From 91899784405e64362c66d961ca5d9506f98e2a66 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 17 Sep 2008 09:29:21 +0000
Subject: [PATCH] LMS-478 DTOs and related classes moved from 'lims_base' to
'openbis'. Project dependencies changed: lims_base, etlserver,
dataset_download depend on openbis.
SVN: 8344
---
.../cisd/common/collections/ListSet.java | 239 +++++++++++
dataset_download/.classpath | 45 ++-
.../datasetdownload/DataSetService.java | 2 +-
.../DatasetDownloadServlet.java | 6 +-
.../HTMLDirectoryRenderer.java | 10 +-
.../datasetdownload/IDirectoryRenderer.java | 2 +-
.../PlainTextRendererFactory.java | 2 +-
.../DatasetDownloadServletTest.java | 18 +-
openbis/.classpath | 5 +-
.../web/server/GenericClientService.java | 6 +-
.../web/server/util/GroupTranslater.java | 2 +-
.../web/server/util/PersonTranslator.java | 2 +-
.../openbis/generic/server/GenericServer.java | 6 +-
.../generic/server/GenericServerLogger.java | 4 +-
.../server/LogMessagePrefixGenerator.java | 4 +-
.../authorization/AuthorizationAdvisor.java | 3 +-
.../DefaultAccessController.java | 4 +-
.../DefaultReturnValueFilter.java | 2 +-
.../server/authorization/IAuthSession.java | 2 +-
.../authorization/PredicateExecutor.java | 2 +-
.../generic/server/authorization/Role.java | 2 +-
.../authorization/RoleWithIdentifier.java | 10 +-
.../authorization/annotation/RoleSet.java | 2 +-
.../AbstractDatabaseInstancePredicate.java | 4 +-
.../predicate/AbstractPredicate.java | 2 +-
.../predicate/ArrayPredicate.java | 2 +-
.../predicate/CollectionPredicate.java | 2 +-
.../DatabaseInstanceIdentifierPredicate.java | 6 +-
.../predicate/DelegatedPredicate.java | 2 +-
.../predicate/GroupIdentifierPredicate.java | 8 +-
.../authorization/predicate/IPredicate.java | 2 +-
.../predicate/NewExperimentPredicate.java | 6 +-
.../predicate/NewSamplePredicate.java | 4 +-
.../predicate/QueryRestrictionPredicate.java | 4 +-
.../predicate/SampleFilterPredicate.java | 10 +-
.../SampleOwnerIdentifierPredicate.java | 4 +-
.../validator/AbstractValidator.java | 2 +-
.../validator/BaseExperimentValidator.java | 6 +-
.../validator/DatabaseInstanceValidator.java | 6 +-
.../validator/ExternalDataValidator.java | 6 +-
.../validator/GroupValidator.java | 6 +-
.../authorization/validator/IValidator.java | 2 +-
.../dataaccess/IAuthorizationDAOFactory.java | 2 +-
.../dataaccess/IDatabaseInstanceDAO.java | 2 +-
.../generic/server/dataaccess/IGroupDAO.java | 4 +-
.../generic/server/dataaccess/IPersonDAO.java | 2 +-
.../server/dataaccess/IRoleAssignmentDAO.java | 4 +-
.../migration/MigrationStepFrom022To023.java | 130 +++---
.../migration/MigrationStepFrom023To024.java | 376 +++++++++---------
.../migration/MigrationStepFrom025To026.java | 294 +++++++-------
.../server/util/GroupIdentifierHelper.java | 14 +-
.../server/util/KeyExtractorFactory.java | 31 +-
.../openbis/generic/server/util/UuidUtil.java | 2 +-
.../shared/GenericSharedConstants.java | 31 ++
.../generic/shared/IGenericServer.java | 4 +-
.../shared/dto/AbstractAttachmentPE.java | 164 ++++++++
.../generic/shared/dto/AbstractEntity.java | 45 +++
.../shared/dto/AbstractIdAndCodeHolder.java | 125 ++++++
.../dto/AbstractRegistratrationHolder.java | 97 +++++
.../generic/shared/dto/AbstractTypePE.java | 86 ++++
.../generic/shared/dto/AttachmentPE.java | 47 +++
.../generic/shared/dto/BaseExperiment.java | 148 +++++++
.../cisd/openbis/generic/shared/dto/Code.java | 112 ++++++
.../generic/shared/dto/CodeConverter.java | 103 +++++
.../generic/shared/dto/ColumnNames.java | 165 ++++++++
.../openbis/generic/shared/dto/DataPE.java | 275 +++++++++++++
.../generic/shared/dto/DataSetType.java | 39 ++
.../generic/shared/dto/DataSetTypePE.java | 70 ++++
.../generic/shared/dto/DataStorePE.java | 135 +++++++
.../generic/shared/dto/DataTypePE.java | 148 +++++++
.../shared/dto/DatabaseInstancePE.java | 183 +++++++++
.../shared/dto/EntityPropertyFiller.java | 74 ++++
.../generic/shared/dto/EntityPropertyPE.java | 164 ++++++++
.../shared/dto/EntityPropertyTypeDTO.java | 103 +++++
.../generic/shared/dto/EntityType.java | 55 +++
.../dto/EntityTypeMandatorilyRelation.java | 110 +++++
.../generic/shared/dto/EntityTypePE.java | 67 ++++
.../shared/dto/EntityTypePropertyTypePE.java | 128 ++++++
.../generic/shared/dto/Experiment.java | 234 +++++++++++
.../generic/shared/dto/ExperimentPE.java | 313 +++++++++++++++
.../shared/dto/ExperimentPlatesFilter.java | 70 ++++
.../shared/dto/ExperimentPropertyPE.java | 98 +++++
.../generic/shared/dto/ExperimentType.java | 29 ++
.../generic/shared/dto/ExperimentTypePE.java | 55 +++
.../dto/ExperimentTypePropertyTypePE.java | 71 ++++
.../generic/shared/dto/ExternalData.java | 223 +++++++++++
.../generic/shared/dto/ExternalDataPE.java | 162 ++++++++
.../generic/shared/dto/ExtractableData.java | 90 +++++
.../generic/shared/dto/FileAttachmentPE.java | 63 +++
.../generic/shared/dto/FileFormatType.java | 41 ++
.../generic/shared/dto/FileFormatTypePE.java | 75 ++++
.../openbis/generic/shared/dto/GroupPE.java | 226 +++++++++++
...ibernateAbstractRegistratrationHolder.java | 116 ++++++
.../shared/dto/IEntityPropertiesHolder.java | 38 ++
.../generic/shared/dto/IEntityProperty.java | 46 +++
.../generic/shared/dto/IEntityType.java | 39 ++
.../shared/dto/IEntityTypePropertyType.java | 36 ++
.../generic/shared/dto/IIdAndCodeHolder.java | 32 ++
.../openbis/generic/shared/dto/IIdHolder.java | 33 ++
.../shared/dto/IRegistratorHolder.java | 48 +++
.../dto/ISimpleEntityPropertiesHolder.java | 36 ++
.../shared/dto/IUntypedValueSetter.java | 30 ++
.../cisd/openbis/generic/shared/dto/Id.java | 91 +++++
.../generic/shared/dto/InvalidationPE.java | 107 +++++
.../generic/shared/dto/LimitFilter.java | 102 +++++
.../generic/shared/dto/LocatorType.java | 41 ++
.../generic/shared/dto/LocatorTypePE.java | 50 +++
.../generic/shared/dto/MaterialBatchPE.java | 158 ++++++++
.../generic/shared/dto/MaterialPE.java | 232 +++++++++++
.../shared/dto/MaterialPropertyPE.java | 107 +++++
.../generic/shared/dto/MaterialTypePE.java | 54 +++
.../dto/MaterialTypePropertyTypePE.java | 75 ++++
.../generic/shared/dto/NewExperiment.java | 135 +++++++
.../generic/shared/dto/NewMaterial.java | 75 ++++
.../shared/dto/NewProcessingInstruction.java | 93 +++++
.../generic/shared/dto/NewPropertyType.java | 97 +++++
.../generic/shared/dto/NewRoleAssignment.java | 112 ++++++
.../openbis/generic/shared/dto/NewSample.java | 145 +++++++
.../shared/dto/NewSampleComponent.java | 49 +++
...wSampleComponentWithFixedMaterialType.java | 50 +++
.../openbis/generic/shared/dto/PersonPE.java | 261 ++++++++++++
.../openbis/generic/shared/dto/Procedure.java | 193 +++++++++
.../generic/shared/dto/ProcedurePE.java | 210 ++++++++++
.../generic/shared/dto/ProcedureType.java | 64 +++
.../generic/shared/dto/ProcedureTypePE.java | 92 +++++
.../shared/dto/ProcessingInstructionDTO.java | 97 +++++
.../shared/dto/ProcessingParameters.java | 72 ++++
.../openbis/generic/shared/dto/ProjectPE.java | 223 +++++++++++
.../dto/PropertyTypeEntityTypeRelation.java | 116 ++++++
.../generic/shared/dto/PropertyTypePE.java | 260 ++++++++++++
.../generic/shared/dto/QueryRestriction.java | 137 +++++++
.../generic/shared/dto/RoleAssignmentPE.java | 188 +++++++++
.../openbis/generic/shared/dto/RoleCode.java | 29 ++
.../openbis/generic/shared/dto/Sample.java | 262 ++++++++++++
.../generic/shared/dto/SampleFilter.java | 98 +++++
.../shared/dto/SampleGenerationDTO.java | 77 ++++
.../openbis/generic/shared/dto/SamplePE.java | 374 +++++++++++++++++
.../generic/shared/dto/SamplePropertyPE.java | 103 +++++
.../generic/shared/dto/SampleType.java | 56 +++
.../generic/shared/dto/SampleTypePE.java | 68 ++++
.../shared/dto/SampleTypePropertyTypePE.java | 76 ++++
.../generic/shared/dto/SequenceNames.java | 99 +++++
.../openbis/generic/shared/dto/Session.java | 2 -
.../shared/dto/SimpleEntityProperty.java | 111 ++++++
.../generic/shared/dto/StorageFormat.java | 75 ++++
.../generic/shared/dto/TableNames.java | 105 +++++
.../generic/shared/dto/TimeInterval.java | 151 +++++++
.../shared/dto/ValidationMessages.java | 147 +++++++
.../generic/shared/dto/VocabularyPE.java | 240 +++++++++++
.../generic/shared/dto/VocabularyTermPE.java | 162 ++++++++
.../exception/UndefinedGroupException.java | 36 ++
.../shared/dto/hibernate/Location.java | 48 +++
.../dto/hibernate/LocationValidator.java | 60 +++
.../DatabaseInstanceIdentifier.java | 139 +++++++
.../dto/identifier/ExperimentIdentifier.java | 124 ++++++
.../dto/identifier/GroupIdentifier.java | 140 +++++++
.../dto/identifier/IdentifierHelper.java | 105 +++++
.../dto/identifier/MaterialIdentifier.java | 69 ++++
.../dto/identifier/ProjectIdentifier.java | 102 +++++
.../dto/identifier/SampleIdentifier.java | 116 ++++++
.../identifier/SampleIdentifierPattern.java | 89 +++++
.../dto/identifier/SampleOwnerIdentifier.java | 182 +++++++++
.../shared/dto/properties/EntityDataType.java | 55 +++
.../shared/dto/properties/EntityKind.java | 90 +++++
.../dto/properties/EntityProperties.java | 122 ++++++
.../EntityPropertyTypeDTOContainer.java | 219 ++++++++++
.../dto/properties/EntityPropertyValue.java | 246 ++++++++++++
.../dto/properties/PropertiesHelper.java | 96 +++++
.../shared/dto/types/DataSetTypeCode.java | 59 +++
.../shared/dto/types/ExperimentTypeCode.java | 59 +++
.../shared/dto/types/MaterialTypeCode.java | 39 ++
.../shared/dto/types/ProcedureTypeCode.java | 58 +++
.../shared/dto/types/SampleTypeCode.java | 79 ++++
.../authorization/AuthorizationTestUtil.java | 12 +-
.../DefaultAccessControllerTest.java | 8 +-
.../DefaultReturnValueFilterTest.java | 2 +-
.../authorization/PredicateExecutorTest.java | 6 +-
.../authorization/RoleWithIdentifierTest.java | 14 +-
...tabaseInstanceIdentifierPredicateTest.java | 10 +-
.../GroupIdentifierPredicateTest.java | 8 +-
.../predicate/NewExperimentPredicateTest.java | 2 +-
.../QueryRestrictionPredicateTest.java | 2 +-
.../validator/GroupValidatorTest.java | 11 +-
.../DatabaseInstanceIdentifierTest.java | 57 +++
.../identifier/ExperimentIdentifierTest.java | 57 +++
.../dto/identifier/GroupIdentifierTest.java | 56 +++
.../dto/identifier/ProjectIdentifierTest.java | 56 +++
.../dto/identifier/SampleIdentifierTest.java | 105 +++++
188 files changed, 14275 insertions(+), 591 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/collections/ListSet.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/GenericSharedConstants.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractAttachmentPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractEntity.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractIdAndCodeHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistratrationHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/BaseExperiment.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Code.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CodeConverter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DatabaseInstancePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyTypeDTO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypeMandatorilyRelation.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePropertyTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Experiment.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPlatesFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileAttachmentPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/GroupPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistratrationHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityPropertiesHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityProperty.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityTypePropertyType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IRegistratorHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ISimpleEntityPropertiesHolder.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Id.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialBatchPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExperiment.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewMaterial.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewPropertyType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewRoleAssignment.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSample.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponentWithFixedMaterialType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PersonPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Procedure.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedurePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProjectPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypeEntityTypeRelation.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/QueryRestriction.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleCode.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Sample.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleFilter.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleGenerationDTO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleEntityProperty.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/exception/UndefinedGroupException.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/LocationValidator.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/MaterialIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierPattern.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleOwnerIdentifier.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityDataType.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityProperties.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyTypeDTOContainer.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyValue.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/PropertiesHelper.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/MaterialTypeCode.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ProcedureTypeCode.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/SampleTypeCode.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifierTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifierTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifierTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierTest.java
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/ListSet.java b/common/source/java/ch/systemsx/cisd/common/collections/ListSet.java
new file mode 100644
index 00000000000..495592f43ef
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/collections/ListSet.java
@@ -0,0 +1,239 @@
+/*
+ * Copyright 2007 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.common.collections;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+
+/**
+ * A set of named lists.
+ * <p>
+ * Naming: every list has an <i>unique</i> name but not necessarily an <i>unique</i> label.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+// TODO 2008-09-05, Christian Ribeaud: Write an Unit test for this class.
+public final class ListSet
+{
+ /**
+ * The lists.
+ * <p>
+ * Each list is identified by a {@link Column} which contains the name and the label of the
+ * corresponding list.<br />
+ * <code>values</code> of this map are <row index>=<table value> pairs.
+ * </p>
+ */
+ private final Map<Column, Map<Integer, String>> lists =
+ new HashMap<Column, Map<Integer, String>>();
+
+ /**
+ * A map containing <i>columns</i> keyed by <i>names</i>.
+ */
+ private final Map<String, Column> columnByName = new LinkedHashMap<String, Column>();
+
+ private final void addColumn(final Column newColumn)
+ {
+ final Column column = columnByName.get(newColumn.name);
+ if (column != null && column.label.equals(newColumn.label) == false)
+ {
+ throw new IllegalArgumentException(String.format(
+ "Different labels detected for the same column name '%s'. "
+ + "The new one is '%s', the previous one was '%s'.", column.name,
+ newColumn.label, column.label));
+ }
+ columnByName.put(newColumn.name, newColumn);
+ }
+
+ private final Column getColumn(final String listName)
+ {
+ final Column column = columnByName.get(listName);
+ if (column == null)
+ {
+ throw new IllegalArgumentException(String.format("List name '%s' not found.", listName));
+ }
+ return column;
+ }
+
+ private final static Map<Integer, String> createIntMap()
+ {
+ return new HashMap<Integer, String>();
+ }
+
+ private final Map<Integer, String> getIntMap(final Column column)
+ {
+ final Map<Integer, String> list = lists.get(column);
+ if (list == null)
+ {
+ throw new IllegalArgumentException(String.format("No list found for column '%s'.",
+ column));
+ }
+ return list;
+ }
+
+ /**
+ * Adds the specified value to the specified list at given <var>rowIndex</var>.
+ *
+ * @param listName can not be <code>null</code>.
+ * @param value can not be <code>null</code>.
+ */
+ public final void addToList(final String listName, final String listLabel, final String value,
+ final int rowIndex)
+ {
+ assert listName != null : "Unspecified list name.";
+ assert value != null : "Unspecified value";
+ assert rowIndex > -1 : "Invalid row index";
+ final Column column = new Column(listName, listLabel);
+ addColumn(column);
+ Map<Integer, String> list = lists.get(column);
+ if (list == null)
+ {
+ list = createIntMap();
+ lists.put(column, list);
+ }
+ if (list.containsKey(rowIndex))
+ {
+ throw new IllegalArgumentException(String.format("List '%s' already contains a "
+ + "value for row index %d", listName, rowIndex));
+ }
+ list.put(rowIndex, value);
+ }
+
+ /** Returns the value at given <var>rowIndex</var> from the list found with given <var>listName</var>. */
+ public final String tryGetValueAt(final String listName, final int rowIndex)
+ {
+ assert listName != null : "Unspecified list name";
+ assert rowIndex > -1 : "Invalid row index";
+ return getIntMap(getColumn(listName)).get(rowIndex);
+ }
+
+ /**
+ * For given <var>listName</var> returns corresponding label.
+ */
+ public final String getLabel(final String listName)
+ {
+ return getColumn(listName).label;
+ }
+
+ /**
+ * Returns a set of all list names.
+ */
+ public final Set<String> getListNames()
+ {
+ return Collections.unmodifiableSet(columnByName.keySet());
+ }
+
+ /**
+ * Merges this list set with given one.
+ */
+ public final void mergeList(final ListSet listSet)
+ {
+ final Set<String> listNames = listSet.getListNames();
+ for (final String listName : listNames)
+ {
+ final Column column = listSet.getColumn(listName);
+ final Map<Integer, String> list = listSet.getIntMap(column);
+ for (final Map.Entry<Integer, String> entry : list.entrySet())
+ {
+ addToList(listName, column.label, entry.getValue(), entry.getKey());
+ }
+ }
+ }
+
+ /**
+ * Returns the list of given name <var>listName</var> as {@link List}.
+ *
+ * @return a list of size <var>rowCount</var>. If no value could be found for a given row
+ * index, is filled with <code>null</code>.
+ */
+ public final List<String> getList(final String listName, final int rowCount)
+ {
+ final List<String> result =
+ new ArrayList<String>(Collections.<String> nCopies(rowCount, null));
+ final Map<Integer, String> list = getIntMap(getColumn(listName));
+ for (final Map.Entry<Integer, String> entry : list.entrySet())
+ {
+ result.set(entry.getKey(), entry.getValue());
+ }
+ return result;
+ }
+
+ //
+ // Helper classes
+ //
+
+ private final static class Column
+ {
+ final String name;
+
+ final String label;
+
+ Column(final String name, final String label)
+ {
+ assert name != null : "Unspecified name";
+ this.name = name;
+ this.label = label;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Column == false)
+ {
+ return false;
+ }
+ final Column that = (Column) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(name, that.name);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(name);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+ }
+}
\ No newline at end of file
diff --git a/dataset_download/.classpath b/dataset_download/.classpath
index 6e36e7b8d0b..21346dc1b2c 100644
--- a/dataset_download/.classpath
+++ b/dataset_download/.classpath
@@ -1,22 +1,23 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry combineaccessrules="false" kind="src" path="/common"/>
- <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
- <classpathentry kind="lib" path="/libraries/jetty/servlet-api-2.5.jar" sourcepath="/libraries/jetty/src/servlet-api-2.5.zip"/>
- <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
- <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
- <classpathentry kind="lib" path="/libraries/jetty/jetty.jar" sourcepath="/libraries/jetty/src/jetty.zip"/>
- <classpathentry kind="lib" path="/libraries/jetty/jetty-util.jar" sourcepath="/libraries/jetty/src/jetty-util.zip"/>
- <classpathentry combineaccessrules="false" kind="src" path="/lims_base"/>
- <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
- <classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
- <classpathentry kind="lib" path="/libraries/cglib/cglib-nodep.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
- <classpathentry kind="output" path="targets/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="source/java"/>
+ <classpathentry kind="src" path="sourceTest/java"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/common"/>
+ <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jetty/servlet-api-2.5.jar" sourcepath="/libraries/jetty/src/servlet-api-2.5.zip"/>
+ <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+ <classpathentry kind="lib" path="/libraries/jetty/jetty.jar" sourcepath="/libraries/jetty/src/jetty.zip"/>
+ <classpathentry kind="lib" path="/libraries/jetty/jetty-util.jar" sourcepath="/libraries/jetty/src/jetty-util.zip"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/lims_base"/>
+ <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
+ <classpathentry kind="lib" path="/libraries/cglib/cglib-nodep.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
+ <classpathentry kind="output" path="targets/classes"/>
+</classpath>
diff --git a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DataSetService.java b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DataSetService.java
index 4c200cb691f..e3651efafe0 100644
--- a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DataSetService.java
+++ b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DataSetService.java
@@ -20,7 +20,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.lims.base.IDataSetService;
import ch.systemsx.cisd.lims.base.ILIMSServiceFactory;
import ch.systemsx.cisd.lims.base.ServiceRegistry;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* A <code>IDataSetService</code> implementation.
diff --git a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServlet.java b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServlet.java
index 4ca18725b32..289cd8f9e10 100644
--- a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServlet.java
+++ b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServlet.java
@@ -49,9 +49,9 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.lims.base.IDataSetService;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
-import ch.systemsx.cisd.lims.base.dto.LocatorType;
-import ch.systemsx.cisd.lims.base.dto.LocatorTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
/**
* @author Franz-Josef Elmer
diff --git a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/HTMLDirectoryRenderer.java b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/HTMLDirectoryRenderer.java
index 6db5091627d..16b1955ac06 100644
--- a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/HTMLDirectoryRenderer.java
+++ b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/HTMLDirectoryRenderer.java
@@ -25,11 +25,11 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.utilities.Template;
-import ch.systemsx.cisd.lims.base.dto.ExperimentPE;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.ProcedurePE;
-import ch.systemsx.cisd.lims.base.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
/**
* An <code>IDirectoryRenderer</code> implementation which renders on HTML pages.
diff --git a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/IDirectoryRenderer.java b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/IDirectoryRenderer.java
index f460c934122..6e2673e0079 100644
--- a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/IDirectoryRenderer.java
+++ b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/IDirectoryRenderer.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.openbis.datasetdownload;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* Interface of a renderer of a directory.
diff --git a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/PlainTextRendererFactory.java b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/PlainTextRendererFactory.java
index 99f2738f92d..6321f5bcbbc 100644
--- a/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/PlainTextRendererFactory.java
+++ b/dataset_download/source/java/ch/systemsx/cisd/openbis/datasetdownload/PlainTextRendererFactory.java
@@ -20,7 +20,7 @@ import java.io.PrintWriter;
import org.apache.commons.io.FileUtils;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* Factory for rendering file system view in plain text.
diff --git a/dataset_download/sourceTest/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServletTest.java b/dataset_download/sourceTest/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServletTest.java
index 93efd75924a..65cdb5f030d 100644
--- a/dataset_download/sourceTest/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServletTest.java
+++ b/dataset_download/sourceTest/java/ch/systemsx/cisd/openbis/datasetdownload/DatasetDownloadServletTest.java
@@ -46,15 +46,15 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.utilities.OSUtilities;
import ch.systemsx.cisd.lims.base.IDataSetService;
-import ch.systemsx.cisd.lims.base.dto.ExperimentPE;
-import ch.systemsx.cisd.lims.base.dto.ExternalData;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.LocatorType;
-import ch.systemsx.cisd.lims.base.dto.LocatorTypePE;
-import ch.systemsx.cisd.lims.base.dto.ProcedurePE;
-import ch.systemsx.cisd.lims.base.dto.ProjectPE;
-import ch.systemsx.cisd.lims.base.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* @author Franz-Josef Elmer
diff --git a/openbis/.classpath b/openbis/.classpath
index 12db228308f..54f8ee2f089 100644
--- a/openbis/.classpath
+++ b/openbis/.classpath
@@ -16,7 +16,6 @@
<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
<classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
<classpathentry kind="lib" path="/libraries/spring/webmvc/spring-webmvc.jar" sourcepath="/libraries/spring/webmvc/src.jar"/>
- <classpathentry combineaccessrules="false" kind="src" path="/lims_base"/>
<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
<classpathentry combineaccessrules="false" kind="src" path="/dbmigration"/>
@@ -24,5 +23,9 @@
<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+ <classpathentry kind="lib" path="/libraries/hibernate-annotations/ejb3-persistence.jar"/>
+ <classpathentry kind="lib" path="/libraries/hibernate-annotations/hibernate-annotations.jar" sourcepath="/libraries/hibernate-annotations/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/hibernate-validator/hibernate-validator.jar" sourcepath="/libraries/hibernate-validator/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/GenericClientService.java
index ce5ee64b8fd..e797d721dc2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/GenericClientService.java
@@ -29,9 +29,6 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
import ch.systemsx.cisd.common.utilities.BuildAndEnvironmentInfo;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.client.web.client.IGenericClientService;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ApplicationInfo;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Group;
@@ -40,7 +37,10 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.User;
import ch.systemsx.cisd.openbis.generic.client.web.server.util.GroupTranslater;
import ch.systemsx.cisd.openbis.generic.client.web.server.util.UserFailureExceptionTranslater;
import ch.systemsx.cisd.openbis.generic.shared.IGenericServer;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/GroupTranslater.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/GroupTranslater.java
index c178ae63a66..86b047356ba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/GroupTranslater.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/GroupTranslater.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.generic.client.web.server.util;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
/**
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/PersonTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/PersonTranslator.java
index 3f1dd12c65d..f381b61cfd9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/PersonTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/util/PersonTranslator.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.generic.client.web.server.util;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServer.java
index c449a550e5a..2d2b261ca86 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServer.java
@@ -27,11 +27,11 @@ import ch.systemsx.cisd.authentication.ISessionManager;
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.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.IGenericServer;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
* Implementation of client-server interface.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServerLogger.java
index 8b56cf94ca3..46c071009d6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/GenericServerLogger.java
@@ -23,10 +23,10 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.IGenericServer;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
* Logger class for {@link GenericServer} which creates readable logs of method invocations.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/LogMessagePrefixGenerator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/LogMessagePrefixGenerator.java
index 32fca099703..0ec02b38d00 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/LogMessagePrefixGenerator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/LogMessagePrefixGenerator.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.generic.server;
import ch.systemsx.cisd.authentication.ILogMessagePrefixGenerator;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationAdvisor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationAdvisor.java
index 5a12b41e3c1..e2863e63140 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationAdvisor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationAdvisor.java
@@ -39,7 +39,6 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.AnnotationUtils;
import ch.systemsx.cisd.common.utilities.ClassUtils;
import ch.systemsx.cisd.common.utilities.AnnotationUtils.Parameter;
-import ch.systemsx.cisd.lims.base.LogMessageProvider;
import ch.systemsx.cisd.openbis.generic.server.authorization.IAccessController.Argument;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
@@ -164,7 +163,7 @@ public final class AuthorizationAdvisor extends DefaultPointcutAdvisor
authorizationLog.info(String.format(
"[USER:'%s' GROUP:%s]: Authorization failure while "
+ "invoking method '%s': %s", session.getUserName(),
- groupCode == null ? LogMessageProvider.UNDEFINED : "'" + groupCode + "'",
+ groupCode == null ? "<UNDEFINED>" : "'" + groupCode + "'",
ClassUtils.describeMethod(method), errorMessage));
throw new AuthorizationFailureException(errorMessage);
}
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 8c8c4c6eeeb..ae0a7673ba6 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
@@ -34,10 +34,10 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.ClassUtils;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
/**
* A default <code>IAccessController</code> implementation.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilter.java
index 59538e2e7ca..be30a3b1ba9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilter.java
@@ -29,9 +29,9 @@ import ch.systemsx.cisd.common.collections.FilteredList;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.ClassUtils;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.IValidator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* A default <code>IReturnValueFilter</code> implementation
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthSession.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthSession.java
index a10b0cd33d1..2c1d5ce1294 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthSession.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthSession.java
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* Session interface used by authorization framework.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
index c2b7afc5474..6aea4115a2f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
@@ -20,12 +20,12 @@ import java.util.List;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.IAccessController.Argument;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ArrayPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.CollectionPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.IPredicate;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* A static class to execute {@link IPredicate}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Role.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Role.java
index 9d413e8f1bf..08a59487b81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Role.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/Role.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.authorization;
import org.apache.commons.lang.builder.EqualsBuilder;
import org.apache.commons.lang.builder.HashCodeBuilder;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
/**
* A well defined role, composed of a {@link RoleLevel} and a {@link RoleCode}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifier.java
index f6ce09bbba5..ef44010ebca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifier.java
@@ -17,11 +17,11 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.lims.base.identifier.IdentifierHelper;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
/**
* Stores the {@link Role} and the "owner" to which this role is connected: database instance or a
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RoleSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RoleSet.java
index 7e1b4e5fbb9..36e5274bcdd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RoleSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/annotation/RoleSet.java
@@ -21,9 +21,9 @@ import java.util.LinkedHashSet;
import java.util.Set;
import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
import ch.systemsx.cisd.openbis.generic.server.authorization.Role;
import ch.systemsx.cisd.openbis.generic.server.authorization.Role.RoleLevel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
/**
* An enumeration which defines some role sets.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractDatabaseInstancePredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractDatabaseInstancePredicate.java
index 632b24b5f0b..d3367ee76f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractDatabaseInstancePredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/AbstractDatabaseInstancePredicate.java
@@ -16,11 +16,11 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.util.GroupIdentifierHelper;
import ch.systemsx.cisd.openbis.generic.server.util.GroupIdentifierHelper.IDatabaseInstanceFinder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
* An {@link AbstractPredicate} extension which works with database instances.
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 7d9508516db..326358a514b 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
@@ -20,8 +20,8 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* An <i>abstract</i> <code>IPredicate</code> implementation which mainly checks method
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ArrayPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ArrayPredicate.java
index 2dd7704381e..cb9142d3ae6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ArrayPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ArrayPredicate.java
@@ -20,9 +20,9 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.StatusFlag;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* An <code>IPredicate</code> implementation based on an array.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicate.java
index 1ddb4ccb85a..ef727012629 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/CollectionPredicate.java
@@ -21,9 +21,9 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.StatusFlag;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* An <code>IPredicate</code> implementation based on a {@link Collection}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicate.java
index 54831682351..8c7b2adc11b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicate.java
@@ -19,11 +19,11 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.Role.RoleLevel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
* An <code>IPredicate</code> implementation for {@link DatabaseInstanceIdentifier}.
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 336b429057a..785498d163c 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
@@ -19,9 +19,9 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* An <code>AbstractPredicate</code> extension which delegates its method calls to the
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicate.java
index 05abc413123..77819e943fb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicate.java
@@ -20,14 +20,14 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.Role.RoleLevel;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.util.GroupIdentifierHelper;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* An <code>IPredicate</code> implementation based on {@link GroupIdentifier}.
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 f49da1ac7c7..bb1893ce7da 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
@@ -19,10 +19,10 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.IPredicateFactory;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* Performs some predicate which returns a {@link Status} based on the input objects.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicate.java
index 4e2132aaa37..c30f3d98773 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicate.java
@@ -16,9 +16,9 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
-import ch.systemsx.cisd.lims.base.dto.NewExperiment;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
-import ch.systemsx.cisd.lims.base.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
/**
* An <code>IPredicate</code> implementation for {@link NewExperiment}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewSamplePredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewSamplePredicate.java
index 144bb3c2ba2..dff1199f7d8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewSamplePredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewSamplePredicate.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
-import ch.systemsx.cisd.lims.base.dto.NewSample;
-import ch.systemsx.cisd.lims.base.identifier.SampleOwnerIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
* An <code>IPredicate</code> implementation for {@link NewSample}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicate.java
index 01529d392fa..e9ebc68bd66 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicate.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
-import ch.systemsx.cisd.lims.base.dto.QueryRestriction;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.QueryRestriction;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* An <code>IPredicate</code> implementation for {@link QueryRestriction}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleFilterPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleFilterPredicate.java
index a596ff8d15e..6be22cc4c31 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleFilterPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleFilterPredicate.java
@@ -19,13 +19,13 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.SampleFilter;
-import ch.systemsx.cisd.lims.base.identifier.SampleIdentifierPattern;
-import ch.systemsx.cisd.lims.base.identifier.SampleOwnerIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleFilter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierPattern;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
* An <code>IPredicate</code> implementation for {@link SampleFilter}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleOwnerIdentifierPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleOwnerIdentifierPredicate.java
index 5e09085e20c..e3926798e3e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleOwnerIdentifierPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleOwnerIdentifierPredicate.java
@@ -19,10 +19,10 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.predicate;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.SampleOwnerIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
/**
* An <code>IPredicate</code> implementation based on {@link SampleOwnerIdentifier}.
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 256074f005b..d56a3c59076 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
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* An <i>abstract</i> <code>IValidator</code> implementation which mainly checks method
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/BaseExperimentValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/BaseExperimentValidator.java
index 3752bd1fdcc..2676ae0dc26 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/BaseExperimentValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/BaseExperimentValidator.java
@@ -16,9 +16,9 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-import ch.systemsx.cisd.lims.base.dto.BaseExperiment;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.BaseExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* A {@link IValidator} implementation suitable for {@link BaseExperiment}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DatabaseInstanceValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DatabaseInstanceValidator.java
index 5cc4da05afd..7fe0f80d2de 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DatabaseInstanceValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/DatabaseInstanceValidator.java
@@ -18,9 +18,9 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
import java.util.List;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
/**
* A {@link IValidator} implementation suitable for {@link DatabaseInstancePE}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidator.java
index 72b1276a612..841a1a7cffc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidator.java
@@ -16,9 +16,9 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-import ch.systemsx.cisd.lims.base.dto.ExternalDataPE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* A {@link IValidator} implementation suitable for {@link ExternalDataPE}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidator.java
index 0200b356d63..5a654c282a4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/GroupValidator.java
@@ -18,9 +18,9 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
import java.util.List;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
/**
* A {@link IValidator} implementation suitable for {@link GroupPE}.
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 3cc26fbd75c..963ddb18ceb 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
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
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
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
index 6f01ed9cc51..8bd39353ff2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
/**
* Factory definition for all Data Access Objects which are needed for managing authorization.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDatabaseInstanceDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDatabaseInstanceDAO.java
index ceedbbf3830..c71caf4495c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDatabaseInstanceDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDatabaseInstanceDAO.java
@@ -22,7 +22,7 @@ import org.springframework.dao.DataAccessException;
import org.springframework.dao.EmptyResultDataAccessException;
import org.springframework.dao.IncorrectResultSizeDataAccessException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
/**
* An interface that contains all data access operations on {@link DatabaseInstancePE}s.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IGroupDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IGroupDAO.java
index e1135b34e78..abee69648e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IGroupDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IGroupDAO.java
@@ -21,8 +21,8 @@ import java.util.List;
import org.springframework.dao.DataAccessException;
import org.springframework.dao.EmptyResultDataAccessException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
/**
* <i>Data Access Object</i> for {@link GroupPE}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPersonDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPersonDAO.java
index 877ecf7237b..5b9340a4e33 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPersonDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IPersonDAO.java
@@ -20,7 +20,7 @@ import java.util.List;
import org.springframework.dao.DataAccessException;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* <i>Data Access Object</i> for persons.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IRoleAssignmentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IRoleAssignmentDAO.java
index 4b06ea00560..42ff809b3c9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IRoleAssignmentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IRoleAssignmentDAO.java
@@ -20,8 +20,8 @@ import java.util.List;
import org.springframework.dao.DataAccessException;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
/**
* <i>Data Access Object</i> for {@link RoleAssignmentPE}.
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 17ca7c69e65..0472709514a 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
@@ -1,65 +1,65 @@
-/*
- * Copyright 2008 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.dataaccess.migration;
-
-import org.springframework.dao.DataAccessException;
-import org.springframework.dao.IncorrectResultSizeDataAccessException;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
-
-import ch.systemsx.cisd.dbmigration.java.IMigrationStep;
-import ch.systemsx.cisd.lims.base.dto.TableNames;
-import ch.systemsx.cisd.openbis.generic.server.util.UuidUtil;
-
-/**
- * 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>.
