Package ch.ethz.sis.openbis.generic

Class OpenBIS

java.lang.Object

ch.ethz.sis.openbis.generic.OpenBIS

public class OpenBIS
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	OpenBIS.AfsServerFacade
class	OpenBIS.DataStoreFacade

Constructor Summary

Constructors

Constructor	Description
OpenBIS(String url)
OpenBIS(String url, int timeout)
OpenBIS(String asURL, String dssURL, String afsURL)
OpenBIS(String asURL, String dssURL, String afsURL, int timeout)
OpenBIS(String asURL, String dssURL, String afsURL, int timeout, int chunkSize)

Method Summary

Modifier and Type	Method	Description
void	archiveDataSets(List<? extends IDataSetId> dataSetIds, DataSetArchiveOptions options)
UUID	beginTransaction()
void	commitTransaction()
void	confirmDeletions(List<? extends IDeletionId> deletionIds)
List<AuthorizationGroupPermId>	createAuthorizationGroups(List<AuthorizationGroupCreation> newAuthorizationGroups)
List<String>	createCodes(String prefix, EntityKind entityKind, int count)
List<DataSetPermId>	createDataSetsAS(List<DataSetCreation> newDataSets)
List<EntityTypePermId>	createDataSetTypes(List<DataSetTypeCreation> newDataSetTypes)
List<ExperimentPermId>	createExperiments(List<ExperimentCreation> newExperiments)
List<EntityTypePermId>	createExperimentTypes(List<ExperimentTypeCreation> newExperimentTypes)
List<ExternalDmsPermId>	createExternalDataManagementSystems(List<ExternalDmsCreation> newExternalDataManagementSystems)
List<String>	createPermIdStrings(int count)
List<PersonalAccessTokenPermId>	createPersonalAccessTokens(List<PersonalAccessTokenCreation> newPersonalAccessTokens)
List<PersonPermId>	createPersons(List<PersonCreation> newPersons)
List<PluginPermId>	createPlugins(List<PluginCreation> newPlugins)
List<ProjectPermId>	createProjects(List<ProjectCreation> newProjects)
List<PropertyTypePermId>	createPropertyTypes(List<PropertyTypeCreation> newPropertyTypes)
List<QueryTechId>	createQueries(List<QueryCreation> newQueries)
List<RoleAssignmentTechId>	createRoleAssignments(List<RoleAssignmentCreation> newRoleAssignments)
List<SamplePermId>	createSamples(List<SampleCreation> newSamples)
List<EntityTypePermId>	createSampleTypes(List<SampleTypeCreation> newSampleTypes)
List<SemanticAnnotationPermId>	createSemanticAnnotations(List<SemanticAnnotationCreation> newAnnotations)
List<SpacePermId>	createSpaces(List<SpaceCreation> newSpaces)
List<TagPermId>	createTags(List<TagCreation> newTags)
List<TypeGroupAssignmentId>	createTypeGroupAssignments(List<TypeGroupAssignmentCreation> newTypeGroupAssignments)
List<TypeGroupId>	createTypeGroups(List<TypeGroupCreation> newTypeGroups)
List<VocabularyPermId>	createVocabularies(List<VocabularyCreation> newVocabularies)
List<VocabularyTermPermId>	createVocabularyTerms(List<VocabularyTermCreation> newVocabularyTerms)
void	deleteAuthorizationGroups(List<? extends IAuthorizationGroupId> groupIds, AuthorizationGroupDeletionOptions deletionOptions)
IDeletionId	deleteDataSets(List<? extends IDataSetId> dataSetIds, DataSetDeletionOptions deletionOptions)
void	deleteDataSetTypes(List<? extends IEntityTypeId> dataSetTypeIds, DataSetTypeDeletionOptions deletionOptions)
IDeletionId	deleteExperiments(List<? extends IExperimentId> experimentIds, ExperimentDeletionOptions deletionOptions)
void	deleteExperimentTypes(List<? extends IEntityTypeId> experimentTypeIds, ExperimentTypeDeletionOptions deletionOptions)
void	deleteExternalDataManagementSystems(List<? extends IExternalDmsId> externalDmsIds, ExternalDmsDeletionOptions deletionOptions)
void	deleteOperationExecutions(List<? extends IOperationExecutionId> executionIds, OperationExecutionDeletionOptions deletionOptions)
void	deletePersonalAccessTokens(List<? extends IPersonalAccessTokenId> personalAccessTokenIds, PersonalAccessTokenDeletionOptions deletionOptions)
void	deletePersons(List<? extends IPersonId> personIds, PersonDeletionOptions deletionOptions)
void	deletePlugins(List<? extends IPluginId> pluginIds, PluginDeletionOptions deletionOptions)
void	deleteProjects(List<? extends IProjectId> projectIds, ProjectDeletionOptions deletionOptions)
void	deletePropertyTypes(List<? extends IPropertyTypeId> propertyTypeIds, PropertyTypeDeletionOptions deletionOptions)
void	deleteQueries(List<? extends IQueryId> queryIds, QueryDeletionOptions deletionOptions)
void	deleteRoleAssignments(List<? extends IRoleAssignmentId> assignmentIds, RoleAssignmentDeletionOptions deletionOptions)
IDeletionId	deleteSamples(List<? extends ISampleId> sampleIds, SampleDeletionOptions deletionOptions)
void	deleteSampleTypes(List<? extends IEntityTypeId> sampleTypeIds, SampleTypeDeletionOptions deletionOptions)
void	deleteSemanticAnnotations(List<? extends ISemanticAnnotationId> annotationIds, SemanticAnnotationDeletionOptions deletionOptions)
void	deleteSpaces(List<? extends ISpaceId> spaceIds, SpaceDeletionOptions deletionOptions)
void	deleteTags(List<? extends ITagId> tagIds, TagDeletionOptions deletionOptions)
void	deleteTypeGroupAssignments(List<? extends ITypeGroupAssignmentId> typeGroupAssignmentIds, TypeGroupAssignmentDeletionOptions deletionOptions)
void	deleteVocabularies(List<? extends IVocabularyId> ids, VocabularyDeletionOptions deletionOptions)
void	deleteVocabularyTerms(List<? extends IVocabularyTermId> termIds, VocabularyTermDeletionOptions deletionOptions)
PluginEvaluationResult	evaluatePlugin(PluginEvaluationOptions options)
TableModel	executeAggregationService(IDssServiceId serviceId, AggregationServiceExecutionOptions options)
Object	executeCustomASService(ICustomASServiceId serviceId, CustomASServiceExecutionOptions options)
ExportResult	executeExport(ExportData exportData, ExportOptions exportOptions)
ImportResult	executeImport(ImportData importData, ImportOptions importOptions)
IOperationExecutionResults	executeOperations(List<? extends IOperation> operations, IOperationExecutionOptions options)
