- AbstractClassIdsOptionsQuery - Class in ome.services.query
-
simple abstract class that provides a common
Definitions containing:
IdsQueryParameterDef and
ClassQueryParameterDef.
- AbstractClassIdsOptionsQuery(Parameters) - Constructor for class ome.services.query.AbstractClassIdsOptionsQuery
-
- AbstractFileDeletions - Class in ome.services.delete.files
-
Base class for managing the removal of files from disk.
- AbstractFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.AbstractFileDeletions
-
- AbstractLevel1Service - Class in ome.logic
-
service level 1
- AbstractLevel1Service() - Constructor for class ome.logic.AbstractLevel1Service
-
- AbstractLevel2Service - Class in ome.logic
-
service level 2
- AbstractLevel2Service() - Constructor for class ome.logic.AbstractLevel2Service
-
- AbstractSecurityFilter - Class in ome.security.basic
-
overrides FilterDefinitionFactoryBean in order to construct our
security filter in code and not in XML.
- AbstractSecurityFilter() - Constructor for class ome.security.basic.AbstractSecurityFilter
-
Default constructor which calls all the necessary setters for this
FactoryBean.
- AbstractSecurityFilter(Roles) - Constructor for class ome.security.basic.AbstractSecurityFilter
-
- AbstractSessionMessage - Class in ome.services.messages
-
InternalMessage implementations which carry relate to some
Session bound event.
- AbstractSessionMessage(Object, String) - Constructor for class ome.services.messages.AbstractSessionMessage
-
- AbstractStatefulBean - Class in ome.services
-
Base bean implementation for stateful services.
- AbstractStatefulBean() - Constructor for class ome.services.AbstractStatefulBean
-
- AbstractStatsMessage - Class in ome.services.messages.stats
-
Published when some limit in user/group/session activity has been reached.
- AbstractStatsMessage(Object) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
-
- AbstractStatsMessage(Object, boolean) - Constructor for class ome.services.messages.stats.AbstractStatsMessage
-
- accept(String, String) - Method in class ome.services.mail.MapAnnotationSubethaListener
-
Accepts all mails.
- accept(Job) - Method in class ome.services.procs.ProcessorSkeleton
-
- acl - Variable in class ome.tools.hibernate.ProxyCleanupFilter
-
- ACLEventListener - Class in ome.security
-
responsible for intercepting all pre-INSERT, pre-UPDATE, pre-DELETE, and
post-LOAD events to apply access control.
- ACLEventListener(ACLVoter) - Constructor for class ome.security.ACLEventListener
-
main constructor.
- aclVoter - Variable in class ome.logic.AdminImpl
-
- ACLVoter - Interface in ome.security
-
helper security interface for all decisions on access control
- aclVoter - Variable in class ome.security.basic.BasicSecuritySystem
-
- acquireContext() - Method in class ome.services.util.BeanHelper
-
Lazy loads the application context, which means that if we're not in
the application server, then the OmeroContext.MANAGED_CONTEXT
should never get loaded.
- action - Variable in class ome.services.graphs.GraphPolicy.Details
-
- action - Variable in class ome.services.messages.EventLogMessage
-
- action - Variable in class ome.tools.hibernate.EventMethodInterceptor
-
- Action() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.Action
-
- activate() - Method in class ome.services.JobBean
-
Does almost nothing.
- activate() - Method in class ome.services.RawFileBean
-
- activate() - Method in class ome.services.RawPixelsBean
-
- activate() - Method in class ome.services.RenderingBean
-
- activate() - Method in class ome.services.SearchBean
-
- activate(long) - Method in class ome.services.sharing.ShareBean
-
- activate() - Method in class ome.services.ThumbnailBean
-
- activeQueries() - Method in class ome.services.SearchBean
-
- add(EventLog) - Method in class ome.services.eventlogs.EventBacklog
-
Adds the given
EventLog instance to the end of a queue for later
popping if no equivalent
EventLog is present.
- add(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- addAction(SearchAction) - Method in class ome.services.SearchBean
-
- addAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
-
- addApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
-
- addApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
-
- addCallback(String, SessionCallback) - Method in class ome.services.sessions.SessionManagerImpl
-
- addCleanup(RegisterServiceCleanupMessage) - Method in class ome.security.basic.CurrentDetails
-
- addCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
-
Deprecated.
- addCodomainMapToChannel(CodomainMapContext, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- addComment(long, String) - Method in class ome.services.sharing.ShareBean
-
- addContents(Document, String, OriginalFile, OriginalFilesService, Map<String, FileParser>, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
Second helper method used when parsing files.
- addDisabled(String) - Method in class ome.security.basic.CurrentDetails
-
- addEnumIfNotNull(Document, String, IEnum, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogLoader
-
Adds an EventLog for the given Class and id to the
backlog.
- addEventLog(Class<? extends IObject>, long) - Method in class ome.services.eventlogs.EventLogQueue
-
Only schedule a new backlog event if there is no currently registered
event of that type.
- addFieldToDocument(String, String, Document) - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- addGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
-
- addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- addGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
-
- addGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
-
- addGuest(long, String) - Method in class ome.services.sharing.ShareBean
-
- addGuests(long, String...) - Method in class ome.services.sharing.ShareBean
-
- addIfNotNull(Document, String, String, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- adding - Variable in class ome.services.eventlogs.EventBacklog
-
Switch between the adding and the removing states.
- additions() - Method in class ome.security.basic.EventListenersFactoryBean
-
- addLocalFile(File, long) - Method in class ome.services.delete.files.AbstractFileDeletions
-
- addLog(String, Class, Long) - Method in class ome.security.basic.BasicSecuritySystem
-
- addLog(String, Class, Long) - Method in class ome.security.basic.CurrentDetails
-
- addManager(String, String) - Method in class ome.security.basic.NodeProviderInDb
-
- addManager(String, String) - Method in class ome.security.basic.NodeProviderInMemory
-
- addManager(String, String) - Method in class ome.security.basic.NodeProviderWrapper
-
- addManager(String, String) - Method in interface ome.security.NodeProvider
-
Adds a manager node.
- addNumericFieldToDocument(String, Object, Document) - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- addObject(long, T) - Method in class ome.services.sharing.ShareBean
-
- addObjects(long, T...) - Method in class ome.services.sharing.ShareBean
-
- addOrderByAsc(String) - Method in class ome.services.SearchBean
-
- addOrderByDesc(String) - Method in class ome.services.SearchBean
-
- addOrReplace(RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- addOrReplace(Session, SqlAction, ServiceFactory, RepoFile, Long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- addParameters(Parameters) - Method in class ome.services.SearchBean
-
- addReply(long, String, CommentAnnotation) - Method in class ome.services.sharing.ShareBean
-
- addResult(List<IObject>) - Method in class ome.services.SearchBean
-
- addSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
-
- addUser(Set<String>, Experimenter) - Method in class ome.services.mail.MailSender
-
- addUser(Set<String>, Experimenter) - Method in class ome.services.mail.ObjectMailSender
-
- addUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
-
- addUsers(long, Experimenter...) - Method in class ome.services.sharing.ShareBean
-
- admin - Variable in class ome.services.delete.DeleteBean
-
- admin - Variable in class ome.services.sharing.ShareBean
-
- AdminAction - Interface in ome.security
-
- adminFlush() - Method in class ome.services.sharing.ShareBean
-
- AdminImpl - Class in ome.logic
-
Provides methods for administering user accounts, passwords, as well as
methods which require special privileges.
- AdminImpl(SqlAction, SessionFactory, MailSender, SimpleMailMessage, ACLVoter, PasswordProvider, RoleProvider, LdapImpl, PasswordUtil, ChmodStrategy, ChecksumProviderFactory, LightAdminPrivileges) - Constructor for class ome.logic.AdminImpl
-
- adminPrivileges - Variable in class ome.logic.AdminImpl
-
- adminPrivileges - Variable in class ome.services.sessions.SessionManagerImpl
-
- advices - Variable in class ome.services.util.Executor.Impl
-
- afs - Variable in class ome.services.delete.Deletion.Builder
-
- afs - Variable in class ome.services.delete.files.AbstractFileDeletions
-
- afterExecute(Runnable, Throwable) - Method in class ome.services.scheduler.ThreadPool
-
Standard
ThreadPoolExecutor extension point which checks for the
BackgroundFutureTask marker and releases a slot in the
ThreadPool.maxBackground
Semaphore.
- afterPropertiesSet() - Method in class ome.security.KeyAndTrustStoreConfiguration
-
- afterTransactionBegin(Transaction) - Method in class ome.security.basic.OmeroInterceptor
-
- afterTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
-
- agent - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- aggByQuery(String, String, String, Parameters) - Method in class ome.logic.QueryImpl
-
- aggMapByQuery(String, String, String, String, Parameters) - Method in class ome.logic.QueryImpl
-
- ALL_PROJECTIONS - Static variable in class ome.services.search.FullText
-
- AllEntitiesPseudoLogLoader<T extends ome.model.IObject> - Class in ome.services.eventlogs
-
EventLogLoader which iterates through each object model type (in no
particular order) and returns each object from lowest to highest id.
- AllEntitiesPseudoLogLoader() - Constructor for class ome.services.eventlogs.AllEntitiesPseudoLogLoader
-
- allEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
-
- AllEventsLogLoader - Class in ome.services.eventlogs
-
- AllEventsLogLoader() - Constructor for class ome.services.eventlogs.AllEventsLogLoader
-
- allgroups - Variable in class ome.security.SecurityFilterHolder
-
- AllGroupsSecurityFilter - Class in ome.security.basic
-
overrides FilterDefinitionFactoryBean in order to construct our
security filter in code and not in XML.
- AllGroupsSecurityFilter(SqlAction) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
-
Default constructor which calls all the necessary setters for this
FactoryBean.
- AllGroupsSecurityFilter(SqlAction, Roles) - Constructor for class ome.security.basic.AllGroupsSecurityFilter
-
- allObjects(Collection<Set<GraphPolicy.Details>>, GraphPolicy.Details, Collection<Set<GraphPolicy.Details>>) - Static method in class ome.services.graphs.GraphPolicy
-
Utility method to return all the objects for review as a single set of objects.
- allowAnnotate(IObject, Details) - Method in interface ome.security.ACLVoter
-
test whether the given object should be annotatable given the trusted
details.
- allowAnnotate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
-
- allowAnnotate(IObject, Details) - Method in class ome.security.CompositeACLVoter
-
- allowAnnotate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
-
- allowChmod(IObject) - Method in interface ome.security.ACLVoter
-
test whether the given object can have its
Permissions changed within the current
security context.
- allowChmod(IObject) - Method in class ome.security.basic.BasicACLVoter
-
- allowChmod(IObject) - Method in class ome.security.CompositeACLVoter
-
- allowChmod(IObject) - Method in class ome.security.sharing.SharingACLVoter
-
- allowCreation(IObject) - Method in interface ome.security.ACLVoter
-
test whether the given object should be insertable into the DB.
- allowCreation(IObject) - Method in class ome.security.basic.BasicACLVoter
-
- allowCreation(IObject) - Method in class ome.security.CompositeACLVoter
-
- allowCreation(IObject) - Method in class ome.security.sharing.SharingACLVoter
-
- allowDelete(IObject, Details) - Method in interface ome.security.ACLVoter
-
test whether the given object should be deleteable given the trusted
details.
- allowDelete(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
-
- allowDelete(IObject, Details) - Method in class ome.security.CompositeACLVoter
-
- allowDelete(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
-
- allowLoad(Session, Class<? extends IObject>, Details, long) - Method in interface ome.security.ACLVoter
-
test whether the object of the given Class with the given
Details should be loadable in the current security context.
- allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.basic.BasicACLVoter
-
delegates to SecurityFilter because that is where the logic is defined
for the
read filter
Ignores the id for the moment.
- allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.CompositeACLVoter
-
- allowLoad(Session, Class<? extends IObject>, Details, long) - Method in class ome.security.sharing.SharingACLVoter
-
- allowUpdate(IObject, Details) - Method in interface ome.security.ACLVoter
-
test whether the given object should be updateable given the trusted
details.
- allowUpdate(IObject, Details) - Method in class ome.security.basic.BasicACLVoter
-
- allowUpdate(IObject, Details) - Method in class ome.security.CompositeACLVoter
-
- allowUpdate(IObject, Details) - Method in class ome.security.sharing.SharingACLVoter
-
- allTypes() - Method in class ome.services.SearchBean
-
- alreadySeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
-
- analyzer - Variable in class ome.logic.QueryImpl
-
- and() - Method in class ome.services.SearchBean
-
- and(String) - Method in class ome.tools.hibernate.QueryBuilder
-
Appends "and" plus your string unless this is the first where-spec in
which case it is simply appended.