- * </p>
- *
- * @author Tomasz Pylak
- */
-public final class MigrationStepFrom022To023 implements IMigrationStep
-{
- //
- // IMigrationStep
- //
-
- public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
- throws DataAccessException
- {
- final String uuid = UuidUtil.generateUUID();
- final int count =
- simpleJdbcTemplate.queryForInt(String.format("select count(*) from %s",
- TableNames.DATABASE_INSTANCES_TABLE));
- if (count == 1)
- {
- simpleJdbcTemplate.update(String.format("update %s set GLOBAL_CODE = ?",
- TableNames.DATABASE_INSTANCES_TABLE), uuid);
- } else
- {
- throw new IncorrectResultSizeDataAccessException(1, count);
- }
- }
-
- public final void performPreMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
- throws DataAccessException
- {
- }
-
-}
+/*
+ * Copyright 2008 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.dataaccess.migration;
+
+import org.springframework.dao.DataAccessException;
+import org.springframework.dao.IncorrectResultSizeDataAccessException;
+import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+
+import ch.systemsx.cisd.dbmigration.java.IMigrationStep;
+import ch.systemsx.cisd.openbis.generic.server.util.UuidUtil;
+import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
+
+/**
+ * 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>.
+ * </p>
+ *
+ * @author Tomasz Pylak
+ */
+public final class MigrationStepFrom022To023 implements IMigrationStep
+{
+ //
+ // IMigrationStep
+ //
+
+ public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
+ throws DataAccessException
+ {
+ final String uuid = UuidUtil.generateUUID();
+ final int count =
+ simpleJdbcTemplate.queryForInt(String.format("select count(*) from %s",
+ TableNames.DATABASE_INSTANCES_TABLE));
+ if (count == 1)
+ {
+ simpleJdbcTemplate.update(String.format("update %s set GLOBAL_CODE = ?",
+ TableNames.DATABASE_INSTANCES_TABLE), uuid);
+ } else
+ {
+ throw new IncorrectResultSizeDataAccessException(1, count);
+ }
+ }
+
+ public final void performPreMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
+ throws DataAccessException
+ {
+ }
+
+}
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 d132a8d79a4..4da1aaee7f8 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
@@ -1,188 +1,188 @@
-/*
- * Copyright 2008 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.dataaccess.migration;
-
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.List;
-
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.log4j.Logger;
-import org.springframework.dao.DataAccessException;
-import org.springframework.dao.DataIntegrityViolationException;
-import org.springframework.dao.IncorrectResultSizeDataAccessException;
-import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
-
-import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
-import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
-import ch.systemsx.cisd.lims.base.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).
- * </p>
- *
- * @author Christian Ribeaud
- */
-public final class MigrationStepFrom023To024 extends MigrationStepAdapter
-{
- private static final String INSTANCE_PREFIX = "Instance_";
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, MigrationStepFrom023To024.class);
-
- private final static ParameterizedRowMapper<DatabaseInstance> DATABASE_ROW_MAPPER =
- new ParameterizedRowMapper<DatabaseInstance>()
- {
-
- //
- // ParameterizedRowMapper
- //
-
- public final DatabaseInstance mapRow(final ResultSet rs, final int rowNum)
- throws SQLException
- {
- final String code = rs.getString("code");
- final String uuid = rs.getString("uuid");
- return new DatabaseInstance(code, uuid);
- }
- };
-
- private final static ParameterizedRowMapper<ExternalData> EXTERNAL_DATA_ROW_MAPPER =
- new ParameterizedRowMapper<ExternalData>()
- {
- //
- // ParameterizedRowMapper
- //
- public final ExternalData mapRow(final ResultSet rs, final int rowNum)
- throws SQLException
- {
- final long id = rs.getLong("data_id");
- final String location = rs.getString("location");
- return new ExternalData(id, location);
- }
- };
-
- private final static DatabaseInstance getDatabaseInstance(
- final SimpleJdbcTemplate simpleJdbcTemplate)
- {
- final DatabaseInstance databaseInstance =
- simpleJdbcTemplate.queryForObject(String.format(
- "select uuid, code from %s where is_original_source = ?",
- TableNames.DATABASE_INSTANCES_TABLE), DATABASE_ROW_MAPPER, true);
- return databaseInstance;
- }
-
- final static String getNewLocation(final ExternalData externalData,
- final DatabaseInstance databaseInstance)
- {
- final String location = externalData.location;
- final int index = location.indexOf('/');
- if (index < 0)
- {
- throw new DataIntegrityViolationException(String.format(
- "No '/' found in location of externa data '%s'.", externalData));
- }
- final String afterInstance = location.substring(index);
- return INSTANCE_PREFIX + databaseInstance.uuid + afterInstance;
- }
-
- //
- // MigrationStepAdapter
- //
-
- @Override
- public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
- throws DataAccessException
- {
- final DatabaseInstance databaseInstance = getDatabaseInstance(simpleJdbcTemplate);
- final List<ExternalData> externalDatas =
- simpleJdbcTemplate.query(String.format(
- "select data_id, location from %s where location like 'Instance_%s%%'",
- TableNames.EXTERNAL_DATA_TABLE, databaseInstance.code),
- EXTERNAL_DATA_ROW_MAPPER);
- if (externalDatas.size() == 0)
- {
- operationLog.info("No data set location has been migrated.");
- } else
- {
- for (final ExternalData externalData : externalDatas)
- {
- final int updated =
- simpleJdbcTemplate.update(String.format(
- "update %s set location = ? where data_id = ?",
- TableNames.EXTERNAL_DATA_TABLE), getNewLocation(externalData,
- databaseInstance), externalData.id);
- if (updated != 1)
- {
- throw new IncorrectResultSizeDataAccessException(1, updated);
- }
- }
- operationLog.info(String.format(
- "Following data set locations '%s' have been migrated.", CollectionUtils
- .abbreviate(externalDatas, 10)));
- }
- }
-
- //
- // Helper classes
- //
-
- final static class DatabaseInstance
- {
-
- final String code;
-
- final String uuid;
-
- DatabaseInstance(final String code, final String uuid)
- {
- this.code = code;
- this.uuid = uuid;
- }
- }
-
- final static class ExternalData
- {
- final long id;
-
- final String location;
-
- ExternalData(final long id, final String location)
- {
- this.id = id;
- this.location = location;
- }
-
- //
- // ExternalData
- //
-
- @Override
- public final String toString()
- {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
- }
-}
+/*
+ * Copyright 2008 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.dataaccess.migration;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.List;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.log4j.Logger;
+import org.springframework.dao.DataAccessException;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.dao.IncorrectResultSizeDataAccessException;
+import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
+import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
+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).
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class MigrationStepFrom023To024 extends MigrationStepAdapter
+{
+ private static final String INSTANCE_PREFIX = "Instance_";
+
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, MigrationStepFrom023To024.class);
+
+ private final static ParameterizedRowMapper<DatabaseInstance> DATABASE_ROW_MAPPER =
+ new ParameterizedRowMapper<DatabaseInstance>()
+ {
+
+ //
+ // ParameterizedRowMapper
+ //
+
+ public final DatabaseInstance mapRow(final ResultSet rs, final int rowNum)
+ throws SQLException
+ {
+ final String code = rs.getString("code");
+ final String uuid = rs.getString("uuid");
+ return new DatabaseInstance(code, uuid);
+ }
+ };
+
+ private final static ParameterizedRowMapper<ExternalData> EXTERNAL_DATA_ROW_MAPPER =
+ new ParameterizedRowMapper<ExternalData>()
+ {
+ //
+ // ParameterizedRowMapper
+ //
+ public final ExternalData mapRow(final ResultSet rs, final int rowNum)
+ throws SQLException
+ {
+ final long id = rs.getLong("data_id");
+ final String location = rs.getString("location");
+ return new ExternalData(id, location);
+ }
+ };
+
+ private final static DatabaseInstance getDatabaseInstance(
+ final SimpleJdbcTemplate simpleJdbcTemplate)
+ {
+ final DatabaseInstance databaseInstance =
+ simpleJdbcTemplate.queryForObject(String.format(
+ "select uuid, code from %s where is_original_source = ?",
+ TableNames.DATABASE_INSTANCES_TABLE), DATABASE_ROW_MAPPER, true);
+ return databaseInstance;
+ }
+
+ final static String getNewLocation(final ExternalData externalData,
+ final DatabaseInstance databaseInstance)
+ {
+ final String location = externalData.location;
+ final int index = location.indexOf('/');
+ if (index < 0)
+ {
+ throw new DataIntegrityViolationException(String.format(
+ "No '/' found in location of externa data '%s'.", externalData));
+ }
+ final String afterInstance = location.substring(index);
+ return INSTANCE_PREFIX + databaseInstance.uuid + afterInstance;
+ }
+
+ //
+ // MigrationStepAdapter
+ //
+
+ @Override
+ public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
+ throws DataAccessException
+ {
+ final DatabaseInstance databaseInstance = getDatabaseInstance(simpleJdbcTemplate);
+ final List<ExternalData> externalDatas =
+ simpleJdbcTemplate.query(String.format(
+ "select data_id, location from %s where location like 'Instance_%s%%'",
+ TableNames.EXTERNAL_DATA_TABLE, databaseInstance.code),
+ EXTERNAL_DATA_ROW_MAPPER);
+ if (externalDatas.size() == 0)
+ {
+ operationLog.info("No data set location has been migrated.");
+ } else
+ {
+ for (final ExternalData externalData : externalDatas)
+ {
+ final int updated =
+ simpleJdbcTemplate.update(String.format(
+ "update %s set location = ? where data_id = ?",
+ TableNames.EXTERNAL_DATA_TABLE), getNewLocation(externalData,
+ databaseInstance), externalData.id);
+ if (updated != 1)
+ {
+ throw new IncorrectResultSizeDataAccessException(1, updated);
+ }
+ }
+ operationLog.info(String.format(
+ "Following data set locations '%s' have been migrated.", CollectionUtils
+ .abbreviate(externalDatas, 10)));
+ }
+ }
+
+ //
+ // Helper classes
+ //
+
+ final static class DatabaseInstance
+ {
+
+ final String code;
+
+ final String uuid;
+
+ DatabaseInstance(final String code, final String uuid)
+ {
+ this.code = code;
+ this.uuid = uuid;
+ }
+ }
+
+ final static class ExternalData
+ {
+ final long id;
+
+ final String location;
+
+ ExternalData(final long id, final String location)
+ {
+ this.id = id;
+ this.location = location;
+ }
+
+ //
+ // ExternalData
+ //
+
+ @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/server/dataaccess/migration/MigrationStepFrom025To026.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/migration/MigrationStepFrom025To026.java
index 8a9b1390cbb..74d5a39e122 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
@@ -1,147 +1,147 @@
-/*
- * Copyright 2008 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.dataaccess.migration;
-
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang.builder.ToStringBuilder;
-import org.apache.log4j.Logger;
-import org.springframework.dao.DataAccessException;
-import org.springframework.dao.IncorrectResultSizeDataAccessException;
-import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
-
-import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
-import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
-import ch.systemsx.cisd.lims.base.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.
- * </p>
- *
- * @author Izabela Adamczyk
- */
-public final class MigrationStepFrom025To026 extends MigrationStepAdapter
-{
-
- private static final String OBSERVABLE_TYPE_PREFIX = "/ObservableType_";
-
- private static final String DATA_SET_TYPE_PREFIX = "/DataSetType_";
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, MigrationStepFrom025To026.class);
-
- private final static ParameterizedRowMapper<ExternalData> EXTERNAL_DATA_ROW_MAPPER =
- new ParameterizedRowMapper<ExternalData>()
- {
- public final ExternalData mapRow(final ResultSet rs, final int rowNum)
- throws SQLException
- {
- final long id = rs.getLong("data_id");
- final String location = rs.getString("location");
- return new ExternalData(id, location);
- }
- };
-
- public final static String getNewLocation(final String oldLocation)
- {
- final int index = oldLocation.indexOf(OBSERVABLE_TYPE_PREFIX);
- if (index < 0)
- {
- StringBuilder builder = new StringBuilder();
- builder.append("WARNING: ");
- builder.append("No ");
- builder.append(OBSERVABLE_TYPE_PREFIX);
- builder.append(" found in external data location '");
- builder.append(oldLocation);
- builder.append("'.");
- operationLog.warn(builder.toString());
- return oldLocation;
- }
- return oldLocation.replaceFirst(OBSERVABLE_TYPE_PREFIX, DATA_SET_TYPE_PREFIX);
- }
-
- //
- // MigrationStepAdapter
- //
-
- @Override
- public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
- throws DataAccessException
- {
-
- final List<ExternalData> externalDatas =
- simpleJdbcTemplate.query(String.format("select data_id, location from %s",
- TableNames.EXTERNAL_DATA_TABLE), EXTERNAL_DATA_ROW_MAPPER);
- if (externalDatas.size() == 0)
- {
- operationLog.info("No data set location has been migrated.");
- } else
- {
- List<ExternalData> migrated = new ArrayList<ExternalData>();
- for (final ExternalData externalData : externalDatas)
- {
- String oldLocation = externalData.location;
- String newLocation = getNewLocation(externalData.location);
- if (newLocation.equals(oldLocation) == false)
- {
- final int updated =
- simpleJdbcTemplate.update(String.format(
- "update %s set location = ? where data_id = ?",
- TableNames.EXTERNAL_DATA_TABLE), newLocation, externalData.id);
- if (updated != 1)
- {
- throw new IncorrectResultSizeDataAccessException(1, updated);
- }
- migrated.add(externalData);
- }
- }
- operationLog.info(String.format(
- "Following data set locations '%s' have been migrated.", CollectionUtils
- .abbreviate(migrated, 10)));
- }
- }
-
- final static class ExternalData
- {
- final long id;
-
- final String location;
-
- ExternalData(final long id, final String location)
- {
- this.id = id;
- this.location = location;
- }
-
- @Override
- public final String toString()
- {
- return ToStringBuilder.reflectionToString(this,
- ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
- }
- }
-}
+/*
+ * Copyright 2008 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.dataaccess.migration;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.log4j.Logger;
+import org.springframework.dao.DataAccessException;
+import org.springframework.dao.IncorrectResultSizeDataAccessException;
+import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
+import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
+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.
+ * </p>
+ *
+ * @author Izabela Adamczyk
+ */
+public final class MigrationStepFrom025To026 extends MigrationStepAdapter
+{
+
+ private static final String OBSERVABLE_TYPE_PREFIX = "/ObservableType_";
+
+ private static final String DATA_SET_TYPE_PREFIX = "/DataSetType_";
+
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, MigrationStepFrom025To026.class);
+
+ private final static ParameterizedRowMapper<ExternalData> EXTERNAL_DATA_ROW_MAPPER =
+ new ParameterizedRowMapper<ExternalData>()
+ {
+ public final ExternalData mapRow(final ResultSet rs, final int rowNum)
+ throws SQLException
+ {
+ final long id = rs.getLong("data_id");
+ final String location = rs.getString("location");
+ return new ExternalData(id, location);
+ }
+ };
+
+ public final static String getNewLocation(final String oldLocation)
+ {
+ final int index = oldLocation.indexOf(OBSERVABLE_TYPE_PREFIX);
+ if (index < 0)
+ {
+ StringBuilder builder = new StringBuilder();
+ builder.append("WARNING: ");
+ builder.append("No ");
+ builder.append(OBSERVABLE_TYPE_PREFIX);
+ builder.append(" found in external data location '");
+ builder.append(oldLocation);
+ builder.append("'.");
+ operationLog.warn(builder.toString());
+ return oldLocation;
+ }
+ return oldLocation.replaceFirst(OBSERVABLE_TYPE_PREFIX, DATA_SET_TYPE_PREFIX);
+ }
+
+ //
+ // MigrationStepAdapter
+ //
+
+ @Override
+ public final void performPostMigration(final SimpleJdbcTemplate simpleJdbcTemplate)
+ throws DataAccessException
+ {
+
+ final List<ExternalData> externalDatas =
+ simpleJdbcTemplate.query(String.format("select data_id, location from %s",
+ TableNames.EXTERNAL_DATA_TABLE), EXTERNAL_DATA_ROW_MAPPER);
+ if (externalDatas.size() == 0)
+ {
+ operationLog.info("No data set location has been migrated.");
+ } else
+ {
+ List<ExternalData> migrated = new ArrayList<ExternalData>();
+ for (final ExternalData externalData : externalDatas)
+ {
+ String oldLocation = externalData.location;
+ String newLocation = getNewLocation(externalData.location);
+ if (newLocation.equals(oldLocation) == false)
+ {
+ final int updated =
+ simpleJdbcTemplate.update(String.format(
+ "update %s set location = ? where data_id = ?",
+ TableNames.EXTERNAL_DATA_TABLE), newLocation, externalData.id);
+ if (updated != 1)
+ {
+ throw new IncorrectResultSizeDataAccessException(1, updated);
+ }
+ migrated.add(externalData);
+ }
+ }
+ operationLog.info(String.format(
+ "Following data set locations '%s' have been migrated.", CollectionUtils
+ .abbreviate(migrated, 10)));
+ }
+ }
+
+ final static class ExternalData
+ {
+ final long id;
+
+ final String location;
+
+ ExternalData(final long id, final String location)
+ {
+ this.id = id;
+ this.location = location;
+ }
+
+ @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/server/util/GroupIdentifierHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/GroupIdentifierHelper.java
index 29f4c3bdc37..ffb0e512a07 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/GroupIdentifierHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/GroupIdentifierHelper.java
@@ -21,15 +21,15 @@ import java.util.List;
import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.exceptions.InternalErr;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.exception.UndefinedGroupException;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
-import ch.systemsx.cisd.lims.base.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGroupDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.exception.UndefinedGroupException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
* Some useful identifier methods on the <i>server</i> side.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
index e8773699c8b..4aeb879fc0e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/KeyExtractorFactory.java
@@ -17,16 +17,15 @@
package ch.systemsx.cisd.openbis.generic.server.util;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.ExperimentPE;
-import ch.systemsx.cisd.lims.base.dto.IIdAndCodeHolder;
-import ch.systemsx.cisd.lims.base.dto.IIdHolder;
-import ch.systemsx.cisd.lims.base.dto.MaterialPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.PropertyTypePE;
-import ch.systemsx.cisd.lims.base.dto.SampleComponentDTO;
-import ch.systemsx.cisd.lims.base.dto.SamplePE;
-import ch.systemsx.cisd.lims.base.dto.VocabularyTermPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IIdAndCodeHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IIdHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
/**
* A <code>IdKeyExtractor</code> factory.
@@ -41,9 +40,6 @@ public final class KeyExtractorFactory
private final static IKeyExtractor<String, DatabaseInstancePE> DATABASE_INSTANCE_BY_UUID_KEY_EXTRACTOR =
new UUIDKeyExtractor();
- private final static IKeyExtractor<String, SampleComponentDTO> SAMPLE_COMPONENT_BY_CODE_KEY_EXTRACTOR =
- createCodeKeyExtractor();
-
private final static IKeyExtractor<Long, ExperimentPE> BASE_EXPERIMENT_BY_ID_KEY_EXTRACTOR =
createIdKeyExtractor();
@@ -159,15 +155,6 @@ public final class KeyExtractorFactory
return PERSON_BY_ID_KEY_EXTRACTOR;
}
- /**
- * Returns an <code>IKeyExtractor</code> for <i>SampleComponentDTO</i> based on
- * {@link SampleComponentDTO#getCode()}.
- */
- public final static IKeyExtractor<String, SampleComponentDTO> getSampleComponentByCode()
- {
- return SAMPLE_COMPONENT_BY_CODE_KEY_EXTRACTOR;
- }
-
//
// Helper classes
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/UuidUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/UuidUtil.java
index fce603852aa..dcd039a4ca8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/UuidUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/UuidUtil.java
@@ -21,7 +21,7 @@ import java.util.regex.Pattern;
import org.apache.commons.lang.StringUtils;
-import ch.systemsx.cisd.lims.base.util.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.CodeConverter;
/**
* Some utility methods based on {@link UUID}.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/GenericSharedConstants.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/GenericSharedConstants.java
new file mode 100644
index 00000000000..6de09a87ec1
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/GenericSharedConstants.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2008 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.shared;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class GenericSharedConstants
+{
+ /**
+ * Everytime some public class in this package or subpackages are are changed, we should
+ * increment this.
+ */
+ public static final int VERSION = 28; // for release S40
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IGenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IGenericServer.java
index 05c003a652f..fa36932570a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IGenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IGenericServer.java
@@ -18,9 +18,9 @@ package ch.systemsx.cisd.openbis.generic.shared;
import java.util.List;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
/**
* Definition of the client-server interface.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractAttachmentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractAttachmentPE.java
new file mode 100644
index 00000000000..d6392da30c8
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractAttachmentPE.java
@@ -0,0 +1,164 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.MappedSuperclass;
+import javax.persistence.SequenceGenerator;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Superclass to store attachment. Does not contain attachment content.
+ *
+ * @author Christian Ribeaud
+ * @author Tomasz Pylak
+ */
+@MappedSuperclass
+public class AbstractAttachmentPE extends HibernateAbstractRegistratrationHolder implements
+ Serializable, Comparable<AbstractAttachmentPE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String fileName;
+
+ private int version;
+
+ transient private Long id;
+
+ // TODO 2008-08-21, Christian Ribeaud: Put the experiment here instead of the id once it has
+ // been hibernated.
+ /**
+ * Id of the parent (e.g. an experiment) to which this attachment belongs.
+ */
+ transient private Long parentId;
+
+ /**
+ * Returns the file name of the property or <code>null</code>.
+ */
+ @Column(name = ColumnNames.FILE_NAME_COLUMN)
+ @NotNull(message = ValidationMessages.FILE_NAME_NOT_NULL_MESSAGE)
+ @Length(max = 100, message = ValidationMessages.FILE_NAME_LENGTH_MESSAGE)
+ public String getFileName()
+ {
+ return fileName;
+ }
+
+ public void setFileName(final String fileName)
+ {
+ this.fileName = fileName;
+ }
+
+ @Column(name = ColumnNames.VERSION_COLUMN)
+ @NotNull(message = ValidationMessages.VERSION_NOT_NULL_MESSAGE)
+ public int getVersion()
+ {
+ return version;
+ }
+
+ public void setVersion(final int version)
+ {
+ this.version = version;
+ }
+
+ @SequenceGenerator(name = SequenceNames.EXPERIMENT_ATTACHMENT_SEQUENCE, sequenceName = SequenceNames.EXPERIMENT_ATTACHMENT_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.EXPERIMENT_ATTACHMENT_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @Column(name = ColumnNames.EXPERIMENT_COLUMN)
+ @NotNull(message = ValidationMessages.EXPERIMENT_NOT_NULL_MESSAGE)
+ public Long getParentId()
+ {
+ return parentId;
+ }
+
+ public void setParentId(final Long parentId)
+ {
+ this.parentId = parentId;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof AbstractAttachmentPE == false)
+ {
+ return false;
+ }
+ final AbstractAttachmentPE that = (AbstractAttachmentPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(fileName, that.fileName);
+ builder.append(version, that.version);
+ builder.append(parentId, that.parentId);
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(fileName);
+ builder.append(version);
+ builder.append(parentId);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Comparable
+ //
+
+ public final int compareTo(final AbstractAttachmentPE o)
+ {
+ final int byFile = getFileName().compareTo(o.getFileName());
+ return byFile == 0 ? Integer.valueOf(getVersion()).compareTo(o.getVersion()) : byFile;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractEntity.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractEntity.java
new file mode 100644
index 00000000000..60b976967d7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractEntity.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * Abstract super class of all Data Transfer Objects having {@link SimpleEntityProperty}s.
+ *
+ * @author Franz-Josef Elmer
+ */
+public abstract class AbstractEntity<T extends AbstractEntity<T>> extends Code<T> implements
+ ISimpleEntityPropertiesHolder
+{
+ private static final long serialVersionUID = 1L;
+
+ private SimpleEntityProperty[] properties;
+
+ //
+ // IEntityPropertiesHolder
+ //
+
+ public final SimpleEntityProperty[] getProperties()
+ {
+ return properties;
+ }
+
+ public final void setProperties(final SimpleEntityProperty[] properties)
+ {
+ this.properties = properties;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractIdAndCodeHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractIdAndCodeHolder.java
new file mode 100644
index 00000000000..f28d33286e7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractIdAndCodeHolder.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * An <i>abstract</i> implementation of {@link IIdAndCodeHolder}
+ *
+ * @author Christian Ribeaud
+ */
+public abstract class AbstractIdAndCodeHolder<T extends IIdAndCodeHolder> implements
+ IIdAndCodeHolder, Comparable<T>, Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static String CODE_PATTERN = "^[A-Z0-9_\\-]+$";
+
+ /**
+ * A static method for comparing two {@link IIdAndCodeHolder}s.
+ */
+ public final static int compare(final IIdAndCodeHolder o1, IIdAndCodeHolder o2)
+ {
+ return IdAndCodeHolderComparator.INSTANCE.compare(o1, o2);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof IIdAndCodeHolder == false)
+ {
+ return false;
+ }
+ final IIdAndCodeHolder that = (IIdAndCodeHolder) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Compare
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(final T o)
+ {
+ return compare(this, o);
+ }
+
+ //
+ // Helper classes
+ //
+
+ private final static class IdAndCodeHolderComparator implements Comparator<IIdAndCodeHolder>
+ {
+
+ static final Comparator<IIdAndCodeHolder> INSTANCE = new IdAndCodeHolderComparator();
+
+ //
+ // Comparator
+ //
+
+ public final int compare(final IIdAndCodeHolder o1, final IIdAndCodeHolder o2)
+ {
+ final String thatCode = o2.getCode();
+ if (o1.getCode() == null)
+ {
+ return thatCode == null ? 0 : -1;
+ }
+ if (thatCode == null)
+ {
+ return 1;
+ }
+ return o1.getCode().compareTo(thatCode);
+
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistratrationHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistratrationHolder.java
new file mode 100644
index 00000000000..1963186759f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractRegistratrationHolder.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.util.Date;
+
+
+/**
+ * Super class of DTOs which hold registration data.
+ *
+ * @author Franz-Josef Elmer
+ */
+public abstract class AbstractRegistratrationHolder extends Id implements IRegistratorHolder
+{
+ private static final long serialVersionUID = 1L;
+
+ /** Technical ID of the person who registered this entity. */
+ private final Long registratorID;
+
+ /**
+ * Person who registered this entity.
+ * <p>
+ * This is specified at insert time.
+ * </p>
+ */
+ private PersonPE registrator;
+
+ /**
+ * Registration date of this entity.
+ * <p>
+ * This is specified at insert time.
+ * </p>
+ */
+ private Date registrationDate;
+
+ protected AbstractRegistratrationHolder(final Long registratorID)
+ {
+ this.registratorID = registratorID;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ //
+ // IRegistratorHolder
+ //
+
+ /**
+ * Returns registratorID.
+ */
+ public final Long getRegistratorID()
+ {
+ return registrator == null ? registratorID : registrator.getId();
+ }
+
+ /**
+ * Returns the registrator or <code>null</code> if not known.
+ */
+ public final PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ /**
+ * Sets the person who has registered the experiment.
+ *
+ * @throws AssertionError if <code>registratorID</code> is defined but unequal
+ * <code>registrator.getId()</code>.
+ */
+ public final void setRegistrator(final PersonPE registrator)
+ {
+ getAndCheckID(registrator, registratorID);
+ this.registrator = registrator;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractTypePE.java
new file mode 100644
index 00000000000..1d0dbf8843c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AbstractTypePE.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.MappedSuperclass;
+
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Abstract Persistence Entity representing a type.
+ *
+ * @author Izabela Adamczyk
+ */
+@MappedSuperclass
+public abstract class AbstractTypePE extends AbstractIdAndCodeHolder<AbstractTypePE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ transient protected Long id;
+
+ private String code;
+
+ private String description;
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ public AbstractTypePE(final long id, final String code, final String description)
+ {
+ setId(id);
+ setCode(code);
+ setDescription(description);
+ }
+
+ public AbstractTypePE()
+ {
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+}
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
new file mode 100644
index 00000000000..14a26d15442
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AttachmentPE.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Contains information about an attachment. Does not contain attachment content.<br>
+ * NOTE: this class does not add anything to the superclass. It exists only because superclasses
+ * cannot be mapped to tables in Hibernate.
+ *
+ * @author Tomasz Pylak
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENT_ATTACHMENTS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.EXPERIMENT_COLUMN, ColumnNames.FILE_NAME_COLUMN, ColumnNames.VERSION_COLUMN }) })
+public class AttachmentPE extends AbstractAttachmentPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final List<AttachmentPE> EMPTY_LIST = new ArrayList<AttachmentPE>();
+
+ public static final AttachmentPE[] EMPTY_ARRAY = new AttachmentPE[0];
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/BaseExperiment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/BaseExperiment.java
new file mode 100644
index 00000000000..74741fef1a3
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/BaseExperiment.java
@@ -0,0 +1,148 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.util.Date;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A basic <code>Experiment</code> object without procedures, samples, and data.
+ *
+ * @author Christian Ribeaud
+ */
+public final class BaseExperiment extends AbstractEntity<BaseExperiment>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private ExperimentType experimentType;
+
+ private Date registrationDate;
+
+ private PersonPE registrator;
+
+ private ProjectPE project;
+
+ private NewMaterial studyObject;
+
+ private ProcessingInstructionDTO[] processingInstructions;
+
+ private boolean invalidated;
+
+ private Date lastDataSetDate;
+
+ public final boolean isInvalidated()
+ {
+ return invalidated;
+ }
+
+ public final void setInvalidated(final boolean invalidated)
+ {
+ this.invalidated = invalidated;
+ }
+
+ public final ProcessingInstructionDTO[] getProcessingInstructions()
+ {
+ return processingInstructions;
+ }
+
+ public final void setProcessingInstructions(
+ final ProcessingInstructionDTO[] processingInstructions)
+ {
+ this.processingInstructions = processingInstructions;
+ }
+
+ public final NewMaterial getStudyObject()
+ {
+ return studyObject;
+ }
+
+ public final void setStudyObject(final NewMaterial material)
+ {
+ this.studyObject = material;
+ }
+
+ public final Date getLastDataSetDate()
+ {
+ return lastDataSetDate;
+ }
+
+ public final void setLastDataSetDate(final Date lastDataSetDate)
+ {
+ this.lastDataSetDate = lastDataSetDate;
+ }
+
+ public Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ public void setRegistrator(final PersonPE registrator)
+ {
+ this.registrator = registrator;
+ }
+
+ public final ProjectPE getProject()
+ {
+ return project;
+ }
+
+ public final void setProject(final ProjectPE project)
+ {
+ this.project = project;
+ }
+
+ public final ExperimentType getExperimentType()
+ {
+ return experimentType;
+ }
+
+ public final void setExperimentType(final ExperimentType experimentType)
+ {
+ this.experimentType = experimentType;
+ }
+
+ //
+ // AbstractEntity
+ //
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ public final EntityType getEntityType()
+ {
+ return getExperimentType();
+ }
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Code.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Code.java
new file mode 100644
index 00000000000..5f9f6f8e62d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Code.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A class that overrides {@link #equals(Object)}, {@link #hashCode()}, {@link #toString()} for a
+ * given <code>code</code>.
+ * <p>
+ * This class also implements {@link Comparable} interface.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public abstract class Code<T extends Code<T>> implements Serializable, Comparable<T>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String code;
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ @BeanProperty(label = "code")
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Code == false)
+ {
+ return false;
+ }
+ final Code<?> that = (Code<?>) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.code, code);
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(code);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public int compareTo(final T o)
+ {
+ final String thatCode = o.code;
+ if (code == null)
+ {
+ return thatCode == null ? 0 : -1;
+ }
+ if (thatCode == null)
+ {
+ return 1;
+ }
+ return code.compareTo(thatCode);
+ }
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CodeConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CodeConverter.java
new file mode 100644
index 00000000000..8c68cf1052d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/CodeConverter.java
@@ -0,0 +1,103 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * Methods for converter codes from business layer to database and from database to business layer.
+ *
+ * @author Bernd Rinn
+ */
+public final class CodeConverter
+{
+ public static final String USER_PROPERTY_PREFIX = "USER.";
+
+ private CodeConverter()
+ {
+ // Cannot be instantiated.
+ }
+
+ /**
+ * Converts a code from database form to business layer form.
+ *
+ * @return The code appropriate for the business layer.
+ */
+ public static String tryToBusinessLayer(final String codeFromDatabaseOrNull)
+ {
+ return tryToBusinessLayer(codeFromDatabaseOrNull, false);
+ }
+
+ /**
+ * Converts a code from database form to business layer form.
+ * <p>
+ * If <var>userNamespace</var> is <code>true</code>, the prefix 'USER.' will be used,
+ * because user properties will be represented as 'NAME' in the database and as USER.NAME in the
+ * business layer.
+ *
+ * @return The code appropriate for the business layer.
+ */
+ public static String tryToBusinessLayer(final String codeFromDatabaseOrNull,
+ final boolean userNamespace)
+ {
+ if (userNamespace && codeFromDatabaseOrNull != null)
+ {
+ return USER_PROPERTY_PREFIX + codeFromDatabaseOrNull;
+ } else
+ {
+ return codeFromDatabaseOrNull;
+ }
+ }
+
+ /**
+ * Converts a property type code from business layer form to database form.
+ * <p>
+ * The code will be translated to upper case. User properties will be represented as 'NAME' in
+ * the database and as USER.NAME in the business layer.
+ *
+ * @return The code appropriate for the database.
+ */
+ public static String tryToDatabase(final String codeFromBusinessLayerOrNull)
+ {
+ if (codeFromBusinessLayerOrNull == null)
+ {
+ return null;
+ }
+ final String upperCaseCode = codeFromBusinessLayerOrNull.toUpperCase();
+ if (upperCaseCode.startsWith(USER_PROPERTY_PREFIX))
+ {
+ return upperCaseCode.substring(USER_PROPERTY_PREFIX.length());
+ } else
+ {
+ return upperCaseCode;
+ }
+ }
+
+ /**
+ * Returns <code>true</code>, if the <var>codeFromBusinessLayerOrNull</var> represents a
+ * user property code.