void	executeProcessingService(IDssServiceId serviceId, ProcessingServiceExecutionOptions options)
TableModel	executeQuery(IQueryId queryId, QueryExecutionOptions options)
TableModel	executeReportingService(IDssServiceId serviceId, ReportingServiceExecutionOptions options)
SearchResult<SearchDomainServiceExecutionResult>	executeSearchDomainService(SearchDomainServiceExecutionOptions options)
TableModel	executeSql(String sql, SqlExecutionOptions options)
OpenBIS.AfsServerFacade	getAfsServerFacade()
Map<IAuthorizationGroupId,AuthorizationGroup>	getAuthorizationGroups(List<? extends IAuthorizationGroupId> groupIds, AuthorizationGroupFetchOptions fetchOptions)
Map<IDataSetId,DataSet>	getDataSets(List<? extends IDataSetId> dataSetIds, DataSetFetchOptions fetchOptions)
Map<IEntityTypeId,DataSetType>	getDataSetTypes(List<? extends IEntityTypeId> dataSetTypeIds, DataSetTypeFetchOptions fetchOptions)
OpenBIS.DataStoreFacade	getDataStoreFacade()
Map<IExperimentId,Experiment>	getExperiments(List<? extends IExperimentId> experimentIds, ExperimentFetchOptions fetchOptions)
Map<IEntityTypeId,ExperimentType>	getExperimentTypes(List<? extends IEntityTypeId> experimentTypeIds, ExperimentTypeFetchOptions fetchOptions)
Map<IExternalDmsId,ExternalDms>	getExternalDataManagementSystems(List<? extends IExternalDmsId> externalDmsIds, ExternalDmsFetchOptions fetchOptions)
String	getInteractiveSessionKey()
PersonalAccessTokenPermId	getManagedPersonalAccessToken(String sessionName)	This utility method returns a well managed personal access token, creating one if no one is found and renews it if is close to expiration.
Map<IOperationExecutionId,OperationExecution>	getOperationExecutions(List<? extends IOperationExecutionId> executionIds, OperationExecutionFetchOptions fetchOptions)
Map<IPersonalAccessTokenId,PersonalAccessToken>	getPersonalAccessTokens(List<? extends IPersonalAccessTokenId> personalAccessTokenIds, PersonalAccessTokenFetchOptions fetchOptions)
Map<IPersonId,Person>	getPersons(List<? extends IPersonId> ids, PersonFetchOptions fetchOptions)
Map<IPluginId,Plugin>	getPlugins(List<? extends IPluginId> pluginIds, PluginFetchOptions fetchOptions)
Map<IProjectId,Project>	getProjects(List<? extends IProjectId> projectIds, ProjectFetchOptions fetchOptions)
Map<IPropertyTypeId,PropertyType>	getPropertyTypes(List<? extends IPropertyTypeId> typeIds, PropertyTypeFetchOptions fetchOptions)
Map<IQueryId,Query>	getQueries(List<? extends IQueryId> queryIds, QueryFetchOptions fetchOptions)
Map<IQueryDatabaseId,QueryDatabase>	getQueryDatabases(List<? extends IQueryDatabaseId> queryDatabaseIds, QueryDatabaseFetchOptions fetchOptions)
Map<IObjectId,Rights>	getRights(List<? extends IObjectId> ids, RightsFetchOptions fetchOptions)
Map<IRoleAssignmentId,RoleAssignment>	getRoleAssignments(List<? extends IRoleAssignmentId> ids, RoleAssignmentFetchOptions fetchOptions)
Map<ISampleId,Sample>	getSamples(List<? extends ISampleId> sampleIds, SampleFetchOptions fetchOptions)
Map<IEntityTypeId,SampleType>	getSampleTypes(List<? extends IEntityTypeId> sampleTypeIds, SampleTypeFetchOptions fetchOptions)
Map<ISemanticAnnotationId,SemanticAnnotation>	getSemanticAnnotations(List<? extends ISemanticAnnotationId> annotationIds, SemanticAnnotationFetchOptions fetchOptions)
static SemanticAnnotationCreation	getSemanticPredicateCreation(String predicateProperty, String predicatePropertyOntologyId, String predicatePropertyOntologyVersion, String predicatePropertyId)	This utility method provides a simplified API to create predicate semantic annotations
static SemanticAnnotationCreation	getSemanticPredicateWithSubjectCreation(EntityKind subjectEntityKind, String subjectClass, String predicateProperty, String predicatePropertyOntologyId, String predicatePropertyOntologyVersion, String predicatePropertyId)	This utility method provides a simplified API to create predicate semantic annotations
static SemanticAnnotationCreation	getSemanticSubjectCreation(EntityKind subjectEntityKind, String subjectClass, String subjectClassOntologyId, String subjectClassOntologyVersion, String subjectClassId)	This utility method provides a simplified API to create subject semantic annotations
Map<String,String>	getServerInformation()
Map<String,String>	getServerPublicInformation()
SessionInformation	getSessionInformation()
String	getSessionToken()
Map<ISpaceId,Space>	getSpaces(List<? extends ISpaceId> spaceIds, SpaceFetchOptions fetchOptions)
Map<ITagId,Tag>	getTags(List<? extends ITagId> tagIds, TagFetchOptions fetchOptions)
UUID	getTransactionId()
Map<ITypeGroupAssignmentId,TypeGroupAssignment>	getTypeGroupAssignments(List<? extends ITypeGroupAssignmentId> ids, TypeGroupAssignmentFetchOptions fetchOptions)
Map<ITypeGroupId,TypeGroup>	getTypeGroups(List<? extends ITypeGroupId> typeGroupIds, TypeGroupFetchOptions fetchOptions)
Map<IVocabularyId,Vocabulary>	getVocabularies(List<? extends IVocabularyId> vocabularyIds, VocabularyFetchOptions fetchOptions)
Map<IVocabularyTermId,VocabularyTerm>	getVocabularyTerms(List<? extends IVocabularyTermId> vocabularyTermIds, VocabularyTermFetchOptions fetchOptions)
boolean	isSessionActive()
void	lockDataSets(List<? extends IDataSetId> dataSetIds, DataSetLockOptions options)
String	login(String userId, String password)
String	loginAs(String userId, String password, String asUserId)
String	loginAsAnonymousUser()
void	logout()
void	revertDeletions(List<? extends IDeletionId> deletionIds)
void	rollbackTransaction()
SearchResult<AggregationService>	searchAggregationServices(AggregationServiceSearchCriteria searchCriteria, AggregationServiceFetchOptions fetchOptions)
SearchResult<AuthorizationGroup>	searchAuthorizationGroups(AuthorizationGroupSearchCriteria searchCriteria, AuthorizationGroupFetchOptions fetchOptions)
SearchResult<CustomASService>	searchCustomASServices(CustomASServiceSearchCriteria searchCriteria, CustomASServiceFetchOptions fetchOptions)
