This package contains the core business logic of BASE.
Interface Summary Interface Description AbsoluteProgressReporterThis is interface is an extension to the
AccessControlledThis interface should be implemented by a class representing items which requires the logged in user to have permission to access them. AnnotatableThis interface is implemented by all items which can be annotated. AnnotatableProxyThis interface is implemented by items that can be used to hold annotations that are intended for other items. BatcherThe basic interface which all batchers must implement. ClonableReporterQueryAn interface that indicates that a query may be used together with cloned reporter information. Controlled DiskConsumableThis interface is implemented by items that can use a lot of disk space. FileAttachableA
FileAttachableitem is an item that can have a
Fileattached to it.
FileStoreEnabledThis interface is implemented by items that can use files instead of the database for storing data. IdentifiableAn
Identifiableitem is an item which has an
ListableTagging interface for items that can be put in an
Metadata.PropertyPath<C,V>Contract for getting the value of a specific property for an item. NameableA
Nameableitem is an item that has a
Ownableitem is an item which has a
Useras its owner.
ProgressReporterCertain methods in BASE can report their progress back to the calling client application if they are giving an object that implements this interface. QueryExecutor.CancelableInterface to be implemented by classes that knows how to cancel a query. QueryRuntimeFilterRepresents a filter that is applied to a query just before it is executed in order to limit the result. RegisteredItems that implements this interface has their registration date stored in the database. RemovableA
Removableitem is an item that can be flagged as removed.
Shareable SubtypableA subtypable item is an item that can have a subtype. SystemItemA
SystemItemis an item which has an additional systemwide unique id in the form of string.
TransactionalThis interface is a tagging interface for items that wants to be notified before a transaction is committed or after it has been completed or rollbacked. TransactionalActionInterface that define hooks for callbacks during transaction commit and rollback. UsableDataFileTypeUtility interface for collecting information about data file requirements when used on a certain platform/variant or item subtype. ValidatableThis interface is a tagging interface for items that needs case 2 validation.
Class Summary Class Description AbstractBatcherThis is an abstract class for batchers that are connected to a single
AbstractEntityQueryAn abstract implementation of the
AbstractHqlQueryAn abstract implementation of the
AbstractQueryAn abstract implementation of the
AbstractResultList<I>This is a list of the result from a query. AbstractSqlQueryAn abstract implementation of the
AnnotatedItemThis is a helper class for items that need to implement the
AnnotationThis class represents an annotation. Annotation.QueryRuntimeFilterImpl AnnotationBatcherBatcher implementation for adding, updating and removing multiple annotations to a large number of items in a single transaction while keeping the memory usage as low as possible. AnnotationBatcher.CurrentAnnotationInfoHolds information about an annotation for the current item. AnnotationBatcher.InsertBatcherBatcher implementation for inserting into tables. AnnotationBatcher.UpdateBatcherBatcher implementation for updating and deleting from tables. AnnotationBetweenRestrictionRestricts a query using annotation values between a low and high value. AnnotationInRestrictionRestricts a query using annotation values that exists in a set of given values. AnnotationRestrictionBase class for creating restrictions based on annotations. AnnotationRestriction.OptionsOptions that specify which annotations to consider when searching. AnnotationSetAn annotation set is the container for all annotations on an item. AnnotationSet.ProjectSpecificAnnotationsRestrictionRestriction for matching project-specific annotations against the currently active project. AnnotationSet.QueryRuntimeFilterImpl AnnotationSimpleRestrictionRestricts a query using annotation values with a simple expression:
annotation operator value.
AnnotationTypeObjects of this class defines an annotation type. AnnotationType.RemoveInheritedAnnotationsAction AnnotationTypeCategoryObjects of this class defines an annotation type category. AnyToAnyAn any-to-any link is a named, directed link from one item to another item. ApplicationThis class represents the BASE application and is the starting point for all client applications. Application.DbCleaner Application.PingerA
Pingeris an object that is used to protect another object from timing out by automatically pinging it.