+ */
+ public static boolean isInternalNamespace(final String codeFromBusinessLayerOrNull)
+ {
+ if (codeFromBusinessLayerOrNull == null)
+ {
+ return false;
+ } else
+ {
+ return codeFromBusinessLayerOrNull.toUpperCase().startsWith(USER_PROPERTY_PREFIX) == false;
+ }
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
new file mode 100644
index 00000000000..1c19152b444
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
@@ -0,0 +1,165 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * This class lists database field names commonly used.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ColumnNames
+{
+
+ public static final String CODE_COLUMN = "code";
+
+ public static final String CONTROL_LAYOUT_SAMPLE_COLUMN = "samp_id_control_layout";
+
+ public static final String CONTROLLED_VOCABULARY_COLUMN = "covo_id";
+
+ public static final String DATA_CHILD_COLUMN = "data_id_child";
+
+ public static final String DATA_ID_COLUMN = "data_id";
+
+ public static final String DATA_PARENT_COLUMN = "data_id_parent";
+
+ public static final String DATA_PRODUCER_CODE_COLUMN = "data_producer_code";
+
+ public static final String DATA_STORE_COLUMN = "dast_id";
+
+ public static final String DATA_TYPE_COLUMN = "daty_id";
+
+ public final static String DATABASE_INSTANCE_COLUMN = "dbin_id";
+
+ public static final String DESCRIPTION_COLUMN = "description";
+
+ public static final String DOWNLOAD_URL_COLUMN = "download_url";
+
+ public static final String EXPERIMENT_COLUMN = "expe_id";
+
+ public static final String EXPERIMENT_TYPE_COLUMN = "exty_id";
+
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN = "etpt_id";
+
+ public static final String FILE_FORMAT_TYPE = "ffty_id";
+
+ public static final String FILE_NAME_COLUMN = "file_name";
+
+ public final static String FIRST_NAME_COLUMN = "first_name";
+
+ public static final String GENERATED_FROM_SAMPLE_COLUMN = "samp_id_generated_from";
+
+ public static final String GROUP_COLUMN = "grou_id";
+
+ public static final String GROUP_PARENT_COLUMN = "grou_id_parent";
+
+ public static final String ID_COLUMN = "id";
+
+ public static final String INHIBITOR_OF_COLUMN = "mate_id_inhibitor_of";
+
+ public static final String INVALIDATION_COLUMN = "inva_id";
+
+ public static final String IS_COMPLETE_COLUMN = "is_complete";
+
+ public static final String IS_DATA_CQUSITION = "is_data_acquisition";
+
+ public static final String IS_INTERNAL_NAMESPACE = "is_internal_namespace";
+
+ public static final String IS_MANAGED_INTERNALLY = "is_managed_internally";
+
+ public static final String IS_MANDATORY = "is_mandatory";
+
+ public static final String IS_ORIGINAL_SOURCE_COLUMN = "is_original_source";
+
+ public static final String IS_PLACEHOLDER_COLUMN = "is_placeholder";
+
+ public static final String LABEL_COLUMN = "label";
+
+ public final static String LAST_NAME_COLUMN = "last_name";
+
+ public static final String LOCATION_COLUMN = "location";
+
+ public static final String LOCATOR_TYPE_COLUMN = "loty_id";
+
+ public static final String MATERIAL_COLUMN = "mate_id";
+
+ public static final String MATERIAL_BATCH_COLUMN = "maba_id";
+
+ public static final String MATERIAL_TYPE_COLUMN = "maty_id";
+
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_COLUMN = "mtpt_id";
+
+ public static final String DATA_SET_TYPE_COLUMN = "dsty_id";
+
+ public static final String PARENT_DATA_SET_CODE_COLUMN = "data_producer_code";
+
+ public static final String PART_OF_SAMPLE_COLUMN = "samp_id_part_of";
+
+ public static final String PERSON_GRANTEE_COLUMN = "pers_id_grantee";
+
+ public static final String PERSON_LEADER_COLUMN = "pers_id_leader";
+
+ public static final String PERSON_REGISTERER_COLUMN = "pers_id_registerer";
+
+ public static final String PROCEDURE_COLUMN = "proc_id";
+
+ public static final String PROCEDURE_PRODUCED_BY_COLUMN = "proc_id_produced_by";
+
+ public static final String PROCEDURE_TYPE_COLUMN = "pcty_id";
+
+ public static final String PRODUCTION_TIMESTAMP_COLUMN = "production_timestamp";
+
+ public static final String PROJECT_COLUMN = "proj_id";
+
+ public static final String PROPERTY_TYPE_COLUMN = "prty_id";
+
+ public static final String REGISTRATION_TIMESTAMP_COLUMN = "registration_timestamp";
+
+ public final static String ROLE_COLUMN = "role_code";
+
+ public static final String SAMPLE_ACQUIRED_FROM = "samp_id_acquired_from";
+
+ public static final String SAMPLE_COLUMN = "samp_id";
+
+ public static final String SAMPLE_DERIVED_FROM = "samp_id_derived_from";
+
+ public static final String SAMPLE_TYPE_COLUMN = "saty_id";
+
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_COLUMN = "stpt_id";
+
+ public static final String STORAGE_FORMAT_COLUMN = "cvte_id_stor_fmt";
+
+ public static final String STUDY_OBJECT_COLUMN = "mate_id_study_object";
+
+ public static final String TOP_SAMPLE_COLUMN = "samp_id_top";
+
+ public final static String USER_COLUMN = "user_id";
+
+ public static final String UUID_COLUMN = "uuid";
+
+ public static final String VALUE = "value";
+
+ public static final String VERSION_COLUMN = "version";
+
+ public static final String VOCABULARY_TERM_COLUMN = "cvte_id";
+
+ public static final String AMOUNT_COLUMN = "amount";
+
+ private ColumnNames()
+ {
+ // Can not be instantiated.
+ }
+}
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
new file mode 100644
index 00000000000..aef8a2f97d7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -0,0 +1,275 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Collections;
+import java.util.Date;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.annotations.Check;
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
+ * know about one DATA.
+ * <p>
+ * This class is the <i>Java Object</i> representation of the corresponding data in the database.
+ * </p>
+ *
+ * @author Bernd Rinn
+ */
+@Entity
+@Table(name = TableNames.DATA_TABLE, uniqueConstraints = @UniqueConstraint(columnNames = ColumnNames.CODE_COLUMN))
+@Check(constraints = "(" + ColumnNames.SAMPLE_ACQUIRED_FROM + " IS NOT NULL AND "
+ + ColumnNames.SAMPLE_DERIVED_FROM + " IS NULL) OR (" + ColumnNames.SAMPLE_ACQUIRED_FROM
+ + " IS NULL AND " + ColumnNames.SAMPLE_DERIVED_FROM + " IS NOT NULL)")
+@Inheritance(strategy = InheritanceType.JOINED)
+public class DataPE extends AbstractIdAndCodeHolder<DataPE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final DataPE[] EMPTY_ARRAY = new DataPE[0];
+
+ public static final List<DataPE> EMPTY_LIST = Collections.emptyList();
+
+ private transient Long id;
+
+ private String code;
+
+ private boolean placeholder;
+
+ /** Registration date of the database instance. */
+ private Date registrationDate;
+
+ private DataSetTypePE dataSetType;
+
+ private ProcedurePE procedure;
+
+ private Date productionDate;
+
+ private String dataProducerCode;
+
+ private SamplePE sampleAcquiredFrom;
+
+ private SamplePE sampleDerivedFrom;
+
+ private List<DataPE> parents = EMPTY_LIST;
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false, updatable = false)
+ @Generated(GenerationTime.INSERT)
+ public Date getRegistrationDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(registrationDate);
+ }
+
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATA_SET_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATA_SET_TYPE_COLUMN, updatable = false)
+ /** Returns <code>dataSetType</code>. */
+ public DataSetTypePE getDataSetType()
+ {
+ return dataSetType;
+ }
+
+ /** Sets <code>dataSetType</code>. */
+ public void setDataSetType(final DataSetTypePE dataSetType)
+ {
+ this.dataSetType = dataSetType;
+ }
+
+ /**
+ * Returns <code>true</code> if this data set is a placeholder for a data set yet to arrive.
+ */
+ @Column(name = ColumnNames.IS_PLACEHOLDER_COLUMN)
+ public boolean isPlaceholder()
+ {
+ return placeholder;
+ }
+
+ /**
+ * Set to <code>true</code> if this data set is a placeholder for a data set yet to arrive.
+ */
+ public void setPlaceholder(final boolean placeholder)
+ {
+ this.placeholder = placeholder;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.SAMPLE_ACQUIRED_FROM, updatable = false)
+ public SamplePE getSampleAcquiredFrom()
+ {
+ return sampleAcquiredFrom;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.SAMPLE_DERIVED_FROM, updatable = false)
+ public SamplePE getSampleDerivedFrom()
+ {
+ return sampleDerivedFrom;
+ }
+
+ public void setSampleAcquiredFrom(final SamplePE sampleAcquiredFrom)
+ {
+ this.sampleAcquiredFrom = sampleAcquiredFrom;
+ }
+
+ public void setSampleDerivedFrom(final SamplePE sampleDerivedFrom)
+ {
+ this.sampleDerivedFrom = sampleDerivedFrom;
+ }
+
+ @Transient
+ public String getAssociatedSampleCode()
+ {
+ final SamplePE sample = sampleAcquiredFrom != null ? sampleAcquiredFrom : sampleDerivedFrom;
+ return sample != null ? sample.getCode() : null;
+ }
+
+ /**
+ * 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>.
+ */
+ @Column(name = ColumnNames.PRODUCTION_TIMESTAMP_COLUMN, updatable = false)
+ public Date getProductionDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(productionDate);
+ }
+
+ /**
+ * Sets the date when the measurement / calculation that produced this external data set has
+ * been performed.
+ */
+ public void setProductionDate(final Date measurementDate)
+ {
+ this.productionDate = measurementDate;
+ }
+
+ /**
+ * 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>.
+ * </p>
+ */
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Column(name = ColumnNames.DATA_PRODUCER_CODE_COLUMN, updatable = false)
+ public String getDataProducerCode()
+ {
+ return dataProducerCode;
+ }
+
+ /**
+ * 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)
+ {
+ this.dataProducerCode = dataProducerCode;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ /**
+ * Sets the code (i.e. the externally used unique identifier) of this external data.
+ */
+ public void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
+ @JoinTable(name = TableNames.DATA_SET_RELATIONSHIPS_TABLE, joinColumns = @JoinColumn(name = ColumnNames.DATA_CHILD_COLUMN), inverseJoinColumns = @JoinColumn(name = ColumnNames.DATA_PARENT_COLUMN))
+ public List<DataPE> getParents()
+ {
+ return parents;
+ }
+
+ public void setParents(final List<DataPE> parents)
+ {
+ this.parents = parents;
+ }
+
+ //
+ // AbstractIdAndCodeHolder
+ //
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.DATA_SEQUENCE, sequenceName = SequenceNames.DATA_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ @Column(unique = true)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ /** Returns <code>procedure</code>. */
+ @ManyToOne(fetch = FetchType.LAZY)
+ @NotNull(message = ValidationMessages.PROCEDURE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.PROCEDURE_PRODUCED_BY_COLUMN, updatable = false)
+ public ProcedurePE getProcedure()
+ {
+ return procedure;
+ }
+
+ /** Sets <code>procedure</code>. */
+ public void setProcedure(final ProcedurePE procedure)
+ {
+ this.procedure = procedure;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetType.java
new file mode 100644
index 00000000000..074c0f40c62
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetType.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about an data set type.
+ *
+ * @author Christian Ribeaud
+ */
+public final class DataSetType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public DataSetType()
+ {
+ }
+
+ public DataSetType(final String code)
+ {
+ setCode(code);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
new file mode 100644
index 00000000000..f0821591c8c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetTypePE.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence Entity representing data set type.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.DATA_SET_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public class DataSetTypePE extends AbstractTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private DatabaseInstancePE databaseInstance;
+
+ @SequenceGenerator(name = SequenceNames.DATA_SET_TYPE_SEQUENCE, sequenceName = SequenceNames.DATA_SET_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_SET_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
new file mode 100644
index 00000000000..dc938c7ef41
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
@@ -0,0 +1,135 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Date;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistence Entity</i> which represents an entry in {@link TableNames#DATA_STORES_TABLE}.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.DATA_STORES_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }))
+public final class DataStorePE extends AbstractIdAndCodeHolder<DataStorePE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ /**
+ * The code of this data store.
+ */
+ private String code;
+
+ /** Registration date of this data store. */
+ private Date registrationDate;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private String downloadUrl;
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @Column(name = ColumnNames.DOWNLOAD_URL_COLUMN, updatable = false)
+ @NotNull(message = ValidationMessages.DOWNLOAD_URL_NOT_NULL_MESSAGE)
+ public final String getDownloadUrl()
+ {
+ return downloadUrl;
+ }
+
+ public final void setDownloadUrl(final String downloadUrl)
+ {
+ this.downloadUrl = downloadUrl;
+ }
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false, updatable = false)
+ @Generated(GenerationTime.INSERT)
+ public final Date getRegistrationDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(registrationDate);
+ }
+
+ public final void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ //
+ // AbstractIdAndCodeHolder
+ //
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public final String getCode()
+ {
+ return code;
+ }
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.DATA_STORE_SEQUENCE, sequenceName = SequenceNames.DATA_STORE_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_STORE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+}
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
new file mode 100644
index 00000000000..4833ea820af
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataTypePE.java
@@ -0,0 +1,148 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityDataType;
+
+/**
+ * Persistence Entity representing 'data type'.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.DATA_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN }) })
+public final class DataTypePE implements IIdHolder, Serializable, Comparable<DataTypePE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ private EntityDataType code;
+
+ private String description;
+
+ @SequenceGenerator(name = SequenceNames.DATA_TYPE_SEQUENCE, sequenceName = SequenceNames.DATA_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATA_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ @Enumerated(EnumType.STRING)
+ public final EntityDataType getCode()
+ {
+ return code;
+ }
+
+ public final void setCode(final EntityDataType code)
+ {
+ this.code = code;
+ }
+
+ @NotNull(message = ValidationMessages.DESCRIPTION_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof DataTypePE == false)
+ {
+ return false;
+ }
+ final DataTypePE that = (DataTypePE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Comparable
+ //
+
+ public final int compareTo(final DataTypePE o)
+ {
+ return getCode().name().compareTo(o.getCode().name());
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DatabaseInstancePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DatabaseInstancePE.java
new file mode 100644
index 00000000000..bb45998f4ab
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DatabaseInstancePE.java
@@ -0,0 +1,183 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Date;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistence Entity</i> which represents a database instance.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.DATABASE_INSTANCES_TABLE)
+public final class DatabaseInstancePE extends AbstractIdAndCodeHolder<DatabaseInstancePE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static String SYSTEM_DEFAULT = "SYSTEM_DEFAULT";
+
+ public final static DatabaseInstancePE[] EMPTY_ARRAY = new DatabaseInstancePE[0];
+
+ private transient Long id;
+
+ /** Registration date of the database instance. */
+ private Date registrationDate;
+
+ /**
+ * The local code of this database instance.
+ * <p>
+ * If <code>SYSTEM_DEFAULT</code>, then {@link #isSystemDefault()} will return
+ * <code>true</code>.
+ * </p>
+ */
+ private String code;
+
+ /**
+ * The global unique code of this database instance (UUID).
+ */
+ private String uuid;
+
+ private boolean isHomeDatabase;
+
+ /** Whether this database instance should get a <i>brand</i>. */
+ private boolean systemDefault;
+
+ private DataStorePE dataStore;
+
+ @OneToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_STORE_COLUMN, updatable = false)
+ public final DataStorePE getDataStore()
+ {
+ return dataStore;
+ }
+
+ public final void setDataStore(final DataStorePE dataStorePE)
+ {
+ this.dataStore = dataStorePE;
+ }
+
+ private final void setSystemDefault(final boolean systemDefault)
+ {
+ this.systemDefault = systemDefault;
+ }
+
+ /**
+ * Whether given <var>code</var> is <code>SYSTEM_DEFAULT</code> code.
+ */
+ public final static boolean isSystemDefault(final String code)
+ {
+ return SYSTEM_DEFAULT.equals(code);
+ }
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false, updatable = false)
+ @Generated(GenerationTime.INSERT)
+ public final Date getRegistrationDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(registrationDate);
+ }
+
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ setSystemDefault(isSystemDefault(code));
+ }
+
+ @Column(name = ColumnNames.UUID_COLUMN)
+ @NotNull(message = ValidationMessages.UUID_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ // Do not call this method 'getUUID' or Hibernate will complain!
+ public String getUuid()
+ {
+ return uuid;
+ }
+
+ // Do not call this method 'setUUID' or Hibernate will complain!
+ public void setUuid(final String uuid)
+ {
+ this.uuid = uuid;
+ }
+
+ @Transient
+ public final boolean isSystemDefault()
+ {
+ return systemDefault;
+ }
+
+ @Column(name = ColumnNames.IS_ORIGINAL_SOURCE_COLUMN, nullable = false)
+ public final boolean isOriginalSource()
+ {
+ return isHomeDatabase;
+ }
+
+ public final void setOriginalSource(final boolean isHomeDatabase)
+ {
+ this.isHomeDatabase = isHomeDatabase;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ //
+ // AbstractIdAndCodeHolder
+ //
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.DATABASE_INSTANCE_SEQUENCE, sequenceName = SequenceNames.DATABASE_INSTANCE_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.DATABASE_INSTANCE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @Column(unique = true)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public final String getCode()
+ {
+ return code;
+ }
+}
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
new file mode 100644
index 00000000000..e9b245ce8db
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyFiller.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * 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
+ */
+public class EntityPropertyFiller extends AbstractHashable implements Serializable
+{
+ public static final EntityPropertyFiller[] EMPTY_ARRAY = new EntityPropertyFiller[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String entityCode;
+
+ private String untypedPropertyValue;
+
+ public EntityPropertyFiller()
+ {
+ }
+
+ public EntityPropertyFiller(final String entityCode, final String untypedPropertyValue)
+ {
+ setEntityCode(entityCode);
+ setPropertyValue(untypedPropertyValue);
+ }
+
+ public final String getEntityCode()
+ {
+ return entityCode;
+ }
+
+ public final String getPropertyValue()
+ {
+ return untypedPropertyValue;
+ }
+
+ @BeanProperty(label = "code")
+ public void setEntityCode(final String entityCode)
+ {
+ assert entityCode != null : "Unspecified entity code.";
+ this.entityCode = entityCode;
+ }
+
+ @BeanProperty(label = "value")
+ public final void setPropertyValue(final String untypedPropertyValue)
+ {
+ assert untypedPropertyValue != null : "Unspecified property value.";
+ this.untypedPropertyValue = untypedPropertyValue;
+ }
+}
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
new file mode 100644
index 00000000000..f4bdaeef23f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyPE.java
@@ -0,0 +1,164 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MappedSuperclass;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+
+import ch.systemsx.cisd.common.utilities.ClassUtils;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+
+/**
+ * Persistence entity representing entity property.
+ *
+ * @author Tomasz Pylak
+ * @author Izabela Adamczyk
+ */
+@MappedSuperclass
+public abstract class EntityPropertyPE extends HibernateAbstractRegistratrationHolder implements
+ IRegistratorHolder, IUntypedValueSetter, IEntityProperty
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /**
+ * The value of this entity property.
+ * <p>
+ * Like in the database, no value is set if <code>value</code> is from controlled vocabulary.
+ * </p>
+ */
+ private String value;
+
+ /**
+ * The vocabulary term.
+ * <p>
+ * Not <code>null</code> if <code>value</code> is from controlled vocabulary.
+ * </p>
+ */
+ private VocabularyTermPE vocabularyTerm;
+
+ protected transient Long id;
+
+ protected transient Long entityId;
+
+ protected EntityTypePropertyTypePE entityTypePropertyType;
+
+ public <T extends EntityTypePropertyTypePE> void setEntityTypePropertyType(
+ final T entityTypePropertyType)
+ {
+ this.entityTypePropertyType = entityTypePropertyType;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ public void setValue(final String value)
+ {
+ this.value = value;
+ }
+
+ @Column(name = ColumnNames.VALUE)
+ @Length(max = 1024, message = ValidationMessages.VALUE_LENGTH_MESSAGE)
+ public String getValue()
+ {
+ return value;
+ }
+
+ // TODO 2008-09-02, Franz-Josef Elmer: Remove this method when
+ // EntityPropertyTypeDAO.createPropertyValue() is no longer used.
+ public void setEntityId(final Long entityId)
+ {
+ this.entityId = entityId;
+ }
+
+ public void setVocabularyTerm(final VocabularyTermPE vt)
+ {
+ this.vocabularyTerm = vt;
+
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.VOCABULARY_TERM_COLUMN, updatable = false)
+ public VocabularyTermPE getVocabularyTerm()
+ {
+ return vocabularyTerm;
+ }
+
+ //
+ // IUntypedValueSetter
+ //
+
+ // TODO 2008-08-29, Christian Ribeaud: How to validate this? A custom validator? It must be a
+ // 'VocabularyTermPE' and not just an id.
+ public final void setUntypedValue(final String value, final Long vocabularyTerm)
+ {
+ assert value != null || vocabularyTerm == null : "Value from controlled vocabulary set cannot be null!";
+ if (vocabularyTerm != null)
+ {
+ if (getVocabularyTerm() == null)
+ {
+ final VocabularyTermPE vt = new VocabularyTermPE();
+ setVocabularyTerm(vt);
+ }
+ getVocabularyTerm().setId(vocabularyTerm);
+ getVocabularyTerm().setCode(value);
+ } else
+ {
+ setValue(value);
+ }
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("entityTypePropertyType", getEntityTypePropertyType());
+ builder.append("value", getValue());
+ builder.append("vocabularyTerm", getVocabularyTerm());
+ return builder.toString();
+ }
+
+ public final String tryGetUntypedValue()
+ {
+ return getVocabularyTerm() == null ? getValue() : getVocabularyTerm().getCode();
+ }
+
+ /**
+ * Creates an {@link EntityPropertyPE} from given <var>entityKind</var>.
+ */
+ public final static <T extends EntityPropertyPE> T createEntityProperty(
+ final EntityKind entityKind)
+ {
+ assert entityKind != null : "Unspecified entity kind";
+ return ClassUtils.createInstance(entityKind.<T> getEntityPropertyClass());
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyTypeDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyTypeDTO.java
new file mode 100644
index 00000000000..e9abbfe9698
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityPropertyTypeDTO.java
@@ -0,0 +1,103 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityDataType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.PropertiesHelper;
+
+/**
+ * Specification of one entity property (name, type, is mandatory).
+ *
+ * @author Tomasz Pylak
+ */
+public final class EntityPropertyTypeDTO extends Id implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private boolean mandatory;
+
+ private Date registrationDate;
+
+ private PersonPE registrator;
+
+ private PropertyTypePE propertyType;
+
+ public EntityPropertyTypeDTO()
+ {
+ }
+
+ public EntityPropertyTypeDTO(final long id, final boolean mandatory,
+ final Date registrationDate, final PersonPE registrator,
+ final PropertyTypePE propertyType)
+ {
+ setId(id);
+ this.mandatory = mandatory;
+ this.registrationDate = registrationDate;
+ this.registrator = registrator;
+ this.propertyType = propertyType;
+ }
+
+ public final EntityDataType getDataTypeCode()
+ {
+ return EntityDataType.valueOf(PropertiesHelper.getSimpleType(propertyType));
+ }
+
+ public final boolean isMandatory()
+ {
+ return mandatory;
+ }
+
+ public final void setMandatory(final boolean mandatory)
+ {
+ this.mandatory = mandatory;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ public final void setRegistrator(final PersonPE registrator)
+ {
+ this.registrator = registrator;
+ }
+
+ public final PropertyTypePE getPropertyType()
+ {
+ return propertyType;
+ }
+
+ public final void setPropertyType(final PropertyTypePE propertyType)
+ {
+ this.propertyType = propertyType;
+ }
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityType.java
new file mode 100644
index 00000000000..59583e32612
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityType.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * An <i>abstract</i> <code>Code</code> extension for types.
+ *
+ * @author Christian Ribeaud
+ */
+public class EntityType extends Code<EntityType> implements IEntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String description;
+
+ public EntityType()
+ {
+ }
+
+ public EntityType(final String code, final String description)
+ {
+ setCode(code);
+ setDescription(description);
+ }
+
+ //
+ // IEntityType
+ //
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypeMandatorilyRelation.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypeMandatorilyRelation.java
new file mode 100644
index 00000000000..147431f0fad
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypeMandatorilyRelation.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class EntityTypeMandatorilyRelation implements Serializable,
+ Comparable<EntityTypeMandatorilyRelation>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final EntityTypeMandatorilyRelation[] EMPTY_ARRAY =
+ new EntityTypeMandatorilyRelation[0];
+
+ private EntityType type;
+
+ private boolean mandatory;
+
+ public final boolean isMandatory()
+ {
+ return mandatory;
+ }
+
+ public final void setMandatory(final boolean mandatory)
+ {
+ this.mandatory = mandatory;
+ }
+
+ public final EntityType getEntityType()
+ {
+ return type;
+ }
+
+ public final void setEntityType(final EntityType materialType)
+ {
+ this.type = materialType;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof EntityTypeMandatorilyRelation == false)
+ {
+ return false;
+ }
+ final EntityTypeMandatorilyRelation that = (EntityTypeMandatorilyRelation) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.type, type);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(type);
+ return builder.toHashCode();
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>type</code>, then they come first.
+ */
+ public final int compareTo(final EntityTypeMandatorilyRelation o)
+ {
+ final EntityType thatType = o.type;
+ if (type == null)
+ {
+ return thatType == null ? 0 : -1;
+ }
+ if (thatType == null)
+ {
+ return 1;
+ }
+ return type.compareTo(thatType);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePE.java
new file mode 100644
index 00000000000..9e581c0a0e4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePE.java
@@ -0,0 +1,67 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MappedSuperclass;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ClassUtils;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+
+/**
+ * Persistence Entity representing entity type.
+ * <p>
+ * Entity is one of: material, sample, experiment
+ * </p>
+ *
+ * @author Franz-Josef Elmer
+ * @author Izabela Adamczyk
+ */
+@MappedSuperclass
+public abstract class EntityTypePE extends AbstractTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private DatabaseInstancePE databaseInstance;
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ /**
+ * Creates an {@link EntityPropertyPE} from given <var>entityKind</var>.
+ */
+ public final static <T extends EntityTypePE> T createEntityTypePE(final EntityKind entityKind)
+ {
+ assert entityKind != null : "Unspecified entity kind.";
+ return ClassUtils.createInstance(entityKind.<T> getTypeClass());
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePropertyTypePE.java
new file mode 100644
index 00000000000..9172f12f692
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityTypePropertyTypePE.java
@@ -0,0 +1,128 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MappedSuperclass;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ClassUtils;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+
+/**
+ * Relation between a {@link EntityTypePE} of something and a {@link PropertyTypePE}.
+ * <p>
+ * This represents an entry in <code>{entity}_type_property_types</code> table.
+ * </p>
+ *
+ * @author Franz-Josef Elmer
+ * @author Tomasz Pylak
+ * @author Izabela Adamczyk
+ */
+@MappedSuperclass
+public abstract class EntityTypePropertyTypePE extends HibernateAbstractRegistratrationHolder
+ implements IEntityTypePropertyType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private boolean mandatory;
+
+ private boolean managedInternally;
+
+ protected transient Long id;
+
+ protected EntityTypePE entityType;
+
+ private PropertyTypePE propertyType;
+
+ final public static <T extends EntityTypePropertyTypePE> T createEntityTypePropertyType(
+ final EntityKind entityKind)
+ {
+ return ClassUtils.createInstance(entityKind.<T> getEntityTypePropertyTypeAssignmentClass());
+ }
+
+ @NotNull(message = ValidationMessages.PROPERTY_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PROPERTY_TYPE_COLUMN, updatable = false)
+ public PropertyTypePE getPropertyType()
+ {
+ return propertyType;
+ }
+
+ public void setPropertyType(final PropertyTypePE propertyType)
+ {
+ this.propertyType = propertyType;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_MANDATORY)
+ public boolean isMandatory()
+ {
+ return mandatory;
+ }
+
+ public void setMandatory(final boolean mandatory)
+ {
+ this.mandatory = mandatory;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_MANAGED_INTERNALLY)
+ public boolean isManagedInternally()
+ {
+ return managedInternally;
+ }
+
+ public void setManagedInternally(final boolean managedInternally)
+ {
+ this.managedInternally = managedInternally;
+ }
+
+ public void setEntityType(final EntityTypePE entityType)
+ {
+ this.entityType = entityType;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("managedInternally", isManagedInternally());
+ builder.append("mandatory", isMandatory());
+ builder.append("propertyType", getPropertyType());
+ builder.append("entityType", getEntityType());
+ return builder.toString();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Experiment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Experiment.java
new file mode 100644
index 00000000000..69cfc371ad9
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Experiment.java
@@ -0,0 +1,234 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.util.Date;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * The full description of a experiment.
+ *
+ * @author Christian Ribeaud
+ */
+public final class Experiment extends AbstractEntity<Experiment>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private NewMaterial studyObject;
+
+ private PersonPE registrator;
+
+ private Date registrationDate;
+
+ private ExperimentType experimentType;
+
+ private AttachmentPE[] attachments = new AttachmentPE[0];
+
+ private Procedure[] procedures = new Procedure[0];
+
+ private ProjectPE project;
+
+ private ProcessingInstructionDTO[] processingInstructions = ProcessingInstructionDTO.EMPTY_ARRAY;
+
+ private InvalidationPE invalidation;
+
+ public final NewMaterial getStudyObject()
+ {
+ return studyObject;
+ }
+
+ public final void setStudyObject(final NewMaterial studyObject)
+ {
+ this.studyObject = studyObject;
+ }
+
+ public final PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ public final void setRegistrator(final PersonPE person)
+ {
+ this.registrator = person;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final ExperimentType getExperimentType()
+ {
+ return experimentType;
+ }
+
+ public final void setExperimentType(final ExperimentType experimentType)
+ {
+ this.experimentType = experimentType;
+ }
+
+ /**
+ * Returns the descriptions of all {@link FileAttachmentPE}s that are stored for this
+ * experiment. If there are no such properties, the array will be empty (have length 0).
+ */
+ public final AttachmentPE[] getAttachments()
+ {
+ if (attachments == null)
+ {
+ return new AttachmentPE[0];
+ }
+ return attachments;
+ }
+
+ /**
+ * Sets the descriptions of all {@link FileAttachmentPE}s.
+ */
+ public final void setAttachments(final AttachmentPE[] attachments)
+ {
+ this.attachments = attachments;
+ }
+
+ /**
+ * Sets procedures.
+ */
+ public final void setProcedures(final Procedure[] procedures)
+ {
+ this.procedures = procedures;
+ }
+
+ /**
+ * Returns procedures. Never returns <code>null</code> but could return an empty array.
+ */
+ public final Procedure[] getProcedures()
+ {
+ if (procedures == null)
+ {
+ return new Procedure[0];
+ }
+ return procedures;
+ }
+
+ public final ProjectPE getProject()
+ {
+ return project;
+ }
+
+ public final void setProject(final ProjectPE project)
+ {
+ this.project = project;
+ }
+
+ public final ProcessingInstructionDTO[] getProcessingInstructions()
+ {
+ if (processingInstructions == null)
+ {
+ return ProcessingInstructionDTO.EMPTY_ARRAY;
+ }
+ return processingInstructions;
+ }
+
+ public final void setProcessingInstructions(final ProcessingInstructionDTO[] processingInstructions)
+ {
+ this.processingInstructions = processingInstructions;
+ }
+
+ public final InvalidationPE getInvalidation()
+ {
+ return invalidation;
+ }
+
+ public final void setInvalidation(final InvalidationPE invalidation)
+ {
+ this.invalidation = invalidation;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Experiment == false)
+ {
+ return false;
+ }
+ final Experiment that = (Experiment) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.project, project);
+ builder.append(that.getCode(), getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(project);
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ @Override
+ public final int compareTo(final Experiment o)
+ {
+ final String thatCode = o.getCode();
+ if (getCode() == null)
+ {
+ return thatCode == null ? 0 : -1;
+ }
+ if (thatCode == null)
+ {
+ return 1;
+ }
+ return getCode().compareTo(thatCode);
+ }
+
+ public final EntityType getEntityType()
+ {
+ return getExperimentType();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPE.java
new file mode 100644
index 00000000000..c50099e4a04
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPE.java
@@ -0,0 +1,313 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Date;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence Entity representing experiment.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENTS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.PROJECT_COLUMN }) })
+public class ExperimentPE extends HibernateAbstractRegistratrationHolder implements
+ IEntityPropertiesHolder<ExperimentPropertyPE>, IIdAndCodeHolder, Comparable<ExperimentPE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final Object EMPTY_ARRAY = new ExperimentPE[0];
+
+ private transient Long id;
+
+ private String code;
+
+ private ProjectPE project;
+
+ private MaterialPE studyObject;
+
+ private ExperimentTypePE experimentType;
+
+ private InvalidationPE invalidation;
+
+ private List<ExperimentPropertyPE> properties = ExperimentPropertyPE.EMPTY_LIST;
+
+ private DataStorePE dataStore;
+
+ private List<AttachmentPE> attachments = AttachmentPE.EMPTY_LIST;
+
+ private List<ProcedurePE> procedures = ProcedurePE.EMPTY_LIST;
+
+ private ProcessingInstructionDTO[] processingInstructions =
+ ProcessingInstructionDTO.EMPTY_ARRAY;
+
+ private Date lastDataSetDate;
+
+ public ExperimentPE()
+ {
+ super();
+ }
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.EXPERIMENT_SEQUENCE, sequenceName = SequenceNames.EXPERIMENT_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.EXPERIMENT_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.PROJECT_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.PROJECT_COLUMN, updatable = false)
+ public ProjectPE getProject()
+ {
+ return project;
+ }
+
+ public void setProject(final ProjectPE project)
+ {
+ this.project = project;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.STUDY_OBJECT_COLUMN, updatable = false)
+ public MaterialPE getStudyObject()
+ {
+ return studyObject;
+ }
+
+ public void setStudyObject(final MaterialPE studyObject)
+ {
+ this.studyObject = studyObject;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.EXPERIMENT_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_TYPE_COLUMN, updatable = false)
+ public ExperimentTypePE getExperimentType()
+ {
+ return experimentType;
+ }
+
+ public void setExperimentType(final ExperimentTypePE experimentType)
+ {
+
+ this.experimentType = experimentType;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.INVALIDATION_COLUMN)
+ public InvalidationPE getInvalidation()
+ {
+ return invalidation;
+ }
+
+ public void setInvalidation(final InvalidationPE invalidation)
+ {
+
+ this.invalidation = invalidation;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "experiment")
+ private List<ExperimentPropertyPE> getExperimentProperties()
+ {
+ return properties;
+ }
+
+ private void setExperimentProperties(final List<ExperimentPropertyPE> properties)
+ {
+ this.properties = properties;
+ }
+
+ @Transient
+ public List<ExperimentPropertyPE> getProperties()
+ {
+ return getExperimentProperties();
+ }
+
+ public void setProperties(final List<ExperimentPropertyPE> properties)
+ {
+ for (final ExperimentPropertyPE experimentProperty : properties)
+ {
+ final ExperimentPE parent = experimentProperty.getExperiment();
+ if (parent != null)
+ {
+ parent.getProperties().remove(experimentProperty);
+ }
+ experimentProperty.setExperiment(this);
+ }
+ setExperimentProperties(properties);
+ }
+
+ @OneToMany(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_COLUMN, updatable = false)
+ public List<AttachmentPE> getAttachments()
+ {
+ return attachments;
+ }
+
+ public void setAttachments(final List<AttachmentPE> attachments)
+ {
+ this.attachments = attachments;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_COLUMN, updatable = false)
+ public List<ProcedurePE> getProcedures()
+ {
+ return procedures;
+ }
+
+ public void setProcedures(final List<ProcedurePE> procedures)
+ {
+ this.procedures = procedures;
+ }
+
+ @Transient
+ public ProcessingInstructionDTO[] getProcessingInstructions()
+ {
+ return processingInstructions;
+ }
+
+ public void setProcessingInstructions(final ProcessingInstructionDTO[] processingInstructions)
+ {
+ this.processingInstructions = processingInstructions;
+ }
+
+ @Transient
+ public Date getLastDataSetDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(lastDataSetDate);
+ }
+
+ public void setLastDataSetDate(final Date lastDataSetDate)
+ {
+ this.lastDataSetDate = lastDataSetDate;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_STORE_COLUMN)
+ public DataStorePE getDataStore()
+ {
+ return dataStore;
+ }
+
+ public void setDataStore(final DataStorePE dataStore)
+ {
+ this.dataStore = dataStore;
+ }
+
+ //
+ // Comparable
+ //
+
+ public int compareTo(final ExperimentPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ExperimentPE == false)
+ {
+ return false;
+ }
+ final ExperimentPE that = (ExperimentPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ builder.append(getProject(), that.getProject());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ builder.append(getProject());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("code", getCode());
+ builder.append("project", getProject());
+ builder.append("experimentType", getExperimentType());
+ builder.append("invalidation", getInvalidation());
+ return builder.toString();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPlatesFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPlatesFilter.java
new file mode 100644
index 00000000000..bd9734830d4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPlatesFilter.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A filter for all Plates which are assigned to a experiment.
+ *
+ * @author Basil Neff
+ */
+public final class ExperimentPlatesFilter implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /** If <code>true</code> only experiment with valid samples are returned. */
+ private boolean hideInvalidated;
+
+ public ExperimentPlatesFilter(final boolean hideInvalidated)
+ {
+ setHideInvalidated(hideInvalidated);
+ }
+
+ /**
+ * Returns, if the invalidated plates should filtered out. If <code>true</code> only
+ * experiment with valid samples are returned.
