searchCustomASServices(systemSessionToken,
- new CustomASServiceSearchCriteria(),
+ SearchResult<CustomASService> result = v3api.searchCustomASServices(systemSessionToken,
+ new CustomASServiceSearchCriteria(),
fetchOptions);
-
+
assertEquals(result.getObjects().toString(), "[CustomASService code: service3]");
assertEquals(result.getTotalCount(), 4);
}
-
+
@Test
public void testSearchServiceByCode()
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
CustomASServiceSearchCriteria searchCriteria = new CustomASServiceSearchCriteria();
searchCriteria.withCode().thatStartsWith("simple");
-
- SearchResult<CustomASService> result = v3api.searchCustomASServices(sessionToken, searchCriteria, new
+
+ SearchResult<CustomASService> result = v3api.searchCustomASServices(sessionToken, searchCriteria, new
CustomASServiceFetchOptions());
-
+
assertEquals(result.getObjects().toString(), "[CustomASService code: simple-service]");
assertEquals(result.getTotalCount(), 1);
}
-
+
}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
index d383409b6af..da0eb6eff2b 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdateExperimentTest.java
@@ -123,41 +123,22 @@ public class UpdateExperimentTest extends AbstractExperimentTest
Experiment experiment = experiments.get(0);
assertEquals(experiment.getIdentifier().getIdentifier(), "/CISD/NOE/TEST_EXPERIMENT");
}
-
- /*
- @Test(groups = "project-samples")
- public void testMovingExperimentWithProjectSamplesToADifferentProject()
- {
- String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sampleCreation = new SampleCreation();
- sampleCreation.setCode("PROJECT-SAMPLE-IN-EXPERIMENT");
- ExperimentIdentifier experimentId = new ExperimentIdentifier("CISD", "NEMO", "EXP1");
- sampleCreation.setExperimentId(experimentId);
- sampleCreation.setSpaceId(new SpacePermId("CISD"));
- sampleCreation.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
- sampleCreation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- v3api.createSamples(sessionToken, Arrays.asList(sampleCreation));
- ExperimentUpdate experimentUpdate = new ExperimentUpdate();
- experimentUpdate.setExperimentId(experimentId);
- ProjectIdentifier projectId = new ProjectIdentifier("/CISD/NOE");
- experimentUpdate.setProjectId(projectId);
-
- v3api.updateExperiments(sessionToken, Arrays.asList(experimentUpdate));
-
- ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions();
- fetchOptions.withProject();
- fetchOptions.withSamples().withProject();
- Map<IExperimentId, Experiment> map = v3api.mapExperiments(sessionToken,
- Arrays.asList(new ExperimentIdentifier("CISD", "NOE", "EXP1")), fetchOptions);
- List<Experiment> experiments = new ArrayList<Experiment>(map.values());
- List<Sample> samples = experiments.get(0).getSamples();
- assertEquals(experiments.get(0).getProject().getCode(), "NOE");
- assertEquals(samples.get(0).getProject().getCode(), "NOE");
- AssertionUtil.assertCollectionSize(samples, 1);
- AssertionUtil.assertCollectionSize(experiments, 1);
- }
-*/
+ /*
+ * @Test(groups = "project-samples") public void testMovingExperimentWithProjectSamplesToADifferentProject() { String sessionToken =
+ * v3api.login(TEST_USER, PASSWORD); SampleCreation sampleCreation = new SampleCreation(); sampleCreation.setCode("PROJECT-SAMPLE-IN-EXPERIMENT");
+ * ExperimentIdentifier experimentId = new ExperimentIdentifier("CISD", "NEMO", "EXP1"); sampleCreation.setExperimentId(experimentId);
+ * sampleCreation.setSpaceId(new SpacePermId("CISD")); sampleCreation.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+ * sampleCreation.setTypeId(new EntityTypePermId("CELL_PLATE")); v3api.createSamples(sessionToken, Arrays.asList(sampleCreation));
+ * ExperimentUpdate experimentUpdate = new ExperimentUpdate(); experimentUpdate.setExperimentId(experimentId); ProjectIdentifier projectId = new
+ * ProjectIdentifier("/CISD/NOE"); experimentUpdate.setProjectId(projectId); v3api.updateExperiments(sessionToken,
+ * Arrays.asList(experimentUpdate)); ExperimentFetchOptions fetchOptions = new ExperimentFetchOptions(); fetchOptions.withProject();
+ * fetchOptions.withSamples().withProject(); Map<IExperimentId, Experiment> map = v3api.mapExperiments(sessionToken, Arrays.asList(new
+ * ExperimentIdentifier("CISD", "NOE", "EXP1")), fetchOptions); List<Experiment> experiments = new ArrayList<Experiment>(map.values());
+ * List<Sample> samples = experiments.get(0).getSamples(); assertEquals(experiments.get(0).getProject().getCode(), "NOE");
+ * assertEquals(samples.get(0).getProject().getCode(), "NOE"); AssertionUtil.assertCollectionSize(samples, 1);
+ * AssertionUtil.assertCollectionSize(experiments, 1); }
+ */
@Test
public void testUpdateWithProjectNull()
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/Change.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/Change.java
index 1d4bb18b8cd..861ee7bca22 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/Change.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/Change.java
@@ -7,7 +7,7 @@ class Change implements Comparable<Change>
public final Date time;
public final String userId;
-
+
public final String value;
public final boolean isRemoval;
@@ -25,7 +25,7 @@ class Change implements Comparable<Change>
this.attachmentContent = attachmentContent;
this.isRemoval = isRemoval;
}
-
+
@Override
public int compareTo(Change other)
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DataSetDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DataSetDeletionTest.java
index 74969716b7d..6be95567bcb 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DataSetDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DataSetDeletionTest.java
@@ -103,8 +103,8 @@ public class DataSetDeletionTest extends DeletionTest
delete(project);
delete(space);
- assertHistory(dataset.getPermId(), "OWNED", experimentSet(experiment.getPermId()),
- sampleSet(spaceSample.getPermId()),
+ assertHistory(dataset.getPermId(), "OWNED", experimentSet(experiment.getPermId()),
+ sampleSet(spaceSample.getPermId()),
sampleSet(experimentSample.getPermId()),
experimentSet(experiment.getPermId()));
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DeletionTest.java
index da6d96f0c1d..e0edca48262 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/DeletionTest.java
@@ -100,86 +100,86 @@ public abstract class DeletionTest extends AbstractTest
private static SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
- public Set<String> attachmentSet(String...values)
+ public Set<String> attachmentSet(String... values)
{
return attachmentSetFor(TEST_USER, values);
}
-
- public Set<String> attachmentSetFor(String userId, String...values)
+
+ public Set<String> attachmentSetFor(String userId, String... values)
{
return entitySet("ATTACHMENT", userId, values);
}
-
- public Set<String> unknownSet(String...values)
+
+ public Set<String> unknownSet(String... values)
{
return unknownSetFor(TEST_USER, values);
}
-
- public Set<String> unknownSetFor(String userId, String...values)
+
+ public Set<String> unknownSetFor(String userId, String... values)
{
return entitySet("UNKNOWN", userId, values);
}
-
- public Set<String> spaceSet(String...values)
+
+ public Set<String> spaceSet(String... values)
{
return spaceSetFor(TEST_USER, values);
}
-
- public Set<String> spaceSetFor(String userId, String...values)
+
+ public Set<String> spaceSetFor(String userId, String... values)
{
return entitySet("SPACE", userId, values);
}
-
- public Set<String> projectSet(String...values)
+
+ public Set<String> projectSet(String... values)
{
return projectSetFor(TEST_USER, values);
}
-
- public Set<String> projectSetFor(String userId, String...values)
+
+ public Set<String> projectSetFor(String userId, String... values)
{
return entitySet("PROJECT", userId, values);
}
-
- public Set<String> experimentSet(String...values)
+
+ public Set<String> experimentSet(String... values)
{
return experimentSetFor(TEST_USER, values);
}
-
- public Set<String> experimentSetFor(String userId, String...values)
+
+ public Set<String> experimentSetFor(String userId, String... values)
{
return entitySet("EXPERIMENT", userId, values);
}
- public Set<String> sampleSet(String...values)
+ public Set<String> sampleSet(String... values)
{
return sampleSetFor(TEST_USER, values);
}
-
- public Set<String> sampleSetFor(String userId, String...values)
+
+ public Set<String> sampleSetFor(String userId, String... values)
{
return entitySet("SAMPLE", userId, values);
}
-
- public Set<String> dataSetSet(String...values)
+
+ public Set<String> dataSetSet(String... values)
{
return dataSetSetFor(TEST_USER, values);
}
-
- public Set<String> dataSetSetFor(String userId, String...values)
+
+ public Set<String> dataSetSetFor(String userId, String... values)
{
return entitySet("DATA_SET", userId, values);
}
-
- public Set<String> propertiesSet(String...values)
+
+ public Set<String> propertiesSet(String... values)
{
return set("PROPERTY", null, TEST_USER, values);
}
-
+
private Set<String> entitySet(String entityType, String userId, String... values)
{
return set("RELATIONSHIP", entityType, userId, values);
}
-
+
private Set<String> set(String type, String entityTypeOrNull, String userId, String... values)
{
Set<String> result = new HashSet<>();
@@ -189,7 +189,7 @@ public abstract class DeletionTest extends AbstractTest
}
return result;
}
-
+
public Set<String> set(String... values)
{
return new HashSet<String>(Arrays.asList(values));
@@ -320,7 +320,7 @@ public abstract class DeletionTest extends AbstractTest
return false;
}
}
-
+
public void assertAttachment(String permId, Set<String> attachments) throws Exception
{
IModificationFilter filter = new IModificationFilter()
@@ -355,7 +355,7 @@ public abstract class DeletionTest extends AbstractTest
@Override
public boolean accept(Modification modification)
{
- return modification.type.equals(AttributeEntry.ATTRIBUTE)
+ return modification.type.equals(AttributeEntry.ATTRIBUTE)
&& modification.key.equals("REGISTRATION_TIMESTAMP") == false;
}
@@ -451,14 +451,14 @@ public abstract class DeletionTest extends AbstractTest
if (expectedList.equals(actualValues) == false)
{
-
+
Assert.assertEquals(render(actualValues), render(expectedList),
- filter.getDescription() + " of entity " + permId + " has wrong value history. Expected <"
- + render(expectedList) + ">, actual <" + render(actualValues) + ">. Raw changes: "
+ filter.getDescription() + " of entity " + permId + " has wrong value history. Expected <"
+ + render(expectedList) + ">, actual <" + render(actualValues) + ">. Raw changes: "
+ builder);
}
}
-
+
private String render(List<Set<String>> values)
{
StringBuilder builder = new StringBuilder();
@@ -483,14 +483,15 @@ public abstract class DeletionTest extends AbstractTest
{
return currentTime == null ? change.time == null : currentTime.equals(change.time);
}
-
+
private static interface IModificationFilter
{
public String getDescription();
+
public boolean accept(Modification modification);
-
+
}
-
+
private static interface IChangeRenderer
{
public String render(Change change);
@@ -502,12 +503,12 @@ public abstract class DeletionTest extends AbstractTest
Query query = session.createQuery("SELECT e FROM EventPE e WHERE :permId IN e.identifiersInternal").setParameter("permId", permId);
EventPE event = (EventPE) query.uniqueResult();
String attachmentContent = getAttachmentContent(event);
-
+
JsonNode tree = new ObjectMapper().reader().readTree(event.getContent());
-
+
List<Modification> allMods =
IteratorUtils.toList(IteratorUtils.transformedIterator(tree.get(permId).elements(), new JsonNodeToModificationTransformer()));
-
+
List<Modification> mods = new ArrayList<>();
for (Modification mod : allMods)
{
@@ -516,7 +517,7 @@ public abstract class DeletionTest extends AbstractTest
mods.add(mod);
}
}
-
+
List<Change> changes = new ArrayList<>();
for (Modification mod : mods)
{
@@ -527,7 +528,7 @@ public abstract class DeletionTest extends AbstractTest
changes.add(new Change(mod.validUntil, mod.key, mod.userId, value, attachmentContent, true));
}
}
-
+
Collections.sort(changes);
return changes;
@@ -573,7 +574,7 @@ public abstract class DeletionTest extends AbstractTest
m.validUntil = asDate(node.get("validUntil"));
return m;
}
-
+
private Date asDate(JsonNode node)
{
String textValue = asString(node);
@@ -585,7 +586,7 @@ public abstract class DeletionTest extends AbstractTest
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
-
+
private String asString(JsonNode node)
{
if (node == null)
@@ -599,13 +600,13 @@ public abstract class DeletionTest extends AbstractTest
private static class Modification
{
public String userId;
-
+
public String type;
-
+
public String key;
public String value;
-
+
public String entityType;
public Date validFrom;
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ExperimentDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ExperimentDeletionTest.java
index 711fd5e2e3c..907fa7edadd 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ExperimentDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ExperimentDeletionTest.java
@@ -25,7 +25,7 @@ public class ExperimentDeletionTest extends DeletionTest
SpacePermId space = createSpace("SPACE");
ProjectPermId project = createProject(space, "PROJECT1");
ExperimentPermId exp = createExperiment(project, "EXPERIMENT");
-
+
AttachmentCreation attachment1 = new AttachmentCreation();
attachment1.setTitle("A1");
attachment1.setDescription("hello A");
@@ -35,21 +35,21 @@ public class ExperimentDeletionTest extends DeletionTest
attachment2.setFileName("hi.txt");
attachment2.setContent("hi world!".getBytes());
addAttachment(exp, attachment1, attachment2);
-
+
newTx();
-
+
delete(exp);
delete(project);
delete(space);
- assertAttachment("experiment/" + exp.getPermId() + "/hello.txt(1)",
+ assertAttachment("experiment/" + exp.getPermId() + "/hello.txt(1)",
set("OWNED = ATTACHMENT:" + exp + "[EXPERIMENT](user:test) <hello world!>"));
- assertAttachment("experiment/" + exp.getPermId() + "/hi.txt(1)",
+ assertAttachment("experiment/" + exp.getPermId() + "/hi.txt(1)",
set("OWNED = ATTACHMENT:" + exp + "[EXPERIMENT](user:test) <hi world!>"));
assertHistory(exp.getPermId(), "OWNER", attachmentSet("experiment/" + exp.getPermId() + "/hello.txt(1)",
"experiment/" + exp.getPermId() + "/hi.txt(1)"));
}
-
+
@Test
@Rollback(false)
public void testAttributes() throws Exception
@@ -87,7 +87,7 @@ public class ExperimentDeletionTest extends DeletionTest
ProjectPermId project2 = createProject(space2, "PROJECT2");
ExperimentPermId experiment = createExperiment(project1, "EXPERIMENT");
-
+
newTx();
ExperimentUpdate update = new ExperimentUpdate();
@@ -101,7 +101,7 @@ public class ExperimentDeletionTest extends DeletionTest
delete(space1);
delete(space2);
- assertHistory(experiment.getPermId(), "OWNED", projectSet(project1.getPermId()),
+ assertHistory(experiment.getPermId(), "OWNED", projectSet(project1.getPermId()),
projectSet(project2.getPermId()));
}
@@ -151,7 +151,7 @@ public class ExperimentDeletionTest extends DeletionTest
delete(project);
delete(space);
- assertHistory(experiment.getPermId(), "OWNER",
+ assertHistory(experiment.getPermId(), "OWNER",
unknownSet(dataset1.getPermId(), dataset2.getPermId()),
unknownSet(dataset2.getPermId()),
set());
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ProjectDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ProjectDeletionTest.java
index 5bd50f794b7..f6241c7b174 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ProjectDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/ProjectDeletionTest.java
@@ -23,7 +23,7 @@ public class ProjectDeletionTest extends DeletionTest
{
SpacePermId space = createSpace("SPACE");
ProjectPermId project = createProject(space, "PROJECT3");
-
+
AttachmentCreation attachment1 = new AttachmentCreation();
attachment1.setTitle("A1");
attachment1.setDescription("hello A");
@@ -41,15 +41,15 @@ public class ProjectDeletionTest extends DeletionTest
projectUpdate.getAttachments().remove(new AttachmentFileName("hello.txt"));
v3api.updateProjects(sessionToken, Arrays.asList(projectUpdate));
- assertAttachment("project/" + project.getPermId() + "/hello.txt(1)",
+ assertAttachment("project/" + project.getPermId() + "/hello.txt(1)",
set("OWNED = ATTACHMENT:" + project + "[PROJECT](user:test) <hello world!>"));
-
+
newTx();
-
+
delete(project);
delete(space);
}
-
+
@Test
@Rollback(false)
public void deleteProjectWithAttachments() throws Exception
@@ -66,20 +66,20 @@ public class ProjectDeletionTest extends DeletionTest
attachment2.setFileName("hi.txt");
attachment2.setContent("hi world!".getBytes());
addAttachment(project, attachment1, attachment2);
-
+
newTx();
-
+
delete(project);
delete(space);
- assertAttachment("project/" + project.getPermId() + "/hello.txt(1)",
+ assertAttachment("project/" + project.getPermId() + "/hello.txt(1)",
set("OWNED = ATTACHMENT:" + project + "[PROJECT](user:test) <hello world!>"));
- assertAttachment("project/" + project.getPermId() + "/hi.txt(1)",
+ assertAttachment("project/" + project.getPermId() + "/hi.txt(1)",
set("OWNED = ATTACHMENT:" + project + "[PROJECT](user:test) <hi world!>"));
assertHistory(project.getPermId(), "OWNER", attachmentSet("project/" + project.getPermId() + "/hello.txt(1)",
"project/" + project.getPermId() + "/hi.txt(1)"));
}
-
+
@Test
@Rollback(false)
public void testAttributes() throws Exception
@@ -152,7 +152,7 @@ public class ProjectDeletionTest extends DeletionTest
delete(project2);
delete(space);
- assertHistory(project1.getPermId(), "OWNER",
+ assertHistory(project1.getPermId(), "OWNER",
experimentSet(experiment1.getPermId(), experiment2.getPermId()), set());
}
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/SampleDeletionTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/SampleDeletionTest.java
index ee13327312f..83fe7e333a8 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/SampleDeletionTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/deletion/SampleDeletionTest.java
@@ -22,7 +22,7 @@ public class SampleDeletionTest extends DeletionTest
{
SpacePermId space = createSpace("SPACE");
SamplePermId sample = createSample(null, space, "SAMPLE");
-
+
AttachmentCreation attachment1 = new AttachmentCreation();
attachment1.setTitle("A1");
attachment1.setDescription("hello A");
@@ -32,15 +32,15 @@ public class SampleDeletionTest extends DeletionTest
attachment2.setFileName("hi.txt");
attachment2.setContent("hi world!".getBytes());
addAttachment(sample, attachment1, attachment2);
-
+
newTx();
-
+
delete(sample);
delete(space);
- assertAttachment("sample/" + sample.getPermId() + "/hello.txt(1)",
+ assertAttachment("sample/" + sample.getPermId() + "/hello.txt(1)",
set("OWNED = ATTACHMENT:" + sample + "[SAMPLE](user:test) <hello world!>"));
- assertAttachment("sample/" + sample.getPermId() + "/hi.txt(1)",
+ assertAttachment("sample/" + sample.getPermId() + "/hi.txt(1)",
set("OWNED = ATTACHMENT:" + sample + "[SAMPLE](user:test) <hi world!>"));
assertHistory(sample.getPermId(), "OWNER", attachmentSet("sample/" + sample.getPermId() + "/hello.txt(1)",
"sample/" + sample.getPermId() + "/hi.txt(1)"));
@@ -51,7 +51,7 @@ public class SampleDeletionTest extends DeletionTest
public void deleteSharedSampleWithAttachments() throws Exception
{
SamplePermId sample = createSample(null, null, "SAMPLE");
-
+
AttachmentCreation attachment1 = new AttachmentCreation();
attachment1.setTitle("A1");
attachment1.setDescription("hello A");
@@ -61,19 +61,19 @@ public class SampleDeletionTest extends DeletionTest
attachment2.setFileName("hi.txt");
attachment2.setContent("hi world!".getBytes());
addAttachment(sample, attachment1, attachment2);
-
+
newTx();
-
+
delete(sample);
-
- assertAttachment("sample/" + sample.getPermId() + "/hello.txt(1)",
+
+ assertAttachment("sample/" + sample.getPermId() + "/hello.txt(1)",
set("OWNED = ATTACHMENT:" + sample + "[SAMPLE](user:test) <hello world!>"));
- assertAttachment("sample/" + sample.getPermId() + "/hi.txt(1)",
+ assertAttachment("sample/" + sample.getPermId() + "/hi.txt(1)",
set("OWNED = ATTACHMENT:" + sample + "[SAMPLE](user:test) <hi world!>"));
assertHistory(sample.getPermId(), "OWNER", attachmentSet("sample/" + sample.getPermId() + "/hello.txt(1)",
"sample/" + sample.getPermId() + "/hi.txt(1)"));
}
-
+
@Test
@Rollback(false)
public void testAttributes() throws Exception
@@ -84,10 +84,10 @@ public class SampleDeletionTest extends DeletionTest
newTx();
Date before = new Date();
-
+
delete(sample);
delete(space);
-
+
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("CODE", "SPACE_SAMPLE");
expectations.put("ENTITY_TYPE", "DELETION_TEST");
@@ -96,7 +96,6 @@ public class SampleDeletionTest extends DeletionTest
assertRegistrationTimestampAttribute(sample.getPermId(), after, before);
}
-
@Test
@Rollback(false)
public void changeSpace() throws Exception
@@ -118,7 +117,7 @@ public class SampleDeletionTest extends DeletionTest
delete(sample);
delete(space1, space2);
- assertHistory(sample.getPermId(), "OWNED", spaceSet(space1.getPermId()),
+ assertHistory(sample.getPermId(), "OWNED", spaceSet(space1.getPermId()),
spaceSetFor(SYSTEM_USER, space2.getPermId()));
}
@@ -150,7 +149,7 @@ public class SampleDeletionTest extends DeletionTest
delete(project1, project2);
delete(space1, space2);
- assertHistory(sample.getPermId(), "OWNED", experimentSet(experiment1.getPermId()),
+ assertHistory(sample.getPermId(), "OWNED", experimentSet(experiment1.getPermId()),
experimentSet(experiment2.getPermId()));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
index e470a2746a3..0a799deee02 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
@@ -123,7 +123,7 @@ public class OpenbisClientTest
final String propertyTypeCode = "IS_VALID";
final String propertyValue = "true";
final Collection<Long> alreadyTracked = Arrays.asList(new Long[]
- { 986L, 987L });
+ { 986L, 987L });
final TrackingSampleCriteria newSampleCriteria =
new TrackingSampleCriteria(sampleTypeCode, propertyTypeCode, propertyValue,
@@ -135,8 +135,7 @@ public class OpenbisClientTest
}
/**
- * Helper class encapsulating methods used for producing readable information about entities
- * returned by {@link ITrackingServer} methods.
+ * Helper class encapsulating methods used for producing readable information about entities returned by {@link ITrackingServer} methods.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/console/LexerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/console/LexerTest.java
index a97d765ffe6..e60ec667940 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/console/LexerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/console/LexerTest.java
@@ -20,8 +20,6 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class LexerTest extends AssertJUnit
@@ -41,7 +39,7 @@ public class LexerTest extends AssertJUnit
check("[a, b, hello 'world']", "a b \"hello 'world'\"");
check("[a=hello world]", "a=\"hello world\"");
}
-
+
private void check(String expectedTokens, String input)
{
assertEquals(expectedTokens, Lexer.extractTokens(input).toString());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/DummyAuthenticationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/DummyAuthenticationTest.java
index bf584aaa536..0cc2f44e5bf 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/DummyAuthenticationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/DummyAuthenticationTest.java
@@ -21,10 +21,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.WaitForAllActiveCallbacksFinish;
/**
- * A shorter version of {@link AuthenticationTest} that just logins to the application. It is
- * supposed to be run at the beginning of each suite (except the first one that should start with
- * full {@link AuthenticationTest}) to do all the GWT initialization and make the next test work
- * faster.
+ * A shorter version of {@link AuthenticationTest} that just logins to the application. It is supposed to be run at the beginning of each suite
+ * (except the first one that should start with full {@link AuthenticationTest}) to do all the GWT initialization and make the next test work faster.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/SearchCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/SearchCommand.java
index 6dbeba3f113..10e3996b698 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/SearchCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/SearchCommand.java
@@ -26,8 +26,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestUtil;
/**
- * A {@link AbstractDefaultTestCommand} extension which triggers a search just after a login has
- * been performed with specified parameters.
+ * A {@link AbstractDefaultTestCommand} extension which triggers a search just after a login has been performed with specified parameters.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/VocabularyRegistrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/VocabularyRegistrationTest.java
index 22f7c6fd628..8ceec7f9ab5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/VocabularyRegistrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/VocabularyRegistrationTest.java
@@ -36,7 +36,7 @@ public class VocabularyRegistrationTest extends AbstractGWTTestCase
private static final String DESCRIPTION = "Color";
private static final String[] TERMS =
- { "RED:01", "BLACK", "Y.E.L.L.O.W" };
+ { "RED:01", "BLACK", "Y.E.L.L.O.W" };
public final void testRegisterVocabulary()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/OpenViewCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/OpenViewCommand.java
index e2f26b58333..1e852bf628d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/OpenViewCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/OpenViewCommand.java
@@ -20,8 +20,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.Client;
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.AbstractDefaultTestCommand;
/**
- * {@link AbstractDefaultTestCommand} extension that does nothing. It should be used if we want to
- * make sure that all callbacks will finish without failure.
+ * {@link AbstractDefaultTestCommand} extension that does nothing. It should be used if we want to make sure that all callbacks will finish without
+ * failure.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/InvokeActionMenu.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/InvokeActionMenu.java
index 95587392bd6..236dd53fc99 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/InvokeActionMenu.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/InvokeActionMenu.java
@@ -22,8 +22,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestUtil;
/**
- * A {@link AbstractDefaultTestCommand} extension for invoking an action attached to
- * {@link ActionMenu} (e.g. opening a tab).
+ * A {@link AbstractDefaultTestCommand} extension for invoking an action attached to {@link ActionMenu} (e.g. opening a tab).
*
* @author Izabela Adamczyk
* @author Piotr Buczek
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckAuthorizationGroupTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckAuthorizationGroupTable.java
index 9e473dcabc4..7702869a51a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckAuthorizationGroupTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckAuthorizationGroupTable.java
@@ -21,8 +21,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of authorization groups
- * has been loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of authorization groups has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckPersonTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckPersonTable.java
index cd09f7f71ab..9e7a35e86a4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckPersonTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckPersonTable.java
@@ -22,8 +22,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTab
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AuthorizationGroup;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of persons has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of persons has been loaded.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckRoleAssignmentTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckRoleAssignmentTable.java
index 5a73404ad21..49cb456eb4c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckRoleAssignmentTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/CheckRoleAssignmentTable.java
@@ -21,8 +21,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of persons has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of persons has been loaded.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/OpenAddPersonDialog.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/OpenAddPersonDialog.java
index cb5a3030075..28e8f940290 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/OpenAddPersonDialog.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/OpenAddPersonDialog.java
@@ -24,8 +24,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestU
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AuthorizationGroup;
/**
- * A {@link AbstractDefaultTestCommand} extension opening a dialog allowing to add a person to the
- * authorization group.
+ * A {@link AbstractDefaultTestCommand} extension opening a dialog allowing to add a person to the authorization group.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/RemovePerson.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/RemovePerson.java
index 724ab61ec6a..92488bfba3c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/RemovePerson.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/RemovePerson.java
@@ -29,8 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AuthorizationGroup;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
/**
- * A {@link AbstractDefaultTestCommand} extension for deleting an authorization group with given
- * code.
+ * A {@link AbstractDefaultTestCommand} extension for deleting an authorization group with given code.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/ShowAuthorizationGroup.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/ShowAuthorizationGroup.java
index de5ff57f520..107a382ca6b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/ShowAuthorizationGroup.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/amc/ShowAuthorizationGroup.java
@@ -28,8 +28,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestU
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AuthorizationGroup;
/**
- * A {@link AbstractDefaultTestCommand} extension for showing an authorization group with given
- * code.
+ * A {@link AbstractDefaultTestCommand} extension for showing an authorization group with given code.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSet.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSet.java
index 5d374468faa..57c22145490 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSet.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSet.java
@@ -27,9 +27,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestU
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
/**
- * A {@link AbstractDefaultTestCommand} extension for showing detail view of a data set with given
- * code. View is displayed because of simulation of a click on show details button in a toolbar of a
- * data set search results browser.
+ * A {@link AbstractDefaultTestCommand} extension for showing detail view of a data set with given code. View is displayed because of simulation of a
+ * click on show details button in a toolbar of a data set search results browser.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSetEditor.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSetEditor.java
index 0c1686ec68e..8270c4dff77 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSetEditor.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/ShowDataSetEditor.java
@@ -27,8 +27,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.dat
*/
/**
- * A {@link AbstractDefaultTestCommand} extension for showing edit view of a data set that assuming
- * that opening its detail view was triggered before.
+ * A {@link AbstractDefaultTestCommand} extension for showing edit view of a data set that assuming that opening its detail view was triggered before.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/CheckExperimentTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/CheckExperimentTable.java
index 21c6a9d9c7f..61bc4313570 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/CheckExperimentTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/CheckExperimentTable.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of experiments has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of experiments has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ShowExperiment.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ShowExperiment.java
index 74f3bf37420..8a1d4aaa458 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ShowExperiment.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ShowExperiment.java
@@ -27,8 +27,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestU
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
/**
- * A {@link AbstractDefaultTestCommand} extension for showing details view of an experiment with
- * given code.
+ * A {@link AbstractDefaultTestCommand} extension for showing details view of an experiment with given code.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/expressions/filter/OpenFilterSettingsCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/expressions/filter/OpenFilterSettingsCommand.java
index 3104346dd9a..d2e910bc96e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/expressions/filter/OpenFilterSettingsCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/expressions/filter/OpenFilterSettingsCommand.java
@@ -22,9 +22,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTab
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestUtil;
/**
- * After the data from table with given id are loaded, the settings dialog is opened and filters tab
- * selected. The command activates loading data with callback id:
- * <code> FilterGrid.createGridId(gridDisplayId)</code>.
+ * After the data from table with given id are loaded, the settings dialog is opened and filters tab selected. The command activates loading data with
+ * callback id: <code> FilterGrid.createGridId(gridDisplayId)</code>.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/material/CheckMaterialTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/material/CheckMaterialTable.java
index dc31ca8d301..66e91cfe6bd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/material/CheckMaterialTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/material/CheckMaterialTable.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of materials has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of materials has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/CheckProjectTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/CheckProjectTable.java
index 123c19d685d..648026ec418 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/CheckProjectTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/CheckProjectTable.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of projects has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of projects has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/FillProjectRegistrationForm.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/FillProjectRegistrationForm.java
index f21685a22f3..208ea5d7840 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/FillProjectRegistrationForm.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/project/FillProjectRegistrationForm.java
@@ -25,8 +25,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestUtil;
/**
- * A {@link AbstractDefaultTestCommand} extension for filling
- * {@link AbstractProjectEditRegisterForm}.
+ * A {@link AbstractDefaultTestCommand} extension for filling {@link AbstractProjectEditRegisterForm}.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeAssignmentTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeAssignmentTable.java
index e72bf9a396b..b09b061ef76 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeAssignmentTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeAssignmentTable.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of property type
- * assignments has been loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of property type assignments has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeTable.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeTable.java
index 389c87cac04..7737bb34d89 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeTable.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/property_type/CheckPropertyTypeTable.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.Abstract
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * A {@link AbstractDefaultTestCommand} extension to check whether a list of property types has been
- * loaded.
+ * A {@link AbstractDefaultTestCommand} extension to check whether a list of property types has been loaded.
*
* @author Izabela Adamczyk
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ExportSamplesTestCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ExportSamplesTestCommand.java
index d3b4e6a7d69..64d0f4dcecd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ExportSamplesTestCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ExportSamplesTestCommand.java
@@ -31,10 +31,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
* System tests for the server side of sample export.<BR>
- * We wait for the listing operation to complete and then initiate 2 subsequent server calls to get
- * the exported table (when preparation is finished it triggers getting the content).<BR>
- * It's hard to have complete tests of the client side due to the fact, that the final response is
- * received from the servlet and is opened in a new browser window which is hard to access.
+ * We wait for the listing operation to complete and then initiate 2 subsequent server calls to get the exported table (when preparation is finished
+ * it triggers getting the content).<BR>
+ * It's hard to have complete tests of the client side due to the fact, that the final response is received from the servlet and is opened in a new
+ * browser window which is hard to access.