- annotatedBetween(AnnotationCriteria) - Method in class ome.services.search.SearchAction
-
- annotatedBetween(QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- annotatedBy(AnnotationCriteria) - Method in class ome.services.search.SearchAction
-
- annotatedBy(QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- annotatedBy - Variable in class ome.services.search.SearchValues
-
- annotatedStart - Variable in class ome.services.search.SearchValues
-
- annotatedStop - Variable in class ome.services.search.SearchValues
-
- AnnotatedWith - Class in ome.services.search
-
Query for Search which uses an example Annotation
instance as the basis for comparison.
- AnnotatedWith(SearchValues, Annotation[], boolean, boolean) - Constructor for class ome.services.search.AnnotatedWith
-
- append(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean
-
appends the objects to the existing list identified by key.
- append(String) - Method in class ome.tools.hibernate.QueryBuilder
-
Simple delegate method to allow appending arbitrary strings.
- appendDate(StringBuilder, Date) - Method in class ome.tools.hibernate.SqlArray
-
- appendSpace() - Method in class ome.tools.hibernate.QueryBuilder
-
- applyContext(Details, boolean) - Method in class ome.security.basic.CurrentDetails
-
- applyIfShareAccessible(QueryBuilder) - Method in class ome.services.sharing.ShareBean
-
If the current user is not an admin, then this methods adds a subclause
to the HQL:
AND ( share.owner.id = :userId or user.id = :userId )
QueryBuilder.where() should already have been called.
- applySettingsToDataset(long, long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- applySettingsToImage(long, long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- applySettingsToImages(long, List<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- applySettingsToPixels(long, long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- applySettingsToProject(long, long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- applySettingsToSet(long, Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- asClassOrNull(String) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- asroot - Variable in class ome.services.sessions.SessionManagerImpl
-
A private session for use only by this instance for running methods via
Executor.
- assemble(Serializable, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- assertManaged(IObject) - Method in class ome.logic.AdminImpl
-
- assertMayProcess(String, long, Details) - Method in interface ome.services.graphs.GraphTraversal.Processor
-
Assert that an object with the given details may be processed.
- assertNoPolicyViolations() - Method in class ome.services.graphs.GraphTraversal
-
Check that there are no policy violations matched by p:error policy rules.
- assertNoUnlinking() - Method in class ome.services.graphs.GraphTraversal
-
- attach(long) - Method in class ome.services.JobBean
-
- AttributeNewUserGroupBean - Class in ome.security.auth
-
Handles the "*_attribute" specifiers from omero-server.properties.
- AttributeNewUserGroupBean(String, boolean, boolean) - Constructor for class ome.security.auth.AttributeNewUserGroupBean
-
- AttributeSet - Class in ome.security.auth
-
Specialized handling of all the attributes, multi or single valued.
- AttributeSet(DirContextAdapter) - Constructor for class ome.security.auth.AttributeSet
-
- available() - Method in class ome.services.pixeldata.PersistentEventLogLoader
-
- AWTScaleService - Class in ome.logic
-
Provides methods for scaling buffered images.
- AWTScaleService() - Constructor for class ome.logic.AWTScaleService
-
- cache - Variable in class ome.services.sessions.SessionManagerImpl
-
- CacheFactory - Class in ome.services.sessions.state
-
- CacheFactory() - Constructor for class ome.services.sessions.state.CacheFactory
-
- CacheListener - Class in ome.services.sessions.state
-
Basic CacheEventListener which does nothing.
- CacheListener() - Constructor for class ome.services.sessions.state.CacheListener
-
- calculateBackOff(int) - Method in class ome.services.db.SelfCorrectingDataSource
-
- calculateMessageDigest() - Method in class ome.services.RawPixelsBean
-
- calculateXYWidths(Pixels, int) - Method in class ome.services.ThumbnailCtx
-
Calculates the ratio of the two sides of a Pixel set and returns the
X and Y widths based on the longest side maintaining aspect ratio.
- call(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
-
- call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.Action
-
- call(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- callWithRetries(String, String, boolean) - Method in class ome.services.db.SelfCorrectingDataSource
-
- canAnnotate(IObject) - Method in interface ome.api.local.LocalAdmin
-
Companion to IAdmin.canUpdate(IObject) but not yet remotely
accessible.
- canAnnotate(IObject) - Method in class ome.logic.AdminImpl
-
- cancel() - Method in interface ome.services.procs.Process
-
- cancel() - Method in class ome.services.procs.ProcessSkeleton
-
- cancel(String) - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
-
- cancelJob() - Method in class ome.services.JobBean
-
- canUpdate(IObject) - Method in class ome.logic.AdminImpl
-
- caseSensitive - Variable in class ome.services.search.SearchValues
-
- cd - Variable in class ome.security.basic.BasicSecuritySystem
-
- cd - Variable in class ome.security.basic.EventLogListener
-
- cd - Variable in class ome.security.SecurityFilterHolder
-
- chainedList - Variable in class ome.services.search.SearchAction
-
List of IObject instances which have currently been found.
- chainedSearch(List<IObject>) - Method in class ome.services.search.SearchAction
-
Set the current list of found ids from previous searches, which should be
chained in this search.
- changeDistinguisedName(String, String) - Method in class ome.security.auth.PasswordProviders
-
- changeExpiredCredentials(String, String, String) - Method in class ome.logic.AdminImpl
-
- changeGroup(IObject, String) - Method in class ome.logic.AdminImpl
-
- changeOwner(IObject, String) - Method in class ome.logic.AdminImpl
-
- changePassword(String) - Method in class ome.logic.AdminImpl
-
- changePassword(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Throws by default.
- changePassword(String, String) - Method in class ome.security.auth.JdbcHashedPasswordProvider
-
- changePassword(String, String) - Method in class ome.security.auth.JdbcPasswordProvider
-
- changePassword(String, String, PasswordUtil.METHOD) - Method in class ome.security.auth.JdbcPasswordProvider
-
Actually perform the password change in the database and log the event against the user.
- changePassword(String, String) - Method in interface ome.security.auth.PasswordProvider
-
Attempts to change the password for the given user.
- changePassword(String, String) - Method in class ome.security.auth.PasswordProviders
-
- changePasswordWithOldPassword(String, String) - Method in class ome.logic.AdminImpl
-
- changePermissions(IObject, Permissions) - Method in class ome.logic.AdminImpl
-
the implementation of this method is somewhat tricky in that
Permissions changes must be allowed even when other updates are
not.
- ChangeSecurityContextEvent - Class in ome.services.sessions.events
-
InternalMessage published by the
SessionManager when
setSecurityContext() is called.
- ChangeSecurityContextEvent(Object, String, IObject, IObject) - Constructor for class ome.services.sessions.events.ChangeSecurityContextEvent
-
- changeUserPassword(String, String) - Method in class ome.logic.AdminImpl
-
- changeUserPasswordById(Long, String) - Method in class ome.security.auth.PasswordUtil
-
- changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil
-
- CHANNELID_QUERY - Static variable in class ome.services.delete.DeleteBean
-
- check(IObject, Object) - Method in class ome.security.basic.GroupChmodStrategy
-
Here we used the checks returned from
ExtendedMetadata to iterate
through every non-system table and check that it has no FKs which point
to back to its rows and violate the read permissions which are being
reduced.
- check(IObject, Object) - Method in interface ome.security.ChmodStrategy
-
- check(String) - Method in class ome.services.query.Query
-
- checkAndCollapseGraph() - Method in class ome.formats.OMEROMetadataStore
-
Checks the entire object graph for sections that may be collapsed if
the data is derived from a Plate.
- checkAndRegister() - Method in class ome.services.JobBean
-
- checkDelayedCallContext(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
-
- checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ObjPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
-
Contacts the remote server to verify that the object implements this type.
- checkedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkedCast(ObjectPrx, String, Map<String, String>) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
-
Contacts the remote server to verify that a facet of the object implements this type.
- checkForScriptUpdates() - Method in class ome.services.scripts.ScriptRepoHelper
-
Check for updates to scripts, modifying database accordingly.
- checkImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
-
- checkManagedDetails(IObject, Details) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkManagedDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
-
- checkManagedDetails(IObject, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
-
- checkManagedDetails(IObject, Details) - Method in interface ome.security.SecuritySystem
-
checks that a non-privileged user has not attempted to edit the entity's
security details.
- checkManagedDetails(IObject, Details) - Method in class ome.security.SecuritySystemHolder
-
- checkManagedDetails(IObject, Details) - Method in class ome.security.sharing.SharingSecuritySystem
-
- checkMethod(Object, Method, Principal, boolean) - Method in class ome.security.basic.BasicMethodSecurity
-
- checkMethod(Object, Method, Principal, boolean) - Method in interface ome.security.MethodSecurity
-
Throws a SecurityViolation exception if the given
Principal does not have the proper permissions to execute the
given method.
- checkParameters() - Method in class ome.services.query.Query
-
check the
Parameters instance against the
Definitions
instance for this Query.
- checkPassword(String, String, boolean) - Method in interface ome.api.local.LocalAdmin
-
Checks password for given user.
- checkPassword(String, String, boolean) - Method in class ome.logic.AdminImpl
-
If ldap plugin turned, creates Ldap accounts and authentication by LDAP
available.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
If this was constructed with the ignoreUnknown argument set to
true, returns null, since the base class knows no users.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.FilePasswordProvider
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.JdbcPasswordProvider
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.LdapPasswordProvider
-
- checkPassword(String, String, boolean) - Method in interface ome.security.auth.PasswordProvider
-
Authenticates the give user given the password token.
- checkPassword(String, String, boolean) - Method in class ome.security.auth.PasswordProviders
-
- checkPassword(String, String, boolean) - Method in class ome.security.auth.providers.LdapPasswordProvider431
-
- checkProperty(String, String) - Method in interface ome.api.local.LocalQuery
-
Checks if a property is defined on a mapped Hibernate type.
- checkProperty(String, String) - Method in class ome.logic.PojosImpl
-
- checkProperty(String, String) - Method in class ome.logic.QueryImpl
-
- checkReady(String) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkRestriction(String, IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
- checkRestriction(IObject) - Method in class ome.security.policy.BasePolicy
-
- checkRestriction(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- checkRestriction(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- checkRestriction(IObject) - Method in interface ome.security.policy.Policy
-
- checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService
-
- checkRestriction(String, IObject) - Method in interface ome.security.SecuritySystem
-
Checks whether or not a
Policy instance of matching
name has been registered, considers itself active,
and
considers the passed context object to be restricted.
- checkRestriction(String, IObject) - Method in class ome.security.SecuritySystemHolder
-
- checkRestriction(String, IObject) - Method in class ome.security.sharing.SharingSecuritySystem
-
- checkState() - Method in class ome.services.procs.ProcessSkeleton
-
- checkType(String) - Method in interface ome.api.local.LocalQuery
-
Checks if a type has been mapped in Hibernate.
- checkType(String) - Method in class ome.logic.PojosImpl
-
- checkType(String) - Method in class ome.logic.QueryImpl
-
- checkWriteOperationAllowed(Session) - Method in class ome.tools.spring.ManualFlushHibernateTemplate
-
- chmod - Variable in class ome.logic.AdminImpl
-
- chmod(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
-
- chmod(IObject, String) - Method in interface ome.security.ChmodStrategy
-
Change the permissions for the given object.
- ChmodStrategy - Interface in ome.security
-
Strategy for changing the permissions of objects in the database
as well as verifying that the permissions for the modified objects
are sensible after the change.
- choose() - Method in class ome.security.CompositeACLVoter
-
- choose() - Method in class ome.security.SecurityFilterHolder
-
- choose() - Method in class ome.security.SecuritySystemHolder
-
- classes - Variable in class ome.services.fulltext.FullTextBridge
-
Deprecated.
- ClassQuerySource - Class in ome.services.query
-
creates a query based on the id string by interpreting it as a Class.
- ClassQuerySource() - Constructor for class ome.services.query.ClassQuerySource
-
- clean() - Method in class ome.services.RawFileBean
-
- clean() - Method in class ome.services.RawPixelsBean
-
- cleanThread() - Method in class ome.tools.hibernate.SessionHandler
-
- cleanup() - Method in class ome.services.util.ServiceHandler
-
- clear() - Method in interface ome.api.local.LocalQuery
-
- clear() - Method in class ome.logic.QueryImpl
-
- clearDisabled() - Method in class ome.security.basic.CurrentDetails
-
- clearLogs() - Method in class ome.security.basic.BasicSecuritySystem
-
- clearLogs() - Method in class ome.security.basic.CurrentDetails
-
- clearQueries() - Method in class ome.services.SearchBean
-
- clearToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
-
- clone() - Method in class ome.services.sessions.state.CacheListener
-
- clone() - Method in class ome.services.sharing.data.Obj
-
- clone() - Method in class ome.services.sharing.data.ShareData
-
- clone() - Method in class ome.services.sharing.data.ShareItem
-
- close(Signal, Integer) - Static method in class ome.services.fulltext.Main
-
- close() - Method in class ome.services.JobBean
-
- close() - Method in class ome.services.messages.ParserOpenFileMessage
-
Used to close the passed in resource.
