A C D E F G H I J K L M N O P Q R S T U V W

A

AbstractDatasetDropboxHandler - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Class which is able to create a copy of incoming data for additional processing.
AbstractDatasetDropboxHandler(Properties) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
 
AbstractDatasetDropboxHandler(Properties, IFileOperations) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
 
add(Project) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
 
add(String, Role) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
 
addAdHocVocabularyTerm(TechId, String, String, String, Long) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
addAdHocVocabularyTerm(Long, NewVocabularyTerm) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
addAdHocVocabularyTerm(TechId, String, String, String, Long) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Deprecated. Please use the IOpenbisServiceFacade.addAdHocVocabularyTerm(Long, NewVocabularyTerm) method instead.
addAdHocVocabularyTerm(Long, NewVocabularyTerm) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.
addChild(DataSetPathInfo) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
Deprecated. 
addDataSet(SimpleDataSetInformationDTO) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
addDataSet(IDataSetId) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
addExperiment(IExperimentId) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
addMatchClause(SearchCriteria.MatchClause) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Add a new match clause.
addMaterial(IMaterialId) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
addMetaproject(Metaproject) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
addMetaproject(Metaproject) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
addMetaproject(Metaproject) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
addMetaproject(Metaproject) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
addPropertyType(PropertyType) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup.PropertyTypeGroupInitializer
 
addPropertyTypeGroup(PropertyTypeGroup) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
addRow(Serializable[]) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel
Adds a row of values.
addSample(ISampleId) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
addSubCriteria(SearchSubCriteria) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Add a new sub search criteria.
addToMetaproject(String, IMetaprojectId, MetaprojectAssignmentsIds) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Adds given entities to an existing metaproject.
addUnofficialVocabularyTerm(String, TechId, String, String, String, Long) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Deprecated. Because the parameters refer to an internal openBIS class (TechID).
addUnofficialVocabularyTerm(String, Long, NewVocabularyTerm) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.
addVersion(RpcServiceInterfaceVersionDTO) - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
afterPropertiesSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
AggregationServiceDescription - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Bean with information about aggregation services that provide data.
AggregationServiceDescription() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
AggregationServiceType - Enum in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
The different kinds of aggregation services.
AndDataSetFilter - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.filter
Combining filters by logical AND.
AndDataSetFilter(IDataSetFilter...) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.AndDataSetFilter
 
appendFileInfos(ArrayList<FileInfoDssDTO>, boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.HierarchicalFileInfoDssBuilder
Append file info starting from the listing root node.
appendFileInfosForFile(File, ArrayList<FileInfoDssDTO>, boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder
Append file info for the requested file or file hierarchy.
appendNameAndObject(StringBuilder, String, Object) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil
Helps in implementing toString() methods
asHierarchicalContent(File, IDelegatedAction) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.PathInfoDBAwareHierarchicalContentFactory
 
asHierarchicalContent(File, IDelegatedAction) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.PathInfoDBOnlyHierarchicalContentFactory
 
asNewDataSetDTO() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
Convert the builder into a NewDataSetDTO object.
AtomicEntityOperationDetails<T extends DataSetInformation> - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
An object that captures the state for performing the registration of one or many openBIS entities atomically.
AtomicEntityOperationDetails(TechId, String, List<NewSpace>, List<ProjectUpdatesDTO>, List<NewProject>, List<ExperimentUpdatesDTO>, List<NewExperiment>, List<SampleUpdatesDTO>, List<NewSample>, Map<String, List<NewMaterial>>, List<MaterialUpdateDTO>, List<DataSetRegistrationInformation<T>>, List<DataSetBatchUpdatesDTO>, List<NewMetaproject>, List<MetaprojectUpdatesDTO>, List<VocabularyUpdatesDTO>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
Attachment - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing an attachment.
Attachment(Attachment.AttachmentInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
 
Attachment.AttachmentInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
Attachment.AttachmentInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
AuthorizationFailureException - Exception in ch.systemsx.cisd.common.exceptions
A UserFailureException for authorization failure.
AuthorizationFailureException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.AuthorizationFailureException
 
AutoSymlink - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Helper application which creates symbolic links for JAR files in DSS core plugins in folder lib.
AutoSymlink() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AutoSymlink
 

C

CACHE_WORKSPACE_FOLDER_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
CACHE_WORKSPACE_MAX_SIZE_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
CACHE_WORKSPACE_MIN_KEEPING_TIME_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
calculateFreeSpace() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Calculates the actual free space (in bytes) of the hard disk on which this share resides.
callWithRetry() - Method in class ch.systemsx.cisd.common.api.retry.RetryCaller
 
ch.systemsx.cisd.common.api - package ch.systemsx.cisd.common.api
 
ch.systemsx.cisd.common.api.retry - package ch.systemsx.cisd.common.api.retry
 
ch.systemsx.cisd.common.api.retry.config - package ch.systemsx.cisd.common.api.retry.config
 
ch.systemsx.cisd.common.exceptions - package ch.systemsx.cisd.common.exceptions
 
ch.systemsx.cisd.openbis.dss.client.api.v1 - package ch.systemsx.cisd.openbis.dss.client.api.v1
 
ch.systemsx.cisd.openbis.dss.client.api.v1.impl - package ch.systemsx.cisd.openbis.dss.client.api.v1.impl
 
ch.systemsx.cisd.openbis.dss.generic.shared.api.v1 - package ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
 
ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation - package ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
 
ch.systemsx.cisd.openbis.dss.generic.shared.content - package ch.systemsx.cisd.openbis.dss.generic.shared.content
 
ch.systemsx.cisd.openbis.dss.generic.shared.dto - package ch.systemsx.cisd.openbis.dss.generic.shared.dto
 
ch.systemsx.cisd.openbis.dss.generic.shared.utils - package ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
ch.systemsx.cisd.openbis.generic.shared.api.v1 - package ch.systemsx.cisd.openbis.generic.shared.api.v1
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample - package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.filter - package ch.systemsx.cisd.openbis.generic.shared.api.v1.filter
 
ch.systemsx.cisd.openbis.generic.shared.api.v1.util - package ch.systemsx.cisd.openbis.generic.shared.api.v1.util
 
ch.systemsx.cisd.openbis.plugin.query.client.api.v1 - package ch.systemsx.cisd.openbis.plugin.query.client.api.v1
API Facade
ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto - package ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Data Transfer Objects
check(List<? extends IDatasetLocation>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetAndPathInfoDBConsistencyChecker
 
checkSession() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Checks whether the session is alive.
checkSession() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
checkSession() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
checkSession() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Checks whether the session is alive.
cleanUp(SimpleDataSetInformationDTO, File, String, IShareIdManager, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Deletes specified data set in the old share if it is already in the new one or in the new one if it is still in the old one.
close() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
close() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
CodeAndLabelUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility class to operate on codes and labels.
CodeAndLabelUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil
 
compareTo(Attachment) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
 
COMPOUND - Static variable in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
Material identifier for a compound.
ConfigurationFailureException - Exception in ch.systemsx.cisd.common.exceptions
The ConfigurationFailureException is the super class of all exceptions that have their cause in an inappropriate configuration of the system.
ConfigurationFailureException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.ConfigurationFailureException
 
ConfigurationFailureException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.ConfigurationFailureException
 
ContentCache - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
Cache for files remotely retrieved from Data Store Servers.
ControlledVocabularyPropertyType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
ControlledVocabularyPropertyType(ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType
 
ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer
 
ControlledVocabularyPropertyType.VocabularyTerm - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
ControlledVocabularyPropertyType.VocabularyTerm(String, String, Long, Boolean, EntityRegistrationDetails) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm
 
convertForDisplayIfNecessary(BufferedImage) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
If the specified image uses grayscale with color depth larger then 8 bits, conversion to 8 bits grayscale is done.
convertForDisplayIfNecessary(BufferedImage, float) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
If the specified image uses grayscale with color depth larger then 8 bits, conversion to 8 bits grayscale is done.
convertPatternListToString(List<String>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetTypeFilter
Takes a List of patterns and serializes them to a single string that this class can later reread.
copyToDirectoryAs(File, File, String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
 
create(T) - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
Creates a new result with status StatusFlag.OK and resultOrNull.
create(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
create() - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.PathInfoDBAwareHierarchicalContentFactory
Returns implementation of IHierarchicalContentFactory based on configuration of Path Info DB.
create() - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.PathInfoDBOnlyHierarchicalContentFactory
 
create(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil
Creates an instance from specified label with optional code prefix in form of <code>.
create(String, String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory
Creates a facade for specified server URL, user Id, and password.
create(String, String) - Static method in class ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory
Creates a facade for specified url and sessionToken.
createAnyFieldMatch(String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Factory method to create a MatchClause matching against any property or attribute.
createAnyPropertyMatch(String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Factory method to create a MatchClause matching against any property.
createAttributeMatch(SearchCriteria.MatchClauseAttribute, String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Factory method to create a MatchClause matching against a specific attribute.
createDataSetChildCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createDataSetContainerCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createDataSetParentCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createDataSetTypeValidationError(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
createError(boolean) - Static method in class ch.systemsx.cisd.common.exceptions.Status
Create an error.
createError(boolean, String) - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createError() - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createError(String) - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createError(String, Object...) - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createError(boolean) - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
Create an error.
createError(boolean, String) - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
createError() - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
createError(String) - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
createExperimentCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createFileValidationError(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
createHelper(BufferedImage) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PngWritingHelper
 
createMasqueradingExceptionIfNeeded(Exception, Collection<String>) - Static method in class ch.systemsx.cisd.common.exceptions.ExceptionUtils
Analyzes given exception and makes it independent to packages outside the specified collection or java.lang, ch.systemsx.cisd.common.
createMetaproject(String, String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Creates a new metaproject.
createOwnerValidationError(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
createPropertyMatch(String, String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Factory method to create a MatchClause matching against a specific property.
createPropertyValidationError(String, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
createProxy(T) - Static method in class ch.systemsx.cisd.common.api.retry.RetryProxyFactory
 
createReport() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetAndPathInfoDBConsistencyChecker
 
createReportFromAggregationService(String, String, Map<String, Object>) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Create the report from the specified aggregation service.
createReportFromAggregationService(AggregationServiceDescription, Map<String, Object>) - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Executes the specified aggregation or ingestion service for the specified parameters and creates a report.
createReportFromDataSets(String, String, List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Creates for the specified data sets a report.
createReportFromDataSets(ReportDescription, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Creates for the specified data sets and specified report description a report.
createReportFromDataSets(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Creates for the specified data sets and specified report key a report.
createRetriableError() - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createRetriableError(String) - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createRetriableError(String, Object...) - Static method in class ch.systemsx.cisd.common.exceptions.Status
 
createRetriableError() - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
createRetriableError(String) - Static method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
createSampleChildCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createSampleContainerCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createSampleCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createSampleParentCriteria(SearchCriteria) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
createThumbnailForDisplay(BufferedImage, int, int) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Re-scales the image to be the biggest one which fits into a (0,0,maxWidth, maxHeight) rectangle.
createTimeAttributeMatch(SearchCriteria.MatchClauseTimeAttribute, SearchCriteria.CompareMode, String, String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Factory method to create a MatchClause matching against registration or modification date.
createValidatorFromScriptPaths(String[]) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
Factory method for creating a ValidationScriptRunner given a path to a script.
createValidatorFromScriptPaths(String[], boolean) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
Factory method for creating a ValidationScriptRunner given a path to a script.
createValidatorFromScriptString(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
Factory method for creating a ValidationScriptRunner given the script as a string.
createValidatorFromScriptString(String, boolean) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
Factory method for creating a ValidationScriptRunner given the script as a string.
CsvFileReaderHelper - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
CsvFileReaderHelper() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper
 
CsvFileReaderHelper.DefaultCsvFileReaderConfiguration - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Default configuration for reading csv file: ';' - column delimiter '#' - comment delimiter ignoring empty records
CsvFileReaderHelper.DefaultCsvFileReaderConfiguration() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
CsvFileReaderHelper.DefaultTsvFileReaderConfiguration - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Default configuration for reading TSV file:
CsvFileReaderHelper.DefaultTsvFileReaderConfiguration() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultTsvFileReaderConfiguration
 
CsvFileReaderHelper.ICsvFileReaderConfiguration - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Configuration for reading csv file.