SearchResult<DataSet>	searchDataSets(DataSetSearchCriteria searchCriteria, DataSetFetchOptions fetchOptions)
SearchResult<DataSetType>	searchDataSetTypes(DataSetTypeSearchCriteria searchCriteria, DataSetTypeFetchOptions fetchOptions)
SearchResult<DataStore>	searchDataStores(DataStoreSearchCriteria searchCriteria, DataStoreFetchOptions fetchOptions)
SearchResult<Deletion>	searchDeletions(DeletionSearchCriteria searchCriteria, DeletionFetchOptions fetchOptions)
SearchResult<Event>	searchEvents(EventSearchCriteria searchCriteria, EventFetchOptions fetchOptions)
SearchResult<Experiment>	searchExperiments(ExperimentSearchCriteria searchCriteria, ExperimentFetchOptions fetchOptions)
SearchResult<ExperimentType>	searchExperimentTypes(ExperimentTypeSearchCriteria searchCriteria, ExperimentTypeFetchOptions fetchOptions)
SearchResult<ExternalDms>	searchExternalDataManagementSystems(ExternalDmsSearchCriteria searchCriteria, ExternalDmsFetchOptions fetchOptions)
SearchResult<GlobalSearchObject>	searchGlobally(GlobalSearchCriteria searchCriteria, GlobalSearchObjectFetchOptions fetchOptions)
SearchResult<ObjectKindModification>	searchObjectKindModifications(ObjectKindModificationSearchCriteria searchCriteria, ObjectKindModificationFetchOptions fetchOptions)
SearchResult<OperationExecution>	searchOperationExecutions(OperationExecutionSearchCriteria searchCriteria, OperationExecutionFetchOptions fetchOptions)
SearchResult<PersonalAccessToken>	searchPersonalAccessTokens(PersonalAccessTokenSearchCriteria searchCriteria, PersonalAccessTokenFetchOptions fetchOptions)
SearchResult<Person>	searchPersons(PersonSearchCriteria searchCriteria, PersonFetchOptions fetchOptions)
SearchResult<Plugin>	searchPlugins(PluginSearchCriteria searchCriteria, PluginFetchOptions fetchOptions)
SearchResult<ProcessingService>	searchProcessingServices(ProcessingServiceSearchCriteria searchCriteria, ProcessingServiceFetchOptions fetchOptions)
SearchResult<Project>	searchProjects(ProjectSearchCriteria searchCriteria, ProjectFetchOptions fetchOptions)
SearchResult<PropertyAssignment>	searchPropertyAssignments(PropertyAssignmentSearchCriteria searchCriteria, PropertyAssignmentFetchOptions fetchOptions)
SearchResult<PropertyType>	searchPropertyTypes(PropertyTypeSearchCriteria searchCriteria, PropertyTypeFetchOptions fetchOptions)
SearchResult<Query>	searchQueries(QuerySearchCriteria searchCriteria, QueryFetchOptions fetchOptions)
SearchResult<QueryDatabase>	searchQueryDatabases(QueryDatabaseSearchCriteria searchCriteria, QueryDatabaseFetchOptions fetchOptions)
SearchResult<ReportingService>	searchReportingServices(ReportingServiceSearchCriteria searchCriteria, ReportingServiceFetchOptions fetchOptions)
SearchResult<RoleAssignment>	searchRoleAssignments(RoleAssignmentSearchCriteria searchCriteria, RoleAssignmentFetchOptions fetchOptions)
SearchResult<Sample>	searchSamples(SampleSearchCriteria searchCriteria, SampleFetchOptions fetchOptions)
SearchResult<SampleType>	searchSampleTypes(SampleTypeSearchCriteria searchCriteria, SampleTypeFetchOptions fetchOptions)
SearchResult<SearchDomainService>	searchSearchDomainServices(SearchDomainServiceSearchCriteria searchCriteria, SearchDomainServiceFetchOptions fetchOptions)
SearchResult<SemanticAnnotation>	searchSemanticAnnotations(SemanticAnnotationSearchCriteria searchCriteria, SemanticAnnotationFetchOptions fetchOptions)
SearchResult<SessionInformation>	searchSessionInformation(SessionInformationSearchCriteria searchCriteria, SessionInformationFetchOptions fetchOptions)
SearchResult<Space>	searchSpaces(SpaceSearchCriteria searchCriteria, SpaceFetchOptions fetchOptions)
SearchResult<Tag>	searchTags(TagSearchCriteria searchCriteria, TagFetchOptions fetchOptions)
SearchResult<TypeGroupAssignment>	searchTypeGroupAssignments(TypeGroupAssignmentSearchCriteria searchCriteria, TypeGroupAssignmentFetchOptions fetchOptions)
SearchResult<Vocabulary>	searchVocabularies(VocabularySearchCriteria searchCriteria, VocabularyFetchOptions fetchOptions)
SearchResult<VocabularyTerm>	searchVocabularyTerms(VocabularyTermSearchCriteria searchCriteria, VocabularyTermFetchOptions fetchOptions)
void	setInteractiveSessionKey(String interactiveSessionKey)
void	setSessionToken(String sessionToken)
void	setTransactionId(UUID transactionId)
void	unarchiveDataSets(List<? extends IDataSetId> dataSetIds, DataSetUnarchiveOptions options)
void	unlockDataSets(List<? extends IDataSetId> dataSetIds, DataSetUnlockOptions options)
void	updateAuthorizationGroups(List<AuthorizationGroupUpdate> authorizationGroupUpdates)
void	updateDataSets(List<DataSetUpdate> dataSetUpdates)
void	updateDataSetTypes(List<DataSetTypeUpdate> dataSetTypeUpdates)
void	updateExperiments(List<ExperimentUpdate> experimentUpdates)
void	updateExperimentTypes(List<ExperimentTypeUpdate> experimentTypeUpdates)
void	updateExternalDataManagementSystems(List<ExternalDmsUpdate> externalDmsUpdates)
void	updateOperationExecutions(List<OperationExecutionUpdate> executionUpdates)
void	updatePersonalAccessTokens(List<PersonalAccessTokenUpdate> personalAccessTokenUpdates)
void	updatePersons(List<PersonUpdate> personUpdates)
void	updatePlugins(List<PluginUpdate> pluginUpdates)
void	updateProjects(List<ProjectUpdate> projectUpdates)
void	updatePropertyTypes(List<PropertyTypeUpdate> propertyTypeUpdates)
void	updateQueries(List<QueryUpdate> queryUpdates)
void	updateSamples(List<SampleUpdate> sampleUpdates)
void	updateSampleTypes(List<SampleTypeUpdate> sampleTypeUpdates)
void	updateSemanticAnnotations(List<SemanticAnnotationUpdate> annotationUpdates)
void	updateSpaces(List<SpaceUpdate> spaceUpdates)
void	updateTags(List<TagUpdate> tagUpdates)
void	updateTypeGroups(List<TypeGroupUpdate> typeGroupUpdates)
void	updateVocabularies(List<VocabularyUpdate> vocabularyUpdates)
void	updateVocabularyTerms(List<VocabularyTermUpdate> vocabularyTermUpdates)
String	uploadToSessionWorkspace(Path fileOrFolder)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