Application.SessionControlCacheCleaner Application.StartupOptionsStartup optins when starting the BASE application. ArrayBatchThis class represents the making of a new batch of microarray slides of a particular design. ArrayDesignAn array design is a description of the design of a microarray slide. ArrayDesignBlock ArrayDesignPlate ArraySlideThis class represents a physical microarray slide. AuthenticationContextGives authentication implementations limited access to the database. BasicBatcher<D extends BatchableData>This is an abstract class for batching functionallity. BasicChildItemAn abstract base class for all items which are child items to a
BasicItemThis is the root superclass of all item classes. BatchedPropertyInfoHolds information about a batchable property. BatchUtilUtility class for batching information. BioAssayRepresents the current intensities of raw data after some transformation has been applied to it. BioAssaySetA bioassayset represents the current intensities of the raw data after some
Transformationhas been applied to it.
BioMaterial BioMaterialEventThis class represents an event in the life of a
BioMaterialEventSourceClass for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay. BioMaterialEventSource.BioMaterialEventSourceTransformer BioPlateThis class is represents physical bio-plates. BioPlateEventA bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates. BioPlateEventParticipantHolds information about a bioplate that is participating in a bioplate event. BioPlateEventTypeThe type of a bioplate event defines what happened in the event. BioPlateTypeThis class represents the type of a bio-plate. BioSourceThis class represent biosource items. BioWell BlockInfoA
BlockInfoobject is used to represent the uniqe identifiers of an
BooleanParameterTypeThis class represent a parameter type that is a boolean. ChangeHistory ChangeHistory.TransactionInfoHolds information about a single transaction. ChildItemAn abstract base class for all items which are child items to a
ClientThis class represents a registered client application. ClientDefaultSettingThis class is used to represent a setting for specific client application. ClonablePropertyRepresents a reporter property that can be cloned to a per-experiment table in the dynamic database. ColoringThis class keeps coloring information for items which can be colored when values are displayed in a client application. CommonItem ConfigUse this class to access the configuration settings for BASE. ContextKey DataCubeA data cube is the main unit for an experiment to store analysed data. DataCube.RawMappingQuerySelect data from Dynamic#RawParents table. DataCubeColumnRepresents the column coordinate in a data cube. DataCubeExtraValueRepresents a set of extra value in a data cube. DataCubeFilterThis represents a filter in a datacube. DataCubeLayerThis represents the layer coordinate in a data cube. DataFileTypeThis class is used to represent types of files that are used to hold data instead of importing the data into into the database. DataQuery<I extends BasicData>An implementation of the
Queryinterface that returns data objects.
DataResultIterator<I extends BasicData>Return the results of a
DataQueryas an iterator.
DateParameterTypeThis class represent a parameter type that is a date. DateUtilUtility methods that will make it easier to handle date values. DbControlA
DbControlobject is the main object used for communicating with the database.
DbControl.SaveIf DbControl.StateMain purpose is to write a warning to the log file in case some user code that created a DbControl instance never called the close() method before the DbControl became uncreachable. DerivedBioAssay DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyActionWhenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes. DirectoryThis is used to represent directory items. DiskUsageThis class is used to represent the disk usage of
DiskUsageStatisticsGet disk usage statistics for the BASE server. DoubleParameterTypeThis class represent a parameter type that is a double. DropDynamicTableActionTransactional action that can drop a table from the dynamic database after a successful commit and/or rollback. DynamicExtraValueQueryRepresents a query for extra values in the dynamic database. DynamicJoinRepresents a join between two virtual tables in a dynamic query:
leftTable JOIN rightTable ON columns.