D

DATA_SET_SIZE_COMPARATOR - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
DATA_SOURCE_NAME - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvider
 
DATA_STREAM_MAX_TIMEOUT - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
DATA_STREAM_TIMEOUT - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
DataSet - Class in ch.systemsx.cisd.openbis.dss.client.api.v1
A class that provides uniform access to data set metadata (from the openBIS AS) and data (from the openBIS DSS).
DataSet(IOpenbisServiceFacade, IDssComponent, DataSet, IDataSetDss) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
Constructor.
DataSet - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a data set.
DataSet(DataSet.DataSetInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Creates a new instance with the provided initializer
DataSet.Connections - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
DataSet.DataSetInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new data set instance.
DataSet.DataSetInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
DATASET_CODE_SEPARATOR_PROPERTY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
Property name which is used to specify the text which will be used to separate the sample code and dataset code in the name of the file which will be created in the dropbox.
DataSetAndPathInfoDBConsistencyChecker - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
DataSetAndPathInfoDBConsistencyChecker(IHierarchicalContentProvider, IHierarchicalContentProvider) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetAndPathInfoDBConsistencyChecker
 
DataSetCodeId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset
Identifies a data set by code.
DataSetCodeId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId
 
DataSetCodesWithStatus - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
 
DataSetCodesWithStatus(List<String>, DataSetArchivingStatus, boolean) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetCodesWithStatus
 
DataSetDss - Class in ch.systemsx.cisd.openbis.dss.client.api.v1.impl
 
DataSetDss(String, IDssServiceRpcGeneric, AuthenticatedState) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
DataSetExistenceChecker - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Helper class checking existence of a data set in a share.
DataSetExistenceChecker(IDataSetDirectoryProvider, Properties) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker
 
DataSetExistenceChecker(IDataSetDirectoryProvider, TimingParameters) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker
 
DataSetExistenceChecker(IDataSetDirectoryProvider, long, int) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker
 
dataSetExists(DeletedDataSet) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker
 
dataSetExists(IDatasetLocation) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetExistenceChecker
 
DataSetFetchOption - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
DataSetFetchOptions - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
DataSetFetchOptions() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOptions
 
DataSetFetchOptions(DataSetFetchOption...) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOptions
 
DataSetFileDTO - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Represents a reference to a file/folder within a data set.
DataSetFileDTO(String, String, boolean) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataSetFileDTO
 
DatasetFileLines - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Stores the lines of a file with tabular data (TSV, CSV, XLS).
DatasetFileLines(File, DatasetDescription, List<String[]>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
 
DatasetFileLines(File, String, List<String[]>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
 
DatasetFileLines(File, String, List<String[]>, boolean) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
 
DataSetInformation - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
Container class for data extracted from the data set directory.
DataSetInformation() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
This constructor is for serialization.
DataSetKind - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Enumeration of all possible data set kinds.
DatasetLocationUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
DatasetLocationUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil
 
DataSetPathInfo - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
 
DataSetPathInfo() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
DataSetRegistrationInformation<T extends DataSetInformation> - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
 
DataSetRegistrationInformation(T, NewExternalData) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation
 
DataSetTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset
Identifies a data set by tech id.
DataSetTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetTechIdId
 
DataSetType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a data set type.
DataSetType(DataSetType.DataSetTypeInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
Creates a new instance with the provided initializer
DataSetType.DataSetTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new DataSetType instance.
DataSetType.DataSetTypeInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
DataSetTypeFilter - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A class that filters out data set types based on a whitelist or blacklist.
DataSetTypeFilter(String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetTypeFilter
Constructor
DataStore - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
DataStore(String, String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore
 
DataStoreApiUrlUtilities - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
 
DataStoreURLForDataSets - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
The data store URL for a set of data sets.
DataStoreURLForDataSets(String, String[]) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets
 
DEFAULT_DATA_SET_FOLDER_NAME - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
When a grayscale image with color depth > 8 bits has to be displayed and user has not decided how it should be converted, then this threshold will be used.
DefaultRetryConfiguration - Class in ch.systemsx.cisd.common.api.retry.config
 
DelayedPersistenceManager - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
 
DelayedPersistenceManager(IPersistenceManager) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.DelayedPersistenceManager
 
DelayedPersistenceManager(IPersistenceManager, long) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.DelayedPersistenceManager
 
deleteDataSet(IDatasetLocation, IDataSetDirectoryProvider, IShareIdManager, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Deletes specified data set.
deleteDataSetInstantly(String, File, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Deletes specified data set at specified location.
deleteMetaproject(String, IMetaprojectId) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Deletes an existing metaproject.
deleteSessionWorkspaceFile(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Delete a file or directory in the session workspace.
deleteSessionWorkspaceFile(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
deleteSessionWorkspaceFile(String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Delete a file or directory in the session workspace.
describe() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
didFinish() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader.FileInfoDssDownloaderListener
 
DOWNLOAD_URL_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
downloadFiles() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader
 
DSS_CODE_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
DSS_RECOVERY_STATE_DIR_PATH - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
Directory for recovery state files.
DSS_REGISTRATION_LOG_DIR_PATH - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
Directory for registration log files.
DSS_SERVICE_NAME - Static variable in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
 
DssComponent - Class in ch.systemsx.cisd.openbis.dss.client.api.v1.impl
Implementation of the IDssComponent interface.
DssComponent(IGeneralInformationService, IRpcServiceFactory, String) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
Constructor for clients that already have an IETLLIMSService; also used for testing.
DssComponentFactory - Class in ch.systemsx.cisd.openbis.dss.client.api.v1
A class that creates DssComponents.
DssComponentFactory() - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory
 
DssCrossOriginFilter - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
A DSS implementation of AbstractCrossOriginFilter.
DssCrossOriginFilter() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssCrossOriginFilter
 
DssPluginType - Enum in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
DssPropertyParametersUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility class to load properties.
DssPropertyParametersUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
DssServiceRpcFactory - Class in ch.systemsx.cisd.openbis.dss.client.api.v1.impl
Client-side factory for DssServiceRpc objects.
DssServiceRpcFactory() - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssServiceRpcFactory
 
DssServiceRpcFactory(long) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssServiceRpcFactory
 
DssServiceRpcGenericFactory - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
Implementation of IDssServiceRpcGenericFactory using on HttpInvokerUtils and caching services in a map.
DssServiceRpcGenericFactory() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.DssServiceRpcGenericFactory
 

E

EntityRegistrationDetails - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A class that encapsulates the details about entity registration.
EntityRegistrationDetails(EntityRegistrationDetails.EntityRegistrationDetailsInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
EntityRegistrationDetails.EntityRegistrationDetailsInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize an EntityRegistrationDetails object.
EntityRegistrationDetails.EntityRegistrationDetailsInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
EntityType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Common attributes of all entity types.
EntityTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Generic part of all entity type initializers.
EnvironmentFailureException - Exception in ch.systemsx.cisd.common.exceptions
The EnvironmentFailureException is the super class of all exceptions that have their cause in the software or hardware environment of the system failing.
EnvironmentFailureException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
 
EnvironmentFailureException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
 
equals(Object) - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
equals(Object) - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
 
equals(Object) - Method in class ch.systemsx.cisd.common.exceptions.Status
 
equals(Object) - Method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectIdentifierId
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectPermIdId
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectTechIdId
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.TimeAttributeMatchClause
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
equals(Object) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns true if and only if the specified object is of type QueryDescription and has the same ID as this.
error() - Static method in exception ch.systemsx.cisd.common.exceptions.InternalErr
 
error(String) - Static method in exception ch.systemsx.cisd.common.exceptions.InternalErr
 
error(Object) - Static method in exception ch.systemsx.cisd.common.exceptions.InternalErr
 
escape(String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
Returns a String where those characters that Lucene expects to be escaped are escaped by a preceding \.
ExcelFileReader - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Reader of tabular data from excel files.
ExcelFileReader(Workbook, boolean) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
ExceptionUtils - Class in ch.systemsx.cisd.common.exceptions
Provides utilities for manipulating and examining Throwable objects.
ExceptionWithStatus - Exception in ch.systemsx.cisd.common.exceptions
 
ExceptionWithStatus(Status) - Constructor for exception ch.systemsx.cisd.common.exceptions.ExceptionWithStatus
 
ExceptionWithStatus(Status, Exception) - Constructor for exception ch.systemsx.cisd.common.exceptions.ExceptionWithStatus
 
executeQuery(long, Map<String, String>) - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Executes specified query by using specified parameter bindings.
exists() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
Experiment - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing an experiment.
Experiment(Experiment.ExperimentInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Creates a new instance with the provided initializer
Experiment.ExperimentInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new experiment instance.
Experiment.ExperimentInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
ExperimentIdentifierId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment
Identifies an experiment by identifier.
ExperimentIdentifierId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.ExperimentIdentifierId
 
ExperimentPermIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment
Identifies an experiment by perm id.
ExperimentPermIdId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.ExperimentPermIdId
 
EXPERIMENTS_PROP - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ShareFactory
 
ExperimentTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment
Identifies an experiment by tech id.
ExperimentTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.ExperimentTechIdId
 
ExperimentType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing an experiment type.
ExperimentType(ExperimentType.ExperimentTypeInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ExperimentType
Creates a new instance with the provided initializer
ExperimentType.ExperimentTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new ExperimentType instance.
ExperimentType.ExperimentTypeInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ExperimentType.ExperimentTypeInitializer
 
extractMetadata(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Tries to extract the data set property key-values (metadata) from the data.
extractMetadata(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
extractMetadata(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
extractMetadata(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Extracts metadata from a file.
extractMetadata(File) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
 
extractMetadata(File) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner.NullValidationScriptRunner
 

F

FacadeFactory - Class in ch.systemsx.cisd.openbis.plugin.query.client.api.v1
Factory of IQueryApiFacade.
FacadeFactory() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory
 
FileExistsException - Exception in ch.systemsx.cisd.common.exceptions
An exception indicating that an output file already exists.
FileExistsException(File) - Constructor for exception ch.systemsx.cisd.common.exceptions.FileExistsException
 
FileInfoDssBuilder - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Helper Class for creating FileInfoDss objects based on file system.
FileInfoDssBuilder(String, String) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder
Constructor for FileInfoDssFactory
FileInfoDssDownloader - Class in ch.systemsx.cisd.openbis.dss.client.api.v1
Utility class for downloading an array of file infos.
FileInfoDssDownloader(IDataSetDss, FileInfoDssDTO[], File) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader
 
FileInfoDssDownloader(IDataSetDss, FileInfoDssDTO[], File, FileInfoDssDownloader.FileInfoDssDownloaderListener) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader
 
FileInfoDssDownloader.FileInfoDssDownloaderListener - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
Interface for listeners to events from the downloader.
FileInfoDssDTO - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Represents information about a file stored in DSS.
FileInfoDssDTO(String, String, boolean, long) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
 
FileInfoDssDTO(String, String, boolean, long, Integer) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
 
fillLine(ImageLine, int) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PngWritingHelper
 
filterDataSetsVisibleToUser(String, List<DataSet>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns a filtered list of allDataSets containing those data sets which are visible to userId.
filterDataSetTypes(List<DataSetType>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetTypeFilter
 
filterExperimentsVisibleToUser(String, List<Experiment>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns a filtered list of allExperiments containing those experiments which are visible to userId.
filterSamplesVisibleToUser(String, List<Sample>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns a filtered list of allSamples containing those samples which are visible to userId.
findIncomingShare(File, File, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Returns first the id of the first incoming share folder of specified store root which allows to move a file from specified incoming folder to the incoming share.
freeSpaceKb(HostAwareFile) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PostgresPlusFileSystemFreeSpaceProvider
 
fromTemplate(String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.ConfigurationFailureException
Creates an ConfigurationFailureException using a Formatter.
fromTemplate(Throwable, String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.ConfigurationFailureException
Creates an ConfigurationFailureException using a Formatter.
fromTemplate(String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
Creates an EnvironmentFailureException using a Formatter.
fromTemplate(Throwable, String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
Creates an EnvironmentFailureException using a Formatter.
fromTemplate(String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.InvalidExternalDataException
Creates an InvalidExternalDataException using a Formatter.
fromTemplate(Throwable, String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.InvalidExternalDataException
Creates an InvalidExternalDataException using a Formatter.
fromTemplate(String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.UserFailureException
Creates an UserFailureException using a Formatter.
fromTemplate(Throwable, String, Object...) - Static method in exception ch.systemsx.cisd.common.exceptions.UserFailureException
Creates an UserFailureException using a Formatter.