- close() - Method in class ome.services.messages.RegisterServiceCleanupMessage
-
Used to close the passed in resource.
- close() - Method in class ome.services.RawFileBean
-
- close() - Method in class ome.services.RawFileBeanReadOnly
-
- close() - Method in class ome.services.RawPixelsBean
-
- close() - Method in class ome.services.RawPixelsBeanReadOnly
-
- close() - Method in class ome.services.RenderingBean
-
- close() - Method in class ome.services.SearchBean
-
- close() - Method in interface ome.services.sessions.SessionCallback
-
- close(String) - Method in interface ome.services.sessions.SessionManager
-
If reference count for the session is less than 1, close the session.
- close(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- close() - Method in class ome.services.sharing.ShareStore
-
- close() - Method in class ome.services.ThumbnailBean
-
- closeAll() - Method in interface ome.services.sessions.SessionManager
-
Close all sessions with checking for the necessary reference counts.
- closeAll() - Method in class ome.services.sessions.SessionManagerImpl
-
- CloseOnNoSessionContext() - Constructor for class ome.security.basic.BasicSecurityWiring.CloseOnNoSessionContext
-
- closeParsedFiles() - Method in class ome.services.fulltext.ParserSession
-
Deprecated.
- closeSession(Session) - Method in class ome.services.sessions.SessionBean
-
- closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderInDb
-
Assumes that the given manager is no longer available and so will not
attempt to call cache.removeSession() since that requires the session to
be in memory.
- closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderInMemory
-
Assumes that the given manager is no longer available and will clean up
all in-memory sessions.
- closeSessionsForManager(String) - Method in class ome.security.basic.NodeProviderWrapper
-
- closeSessionsForManager(String) - Method in interface ome.security.NodeProvider
-
Closes all sessions for a given manager node.
- closeShare(long) - Method in class ome.services.sharing.ShareBean
-
- collect(UnloadedCollector, Image) - Method in class ome.services.delete.DeleteBean
-
Walks the Image graph collecting unloaded instances of all
entities for later delete.
- CollectionCountQueryDefinition - Class in ome.services.query
-
counts the number of members in a collection.
- CollectionCountQueryDefinition(Parameters) - Constructor for class ome.services.query.CollectionCountQueryDefinition
-
- CollectionQueryParameterDef - Class in ome.services.query
-
extension of
QueryParameterDef which restricts the
type to a
Collection, and specifies the element types of that
Collection.
- CollectionQueryParameterDef(String, boolean, Class) - Constructor for class ome.services.query.CollectionQueryParameterDef
-
- COMBINED - Static variable in class ome.services.fulltext.BridgeHelper
-
Deprecated.
Name of the Field which contains the union of all fields.
- comparePasswords(String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Compares the password provided by the user (unhashed) against the given
trusted password.
- comparePasswords(Long, String, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
Compares the password provided by the user (unhashed) against the given
trusted password.
- comparePasswords(Long, String, String, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- comparePasswords(String, String) - Method in interface ome.security.auth.PasswordUtility
-
- Complement - Class in ome.services.search
-
Complement
SearchAction which combines two other search actions into
one logical unit, e.g.
- Complement(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Complement
-
- completeFast - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- completeSlow - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- CompositeACLVoter - Class in ome.security
-
- CompositeACLVoter(CurrentDetails, BasicACLVoter, SharingACLVoter) - Constructor for class ome.security.CompositeACLVoter
-
- CompressImpl - Class in ome.logic
-
- CompressImpl() - Constructor for class ome.logic.CompressImpl
-
- compressToStream(BufferedImage, OutputStream) - Method in interface ome.api.local.LocalCompress
-
Compresses a buffered image to an output stream.
- compressToStream(BufferedImage, OutputStream) - Method in class ome.logic.CompressImpl
-
- configGroup(EventContext, List<Long>) - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- ConfigImpl - Class in ome.logic
-
implementation of the IConfig service interface.
- ConfigImpl() - Constructor for class ome.logic.ConfigImpl
-
- ConfigurablePasswordProvider - Class in ome.security.auth
-
Base class for most
PasswordProvider implementations, providing
configuration for default behaviors.
- ConfigurablePasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- ConfigurablePasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.ConfigurablePasswordProvider
-
- configure(List<HardWiredInterceptor>, OmeroContext) - Static method in class ome.logic.HardWiredInterceptor
-
- configure(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
-
- configure(Type, Properties, Dialect) - Method in class ome.tools.hibernate.MySeqGenerator
-
If the parameters do not contain a SequenceGenerator.SEQUENCE
name, we assign one based on the table name.
- containedExperimenters(long) - Method in class ome.logic.AdminImpl
-
- containedGroups(long) - Method in class ome.logic.AdminImpl
-
- contains(Object) - Method in interface ome.api.local.LocalQuery
-
Tests if an object is currently contained in the session.
- contains(Object) - Method in class ome.logic.QueryImpl
-
- contains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
-
- containsKey(Object) - Method in class ome.services.query.Definitions
-
- context - Variable in class ome.logic.AdminImpl
-
- context - Variable in class ome.services.fulltext.FileParser
-
- context - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- context - Variable in class ome.services.messages.ContextMessage
-
- context - Variable in class ome.services.sessions.SessionManagerImpl
-
- context - Variable in class ome.services.util.Executor.Impl
-
- ContextMessage - Class in ome.services.messages
-
- ContextMessage(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage
-
- ContextMessage.Pop - Class in ome.services.messages
-
Published when an internal service is finished with
the context previously signaled through publishing
a
ContextMessage.Push.
- ContextMessage.Push - Class in ome.services.messages
-
Published when an internal service would like to
modify the current EventContext.
- copy(SearchValues) - Method in class ome.services.search.SearchValues
-
- copy(Parameters) - Method in class ome.services.search.SearchValues
-
Copies all known values from Parameters
- copy(Session) - Method in class ome.services.sessions.SessionManagerImpl
-
- copy(Map) - Static method in class ome.tools.hibernate.HibernateUtils
-
- copy(Collection) - Static method in class ome.tools.hibernate.HibernateUtils
-
- copyAndResizeImage(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
-
- copyAndResizePixels(long, Integer, Integer, Integer, Integer, List<Integer>, String, boolean) - Method in class ome.logic.PixelsImpl
-
- copyClassListToArray(List<Class>) - Static method in class ome.services.search.SearchValues
-
- copyDetails(Details) - Static method in class ome.services.search.SearchValues
-
- copyGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- copyList(List<T>) - Static method in class ome.services.search.SearchValues
-
- copyOfValues() - Method in class ome.services.search.SearchAction
-
- copyTimestamp(Timestamp) - Static method in class ome.services.search.SearchValues
-
- copyToken(IObject, IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
- copyToken(IObject, IObject) - Method in class ome.security.basic.TokenHolder
-
copy a token from one IObject to another.
- copyUser(Experimenter) - Method in class ome.security.auth.SimpleRoleProvider
-
- copyValues(EntityPersister, Object, Object, SessionImplementor, Map) - Method in class ome.security.basic.MergeEventListener
-
- copyValues(EntityPersister, Object, Object, SessionImplementor, Map, ForeignKeyDirection) - Method in class ome.security.basic.MergeEventListener
-
- count() - Method in class ome.services.messages.DeleteLogMessage
-
- count() - Method in interface ome.services.sessions.SessionContext
-
- Count(String) - Constructor for class ome.services.sessions.SessionContext.Count
-
- count() - Method in class ome.services.sessions.SessionContextImpl
-
- count - Variable in class ome.services.sessions.stats.LongCounter
-
- countAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
-
- CounterFactory - Class in ome.services.sessions.stats
-
Factory for creating counter objects.
- CounterFactory() - Constructor for class ome.services.sessions.stats.CounterFactory
-
- countInDb() - Method in class ome.services.scripts.ScriptRepoHelper
-
- countInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
-
- countLocks(Session, Long, String[][], String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper
-
- countSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
-
- cpf - Variable in class ome.logic.AdminImpl
-
- createAndPrepareMissingRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Resets a given set of Pixels rendering settings to the default
effectively creating any which do not exist.
- createBufferedImage() - Method in class ome.services.SVGRasterizer
-
Returns the image that represents the SVG document.
- createCache(CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
-
- createCache(String, boolean, int) - Method in class ome.services.sessions.state.SessionCache
-
- createDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
-
- createDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
-
- createDetails() - Method in class ome.security.basic.CurrentDetails
-
Creates a Details object for the current security context.
- createdOrModified(Class, Criteria) - Method in class ome.services.search.SearchAction
-
- createdOrModified(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- createdStart - Variable in class ome.services.search.SearchValues
-
- createdStop - Variable in class ome.services.search.SearchValues
-
- createEnumeration(T) - Method in class ome.logic.TypesImpl
-
- createException(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
-
- createExperimenter(Experimenter, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
-
- createExperimenterWithPassword(Experimenter, String, ExperimenterGroup, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- createFromRequest(SessionManager.CreationRequest) - Method in interface ome.services.sessions.SessionManager
-
- createFromRequest(SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
-
- createFullTextThread(EventLogLoader) - Static method in class ome.services.fulltext.Main
-
- createFullTextThread(EventLogLoader, boolean) - Static method in class ome.services.fulltext.Main
-
- createGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
-
- createGroup(ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean, boolean) - Method in interface ome.security.auth.RoleProvider
-
- createGroup(String, Permissions, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- createGroup(String, Permissions, boolean, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- createGroup(ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- createImage(int, int, int, int, List<Integer>, PixelsType, String, String) - Method in class ome.logic.PixelsImpl
-
- createImage(int, int) - Method in class ome.services.SVGRasterizer.Rasterizer
-
- createInstance() - Method in class ome.security.basic.EventListenersFactoryBean
-
First, adds all default listeners.
- createInstance() - Method in class ome.services.delete.Deletion.Builder
-
- createJPEG(OutputStream) - Method in class ome.services.SVGRasterizer
-
Returns the image that represents the SVG document as a JPEG.
- createNewRenderingDef(Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- createRestrictedSystemUser(Experimenter, List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
-
- createRestrictedSystemUserWithPassword(Experimenter, List<AdminPrivilege>, String) - Method in class ome.logic.AdminImpl
-
- createRoot() - Method in class ome.formats.OMEROMetadataStore
-
- createSafeInputStream(Communicator, byte[]) - Static method in class ome.services.util.IceUtil
-
Creates an InputStream with the appropriate encoding.
- createSafeOutputStream(Communicator) - Static method in class ome.services.util.IceUtil
-
Creates an OutputStream with the appropriate encoding.
- createSession(Principal, String) - Method in class ome.services.sessions.SessionBean
-
- createSessionContext(List<?>, SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
-
- CreateSessionMessage - Class in ome.services.messages
-
Published after a successful session creation.
- CreateSessionMessage(Object, String) - Constructor for class ome.services.messages.CreateSessionMessage
-
- createSessionWithTimeout(Principal, long) - Method in class ome.services.sessions.SessionBean
-
- createSessionWithTimeouts(Principal, long, long) - Method in class ome.services.sessions.SessionBean
-
- createShare(Principal, boolean, long, String, String, long) - Method in interface ome.services.sessions.SessionManager
-
- createShare(Principal, boolean, long, String, String, long) - Method in class ome.services.sessions.SessionManagerImpl
-
- createShare(String, Timestamp, List<T>, List<Experimenter>, List<String>, boolean) - Method in class ome.services.sharing.ShareBean
-
- createStats() - Method in class ome.services.sessions.stats.CounterFactory
-
- createSystemUser(Experimenter) - Method in class ome.logic.AdminImpl
-
- createThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- createThumbnailMetadata(Pixels, Dimension) - Method in class ome.services.ThumbnailCtx
-
Creates metadata for a thumbnail of a given set of pixels set and X-Y
dimensions.
- createThumbnails() - Method in class ome.services.ThumbnailBean
-
- createThumbnailsByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- createUser(Experimenter, String) - Method in class ome.logic.AdminImpl
-
- createUser(String) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter based on the supplied LDAP username.
- createUser(String, String) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter based on the supplied LDAP username.