OpenBIS

public OpenBIS(String url)

OpenBIS

public OpenBIS(String url,
 int timeout)

OpenBIS

public OpenBIS(String asURL,
 String dssURL,
 String afsURL)

OpenBIS

public OpenBIS(String asURL,
 String dssURL,
 String afsURL,
 int timeout)

OpenBIS

public OpenBIS(String asURL,
 String dssURL,
 String afsURL,
 int timeout,
 int chunkSize)

Method Details

login

public String login(String userId,
 String password)

loginAs

public String loginAs(String userId,
 String password,
 String asUserId)

loginAsAnonymousUser

public String loginAsAnonymousUser()

logout

public void logout()

getSessionInformation

public SessionInformation getSessionInformation()

isSessionActive

public boolean isSessionActive()

beginTransaction

public UUID beginTransaction()

commitTransaction

public void commitTransaction()

rollbackTransaction

public void rollbackTransaction()

createSpaces

public List<SpacePermId> createSpaces(List<SpaceCreation> newSpaces)

createProjects

public List<ProjectPermId> createProjects(List<ProjectCreation> newProjects)

createExperiments

public List<ExperimentPermId> createExperiments(List<ExperimentCreation> newExperiments)

createExperimentTypes

public List<EntityTypePermId> createExperimentTypes(List<ExperimentTypeCreation> newExperimentTypes)

createSamples

public List<SamplePermId> createSamples(List<SampleCreation> newSamples)

createSampleTypes

public List<EntityTypePermId> createSampleTypes(List<SampleTypeCreation> newSampleTypes)

createDataSetsAS

public List<DataSetPermId> createDataSetsAS(List<DataSetCreation> newDataSets)

createDataSetTypes

public List<EntityTypePermId> createDataSetTypes(List<DataSetTypeCreation> newDataSetTypes)