G

GENE - Static variable in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
Material identifier for a gene.
getAttachmentHolderId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getAttachmentHolderId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the id of the entity holding this attachment.
getAttribute() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.AttributeMatchClause
Return the code of the attribute to compare against.
getAttribute() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.TimeAttributeMatchClause
Return the code of the attribute to compare against.
getAugmentedCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
getChecksumCRC32() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getChecksumCRC32() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getChildNodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getChildren() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
Deprecated. 
getChildren() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Return the children.
getChildren() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getChildrenCodes() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getChildrenCodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getChildrenCodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Return the children codes.
getChildrenJson() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getClassName() - Method in class ch.systemsx.cisd.common.exceptions.NotImplementedException.StackTraceExtractor
 
getCode() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getCode() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
The code of this data set.
getCode() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Returns the data set code;
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
Returns the unique entity type code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Returns the experiment code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialCodeAndTypeCodeId
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Return the term's code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Returns the project code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
Return the code of this property type.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
Returns role code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
Returns the space code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns the vocabulary code.
getCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
getCodePrefix() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns code prefix used to create sample code automatically.
getCodePrefix() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
getCols() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PngWritingHelper
 
getColumnDelimiter() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
getColumnDelimiter() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultTsvFileReaderConfiguration
 
getColumnDelimiter() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration
 
getColumns() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel
Returns columns as specified in the constructor.
getCommentDelimiter() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
getCommentDelimiter() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration
 
getCompareMode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
 
getContainedDataSetCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getContainedDataSets() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getContainedDataSets() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getContainedDataSets() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getContainerOrNull() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getContainerOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getContainerOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getCriteria() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
getCsvReader(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper
Get a CsvReader for parsing a tabular data file with default configuration.
getCsvReader(File, CsvFileReaderHelper.ICsvFileReaderConfiguration) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper
Get a CsvReader for parsing a tabular data file with specified configuration.
getDataLines() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
 
getDataLines() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData
 
getDataSet(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Get a proxy to the data set designated by the given data set code.
getDataSet(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
getDataSet(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getDataSet(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return a DataSet object for for the given code.
getDataSetCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataSetFileDTO
The code of the data set that owns this file
getDataSetCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getDataSetCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetCodesWithStatus
 
getDataSetCodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets
A set of data sets that can be found in this data store.
getDataSetDss() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
Internal accessor, made public for testing, but clients should not need it.
getDataSetDss(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getDatasetFileLines(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper
Return the tabular data as a DatasetFileLines with default configuration.
getDatasetFileLines(File, CsvFileReaderHelper.ICsvFileReaderConfiguration) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper
Return the tabular data as a DatasetFileLines with specified configuration.
getDataSetFolderName() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
The name of the folder containing the files in the data set.
getDataSetInformation() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation
 
getDataSetKind() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
getDataSetKind() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
Returns the kind of data sets of this type.
getDatasetLocationPath(File, String, String, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil
Creates a location where a dataset can be found in a specified base directory.
getDatasetLocationPath(String, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil
returns location (path relative to the share)
getDatasetLocationPathCheckingIfExists(String, String, DatabaseInstance, File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil
Creates a location where a dataset can be found in a specified base directory.
getDataSetMetadata() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
The metadata data for the data set, including type and properties.
getDataSetMetaData(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns meta data for all specified data sets.
getDataSetMetaData(String, List<String>, EnumSet<DataSetFetchOption>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns meta data for all specified data sets.
getDataSetOwner() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
The direct owner of the data set, either an experiment or a sample.
getDataSetOwner() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
The owner may be null during construction but is non-null in a well-formed object.
getDataSetOwnerIdentifier() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
The owner identifier may be and empty during construction but is non-null in a well-formed object.
getDataSetOwnerType() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
The owner type should never be null.
getDataSetProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getDataSetRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getDataSets(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getDataSets(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return DataSet objects for given a set of codes.
getDataSets() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
getDataSets() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
getDataSetsOrderedBySize() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns all data sets of this shared ordered by size starting with the largest data set.
getDataSetType() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getDataSetTypeCode() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getDataSetTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getDataSetTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getDataSetTypes() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
getDataSetUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getDataSource() - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvider
 
getDataStoreBaseUrl() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
Returns the base URL of the data store that provides this service.
getDataStoreBaseURLs(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns the download URL for the data store of specified data sets.
getDataStoreCode(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDataStoreCode() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
The code of the data store that provides this service.
getDataStoreCode() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
getDataStoreURL() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets
The base URL of the data store.
getDataStoreUrlFromDownloadUrl(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataStoreApiUrlUtilities
Converts the download url to a server url.
getDataStreamMaxTimeout(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDataStreamTimeout(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDataType() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
 
getDataType() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
getDataType() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn
Returns the data type.
getDefaultPutDataStoreBaseURL(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns the URL for the default data store server for this openBIS AS.
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the description given by the user when uploading this attachment.
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
Returns the description or null if undefined.
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Return the term's description.
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
Return the extended description.
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
getDescription() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns the vocabulary description.
getDescription() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns an optional description or empty string if undefined.
getDesiredValue() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
 
getDownloadLink() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getDownloadLink() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the download link.
getDownloadUrl(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDownloadUrl() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore
 
getDownloadUrlForFileForDataSet(String, DataSetFileDTO) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns an URL from which the requested file.
getDownloadUrlForFileForDataSet(String, String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns an URL from which the requested file of the specified data set can be downloaded.
getDownloadUrlForFileForDataSetWithTimeout(String, DataSetFileDTO, long) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns an URL from which the requested file.
getDownloadUrlForFileForDataSetWithTimeout(String, String, String, long) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns an URL from which the requested file of the specified data set can be downloaded.
getDownloadUrlFromDataStoreUrl(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataStoreApiUrlUtilities
Converts a data store server URL to a URL that can be used to download files.
getDssInternalTempDir(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDssRecoveryStateDir(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getDssRegistrationLogDir(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getEmail() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getEndOfChain(Throwable) - Static method in class ch.systemsx.cisd.common.exceptions.ExceptionUtils
Returns the last Throwable of a chain of throwables.
getErrorMessage() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
getExcelWorkbook(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Returns the identifier of experiment which makes it unique.
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getExperimentIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Returns the identifier of the Experiment to which this data set belongs.
getExperimentIdentifierOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getExperimentIdentifierOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getExperimentIdentifiers() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns the set of experiment identifier or an empty set if undefined.
getExperimentRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getExperiments(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getExperiments(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return Experiment objects for a set of given experiment identifiers.
getExperiments() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
getExperiments() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
getExperimentTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getExperimentTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Returns the experiment type code.
getExperimentUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getExternalCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getExternalData() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation
 
getExternalDataManagementSystem() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getExternalDataManagementSystem() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getExternalDataManagementSystem() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getExternalDataManagementSystem() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getExternalDataSetCode() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getExternalDataSetCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getExternalDataSetCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getExternalDataSetLink() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getExternalDataSetLink() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getExternalDataSetLink() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getExtractableData() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getFetchOptions() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getFieldType() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
The field type this MatchClause matches against.
getFile(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getFile(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Get an InputStream with contents of a file contained in this data set.
getFile(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getFile() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
The file that contains the data set.
getFile(String, IDatasetLocation, DataSetPathInfo) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
getFile(String, IDatasetLocation, DataSetPathInfo) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.content.IContentCache
 
getFile() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getFile() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
 
getFileContent() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getFileForDataSet(String, DataSetFileDTO) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Deprecated. use IDssServiceRpcGeneric.getDownloadUrlForFileForDataSet(String, DataSetFileDTO).
getFileForDataSet(String, String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Deprecated. use IDssServiceRpcGeneric.getDownloadUrlForFileForDataSet(String, String, String).
getFileFromSessionWorkspace(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Downloads a file from the session workspace.
getFileFromSessionWorkspace(String, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Downloads a file from the session workspace.
getFileFromSessionWorkspace(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
getFileFromSessionWorkspace(String, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
getFileFromSessionWorkspace(String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Download a file from the user's session workspace.
getFileInfos(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder
Return a list of FileInfoDssDTO objects corresponding to all files existing within a certain folder.
getFileInfos() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
FileInfoDssDTO objects describing the files within the data set.
getFileInfos() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
 
getFileLength() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getFileName() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getFileName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getFileName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the file name of this attachment.
getFileSize() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
Return the file size if this FileInfo represents a file.
getFirstName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getFlag() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
getFreeSpace() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
getGeneralInformationService() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Returns a remote access to the IGeneralInformationService.
getHeaderCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
Returns the normalized headers.
getHeaderCodes() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData
 
getHeaderLabels() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines
Returns the headers as defined in the file.
getHeaderLabels() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData
 
getHeight() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
getHostUrl() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore
 
getId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Returns tech id of the data set.
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Returns the experiment id.
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Returns the techical database id of the project.
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample id.
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns the vocabulary id.
getId() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns the ID of the query.
getIdentifier() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner
 
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Returns the experiment identifier.
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectIdentifierId
 
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
 
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample identifier;
getIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getImageInfo() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PngWritingHelper
 
getInputStream(String, IDatasetLocation, DataSetPathInfo) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.ContentCache
 
getInputStream(String, IDatasetLocation, DataSetPathInfo) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.content.IContentCache
 
getInputStream() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getInstance() - Static method in class ch.systemsx.cisd.common.api.retry.config.DefaultRetryConfiguration
 
getInstanceCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getInstanceUUID() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getInterfaceName() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
The name of this interface used for identification.
getInterfaceName() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
The name of this interface used for identification.
getIsCompleteFlag() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getKey() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
getKeyOfKeyListPropertyOrNull() - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
 
getLabel() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Return the term's label.
getLabel() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
Return the label shown in forms.
getLabel() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
getLabel() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
Returns the label of the service.
getLabel() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
getLastModified() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getLastModified() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getLastName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getLinkOrCopyOfContent(String, File, String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getLinkOrCopyOfContent(String, File, String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Returns a File, if possible, that directly references some specified content of a data set in the data store server.
getLinkOrCopyOfContent(String, File, String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getLinkOrCopyOfContents(String, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getLinkOrCopyOfContents(String, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Returns a File, if possible, that directly references the contents of a data set in the data store server.
getLinkOrCopyOfContents(String, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getMainDataSetPath() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
getMainDataSetPath() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
Returns main data set path if defined.
getMainDataSetPattern() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
getMainDataSetPattern() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
Returns main data set pattern if defined.
getMajorVersion() - Method in interface ch.systemsx.cisd.common.api.IRpcService
Returns the major version of the server side interface.
getMajorVersion() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
The major version of the interface.
getMatchClauses() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Get a list of MatchClause objects this SearchCriteria will match against.
getMaterialByCodes(String, List<MaterialIdentifier>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns the materials with specified identifiers (i.e.
getMaterialCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getMaterialCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
getMaterialProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
getMaterialProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getMaterialRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getMaterials() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
getMaterials() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
getMaterialTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
Returns the code of this material type.
getMaterialTypeIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getMaterialTypeIdentifier() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
getMaterialUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getMaximumNumberOfRetries() - Method in interface ch.systemsx.cisd.common.api.retry.config.RetryConfiguration
 