*
* @author Tomasz Pylak
*/
@@ -105,8 +105,8 @@ public class ExportSamplesTestCommand extends AbstractDefaultTestCommand
}
/**
- * A command is executed when export preparation operation and saving the result operation have
- * successfully completed. The result is compared with the specified expected content.
+ * A command is executed when export preparation operation and saving the result operation have successfully completed. The result is compared
+ * with the specified expected content.
*/
public ITestCommand createCheckExportCommand(String expectedHeader,
String expectedFirstLineOrNull, int expectedTotalLines)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ShowSample.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ShowSample.java
index 056405aff1b..29789db15af 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ShowSample.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/ShowSample.java
@@ -27,8 +27,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.GWTTestU
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
- * A {@link AbstractDefaultTestCommand} extension for showing details view of a sample with given
- * code.
+ * A {@link AbstractDefaultTestCommand} extension for showing details view of a sample with given code.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/util/GridTestUtils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/util/GridTestUtils.java
index 5cfa781126e..f7e6d959716 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/util/GridTestUtils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/util/GridTestUtils.java
@@ -49,8 +49,7 @@ public class GridTestUtils
}
/**
- * Fires a double click event on a first row which contains given value in a column with a
- * specified id.
+ * Fires a double click event on a first row which contains given value in a column with a specified id.
*/
public static <T extends ModelData> void fireDoubleClick(final Grid<T> table, String columnId,
String columnValue)
@@ -60,8 +59,7 @@ public class GridTestUtils
}
/**
- * Fires a single click event on a first row which contains given value in a column with a
- * specified id.
+ * Fires a single click event on a first row which contains given value in a column with a specified id.
*/
public static <T extends ModelData> void fireSingleClick(final Grid<T> table, String columnId,
String columnValue)
@@ -71,8 +69,7 @@ public class GridTestUtils
}
/**
- * Fires a selection of a first row in given table which contains given value in a column with a
- * specified id.
+ * Fires a selection of a first row in given table which contains given value in a column with a specified id.
*/
public static <T extends ModelData> void fireSelectRow(final Grid<T> table, String columnId,
String columnValue)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractDefaultTestCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractDefaultTestCommand.java
index 83ce5dbb333..95aa9d90462 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractDefaultTestCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractDefaultTestCommand.java
@@ -21,8 +21,8 @@ import junit.framework.Assert;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
/**
- * Abstract super class of all test commands which are executed if there are no active callbacks
- * (all callbacks were detected by {@link RemoteConsole}).
+ * Abstract super class of all test commands which are executed if there are no active callbacks (all callbacks were detected by {@link RemoteConsole}
+ * ).
*
* @author Franz-Josef Elmer
* @author Piotr Buczek
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractGWTTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractGWTTestCase.java
index 492d46f0ea8..5d443e942d7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractGWTTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractGWTTestCase.java
@@ -59,8 +59,8 @@ public abstract class AbstractGWTTestCase extends GWTTestCase
}
/**
- * Delays test termination until the specified timeout (in milliseconds). Wrapper of
- * {@link #delayTestFinish(int)}. Will be used in {@link RemoteConsole}.
+ * Delays test termination until the specified timeout (in milliseconds). Wrapper of {@link #delayTestFinish(int)}. Will be used in
+ * {@link RemoteConsole}.
*/
void delayTestTermination(final int timeoutMillis)
{
@@ -111,8 +111,7 @@ public abstract class AbstractGWTTestCase extends GWTTestCase
}
/**
- * Starts the tests. Sets the timeout after which the test is terminated to
- * {@value #DEFAULT_TIMEOUT}.
+ * Starts the tests. Sets the timeout after which the test is terminated to {@value #DEFAULT_TIMEOUT}.
*/
protected void launchTest()
{
@@ -189,8 +188,7 @@ public abstract class AbstractGWTTestCase extends GWTTestCase
}
/**
- * Returns a command that executes specified <var>preprocessingAction</var> before preparing the
- * specified <var>command</var>.
+ * Returns a command that executes specified <var>preprocessingAction</var> before preparing the specified <var>command</var>.
*/
protected ITestCommand createCommandWrapper(final ITestCommand command,
final IDelegatedAction preprocessingAction)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractProperty.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractProperty.java
index cff00732d79..a969e843599 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractProperty.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/AbstractProperty.java
@@ -25,8 +25,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
/**
- * Abstract superclass of a generic {@link IProperty} which implements convenient property value
- * expectations. It uses a fluent API approach for its methods to prepare expectations.
+ * Abstract superclass of a generic {@link IProperty} which implements convenient property value expectations. It uses a fluent API approach for its
+ * methods to prepare expectations.
*
* @author Franz-Josef Elmer
*/
@@ -106,8 +106,7 @@ public abstract class AbstractProperty<C extends IPropertyChecker<?>> implements
}
/**
- * Sets assertion that the property value is of type {@link ICodeHolder} with a code equals the
- * specified code.
+ * Sets assertion that the property value is of type {@link ICodeHolder} with a code equals the specified code.
*/
public C asCode(final String expectedCode)
{
@@ -122,8 +121,7 @@ public abstract class AbstractProperty<C extends IPropertyChecker<?>> implements
}
/**
- * Sets assertion that the property value is of type {@link IDeletionProvider} with no
- * {@link Deletion} object.
+ * Sets assertion that the property value is of type {@link IDeletionProvider} with no {@link Deletion} object.
*/
public C asValidEntity()
{
@@ -139,8 +137,7 @@ public abstract class AbstractProperty<C extends IPropertyChecker<?>> implements
}
/**
- * Sets assertion that the property value is of type {@link IDeletionProvider} with an
- * {@link Deletion} object.
+ * Sets assertion that the property value is of type {@link IDeletionProvider} with an {@link Deletion} object.
*/
public C asDeletedEntity()
{
@@ -156,8 +153,7 @@ public abstract class AbstractProperty<C extends IPropertyChecker<?>> implements
}
/**
- * Sets assertion that the property value is of type {@link EntityProperty} with a value equals
- * the specified string.
+ * Sets assertion that the property value is of type {@link EntityProperty} with a value equals the specified string.
*/
public C asProperty(final String expectedValue)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/CheckTableCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/CheckTableCommand.java
index 0bb7b5547c3..8a7bfbeac05 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/CheckTableCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/CheckTableCommand.java
@@ -29,8 +29,8 @@ import com.extjs.gxt.ui.client.widget.grid.Grid;
import ch.systemsx.cisd.openbis.generic.shared.basic.Row;
/**
- * Command for checking the content (i.e. <code>ListStore</code>) of a table (i.e. <code>Grid</code>
- * ). It uses a fluent API approach for its methods to prepare expectations.
+ * Command for checking the content (i.e. <code>ListStore</code>) of a table (i.e. <code>Grid</code> ). It uses a fluent API approach for its methods
+ * to prepare expectations.
*
* @author Franz-Josef Elmer
*/
@@ -140,8 +140,7 @@ public class CheckTableCommand extends AbstractDefaultTestCommand
}
/**
- * Prepares this with the expectation upon the number of table columns, including hidden
- * columns.
+ * Prepares this with the expectation upon the number of table columns, including hidden columns.
*/
public CheckTableCommand expectedColumnsNumber(final int expectedNumberOfColumns)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/GWTTestUtil.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/GWTTestUtil.java
index 4d72ff0bc44..3fc5260c96c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/GWTTestUtil.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/GWTTestUtil.java
@@ -116,8 +116,7 @@ public final class GWTTestUtil
}
/**
- * Simulates click on the {@link CheckBox} with specified id (modifies check box value and fires
- * {@link Events#Change} event).
+ * Simulates click on the {@link CheckBox} with specified id (modifies check box value and fires {@link Events#Change} event).
*
* @throws AssertionError if not found, isn't a CheckBox or is not enabled.
*/
@@ -148,8 +147,7 @@ public final class GWTTestUtil
}
/**
- * sets value of a property field with id specified by given {@link PropertyField} (handles both
- * simple and comboBox fields)
+ * sets value of a property field with id specified by given {@link PropertyField} (handles both simple and comboBox fields)
*/
public final static void setPropertyFieldValue(PropertyField property)
{
@@ -157,8 +155,8 @@ public final class GWTTestUtil
}
/**
- * sets value of a property field with id specified by given {@link PropertyField} and
- * <var>formIdPrefix</var> (handles both simple and comboBox fields)
+ * sets value of a property field with id specified by given {@link PropertyField} and <var>formIdPrefix</var> (handles both simple and comboBox
+ * fields)
*/
public final static void setPropertyFieldValue(String formIdPrefix, PropertyField property)
{
@@ -383,8 +381,7 @@ public final class GWTTestUtil
/**
* Tries to find the widget with id that matches given <var>id</var>.
*
- * @param id a regular expression of an id (usually exactly an id string but it may contain some
- * regular expression wildcards inside)
+ * @param id a regular expression of an id (usually exactly an id string but it may contain some regular expression wildcards inside)
* @return <code>null</code> if not found.
*/
public static Widget tryToFindByID(final String id)
@@ -395,8 +392,8 @@ public final class GWTTestUtil
}
/**
- * Traverses root panel tree with the specified widget handler. Traversal is stopped when
- * {@link IWidgetHandler#handle(Widget)} returns <code>true</code>.
+ * Traverses root panel tree with the specified widget handler. Traversal is stopped when {@link IWidgetHandler#handle(Widget)} returns
+ * <code>true</code>.
*/
public static void traverseRootPanel(final IWidgetHandler<Widget> handler)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IMessageValidator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IMessageValidator.java
index 178a593c35f..033addcd7a5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IMessageValidator.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IMessageValidator.java
@@ -17,8 +17,6 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.testframework;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public interface IMessageValidator
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IProperty.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IProperty.java
index ff6b1404e79..f8ccfe4b7fa 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IProperty.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IProperty.java
@@ -16,11 +16,9 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.testframework;
-
/**
- * Interface of an assertion preparation for a property checked by a
- * {@link IPropertyChecker} of type <code>C</code>.
- * It uses a fluent API approach for its methods to prepare expectations.
+ * Interface of an assertion preparation for a property checked by a {@link IPropertyChecker} of type <code>C</code>. It uses a fluent API approach
+ * for its methods to prepare expectations.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IPropertyChecker.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IPropertyChecker.java
index 0b8f3d806e7..b214dd5d549 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IPropertyChecker.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/IPropertyChecker.java
@@ -17,8 +17,7 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.testframework;
/**
- * Interface for preparing expectation on a property checking class.
- * It uses a fluent API approach for its methods to prepare expectations.
+ * Interface for preparing expectation on a property checking class. It uses a fluent API approach for its methods to prepare expectations.
*
* @author Franz-Josef Elmer
*/
@@ -28,10 +27,9 @@ public interface IPropertyChecker<C extends IPropertyChecker<?>>
* Creates an expectation for the property of specified name.
*/
public IProperty<C> property(String name);
-
+
/**
- * Adds an expectation of a property with specified name and specified
- * assertion object which checks the property value.
+ * Adds an expectation of a property with specified name and specified assertion object which checks the property value.
*
* @return this checker.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/ITestCommand.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/ITestCommand.java
index 01c8d0eb3fb..3d2cbabcb85 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/ITestCommand.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/ITestCommand.java
@@ -21,8 +21,7 @@ import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
/**
- * A command which will be executed after a successful invocation of
- * {@link AsyncCallback#onSuccess(Object)}.
+ * A command which will be executed after a successful invocation of {@link AsyncCallback#onSuccess(Object)}.
*
* @author Franz-Josef Elmer
* @author Piotr Buczek
@@ -35,16 +34,14 @@ public interface ITestCommand
public void execute();
/**
- * @return <tt>true</tt> if the specified result should trigger this command in case of an
- * invocation of {@link AsyncCallback#onSuccess(Object)}, otherwise <tt>false</tt>
+ * @return <tt>true</tt> if the specified result should trigger this command in case of an invocation of {@link AsyncCallback#onSuccess(Object)},
+ * otherwise <tt>false</tt>
*/
public boolean isValidOnSucess(Object result);
/**
- * @return <tt>true</tt> if the specified <var>failureMessage</var> and <var>throwable</var>
- * should trigger this command in case of an invocation of
- * {@link AsyncCallback#onFailure(Throwable)} of specified <var>callback</var>,
- * otherwise <tt>false</tt>
+ * @return <tt>true</tt> if the specified <var>failureMessage</var> and <var>throwable</var> should trigger this command in case of an invocation
+ * of {@link AsyncCallback#onFailure(Throwable)} of specified <var>callback</var>, otherwise <tt>false</tt>
*/
public boolean isValidOnFailure(AbstractAsyncCallback<?> callback, String failureMessage,
Throwable throwable);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/PropertyCheckingManager.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/PropertyCheckingManager.java
index 19a8768661b..ed05009ec0c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/PropertyCheckingManager.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/PropertyCheckingManager.java
@@ -59,7 +59,7 @@ public class PropertyCheckingManager extends Assert
* Checks the assertion for the specified properties.
*/
@SuppressWarnings(
- { "unchecked", "rawtypes" })
+ { "unchecked", "rawtypes" })
public void assertProperties(final Map<String, ?> actualProperties)
{
for (final Map.Entry<String, IValueAssertion> expectedProperty : expectedProperties
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/RemoteConsole.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/RemoteConsole.java
index c11783c7595..41e8553385d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/RemoteConsole.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/RemoteConsole.java
@@ -29,11 +29,10 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ICallbackL
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
/**
- * A class which allows to execute a sequence of {@link ITestCommand} instances. The commands are
- * executed in the order they have been added by {@link #prepare(ITestCommand)}. In order to be
- * executed a command has to be valid for the kind of {@link AsyncCallback} invocation. With the
- * method {@link #finish(int)} a timeout will be specified after which the test will be terminated
- * independent whether all commands have been executed or not. In the later case the test fails.
+ * A class which allows to execute a sequence of {@link ITestCommand} instances. The commands are executed in the order they have been added by
+ * {@link #prepare(ITestCommand)}. In order to be executed a command has to be valid for the kind of {@link AsyncCallback} invocation. With the method
+ * {@link #finish(int)} a timeout will be specified after which the test will be terminated independent whether all commands have been executed or
+ * not. In the later case the test fails.
*
* @author Franz-Josef Elmer
* @author Piotr Buczek
@@ -69,8 +68,7 @@ public class RemoteConsole
}
/**
- * Prepares the console with the specified command which will be executed if the specified
- * condition is fulfilled.
+ * Prepares the console with the specified command which will be executed if the specified condition is fulfilled.
*/
public RemoteConsole prepare(final ITestCommand command)
{
@@ -154,10 +152,8 @@ public class RemoteConsole
/**
* Does necessary cleanup after the test has completed.
*
- * @param delayInMillisecondsOrZero The max duration the test was allowed to run. This is only
- * used to construct an error message if the duration ran out before the test
- * completed. In cases where it is known that the test completed properly, this can
- * be set to 0.
+ * @param delayInMillisecondsOrZero The max duration the test was allowed to run. This is only used to construct an error message if the duration
+ * ran out before the test completed. In cases where it is known that the test completed properly, this can be set to 0.
*/
private void cleanupAfterTests(final int delayInMillisecondsOrZero)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/TestUtil.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/TestUtil.java
index a097809b3fc..1d4c471e900 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/TestUtil.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/TestUtil.java
@@ -46,9 +46,8 @@ public class TestUtil
}
/**
- * Returns the specified object as a normalised string. Normalization includes trimming,
- * conversion to lower case, stripping off <code><div></code> and <code><a></code>
- * wrappers.
+ * Returns the specified object as a normalised string. Normalization includes trimming, conversion to lower case, stripping off
+ * <code><div></code> and <code><a></code> wrappers.
*
* @return {@link #NULL} if <code>objectOrNull == null</code>
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WaitForAllActiveCallbacksFinish.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WaitForAllActiveCallbacksFinish.java
index 5547d1f1759..aa284853847 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WaitForAllActiveCallbacksFinish.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WaitForAllActiveCallbacksFinish.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.testframework;
/**
- * {@link AbstractDefaultTestCommand} extension that does nothing. It should be used if we want to
- * make sure that all callbacks will finish without failure.
+ * {@link AbstractDefaultTestCommand} extension that does nothing. It should be used if we want to make sure that all callbacks will finish without
+ * failure.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WidgetPicker.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WidgetPicker.java
index 3b76f349213..16423e61955 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WidgetPicker.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/client/testframework/WidgetPicker.java
@@ -19,8 +19,7 @@ package ch.systemsx.cisd.openbis.generic.client.web.client.testframework;
import com.google.gwt.user.client.ui.Widget;
/**
- * Widget handler which picks the first widget having a specified ID. Allows to use regular
- * expression wildcards.
+ * Widget handler which picks the first widget having a specified ID. Allows to use regular expression wildcards.
*
* @author Franz-Josef Elmer
* @author Piotr Buczek
@@ -32,8 +31,7 @@ public class WidgetPicker implements IWidgetHandler<Widget>
private Widget pickedWidget;
/**
- * Creates an instance for the specified widget ID. Given <var>id</var> may contain regular
- * expression wildcards.
+ * Creates an instance for the specified widget ID. Given <var>id</var> may contain regular expression wildcards.
*/
public WidgetPicker(final String id)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/HelpPageIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/HelpPageIdentifierTest.java
index 0e2e57a45bc..bc33aed36e4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/HelpPageIdentifierTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/HelpPageIdentifierTest.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpP
* @author Piotr Buczek
*/
@Friend(toClasses =
- { HelpPageIdentifier.class })
+{ HelpPageIdentifier.class })
public class HelpPageIdentifierTest extends AssertJUnit
{
@@ -43,7 +43,7 @@ public class HelpPageIdentifierTest extends AssertJUnit
final HelpPageDomain baseDomain = HelpPageDomain.CHANGE_USER_SETTINGS;
assertNull(baseDomain.getSuperDomainOrNull());
assertDomainPathsEquals(new HelpPageDomain[]
- { HelpPageDomain.CHANGE_USER_SETTINGS }, baseDomain.getDomainPath());
+ { HelpPageDomain.CHANGE_USER_SETTINGS }, baseDomain.getDomainPath());
}
@Test
@@ -52,7 +52,7 @@ public class HelpPageIdentifierTest extends AssertJUnit
final HelpPageDomain subDomain = HelpPageDomain.USERS;
assertNotNull(subDomain.getSuperDomainOrNull());
assertDomainPathsEquals(new HelpPageDomain[]
- { HelpPageDomain.ADMINISTRATION, HelpPageDomain.AUTHORIZATION, HelpPageDomain.USERS },
+ { HelpPageDomain.ADMINISTRATION, HelpPageDomain.AUTHORIZATION, HelpPageDomain.USERS },
subDomain.getDomainPath());
}
@@ -73,13 +73,13 @@ public class HelpPageIdentifierTest extends AssertJUnit
protected Object[][] getPageTitlesToTest()
{
return new Object[][]
- {
- { HelpPageDomain.CHANGE_USER_SETTINGS, HelpPageAction.ACTION,
- "HELP__CHANGE_USER_SETTINGS__ACTION" },
- { HelpPageDomain.USERS, HelpPageAction.BROWSE,
- "HELP__ADMINISTRATION__AUTHORIZATION__USERS__BROWSE" },
+ {
+ { HelpPageDomain.CHANGE_USER_SETTINGS, HelpPageAction.ACTION,
+ "HELP__CHANGE_USER_SETTINGS__ACTION" },
+ { HelpPageDomain.USERS, HelpPageAction.BROWSE,
+ "HELP__ADMINISTRATION__AUTHORIZATION__USERS__BROWSE" },
- };
+ };
}
@SuppressWarnings("deprecation")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/URLListEncoderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/URLListEncoderTest.java
index 6af1c65b6b3..5f0aed1016f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/URLListEncoderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/URLListEncoderTest.java
@@ -31,15 +31,15 @@ public class URLListEncoderTest extends AssertJUnit
protected Object[][] getLists()
{
return new Object[][]
- {
+ {
{ new String[]
- { "a +:\"\\b", "bobo" } },
+ { "a +:\"\\b", "bobo" } },
{ new String[]
- { "a ,,", ",, b" } },
+ { "a ,,", ",, b" } },
{ new String[]
- { "a,,b ", " ", " c,d,e" } },
+ { "a,,b ", " ", " c,d,e" } },
- };
+ };
}
@Test(dataProvider = "lists")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/ViewLocatorResolverRegistryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/ViewLocatorResolverRegistryTest.java
index a6113809824..e6197beaec3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/ViewLocatorResolverRegistryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/clientnonjs/ViewLocatorResolverRegistryTest.java
@@ -42,10 +42,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
/**
- * A test of the ViewLocatorHandlerRegistry functionality from the Java side. The JavaScript side is
- * tested by
- * {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocatorResolverRegistryTest}
- * .
+ * A test of the ViewLocatorHandlerRegistry functionality from the Java side. The JavaScript side is tested by
+ * {@link ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocatorResolverRegistryTest} .
*
* @author Chandrasekhar Ramakrishnan
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
index d2bd0d7d98e..ea55ce95833 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
@@ -520,7 +520,7 @@ public final class CommonClientServiceTest extends AbstractClientServiceTest
{
prepareGetSessionToken(this);
allowing(httpSession).getAttribute(SessionConstants.OPENBIS_RESULT_SET_MANAGER);
- will(returnValue(new CachedResultSetManager<String>(tableDataCache,
+ will(returnValue(new CachedResultSetManager<String>(tableDataCache,
new TokenBasedResultSetKeyGenerator(), new ICustomColumnsProvider()
{
@Override
@@ -534,7 +534,7 @@ public final class CommonClientServiceTest extends AbstractClientServiceTest
one(commonServer).listExperimentExternalData(SESSION_TOKEN, experimentId, true);
will(returnValue(Collections.singletonList(ds)));
-
+
one(commonServer).listDataSetTypes(SESSION_TOKEN);
will(returnValue(Arrays.asList(ds.getDataSetType())));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/WebClientConfigurationProviderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/WebClientConfigurationProviderTest.java
index 8201dcf642b..4657a6add1f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/WebClientConfigurationProviderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/WebClientConfigurationProviderTest.java
@@ -25,8 +25,6 @@ import ch.systemsx.cisd.openbis.generic.shared.WebClientConfigurationProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.WebClientConfiguration;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class WebClientConfigurationProviderTest extends AssertJUnit
@@ -37,21 +35,20 @@ public class WebClientConfigurationProviderTest extends AssertJUnit
WebClientConfigurationProvider provider = new WebClientConfigurationProvider(new Properties());
assertEquals(null, provider.getWebClientConfiguration().getPropertyOrNull("hello", "world"));
}
-
+
@Test
public void testTechnologyProperties()
{
Properties properties = new Properties();
properties.setProperty(WebClientConfigurationProvider.TECHNOLOGIES, "t1, t2");
- properties.setProperty("t1.a" , "alpha1");
- properties.setProperty("t2.b" , "beta1");
-
+ properties.setProperty("t1.a", "alpha1");
+ properties.setProperty("t2.b", "beta1");
+
WebClientConfigurationProvider provider = new WebClientConfigurationProvider(properties);
WebClientConfiguration webClientConfiguration = provider.getWebClientConfiguration();
-
+
assertEquals("alpha1", webClientConfiguration.getPropertyOrNull("t1", "a"));
assertEquals(null, provider.getWebClientConfiguration().getPropertyOrNull("t2", "a"));
}
-
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowTest.java
index 972ba950711..d7cf8ef687a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/calculator/RowTest.java
@@ -31,19 +31,18 @@ import org.testng.annotations.Test;
*/
public class RowTest extends AssertJUnit
{
- private static final List<Comparable<?>> EXAMPLE_ROW = Arrays.<Comparable<?>>asList("hello", new Double(42.5));
+ private static final List<Comparable<?>> EXAMPLE_ROW = Arrays.<Comparable<?>> asList("hello", new Double(42.5));
private static final String COL1 = "col1";
private static final String COL2 = "col2";
-
+
private static final String PROPERTY_KEY = "key";
private static final String PROPERTY_VALUE = "value";
private static final String PROPERTY_VALUE2 = "value2";
-
private Mockery context;
private Row row;
@@ -56,15 +55,15 @@ public class RowTest extends AssertJUnit
context = new Mockery();
dataProvider = context.mock(ITableDataProvider.class);
context.checking(new Expectations()
- {
{
- allowing(dataProvider).getValue(COL1, EXAMPLE_ROW);
- will(returnValue(EXAMPLE_ROW.get(0)));
+ {
+ allowing(dataProvider).getValue(COL1, EXAMPLE_ROW);
+ will(returnValue(EXAMPLE_ROW.get(0)));
- allowing(dataProvider).getValue(COL2, EXAMPLE_ROW);
- will(returnValue(EXAMPLE_ROW.get(1)));
- }
- });
+ allowing(dataProvider).getValue(COL2, EXAMPLE_ROW);
+ will(returnValue(EXAMPLE_ROW.get(1)));
+ }
+ });
row = new Row(dataProvider);
row.setRowData(EXAMPLE_ROW);
@@ -117,7 +116,7 @@ public class RowTest extends AssertJUnit
public void testColDefsWithNullArgument()
{
prepareColDefs(PROPERTY_VALUE, PROPERTY_VALUE2, 0);
-
+
List<ColumnDefinition> defs = row.colDefs(null);
assertEquals(2, defs.size());
@@ -198,7 +197,7 @@ public class RowTest extends AssertJUnit
public void testColsGroupedByWithOneGroup()
{
prepareColDefs(PROPERTY_VALUE, PROPERTY_VALUE, 2);
-
+
List<ColumnGroup> groups = row.colsGroupedBy(PROPERTY_KEY);
assertEquals(1, groups.size());
@@ -235,7 +234,7 @@ public class RowTest extends AssertJUnit
{
prepareColDefs(propertyValueOfFirstDefinition, propertyValueOfSecondDefinition, 1);
}
-
+
private void prepareColDefs(final String propertyValueOfFirstDefinition,
final String propertyValueOfSecondDefinition, final int numberOfTryToGetPropertyInvocations)
{
@@ -244,10 +243,10 @@ public class RowTest extends AssertJUnit
{
one(dataProvider).getAllColumnIDs();
will(returnValue(Arrays.asList(COL1, COL2)));
-
+
exactly(numberOfTryToGetPropertyInvocations).of(dataProvider).tryToGetProperty(COL1, PROPERTY_KEY);
will(returnValue(propertyValueOfFirstDefinition));
-
+
exactly(numberOfTryToGetPropertyInvocations).of(dataProvider).tryToGetProperty(COL2, PROPERTY_KEY);
will(returnValue(propertyValueOfSecondDefinition));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/ScriptProviderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/ScriptProviderTest.java
index bed3ca927c5..82018af27cc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/ScriptProviderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/ScriptProviderTest.java
@@ -85,7 +85,7 @@ public class ScriptProviderTest extends AbstractProviderTest
script.setName("my-" + kind + "-script");
script.setDescription("A script for " + kind);
script.setEntityKind(kind == null ? null : new EntityKind[]
- { kind });
+ { kind });
script.setScript("do something with " + kind);
script.setScriptType(ScriptType.DYNAMIC_PROPERTY);
script.setPluginType(PluginType.JYTHON);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/FilterUtilsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/FilterUtilsTest.java
index 2b1fe000e4e..88d24e27edf 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/FilterUtilsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/FilterUtilsTest.java
@@ -38,6 +38,7 @@ public class FilterUtilsTest extends AssertJUnit
private static final class MockDataProvider implements ITableDataProvider
{
private final String expectedColumnID;
+
private final List<List<? extends Comparable<?>>> rows;
MockDataProvider(String expectedColumnID, List<? extends Comparable<?>>... rows)
@@ -71,14 +72,14 @@ public class FilterUtilsTest extends AssertJUnit
{
return null;
}
-
+
@Override
public String tryToGetProperty(String columnID, String key)
{
return null;
}
}
-
+
private ITableDataProvider dataProvider;
@SuppressWarnings("unchecked")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/TSVRendererTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/TSVRendererTest.java
index 70523e18874..d4f2365a143 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/TSVRendererTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/TSVRendererTest.java
@@ -69,13 +69,13 @@ public class TSVRendererTest extends AssertJUnit
will(returnValue(entities));
}
});
-
+
String content = TSVRenderer.createTable(dataProvider, "#");
-
+
assertEquals("h0\th1#x\ty#a\tb#", content);
context.assertIsSatisfied();
}
-
+
@Test
public void testRendererNoRows()
{
@@ -88,9 +88,9 @@ public class TSVRendererTest extends AssertJUnit
will(returnValue(entities));
}
});
-
+
String content = TSVRenderer.createTable(dataProvider, "\n");
-
+
assertEquals("h0\th1\n", content);
context.assertIsSatisfied();
}
@@ -98,13 +98,13 @@ public class TSVRendererTest extends AssertJUnit
private void prepareGetAllColumnTitles(final String... titles)
{
context.checking(new Expectations()
- {
{
- one(dataProvider).getAllColumnTitles();
- will(returnValue(Arrays.asList(titles)));
- }
- });
-
+ {
+ one(dataProvider).getAllColumnTitles();
+ will(returnValue(Arrays.asList(titles)));
+ }
+ });
+
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/XMLPropertyTransformerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/XMLPropertyTransformerTest.java
index 256df40f251..ed6dc6ffd63 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/XMLPropertyTransformerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/XMLPropertyTransformerTest.java
@@ -48,7 +48,7 @@ public class XMLPropertyTransformerTest extends AssertJUnit
sample.setProperties(Arrays.<IEntityProperty> asList(p1, p2, p3));
new XMLPropertyTransformer().transformXMLProperties(Arrays.asList(sample));
-
+
IEntityProperty transformed1 = sample.getProperties().get(0);
assertEquals("<?xml version=\"1.0\" encoding=\"UTF-8\"?><b>hello world</b>",
transformed1.tryGetAsString());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index 33e4662eac8..41d4a2848db 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -1729,7 +1729,7 @@ public final class CommonServerTest extends AbstractServerTestCase
{
one(commonBusinessObjectFactory).createDataSetTable(session);
will(returnValue(dataSetTable));