+ */
+ public final boolean isHideInvalidated()
+ {
+ return hideInvalidated;
+ }
+
+ public final void setHideInvalidated(final boolean hideInvalidated)
+ {
+ this.hideInvalidated = hideInvalidated;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("hideInvalidated", isHideInvalidated());
+ return builder.toString();
+ }
+}
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
new file mode 100644
index 00000000000..186cd5a8e05
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentPropertyPE.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing experiment property.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENT_PROPERTIES_TABLE)
+public class ExperimentPropertyPE extends EntityPropertyPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static ExperimentPropertyPE[] EMPTY_ARRAY = new ExperimentPropertyPE[0];
+
+ public static final List<ExperimentPropertyPE> EMPTY_LIST = Collections.emptyList();
+
+ private ExperimentPE experiment;
+
+ //
+ // EntityPropertyPE
+ //
+
+ @NotNull(message = ValidationMessages.EXPERIMENT_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = ExperimentTypePropertyTypePE.class)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_TYPE_PROPERTY_TYPE_COLUMN, updatable = false)
+ public EntityTypePropertyTypePE getEntityTypePropertyType()
+ {
+ return entityTypePropertyType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.EXPERIMENT_PROPERTY_SEQUENCE, sequenceName = SequenceNames.EXPERIMENT_PROPERTY_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.EXPERIMENT_PROPERTY_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ @Transient
+ public Long getEntityId()
+ {
+ return experiment.getId();
+ }
+
+ @Override
+ public void setEntityId(final Long entityId)
+ {
+ experiment = new ExperimentPE();
+ experiment.setId(entityId);
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_COLUMN, updatable = false)
+ public ExperimentPE getExperiment()
+ {
+ return experiment;
+ }
+
+ void setExperiment(final ExperimentPE experiment)
+ {
+ this.experiment = experiment;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentType.java
new file mode 100644
index 00000000000..8e5eff2b454
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentType.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * The type of an experiment.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ExperimentType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePE.java
new file mode 100644
index 00000000000..9feb7103bdd
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePE.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing type of experiment.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENT_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class ExperimentTypePE extends EntityTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ //
+ // EntityTypePE
+ //
+
+ @SequenceGenerator(name = SequenceNames.EXPERIMENT_TYPE_SEQUENCE, sequenceName = SequenceNames.EXPERIMENT_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.EXPERIMENT_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..0e19fcae1ab
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExperimentTypePropertyTypePE.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing experiment type - property type relation.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENT_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.ID_COLUMN }) })
+public class ExperimentTypePropertyTypePE extends EntityTypePropertyTypePE
+{
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final ExperimentTypePropertyTypePE[] EMPTY_ARRAY =
+ new ExperimentTypePropertyTypePE[0];
+
+ //
+ // EntityTypePropertyTypePE
+ //
+
+ @NotNull(message = ValidationMessages.EXPERIMENT_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = ExperimentTypePE.class)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_TYPE_COLUMN)
+ public EntityTypePE getEntityType()
+ {
+ return entityType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
new file mode 100644
index 00000000000..b1e22b67f22
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
@@ -0,0 +1,223 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.util.Date;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.common.types.BooleanOrUnknown;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about external data.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ExternalData extends ExtractableData
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String location;
+
+ private StorageFormat storageFormat;
+
+ private Date registrationDate;
+
+ private FileFormatType fileFormatType;
+
+ private DataSetType dataSetType;
+
+ private LocatorType locatorType;
+
+ private Procedure procedure;
+
+ private BooleanOrUnknown complete = BooleanOrUnknown.U;
+
+ private String associatedSampleCode;
+
+ /** Returns <code>dataSetType</code>. */
+ public final DataSetType getDataSetType()
+ {
+ return dataSetType;
+ }
+
+ /** Sets <code>dataSetType</code>. */
+ public final void setDataSetType(final DataSetType dataSetType)
+ {
+ this.dataSetType = dataSetType;
+ }
+
+ /** Returns <code>locator</code>. */
+ public final String getLocation()
+ {
+ return location;
+ }
+
+ /** Sets <code>locator</code>. */
+ public final void setLocation(final String locator)
+ {
+ this.location = locator;
+ }
+
+ /**
+ * Returns the storage format (proprietary or BDS) of this external data set.
+ */
+ public StorageFormat getStorageFormat()
+ {
+ return storageFormat;
+ }
+
+ /**
+ * Sets the storage format (proprietary or BDS) of this external data set.
+ */
+ public void setStorageFormat(final StorageFormat storageFormat)
+ {
+ this.storageFormat = storageFormat;
+ }
+
+ /** Returns the date when the data set has been registered to the database. */
+ public Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ /** Sets the date when the data set has been registered to the database. */
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ /** Returns <code>fileFormatType</code>. */
+ public final FileFormatType getFileFormatType()
+ {
+ return fileFormatType;
+ }
+
+ /** Sets <code>fileFormatType</code>. */
+ public final void setFileFormatType(final FileFormatType fileFormatType)
+ {
+ this.fileFormatType = fileFormatType;
+ }
+
+ /** Returns <code>locatorType</code>. */
+ public final LocatorType getLocatorType()
+ {
+ return locatorType;
+ }
+
+ /** Sets <code>locatorType</code>. */
+ public final void setLocatorType(final LocatorType locatorType)
+ {
+ this.locatorType = locatorType;
+ }
+
+ public Procedure getProcedure()
+ {
+ return procedure;
+ }
+
+ public final void setProcedure(final Procedure procedure)
+ {
+ this.procedure = procedure;
+ }
+
+ /**
+ * 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()
+ {
+ return complete;
+ }
+
+ /**
+ * 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)
+ {
+ this.complete = complete;
+ }
+
+ public String getAssociatedSampleCode()
+ {
+ return associatedSampleCode;
+ }
+
+ public void setAssociatedSampleCode(final String sampleCode)
+ {
+ this.associatedSampleCode = sampleCode;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ExternalData == false)
+ {
+ return false;
+ }
+ final ExternalData that = (ExternalData) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.location, location);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(location);
+ return builder.toHashCode();
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ @Override
+ public final int compareTo(final ExtractableData o)
+ {
+ final String thatLocation = ((ExternalData) o).location;
+ if (location == null)
+ {
+ return thatLocation == null ? 0 : -1;
+ }
+ if (thatLocation == null)
+ {
+ return 1;
+ }
+ return location.compareTo(thatLocation);
+ }
+
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..5996c342726
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.PrimaryKeyJoinColumn;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.types.BooleanOrUnknown;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.Location;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
+ * know about one EXTERNAL DATA.
+ * <p>
+ * This class is the <i>Java Object</i> representation of the corresponding data in the database.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.EXTERNAL_DATA_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
+ { ColumnNames.LOCATION_COLUMN, ColumnNames.LOCATOR_TYPE_COLUMN }))
+@PrimaryKeyJoinColumn(name = ColumnNames.DATA_ID_COLUMN)
+public final class ExternalDataPE extends DataPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /** An empty array of <code>ExternalData</code>. */
+ @SuppressWarnings("hiding")
+ public final static ExternalDataPE[] EMPTY_ARRAY = new ExternalDataPE[0];
+
+ private String location;
+
+ private VocabularyTermPE storageFormatVocabularyTerm;
+
+ private FileFormatTypePE fileFormatType;
+
+ private LocatorTypePE locatorType;
+
+ private BooleanOrUnknown complete = BooleanOrUnknown.U;
+
+ /**
+ * Returns the id of the locator type of the location of this external data, or
+ * <code>null</code> if not yet set.
+ */
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.LOCATOR_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.LOCATOR_TYPE_COLUMN, updatable = false)
+ public final LocatorTypePE getLocatorType()
+ {
+ return locatorType;
+ }
+
+ public void setLocatorType(final LocatorTypePE locatorType)
+ {
+ this.locatorType = locatorType;
+ }
+
+ /** Returns <code>locator</code>. */
+ @Column(name = ColumnNames.LOCATION_COLUMN)
+ @Length(max = 1024, message = ValidationMessages.LOCATION_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.LOCATION_NOT_NULL_MESSAGE)
+ @Location(relative = true, message = ValidationMessages.LOCATION_NOT_RELATIVE)
+ public String getLocation()
+ {
+ return location;
+ }
+
+ /** Sets <code>locator</code>. */
+ public void setLocation(final String location)
+ {
+ this.location = location;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.STORAGE_FORMAT_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.STORAGE_FORMAT_COLUMN, updatable = false)
+ public VocabularyTermPE getStorageFormatVocabularyTerm()
+ {
+ return storageFormatVocabularyTerm;
+ }
+
+ public void setStorageFormatVocabularyTerm(final VocabularyTermPE storageFormatVocabularyTerm)
+ {
+ this.storageFormatVocabularyTerm = storageFormatVocabularyTerm;
+ }
+
+ /**
+ * Returns the storage format (proprietary or BDS) of this external data set.
+ */
+ @Transient
+ public StorageFormat getStorageFormat()
+ {
+ return StorageFormat.tryGetFromCode(storageFormatVocabularyTerm.getCode());
+ }
+
+ /** Returns <code>fileFormatType</code>. */
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.FILE_FORMAT_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.FILE_FORMAT_TYPE, updatable = false)
+ public FileFormatTypePE getFileFormatType()
+ {
+ return fileFormatType;
+ }
+
+ /** Sets <code>fileFormatType</code>. */
+ public void setFileFormatType(final FileFormatTypePE fileFormatType)
+ {
+ this.fileFormatType = fileFormatType;
+ }
+
+ @NotNull(message = ValidationMessages.IS_COMPLETE_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.IS_COMPLETE_COLUMN)
+ @Enumerated(EnumType.STRING)
+ /**
+ * 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 BooleanOrUnknown getComplete()
+ {
+ return complete;
+ }
+
+ /**
+ * 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 void setComplete(final BooleanOrUnknown complete)
+ {
+ this.complete = complete;
+ }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..e7cf5d9721d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExtractableData.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Date;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A basic {@link ExternalData} object.
+ * <p>
+ * {@link ExternalData} extends this class and completes it with additional fields.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public class ExtractableData extends Code<ExtractableData>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private Date productionDate;
+
+ private String dataProducerCode;
+
+ private String parentDataSetCode;
+
+ /**
+ * 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>.
+ */
+ public Date getProductionDate()
+ {
+ return productionDate;
+ }
+
+ /**
+ * Sets the date when the measurement / calculation that produced this external data set has
+ * been performed.
+ */
+ public void setProductionDate(final Date productionDate)
+ {
+ this.productionDate = productionDate;
+ }
+
+ /**
+ * 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>.
+ */
+ public String getDataProducerCode()
+ {
+ return dataProducerCode;
+ }
+
+ /**
+ * 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)
+ {
+ this.dataProducerCode = dataProducerCode;
+ }
+
+ public final String getParentDataSetCode()
+ {
+ return parentDataSetCode;
+ }
+
+ public final void setParentDataSetCode(String parentDataSetCode)
+ {
+ this.parentDataSetCode = parentDataSetCode;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileAttachmentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileAttachmentPE.java
new file mode 100644
index 00000000000..0d194c4a53a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileAttachmentPE.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Contains information about an attachment together with its content.
+ *
+ * @author Bernd Rinn
+ */
+@Entity
+@Table(name = TableNames.EXPERIMENT_ATTACHMENTS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.EXPERIMENT_COLUMN, ColumnNames.FILE_NAME_COLUMN, ColumnNames.VERSION_COLUMN }) })
+public class FileAttachmentPE extends AbstractAttachmentPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private byte[] value;
+
+ /**
+ * Returns bytes blob stored in the attachment.
+ */
+ @NotNull(message = ValidationMessages.ATTACHMENT_CONTENT_NOT_NULL_MESSAGE)
+ public byte[] getValue()
+ {
+ return value;
+ }
+
+ public void setValue(byte[] value)
+ {
+ this.value = value;
+ }
+
+ @Override
+ public final String toString()
+ {
+ return getClass().getSimpleName() + "{len(value)="
+ + (value != null ? value.length : "<null>") + ",attachment=" + super.toString()
+ + "}";
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatType.java
new file mode 100644
index 00000000000..facdd283e7c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatType.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a file format type.
+ *
+ * @author Christian Ribeaud
+ */
+public final class FileFormatType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final String DEFAULT_FILE_FORMAT_TYPE_CODE = "TIFF";
+
+ public FileFormatType()
+ {
+ }
+
+ public FileFormatType(final String code)
+ {
+ setCode(code);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatTypePE.java
new file mode 100644
index 00000000000..0beec72892a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/FileFormatTypePE.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence Entity representing the type of file format.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.FILE_FORMAT_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class FileFormatTypePE extends AbstractTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private DatabaseInstancePE databaseInstance;
+
+ @SequenceGenerator(name = SequenceNames.FILE_FORMAT_TYPE_SEQUENCE, sequenceName = SequenceNames.FILE_FORMAT_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.FILE_FORMAT_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ public FileFormatTypePE()
+ {
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/GroupPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/GroupPE.java
new file mode 100644
index 00000000000..611244ac741
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/GroupPE.java
@@ -0,0 +1,226 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistence Entity</i> which represents a group.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.GROUPS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class GroupPE extends HibernateAbstractRegistratrationHolder implements
+ IIdAndCodeHolder, Comparable<GroupPE>, Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final GroupPE[] EMPTY_ARRAY = new GroupPE[0];
+
+ private transient Long id;
+
+ private String code;
+
+ private String description;
+
+ private PersonPE groupLeader;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private GroupPE parent;
+
+ // null if unknown
+ private Boolean home;
+
+ private DataStorePE dataStore;
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_STORE_COLUMN, updatable = false)
+ public final DataStorePE getDataStore()
+ {
+ return dataStore;
+ }
+
+ public final void setDataStore(final DataStorePE dataStorePE)
+ {
+ this.dataStore = dataStorePE;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 250, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PERSON_LEADER_COLUMN, updatable = false)
+ public final PersonPE getGroupLeader()
+ {
+ return groupLeader;
+ }
+
+ public final void setGroupLeader(final PersonPE groupLeader)
+ {
+ this.groupLeader = groupLeader;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.GROUP_PARENT_COLUMN, updatable = false)
+ public final GroupPE getParent()
+ {
+ return parent;
+ }
+
+ public final void setParent(final GroupPE parent)
+ {
+ this.parent = parent;
+ }
+
+ @Transient
+ public final Boolean isHome()
+ {
+ return home;
+ }
+
+ public final void setHome(final Boolean home)
+ {
+ this.home = home;
+ }
+
+ //
+ // IIdAndCodeHolder
+ //
+
+ @SequenceGenerator(name = SequenceNames.GROUP_SEQUENCE, sequenceName = SequenceNames.GROUP_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.GROUP_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public final String getCode()
+ {
+ return code;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof GroupPE == false)
+ {
+ return false;
+ }
+ final GroupPE that = (GroupPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(code, that.code);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(code);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Compare
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(final GroupPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistratrationHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistratrationHolder.java
new file mode 100644
index 00000000000..f27d283f57b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/HibernateAbstractRegistratrationHolder.java
@@ -0,0 +1,116 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import javax.persistence.Column;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.MappedSuperclass;
+import javax.persistence.Transient;
+
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+
+
+/**
+ * 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).
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+@MappedSuperclass
+public abstract class HibernateAbstractRegistratrationHolder implements IRegistratorHolder,
+ Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Person who registered this entity.
+ * <p>
+ * This is specified at insert time.
+ * </p>
+ */
+ private PersonPE registrator;
+
+ /**
+ * Registration date of this entity.
+ * <p>
+ * This is specified at insert time.
+ * </p>
+ */
+ 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.
+ */
+ public final static Date getDate(final Date date)
+ {
+ if (date == null)
+ {
+ return null;
+ }
+ final String packageName = date.getClass().getPackage().getName();
+ if (packageName.equals("java.sql"))
+ {
+ return new Date(date.getTime());
+ }
+ return date;
+ }
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false, updatable = false)
+ @Generated(GenerationTime.INSERT)
+ public Date getRegistrationDate()
+ {
+ return getDate(registrationDate);
+ }
+
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ //
+ // IRegistratorHolder
+ //
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PERSON_REGISTERER_COLUMN, updatable = false)
+ public PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ public void setRegistrator(final PersonPE registrator)
+ {
+ this.registrator = registrator;
+ }
+
+ @Transient
+ public Long getRegistratorID()
+ {
+ return registrator.getId();
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityPropertiesHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityPropertiesHolder.java
new file mode 100644
index 00000000000..60d9d7e4929
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityPropertiesHolder.java
@@ -0,0 +1,38 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.List;
+
+/**
+ * Interface of classes having entity properties.
+ *
+ * @author Christian Ribeaud
+ */
+public interface IEntityPropertiesHolder<T extends EntityPropertyPE>
+{
+ /**
+ * Gets the entity properties.
+ */
+ public List<T> getProperties();
+
+ /**
+ * Sets the entity properties.
+ */
+ public void setProperties(final List<T> properties);
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityProperty.java
new file mode 100644
index 00000000000..4b8325d087f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityProperty.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+
+/**
+ * An entity property is composed of:
+ * <ol>
+ * <li>{@link IIdHolder#getId()}</li>
+ * <li>{@link #getEntityId()}</li>
+ * <li>{@link #getEntityTypePropertyType()}</li>
+ * </ol>
+ *
+ * @author Christian Ribeaud
+ */
+public interface IEntityProperty extends IIdHolder
+{
+ /**
+ * Returns the entity type property type for this entity property.
+ */
+ public EntityTypePropertyTypePE getEntityTypePropertyType();
+
+ /**
+ * Returns the entity id for this entity property.
+ */
+ public Long getEntityId();
+
+ /**
+ * Return untyped value or <code>null</code>.
+ */
+ public String tryGetUntypedValue();
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityType.java
new file mode 100644
index 00000000000..d133c1a8383
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityType.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+/**
+ * Getters and Setters of all DTOs which are Entity Types (e.g. Material Type, Experiment Type).
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IEntityType
+{
+
+ /** Returns the code of this type. */
+ public String getCode();
+
+ /** Sets the code of this type. */
+ public void setCode(final String code);
+
+ /** Returns a description of this type. */
+ public String getDescription();
+
+ /** Sets the description of this type. */
+ public void setDescription(final String description);
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityTypePropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityTypePropertyType.java
new file mode 100644
index 00000000000..9e9c4ba17a7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IEntityTypePropertyType.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+
+/**
+ * An entity property is composed of:
+ * <ol>
+ * <li>{@link IIdHolder#getId()}</li>
+ * <li>{@link #getEntityType()}</li>
+ * </ol>
+ *
+ * @author Christian Ribeaud
+ */
+public interface IEntityTypePropertyType extends IIdHolder
+{
+
+ /**
+ * Returns the entity type for this entity type property type.
+ */
+ public EntityTypePE getEntityType();
+}
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
new file mode 100644
index 00000000000..723d198abb8
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdAndCodeHolder.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+
+/**
+ * Read-only interface for beans with a (unique) business code as a string and a unique technical
+ * ID.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IIdAndCodeHolder extends IIdHolder
+{
+ /**
+ * Returns the business code of this instance.
+ */
+ public String getCode();
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdHolder.java
new file mode 100644
index 00000000000..61cf20cbfc3
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IIdHolder.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * Read-only interface for beans with a unique technical Id.
+ *
+ * @author Christian Ribeaud
+ */
+public interface IIdHolder
+{
+
+ /**
+ * Returns the technical ID of this instance.
+ *
+ * @return <code>null</code> if there is no Id.
+ */
+ public Long getId();
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IRegistratorHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IRegistratorHolder.java
new file mode 100644
index 00000000000..7d569c24347
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IRegistratorHolder.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+
+/**
+ * Implementations are aware of the registrator.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IRegistratorHolder
+{
+
+ /**
+ * Returns registratorID.
+ */
+ public Long getRegistratorID();
+
+ /**
+ * Returns the registrator.
+ *
+ * @return <code>null</code> if undefined.
+ */
+ public PersonPE getRegistrator();
+
+ /**
+ * Sets the person who has registered something.
+ *
+ * @throws AssertionError if {@link #getRegistratorID()} is not <code>null</code> but unequal
+ * <code>registrator.getId()</code>.
+ */
+ public void setRegistrator(final PersonPE registrator);
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ISimpleEntityPropertiesHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ISimpleEntityPropertiesHolder.java
new file mode 100644
index 00000000000..76fee88d1fe
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ISimpleEntityPropertiesHolder.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * Interface of classes having entity properties.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ISimpleEntityPropertiesHolder
+{
+ /**
+ * Gets the entity properties.
+ */
+ public SimpleEntityProperty[] getProperties();
+
+ /**
+ * Sets the entity properties.
+ */
+ public void setProperties(final SimpleEntityProperty[] properties);
+
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..d07ea6eec9c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/IUntypedValueSetter.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * Holds the untyped property value.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IUntypedValueSetter
+{
+
+ /** Internally sets the untyped property value. */
+ public void setUntypedValue(final String valueOrNull, final Long vocabularyTermIdOrNull);
+
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Id.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Id.java
new file mode 100644
index 00000000000..cf25ee05305
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Id.java
@@ -0,0 +1,91 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * An abstract class which based equality and comparability on in its unique field <code>id</code>.
+ *
+ * @author Christian Ribeaud
+ */
+public class Id implements Serializable, IIdHolder
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static Long getAndCheckID(final IIdHolder objectWithID, final Long id)
+ {
+ if (objectWithID == null)
+ {
+ return id;
+ }
+ assert id == null || id.equals(objectWithID.getId());
+ return objectWithID.getId();
+ }
+
+ transient private Long id;
+
+ /**
+ * Sets id.
+ *
+ * @param id New value. Can be <code>null</code>.
+ */
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ //
+ // IIdHolder
+ //
+
+ public Long getId()
+ {
+ return id;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ return EqualsBuilder.reflectionEquals(this, obj);
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return HashCodeBuilder.reflectionHashCode(this);
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
new file mode 100644
index 00000000000..24acb05d946
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Class representing invalidation.
+ *
+ * @author Franz-Josef Elmer
+ */
+@Entity
+@Table(name = TableNames.INVALIDATION_TABLE)
+public class InvalidationPE extends HibernateAbstractRegistratrationHolder implements IIdHolder,
+ Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ private String reason;
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.INVALIDATION_SEQUENCE, sequenceName = SequenceNames.INVALIDATION_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.INVALIDATION_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @Length(max = 250, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public String getReason()
+ {
+ return reason;
+ }
+
+ public void setReason(final String description)
+ {
+ this.reason = description;
+ }
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof InvalidationPE == false)
+ {
+ return false;
+ }
+ final InvalidationPE that = (InvalidationPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(id, that.id);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(id);
+ 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/LimitFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
new file mode 100644
index 00000000000..8dc0224153f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LimitFilter.java
@@ -0,0 +1,102 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * 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.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class LimitFilter extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private final static int NO_LIMIT = -1;
+
+ public LimitFilter(int limit)
+ {
+ this.limit = limit;
+ }
+
+ /**
+ * Creates the empty filter.
+ */
+ public LimitFilter()
+ {
+ this(NO_LIMIT);
+ }
+
+ public final static LimitFilter createEmpty()
+ {
+ return new LimitFilter();
+ }
+
+ /**
+ * The maximum number of items the returned list should be composed of.
+ */
+ private int limit;
+
+ /** At which index to apply {@link #limit}. */
+ private int start;
+
+ /**
+ * Returns <code>limit</code>.
+ * <p>
+ * Never returns a value smaller than <code>NO_LIMIT</code>.
+ * </p>
+ */
+ public final int getLimit()
+ {
+ return Math.max(limit, NO_LIMIT);
+ }
+
+ public final void setLimit(int limit)
+ {
+ this.limit = limit;
+ }
+
+ /**
+ * Returns <code>limit</code>.
+ * <p>
+ * Never returns a negative value.
+ * </p>
+ */
+ public final int getStart()
+ {
+ return Math.max(start, 0);
+ }
+
+ public final void setStart(int start)
+ {
+ this.start = start;
+ }
+
+ /** @return true if the filter has no effect */
+ public final boolean isEmpty()
+ {
+ return this.equals(createEmpty());
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorType.java
new file mode 100644
index 00000000000..a5a6f593624
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorType.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
+ * know about a locator type.
+ *
+ * @author Christian Ribeaud
+ */
+public final class LocatorType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final String DEFAULT_LOCATOR_TYPE_CODE = "RELATIVE_LOCATION";
+
+ public LocatorType()
+ {
+ }
+
+ public LocatorType(final String code)
+ {
+ setCode(code);
+ }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..98d7dd89800
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LocatorTypePE.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence Entity representing type of locator.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.LOCATOR_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN }) })
+public final class LocatorTypePE extends AbstractTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ @SequenceGenerator(name = SequenceNames.LOCATOR_TYPE_SEQUENCE, sequenceName = SequenceNames.LOCATOR_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.LOCATOR_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialBatchPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialBatchPE.java
new file mode 100644
index 00000000000..530c9b80a7e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialBatchPE.java
@@ -0,0 +1,158 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which contains any information we would like to
+ * know about one material batch.
+ * <p>
+ * This class is the <i>Java Object</i> representation of the corresponding data in the database.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.MATERIAL_BATCHES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.MATERIAL_COLUMN }) })
+public final class MaterialBatchPE extends HibernateAbstractRegistratrationHolder implements
+ IIdAndCodeHolder, Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private transient Long id;
+
+ private String code;
+
+ private Double amount;
+
+ private transient List<SamplePE> samples;
+
+ private MaterialPE material;
+
+ /**
+ * Creates an instance for specified technical ID of the person who has registered the material
+ * batch.
+ */
+ public MaterialBatchPE(final Long registratorID)
+ {
+ PersonPE registrator = new PersonPE();
+ registrator.setId(registratorID);
+ setRegistrator(registrator);
+ }
+
+ public MaterialBatchPE()
+ {
+ }
+
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ /** Returns <code>code</code>. */
+ public final String getCode()
+ {
+ return code;
+ }
+
+ /** Sets <code>code</code>. */
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @Column(name = ColumnNames.AMOUNT_COLUMN)
+ public final Double getAmount()
+ {
+ return amount;
+ }
+
+ public final void setAmount(final Double ammount)
+ {
+ this.amount = ammount;
+ }
+
+ @ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
+ @JoinTable(name = TableNames.SAMPLE_MATERIAL_BATCHES_TABLE, joinColumns = @JoinColumn(name = ColumnNames.MATERIAL_BATCH_COLUMN), inverseJoinColumns = @JoinColumn(name = ColumnNames.SAMPLE_COLUMN))
+ public List<SamplePE> getSamples()
+ {
+ return samples;
+ }
+
+ public void setSamples(List<SamplePE> samples)
+ {
+ this.samples = samples;
+ }
+
+ /**
+ * @return <code>null</code> when undefined.
+ */
+ @Transient
+ public final Long getMaterialID()
+ {
+ return material == null ? null : material.getId();
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @NotNull(message = ValidationMessages.MATERIAL_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.MATERIAL_COLUMN, updatable = false)
+ public final MaterialPE getMaterial()
+ {
+ return material;
+ }
+
+ public final void setMaterial(final MaterialPE material)
+ {
+ this.material = material;
+ }
+
+ @SequenceGenerator(name = SequenceNames.MATERIAL_BATCH_SEQUENCE, sequenceName = SequenceNames.MATERIAL_BATCH_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.MATERIAL_BATCH_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..ea92bea498a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPE.java
@@ -0,0 +1,232 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistent Entity</i> which is a material.
+ *
+ * @author Franz-Josef Elmer
+ */
+@Entity
+@Table(name = TableNames.MATERIALS_TABLE, uniqueConstraints = @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.MATERIAL_TYPE_COLUMN,
+ ColumnNames.DATABASE_INSTANCE_COLUMN }))
+public class MaterialPE extends HibernateAbstractRegistratrationHolder implements IIdAndCodeHolder,
+ Comparable<MaterialPE>, IEntityPropertiesHolder<MaterialPropertyPE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ private MaterialTypePE materialType;
+
+ private String code;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private List<MaterialPropertyPE> properties = MaterialPropertyPE.EMPTY_LIST;
+
+ public static final MaterialPE[] EMPTY_ARRAY = new MaterialPE[0];
+
+ private MaterialPE inhibitorOf;
+
+ public MaterialPE()
+ {
+ }
+
+ @Id
+ @SequenceGenerator(name = SequenceNames.MATERIAL_SEQUENCE, sequenceName = SequenceNames.MATERIAL_SEQUENCE, allocationSize = 1)
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.MATERIAL_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.MATERIAL_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.MATERIAL_TYPE_COLUMN, updatable = false)
+ public MaterialTypePE getMaterialType()
+ {
+ return materialType;
+ }
+
+ public void setMaterialType(final MaterialTypePE materialType)
+ {
+ this.materialType = materialType;
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.INHIBITOR_OF_COLUMN)
+ public MaterialPE getInhibitorOf()
+ {
+ return inhibitorOf;
+ }
+
+ public void setInhibitorOf(final MaterialPE inhibitorOf)
+ {
+ this.inhibitorOf = inhibitorOf;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "material")
+ @Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+ private List<MaterialPropertyPE> getMaterialProperties()
+ {
+ return properties;
+ }
+
+ private void setMaterialProperties(final List<MaterialPropertyPE> properties)
+ {
+ this.properties = properties;
+ }
+
+ //
+ // IEntityPropertiesHolder
+ //
+
+ @Transient
+ public List<MaterialPropertyPE> getProperties()
+ {
+ return getMaterialProperties();
+ }
+
+ public void setProperties(final List<MaterialPropertyPE> properties)
+ {
+ for (MaterialPropertyPE materialProperty : properties)
+ {
+ MaterialPE parent = materialProperty.getMaterial();
+ if (parent != null)
+ {
+ parent.getProperties().remove(materialProperty);
+ }
+ materialProperty.setMaterial(this);
+ }
+ setMaterialProperties(properties);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof MaterialPE == false)
+ {
+ return false;
+ }
+ final MaterialPE that = (MaterialPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ builder.append(getMaterialType(), that.getMaterialType());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ builder.append(getMaterialType());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("code", getCode());
+ builder.append("materialType", getMaterialType());
+ return builder.toString();
+ }
+
+ //
+ // Comparable
+ //
+
+ public final int compareTo(final MaterialPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+}
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
new file mode 100644
index 00000000000..6abd75a346e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialPropertyPE.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.hibernate.annotations.Cache;
+import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing material property.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.MATERIAL_PROPERTIES_TABLE)
+@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
+public class MaterialPropertyPE extends EntityPropertyPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static MaterialPropertyPE[] EMPTY_ARRAY = new MaterialPropertyPE[0];
+
+ public static final List<MaterialPropertyPE> EMPTY_LIST =
+ Collections.<MaterialPropertyPE> emptyList();
+
+ private MaterialPE material;
+
+ //
+ // EntityPropertyPE
+ //
+
+ @NotNull(message = ValidationMessages.MATERIAL_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = MaterialTypePropertyTypePE.class)
+ @JoinColumn(name = ColumnNames.MATERIAL_TYPE_PROPERTY_TYPE_COLUMN, updatable = false)
+ public EntityTypePropertyTypePE getEntityTypePropertyType()
+ {
+ return entityTypePropertyType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.MATERIAL_PROPERTY_SEQUENCE, sequenceName = SequenceNames.MATERIAL_PROPERTY_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.MATERIAL_PROPERTY_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ // TODO 2008-09-02, Franz-Josef Elmer: Remove this method when
+ // EntityPropertyTypeDAO.createPropertyValue() is no longer used.
+ @Transient
+ public Long getEntityId()
+ {
+ return material.getId();
+ }
+
+ // TODO 2008-09-02, Franz-Josef Elmer: Remove this method when
+ // EntityPropertyTypeDAO.createPropertyValue() is no longer used.
+ @Override
+ public void setEntityId(final Long entityId)
+ {
+ material = new MaterialPE();
+ material.setId(entityId);
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.MATERIAL_COLUMN, updatable = false)
+ public MaterialPE getMaterial()
+ {
+ return material;
+ }
+
+ void setMaterial(final MaterialPE materialID)
+ {
+ this.material = materialID;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePE.java
new file mode 100644
index 00000000000..a3f387ac580
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePE.java
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing type of material.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.MATERIAL_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class MaterialTypePE extends EntityTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ //
+ // EntityTypePE
+ //
+
+ @SequenceGenerator(name = SequenceNames.MATERIAL_TYPE_SEQUENCE, sequenceName = SequenceNames.MATERIAL_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.MATERIAL_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..9541a6f2568
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/MaterialTypePropertyTypePE.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing material type - property type relation.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.MATERIAL_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.ID_COLUMN }) })
+public class MaterialTypePropertyTypePE extends EntityTypePropertyTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final MaterialTypePropertyTypePE[] EMPTY_ARRAY =
+ new MaterialTypePropertyTypePE[0];
+
+ public MaterialTypePropertyTypePE()
+ {
+ }
+
+ //
+ // EntityTypePropertyTypePE
+ //
+
+ @NotNull(message = ValidationMessages.MATERIAL_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = MaterialTypePE.class)
+ @JoinColumn(name = ColumnNames.MATERIAL_TYPE_COLUMN)
+ public EntityTypePE getEntityType()
+ {
+ return entityType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE)
+ @Column(insertable = false, updatable = false)
+ public Long getId()
+ {
+ return id;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExperiment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExperiment.java
new file mode 100644
index 00000000000..15162ac0234
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExperiment.java
@@ -0,0 +1,135 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * The full description of a new experiment. Used when registering an experiment to the LIMS.
+ *
+ * @author Bernd Rinn
+ */
+public final class NewExperiment extends AbstractEntity<NewExperiment>
+{
+
+ public final static NewExperiment[] EMPTY_ARRAY = new NewExperiment[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private ProjectIdentifier projectIdentifier;
+
+ private String studyObjectCode;
+
+ private String studyObjectTypeCode;
+
+ private String experimentTypeCode;
+
+ private String description;
+
+ /**
+ * Processing instructions related to this experiment.
+ * <p>
+ * Processing instructions are procedure type specific.
+ * </p>
+ */
+ private NewProcessingInstruction[] processingInstructions = new NewProcessingInstruction[0];
+
+ /** List of cell plates that are related to this experiment. */
+ private SampleIdentifier[] cellPlates = SampleIdentifier.EMPTY_ARRAY;
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ public EntityType getEntityType()
+ {
+ return new EntityType(experimentTypeCode, "Experiment of type " + experimentTypeCode);
+ }
+
+ public final String getExperimentTypeCode()
+ {
+ return experimentTypeCode;
+ }
+
+ public final void setExperimentTypeCode(final String experimentTypeCode)
+ {
+ this.experimentTypeCode = experimentTypeCode;
+ }
+
+ public final String getStudyObjectCode()
+ {
+ return studyObjectCode;
+ }
+
+ public final void setStudyObjectCode(final String studyObjectCode)
+ {
+ this.studyObjectCode = studyObjectCode;
+ }
+
+ public ProjectIdentifier getProjectIdentifier()
+ {
+ return projectIdentifier;
+ }
+
+ public final void setProjectIdentifier(final ProjectIdentifier projectIdentifier)
+ {
+ this.projectIdentifier = projectIdentifier;
+ }
+
+ /** Never returns <code>null</code> but could return an empty array. */
+ public final SampleIdentifier[] getCellPlates()
+ {
+ return cellPlates == null ? SampleIdentifier.EMPTY_ARRAY : cellPlates;
+ }
+
+ public final void setCellPlates(final SampleIdentifier[] cellPlateCodes)
+ {
+ this.cellPlates = cellPlateCodes;
+ }
+
+ public final void setProcessingInstructions(
+ final NewProcessingInstruction[] processingInstructions)
+ {
+ this.processingInstructions = processingInstructions;
+ }
+
+ /** Never returns <code>null</code> but could return an empty array. */
+ public final NewProcessingInstruction[] getProcessingInstructions()
+ {
+ return processingInstructions == null ? new NewProcessingInstruction[0]
+ : processingInstructions;
+ }
+
+ public final String getStudyObjectTypeCode()
+ {
+ return studyObjectTypeCode;
+ }
+
+ public final void setStudyObjectTypeCode(final String studyObjectTypeCode)
+ {
+ this.studyObjectTypeCode = studyObjectTypeCode;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewMaterial.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewMaterial.java
new file mode 100644
index 00000000000..d580dd6d3c6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewMaterial.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Class representing a new material.