getMaximumNumberOfRetries() - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
getMessage() - Method in exception ch.systemsx.cisd.common.exceptions.NotImplementedException
Returns the error message for this exception.
getMetaproject() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
getMetaproject(String, IMetaprojectId) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all entities tagged with given metaproject.
getMetaprojectOnBehalfOfUser(String, IMetaprojectId, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all entities tagged with given metaproject for specified user.
getMetaprojectRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getMetaprojects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getMetaprojectsJson() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getMetaprojectUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getMethodName() - Method in class ch.systemsx.cisd.common.exceptions.NotImplementedException.StackTraceExtractor
 
getMinorVersion() - Method in interface ch.systemsx.cisd.common.api.IRpcService
Returns the minor version of this server side interface.
getMinorVersion() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
The major version of the interface.
getMinorVersionInformationService() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getMinorVersionInformationService() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns the minor version of the general information service.
getModificationDate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getModificationDate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getModifierEmail() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getModifierEmail() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getModifierFirstName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getModifierFirstName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getModifierLastName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getModifierLastName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getModifierUserId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getModifierUserId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getName() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
Returns the name of this group (section).
getName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup.PropertyTypeGroupInitializer
 
getName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
getName() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns the name of the query.
getNode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
getOpenBisServerUrl(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getOperator() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Gets the operator for combining MatchClause objects.
getOrdinal() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
getParameters() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns the list of parameters to which values should be bound when executing the query.
getParent() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getParent() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
Deprecated. 
getParentCodes() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getParentCodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getParentCodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Return the parent codes.
getParentDataSetCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
The codes of the parent data sets for this new data set.
getParentDataSetCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
The codes of the parent data sets for this new data set.
getParentDataSetCodes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getParentRelativePath() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getParents() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Return the parents.
getParents() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getParentsJson() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getPath() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataSetFileDTO
The path within the data set of the file
getPathInDataSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
The path of this file in the data set (i.e., the root of the data set has a path of "").
getPathInListing() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
The path of this file relative to the path of the request that produced this FileInfoDss
getPathToDataSet(String, String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Get a path to the data set.
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
Returns the experiment permanent id.
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectPermIdId
 
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Returns the permanent id of the project.
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample permanent id.
getPermId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getPluginKey(String, String, Properties) - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
 
getPrefix() - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
 
getPreviousTermOrdinal() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Return the position of predecessor term in the vocabulary.
getPrimaryDataSetOrNull() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
Returns the primary data set.
getProducerCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getProductionDate() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getProjectRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getProjects() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
Returns all projects of this space.
getProjectUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getProperties() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
getProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
The properties for the new data set.
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getProperties() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getPropertiesJson() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
getPropertyCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.PropertyMatchClause
Return the code of the property to compare against.
getPropertyCodeOrNull() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
getPropertyTypeGroups() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
Return the grouped property types for this entity type.
getPropertyTypeGroups() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
getPropertyTypes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
 
getPropertyTypes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup.PropertyTypeGroupInitializer
 
getRegistrationDate() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getRegistrationDate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getRegistrationDate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getRegistrationDate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Return the registration details.
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
Return the data set registration details.
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Return the vocabulary term registration details.
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Return the sample registration details.
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getRegistrationDetails() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
Return the vocabulary term registration details.
getRegistrationId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getRelativePath() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
getRelativePath() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getRetrievedConnections() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getRetrievedConnections() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getRetrievedConnections() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getRetrievedFetchOptions() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns fetch options used to retrieved this sample object.
getRetrievedFetchOptions() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getRoles(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
Returns all access roles the specified user has on this space.
getRootExceptionClassName() - Method in exception ch.systemsx.cisd.common.exceptions.MasqueradingException
 
getRootNode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
getRows() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PngWritingHelper
 
getRows() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel
Gets all rows.
getSampleCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getSampleIdentifier() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Returns the sample identifier.
getSampleIdentifierOrNull() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getSampleIdentifierOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
getSampleIdentifierOrNull() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
getSampleProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Returns the sample properties.
getSampleRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getSamples(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getSamples(List<String>, EnumSet<SampleFetchOption>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getSamples(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return Sample objects for a set of given sample identifiers.
getSamples(List<String>, EnumSet<SampleFetchOption>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return Sample objects for a set of given sample identifiers.
getSamples() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
getSamples() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
getSampleTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample type code.
getSampleTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getSampleTypeId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the sample type id.
getSampleTypeId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getSampleUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getScriptString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
 
getService(RpcServiceInterfaceVersionDTO, Class<T>, String, boolean) - Method in interface ch.systemsx.cisd.common.api.IRpcServiceFactory
Get a proxy to the RPC service interface specified by ifaceVersion.
getService() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getService(RpcServiceInterfaceVersionDTO, Class<T>, String, boolean) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssServiceRpcFactory
 
getService(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.DssServiceRpcGenericFactory
 
getService(String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.content.IDssServiceRpcGenericFactory
Returns the service for the specified base URL.
getServiceKey() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
The key that identifies this particular service.
getServletClass() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig
 
getServletPath() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig
URL path at which the servlet will be deployed
getServletProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig
Any additional properties specified in the properties file
getSessionToken() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Returns the session token.
getSessionToken() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
getSessionToken() - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IWebInformationService
Returns the server side session token for the current HTTP session.
getSessionToken() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Return the session token for the logged-in user.
getSessionURLForFile(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getSessionURLForFile(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Get a URL that will return the contents of a file contained in this data set.
getSessionURLForFile(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getSessionWorkspace(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SessionWorkspaceUtil
 
getSettings() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings
 
getShare() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns the root directory of this share.
getShareId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
getShareId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getShareId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns the share Id of this share.
getShares(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Lists all folders in specified store root directory which match share pattern.
getSharesWithDataSets(File, String, boolean, Set<String>, IFreeSpaceProvider, IEncapsulatedOpenBISService, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Gets a list of all shares of specified store root directory.
getShufflePriority() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
getSimpleClassName() - Method in class ch.systemsx.cisd.common.exceptions.NotImplementedException.StackTraceExtractor
 
getSizeInBytes() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
getSpaceCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getSpaceCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Returns the space code.
getSpaceCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Returns the space code.
getSpaceCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
getSpaceRegistrations() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getSpacesWithProjects() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getSpacesWithProjects() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all spaces enriched with their projects and role assignments.
getSpeed() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns the speed of this share.
getSpeedHint() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getStatus() - Method in exception ch.systemsx.cisd.common.exceptions.ExceptionWithStatus
 
getStatus() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetCodesWithStatus
 
getStatus() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetAndPathInfoDBConsistencyChecker
 
getStoreRootDir(Properties) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
getSubCriterias() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Get a list of SearchSubCriteria objects for this SearchCriteria.
getSubFolderName() - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
 
getSupportedInterfaces(String, boolean) - Method in interface ch.systemsx.cisd.common.api.IRpcServiceFactory
Get the RPC service interfaces supported by the server.
getSupportedInterfaces() - Method in interface ch.systemsx.cisd.common.api.IRpcServiceNameServer
Return a collection of interfaces supported by this server
getSupportedInterfaces(String, boolean) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssServiceRpcFactory
 
getTarget() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
getTargetEntityKind() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
getTechId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectTechIdId
 
getTerms() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType
 
getTerms() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns the vocabulary terms.
getTimeZone() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.TimeAttributeMatchClause
Return the time zone to compare against.
getTitle() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getTitle() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the title given by the user when uploading this attachment.
getTitle() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn
Returns the title.
getTotalSizeOfDataSets() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns the total size (in bytes) of all data sets.
getType() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner
 
getType() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
The type of the service.
getType() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
getTypeCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialCodeAndTypeCodeId
 
getUnmodifiableProperties() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
The unmodifiable property types (as strings).
getUploadingUserIdOrNull() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
getURLForFileWithTimeout(String, long) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
getURLForFileWithTimeout(String, long) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Get a URL that will return the contents of a file contained in this data set.
getURLForFileWithTimeout(String, long) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
getUrlForRpcService(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataStoreApiUrlUtilities
 
getUrlSuffix() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
The suffix added to the server's URL to produce the URL for this interface.
getUrlTemplate() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns a URL template (e.g a search query) that can display additional information for concrete vocabulary terms.
getUserEmail() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getUserFirstName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getUserId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
getUserId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getUserLastName() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
getUsers() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
Returns the set of all users that have a role in this space.
getValidationPluginInfo() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
 
getValidationPluginInfo() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
getValidationScript(String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Get the validation script for the specified data set type.
getValue() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
getVersion() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
getVersion() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
Returns the version of this attachment.
getVersions() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
getVocabulary() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType
 
getVocabularyTermsMap() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getVocabularyTermsMap() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Deprecated. Please use the ISimpleOpenbisServiceFacade.listVocabularies() method instead.
getVocabularyTermsMap(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Deprecated. Please use IGeneralInformationService.listVocabularies(String) instead.
getVocabularyUpdates() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
getWaitingTimeBetweenRetries() - Method in interface ch.systemsx.cisd.common.api.retry.config.RetryConfiguration
 
getWaitingTimeBetweenRetries() - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
getWaitingTimeBetweenRetriesIncreasingFactor() - Method in interface ch.systemsx.cisd.common.api.retry.config.RetryConfiguration
 
getWaitingTimeBetweenRetriesIncreasingFactor() - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
getWebAppId() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings
 
getWebAppSettings(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
getWebAppSettings(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Returns the persistent settings for a given custom web app.
getWebAppSettings(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Returns the persistent settings for a given custom web app.
getWidth() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
GIF_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 

H

handle(File, DataSetInformation, Map<String, String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
 
hashCode() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
hashCode() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
 
hashCode() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
hashCode() - Method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
hashCode() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
hashCode() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityType
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectIdentifierId
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectPermIdId
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectTechIdId
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.TimeAttributeMatchClause
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
 
hashCode() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
hashCode() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns the ID.
HierarchicalFileInfoDssBuilder - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Helper Class for creating FileInfoDss objects based on file system abstraction.
HierarchicalFileInfoDssBuilder(IHierarchicalContentNode) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.HierarchicalFileInfoDssBuilder
Constructor for FileInfoDssFactory
HighLevelException - Exception in ch.systemsx.cisd.common.exceptions
An exception that is "high-level" in the sense that we have a pretty good understanding what the failure means in the context where the exception has been thrown.