- createUser(String, String, boolean) - Method in class ome.logic.LdapImpl
-
Creates an Experimenter based on the supplied LDAP username.
- createUserFromLdap(String, String) - Method in class ome.logic.LdapImpl
-
Deprecated.
- createUserSession(long, long, String) - Method in class ome.services.sessions.SessionBean
-
- createWithAgent(Principal, String, String, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String, String) - Method in interface ome.services.sessions.SessionManager
-
- createWithAgent(Principal, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- createWithAgent(Principal, String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- CreationRequest() - Constructor for class ome.services.sessions.SessionManager.CreationRequest
-
- credentials - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- CRITICAL_USAGE - Static variable in class ome.logic.RepositoryInfoImpl
-
- ctx - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
- ctx - Variable in class ome.security.basic.BasicSecuritySystem
-
- ctx - Variable in class ome.services.delete.Deletion.Builder
-
- ctx - Variable in class ome.services.sharing.BlobShareStore
-
- current - Variable in class ome.security.SecurityFilterHolder
-
- current - Variable in class ome.security.SecuritySystemHolder
-
- current - Variable in class ome.tools.hibernate.ProxyCleanupFilter
-
- current_group - Static variable in class ome.security.basic.OneGroupSecurityFilter
-
- current_user - Static variable in interface ome.security.SecurityFilter
-
- CurrentDetails - Class in ome.security.basic
-
Stores information related to the security context of the current thread.
- CurrentDetails() - Constructor for class ome.security.basic.CurrentDetails
-
Default constructor.
- CurrentDetails(SessionCache) - Constructor for class ome.security.basic.CurrentDetails
-
- CurrentDetails(SessionCache, Roles, SystemTypes, LightAdminPrivileges, Set<String>, Set<String>) - Constructor for class ome.security.basic.CurrentDetails
-
- currentMetadata() - Method in class ome.services.SearchBean
-
- currentMetadataList() - Method in class ome.services.SearchBean
-
- CurrentSessionContext - Class in ome.tools.hibernate
-
Implementation of Hibernate's current_session_context_class extension point.
- CurrentSessionContext(SessionFactoryImplementor) - Constructor for class ome.tools.hibernate.CurrentSessionContext
-
- CurrentSessionStats - Class in ome.services.sessions.stats
-
Wrapper which delegates to a
SessionStats instance acquired during
construction.
- CurrentSessionStats(CurrentDetails, SessionManager) - Constructor for class ome.services.sessions.stats.CurrentSessionStats
-
- currentUser - Variable in class ome.security.basic.BasicACLVoter
-
- elementType - Variable in class ome.services.query.CollectionQueryParameterDef
-
- em - Variable in class ome.services.delete.Deletion.Builder
-
- EMPTY - Static variable in class ome.services.fulltext.FileParser
-
Iterable which returns an empty Iterator.
- emptyCleanups() - Method in class ome.security.basic.CurrentDetails
-
Returns the current cleanups and resets the Set.
- enable(Session, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter
-
Since we assume that the group is "-1" for this method, we have to pass
in lists of all groups as we did before group permissions (~4.2).
- enable(String...) - Method in class ome.security.basic.BasicSecuritySystem
-
- enable(Session, EventContext) - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
-
Deprecated.
- enable(Session, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
-
- enable(Session, EventContext) - Method in class ome.security.basic.SharingSecurityFilter
-
- enable(Session, EventContext) - Method in interface ome.security.SecurityFilter
-
Enables this filter with the settings from this filter.
- enable(Session, EventContext) - Method in class ome.security.SecurityFilterHolder
-
- enable(String...) - Method in interface ome.security.SecuritySystem
-
enables components of the backend for the current Thread.
- enable(String...) - Method in class ome.security.SecuritySystemHolder
-
- enable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
-
- enableBaseFilters(Session, int, Long) - Method in class ome.security.basic.AbstractSecurityFilter
-
- enabled - Variable in class ome.services.sharing.data.ShareData
-
- enableFilters(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
-
- enableFilters(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
-
- enableFilters(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
-
- enableFilters(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
-
- enableFilters(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
-
- enableFilters(Session) - Method in class ome.services.query.Query
-
does nothing by default, but can be overridden by subclasses to enable
particular filters.
- enableQueryCache() - Method in class ome.services.query.Query
-
Enable the Hibernate level 2 cache for this query.
- enableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem
-
enables the read filter such that graph queries will have non-visible
entities silently removed from the return value.
- encodePassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- encodePassword(Long, String, boolean, PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- encodePassword(String) - Method in interface ome.security.auth.PasswordUtility
-
- encodeSaltedPassword(Long, String) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- ensure(Class<E>, Collection<String>) - Method in class ome.services.util.EnsureEnum
-
Ensure that the given enumerations exist.
- EnsureEnum - Class in ome.services.util
-
Utility bean for ensuring that enumeration values do exist in the database.
- EnsureEnum(Executor, String, Roles, ReadOnlyStatus) - Constructor for class ome.services.util.EnsureEnum
-
Construct a new enumeration ensurer.
- entityIds - Variable in class ome.services.messages.EventLogMessage
-
- entityIsDetached(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
-
- entityIsTransient(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
-
- entityToStringLong(E) - Method in class ome.services.query.HierarchyNavigatorWrap
-
- entityType - Variable in class ome.services.messages.EventLogMessage
-
- ENUM(E[]) - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
-
- environment(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- EPSILON - Static variable in class ome.logic.RenderingSettingsImpl
-
The value used to compare double and float.
- equals(Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- error(SqlAction.DeleteLog, Throwable) - Method in class ome.services.messages.DeleteLogMessage
-
- errorIfInvalid(QueryParameter) - Method in class ome.services.query.CollectionQueryParameterDef
-
- errorIfInvalid(QueryParameter) - Method in class ome.services.query.QueryParameterDef
-
- errorIfInvalidState() - Method in class ome.services.JobBean
-
- errorIfInvalidState() - Method in class ome.services.RenderingBean
-
- errorIfInvalidState() - Method in class ome.services.ThumbnailBean
-
- errorIfNullPixels() - Method in class ome.services.RenderingBean
-
Throws an ApiUsageException if the pixels are not set.
- errorIfNullPixels() - Method in class ome.services.ThumbnailBean
-
- errorIfNullPixelsAndRenderingDef() - Method in class ome.services.ThumbnailBean
-
- errorIfNullRenderer() - Method in class ome.services.RenderingBean
-
Reloads the rendering engine if null and has been
made passive or throws an ApiUsageException if the rendering
engine is not set.
- errorIfNullRenderingDef() - Method in class ome.services.RenderingBean
-
Throws an ApiUsageException if the rendering settings are not
set.
- errorIfNullRenderingDef() - Method in class ome.services.ThumbnailBean
-
- evaluateLinkages(IObject) - Method in class ome.security.basic.OmeroInterceptor
-
Checks the details of the objects which the given object links to in
order to guarantee that linkages are valid.
- EventBacklog - Class in ome.services.eventlogs
-
Thread-safe java.util-like Container for storing EventLog instances
for later parsing.
- EventBacklog() - Constructor for class ome.services.eventlogs.EventBacklog
-
- EventHandler - Class in ome.security.basic
-
method interceptor responsible for login and creation of Events.
- EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource) - Constructor for class ome.security.basic.EventHandler
-
Deprecated.
- EventHandler(SqlAction, BasicSecuritySystem, SessionFactory, TransactionAttributeSource, ReadOnlyStatus) - Constructor for class ome.security.basic.EventHandler
-
- EventListenersFactoryBean - Class in ome.security.basic
-
configuring all the possible event listeners within
XML can be cumbersome.
- EventListenersFactoryBean(CurrentDetails, TokenHolder, ACLVoter, OmeroInterceptor) - Constructor for class ome.security.basic.EventListenersFactoryBean
-
- EventLogFailure - Class in ome.services.eventlogs
-
Signifies that the processing of a EventLog has failed.
- EventLogFailure(EventLogLoader, EventLog, Throwable) - Constructor for class ome.services.eventlogs.EventLogFailure
-
- EventLogListener - Class in ome.security.basic
-
responsible for responding to all Hibernate Events.
- EventLogListener(CurrentDetails) - Constructor for class ome.security.basic.EventLogListener
-
main constructor.
- EventLogLoader - Class in ome.services.eventlogs
-
Data access object for the
FullTextIndexer which provides an
Iterator interface for
EventLog instances to be properly
indexed.
- EventLogLoader() - Constructor for class ome.services.eventlogs.EventLogLoader
-
- EventLogMessage - Class in ome.services.messages
-
Published only when an event log should be saved at the end of a transaction.
- EventLogMessage(Object, String, Class<? extends IObject>, List<Long>) - Constructor for class ome.services.messages.EventLogMessage
-
- EventLogQueue - Class in ome.services.eventlogs
-
PersistentEventLogLoader implementation which loads many rows at the
same time, culling out duplicates in order to speed up indexing.
- EventLogQueue() - Constructor for class ome.services.eventlogs.EventLogQueue
-
- EventLogQueue(Metrics, int, String[], String[]) - Constructor for class ome.services.eventlogs.EventLogQueue
-
- EventLogsMessage - Class in ome.services.messages
-
Published with the final collection of EventLog instances which
will be saved.
- EventLogsMessage(Object, Multimap<String, EventLog>) - Constructor for class ome.services.messages.EventLogsMessage
-
- EventMethodInterceptor - Class in ome.tools.hibernate
-
filter which can be added to any event type in order to catch execution.
- EventMethodInterceptor() - Constructor for class ome.tools.hibernate.EventMethodInterceptor
-
- EventMethodInterceptor(EventMethodInterceptor.Action) - Constructor for class ome.tools.hibernate.EventMethodInterceptor
-
- EventMethodInterceptor.Action - Class in ome.tools.hibernate
-
- EventMethodInterceptor.DisableAction - Class in ome.tools.hibernate
-
- eventProvider - Variable in class ome.security.basic.BasicSecuritySystem
-
- EventProvider - Interface in ome.security
-
Provider for Event objects which is responsible for persisting and
populating such entities.
- EventProviderInDb - Class in ome.security.basic
-
Provider for Event objects which is responsible for persisting and
populating such entities using Hibernate in accordance with the currently
available IUpdate implementation.
- EventProviderInDb(ServiceFactory) - Constructor for class ome.security.basic.EventProviderInDb
-
- EventProviderInMemory - Class in ome.security.basic
-
Provider for Event objects which is responsible for persisting and
populating such entities in-memory.
- EventProviderInMemory() - Constructor for class ome.security.basic.EventProviderInMemory
-
- EventProviderWrapper<P extends EventProvider & ReadOnlyStatus.IsAware> - Class in ome.security.basic
-
An event provider that offers a unified view of multiple underlying event providers.
- EventProviderWrapper(ReadOnlyStatus, List<P>) - Constructor for class ome.security.basic.EventProviderWrapper
-
Construct a new event provider.
- evict(Object) - Method in interface ome.api.local.LocalQuery
-
Removes an object graph from the session.
- evict(Object) - Method in class ome.logic.QueryImpl
-
- excludes - Variable in class ome.services.eventlogs.EventLogLoader
-
Array of class types which will get excluded from indexing.
- execute(HibernateCallback) - Method in interface ome.api.local.LocalQuery
-
Executes a HibernateCallback
- execute(Query<T>) - Method in interface ome.api.local.LocalQuery
-
Executes a locally defined Query.
- execute(HibernateCallback) - Method in class ome.logic.QueryImpl
-
- execute(Query<T>) - Method in class ome.logic.QueryImpl
-
- execute() - Method in interface ome.services.graphs.GraphTraversal.PlanExecutor
-
Perform the planned action.
- execute(Principal, Executor.Work<T>) - Method in interface ome.services.util.Executor
-
- execute(Map<String, String>, Principal, Executor.Work<T>) - Method in interface ome.services.util.Executor
-
- execute(Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl
-
- execute(Map<String, String>, Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl
-
- executeCloseSession(String) - Method in interface ome.services.sessions.SessionProvider
-
Loads a session directly, sets its "closed" value and immediately
saves it.
- executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderInDb
-
- executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderInMemory
-
- executeCloseSession(String) - Method in class ome.services.sessions.SessionProviderWrapper
-
- executeInternalSession(String, Session) - Method in interface ome.services.sessions.SessionProvider
-
- executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderInDb
-
- executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderInMemory
-
- executeInternalSession(String, Session) - Method in class ome.services.sessions.SessionProviderWrapper
-
- executeNextSessionId() - Method in interface ome.services.sessions.SessionProvider
-
Added as an attempt to cure ticket:1176
- executeNextSessionId() - Method in class ome.services.sessions.SessionProviderInDb
-
- executeNextSessionId() - Method in class ome.services.sessions.SessionProviderInMemory
-
- executeNextSessionId() - Method in class ome.services.sessions.SessionProviderWrapper
-
- executePasswordCheck(String, String) - Method in interface ome.services.sessions.SessionManager
-
Executes a password check using the
Executor framework.