-
+
one(daoFactory).getTransactionTimestamp();
will(returnValue(new Date()));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceRegistratorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceRegistratorTest.java
index 9da6c07c2e6..61d320afc6c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceRegistratorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceRegistratorTest.java
@@ -108,10 +108,10 @@ public class DataStoreServiceRegistratorTest extends AssertJUnit
dataStore.setCode(DATASTORE_CODE);
DatastoreServiceDescription r1 =
DatastoreServiceDescription.reporting("R1", "r1", new String[]
- { "A.*", "B" }, DATASTORE_CODE, ReportingPluginType.TABLE_MODEL);
+ { "A.*", "B" }, DATASTORE_CODE, ReportingPluginType.TABLE_MODEL);
DatastoreServiceDescription p1 =
DatastoreServiceDescription.processing("P1", "p1", new String[]
- { "A.*", "C.*", "D" }, DATASTORE_CODE);
+ { "A.*", "C.*", "D" }, DATASTORE_CODE);
context.checking(new Expectations()
{
{
@@ -154,10 +154,10 @@ public class DataStoreServiceRegistratorTest extends AssertJUnit
dataStore.setCode(DATASTORE_CODE);
DatastoreServiceDescription r1 =
DatastoreServiceDescription.reporting("R1", "r1", new String[]
- { "A.*", "B" }, DATASTORE_CODE, ReportingPluginType.TABLE_MODEL);
+ { "A.*", "B" }, DATASTORE_CODE, ReportingPluginType.TABLE_MODEL);
DatastoreServiceDescription p1 =
DatastoreServiceDescription.processing("P1", "p1", new String[]
- { "A.*", "C.*", "D" }, DATASTORE_CODE);
+ { "A.*", "C.*", "D" }, DATASTORE_CODE);
context.checking(new Expectations()
{
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DatabaseLastModificationAdvisorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DatabaseLastModificationAdvisorTest.java
index e20fff2e824..90a151996ce 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DatabaseLastModificationAdvisorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/DatabaseLastModificationAdvisorTest.java
@@ -107,13 +107,13 @@ public class DatabaseLastModificationAdvisorTest extends AssertJUnit
private Method getCreateMethod() throws Exception
{
return ICommonServer.class.getMethod("registerDataSetType", new Class[]
- { String.class, DataSetType.class });
+ { String.class, DataSetType.class });
}
private Method getUpdateMethod() throws Exception
{
return ICommonServer.class.getMethod("updateDataSet", new Class[]
- { String.class, DataSetUpdatesDTO.class });
+ { String.class, DataSetUpdatesDTO.class });
}
private void waitForClockChange()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
index bac6f852838..216efad596b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
@@ -285,7 +285,7 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
for (AbstractExternalData dataSetWithNewValue : dataSetsWithNewValue)
{
Date modificationDate = dataSetWithNewValue.getModificationDate();
- assertTrue("The modification date (" + modificationDate + ") should be current (" + now + ")",
+ assertTrue("The modification date (" + modificationDate + ") should be current (" + now + ")",
modificationDate.compareTo(now) >= 0);
String savedComment = EntityHelper.tryFindPropertyValue(dataSetWithNewValue, "COMMENT");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/JythonEvaluatorPoolTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/JythonEvaluatorPoolTest.java
index 9f74240f4a2..1bf0a4fbbf0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/JythonEvaluatorPoolTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/JythonEvaluatorPoolTest.java
@@ -213,13 +213,13 @@ public class JythonEvaluatorPoolTest
{
return pool.getManagedPropertiesRunner(script).evaluate(
new IAtomicEvaluation<IJythonEvaluator>()
- {
- @Override
- public IJythonEvaluator evaluate(IJythonEvaluator evaluator)
- {
- return evaluator;
- }
- });
+ {
+ @Override
+ public IJythonEvaluator evaluate(IJythonEvaluator evaluator)
+ {
+ return evaluator;
+ }
+ });
}
};
}
@@ -235,17 +235,17 @@ public class JythonEvaluatorPoolTest
{
return pool.getManagedPropertiesRunner(script).evaluate(
new IAtomicEvaluation<Integer>()
- {
- @Override
- public Integer evaluate(IJythonEvaluator evaluator)
- {
- Integer x =
- (Integer) evaluator
- .evalFunction("return_x_if_defined_else_0");
- evaluator.evalFunction("set_x", 3);
- return x;
- }
- });
+ {
+ @Override
+ public Integer evaluate(IJythonEvaluator evaluator)
+ {
+ Integer x =
+ (Integer) evaluator
+ .evalFunction("return_x_if_defined_else_0");
+ evaluator.evalFunction("set_x", 3);
+ return x;
+ }
+ });
}
};
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ServerInterfaceRegressionTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ServerInterfaceRegressionTest.java
index f9b18bbae72..53424e5cf4e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ServerInterfaceRegressionTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ServerInterfaceRegressionTest.java
@@ -37,7 +37,7 @@ public class ServerInterfaceRegressionTest extends AnnotationAppliedTestCase
{
List<String> exemptMethods = new ArrayList<String>();
exemptMethods.add("getDisabledText");
-
+
assertMandatoryMethodAnnotations(ICommonServer.class, CommonServer.class,
"getLastModificationState: Transactional\n", exemptMethods);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessControllerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessControllerTest.java
index 6d8b4b13c5d..e4d24abc7a8 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessControllerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultAccessControllerTest.java
@@ -90,7 +90,7 @@ public final class DefaultAccessControllerTest
try
{
FileUtils.writeLines(capFile,
- Arrays.asList("# Test overriding annotation",
+ Arrays.asList("# Test overriding annotation",
"MY_CAP: SPACE_OBSERVER; ARG1 = SPACE_USER",
"my_cap2: arg1 = space_user"));
} catch (IOException ex)
@@ -114,7 +114,7 @@ public final class DefaultAccessControllerTest
{
allowing(daoFactory).getProjectDAO();
will(returnValue(projectDAO));
-
+
allowing(projectDAO).tryGetByPermID("42");
will(returnValue(project));
}
@@ -272,7 +272,7 @@ public final class DefaultAccessControllerTest
{
final IAuthSession session = AuthorizationTestUtil.createSession();
session.tryGetPerson().setRoleAssignments(createRoleAssignments());
- final Method method = MyInterface.class.getMethod("myMethodWithGardedArgument",
+ final Method method = MyInterface.class.getMethod("myMethodWithGardedArgument",
String.class, String.class, String.class);
assertNotNull(method);
Argument<?>[] arguments = createArguments(method);
@@ -290,19 +290,19 @@ public final class DefaultAccessControllerTest
{
final IAuthSession session = AuthorizationTestUtil.createSession();
session.tryGetPerson().setRoleAssignments(createRoleAssignments());
- final Method method = MyInterface.class.getMethod("myMethodWithGardedArgument",
+ final Method method = MyInterface.class.getMethod("myMethodWithGardedArgument",
String.class, String.class, String.class);
assertNotNull(method);
Argument<?>[] arguments = createArguments(method);
project.setId(1L);
-
+
final Status authorized = accessController.isAuthorized(session, method, arguments);
-
+
assertEquals("ERROR", authorized.toString());
assertEquals("person: john_doe, roles: [INSTANCE_OBSERVER, SPACE_USER], value: arg0", project.getDescription());
context.assertIsSatisfied();
}
-
+
@Test
public void testIsNotAuthorizedWithGardedArgumentWithDifferentRoles() throws Exception
{
@@ -320,7 +320,7 @@ public final class DefaultAccessControllerTest
assertEquals(null, project.getDescription());
context.assertIsSatisfied();
}
-
+
@Test
public void testIsAuthorizedWithGardedArgumentWithRolesOverridden() throws Exception
{
@@ -330,9 +330,9 @@ public final class DefaultAccessControllerTest
String.class, String.class);
assertNotNull(method);
Argument<?>[] arguments = createArguments(method);
-
+
final Status authorized = accessController.isAuthorized(session, method, arguments);
-
+
assertEquals("OK", authorized.toString());
assertEquals("person: john_doe, roles: [SPACE_USER], value: arg0", project.getDescription());
context.assertIsSatisfied();
@@ -347,14 +347,14 @@ public final class DefaultAccessControllerTest
String.class, String.class);
assertNotNull(method);
Argument<?>[] arguments = createArguments(method);
-
+
final Status authorized = accessController.isAuthorized(session, method, arguments);
-
+
assertEquals("OK", authorized.toString());
assertEquals("person: john_doe, roles: [SPACE_USER], value: arg0", project.getDescription());
context.assertIsSatisfied();
}
-
+
@Test
public void testIsAuthorizedWithGardedArgumentWithRolesOverridden3() throws Exception
{
@@ -364,15 +364,15 @@ public final class DefaultAccessControllerTest
String.class, String.class, String.class);
assertNotNull(method);
Argument<?>[] arguments = createArguments(method);
-
+
final Status authorized = accessController.isAuthorized(session, method, arguments);
-
+
assertEquals("ERROR: \"None of method roles '[SPACE_POWER_USER, SPACE_ADMIN, INSTANCE_ADMIN]' "
+ "could be found in roles of user 'John Doe'.\"", authorized.toString());
assertEquals(null, project.getDescription());
context.assertIsSatisfied();
}
-
+
private Argument<?>[] createArguments(final Method method)
{
List<Argument<?>> arguments = new ArrayList<>();
@@ -414,38 +414,33 @@ public final class DefaultAccessControllerTest
public void myMethodWithUngardedArgument(String sessionToken, String argument1);
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
- public void myMethodWithGardedArgument(String sessionToken,
+ public void myMethodWithGardedArgument(String sessionToken,
@AuthorizationGuard(guardClass = MockPredicate.class) String argument1,
@AuthorizationGuard(guardClass = MockPredicate.class) String argument2);
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public void myMethodWithGardedArgumentWithDifferentRoles(String sessionToken,
@AuthorizationGuard(guardClass = MockPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER })
- String argument1);
-
+ rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER }) String argument1);
+
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@Capability("MY_CAP")
public void myMethodWithGardedArgumentWithRolesOverridden(String sessionToken,
@AuthorizationGuard(name = "ARG1", guardClass = MockPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER })
- String argument1);
+ rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER }) String argument1);
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@Capability("MY_CAP2")
public void myMethodWithGardedArgumentWithRolesOverridden2(String sessionToken,
@AuthorizationGuard(name = "ARG1", guardClass = MockPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER })
- String argument1);
+ rolesAllowed = { RoleWithHierarchy.SPACE_ETL_SERVER }) String argument1);
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public void myMethodWithGardedArgumentWithRolesOverridden3(String sessionToken,
@AuthorizationGuard(name = "ARG1", guardClass = MockPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_POWER_USER })
- String argument1,
+ rolesAllowed = { RoleWithHierarchy.SPACE_POWER_USER }) String argument1,
@AuthorizationGuard(name = "ARG2", guardClass = MockPredicate.class,
- rolesAllowed = { RoleWithHierarchy.SPACE_USER })
- String argument2);
+ rolesAllowed = { RoleWithHierarchy.SPACE_USER }) String argument2);
}
/**
@@ -464,7 +459,7 @@ public final class DefaultAccessControllerTest
roles.add(roleWithIdentifier.getRole());
}
Collections.sort(roles);
-
+
String description = "person: " + person.getUserId() + ", roles: " + roles + ", value: " + valueOrNull;
if (project.getDescription() != null)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicateTest.java
index dbe50eaddb0..e80f23ad8a2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicateTest.java
@@ -32,8 +32,6 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.IPredicat
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class CollectionPredicateTest extends AuthorizationTestCase
@@ -60,14 +58,14 @@ public class CollectionPredicateTest extends AuthorizationTestCase
{
CollectionPredicate<String> arrayPredicate = new CollectionPredicate<String>(predicate);
arrayPredicate.init(provider);
-
+
List<String> emptyList = Collections.<String> emptyList();
Status status = arrayPredicate.evaluate(createPerson(), createRoles(true), emptyList);
-
+
assertEquals(false, status.isError());
context.assertIsSatisfied();
}
-
+
@Test
public void testWithTwoElements()
{
@@ -85,13 +83,13 @@ public class CollectionPredicateTest extends AuthorizationTestCase
will(returnValue(Status.OK));
}
});
-
+
Status status = arrayPredicate.evaluate(person, roles, Arrays.asList("a", "b"));
-
+
assertEquals(false, status.isError());
context.assertIsSatisfied();
}
-
+
@Test
public void testWithTwoElementsOneFailing()
{
@@ -109,9 +107,9 @@ public class CollectionPredicateTest extends AuthorizationTestCase
will(returnValue(Status.createError()));
}
});
-
+
Status status = arrayPredicate.evaluate(person, roles, Arrays.asList("a", "b"));
-
+
assertEquals(true, status.isError());
context.assertIsSatisfied();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
index 671579db982..a6ba1920aba 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
@@ -39,7 +39,7 @@ public class ExternalDataValidatorTest extends AuthorizationTestCase
"http://someURL", null, new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool())));
return data;
}
-
+
private PhysicalDataSet createDataForSample(SpacePE space)
{
PhysicalDataSet data = new PhysicalDataSet();
@@ -63,7 +63,7 @@ public class ExternalDataValidatorTest extends AuthorizationTestCase
PersonPE person = createPersonWithRoleAssignments();
assertEquals(true, validator.isValid(person, createDataForSample(createAnotherSpace())));
}
-
+
@Test
public void testIsValidWithDataInTheRightDatabaseInstance()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidatorTest.java
index 9094c157d8d..d04561f8db5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidatorTest.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationTestCase;
@@ -44,7 +43,7 @@ public final class GroupValidatorTest extends AuthorizationTestCase
{
assertEquals("Unspecified person", e.getMessage());
}
-
+
context.assertIsSatisfied();
}
@@ -55,7 +54,7 @@ public final class GroupValidatorTest extends AuthorizationTestCase
final PersonPE personPE = createPerson();
final SpacePE groupPE = createSpace();
final Space space = SpaceTranslator.translate(groupPE);
-
+
assertFalse(groupValidator.isValid(personPE, space));
context.assertIsSatisfied();
@@ -71,7 +70,7 @@ public final class GroupValidatorTest extends AuthorizationTestCase
assertTrue(groupValidator.isValid(personPE, space));
context.assertIsSatisfied();
}
-
+
@Test
public final void testIsValidWithMatchingRoleAssignmentOnDatabaseinstanceLevel()
{
@@ -82,5 +81,5 @@ public final class GroupValidatorTest extends AuthorizationTestCase
assertTrue(groupValidator.isValid(personPE, space));
context.assertIsSatisfied();
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrorsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrorsTest.java
index 0a8b061937c..edefe6c7362 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrorsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/PropertiesBatchEvaluationErrorsTest.java
@@ -45,7 +45,6 @@ public class PropertiesBatchEvaluationErrorsTest extends AssertJUnit
private ScriptPE script;
-
@BeforeMethod
public void setUp()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
index e2fb8a95ede..70ea85e901a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
@@ -472,12 +472,12 @@ public class DataBOTest extends AbstractBOTest
{
assertEquals("Unknown data set code '" + COMPONENT_CODE + "'", e.getMessage());
}
- DataPE data = dataBO.getData();
-
- assertSame(experiment, data.getExperiment());
- assertEquals(null, data.tryGetSample());
- assertSame(true, data.isMeasured());
- assertSame(dataStore, data.getDataStore());
+ DataPE data = dataBO.getData();
+
+ assertSame(experiment, data.getExperiment());
+ assertEquals(null, data.tryGetSample());
+ assertSame(true, data.isMeasured());
+ assertSame(dataStore, data.getDataStore());
context.assertIsSatisfied();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
index e83c9101c8b..fa6731952df 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
@@ -229,8 +229,7 @@ public final class ExperimentBOTest extends AbstractBOTest
final ProjectPE project = createProject(groupCode, projectCode);
final ExperimentTypePE type = createExperimentType(expTypeCode);
final ExperimentPE experiment = createExperiment(project, expCode, type);
- TimeIntervalChecker timeIntervalChecker
- = new TimeIntervalChecker(daoFactory.getTransactionTimestamp());
+ TimeIntervalChecker timeIntervalChecker = new TimeIntervalChecker(daoFactory.getTransactionTimestamp());
prepareAnyDaoCreation();
context.checking(new Expectations()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyValidatorTest.java
index c556f96dd63..111c513b96f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/PropertyValidatorTest.java
@@ -108,35 +108,35 @@ public final class PropertyValidatorTest extends AbstractBOTest
private final static Object[][] getNonWorkingValues()
{
return new Object[][]
- {
- { createTimestampPropertyType(), DateFormatUtils.format(new Date(), "yyyy") },
- { createIntegerPropertyType(), "a" },
- { createIntegerPropertyType(), "1.1" },
- { createRealPropertyType(), "b" },
- { createBooleanPropertyType(), "BOB" }, };
+ {
+ { createTimestampPropertyType(), DateFormatUtils.format(new Date(), "yyyy") },
+ { createIntegerPropertyType(), "a" },
+ { createIntegerPropertyType(), "1.1" },
+ { createRealPropertyType(), "b" },
+ { createBooleanPropertyType(), "BOB" }, };
}
@DataProvider
private final static Object[][] getWorkingValues()
{
return new Object[][]
- {
- { createVarcharPropertyType(), "" },
- { createVarcharPropertyType(), "varchar" },
- {
- createTimestampPropertyType(),
- DateFormatUtils.format(new Date(),
- SupportedDatePattern.CANONICAL_DATE_PATTERN.getPattern()) },
- {
- createTimestampPropertyType(),
- DateFormatUtils.format(new Date(),
- SupportedDatePattern.US_DATE_TIME_24_PATTERN.getPattern()) },
- { createIntegerPropertyType(), "1" },
- { createRealPropertyType(), "1" },
- { createRealPropertyType(), "1.1" },
- { createBooleanPropertyType(), "yes" },
- { createBooleanPropertyType(), "1" },
- { createBooleanPropertyType(), "true" } };
+ {
+ { createVarcharPropertyType(), "" },
+ { createVarcharPropertyType(), "varchar" },
+ {
+ createTimestampPropertyType(),
+ DateFormatUtils.format(new Date(),
+ SupportedDatePattern.CANONICAL_DATE_PATTERN.getPattern()) },
+ {
+ createTimestampPropertyType(),
+ DateFormatUtils.format(new Date(),
+ SupportedDatePattern.US_DATE_TIME_24_PATTERN.getPattern()) },
+ { createIntegerPropertyType(), "1" },
+ { createRealPropertyType(), "1" },
+ { createRealPropertyType(), "1.1" },
+ { createBooleanPropertyType(), "yes" },
+ { createBooleanPropertyType(), "1" },
+ { createBooleanPropertyType(), "true" } };
}
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
index f8e6d4aa923..4c640c4560e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
@@ -432,7 +432,6 @@ public final class SampleBOTest extends AbstractBOTest
allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
-
one(relationshipService).shareSample(with(any(IAuthSession.class)),
with(any(SamplePE.class)));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
index 6e80885bc51..c101a2f0856 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
@@ -143,27 +143,27 @@ public class SearchDomainSearcherTest extends AbstractBOTest
assertEquals("E1", results.get(0).getEntity().getPermId());
assertEquals("Search Domain: test-db, Score: [Score: 11.5, bit score: 5.75, evalue: 12.5], Result location: "
+ "[Experiment type: UNKNOWN-E, perm id: E1, code: CODE-E1, property type: S, alignment in sequence: [42-45], "
- + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
+ + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(0).getSearchResult().toString());
assertEquals("S2", results.get(1).getEntity().getPermId());
assertEquals("Search Domain: test-db, Score: [Score: 10.5, bit score: 5.25, evalue: 11.5], Result location: "
+ "[Sample type: TYPE, perm id: S2, code: CODE-S2, property type: OLIGO, alignment in sequence: [42-45], "
- + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
+ + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(1).getSearchResult().toString());
assertEquals("S1", results.get(2).getEntity().getPermId());
assertEquals("Search Domain: test-db, Score: [Score: 9.5, bit score: 4.75, evalue: 10.5], Result location: "
+ "[Sample type: TYPE, perm id: S1, code: CODE-S1, property type: OLIGO, alignment in sequence: [42-45], "
- + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
+ + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(2).getSearchResult().toString());
assertEquals("DS1", results.get(3).getEntity().getPermId());
assertEquals("Search Domain: test-db, Score: [Score: 0.5, bit score: 0.25, evalue: 1.5], Result location: "
+ "[Data set type: UNKNOWN, perm id: DS1, code: DS1, property type: SEQ, alignment in sequence: [42-45], "
- + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
+ + "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(3).getSearchResult().toString());
assertEquals(4, results.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testSearchForDataSetsWithSequences()
{
@@ -259,7 +259,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
}
});
}
-
+
private void prepareSearchForEntityPropertiesWithSequences(final DataStorePE dataStore,
final IDataStoreService service, final double initialScore, final String... foundLocations)
{
@@ -355,7 +355,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
data.setFileFormatType(fileFormatType);
return data;
}
-
+
private SamplePE createSample(String permID)
{
SamplePE sample = new SamplePE();
@@ -372,7 +372,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
sample.setSampleType(sampleType);
return sample;
}
-
+
private ExperimentPE createExperiment(String permID)
{
ExperimentPE experiment = new ExperimentPE();
@@ -402,7 +402,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
}
return permIds;
}
-
+
private ISearchDomainResultScore createScore(double score)
{
BlastScore blastScore = new BlastScore();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBOTest.java
index 1f45068e04f..9b731df54ff 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBOTest.java
@@ -74,6 +74,7 @@ public final class TrashBOTest extends AbstractBOTest
private static String EXAMPLE_REASON = "example reason";
private static Long COMPONENT_CONTAINER_RELATIONSHIP_ID = 1001L;
+
private static Long CHILDREN_PARENT_RELATIONSHIP_ID = 1002L;
private static TechId EXAMPLE_ID = new TechId(1L);
@@ -117,10 +118,10 @@ public final class TrashBOTest extends AbstractBOTest
type = new RelationshipTypePE();
type.setId(CHILDREN_PARENT_RELATIONSHIP_ID);
will(returnValue(type));
-
+
allowing(boFactory).createSampleLister(session);
will(returnValue(sampleLister));
-
+
allowing(boFactory).createDatasetLister(session);
will(returnValue(datasetLister));
}
@@ -238,7 +239,7 @@ public final class TrashBOTest extends AbstractBOTest
context.assertIsSatisfied();
}
-
+
private void prepareEntityGraph(EntityGraphGenerator g)
{
g.assertConsistency();
@@ -297,7 +298,7 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private void prepareListDataSetIdsByExperimentIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<List<TechId>> handler = new AbstractMockHandler<List<TechId>>()
@@ -318,7 +319,7 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private void prepareListDataSetIdsBySampleIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<Collection<TechId>> handler = new AbstractMockHandler<Collection<TechId>>()
@@ -339,29 +340,29 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private void prepareGetByTechId(final EntityGraphGenerator g)
{
final AbstractMockHandler<TechId> handler = new AbstractMockHandler<TechId>()
+ {
+ @Override
+ public Object invoke(Invocation invocation) throws Throwable
{
- @Override
- public Object invoke(Invocation invocation) throws Throwable
+ DataSetNode dataSetNode = g.getDataSets().get(argument.getId());
+ ExternalDataPE dataSet = Utils.createData(dataSetNode);
+ print("getByTechId(" + argument + ") = " + dataSet);
+ return dataSet;
+ }
+ };
+ context.checking(new Expectations()
{
- DataSetNode dataSetNode = g.getDataSets().get(argument.getId());
- ExternalDataPE dataSet = Utils.createData(dataSetNode);
- print("getByTechId(" + argument + ") = " + dataSet);
- return dataSet;
- }
- };
- context.checking(new Expectations()
{
- {
- allowing(dataDAO).getByTechId(with(handler));
- will(handler);
- }
- });
+ allowing(dataDAO).getByTechId(with(handler));
+ will(handler);
+ }
+ });
}
-
+
private void prepareFindChildrenOrComponentIds(final EntityGraphGenerator g)
{
class FindChildrenIdsMockHandler
@@ -478,84 +479,84 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private void prepareListExperimentsByIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<Collection<Long>> handler = new AbstractMockHandler<Collection<Long>>()
- {
- @Override
- public Object invoke(Invocation invocation) throws Throwable
{
- List<ExperimentPE> experiments = new ArrayList<ExperimentPE>();
- Map<Long, ExperimentNode> experimentNodes = g.getExperiments();
- for (Long id : argument)
- {
- ExperimentNode experimentNode = experimentNodes.get(id);
- experiments.add(Utils.createExperimentPE(experimentNode));
- }
- print("listByExperimentIds(" + argument + ") = " + experiments);
- return experiments;
- }
- };
- context.checking(new Expectations()
+ @Override
+ public Object invoke(Invocation invocation) throws Throwable
{
+ List<ExperimentPE> experiments = new ArrayList<ExperimentPE>();
+ Map<Long, ExperimentNode> experimentNodes = g.getExperiments();
+ for (Long id : argument)
{
- allowing(experimentDAO).listByIDs(with(handler));
- will(handler);
+ ExperimentNode experimentNode = experimentNodes.get(id);
+ experiments.add(Utils.createExperimentPE(experimentNode));
}
- });
+ print("listByExperimentIds(" + argument + ") = " + experiments);
+ return experiments;
+ }
+ };
+ context.checking(new Expectations()
+ {
+ {
+ allowing(experimentDAO).listByIDs(with(handler));
+ will(handler);
+ }
+ });
}
-
+
private void prepareListByDataSetIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<Collection<Long>> handler = new AbstractMockHandler<Collection<Long>>()
- {
- @Override
- public Object invoke(Invocation invocation) throws Throwable
{
- List<AbstractExternalData> dataSets = new ArrayList<AbstractExternalData>();
- Map<Long, DataSetNode> dataSetNodes = g.getDataSets();
- for (Long id : argument)
- {
- DataSetNode dataSetNode = dataSetNodes.get(id);
- dataSets.add(Utils.createExternalData(dataSetNode));
- }
- print("listByDataSetIds(" + argument + ") = " + dataSets);
- return dataSets;
- }
- };
- context.checking(new Expectations()
+ @Override
+ public Object invoke(Invocation invocation) throws Throwable
{
+ List<AbstractExternalData> dataSets = new ArrayList<AbstractExternalData>();
+ Map<Long, DataSetNode> dataSetNodes = g.getDataSets();
+ for (Long id : argument)
{
- allowing(datasetLister).listByDatasetIds(with(handler), with(TrashBO.DATA_SET_FETCH_OPTIONS));
- will(handler);
+ DataSetNode dataSetNode = dataSetNodes.get(id);
+ dataSets.add(Utils.createExternalData(dataSetNode));
}
- });
+ print("listByDataSetIds(" + argument + ") = " + dataSets);
+ return dataSets;
+ }
+ };
+ context.checking(new Expectations()
+ {
+ {
+ allowing(datasetLister).listByDatasetIds(with(handler), with(TrashBO.DATA_SET_FETCH_OPTIONS));
+ will(handler);
+ }
+ });
}
private void prepareListDataSetContainerIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<Collection<Long>> handler = new AbstractMockHandler<Collection<Long>>()
+ {
+ @Override
+ public Object invoke(Invocation invocation) throws Throwable
{
- @Override
- public Object invoke(Invocation invocation) throws Throwable
+ Map<Long, Set<Long>> idsMap = g.getContainerDataSetIdsMap(
+ TechId.createList(new ArrayList<Long>(argument)));
+ print("listContainerIds(" + argument + ") = " + idsMap);
+ return idsMap;
+ }
+ };
+ context.checking(new Expectations()
{
- Map<Long, Set<Long>> idsMap = g.getContainerDataSetIdsMap(
- TechId.createList(new ArrayList<Long>(argument)));
- print("listContainerIds(" + argument + ") = " + idsMap);
- return idsMap;
- }
- };
- context.checking(new Expectations()
{
- {
- allowing(datasetLister).listContainerIds(with(handler));
- will(handler);
- }
- });
+ allowing(datasetLister).listContainerIds(with(handler));
+ will(handler);
+ }
+ });
}
-
+
private void prepareListDataSetComponentIds(final EntityGraphGenerator g)
{
final AbstractMockHandler<Collection<Long>> handler = new AbstractMockHandler<Collection<Long>>()
@@ -577,12 +578,13 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private void prepareGetDataSetsAndNonDeletableDataSets(final EntityGraphGenerator g)
{
class DataSetTableMockHandler extends BaseMatcher<List<TechId>>
{
private List<DataPE> dataSets = new ArrayList<DataPE>();
+
private List<ExternalDataPE> nonDeletableDataSets = new ArrayList<ExternalDataPE>();
@Override
@@ -614,7 +616,7 @@ public final class TrashBOTest extends AbstractBOTest
}
return true;
}
-
+
}
final DataSetTableMockHandler handler = new DataSetTableMockHandler();
@@ -635,7 +637,7 @@ public final class TrashBOTest extends AbstractBOTest
}
});
}
-
+
private static abstract class AbstractMockHandler<T> extends BaseMatcher<T> implements Action
{
protected T argument;
@@ -654,12 +656,12 @@ public final class TrashBOTest extends AbstractBOTest
return true;
}
}
-
- private List<TechId> asIds(IIdHolder...entities)
+
+ private List<TechId> asIds(IIdHolder... entities)
{
return TechId.createList(Arrays.asList(entities));
}
-
+
private static final void print(Object message)
{
String methodName = null;
@@ -673,5 +675,5 @@ public final class TrashBOTest extends AbstractBOTest
}
System.out.println(methodName + ": " + message);
}
-
+
}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
index 804a4d9ab38..3d051bc351e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
@@ -79,7 +79,7 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
propertyType.setId(PROPERTY_TYPE_ID);
propertyType.setDataType(new DataType(DataTypeCode.CONTROLLEDVOCABULARY));
will(returnValue(new PropertyType[]
- { propertyType }));
+ { propertyType }));
allowing(resolver).get(ENTITY_ID);
will(returnValue(holder));
@@ -114,7 +114,7 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
codeRecord.id = VOCABULARY_ID;
codeRecord.code = "http://my.url.org/?q=${term}";
will(returnValue(new CodeRecord[]
- { codeRecord }));
+ { codeRecord }));
one(setQuery).getEntityPropertyVocabularyTermValues(entityIDs);
VocabularyTermRecord termRecord = new VocabularyTermRecord();
@@ -152,7 +152,7 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
codeRecord.id = VOCABULARY_ID;
codeRecord.code = "http://my.url.org/?q=$term$";
will(returnValue(new CodeRecord[]
- { codeRecord }));
+ { codeRecord }));
one(setQuery).getEntityPropertyVocabularyTermValues(entityIDs);
VocabularyTermRecord termRecord = new VocabularyTermRecord();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
index d7aa311ad98..79f5b55ca59 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
@@ -47,10 +47,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
* @author Tomasz Pylak
*/
@Friend(toClasses =
- { ExperimentProjectSpaceCodeRecord.class, ISecondaryEntityListingQuery.class,
- SecondaryEntityDAO.class })
+{ ExperimentProjectSpaceCodeRecord.class, ISecondaryEntityListingQuery.class,
+ SecondaryEntityDAO.class })
@Test(groups =
- { "db", "misc" })
+{ "db", "misc" })
public class SecondaryEntityListingQueryTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
index 90b9ee8a9ff..bbb2ab1d257 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
@@ -149,11 +149,11 @@ public class DatasetListingQueryTest extends AbstractDAOTest
{
ExperimentPE experiment1 =
getExperiment(dbInstance.getCode(), "CISD", "NEMO", "EXP-TEST-1", daoFactory);
-
+
Long relationshipTypeId = RelationshipUtils.getParentChildRelationshipType(daoFactory.getRelationshipTypeDAO()).getId();
List<DatasetRecord> datasets = asList(query.getDataSetsForExperimentAndDescendents(experiment1.getId(), relationshipTypeId));
-
+
for (DatasetRecord record : datasets)
{
assertTrue(record.is_post_registered != null);
@@ -171,7 +171,7 @@ public class DatasetListingQueryTest extends AbstractDAOTest
{
assertTrue(record.is_post_registered != null);
}
- }
+ }
@Test
public void testQueryUsingSelectAllExternalDatasReturnsNotNullPostRegistered()
@@ -181,7 +181,7 @@ public class DatasetListingQueryTest extends AbstractDAOTest
{
assertTrue(record.is_post_registered != null);
}
- }
+ }
@Test
public void testQueryUsingSelectAllExternalDatasReturnsCorrectPostRegistered()
@@ -189,14 +189,16 @@ public class DatasetListingQueryTest extends AbstractDAOTest
List<DatasetRecord> datasets = asList(query.getDatasetsByDataStoreId(1));
for (DatasetRecord record : datasets)
{
- if(record.code.equals("COMPONENT_1A")) {
+ if (record.code.equals("COMPONENT_1A"))
+ {
assertTrue(record.is_post_registered == false);
}
- else {
+ else
+ {
assertTrue(record.is_post_registered == true);
}
}
- }
+ }
@Test
public void testDatasetsForSample()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
index 51a7311d118..f21517c0e33 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/DataSetNode.java
@@ -19,11 +19,10 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.entitygraph;
import java.util.ArrayList;
import java.util.List;
-
public final class DataSetNode extends EntityNode
{
private boolean deletable = true;
-
+
ExperimentNode experiment;
SampleNode sample;
@@ -40,7 +39,7 @@ public final class DataSetNode extends EntityNode
{
super("DS", id);
}
-
+
public boolean isDeletable()
{
return deletable;
@@ -50,12 +49,12 @@ public final class DataSetNode extends EntityNode
{
return experiment;
}
-
+
public SampleNode getSample()
{
return sample;
}
-
+
public List<DataSetNode> getChildren()