I

IContentCache - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.content
Interface for cache for files remotely retrieved from Data Store Servers.
IDataSetDss - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
The representation of a Data Set managed by a DSS server.
IDataSetFilter - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.filter
Interface filters of DataSet instances.
IDataSetId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset
Holds information that uniquely identifies a data set in openBIS.
IDssComponent - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
A component that manages a connection to openBIS and 1 or more data store servers.
IDssServiceRpcGeneric - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Generic functionality for interacting with the DSS.
IDssServiceRpcGenericFactory - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.content
Factory for remote IDssServiceRpcGeneric based on an URL.
IExperimentId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment
Holds information that uniquely identifies an experiment in openBIS.
IGeneralInformationChangingService - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1
Service for changing general informations.
IGeneralInformationService - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1
Service for retrieving general informations.
IGNORED_FOR_SHUFFLING_PROP - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ShareFactory
 
imageToPng(BufferedImage) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image.
imageToPng(BufferedImage, PngFilterType, int) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image.
imageToPngFast(BufferedImage) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image.
ImageUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility function on images.
ImageUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 
IMaterialId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material
Holds information that uniquely identifies a material in openBIS.
IMetaprojectId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject
Holds information that uniquely identifies a metaproject in openBIS.
IncompatibleAPIVersionsException - Exception in ch.systemsx.cisd.common.api
Exception that is thrown if the client can not talk to the server because of API version incompatibility.
IncompatibleAPIVersionsException(int, int) - Constructor for exception ch.systemsx.cisd.common.api.IncompatibleAPIVersionsException
 
initializeFromTemplate(NewDataSetDTOBuilder) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
Take over any appropriate values from the template.
INSTANCE - Static variable in class ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory
 
INSTANCE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
InternalErr - Exception in ch.systemsx.cisd.common.exceptions
Exception representing internal error in the program caused by programmer error.
InvalidAuthenticationException - Exception in ch.systemsx.cisd.common.exceptions
Exception to be thrown when authentication of a service at another service fails.
InvalidAuthenticationException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException
 
InvalidAuthenticationException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException
 
InvalidExternalDataException - Exception in ch.systemsx.cisd.common.exceptions
Data provided to the system from another system is invalid.
InvalidExternalDataException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.InvalidExternalDataException
 
InvalidExternalDataException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.InvalidExternalDataException
 
InvalidSessionException - Exception in ch.systemsx.cisd.common.exceptions
This UserFailureException extension signals that a session has expired.
InvalidSessionException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.InvalidSessionException
 
invoke(MethodInvocation) - Method in class ch.systemsx.cisd.common.api.retry.RetryInterceptor
 
IObjectId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id
Holds information that uniquely identifies an object in openBIS.
IOpenbisServiceFacade - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
Provides a fully-blown API for openBIS integration.
IOpenbisServiceFacadeFactory - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
 
IPersistenceManager - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.content
Manages persistence of a statefull object.
IProjectId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project
Holds information that uniquely identifies a project in openBIS.
IQueryApiFacade - Interface in ch.systemsx.cisd.openbis.plugin.query.client.api.v1
Facade for openBIS query service.
IRpcService - Interface in ch.systemsx.cisd.common.api
The most generic interface for RPC invocations into openBIS.
IRpcServiceFactory - Interface in ch.systemsx.cisd.common.api
A factory for creating proxies to RPC services on a data store server.
IRpcServiceNameServer - Interface in ch.systemsx.cisd.common.api
An Interface for finding out about the IRpcService interfaces supported by a server.
ISampleId - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample
Holds information that uniquely identifies a sample in openBIS.
isAutomaticCodeGeneration() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if the sample code is created automatically.
isAutomaticCodeGeneration() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isChecksumCRC32Precalculated() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
isChosenFromList() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Return true if the vocabulary was chosen from a list.
isContainerDataSet() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
isContainerDataSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
isContainerDataSet() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
isContainerDataSet() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
isDataSourceDefined() - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvider
 
isDeletionDisallowed() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
isDeletionDisallowed() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
Returns true if deletion for data sets of this type are disallowed.
isDirectory() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
Return true if this FileInfo represents a folder.
isDirectory() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
isDirectory() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
isError() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
isExcelFile(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
Uses file extension to figure out if given file is supported Excel file.
isGif(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Returns true if the fileTypeOrNull is a gif file.
isIgnoreComments() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
isIgnoreComments() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration
 
isIgnoredForShuffling() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
Returns true if the share should not be used by shuffling maintenance or post-registration tasks.
isIgnoredForShuffling() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
isImageFile(File) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Returns true if the specified file is a supported image file.
ISimpleOpenbisServiceFacade - Interface in ch.systemsx.cisd.openbis.dss.client.api.v1
Provides a simplified view of an openBIS backend by allowing the following operations :
isIncoming() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
Returns true if the share is associated with one or more incoming directories.
isIncoming() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
Returns true if this is an incoming share.
isInternalNamespace() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns true if the vocabulary is in the internal openBIS namespace.
isJpeg(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Returns true if the fileTypeOrNull is a jpeg file.
isLinkDataSet() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
isLinkDataSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
isLinkDataSet() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
isLinkDataSet() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
isLinkSample() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
isListable() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if this is a sample type of listable samples.
isListable() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isManagedInternally() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Returns true if the vocabulary is managed internally.
isMandatory() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
 
isMandatory() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
isNoFileDataSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
isNonRetriableError() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
isOfficial() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
isOK() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
isPng(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Returns true if the fileTypeOrNull is a png file.
isPresentInArchive() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetCodesWithStatus
 
isRecursive() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataSetFileDTO
If true, this object includes sub folders
isRetriable() - Method in exception ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
Returns the assessment of the subsystem throwing the exception whether the failure could be temporarily and thus retrying the operation (on a higher level) could possibly help to cure the problem.
isRetriable() - Method in exception ch.systemsx.cisd.common.exceptions.HighLevelException
Returns the assessment of the subsystem throwing the exception whether the failure could be temporarily and thus retrying the operation (on a higher level) could possibly help to cure the problem.
isRetriable(Throwable) - Static method in exception ch.systemsx.cisd.common.exceptions.HighLevelException
Returns the assessment of the subsystem throwing the exception whether the failure could be temporarily and thus retrying the operation (on a higher level) could possibly help to cure the problem.
isRetriableError() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
isSessionActive(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns true if session with the specified token is still active, false otherwise.
isShowContainer() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if for samples of this type the container field is shown in edit/registration form.
isShowContainer() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isShowParentMetaData() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if meta data of parents of samples of this type should be shown.
isShowParentMetaData() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isShowParents() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if for sample of this type the parents field is shown in edit/registration form.
isShowParents() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isSkipEmptyRecords() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.DefaultCsvFileReaderConfiguration
 
isSkipEmptyRecords() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration
 
isSpaceLevel() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
Returns true if this role is for a particular space.
isStorageConfirmed() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
isStorageConfirmed() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
isStub() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
isStub() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
isStub() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
isTiff(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Returns true if the fileTypeOrNull is a tiff file.
isUniquePluginNameRequired() - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
 
isUniqueSubcodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Returns true if the sub code of samples of this type has to be unique.
isUniqueSubcodes() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
isUnmodifiableProperty(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
isWithdrawShare() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
Returns true if the share should be emptied by shuffling maintenance tasks.
isWithdrawShare() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
ITabularData - Interface in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
IWebInformationService - Interface in ch.systemsx.cisd.openbis.generic.shared.api.v1
Service for retrieving web information.

J

JPEG_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 
JSON_SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
URL where the service is exposed via JSON interface.
JSON_SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
 
JSON_SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IWebInformationService
Application part of the URL to access this service remotely.
JsonPropertyUtil - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.util
 
JsonPropertyUtil() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.util.JsonPropertyUtil
 

K

knowsContainer() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
Returns true, if result of DataSet.getContainerOrNull() can be trusted and false, if it cannot be trusted because the server is too old to deliver this information.

L

listAggregationServices(String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns metadata for all aggregation services.
listAggregationServices() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
List the available aggregation and ingestion services
listAllShares(String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Lists all shares.
listAttachmentsForExperiment(String, IExperimentId, boolean) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists attachments of specified experiment.
listAttachmentsForProject(String, IProjectId, boolean) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists attachments of specified project.
listAttachmentsForSample(String, ISampleId, boolean) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists attachments of specified sample.
listDataSets(List<Sample>, EnumSet<DataSet.Connections>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSets(List<Sample>, EnumSet<DataSet.Connections>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Return all data sets attached to the given samples with connections.
listDataSets(String, List<Sample>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets attached to the given samples.
listDataSets(String, List<Sample>, EnumSet<DataSet.Connections>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets attached to the given samples with connections.
listDataSetsForExperiment(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSetsForExperiment(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all data sets of specified experiment.
listDataSetsForExperiments(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSetsForExperiments(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all data sets for a given list of experiments identifiers.
listDataSetsForExperiments(String, List<Experiment>, EnumSet<DataSet.Connections>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets attached to the given experiments with connections.
listDataSetsForExperimentsOnBehalfOfUser(String, List<Experiment>, EnumSet<DataSet.Connections>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets attached to the given experiments with connections that the user userId is allowed to see.
listDataSetsForSample(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSetsForSample(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all data sets of specified sample.
listDataSetsForSample(String, Sample, boolean) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return the data sets attached to the specified sample, optionally including child samples.
listDataSetsForSamples(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSetsForSamples(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all data sets for a given list of sample identifiers.
listDataSetsOnBehalfOfUser(String, List<Sample>, EnumSet<DataSet.Connections>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets attached to the given samples with connections that the user userId is allowed to see.
listDataSetTypes() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listDataSetTypes() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all data set types available in openBIS.
listDataSetTypes(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all data set types.
listDataStores(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists all DSS server registered this openBIS server instance.
listExperiments(String, List<Project>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all experiments of the given type that belong to the supplied projects.
listExperiments(String, List<String>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all experiments matching a specified set of identifiers.
listExperimentsForProjects(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listExperimentsForProjects(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all experiments for a given list of project identifiers.
listExperimentsHavingDataSets(String, List<Project>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all experiments of the given type that belong to the supplied projects and have registered data sets.
listExperimentsHavingDataSetsForProjects(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listExperimentsHavingDataSetsForProjects(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all experiments having data sets for a given list of project identifiers.
listExperimentsHavingSamples(String, List<Project>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all experiments of the given type that belong to the supplied projects and have registered samles.
listExperimentsHavingSamplesForProjects(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listExperimentsHavingSamplesForProjects(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all experiments having samples for a given list of project identifiers.
listExperimentTypes() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listExperimentTypes() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all experiment types available in openBIS.
listExperimentTypes(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all experiment types.
listFiles(String, boolean) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
listFiles(String, boolean) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
List files contained in this data set.
listFiles(String, boolean) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
listFilesForDataSet(String, DataSetFileDTO) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Get an array of FileInfoDss objects that describe the file-system structure of the data set.
listFilesForDataSet(String, String, String, boolean) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Get an array of FileInfoDss objects that describe the file-system structure of the data set.
listMatchingNodes(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
listMatchingNodes(String, String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
listMetaprojects(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists all metaprojects belonging to current user.
listMetaprojectsOnBehalfOfUser(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Lists all metaprojects belonging to specified user.
listNamedRoleSets(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all named role sets.
listProjects() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listProjects() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all available projects.
listProjects(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all available projects.
listProjectsOnBehalfOfUser(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all available projects that a particular user is allowed to see.
listQueries() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Lists all queries the user has access rights.
listSamplesForExperiment(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all samples that belong to the supplied experiment.
listSamplesForExperimentAndSampleType(String, String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesForExperimentAndSampleType(String, String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all samples for specified experiment and of specified type.
listSamplesForExperimentOnBehalfOfUser(String, String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all samples that belong to the supplied experiment that are visible to user userId.
listSamplesForExperiments(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesForExperiments(List<String>, EnumSet<SampleFetchOption>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesForExperiments(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all samples for a given list of experiments identifiers.
listSamplesForExperiments(List<String>, EnumSet<SampleFetchOption>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all samples for a given list of experiments identifiers.
listSamplesForProjects(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesForProjects(List<String>, EnumSet<SampleFetchOption>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesForProjects(List<String>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all samples for a given list of project identifiers.
listSamplesForProjects(List<String>, EnumSet<SampleFetchOption>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all samples for a given list of project identifiers.
listSamplesOfSample(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSamplesOfSample(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all samples which are components or children of the specified sample.
listSampleTypes() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listSampleTypes() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Returns all sample types available in openBIS.
listSampleTypes(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all sample types.
listSpacesWithProjectsAndRoleAssignments(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all spaces of specified database instance enriched with their projects and role assignments.
listTableReportDescriptions(String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Returns meta data for all reporting plugins which deliver a table.
listTableReportDescriptions() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Returns meta data for all reporting plugins which deliver a table.
listVocabularies() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
listVocabularies() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Return all vocabularies available in openBIS together with the contained vocabulary terms.
listVocabularies(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all available vocabularies together with the contained terms.
load(Serializable) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.DelayedPersistenceManager
 
load(Serializable) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.content.IPersistenceManager
Loads and returns the persistent object.
load(Serializable) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.SimpleFileBasePersistenceManager
 
loadColorDepthJavaAdvancedImagingTiff(IRandomAccessFile, ImageID) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
For experts only! Loads some kinds of TIFF images handled by JAI library.
loadDimensionJavaAdvancedImagingTiff(IRandomAccessFile, ImageID) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
For experts only! Loads some kinds of TIFF images handled by JAI library.
loadImageForDisplay(IHierarchicalContentNode) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Loads an image from specified file node.
loadJavaAdvancedImagingTiff(IRandomAccessFile, ImageID) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
For experts only! Loads some kinds of TIFF images handled by JAI library.
loadProperties(String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
loadServiceProperties() - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
loads server configuration
loadUnchangedImage(IHierarchicalContentNode, String, String, String, IReadParams) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Loads the image specified by imageIdOrNull from the given inputStream.
loadUnchangedImageColorDepth(IHierarchicalContentNode, String, String, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Loads the color depth of image specified by imageIdOrNull from the given inputStream.
loadUnchangedImageDimension(IHierarchicalContentNode, String, String, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Loads the size of image specified by imageIdOrNull from the given inputStream.
logout() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Logs the current user out.
logout() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
logout() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
logout() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Logs out from openBIS and frees all associated resources on the server.
logout(String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Logout the session with the specified session token.
logout() - Method in interface ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade
Logs current user out.