DynamicPositionQueryRepresents a query for position information against the dynamic database. DynamicPositionQueryJoinersThis class collects
DynamicPositionQueryJoiners.ExtraValueJoinerJoiner for extra values. DynamicPositionQueryJoiners.ReporterJoinerJoiner for reporters DynamicPositionQueryJoiners.ReporterListJoinerAuto joiner for reporter lists. DynamicQueryRepresents a query against the dynamic database. DynamicRawDataQueryRepresents a query for raw data in a "dynamic" way. DynamicRawDataQuery.RawBioAssayJoinerAuto joiner for raw bioassays. DynamicRawDataQuery.ReporterJoinerAuto joiner for reporters. DynamicRawDataQuery.ReporterListJoinerAuto joiner for reporter lists. DynamicReporterQueryRepresents a query for reporter data in a "dynamic" way. DynamicReporterQuery.MasterReporterJoinerAuto joiner for master reporter table. DynamicReporterQuery.ReporterListJoinerAuto joiner for reporter lists. DynamicRestrictionCreates a restriction that compares a dynamic column with a constant value:
tableAlias.column = valueor
queryRootAlias.column = value
DynamicResultIteratorAn iterator view of the result of an
DynamicSpotQueryRepresents a query for spot information in the dynamic database. DynamicSpotQueryJoinersThis class collects
DynamicSpotQueryJoiners.ExtraValueJoinerJoiner for extra values. DynamicSpotQueryJoiners.RawDataJoinerJoiner for raw data. DynamicSpotQueryJoiners.ReporterJoinerJoiner for reporters DynamicSpotQueryJoiners.ReporterListJoinerJoiner for reporter lists. ExperimentAn experiment is the starting point of the analysis in BASE. ExtendedPropertiesThis class is used for reading XML files with information about extended properties. ExtendedPropertyHolds information about an extended property for a class. ExtendedPropertyAccessorThis class is used to interface with Hibernate for extended properties. ExtendedPropertyAccessor.GetterSetterThis class implements the Hibernate
ExtendedPropertyLinkerUsed to create links from extended property values. ExtractThis class is used to represent extract items. ExtraValueRepresents extra values attached to a
ExtraValueExpressionRepresents the value of an extra value in a dynamic query:
ExtraValueJoinRepresents a join to an extra value in a dynamic query:
leftTable JOIN extraValueTable ON ...
ExtraValueTypeDefines extra values that can be calculated by plugins or some other application and inserted as part of a
FeatureThis is a utility class for Features. FeatureBatcherBatcher class for Features or AffyFeatures. FeatureCoordinateRepresents the coordinate of a feature on an array design. FileThis class is used to represent individual file items and information about them. FileParameterTypeThis class represent a parameter type that is a file. FileServerThis class represents a file server that is used to store external files. FileSetA file set is the container for files that have been attach to an item to hold data instead of importing it to the database. FileSet.QueryRuntimeFilterImpl FileSetMemberThis class represents a file that is member of a file set. FileSetMember.QueryRuntimeFilterImpl FileStoreUtilUtility class working with
FilterBatcherBatcher class for filtered bioassaysets. FloatParameterTypeThis class represent a parameter type that is a float. FormulaThis class represents a formula. GlobalDefaultSettingThis class is used to represent a global default setting. GroupThis class is used to represent groups. Group.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return groups where the logged in user is a member unless the logged in user has generic read permission. GroupPermissionsThis class is used to specify permissions to share an item to groups. HardwareThis class is used to represent individual hardware items and information about them. HasAnnotationRestrictionRestricts a query by the presence of absence of an annotation. HelpThis class is used to represent a help text for a client application. HibernateUtilThis class collects most of the functionality we need for using Hibernate. HibernateUtil.DelayedFilterDef HibernateUtil.FilterConfiguratorHelper class for defining filters at runtime. HqlQueryJoinersThis class collects
HqlQueryJoiners.AnnotationJoinerJoiner for annotations. HqlQueryJoiners.ReporterListJoinerJoiner for reporter lists. InstallThis class contains static methods used to install items into an empty database. Install.ItemSubtypeFT Install.PlatformFT IntegerParameterTypeThis class represent a parameter type that is an integer. IntegerUtilUtility methods that will make it easier to implement data validation for integer attributes. IntensityFormulaHolds information about the formulas used to calculate intensities from a raw data spot. InternalJobQueueA simple implementation of a job queue that executes jobs in order of priority and longest waiting time. InternalJobQueue.JobQueueKeyringOur own keyring containing the permissions we need to execute the jobs. Item.DefinedPermissionsHelper class to make it easier to set up the defined permissions. ItemContextThis item is a helper class for client applications when they need to store information about the current context for plugins that needs to find out the current context of the running client application. ItemContext.PropertyFilterPairHolds a pair of filter. ItemContext.QueryRestrictions ItemContext.RowRestrictions ItemKeyThis class is used to get information about which users and groups a
Shareableitem has been shared to.
ItemListThis class represents a list of items. ItemList.DelayedAdditionManagerHandles items that should be added as members to the list, but since they were created in the same transaction doesn't have any ID until later in the commit phase. ItemParameterType<T extends BasicItem>This class represent a parameter type that is an object derived from
ItemProxy ItemQuery<I extends BasicItem>An implementation of the
Queryinterface that returns item objects.
ItemResultIterator<I extends BasicItem>Return the results of an
ItemQueryas an iterator.
ItemResultList<I extends BasicItem>Return the results of an
ItemQueryas a list.