{
return children;
@@ -65,23 +64,23 @@ public final class DataSetNode extends EntityNode
{
return parents;
}
-
+
public List<DataSetNode> getComponents()
{
return components;
}
-
+
public List<DataSetNode> getContainers()
{
return containers;
}
-
+
public DataSetNode nonDeletable()
{
deletable = false;
return this;
}
-
+
void hasComponents(DataSetNode... someComponentDataSets)
{
for (DataSetNode componentDataSet : someComponentDataSets)
@@ -99,8 +98,8 @@ public final class DataSetNode extends EntityNode
childDataSet.parents.add(this);
}
}
-
- void hasParents(DataSetNode...someParentDataSets)
+
+ void hasParents(DataSetNode... someParentDataSets)
{
for (DataSetNode parentDataSet : someParentDataSets)
{
@@ -108,7 +107,7 @@ public final class DataSetNode extends EntityNode
parentDataSet.children.add(this);
}
}
-
+
@Override
public String toString()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
index 7419487dcc0..c15f73725d7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityGraphGenerator.java
@@ -31,19 +31,31 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
public final class EntityGraphGenerator
{
- private static enum Kind { E, S, DS}
-
+ private static enum Kind
+ {
+ E, S, DS
+ }
+
private static final class EntityDescription
{
private static final Pattern EXPERIMENT_PATTERN = Pattern.compile("(/S\\d+/P\\d+/)?E\\d+");
+
private static final Pattern SAMPLE_PATTERN = Pattern.compile("(/(S\\d+/(P\\d+/)?)?)?S\\d+");
+
private static final Pattern DATA_SET_PATTERN = Pattern.compile("DS\\d+");
+
Kind kind;
+
boolean shared;
+
String space;
+
String project;
+
int id;
+
String type;
+
EntityDescription(String description)
{
int indexOfBracket = description.indexOf('[');
@@ -58,7 +70,7 @@ public final class EntityGraphGenerator
throw new IllegalArgumentException("Missing ']' at the end of " + description);
}
identifier = description.substring(0, indexOfBracket);
- type = description.substring(indexOfBracket + 1, description.length() - 1);
+ type = description.substring(indexOfBracket + 1, description.length() - 1);
}
String[] elements = identifier.split("/");
if (EXPERIMENT_PATTERN.matcher(identifier).matches())
@@ -91,12 +103,12 @@ public final class EntityGraphGenerator
id = Integer.parseInt(elements[elements.length - 1].substring(kind.name().length()));
}
}
-
+
private static interface IEntitiesProvider<T extends EntityNode>
{
public Collection<? extends EntityNode> getEntities(T entityNode);
}
-
+
private class Parser
{
private void parse(List<String> parts)
@@ -116,7 +128,7 @@ public final class EntityGraphGenerator
handle(ds, rest);
}
}
-
+
private void handle(ExperimentNode experiment, List<String> parts)
{
experiment.has(getSamples("samples", parts));
@@ -136,7 +148,7 @@ public final class EntityGraphGenerator
dataSet.hasParents(getDataSets("parents", parts));
dataSet.hasComponents(getDataSets("components", parts));
}
-
+
private SampleNode[] getSamples(String name, List<String> parts)
{
List<SampleNode> sampleNodes = new ArrayList<SampleNode>();
@@ -147,7 +159,7 @@ public final class EntityGraphGenerator
}
return sampleNodes.toArray(new SampleNode[descriptions.size()]);
}
-
+
private DataSetNode[] getDataSets(String name, List<String> parts)
{
List<DataSetNode> dataSetNodes = new ArrayList<DataSetNode>();
@@ -160,7 +172,7 @@ public final class EntityGraphGenerator
}
return dataSetNodes.toArray(new DataSetNode[descriptions.size()]);
}
-
+
private List<EntityDescription> getDescriptions(String name, Kind kind, List<String> parts)
{
String descriptionsConcatenated = getValue(name, parts);
@@ -181,7 +193,7 @@ public final class EntityGraphGenerator
}
return result;
}
-
+
private String getValue(String name, List<String> parts)
{
for (String part : parts)
@@ -195,13 +207,13 @@ public final class EntityGraphGenerator
return null;
}
}
-
+
private final Map<Long, ExperimentNode> experiments = new TreeMap<Long, ExperimentNode>();
private final Map<Long, SampleNode> samples = new TreeMap<Long, SampleNode>();
private final Map<Long, DataSetNode> dataSets = new TreeMap<Long, DataSetNode>();
-
+
public void parse(String definition)
{
Parser parser = new Parser();
@@ -239,12 +251,12 @@ public final class EntityGraphGenerator
SampleNode sample = dataSetNode.getSample();
if (experiment == null && sample == null)
{
- throw new IllegalStateException("Data set " + dataSetNode.getCode()
+ throw new IllegalStateException("Data set " + dataSetNode.getCode()
+ " should belong to an experiment or a sample.");
}
if (sample != null && sample.getExperiment() != experiment)
{
- throw new IllegalStateException("Data set " + dataSetNode.getCode()
+ throw new IllegalStateException("Data set " + dataSetNode.getCode()
+ " should belong to the same experiment as the sample.");
}
}
@@ -260,7 +272,7 @@ public final class EntityGraphGenerator
}
return experimentNode;
}
-
+
private ExperimentNode createExperiment(EntityDescription entityDescription)
{
ExperimentNode experimentNode = e(entityDescription.id);
@@ -279,7 +291,7 @@ public final class EntityGraphGenerator
}
return sampleNode;
}
-
+
private SampleNode createSample(EntityDescription entityDescription)
{
SampleNode sampleNode = s(entityDescription.id);
@@ -314,7 +326,7 @@ public final class EntityGraphGenerator
{
return dataSets;
}
-
+
public List<TechId> getSampleIdsByExperimentIds(Collection<TechId> experimentIds)
{
return getRelatedIds(experimentIds, experiments, new EntityGraphGenerator.IEntitiesProvider<ExperimentNode>()
@@ -342,13 +354,13 @@ public final class EntityGraphGenerator
public List<TechId> getDataSetIdsByExperimentIds(Collection<TechId> experimentIds)
{
return getRelatedIds(experimentIds, experiments, new EntityGraphGenerator.IEntitiesProvider<ExperimentNode>()
+ {
+ @Override
+ public Collection<? extends EntityNode> getEntities(ExperimentNode experiment)
{
- @Override
- public Collection<? extends EntityNode> getEntities(ExperimentNode experiment)
- {
- return experiment.getDataSets();
- }
- });
+ return experiment.getDataSets();
+ }
+ });
}
public List<TechId> getDataSetIdsBySampleIds(Collection<TechId> experimentIds)
@@ -386,7 +398,7 @@ public final class EntityGraphGenerator
}
});
}
-
+
public Map<Long, Set<Long>> getContainerDataSetIdsMap(Collection<TechId> dataSetIds)
{
return getRelatedIdsMap(dataSetIds, dataSets, new EntityGraphGenerator.IEntitiesProvider<DataSetNode>()
@@ -402,15 +414,15 @@ public final class EntityGraphGenerator
public Map<Long, Set<Long>> getComponentDataSetIdsMap(Collection<TechId> dataSetIds)
{
return getRelatedIdsMap(dataSetIds, dataSets, new EntityGraphGenerator.IEntitiesProvider<DataSetNode>()
- {
- @Override
- public Collection<? extends EntityNode> getEntities(DataSetNode dataSet)
{
- return dataSet.getComponents();
- }
- });
+ @Override
+ public Collection<? extends EntityNode> getEntities(DataSetNode dataSet)
+ {
+ return dataSet.getComponents();
+ }
+ });
}
-
+
public Map<Long, Set<Long>> getParentsDataSetIdsMap(Collection<TechId> dataSetIds)
{
return getRelatedIdsMap(dataSetIds, dataSets, new EntityGraphGenerator.IEntitiesProvider<DataSetNode>()
@@ -432,7 +444,7 @@ public final class EntityGraphGenerator
appendTo(builder, "#Data Sets", dataSets);
return builder.toString();
}
-
+
private void appendTo(StringBuilder builder, String name, Map<Long, ? extends EntityNode> nodes)
{
if (nodes.isEmpty())
@@ -446,7 +458,7 @@ public final class EntityGraphGenerator
}
}
- private <T extends EntityNode> List<TechId> getRelatedIds(Collection<TechId> entityIds, Map<Long, T> entities,
+ private <T extends EntityNode> List<TechId> getRelatedIds(Collection<TechId> entityIds, Map<Long, T> entities,
EntityGraphGenerator.IEntitiesProvider<T> provider)
{
List<TechId> ids = new ArrayList<TechId>();
@@ -460,8 +472,8 @@ public final class EntityGraphGenerator
}
return ids;
}
-
- private <T extends EntityNode> Map<Long, Set<Long>> getRelatedIdsMap(Collection<TechId> entityIds, Map<Long, T> entities,
+
+ private <T extends EntityNode> Map<Long, Set<Long>> getRelatedIdsMap(Collection<TechId> entityIds, Map<Long, T> entities,
EntityGraphGenerator.IEntitiesProvider<T> provider)
{
Map<Long, Set<Long>> idsMap = new LinkedHashMap<Long, Set<Long>>();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
index a90b4922dc5..490cc8338f5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/EntityNode.java
@@ -23,7 +23,7 @@ public class EntityNode implements IIdHolder, Comparable<EntityNode>
private final long id;
private final String code;
-
+
private String type;
EntityNode(String codePrefix, long id)
@@ -42,7 +42,7 @@ public class EntityNode implements IIdHolder, Comparable<EntityNode>
{
return code;
}
-
+
public String getIdentifier()
{
return getCode();
@@ -52,7 +52,7 @@ public class EntityNode implements IIdHolder, Comparable<EntityNode>
{
return type;
}
-
+
public String getIdentifierAndType()
{
return getCodeAndType();
@@ -78,11 +78,11 @@ public class EntityNode implements IIdHolder, Comparable<EntityNode>
{
return this.getCode().compareTo(that.getCode());
}
-
+
@Override
public String toString()
{
return getIdentifierAndType();
}
-
+
}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
index 573e3d096c1..59daae0d664 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/ExperimentNode.java
@@ -24,16 +24,16 @@ public final class ExperimentNode extends EntityNode
private final List<SampleNode> samples = new ArrayList<SampleNode>();
private final List<DataSetNode> dataSets = new ArrayList<DataSetNode>();
-
+
private String space;
-
+
private String project;
ExperimentNode(long id)
{
super("E", id);
}
-
+
public String getSpace()
{
return space;
@@ -58,12 +58,12 @@ public final class ExperimentNode extends EntityNode
{
return samples;
}
-
+
public List<DataSetNode> getDataSets()
{
return dataSets;
}
-
+
void has(SampleNode... someSamples)
{
for (SampleNode sample : someSamples)
@@ -81,7 +81,7 @@ public final class ExperimentNode extends EntityNode
dataSets.add(dataSet);
}
}
-
+
@Override
public String getIdentifier()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
index d08074b82b7..0ed3034275d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/SampleNode.java
@@ -22,21 +22,28 @@ import java.util.List;
public final class SampleNode extends EntityNode
{
private final List<SampleNode> components = new ArrayList<SampleNode>();
+
private final List<SampleNode> parents = new ArrayList<SampleNode>();
+
private final List<SampleNode> children = new ArrayList<SampleNode>();
+
private final List<DataSetNode> dataSets = new ArrayList<DataSetNode>();
private boolean shared;
+
private String space;
+
private String project;
+
private ExperimentNode experiment;
+
private SampleNode container;
SampleNode(long id)
{
super("S", id);
}
-
+
public boolean isShared()
{
return shared;
@@ -76,7 +83,7 @@ public final class SampleNode extends EntityNode
{
this.experiment = experiment;
}
-
+
public SampleNode getContainer()
{
return container;
@@ -86,7 +93,7 @@ public final class SampleNode extends EntityNode
{
this.container = container;
}
-
+
public List<SampleNode> getComponents()
{
return components;
@@ -96,17 +103,17 @@ public final class SampleNode extends EntityNode
{
return parents;
}
-
+
public List<SampleNode> getChildren()
{
return children;
}
-
+
public List<DataSetNode> getDataSets()
{
return dataSets;
}
-
+
void hasComponents(SampleNode... someComponentSamples)
{
for (SampleNode componentSample : someComponentSamples)
@@ -115,7 +122,7 @@ public final class SampleNode extends EntityNode
componentSample.container = this;
}
}
-
+
void hasChildren(SampleNode... someChildSamples)
{
for (SampleNode childSample : someChildSamples)
@@ -124,7 +131,7 @@ public final class SampleNode extends EntityNode
childSample.parents.add(this);
}
}
-
+
void has(DataSetNode... someDataSets)
{
for (DataSetNode dataSet : someDataSets)
@@ -137,7 +144,7 @@ public final class SampleNode extends EntityNode
dataSets.add(dataSet);
}
}
-
+
@Override
public String getIdentifier()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/Utils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/Utils.java
index 525abd23f8d..228906a3527 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/Utils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/entitygraph/Utils.java
@@ -32,8 +32,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class Utils
@@ -52,7 +50,7 @@ public class Utils
sample.setContainer(createSample(sampleNode.getContainer()));
return sample;
}
-
+
public static ExternalDataPE createData(DataSetNode dataSetNode)
{
ExternalDataPE data = new ExternalDataPE();
@@ -135,7 +133,7 @@ public class Utils
experiment.setIdentifier(experimentNode.getCode());
return experiment;
}
-
+
public static ExperimentPE createExperimentPE(ExperimentNode experimentNode)
{
if (experimentNode == null)
@@ -159,7 +157,7 @@ public class Utils
experiment.setProject(project);
return experiment;
}
-
+
static final void appendTo(StringBuilder builder, String label, List<? extends EntityNode> entityNodes)
{
if (entityNodes.isEmpty())
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleListerTest.java
index 4441778e1de..f4c38598a47 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleListerTest.java
@@ -112,7 +112,7 @@ public class SampleListerTest extends AssertJUnit
SampleRecord r101 = record(101);
SampleRecord r102 = record(102);
LongOpenHashSet sampleIdSet = new LongOpenHashSet(new long[]
- { r101.s_id, r102.s_id });
+ { r101.s_id, r102.s_id });
one(query).listSamplesByIds(sampleIdSet);
will(returnValue(Arrays.asList(r101, r102)));
@@ -123,7 +123,7 @@ public class SampleListerTest extends AssertJUnit
will(returnValue(Arrays.asList(sampleMetaproject(102, 42))));
one(query).getMetaprojects(new LongOpenHashSet(new long[]
- { 42 }));
+ { 42 }));
will(returnValue(Arrays.asList(metaproject(42, "answer"))));
atLeast(1).of(filter).isValid(user, sample(r101));
@@ -162,7 +162,7 @@ public class SampleListerTest extends AssertJUnit
SampleRecord r101 = record(101);
SampleRecord r102 = record(102);
one(query).listSamplesByIds(new LongOpenHashSet(new long[]
- { r1.s_id, r2.s_id, r3.s_id, r101.s_id, r102.s_id }));
+ { r1.s_id, r2.s_id, r3.s_id, r101.s_id, r102.s_id }));
will(returnValue(Arrays.asList(r1, r2, r3, r101, r102)));
atLeast(1).of(filter).isValid(user, sample(r1));
@@ -220,8 +220,8 @@ public class SampleListerTest extends AssertJUnit
SampleRecord r401 = record(401);
one(query).listSamplesByIds(
new LongOpenHashSet(new long[]
- { r1.s_id, r2.s_id, r3.s_id, r101.s_id, r102.s_id, r201.s_id,
- r202.s_id, r301.s_id, r302.s_id, r401.s_id }));
+ { r1.s_id, r2.s_id, r3.s_id, r101.s_id, r102.s_id, r201.s_id,
+ r202.s_id, r301.s_id, r302.s_id, r401.s_id }));
will(returnValue(Arrays.asList(r1, r2, r3, r101, r102, r201, r202, r301, r302,
r401)));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
index 0b8a7db3956..f6b78c353c7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
@@ -46,9 +46,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
* @author Bernd Rinn
*/
@Friend(toClasses =
- { SampleRecord.class, ISampleListingQuery.class })
+{ SampleRecord.class, ISampleListingQuery.class })
@Test(groups =
- { "db", "sample" })
+{ "db", "sample" })
public class SampleSetListingQueryTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAOTest.java
index e231e9fbb28..0895df858b2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AttachmentDAOTest.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
* @author Kaloyan Enimanev
*/
@Test(groups =
- { "db" })
+{ "db" })
public final class AttachmentDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationGroupDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationGroupDAOTest.java
index 7aa2f0d89d8..d9af20c386b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationGroupDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationGroupDAOTest.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
* @author Izabela Adamczyk
*/
@Test(groups =
- { "db", "authorization_group" })
+{ "db", "authorization_group" })
public class AuthorizationGroupDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/CorePluginDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/CorePluginDAOTest.java
index 19279af825f..a77c427b2a7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/CorePluginDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/CorePluginDAOTest.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.CorePluginPE;
* @author Kaloyan Enimanev
*/
@Test(groups =
- { "db", "slow" })
+{ "db", "slow" })
public final class CorePluginDAOTest extends AbstractDAOTest
{
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAOTest.java
index 5c3ab7b36fe..9315a229534 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAOTest.java
@@ -303,14 +303,14 @@ public final class DataDAOTest extends AbstractDAOTest
data.setStorageFormatVocabularyTerm(pickAStorageFormatVocabularyTerm());
data.setStatus(DataSetArchivingStatus.AVAILABLE);
dataDAO.createDataSet(data, getSystemPerson());
-
+
ExternalDataPE externalData = dataDAO.tryToFindDataSetByCode(dataSetCode).tryAsExternalData();
int version = externalData.getVersion();
externalData.setShareId("share-43");
externalData.setSize(size);
-
+
dataDAO.updateDataSet(externalData, getTestPerson());
-
+
ExternalDataPE dataSet = dataDAO.tryToFindDataSetByCode(dataSetCode).tryAsExternalData();
assertEquals(externalData.getCode(), dataSet.getCode());
assertEquals(externalData.getDataSetType(), dataSet.getDataSetType());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseCreationUtil.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseCreationUtil.java
index 961a9febf40..5a39142741e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseCreationUtil.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseCreationUtil.java
@@ -55,15 +55,15 @@ public final class DatabaseCreationUtil
{
final AbstractApplicationContext applicationContext =
new ClassPathXmlApplicationContext(new String[]
- { "dbConfigurationContext.xml" }, true);
+ { "dbConfigurationContext.xml" }, true);
DatabaseCreationUtil.beanFactory = applicationContext;
}
return beanFactory;
}
/**
- * Creates all files in <code>sourceTest/sql/postgresql</code> necessary to set up a database of
- * the current version by dumping a database migrated from the specified version.
+ * Creates all files in <code>sourceTest/sql/postgresql</code> necessary to set up a database of the current version by dumping a database
+ * migrated from the specified version.
*/
private final static void createFilesFromADumpOfAMigratedDatabase(final String databaseVersion)
throws Exception
@@ -85,8 +85,7 @@ public final class DatabaseCreationUtil
}
/**
- * Creates all files in <var>destinationDir</var> necessary to set up the database
- * <var>databaseKind</var> in its current state.
+ * Creates all files in <var>destinationDir</var> necessary to set up the database <var>databaseKind</var> in its current state.
*/
private static final void createDumpForJava(final String databaseKind, final File destinationDir)
throws IOException
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAOTest.java
index aa411ecab57..67c3a99770b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAOTest.java
@@ -49,7 +49,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
* @author Piotr Buczek
*/
@Test(groups =
- { "db" })
+{ "db" })
public class DeletionDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAOTest.java
index 8d6b36d3262..63bb6de6980 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAOTest.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE;
* @author Chandrasekhar Ramakrishnan
*/
@Test(groups =
- { "db" })
+{ "db" })
public final class EntityOperationsLogDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAOTest.java
index 8139a043765..22f6bfd3abc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityPropertyTypeDAOTest.java
@@ -44,7 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
* @author Izabela Adamczyk
*/
@Test(groups =
- { "db", "property" })
+{ "db", "property" })
public class EntityPropertyTypeDAOTest extends AbstractDAOTest
{
@@ -172,19 +172,19 @@ public class EntityPropertyTypeDAOTest extends AbstractDAOTest
private final static Object[][] entityKindsWithEntityTypeAndPropertyTypeMandatory()
{
return new Object[][]
- {
- { EntityKind.EXPERIMENT, "SIRNA_HCS", "DESCRIPTION" },
- { EntityKind.SAMPLE, "CONTROL_LAYOUT", "$PLATE_GEOMETRY" },
- { EntityKind.MATERIAL, "BACTERIUM", "DESCRIPTION" } };
+ {
+ { EntityKind.EXPERIMENT, "SIRNA_HCS", "DESCRIPTION" },
+ { EntityKind.SAMPLE, "CONTROL_LAYOUT", "$PLATE_GEOMETRY" },
+ { EntityKind.MATERIAL, "BACTERIUM", "DESCRIPTION" } };
}
@DataProvider
private final static Object[][] entityKindsWithEntityTypeAndPropertyTypeNotAssigned()
{
return new Object[][]
- {
- { EntityKind.EXPERIMENT, "SIRNA_HCS", "IS_VALID" },
- { EntityKind.SAMPLE, "CONTROL_LAYOUT", "IS_VALID" },
- { EntityKind.MATERIAL, "BACTERIUM", "IS_VALID" }, };
+ {
+ { EntityKind.EXPERIMENT, "SIRNA_HCS", "IS_VALID" },
+ { EntityKind.SAMPLE, "CONTROL_LAYOUT", "IS_VALID" },
+ { EntityKind.MATERIAL, "BACTERIUM", "IS_VALID" }, };
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityResolverQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityResolverQueryTest.java
index b2d645617b7..e99beecdd12 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityResolverQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityResolverQueryTest.java
@@ -30,7 +30,7 @@ import org.testng.annotations.Test;
* @author Bernd Rinn
*/
@Test(groups =
- { "db" })
+{ "db" })
public class EntityResolverQueryTest extends AbstractDAOTest
{
private IEntityResolverQuery query;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EventDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EventDAOTest.java
index 555db6c4402..3f7e9f7ebb1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EventDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EventDAOTest.java
@@ -40,7 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
* @author Izabela Adamczyk
*/
@Test(groups =
- { "db", "event" })
+{ "db", "event" })
public class EventDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomColumnDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomColumnDAOTest.java
index 3054b3ae0f6..15a1fd43266 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomColumnDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomColumnDAOTest.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
* @author Tomasz Pylak
*/
@Test(groups =
- { "db", "column" })
+{ "db", "column" })
public final class GridCustomColumnDAOTest extends AbstractDAOTest
{
public void testCreateAndListColumn() throws Exception
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomFilterDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomFilterDAOTest.java
index 6ec4cf8ccea..d9eca3340e5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomFilterDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/GridCustomFilterDAOTest.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
* @author Izabela Adamczyk
*/
@Test(groups =
- { "db", "filter" })
+{ "db", "filter" })
public final class GridCustomFilterDAOTest extends AbstractDAOTest
{
private static final boolean PUBLIC = true;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
index 1da3f963328..abafc69cf8e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
@@ -195,7 +195,7 @@ public class MetaprojectDAOTest extends AbstractDAOTest
Collection<MetaprojectAssignmentPE> assignments =
daoFactory.getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
getTestPerson(), Arrays.asList(new IEntityInformationWithPropertiesHolder[]
- { experiment1, experiment2 }), EntityKind.EXPERIMENT);
+ { experiment1, experiment2 }), EntityKind.EXPERIMENT);
assertEquals(3, assignments.size());
for (MetaprojectAssignmentPE assignment : assignments)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/PermIdDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/PermIdDAOTest.java
index d88eea5dc91..1f7dbab25ba 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/PermIdDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/PermIdDAOTest.java
@@ -28,7 +28,7 @@ import org.testng.annotations.Test;
* @author Izabela Adamczyk
*/
@Test(groups =
- { "db" })
+{ "db" })
public final class PermIdDAOTest extends AbstractDAOTest
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlDataMigrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlDataMigrationTest.java
index efa34fbc2e5..39c659d098d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlDataMigrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlDataMigrationTest.java
@@ -59,7 +59,7 @@ public final class SqlDataMigrationTest
}
@Test(groups =
- { "slow" })
+ { "slow" })
/* runs unit tests written in SQL. The tests should check if the migration went fine. */
public final void testMigration() throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlMigrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlMigrationTest.java
index a24684bafe1..d4008aeaf26 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlMigrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlMigrationTest.java
@@ -29,7 +29,7 @@ public class SqlMigrationTest extends SqlMigrationTestAbstract
{
@Test(groups =
- { "slow" })
+ { "slow" })
public void test_migration() throws Exception
{
testMigration(DatabaseVersionHolder.getDatabaseVersion());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilderTest.java
index 38539257373..a0bb9a4b513 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/search/LuceneQueryBuilderTest.java
@@ -32,7 +32,7 @@ public class LuceneQueryBuilderTest extends AssertJUnit
protected Object[][] getQueriesToTestInBasicMode()
{
return new Object[][]
- {
+ {
{ "abc", "(*abc*)" },
{ "code:CP registrator:Joe", "(*code\\:CP*) (*registrator\\:Joe*)" },
{ "ab#c OR d", "(*ab* AND *c*) OR (*d*)" } };
@@ -42,7 +42,7 @@ public class LuceneQueryBuilderTest extends AssertJUnit
protected Object[][] getQueriesToTestInWildcardMode()
{
return new Object[][]
- {
+ {
{ "abc", "abc" },
{ "code:CP registrator:Joe", "code\\:CP registrator\\:Joe" },
{ "*ab#c OR d", "*ab#c OR d" } };
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTaskTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTaskTest.java
index ec45da86a93..722e7198599 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTaskTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/DataSetRegistrationSummaryTaskTest.java
@@ -347,7 +347,7 @@ public class DataSetRegistrationSummaryTaskTest extends AssertJUnit
one(mailClient).sendEmailMessage(with(checker.getSubjectMatcher()),
with(checker.getReportMatcher()), with((EMailAddress) null),
with((EMailAddress) null), with(new EMailAddress[]
- { new EMailAddress(address) }));
+ { new EMailAddress(address) }));
}
}
});
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTaskTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTaskTest.java
index a6336961efb..a2e7f986de6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTaskTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/task/MaterialExternalDBSyncTaskTest.java
@@ -67,7 +67,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
* @author Franz-Josef Elmer
*/
@Friend(toClasses =
- { MaterialExternalDBSyncTask.class, MappingInfo.class })
+{ MaterialExternalDBSyncTask.class, MappingInfo.class })
public class MaterialExternalDBSyncTaskTest extends AbstractFileSystemTestCase
{
private static final String SESSION_TOKEN = "session-token";
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/AnnotationAppliedTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/AnnotationAppliedTestCase.java
index b78b7b0f56e..6d7f34d49d8 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/AnnotationAppliedTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/AnnotationAppliedTestCase.java
@@ -30,16 +30,14 @@ import org.testng.AssertJUnit;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
/**
- * Test case for test classes testing whether an interface and/or its implementation have all
- * mandatory annotations.
+ * Test case for test classes testing whether an interface and/or its implementation have all mandatory annotations.
*
* @author Franz-Josef Elmer
*/
public class AnnotationAppliedTestCase extends AssertJUnit
{
/**
- * Asserts that the specified class is an interface and all its methods have the annotations
- * {@link RolesAllowed} and {@link Transactional}.
+ * Asserts that the specified class is an interface and all its methods have the annotations {@link RolesAllowed} and {@link Transactional}.
*/
protected void assertMandatoryMethodAnnotations(Class<?> interfaceClass, List<String> exemptMethods)
{
@@ -47,9 +45,8 @@ public class AnnotationAppliedTestCase extends AssertJUnit
}
/**
- * Asserts that the specified interface class is an interface, the implementing class really
- * implements that interface, and all interface methods or their implementations have the
- * annotations {@link RolesAllowed} and {@link Transactional}.
+ * Asserts that the specified interface class is an interface, the implementing class really implements that interface, and all interface methods
+ * or their implementations have the annotations {@link RolesAllowed} and {@link Transactional}.
*/
protected void assertMandatoryMethodAnnotations(Class<?> interfaceClass,
Class<?> implementingClass, List<String> exemptMethods)
@@ -58,10 +55,8 @@ public class AnnotationAppliedTestCase extends AssertJUnit
}
/**
- * Asserts that the specified interface class is an interface, the implementing class really
- * implements that interface, and all interface methods or their implementations have the
- * annotations {@link RolesAllowed} and {@link Transactional}. The specified exceptions are
- * allowed.
+ * Asserts that the specified interface class is an interface, the implementing class really implements that interface, and all interface methods
+ * or their implementations have the annotations {@link RolesAllowed} and {@link Transactional}. The specified exceptions are allowed.
*/
protected void assertMandatoryMethodAnnotations(Class<?> interfaceClass,
Class<?> implementingClass, String exceptions, List<String> exemptMethods)
@@ -76,9 +71,8 @@ public class AnnotationAppliedTestCase extends AssertJUnit
}
/**
- * Asserts that the specified interface class is an interface, the implementing class really
- * implements that interface, and all interface methods or their implementations have the
- * specified annotations. The specified exceptions are allowed.
+ * Asserts that the specified interface class is an interface, the implementing class really implements that interface, and all interface methods
+ * or their implementations have the specified annotations. The specified exceptions are allowed.
*/
protected void assertMandatoryMethodAnnotations(
List<Class<? extends Annotation>> mandatoryAnnotations, Class<?> interfaceClass,
@@ -103,10 +97,11 @@ public class AnnotationAppliedTestCase extends AssertJUnit
});
for (Method interfaceMethod : declaredMethods)
{
- if(exemptMethods != null && exemptMethods.contains(interfaceMethod.getName())) {
+ if (exemptMethods != null && exemptMethods.contains(interfaceMethod.getName()))
+ {
continue;
}
-
+
List<String> missingAnnotations = new ArrayList<String>();
for (Class<? extends Annotation> annotationClass : mandatoryAnnotations)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/SimpleDateRendererTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/SimpleDateRendererTest.java
index 50e4856adbe..100caf9537a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/SimpleDateRendererTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/SimpleDateRendererTest.java
@@ -27,8 +27,8 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.basic.SimpleDateRenderer;
/**
- * Tests of {@link SimpleDateRenderer}. The test is in the different package than the tested class
- * to have access to TimeZone class (GWT does not support it).
+ * Tests of {@link SimpleDateRenderer}. The test is in the different package than the tested class to have access to TimeZone class (GWT does not
+ * support it).
*
* @author Tomasz Pylak
*/
@@ -38,10 +38,10 @@ public class SimpleDateRendererTest extends AssertJUnit
private Object[][] getDates()
{
return new Object[][]
- {
- { toDate(1991, 12, 3, 3, 13, 59, "CET"), "1991-12-03 03:13:59 GMT+01:00" },
- { toDate(2008, 12, 6, 15, 35, 17, "CET"), "2008-12-06 15:35:17 GMT+01:00" },
- { toDate(2008, 7, 31, 1, 2, 3, "CET"), "2008-07-31 01:02:03 GMT+02:00" } };
+ {
+ { toDate(1991, 12, 3, 3, 13, 59, "CET"), "1991-12-03 03:13:59 GMT+01:00" },
+ { toDate(2008, 12, 6, 15, 35, 17, "CET"), "2008-12-06 15:35:17 GMT+01:00" },
+ { toDate(2008, 7, 31, 1, 2, 3, "CET"), "2008-07-31 01:02:03 GMT+02:00" } };
}
@Test(dataProvider = "dates")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TimeIntervalChecker.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TimeIntervalChecker.java
index 03b93da8d5b..1096191efd5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TimeIntervalChecker.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TimeIntervalChecker.java
@@ -22,11 +22,9 @@ import java.util.Date;
import org.testng.AssertJUnit;
/**
- * Helper class to check that a time stamp is between now and a time in the past when an instance of
- * this class has been created.
+ * Helper class to check that a time stamp is between now and a time in the past when an instance of this class has been created.
* <p>
- * This class is useful in tests where some productive code creates a time stamp which should be
- * checked.
+ * This class is useful in tests where some productive code creates a time stamp which should be checked.
*
* @author Franz-Josef Elmer
*/
@@ -49,7 +47,7 @@ public class TimeIntervalChecker extends AssertJUnit
{
this(new Timestamp(System.currentTimeMillis() - shiftInMillisecond));
}
-
+
/**
* Creates an instance for the specified date object.
*/
@@ -59,8 +57,7 @@ public class TimeIntervalChecker extends AssertJUnit
}
/**
- * Asserts that the specified date is after the time stamp of creation of this instance and
- * before now.
+ * Asserts that the specified date is after the time stamp of creation of this instance and before now.