- executePasswordCheck(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- executeSql(Executor.SqlWork) - Method in interface ome.services.util.Executor
-
- executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl
-
- executeUpdate(ServiceFactory, Session, String, long, Long) - Method in interface ome.services.sessions.SessionProvider
-
- executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderInDb
-
- executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderInMemory
-
- executeUpdate(ServiceFactory, Session, String, long, Long) - Method in class ome.services.sessions.SessionProviderWrapper
-
- ExecutionThread - Class in ome.services.util
-
Thread which can be started and will appropriately acquire a session, then
use the
Executor to complete its work.
- ExecutionThread(SessionManager, Executor, Executor.Work, Principal) - Constructor for class ome.services.util.ExecutionThread
-
Main constructor.
- executor - Variable in class ome.logic.UpdateImpl
-
- executor - Variable in class ome.services.sessions.SessionManagerImpl
-
- executor - Variable in class ome.services.sharing.ShareBean
-
- executor - Variable in class ome.services.util.ExecutionThread
-
- Executor - Interface in ome.services.util
-
Simple execution/work interface which can be used for internal tasks
which need to have a full working implementation.
- Executor.Descriptive - Class in ome.services.util
-
- Executor.Impl - Class in ome.services.util
-
- Executor.LoggedWork<X> - Interface in ome.services.util
-
- Executor.Priority - Enum in ome.services.util
-
- Executor.SimpleSqlWork - Class in ome.services.util
-
- Executor.SimpleWork<T> - Class in ome.services.util
-
- Executor.SqlWork - Interface in ome.services.util
-
Work SPI to perform actions related to
stateless
sessions.
- Executor.StatefulWork - Interface in ome.services.util
-
In the case of a stateful work order, the bean itself needs to be
associated with the sessionHandler and thread rather than the word
instance itself.
- Executor.Work<X> - Interface in ome.services.util
-
Work SPI to perform actions within the server as if they were fully
wrapped in our service logic.
- exists() - Method in class ome.services.RawFileBean
-
- expirationAsLong(long, Timestamp) - Static method in class ome.services.sharing.ShareBean
-
Convert a expiration into a long which can be set on
Session.setTimeToLive(Long).
- ExtendedMetadata - Interface in ome.tools.hibernate
-
- ExtendedMetadata.Immutables - Class in ome.tools.hibernate
-
- ExtendedMetadata.Impl - Class in ome.tools.hibernate
-
Sole implementation of ExtendedMetadata.
- ExtendedMetadata.Locks - Class in ome.tools.hibernate
-
inner class which wraps the information (index number, path, etc) related to
what fields a particular object can lock.
- ExtendedMetadata.Relationship - Class in ome.tools.hibernate
-
- generateRandomPasswd() - Method in class ome.security.auth.PasswordUtil
-
- get(Class, long) - Method in class ome.logic.QueryImpl
-
- get(String, DirContextAdapter) - Method in class ome.security.auth.GroupContextMapper
-
- get(String, DirContextAdapter) - Method in class ome.security.auth.PersonContextMapper
-
- get(Session, Class, long) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- get(Object) - Method in class ome.services.query.Definitions
-
- get(String) - Method in class ome.services.query.Query
-
get the QueryParameter for this name argument.
- get() - Method in class ome.services.sessions.SessionContext.Count
-
Return the current number of references which this session is aware of.
- get(long) - Method in class ome.services.sharing.BlobShareStore
-
- get(long) - Method in class ome.services.sharing.ShareStore
-
- get(Future<T>) - Method in interface ome.services.util.Executor
-
Helper method to perform Future.get() and properly unwrap the
exceptions.
- get(Future<T>) - Method in class ome.services.util.Executor.Impl
-
- getAction() - Method in class ome.services.mail.ObjectMailSender
-
- getActiveConnections(long) - Method in class ome.services.sharing.ShareBean
-
- getAdminPrivileges(Experimenter) - Method in class ome.logic.AdminImpl
-
- getAdminPrivileges() - Method in class ome.security.basic.BasicEventContext
-
- getAdminPrivileges() - Method in class ome.security.basic.CurrentDetails
-
- getAdminsWithPrivileges(List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
-
- getAll(String) - Method in class ome.security.auth.AttributeSet
-
- getAllClasses() - Method in class ome.services.graphs.GraphPathBean
-
Get all the classes mapped by Hibernate.
- getAllEnumerations(Class<T>) - Method in class ome.logic.PixelsImpl
-
Deprecated.
- getAllGuests(long) - Method in class ome.services.sharing.ShareBean
-
- getAllMembers(long) - Method in class ome.services.sharing.ShareBean
-
- getAllPrivileges() - Static method in class ome.security.basic.LightAdminPrivileges
-
- getAllSystemUsers(boolean) - Method in class ome.services.mail.MailSender
-
- getAllUsers(long) - Method in class ome.services.sharing.ShareBean
-
- getAndLogException(Throwable) - Method in class ome.services.util.ServiceHandler
-
- getAnnotatableTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns all the classes which implement IAnnotated
- getAnnotatableTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getAnnotationTypes() - Method in class ome.logic.TypesImpl
-
- getAnnotationTypes() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns all the classes which subclass Annotation
- getAnnotationTypes() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getArray() - Method in class ome.tools.hibernate.SqlArray
-
- getArray(long, int) - Method in class ome.tools.hibernate.SqlArray
-
- getArray(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getArray(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getAttribute(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- getAttributeSet(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- getAuthority() - Method in class ome.services.db.DatabaseIdentity
-
- getAvailableFamilies() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getAvailableModels() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getBaseType() - Method in class ome.tools.hibernate.SqlArray
-
- getBaseTypeName() - Method in class ome.tools.hibernate.SqlArray
-
- getBatchSize() - Method in class ome.services.eventlogs.EventLogLoader
-
- getBatchSize() - Method in class ome.services.SearchBean
-
- getBeanHelper() - Method in class ome.logic.AbstractLevel1Service
-
- getBeanHelper() - Method in class ome.logic.AbstractLevel2Service
-
- getBeanHelper() - Method in class ome.services.AbstractStatefulBean
-
- getBitDepth(PixelsType) - Method in class ome.logic.PixelsImpl
-
- getBoost() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- getBytesFailed() - Method in class ome.services.delete.files.AbstractFileDeletions
-
- getByteWidth() - Method in class ome.services.RawPixelsBean
-
- getCallbackObject(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getCallContext() - Method in class ome.security.basic.BasicEventContext
-
- getChannelCurveCoefficient(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getChannelFamily(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getChannelLookupTable(int) - Method in class ome.services.RenderingBean
-
- getChannelNoiseReduction(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getChannelStats(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getChannelWindowEnd(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getChannelWindowStart(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getCheckDone() - Method in class ome.services.util.DBEnumCheck
-
- getCheckDone() - Method in class ome.services.util.DBMappedEnumCheck
-
- getChecks(IObject, String) - Method in class ome.security.basic.GroupChmodStrategy
-
- getChecks(IObject, String) - Method in interface ome.security.ChmodStrategy
-
Return all the checks necessary to validate the
given object if it were to have its permissions.
- getChildTransformer(Class) - Static method in class ome.services.query.Hierarchy
-
- getClasses() - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getClasses() - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getClassForSimpleName(String) - Method in class ome.services.graphs.GraphPathBean
-
- getCleanInstance() - Method in class ome.services.graphs.GraphPolicy
-
Create a clone of this graph policy that has fresh state.
- getClientConfigDefaults() - Method in class ome.logic.ConfigImpl
-
- getClientConfigValues() - Method in class ome.logic.ConfigImpl
-
- getCodomainMapContext(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getCol(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getCollectionCount(String, String, Set, Parameters) - Method in class ome.logic.PojosImpl
-
- getCommentCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
-
- getComments(long) - Method in class ome.services.sharing.ShareBean
-
- getCompressionLevel() - Method in interface ome.api.local.LocalCompress
-
Returns the current compression level for the service.
- getCompressionLevel() - Method in class ome.logic.CompressImpl
-
- getCompressionLevel() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getConfigDefaults() - Method in class ome.logic.ConfigImpl
-
- getConfigNameForPrivilege(AdminPrivilege) - Method in class ome.security.basic.LightAdminPrivileges
-
- getConfigValue(String) - Method in class ome.logic.ConfigImpl
-
see IConfig.getConfigValue(String)
- getConfigValues(String) - Method in class ome.logic.ConfigImpl
-
- getConnection() - Method in class ome.services.db.SelfCorrectingDataSource
-
- getConnection(String, String) - Method in class ome.services.db.SelfCorrectingDataSource
-
- getContainerTypes() - Method in class ome.logic.TypesImpl
-
- getContentMap(long) - Method in class ome.services.sharing.ShareBean
-
- getContents(long) - Method in class ome.services.sharing.ShareBean
-
- getContentSize(long) - Method in class ome.services.sharing.ShareBean
-
- getContentSubList(long, int, int) - Method in class ome.services.sharing.ShareBean
-
- getContext() - Method in class ome.security.basic.CurrentDetails
-
- getContext() - Method in interface ome.services.util.Executor
-
Provides access to the context for Work-API consumers who need to publish
events, etc.
- getContext() - Method in class ome.services.util.Executor.Impl
-
- getControls() - Method in class ome.security.auth.GroupContextMapper
-
- getControls() - Method in class ome.security.auth.PersonContextMapper
-
- getCountQuery(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Returns the query for obtaining the number of collection items to a
particular instance.
- getCountQuery(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Returns the query for obtaining the number of collection items to a
particular instance.
- getCurrentAdminPrivileges() - Method in class ome.logic.AdminImpl
-
- getCurrentAdminPrivileges() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
-
- getCurrentEventContext() - Method in class ome.services.AbstractStatefulBean
-
- getCurrentEventContext() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getCurrentEventContext() - Method in class ome.services.ThumbnailBean
-
- getCurrentEventId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentEventType() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupName() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentGroupPermissions() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
Get current EventLog id.
- getCurrentSessionId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentSessionUuid() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentShareId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentSudoerId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentSudoerName() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUmask() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUserId() - Method in class ome.services.sessions.SessionContextImpl
-
- getCurrentUserName() - Method in class ome.services.sessions.SessionContextImpl
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
-
- getDataAsArray(Connection, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
-
- getDatabaseTime() - Method in class ome.logic.ConfigImpl
-
see IConfig.getDatabaseTime()
- getDatabaseUuid() - Method in class ome.logic.ConfigImpl
-
- getDatabaseVersion() - Method in interface ome.api.local.LocalConfig
-
Retrieves the newest database patch.
- getDatabaseVersion() - Method in class ome.logic.ConfigImpl
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.ENUM
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
-
- getDataFromArray(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
-
- getDataset() - Method in class ome.formats.importer.util.TinyImportFixture
-
Deprecated.
provides access to the created Dataset instance.
- getDefaultBody() - Method in class ome.services.mail.MailSender
-
- getDefaultCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- getDefaultCondition() - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
-
Deprecated.
- getDefaultCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
-
- getDefaultCondition() - Method in class ome.security.basic.SharingSecurityFilter
-
- getDefaultCondition() - Method in interface ome.security.SecurityFilter
-
Return the string to be used as the condition.
- getDefaultCondition() - Method in class ome.security.SecurityFilterHolder
-
- getDefaultContext() - Method in class ome.tools.spring.InternalServiceFactory
-
returns null to prevent the lookup of any context, but rather wait on
injection as a ApplicationContextAware
- getDefaultContext() - Method in class ome.tools.spring.ManagedServiceFactory
-
returns null to prevent the lookup of any context, but rather wait on
injection as a ApplicationContextAware
- getDefaultGroup(long) - Method in class ome.logic.AdminImpl
-
- getDefaultScriptDir() - Static method in class ome.services.scripts.ScriptRepoHelper
-
Directory which will be used as the root of this repository if no
directory is passed to a constructor.
- getDefaultT() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getDefaultZ() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getDetails(Object[], String[]) - Static method in class ome.tools.hibernate.HibernateUtils
-
- getDirectSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the direct subclasses of the given class, if any.
- getDirectSuperclassOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the direct superclass of the given class, if any.