createPropertyTypes

public List<PropertyTypePermId> createPropertyTypes(List<PropertyTypeCreation> newPropertyTypes)

createPlugins

public List<PluginPermId> createPlugins(List<PluginCreation> newPlugins)

createVocabularies

public List<VocabularyPermId> createVocabularies(List<VocabularyCreation> newVocabularies)

createVocabularyTerms

public List<VocabularyTermPermId> createVocabularyTerms(List<VocabularyTermCreation> newVocabularyTerms)

createTags

public List<TagPermId> createTags(List<TagCreation> newTags)

createAuthorizationGroups

public List<AuthorizationGroupPermId> createAuthorizationGroups(List<AuthorizationGroupCreation> newAuthorizationGroups)

createRoleAssignments

public List<RoleAssignmentTechId> createRoleAssignments(List<RoleAssignmentCreation> newRoleAssignments)

createPersons

public List<PersonPermId> createPersons(List<PersonCreation> newPersons)

createExternalDataManagementSystems

public List<ExternalDmsPermId> createExternalDataManagementSystems(List<ExternalDmsCreation> newExternalDataManagementSystems)

createQueries

public List<QueryTechId> createQueries(List<QueryCreation> newQueries)

createSemanticAnnotations

public List<SemanticAnnotationPermId> createSemanticAnnotations(List<SemanticAnnotationCreation> newAnnotations)

createPersonalAccessTokens

public List<PersonalAccessTokenPermId> createPersonalAccessTokens(List<PersonalAccessTokenCreation> newPersonalAccessTokens)

createTypeGroups

public List<TypeGroupId> createTypeGroups(List<TypeGroupCreation> newTypeGroups)

createTypeGroupAssignments

public List<TypeGroupAssignmentId> createTypeGroupAssignments(List<TypeGroupAssignmentCreation> newTypeGroupAssignments)

updateSpaces

public void updateSpaces(List<SpaceUpdate> spaceUpdates)

updateProjects

public void updateProjects(List<ProjectUpdate> projectUpdates)

updateExperiments

public void updateExperiments(List<ExperimentUpdate> experimentUpdates)

updateExperimentTypes

public void updateExperimentTypes(List<ExperimentTypeUpdate> experimentTypeUpdates)

updateSamples

public void updateSamples(List<SampleUpdate> sampleUpdates)

updateSampleTypes

public void updateSampleTypes(List<SampleTypeUpdate> sampleTypeUpdates)

updateDataSets

public void updateDataSets(List<DataSetUpdate> dataSetUpdates)

updateDataSetTypes

public void updateDataSetTypes(List<DataSetTypeUpdate> dataSetTypeUpdates)

updateExternalDataManagementSystems

public void updateExternalDataManagementSystems(List<ExternalDmsUpdate> externalDmsUpdates)

updatePropertyTypes

public void updatePropertyTypes(List<PropertyTypeUpdate> propertyTypeUpdates)

updatePlugins

public void updatePlugins(List<PluginUpdate> pluginUpdates)

updateVocabularies

public void updateVocabularies(List<VocabularyUpdate> vocabularyUpdates)

updateVocabularyTerms

public void updateVocabularyTerms(List<VocabularyTermUpdate> vocabularyTermUpdates)

updateTags

public void updateTags(List<TagUpdate> tagUpdates)

updateAuthorizationGroups

public void updateAuthorizationGroups(List<AuthorizationGroupUpdate> authorizationGroupUpdates)

updatePersons

public void updatePersons(List<PersonUpdate> personUpdates)

updateOperationExecutions

public void updateOperationExecutions(List<OperationExecutionUpdate> executionUpdates)

updateSemanticAnnotations

public void updateSemanticAnnotations(List<SemanticAnnotationUpdate> annotationUpdates)

updateQueries

public void updateQueries(List<QueryUpdate> queryUpdates)

updatePersonalAccessTokens

public void updatePersonalAccessTokens(List<PersonalAccessTokenUpdate> personalAccessTokenUpdates)

updateTypeGroups

public void updateTypeGroups(List<TypeGroupUpdate> typeGroupUpdates)

getRights

public Map<IObjectId,Rights> getRights(List<? extends IObjectId> ids,
 RightsFetchOptions fetchOptions)

getSpaces

public Map<ISpaceId,Space> getSpaces(List<? extends ISpaceId> spaceIds,
 SpaceFetchOptions fetchOptions)

getProjects

public Map<IProjectId,Project> getProjects(List<? extends IProjectId> projectIds,
 ProjectFetchOptions fetchOptions)

getExperiments

public Map<IExperimentId,Experiment> getExperiments(List<? extends IExperimentId> experimentIds,
 ExperimentFetchOptions fetchOptions)

getExperimentTypes

public Map<IEntityTypeId,ExperimentType> getExperimentTypes(List<? extends IEntityTypeId> experimentTypeIds,
 ExperimentTypeFetchOptions fetchOptions)

getSamples

public Map<ISampleId,Sample> getSamples(List<? extends ISampleId> sampleIds,
 SampleFetchOptions fetchOptions)

getSampleTypes

public Map<IEntityTypeId,SampleType> getSampleTypes(List<? extends IEntityTypeId> sampleTypeIds,
 SampleTypeFetchOptions fetchOptions)

getDataSets

public Map<IDataSetId,DataSet> getDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetFetchOptions fetchOptions)

getDataSetTypes

public Map<IEntityTypeId,DataSetType> getDataSetTypes(List<? extends IEntityTypeId> dataSetTypeIds,
 DataSetTypeFetchOptions fetchOptions)

getPropertyTypes

public Map<IPropertyTypeId,PropertyType> getPropertyTypes(List<? extends IPropertyTypeId> typeIds,
 PropertyTypeFetchOptions fetchOptions)