+ *
+ * @author Franz-Josef Elmer
+ * @author Tomasz Pylak
+ */
+public final class NewMaterial extends AbstractEntity<NewMaterial>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private EntityType materialType;
+
+ private NewMaterial inhibitorOfOrNull;
+
+ public NewMaterial(final String code, final EntityType materialType)
+ {
+ setCode(code);
+ this.materialType = materialType;
+ this.inhibitorOfOrNull = null;
+ setProperties(new SimpleEntityProperty[0]);
+ }
+
+ public NewMaterial()
+ {
+ }
+
+ public NewMaterial getInhibitorOf()
+ {
+ return inhibitorOfOrNull;
+ }
+
+ public void setInhibitorOf(final NewMaterial inhibitorOfOrNull)
+ {
+ this.inhibitorOfOrNull = inhibitorOfOrNull;
+ }
+
+ public final EntityType getMaterialType()
+ {
+ return materialType;
+ }
+
+ public final void setMaterialType(final EntityType materialType)
+ {
+ this.materialType = materialType;
+ }
+
+ //
+ // AbstractEntity
+ //
+
+ public final EntityType getEntityType()
+ {
+ return getMaterialType();
+ }
+}
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
new file mode 100644
index 00000000000..05ec1d2e401
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewProcessingInstruction.java
@@ -0,0 +1,93 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Processing instruction is a specific experiment attachment.
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class NewProcessingInstruction extends AbstractHashable implements Serializable
+{
+ public final static NewProcessingInstruction[] EMPTY_ARRAY = new NewProcessingInstruction[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String procedureTypeCode;
+
+ private String path;
+
+ private String description;
+
+ private ProcessingParameters parameters;
+
+ public final String getPath()
+ {
+ return path;
+ }
+
+ @BeanProperty(label = "path")
+ public final void setPath(final String path)
+ {
+ this.path = path;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ @BeanProperty(optional = true, label = "description")
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ /** can be null */
+ public final byte[] getParameters()
+ {
+ return parameters == null ? null : parameters.getProcessingParameters();
+ }
+
+ public String getParametersFileDescription()
+ {
+ return parameters == null ? null : parameters.getFileDescription();
+ }
+
+ @BeanProperty(optional = true, label = "parameters")
+ public final void setProcessingParameters(final ProcessingParameters parameters)
+ {
+ this.parameters = parameters;
+ }
+
+ public final String getProcedureTypeCode()
+ {
+ return procedureTypeCode;
+ }
+
+ @BeanProperty(label = "procedure_type")
+ public final void setProcedureTypeCode(final String procedureTypeCode)
+ {
+ this.procedureTypeCode = procedureTypeCode;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewPropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewPropertyType.java
new file mode 100644
index 00000000000..5ff794a292f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewPropertyType.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * <i>Bean</i> for registering new property type.
+ * <p>
+ * It is used by the parser. This explains the {@link BeanProperty} annotations.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class NewPropertyType extends Code<NewPropertyType>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final NewPropertyType[] EMPTY_ARRAY = new NewPropertyType[0];
+
+ private String type;
+
+ private String description;
+
+ private String label;
+
+ private String vocabularyCode;
+
+ @BeanProperty(label = "data_type")
+ public final void setType(final String type)
+ {
+ this.type = type;
+ }
+
+ @BeanProperty(label = "description")
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ @BeanProperty(label = "label")
+ public final void setLabel(final String label)
+ {
+ this.label = label;
+ }
+
+ @BeanProperty(optional = true, label = "vocabulary")
+ public void setVocabularyCode(final String vocabularyCode)
+ {
+ this.vocabularyCode = vocabularyCode;
+ }
+
+ public final String getType()
+ {
+ return type;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final String getLabel()
+ {
+ return label;
+ }
+
+ public final String getVocabularyCode()
+ {
+ return vocabularyCode;
+ }
+
+ //
+ // Code
+ //
+
+ @Override
+ public final String toString()
+ {
+ return getCode();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewRoleAssignment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewRoleAssignment.java
new file mode 100644
index 00000000000..c1cbf11c72d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewRoleAssignment.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+
+/**
+ * <i>Bean</i> for registering new role assignments.
+ * <p>
+ * It is used by the parser. This explains the {@link BeanProperty} annotations.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class NewRoleAssignment extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final NewRoleAssignment[] EMPTY_ARRAY = new NewRoleAssignment[0];
+
+ private DatabaseInstanceIdentifier databaseInstanceIdentifier;
+
+ private GroupIdentifier groupIdentifier;
+
+ private String userId;
+
+ private RoleCode role;
+
+ public final RoleCode getRole()
+ {
+ return role;
+ }
+
+ @BeanProperty(label = "role")
+ public final void setRole(final RoleCode role)
+ {
+ this.role = role;
+ }
+
+ public final DatabaseInstanceIdentifier getDatabaseInstanceIdentifier()
+ {
+ return databaseInstanceIdentifier;
+ }
+
+ @BeanProperty(label = "instance")
+ public final void setDatabaseInstanceIdentifier(
+ final DatabaseInstanceIdentifier databaseInstanceIdentifier)
+ {
+ this.databaseInstanceIdentifier = databaseInstanceIdentifier;
+ }
+
+ public final GroupIdentifier getGroupIdentifier()
+ {
+ return groupIdentifier;
+ }
+
+ @BeanProperty(label = "group")
+ public final void setGroupIdentifier(final GroupIdentifier groupIdentifier)
+ {
+ this.groupIdentifier = groupIdentifier;
+ }
+
+ public final String getUserId()
+ {
+ return userId;
+ }
+
+ @BeanProperty(label = "user")
+ public final void setUserId(final String userId)
+ {
+ this.userId = userId;
+ }
+
+ //
+ // AbstractHashable
+ //
+
+ @Override
+ public final String toString()
+ {
+ final StringBuilder builder = new StringBuilder();
+ builder.append(userId).append("=").append(role).append("@");
+ if (getGroupIdentifier() == null)
+ {
+ builder.append(getDatabaseInstanceIdentifier());
+ } else
+ {
+ builder.append(getGroupIdentifier());
+ }
+ return builder.toString();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSample.java
new file mode 100644
index 00000000000..19b1866d7d4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSample.java
@@ -0,0 +1,145 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.SampleTypeCode;
+
+/**
+ * The full description of a new sample component.
+ * <p>
+ * Used when registering a sample component to the LIMS.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class NewSample implements Serializable, ISimpleEntityPropertiesHolder
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private SampleIdentifier sampleIdentifier;
+
+ private SampleTypeCode sampleTypeCode;
+
+ private SampleIdentifier parentSampleIdentifier;
+
+ private SampleIdentifier controlLayoutIdentifierOrNull;
+
+ private SimpleEntityProperty[] properties;
+
+ public NewSample()
+ {
+ }
+
+ public NewSample(final SampleIdentifier sampleIdentifier, final SampleTypeCode sampleTypeCode,
+ final SampleIdentifier controlLayoutOrNull)
+ {
+ this.sampleIdentifier = sampleIdentifier;
+ this.controlLayoutIdentifierOrNull = controlLayoutOrNull;
+ this.sampleTypeCode = sampleTypeCode;
+ }
+
+ public SimpleEntityProperty[] getProperties()
+ {
+ return properties;
+ }
+
+ public void setProperties(final SimpleEntityProperty[] properties)
+ {
+ this.properties = properties;
+ }
+
+ public final SampleIdentifier getSampleIdentifier()
+ {
+ return sampleIdentifier;
+ }
+
+ public final SampleIdentifier getParentSampleIdentifier()
+ {
+ return parentSampleIdentifier;
+ }
+
+ public final void setParentSampleIdentifier(final SampleIdentifier parentSampleIdentifier)
+ {
+ this.parentSampleIdentifier = parentSampleIdentifier;
+ }
+
+ public final SampleTypeCode getSampleTypeCode()
+ {
+ return sampleTypeCode;
+ }
+
+ /**
+ * Return the <i>Control Layout</i> {@link SampleIdentifier}.
+ *
+ * @return <code>null</code> if not specified.
+ */
+ public final SampleIdentifier getControlLayoutIdentifier()
+ {
+ return controlLayoutIdentifierOrNull;
+ }
+
+ public final void setControlLayoutIdentifier(final SampleIdentifier controlLayoutIdentifier)
+ {
+ this.controlLayoutIdentifierOrNull = controlLayoutIdentifier;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof NewSample == false)
+ {
+ return false;
+ }
+ final NewSample that = (NewSample) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.getSampleIdentifier(), getSampleIdentifier());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getSampleIdentifier());
+ 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/NewSampleComponent.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
new file mode 100644
index 00000000000..b8f48dfaac8
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponent.java
@@ -0,0 +1,49 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * The full description of a new sample component.
+ * <p>
+ * Used when registering a sample component to the LIMS.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class NewSampleComponent extends NewSampleComponentWithFixedMaterialType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ @SuppressWarnings("hiding")
+ public final static NewSampleComponent[] EMPTY_ARRAY = new NewSampleComponent[0];
+
+ private String materialTypeCode;
+
+ public final String getMaterialTypeCode()
+ {
+ return materialTypeCode;
+ }
+
+ @BeanProperty(label = "material_type")
+ public final void setMaterialTypeCode(final String materialTypeCode)
+ {
+ this.materialTypeCode = materialTypeCode;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponentWithFixedMaterialType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponentWithFixedMaterialType.java
new file mode 100644
index 00000000000..0b639c936f6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewSampleComponentWithFixedMaterialType.java
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * The full description of a new sample component.
+ * <p>
+ * Used when registering a sample component to the LIMS.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public class NewSampleComponentWithFixedMaterialType extends
+ Code<NewSampleComponentWithFixedMaterialType>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static NewSampleComponentWithFixedMaterialType[] EMPTY_ARRAY =
+ new NewSampleComponentWithFixedMaterialType[0];
+
+ private String materialCode;
+
+ public final String getMaterialCode()
+ {
+ return materialCode;
+ }
+
+ @BeanProperty(label = "material")
+ public final void setMaterialCode(final String materialCode)
+ {
+ this.materialCode = materialCode;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PersonPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PersonPE.java
new file mode 100644
index 00000000000..28e68def87e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PersonPE.java
@@ -0,0 +1,261 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Email;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistence Entity</i> which represents a person.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.PERSONS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.USER_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class PersonPE extends HibernateAbstractRegistratrationHolder implements
+ Comparable<PersonPE>, IIdHolder, Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /**
+ * The user id of the system user.
+ */
+ public static final String SYSTEM_USER_ID = "system";
+
+ private GroupPE homeGroup;
+
+ private transient Long id;
+
+ private String userId;
+
+ private String firstName;
+
+ private String lastName;
+
+ private String email;
+
+ private boolean systemUser;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private List<RoleAssignmentPE> roleAssignments = RoleAssignmentPE.EMPTY_LIST;
+
+ private final void setSystemUser(final boolean systemUser)
+ {
+ this.systemUser = systemUser;
+ }
+
+ @Column(name = ColumnNames.FIRST_NAME_COLUMN)
+ @Length(max = 30, message = ValidationMessages.FIRST_NAME_LENGTH_MESSAGE)
+ public final String getFirstName()
+ {
+ return firstName;
+ }
+
+ public final void setFirstName(final String firstName)
+ {
+ this.firstName = firstName;
+ }
+
+ @Column(name = ColumnNames.LAST_NAME_COLUMN)
+ @Length(max = 30, message = ValidationMessages.LAST_NAME_LENGTH_MESSAGE)
+ public final String getLastName()
+ {
+ return lastName;
+ }
+
+ public final void setLastName(final String lastName)
+ {
+ this.lastName = lastName;
+ }
+
+ @Email(message = ValidationMessages.EMAIL_EMAIL_MESSAGE)
+ @Length(max = 50, message = ValidationMessages.EMAIL_LENGTH_MESSAGE)
+ public final String getEmail()
+ {
+ return email;
+ }
+
+ public final void setEmail(final String email)
+ {
+ this.email = email;
+ }
+
+ @Column(name = ColumnNames.USER_COLUMN)
+ @Length(max = 20, message = ValidationMessages.USER_ID_LENGTH_MESSAGE)
+ @NotNull(message = ValidationMessages.USER_ID_NOT_NULL_MESSAGE)
+ public final String getUserId()
+ {
+ return userId;
+ }
+
+ public final void setUserId(final String userId)
+ {
+ this.userId = userId;
+ setSystemUser(SYSTEM_USER_ID.equals(userId));
+ }
+
+ @Transient
+ public final boolean isSystemUser()
+ {
+ return systemUser;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.GROUP_COLUMN)
+ public final GroupPE getHomeGroup()
+ {
+ return homeGroup;
+ }
+
+ public final void setHomeGroup(final GroupPE homeGroup)
+ {
+ this.homeGroup = homeGroup;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, mappedBy = "person", cascade = CascadeType.ALL)
+ public final List<RoleAssignmentPE> getRoleAssignments()
+ {
+ return roleAssignments;
+ }
+
+ public final void setRoleAssignments(final List<RoleAssignmentPE> rolesAssignments)
+ {
+ this.roleAssignments = rolesAssignments;
+ }
+
+ //
+ // IIdHolder
+ //
+
+ @SequenceGenerator(name = SequenceNames.PERSON_SEQUENCE, sequenceName = SequenceNames.PERSON_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PERSON_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof PersonPE == false)
+ {
+ return false;
+ }
+ final PersonPE that = (PersonPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(userId, that.userId);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(userId);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("userId", userId);
+ builder.append("firstName", firstName);
+ builder.append("lastName", lastName);
+ builder.append("email", email);
+ builder.append("systemUser", systemUser);
+ return builder.toString();
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(final PersonPE o)
+ {
+ final String thatUserID = o.userId;
+ if (userId == null)
+ {
+ return thatUserID == null ? 0 : -1;
+ }
+ if (thatUserID == null)
+ {
+ return 1;
+ }
+ return userId.compareTo(thatUserID);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Procedure.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Procedure.java
new file mode 100644
index 00000000000..37409c11eb5
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Procedure.java
@@ -0,0 +1,193 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a procedure.
+ * <p>
+ * <i>Note that equality, hash code calculation and comparison is based on the code of the
+ * {@link ProcedureType} since the procedure itself does not have a code.</i>
+ *
+ * @author Christian Ribeaud
+ */
+public final class Procedure implements Comparable<Procedure>, Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private Date registrationDate;
+
+ private ProcedureType procedureType;
+
+ private Experiment experiment;
+
+ private Sample[] resultSamples = new Sample[0];
+
+ private Sample[] inputSamples = new Sample[0];
+
+ public final ProcedureType getProcedureType()
+ {
+ return procedureType;
+ }
+
+ public final void setProcedureType(ProcedureType procedureType)
+ {
+ this.procedureType = procedureType;
+ }
+
+ /**
+ * Returns registrationDate.
+ *
+ * @return <code>null</code> when undefined.
+ */
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ /**
+ * Sets registrationDate.
+ *
+ * @param registrationDate New value. Can be <code>null</code>.
+ */
+ public final void setRegistrationDate(Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final void setResultSamples(Sample[] samples)
+ {
+ this.resultSamples = samples;
+ }
+
+ /**
+ * Returns experiment.
+ *
+ * @return <code>null</code> when undefined.
+ */
+ public final Experiment getExperiment()
+ {
+ return experiment;
+ }
+
+ /**
+ * Sets experiment.
+ *
+ * @param experiment New value. Can be <code>null</code>.
+ */
+ public final void setExperiment(Experiment experiment)
+ {
+ this.experiment = experiment;
+ }
+
+ /**
+ * Never returns <code>null</code> but could return an empty array.
+ */
+ public final Sample[] getResultSamples()
+ {
+ if (resultSamples == null)
+ {
+ return new Sample[0];
+ }
+ return resultSamples;
+ }
+
+ /**
+ * Never returns <code>null</code> but could return an empty array.
+ */
+ public final Sample[] getInputSamples()
+ {
+ if (inputSamples == null)
+ {
+ return new Sample[0];
+ }
+ return inputSamples;
+ }
+
+ public final void setInputSamples(Sample[] inputSamples)
+ {
+ this.inputSamples = inputSamples;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Procedure == false)
+ {
+ return false;
+ }
+ Procedure that = (Procedure) obj;
+ EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.registrationDate, registrationDate);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(registrationDate);
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(Procedure o)
+ {
+ final String code = procedureType.getCode();
+ final String thatCode = o.procedureType.getCode();
+ if (code == null)
+ {
+ return thatCode == null ? 0 : -1;
+ }
+ if (thatCode == null)
+ {
+ return 1;
+ }
+ return code.compareTo(thatCode);
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedurePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedurePE.java
new file mode 100644
index 00000000000..eef9eb4c145
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedurePE.java
@@ -0,0 +1,210 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * <i>Persistent Entity</i> object of an entity 'procedure'.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.PROCEDURES_TABLE)
+public class ProcedurePE implements IIdHolder, Serializable
+{
+ public final static ProcedurePE[] EMPTY_ARRAY = new ProcedurePE[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final List<ProcedurePE> EMPTY_LIST = new ArrayList<ProcedurePE>();
+
+ private ProcedureTypePE procedureType;
+
+ private Date registrationDate;
+
+ private transient Long id;
+
+ private ExperimentPE experiment;
+
+ private SamplePE[] resultSamples = SamplePE.EMPTY_ARRAY;
+
+ // TODO 2008-09-10, Tomasz Pylak: this is a deprecated field for control layouts connected
+ // directly to procedures. The workflow which used it has been deleted. We can get rid of this
+ // field if we write a migration script which connection all the experiment samples to the
+ // control layout directly.
+ private SamplePE[] inputSamples = SamplePE.EMPTY_ARRAY;
+
+ private List<DataPE> data = DataPE.EMPTY_LIST;
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.PROPERTY_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.PROCEDURE_TYPE_COLUMN, updatable = false)
+ public ProcedureTypePE getProcedureType()
+ {
+ return procedureType;
+ }
+
+ public void setProcedureType(final ProcedureTypePE procedureType)
+ {
+ this.procedureType = procedureType;
+ }
+
+ @Column(name = ColumnNames.REGISTRATION_TIMESTAMP_COLUMN, nullable = false, insertable = false, updatable = false)
+ @Generated(GenerationTime.INSERT)
+ public Date getRegistrationDate()
+ {
+ return HibernateAbstractRegistratrationHolder.getDate(registrationDate);
+ }
+
+ public void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ //
+ // IIdHolder
+ //
+
+ @SequenceGenerator(name = SequenceNames.PROCEDURE_SEQUENCE, sequenceName = SequenceNames.PROCEDURE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROCEDURE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public void setExperiment(final ExperimentPE experiment)
+ {
+ this.experiment = experiment;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @NotNull(message = ValidationMessages.EXPERIMENT_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.EXPERIMENT_COLUMN, updatable = false)
+ public ExperimentPE getExperiment()
+ {
+ return experiment;
+ }
+
+ @Transient
+ public SamplePE[] getInputSamples()
+ {
+ return inputSamples;
+ }
+
+ @Transient
+ public SamplePE[] getResultSamples()
+ {
+ return resultSamples;
+ }
+
+ public void setResultSamples(final SamplePE[] resultSamples)
+ {
+ this.resultSamples = resultSamples;
+ }
+
+ public void setInputSamples(final SamplePE[] inputSamples)
+ {
+ this.inputSamples = inputSamples;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.PROCEDURE_PRODUCED_BY_COLUMN, updatable = false)
+ public List<DataPE> getData()
+ {
+ return data;
+ }
+
+ public void setData(final List<DataPE> data)
+ {
+ this.data = data;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("procedureType", getProcedureType());
+ builder.append("experiment", getExperiment());
+ return builder.toString();
+ }
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ProcedurePE == false)
+ {
+ return false;
+ }
+ final ProcedurePE that = (ProcedurePE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getProcedureType(), that.getProcedureType());
+ builder.append(getExperiment(), that.getExperiment());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getProcedureType());
+ builder.append(getExperiment());
+ return builder.toHashCode();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureType.java
new file mode 100644
index 00000000000..4cb6478b399
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureType.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a procedure type.
+ *
+ * @author Christian Ribeaud
+ */
+public final class ProcedureType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private boolean dataAcquisition;
+
+ public ProcedureType()
+ {
+ }
+
+ public ProcedureType(final String code)
+ {
+ ProcedureTypeCode procedureTypeCode = ProcedureTypeCode.getProcedureTypeCode(code);
+ setCode(procedureTypeCode.getCode());
+ // TODO 2008-04-17, Franz-Josef Elmer: data acquisition flag should come from application
+ // server
+ setDataAcquisition(procedureTypeCode == ProcedureTypeCode.DATA_ACQUISITION);
+ }
+
+ /**
+ * Returns <code>true</code> if and only if this procedure type represents a data acquisition
+ * (or measurement) rather than a data processing (or derivation) step in a workflow.
+ */
+ public final boolean isDataAcquisition()
+ {
+ return dataAcquisition;
+ }
+
+ /**
+ * Sets the attribute which determines whether this procedure type represents a data acquisition
+ * (or measurement) rather than a data processing (or derivation) step in a workflow.
+ */
+ public final void setDataAcquisition(final boolean dataAcquisition)
+ {
+ this.dataAcquisition = dataAcquisition;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureTypePE.java
new file mode 100644
index 00000000000..ccc54233795
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcedureTypePE.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence Entity representing procedure type.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.PROCEDURE_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class ProcedureTypePE extends AbstractTypePE
+{
+ private boolean dataAcquisition;
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private DatabaseInstancePE databaseInstance;
+
+ @SequenceGenerator(name = SequenceNames.PROCEDURE_TYPE_SEQUENCE, sequenceName = SequenceNames.PROCEDURE_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROCEDURE_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ /**
+ * Returns <code>true</code> if and only if this procedure type represents a data acquisition
+ * (or measurement) rather than a data processing (or derivation) step in a workflow.
+ */
+ @Column(name = ColumnNames.IS_DATA_CQUSITION, nullable = false)
+ public final boolean isDataAcquisition()
+ {
+ return dataAcquisition;
+ }
+
+ /**
+ * Sets the attribute which determines whether this procedure type represents a data acquisition
+ * (or measurement) rather than a data processing (or derivation) step in a workflow.
+ */
+ public final void setDataAcquisition(final boolean dataAcquisition)
+ {
+ this.dataAcquisition = dataAcquisition;
+ }
+}
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
new file mode 100644
index 00000000000..dcac257414c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingInstructionDTO.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+
+/**
+ * Processing instruction needed to process raw data.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProcessingInstructionDTO extends AbstractRegistratrationHolder
+{
+ private static final long serialVersionUID = 1L;
+
+ public static final ProcessingInstructionDTO[] EMPTY_ARRAY = new ProcessingInstructionDTO[0];
+
+ transient private Long experimentID;
+
+ private String procedureTypeCode;
+
+ private String path;
+
+ private String description;
+
+ private byte[] parameters;
+
+ public ProcessingInstructionDTO()
+ {
+ super(null);
+ }
+
+ public final Long getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(final Long experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+ public final String getProcedureTypeCode()
+ {
+ return procedureTypeCode;
+ }
+
+ public final void setProcedureTypeCode(final String procedureTypeCode)
+ {
+ this.procedureTypeCode = procedureTypeCode;
+ }
+
+ public final String getPath()
+ {
+ return path;
+ }
+
+ public final void setPath(final String path)
+ {
+ this.path = path;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ /** can be null */
+ public final byte[] getParameters()
+ {
+ return parameters;
+ }
+
+ public final void setParameters(final byte[] parameters)
+ {
+ this.parameters = parameters;
+ }
+
+}
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
new file mode 100644
index 00000000000..bcf741b0cc2
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProcessingParameters.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * 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
+ */
+public class ProcessingParameters implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /**
+ * Creates an instance based on the specified byte array.
+ *
+ * @return <code>null</code> if the argument is also <code>null</code>.
+ */
+ public final static ProcessingParameters tryCreateFrom(final byte[] bytesOrNull)
+ {
+ if (bytesOrNull == null)
+ {
+ return null;
+ }
+ final ProcessingParameters processingParameters = new ProcessingParameters();
+ processingParameters.setProcessingParameters(bytesOrNull);
+ return processingParameters;
+ }
+
+ private byte[] processingParameters;
+
+ private String fileDescription;
+
+ public final String getFileDescription()
+ {
+ return fileDescription;
+ }
+
+ public final void setFileDescription(final String fileDescription)
+ {
+ this.fileDescription = fileDescription;
+ }
+
+ public final byte[] getProcessingParameters()
+ {
+ return processingParameters;
+ }
+
+ public final void setProcessingParameters(final byte[] encodedProcessingParameters)
+ {
+ this.processingParameters = encodedProcessingParameters;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProjectPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProjectPE.java
new file mode 100644
index 00000000000..86d88834fd9
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ProjectPE.java
@@ -0,0 +1,223 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <i>Persistence Entity</i> which represents a project.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.PROJECTS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.GROUP_COLUMN }) })
+public final class ProjectPE extends HibernateAbstractRegistratrationHolder implements
+ Comparable<ProjectPE>, IIdAndCodeHolder, Serializable
+{
+ public static final ProjectPE[] EMPTY_ARRAY = new ProjectPE[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ private GroupPE group;
+
+ private String code;
+
+ private String description;
+
+ private PersonPE projectLeader;
+
+ /** The number of experiments this project contains. */
+ private int size;
+
+ private DataStorePE dataStore;
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_STORE_COLUMN, updatable = false)
+ public final DataStorePE getDataStore()
+ {
+ return dataStore;
+ }
+
+ public final void setDataStore(final DataStorePE dataStorePE)
+ {
+ this.dataStore = dataStorePE;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ /**
+ * Sets the group which this <code>ProjectDTO</code> is related to.
+ *
+ * @throws AssertionError if <code>groupId</code> is defined but unequal
+ * <code>group.getId()</code>.
+ */
+ public final void setGroup(final GroupPE group)
+ {
+ this.group = group;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.GROUP_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.GROUP_COLUMN, updatable = false)
+ public final GroupPE getGroup()
+ {
+ return group;
+ }
+
+ @Transient
+ public final int getSize()
+ {
+ return size;
+ }
+
+ public final void setSize(final int size)
+ {
+ this.size = size;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PERSON_LEADER_COLUMN, updatable = false)
+ public final PersonPE getProjectLeader()
+ {
+ return projectLeader;
+ }
+
+ public final void setProjectLeader(final PersonPE projectLeader)
+ {
+ this.projectLeader = projectLeader;
+ }
+
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 1000, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ProjectPE == false)
+ {
+ return false;
+ }
+ final ProjectPE that = (ProjectPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("code", getCode());
+ builder.append("description", getDescription());
+ return builder.toString();
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(final ProjectPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+ //
+ // IIdHolder
+ //
+
+ @SequenceGenerator(name = SequenceNames.PROJECT_SEQUENCE, sequenceName = SequenceNames.PROJECT_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROJECT_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @Column(unique = true)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public final String getCode()
+ {
+ return code;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypeEntityTypeRelation.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypeEntityTypeRelation.java
new file mode 100644
index 00000000000..f1b9b2dee57
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypeEntityTypeRelation.java
@@ -0,0 +1,116 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Class that defines a relation between a {@link PropertyTypePE} and a
+ * {@link EntityTypeMandatorilyRelation}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class PropertyTypeEntityTypeRelation implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final PropertyTypeEntityTypeRelation[] EMPTY_ARRAY =
+ new PropertyTypeEntityTypeRelation[0];
+
+ private PropertyTypePE property;
+
+ private EntityTypeMandatorilyRelation[] relations = new EntityTypeMandatorilyRelation[0];
+
+ public final PropertyTypePE getProperty()
+ {
+ return property;
+ }
+
+ public final void setProperty(final PropertyTypePE property)
+ {
+ this.property = property;
+ }
+
+ public final EntityTypeMandatorilyRelation[] getRelations()
+ {
+ return relations;
+ }
+
+ public final void setRelations(final EntityTypeMandatorilyRelation[] relations)
+ {
+ this.relations = relations;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof PropertyTypeEntityTypeRelation == false)
+ {
+ return false;
+ }
+ final PropertyTypeEntityTypeRelation that = (PropertyTypeEntityTypeRelation) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.property, property);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(property);
+ return builder.toHashCode();
+ }
+
+ public static Comparator<PropertyTypeEntityTypeRelation> cerateComparator()
+ {
+ return new Comparator<PropertyTypeEntityTypeRelation>()
+ {
+
+ public int compare(final PropertyTypeEntityTypeRelation o1,
+ final PropertyTypeEntityTypeRelation o2)
+ {
+ final PropertyTypePE property1 = o1.getProperty();
+ final PropertyTypePE property2 = o2.getProperty();
+ if (property1 == null)
+ {
+ return property2 == null ? 0 : -1;
+ }
+ if (property2 == null)
+ {
+ return 1;
+ }
+ return property1.compareTo(property2);
+ }
+
+ };
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
new file mode 100644
index 00000000000..ad1619badd5
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
@@ -0,0 +1,260 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing property type.
+ * <p>
+ * Example of property types: DESCRIPTION, PLATE_GEOMETRY.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.PROPERTY_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.IS_INTERNAL_NAMESPACE,
+ ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class PropertyTypePE extends HibernateAbstractRegistratrationHolder implements
+ Comparable<PropertyTypePE>, IIdAndCodeHolder
+{
+ public static final PropertyTypePE[] EMPTY_ARRAY = new PropertyTypePE[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String simpleCode;
+
+ private DataTypePE type;
+
+ private String description;
+
+ private String label;
+
+ private VocabularyPE vocabulary;
+
+ private boolean internalNamespace;
+
+ private boolean managedInternally;
+
+ private transient Long id;
+
+ private DatabaseInstancePE databaseInstance;
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.CONTROLLED_VOCABULARY_COLUMN, updatable = false)
+ public VocabularyPE getVocabulary()
+ {
+ return vocabulary;
+ }
+
+ public void setVocabulary(final VocabularyPE vocabulary)
+ {
+ this.vocabulary = vocabulary;
+ }
+
+ /**
+ * Sets code in 'database format' - without 'user prefix'. To set full code (with user prefix
+ * use {@link #setCode(String)}).
+ */
+ private void setSimpleCode(final String simpleCode)
+ {
+ this.simpleCode = simpleCode.toUpperCase();
+ }
+
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ private String getSimpleCode()
+ {
+ return simpleCode;
+ }
+
+ public void setCode(final String fullCode)
+ {
+ setInternalNamespace(CodeConverter.isInternalNamespace(fullCode));
+ setSimpleCode(CodeConverter.tryToDatabase(fullCode));
+ }
+
+ @Transient
+ public String getCode()
+ {
+ return CodeConverter.tryToBusinessLayer(getSimpleCode(), isInternalNamespace() == false);
+ }
+
+ @NotNull(message = ValidationMessages.DATA_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_TYPE_COLUMN, updatable = false)
+ public final DataTypePE getType()
+ {
+ return type;
+ }
+
+ public final void setType(final DataTypePE type)
+ {
+ this.type = type;
+ }
+
+ @NotNull(message = ValidationMessages.DESCRIPTION_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(final String description)
+ {
+ this.description = description;
+ }
+
+ @NotNull(message = ValidationMessages.LABEL_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.LABEL_COLUMN)
+ @Length(max = 40, message = ValidationMessages.LABEL_LENGTH_MESSAGE)
+ public final String getLabel()
+ {
+ return label;
+ }
+
+ public final void setLabel(final String label)
+ {
+ this.label = label;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_MANAGED_INTERNALLY)
+ public boolean isManagedInternally()
+ {
+ return managedInternally;
+ }
+
+ public void setManagedInternally(final boolean managedInternally)
+ {
+ this.managedInternally = managedInternally;
+ }
+
+ @NotNull
+ @Column(name = ColumnNames.IS_INTERNAL_NAMESPACE)
+ public boolean isInternalNamespace()
+ {
+ return internalNamespace;
+ }
+
+ public void setInternalNamespace(final boolean internalNamespace)
+ {
+ this.internalNamespace = internalNamespace;
+ }
+
+ @SequenceGenerator(name = SequenceNames.PROPERTY_TYPES_SEQUENCE, sequenceName = SequenceNames.PROPERTY_TYPES_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.PROPERTY_TYPES_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ //
+ // Comparable
+ //
+
+ /**
+ * If <code>null</code> values are present for <code>code</code>, then they come first.
+ */
+ public final int compareTo(final PropertyTypePE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof PropertyTypePE == false)
+ {
+ return false;
+ }
+ final PropertyTypePE that = (PropertyTypePE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getSimpleCode(), that.getSimpleCode());
+ builder.append(getDatabaseInstance(), that.getDatabaseInstance());
+ builder.append(isInternalNamespace(), that.isInternalNamespace());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getSimpleCode());
+ builder.append(getDatabaseInstance());
+ builder.append(isInternalNamespace());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ return getCode();
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/QueryRestriction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/QueryRestriction.java
new file mode 100644
index 00000000000..13c58cdd32d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/QueryRestriction.java
@@ -0,0 +1,137 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+
+/**
+ * A query restriction that is applied to experiments.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QueryRestriction implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private boolean suppressInvalidated;
+
+ private ProjectIdentifier projectIdentifier;
+
+ private GroupIdentifier groupIdentifier;
+
+ private MaterialIdentifier materialIdentifier;
+
+ private TimeInterval timeInterval;
+
+ /**
+ * The experiment type code.
+ */
+ private String experimentTypeCode;
+
+ public final boolean isSuppressInvalidated()
+ {
+ return suppressInvalidated;
+ }
+
+ public final void setSuppressInvalidated(final boolean suppressInvalid)
+ {
+ this.suppressInvalidated = suppressInvalid;
+ }
+
+ public final MaterialIdentifier getMaterialIdentifier()
+ {
+ return materialIdentifier;
+ }
+
+ public final void setMaterialIdentifier(final MaterialIdentifier materialIdentifier)
+ {
+ this.materialIdentifier = materialIdentifier;
+ }
+
+ public final ProjectIdentifier tryGetProjectIdentifier()
+ {
+ return projectIdentifier;
+ }
+
+ public final void setProjectIdentifier(final ProjectIdentifier projectIdentifier)
+ {
+ this.projectIdentifier = projectIdentifier;
+ }
+
+ public final GroupIdentifier tryGetGroupIdentifier()
+ {
+ return groupIdentifier;
+ }
+
+ public final void setGroupIdentifier(final GroupIdentifier groupIdentifier)
+ {
+ this.groupIdentifier = groupIdentifier;
+ }
+
+ public final TimeInterval getTimeInterval()
+ {
+ return timeInterval;
+ }
+
+ public final void setTimeInterval(final TimeInterval timeInterval)
+ {
+ this.timeInterval = timeInterval;
+ }
+
+ public final String getExperimentTypeCode()
+ {
+ return experimentTypeCode;
+ }
+
+ public final void setExperimentTypeCode(final String experimentTypeCode)
+ {
+ this.experimentTypeCode = experimentTypeCode;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ return EqualsBuilder.reflectionEquals(this, obj);
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return HashCodeBuilder.reflectionHashCode(this);
+ }
+
+ @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/RoleAssignmentPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
new file mode 100644
index 00000000000..4ad1e6de598
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleAssignmentPE.java
@@ -0,0 +1,188 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.annotations.Check;
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistent Entity corresponding containing informations about role assignment.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Check(constraints = ColumnNames.DATABASE_INSTANCE_COLUMN + " IS NOT NULL AND "
+ + ColumnNames.GROUP_COLUMN + " IS NULL OR " + ColumnNames.DATABASE_INSTANCE_COLUMN
+ + " IS NULL AND " + ColumnNames.GROUP_COLUMN + " IS NOT NULL")
+@Table(name = TableNames.ROLE_ASSIGNMENTS_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.PERSON_GRANTEE_COLUMN, ColumnNames.ROLE_COLUMN, ColumnNames.GROUP_COLUMN,
+ ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class RoleAssignmentPE extends HibernateAbstractRegistratrationHolder implements
+ IIdHolder, Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final RoleAssignmentPE[] EMPTY_ARRAY = new RoleAssignmentPE[0];
+
+ public static final List<RoleAssignmentPE> EMPTY_LIST =
+ Collections.<RoleAssignmentPE> emptyList();
+
+ private transient Long id;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private GroupPE group;
+
+ private PersonPE person;
+
+ 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;
+ }
+
+ @NotNull(message = ValidationMessages.PERSON_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.PERSON_GRANTEE_COLUMN, updatable = false)
+ public final PersonPE getPerson()
+ {
+ return person;
+ }
+
+ public final void setPerson(final PersonPE person)
+ {
+ this.person = person;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.GROUP_COLUMN, updatable = false)
+ public final GroupPE getGroup()
+ {
+ return group;
+ }
+
+ public final void setGroup(final GroupPE group)
+ {
+ this.group = group;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public final DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public final void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ //
+ // IIdHolder
+ //
+
+ @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)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof RoleAssignmentPE == false)
+ {
+ return false;
+ }
+ final RoleAssignmentPE that = (RoleAssignmentPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(role, that.role);
+ builder.append(person, that.person);
+ builder.append(databaseInstance, that.databaseInstance);
+ builder.append(group, that.group);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(role);
+ builder.append(person);
+ builder.append(databaseInstance);
+ builder.append(group);
+ 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/RoleCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleCode.java
new file mode 100644
index 00000000000..cbcd81039ad
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/RoleCode.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * The <i>openBIS</i> role codes.