- getDisabledSubsystems() - Method in class ome.security.basic.BasicEventContext
-
- getDn(T) - Method in class ome.security.auth.OmeroModelContextMapper
-
- getDnById(Long) - Method in class ome.security.auth.PasswordUtil
-
- getEffectiveUID() - Method in class ome.security.basic.BasicSecuritySystem
-
Returns the Id of the currently logged in user.
- getEffectiveUID() - Method in interface ome.security.SecuritySystem
-
Returns UID based on whether a share is active, etc.
- getEffectiveUID() - Method in class ome.security.SecuritySystemHolder
-
- getEffectiveUID() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEntity(String, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
- getEntityName(Object) - Method in class ome.security.basic.OmeroInterceptor
-
- getEnumeration(Class<T>, String) - Method in class ome.logic.PixelsImpl
-
Deprecated.
- getEnumeration(Class<T>, String) - Method in class ome.logic.TypesImpl
-
- getEnumerationsWithEntries() - Method in class ome.logic.TypesImpl
-
- getEnumerationTypes() - Method in class ome.logic.TypesImpl
-
- getEvent() - Method in class ome.security.basic.BasicEventContext
-
- getEvent() - Method in class ome.security.basic.CurrentDetails
-
- getEventContext() - Method in class ome.logic.AdminImpl
-
- getEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
-
- getEventContext() - Method in class ome.security.basic.BasicSecuritySystem
-
- getEventContext() - Method in interface ome.security.SecuritySystem
-
- getEventContext(boolean) - Method in interface ome.security.SecuritySystem
-
If refresh is false, returns the current EventContext stored
in the session.
- getEventContext() - Method in class ome.security.SecuritySystemHolder
-
- getEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
-
- getEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
-
- getEventContext(Principal) - Method in interface ome.services.sessions.SessionManager
-
Provides a partial EventContext for the current Session.
- getEventContext(Principal) - Method in class ome.services.sessions.SessionManagerImpl
-
- getEventContextQuiet() - Method in interface ome.api.local.LocalAdmin
-
Like IAdmin.getEventContext() but will not reload the context.
- getEventContextQuiet() - Method in class ome.logic.AdminImpl
-
- getEvents(long, Experimenter, Timestamp, Timestamp) - Method in class ome.services.sharing.ShareBean
-
- getExecutor() - Method in class ome.services.mail.MailSender
-
- getExecutor() - Method in class ome.services.scheduler.ThreadPool
-
Deprecated.
- getExperimenter(long) - Method in class ome.logic.AdminImpl
-
- getExtendedMetadata() - Method in class ome.logic.AbstractLevel2Service
-
- getFailedFilesCount() - Method in class ome.services.delete.files.FileDeleter
-
- getFileFilter() - Method in class ome.services.scripts.ScriptFileType
-
A file-pattern (most likely of the form "*.EXT") which will be used
to determine if a file is of this type.
- getFileId() - Method in class ome.services.messages.DeleteLogMessage
-
- getFileId() - Method in class ome.services.RawFileBean
-
- getFileIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of file ids that require
deletion from the disk repository.
- getFirst(String) - Method in class ome.security.auth.AttributeSet
-
- getFreeSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
-
- getGroup(long) - Method in class ome.logic.AdminImpl
-
- getGroup() - Method in class ome.security.basic.BasicEventContext
-
- getGroup() - Method in class ome.security.basic.CurrentDetails
-
- getGroupAttribute(String) - Method in class ome.security.auth.LdapConfig
-
- getGroupFilter() - Method in class ome.security.auth.LdapConfig
-
- getHibernateClass(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Given the name of a database table or alternatively the simple class name
(non-fully qualified) of an IObject, this method returns the class which
Hibernate will map that table to.
- getHibernateClass(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getHistogram(int[], int, boolean, PlaneDef) - Method in class ome.services.RawPixelsBean
-
- getHypercube(List<Integer>, List<Integer>, List<Integer>) - Method in class ome.services.RawPixelsBean
-
- getIdentifierProperty(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the identifier property for the given class.
- getIds() - Method in class ome.services.sessions.state.SessionCache
-
Since all methods which use
SessionCache.getIds() will subsequently check for
the existing session, we do not block here.
- getImageAndCount(Image[], long, UnloadedCollector) - Method in class ome.services.delete.DeleteBean
-
- getImages(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
-
- getImagesByOptions(Parameters) - Method in class ome.logic.PojosImpl
-
- getImagesBySplitFilesets(Map<Class<? extends IObject>, List<Long>>, Parameters) - Method in class ome.logic.PojosImpl
-
- getImmutableFields() - Method in class ome.tools.hibernate.ExtendedMetadata.Immutables
-
- getImmutableFields(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getImportTypes() - Method in class ome.logic.TypesImpl
-
- getIndex() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- getInput(String, String) - Method in class ome.services.sessions.SessionBean
-
- getInput(String, String) - Method in interface ome.services.sessions.SessionManager
-
Returns the input environment Object stored under the given key
or null if none present.
- getInput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getInputKeys(String) - Method in class ome.services.sessions.SessionBean
-
- getInputs(String) - Method in class ome.services.sessions.SessionBean
-
- getInterfaceImplemented(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Get the interface whose method is implemented by a specific class property, if any.
- getInternalValue(String) - Method in interface ome.api.local.LocalConfig
-
Provides a configuration value, ignoring the visibility of the given
value.
- getInternalValue(String) - Method in class ome.logic.ConfigImpl
-
- getJob() - Method in class ome.services.JobBean
-
- getKey() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- getLast() - Method in class ome.security.basic.CurrentDetails
-
- getLast() - Method in interface ome.security.basic.PrincipalHolder
-
Get the last, i.e.
- getLastUpdated() - Method in class ome.services.sessions.state.SessionCache
-
- getLauncher() - Method in class ome.services.scripts.ScriptFileType
-
Return the name of the launcher ("./run.exe") that is used for
scripts of this type.
- getLauncher(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
Find an "omero.launcher..." property string for the given mimetype or
return "" if none is found.
- getLeaderOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
-
- getLeaderOfGroupsList() - Method in class ome.security.basic.BasicEventContext
-
- getLeaderOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
-
- getLinkedBy(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the classes and properties that link to the given class.
- getLinkeds(String, String, Long) - Method in class ome.services.graphs.GraphTraversal
-
Get the model objects that are linked to by the given object via the given property.
- getLinkedTo(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the classes and properties to which the given class links.
- getLinkers(String, String, Long) - Method in class ome.services.graphs.GraphTraversal
-
Get the model objects that link to the given object via the given property.
- getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getLockCandidateChecks(Class<? extends IObject>, boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getLockCandidateChecks(boolean) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getLockCandidates() - Method in class ome.security.basic.BasicEventContext
-
- getLockCandidates(IObject) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
walks the IObject argument non-recursively and gathers
all IObject instances which will be linked to by the
creation or updating of the argument.
- getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
walks the IObject argument non-recursively and gathers
all IObject instances which will be linked to by the
creation or updating of the argument.
- getLockCandidates(IObject) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getLockChecks(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
returns all class/field name pairs which may possibly link to an object
of type klass.
- getLockChecks(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
returns all class/field name pairs which may possibly link to an object
of type klass.
- getLockingIds(Class<IObject>, long, Long) - Method in interface ome.api.local.LocalAdmin
-
Returns a map from Class (as string) to a count for all entities
which point to the given IObject.
- getLockingIds(IObject) - Method in class ome.logic.AdminImpl
-
- getLockingIds(Class<IObject>, long, Long) - Method in class ome.logic.AdminImpl
-
- getLogger() - Method in class ome.services.util.BeanHelper
-
- getLogs() - Method in class ome.security.basic.BasicEventContext
-
- getLogs() - Method in class ome.security.basic.BasicSecuritySystem
-
- getLogs() - Method in class ome.security.basic.CurrentDetails
-
- getLogString(SelfConfigurableService) - Method in class ome.services.util.BeanHelper
-
- getLutReaders(ChannelBinding[]) - Method in class ome.logic.LutProviderImpl
-
- getMailUtil() - Method in class ome.services.mail.MailSender
-
- getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderInDb
-
- getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderInMemory
-
- getManagerByUuid(String, ServiceFactory) - Method in class ome.security.basic.NodeProviderWrapper
-
- getManagerByUuid(String, ServiceFactory) - Method in interface ome.security.NodeProvider
-
Retrieves a given manager node.
- getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderInDb
-
- getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderInMemory
-
- getManagerIdByUuid(String, SqlAction) - Method in class ome.security.basic.NodeProviderWrapper
-
- getManagerIdByUuid(String, SqlAction) - Method in interface ome.security.NodeProvider
-
Retrieves a given manager node ID.
- getManagerList(boolean) - Method in class ome.security.basic.NodeProviderInDb
-
- getManagerList(boolean) - Method in class ome.security.basic.NodeProviderInMemory
-
- getManagerList(boolean) - Method in class ome.security.basic.NodeProviderWrapper
-
- getManagerList(boolean) - Method in interface ome.security.NodeProvider
-
- getMapProperties(String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Get the names of any String→RString map properties this class has, otherwise an empty set if none.
- getMapProperties(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
- getMemberCount(Set<Long>) - Method in class ome.services.sharing.ShareBean
-
- getMemberOfGroupIds(Experimenter) - Method in class ome.logic.AdminImpl
-
- getMemberOfGroupsList() - Method in class ome.security.basic.BasicEventContext
-
- getMemberOfGroupsList() - Method in class ome.services.sessions.SessionContextImpl
-
- getMemberShares(boolean) - Method in class ome.services.sharing.ShareBean
-
- getMemberSharesFor(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
-
- getMessages() - Method in class ome.services.messages.DeleteLogsMessage
-
- getMetadata(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the Thumbnail object for a given Pixels ID.
- getMetadataSimple(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the Thumbnail object for a given Pixels ID.
- getMethodCount() - Method in class ome.services.messages.stats.MethodStatsMessage
-
- getMimetype() - Method in class ome.services.scripts.ScriptFileType
-
Returns the mimetype that must be set on an original file instance
in order to be considered of this type.
- getModel() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getMyOpenAgentSessions(String) - Method in class ome.services.sessions.SessionBean
-
- getMyOpenClientSessions() - Method in class ome.services.sessions.SessionBean
-
- getMyOpenSessions() - Method in class ome.services.sessions.SessionBean
-
- getMyUserPhotos() - Method in class ome.logic.AdminImpl
-
- getName() - Method in class ome.logic.HardWiredInterceptor
-
- getName() - Method in class ome.security.basic.AbstractSecurityFilter
-
- getName() - Method in class ome.security.basic.BasicSecurityWiring
-
Lookup name.
- getName() - Method in class ome.security.policy.BasePolicy
-
- getName() - Method in class ome.security.policy.BinaryAccessPolicy
-
- getName() - Method in interface ome.security.policy.Policy
-
Unique name for a class of restrictions that this
Policy
will enforce.
- getName() - Method in interface ome.security.SecurityFilter
-
Name of this security filter.
- getName() - Method in class ome.security.SecurityFilterHolder
-
- getName() - Method in interface ome.services.graphs.GraphPolicyRulePredicate
-
- getName() - Method in class ome.services.graphs.GroupPredicate
-
- getName() - Method in class ome.services.graphs.PermissionsPredicate
-
- getName() - Method in interface ome.services.sessions.SessionCallback
-
- getName() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
-
- getNewUserGroup() - Method in class ome.security.auth.LdapConfig
-
- getNewUserGroupOwner() - Method in class ome.security.auth.LdapConfig
-
- getObject() - Method in interface ome.services.sessions.SessionCallback
-
- getObject() - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
-
- getObject() - Method in class ome.services.sessions.state.CacheFactory
-
- getObjectByLSID(LSID) - Method in class ome.formats.OMEROMetadataStore
-
Retrieves an object from the internal object graph by LSID.
- getObjectClass() - Method in class ome.services.mail.ObjectMailSender
-
- getObjectsRead() - Method in class ome.services.messages.stats.ObjectsReadStatsMessage
-
- getObjectsWritten() - Method in class ome.services.messages.stats.ObjectsWrittenStatsMessage
-
- getObjectType() - Method in class ome.security.basic.EventListenersFactoryBean
-
this FactoryBean produces a Map instance for use in
LocalSessionFactoryBean.setEventListeners(Map)
- getObjectType() - Method in class ome.services.delete.Deletion.Builder
-
- getOriginalEnumerations() - Method in class ome.logic.TypesImpl
-
- getOriginalFilePath(AbstractFileSystemService, Pixels) - Method in class ome.services.OmeroFilePathResolver
-
- getOutput(String, String) - Method in class ome.services.sessions.SessionBean
-
- getOutput(String, String) - Method in interface ome.services.sessions.SessionManager
-
Returns the output environment Object stored under the given key
or null if none present.