getPlugins

public Map<IPluginId,Plugin> getPlugins(List<? extends IPluginId> pluginIds,
 PluginFetchOptions fetchOptions)

getVocabularies

public Map<IVocabularyId,Vocabulary> getVocabularies(List<? extends IVocabularyId> vocabularyIds,
 VocabularyFetchOptions fetchOptions)

getVocabularyTerms

public Map<IVocabularyTermId,VocabularyTerm> getVocabularyTerms(List<? extends IVocabularyTermId> vocabularyTermIds,
 VocabularyTermFetchOptions fetchOptions)

getTags

public Map<ITagId,Tag> getTags(List<? extends ITagId> tagIds,
 TagFetchOptions fetchOptions)

getAuthorizationGroups

public Map<IAuthorizationGroupId,AuthorizationGroup> getAuthorizationGroups(List<? extends IAuthorizationGroupId> groupIds,
 AuthorizationGroupFetchOptions fetchOptions)

getRoleAssignments

public Map<IRoleAssignmentId,RoleAssignment> getRoleAssignments(List<? extends IRoleAssignmentId> ids,
 RoleAssignmentFetchOptions fetchOptions)

getPersons

public Map<IPersonId,Person> getPersons(List<? extends IPersonId> ids,
 PersonFetchOptions fetchOptions)

getExternalDataManagementSystems

public Map<IExternalDmsId,ExternalDms> getExternalDataManagementSystems(List<? extends IExternalDmsId> externalDmsIds,
 ExternalDmsFetchOptions fetchOptions)

getSemanticAnnotations

public Map<ISemanticAnnotationId,SemanticAnnotation> getSemanticAnnotations(List<? extends ISemanticAnnotationId> annotationIds,
 SemanticAnnotationFetchOptions fetchOptions)

getOperationExecutions

public Map<IOperationExecutionId,OperationExecution> getOperationExecutions(List<? extends IOperationExecutionId> executionIds,
 OperationExecutionFetchOptions fetchOptions)

getQueries

public Map<IQueryId,Query> getQueries(List<? extends IQueryId> queryIds,
 QueryFetchOptions fetchOptions)

getQueryDatabases

public Map<IQueryDatabaseId,QueryDatabase> getQueryDatabases(List<? extends IQueryDatabaseId> queryDatabaseIds,
 QueryDatabaseFetchOptions fetchOptions)

getPersonalAccessTokens

public Map<IPersonalAccessTokenId,PersonalAccessToken> getPersonalAccessTokens(List<? extends IPersonalAccessTokenId> personalAccessTokenIds,
 PersonalAccessTokenFetchOptions fetchOptions)

getTypeGroups

public Map<ITypeGroupId,TypeGroup> getTypeGroups(List<? extends ITypeGroupId> typeGroupIds,
 TypeGroupFetchOptions fetchOptions)

getTypeGroupAssignments

public Map<ITypeGroupAssignmentId,TypeGroupAssignment> getTypeGroupAssignments(List<? extends ITypeGroupAssignmentId> ids,
 TypeGroupAssignmentFetchOptions fetchOptions)

searchSpaces

public SearchResult<Space> searchSpaces(SpaceSearchCriteria searchCriteria,
 SpaceFetchOptions fetchOptions)

searchProjects

public SearchResult<Project> searchProjects(ProjectSearchCriteria searchCriteria,
 ProjectFetchOptions fetchOptions)

searchExperiments

public SearchResult<Experiment> searchExperiments(ExperimentSearchCriteria searchCriteria,
 ExperimentFetchOptions fetchOptions)

searchExperimentTypes

public SearchResult<ExperimentType> searchExperimentTypes(ExperimentTypeSearchCriteria searchCriteria,
 ExperimentTypeFetchOptions fetchOptions)

searchSamples

public SearchResult<Sample> searchSamples(SampleSearchCriteria searchCriteria,
 SampleFetchOptions fetchOptions)

searchSampleTypes

public SearchResult<SampleType> searchSampleTypes(SampleTypeSearchCriteria searchCriteria,
 SampleTypeFetchOptions fetchOptions)

searchDataSets

public SearchResult<DataSet> searchDataSets(DataSetSearchCriteria searchCriteria,
 DataSetFetchOptions fetchOptions)

searchDataSetTypes

public SearchResult<DataSetType> searchDataSetTypes(DataSetTypeSearchCriteria searchCriteria,
 DataSetTypeFetchOptions fetchOptions)

searchExternalDataManagementSystems

public SearchResult<ExternalDms> searchExternalDataManagementSystems(ExternalDmsSearchCriteria searchCriteria,
 ExternalDmsFetchOptions fetchOptions)

searchPlugins

public SearchResult<Plugin> searchPlugins(PluginSearchCriteria searchCriteria,
 PluginFetchOptions fetchOptions)

searchVocabularies

public SearchResult<Vocabulary> searchVocabularies(VocabularySearchCriteria searchCriteria,
 VocabularyFetchOptions fetchOptions)

searchVocabularyTerms

public SearchResult<VocabularyTerm> searchVocabularyTerms(VocabularyTermSearchCriteria searchCriteria,
 VocabularyTermFetchOptions fetchOptions)

searchTags

public SearchResult<Tag> searchTags(TagSearchCriteria searchCriteria,
 TagFetchOptions fetchOptions)

searchAuthorizationGroups

public SearchResult<AuthorizationGroup> searchAuthorizationGroups(AuthorizationGroupSearchCriteria searchCriteria,
 AuthorizationGroupFetchOptions fetchOptions)

searchRoleAssignments

public SearchResult<RoleAssignment> searchRoleAssignments(RoleAssignmentSearchCriteria searchCriteria,
 RoleAssignmentFetchOptions fetchOptions)