M

main(String[]) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AutoSymlink
 
main(String[]) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
main(String[]) - Static method in class ch.systemsx.cisd.openbis.plugin.query.client.api.v1.QueryApiTest
 
MasqueradingException - Exception in ch.systemsx.cisd.common.exceptions
A RuntimeException extension which almost clones given rootException without saving it as cause.
MasqueradingException(Exception, String) - Constructor for exception ch.systemsx.cisd.common.exceptions.MasqueradingException
 
MasqueradingException(Exception) - Constructor for exception ch.systemsx.cisd.common.exceptions.MasqueradingException
 
Material - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
Material(Material.MaterialInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material
 
Material.MaterialInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
Material.MaterialInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
MaterialCodeAndTypeCodeId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material
Identifies a material by code and material type code.
MaterialCodeAndTypeCodeId(String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialCodeAndTypeCodeId
 
MaterialIdentifier - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
MaterialIdentifier(MaterialTypeIdentifier, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
MaterialTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material
Identifies a material by tech id.
MaterialTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialTechIdId
 
MaterialTypeIdentifier - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
duplicated from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier
MaterialTypeIdentifier(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
 
MAXIMUM_TIME_TO_KEEP_STREAMS_DEFAULT - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
MetaprojectAssignments - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
MetaprojectAssignments() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
MetaprojectAssignmentsIds - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
MetaprojectAssignmentsIds() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds
 
MetaprojectIdentifierId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject
Identifies a metaproject by identifier.
MetaprojectIdentifierId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.MetaprojectIdentifierId
 
MetaprojectIdentifierId(MetaprojectIdentifier) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.MetaprojectIdentifierId
 
MetaprojectIdentifierId(String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.MetaprojectIdentifierId
 
MetaprojectTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject
Identifies a metaproject by tech id.
MetaprojectTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.MetaprojectTechIdId
 
MetaprojectTechIdId(TechId) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.MetaprojectTechIdId
 
MinimalMinorVersion - Annotation Type in ch.systemsx.cisd.common.api
The minimal minor version that a service needs to have in order to possess this method.
MINIMUM_TIME_TO_KEEP_STREAMS_DEFAULT - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
moveDataSetToAnotherShare(File, File, IEncapsulatedOpenBISService, IShareIdManager, IChecksumProvider, ISimpleLogger) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
Moves the specified data set to the specified share.

N

NewDataSetDTO - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Represents a new data set that the DSS should register.
NewDataSetDTO(NewDataSetDTO.DataSetOwner, File) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
Constructor
NewDataSetDTO(NewDataSetDTO.DataSetOwner, String, List<FileInfoDssDTO>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
Constructor
NewDataSetDTO(String, NewDataSetDTO.DataSetOwner, String, List<FileInfoDssDTO>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
Constructor
NewDataSetDTO(NewDataSetMetadataDTO, NewDataSetDTO.DataSetOwner, String, List<FileInfoDssDTO>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
Constructor
NewDataSetDTO.DataSetOwner - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
The identifier of the owner of the new data set.
NewDataSetDTO.DataSetOwner(NewDataSetDTO.DataSetOwnerType, String) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner
 
NewDataSetDTO.DataSetOwnerType - Enum in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
The different types of owners of data sets; there are two: experiment and sample.
NewDataSetDTOBuilder - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
A mutable object for building NewDataSetDTO objects.
NewDataSetDTOBuilder() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
 
NewDataSetMetadataDTO - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Represents optional metadata (data set type and properties) of a new data set that the DSS should register.
NewDataSetMetadataDTO(String, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
NewDataSetMetadataDTO(String, Map<String, String>, List<String>) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
NewDataSetMetadataDTO() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
NewVocabularyTerm - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A value object representing a new vocabulary term to be created by the openBIS backend.
NewVocabularyTerm() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
 
noErrorAndInconsitencyFound() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DataSetAndPathInfoDBConsistencyChecker
 
NotImplementedException - Exception in ch.systemsx.cisd.common.exceptions
This is an extension to the RuntimeException for unimplemented methods.
NotImplementedException() - Constructor for exception ch.systemsx.cisd.common.exceptions.NotImplementedException
 
NotImplementedException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.NotImplementedException
 
NotImplementedException(Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.NotImplementedException
 
NotImplementedException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.NotImplementedException
 
NotImplementedException.StackTraceExtractor - Class in ch.systemsx.cisd.common.exceptions
An automatic stack trace extractor.
NotImplementedException.StackTraceExtractor(Throwable) - Constructor for class ch.systemsx.cisd.common.exceptions.NotImplementedException.StackTraceExtractor
 
NotImplementedException.StackTraceExtractor(Throwable, int) - Constructor for class ch.systemsx.cisd.common.exceptions.NotImplementedException.StackTraceExtractor
 
NULL_SIZE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
NULL_SIZE can be encode special conditions e.g.

O

ObjectIdentifierId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id
Base class for ids that identify objects by identifier.
ObjectIdentifierId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectIdentifierId
 
ObjectPermIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id
Base class for ids that identify objects by perm id.
ObjectPermIdId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectPermIdId
 
ObjectTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id
Base class for ids that identify objects by tech id.
ObjectTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectTechIdId
 
OK - Static variable in class ch.systemsx.cisd.common.exceptions.Status
The status indicating that the operation went fine.
OLIGO - Static variable in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
Material identifier for an siRNA-nucleotide
OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
Prefix of system properties which may override service.properties.
OpenbisServiceFacade - Class in ch.systemsx.cisd.openbis.dss.client.api.v1.impl
Default implementation for IOpenbisServiceFacade.
OpenbisServiceFacade(String, IGeneralInformationService, IGeneralInformationChangingService, IDssComponent) - Constructor for class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
OpenbisServiceFacadeFactory - Class in ch.systemsx.cisd.openbis.dss.client.api.v1
A factory creating IOpenbisServiceFacade instances.

P

parseImageID(String, IHierarchicalContentNode) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Parses specified string representation of an ImageID.
pass(DataSet) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.AndDataSetFilter
 
pass(DataSet) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter
Returns true if the specified data set passes the filter.
pass(DataSet) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.PropertiesBasedDataSetFilter
 
pass(DataSet) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter
Return true if the data set type code of the specified data set matches the regular expression provided as constructor argument.
PathInfoDataSourceProvider - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Helper method for providing data source to pathinfo database.
PathInfoDataSourceProvider() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvider
 
PathInfoDBAwareHierarchicalContentFactory - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
The implementation of IHierarchicalContentFactory that aware of Path Info DB.
PathInfoDBOnlyHierarchicalContentFactory - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
 
PluginServletConfig - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
Configuration parameters for Servlets.
PluginServletConfig(String, String, Properties) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig
 
PNG_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 
PngWritingHelper - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
An object that encapsulates some knowledge about how PNG files should be created.
PostgresPlusFileSystemFreeSpaceProvider - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
PostgreSQL database files are designed to grow until they take up the entire available disk space.
PostgresPlusFileSystemFreeSpaceProvider(Properties) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.PostgresPlusFileSystemFreeSpaceProvider
 
PREFFERED_BEAN_NAME - Static variable in interface ch.systemsx.cisd.common.api.IRpcServiceNameServer
The preferred name of the bean in Spring
PREFFERED_SERVICE_NAME - Static variable in interface ch.systemsx.cisd.common.api.IRpcServiceNameServer
The preferred name of the bean in Spring
PREFFERED_URL_SUFFIX - Static variable in interface ch.systemsx.cisd.common.api.IRpcServiceNameServer
The preferred suffix of the url of the name server service
Project - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a project.
Project(Long, String, String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Creates a new instance for the specified tech id, perm id, space code and project code.
Project(String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Creates a new instance for the specified space code and project code.
Project(String, String, EntityRegistrationDetails) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Creates a new instance for the specified tech id, perm id, space code and project code.
Project(Long, String, String, String, EntityRegistrationDetails) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
Creates a new instance for the specified space code and project code.
ProjectIdentifierId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project
Identifies a project by identifier.
ProjectIdentifierId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project.ProjectIdentifierId
 
ProjectPermIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project
Identifies a project by perm id.
ProjectPermIdId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project.ProjectPermIdId
 
ProjectTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project
Identifies a project by tech id.
ProjectTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.project.ProjectTechIdId
 
PropertiesBasedDataSetFilter - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.filter
Filter based on data set properties.
PropertiesBasedDataSetFilter(Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.PropertiesBasedDataSetFilter
 
PropertyType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a property type.
PropertyType(PropertyType.PropertyTypeInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
Creates a new instance with the provided initializer
PropertyType.PropertyTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new data set instance.
PropertyType.PropertyTypeInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
PropertyTypeGroup - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a data set type.
PropertyTypeGroup(PropertyTypeGroup.PropertyTypeGroupInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
Creates a new instance with the provided initializer
PropertyTypeGroup.PropertyTypeGroupInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new data set instance.
PropertyTypeGroup.PropertyTypeGroupInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup.PropertyTypeGroupInitializer
 
putDataSet(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Upload a new data set to the DSS.
putDataSet(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
putDataSet(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
putDataSet(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Upload a new data set to the DSS.
putDataSet(String, NewDataSetDTO, InputStream) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Upload a new data set to the DSS.
putFileSliceToSessionWorkspace(String, String, long, InputStream) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Upload a file slice to the user's session workspace.
putFileToSessionWorkspace(String, InputStream) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Uploads a file to the session workspace.
putFileToSessionWorkspace(String, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Uploads a file to the session workspace.
putFileToSessionWorkspace(String, InputStream) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
putFileToSessionWorkspace(String, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
putFileToSessionWorkspace(String, String, InputStream) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Upload a new file to the user's session workspace.
putProperty(String, String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
putProperty(String, String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
putProperty(String, String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 

Q

QueryApiTest - Class in ch.systemsx.cisd.openbis.plugin.query.client.api.v1
Example of usage of Query API.
QueryApiTest() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.client.api.v1.QueryApiTest
 
QueryDescription - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Description of a query.
QueryDescription() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
 
QueryTableColumn - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Column of query data.
QueryTableColumn(String, QueryTableColumnDataType) - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn
Creates an instance for specified title and data type.
QueryTableColumnDataType - Enum in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Data types of QueryTableModel.
QueryTableModel - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Model of query data.
QueryTableModel(List<QueryTableColumn>) - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel
Creates an instance for the specified columns.