+ * <p>
+ * These names reflect the ones that could be found in the database.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public enum RoleCode
+{
+ ADMIN, USER, OBSERVER, ETL_SERVER;
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Sample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Sample.java
new file mode 100644
index 00000000000..64624d91855
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Sample.java
@@ -0,0 +1,262 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a sample.
+ *
+ * @author Christian Ribeaud
+ */
+public final class Sample implements Serializable, Comparable<Sample>, ISimpleEntityPropertiesHolder
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private SampleIdentifier sampleIdentifier;
+
+ private SampleType sampleType;
+
+ private PersonPE registrator;
+
+ private ExternalData[] measurementData = new ExternalData[0];
+
+ private ExternalData[] derivedData = new ExternalData[0];
+
+ private Procedure procedure;
+
+ private Sample generatedFrom;
+
+ private Sample top;
+
+ private InvalidationPE invalidationOrNull;
+
+ /**
+ * The identifier of control layout assigned to the sample or null if nothing is assigned.
+ */
+ private SampleIdentifier controlLayoutIdentifierOrNull;
+
+ /** Registration date of this sample. */
+ private Date registrationDate;
+
+ private SimpleEntityProperty[] properties;
+
+ public EntityType getEntityType()
+ {
+ return getSampleType();
+ }
+
+ public final SampleType getSampleType()
+ {
+ return sampleType;
+ }
+
+ public final void setSampleType(final SampleType sampleType)
+ {
+ this.sampleType = sampleType;
+ }
+
+ /**
+ * Returns registrator.
+ *
+ * @return <code>null</code> when undefined.
+ */
+ public final PersonPE getRegistrator()
+ {
+ return registrator;
+ }
+
+ /**
+ * Sets registrator.
+ *
+ * @param registrator New value. Can be <code>null</code>.
+ */
+ public final void setRegistrator(final PersonPE registrator)
+ {
+ this.registrator = registrator;
+ }
+
+ public final Procedure getProcedure()
+ {
+ return procedure;
+ }
+
+ public final void setProcedure(final Procedure procedure)
+ {
+ this.procedure = procedure;
+ }
+
+ /**
+ * Never returns <code>null</code> but could return an empty array of
+ * <code>ExternalData</code>.
+ */
+ public final ExternalData[] getMeasurementData()
+ {
+ if (measurementData == null)
+ {
+ return new ExternalData[0];
+ }
+ return measurementData;
+ }
+
+ /**
+ * Sets <code>measurementData</code>.
+ *
+ * @param externalData new value. Could be <code>null</code>.
+ */
+ public final void setMeasurementData(final ExternalData[] externalData)
+ {
+ this.measurementData = externalData;
+ }
+
+ /**
+ * Never returns <code>null</code> but could return an empty array of
+ * <code>ExternalData</code>.
+ */
+ public final ExternalData[] getDerivedData()
+ {
+ if (derivedData == null)
+ {
+ return new ExternalData[0];
+ }
+ return derivedData;
+ }
+
+ /**
+ * Sets <code>derivedData</code>.
+ *
+ * @param externalData new value. Could be <code>null</code>.
+ */
+ public final void setDerivedData(final ExternalData[] externalData)
+ {
+ this.derivedData = externalData;
+ }
+
+ public final Sample getGeneratedFrom()
+ {
+ return generatedFrom;
+ }
+
+ public final void setGeneratedFrom(final Sample generatedFrom)
+ {
+ this.generatedFrom = generatedFrom;
+ }
+
+ public final Sample getTop()
+ {
+ return top;
+ }
+
+ public final void setTop(final Sample top)
+ {
+ this.top = top;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(final Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ /** Returns invalidation data or null */
+ public InvalidationPE getInvalidation()
+ {
+ return invalidationOrNull;
+ }
+
+ public void setInvalidation(final InvalidationPE invalidation)
+ {
+ this.invalidationOrNull = invalidation;
+ }
+
+ public SampleIdentifier getSampleIdentifier()
+ {
+ return sampleIdentifier;
+ }
+
+ public void setSampleIdentifier(SampleIdentifier sampleIdentifier)
+ {
+ this.sampleIdentifier = sampleIdentifier;
+ }
+
+ /** can be null */
+ public final SampleIdentifier getControlLayoutIdentifier()
+ {
+ return controlLayoutIdentifierOrNull;
+ }
+
+ public final void setControlLayoutIdentifier(SampleIdentifier controlLayoutIdentifierOrNull)
+ {
+ this.controlLayoutIdentifierOrNull = controlLayoutIdentifierOrNull;
+ }
+
+ //
+ // IEntityPropertiesHolder
+ //
+
+ public final SimpleEntityProperty[] getProperties()
+ {
+ return properties;
+ }
+
+ public final void setProperties(final SimpleEntityProperty[] properties)
+ {
+ this.properties = properties;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || obj instanceof Sample == false)
+ {
+ return false;
+ }
+ Sample sample = (Sample) obj;
+ return sampleIdentifier.equals(sample.getSampleIdentifier());
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return sampleIdentifier == null ? 43 : sampleIdentifier.hashCode();
+ }
+
+ public int compareTo(Sample sample)
+ {
+ SampleIdentifier thatIdent = sample.getSampleIdentifier();
+ SampleIdentifier thisIdent = getSampleIdentifier();
+ if (thisIdent == null)
+ {
+ return thatIdent == null ? 0 : -1;
+ }
+ if (thatIdent == null)
+ {
+ return 1;
+ }
+
+ return thisIdent.compareTo(thatIdent);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleFilter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleFilter.java
new file mode 100644
index 00000000000..0793b58506d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleFilter.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierPattern;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
+
+/**
+ * Bean specifying a {@link SamplePE} filter.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SampleFilter extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private SampleIdentifierPattern[] patterns;
+
+ private boolean notRegisteredToExperiment;
+
+ private boolean hideInvalidated;
+
+ /** see class getters documentation */
+ public SampleFilter(final SampleIdentifierPattern[] patterns,
+ final boolean notRegisteredToExperiment, final boolean hideInvalidated)
+ {
+ assert patterns != null : "Unspecified patterns";
+ this.patterns = patterns;
+ this.notRegisteredToExperiment = notRegisteredToExperiment;
+ this.hideInvalidated = hideInvalidated;
+ }
+
+ /**
+ * Returns whether only those samples should be passing the filters that are not registered to
+ * an experiment.
+ */
+ public final boolean isNotRegisteredToExperiment()
+ {
+ return notRegisteredToExperiment;
+ }
+
+ /**
+ * Filters samples visible for specified owner and with code matching the wildcards pattern (* =
+ * any string, ? = any character). Note, that if there are no patterns, no sample will match.
+ */
+ public final SampleIdentifierPattern[] getPatterns()
+ {
+ return patterns;
+ }
+
+ /**
+ * Returns either the patterns specified in the constructor or if not defined default patterns
+ * based on the specified home group.
+ */
+ public SampleIdentifierPattern[] getPatternsOrDefaultPatterns(GroupPE homeGroupOrNull)
+ {
+ if (patterns.length > 0)
+ {
+ return patterns;
+ }
+ if (homeGroupOrNull == null || homeGroupOrNull.getCode() == null)
+ {
+ SampleOwnerIdentifier owner =
+ new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
+ return new SampleIdentifierPattern[]
+ { SampleIdentifierPattern.createOwnedBy(owner, "*") };
+ }
+ GroupIdentifier groupIdentifier =
+ new GroupIdentifier(DatabaseInstanceIdentifier.HOME, homeGroupOrNull.getCode());
+ return SampleIdentifierPattern.createGroupVisible(groupIdentifier, "*");
+ }
+
+ /** If <code>true</code> only valid samples are returned. */
+ public final boolean isHideInvalidated()
+ {
+ return hideInvalidated;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleGenerationDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleGenerationDTO.java
new file mode 100644
index 00000000000..c1223535133
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleGenerationDTO.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A <code>SampleGeneration</code> encapsulates a generator <code>SampleDTO</code> and its
+ * generated <code>SampleDTO</code>s.
+ *
+ * @author Christian Ribeaud
+ */
+public final class SampleGenerationDTO implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /**
+ * The <code>Sample</code> parent.
+ */
+ private SamplePE generator;
+
+ /** The <code>Sample</code> children. */
+ private SamplePE[] generated;
+
+ public SampleGenerationDTO()
+ {
+
+ }
+
+ public SampleGenerationDTO(final SamplePE generator, final List<SamplePE> generated)
+ {
+ assert generator != null : "Generator can not be null.";
+ assert generated != null : "Generated can not be null.";
+ setGenerator(generator);
+ setGenerated(generated.toArray(SamplePE.EMPTY_ARRAY));
+ }
+
+ /**
+ * Never returns <code>null</code> but could return an empty list.
+ */
+ public final SamplePE[] getGenerated()
+ {
+ return generated;
+ }
+
+ public final SamplePE getGenerator()
+ {
+ return generator;
+ }
+
+ public void setGenerator(final SamplePE generator)
+ {
+ this.generator = generator;
+ }
+
+ public void setGenerated(final SamplePE[] generated)
+ {
+ this.generated = generated;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
new file mode 100644
index 00000000000..f27725e6287
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
@@ -0,0 +1,374 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.annotations.Check;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * <i>Persistent Entity</i> object of an entity 'sample'.
+ *
+ * @author Christian Ribeaud
+ */
+@Entity
+@Table(name = TableNames.SAMPLES_TABLE)
+@Check(constraints = "(" + ColumnNames.DATABASE_INSTANCE_COLUMN + " IS NOT NULL AND "
+ + ColumnNames.GROUP_COLUMN + " IS NULL) OR (" + ColumnNames.DATABASE_INSTANCE_COLUMN
+ + " IS NULL AND " + ColumnNames.GROUP_COLUMN + " IS NOT NULL)")
+public class SamplePE extends HibernateAbstractRegistratrationHolder implements IIdAndCodeHolder,
+ Comparable<SamplePE>, IEntityPropertiesHolder<SamplePropertyPE>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SamplePE[] EMPTY_ARRAY = new SamplePE[0];
+
+ public static final List<SamplePE> EMPTY_LIST = Collections.emptyList();
+
+ private Long id;
+
+ private String code;
+
+ private SampleTypePE sampleType;
+
+ private DatabaseInstancePE databaseInstance;
+
+ private GroupPE group;
+
+ private SampleIdentifier sampleIdentifier;
+
+ private SamplePE controlLayout;
+
+ private SamplePE container;
+
+ private SamplePE top;
+
+ private SamplePE generatedFrom;
+
+ private List<ProcedurePE> procedures = ProcedurePE.EMPTY_LIST;
+
+ private ProcedurePE validProcedure;
+
+ private ExternalDataPE[] measurementData = ExternalDataPE.EMPTY_ARRAY;
+
+ private ExternalDataPE[] derivedData = ExternalDataPE.EMPTY_ARRAY;
+
+ /**
+ * Invalidation information.
+ * <p>
+ * If not <code>null</code>, then this sample is considered as <i>invalid</i>.
+ * </p>
+ */
+ private InvalidationPE invalidation;
+
+ private List<SamplePropertyPE> properties = SamplePropertyPE.EMPTY_LIST;
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.INVALIDATION_COLUMN)
+ public InvalidationPE getInvalidation()
+ {
+ return invalidation;
+ }
+
+ public void setInvalidation(final InvalidationPE invalidation)
+ {
+ this.invalidation = invalidation;
+ }
+
+ @Transient
+ public SampleIdentifier getSampleIdentifier()
+ {
+ if (sampleIdentifier == null)
+ {
+ sampleIdentifier = IdentifierHelper.createIdentifier(this);
+ }
+ return sampleIdentifier;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.GROUP_COLUMN, updatable = false)
+ public GroupPE getGroup()
+ {
+ return group;
+ }
+
+ public void setGroup(final GroupPE group)
+ {
+ this.group = group;
+ }
+
+ public void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public final void setId(final Long id)
+ {
+ this.id = id;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.SAMPLE_TYPE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.SAMPLE_TYPE_COLUMN, updatable = false)
+ public SampleTypePE getSampleType()
+ {
+ return sampleType;
+ }
+
+ public void setSampleType(final SampleTypePE sampleType)
+ {
+ this.sampleType = sampleType;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "sample")
+ private List<SamplePropertyPE> getSampleProperties()
+ {
+ return properties;
+ }
+
+ private void setSampleProperties(final List<SamplePropertyPE> properties)
+ {
+ this.properties = properties;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.CONTROL_LAYOUT_SAMPLE_COLUMN, updatable = false)
+ public SamplePE getControlLayout()
+ {
+ return controlLayout;
+ }
+
+ public void setControlLayout(final SamplePE controlLayout)
+ {
+ this.controlLayout = controlLayout;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.PART_OF_SAMPLE_COLUMN, updatable = false)
+ public SamplePE getContainer()
+ {
+ return container;
+ }
+
+ public void setContainer(final SamplePE container)
+ {
+ this.container = container;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.TOP_SAMPLE_COLUMN)
+ public SamplePE getTop()
+ {
+ return top;
+ }
+
+ public void setTop(final SamplePE top)
+ {
+ this.top = top;
+ }
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.GENERATED_FROM_SAMPLE_COLUMN)
+ public SamplePE getGeneratedFrom()
+ {
+ return generatedFrom;
+ }
+
+ public void setGeneratedFrom(final SamplePE generatedFrom)
+ {
+ this.generatedFrom = generatedFrom;
+ }
+
+ @ManyToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
+ @JoinTable(name = TableNames.SAMPLE_INPUTS_TABLE, joinColumns = @JoinColumn(name = ColumnNames.SAMPLE_COLUMN), inverseJoinColumns = @JoinColumn(name = ColumnNames.PROCEDURE_COLUMN))
+ public List<ProcedurePE> getProcedures()
+ {
+ return procedures;
+ }
+
+ public void setProcedures(final List<ProcedurePE> procedures)
+ {
+ this.procedures = procedures;
+ }
+
+ @Transient
+ public ProcedurePE getValidProcedure()
+ {
+ return validProcedure;
+ }
+
+ public void setValidProcedure(final ProcedurePE validProcedure)
+ {
+ this.validProcedure = validProcedure;
+ }
+
+ @Transient
+ public ExternalDataPE[] getMeasurementData()
+ {
+ return measurementData;
+ }
+
+ public void setMeasurementData(final ExternalDataPE[] measurementData)
+ {
+ this.measurementData = measurementData;
+ }
+
+ @Transient
+ public ExternalDataPE[] getDerivedData()
+ {
+ return derivedData;
+ }
+
+ public void setDerivedData(final ExternalDataPE[] derivedData)
+ {
+ this.derivedData = derivedData;
+ }
+
+ //
+ // IIdAndCodeHolder
+ //
+
+ @SequenceGenerator(name = SequenceNames.SAMPLE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof SamplePE == false)
+ {
+ return false;
+ }
+ final SamplePE that = (SamplePE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ builder.append(getSampleType(), that.getSampleType());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ builder.append(getSampleType());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("code", getCode());
+ builder.append("sampleType", getSampleType());
+ return builder.toString();
+ }
+
+ //
+ // Compare
+ //
+
+ public final int compareTo(final SamplePE o)
+ {
+ return getSampleIdentifier().compareTo(o.getSampleIdentifier());
+ }
+
+ //
+ // IEntityPropertiesHolder
+ //
+
+ @Transient
+ public List<SamplePropertyPE> getProperties()
+ {
+ return getSampleProperties();
+ }
+
+ public void setProperties(final List<SamplePropertyPE> properties)
+ {
+ for (final SamplePropertyPE sampleProperty : properties)
+ {
+ final SamplePE parent = sampleProperty.getSample();
+ if (parent != null)
+ {
+ parent.getProperties().remove(sampleProperty);
+ }
+ sampleProperty.setSample(this);
+ }
+ setSampleProperties(properties);
+ }
+}
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
new file mode 100644
index 00000000000..8c4d5b09f33
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePropertyPE.java
@@ -0,0 +1,103 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing sample property.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.SAMPLE_PROPERTIES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.ID_COLUMN }) })
+public class SamplePropertyPE extends EntityPropertyPE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SamplePropertyPE[] EMPTY_ARRAY = new SamplePropertyPE[0];
+
+ public static final List<SamplePropertyPE> EMPTY_LIST =
+ Collections.<SamplePropertyPE> emptyList();
+
+ private SamplePE sample;
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = ColumnNames.SAMPLE_COLUMN, updatable = false)
+ public SamplePE getSample()
+ {
+ return sample;
+ }
+
+ public void setSample(final SamplePE sample)
+ {
+ this.sample = sample;
+ }
+
+ //
+ // EntityPropertyPE
+ //
+
+ @NotNull(message = ValidationMessages.SAMPLE_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = SampleTypePropertyTypePE.class)
+ @JoinColumn(name = ColumnNames.SAMPLE_TYPE_PROPERTY_TYPE_COLUMN, updatable = false)
+ public EntityTypePropertyTypePE getEntityTypePropertyType()
+ {
+ return entityTypePropertyType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.SAMPLE_PROPERTY_SEQUENCE, sequenceName = SequenceNames.SAMPLE_PROPERTY_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_PROPERTY_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ @Transient
+ public Long getEntityId()
+ {
+ return entityId;
+ }
+
+ @Override
+ public void setEntityId(final Long entityId)
+ {
+ sample = new SamplePE();
+ sample.setId(entityId);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleType.java
new file mode 100644
index 00000000000..50382371e4e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleType.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Kind of <i>Java Bean</i> or <i>Value Object</i> which transports through Web Service any
+ * information we would like to know about a sample type.
+ *
+ * @author Christian Ribeaud
+ */
+public final class SampleType extends EntityType
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SampleType[] EMPTY_ARRAY = new SampleType[0];
+
+ private boolean plate;
+
+ private boolean controlLayout;
+
+ public final boolean isPlate()
+ {
+ return plate;
+ }
+
+ public final void setPlate(boolean plate)
+ {
+ this.plate = plate;
+ }
+
+ public final boolean isControlLayout()
+ {
+ return controlLayout;
+ }
+
+ public final void setControlLayout(final boolean controlLayout)
+ {
+ this.controlLayout = controlLayout;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePE.java
new file mode 100644
index 00000000000..cf1a436f075
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePE.java
@@ -0,0 +1,68 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.SampleTypeCode;
+
+/**
+ * Persistence Entity representing 'sample type'.
+ *
+ * @author Christian Ribeaud
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.SAMPLE_TYPES_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public final class SampleTypePE extends EntityTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ @Transient
+ public final boolean isPlate()
+ {
+ return getCode().endsWith("_PLATE");
+ }
+
+ @Transient
+ public final boolean isControlLayout()
+ {
+ return SampleTypeCode.CONTROL_LAYOUT.getCode().equals(getCode());
+ }
+
+ //
+ // EntityTypePE
+ //
+
+ @SequenceGenerator(name = SequenceNames.SAMPLE_TYPE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_TYPE_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+}
\ No newline at end of file
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
new file mode 100644
index 00000000000..cc909d5a280
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleTypePropertyTypePE.java
@@ -0,0 +1,76 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing sample type - property type relation.
+ *
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.SAMPLE_TYPE_PROPERTY_TYPE_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.SAMPLE_TYPE_COLUMN, ColumnNames.PROPERTY_TYPE_COLUMN }) })
+public class SampleTypePropertyTypePE extends EntityTypePropertyTypePE
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SampleTypePropertyTypePE[] EMPTY_ARRAY = new SampleTypePropertyTypePE[0];
+
+ public SampleTypePropertyTypePE()
+ {
+
+ }
+
+ //
+ // EntityTypePropertyTypePE
+ //
+
+ @NotNull(message = ValidationMessages.SAMPLE_TYPE_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER, targetEntity = SampleTypePE.class)
+ @JoinColumn(name = ColumnNames.SAMPLE_TYPE_COLUMN)
+ public EntityTypePE getEntityType()
+ {
+ return entityType;
+ }
+
+ @SequenceGenerator(name = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE)
+ @Column(insertable = false, updatable = false)
+ public Long getId()
+ {
+ return id;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
new file mode 100644
index 00000000000..b852fca8a07
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
@@ -0,0 +1,99 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * The database sequence names.
+ *
+ * @author Christian Ribeaud
+ */
+public final class SequenceNames
+{
+
+ public static final String CONTROLLED_VOCABULARY_SEQUENCE = "CONTROLLED_VOCABULARY_ID_SEQ";
+
+ public static final String CONTROLLED_VOCABULARY_TERM_SEQUENCE = "CVTE_ID_SEQ";
+
+ public static final String DATA_SEQUENCE = "DATA_ID_SEQ";
+
+ public static final String DATA_SET_RELATIONSHIP_SEQUENCE = "DATA_SET_RELATIONSHIP_ID_SEQ";
+
+ public static final String DATA_STORE_SEQUENCE = "DATA_STORE_ID_SEQ";
+
+ public static final String DATA_TYPE_SEQUENCE = "DATA_TYPE_ID_SEQ";
+
+ public static final String DATABASE_INSTANCE_SEQUENCE = "DATABASE_INSTANCE_ID_SEQ";
+
+ public static final String EXPERIMENT_ATTACHMENT_SEQUENCE = "EXPERIMENT_ATTACHMENT_ID_SEQ";
+
+ public static final String EXPERIMENT_PROPERTY_SEQUENCE = "EXPERIMENT_PROPERTY_ID_SEQ";
+
+ public static final String EXPERIMENT_SEQUENCE = "EXPERIMENT_ID_SEQ";
+
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_SEQUENCE = "ETPT_ID_SEQ";
+
+ public static final String EXPERIMENT_TYPE_SEQUENCE = "EXPERIMENT_TYPE_ID_SEQ";
+
+ public static final String FILE_FORMAT_TYPE_SEQUENCE = "FILE_FORMAT_TYPE_ID_SEQ";
+
+ public static final String GROUP_SEQUENCE = "GROUP_ID_SEQ";
+
+ public static final String INVALIDATION_SEQUENCE = "INVALIDATION_ID_SEQ";
+
+ public static final String LOCATOR_TYPE_SEQUENCE = "LOCATOR_TYPE_ID_SEQ";
+
+ public static final String MATERIAL_BATCH_SEQUENCE = "MATERIAL_BATCH_ID_SEQ";
+
+ public static final String MATERIAL_PROPERTY_SEQUENCE = "MATERIAL_PROPERTY_ID_SEQ";
+
+ public static final String MATERIAL_SEQUENCE = "MATERIAL_ID_SEQ";
+
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_SEQUENCE = "MTPT_ID_SEQ";
+
+ public static final String DATA_SET_TYPE_SEQUENCE = "DATA_SET_TYPE_ID_SEQ";
+
+ public final static String PERSON_SEQUENCE = "PERSON_ID_SEQ";
+
+ public static final String MATERIAL_TYPE_SEQUENCE = "MATERIAL_TYPE_ID_SEQ";
+
+ public static final String PROCEDURE_SEQUENCE = "PROCEDURE_ID_SEQ";
+
+ public static final String PROCEDURE_TYPE_SEQUENCE = "PROCEDURE_TYPE_ID_SEQ";
+
+ public static final String PROJECT_SEQUENCE = "PROJECT_ID_SEQ";
+
+ public static final String PROPERTY_TYPES_SEQUENCE = "PROPERTY_TYPE_ID_SEQ";
+
+ public static final String ROLE_ASSIGNMENT_SEQUENCE = "ROLE_ASSIGNMENT_ID_SEQ";
+
+ public static final String SAMPLE_INPUT_SEQUENCE = "SAMPLE_INPUT_ID_SEQ";
+
+ public static final String SAMPLE_MATERIAL_BATCH_SEQUENCE = "SAMPLE_MATERIAL_BATCH_ID_SEQ";
+
+ public static final String SAMPLE_PROPERTY_SEQUENCE = "SAMPLE_PROPERTY_ID_SEQ";
+
+ public static final String SAMPLE_SEQUENCE = "SAMPLE_ID_SEQ";
+
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_SEQUENCE = "STPT_ID_SEQ";
+
+ public static final String SAMPLE_TYPE_SEQUENCE = "SAMPLE_TYPE_ID_SEQ";
+
+ private SequenceNames()
+ {
+ // Can not be instantiated.
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Session.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Session.java
index 42dc5012498..a370a583682 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Session.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/Session.java
@@ -20,8 +20,6 @@ import org.apache.commons.lang.time.DateFormatUtils;
import ch.systemsx.cisd.authentication.BasicSession;
import ch.systemsx.cisd.authentication.Principal;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
/**
* Extendion of {@link BasicSession} which may holds a {@link PersonPE} instance.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleEntityProperty.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleEntityProperty.java
new file mode 100644
index 00000000000..5f7961bce8c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleEntityProperty.java
@@ -0,0 +1,111 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityDataType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityPropertyValue;
+
+/**
+ * Simple version of EntityProperty which can be expressed in web service definition language<br>
+ * Deprecated methods should be used only during bean conversion.
+ *
+ * @author Tomasz Pylak
+ */
+public final class SimpleEntityProperty extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public final static SimpleEntityProperty[] EMPTY_ARRAY = new SimpleEntityProperty[0];
+
+ /** Label of the property, which is shown to the user. */
+ private String label;
+
+ private String code;
+
+ private EntityDataType dataType;
+
+ private Serializable value;
+
+ public SimpleEntityProperty()
+ {
+ }
+
+ public SimpleEntityProperty(final String name, final String label,
+ final EntityDataType dataType, final Serializable valueOrNull)
+ {
+ this.code = name;
+ this.label = label;
+ this.dataType = dataType;
+ this.value = valueOrNull;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ public final EntityDataType getDataType()
+ {
+ return dataType;
+ }
+
+ public final Serializable getValue()
+ {
+ return value;
+ }
+
+ // can be null
+ public String getUntypedValue()
+ {
+ return EntityPropertyValue.createFromSimple(this).tryGetUntypedValue();
+ }
+
+ public final String getLabel()
+ {
+ return label;
+ }
+
+ public final void setLabel(final String label)
+ {
+ this.label = label;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public final void setDataType(final EntityDataType dataType)
+ {
+ this.dataType = dataType;
+ }
+
+ public final void setValue(final Serializable value)
+ {
+ this.value = value;
+ }
+
+ public final void setValue(final String value)
+ {
+ this.value = value;
+ }
+
+}
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
new file mode 100644
index 00000000000..7a9dba1a7f8
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/StorageFormat.java
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * An enumeration that describes what format an external data set is stored in.
+ *
+ * @author Bernd Rinn
+ */
+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.
+ */
+ BDS_DIRECTORY("BDS_DIRECTORY");
+
+ private static final Map<String, StorageFormat> codeMap = new HashMap<String, StorageFormat>();
+
+ static
+ {
+ for (final StorageFormat format : values())
+ {
+ assert codeMap.containsKey(format.code) == false : "Duplicate code";
+ codeMap.put(format.code, format);
+ }
+ }
+
+ private final String code;
+
+ private StorageFormat(final String code)
+ {
+ this.code = code;
+ }
+
+ /**
+ * Returns the code (string representation) of this storage format.
+ * <p>
+ * Use this instead of {@link #toString()} when storing in the database.
+ */
+ public final String getCode()
+ {
+ return code;
+ }
+
+ /**
+ * 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)
+ {
+ return codeMap.get(code);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
new file mode 100644
index 00000000000..caa8242d38f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+/**
+ * This class lists the tables that can be found in the database.
+ *
+ * @author Christian Ribeaud
+ */
+public final class TableNames
+{
+
+ public static final String CONTROLLED_VOCABULARY_TABLE = "controlled_vocabularies";
+
+ public static final String CONTROLLED_VOCABULARY_TERM_TABLE = "controlled_vocabulary_terms";
+
+ public static final Object CONTROLLED_VOCABULARY_TERMS_TABLE = "controlled_vocabulary_terms";
+
+ public static final String DATA_SET_RELATIONSHIPS_TABLE = "data_set_relationships";
+
+ public static final String DATA_STORES_TABLE = "data_stores";
+
+ public static final String DATA_TABLE = "data";
+
+ public static final String DATA_TYPES_TABLE = "data_types";
+
+ public static final String DATABASE_INSTANCES_TABLE = "database_instances";
+
+ public static final String EXPERIMENT_ATTACHMENTS_TABLE = "experiment_attachments";
+
+ public static final String EXPERIMENT_PROPERTIES_TABLE = "experiment_properties";
+
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_TABLE =
+ "experiment_type_property_types";
+
+ public static final String EXPERIMENT_TYPES_TABLE = "experiment_types";
+
+ public static final String EXPERIMENTS_TABLE = "experiments";
+
+ public static final String EXTERNAL_DATA_TABLE = "external_data";
+
+ public static final String FILE_FORMAT_TYPES_TABLE = "file_format_types";
+
+ public static final String GROUPS_TABLE = "groups";
+
+ public static final String INVALIDATION_TABLE = "invalidations";
+
+ public static final String LOCATOR_TYPES_TABLE = "locator_types";
+
+ public static final String MATERIAL_BATCHES_TABLE = "material_batches";
+
+ public static final String MATERIAL_PROPERTIES_TABLE = "material_properties";
+
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_TABLE = "material_type_property_types";
+
+ public static final String MATERIAL_TYPES_TABLE = "material_types";
+
+ public static final String MATERIALS_TABLE = "materials";
+
+ public static final String DATA_SET_TYPES_TABLE = "data_set_types";
+
+ public static final String PERSONS_TABLE = "persons";
+
+ public static final String PROCEDURE_TYPES_TABLE = "procedure_types";
+
+ public static final String PROCEDURES_TABLE = "procedures";
+
+ public static final String PROJECTS_TABLE = "projects";
+
+ public static final String PROPERTY_TYPES_TABLE = "property_types";
+
+ public static final String ROLE_ASSIGNMENTS_TABLE = "role_assignments";
+
+ public static final String SAMPLE_INPUTS_TABLE = "sample_inputs";
+
+ public static final String SAMPLE_MATERIAL_BATCHES_TABLE = "sample_material_batches";
+
+ public static final String SAMPLE_PROPERTIES_TABLE = "sample_properties";
+
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_TABLE = "sample_type_property_types";
+
+ public static final String SAMPLE_TYPES_TABLE = "sample_types";
+
+ public static final String SAMPLES_TABLE = "samples";
+
+ private TableNames()
+ {
+ // This class can not be instantiated.
+ }
+
+}
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
new file mode 100644
index 00000000000..d4f83d05939
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TimeInterval.java
@@ -0,0 +1,151 @@
+/*
+ * Copyright 2007 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * A time range composed of a <code>from</code> and of an <code>until</code> date.
+ * <p>
+ * Note that both dates can be <code>null</code>.
+ * </p>
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class TimeInterval implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private Date from;
+
+ private Date until;
+
+ public TimeInterval()
+ {
+ }
+
+ public TimeInterval(final Date from, final Date until)
+ {
+ check(from, until);
+ this.from = from;
+ this.until = until;
+ }
+
+ private void check(final Date fromDate, final Date untilDate)
+ {
+ if (fromDate != null && untilDate != null && fromDate.getTime() > untilDate.getTime())
+ {
+ throw new IllegalArgumentException("From date is after until date: " + fromDate + " > "
+ + untilDate);
+ }
+ }
+
+ public final Date getFrom()
+ {
+ return from;
+ }
+
+ public final void setFrom(final Date from)
+ {
+ check(until, from);
+ this.from = from;
+ }
+
+ public final Date getUntil()
+ {
+ return until;
+ }
+
+ public final void setUntil(final Date until)
+ {
+ check(until, from);
+ this.until = until;
+ }
+
+ public final boolean isInside(final Date date)
+ {
+ assert date != null : "Unspecified date.";
+ final long time = date.getTime();
+ return (from == null || from.getTime() <= time)
+ && (until == null || time <= until.getTime());
+ }
+
+ public final boolean overlapsWith(final TimeInterval timeInterval)
+ {
+ assert timeInterval != null : "Unspecified time interval.";
+ return isBeforeOrEqual(from, timeInterval.getUntil())
+ && isBeforeOrEqual(timeInterval.getFrom(), until);
+ }
+
+ /**
+ * Whether given <var>olderDate</var> is before or equal to given <var>youngerDate</var>.
+ * <p>
+ * Returns <code>true</code> if one of given arguments is <code>null</code>.
+ * </p>
+ */
+ private final static boolean isBeforeOrEqual(final Date olderDate, final Date youngerDate)
+ {
+ return olderDate == null || youngerDate == null
+ || olderDate.getTime() <= youngerDate.getTime();
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof TimeInterval == false)
+ {
+ return false;
+ }
+ final TimeInterval that = (TimeInterval) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(that.from, from);
+ builder.append(that.until, until);
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(from);
+ builder.append(until);
+ 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/ValidationMessages.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
new file mode 100644
index 00000000000..5fa54478317
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+/**
+ * This class lists the validation messages.
+ * <p>
+ * Each field definition follows schema:
+ * <code><field-name>_<validation-annotation>_MESSAGE</code>.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class ValidationMessages
+{
+
+ private static final String CAN_NOT_BE_NULL = " can not be null.";
+
+ private static final String LENGTH_PREFIX = "Given ";
+
+ private static final String LENGTH_SUFFIX =
+ " '%s' is too long (maximal length: {max} characters).";
+
+ public static final String ATTACHMENT_CONTENT_NOT_NULL_MESSAGE =
+ "The content of the attachment" + CAN_NOT_BE_NULL;
+
+ public static final String CODE_LENGTH_MESSAGE =
+ "Given code '%s' is either too short (minimal length: {min} character) "
+ + "or too long (maximal length: {max} characters).";
+
+ public static final String CODE_NOT_NULL_MESSAGE = "Code" + CAN_NOT_BE_NULL;
+
+ public static final String CODE_PATTERN_MESSAGE =
+ "Given code '%s' contains illegal characters (allowed: A-Z, a-z, 0-9, _ and -)";
+
+ public static final String DATA_TYPE_NOT_NULL_MESSAGE = "Data type" + CAN_NOT_BE_NULL;
+
+ public static final String DATABASE_INSTANCE_NOT_NULL_MESSAGE =
+ "Database instance" + CAN_NOT_BE_NULL;
+
+ public final static String DESCRIPTION_LENGTH_MESSAGE =
+ LENGTH_PREFIX + "description" + LENGTH_SUFFIX;
+
+ public static final String DESCRIPTION_NOT_NULL_MESSAGE = "Description" + CAN_NOT_BE_NULL;
+
+ public static final String DOWNLOAD_URL_NOT_NULL_MESSAGE = "Download URL" + CAN_NOT_BE_NULL;
+
+ public static final String EMAIL_EMAIL_MESSAGE = "Given email address '%s' is not a valid one.";
+
+ public static final String EMAIL_LENGTH_MESSAGE =
+ LENGTH_PREFIX + "email address" + LENGTH_SUFFIX;
+
+ public static final String EXPERIMENT_NOT_NULL_MESSAGE = "Experiment " + CAN_NOT_BE_NULL;
+
+ public static final String EXPERIMENT_TYPE_NOT_NULL_MESSAGE =
+ "Experiment type" + CAN_NOT_BE_NULL;
+
+ public static final String EXPERIMENT_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
+ "Experiment type - property type" + CAN_NOT_BE_NULL;
+
+ public static final String FILE_FORMAT_TYPE_NOT_NULL_MESSAGE =
+ "File format type" + CAN_NOT_BE_NULL;
+
+ public static final String FILE_NAME_LENGTH_MESSAGE =
+ LENGTH_PREFIX + "file name" + LENGTH_SUFFIX;
+
+ public static final String FILE_NAME_NOT_NULL_MESSAGE = "File name" + CAN_NOT_BE_NULL;
+
+ public static final String FIRST_NAME_LENGTH_MESSAGE =
+ LENGTH_PREFIX + "first name" + LENGTH_SUFFIX;
+
+ public static final String GROUP_NOT_NULL_MESSAGE = "Group" + CAN_NOT_BE_NULL;
+
+ public static final String IS_COMPLETE_NOT_NULL_MESSAGE = "Complete flag" + CAN_NOT_BE_NULL;
+
+ public static final String LABEL_LENGTH_MESSAGE = LENGTH_PREFIX + "label" + LENGTH_SUFFIX;
+
+ public static final String LABEL_NOT_NULL_MESSAGE = "Label" + CAN_NOT_BE_NULL;
+
+ public static final String LAST_NAME_LENGTH_MESSAGE =
+ LENGTH_PREFIX + "last name" + LENGTH_SUFFIX;
+
+ public static final String LOCATION_LENGTH_MESSAGE = LENGTH_PREFIX + "location" + LENGTH_SUFFIX;
+
+ public static final String LOCATION_NOT_NULL_MESSAGE = "Location" + CAN_NOT_BE_NULL;
+
+ public static final String LOCATION_NOT_RELATIVE = "Location is not relative";
+
+ public static final String LOCATOR_TYPE_NOT_NULL_MESSAGE = "Locator type" + CAN_NOT_BE_NULL;
+
+ public static final String MATERIAL_TYPE_NOT_NULL_MESSAGE = "Material type" + CAN_NOT_BE_NULL;
+
+ public static final String MATERIAL_NOT_NULL_MESSAGE = "Material" + CAN_NOT_BE_NULL;
+
+ public static final String MATERIAL_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
+ "Material type - property type" + CAN_NOT_BE_NULL;
+
+ public static final String DATA_SET_TYPE_NOT_NULL_MESSAGE = "Data set type" + CAN_NOT_BE_NULL;
+
+ public static final String PERSON_NOT_NULL_MESSAGE = "Person" + CAN_NOT_BE_NULL;
+
+ public static final String PROCEDURE_NOT_NULL_MESSAGE = "Procedure" + CAN_NOT_BE_NULL;
+
+ public static final String PROPERTY_TYPE_NOT_NULL_MESSAGE = "Property type" + CAN_NOT_BE_NULL;
+
+ public static final String ROLE_NOT_NULL_MESSAGE = "Role" + CAN_NOT_BE_NULL;
+
+ public static final String SAMPLE_TYPE_NOT_NULL_MESSAGE = "Sample type" + CAN_NOT_BE_NULL;
+
+ public static final String SAMPLE_TYPE_PROPERTY_TYPE_NOT_NULL_MESSAGE =
+ "Sample type - property type" + CAN_NOT_BE_NULL;
+
+ public static final String STORAGE_FORMAT_NOT_NULL_MESSAGE = "Storage format" + CAN_NOT_BE_NULL;
+
+ public static final String USER_ID_LENGTH_MESSAGE = LENGTH_PREFIX + "user id" + LENGTH_SUFFIX;
+
+ public static final String USER_ID_NOT_NULL_MESSAGE = "User id" + CAN_NOT_BE_NULL;
+
+ public static final String UUID_NOT_NULL_MESSAGE = "UUID" + CAN_NOT_BE_NULL;
+
+ public static final String VALUE_LENGTH_MESSAGE = LENGTH_PREFIX + "value" + LENGTH_SUFFIX;
+
+ public static final String VERSION_NOT_NULL_MESSAGE = "Version" + CAN_NOT_BE_NULL;
+
+ public static final String VOCABULARY_NOT_NULL_MESSAGE = "Vocabulary" + CAN_NOT_BE_NULL;
+
+ public static final String PROJECT_NOT_NULL_MESSAGE = "Project" + CAN_NOT_BE_NULL;
+
+ private ValidationMessages()
+ {
+ // Can not be instantiated.