searchPersons

public SearchResult<Person> searchPersons(PersonSearchCriteria searchCriteria,
 PersonFetchOptions fetchOptions)

searchCustomASServices

public SearchResult<CustomASService> searchCustomASServices(CustomASServiceSearchCriteria searchCriteria,
 CustomASServiceFetchOptions fetchOptions)

searchSearchDomainServices

public SearchResult<SearchDomainService> searchSearchDomainServices(SearchDomainServiceSearchCriteria searchCriteria,
 SearchDomainServiceFetchOptions fetchOptions)

searchAggregationServices

public SearchResult<AggregationService> searchAggregationServices(AggregationServiceSearchCriteria searchCriteria,
 AggregationServiceFetchOptions fetchOptions)

searchReportingServices

public SearchResult<ReportingService> searchReportingServices(ReportingServiceSearchCriteria searchCriteria,
 ReportingServiceFetchOptions fetchOptions)

searchProcessingServices

public SearchResult<ProcessingService> searchProcessingServices(ProcessingServiceSearchCriteria searchCriteria,
 ProcessingServiceFetchOptions fetchOptions)

searchObjectKindModifications

public SearchResult<ObjectKindModification> searchObjectKindModifications(ObjectKindModificationSearchCriteria searchCriteria,
 ObjectKindModificationFetchOptions fetchOptions)

searchGlobally

public SearchResult<GlobalSearchObject> searchGlobally(GlobalSearchCriteria searchCriteria,
 GlobalSearchObjectFetchOptions fetchOptions)

searchOperationExecutions

public SearchResult<OperationExecution> searchOperationExecutions(OperationExecutionSearchCriteria searchCriteria,
 OperationExecutionFetchOptions fetchOptions)

searchDataStores

public SearchResult<DataStore> searchDataStores(DataStoreSearchCriteria searchCriteria,
 DataStoreFetchOptions fetchOptions)

searchSemanticAnnotations

public SearchResult<SemanticAnnotation> searchSemanticAnnotations(SemanticAnnotationSearchCriteria searchCriteria,
 SemanticAnnotationFetchOptions fetchOptions)

searchPropertyTypes

public SearchResult<PropertyType> searchPropertyTypes(PropertyTypeSearchCriteria searchCriteria,
 PropertyTypeFetchOptions fetchOptions)

searchPropertyAssignments

public SearchResult<PropertyAssignment> searchPropertyAssignments(PropertyAssignmentSearchCriteria searchCriteria,
 PropertyAssignmentFetchOptions fetchOptions)

searchQueries

public SearchResult<Query> searchQueries(QuerySearchCriteria searchCriteria,
 QueryFetchOptions fetchOptions)

searchQueryDatabases

public SearchResult<QueryDatabase> searchQueryDatabases(QueryDatabaseSearchCriteria searchCriteria,
 QueryDatabaseFetchOptions fetchOptions)

searchTypeGroupAssignments

public SearchResult<TypeGroupAssignment> searchTypeGroupAssignments(TypeGroupAssignmentSearchCriteria searchCriteria,
 TypeGroupAssignmentFetchOptions fetchOptions)

deleteSpaces

public void deleteSpaces(List<? extends ISpaceId> spaceIds,
 SpaceDeletionOptions deletionOptions)

deleteProjects

public void deleteProjects(List<? extends IProjectId> projectIds,
 ProjectDeletionOptions deletionOptions)

deleteExperiments

public IDeletionId deleteExperiments(List<? extends IExperimentId> experimentIds,
 ExperimentDeletionOptions deletionOptions)

deleteSamples

public IDeletionId deleteSamples(List<? extends ISampleId> sampleIds,
 SampleDeletionOptions deletionOptions)

deleteDataSets

public IDeletionId deleteDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetDeletionOptions deletionOptions)

deletePlugins

public void deletePlugins(List<? extends IPluginId> pluginIds,
 PluginDeletionOptions deletionOptions)

deletePropertyTypes

public void deletePropertyTypes(List<? extends IPropertyTypeId> propertyTypeIds,
 PropertyTypeDeletionOptions deletionOptions)

deleteVocabularies

public void deleteVocabularies(List<? extends IVocabularyId> ids,
 VocabularyDeletionOptions deletionOptions)

deleteVocabularyTerms

public void deleteVocabularyTerms(List<? extends IVocabularyTermId> termIds,
 VocabularyTermDeletionOptions deletionOptions)

deleteExperimentTypes

public void deleteExperimentTypes(List<? extends IEntityTypeId> experimentTypeIds,
 ExperimentTypeDeletionOptions deletionOptions)

deleteSampleTypes

public void deleteSampleTypes(List<? extends IEntityTypeId> sampleTypeIds,
 SampleTypeDeletionOptions deletionOptions)

deleteDataSetTypes

public void deleteDataSetTypes(List<? extends IEntityTypeId> dataSetTypeIds,
 DataSetTypeDeletionOptions deletionOptions)

deleteExternalDataManagementSystems

public void deleteExternalDataManagementSystems(List<? extends IExternalDmsId> externalDmsIds,
 ExternalDmsDeletionOptions deletionOptions)

deleteTags

public void deleteTags(List<? extends ITagId> tagIds,
 TagDeletionOptions deletionOptions)

deleteAuthorizationGroups

public void deleteAuthorizationGroups(List<? extends IAuthorizationGroupId> groupIds,
 AuthorizationGroupDeletionOptions deletionOptions)

deleteRoleAssignments

public void deleteRoleAssignments(List<? extends IRoleAssignmentId> assignmentIds,
 RoleAssignmentDeletionOptions deletionOptions)

deleteOperationExecutions

public void deleteOperationExecutions(List<? extends IOperationExecutionId> executionIds,
 OperationExecutionDeletionOptions deletionOptions)