*/
public void assertDateInInterval(Date date)
{
@@ -71,7 +68,7 @@ public class TimeIntervalChecker extends AssertJUnit
assertFalse("Actual date [" + date + "] is after now [" + now + "].",
now.before(timestamp));
}
-
+
private Timestamp asTimestamp(Date date)
{
return date instanceof Timestamp ? (Timestamp) date : new Timestamp(date.getTime());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
index 4866c47dc09..407777d67cc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/DataSetInfoHelperTest.java
@@ -51,7 +51,7 @@ public class DataSetInfoHelperTest extends AssertJUnit
String dataSetType = "dataSetTypeC";
String fileType = "fileTypeD";
String[] parents =
- { "p1", "p2", "p3" };
+ { "p1", "p2", "p3" };
DataSetUploadInfo info =
new DataSetUploadInfo(sample, experiment, parents, dataSetType, fileType);
checkInfo(info, sample, experiment, parents, dataSetType, fileType);
@@ -110,7 +110,7 @@ public class DataSetInfoHelperTest extends AssertJUnit
String sample = null;
String experiment = "eB";
String[] parents =
- { "p1", "p2", "p3" };
+ { "p1", "p2", "p3" };
String dataSetType = "dsC";
String fileType = "ftD";
DataSetUploadInfo info =
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/INormalizer.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/INormalizer.java
index 8da91428930..4edcd1c2fd0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/INormalizer.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/INormalizer.java
@@ -17,8 +17,6 @@
package ch.systemsx.cisd.openbis.generic.shared;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public interface INormalizer
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ServletParamsParsingTestUtils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ServletParamsParsingTestUtils.java
index acb3c05e0d1..58573e023aa 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ServletParamsParsingTestUtils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ServletParamsParsingTestUtils.java
@@ -85,7 +85,7 @@ public class ServletParamsParsingTestUtils extends AssertJUnit
for (int i = 0; i < keyValuePairs.length / 2; i++)
{
paramsMap.put(keyValuePairs[i * 2], new String[]
- { keyValuePairs[i * 2 + 1] });
+ { keyValuePairs[i * 2 + 1] });
}
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/TranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/TranslatorTest.java
index 5c1f1eca44b..8b573fcb72b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/TranslatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/TranslatorTest.java
@@ -67,14 +67,14 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
public class TranslatorTest extends AssertJUnit
{
private static final IKeyExtractor<String, DataSet> KEY_EXTRACTOR = new IKeyExtractor<String, DataSet>()
+ {
+ @Override
+ public String getKey(DataSet e)
{
- @Override
- public String getKey(DataSet e)
- {
- return e.getCode();
- }
- };
-
+ return e.getCode();
+ }
+ };
+
private DataSetBuilder ds1;
private DataSetBuilder ds2;
@@ -133,13 +133,13 @@ public class TranslatorTest extends AssertJUnit
new LinkDataSetBuilder(4).code("lds").type("L1").experiment(experiment)
.sample(sample).registrationDate(new Date(123456789L))
.modificationDate(new Date(123459999L)).externalCode("EX_CODE").edms(edms);
-
+
dsp1 = new DataSetBuilder(10).code("ds-p1").type("T2").experiment(experiment).getDataSet();
dsp2 = new DataSetBuilder(11).code("ds-p2").type("T2").experiment(experiment).getDataSet();
dsc1 = new ContainerDataSetBuilder(12).code("ds-c1").type("T3")
- .experiment(experiment).component(dsp1).component(dsp2).getContainerDataSet();
+ .experiment(experiment).component(dsp1).component(dsp2).getContainerDataSet();
dsc2 = new ContainerDataSetBuilder(13).code("ds-c2").type("T3")
- .experiment(experiment).component(dsp1).component(dsp2).getContainerDataSet();
+ .experiment(experiment).component(dsp1).component(dsp2).getContainerDataSet();
dsp1.addContainer(dsc1, 0);
dsp1.addContainer(dsc2, 1);
dsp2.addContainer(dsc1, 0);
@@ -406,12 +406,12 @@ public class TranslatorTest extends AssertJUnit
assertEquals("[ds2]", translated.getChildrenCodes().toString());
assertEquals("[ds1]", translated.getParentCodes().toString());
}
-
+
@Test
public void testTranslateCyclicGraphOfDataSets()
{
- List<DataSet> translatedDatasets = Translator.translate(Arrays.<AbstractExternalData>asList(dsc1, dsc2), EnumSet.noneOf(Connections.class));
-
+ List<DataSet> translatedDatasets = Translator.translate(Arrays.<AbstractExternalData> asList(dsc1, dsc2), EnumSet.noneOf(Connections.class));
+
DataSet dsc1t = translatedDatasets.get(0);
TableMap<String, DataSet> dsc1tc = new TableMap<String, DataSet>(dsc1t.getContainedDataSets(), KEY_EXTRACTOR);
assertEquals(2, dsc1tc.keySet().size());
@@ -431,7 +431,7 @@ public class TranslatorTest extends AssertJUnit
TableMap<String, DataSet> dsp2tc = new TableMap<String, DataSet>(dsp2t.getContainerDataSets(), KEY_EXTRACTOR);
assertSame(dsc1t2, dsp2tc.getOrDie("ds-c1"));
assertSame(dsc2t2, dsp2tc.getOrDie("ds-c2"));
-
+
assertEquals(2, translatedDatasets.size());
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
index 9763184ee1f..3b6e8ab1476 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetBuilder.java
@@ -35,40 +35,40 @@ public class DataSetBuilder
new EntityRegistrationDetails(new EntityRegistrationDetailsInitializer());
initializer.setRegistrationDetails(registrationDetails);
}
-
+
public DataSet getDataSet()
{
return new DataSet(initializer);
}
-
+
public DataSetBuilder code(String code)
{
initializer.setCode(code);
return this;
}
-
+
public DataSetBuilder type(String type)
{
initializer.setDataSetTypeCode(type);
return this;
}
-
+
public DataSetBuilder experiment(String experimentIdentifier)
{
initializer.setExperimentIdentifier(experimentIdentifier);
return this;
}
-
+
public DataSetBuilder sample(String sampleIdentifier)
{
initializer.setSampleIdentifierOrNull(sampleIdentifier);
return this;
}
-
+
public DataSetBuilder property(String key, String value)
{
initializer.getProperties().put(key, value);
return this;
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTest.java
index eb6a1393d5b..d7013b1700e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTest.java
@@ -51,7 +51,7 @@ public class DataSetTest extends AssertJUnit
}
@Test(expectedExceptions =
- { IllegalArgumentException.class })
+ { IllegalArgumentException.class })
public void testInitialization()
{
DataSetInitializer initializer = new DataSetInitializer();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTypeTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTypeTest.java
index 6c92ced8b53..92b3c7732a4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTypeTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetTypeTest.java
@@ -63,7 +63,7 @@ public class DataSetTypeTest extends AssertJUnit
}
@Test(expectedExceptions =
- { IllegalArgumentException.class })
+ { IllegalArgumentException.class })
public void testInitialization()
{
DataSetTypeInitializer initializer = new DataSetTypeInitializer();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleBuilder.java
index 20bb31e289c..fa9f964ddc5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleBuilder.java
@@ -20,14 +20,12 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDeta
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SampleBuilder
{
private SampleInitializer initializer = new SampleInitializer();
-
+
public SampleBuilder(long id)
{
initializer.setId(id);
@@ -35,46 +33,46 @@ public class SampleBuilder
new EntityRegistrationDetailsInitializer();
initializer.setRegistrationDetails(new EntityRegistrationDetails(entityRegInitializer));
}
-
+
public Sample getSample()
{
return new Sample(initializer);
}
-
+
public SampleBuilder code(String code)
{
initializer.setCode(code);
return this;
}
-
+
public SampleBuilder type(String type)
{
initializer.setSampleTypeCode(type);
return this;
}
-
+
public SampleBuilder typeID(long typeId)
{
initializer.setSampleTypeId(typeId);
return this;
}
-
+
public SampleBuilder identifier(String identifier)
{
initializer.setIdentifier(identifier);
return this;
}
-
+
public SampleBuilder permID(String permId)
{
initializer.setPermId(permId);
return this;
}
-
+
public SampleBuilder experiment(String experimentIdentifier)
{
initializer.setExperimentIdentifierOrNull(experimentIdentifier);
return this;
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
index e3625fb932a..e026ce4c863 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
@@ -64,7 +64,7 @@ public class SampleTest extends AssertJUnit
}
@Test(expectedExceptions =
- { IllegalArgumentException.class })
+ { IllegalArgumentException.class })
public void testInitialization()
{
SampleInitializer initializer = new SampleInitializer();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
index d4a0ee46a4e..b44306b3bc3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/PropertiesBasedDataSetFilterTest.java
@@ -24,8 +24,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetBuilder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class PropertiesBasedDataSetFilterTest extends AssertJUnit
@@ -34,19 +32,19 @@ public class PropertiesBasedDataSetFilterTest extends AssertJUnit
public void testNoProperties()
{
IDataSetFilter filter = new PropertiesBasedDataSetFilter(new HashMap<String, String>());
-
+
DataSetBuilder builder = new DataSetBuilder().code("A").type("A").experiment("E");
assertEquals(true, filter.pass(builder.getDataSet()));
assertEquals(true, filter.pass(builder.property("a", "alpha").getDataSet()));
}
-
+
@Test
public void testWithProperties()
{
HashMap<String, String> properties = new HashMap<String, String>();
properties.put("a", "alpha");
PropertiesBasedDataSetFilter filter = new PropertiesBasedDataSetFilter(properties);
-
+
DataSetBuilder builder = new DataSetBuilder().code("A").type("A").experiment("E");
assertEquals(false, filter.pass(builder.getDataSet()));
assertEquals(true, filter.pass(builder.property("a", "alpha").getDataSet()));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
index 6013c718040..e9f5fb8d7b1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/filter/TypeBasedDataSetFilterTest.java
@@ -22,8 +22,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetBuilder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class TypeBasedDataSetFilterTest extends AssertJUnit
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicURLEncoderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicURLEncoderTest.java
index e2b2a514924..0b5172fa665 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicURLEncoderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicURLEncoderTest.java
@@ -29,7 +29,7 @@ public class BasicURLEncoderTest extends AssertJUnit
protected Object[][] getChars()
{
return new Object[][]
- {
+ {
/* original char, encoded */
{ ' ', "+" },
/* Reserved characters: */
@@ -59,7 +59,7 @@ public class BasicURLEncoderTest extends AssertJUnit
{ ']', "%5D" },
{ '`', "%60" },
- };
+ };
}
@Test(dataProvider = "chars")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtilTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtilTest.java
index 422aaa24aef..61a4412faff 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtilTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/ExpressionUtilTest.java
@@ -58,14 +58,14 @@ public class ExpressionUtilTest extends AssertJUnit
String expression = "${abc} ${def} ${abc} ${ghi}.";
assertEquals("[abc, def, abc, ghi]", extractParameters(expression).toString());
}
-
+
@Test
public void testCreateDistinctParametersList()
{
assertEquals("[a, b, c]", createDistinctList("a", "b", "a", "c", "b").toString());
}
-
- private Collection<String> createDistinctList(String...strings)
+
+ private Collection<String> createDistinctList(String... strings)
{
return ExpressionUtil.createDistinctParametersList(Arrays.asList(strings));
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/Row.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/Row.java
index caa444ddb01..591bd52e2d4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/Row.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/Row.java
@@ -23,8 +23,8 @@ import java.util.Map;
import ch.systemsx.cisd.openbis.generic.client.web.client.testframework.CheckTableCommand;
/**
- * Class which contains all expected cell values to be checked by {@link CheckTableCommand}. It uses
- * a fluent API approach for its methods to prepare expectations.
+ * Class which contains all expected cell values to be checked by {@link CheckTableCommand}. It uses a fluent API approach for its methods to prepare
+ * expectations.
*
* @author Franz-Josef Elmer
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/WebAppsPropertiesTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/WebAppsPropertiesTest.java
index 2032666f6ec..aa9c5ff6174 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/WebAppsPropertiesTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/WebAppsPropertiesTest.java
@@ -63,11 +63,11 @@ public class WebAppsPropertiesTest
Assert.assertEquals("Web app 1", webApp.getLabel());
Assert.assertEquals(Integer.valueOf(100), webApp.getSorting());
Assert.assertTrue(Arrays.equals(new String[]
- { "queries-menu", "experiment-details-view" }, webApp.getContexts()));
+ { "queries-menu", "experiment-details-view" }, webApp.getContexts()));
Assert.assertTrue(Arrays.equals(new String[]
- { "EXP1", "EXP2" }, webApp.getEntityTypes().get(EntityKind.EXPERIMENT)));
+ { "EXP1", "EXP2" }, webApp.getEntityTypes().get(EntityKind.EXPERIMENT)));
Assert.assertTrue(Arrays.equals(new String[]
- { "SAM1" }, webApp.getEntityTypes().get(EntityKind.SAMPLE)));
+ { "SAM1" }, webApp.getEntityTypes().get(EntityKind.SAMPLE)));
Assert.assertTrue(Arrays.equals(new String[] {},
webApp.getEntityTypes().get(EntityKind.DATA_SET)));
Assert.assertTrue(Arrays.equals(new String[] {},
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PrimitiveValueTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PrimitiveValueTest.java
index 188c295ce38..c3d212a35ec 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PrimitiveValueTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/PrimitiveValueTest.java
@@ -20,7 +20,7 @@ public class PrimitiveValueTest extends AssertJUnit
protected Object[][] getValues()
{
return new Object[][]
- {
+ {
/* NULL == NULL == "" */
{ PrimitiveValue.NULL, PrimitiveValue.NULL, ExpectedResult.EQUAL },
{ PrimitiveValue.NULL, new PrimitiveValue(""), ExpectedResult.EQUAL },
@@ -74,7 +74,7 @@ public class PrimitiveValueTest extends AssertJUnit
{ new PrimitiveValue(-10L), new PrimitiveValue(-5.0), ExpectedResult.LOWER },
{ new PrimitiveValue(9.9), new PrimitiveValue(10L), ExpectedResult.LOWER },
- };
+ };
}
@Test(dataProvider = "values")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/WebAppTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/WebAppTest.java
index b27786c8709..7c2c27765aa 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/WebAppTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/WebAppTest.java
@@ -55,7 +55,7 @@ public class WebAppTest
public void testMatchesContextWithExactMatchInContextsList()
{
WebApp webApp = new WebApp("webapp", null, null, new String[]
- { "experiment-details-view" }, null);
+ { "experiment-details-view" }, null);
for (WebAppContext context : WebAppContext.values())
{
@@ -73,7 +73,7 @@ public class WebAppTest
public void testMatchesContextWithRegexpMatchInContextsList()
{
WebApp webApp = new WebApp("webapp", null, null, new String[]
- { ".*-details-view" }, null);
+ { ".*-details-view" }, null);
for (WebAppContext context : WebAppContext.values())
{
@@ -118,7 +118,7 @@ public class WebAppTest
{
Map<EntityKind, String[]> entityTypes = new HashMap<EntityKind, String[]>();
entityTypes.put(EntityKind.EXPERIMENT, new String[]
- { "EXP0", "EXP1" });
+ { "EXP0", "EXP1" });
WebApp webApp = new WebApp("webapp", null, null, null, entityTypes);
for (EntityKind kind : EntityKind.values())
@@ -143,7 +143,7 @@ public class WebAppTest
{
Map<EntityKind, String[]> entityTypes = new HashMap<EntityKind, String[]>();
entityTypes.put(EntityKind.EXPERIMENT, new String[]
- { "EXP0", "EXP.*" });
+ { "EXP0", "EXP.*" });
WebApp webApp = new WebApp("webapp", null, null, null, entityTypes);
for (EntityKind kind : EntityKind.values())
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataStoreBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataStoreBuilder.java
index 4c0c9eb24a2..b3b4049b213 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataStoreBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataStoreBuilder.java
@@ -26,12 +26,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
public class DataStoreBuilder
{
private DataStore store = new DataStore();
-
+
public DataStoreBuilder(String dataStoreCode)
{
store.setCode(dataStoreCode);
}
-
+
public DataStoreBuilder hostUrl(String hostUrl)
{
store.setHostUrl(hostUrl);
@@ -43,10 +43,10 @@ public class DataStoreBuilder
store.setDownloadUrl(downloadUrl);
return this;
}
-
+
public DataStore getStore()
{
return store;
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/PropertyBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/PropertyBuilder.java
index 3360ea6cbbc..ec4bd3660d0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/PropertyBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/PropertyBuilder.java
@@ -58,8 +58,7 @@ public class PropertyBuilder
private final ExtendedEntityProperty property = new ExtendedEntityProperty();
/**
- * Creates an instance for specified property type code which also the simple code. Data type is
- * {@link DataTypeCode#VARCHAR}.
+ * Creates an instance for specified property type code which also the simple code. Data type is {@link DataTypeCode#VARCHAR}.
*/
public PropertyBuilder(String key)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/utils/GroupByMapTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/utils/GroupByMapTest.java
index 47d51e7b841..29fdbe6b264 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/utils/GroupByMapTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/utils/GroupByMapTest.java
@@ -45,7 +45,7 @@ public class GroupByMapTest extends AssertJUnit
public void test()
{
List<Integer> list = Arrays.asList(new Integer[]
- { 1, 100, 1, 5, 100, 100 });
+ { 1, 100, 1, 5, 100, 100 });
GroupByMap<Integer, Integer> map = GroupByMap.create(list, createKeyExtractor());
assertNull(map.tryGet(9));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsInjectorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsInjectorTest.java
index 28ffc66e0c5..06b49312679 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsInjectorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/coreplugin/CorePluginsInjectorTest.java
@@ -104,7 +104,7 @@ public class CorePluginsInjectorTest extends AbstractFileSystemTestCase
};
PluginType typeWebapps = new PluginType("webapps", "webapps");
injector = new CorePluginsInjector(ScannerType.DSS, new IPluginType[]
- { type1, type2, type3, type4, type5, type6, typeWebapps }, logger);
+ { type1, type2, type3, type4, type5, type6, typeWebapps }, logger);
corePluginsFolder = new File(workingDirectory, "core-plugins");
corePluginsFolder.mkdirs();
corePluginsFolderProperty =
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/AbstractEntityTypePEBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/AbstractEntityTypePEBuilder.java
index 7b8f2e8112e..422849db805 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/AbstractEntityTypePEBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/AbstractEntityTypePEBuilder.java
@@ -32,6 +32,6 @@ abstract class AbstractEntityTypePEBuilder
propertyType.setCode(propertyTypeCode);
return assign(propertyType);
}
-
+
public abstract EntityTypePropertyTypePEBuilder assign(PropertyTypePE propertyType);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/SamplePEBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/SamplePEBuilder.java
index d90fa34f6c6..f1c8dce02af 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/SamplePEBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/SamplePEBuilder.java
@@ -33,51 +33,51 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
public class SamplePEBuilder
{
private final SamplePE sample = new SamplePE();
-
+
public SamplePEBuilder()
{
}
-
+
public SamplePEBuilder(long id)
{
sample.setId(id);
}
-
+
public SamplePE getSample()
{
return sample;
}
-
+
public SamplePEBuilder id(long id)
{
sample.setId(id);
return this;
}
-
+
public SamplePEBuilder code(String code)
{
sample.setCode(code);
return this;
}
-
+
public SamplePEBuilder space(SpacePE space)
{
sample.setSpace(space);
return this;
}
-
+
public SamplePEBuilder permID(String permID)
{
sample.setPermId(permID);
return this;
}
-
+
public SamplePEBuilder type(SampleTypePE type)
{
sample.setSampleType(type);
return this;
}
-
+
public SamplePEBuilder property(String code, DataTypeCode dataType, String value)
{
SampleTypePEBuilder sampleTypeBuilder = new SampleTypePEBuilder().code("my-type");
@@ -87,7 +87,7 @@ public class SamplePEBuilder
sampleTypeBuilder.assign(propertyType).getEntityTypePropertyType();
return property(etpt, value);
}
-
+
public SamplePEBuilder property(EntityTypePropertyTypePE etpt, String value)
{
SamplePropertyPE property = new SamplePropertyPE();
@@ -95,14 +95,11 @@ public class SamplePEBuilder
property.setValue(value);
return property(property);
}
-
+
public SamplePEBuilder property(SamplePropertyPE property)
{
sample.addProperty(property);
return this;
}
-
-
-
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/JythonManagedPropertyEvaluatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/JythonManagedPropertyEvaluatorTest.java
index 9bc6e4b70e0..fb5b95fa596 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/JythonManagedPropertyEvaluatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/JythonManagedPropertyEvaluatorTest.java
@@ -234,7 +234,7 @@ public class JythonManagedPropertyEvaluatorTest extends AssertJUnit
widgetFactory.createMultilineTextInputField("multi").setValue("multi\nline\ninput");
IManagedInputWidgetDescription action1w4 =
widgetFactory.createComboBoxInputField("combo", new String[]
- { "cv1", "cv2", "cv3" }).setValue("cv1");
+ { "cv1", "cv2", "cv3" }).setValue("cv1");
action1.addInputWidgets(action1w1, action1w2, action1w3, action1w4);
assertEquals(null, action1.getInputValue("t1"));
assertEquals("v2", action1.getInputValue("t2"));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
index bd98454124a..dbb82fc0f57 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
@@ -55,7 +55,7 @@ public final class NewSampleParserObjectFactoryTest
private final static IPropertyMapper createPropertyMapper()
{
final String[] properties = new String[]
- { "!toBeIgnored", "identifier", "container", "parent", "prop1", "prop2" };
+ { "!toBeIgnored", "identifier", "container", "parent", "prop1", "prop2" };
final DefaultPropertyMapper propertyMapper = new DefaultPropertyMapper(properties, null);
return propertyMapper;
}
@@ -63,7 +63,7 @@ public final class NewSampleParserObjectFactoryTest
private final static IPropertyMapper createPropertyMapperWithoutIdentifier()
{
final String[] properties = new String[]
- { "prop1", "prop2" };
+ { "prop1", "prop2" };
final DefaultPropertyMapper propertyMapper = new DefaultPropertyMapper(properties, null);
return propertyMapper;
}
@@ -97,29 +97,29 @@ public final class NewSampleParserObjectFactoryTest
private final static Object[][] getLineTokensForAutoGeneratedCodes()
{
return new Object[][]
- {
- { new String[]
- { "", "" }, 0 },
- { new String[]
- { null, null }, 0 },
- { new String[]
- { "1", "hello" }, 2 },
+ {
+ { new String[]
+ { "", "" }, 0 },
+ { new String[]
+ { null, null }, 0 },
+ { new String[]
+ { "1", "hello" }, 2 },
};
-}
+ }
@DataProvider
private final static Object[][] getLineTokens()
{
return new Object[][]
- {
- { new String[]
- { "", "", "", "", "", "" }, 0 },
- { new String[]
- { "ignoreMe", "id1", "cont1", "par1", "1", "hello" }, 2 },
+ {
+ { new String[]
+ { "", "", "", "", "", "" }, 0 },
+ { new String[]
+ { "ignoreMe", "id1", "cont1", "par1", "1", "hello" }, 2 },
};
-}
+ }
@Test(dataProvider = "getLineTokens")
public final void testFailCreateObjectForAutoGeneratedCodesWithIdentifierSpecified(
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
index f15efeb94e4..c12f4f08b9c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
@@ -60,7 +60,7 @@ public final class UpdatedSampleParserObjectFactoryTest
private final static IPropertyMapper createPropertyMapper()
{
final String[] properties = new String[]
- { Identifier.IDENTIFIER_COLUMN, NewSample.CONTAINER, PROPERTY_1, PROPERTY_2 };
+ { Identifier.IDENTIFIER_COLUMN, NewSample.CONTAINER, PROPERTY_1, PROPERTY_2 };
final DefaultPropertyMapper propertyMapper = new DefaultPropertyMapper(properties, null);
return propertyMapper;
}
@@ -69,19 +69,19 @@ public final class UpdatedSampleParserObjectFactoryTest
private final static Object[][] getLineTokens()
{
return new Object[][]
- {
- { new String[]
- { "", "", "", "" }, 0, 0 },
- { new String[]
- { "id1", "cont1", "1", "hello" }, 2, 2 },
- { new String[]
- { "id1", "", "1", "" }, 1, 1 },
- { new String[]
- { "", "cont1", "", "hello" }, 1, 1 },
- { new String[]
- { "id1", "cont1", "--DELETE--", "__DELETE__" }, 0, 2 },
- { new String[]
- { "__DELETE__", "--DELETE--", "--DELETE--", "hello" }, 1, 2 } };
+ {
+ { new String[]
+ { "", "", "", "" }, 0, 0 },
+ { new String[]
+ { "id1", "cont1", "1", "hello" }, 2, 2 },
+ { new String[]
+ { "id1", "", "1", "" }, 1, 1 },
+ { new String[]
+ { "", "cont1", "", "hello" }, 1, 1 },
+ { new String[]
+ { "id1", "cont1", "--DELETE--", "__DELETE__" }, 0, 2 },
+ { new String[]
+ { "__DELETE__", "--DELETE--", "--DELETE--", "hello" }, 1, 2 } };
}
@Test(dataProvider = "getLineTokens")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManagerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManagerTest.java
index f58fb553850..766a8041fd2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManagerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/CacheManagerTest.java
@@ -43,23 +43,27 @@ import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.WebClientConfiguration;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-@Friend(toClasses=CacheManager.class)
+@Friend(toClasses = CacheManager.class)
public class CacheManagerTest extends AbstractFileSystemTestCase
{
private static final String TECHNOLOGY = "test-technology";
+
private static final String CACHE_VERSION = "42";
+
private static final long DAY = 24 * 60 * 60 * 1000;
-
+
private Mockery context;
+
private IFreeSpaceProvider freeSpaceProvider;
+
private WebClientConfiguration webClientConfiguration;
+
private File cacheFolder;
+
private ITimeProvider timeProvider;
-
+
@BeforeMethod
public void beforeMethod()
{
@@ -83,29 +87,29 @@ public class CacheManagerTest extends AbstractFileSystemTestCase
// Otherwise one do not known which test failed.
context.assertIsSatisfied();
}
-
+
@Test
public void testEmptyCache()
{
CacheManager cacheManager = createCacheManager();
-
+
Object data = cacheManager.tryToGetData(new Key("a"));
-
+
assertEquals(null, data);
checkCacheFolder(CACHE_VERSION);
context.assertIsSatisfied();
}
-
+
@Test
public void testStoreDataButNotEnoughMemory()
{
prepareTimeProvider(1L, 2L, 3L);
prepareFreeSpaceProvider(0L);
CacheManager cacheManager = createCacheManager();
-
+
String data = "hello";
cacheManager.storeData(new Key("a"), data);
-
+
assertEquals(null, cacheManager.tryToGetData(new Key("a")));
checkCacheFolder(CACHE_VERSION);
context.assertIsSatisfied();
@@ -117,10 +121,10 @@ public class CacheManagerTest extends AbstractFileSystemTestCase
prepareTimeProvider(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L);
prepareFreeSpaceProvider(2048L, 2048L);
CacheManager cacheManager = createCacheManager();
-
+
String data = "hello";
cacheManager.storeData(new Key("a"), data);
-
+
assertEquals(data, cacheManager.tryToGetData(new Key("a")));
checkCacheFolder(CACHE_VERSION, "19700101010000007-1");
assertEquals(data, cacheManager.tryToGetData(new Key("a")));
@@ -128,76 +132,76 @@ public class CacheManagerTest extends AbstractFileSystemTestCase
checkCacheFolder(CACHE_VERSION, "19700101010000010-2");
context.assertIsSatisfied();
}
-
+
@Test
public void testStoreShutdownAndRetrieveFromCache()
{
prepareTimeProvider(1L, 2L, 3L, 4L, 5L, 6L, 7L);
prepareFreeSpaceProvider(2048L, 2048L);
CacheManager cacheManager = createCacheManager();
-
+
String data = "hello";
cacheManager.storeData(new Key("a"), data);
-
+
cacheManager = createCacheManager();
assertEquals(data, cacheManager.tryToGetData(new Key("a")));
assertEquals(null, cacheManager.tryToGetData(new Key("b")));
checkCacheFolder(CACHE_VERSION, "19700101010000007-0");
context.assertIsSatisfied();
}
-
+
@Test
public void testStoreShutdownAndTryToRetrieveFromCacheWithChangedCacheVersion()
{
prepareTimeProvider(1L, 2L, 3L, 4L);
prepareFreeSpaceProvider(2048L, 2048L);
CacheManager cacheManager = createCacheManager("1");
-
+
String data = "hello";
cacheManager.storeData(new Key("a"), data);
-
+
cacheManager = createCacheManager("2");
assertEquals(null, cacheManager.tryToGetData(new Key("a")));
checkCacheFolder("2");
context.assertIsSatisfied();
}
-
+
@Test
public void testCleanUpForLargeFiles()
{
prepareTimeProvider(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L);
prepareFreeSpaceProvider(2048L, 2048L, 0L, 2048L, 2048L);
CacheManager cacheManager = createCacheManager();
-
+
String data1 = "hello";
cacheManager.storeData(new Key("a"), data1);
String data2 = "hi";
cacheManager.storeData(new Key("b"), data2);
-
+
assertEquals(null, cacheManager.tryToGetData(new Key("a")));
assertEquals(data2, cacheManager.tryToGetData(new Key("b")));
checkCacheFolder(CACHE_VERSION, "19700101010000011-1");
context.assertIsSatisfied();
}
-
+
@Test
public void testCleanUpForOldFiles()
{
prepareTimeProvider(1L, 2L, 3L, 4L, DAY + 5L, DAY + 6L, DAY + 7L, DAY + 8L, DAY + 9L, DAY + 10L, DAY + 11L);
prepareFreeSpaceProvider(2048L, 2048L, 2048L, 2048L);
CacheManager cacheManager = createCacheManager();
-
+
String data1 = "hello";
cacheManager.storeData(new Key("a"), data1);
String data2 = "hi";
cacheManager.storeData(new Key("b"), data2);
-
+
assertEquals(null, cacheManager.tryToGetData(new Key("a")));
assertEquals(data2, cacheManager.tryToGetData(new Key("b")));
checkCacheFolder(CACHE_VERSION, "19700102010000011-1");
context.assertIsSatisfied();
}
-
+
private void checkCacheFolder(String cacheVersion, String... fileNames)
{
File versionFile = new File(cacheFolder, CacheManager.CACHE_VERSION_FILE_NAME);
@@ -259,7 +263,7 @@ public class CacheManagerTest extends AbstractFileSystemTestCase
}
});
}
-
+
private CacheManager createCacheManager()
{
return createCacheManager(CACHE_VERSION);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelperTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelperTest.java
index b9ac343c65d..0c5d9942da4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelperTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelperTest.java
@@ -42,7 +42,7 @@ public class EntityHelperTest extends AssertJUnit
assertEquals(1, properties.size());
assertEquals("A", properties.get(0).getPropertyCode());
}
-
+
@Test
public void testEqualEntities()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/CheckDataSet.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/CheckDataSet.java
index e41a350862f..e54a0f5da6d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/CheckDataSet.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/CheckDataSet.java
@@ -25,8 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelationshipRole;
/**
- * * {@link AbstractDefaultTestCommand} extension checking e.g. properties displayed in data set
- * detail view.
+ * * {@link AbstractDefaultTestCommand} extension checking e.g. properties displayed in data set detail view.
*
* @author Piotr Buczek
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewerTest.java
index ce7bb7e795f..1f2867552da 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetViewerTest.java
@@ -70,7 +70,7 @@ public class GenericDataSetViewerTest extends AbstractGWTTestCase
{
final String parentCodes[] = {};
final String childCodes[] =
- { "20081105092259000-9" };
+ { "20081105092259000-9" };
prepareShowDataSet(PARENT_DATASET_CODE_WITH_SAMPLE);
@@ -103,10 +103,10 @@ public class GenericDataSetViewerTest extends AbstractGWTTestCase
public final void testShowExperimentDataSetWithParents()
{
final String parentCodes[] =
- { "20081105092158673-1", "20081105092159111-1", "20081105092159222-2",
- "20081105092159333-3" };
+ { "20081105092158673-1", "20081105092159111-1", "20081105092159222-2",
+ "20081105092159333-3" };
final String childCodes[] =
- { "20081105092259900-0", "20081105092259900-1" };
+ { "20081105092259900-0", "20081105092259900-1" };
prepareShowDataSet(CHILD_DATASET_CODE);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentRegistrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentRegistrationTest.java
index 47c5779edd6..ccd00a4074a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentRegistrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentRegistrationTest.java
@@ -36,7 +36,6 @@ import ch.systemsx.cisd.openbis.systemtest.plugin.generic.ExperimentRegistration
/**
* A {@link AbstractGWTTestCase} extension to test {@link GenericExperimentRegistrationForm}.
*
- *
* @author Izabela Adamczyk
* @see ExperimentRegistrationTest
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentViewerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentViewerTest.java
index c54f062bb2d..bd05e4e3089 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentViewerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentViewerTest.java
@@ -125,9 +125,8 @@ public class GenericExperimentViewerTest extends AbstractGWTTestCase
/**
* Tests that authorization annotations of
- * {@link ICommonServer#getExperimentInfo(String, ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier)}
- * are obeyed. This is done by a direct invocation of
- * {@link ICommonClientServiceAsync#getExperimentInfo(String,com.google.gwt.user.client.rpc.AsyncCallback)}
+ * {@link ICommonServer#getExperimentInfo(String, ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier)} are obeyed. This
+ * is done by a direct invocation of {@link ICommonClientServiceAsync#getExperimentInfo(String,com.google.gwt.user.client.rpc.AsyncCallback)}
* because the normal GUI only list experiments which are accessible by the user.