ItemSubtypeItem subtypes can be used to classify items into sub-categories. ItemSubtypeFileTypeThis class represents a specific
DataFileTypethat is associated with an item subtype.
JobThis class represents the execution of a job. Job.ProgressReporterImplImplements the ProgressReporter interface and stores the percentage completed for the current job. Job.SignalKeyringOur own keyring containing the permissions signal handlers may need to update job status, eq. JobAgentThis class represents a job agent, which is a program running in another virtual machine on the same or a different server. JobAgentSettingsThis class contains a job agent's settings for a specific plugin. KeyThis is the base class for keys. KeyringObjects of this class holds information about a user's access permissions, group and role membership. KitThis class is used to represent a kit of reagents and other stuff used in the lab process. LogControlGives information about the current transaction and gives log implementations limited access to the database. LogUtilUtility class for LOG4J logging. LongParameterTypeThis class represent a parameter type that is a long. MappingBatcherBatcher class for inserting parent mapping information in the dynamic database. MeanRawDataPropertyExpressionAn expression representing the mean value of property of a raw data spot. MeasuredBioMaterialThis class is the base class for measured biomaterial items. MeasuredBioMaterial.RemainingQuantityActionTransaction handler for updating the remaining quantity of a biomaterial based on the sum of the used quantity in this transaction. MessageThis class represents a message. Message.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return messages for the currently logged in user unless the logged in user has generic read permission. Metadata<C>Utility methods for retreiving metadata about items. Metadata.BasicData2ItemPropertyPath<C extends BasicData,V extends BasicItem>Property path implementation that converts a BasicData object to a BasicItem. Metadata.BasicItem2DataPropertyPath<C extends BasicItem,V extends BasicData>Property path implementation that converts a BasicItem to a BasicData object. Metadata.CollectionPropertyPath<C>Property path implementation which wraps a collection inside an unmodifiable collection. Metadata.CombinedPropertyPath<C,V>Property path implementation that combines a list of property paths to create a long chain. Metadata.ComponentPropertyPath<C,V>Property path implementation which gets a value from a component. Metadata.DateCopyPropertyPathProperty path implementation clones a Date. Metadata.EntityPropertyPath<C,V>Property path implementation which gets a value from an entity. Metadata.EvictPropertyPath<C>Property path implementation that evicts the selected item from the Hibernate first-level cache. Metadata.IdentifierPropertyPathProperty path implementation which gets the id from an entity. Metadata.MapPropertyPathProperty path implementation which wraps a map inside an unmodifiable map. Metadata.NoopPropertyPath<C>Property path implementation that does nothing. Metadata.ReporterScore2DataPropertyPathProperty path implementation that converts a ReporterScore to a ReporterListScoreData object. MigrationClass for migrating a database to PostgreSQL. MimeTypeThis class is used to represent mime types. MultiPermissionsThis is a helper class that is very useful when you have a collection of
Shareableitems and want to modify some permissions on all of them without affecting the rest of the permissions.
NameableUtilUtility methods that will make it easier to implement the
Nameableinterface, including data validation.
NewsThis class represents news items. News.QueryRuntimeFilterImpl OwnableUtilUtility methods that will make it easier to implement the
Ownableinterface, including data validation.
OwnedItem ParameterInfoGet information about a plugin configuration or parameter. ParameterType<T>This is the base class for all parameter types. ParameterValuesImplAn implementation of the
ParameterValuesinterface that lets a plugin write the job's configuration.
PasswordParameterTypeThis class represent a parameter type that is a password (or any other type of masked string). Path PathParameterTypeThis class represent a parameter type that is a path to either a directory or a file. PermissionTemplateA permission template with permissions to users, groups and projects. PhysicalBioAssayA physical bioassay is a representation of the process of performing an experiment one or more
PlateThis class is represents physical plates. PlateEventThis class represents an event in the life of a
PlateEventTypeThis class is used together with the
PlateTypeclass to define event types for plates.
PlateGeometryThis class defines a plate geometry, which is the number of rows and columns of wells on a
PlateMappingThis class represents a mapping from one plate geometry to another. PlateTypeThis class represents plate types, which is a name, description, geometry and a list of event types. PlatformThis class is used to represent an experimental platform in BASE. PlatformFileTypeThis class represents a specific
DataFileTypethat is part of a platform.