deleteSemanticAnnotations

public void deleteSemanticAnnotations(List<? extends ISemanticAnnotationId> annotationIds,
 SemanticAnnotationDeletionOptions deletionOptions)

deleteQueries

public void deleteQueries(List<? extends IQueryId> queryIds,
 QueryDeletionOptions deletionOptions)

deletePersons

public void deletePersons(List<? extends IPersonId> personIds,
 PersonDeletionOptions deletionOptions)

deletePersonalAccessTokens

public void deletePersonalAccessTokens(List<? extends IPersonalAccessTokenId> personalAccessTokenIds,
 PersonalAccessTokenDeletionOptions deletionOptions)

deleteTypeGroupAssignments

public void deleteTypeGroupAssignments(List<? extends ITypeGroupAssignmentId> typeGroupAssignmentIds,
 TypeGroupAssignmentDeletionOptions deletionOptions)

searchDeletions

public SearchResult<Deletion> searchDeletions(DeletionSearchCriteria searchCriteria,
 DeletionFetchOptions fetchOptions)

searchEvents

public SearchResult<Event> searchEvents(EventSearchCriteria searchCriteria,
 EventFetchOptions fetchOptions)

searchPersonalAccessTokens

public SearchResult<PersonalAccessToken> searchPersonalAccessTokens(PersonalAccessTokenSearchCriteria searchCriteria,
 PersonalAccessTokenFetchOptions fetchOptions)

searchSessionInformation

public SearchResult<SessionInformation> searchSessionInformation(SessionInformationSearchCriteria searchCriteria,
 SessionInformationFetchOptions fetchOptions)

revertDeletions

public void revertDeletions(List<? extends IDeletionId> deletionIds)

confirmDeletions

public void confirmDeletions(List<? extends IDeletionId> deletionIds)

executeCustomASService

public Object executeCustomASService(ICustomASServiceId serviceId,
 CustomASServiceExecutionOptions options)

executeSearchDomainService

public SearchResult<SearchDomainServiceExecutionResult> executeSearchDomainService(SearchDomainServiceExecutionOptions options)

executeAggregationService

public TableModel executeAggregationService(IDssServiceId serviceId,
 AggregationServiceExecutionOptions options)

executeReportingService

public TableModel executeReportingService(IDssServiceId serviceId,
 ReportingServiceExecutionOptions options)

executeProcessingService

public void executeProcessingService(IDssServiceId serviceId,
 ProcessingServiceExecutionOptions options)

executeQuery

public TableModel executeQuery(IQueryId queryId,
 QueryExecutionOptions options)

executeSql

public TableModel executeSql(String sql,
 SqlExecutionOptions options)

evaluatePlugin

public PluginEvaluationResult evaluatePlugin(PluginEvaluationOptions options)

archiveDataSets

public void archiveDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetArchiveOptions options)

unarchiveDataSets

public void unarchiveDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetUnarchiveOptions options)

lockDataSets

public void lockDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetLockOptions options)

unlockDataSets

public void unlockDataSets(List<? extends IDataSetId> dataSetIds,
 DataSetUnlockOptions options)

executeOperations

public IOperationExecutionResults executeOperations(List<? extends IOperation> operations,
 IOperationExecutionOptions options)

getServerInformation

public Map<String,String> getServerInformation()

getServerPublicInformation

public Map<String,String> getServerPublicInformation()

createPermIdStrings

public List<String> createPermIdStrings(int count)

createCodes

public List<String> createCodes(String prefix,
 EntityKind entityKind,
 int count)

executeImport

public ImportResult executeImport(ImportData importData,
 ImportOptions importOptions)

executeExport

public ExportResult executeExport(ExportData exportData,
 ExportOptions exportOptions)

uploadToSessionWorkspace

public String uploadToSessionWorkspace(Path fileOrFolder)

getDataStoreFacade

public OpenBIS.DataStoreFacade getDataStoreFacade()

getAfsServerFacade

public OpenBIS.AfsServerFacade getAfsServerFacade()

getSessionToken

public String getSessionToken()

setSessionToken

public void setSessionToken(String sessionToken)

setInteractiveSessionKey

public void setInteractiveSessionKey(String interactiveSessionKey)

getInteractiveSessionKey

public String getInteractiveSessionKey()

setTransactionId

public void setTransactionId(UUID transactionId)

getTransactionId

public UUID getTransactionId()

getManagedPersonalAccessToken

public PersonalAccessTokenPermId getManagedPersonalAccessToken(String sessionName)

This utility method returns a well managed personal access token, creating one if no one is found and renews it if is close to expiration. Requires are real session token since it uses other methods.

Throws:

UserFailureException - in case of any problems

getSemanticSubjectCreation

public static SemanticAnnotationCreation getSemanticSubjectCreation(EntityKind subjectEntityKind,
 String subjectClass,
 String subjectClassOntologyId,
 String subjectClassOntologyVersion,
 String subjectClassId)

This utility method provides a simplified API to create subject semantic annotations

getSemanticPredicateWithSubjectCreation

public static SemanticAnnotationCreation getSemanticPredicateWithSubjectCreation(EntityKind subjectEntityKind,
 String subjectClass,
 String predicateProperty,
 String predicatePropertyOntologyId,
 String predicatePropertyOntologyVersion,
 String predicatePropertyId)

This utility method provides a simplified API to create predicate semantic annotations

getSemanticPredicateCreation

public static SemanticAnnotationCreation getSemanticPredicateCreation(String predicateProperty,
 String predicatePropertyOntologyId,
 String predicatePropertyOntologyVersion,
 String predicatePropertyId)

This utility method provides a simplified API to create predicate semantic annotations