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyPE.java
new file mode 100644
index 00000000000..97f6d55b670
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyPE.java
@@ -0,0 +1,240 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.List;
+
+import javax.persistence.CascadeType;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing controlled vocabulary.
+ *
+ * @author Tomasz Pylak
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.CONTROLLED_VOCABULARY_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.IS_INTERNAL_NAMESPACE,
+ ColumnNames.DATABASE_INSTANCE_COLUMN }) })
+public class VocabularyPE extends HibernateAbstractRegistratrationHolder implements
+ IIdAndCodeHolder, Comparable<VocabularyPE>, Serializable
+{
+
+ public final static VocabularyPE[] EMPTY_ARRAY = new VocabularyPE[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private transient Long id;
+
+ private String simpleCode;
+
+ private String description;
+
+ private List<VocabularyTermPE> terms = VocabularyTermPE.EMPTY_LIST;
+
+ private boolean managedInternally;
+
+ private boolean internalNamespace;
+
+ private DatabaseInstancePE databaseInstance;
+
+ public VocabularyPE()
+ {
+ }
+
+ @Column(name = ColumnNames.CODE_COLUMN)
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ private String getSimpleCode()
+ {
+ return simpleCode;
+ }
+
+ /**
+ * Sets code in 'database format' - without 'user prefix'. To set full code (with user prefix
+ * use {@link #setCode(String)}).
+ */
+ private void setSimpleCode(final String simpleCode)
+ {
+ this.simpleCode = simpleCode;
+ }
+
+ @Column(name = ColumnNames.DESCRIPTION_COLUMN)
+ @Length(max = 80, message = ValidationMessages.DESCRIPTION_LENGTH_MESSAGE)
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(final String descriptionOrNull)
+ {
+ this.description = descriptionOrNull;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+ @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "vocabulary")
+ public List<VocabularyTermPE> getTerms()
+ {
+ return terms;
+ }
+
+ @SequenceGenerator(name = SequenceNames.CONTROLLED_VOCABULARY_SEQUENCE, sequenceName = SequenceNames.CONTROLLED_VOCABULARY_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.CONTROLLED_VOCABULARY_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public void setTerms(final List<VocabularyTermPE> terms)
+ {
+ for (final VocabularyTermPE term : terms)
+ {
+ term.setVocabulary(this);
+ }
+ this.terms = terms;
+ }
+
+ @Column(name = ColumnNames.IS_MANAGED_INTERNALLY, nullable = false)
+ public boolean isManagedInternally()
+ {
+ return managedInternally;
+ }
+
+ public void setManagedInternally(final boolean managedInternally)
+ {
+ this.managedInternally = managedInternally;
+ }
+
+ @Column(name = ColumnNames.IS_INTERNAL_NAMESPACE, nullable = false)
+ public boolean isInternalNamespace()
+ {
+ return internalNamespace;
+ }
+
+ public void setInternalNamespace(final boolean internalNamespace)
+ {
+ this.internalNamespace = internalNamespace;
+ }
+
+ public void setId(final long id)
+ {
+ this.id = id;
+
+ }
+
+ public void setCode(final String fullCode)
+ {
+ setInternalNamespace(CodeConverter.isInternalNamespace(fullCode));
+ setSimpleCode(CodeConverter.tryToDatabase(fullCode));
+ }
+
+ @Transient
+ public String getCode()
+ {
+ return CodeConverter.tryToBusinessLayer(getSimpleCode(), isInternalNamespace() == false);
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof VocabularyPE == false)
+ {
+ return false;
+ }
+ final VocabularyPE that = (VocabularyPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("simpleCode", getSimpleCode());
+ builder.append("internalNamespace", isInternalNamespace());
+ builder.append("managedInternally", isManagedInternally());
+ return builder.toString();
+ }
+
+ //
+ // Comparable
+ //
+
+ public final int compareTo(final VocabularyPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+}
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
new file mode 100644
index 00000000000..0139df65fea
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/VocabularyTermPE.java
@@ -0,0 +1,162 @@
+/*
+ * Copyright 2008 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.shared.dto;
+
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.List;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.hibernate.validator.Length;
+import org.hibernate.validator.NotNull;
+import org.hibernate.validator.Pattern;
+
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Persistence entity representing vocabulary term.
+ *
+ * @author Tomasz Pylak
+ * @author Izabela Adamczyk
+ */
+@Entity
+@Table(name = TableNames.CONTROLLED_VOCABULARY_TERM_TABLE, uniqueConstraints =
+ { @UniqueConstraint(columnNames =
+ { ColumnNames.CODE_COLUMN, ColumnNames.CONTROLLED_VOCABULARY_COLUMN }) })
+public class VocabularyTermPE extends HibernateAbstractRegistratrationHolder implements
+ IIdAndCodeHolder, Comparable<VocabularyTermPE>, Serializable
+{
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final List<VocabularyTermPE> EMPTY_LIST = Collections.emptyList();
+
+ public static final VocabularyTermPE[] EMPTY_ARRAY = new VocabularyTermPE[0];
+
+ private transient Long id;
+
+ private String code;
+
+ private VocabularyPE vocabulary;
+
+ public VocabularyTermPE()
+ {
+ }
+
+ @NotNull(message = ValidationMessages.CODE_NOT_NULL_MESSAGE)
+ @Length(min = 1, max = 40, message = ValidationMessages.CODE_LENGTH_MESSAGE)
+ @Pattern(regex = AbstractIdAndCodeHolder.CODE_PATTERN, flags = java.util.regex.Pattern.CASE_INSENSITIVE, message = ValidationMessages.CODE_PATTERN_MESSAGE)
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(final String code)
+ {
+ this.code = CodeConverter.tryToDatabase(code);
+ }
+
+ public void setId(final long id)
+ {
+ this.id = id;
+
+ }
+
+ @SequenceGenerator(name = SequenceNames.CONTROLLED_VOCABULARY_TERM_SEQUENCE, sequenceName = SequenceNames.CONTROLLED_VOCABULARY_TERM_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.CONTROLLED_VOCABULARY_TERM_SEQUENCE)
+ public Long getId()
+ {
+ return id;
+ }
+
+ @NotNull(message = ValidationMessages.VOCABULARY_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.CONTROLLED_VOCABULARY_COLUMN, updatable = false)
+ public VocabularyPE getVocabulary()
+ {
+ return vocabulary;
+ }
+
+ public void setVocabulary(final VocabularyPE vocabulary)
+ {
+ this.vocabulary = vocabulary;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof VocabularyTermPE == false)
+ {
+ return false;
+ }
+ final VocabularyTermPE that = (VocabularyTermPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getCode(), that.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public final String toString()
+ {
+ final ToStringBuilder builder =
+ new ToStringBuilder(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ builder.append("code", getCode());
+ return builder.toString();
+ }
+
+ //
+ // Comparable
+ //
+
+ public final int compareTo(final VocabularyTermPE o)
+ {
+ return AbstractIdAndCodeHolder.compare(this, o);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/exception/UndefinedGroupException.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/exception/UndefinedGroupException.java
new file mode 100644
index 00000000000..0f4f210f89e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/exception/UndefinedGroupException.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2007 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.shared.dto.exception;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * This <code>UserFailureException</code> extension signals that no group has been specified.
+ *
+ * @author Christian Ribeaud
+ */
+public final class UndefinedGroupException extends UserFailureException
+{
+ private static final long serialVersionUID = 1L;
+
+ private final static String MESSAGE = "Group not specified, home group unknown";
+
+ public UndefinedGroupException()
+ {
+ super(MESSAGE);
+ }
+}
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
new file mode 100644
index 00000000000..3037e5a93ed
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/Location.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright 2008 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.shared.dto.hibernate;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.ElementType.METHOD;
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+import org.hibernate.validator.ValidatorClass;
+
+/**
+ * The string has to be a location
+ *
+ * @author Christian Ribeaud
+ */
+@Target(
+ { METHOD, FIELD })
+@Retention(RetentionPolicy.RUNTIME)
+@Documented
+@ValidatorClass(LocationValidator.class)
+public @interface Location
+{
+
+ /**
+ * Whether given location must be relative or not. Default is <code>true</code>.
+ */
+ boolean relative() default true;
+
+ String message() default "{validator.location}";
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/LocationValidator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/LocationValidator.java
new file mode 100644
index 00000000000..232205c4b37
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/hibernate/LocationValidator.java
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2008 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.shared.dto.hibernate;
+
+import java.io.Serializable;
+
+import org.apache.commons.io.FilenameUtils;
+import org.hibernate.validator.Validator;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Check a specified location.
+ *
+ * @author Christian Ribeaud
+ */
+public final class LocationValidator implements Validator<Location>, Serializable
+{
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private boolean relative;
+
+ //
+ // Validator
+ //
+
+ public final void initialize(final Location location)
+ {
+ relative = location.relative();
+ }
+
+ public final boolean isValid(final Object value)
+ {
+ final String location = (String) value;
+ final int prefixLength = FilenameUtils.getPrefixLength(location);
+ if (relative)
+ {
+ return prefixLength == 0;
+ } else
+ {
+ return prefixLength > 0;
+ }
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifier.java
new file mode 100644
index 00000000000..10f0205b262
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifier.java
@@ -0,0 +1,139 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.common.utilities.StringUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Uniquely identifies a database instance.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DatabaseInstanceIdentifier implements Serializable
+{
+ public final static class Constants
+ {
+ public static final char IDENTIFIER_SEPARATOR = '/';
+
+ public static final char DATABASE_INSTANCE_SEPARATOR = ':';
+ }
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /** see {@link #getDatabaseInstanceCode()} documentation */
+ private String databaseInstanceCode;
+
+ public static final String HOME = null;
+
+ public static DatabaseInstanceIdentifier createHome()
+ {
+ return new DatabaseInstanceIdentifier(HOME);
+ }
+
+ public DatabaseInstanceIdentifier(final String databaseInstanceCode)
+ {
+ this.databaseInstanceCode = databaseInstanceCode;
+ }
+
+ /**
+ * Usually you should not access database instance code directly. Look for appropriate helpers.
+ *
+ * @return local or <i>UUID</i> of the database instance. It is treated as <i>UUID</i> if it
+ * has a canonical UUID format.
+ */
+ public final String getDatabaseInstanceCode()
+ {
+ return StringUtils.upperCase(databaseInstanceCode);
+ }
+
+ public final void setDatabaseInstanceCode(final String databaseInstanceCode)
+ {
+ this.databaseInstanceCode = databaseInstanceCode;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof DatabaseInstanceIdentifier == false)
+ {
+ return false;
+ }
+ final DatabaseInstanceIdentifier that = (DatabaseInstanceIdentifier) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getDatabaseInstanceCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ if (databaseInstanceCode == null)
+ {
+ return "";
+ } else
+ {
+ return databaseInstanceCode;
+ }
+ }
+
+ public boolean isHomeDatabase()
+ {
+ return databaseInstanceCode == null;
+ }
+
+ /** Do not use this method. It exists just to make automatic bean conversion possible */
+ @Deprecated
+ public void setHomeDatabase(boolean isHomeDatabase)
+ {
+ // empty
+ }
+
+ /** Do not use this constructor. It exists just to make automatic bean conversion possible */
+ @Deprecated
+ public DatabaseInstanceIdentifier()
+ {
+ }
+
+ public int compareTo(DatabaseInstanceIdentifier other)
+ {
+ return StringUtilities.compareNullable(databaseInstanceCode, other
+ .getDatabaseInstanceCode());
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifier.java
new file mode 100644
index 00000000000..28b54034a85
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifier.java
@@ -0,0 +1,124 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifies an experiment.
+ *
+ * @author Izabela Adamczyk
+ */
+public final class ExperimentIdentifier extends ProjectIdentifier
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ final static String CODE_SEPARATOR = "/";
+
+ private String experimentCode;
+
+ public ExperimentIdentifier()
+ {
+ this(null, null, null, null);
+ }
+
+ public ExperimentIdentifier(final ProjectIdentifier projectIdentifier, final String experimentCode)
+ {
+ this(projectIdentifier.getDatabaseInstanceCode(), projectIdentifier.getGroupCode(),
+ projectIdentifier.getProjectCode(), experimentCode);
+ }
+
+ public ExperimentIdentifier(final String projectCode, final String experimentCode)
+ {
+ this(DatabaseInstanceIdentifier.HOME, GroupIdentifier.HOME_GROUP, projectCode,
+ experimentCode);
+ }
+
+ public ExperimentIdentifier(final String databaseInstanceCode, final String groupCode,
+ final String projectCode, final String experimentCode)
+ {
+ super(databaseInstanceCode, groupCode, projectCode);
+ setExperimentCode(experimentCode);
+ }
+
+ public String getExperimentCode()
+ {
+ return StringUtils.upperCase(experimentCode);
+ }
+
+ public void setExperimentCode(final String experimentCode)
+ {
+ this.experimentCode = experimentCode;
+ }
+
+ /**
+ * Returns an unique description of this object.
+ */
+ public final String describe()
+ {
+ final StringBuilder builder = new StringBuilder();
+ builder.append(getProjectCode());
+ builder.append(CODE_SEPARATOR);
+ builder.append(getExperimentCode());
+ return builder.toString();
+ }
+
+ //
+ // ProjectIdentifier
+ //
+
+ @Override
+ public final String toString()
+ {
+ return super.toString() + Constants.IDENTIFIER_SEPARATOR + experimentCode;
+ }
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ExperimentIdentifier == false)
+ {
+ return false;
+ }
+ final ExperimentIdentifier that = (ExperimentIdentifier) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ builder.append(getGroupCode(), that.getGroupCode());
+ builder.append(getProjectCode(), that.getProjectCode());
+ builder.append(getExperimentCode(), that.getExperimentCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getDatabaseInstanceCode());
+ builder.append(getGroupCode());
+ builder.append(getProjectCode());
+ builder.append(getExperimentCode());
+ return builder.toHashCode();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifier.java
new file mode 100644
index 00000000000..1a055b98212
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifier.java
@@ -0,0 +1,140 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.common.utilities.StringUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifies a group.
+ *
+ * @author Izabela Adamczyk
+ */
+public class GroupIdentifier extends DatabaseInstanceIdentifier
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String groupCodeOrNull;
+
+ public static final String HOME_GROUP = null;
+
+ public static GroupIdentifier createHome()
+ {
+ return new GroupIdentifier(HOME_GROUP, DatabaseInstanceIdentifier.HOME);
+ }
+
+ public GroupIdentifier(final DatabaseInstanceIdentifier databaseInstanceIdentifier,
+ final String groupCode)
+ {
+ this(databaseInstanceIdentifier.getDatabaseInstanceCode(), groupCode);
+ }
+
+ public GroupIdentifier(final String databaseInstanceCode, final String groupCode)
+ {
+ super(databaseInstanceCode);
+ setGroupCode(groupCode);
+ }
+
+ public final String getGroupCode()
+ {
+ return StringUtils.upperCase(groupCodeOrNull);
+ }
+
+ public final void setGroupCode(final String groupCode)
+ {
+ this.groupCodeOrNull = groupCode;
+ }
+
+ //
+ // DatabaseInstanceIdentifier
+ //
+
+ @Override
+ public boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof GroupIdentifier == false)
+ {
+ return false;
+ }
+ final GroupIdentifier that = (GroupIdentifier) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ builder.append(getGroupCode(), that.getGroupCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getDatabaseInstanceCode());
+ builder.append(getGroupCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ if (getDatabaseInstanceCode() == null)
+ {
+ return Constants.IDENTIFIER_SEPARATOR + groupCodeOrNull;
+ } else
+ {
+ return super.toString() + Constants.DATABASE_INSTANCE_SEPARATOR
+ + Constants.IDENTIFIER_SEPARATOR + groupCodeOrNull;
+ }
+ }
+
+ public boolean isHomeGroup()
+ {
+ return groupCodeOrNull == null;
+ }
+
+ /** Do not use this constructor. It exists just to make automatic bean conversion possible */
+ @Deprecated
+ public GroupIdentifier()
+ {
+ super();
+ }
+
+ /** this method exists just to make automatic bean conversion possible */
+ @Deprecated
+ public void setHomeGroup(boolean isHomeGroup)
+ {
+ // empty
+ }
+
+ public int compareTo(GroupIdentifier other)
+ {
+ int dbCompare = super.compareTo(other);
+ if (dbCompare == 0)
+ {
+ return StringUtilities.compareNullable(getGroupCode(), other.getGroupCode());
+ } else
+ {
+ return dbCompare;
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
new file mode 100644
index 00000000000..d8e46c1ac4b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/IdentifierHelper.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * Some useful methods around identifiers.
+ *
+ * @author Christian Ribeaud
+ */
+public final class IdentifierHelper
+{
+
+ private IdentifierHelper()
+ {
+ // Can not be instantiated.
+ }
+
+ /**
+ * Creates a {@link GroupIdentifier} from given <var>groupPE</var>.
+ */
+ public final static GroupIdentifier createIdentifier(final GroupPE groupPE)
+ {
+ assert groupPE != null : "Unspecified group";
+ assert groupPE.getDatabaseInstance() != null : "Any group must "
+ + "be attached to a database instance";
+ return new GroupIdentifier(groupPE.getDatabaseInstance().getCode(), groupPE.getCode());
+ }
+
+ /**
+ * Creates a {@link GroupIdentifier} from given <var>groupPE</var>.
+ */
+ public final static DatabaseInstanceIdentifier createIdentifier(
+ final DatabaseInstancePE databaseInstancePE)
+ {
+ assert databaseInstancePE != null : "Unspecified database instance";
+ return new DatabaseInstanceIdentifier(databaseInstancePE.getCode());
+ }
+
+ /**
+ * Creates a {@link SampleIdentifier} from given <var>samplePE</var>.
+ */
+ public final static SampleIdentifier createIdentifier(final SamplePE samplePE)
+ {
+ assert samplePE != null : "Unspecified sample";
+ final DatabaseInstancePE databaseInstance = samplePE.getDatabaseInstance();
+ final GroupPE group = samplePE.getGroup();
+ final String sampleCode = samplePE.getCode();
+ if (databaseInstance != null)
+ {
+ return new SampleIdentifier(createIdentifier(databaseInstance), sampleCode);
+ } else if (group != null)
+ {
+ return new SampleIdentifier(createIdentifier(group), samplePE.getCode());
+ } else
+ {
+ return SampleIdentifier.createHomeGroup(sampleCode);
+ }
+ }
+
+ /**
+ * Creates a {@link ProjectIdentifier} from given <var>project</var>.
+ */
+ public final static ProjectIdentifier createIdentifier(final ProjectPE project)
+ {
+ assert project != null : "Unspecified project";
+ final GroupPE group = project.getGroup();
+ final DatabaseInstancePE databaseInstance = group.getDatabaseInstance();
+ final ProjectIdentifier identifier =
+ new ProjectIdentifier(databaseInstance.getCode(), group.getCode(), project
+ .getCode());
+ return identifier;
+ }
+
+ /**
+ * Creates a {@link ExperimentIdentifier} from given <var>experiment</var>.
+ */
+ public final static ExperimentIdentifier createIdentifier(final ExperimentPE experiment)
+ {
+ assert experiment != null : "Unspecified experiment";
+ final ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifier(createIdentifier(experiment.getProject()), experiment
+ .getCode());
+ return experimentIdentifier;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/MaterialIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/MaterialIdentifier.java
new file mode 100644
index 00000000000..af69d5e3a99
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/MaterialIdentifier.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2007 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.shared.dto.identifier;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifier for searching material through <i>Web Service</i> lookup methods in the database.
+ *
+ * @author Christian Ribeaud
+ */
+public final class MaterialIdentifier extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ /**
+ * The material code of this material: together with typeCode uniquely identifies the material.
+ * <p>
+ * Could not be <code>null</code>.
+ * </p>
+ */
+ private String code;
+
+ /**
+ * The code of material type of this material: together with code uniquely identifies the
+ * material.
+ * <p>
+ * Could not be <code>null</code>.
+ * </p>
+ */
+ private String typeCode;
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ public final void setCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public String getTypeCode()
+ {
+ return typeCode;
+ }
+
+ public void setTypeCode(final String typeCode)
+ {
+ this.typeCode = typeCode;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifier.java
new file mode 100644
index 00000000000..47f3a07d95f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifier.java
@@ -0,0 +1,102 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifies a project.
+ *
+ * @author Izabela Adamczyk
+ */
+public class ProjectIdentifier extends GroupIdentifier
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String projectCode;
+
+ public ProjectIdentifier(final String instanceCode, final String groupCode,
+ final String projectCode)
+ {
+ super(instanceCode, groupCode);
+ setProjectCode(projectCode);
+ }
+
+ public ProjectIdentifier(final String groupCode, final String projectCode)
+ {
+ this(null, groupCode, projectCode);
+ }
+
+ public String getProjectCode()
+ {
+ return StringUtils.upperCase(projectCode);
+ }
+
+ public void setProjectCode(final String projectCode)
+ {
+ this.projectCode = projectCode;
+ }
+
+ //
+ // GroupIdentifier
+ //
+
+ @Override
+ public boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof ProjectIdentifier == false)
+ {
+ return false;
+ }
+ final ProjectIdentifier that = (ProjectIdentifier) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ builder.append(getGroupCode(), that.getGroupCode());
+ builder.append(getProjectCode(), that.getProjectCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getDatabaseInstanceCode());
+ builder.append(getGroupCode());
+ builder.append(getProjectCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ if (getGroupCode() == null)
+ {
+ return projectCode;
+ } else
+ {
+ return super.toString() + Constants.IDENTIFIER_SEPARATOR + projectCode;
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
new file mode 100644
index 00000000000..5d0e27a7f7d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifier.java
@@ -0,0 +1,116 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import ch.systemsx.cisd.common.exceptions.InternalErr;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifies a sample.
+ *
+ * @author Izabela Adamczyk
+ * @author Tomasz Pylak
+ */
+public class SampleIdentifier extends SampleOwnerIdentifier implements Comparable<SampleIdentifier>
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ public static final SampleIdentifier[] EMPTY_ARRAY = new SampleIdentifier[0];
+
+ private String sampleCode;
+
+ private SampleIdentifier(final DatabaseInstanceIdentifier databaseInstanceIdentOrNull,
+ final GroupIdentifier groupIdentOrNull, final String sampleCode)
+ {
+ super(databaseInstanceIdentOrNull, groupIdentOrNull);
+ this.sampleCode = sampleCode;
+ }
+
+ public static SampleIdentifier createOwnedBy(final SampleOwnerIdentifier owner,
+ final String sampleCode)
+ {
+ if (owner.isDatabaseInstanceLevel())
+ {
+ return new SampleIdentifier(owner.getDatabaseInstanceLevel(), sampleCode);
+ } else if (owner.isGroupLevel())
+ {
+ return new SampleIdentifier(owner.getGroupLevel(), sampleCode);
+ } else
+ {
+ throw InternalErr.error();
+ }
+ }
+
+ /** Database-instance level {@link SampleIdentifier}. */
+ public SampleIdentifier(final DatabaseInstanceIdentifier instanceIdentifier,
+ final String sampleCode)
+ {
+ this(instanceIdentifier, null, sampleCode);
+ }
+
+ /** Group level {@link SampleIdentifier}. */
+ public SampleIdentifier(final GroupIdentifier groupIdentifier, final String sampleCode)
+ {
+ this(null, groupIdentifier, sampleCode);
+ }
+
+ /** Home group level {@link SampleIdentifier} with type. */
+ public static SampleIdentifier createHomeGroup(final String sampleCode)
+ {
+ return new SampleIdentifier(GroupIdentifier.createHome(), sampleCode);
+ }
+
+ public String getSampleCode()
+ {
+ return sampleCode;
+ }
+
+ @Override
+ public String toString()
+ {
+ return super.toString() + sampleCode;
+ }
+
+ @Deprecated
+ public void setSampleCode(final String sampleCode)
+ {
+ this.sampleCode = sampleCode;
+ }
+
+ // for bean conversion only!
+ @Deprecated
+ public SampleIdentifier()
+ {
+ super(null, null);
+ }
+
+ //
+ // Comparable
+ //
+
+ public int compareTo(final SampleIdentifier o)
+ {
+ final int ownerCmp = super.compareTo(o);
+ if (ownerCmp == 0)
+ {
+ return sampleCode.compareTo(o.sampleCode);
+ } else
+ {
+ return ownerCmp;
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierPattern.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierPattern.java
new file mode 100644
index 00000000000..b14322ec906
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierPattern.java
@@ -0,0 +1,89 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Identifies a group of samples on the same level (in certain group or on database level)
+ *
+ * @author Tomasz Pylak
+ */
+public class SampleIdentifierPattern extends AbstractHashable implements Serializable
+{
+ public final static SampleIdentifierPattern[] EMPTY_ARRAY = new SampleIdentifierPattern[0];
+
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private final SampleOwnerIdentifier owner;
+
+ private final String sampleCodePattern;
+
+ /**
+ * Matches samples from the specified group and the database instance to which this group
+ * belongs. Only samples with the code matching sampleCodePattern will be selected.
+ */
+ public static SampleIdentifierPattern[] createGroupVisible(GroupIdentifier groupIdentifier,
+ String sampleCodePattern)
+ {
+ SampleOwnerIdentifier groupOwner = new SampleOwnerIdentifier(groupIdentifier);
+ SampleIdentifierPattern groupPattern =
+ new SampleIdentifierPattern(sampleCodePattern, groupOwner);
+
+ SampleOwnerIdentifier dbOwner =
+ new SampleOwnerIdentifier((DatabaseInstanceIdentifier) groupIdentifier);
+ SampleIdentifierPattern dbPattern = new SampleIdentifierPattern(sampleCodePattern, dbOwner);
+
+ return new SampleIdentifierPattern[]
+ { groupPattern, dbPattern };
+ }
+
+ /**
+ * Matches samples owned by the specified owner. Only samples with the code matching
+ * sampleCodePattern will be selected.
+ */
+ public static SampleIdentifierPattern createOwnedBy(SampleOwnerIdentifier owner,
+ String sampleCodePattern)
+ {
+ return new SampleIdentifierPattern(sampleCodePattern, owner);
+ }
+
+ private SampleIdentifierPattern(String sampleCodePattern, SampleOwnerIdentifier owner)
+ {
+ this.owner = owner;
+ this.sampleCodePattern = sampleCodePattern;
+ }
+
+ public SampleOwnerIdentifier getSampleOwner()
+ {
+ return owner;
+ }
+
+ public String getSampleCodePattern()
+ {
+ return sampleCodePattern;
+ }
+
+ @Override
+ public String toString()
+ {
+ return owner.toString() + sampleCodePattern;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleOwnerIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleOwnerIdentifier.java
new file mode 100644
index 00000000000..26ab745b2c2
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleOwnerIdentifier.java
@@ -0,0 +1,182 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier.Constants;
+
+/**
+ * Identifies an owner of a sample: group or database instance.
+ *
+ * @author Tomasz Pylak
+ */
+public class SampleOwnerIdentifier extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ // if not null, sample is defined on the group level
+ private GroupIdentifier groupIdentOrNull;
+
+ // if not null, sample is defined on the database instance level
+ private DatabaseInstanceIdentifier databaseInstanceIdentOrNull;
+
+ protected SampleOwnerIdentifier(final DatabaseInstanceIdentifier databaseInstanceIdentOrNull,
+ final GroupIdentifier groupIdentOrNull)
+ {
+ this.databaseInstanceIdentOrNull = databaseInstanceIdentOrNull;
+ this.groupIdentOrNull = groupIdentOrNull;
+ }
+
+ /** Database-instance level {@link SampleOwnerIdentifier}. */
+ public SampleOwnerIdentifier(final DatabaseInstanceIdentifier instanceIdentifier)
+ {
+ this(checkNotNull(instanceIdentifier), null);
+ }
+
+ private static DatabaseInstanceIdentifier checkNotNull(DatabaseInstanceIdentifier identifier)
+ {
+ assert identifier != null : "database identifier cannot be null";
+ return identifier;
+ }
+
+ /** Group level {@link SampleOwnerIdentifier}. */
+ public SampleOwnerIdentifier(final GroupIdentifier groupIdentifier)
+ {
+ this(null, checkNotNull(groupIdentifier));
+ }
+
+ private static GroupIdentifier checkNotNull(GroupIdentifier identifier)
+ {
+ assert identifier != null : "group identifier cannot be null";
+ return identifier;
+ }
+
+ /** @return if sample is connected to its home group */
+ public boolean isInsideHomeGroup()
+ {
+ return isGroupLevel() && groupIdentOrNull.isHomeGroup();
+ }
+
+ /**
+ * true if sample belongs to the group. {@link #isDatabaseInstanceLevel()} will return false in
+ * such a case.
+ */
+ public boolean isGroupLevel()
+ {
+ return groupIdentOrNull != null;
+ }
+
+ /**
+ * true if sample belongs to the database instance. {@link #isGroupLevel()} will return false in
+ * such a case.
+ */
+ public boolean isDatabaseInstanceLevel()
+ {
+ return databaseInstanceIdentOrNull != null;
+ }
+
+ @Override
+ public String toString()
+ {
+ if (isGroupLevel())
+ {
+ if (isInsideHomeGroup())
+ {
+ return "";
+ } else
+ {
+ return groupIdentOrNull.toString() + Constants.IDENTIFIER_SEPARATOR;
+ }
+ } else if (isDatabaseInstanceLevel())
+ {
+ if (databaseInstanceIdentOrNull.isHomeDatabase())
+ {
+ return "" + Constants.IDENTIFIER_SEPARATOR;
+ } else
+ {
+ return databaseInstanceIdentOrNull.getDatabaseInstanceCode()
+ + Constants.DATABASE_INSTANCE_SEPARATOR + Constants.IDENTIFIER_SEPARATOR;
+ }
+ } else
+ {
+ throw new IllegalStateException("sample owner is unknown");
+ }
+ }
+
+ /**
+ * It is a good pattern to use {@link #isDatabaseInstanceLevel()} before calling this method.
+ *
+ * @return The database instance which is the owner or null if the owner is not a database
+ * instance but a group.
+ */
+ public DatabaseInstanceIdentifier getDatabaseInstanceLevel()
+ {
+ return databaseInstanceIdentOrNull;
+ }
+
+ /**
+ * It is a good pattern to use {@link #isGroupLevel()} before calling this method.
+ *
+ * @return The group which is the owner or null if the owner is not a group, but database
+ * instance.
+ */
+ public GroupIdentifier getGroupLevel()
+ {
+ return groupIdentOrNull;
+ }
+
+ // for bean conversion only!
+ @Deprecated
+ public void setGroupLevel(GroupIdentifier groupIdentOrNull)
+ {
+ this.groupIdentOrNull = groupIdentOrNull;
+ }
+
+ // for bean conversion only!
+ @Deprecated
+ public void setDatabaseInstanceLevel(DatabaseInstanceIdentifier databaseInstanceIdentOrNull)
+ {
+ this.databaseInstanceIdentOrNull = databaseInstanceIdentOrNull;
+ }
+
+ public int compareTo(SampleOwnerIdentifier other)
+ {
+ if (isGroupLevel())
+ {
+ if (other.isGroupLevel())
+ {
+ return getGroupLevel().compareTo(other.getGroupLevel());
+ } else
+ {
+ return 1;
+ }
+ } else if (isDatabaseInstanceLevel())
+ {
+ if (other.isGroupLevel())
+ {
+ return -1;
+ } else
+ {
+ return getDatabaseInstanceLevel().compareTo(other.getDatabaseInstanceLevel());
+ }
+ } else
+ throw new IllegalStateException("sample owner is unknown");
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityDataType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityDataType.java
new file mode 100644
index 00000000000..9bce0957a85
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityDataType.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2007 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.shared.dto.properties;
+
+import java.io.Serializable;
+
+/**
+ * Available types of entity properties in the database.
+ *
+ * @author Tomasz Pylak
+ */
+public enum EntityDataType implements Serializable
+{
+ INTEGER("INT"), VARCHAR("STRING"), REAL("DOUBLE"), TIMESTAMP("DATE"), BOOLEAN("BOOLEAN"),
+ CONTROLLEDVOCABULARY("VOCABULARY");
+
+ private final String niceRepresentation;
+
+ private EntityDataType(final String niceRepresentation)
+ {
+ this.niceRepresentation = niceRepresentation;
+ }
+
+ /**
+ * Returns a nice representation of this enumeration item.
+ */
+ public final String getNiceRepresentation()
+ {
+ return niceRepresentation;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public final String toString()
+ {
+ return getNiceRepresentation();
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
new file mode 100644
index 00000000000..cc46d50bb19
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityKind.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2007 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.shared.dto.properties;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
+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.ExperimentPropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePropertyTypePE;
+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.SampleTypePropertyTypePE;
+
+/**
+ * Enumeration of entity kinds.