PlatformVariantRepresents variants of a
PluginConfigurationThis class is used to configure a plugin. PluginConfigurationRequestConfigures a plugin or job. PluginDefinitionA plugin definition represents the executable plugin. PluginExecutionRequestExecutes a job. PluginParameter<T>Contains information about a single parameter that the plugin needs for a request. PluginPermission PluginRequest<P extends Plugin>Configures or executes a plugin. PluginResponseGet the response from a configuration step or execution of a plugin. PluginSessionControlThis is a special session control implementation that is used for executing plugins that prevents them from logging in or out. PluginType PositionBatcherBatcher class for per-position data in the dynamic database. PositionExtraValueBatcher<I>Batcher class for per-position extra values. PredefinedQueryThis class is used for reading XML files with information about predefined queries. PresetsThis is a generic class for handling named presets consisting of multiple key/value pairs. Presets.PresetRepresents a single preset. ProjectThis class is used to represent projects. Project.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission. ProjectKeyThis class is used to get information about which projects a
Shareableitem has been shared to.
ProjectPermissionsThis class is used to specify permissions to share an item to projects. ProjectSpecificAnnotationsManagerInternal class for keeping the "override_id" column in the "Annotations" table synchronized when annotations are creted and deleted. ProjectSpecificAnnotationsManager.AnnotationInfoHolds some information about the annotation that has been created. PropertyFilterUsed to store filter settings in the current context. ProtocolThis class is used to represent individual protocol items and information about them. QuantityThis class is used to represent a quantity for specifying units to annotations. QueryExecutorUtility class for executing SQL and Hibernate queries. QueryExecutor.CancelableSessionCancels the query running in a Hibernate session. QueryExecutor.CancelableStatelessSessionCancels a query running in a stateless Hibernate session. QueryExecutor.CancelableStatementCancels a statement by calling
QueryExecutor.FutureItem<T> QueryExecutor.FutureResultSetA callable implementation the calls
QueryExecutor.FutureScrollIterator<T> QueryExecutor.FutureUpdateA callable implementation the calls
QueryRuntimeFilterFactoryThis is a factory class for
QueryRuntimeFilterFactory.AnnotatableFilterA required filter for
QueryRuntimeFilterFactory.BasicFilter QueryRuntimeFilterFactory.ChainedFilterChains one or more filters into a single filter. QueryRuntimeFilterFactory.ChildFilter QueryRuntimeFilterFactory.DenyAllFilterA required filter for all items, which checks if the logged in user has been "granted" the
Permission.DENIEDpermission for a specific item type.
QueryRuntimeFilterFactory.OwnableFilter QueryRuntimeFilterFactory.RemovableFilterA required filter for
QueryRuntimeFilterFactory.ShareableFilterAn optional default filter for
QueryRuntimeFilterManagerThis class manages the enabling/disabling of
QuotaThis class is used to represent disk quota settings for users and groups. Quota.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return the quota assigned to the logged in user unless the logged in user has generic read permission. QuotaTypeThis class represents the different types a quota can have. RawBioAssayA rawbioassay represents the raw data generated from a single
RawBioAssayPropertyExpressionAn expression representing the property of a raw bioassay. RawDataBatcherBatcher class for raw data. RawDataBatcher.FeatureInfo RawDataBatcher.FeatureProxy RawDataBatcher.ReporterProxy RawDataPropertyHolds information about an extended property for raw data. RawDataPropertyExpressionAn expression representing the property of a raw data spot. RawDataTypeThis class holds information about a raw data type. RawDataTypesThis class is used for reading the XML configuration file with information about raw data types. RawDataTypes.NameComparatorComparator implementation that sorts raw data types according to their name. RawDataUtilUtiltity class for getting and setting non-public properties of raw data objects. RealJoinRepresents a join from one virtual table in the dynamic database to a table in the regular database or between two tables in the regular database. RealTableThis class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries. ReporterThis is an utilitiy class for reporters. ReporterBatcherBatcher class for reporters. ReporterCloneBatcherBatcher implementation that is used to handle cloned reporter information in the dynamic database. ReporterCloneTemplateA reporter clone template is a definition of which reporter properties/annotations that should be cloned to a per-experiment table in the dynamic database. ReporterList ReporterListJoinRepresents a join to a reporter list in a dynamic query:
leftTable JOIN ReporterListScores ON ...