*/
public final void testDirectInvocationOfGetExperimentInfoByAnUnauthorizedUser()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationTest.java
index 7475245ee0e..5f917575d33 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationTest.java
@@ -90,8 +90,7 @@ public class GenericSampleRegistrationTest extends AbstractGWTTestCase
}
/**
- * Tests that authorization annotations of {@link IGenericClientService#registerSample} are
- * obeyed.
+ * Tests that authorization annotations of {@link IGenericClientService#registerSample} are obeyed.
*/
public final void testRegisterSampleByAnUnauthorizedUser()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewerTest.java
index 3d0b2cd1f8a..6397aef9a23 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewerTest.java
@@ -219,7 +219,7 @@ public class GenericSampleViewerTest extends AbstractGWTTestCase
final String differentExperimentIdentifier = "/CISD/DEFAULT/EXP-REUSE";
assert differentExperimentIdentifier.equals(CELL_PLATE_EXAMPLE_EXPERIMENT_ID) == false;
final String[] indirectlyConnectedDataSetLocations =
- { "xml/result-9", "xml/result-10", "xml/result-11", "xml/result-12" };
+ { "xml/result-9", "xml/result-10", "xml/result-11", "xml/result-12" };
for (String location : indirectlyConnectedDataSetLocations)
{
checkIndirectlyConnectedDataTable.expectedRow(new DataSetRow().valid().withSample("")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/Property.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/Property.java
index 268b2dc2b0e..2c0bb379f24 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/Property.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/Property.java
@@ -24,18 +24,17 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
- * Extends {@link AbstractProperty} with methods for {@link Person} and arrays of generated
- * {@link Sample}.
+ * Extends {@link AbstractProperty} with methods for {@link Person} and arrays of generated {@link Sample}.
*
* @author Franz-Josef Elmer
*/
-public class Property extends AbstractProperty<CheckSample>
+public class Property extends AbstractProperty<CheckSample>
{
public Property(String key, CheckSample checker)
{
super(key, checker);
}
-
+
public CheckSample asPerson(final String personAsString)
{
return by(new IValueAssertion<Person>()
@@ -48,7 +47,7 @@ public class Property extends AbstractProperty<CheckSample>
}
});
}
-
+
public CheckSample asGeneratedSamples(final String... samples)
{
return by(new IValueAssertion<Sample[]>()
@@ -67,5 +66,5 @@ public class Property extends AbstractProperty<CheckSample>
}
});
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/RemoteApiTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/RemoteApiTestCase.java
index df7fad3bb85..c95ce5c86a6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/RemoteApiTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/remoteapitest/RemoteApiTestCase.java
@@ -37,9 +37,8 @@ import ch.systemsx.cisd.openbis.generic.server.util.TestInitializer;
import ch.systemsx.cisd.openbis.generic.shared.util.TestInstanceHostUtils;
/**
- * Test cases which have access to the public API services of a running, fully-fledged openBIS
- * server. The tests do not see the server internals and thus they must employ black-box testing
- * strategies.
+ * Test cases which have access to the public API services of a running, fully-fledged openBIS server. The tests do not see the server internals and
+ * thus they must employ black-box testing strategies.
*
* @author Kaloyan Enimanev
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
index d20b983fa63..4d04313cc8c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractDataSetAssignmentTestCase.java
@@ -131,6 +131,7 @@ public abstract class AbstractDataSetAssignmentTestCase extends BaseTest
return RolePermutator.getAcceptedPermutations(assignDataSetToExperimentRule, source,
destination, instance);
}
+
@DataProvider
public Object[][] rolesNotAllowedToAssignDataSetToExperiment()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
index f97bda93c2f..847f9e2ebac 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AbstractEntityDeletionTestCase.java
@@ -51,10 +51,10 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
{
EntityGraphGenerator g = parseAndCreateGraph(
"E1, samples: S50, data sets: DS60 DS61\n"
- + "E2, samples: S51\n"
- + "E3\n"
+ + "E2, samples: S51\n"
+ + "E3\n"
);
-
+
deleteExperiments(g.e(1), g.e(2), g.e(3));
assertEquals("", renderGraph(g));
@@ -63,7 +63,7 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(60), g.ds(61));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentsWithDeepDependencies()
{
@@ -82,22 +82,22 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(60), g.ds(61), g.ds(70), g.ds(71));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentWithSampleWhichIsAComponentOfASpaceSample()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S2\n"
+ "S1, components: S2\n");
-
+
deleteExperiments(g.e(1));
-
+
assertEquals("", renderGraph(g));
assertModified(g.s(1));
assertDeleted(g.e(1));
assertDeleted(g.s(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public void testTrashExperimentWithSampleWhichHasAChild()
{
@@ -105,14 +105,14 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "S1, children: S3\n");
deleteExperiments(g.e(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.e(1));
assertDeleted(g.s(1));
assertModified(g.s(3));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(false)
public final void testTrashExperimentWithSampleAndDataSet()
@@ -121,14 +121,14 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "S1, data sets: DS1\n", false);
deleteExperiments(g.e(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.e(1));
assertDeleted(g.s(1));
assertDeleted(g.ds(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentsWithSampleAndDataSetsAndNoExternalLinks()
{
@@ -136,16 +136,16 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "E2, data sets: DS2\n"
+ "S1, data sets: DS1\n"
+ "DS1, components: DS2\n");
-
+
deleteExperiments(g.e(1), g.e(2));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.e(1), g.e(2));
assertDeleted(g.s(1));
assertDeleted(g.ds(1), g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentWithARelatedDataSetComponentWhichBelongsToAnExternalExperiment()
{
@@ -153,16 +153,16 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "E2, data sets: DS2\n"
+ "S1, data sets: DS1\n"
+ "DS1, components: DS2\n");
-
+
deleteExperiments(g.e(1));
-
+
assertEquals("E2, data sets: DS2\n", renderGraph(g));
assertDeleted(g.e(1));
assertDeleted(g.s(1));
assertDeleted(g.ds(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public final void testTrashExperimentWithARelatedDataSetInAnExternalContainer()
@@ -171,16 +171,16 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "E2, data sets: DS2\n"
+ "S1, data sets: DS1\n"
+ "DS1, components: DS2\n", false);
-
+
failTrashExperiment(g.e(2), createExpectedErrorMessage(g.ds(2), g.ds(1), g.s(1)));
-
+
assertEquals("E1, samples: S1, data sets: DS1\n"
+ "E2, data sets: DS2\n"
+ "S1, data sets: DS1\n"
+ "DS1, components: DS2\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public void testTrashPublishedExperiment()
{
@@ -190,9 +190,9 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "DS2, components: DS6\n"
+ "DS3, components: DS4\n"
+ "DS5, parents: DS6\n");
-
+
deleteExperiments(g.e(2));
-
+
assertEquals("E1, data sets: DS3 DS4 DS5 DS6\n"
+ "DS3, components: DS4\n"
+ "DS5, parents: DS6\n", renderGraph(g));
@@ -200,7 +200,7 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(1), g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashPublishedExperimentWithOrginalExperimentWithSamples()
{
@@ -210,9 +210,9 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "DS1, components: DS2\n"
+ "DS2, components: DS3\n"
);
-
+
deleteExperiments(g.e(2));
-
+
assertEquals("E1, samples: S1, data sets: DS2 DS3\n"
+ "S1, data sets: DS2 DS3\n"
+ "DS2, components: DS3\n", renderGraph(g));
@@ -220,7 +220,7 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public final void testTrashOrginalExperimentWithSample()
@@ -230,9 +230,9 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "S1, data sets: DS2 DS3\n"
+ "DS1, components: DS2\n"
+ "DS2, components: DS3\n", false);
-
+
failTrashExperiment(g.e(1), createExpectedErrorMessage(g.ds(2), g.ds(1), g.e(2)));
-
+
assertEquals("E1, samples: S1, data sets: DS2 DS3\n"
+ "E2, data sets: DS1\n"
+ "S1, data sets: DS2 DS3\n"
@@ -240,28 +240,27 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "DS2, components: DS3\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentsWithContainerDataSetWithPhysicalDataSetFromAnotherExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1\n"
+ "E2, data sets: DS2\n"
+ "DS1, components: DS2\n");
-
+
deleteExperiments(g.e(1));
-
+
assertEquals("E2, data sets: DS2\n", renderGraph(g));
assertDeleted(g.e(1));
assertDeleted(g.ds(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSamplesAlreadyTrashed()
{
EntityGraphGenerator g = parseAndCreateGraph("S1\nS2\n");
-
-
+
assertEquals("", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
@@ -272,135 +271,135 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
EntityGraphGenerator g = parseAndCreateGraph("S1, components: S20\n"
+ "S3, data sets: DS60[NET]\n"
+ "S20, data sets: DS61[NET]\n");
-
+
deleteSamples(g.s(1), g.s(3));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(3), g.s(20));
assertDeleted(g.ds(60), g.ds(61));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSampleWithTwoLevelOfDependencies()
{
EntityGraphGenerator g = parseAndCreateGraph("S1, components: S2 S3, data sets: DS1[NET]\n"
+ "S2, data sets: DS2[NET]\n"
+ "S3, data sets: DS3[NET]\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(2), g.s(3));
assertDeleted(g.ds(1), g.ds(2), g.ds(3));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashComponentSample()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S2\n"
+ "S1, components: S2\n");
-
+
deleteSamples(g.s(2));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(2));
assertModified(g.e(1));
assertModified(g.s(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSampleWithAComponentWithAContainerDataSetWithAComponentDataSetOfFirstSample()
{
EntityGraphGenerator g = parseAndCreateGraph("S1, components: S2, data sets: DS2[NET]\n"
+ "S2, data sets: DS1[NECT]\n"
+ "DS1[NECT], components: DS2[NET]\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(2));
assertDeleted(g.ds(1), g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSampleWithAComponentWithAComponentDataSetOfAContainerDataSetOfFirstSample()
{
EntityGraphGenerator g = parseAndCreateGraph("S1, components: S2, data sets: DS1[NECT]\n"
+ "S2, data sets: DS2[NET]\n"
+ "DS1[NECT], components: DS2[NET]\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(2));
assertDeleted(g.ds(1), g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSampleWithAnExperimentSample()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S2\n"
+ "S1, components: S2\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(2));
assertModified(g.e(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashSampleWithAnExperimentSampleWithADataSet()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S2, data sets: DS1\n"
+ "S1, components: S2\n"
+ "S2, data sets: DS1\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertDeleted(g.s(1), g.s(2));
assertDeleted(g.ds(1));
assertModified(g.e(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentSampleWithADataSet()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1\n"
+ "S1, data sets: DS1\n");
-
+
deleteSamples(g.s(1));
-
+
assertEquals("", renderGraph(g));
assertModified(g.e(1));
assertDeleted(g.s(1));
assertDeleted(g.ds(1));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashExperimentSampleWhichIsAComponentOfASpaceSample()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S2\n"
+ "S1, components: S2\n");
-
+
deleteSamples(g.s(2));
-
+
assertEquals("", renderGraph(g));
assertModified(g.e(1));
assertModified(g.s(1));
assertDeleted(g.s(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public final void testTrashSampleWithComponentWithDataSetWithComponentOfAnotherSample()
@@ -409,16 +408,16 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "S2, data sets: DS2[NET]\n"
+ "S3, data sets: DS1[NECT]\n"
+ "DS1[NECT], components: DS2[NET]\n", false);
-
+
failTrashSample(g.s(1), createExpectedErrorMessage(g.ds(2), g.ds(1), g.s(3)));
-
+
assertEquals("S1, components: S2\n"
+ "S2, data sets: DS2[NET]\n"
+ "S3, data sets: DS1[NECT]\n"
+ "DS1[NECT], components: DS2[NET]\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public final void testTrashSampleWithComponentWithDataSetWithComponentOfAnotherExperiment()
@@ -427,16 +426,16 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "S1, components: S2\n"
+ "S2, data sets: DS2[NET]\n"
+ "DS1, components: DS2[NET]\n", false);
-
+
failTrashSample(g.s(1), createExpectedErrorMessage(g.ds(2), g.ds(1), g.e(1)));
-
+
assertEquals("E1, data sets: DS1\n"
+ "S1, components: S2\n"
+ "S2, data sets: DS2[NET]\n"
+ "DS1, components: DS2[NET]\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public void testTrashSampleWithDataSetWithDataSetComponentIndirectlyDependentOnOutsideContainer()
@@ -446,9 +445,9 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "DS1[NECT], components: DS3[NET] DS4[NECT] DS5[NET]\n"
+ "DS2[NECT], components: DS4[NECT]\n"
+ "DS4[NECT], components: DS5[NET] DS6[NET]\n", false);
-
+
failTrashSample(g.s(1), createExpectedErrorMessage(g.ds(4), g.ds(2), g.s(2)));
-
+
assertEquals("S1, data sets: DS1[NECT] DS3[NET] DS4[NECT] DS5[NET] DS6[NET]\n"
+ "S2, data sets: DS2[NECT]\n"
+ "DS1[NECT], components: DS3[NET] DS4[NECT] DS5[NET]\n"
@@ -456,20 +455,20 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
+ "DS4[NECT], components: DS5[NET] DS6[NET]\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
@Rollback(true)
public void testTrashSampleWithComponentsFromAnInvisibleSpace()
{
EntityGraphGenerator g = parseAndCreateGraph("/S1/S1, components: /S2/S2\n", false);
- SessionBuilder sessionBuilder = aSession().withSpaceRole(RoleWithHierarchy.SPACE_ADMIN,
+ SessionBuilder sessionBuilder = aSession().withSpaceRole(RoleWithHierarchy.SPACE_ADMIN,
entityGraphManager.getSample(g.s(1)).getSpace());
String userSessionToken = create(sessionBuilder);
-
+
String userID = sessionBuilder.getUserID();
String sample = entityGraphManager.getSample(g.s(2)).getIdentifier();
failTrashSample(userSessionToken, g.s(1), createExpectedErrorMessage(userID, sample));
-
+
assertEquals("/S1/S1, components: /S2/S2\n", renderGraph(g));
assertUnmodifiedAndUndeleted(g);
}
@@ -480,54 +479,54 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
EntityGraphGenerator g = parseAndCreateGraph("S1, data sets: DS1[NECT] DS2[NECT] DS3[NET] DS4[NET] DS5[NET] DS6[NET]\n"
+ "DS1[NECT], components: DS5[NET]\n"
+ "DS2[NECT], components: DS6[NET]\n");
-
+
deleteDataSets(g.ds(1), g.ds(2), g.ds(3));
-
+
assertEquals("S1, data sets: DS4[NET]\n", renderGraph(g));
assertModified(g.s(1));
assertDeleted(g.ds(1), g.ds(2), g.ds(3), g.ds(5), g.ds(6));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashDataSetAndComponentsBelongingToSameExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1 DS2\n"
+ "E2, data sets: DS3\n"
+ "DS1, components: DS2 DS3\n");
-
+
deleteDataSets(g.ds(1));
-
+
assertEquals("E2, data sets: DS3\n", renderGraph(g));
assertModified(g.e(1));
assertDeleted(g.ds(1), g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashDataSetOfAContainerWhichBelongingToSameExperiment()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, data sets: DS1 DS2\n"
+ "DS1, components: DS2\n");
-
+
deleteDataSets(g.ds(2));
-
+
assertEquals("E1, data sets: DS1\n", renderGraph(g));
assertModified(g.e(1));
assertModified(g.ds(1));
assertDeleted(g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public final void testTrashDataSetOfAContainerWhichBelongingToSameExperimentButDifferentSample()
{
EntityGraphGenerator g = parseAndCreateGraph("E1, samples: S1, data sets: DS1 DS2\n"
+ "S1, data sets: DS2\n"
+ "DS1, components: DS2\n");
-
+
deleteDataSets(g.ds(2));
-
+
assertEquals("E1, samples: S1, data sets: DS1\n", renderGraph(g));
assertModified(g.e(1));
assertModified(g.s(1));
@@ -535,23 +534,23 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(2));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public void testTrashDataSetsWithDataSetInAContainer()
{
EntityGraphGenerator g = parseAndCreateGraph("S1, data sets: DS1[NECT] DS2[NECT] DS3[NET]\n"
+ "DS1[NECT], components: DS2[NECT]\n"
+ "DS2[NECT], components: DS3[NET]\n");
-
+
deleteDataSets(g.ds(2));
-
+
assertEquals("S1, data sets: DS1[NECT]\n", renderGraph(g));
assertModified(g.s(1));
assertModified(g.ds(1));
assertDeleted(g.ds(2), g.ds(3));
assertUnmodifiedAndUndeleted(g);
}
-
+
@Test
public void testTrashDataSetsWithDataSetComponentIndirectlyDependentOnOutsideContainer()
{
@@ -569,7 +568,7 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertDeleted(g.ds(1), g.ds(3));
assertUnmodifiedAndUndeleted(g);
}
-
+
private void failTrashExperiment(ExperimentNode experimentNode, String expectedErrorMessage)
{
try
@@ -578,11 +577,11 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals(expectedErrorMessage,
- ex.getMessage());
+ assertEquals(expectedErrorMessage,
+ ex.getMessage());
}
}
-
+
private void failTrashSample(SampleNode sampleNode, String expectedErrorMessage)
{
String userSessionToken = createAdminUser();
@@ -600,27 +599,26 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
assertEquals(expectedErrorMessage, ex.getMessage());
}
}
-
+
protected String createExpectedErrorMessage(SampleNode relatedSample, EntityNode outsiderNode)
{
String relation = outsiderNode instanceof ExperimentNode ? "belongs to" : "is a component of";
- return "The sample " + entityGraphManager.getSample(relatedSample).getIdentifier()
+ return "The sample " + entityGraphManager.getSample(relatedSample).getIdentifier()
+ " " + relation + " the " + render(outsiderNode) + " which is outside the deletion set.";
}
protected String createExpectedErrorMessage(EntityNode originalNode, EntityNode relatedEntity, EntityNode outsiderNode)
{
- return "The " + render(originalNode)
- + " is a component of the " + render(relatedEntity)
+ return "The " + render(originalNode)
+ + " is a component of the " + render(relatedEntity)
+ " which belongs to the " + render(outsiderNode) + " which is outside the deletion set.";
}
-
+
protected String createExpectedErrorMessage(String userID, String... samples)
{
- return "Authorization failure: Can not delete samples " + Arrays.asList(samples)
+ return "Authorization failure: Can not delete samples " + Arrays.asList(samples)
+ " because user " + userID + " does not have enough privileges.";
}
-
private String render(EntityNode entityNode)
{
@@ -641,8 +639,8 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
}
return type + " " + identifier;
}
-
- private void deleteExperiments(ExperimentNode...experimentNodes)
+
+ private void deleteExperiments(ExperimentNode... experimentNodes)
{
List<String> experimentIdentifiers = new ArrayList<String>();
for (ExperimentNode experimentNode : experimentNodes)
@@ -653,7 +651,7 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
flushAndClearHibernateSession();
}
- private void deleteSamples(SampleNode...sampleNodes)
+ private void deleteSamples(SampleNode... sampleNodes)
{
deleteSamples(createAdminUser(), sampleNodes);
}
@@ -668,8 +666,8 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
deleteSamples(samplePermIds, userSessionToken);
flushAndClearHibernateSession();
}
-
- private void deleteDataSets(DataSetNode...dataSetNodes)
+
+ private void deleteDataSets(DataSetNode... dataSetNodes)
{
List<String> dataSetCodes = new ArrayList<String>();
for (DataSetNode dataSetNode : dataSetNodes)
@@ -679,17 +677,17 @@ public abstract class AbstractEntityDeletionTestCase extends BaseTest
deleteDataSets(dataSetCodes, createAdminUser());
flushAndClearHibernateSession();
}
-
+
private String createAdminUser()
{
return create(aSession().withInstanceRole(RoleCode.ADMIN));
}
-
+
/**
* Trashes specified experiments for specified user session token.
*/
protected abstract void deleteExperiments(List<String> experimentIdentifiers, String userSessionToken);
-
+
/**
* Trashes specified samples for specified user session token.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleTest.java
index f744a378d26..3d8e731af4b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleTest.java
@@ -38,7 +38,7 @@ public class AssignDataSetToExperimentAndSampleTest extends AbstractDataSetAssig
AbstractExternalData dataSet = etlService.tryGetDataSet(systemSessionToken, dataSetCode);
if (experimentIdentifierOrNull != null)
{
- Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
+ Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
ExperimentIdentifierFactory.parse(experimentIdentifierOrNull));
perform(anUpdateOf(dataSet).toExperiment(experiment).as(userSessionToken));
} else
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleViaDropBoxAPITest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleViaDropBoxAPITest.java
index be6a49b5689..0bc07232b46 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleViaDropBoxAPITest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignDataSetToExperimentAndSampleViaDropBoxAPITest.java
@@ -36,8 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
- * Data set assignment tests for Drop Box API V1/V2 (that is, via {@link IServiceForDataStoreServer#performEntityOperations(String,
- * ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails)}).
+ * Data set assignment tests for Drop Box API V1/V2 (that is, via
+ * {@link IServiceForDataStoreServer#performEntityOperations(String, ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails)}).
*
* @author Franz-Josef Elmer
*/
@@ -73,7 +73,7 @@ public class AssignDataSetToExperimentAndSampleViaDropBoxAPITest extends Abstrac
AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
etlService.performEntityOperations(userSessionToken, builder.dataSetUpdate(dataSetUpdate).getDetails());
}
-
+
private DataSetBatchUpdatesDTO createUpdatesObject(String dataSetCode)
{
AbstractExternalData dataSet = etlService.tryGetDataSet(systemSessionToken, dataSetCode);
@@ -93,7 +93,7 @@ public class AssignDataSetToExperimentAndSampleViaDropBoxAPITest extends Abstrac
{
dataSetUpdate.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(sample));
}
- dataSetUpdate.setProperties(Collections.<IEntityProperty>emptyList());
+ dataSetUpdate.setProperties(Collections.<IEntityProperty> emptyList());
updateDetails.setPropertiesToUpdate(new HashSet<String>());
return dataSetUpdate;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignExperimentToProjectTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignExperimentToProjectTest.java
index 3f6f98ae2d2..77fe313cab2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignExperimentToProjectTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignExperimentToProjectTest.java
@@ -94,7 +94,7 @@ public class AssignExperimentToProjectTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAssignExperimentToProject", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void assigningExperimentToProjectIsNotAllowedFor(RoleWithHierarchy sourceSpaceRole,
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignProjectToSpaceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignProjectToSpaceTest.java
index e2b8cac271d..dcb03701d6b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignProjectToSpaceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignProjectToSpaceTest.java
@@ -90,7 +90,7 @@ public class AssignProjectToSpaceTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAssignProjectToSpace", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void assigningProjectToSpaceIsNotAllowedFor(RoleWithHierarchy sourceSpaceRole,
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
index 5d00d24e0f6..93be25ef514 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentTest.java
@@ -32,24 +32,24 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
public class AssignSampleToExperimentTest extends AbstractAssignmentSampleToExperimentTestCase
{
@Override
- protected void updateExperimentChangeSamples(String experimentIdentifier, List<String> samplePermIds,
+ protected void updateExperimentChangeSamples(String experimentIdentifier, List<String> samplePermIds,
String userSessionToken)
{
- Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
+ Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
ExperimentIdentifierFactory.parse(experimentIdentifier));
perform(anUpdateOf(experiment).withSamples(loadSamples(samplePermIds)).as(userSessionToken));
-
+
}
-
+
@Override
- protected void updateSampleChangeExperiment(String samplePermId, String experimentIdentifierOrNull,
+ protected void updateSampleChangeExperiment(String samplePermId, String experimentIdentifierOrNull,
String userSessionToken)
{
SampleIdentifier sampleIdentifier = etlService.tryGetSampleIdentifier(systemSessionToken, samplePermId);
Sample sample = etlService.tryGetSampleWithExperiment(systemSessionToken, sampleIdentifier);
if (experimentIdentifierOrNull != null)
{
- Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
+ Experiment experiment = etlService.tryGetExperiment(systemSessionToken,
ExperimentIdentifierFactory.parse(experimentIdentifierOrNull));
perform(anUpdateOf(sample).toExperiment(experiment).as(userSessionToken));
} else
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentViaDropBoxAPITest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentViaDropBoxAPITest.java
index b1f80d94828..fbb0bb23ec6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentViaDropBoxAPITest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToExperimentViaDropBoxAPITest.java
@@ -42,7 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
public class AssignSampleToExperimentViaDropBoxAPITest extends AbstractAssignmentSampleToExperimentTestCase
{
@Override
- protected void updateExperimentChangeSamples(String experimentIdentifier, List<String> samplePermIds,
+ protected void updateExperimentChangeSamples(String experimentIdentifier, List<String> samplePermIds,
String userSessionToken)
{
ExperimentIdentifier identifier = ExperimentIdentifierFactory.parse(experimentIdentifier);
@@ -51,16 +51,16 @@ public class AssignSampleToExperimentViaDropBoxAPITest extends AbstractAssignmen
experimentUpdate.setExperimentId(new TechId(experiment));
experimentUpdate.setProjectIdentifier(identifier);
experimentUpdate.setVersion(experiment.getVersion());
- experimentUpdate.setProperties(Collections.<IEntityProperty>emptyList());
- experimentUpdate.setAttachments(Collections.<NewAttachment>emptyList());
+ experimentUpdate.setProperties(Collections.<IEntityProperty> emptyList());
+ experimentUpdate.setAttachments(Collections.<NewAttachment> emptyList());
Sample[] samples = loadSamples(samplePermIds);
experimentUpdate.setSampleCodes(Code.extractCodesToArray(Arrays.asList(samples)));
AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
etlService.performEntityOperations(userSessionToken, builder.experimentUpdate(experimentUpdate).getDetails());
}
-
+
@Override
- protected void updateSampleChangeExperiment(String samplePermId, String experimentIdentifierOrNull,
+ protected void updateSampleChangeExperiment(String samplePermId, String experimentIdentifierOrNull,
String userSessionToken)
{
SampleIdentifier sampleIdentifier = etlService.tryGetSampleIdentifier(systemSessionToken, samplePermId);
@@ -82,5 +82,5 @@ public class AssignSampleToExperimentViaDropBoxAPITest extends AbstractAssignmen
sampleIdentifier, containerIdentifier, null));
etlService.performEntityOperations(userSessionToken, builder.getDetails());
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToSpaceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToSpaceTest.java
index 7a3f1a1eb27..0a3dc66e6dd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToSpaceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AssignSampleToSpaceTest.java
@@ -204,7 +204,7 @@ public class AssignSampleToSpaceTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAssignSampleToSpace", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void assigningSampleToAnotherSpaceIsNotAllowedFor(RoleWithHierarchy sourceSpaceRole,
RoleWithHierarchy destinationSpaceRole, RoleWithHierarchy instanceRole)
throws Exception
@@ -235,7 +235,7 @@ public class AssignSampleToSpaceTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAssignSharedSampleToSpace", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void assigningSharedSampleToSpaceIsNotAllowedFor(RoleWithHierarchy destinationSpaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AttachmentUploadTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AttachmentUploadTest.java
index 1ee5e6358fa..a6520506bad 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AttachmentUploadTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AttachmentUploadTest.java
@@ -36,14 +36,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@Test(groups = "system test")
public class AttachmentUploadTest extends SystemTestCase
{
private static final String FILE_CONTENT = "hello world";
+
private static final String FILE_NAME = "hello.txt";
@Test
@@ -70,33 +69,33 @@ public class AttachmentUploadTest extends SystemTestCase
{
SessionContext sessionContext = logIntoCommonClientService();
TechId experimentID = new TechId(2);
-
+
uploadFile(FILE_NAME, FILE_CONTENT);
commonClientService.addAttachment(experimentID, SESSION_KEY, AttachmentHolderKind.EXPERIMENT,
new NewAttachment(FILE_NAME, "my file", "example file"));
-
+
AttachmentWithContent attachmentWithContent =
- genericServer.getExperimentFileAttachment(sessionContext.getSessionID(), experimentID,
- FILE_NAME, 1);
+ genericServer.getExperimentFileAttachment(sessionContext.getSessionID(), experimentID,
+ FILE_NAME, 1);
checkUploadedAttachment(experimentID, AttachmentHolderKind.EXPERIMENT, attachmentWithContent);
}
-
+
@Test
public void testUploadSampleAttachment()
{
SessionContext sessionContext = logIntoCommonClientService();
TechId sampleID = new TechId(1);
-
+
uploadFile(FILE_NAME, FILE_CONTENT);
commonClientService.addAttachment(sampleID, SESSION_KEY, AttachmentHolderKind.SAMPLE,
new NewAttachment(FILE_NAME, "my file", "example file"));
-
+
AttachmentWithContent attachmentWithContent =
- genericServer.getSampleFileAttachment(sessionContext.getSessionID(), sampleID,
- FILE_NAME, 1);
+ genericServer.getSampleFileAttachment(sessionContext.getSessionID(), sampleID,
+ FILE_NAME, 1);
checkUploadedAttachment(sampleID, AttachmentHolderKind.SAMPLE, attachmentWithContent);
}
-
+
private void checkUploadedAttachment(TechId holderID, AttachmentHolderKind holderKind,
AttachmentWithContent attachmentWithContent)
{
@@ -108,17 +107,19 @@ public class AttachmentUploadTest extends SystemTestCase
new DefaultResultSetConfig<String, TableModelRowWithObject<AttachmentVersions>>());
GridRowModels<TableModelRowWithObject<AttachmentVersions>> list = attachmentVersions.getResultSet().getList();
- for (GridRowModel<TableModelRowWithObject<AttachmentVersions>> tmrl : list) {
- Attachment attachment = tmrl.getOriginalObject().getObjectOrNull().getVersions().get(0);
- if (attachment.getFileName().equals(FILE_NAME)) {
+ for (GridRowModel<TableModelRowWithObject<AttachmentVersions>> tmrl : list)
+ {
+ Attachment attachment = tmrl.getOriginalObject().getObjectOrNull().getVersions().get(0);
+ if (attachment.getFileName().equals(FILE_NAME))
+ {
assertEquals("my file", attachment.getTitle());
assertEquals("example file", attachment.getDescription());
assertEquals(1, attachment.getVersion());
assertEquals(FILE_CONTENT, new String(attachmentWithContent.getContent()));
- return;
- }
+ return;
+ }
}
-
- fail("Attachment with file name "+FILE_NAME+" was not found");
+
+ fail("Attachment with file name " + FILE_NAME + " was not found");
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AuthenticationSystemTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AuthenticationSystemTest.java
index 9c8f5c9c2cd..81c2065e8b0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AuthenticationSystemTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/AuthenticationSystemTest.java
@@ -28,8 +28,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@Test(groups = "system test")
@@ -47,7 +45,7 @@ public class AuthenticationSystemTest extends SystemTestCase
assertEquals("No 'password' specified.", ex.getMessage());
}
}
-
+
@Test
public void testTryToAuthenticateAsSystem()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityDeletionTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityDeletionTest.java
index 467002aa4a3..52ad4b53fd6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityDeletionTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityDeletionTest.java
@@ -50,7 +50,7 @@ public class EntityDeletionTest extends AbstractEntityDeletionTestCase
List<TechId> experimentIds = TechId.createList(commonServer.listExperiments(userSessionToken, identifiers));
commonServer.deleteExperiments(userSessionToken, experimentIds, "test", DeletionType.TRASH);
}
-
+
/**
* Trashes specified samples for specified user session token.