- getOutput(String, String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getOutputKeys(String) - Method in class ome.services.sessions.SessionBean
-
- getOutputs(String) - Method in class ome.services.sessions.SessionBean
-
- getOwnedGroups() - Method in class ome.logic.LdapImpl.GroupLoader
-
Return the found owned groups for the given username.
- getOwner() - Method in class ome.security.basic.BasicEventContext
-
- getOwner() - Method in class ome.security.basic.CurrentDetails
-
- getOwnShares(boolean) - Method in class ome.services.sharing.ShareBean
-
- getParameterTypes() - Method in class ome.security.basic.AllGroupsSecurityFilter
-
- getParameterTypes() - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
-
Deprecated.
- getParameterTypes() - Method in class ome.security.basic.OneGroupSecurityFilter
-
- getParameterTypes() - Method in class ome.security.basic.SharingSecurityFilter
-
- getParameterTypes() - Method in interface ome.security.SecurityFilter
-
Return a mapping of the hibernate types for each of the parameters
that the condition takes.
- getParameterTypes() - Method in class ome.security.SecurityFilterHolder
-
- getParentTransformer(Class) - Static method in class ome.services.query.Hierarchy
-
- getPasswordAuthentication() - Method in class ome.security.SmtpAuthenticator
-
- getPastConnections(long) - Method in class ome.services.sharing.ShareBean
-
- getPermissionsForGroup(Long) - Method in class ome.security.basic.BasicEventContext
-
Never returns Permissions.DUMMY.
- getPhysicalMemory() - Static method in class ome.services.util.JvmSettingsCheck
-
- getPixelIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of pixel ids that require
deletion from the disk repository.
- getPixels() - Method in class ome.formats.importer.util.TinyImportFixture
-
Deprecated.
- getPixels(Long, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
-
- getPixels() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getPixels(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the Pixels object for a given Pixels ID.
- getPixelsId() - Method in class ome.services.RawPixelsBean
-
- getPixelsPath() - Method in class ome.services.RawPixelsBean
-
- getPixelsTypeLowerBound(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getPixelsTypeUpperBound(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getPlane(int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlaneOffset(int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlaneRegion(int, int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getPlaneSize() - Method in class ome.services.RawPixelsBean
-
- getPojoTypes() - Method in class ome.logic.TypesImpl
-
- getPrefix() - Method in class ome.tools.spring.InternalServiceFactory
-
- getPrefix() - Method in class ome.tools.spring.ManagedServiceFactory
-
- getPrincipal(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
-
- getPrincipal() - Method in class ome.security.basic.BasicEventContext
-
- getPrincipal() - Method in class ome.services.util.ExecutionThread
-
- getPrivilege(String) - Method in class ome.security.basic.LightAdminPrivileges
-
- getPrivilegeForConfigName(String) - Method in class ome.security.basic.LightAdminPrivileges
-
- getProcess() - Method in class ome.services.scripts.ScriptFileType
-
Return the import name of the process class which will be used
to invoke scripts of this type.
- getProcess(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
Find an "omero.process..." property string for the given mimetype or
return "" if none is found.
- getProjections(IObject) - Method in class ome.services.search.FullText
-
- getProperties() - Method in class ome.security.auth.FilePasswordProvider
-
- getPropertyKind(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Get what kind of property a specific class property is.
- getPropertyType(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Get the Hibernate type of a specific class property.
- getProxiedObject(T) - Static method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
Simpler wrapper to handle superclass proxy objects (e.g.
- getQuantumDef() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getQueryFactory() - Method in class ome.logic.AbstractLevel1Service
-
- getQueryFactory() - Method in class ome.logic.AbstractLevel2Service
-
- getQueryService() - Method in class ome.services.mail.MailSender
-
- getQueryString() - Method in class ome.services.mail.ObjectMailSender
-
- getReferenceCount(String) - Method in class ome.services.sessions.SessionBean
-
- getReferenceCount(String) - Method in interface ome.services.sessions.SessionManager
-
Return the number of client which are presumed to be attached to this
session or throw an exception if there's no such session.
- getReferenceCount(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getRegion(int, long) - Method in class ome.services.RawPixelsBean
-
- getRelationship(String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
Walks the data on what locks what
for "from" argument to see if there is any direct relationship to the
"to" argument.
- getRelationship(String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Walks the data on what locks what
for "from" argument to see if there is any direct relationship to the
"to" argument.
- getRenderingDefId() - Method in class ome.services.RenderingBean
-
- getRenderingDefId() - Method in class ome.services.ThumbnailBean
-
- getRenderingSettings(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- getRequiredPermissions() - Method in interface ome.services.graphs.GraphTraversal.Processor
-
- getResolutionDescriptions() - Method in class ome.services.RawPixelsBean
-
- getResolutionDescriptions() - Method in class ome.services.RenderingBean
-
- getResolutionLevel() - Method in class ome.services.RawPixelsBean
-
- getResolutionLevel() - Method in class ome.services.RenderingBean
-
- getResolutionLevels() - Method in class ome.services.RawPixelsBean
-
- getResolutionLevels() - Method in class ome.services.RenderingBean
-
- getResults() - Method in class ome.services.delete.QueryConstraints
-
- getResultSet() - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(long, int) - Method in class ome.tools.hibernate.SqlArray
-
- getResultSet(long, int, Map<String, Class<?>>) - Method in class ome.tools.hibernate.SqlArray
-
- getResultsString(Object, IdentityHashMap<Object, String>) - Static method in class ome.services.util.ServiceHandler
-
public for testing purposes.
- getResultTypes() - Method in class ome.logic.TypesImpl
-
- getRGBA(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- getRoles() - Method in class ome.services.mail.MailSender
-
- getRoles() - Method in class ome.services.util.DBUserCheck
-
- getRow(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getRowOffset(int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getRowSize() - Method in class ome.services.RawPixelsBean
-
- getScore(IObject) - Method in class ome.services.search.FullText
-
- getScriptDir() - Method in class ome.services.scripts.ScriptRepoHelper
-
Returns the actual root of this repository.
- getSecurityRoles() - Method in class ome.logic.AdminImpl
-
- getSecurityRoles() - Method in class ome.security.basic.BasicSecuritySystem
-
- getSecurityRoles() - Method in interface ome.security.SecuritySystem
-
- getSecurityRoles() - Method in class ome.security.SecuritySystemHolder
-
- getSecurityRoles() - Method in class ome.security.sharing.SharingSecuritySystem
-
- getSecuritySystem() - Method in class ome.logic.AbstractLevel2Service
-
- getSender() - Method in class ome.services.mail.MailUtil
-
Helper method that returns value of omero.mail.from.
- getServerTime() - Method in class ome.logic.ConfigImpl
-
see IConfig.getServerTime()
- getService() - Method in interface ome.services.util.Executor
-
Returns the ExecutorService assigned to this instance.
- getService() - Method in class ome.services.util.Executor.Impl
-
- getServiceCleanups() - Method in class ome.security.basic.BasicEventContext
-
- getServiceFactory(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
-
- getServiceInterface() - Method in class ome.logic.AdminImpl
-
- getServiceInterface() - Method in class ome.logic.ConfigImpl
-
- getServiceInterface() - Method in class ome.logic.LdapImpl
-
- getServiceInterface() - Method in class ome.logic.MetadataImpl
-
Returns the Interface implemented by this class.
- getServiceInterface() - Method in class ome.logic.PixelsImpl
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.logic.PojosImpl
-
Returns the Interface implemented by this class.
- getServiceInterface() - Method in class ome.logic.QueryImpl
-
- getServiceInterface() - Method in class ome.logic.RenderingSettingsImpl
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.logic.RepositoryInfoImpl
-
- getServiceInterface() - Method in class ome.logic.TypesImpl
-
- getServiceInterface() - Method in class ome.logic.UpdateImpl
-
- getServiceInterface() - Method in class ome.services.delete.DeleteBean
-
- getServiceInterface() - Method in class ome.services.JobBean
-
- getServiceInterface() - Method in class ome.services.projection.ProjectionBean
-
Returns the interface this implementation is for.
- getServiceInterface() - Method in class ome.services.RawFileBean
-
- getServiceInterface() - Method in class ome.services.RawPixelsBean
-
- getServiceInterface() - Method in class ome.services.RenderingBean
-
Returns the service corresponding to this class.
- getServiceInterface() - Method in class ome.services.SearchBean
-
- getServiceInterface() - Method in class ome.services.sessions.SessionBean
-
- getServiceInterface() - Method in class ome.services.sharing.ShareBean
-
- getServiceInterface() - Method in class ome.services.ThumbnailBean
-
- getSession(String) - Method in class ome.services.sessions.SessionBean
-
- getSession() - Method in interface ome.services.sessions.SessionContext
-
- getSession() - Method in class ome.services.sessions.SessionContextImpl
-
- getSession() - Method in class ome.tools.hibernate.SessionFactory
-
Returns a session active for the current thread.
- getSessionContext(String) - Method in class ome.services.sessions.state.SessionCache
-
Retrieve a session possibly raising either
RemovedSessionException or SessionTimeoutException.
- getSessionContext(String, boolean) - Method in class ome.services.sessions.state.SessionCache
-
Retrieve a session possibly raising either
RemovedSessionException or SessionTimeoutException.
- getSessionData() - Method in interface ome.services.sessions.SessionManager
-
Return all sessions that are active with associated possibly varying
session data information.
- getSessionData() - Method in class ome.services.sessions.SessionManagerImpl
-
- getSessionData(String, boolean) - Method in class ome.services.sessions.state.SessionCache
-
Returns all the data contained in the internal implementation of
this manager.
- getSessionFactory() - Method in class ome.logic.AbstractLevel1Service
-
delegates to HibernateDaoSupport to get the current
SessionFactory
- getSessionId() - Method in class ome.services.messages.AbstractSessionMessage
-
- getSessionPrivileges(Session) - Method in class ome.security.basic.LightAdminPrivileges
-
Determine the light administrator privileges associated with a session.
- getSessionQuietly(String) - Method in interface ome.api.local.LocalSession
-
Lookups a Session without updating the last access time.
- getSessionQuietly(String) - Method in class ome.services.sessions.SessionBean
-
- getSessionStats(String) - Method in interface ome.services.sessions.SessionManager
-
Return the
SessionStats which are being counted for the given
session or throw an exception if it has been removed.
- getSessionStats(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getSetting() - Method in class ome.logic.LdapImpl
-
- getSettings(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves the RenderingDef object for a given Pixels ID.
- getShare(long) - Method in class ome.services.sharing.ShareBean
-
- getShareIfAccessible(long) - Method in class ome.services.sharing.ShareBean
-
Loads share and checks it's owner and member data against the current
context (owner/member/admin).
- getShareIfAccessible(long, boolean, long) - Method in class ome.services.sharing.ShareStore
-
Loads share and checks its owner and member data against the current
context (owner/member/admin).
- getShares(long, boolean, boolean) - Method in class ome.services.sharing.BlobShareStore
-
- getShares(long, boolean, boolean) - Method in class ome.services.sharing.ShareStore
-
- getSharesOwnedBy(Experimenter, boolean) - Method in class ome.services.sharing.ShareBean
-
- getSimpleProperties(String) - Method in class ome.services.graphs.GraphPathBean
-
- getSimpleProperties(String, boolean) - Method in class ome.services.graphs.GraphPathBean
-
Get the simple
properties for the given class, not linking to other mapped classes.
- getSqlAction() - Method in class ome.services.util.Executor.SimpleWork
-
- getSQLJoin(String, String, String, String) - Method in interface ome.tools.hibernate.ExtendedMetadata
-
- getSQLJoin(String, String, String, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Note: this implementation does not yet take into account the mapping
of joined subclasses like Job -> UpdateJob.
- getStack(int, int) - Method in class ome.services.RawPixelsBean
-
- getStackOffset(int, int) - Method in class ome.services.RawPixelsBean
-
- getStackSize() - Method in class ome.services.RawPixelsBean
-
- getStats() - Method in class ome.security.basic.BasicEventContext
-
- getStats() - Method in class ome.security.basic.CurrentDetails
-
- getStore() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- getSubclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the subclasses of the given class, if any.
- getSubclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the name of this class and of its mapped subclasses.
- getSubjectPrefix() - Method in class ome.services.mail.MailSender
-
- getSubtypeValue(int, int, Object) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
- getSudoer() - Method in class ome.security.basic.BasicEventContext
-
- getSudoer() - Method in class ome.security.basic.CurrentDetails
-
- getSuperclassesOf(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the superclasses of the given class, if any.
- getSuperclassesOfReflexive(String) - Method in class ome.services.graphs.GraphPathBean
-
Get the name of this class and of its mapped superclasses.