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum EntityKind
+{
+ MATERIAL("material", MaterialTypePE.class, MaterialTypePropertyTypePE.class,
+ MaterialPropertyPE.class),
+
+ EXPERIMENT("experiment", ExperimentTypePE.class, ExperimentTypePropertyTypePE.class,
+ ExperimentPropertyPE.class),
+
+ SAMPLE("sample", SampleTypePE.class, SampleTypePropertyTypePE.class, SamplePropertyPE.class);
+
+ private final String entityLabel;
+
+ private transient final Class<?> typeClass;
+
+ private transient final Class<?> assignmentClass;
+
+ private transient final Class<?> propertyClass;
+
+ private EntityKind(final String entityLabel, final Class<?> typeClass,
+ final Class<?> assignmentClass, Class<?> propertyClass)
+ {
+ this.entityLabel = entityLabel;
+ this.typeClass = typeClass;
+ this.assignmentClass = assignmentClass;
+ this.propertyClass = propertyClass;
+ }
+
+ @SuppressWarnings("unchecked")
+ private final static <T> Class<T> cast(final Class<?> clazz)
+ {
+ return (Class<T>) clazz;
+ }
+
+ public final String getLabel()
+ {
+ return entityLabel;
+ }
+
+ public final <T extends EntityTypePE> Class<T> getTypeClass()
+ {
+ return cast(typeClass);
+ }
+
+ public final <T extends EntityTypePropertyTypePE> Class<T> getEntityTypePropertyTypeAssignmentClass()
+ {
+ return cast(assignmentClass);
+ }
+
+ public <T extends EntityPropertyPE> Class<T> getEntityPropertyClass()
+ {
+ return cast(propertyClass);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityProperties.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityProperties.java
new file mode 100644
index 00000000000..5d919b517fb
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityProperties.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2007 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.shared.dto.properties;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyTypeDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleEntityProperty;
+
+/**
+ * Type property implementation with some extensions used by DAOs.<br>
+ * Note that "orNull" and "try" naming convention is used everywhere.
+ *
+ * @author Tomasz Pylak
+ */
+public class EntityProperties extends AbstractHashable
+{
+ // TODO 2008-02-16, Tomasz Pylak: this field should be removed, setProperty has to have schema
+ // as parameter.
+ // It will make instance of this class smaller, so we could delete SimpleEntityProperty class
+ // and replace it with this class when axis web-service interface will not be used anymore.
+ private final EntityPropertyTypeDTOContainer propertyTypeContainer;
+
+ private final Map<String, EntityPropertyValue> properties;
+
+ public EntityProperties(final EntityPropertyTypeDTOContainer propertiesSchema)
+ {
+ this.properties = new LinkedHashMap<String, EntityPropertyValue>();
+ this.propertyTypeContainer = propertiesSchema;
+ createInitialProperties();
+ }
+
+ private final void createInitialProperties()
+ {
+ for (final String name : propertyTypeContainer.getAllPropertyCodes())
+ {
+ final EntityPropertyTypeDTO spec = propertyTypeContainer.getPropertyType(name);
+ final EntityPropertyValue value =
+ EntityPropertyValue.createFromUntyped(null, spec.getDataTypeCode());
+ properties.put(name, value);
+ }
+ }
+
+ public boolean hasProperty(final String name)
+ {
+ return properties.containsKey(name);
+ }
+
+ public final EntityPropertyValue getProperty(final String name) throws IllegalArgumentException
+ {
+ final EntityPropertyValue value = properties.get(name);
+ if (value == null)
+ {
+ throw new IllegalArgumentException("No entity property value for '" + name + "'.");
+ }
+ return value;
+ }
+
+ // checks if value is mandatory and casts it to appropriate type
+ public final void setProperty(final String name, final String untypedValueOrNull)
+ {
+ final EntityPropertyValue value =
+ propertyTypeContainer.validateAndCreateValue(name, untypedValueOrNull);
+ properties.put(name, value);
+ }
+
+ public static EntityProperties createFromSimple(final SimpleEntityProperty[] simpleProperties,
+ final EntityPropertyTypeDTOContainer propertySchema)
+ {
+ if (simpleProperties == null)
+ {
+ return null;
+ }
+ final EntityProperties properties = new EntityProperties(propertySchema);
+ for (int i = 0; i < simpleProperties.length; i++)
+ {
+ final SimpleEntityProperty property = simpleProperties[i];
+ final String name = property.getCode();
+ if (propertySchema.hasPropertySchema(name))
+ {
+ properties.setProperty(name, EntityPropertyValue.createFromSimple(property)
+ .tryGetUntypedValue());
+ } else
+ {
+ throw new IllegalArgumentException("Unknown property '" + name + "'.");
+ }
+ }
+ return properties;
+ }
+
+ public SimpleEntityProperty[] createSimple()
+ {
+ final List<SimpleEntityProperty> result = new ArrayList<SimpleEntityProperty>();
+ for (final Map.Entry<String, EntityPropertyValue> entry : properties.entrySet())
+ {
+ final String label =
+ propertyTypeContainer.getPropertyType(entry.getKey()).getPropertyType()
+ .getLabel();
+ SimpleEntityProperty property = entry.getValue().createSimple(entry.getKey(), label);
+ result.add(property);
+ }
+ return result.toArray(new SimpleEntityProperty[result.size()]);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyTypeDTOContainer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyTypeDTOContainer.java
new file mode 100644
index 00000000000..b00f37ad8fc
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyTypeDTOContainer.java
@@ -0,0 +1,219 @@
+/*
+ * Copyright 2007 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.shared.dto.properties;
+
+import java.util.Date;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyTypeDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+
+/**
+ * Stores a set ({@link Map}) of {@link EntityPropertyTypeDTO}s and provides useful methods.
+ *
+ * @author Tomasz Pylak
+ */
+public class EntityPropertyTypeDTOContainer extends AbstractHashable
+{
+ /**
+ * Factory method for creating {@link EntityPropertyTypeDTOContainer}s from
+ * {@link EntityPropertyTypeDTO} lists.
+ *
+ * @param propertyTypes
+ */
+ public static EntityPropertyTypeDTOContainer create(
+ final List<EntityPropertyTypeDTO> propertyTypes)
+ {
+ final EntityPropertyTypeDTOContainer container = new EntityPropertyTypeDTOContainer();
+ for (final EntityPropertyTypeDTO entityPropertyType : propertyTypes)
+ {
+ container.addEntityPropertyType(entityPropertyType);
+ }
+ return container;
+ }
+
+ /**
+ * Factory method for creating {@link EntityPropertyTypeDTOContainer}s from
+ * {@link EntityPropertyTypeDTO} array.
+ *
+ * @param entityPropertyTypeTable
+ */
+ public static EntityPropertyTypeDTOContainer createFromTable(
+ final EntityPropertyTypeDTO[] entityPropertyTypeTable)
+ {
+ if (entityPropertyTypeTable == null)
+ {
+ return null;
+ }
+ final EntityPropertyTypeDTOContainer schema = new EntityPropertyTypeDTOContainer();
+ for (final EntityPropertyTypeDTO entityPropertyType : entityPropertyTypeTable)
+ {
+ schema.addEntityPropertyType(entityPropertyType);
+ }
+ return schema;
+ }
+
+ private static UserFailureException createMandatoryException(final String name)
+ {
+ return UserFailureException.fromTemplate(
+ "Property '%s' is mandatory and cannot be set to the empty value.", name);
+ }
+
+ private final Map<String, EntityPropertyTypeDTO> container;
+
+ private EntityPropertyTypeDTOContainer()
+ {
+ this.container = new LinkedHashMap<String, EntityPropertyTypeDTO>();
+ }
+
+ /**
+ * Returns an array of {@link EntityPropertyTypeDTO} which typeCodes were stored in container.
+ */
+ public EntityPropertyTypeDTO[] createTable()
+ {
+ final Set<String> allCodes = container.keySet();
+ final EntityPropertyTypeDTO[] result = new EntityPropertyTypeDTO[allCodes.size()];
+ int i = 0;
+ for (final String code : allCodes)
+ {
+ final EntityPropertyTypeDTO orig = getPropertyType(code);
+ result[i] = orig;
+ i++;
+ }
+ return result;
+ }
+
+ /**
+ * Returns an array of propertyTypeCodes stored in the container.
+ */
+ public String[] getAllPropertyCodes()
+ {
+ return container.keySet().toArray(new String[0]);
+ }
+
+ /**
+ * Returns {@link EntityPropertyTypeDTO} for given <var>propertyTypeCode</var>.
+ *
+ * @param propertyTypeCode
+ * @throws UserFailureException if there is no {@link EntityPropertyTypeDTO} with specified
+ * <var>propertyTypeCode</var>.
+ */
+ public EntityPropertyTypeDTO getPropertyType(final String propertyTypeCode)
+ {
+ final EntityPropertyTypeDTO type = tryGetPropertyType(propertyTypeCode);
+ if (type == null)
+ {
+ throw UserFailureException.fromTemplate("Unknown property '%s'", propertyTypeCode);
+ }
+ return type;
+ }
+
+ /**
+ * Returns true if container contains given propertyTypeCode.
+ *
+ * @param propertyTypeCode
+ */
+ public boolean hasPropertySchema(final String propertyTypeCode)
+ {
+ return container.containsKey(propertyTypeCode);
+ }
+
+ /**
+ * Returns {@link EntityPropertyTypeDTO} or null for given propertyTypeCode.
+ *
+ * @param propertyTypeCode
+ */
+ public EntityPropertyTypeDTO tryGetPropertyType(final String propertyTypeCode)
+ {
+ return container.get(StringUtils.upperCase(propertyTypeCode));
+ }
+
+ /**
+ * Checks if value is mandatory and casts it to appropriate type.
+ *
+ * @param propertyTypeCode
+ * @param untypedValueOrNull
+ */
+ public EntityPropertyValue validateAndCreateValue(final String propertyTypeCode,
+ final String untypedValueOrNull)
+ {
+ final String upperCaseCode = StringUtils.upperCase(propertyTypeCode);
+ final EntityPropertyTypeDTO propertyType = getPropertyType(upperCaseCode);
+ assert propertyType != null;
+ if (propertyType.isMandatory() && untypedValueOrNull == null)
+ {
+ throw createMandatoryException(upperCaseCode);
+ }
+ return EntityPropertyValue.createFromUntyped(untypedValueOrNull, propertyType
+ .getDataTypeCode());
+ }
+
+ /**
+ * Adds {@link EntityPropertyTypeDTO} to container.
+ *
+ * @param entityPropertyType
+ * @throws IllegalArgumentException if property was already present
+ */
+ private void addEntityPropertyType(final EntityPropertyTypeDTO entityPropertyType)
+ {
+ final String propertyTypeCode = entityPropertyType.getPropertyType().getCode();
+ if (container.get(propertyTypeCode) != null)
+ {
+ throw new IllegalArgumentException("property already present: " + propertyTypeCode);
+ }
+ container.put(propertyTypeCode, entityPropertyType);
+ }
+
+ //
+ // Methods introduced for testing purposes
+ //
+
+ /**
+ * <i>Only to be used in unit tests.</i>
+ */
+ public static EntityPropertyTypeDTOContainer only4TestingCreateEmpty()
+ {
+ return new EntityPropertyTypeDTOContainer();
+ }
+
+ /**
+ * <i>Only to be used in unit tests.</i>
+ * <p>
+ * Fails if property was already present.
+ */
+ @Private
+ public EntityPropertyTypeDTO only4TestingAddEntityPropertyType(final long id,
+ final boolean isMandatory, final Date registrationDate, final PersonPE registrator,
+ final PropertyTypePE propertyType)
+ {
+ final EntityPropertyTypeDTO entityPropertyType =
+ new EntityPropertyTypeDTO(id, isMandatory, registrationDate, registrator,
+ propertyType);
+ addEntityPropertyType(entityPropertyType);
+ return entityPropertyType;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyValue.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyValue.java
new file mode 100644
index 00000000000..3baee030f8c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/EntityPropertyValue.java
@@ -0,0 +1,246 @@
+/*
+ * Copyright 2007 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.shared.dto.properties;
+
+import java.io.Serializable;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import ch.systemsx.cisd.common.exceptions.InternalErr;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.common.utilities.DateFormatThreadLocal;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleEntityProperty;
+
+/**
+ * Storage of entity property value. Use casting methods with tryAs prefix to extract a value. Note
+ * that if a value of a certain type is stored (e.g. integer), than using a casting method different
+ * than tryAsInteger is a programming error! Use {@code getType()} method to figure out the type of
+ * value, which is stored.
+ *
+ * @author Tomasz Pylak
+ */
+// TODO 2007-11-22, Christian Ribeaud: typed methods 'tryAsDouble', 'tryAsInteger' and 'tryAsString'
+// should be removed as they are only used inside the property type framework.
+public class EntityPropertyValue extends AbstractHashable
+{
+ private static final String TRUE_VALUE = "true";
+
+ private static final String FALSE_VALUE = "false";
+
+ public static final ThreadLocal<SimpleDateFormat> CANONICAL_DATE_FORMAT =
+ new DateFormatThreadLocal("yyyy-MM-dd HH:mm:ss Z");
+
+ private final EntityDataType type;
+
+ private final Object valueOrNull;
+
+ private EntityPropertyValue(final Object valueOrNull, final EntityDataType type)
+ {
+ this.valueOrNull = valueOrNull;
+ this.type = type;
+ }
+
+ /** @return the type of value, which is stored */
+ public EntityDataType getType()
+ {
+ return type;
+ }
+
+ /** @return true if the stored value is null (type independent) */
+ public boolean isNull()
+ {
+ return valueOrNull == null;
+ }
+
+ /** throws exception when value cannot be properly casted */
+ public static EntityPropertyValue createFromUntyped(final String untypedValueOrNull,
+ final EntityDataType type) throws UserFailureException
+ {
+ if (untypedValueOrNull == null)
+ {
+ return new EntityPropertyValue(null, type);
+ }
+ try
+ {
+ return internalCreateFromUntyped(untypedValueOrNull, type);
+ } catch (final NumberFormatException e)
+ {
+ throw UserFailureException.fromTemplate(
+ "Value '%s' has improper format. It should be of type '%s'",
+ untypedValueOrNull, type.getNiceRepresentation());
+ }
+ }
+
+ private static EntityPropertyValue internalCreateFromUntyped(final String untypedValue,
+ final EntityDataType type)
+ {
+ if (type.equals(EntityDataType.INTEGER))
+ {
+ return createInteger(Integer.parseInt(untypedValue));
+ } else if (type.equals(EntityDataType.REAL))
+ {
+ return createDouble(Double.parseDouble(untypedValue));
+ } else if (type.equals(EntityDataType.VARCHAR))
+ {
+ return createString(untypedValue);
+ } else if (type.equals(EntityDataType.BOOLEAN))
+ {
+ return createBoolean(parseBoolean(untypedValue));
+ } else if (type.equals(EntityDataType.TIMESTAMP))
+ {
+ return createDate(parseDate(untypedValue));
+ } else if (type.equals(EntityDataType.CONTROLLEDVOCABULARY))
+ {
+ return createVocabularyTerm(untypedValue);
+ } else
+ {
+ throw InternalErr.error();
+ }
+ }
+
+ private static Date parseDate(final String untypedValue)
+ {
+ try
+ {
+ return CANONICAL_DATE_FORMAT.get().parse(untypedValue);
+ } catch (final ParseException ex)
+ {
+ throw UserFailureException.fromTemplate(
+ "Date value '%s' has improper format. The proper format is '%s'.",
+ untypedValue, CANONICAL_DATE_FORMAT.get().toPattern());
+ }
+ }
+
+ private static Boolean parseBoolean(final String untypedValue)
+ {
+ if (untypedValue.equalsIgnoreCase(TRUE_VALUE))
+ {
+ return Boolean.TRUE;
+ } else if (untypedValue.equalsIgnoreCase(FALSE_VALUE))
+ {
+ return Boolean.FALSE;
+ } else
+ {
+ throw UserFailureException.fromTemplate(
+ "Boolean value '%s' has improper format. It should be either '%s' or '%s',",
+ untypedValue, TRUE_VALUE, FALSE_VALUE);
+ }
+ }
+
+ public static EntityPropertyValue createInteger(final Integer valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.INTEGER);
+ }
+
+ public static EntityPropertyValue createDouble(final Double valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.REAL);
+ }
+
+ public static EntityPropertyValue createString(final String valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.VARCHAR);
+ }
+
+ public static EntityPropertyValue createVocabularyTerm(final String valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.CONTROLLEDVOCABULARY);
+ }
+
+ public static EntityPropertyValue createBoolean(final Boolean valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.BOOLEAN);
+ }
+
+ public static EntityPropertyValue createDate(final Date valOrNull)
+ {
+ return new EntityPropertyValue(valOrNull, EntityDataType.TIMESTAMP);
+ }
+
+ // --- casting methods, fail if type does not match
+
+ public String tryAsString()
+ {
+ ensure(type.equals(EntityDataType.VARCHAR));
+ return (String) valueOrNull;
+ }
+
+ public Integer tryAsInteger()
+ {
+ ensure(type.equals(EntityDataType.INTEGER));
+ return (Integer) valueOrNull;
+ }
+
+ public Double tryAsDouble()
+ {
+ ensure(type.equals(EntityDataType.REAL));
+ return (Double) valueOrNull;
+ }
+
+ public Boolean tryAsBoolean()
+ {
+ ensure(type.equals(EntityDataType.BOOLEAN));
+ return (Boolean) valueOrNull;
+ }
+
+ public Date tryAsDate()
+ {
+ ensure(type.equals(EntityDataType.TIMESTAMP));
+ return (Date) valueOrNull;
+ }
+
+ /** returns canonical representation of the value */
+ public String tryGetUntypedValue()
+ {
+ if (valueOrNull == null)
+ {
+ return null;
+ }
+ if (type.equals(EntityDataType.INTEGER) || type.equals(EntityDataType.REAL)
+ || type.equals(EntityDataType.VARCHAR)
+ || type.equals(EntityDataType.CONTROLLEDVOCABULARY))
+ {
+ return valueOrNull.toString();
+ } else if (type.equals(EntityDataType.BOOLEAN))
+ {
+ return tryAsBoolean() ? TRUE_VALUE : FALSE_VALUE;
+ } else if (type.equals(EntityDataType.TIMESTAMP))
+ {
+ return CANONICAL_DATE_FORMAT.get().format(tryAsDate());
+ } else
+ {
+ throw InternalErr.error();
+ }
+ }
+
+ private void ensure(final boolean value)
+ {
+ assert value : "Type does not match";
+ }
+
+ public SimpleEntityProperty createSimple(final String code, final String label)
+ {
+ return new SimpleEntityProperty(code, label, type, (Serializable) this.valueOrNull);
+ }
+
+ public static EntityPropertyValue createFromSimple(SimpleEntityProperty property)
+ {
+ return new EntityPropertyValue(property.getValue(), property.getDataType());
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/PropertiesHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/PropertiesHelper.java
new file mode 100644
index 00000000000..2b96970699c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/properties/PropertiesHelper.java
@@ -0,0 +1,96 @@
+/*
+ * Copyright 2008 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.shared.dto.properties;
+
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.collections.ListSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ISimpleEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
+
+/**
+ * A static helper class which contains helpful methods around {@link PropertyTypePE},
+ * {@link ISimpleEntityPropertiesHolder}.
+ *
+ * @author Tomasz Pylak
+ */
+public final class PropertiesHelper
+{
+
+ private PropertiesHelper()
+ {
+ // Can not be instantiated.
+ }
+
+ /**
+ * Returns a description of given <var>propertyType</var>.
+ */
+ public static final String getTypeDescription(final PropertyTypePE propertyType)
+ {
+ assert propertyType != null : "Unspecified property type";
+ final DataTypePE dataType = propertyType.getType();
+ String type = dataType != null ? dataType.getCode().name() : getSimpleType(propertyType);
+ final String vocabularyCode = getVocabularyCode(propertyType);
+ if (vocabularyCode != null)
+ {
+ type = type + "(" + vocabularyCode + ")";
+ }
+ return type;
+ }
+
+ public static final String getSimpleType(final PropertyTypePE propertyType)
+ {
+ return propertyType.getType() == null ? null : propertyType.getType().getCode().name();
+ }
+
+ public static String getVocabularyCode(final PropertyTypePE propertyType)
+ {
+ final VocabularyPE vocabulary = propertyType.getVocabulary();
+ if (vocabulary == null || StringUtils.isEmpty(vocabulary.getCode()))
+ {
+ return null;
+ } else
+ {
+ return vocabulary.getCode();
+ }
+ }
+
+ public final static <T extends EntityPropertyPE> ListSet createPropertiesListSet(
+ final IEntityPropertiesHolder<T>[] entities)
+ {
+ final ListSet table = new ListSet();
+ for (int rowIndex = 0; rowIndex < entities.length; rowIndex++)
+ {
+ final List<T> properties = entities[rowIndex].getProperties();
+ assert properties != null : "Unspecified properties";
+ for (final EntityPropertyPE property : properties)
+ {
+ final PropertyTypePE propertyType =
+ property.getEntityTypePropertyType().getPropertyType();
+ table.addToList(propertyType.getCode(), propertyType.getLabel(), property
+ .tryGetUntypedValue(), rowIndex);
+ }
+ }
+ return table;
+ }
+}
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
new file mode 100644
index 00000000000..58e56881ae4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/DataSetTypeCode.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2008 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.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.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public enum DataSetTypeCode
+{
+ HCS_IMAGE("HCS_IMAGE"), HCS_IMAGE_ANALYSIS_DATA("HCS_IMAGE_ANALYSIS_DATA"), UNKNOWN("UNKNOWN");
+
+ private final String code;
+
+ private DataSetTypeCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ /** For given <var>typeCode</var> returns the corresponding <code>DataSetTypeCode</code>. */
+ public final static DataSetTypeCode getDataSetTypeCode(final String typeCode)
+ {
+ assert typeCode != null : "Unspecified data set type code.";
+ for (final DataSetTypeCode dataSetTypeCode : values())
+ {
+ if (dataSetTypeCode.code.equalsIgnoreCase(typeCode))
+ {
+ return dataSetTypeCode;
+ }
+ }
+ throw new IllegalArgumentException(String.format("No data set type for given code '%s'.",
+ typeCode));
+ }
+
+}
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
new file mode 100644
index 00000000000..1bd6015c4b4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ExperimentTypeCode.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2008 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.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.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public enum ExperimentTypeCode
+{
+ SIRNA_HCS("SIRNA_HCS"), COMPOUND_HCS("COMPOUND_HCS");
+
+ private final String code;
+
+ private ExperimentTypeCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ /** For given <var>typeCode</var> returns the corresponding <code>ExperimentTypeCode</code>. */
+ public final static ExperimentTypeCode getExperimentTypeCode(final String typeCode)
+ {
+ assert typeCode != null : "Unspecified experiment type code.";
+ for (final ExperimentTypeCode experimentTypeCode : values())
+ {
+ if (experimentTypeCode.code.equalsIgnoreCase(typeCode))
+ {
+ return experimentTypeCode;
+ }
+ }
+ throw new IllegalArgumentException(String.format("No experiment type for given code '%s'.",
+ typeCode));
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/MaterialTypeCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/MaterialTypeCode.java
new file mode 100644
index 00000000000..fde7c1f1557
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/MaterialTypeCode.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright 2007 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.shared.dto.types;
+
+/**
+ * The current <code>MaterialType</code> codes.
+ *
+ * @author Christian Ribeaud
+ */
+public final class MaterialTypeCode
+{
+ private MaterialTypeCode()
+ {
+ // Can not be instantiated.
+ }
+
+ public static final String GENE = "GENE";
+
+ public static final String OLIGO = "OLIGO";
+
+ public static final String VIRUS = "VIRUS";
+
+ public static final String CONTROL = "CONTROL";
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ProcedureTypeCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ProcedureTypeCode.java
new file mode 100644
index 00000000000..99a39199a4f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/ProcedureTypeCode.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright 2007 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.shared.dto.types;
+
+/**
+ * The current <code>ProcedureType</code> codes.
+ * <p>
+ * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure
+ * this point.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public enum ProcedureTypeCode
+{
+ DATA_ACQUISITION("DATA_ACQUISITION"), IMAGE_ANALYSIS("IMAGE_ANALYSIS"), UNKNOWN("UNKNOWN");
+
+ private final String code;
+
+ private ProcedureTypeCode(final String code)
+ {
+ this.code = code;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ /** For given <var>typeCode</var> returns the corresponding <code>ProcedureTypeCode</code>. */
+ public final static ProcedureTypeCode getProcedureTypeCode(final String typeCode)
+ {
+ assert typeCode != null : "Unspecified procedure type code.";
+ for (final ProcedureTypeCode procedureTypeCode : values())
+ {
+ if (procedureTypeCode.code.equalsIgnoreCase(typeCode))
+ {
+ return procedureTypeCode;
+ }
+ }
+ throw new IllegalArgumentException(String.format("No procedure type for given code '%s'.",
+ typeCode));
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/SampleTypeCode.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/SampleTypeCode.java
new file mode 100644
index 00000000000..ed247aa80d0
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/types/SampleTypeCode.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2007 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.shared.dto.types;
+
+/**
+ * The current <code>SampleType</code> codes.
+ * <p>
+ * This enumeration should reflect the values in the database and is <i>Unit</i> tested to ensure
+ * this point.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public enum SampleTypeCode
+{
+ CELL_PLATE("CELL_PLATE", true, "cell plate"),
+ CONTROL_LAYOUT("CONTROL_LAYOUT", false, "control layout"),
+ DILUTION_PLATE("DILUTION_PLATE", true, "dilution plate"),
+ MASTER_PLATE("MASTER_PLATE", false, "master plate"),
+ REINFECT_PLATE("REINFECT_PLATE", true, "reinfection plate"),
+ WELL("WELL", false, "well");
+
+ private final String code;
+
+ private final boolean parentRequired;
+
+ private final String description;
+
+ private SampleTypeCode(final String code, final boolean parentRequired, final String description)
+ {
+ this.code = code;
+ this.parentRequired = parentRequired;
+ this.description = description;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ public final boolean isParentRequired()
+ {
+ return parentRequired;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ /** For given <var>typeCode</var> returns the corresponding <code>SampleTypeCode</code>. */
+ public final static SampleTypeCode getSampleTypeCode(final String typeCode)
+ {
+ assert typeCode != null : "Unspecified sample type code.";
+ for (final SampleTypeCode sampleTypeCode : values())
+ {
+ if (sampleTypeCode.code.equalsIgnoreCase(typeCode))
+ {
+ return sampleTypeCode;
+ }
+ }
+ throw new IllegalArgumentException(String.format("No sample type for given code '%s'.",
+ typeCode));
+ }
+}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationTestUtil.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationTestUtil.java
index c88ea744587..53aec475e29 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationTestUtil.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationTestUtil.java
@@ -31,15 +31,15 @@ import org.springframework.aop.framework.autoproxy.AbstractAutoProxyCreator;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.config.BeanPostProcessor;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
-import ch.systemsx.cisd.lims.base.util.CodeConverter;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGroupDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
/**
* Utility methods for {@link AuthorizationAdvisor}. Can be used to test authorization of concrete
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 4ba01e085e3..a2a16e6e48d 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
@@ -30,13 +30,13 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.StatusFlag;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
import ch.systemsx.cisd.openbis.generic.server.authorization.IAccessController.Argument;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
/**
* Test cases for corresponding {@link DefaultAccessController} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilterTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilterTest.java
index d2dea5b6a84..6946eb687eb 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilterTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/DefaultReturnValueFilterTest.java
@@ -42,9 +42,9 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.common.test.LogMonitoringAppender;
import ch.systemsx.cisd.common.utilities.StringUtilities;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.server.authorization.DefaultReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.IValidator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* Test cases for corresponding {@link DefaultReturnValueFilter} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutorTest.java
index 0e08e1e7a43..b2ee0080dea 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutorTest.java
@@ -31,11 +31,11 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.utilities.StringUtilities;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.IPredicate;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* Test cases for corresponding {@link PredicateExecutor} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifierTest.java
index d169842ed77..54499e66d54 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifierTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/RoleWithIdentifierTest.java
@@ -27,15 +27,13 @@ import java.util.Set;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
-import ch.systemsx.cisd.openbis.generic.server.authorization.Role;
-import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.Role.RoleLevel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* Test cases for corresponding {@link RoleWithIdentifier} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicateTest.java
index 4313747463e..47730520304 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/DatabaseInstanceIdentifierPredicateTest.java
@@ -33,15 +33,15 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.StatusFlag;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifierTest;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* Test cases for corresponding {@link DatabaseInstanceIdentifierPredicate} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicateTest.java
index 8f846a12b3f..2e1ebd3a9d6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/GroupIdentifierPredicateTest.java
@@ -33,13 +33,13 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.StatusFlag;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGroupDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
* Test cases for corresponding {@link GroupIdentifierPredicate} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicateTest.java
index e4084df64d2..0a2f21e6043 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/NewExperimentPredicateTest.java
@@ -20,8 +20,8 @@ import static org.testng.AssertJUnit.assertFalse;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.lims.base.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.NewExperimentPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExperiment;
/**
* Test cases for corresponding {@link NewExperimentPredicate} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicateTest.java
index f895e02269e..1ce0d2d99a3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/QueryRestrictionPredicateTest.java
@@ -20,8 +20,8 @@ import static org.testng.AssertJUnit.assertFalse;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.lims.base.dto.QueryRestriction;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.QueryRestrictionPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.QueryRestriction;
/**
* Test cases for corresponding {@link QueryRestrictionPredicate} class.
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 1f07de0c749..6c383a238e7 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
@@ -24,12 +24,11 @@ import java.util.List;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.lims.base.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.lims.base.dto.GroupPE;
-import ch.systemsx.cisd.lims.base.dto.PersonPE;
-import ch.systemsx.cisd.lims.base.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.lims.base.role.RoleCode;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.GroupValidator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.RoleCode;
/**
* Test cases for corresponding {@link GroupValidator} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifierTest.java
new file mode 100644
index 00000000000..7264b9de553
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/DatabaseInstanceIdentifierTest.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+
+/**
+ * Test cases for corresponding {@link DatabaseInstanceIdentifier} class.
+ *
+ * @author Christian Ribeaud
+ */
+@Test
+public final class DatabaseInstanceIdentifierTest extends
+ EqualsHashCodeTestCase<DatabaseInstanceIdentifier>
+{
+
+ //
+ // EqualsHashCodeTestCase
+ //
+
+ @Override
+ protected final DatabaseInstanceIdentifier createInstance() throws Exception
+ {
+ return new DatabaseInstanceIdentifier("DB1");
+ }
+
+ @Override
+ protected final DatabaseInstanceIdentifier createNotEqualInstance() throws Exception
+ {
+ return new DatabaseInstanceIdentifier("db2");
+ }
+
+ @Test
+ public final void testEqualsIgnoreCase()
+ {
+ assertEquals(new DatabaseInstanceIdentifier("db2"), new DatabaseInstanceIdentifier("DB2"));
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierTest.java
new file mode 100644
index 00000000000..ab3a3c1737f
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierTest.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * Test cases for corresponding {@link ExperimentIdentifier} class.
+ *
+ * @author Christian Ribeaud
+ */
+@Test
+public final class ExperimentIdentifierTest extends EqualsHashCodeTestCase<ExperimentIdentifier>
+{
+
+ //
+ // EqualsHashCodeTestCase
+ //
+
+ @Override
+ protected final ExperimentIdentifier createInstance() throws Exception
+ {
+ return new ExperimentIdentifier("DB1", "G", "P1", "E1");
+ }
+
+ @Override
+ protected final ExperimentIdentifier createNotEqualInstance() throws Exception
+ {
+ return new ExperimentIdentifier("DB1", "G", "p1", "e2");
+ }
+
+ @Test
+ public final void testEqualsIgnoreCase()
+ {
+ assertEquals(new ExperimentIdentifier("DB1", "G", "P", "E"), new ExperimentIdentifier(
+ "DB1", "G", "p", "e"));
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifierTest.java
new file mode 100644
index 00000000000..887366223cf
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/GroupIdentifierTest.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+
+/**
+ * Test cases for corresponding {@link GroupIdentifier} class.
+ *
+ * @author Christian Ribeaud
+ */
+@Test
+public class GroupIdentifierTest extends EqualsHashCodeTestCase<GroupIdentifier>
+{
+
+ //
+ // EqualsHashCodeTestCase
+ //
+
+ @Override
+ protected final GroupIdentifier createInstance() throws Exception
+ {
+ return new GroupIdentifier("DB1", "G");
+ }
+
+ @Override
+ protected final GroupIdentifier createNotEqualInstance() throws Exception
+ {
+ return new GroupIdentifier((String) null, "G");
+ }
+
+ @Test
+ public final void testEqualsIgnoreCase()
+ {
+ assertEquals(new GroupIdentifier("DB2", "G"), new GroupIdentifier("DB2", "g"));
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifierTest.java
new file mode 100644
index 00000000000..c5913759225
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ProjectIdentifierTest.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.EqualsHashCodeTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+
+/**
+ * Test cases for corresponding {@link ProjectIdentifier} class.
+ *
+ * @author Christian Ribeaud
+ */
+@Test
+public final class ProjectIdentifierTest extends EqualsHashCodeTestCase<ProjectIdentifier>
+{
+
+ //
+ // EqualsHashCodeTestCase
+ //
+
+ @Override
+ protected final ProjectIdentifier createInstance() throws Exception
+ {
+ return new ProjectIdentifier("DB1", "G", "P1");
+ }
+
+ @Override
+ protected final ProjectIdentifier createNotEqualInstance() throws Exception
+ {
+ return new ProjectIdentifier("DB1", "G", "p2");
+ }
+
+ @Test
+ public final void testEqualsIgnoreCase()
+ {
+ assertEquals(new ProjectIdentifier("DB1", "G", "P"), new ProjectIdentifier("DB1", "G", "p"));
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierTest.java
new file mode 100644
index 00000000000..f54b6ce5368
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/SampleIdentifierTest.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright 2008 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.shared.dto.identifier;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.util.Arrays;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * Test cases for corresponding {@link SampleIdentifier} class.
+ *
+ * @author Izabela Adamczyk
+ */
+public final class SampleIdentifierTest
+{
+ final static String SAMPLE_TYPE = "TYPE1";
+
+ @Test
+ public final void testToStringDbLevel()
+ {
+ final SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new DatabaseInstanceIdentifier("DB"), "SAMP");
+ assertEquals(sampleIdentifier.toString(), "DB:/SAMP");
+ }
+
+ @Test
+ public final void testToStringGroupLevelHomeBd()
+ {
+ final SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new GroupIdentifier(DatabaseInstanceIdentifier.HOME, "GR"),
+ "SAMP");
+ assertEquals(sampleIdentifier.toString(), "/GR/SAMP");
+ }
+
+ @Test
+ public final void testToStringGroupLevel()
+ {
+ final SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new GroupIdentifier("DB", "GR"), "SAMP");
+ assertEquals(sampleIdentifier.toString(), "DB:/GR/SAMP");
+ }
+
+ @Test
+ public final void testToStringHomeGroupLevel()
+ {
+ final SampleIdentifier sampleIdentifier = SampleIdentifier.createHomeGroup("SAMP");
+ assertEquals(sampleIdentifier.toString(), "SAMP");
+ }
+
+ @Test
+ public final void testCompareIdentifiers()
+ {
+ DatabaseInstanceIdentifier homeDb = DatabaseInstanceIdentifier.createHome();
+ DatabaseInstanceIdentifier otherDb = new DatabaseInstanceIdentifier("db");
+
+ String g1 = "AG";
+ String g2 = "BG";
+ String c1 = "A";
+ String c2 = "B";
+ SampleIdentifier[] expectedOrder =
+ new SampleIdentifier[]
+ { SampleIdentifier.createHomeGroup(c1), SampleIdentifier.createHomeGroup(c2),
+ new SampleIdentifier(new GroupIdentifier(homeDb, g1), c1),
+ new SampleIdentifier(new GroupIdentifier(homeDb, g2), c1),
+ new SampleIdentifier(new GroupIdentifier(homeDb, g2), c2),
+ new SampleIdentifier(new GroupIdentifier(otherDb, g1), c1),
+ new SampleIdentifier(new GroupIdentifier(otherDb, g1), c2),
+ new SampleIdentifier(new GroupIdentifier(otherDb, g2), c1),
+ new SampleIdentifier(new GroupIdentifier(otherDb, g2), c2) };
+
+ SampleIdentifier[] idents = revert(expectedOrder);
+ Arrays.sort(idents);
+ assertEquals(Arrays.asList(expectedOrder), Arrays.asList(idents));
+ }
+
+ private static SampleIdentifier[] revert(SampleIdentifier[] expectedOrder)
+ {
+ SampleIdentifier[] idents = new SampleIdentifier[expectedOrder.length];
+ for (int i = 0; i < idents.length; i++)
+ {
+ idents[idents.length - i - 1] = expectedOrder[i];
+ }
+ return idents;
+ }
+}
--
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