ReporterPropertyExpressionAn expression representing the property of a reporter. ReporterScoreGet information about the reporters and their score in a reporter list. ReporterScoreQueryThis is a temporary solution to query against the reporter list's score. ReporterScoreResultIteratorThis is a temporary solution for returning reporter list scores as an iterator. ReporterTypeThis class holds reporter type information. RequestInformationGet information about the parameters the plugin needs for a particular request. RoleThis class is used to represent roles. Role.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return roles where the logged in user is a member unless the logged in user has generic read permission. RoleKeyThis class is used to represent a role key. RootRawBioAssayRepresents the use of a raw bioassay in an experiment. SampleThis class is used to represent sample items. ScrollIterator<E>This is an iterator view of the result from a query using the Hibernate
ServiceSessionControlA special session control implementation used for services. ServiceSessionControl.FlushSessionActionFlushes the given session before the transaction is committed. ServiceSessionControl.ServicesKeyringOur own keyring containing the only permission:
ServicesUtilUtility class for the "services" extension point. SessionA session represents the time between login and logout for a single user. Session.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return sessions for the currently logged in user unless the logged in user has generic read permission. SessionControlThis class handles user sessions. SessionControl.ClientInfo SessionControl.LoginInfoInternal class to hold information about the logged in user. SessionControl.SettingInfoInternal class to hold information about a setting SessionControl.UnverifiedDeviceInfoClass for storing temporary device information for a user that has been authenticated but before a device has been verified. SettingThis is the base class for all setting items. ShareableUtilUtility methods that will make it easier to implement the
Shareableinterface, including data validation.
SharedItem SimpleAbsoluteProgressReporterThis is a simple implementation of the
AbsoluteProgressReporterinterface, which simply remembers that last values.
SimpleProgressReporterThis is a simple implementation of the
ProgressReporterinterface, which simply remembers that last values.
SoftwareThis class is used to represent individual software items and information about them. SpecialQuery<C>A special HQL query implementation that can return almost any kind of object. SpotBatcherBatcher class for per-spot intensity values for bioassaysets. SpotExtraValueBatcher<I>Batcher class for per-spot extra values. StringParameterTypeThis class represent a parameter type that is a string. StringUtilUtility methods that will make it easier to implement data validation for string attributes. SyncFilterHolds information about a synchronization filter used by an item list. SystemItemsThis class is used to map the system id of all
SystemDataitems to the numerical internal id in the current installation.
TagThis class represents a tag. TimestampParameterTypeThis class represent a parameter type that is a timestamp. TransformationA transformation represents an analysis step for an
TrashcanThis class contains functionality to manage items that have been marked for deletion. Trashcan.CircularRefInfoHelper class for holding information about a single item, other items using it and other information that is relevant for resolving circular references. UnitThis class is used to represent a specific unit that can be used with annotations. UnmodifiableResultList<T> UpdateThis class contains static methods used to update items already in the database. Update.DropColumnChangeAction that drops a column in a table. Update.SchemaChangeAction that need to make some change to the database schem after the main transaction in
Update.adjustExistingItems(ProgressReporter, int, String, String)has finished.
UserThis class is used to represent a user in BASE. User.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return users which are members of at least one group where the logged in user is also a member unless the logged in user has generic read permission. UserClientSettingThis class is used to represent a setting valid for a specific user using a specific client application. UserDefaultSettingThis class is used to represent a setting valid for a specific user using any client application. UserDeviceA user device represents a verified device a user may use for accessing BASE. UserDevice.QueryRuntimeFilterImplA runtime filter implementation that limits a query to only return devices for the currently logged in user unless the logged in user has generic read permission. UserPermissionsThis class is used to specify permissions to share an item to users. ValuesUtility class to handle the conversion between data objects and item objects. VersionGet information about the BASE version. VirtualColumnThis class is used to define columns in the virtual tables in the dynamic part of the database that are storing analysed data. VirtualDbA virtual database represents the set of tables in the dynamic database used by a single experiment to store it's analysed data. Well
Enum Summary Enum Description Annotation.SourceThe annotation source. AnnotationBatcher.ChangeA flag indicating what type of change that was made to an annotation as a result of calling
AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)
BioMaterialEvent.TypeThe type of the event. BioWell.LockModeThe lock mode for a well is determined by the plate's bio plate type. ExtraValue.CoordinateTypeDefines which coordinates in the data cube the extra values are attached to. FeatureIdentificationMethodThis enumeration defines constants that are used to specify which method to use for identifying features on an array design. Formula.AverageMethodThe average method used for the values of this formula. Formula.ParserThe parser used to parse the formula. Formula.TypeThe type of formula indicats in which situations it can be used. IncludeThis enumeration defines constants that are used to specify which items to include in a query. IntensityTransformGives information in what way spot intensities has been transformed before they were stored in the database. ItemThis class defines constants for various items in BASE. ItemContext.SortDirectionEnumeration used to specify the sort direction. ItemList.SynchronizeOptionOptions for synchronizing an existing item list with a current settings in an
Job.ExecutionTimeA rough estimate of the execution time of a job. Job.StatusThe status of a job. Job.TypeThe type of job. LocationThis enumeration defines constants that are used to specify different file storage locations. Operator Path.TypeAn enum that describes what type the path is PermissionThis enumeration defined constants for permissions. ReporterCloneBatcher.CloneSourceSpecifies which source table to use for finding out which reporters that are part of the current experiment. SyncFilter.SourceItemTransform Transactional.ActionEnumeration constants used to tell the item what is going on in the core. TypeThis class defines constants for supported value types in BASE. VirtualTableThis enumeration defines constants that are used to specify different virtual tables in the dynamic part of the database used for analysis.