R

readLines() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
readLines(int) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
readLines(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ExcelFileReader
 
RemoteHierarchicalContent - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
Implementation of HierchicalContent that is stored on remote datastore server.
RemoteHierarchicalContent(IDatasetLocationNode, ISingleDataSetPathInfoProvider, IDssServiceRpcGenericFactory, ISessionTokenProvider, IContentCache) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
RemoteHierarchicalContentNode - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
A node of hierarchical content that stored on a remote datastore server.
RemoteHierarchicalContentNode(IDatasetLocation, DataSetPathInfo, ISingleDataSetPathInfoProvider, IDssServiceRpcGenericFactory, ISessionTokenProvider, IContentCache) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
removeFromMetaproject(String, IMetaprojectId, MetaprojectAssignmentsIds) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Removes given entities from an existing metaproject.
ReportDescription - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
Bean with basic meta data of a service offered by a Data Store Server.
ReportDescription() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
requestPersistence() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.DelayedPersistenceManager
 
requestPersistence() - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.content.IPersistenceManager
Requests for persisting the object.
requestPersistence() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.SimpleFileBasePersistenceManager
 
rescale(BufferedImage, int, int, boolean, boolean) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Re-scales the image to be the biggest one which fits into a (0,0,maxWidth, maxHeight) rectangle.
reset() - Method in class ch.systemsx.cisd.common.api.retry.config.DefaultRetryConfiguration
 
Retry - Annotation Type in ch.systemsx.cisd.common.api.retry
 
RetryCaller<T,E extends java.lang.Throwable> - Class in ch.systemsx.cisd.common.api.retry
 
RetryCaller() - Constructor for class ch.systemsx.cisd.common.api.retry.RetryCaller
 
RetryCaller(RetryConfiguration) - Constructor for class ch.systemsx.cisd.common.api.retry.RetryCaller
 
RetryCaller(RetryConfiguration, ISimpleLogger) - Constructor for class ch.systemsx.cisd.common.api.retry.RetryCaller
 
RetryConfiguration - Interface in ch.systemsx.cisd.common.api.retry.config
 
RetryInterceptor - Class in ch.systemsx.cisd.common.api.retry
 
RetryInterceptor() - Constructor for class ch.systemsx.cisd.common.api.retry.RetryInterceptor
 
RetryProxy - Interface in ch.systemsx.cisd.common.api.retry
 
RetryProxyFactory - Class in ch.systemsx.cisd.common.api.retry
 
RetryProxyFactory() - Constructor for class ch.systemsx.cisd.common.api.retry.RetryProxyFactory
 
Role - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing an authorization role.
Role(String, boolean) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
Creates a new instance from specified code and space level flag.
RpcServiceInterfaceDTO - Class in ch.systemsx.cisd.common.api
Describes an RPC interface supported by the server.
RpcServiceInterfaceDTO(String) - Constructor for class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
RpcServiceInterfaceVersionDTO - Class in ch.systemsx.cisd.common.api
Describes an RPC interface supported by the server.
RpcServiceInterfaceVersionDTO(String, String, int, int) - Constructor for class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
 

S

Sample - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a sample.
Sample(Sample.SampleInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
Creates a new instance with the provided initializer
Sample.SampleInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new sample instance.
Sample.SampleInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
SampleFetchOption - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Fetch options for IGeneralInformationService.searchForSamples(String, SearchCriteria, java.util.EnumSet).
SampleIdentifierId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample
Identifies a sample by identifier.
SampleIdentifierId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.SampleIdentifierId
 
SamplePermIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample
Identifies a sample by perm id.
SamplePermIdId(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.SamplePermIdId
 
SampleTechIdId - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample
Identifies a sample by tech id.
SampleTechIdId(Long) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.SampleTechIdId
 
SampleType - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing a sample type.
SampleType(SampleType.SampleTypeInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
Creates a new instance with the provided initializer
SampleType.SampleTypeInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Class used to initialize a new SampleType instance.
SampleType.SampleTypeInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
SearchableEntityKind - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
An enum listing the different kinds of entities that are searchable.
SearchCriteria - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A (mutable) object representing the specification of a search.
SearchCriteria() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
 
SearchCriteria.AnyFieldMatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A MatchClause for checking that any of the properties or attributes equals a desired value.
SearchCriteria.AnyPropertyMatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A MatchClause for checking that any of the properties equals a desired value.
SearchCriteria.AttributeMatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A MatchClause for checking that an attribute equals a desired value.
SearchCriteria.CompareMode - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
SearchCriteria.MatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A specification of one field (either property or attribute) and desired value for that field.
SearchCriteria.MatchClauseAttribute - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
An enum listing the different attributes that can be compared against.
SearchCriteria.MatchClauseFieldType - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
An enum listing the different field types that can be compared against.
SearchCriteria.MatchClauseTimeAttribute - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
An enum listing the different attributes containing time values that can be compared against.
SearchCriteria.PropertyMatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A MatchClause for checking that a property equals a desired value.
SearchCriteria.SearchOperator - Enum in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Operators for combining MatchClause objects.
SearchCriteria.TimeAttributeMatchClause - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A MatchClause for comparing a time attribute to a specified value.
searchForDataSets(SearchCriteria) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
searchForDataSets(SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Return all data sets matching a specified search criteria.
searchForDataSets(String, SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets matching specified search criteria.
searchForDataSetsOnBehalfOfUser(String, SearchCriteria, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all data sets matching specified search criteria and visible to user userId.
searchForExperiments(SearchCriteria) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
searchForExperiments(SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Returns all experiments matching specified search criteria.
searchForExperiments(String, SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all experiments matching specified search criteria.
searchForMaterials(String, SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns all material fulfilling specified search criteria.
searchForSamples(SearchCriteria) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
searchForSamples(SearchCriteria, EnumSet<SampleFetchOption>) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
searchForSamples(SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Return all samples that match the search criteria.
searchForSamples(SearchCriteria, EnumSet<SampleFetchOption>) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Return all samples that match the search criteria.
searchForSamples(String, SearchCriteria) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all samples that match the search criteria.
searchForSamples(String, SearchCriteria, EnumSet<SampleFetchOption>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all samples that match the search criteria.
searchForSamplesOnBehalfOfUser(String, SearchCriteria, EnumSet<SampleFetchOption>, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Return all samples that match the search criteria and that a particular user is allowed to see.
SearchSubCriteria - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A specification of criteria for a subquery about a connected entity.
SegmentedStoreUtils - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility methods for segmented stores.
SegmentedStoreUtils() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils
 
SERVER_URL_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
SERVICE_NAME - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Name of this service for which it is registered at the RPC name server.
SERVICE_NAME - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Name of this service for which it is registered at the RPC name server.
SERVICE_NAME - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IWebInformationService
Name of this service for which it is registered at the RPC name server.
SERVICE_PROPERTIES_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
Location of service properties file.
SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Application part of the URL to access this service remotely.
SERVICE_URL - Static variable in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Application part of the URL to access this service remotely.
SESSION_WORKSPACE_ROOT_DIR_DEFAULT - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SessionWorkspaceUtil
 
SESSION_WORKSPACE_ROOT_DIR_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SessionWorkspaceUtil
 
SessionWorkspaceUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility functions for session workspace.
SessionWorkspaceUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SessionWorkspaceUtil
 
setAttachmentHolderId(IObjectId) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setAutomaticCodeGeneration(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setChecksumCRC32(Integer) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setChildReferences(List<Long>, Map<Long, Sample>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setChildren(List<Sample>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setChildrenCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setChosenFromList(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Set the term's code.
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setCodePrefix(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setComplete(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setContainedDataSetCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setContainedDataSets(List<DataSet>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setContainerDataSet(AbstractExternalData) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setContainerDataSet(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setContainerDatasetPermId(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setContainerOrNull(DataSet) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setDataSetCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setDataSetKind(DataSetKind) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
setDataSetOwnerIdentifier(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
 
setDataSetOwnerType(NewDataSetDTO.DataSetOwnerType) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
 
setDataSetProperties(List<NewProperty>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setDataSets(List<DataSet>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
setDataSetType(DataSetType) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setDataSetTypeCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setDataSetTypeOrNull(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
setDataSetTypeOrNull(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
setDataSetTypes(List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
setDataStoreBaseUrl(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
setDataStoreCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
setDataStoreCode(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
setDataType(DataTypeCode) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
setDeletionDisallowed(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
setDescription(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setDescription(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
setDescription(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Set the term's description.
setDescription(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
setDescription(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setDescription(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
 
setDirectory(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setDownloadLink(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setEmail(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setExperiment(Experiment) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setExperimentIdentifier(ExperimentIdentifier) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Sets experimentIdentifier.
setExperimentIdentifier(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setExperimentIdentifierOrNull(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setExperimentIdentifiers(Set<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
setExperiments(List<Experiment>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
setExperimentTypeCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setExternalCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setExternalDataManagementSystem(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setExternalDataManagementSystem(ExternalDataManagementSystem) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setExternalDataSetCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setExternalDataSetLink(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setExtractableData(ExtractableData) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setFetchOptions(DataSetFetchOptions) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
setFile(File) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder
Set the file that contains the data set.
setFileName(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setFileName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setFirstName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setId(long) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setId(long) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
 
setIdentifier(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setIdentifier(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setIgnoredForShuffling(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
setIgnoredForShuffling(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
setIncoming(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
setIncoming(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
setInstanceCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setInstanceUUID(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setInternalNamespace(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setIsStub(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setKey(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
setLabel(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Set the term's label.
setLabel(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
setLabel(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
setLabel(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
 
setLastModified(Date) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setLastName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setLinkDataSet(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setLinkSample(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setListable(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setMainDataSetPath(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
setMainDataSetPattern(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer
 
setManagedInternally(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setMandatory(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer
 
setMaterialCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setMaterialProperties(Map<String, Material>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setMaterials(List<Material>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
setMaterialTypeIdentifier(MaterialTypeIdentifier) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setMaximumNumberOfRetries(int) - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
setMetaproject(Metaproject) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
setModificationDate(Date) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setModifierEmail(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setModifierFirstName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setModifierLastName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setModifierUserId(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setName(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup.PropertyTypeGroupInitializer
 
setName(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
 
setOperator(SearchCriteria.SearchOperator) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
Set the operator for combining MatchClause objects.
setParameters(List<String>) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
 
setParent(DataSetPathInfo) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setParentCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setParentDataSetCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
Sets the parent data sets of this data set.
setParentDataSetCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
Sets the parent data sets of this data set.
setParentDataSetCodes(List<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setParentReferences(List<Long>, Map<Long, Sample>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setParents(List<Sample>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setPermId(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setPermId(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setPreviousTermOrdinal(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
Set the position of predecessor term in the vocabulary.
setProducerCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setProductionDate(Date) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setProperties(Map<String, String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
setProperties(Map<String, String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
setProperties(Map<String, String>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setRegistrationDate(Date) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setRegistrationDetails(EntityRegistrationDetails) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setRegistrationDetails(EntityRegistrationDetails) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setRegistrationDetails(EntityRegistrationDetails) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer
 
setRegistrationDetails(EntityRegistrationDetails) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer
 
setRegistrationDetails(EntityRegistrationDetails) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setRelativePath(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setRetrievedConnections(EnumSet<DataSet.Connections>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setRetrievedFetchOptions(EnumSet<SampleFetchOption>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setSample(Sample) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setSampleCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setSampleIdentifier(SampleIdentifier) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Sets the sample identifier.
setSampleIdentifier(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setSampleIdentifierOrNull(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setSampleProperties(IEntityProperty[]) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setSamples(List<Sample>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments
 
setSampleTypeCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setSampleTypeId(Long) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setServiceKey(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
setShareId(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setShowContainer(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setShowParentMetaData(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setShowParents(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setShufflePriority(Share.ShufflePriority) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
setSizeInBytes(long) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetPathInfo
 
setSpaceCode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setSpaceCode(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setSpeedHint(int) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setStorageConfirmed(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setStorageConfirmed(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
setStub(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer
 
setStub(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer
 
setTerms(List<ControlledVocabularyPropertyType.VocabularyTerm>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer
 
setTerms(List<VocabularyTerm>) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setTitle(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setType(AggregationServiceType) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
setType(QueryTableColumnDataType) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
setUniqueSubcodes(boolean) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType.SampleTypeInitializer
 
setUnmodifiableProperties(Set<String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
setUnmodifiableProperties(Map<String, String>) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
setUploadingUserEmail(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setUploadingUserId(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
setUrlTemplate(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
setUserId(String) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer
 
setValidationPluginInfo(ValidationPluginInfo) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer
 
setValue(String) - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
setVersion(int) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment.AttachmentInitializer
 
setVocabulary(Vocabulary) - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer
 
setWaitingTimeBetweenRetries(int) - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
setWaitingTimeBetweenRetriesIncreasingFactor(float) - Method in class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
setWebAppSettings(WebAppSettings) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
setWebAppSettings(WebAppSettings) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade
Sets the persistent settings for a given custom web app.
setWebAppSettings(String, WebAppSettings) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Sets the persistent settings for a given custom web app.
setWithdrawShare(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
setWithdrawShare(boolean) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
Share - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Represents a share of a segmented store.
Share(File, int, IFreeSpaceProvider) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
Share(SharesHolder, File, int, IFreeSpaceProvider) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share
 