*/
@@ -69,5 +69,5 @@ public class EntityDeletionTest extends AbstractEntityDeletionTestCase
{
commonServer.deleteDataSets(userSessionToken, dataSetCodes, "test", DeletionType.TRASH, true);
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
index 75299eb069e..d09fbe594fc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
@@ -660,7 +660,7 @@ public class EntityOperationTest extends SystemTestCase
assertEquals("[COMMENT: my data]", dataSet.getProperties().toString());
assertEquals("/CISD/PLATE_WELLSEARCH:WELL-A01", dataSet.getSampleIdentifier());
}
-
+
@Test
public void testCreateDataSetForUnknownSample()
{
@@ -669,11 +669,11 @@ public class EntityOperationTest extends SystemTestCase
AtomicEntityOperationDetails eo =
new EntityOperationBuilder().dataSet(
new DataSetBuilder().code(dataSetCode).type("HCS_IMAGE")
- .store(new DataStoreBuilder("STANDARD").getStore())
- .fileFormat("XML").location("a/b/c").property("COMMENT", "my data")
- .sample(new SampleBuilder().identifier("/CISD/A01").getSample())
- .getDataSet()).create();
-
+ .store(new DataStoreBuilder("STANDARD").getStore())
+ .fileFormat("XML").location("a/b/c").property("COMMENT", "my data")
+ .sample(new SampleBuilder().identifier("/CISD/A01").getSample())
+ .getDataSet()).create();
+
try
{
etlService.performEntityOperations(sessionToken, eo);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/FilterSystemTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/FilterSystemTest.java
index cffa26c2a65..154322c6880 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/FilterSystemTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/FilterSystemTest.java
@@ -143,8 +143,8 @@ public class FilterSystemTest extends SystemTestCase
new HashSet<IColumnDefinition<TableModelRowWithObject<GridCustomFilter>>>();
String[] headerIds =
- { "NAME", "DESCRIPTION", "EXPRESSION", "IS_PUBLIC", "REGISTRATOR",
- "REGISTRATION_DATE", "MODIFICATION_DATE" };
+ { "NAME", "DESCRIPTION", "EXPRESSION", "IS_PUBLIC", "REGISTRATOR",
+ "REGISTRATION_DATE", "MODIFICATION_DATE" };
for (int i = 0; i < headerIds.length; i++)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/RegisterDataSetTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/RegisterDataSetTest.java
index dbcbc075788..53826844bae 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/RegisterDataSetTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/RegisterDataSetTest.java
@@ -44,14 +44,12 @@ import ch.systemsx.cisd.openbis.systemtest.base.BaseTest;
import ch.systemsx.cisd.openbis.systemtest.base.builder.ExternalDataBuilder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class RegisterDataSetTest extends BaseTest
{
private Sample sampleWithExperiment;
-
+
private Sample spaceSampleWithoutExperiment;
private Sample sharedSample;
@@ -74,10 +72,10 @@ public class RegisterDataSetTest extends BaseTest
public void testRegisterDataSetForAnExperiment() throws Exception
{
AbstractExternalData dataSet = create(aDataSet().inExperiment(experiment));
-
+
assertThat(dataSet, is(inExperiment(experiment)));
}
-
+
@Test
public void testRegisterContainerWithNonExistingDataSetForAnExperimentFails() throws Exception
{
@@ -100,10 +98,10 @@ public class RegisterDataSetTest extends BaseTest
List<String> componentDSCodes = new ArrayList<String>();
componentDSCodes.add(component1.getCode());
componentDSCodes.add(component2.getCode());
-
+
AbstractExternalData dataSet = create(aDataSet().asContainer().withComponents(component1.getCode(), component2.getCode())
.inExperiment(experiment));
-
+
assertThat(dataSet, is(inExperiment(experiment)));
List<AbstractExternalData> components = dataSet.tryGetAsContainerDataSet().getContainedDataSets();
List<String> codes = Code.extractCodes(components);
@@ -114,16 +112,16 @@ public class RegisterDataSetTest extends BaseTest
assertThat(components.get(1), is(inExperiment(experiment)));
assertThat(components.size(), equalTo(2));
}
-
+
@Test
public void testRegisterDataSetForADeletedExperiment() throws Exception
{
- commonServer.deleteExperiments(systemSessionToken, Arrays.asList(new TechId(experiment)),
+ commonServer.deleteExperiments(systemSessionToken, Arrays.asList(new TechId(experiment)),
"t", DeletionType.TRASH);
createWithExpectedError(aDataSet().inExperiment(experiment),
"Unknown experiment '" + experiment.getIdentifier() + "'.");
}
-
+
@Test
public void testRegisterDataSetAsContainerForADeletedDataSetFails() throws Exception
{
@@ -133,7 +131,8 @@ public class RegisterDataSetTest extends BaseTest
commonServer.deleteDataSets(systemSessionToken, Arrays.asList(componentDataSet.getCode()),
"t", DeletionType.TRASH, true);
- try {
+ try
+ {
create(aDataSet().asContainer().withComponents(componentDataSet.getCode()).inExperiment(experiment));
fail("UserFailureExcpetion expected");
} catch (UserFailureException ex)
@@ -146,11 +145,11 @@ public class RegisterDataSetTest extends BaseTest
public void testRegisterDataSetForASampleWithExperiment() throws Exception
{
AbstractExternalData dataSet = create(aDataSet().inSample(sampleWithExperiment));
-
+
assertThat(dataSet, is(inSample(sampleWithExperiment)));
assertThat(dataSet, is(inExperiment(experiment)));
}
-
+
@Test
public void testRegisterContainerDataSetForASampleWithExperiment() throws Exception
{
@@ -162,7 +161,7 @@ public class RegisterDataSetTest extends BaseTest
AbstractExternalData dataSet = create(aDataSet().asContainer().withComponents(component1.getCode(), component2.getCode())
.inSample(sampleWithExperiment));
-
+
assertThat(dataSet, is(inSample(sampleWithExperiment)));
assertThat(dataSet, is(inExperiment(experiment)));
List<AbstractExternalData> components = dataSet.tryGetAsContainerDataSet().getContainedDataSets();
@@ -175,33 +174,33 @@ public class RegisterDataSetTest extends BaseTest
assertThat(components.get(1), is(inExperiment(experiment)));
assertThat(components.size(), equalTo(2));
}
-
+
@Test
public void testRegisterDataSetForADeletedSampleWithExperiment() throws Exception
{
- commonServer.deleteSamples(systemSessionToken, Arrays.asList(new TechId(sampleWithExperiment)),
+ commonServer.deleteSamples(systemSessionToken, Arrays.asList(new TechId(sampleWithExperiment)),
"t", DeletionType.TRASH);
- createWithExpectedError(aDataSet().inSample(sampleWithExperiment),
+ createWithExpectedError(aDataSet().inSample(sampleWithExperiment),
"No sample could be found with given identifier '" + sampleWithExperiment.getIdentifier() + "'.");
}
@Test
public void testRegisterDataSetForASampleWithDeletedExperiment() throws Exception
{
- commonServer.deleteExperiments(systemSessionToken, Arrays.asList(new TechId(experiment)),
+ commonServer.deleteExperiments(systemSessionToken, Arrays.asList(new TechId(experiment)),
"t", DeletionType.TRASH);
- createWithExpectedError(aDataSet().inSample(sampleWithExperiment),
+ createWithExpectedError(aDataSet().inSample(sampleWithExperiment),
"No sample could be found with given identifier '" + sampleWithExperiment.getIdentifier() + "'.");
}
-
+
@Test
public void testRegisterDataSetForASampleWithoutExperiment() throws Exception
{
AbstractExternalData dataSet = create(aDataSet().withType("NO-EXP-TYPE").inSample(spaceSampleWithoutExperiment));
-
+
assertThat(dataSet, is(inSample(spaceSampleWithoutExperiment)));
}
-
+
@Test
public void testRegisterContainerDataSetAndItsComponentsForASampleWithoutExperiment() throws Exception
{
@@ -230,7 +229,7 @@ public class RegisterDataSetTest extends BaseTest
AbstractExternalData componentDataSet = create(aDataSet().inSample(sampleWithExperiment));
AbstractExternalData dataSet = create(aDataSet().withType("NEXP-CONTAINER-TYPE")
.asContainer().withComponent(componentDataSet).inSample(spaceSampleWithoutExperiment));
-
+
assertThat(dataSet, is(inSample(spaceSampleWithoutExperiment)));
List<AbstractExternalData> components = dataSet.tryGetAsContainerDataSet().getContainedDataSets();
List<String> codes = Code.extractCodes(components);
@@ -240,37 +239,37 @@ public class RegisterDataSetTest extends BaseTest
assertThat(components.get(0), is(inExperiment(experiment)));
assertThat(components.size(), equalTo(1));
}
-
+
@Test
public void testRegisterDataSetForASampleWithoutExperimentButWrongDataSetType() throws Exception
{
- createWithExpectedError(aDataSet().inSample(spaceSampleWithoutExperiment),
- "Data set can not be registered because no experiment found for sample '"
- + spaceSampleWithoutExperiment.getIdentifier() + "'.");
+ createWithExpectedError(aDataSet().inSample(spaceSampleWithoutExperiment),
+ "Data set can not be registered because no experiment found for sample '"
+ + spaceSampleWithoutExperiment.getIdentifier() + "'.");
}
@Test
public void testRegisterDataSetForASharedSample() throws Exception
{
- createWithExpectedError(aDataSet().withType("NEXP-TYPE").inSample(sharedSample),
- "Data set can not be registered because sample '" + sharedSample.getIdentifier()
- + "' is a shared sample.");
+ createWithExpectedError(aDataSet().withType("NEXP-TYPE").inSample(sharedSample),
+ "Data set can not be registered because sample '" + sharedSample.getIdentifier()
+ + "' is a shared sample.");
}
-
+
@Test
public void testRegisterDataSetForSampleWithoutExperimentViaPerformEntityOperation() throws Exception
{
NewExternalData newDataSet = aDataSet().withType("NO-EXP-TYPE2")
.inSample(spaceSampleWithoutExperiment).get();
AtomicEntityOperationDetails operationDetails = new EntityOperationBuilder().dataSet(newDataSet).create();
-
+
AtomicEntityOperationResult operationResult = etlService.performEntityOperations(systemSessionToken, operationDetails);
-
+
assertThat((int) operationResult.getDataSetsCreatedCount(), equalTo(1));
AbstractExternalData dataSet = etlService.tryGetDataSet(systemSessionToken, newDataSet.getCode());
assertThat(dataSet, is(inSample(spaceSampleWithoutExperiment)));
}
-
+
private void createWithExpectedError(ExternalDataBuilder dataSetBuilder, String expectedErrorMessage)
{
try
@@ -282,6 +281,5 @@ public class RegisterDataSetTest extends BaseTest
assertEquals(expectedErrorMessage, ex.getMessage());
}
}
-
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/SystemTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/SystemTestCase.java
index 9c2f9407b49..67d98c2f940 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/SystemTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/SystemTestCase.java
@@ -82,7 +82,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
public abstract class SystemTestCase extends AbstractTransactionalTestNGSpringContextTests
{
private static final String SOURCE_TEST_CORE_PLUGINS = "sourceTest/core-plugins";
-
+
protected static final String SESSION_KEY = "session-key";
protected ICommonServerForInternalUse commonServer;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/TypedTableAssertions.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/TypedTableAssertions.java
index 6f126b9c427..a97234a1343 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/TypedTableAssertions.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/TypedTableAssertions.java
@@ -20,8 +20,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
/**
- * A utility class that can be used to simplify assertions in {@link TypedTableGrid}-related
- * headless system tests.
+ * A utility class that can be used to simplify assertions in {@link TypedTableGrid}-related headless system tests.
*
* @author Kaloyan Enimanev
*/
@@ -29,8 +28,7 @@ public class TypedTableAssertions<T extends Serializable> extends AssertJUnit
{
/**
- * a convenience method, that can be used as a static import to achieve a fluent-API like
- * programming style.
+ * a convenience method, that can be used as a static import to achieve a fluent-API like programming style.
*/
public static <S extends Serializable> TypedTableAssertions<S> assertTable(
TypedTableResultSet<S> tableResultSet)
@@ -39,8 +37,7 @@ public class TypedTableAssertions<T extends Serializable> extends AssertJUnit
}
/**
- * a convenience method, that can be used as a static import to achieve a fluent-API like
- * programming style.
+ * a convenience method, that can be used as a static import to achieve a fluent-API like programming style.
*/
public static <S extends Serializable> TypedTableAssertions<S>.ColumnAssertions assertColumn(
TypedTableResultSet<S> tableResultSet, String columnName)
@@ -53,8 +50,7 @@ public class TypedTableAssertions<T extends Serializable> extends AssertJUnit
private Map<String, TableModelColumnHeader> headers;
/**
- * the constructor is tentatively marked as "private" for now. We could make it public in the
- * future if we decide it will suite our tests better.
+ * the constructor is tentatively marked as "private" for now. We could make it public in the future if we decide it will suite our tests better.
*
* @param tableResultSet the typed-table result set
*/
@@ -208,8 +204,7 @@ public class TypedTableAssertions<T extends Serializable> extends AssertJUnit
}
/**
- * just a convenience method redirecting to the {@link #containsValue(String)} with a single
- * parameter.
+ * just a convenience method redirecting to the {@link #containsValue(String)} with a single parameter.
*/
public void containsValues(String... values)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromExperimentTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromExperimentTest.java
index 827f840af89..866b235fd84 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromExperimentTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromExperimentTest.java
@@ -67,7 +67,7 @@ public class UnassignSampleFromExperimentTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void unassigningFailsIfTheSampleHasDataSets() throws Exception
{
Sample sample = create(aSample().inExperiment(experiment));
@@ -199,7 +199,7 @@ public class UnassignSampleFromExperimentTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToUnassignSampleFromExperiment", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void unassigningIsNotAllowedFor(RoleWithHierarchy spaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromSpaceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromSpaceTest.java
index 03aef15ee9d..14175113471 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromSpaceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UnassignSampleFromSpaceTest.java
@@ -78,7 +78,7 @@ public class UnassignSampleFromSpaceTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void sampleWithDataSetCannotBeUnassignedFromSpace() throws Exception
{
Sample sample = create(aSample().inExperiment(experiment));
@@ -88,7 +88,7 @@ public class UnassignSampleFromSpaceTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void childSampleCantBeUnassignedFromSpace() throws Exception
{
Sample parent = create(aSample().inExperiment(experiment));
@@ -122,7 +122,7 @@ public class UnassignSampleFromSpaceTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void componentOfSpaceLevelSampleCantBeUnassignedFromSpace() throws Exception
{
Sample container = create(aSample().inExperiment(experiment));
@@ -174,7 +174,7 @@ public class UnassignSampleFromSpaceTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToUnassignSampleFromSpace", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void unassigningIsNotAllowedFor(RoleWithHierarchy spaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetParentsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetParentsTest.java
index 21868af0a5c..bb0b70cdd88 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetParentsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetParentsTest.java
@@ -111,7 +111,7 @@ public class UpdateDataSetParentsTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void dataSetCannotBeItsOwnParent() throws Exception
{
AbstractExternalData data = create(aDataSet().inSample(sample));
@@ -120,7 +120,7 @@ public class UpdateDataSetParentsTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void dataSetCannotBeItsOwnGrandParent() throws Exception
{
AbstractExternalData parent = create(aDataSet().inSample(sample));
@@ -170,7 +170,7 @@ public class UpdateDataSetParentsTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAddParentToDataSet", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void addingParentToDataSetNotIsAllowedFor(RoleWithHierarchy childSpaceRole,
RoleWithHierarchy parentSpaceRole, RoleWithHierarchy instanceRole) throws Exception
{
@@ -203,7 +203,7 @@ public class UpdateDataSetParentsTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToRemoveParentFromDataSet", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void removingParentFromDataSetNotIsAllowedFor(RoleWithHierarchy childSpaceRole,
RoleWithHierarchy parentSpaceRole, RoleWithHierarchy instanceRole) throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetTest.java
index bf0a117e4dd..dbf31561d7a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateDataSetTest.java
@@ -19,35 +19,36 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.systemtest.base.BaseTest;
-public class UpdateDataSetTest extends BaseTest{
-
+public class UpdateDataSetTest extends BaseTest
+{
+
Sample sample;
-
- @BeforeMethod
- void createFixture() throws Exception
- {
- Space space = create(aSpace());
- Project project = create(aProject().inSpace(space));
- Experiment experiment = create(anExperiment().inProject(project));
- sample = create(aSample().inExperiment(experiment));
- }
-
- @Test
- public void dataSetUpdateDoesntSetSampleToNull() {
- AbstractExternalData dataSet = create(aDataSet().inSample(sample));
- DataSetBatchUpdatesDTO update = new DataSetBatchUpdatesDTO();
- update.setDatasetId(new TechId(dataSet));
- update.setDatasetCode(dataSet.getCode());
- update.setVersion(dataSet.getVersion());
- update.setDetails(new DataSetBatchUpdateDetails());
- update.setProperties(Collections.<IEntityProperty>emptyList());
- update.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(dataSet.getSample()));
- update.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(dataSet.getExperiment().getIdentifier()));
-
- etlService.performEntityOperations(systemSessionToken, new AtomicEntityOperationDetailsBuilder().dataSetUpdate(update).getDetails());
-
- assertThat(dataSet, inSample(sample));
- assertThat(dataSet, inExperiment(sample.getExperiment()));
- }
+ @BeforeMethod
+ void createFixture() throws Exception
+ {
+ Space space = create(aSpace());
+ Project project = create(aProject().inSpace(space));
+ Experiment experiment = create(anExperiment().inProject(project));
+ sample = create(aSample().inExperiment(experiment));
+ }
+
+ @Test
+ public void dataSetUpdateDoesntSetSampleToNull()
+ {
+ AbstractExternalData dataSet = create(aDataSet().inSample(sample));
+ DataSetBatchUpdatesDTO update = new DataSetBatchUpdatesDTO();
+ update.setDatasetId(new TechId(dataSet));
+ update.setDatasetCode(dataSet.getCode());
+ update.setVersion(dataSet.getVersion());
+ update.setDetails(new DataSetBatchUpdateDetails());
+ update.setProperties(Collections.<IEntityProperty> emptyList());
+ update.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(dataSet.getSample()));
+ update.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(dataSet.getExperiment().getIdentifier()));
+
+ etlService.performEntityOperations(systemSessionToken, new AtomicEntityOperationDetailsBuilder().dataSetUpdate(update).getDetails());
+
+ assertThat(dataSet, inSample(sample));
+ assertThat(dataSet, inExperiment(sample.getExperiment()));
+ }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleContainmentTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleContainmentTest.java
index c45ee31b559..b9044fe163e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleContainmentTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleContainmentTest.java
@@ -75,7 +75,7 @@ public class UpdateSampleContainmentTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void componentCantBeSharedSample() throws Exception
{
Sample container = create(aSample().inSpace(space));
@@ -109,7 +109,7 @@ public class UpdateSampleContainmentTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void sampleCannotBeUpdatedToBeComponentOfComponentSample() throws Exception
{
Sample container = create(aSample().inSpace(space));
@@ -120,7 +120,7 @@ public class UpdateSampleContainmentTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void sampleCanContainItself() throws Exception
{
Sample sample = create(aSample().inSpace(space));
@@ -155,7 +155,7 @@ public class UpdateSampleContainmentTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToSetContainerToSample", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void settingContainerToSampleIsNotAllowedFor(RoleWithHierarchy containerSpaceRole,
RoleWithHierarchy componentSpaceRole, RoleWithHierarchy instanceRole) throws Exception
{
@@ -188,7 +188,7 @@ public class UpdateSampleContainmentTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToRemoveContainerFromSample", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void removingContainerFromSampleIsNotAllowedFor(RoleWithHierarchy containerSpaceRole,
RoleWithHierarchy componentSpaceRole, RoleWithHierarchy instanceRole) throws Exception
{
@@ -237,7 +237,7 @@ public class UpdateSampleContainmentTest extends BaseTest
rule(containerDomain, RoleWithHierarchy.SPACE_ETL_SERVER)),
rule(componentDomain, RoleWithHierarchy.SPACE_POWER_USER)
- ),
+ ),
and(rule(componentDomain, RoleWithHierarchy.SPACE_USER),
rule(instance, RoleWithHierarchy.INSTANCE_ETL_SERVER)));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleParentsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleParentsTest.java
index f06dedd2735..228e9f069f5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleParentsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/UpdateSampleParentsTest.java
@@ -102,7 +102,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void sampleCantBeItsOwnParent() throws Exception
{
Sample sample = create(aSample().inSpace(space));
@@ -111,7 +111,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void sampleCantBeItsOwnGrandParent() throws Exception
{
Sample parent = create(aSample().inSpace(space));
@@ -133,7 +133,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(expectedExceptions =
- { UserFailureException.class })
+ { UserFailureException.class })
public void childCannotBeShared() throws Exception
{
Sample parent = create(aSample().inSpace(space));
@@ -163,7 +163,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAddParentToSample", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void addingParentToSampleIsNotAllowedFor(RoleWithHierarchy spaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
@@ -193,7 +193,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAddParentToSample", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void addingParentToSampleInDifferentSpaceIsNotAllowedFor(RoleWithHierarchy spaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
@@ -224,7 +224,7 @@ public class UpdateSampleParentsTest extends BaseTest
}
@Test(dataProvider = "rolesNotAllowedToAddParentToSample", expectedExceptions =
- { AuthorizationFailureException.class }, groups = "authorization")
+ { AuthorizationFailureException.class }, groups = "authorization")
public void removingParentToSampleIsNotAllowedFor(RoleWithHierarchy spaceRole,
RoleWithHierarchy instanceRole) throws Exception
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/common/json/JsonApiClient.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/common/json/JsonApiClient.java
index be76ee7a6ce..5dd2530d3c4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/common/json/JsonApiClient.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/common/json/JsonApiClient.java
@@ -36,37 +36,15 @@ public class JsonApiClient
public JsonNode sendRequest(String json, Object... params) throws Exception
{
/*
- String jsonWithParams = String.format(json, params);
-
- HttpClient client = new DefaultHttpClient();
- HttpPost post = new HttpPost(apiUrl);
-
- // add header
- post.setHeader("User-Agent", USER_AGENT);
-
- post.setEntity(new StringEntity(jsonWithParams));
-
- HttpResponse response = client.execute(post);
- System.out.println(">>>>>");
- System.out.println("Sending 'POST' request to URL : " + apiUrl);
- System.out.println("Post parameters : " + jsonWithParams.trim());
- System.out.println("Response Code : " +
- response.getStatusLine().getStatusCode());
-
- BufferedReader rd = new BufferedReader(
- new InputStreamReader(response.getEntity().getContent()));
-
- StringBuffer result = new StringBuffer();
- String line = "";
- while ((line = rd.readLine()) != null)
- {
- result.append(line);
- }
-
- System.out.println("Response : " + result.toString());
- System.out.println("<<<<<");
- return new ObjectMapper().readTree(result.toString());
- */
+ * String jsonWithParams = String.format(json, params); HttpClient client = new DefaultHttpClient(); HttpPost post = new HttpPost(apiUrl); //
+ * add header post.setHeader("User-Agent", USER_AGENT); post.setEntity(new StringEntity(jsonWithParams)); HttpResponse response =
+ * client.execute(post); System.out.println(">>>>>"); System.out.println("Sending 'POST' request to URL : " + apiUrl);
+ * System.out.println("Post parameters : " + jsonWithParams.trim()); System.out.println("Response Code : " +
+ * response.getStatusLine().getStatusCode()); BufferedReader rd = new BufferedReader( new
+ * InputStreamReader(response.getEntity().getContent())); StringBuffer result = new StringBuffer(); String line = ""; while ((line =
+ * rd.readLine()) != null) { result.append(line); } System.out.println("Response : " + result.toString()); System.out.println("<<<<<"); return
+ * new ObjectMapper().readTree(result.toString());
+ */
return null;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index b9b790d1a5f..e6ef8d91fdb 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -2077,7 +2077,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
new MetaprojectTechIdId(metaProjects.get(1).getId()), "test");
assertEquals("[MaterialIdentifier [materialCode=AD3, "
+ "materialTypeIdentifier=MaterialTypeIdentifier [materialTypeCode=VIRUS]]]", mas
- .getMaterials().toString());
+ .getMaterials().toString());
assertEntities("[/CISD/NEMO/EXP11, /TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST]",
mas.getExperiments());
assertEquals("[Sample[/TEST-SPACE/EV-TEST,VALIDATE_CHILDREN,{},parents=?,children=?]]", mas
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonServerAuthorizationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonServerAuthorizationTest.java
index a13810cd58d..91be8ea0ac7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonServerAuthorizationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/CommonServerAuthorizationTest.java
@@ -59,8 +59,8 @@ public class CommonServerAuthorizationTest extends BaseTest
assertEquals("S2", space.getCode());
TechId ds3Id = new TechId(ds3.getId());
String user = create(aSession().withSpaceRole(RoleCode.ADMIN, space));
-
- List<AbstractExternalData> children = commonServer.listDataSetRelationships(user, ds3Id,DataSetRelationshipRole.PARENT);
+
+ List<AbstractExternalData> children = commonServer.listDataSetRelationships(user, ds3Id, DataSetRelationshipRole.PARENT);
assertEquals("[" + ds2.getCode() + "]", Code.extractCodes(children).toString());
List<AbstractExternalData> parents = commonServer.listDataSetRelationships(user, ds3Id, DataSetRelationshipRole.CHILD);
assertEquals("[" + ds5.getCode() + "]", Code.extractCodes(parents).toString());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ETLServiceAuthorizationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ETLServiceAuthorizationTest.java
index a5c09442550..adea353f539 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ETLServiceAuthorizationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ETLServiceAuthorizationTest.java
@@ -96,7 +96,7 @@ public class ETLServiceAuthorizationTest extends BaseTest
}
@Test(expectedExceptions =
- { AuthorizationFailureException.class })
+ { AuthorizationFailureException.class })
public void testListSamplesForObserverForAnotherSpace()
{
String sessionToken =
@@ -129,7 +129,7 @@ public class ETLServiceAuthorizationTest extends BaseTest
}
@Test(expectedExceptions =
- { AuthorizationFailureException.class })
+ { AuthorizationFailureException.class })
public void testRegistrationOfSamplesForUnauthorizedUser()
{
String sessionToken = create(aSession().withInstanceRole(RoleWithHierarchy.INSTANCE_ADMIN));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/PersonManagementTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/PersonManagementTest.java
index ea6528c23c6..b48e9255ac4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/PersonManagementTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/PersonManagementTest.java
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
public class PersonManagementTest extends BaseTest
{
private BufferedAppender logRecorder;
+
private int initialNumberOfActivePersons;
@BeforeMethod
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
index 60d27e7006a..7d0e6914943 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/BaseTest.java
@@ -510,7 +510,7 @@ public abstract class BaseTest extends AbstractTransactionalTestNGSpringContextT
{
return parseAndCreateGraph(graphDefinition, true);
}
-
+
protected EntityGraphGenerator parseAndCreateGraph(String graphDefinition, boolean startNewTransaction)
{
EntityGraphGenerator graphGenerator = entityGraphManager.parseAndCreateGraph(graphDefinition);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/RelationshipServiceStub.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/RelationshipServiceStub.java
index f9d9ed13b30..1eeb0e0e26f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/RelationshipServiceStub.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/RelationshipServiceStub.java
@@ -130,13 +130,13 @@ public class RelationshipServiceStub implements IRelationshipService
public void assignSampleToProject(IAuthSession session, SamplePE sample, ProjectPE project)
{
// TODO Auto-generated method stub
-
+
}
@Override
public void unassignSampleFromProject(IAuthSession session, SamplePE sample)
{
// TODO Auto-generated method stub
-
+
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/Builder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/Builder.java
index c58b8ce407b..d6f1991a870 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/Builder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/Builder.java
@@ -42,6 +42,6 @@ public abstract class Builder<T>
this.sessionToken = token;
return this;
}
-
+
public abstract T create();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
index 05562e991d1..cc16956e0b2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/DataSetUpdateBuilder.java
@@ -115,7 +115,7 @@ public class DataSetUpdateBuilder extends UpdateBuilder<DataSetUpdatesDTO>
this.sampleIdentifier = null;
return this;
}
-
+
public DataSetUpdateBuilder withContainer(AbstractExternalData dataSet)
{
this.containerCode = dataSet.getCode();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
index accaffc8ddb..6015bd0bc83 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/ExternalDataBuilder.java
@@ -63,11 +63,11 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
private List<String> parentCodes;
private List<String> componentCodes;
-
+
private Map<String, String> properties;
private String code;
-
+
private String dataSetTypeCode;
private boolean container;
@@ -99,7 +99,7 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
}
return this;
}
-
+
public ExternalDataBuilder inExperiment(Experiment experiment)
{
this.experimentIdentifier = new ExperimentIdentifier(experiment);
@@ -131,7 +131,7 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
componentCodes.addAll(Arrays.asList(dataSetCodes));
return this;
}
-
+
public ExternalDataBuilder withComponent(AbstractExternalData data)
{
return this.withComponents(data.getCode());
@@ -142,7 +142,7 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
properties.put(propertyTypeCode, value);
return this;
}
-
+
@Override
public AbstractExternalData create()
{
@@ -216,7 +216,7 @@ public class ExternalDataBuilder extends Builder<AbstractExternalData>
{
if (properties.isEmpty() == false)
{
- Set<String> knownPropertyTypes = new HashSet<String>();
+ Set<String> knownPropertyTypes = new HashSet<String>();
List<DataSetTypePropertyType> assignedPropertyTypes = type.getAssignedPropertyTypes();
for (DataSetTypePropertyType dtpt : assignedPropertyTypes)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/UpdateBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/UpdateBuilder.java
index 54cd93c58f3..987bc4797c6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/UpdateBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/base/builder/UpdateBuilder.java
@@ -35,6 +35,6 @@ public abstract class UpdateBuilder<T> extends Builder<T>
this.sessionToken = token;
return this;
}
-
+
public abstract void perform();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
index aa784dd92f0..44334e3ef05 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/entitygraph/EntityGraphManager.java
@@ -75,50 +75,54 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
- * Helper class which creates a graph of entities of kind experiment, sample, and data set based on a
- * textual description. A simple language defines the entities (experiments, samples, and data sets) and its relations.