Exception Summary Exception Description AccountExpiredExceptionThis exception is thrown if you try to log in with an account that has expired. AlreadyLoggedInExceptionThis exception is thrown if you try to log in but are already logged in. BaseExceptionThis is the base class for exceptions in BASE. ConfigurationExceptionThis exception is thrown by the
Configclass if there is a problem with finding or loading the configuration settings.
ConnectionClosedExceptionThis exception is thrown when trying to use a
DbControlobject that has been closed.
DatabaseExceptionExceptions of this type are thrown when there is an error from the database. DateFormatExceptionThis exception is thrown when parsing a string into a date failed. DetachedItemExceptionThis exception is thrown when trying to use an item that has been detached from the
DbControlthat manages it.
DeviceNotVerifiedExceptionThis exception can be thrown when a user is trying to login from a device that has not been verified. DisallowedValueExceptionException that is thrown when a value is not found among a set of allowed values, for example, when setting an annotation value. InvalidAnnotationException InvalidDataExceptionExceptions of this type are thrown when invalid data is encountered. InvalidPasswordExceptionExceptions of this type are thrown when user tries to log in, but the password is incorrect. InvalidPathExceptionThis exception is thrown when BASE is trying to parse a path which is invalid. InvalidRelationExceptionExceptions of this type are thrown when a
ValidationActionhas detected that a file related to the main file is invalid.
InvalidUseOfNullExceptionThis exception is thrown when an object field or a parameter that mustn't be null is set to null. ItemAlreadyExistsExceptionThis exception is thrown when trying to save an object and another object with the same ID already exists. ItemInUseExceptionThis exception is thrown when trying delete an item that is used (reference to) by some other item or items. ItemModifiedExceptionThis exception is thrown when trying to save an item to the database that has been updated (or deleted) by another process in the meantime. ItemNotFoundExceptionThis exception is thrown when trying to load an item from the database that does not exist. LoginExceptionExceptions of this type are thrown when the BASE server uses an external authentication plug-in and it is not clear if the login or password is causing the failure. NotLoggedInExceptionThis exception is thrown if you try to perform a function that requires a user to be logged in without beeing logged in. NumberOutOfRangeExceptionThis exception is thrown when an item's field or a parameter that only accepts numeric values within a certain range are passed a value outside that range. ParameterException PermissionDeniedExceptionThis exception is thrown when trying to load or manipulate an item in the database and you don't have the required permission. QuotaExceptionThis exception is thrown to signal that the user's quota has been exceeded and that an
DiskConsumableitem cannot be saved.
StringTooLongExceptionThis exception is thrown when an item's field or a parameter which must be shorter than a specified length exceeds that length. UnsavedItemExceptionThis exception is thrown when trying to use an item that has not been saved to the database in places where this is required. UnsupportedFileFormatExceptionThrown when an import plug-in is forced to use a file that is not of the correct format.
Annotation Types Summary Annotation Type Description SubtypableRelatedItemsAnnotation that can be used by
Subtypableitems to tell about related items.
SupportsPushAnnotationsAnnotation (java) that can be used by
Subtypableitems to enable/disable support for pushing annotations (BASE) to parent items.