Share.ShufflePriority - Enum in ch.systemsx.cisd.openbis.dss.generic.shared.utils
different factors that have priority when moving a data set to the share.
SHARE_PROPS_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ShareFactory
 
ShareFactory - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
A factory that constructs Share objects.
ShareFactory() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ShareFactory
 
ShareInfo - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1
Information about a share.
ShareInfo(String, long) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.ShareInfo
 
shuffleDataSet(String, String, String) - Method in interface ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric
Moves specified data set to specified share.
SimpleFileBasePersistenceManager - Class in ch.systemsx.cisd.openbis.dss.generic.shared.content
Simple implementation of IPersistenceManager using a file.
SimpleFileBasePersistenceManager(File, String) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.content.SimpleFileBasePersistenceManager
Creates an instance for the specified file storing the object.
Size - Class in ch.systemsx.cisd.openbis.dss.generic.shared.dto
 
Size(int, int) - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
SpaceWithProjectsAndRoleAssignments - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Bean which represents a space, all its projects, and all its relevant role assignments
SpaceWithProjectsAndRoleAssignments(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments
Creates a new instance for the specified code.
SpeedUtils - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
Utility method for speed.
SpeedUtils() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SpeedUtils
 
StaticRetryConfiguration - Class in ch.systemsx.cisd.common.api.retry.config
 
StaticRetryConfiguration() - Constructor for class ch.systemsx.cisd.common.api.retry.config.StaticRetryConfiguration
 
Status - Class in ch.systemsx.cisd.common.exceptions
A class that holds the information about the status of an operation.
StatusFlag - Enum in ch.systemsx.cisd.common.exceptions
The status of an operation.
StatusWithResult<T> - Class in ch.systemsx.cisd.common.exceptions
A Status that can also hold a result.
STOREROOT_DIR_KEY - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil
 
SystemExitException - Exception in ch.systemsx.cisd.common.exceptions
Thrown by SystemExit instead of plain RuntimeException
SystemExitException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.SystemExitException
 

T

TIFF_FILE - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 
toLongOrNull(String) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.util.JsonPropertyUtil
 
toSerializable() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
toString() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceDTO
 
toString() - Method in class ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO
 
toString() - Method in exception ch.systemsx.cisd.common.exceptions.MasqueradingException
 
toString() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
toString() - Method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.DataSetFileDTO
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner
 
toString() - Method in enum ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetCodesWithStatus
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.PluginServletConfig
 
toString() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Attachment
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ExperimentType
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialCodeAndTypeCodeId
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectIdentifierId
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectPermIdId
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.ObjectTechIdId
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.AndDataSetFilter
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.PropertiesBasedDataSetFilter
 
toString() - Method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter
 
toString() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription
 
toString() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription
Returns the name.
toString() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription
Returns the label.
toString() - Method in class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
toStringOrNull(Long) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.util.JsonPropertyUtil
 
ToStringUtil - Class in ch.systemsx.cisd.openbis.dss.generic.shared.utils
 
ToStringUtil() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil
 
translate(RoleWithHierarchy) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(RoleWithHierarchy.RoleCode, boolean) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(DataStore) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Project) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Sample) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Experiment) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(DataSetType, HashMap<Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(SampleType, HashMap<Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(ExperimentType, HashMap<Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Collection<VocabularyTerm>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Iterable<AbstractExternalData>, EnumSet<DataSet.Connections>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
Translates specified iterable collection of AbstractExternalData into a list of DataSet instance.
translate(AbstractExternalData, EnumSet<DataSet.Connections>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
Translates the specified AbstractExternalData instance into a DataSet instance.
translate(Vocabulary) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translate(Material, Map<Long, Material>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateAttachments(String, IObjectId, AttachmentHolderPE, List<AttachmentPE>, boolean) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateDataStores(List<DataStore>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateExperiments(Collection<Experiment>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateMaterials(Collection<Material>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateProjects(List<Project>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translatePropertyTypeTerms(Collection<VocabularyTerm>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
translateSamples(Collection<Sample>) - Static method in class ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator
 
Translator - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1
 
trim(int) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SpeedUtils
Returns trimmed speed.
trimSpeedHint(int) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.SpeedUtils
Returns trimmed speed hint.
tryCreate(String, String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory
Public factory method for creating an IDssComponent with a username and password.
tryCreate(String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory
Public factory method for creating an IDssComponent for a user that has already been authenticated.
tryCreate(String, String, String) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory
See DssComponentFactory.tryCreate(String, String, String, long).
tryCreate(String, String) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory
See DssComponentFactory.tryCreate(String, String, long).
tryCreate(String, String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
Public factory method for creating a DssComponent with a username and password.
tryCreate(String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
Public factory method for creating a DssComponent for a user that has already been authenticated.
tryCreate(String, String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
tryCreate(String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
tryCreate(String, String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory
Creates an OpenbisServiceFacade instance that can be used to interact with an openBIS backend.
tryCreate(String, String, long) - Static method in class ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory
Creates an OpenbisServiceFacade instance that can be used to interact with an openBIS backend.
tryDataSetType() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO
 
tryDataSetType() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO
The code for the type of the new data set.
tryGetContainerDataSet() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
tryGetContainerDatasetPermId() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
tryGetCrc32Checksum() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO
Return the CRC32 checksum, if it is available and null otherwise.
tryGetDataStoreBaseURL(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Returns the download URL for the data store of specified data set or null if such data set does not exist.
tryGetErrorMessage() - Method in class ch.systemsx.cisd.common.exceptions.Status
 
tryGetFile() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContentNode
 
tryGetInternalPathInDataStore() - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Returns the internal storage path of this data set in the datastore.
tryGetInternalPathInDataStore() - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
tryGetNode(String) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.content.RemoteHierarchicalContent
 
tryGetResult() - Method in class ch.systemsx.cisd.common.exceptions.StatusWithResult
Returns the result of the operation (may be null).
tryGetThrowableOfClass(Throwable, Class<T>) - Static method in class ch.systemsx.cisd.common.exceptions.ExceptionUtils
Returns the first found Throwable of given clazz from the exception chain of given throwable.
tryGetUploadingUserEmail() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
tryLinkToContents(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet
 
tryLinkToContents(String) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss
Returns a File, if possible, that directly references the contents of a data set in the data store server.
tryLinkToContents(String) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DataSetDss
 
tryReadValidationScript(String[]) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptReader
Reads and appends a collection of Jython validation files into a single interpretable script.
tryToAuthenticateForAllServices(String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService
Tries to authenticate specified user with specified password.
tryToCreate(String, String, String, long) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacadeFactory
Creates an OpenbisServiceFacade instance that can be used to interact with an openBIS backend.
tryToCreate(String, String, long) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacadeFactory
Creates an OpenbisServiceFacade instance that can be used to interact with an openBIS backend.
tryToCreate(String, String, long) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory
 
tryToCreate(String, String, String, long) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory
 
tryToFigureOutFileTypeOf(IRandomAccessFile) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Tries to figure out the file type of the specified binary content.
tryToGetExperiment() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
Returns the basic information about the experiment.
tryToGetSample() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation
 
tryUserIdOrNull() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails
 
TypeBasedDataSetFilter - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.filter
Filter which will be passed only by data sets with a data set type code matching a certain regular expression.
TypeBasedDataSetFilter(String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter
Creates an instance for the specified regular expression.
TypedStringValue - Class in ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto
A bean that stores a primitive value as a string with a type.
TypedStringValue() - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 
TypedStringValue(QueryTableColumnDataType, String) - Constructor for class ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.TypedStringValue
 

U

undoLastOperation() - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler
 
UnknownLastChangedException - Exception in ch.systemsx.cisd.common.exceptions
Used to signal the error of getting last modification time of a store item
UnknownLastChangedException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.UnknownLastChangedException
 
updateMetaproject(String, IMetaprojectId, String, String) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
Updates an existing metaproject.
updateSampleProperties(String, long, Map<String, String>) - Method in interface ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService
 
UserFailureException - Exception in ch.systemsx.cisd.common.exceptions
The UserFailureException is the super class of all exceptions that have their cause in an inappropriate usage of the system.
UserFailureException(String) - Constructor for exception ch.systemsx.cisd.common.exceptions.UserFailureException
 
UserFailureException(String, Throwable) - Constructor for exception ch.systemsx.cisd.common.exceptions.UserFailureException
 

V

validate(File) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner.NullValidationScriptRunner
 
validate(File) - Method in class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner
 
validateDataSet(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent
Validate a data set.
validateDataSet(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent
 
validateDataSet(NewDataSetDTO, File) - Method in class ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade
 
validateDataSet(NewDataSetDTO, File) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.ISimpleOpenbisServiceFacade
Validates a data set.
ValidationError - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
 
ValidationError.ValidationErrorTarget - Enum in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
 
ValidationPluginInfo - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Value object with name and optional description of a validation plugin.
ValidationPluginInfo(String, String) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ValidationPluginInfo
 
ValidationScriptReader - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
A helper class that reads validation scripts.
ValidationScriptReader() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptReader
 
ValidationScriptRunner - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
 
ValidationScriptRunner.NullValidationScriptRunner - Class in ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation
 
ValidationScriptRunner.NullValidationScriptRunner() - Constructor for class ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationScriptRunner.NullValidationScriptRunner
 
valueOf(String) - Static method in enum ch.systemsx.cisd.common.exceptions.StatusFlag
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError.ValidationErrorTarget
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share.ShufflePriority
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetKind
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchableEntityKind
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.CompareMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseFieldType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseTimeAttribute
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumnDataType
Returns the enum constant of this type with the specified name.
values() - Static method in enum ch.systemsx.cisd.common.exceptions.StatusFlag
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError.ValidationErrorTarget
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPluginType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.dss.generic.shared.utils.Share.ShufflePriority
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetKind
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchableEntityKind
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.CompareMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseFieldType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseTimeAttribute
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumnDataType
Returns an array containing the constants of this enum type, in the order they are declared.
Vocabulary - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
Immutable value object representing an openBIS vocabulary.
Vocabulary(Vocabulary.VocabularyInitializer) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary
Creates a new instance with the provided initializer
Vocabulary.VocabularyInitializer - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
Vocabulary.VocabularyInitializer() - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Vocabulary.VocabularyInitializer
 
VocabularyTerm - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
 
VocabularyTerm(String, String, Long, Boolean, EntityRegistrationDetails) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.VocabularyTerm
 

W

WebAppSettings - Class in ch.systemsx.cisd.openbis.generic.shared.api.v1.dto
A map containing persistent settings for an openBIS web app.
WebAppSettings(String, Map<String, String>) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings
 
WebAppSettings(String, WebAppSettings) - Constructor for class ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings
 
willCreateDirectory(FileInfoDssDTO) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader.FileInfoDssDownloaderListener
 
willDownload(FileInfoDssDTO) - Method in interface ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader.FileInfoDssDownloaderListener
 
WITHDRAW_SHARE_PROP - Static variable in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ShareFactory
 
writeImageToPng(BufferedImage, OutputStream) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image and writes it to the given output stream.
writeImageToPng(BufferedImage, OutputStream, PngFilterType, int) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image and writes it to the given output stream.
writeImageToPngFast(BufferedImage, OutputStream) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
Converts the given image to a PNG image and writes it to the given output stream.
writeImageUsingImageIO(BufferedImage, OutputStream, String) - Static method in class ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil
 

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