- * From the textual definition of the graph real entities are created in the database. The actual graph of
- * entities as stored in the data base can be rendered in the same language used for parsing. This allows to
- * checked expected changes after some (re-)assignment between the entities has been performed. It is also
- * possible to checked whether the entities have been modified (i.e. modifier and modification date have been changed)
- * or not. Here is an example:
+ * Helper class which creates a graph of entities of kind experiment, sample, and data set based on a textual description. A simple language defines
+ * the entities (experiments, samples, and data sets) and its relations. From the textual definition of the graph real entities are created in the
+ * database. The actual graph of entities as stored in the data base can be rendered in the same language used for parsing. This allows to checked
+ * expected changes after some (re-)assignment between the entities has been performed. It is also possible to checked whether the entities have been
+ * modified (i.e. modifier and modification date have been changed) or not. Here is an example:
+ *
* <pre>
- * EntityGraphGenerator g = entityGraphManager.parseAndCreateGraph("E1, data sets: DS4\n"
- + "S1, data sets: DS1[NECT] DS2[NECT]\n"
- + "S2\n"
- + "S3, data sets: DS3[NET]\n"
- + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
- + "DS2[NECT], components: DS4");
-
- reassignToSample(g.ds(1), g.s(2));
-
- assertEquals("E1, data sets: DS4\n"
- + "S2, data sets: DS1[NECT] DS2[NECT]\n"
- + "S3, data sets: DS3[NET]\n"
- + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
- + "DS2[NECT], components: DS4\n", entityGraphManager.renderGraph(g));
- entityGraphManager.assertModified(g.s(1), g.s(2));
- entityGraphManager.assertModified(g.ds(1), g.ds(2));
- entityGraphManager.assertUnmodified(g);
+ * EntityGraphGenerator g = entityGraphManager.parseAndCreateGraph("E1, data sets: DS4\n"
+ * + "S1, data sets: DS1[NECT] DS2[NECT]\n"
+ * + "S2\n"
+ * + "S3, data sets: DS3[NET]\n"
+ * + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ * + "DS2[NECT], components: DS4");
+ *
+ * reassignToSample(g.ds(1), g.s(2));
+ *
+ * assertEquals("E1, data sets: DS4\n"
+ * + "S2, data sets: DS1[NECT] DS2[NECT]\n"
+ * + "S3, data sets: DS3[NET]\n"
+ * + "DS1[NECT], components: DS2[NECT] DS3[NET]\n"
+ * + "DS2[NECT], components: DS4\n", entityGraphManager.renderGraph(g));
+ * entityGraphManager.assertModified(g.s(1), g.s(2));
+ * entityGraphManager.assertModified(g.ds(1), g.ds(2));
+ * entityGraphManager.assertUnmodified(g);
* </pre>
*
- *
* @author Franz-Josef Elmer
*/
public class EntityGraphManager
{
private final IServiceForDataStoreServer service;
+
private final ICommonServerForInternalUse commonService;
+
private final SessionFactory sessionFactory;
+
private final String sessionToken;
-
+
private Space defaultSpace;
+
private Project defaultProject;
+
private ExperimentType defaultExperimentType;
+
private SampleType defaultSampleType;
-
+
private EntityRepository repository;
-
+
public EntityGraphManager(IServiceForDataStoreServer service, ICommonServerForInternalUse commonService,
SessionFactory sessionFactory, String sessionToken)
{
@@ -127,7 +131,7 @@ public class EntityGraphManager
this.sessionFactory = sessionFactory;
this.sessionToken = sessionToken;
}
-
+
public EntityGraphGenerator parseAndCreateGraph(String graphDefinition)
{
EntityGraphGenerator g = new EntityGraphGenerator();
@@ -137,7 +141,7 @@ public class EntityGraphManager
repository.gatherModifictaionInfos();
return g;
}
-
+
public void addToRepository(ExperimentNode experimentNode, Experiment experiment)
{
repository.put(experimentNode, experiment);
@@ -152,7 +156,7 @@ public class EntityGraphManager
{
repository.assertDeleted(experimentNodes);
}
-
+
public void assertModified(SampleNode[] sampleNodes)
{
repository.assertModified(sampleNodes);
@@ -162,7 +166,7 @@ public class EntityGraphManager
{
repository.assertDeleted(sampleNodes);
}
-
+
public void assertModified(DataSetNode[] dataSetNodes)
{
repository.assertModified(dataSetNodes);
@@ -172,7 +176,7 @@ public class EntityGraphManager
{
repository.assertDeleted(dataSetNodes);
}
-
+
public void assertUnmodified(EntityGraphGenerator g)
{
repository.assertUnmodified(g);
@@ -182,7 +186,7 @@ public class EntityGraphManager
{
repository.assertUndeleted(g);
}
-
+
public String getIdentifierOfDefaultProject()
{
return defaultProject.getIdentifier();
@@ -192,12 +196,12 @@ public class EntityGraphManager
{
return repository.getExperimentIdentifierOrNull(experimentNodeOrNull);
}
-
+
public Sample getSample(SampleNode sampleNode)
{
return repository.getSample(sampleNode);
}
-
+
public Sample tryGetSample(SampleNode sampleNode)
{
return repository.tryGetSample(sampleNode);
@@ -207,12 +211,12 @@ public class EntityGraphManager
{
return repository.getSamplePermIdOrNull(sampleNodeOrNull);
}
-
+
public AbstractExternalData getDataSet(DataSetNode dataSetNode)
{
return repository.getDataSet(dataSetNode);
}
-
+
public AbstractExternalData tryGetDataSet(DataSetNode dataSetNode)
{
return repository.tryGetDataSet(dataSetNode);
@@ -222,12 +226,12 @@ public class EntityGraphManager
{
return repository.getDataSetCodeOrNull(dataSetNodeOrNull);
}
-
+
public String renderGraph(EntityGraphGenerator g)
{
return renderGraph(g, false);
}
-
+
public String renderGraph(EntityGraphGenerator g, boolean showWhereIAm)
{
repository.refreshGraph(showWhereIAm);
@@ -293,7 +297,7 @@ public class EntityGraphManager
}
return sampleNode.getIdentifierAndType();
}
-
+
private String removeSolitaryNodes(String graphDefinition)
{
StringBuilder builder = new StringBuilder();
@@ -307,7 +311,7 @@ public class EntityGraphManager
}
return builder.toString();
}
-
+
private void appendNodeTo(StringBuilder builder, String identifierAndType, StringBuilder builder2)
{
if (builder2.length() > 0)
@@ -316,12 +320,12 @@ public class EntityGraphManager
builder.append(builder2).append("\n");
}
}
-
+
private void render(StringBuilder builder, String name, Collection<? extends EntityNode> nodes)
{
render(builder, name, getIdentifiers(nodes));
}
-
+
private List<String> getIdentifiers(Collection<? extends EntityNode> nodes)
{
List<String> identifiers = new ArrayList<String>();
@@ -336,7 +340,7 @@ public class EntityGraphManager
}
return identifiers;
}
-
+
private void render(StringBuilder builder, String name, List<String> identifiers)
{
if (identifiers.isEmpty())
@@ -349,7 +353,7 @@ public class EntityGraphManager
builder.append(' ').append(identifier);
}
}
-
+
private Space createSpace(String spaceCode)
{
SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
@@ -361,7 +365,7 @@ public class EntityGraphManager
commonService.registerSpace(sessionToken, spaceCode, null);
return service.tryGetSpace(sessionToken, spaceIdentifier);
}
-
+
private Project createProject(Space space, String projectCode)
{
ProjectIdentifier projectIdentifier = new ProjectIdentifier(space.getCode(), projectCode);
@@ -370,11 +374,11 @@ public class EntityGraphManager
{
return project;
}
- commonService.registerProject(sessionToken, projectIdentifier, null, null,
- Collections.<NewAttachment>emptyList());
+ commonService.registerProject(sessionToken, projectIdentifier, null, null,
+ Collections.<NewAttachment> emptyList());
return commonService.getProjectInfo(sessionToken, projectIdentifier);
}
-
+
private ExperimentType createExperimentType(String typeCode)
{
for (ExperimentType experimentType : commonService.listExperimentTypes(sessionToken))
@@ -389,7 +393,7 @@ public class EntityGraphManager
commonService.registerExperimentType(sessionToken, experimentType);
return service.getExperimentType(sessionToken, typeCode);
}
-
+
private SampleType createSampleType(String typeCode)
{
for (SampleType sampleType : commonService.listSampleTypes(sessionToken))
@@ -405,7 +409,7 @@ public class EntityGraphManager
commonService.registerSampleType(sessionToken, sampleType);
return service.getSampleType(sessionToken, typeCode);
}
-
+
private DataSetType createDataSetType(String typeCode, DataSetKind dataSetKind)
{
for (DataSetType dataSetType : commonService.listDataSetTypes(sessionToken))
@@ -422,7 +426,7 @@ public class EntityGraphManager
dataSetType = service.getDataSetType(sessionToken, typeCode).getDataSetType();
return dataSetType;
}
-
+
private Experiment createExperiment(ExperimentNode experimentNode, Project project)
{
try
@@ -438,7 +442,7 @@ public class EntityGraphManager
return service.tryGetExperiment(sessionToken, ExperimentIdentifierFactory.parse(identifier));
} catch (Exception ex)
{
- throw new RuntimeException("Error while creating experiment for node " + experimentNode.getCode()
+ throw new RuntimeException("Error while creating experiment for node " + experimentNode.getCode()
+ ": " + ex.getMessage(), ex);
}
}
@@ -463,19 +467,19 @@ public class EntityGraphManager
Sample containerSample = repository.tryGetSample(container);
if (containerSample == null)
{
- throw new IllegalStateException("Sample " + container.getCode()
- + " is specified as container of " + sampleNode.getCode()
+ throw new IllegalStateException("Sample " + container.getCode()
+ + " is specified as container of " + sampleNode.getCode()
+ " but hasn't yet created.");
}
sample.setContainerIdentifier(containerSample.getIdentifier());
}
sample.setProperties(new IEntityProperty[0]);
- sample.setAttachments(Collections.<NewAttachment>emptyList());
+ sample.setAttachments(Collections.<NewAttachment> emptyList());
service.registerSample(sessionToken, sample, null);
return service.tryGetSampleWithExperiment(sessionToken, SampleIdentifierFactory.parse(sample));
} catch (Exception ex)
{
- throw new RuntimeException("Error while creating sample for node " + sampleNode.getCode()
+ throw new RuntimeException("Error while creating sample for node " + sampleNode.getCode()
+ ": " + ex.getMessage(), ex);
}
}
@@ -488,8 +492,8 @@ public class EntityGraphManager
Sample parentSample = repository.tryGetSample(parent);
if (parentSample == null)
{
- throw new IllegalStateException("Sample " + parent.getCode()
- + " is specified as parent of " + sampleNode.getCode()
+ throw new IllegalStateException("Sample " + parent.getCode()
+ + " is specified as parent of " + sampleNode.getCode()
+ " but hasn't yet created.");
}
parentIdentifiers.add(parentSample.getIdentifier());
@@ -509,7 +513,7 @@ public class EntityGraphManager
}
return prefix + sampleNode.getCode() + generateUniqueId();
}
-
+
private AbstractExternalData createDataSet(DataSetNode dataSetNode)
{
try
@@ -548,7 +552,7 @@ public class EntityGraphManager
return service.tryGetDataSet(sessionToken, dataSet.getCode());
} catch (Exception ex)
{
- throw new RuntimeException("Error while creating data set for node " + dataSetNode.getIdentifierAndType()
+ throw new RuntimeException("Error while creating data set for node " + dataSetNode.getIdentifierAndType()
+ ": " + ex.getMessage(), ex);
}
}
@@ -574,8 +578,8 @@ public class EntityGraphManager
AbstractExternalData parentDataSet = repository.tryGetDataSet(parent);
if (parentDataSet == null)
{
- throw new IllegalStateException("Data set " + parent.getCode()
- + " is specified as " + relationType + " of " + dataSetNode.getCode()
+ throw new IllegalStateException("Data set " + parent.getCode()
+ + " is specified as " + relationType + " of " + dataSetNode.getCode()
+ " but hasn't yet created.");
}
parentCodes.add(parentDataSet.getCode());
@@ -592,7 +596,7 @@ public class EntityGraphManager
{
return "-" + service.createPermId(sessionToken);
}
-
+
private void createGraph(EntityGraphGenerator g)
{
repository = new EntityRepository();
@@ -621,13 +625,13 @@ public class EntityGraphManager
private void createSamples(Space space, EntityGraphGenerator g)
{
ArrayList<SampleNode> sampleNodes = new ArrayList<SampleNode>(g.getSamples().values());
-// Collections.reverse(sampleNodes);
+ // Collections.reverse(sampleNodes);
for (SampleNode sampleNode : sampleNodes)
{
repository.put(sampleNode, createSample(sampleNode, space));
}
}
-
+
private void createExperiments(Project project, EntityGraphGenerator g)
{
for (ExperimentNode experimentNode : g.getExperiments().values())
@@ -635,34 +639,51 @@ public class EntityGraphManager
repository.put(experimentNode, createExperiment(experimentNode, project));
}
}
-
+
private final class EntityRepository
{
private Map<Long, Experiment> experimentsNodeToDtoMap = new TreeMap<Long, Experiment>();
+
private Map<Long, ModificationInfo> experimentModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
+
private Set<ExperimentNode> modifiedExperimentNodes = new HashSet<ExperimentNode>();
+
private Set<ExperimentNode> deletedExperimentNodes = new HashSet<ExperimentNode>();
-
+
private Map<Long, Sample> samplesNodeToDtoMap = new TreeMap<Long, Sample>();
+
private Map<Long, SampleNode> samplesDtoToNodeMap = new TreeMap<Long, SampleNode>();
+
private Map<Long, ModificationInfo> sampleModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
+
private Set<SampleNode> modifiedSampleNodes = new HashSet<SampleNode>();
+
private Set<SampleNode> deletedSampleNodes = new HashSet<SampleNode>();
private Map<Long, AbstractExternalData> dataSetsNodeToDtoMap = new TreeMap<Long, AbstractExternalData>();
+
private Map<Long, DataSetNode> dataSetsDtoToNodeMap = new TreeMap<Long, DataSetNode>();
+
private Map<Long, ModificationInfo> dataSetModificationInfoByNodeId = new HashMap<Long, ModificationInfo>();
+
private Set<DataSetNode> modifiedDataSetNodes = new HashSet<DataSetNode>();
+
private Set<DataSetNode> deletedDataSetNodes = new HashSet<DataSetNode>();
private Map<Long, Set<Long>> experimentSamplesMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> childrenSamplesMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> componentSamplesMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> experimentDataSetsMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> sampleDataSetsMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> componentDataSetsMap = new HashMap<Long, Set<Long>>();
+
private Map<Long, Set<Long>> parentDataSetsMap = new HashMap<Long, Set<Long>>();
-
+
public String renderNodeToDtoMapping()
{
StringBuilder builder = new StringBuilder();
@@ -680,8 +701,8 @@ public class EntityGraphManager
}
return builder.toString();
}
-
- private void render(StringBuilder builder, String prefix, Long id,
+
+ private void render(StringBuilder builder, String prefix, Long id,
CodeWithRegistrationAndModificationDate<?> entity)
{
builder.append(prefix).append(id).append(" -> ").append(entity.getCode()).append(" (");
@@ -693,12 +714,12 @@ public class EntityGraphManager
builder.append(entity.getModifier().getUserId()).append(", ");
builder.append(entity.getModificationDate()).append(")\n");
}
-
+
public String getExperimentIdentifierOrNull(ExperimentNode experimentNodeOrNull)
{
return experimentNodeOrNull == null ? null : getExperiment(experimentNodeOrNull).getIdentifier();
}
-
+
public Experiment getExperiment(ExperimentNode experimentNode)
{
Experiment experiment = tryGetExperiment(experimentNode);
@@ -708,17 +729,17 @@ public class EntityGraphManager
}
return experiment;
}
-
+
public Experiment tryGetExperiment(ExperimentNode experimentNode)
{
return experimentsNodeToDtoMap.get(experimentNode.getId());
}
-
+
public String getSamplePermIdOrNull(SampleNode sampleNodeOrNull)
{
return sampleNodeOrNull == null ? null : getSample(sampleNodeOrNull).getPermId();
}
-
+
public Sample getSample(SampleNode sampleNode)
{
Sample sample = tryGetSample(sampleNode);
@@ -728,17 +749,17 @@ public class EntityGraphManager
}
return sample;
}
-
+
public Sample tryGetSample(SampleNode sampleNode)
{
return samplesNodeToDtoMap.get(sampleNode.getId());
}
-
+
public String getDataSetCodeOrNull(DataSetNode dataSetNodeOrNull)
{
return dataSetNodeOrNull == null ? null : getDataSet(dataSetNodeOrNull).getCode();
}
-
+
public AbstractExternalData getDataSet(DataSetNode dataSetNode)
{
AbstractExternalData dataSet = tryGetDataSet(dataSetNode);
@@ -748,12 +769,12 @@ public class EntityGraphManager
}
return dataSet;
}
-
+
public AbstractExternalData tryGetDataSet(DataSetNode dataSetNode)
{
return dataSetsNodeToDtoMap.get(dataSetNode.getId());
}
-
+
void refreshGraph(boolean showWhereIAm)
{
refreshExperimentDtos();
@@ -770,8 +791,8 @@ public class EntityGraphManager
private void refreshDataSetDtos()
{
- List<Entry<Long, AbstractExternalData>> nodeToDtoMapping
- = new ArrayList<Entry<Long, AbstractExternalData>>(dataSetsNodeToDtoMap.entrySet());
+ List<Entry<Long, AbstractExternalData>> nodeToDtoMapping =
+ new ArrayList<Entry<Long, AbstractExternalData>>(dataSetsNodeToDtoMap.entrySet());
dataSetsNodeToDtoMap.clear();
for (Entry<Long, AbstractExternalData> entry : nodeToDtoMapping)
{
@@ -904,7 +925,7 @@ public class EntityGraphManager
}
System.out.println("...");
}
-
+
private void addToEntitiesMap(Map<Long, Set<Long>> entityToEntitiesMap, IIdHolder keyEntity, IIdHolder valueEntity)
{
if (keyEntity != null)
@@ -919,7 +940,7 @@ public class EntityGraphManager
entityIds.add(valueEntity.getId());
}
}
-
+
void gatherModifictaionInfos()
{
for (Entry<Long, Experiment> entry : experimentsNodeToDtoMap.entrySet())
@@ -935,63 +956,63 @@ public class EntityGraphManager
dataSetModificationInfoByNodeId.put(entry.getKey(), new ModificationInfo(entry.getValue()));
}
}
-
+
void put(ExperimentNode experimentNode, Experiment experiment)
{
experimentsNodeToDtoMap.put(experimentNode.getId(), experiment);
}
-
- public void assertModified(ExperimentNode...experimentNodes)
+
+ public void assertModified(ExperimentNode... experimentNodes)
{
- assertModificationInfo(true, experimentModificationInfoByNodeId, experimentsNodeToDtoMap,
- Arrays.<EntityNode>asList(experimentNodes));
+ assertModificationInfo(true, experimentModificationInfoByNodeId, experimentsNodeToDtoMap,
+ Arrays.<EntityNode> asList(experimentNodes));
modifiedExperimentNodes.addAll(Arrays.asList(experimentNodes));
}
-
- public void assertDeleted(ExperimentNode...experimentNodes)
+
+ public void assertDeleted(ExperimentNode... experimentNodes)
{
- assertDeleted(experimentsNodeToDtoMap, Arrays.<EntityNode>asList(experimentNodes));
+ assertDeleted(experimentsNodeToDtoMap, Arrays.<EntityNode> asList(experimentNodes));
deletedExperimentNodes.addAll(Arrays.asList(experimentNodes));
}
-
+
void put(SampleNode sampleNode, Sample sample)
{
samplesNodeToDtoMap.put(sampleNode.getId(), sample);
samplesDtoToNodeMap.put(sample.getId(), sampleNode);
}
- public void assertModified(SampleNode...sampleNodes)
+ public void assertModified(SampleNode... sampleNodes)
{
- assertModificationInfo(true, sampleModificationInfoByNodeId, samplesNodeToDtoMap,
- Arrays.<EntityNode>asList(sampleNodes));
+ assertModificationInfo(true, sampleModificationInfoByNodeId, samplesNodeToDtoMap,
+ Arrays.<EntityNode> asList(sampleNodes));
modifiedSampleNodes.addAll(Arrays.asList(sampleNodes));
}
-
- public void assertDeleted(SampleNode...sampleNodes)
+
+ public void assertDeleted(SampleNode... sampleNodes)
{
- assertDeleted(samplesNodeToDtoMap, Arrays.<EntityNode>asList(sampleNodes));
+ assertDeleted(samplesNodeToDtoMap, Arrays.<EntityNode> asList(sampleNodes));
deletedSampleNodes.addAll(Arrays.asList(sampleNodes));
}
-
+
void put(DataSetNode dataSetNode, AbstractExternalData dataSet)
{
dataSetsNodeToDtoMap.put(dataSetNode.getId(), dataSet);
dataSetsDtoToNodeMap.put(dataSet.getId(), dataSetNode);
}
-
- public void assertModified(DataSetNode...dataSetNodes)
+
+ public void assertModified(DataSetNode... dataSetNodes)
{
- assertModificationInfo(true, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap,
- Arrays.<EntityNode>asList(dataSetNodes));
+ assertModificationInfo(true, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap,
+ Arrays.<EntityNode> asList(dataSetNodes));
modifiedDataSetNodes.addAll(Arrays.asList(dataSetNodes));
}
-
- public void assertDeleted(DataSetNode...dataSetNodes)
+
+ public void assertDeleted(DataSetNode... dataSetNodes)
{
- assertDeleted(dataSetsNodeToDtoMap, Arrays.<EntityNode>asList(dataSetNodes));
+ assertDeleted(dataSetsNodeToDtoMap, Arrays.<EntityNode> asList(dataSetNodes));
deletedDataSetNodes.addAll(Arrays.asList(dataSetNodes));
}
-
+
public void assertUnmodified(EntityGraphGenerator g)
{
Set<EntityNode> unmodifiedExperimentNodes = new HashSet<EntityNode>(g.getExperiments().values());
@@ -1004,7 +1025,7 @@ public class EntityGraphManager
unmodifiedDataSetNodes.removeAll(modifiedDataSetNodes);
assertModificationInfo(false, dataSetModificationInfoByNodeId, dataSetsNodeToDtoMap, unmodifiedDataSetNodes);
}
-
+
private void assertModificationInfo(boolean modified, Map<Long, ModificationInfo> previousInfos,
Map<Long, ? extends CodeWithRegistrationAndModificationDate<?>> nodeToDtoMap,
Collection<EntityNode> entityNodes)
@@ -1029,22 +1050,22 @@ public class EntityGraphManager
ModificationInfo current = new ModificationInfo(entity);
if (modified)
{
- assertEquals(node.getCode() + " has unexpectedly still the old modifier: " + current.modifier,
+ assertEquals(node.getCode() + " has unexpectedly still the old modifier: " + current.modifier,
false, current.modifier.equals(previous.modifier));
- assertEquals(node.getCode() + " has unexpectedly still the old modification date: "
- + current.modificationDate + " > " + previous.modificationDate,
+ assertEquals(node.getCode() + " has unexpectedly still the old modification date: "
+ + current.modificationDate + " > " + previous.modificationDate,
true, current.modificationDate.getTime() > previous.modificationDate.getTime());
} else
{
assertEquals(node.getCode() + " has unexpectedly a new modifier: ",
previous.modifier, current.modifier);
- assertEquals(node.getCode() + " has unexpectedly a new modification date:",
+ assertEquals(node.getCode() + " has unexpectedly a new modification date:",
previous.modificationDate, current.modificationDate);
}
}
}
}
-
+
private void assertDeleted(Map<Long, ? extends CodeWithRegistrationAndModificationDate<?>> nodeToDtoMap,
Collection<EntityNode> entityNodes)
{
@@ -1056,7 +1077,7 @@ public class EntityGraphManager
}
}
}
-
+
public void assertUndeleted(EntityGraphGenerator g)
{
Set<EntityNode> undeletedExperimentNodes = new HashSet<EntityNode>(g.getExperiments().values());
@@ -1069,7 +1090,7 @@ public class EntityGraphManager
undeletedDataSetNodes.removeAll(deletedDataSetNodes);
assertUndeleted(dataSetsNodeToDtoMap, undeletedDataSetNodes);
}
-
+
private void assertUndeleted(Map<Long, ? extends CodeWithRegistrationAndModificationDate<?>> nodeToDtoMap,
Collection<EntityNode> entityNodes)
{
@@ -1087,26 +1108,25 @@ public class EntityGraphManager
fail("The following nodes have been deleted: " + deletedNodes);
}
}
-
Set<SampleNode> getSampleNodes(ExperimentNode experimentNode)
{
- return getEntityNodes(experimentSamplesMap, experimentsNodeToDtoMap.get(experimentNode.getId()),
+ return getEntityNodes(experimentSamplesMap, experimentsNodeToDtoMap.get(experimentNode.getId()),
samplesDtoToNodeMap);
}
-
+
Set<SampleNode> getChildrenSampleNodes(SampleNode sampleNode)
{
- return getEntityNodes(childrenSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
+ return getEntityNodes(childrenSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
samplesDtoToNodeMap);
}
-
+
Set<SampleNode> getComponentSampleNodes(SampleNode sampleNode)
{
- return getEntityNodes(componentSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
+ return getEntityNodes(componentSamplesMap, samplesNodeToDtoMap.get(sampleNode.getId()),
samplesDtoToNodeMap);
}
-
+
Set<DataSetNode> getDataSetNodes(ExperimentNode experimentNode)
{
return getDataSetNodes(experimentDataSetsMap, experimentsNodeToDtoMap.get(experimentNode.getId()));
@@ -1116,23 +1136,23 @@ public class EntityGraphManager
{
return getDataSetNodes(sampleDataSetsMap, samplesNodeToDtoMap.get(sampleNode.getId()));
}
-
+
Set<DataSetNode> getComponentDataSetNodes(DataSetNode containerDataSetNode)
{
return getDataSetNodes(componentDataSetsMap, dataSetsNodeToDtoMap.get(containerDataSetNode.getId()));
}
-
+
Set<DataSetNode> getParentDataSetNodes(DataSetNode childDataSetNode)
{
return getDataSetNodes(parentDataSetsMap, dataSetsNodeToDtoMap.get(childDataSetNode.getId()));
}
-
+
private Set<DataSetNode> getDataSetNodes(Map<Long, Set<Long>> idHolderDataSetsMap, IIdHolder idHolder)
{
return getEntityNodes(idHolderDataSetsMap, idHolder, dataSetsDtoToNodeMap);
}
- private <T extends EntityNode> Set<T> getEntityNodes(Map<Long, Set<Long>> idHolderEntitiesMap, IIdHolder idHolder,
+ private <T extends EntityNode> Set<T> getEntityNodes(Map<Long, Set<Long>> idHolderEntitiesMap, IIdHolder idHolder,
Map<Long, T> dtoToNodeMap)
{
Set<T> result = new TreeSet<T>();
@@ -1150,10 +1170,11 @@ public class EntityGraphManager
return result;
}
}
-
+
private static final class ModificationInfo
{
private final String modifier;
+
private final Date modificationDate;
ModificationInfo(CodeWithRegistrationAndModificationDate<?> entity)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadOptimisticLockingTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadOptimisticLockingTestCase.java
index be70605def9..05fdf33cd27 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadOptimisticLockingTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadOptimisticLockingTestCase.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.systemtest.PersistentSystemTestCase;
public class MultiThreadOptimisticLockingTestCase extends PersistentSystemTestCase
{
static final String CREATING_ENTITIES = "creating entities";
+
protected ToolBox toolBox;
@BeforeMethod
@@ -53,5 +54,5 @@ public class MultiThreadOptimisticLockingTestCase extends PersistentSystemTestCa
throw new Error(m.getName() + "() : ", t);
}
}
-
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadProjectOptimisticLockingTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadProjectOptimisticLockingTest.java
index b4539cd66b8..090d2686d0d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadProjectOptimisticLockingTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadProjectOptimisticLockingTest.java
@@ -49,11 +49,9 @@ public class MultiThreadProjectOptimisticLockingTest extends MultiThreadOptimist
private static final String CREATE_EXPERIMENTS_PHASE = "createExperiments";
/*
- * This test registers three experiments for the same project. Two of them are registered by the
- * main thread using performEntityOperations(). A second thread registers an experiment between
- * the registration of the two other experiments. This is done by using a
- * IServiceConversationProgressListener together with two message channels to coordinate the
- * order of actions in both threads.
+ * This test registers three experiments for the same project. Two of them are registered by the main thread using performEntityOperations(). A
+ * second thread registers an experiment between the registration of the two other experiments. This is done by using a
+ * IServiceConversationProgressListener together with two message channels to coordinate the order of actions in both threads.
*/
@Test
public void testRegisterExperimentsInTwoThreads()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadSampleOptimisticLockingTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadSampleOptimisticLockingTest.java
index d8bcd226f13..774fb1c6ecf 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadSampleOptimisticLockingTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/MultiThreadSampleOptimisticLockingTest.java
@@ -164,12 +164,8 @@ public class MultiThreadSampleOptimisticLockingTest extends MultiThreadOptimisti
}
/**
- * This test is flaky.
- *
- * If the transaction of performEntityOperations() call in the new thread ends before
- * the transaction of performEntityOperations() call in the main thread, the modifier of
- * the sample will be "optimist" and the test fails.
- *
+ * This test is flaky. If the transaction of performEntityOperations() call in the new thread ends before the transaction of
+ * performEntityOperations() call in the main thread, the modifier of the sample will be "optimist" and the test fails.
*/
@Test
public void testRegisterDataSetsForSameSampleInTwoThreads()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
index 3f20d81a796..4ca0b6b323c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
@@ -117,7 +117,7 @@ public class ToolBox
private final IServiceForDataStoreServer etlService;
private final IDAOFactory daoFactory;
-
+
private final String systemSessionToken;
public Space space1;
@@ -129,7 +129,7 @@ public class ToolBox
public Project project2;
public ToolBox(ICommonServer commonServer, IGenericServer genericServer,
- IServiceForDataStoreServer etlService, String systemSessionToken,
+ IServiceForDataStoreServer etlService, String systemSessionToken,
ApplicationContext applicationContext)
{
this.commonServer = commonServer;
@@ -138,7 +138,7 @@ public class ToolBox
this.systemSessionToken = systemSessionToken;
daoFactory = applicationContext.getBean(IDAOFactory.class);
}
-
+
TimeIntervalChecker createTimeIntervalChecker()
{
return new TimeIntervalChecker(daoFactory.getTransactionTimestamp());
@@ -226,14 +226,14 @@ public class ToolBox
List<String> dataSetCodes = new ArrayList<String>(codes);
commonServer.deleteDataSets(systemSessionToken, dataSetCodes, "cleanup", DeletionType.TRASH, true);
}
-
+
private List<TechId> listExperimentIds(Space space)
{
ExperimentType experimentType = new ExperimentTypeBuilder().code(EXPERIMENT_TYPE_CODE).getExperimentType();
SpaceIdentifier spaceIdentifier = new SpaceIdentifierFactory(space.getIdentifier()).createIdentifier();
return TechId.createList(commonServer.listExperiments(systemSessionToken, experimentType, spaceIdentifier));
}
-
+
private List<TechId> listSampleIds(Space space)
{
ListSampleCriteria criteria = new ListSampleCriteria();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/EntityValidationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/EntityValidationTest.java
index f519624bc5e..6252997980e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/EntityValidationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/EntityValidationTest.java
@@ -77,7 +77,7 @@ public class EntityValidationTest extends GenericSystemTestCase
private static final String IMPOSSIBLE_TO_UPDATE_TYPE = "IMPOSSIBLE_TO_UPDATE";
private static final int TEST_SCRIPT_ID = 8;
-
+
@Autowired
private IDAOFactory daoFactory;
@@ -340,7 +340,7 @@ public class EntityValidationTest extends GenericSystemTestCase
AbstractExternalData dataset =
commonServer.getDataSetInfo(systemSessionToken, new TechId(26l));
-
+
DataSetUpdatesDTO updates = new DataSetUpdatesDTO();
updates.setDatasetId(new TechId(26));
updates.setVersion(dataset.getVersion());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/FileFormatTypeHeadlessTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/FileFormatTypeHeadlessTest.java
index ee26c6b5419..daed4cd77c3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/FileFormatTypeHeadlessTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/FileFormatTypeHeadlessTest.java
@@ -73,7 +73,6 @@ public class FileFormatTypeHeadlessTest extends SystemTestCase
TypedTableResultSet<FileFormatType> tableResultSet =
commonClientService.listFileTypes(criteria);
-
Row expectedRow =
new Row().withCell("CODE", fft.getCode()).withCell("DESCRIPTION",
fft.getDescription());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/query/QuerySystemTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/query/QuerySystemTestCase.java
index b666241c975..9829f4fd886 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/query/QuerySystemTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/query/QuerySystemTestCase.java
@@ -22,19 +22,16 @@ import ch.systemsx.cisd.openbis.plugin.query.client.web.client.IQueryClientServi
import ch.systemsx.cisd.openbis.systemtest.SystemTestCase;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class QuerySystemTestCase extends SystemTestCase
{
protected IQueryClientService queryClientService;
-
+
@Autowired
public final void setQueryClientService(IQueryClientService queryClientService)
{
this.queryClientService = queryClientService;
}
-
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/relationshipshistory/SampleToSampleRelationshipsHistoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/relationshipshistory/SampleToSampleRelationshipsHistoryTest.java
index bcb03445a51..661bb8bd9bc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/relationshipshistory/SampleToSampleRelationshipsHistoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/relationshipshistory/SampleToSampleRelationshipsHistoryTest.java
@@ -156,7 +156,7 @@ public class SampleToSampleRelationshipsHistoryTest extends AbstractRelationship
updates.setExperimentIdentifierOrNull(child.getExperiment() == null ? null
: ExperimentIdentifier.createIdentifier(child.getExperiment()));
updates.setModifiedParentCodesOrNull(new String[]
- { parent.getIdentifier() });
+ { parent.getIdentifier() });
genericClientService.updateSample(updates);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/util/LogRecordingUtils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/util/LogRecordingUtils.java
index 60330dd40d4..04b73dcbb04 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/util/LogRecordingUtils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/util/LogRecordingUtils.java
@@ -21,8 +21,7 @@ import org.apache.log4j.Level;
import ch.systemsx.cisd.common.logging.BufferedAppender;
/**
- * Helper methods to create a log recorder which suppresses log entries from MonitoringPoolingDataSource
- * and full text indexer.
+ * Helper methods to create a log recorder which suppresses log entries from MonitoringPoolingDataSource and full text indexer.
*
* @author Franz-Josef Elmer
*/
@@ -32,22 +31,22 @@ public class LogRecordingUtils
{
return suppress(new BufferedAppender());
}
-
+
public static BufferedAppender createRecorder(Level logLevel)
{
return suppress(new BufferedAppender(logLevel));
}
-
+
public static BufferedAppender createRecorder(String pattern, Level logLevel)
{
return suppress(new BufferedAppender(pattern, logLevel));
}
-
+
public static BufferedAppender createRecorder(String pattern, Level logLevel, String loggerNameRegex)
{
return suppress(new BufferedAppender(pattern, logLevel, loggerNameRegex));
}
-
+
private static BufferedAppender suppress(BufferedAppender logRecorder)
{
logRecorder.addRegexForLoggingEventsToBeDropped("OPERATION.*FullTextIndex.*");
--
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