- getTaggedObjectsCount(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
-
- getTargetType(String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Returns the IObject type which a given field points to.
- getTermVector() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- getThis() - Method in interface ome.services.util.Executor.StatefulWork
-
- getThis(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
-
- getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnail(Integer, Integer) - Method in class ome.services.ThumbnailBeanReadOnly
-
- getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailByLongestSide(Integer) - Method in class ome.services.ThumbnailBeanReadOnly
-
- getThumbnailByLongestSideDirect(Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- getThumbnailByLongestSideSet(Integer, Set<Long>) - Method in class ome.services.ThumbnailBeanReadOnly
-
- getThumbnailDirect(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailForSectionByLongestSideDirect(int, int, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailForSectionDirect(int, int, Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getThumbnailIds() - Method in class ome.tools.RepositoryTask
-
This public method is used to return a list of thumbnail ids that require
deletion from the disk repository.
- getThumbnailSet(Integer, Integer, Set<Long>) - Method in class ome.services.ThumbnailBean
-
- getThumbnailWithoutDefault(Integer, Integer) - Method in class ome.services.ThumbnailBean
-
- getTile(int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- getTileSize() - Method in class ome.services.RawPixelsBean
-
- getTileSize() - Method in class ome.services.RenderingBean
-
- getTimepoint(int) - Method in class ome.services.RawPixelsBean
-
- getTimepointOffset(int) - Method in class ome.services.RawPixelsBean
-
- getTimepointSize() - Method in class ome.services.RawPixelsBean
-
- getTotalSize() - Method in class ome.services.RawPixelsBean
-
- getTotalSize(IObject) - Method in class ome.services.search.FullText
-
- getTransactionAttribute(Method, Class) - Method in class ome.services.sharing.ShareRestrictionTransactionAttributeSource
-
- getTransactionAttribute(Method, Class) - Method in class ome.tools.spring.ForceTransactionAttributeSource
-
- getType(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
-
- getTypes() - Method in class ome.security.policy.BasePolicy
-
- getTypes() - Method in interface ome.security.policy.Policy
-
- getUndeletedFiles() - Method in class ome.services.delete.files.AbstractFileDeletions
-
- getUndeletedFiles() - Method in class ome.services.delete.files.FileDeleter
-
- getUsageFraction() - Method in class ome.logic.RepositoryInfoImpl
-
Deprecated.
- getUsedSpaceInKilobytes() - Method in class ome.logic.RepositoryInfoImpl
-
Deprecated.
- getUserAttribute(String) - Method in class ome.security.auth.LdapConfig
-
- getUserEmail(String) - Method in class ome.services.mail.MailSender
-
- getUserFilter() - Method in class ome.security.auth.LdapConfig
-
- getUserId() - Method in class ome.services.ThumbnailCtx
-
Retrieves the current user ID to use for queries.
- getUserImages(Parameters) - Method in class ome.logic.PojosImpl
-
- getUserPasswordHash(Long) - Method in class ome.security.auth.PasswordUtil
-
- getUserRoles(Experimenter) - Method in interface ome.api.local.LocalAdmin
-
Finds the group names for all groups for which the given Experimenter is
a member.
- getUserRoles(Experimenter) - Method in class ome.logic.AdminImpl
-
- getUserRoles() - Method in interface ome.services.sessions.SessionContext
-
- getUserRoles() - Method in class ome.services.sessions.SessionContextImpl
-
- getUserRoles(String) - Method in interface ome.services.sessions.SessionManager
-
- getUserRoles(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- getUuid() - Method in class ome.services.db.DatabaseIdentity
-
- getUuid() - Method in class ome.services.scripts.ScriptRepoHelper
-
Uuid of this repository.
- getUuid() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
-
- getVersion() - Method in class ome.logic.ConfigImpl
-
see IConfig.getVersion()
- getWarning() - Method in class ome.services.delete.files.FileDeleter
-
- GlobalMulticaster - Class in ome.services.messages
-
Global ApplicationEventMulticaster which can be used to integrate
parent and child OmeroContext instances.
- GlobalMulticaster() - Constructor for class ome.services.messages.GlobalMulticaster
-
Keeps track of which instance this is.
- GraphException - Exception in ome.services.graphs
-
Exception which will be thrown by traversing the graph if an error occurred.
- GraphException(String) - Constructor for exception ome.services.graphs.GraphException
-
- GraphPathBean - Class in ome.services.graphs
-
The graph path bean holds the Hibernate object mapping and assists navigation thereof.
- GraphPathBean() - Constructor for class ome.services.graphs.GraphPathBean
-
- GraphPathReport - Class in ome.services.graphs
-
A standalone tool for producing a summary of the Hibernate object mapping for our Sphinx documentation.
- GraphPathReport() - Constructor for class ome.services.graphs.GraphPathReport
-
- GraphPolicy - Class in ome.services.graphs
-
A policy guides how to traverse the graph.
- GraphPolicy() - Constructor for class ome.services.graphs.GraphPolicy
-
- GraphPolicy.Ability - Enum in ome.services.graphs
-
Abilities that the user may have to operate upon model objects.
- GraphPolicy.Action - Enum in ome.services.graphs
-
The action to take on an object instance.
- GraphPolicy.Details - Class in ome.services.graphs
-
A tuple noting the state of a mapped object instance in the current graph traversal.
- GraphPolicy.Orphan - Enum in ome.services.graphs
-
- GraphPolicyRule - Class in ome.services.graphs
-
A graph policy rule specifies a component of a
GraphPolicy.
- GraphPolicyRule() - Constructor for class ome.services.graphs.GraphPolicyRule
-
- GraphPolicyRulePredicate - Interface in ome.services.graphs
-
A plug-in for graph policy rule matches whereby an object may be matched against named values.
- GraphTraversal - Class in ome.services.graphs
-
An alternative implementation of model object graph traversal, relying on SELECTing in advance for making decisions,
instead of rolling back to savepoints to recover from failed attempts to act.
- GraphTraversal(Session, EventContext, ACLVoter, GraphPathBean, SetMultimap<String, String>, GraphPolicy, GraphTraversal.Processor) - Constructor for class ome.services.graphs.GraphTraversal
-
Construct a new instance of a graph traversal manager.
- GraphTraversal.PlanExecutor - Interface in ome.services.graphs
-
Executor that allows callers to actually perform the planned action.
- GraphTraversal.Processor - Interface in ome.services.graphs
-
Executes the planned operation.
- GROUP_SUDO_NS - Static variable in class ome.services.sessions.SessionManagerImpl
-
- GroupAttributeMapper - Class in ome.security.auth
-
- GroupAttributeMapper(LdapConfig) - Constructor for class ome.security.auth.GroupAttributeMapper
-
- GroupChmodStrategy - Class in ome.security.basic
-
ChmodStrategy which only permits modifying
the permissions on groups.
- GroupChmodStrategy(BasicACLVoter, SessionFactory, SqlAction, ExtendedMetadata) - Constructor for class ome.security.basic.GroupChmodStrategy
-
- GroupContextMapper - Class in ome.security.auth
-
Specialized OME ExperimenterGroup context mapper.
- GroupContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.GroupContextMapper
-
- GroupContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.GroupContextMapper
-
- groupId - Variable in class ome.services.graphs.GraphPolicy.Details
-
the ID of the object's ExperimenterGroup,
or null if the object does not have a group
- groupnameFilter(String) - Method in class ome.security.auth.LdapConfig
-
- GroupPredicate - Class in ome.services.graphs
-
A predicate that allows group=system and similar to be used in graph policy rule matches.
- GroupPredicate(Roles) - Constructor for class ome.services.graphs.GroupPredicate
-
Construct a new group predicate.
- groupProxy(Long) - Method in interface ome.api.local.LocalAdmin
-
returns a possibly uninitialized proxy for the given
group id.
- groupProxy(String) - Method in interface ome.api.local.LocalAdmin
-
returns a possibly uninitialized proxy for the given
group name.
- groupProxy(Long) - Method in class ome.logic.AdminImpl
-
- groupProxy(String) - Method in class ome.logic.AdminImpl
-
- groupRestrictions(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.AttributeNewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.OrgUnitNewUserGroupBean
-
- groups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
-
- groupsLed - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- guests - Variable in class ome.services.sharing.data.ShareData
-
- guests - Variable in class ome.services.sharing.data.ShareItem
-
- ic - Variable in class ome.services.sharing.ShareStore
-
- ice_factory() - Static method in class ome.services.sharing.data.Obj
-
- ice_factory() - Static method in class ome.services.sharing.data.ShareData
-
- ice_factory() - Static method in class ome.services.sharing.data.ShareItem
-
- ice_id() - Method in class ome.services.sharing.data.Obj
-
- ice_id(Current) - Method in class ome.services.sharing.data.Obj
-
- ice_id() - Method in class ome.services.sharing.data.ShareData
-
- ice_id(Current) - Method in class ome.services.sharing.data.ShareData
-
- ice_id() - Method in class ome.services.sharing.data.ShareItem
-
- ice_id(Current) - Method in class ome.services.sharing.data.ShareItem
-
- ice_ids() - Method in class ome.services.sharing.data.Obj
-
- ice_ids(Current) - Method in class ome.services.sharing.data.Obj
-
- ice_ids() - Method in class ome.services.sharing.data.ShareData
-
- ice_ids(Current) - Method in class ome.services.sharing.data.ShareData
-
- ice_ids() - Method in class ome.services.sharing.data.ShareItem
-
- ice_ids(Current) - Method in class ome.services.sharing.data.ShareItem
-
- ice_isA(String) - Method in class ome.services.sharing.data.Obj
-
- ice_isA(String, Current) - Method in class ome.services.sharing.data.Obj
-
- ice_isA(String) - Method in class ome.services.sharing.data.ShareData
-
- ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareData
-
- ice_isA(String) - Method in class ome.services.sharing.data.ShareItem
-
- ice_isA(String, Current) - Method in class ome.services.sharing.data.ShareItem
-
- ice_staticId() - Static method in class ome.services.sharing.data.Obj
-
- ice_staticId() - Static method in class ome.services.sharing.data.ObjPrxHelper
-
Provides the Slice type ID of this type.
- ice_staticId() - Static method in class ome.services.sharing.data.ShareData
-
- ice_staticId() - Static method in class ome.services.sharing.data.ShareDataPrxHelper
-
Provides the Slice type ID of this type.
- ice_staticId() - Static method in class ome.services.sharing.data.ShareItem
-
- ice_staticId() - Static method in class ome.services.sharing.data.ShareItemPrxHelper
-
Provides the Slice type ID of this type.
- IceUtil - Class in ome.services.util
-
Methods for working with Ice.
- IceUtil() - Constructor for class ome.services.util.IceUtil
-
- id - Variable in class ome.services.sharing.data.Obj
-
- id - Variable in class ome.services.sharing.data.ShareData
-
- id - Variable in class ome.services.sharing.data.ShareItem
-
- idEqual(IObject, IObject) - Static method in class ome.tools.hibernate.HibernateUtils
-
returns true under the following circumstances:
both arguments are null, or
both arguments are identical (==), or
both arguments have the same id value(equals)
- IdMapHelper - Class in ome.services.sharing.data
-
- IdMapHelper() - Constructor for class ome.services.sharing.data.IdMapHelper
-
- IdMapHolder - Class in ome.services.sharing.data
-
- IdMapHolder() - Constructor for class ome.services.sharing.data.IdMapHolder
-
- IdMapHolder(Map<String, List<Long>>) - Constructor for class ome.services.sharing.data.IdMapHolder
-
- idOnly - Variable in class ome.services.search.SearchValues
-
- ids(Criteria) - Method in class ome.services.search.SearchAction
-
- ids(QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- idsInDb() - Method in class ome.services.scripts.ScriptRepoHelper
-
- idsInDb(SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
-
- idToUuid(long) - Method in class ome.services.sharing.ShareBean
-
- ignoreUnknown - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
- IMAGE_QUERY - Static variable in class ome.services.delete.DeleteBean
-
Loads an Image graph including: Pixels, Channel, LogicalChannel,
StatsInfo, PlaneInfo, Thumbnails, file maps, OriginalFiles, and Settings
- img - Variable in class ome.services.SVGRasterizer
-
The image that represents the SVG document.
- Impl(CurrentDetails, SessionFactory, SqlAction, String[]) - Constructor for class ome.services.util.Executor.Impl
-
- Impl(CurrentDetails, SessionFactory, SqlAction, String[], ThreadPool) - Constructor for class ome.services.util.Executor.Impl
-
- Impl() - Constructor for class ome.tools.hibernate.ExtendedMetadata.Impl
-
- include(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
returns true if this offset points to a field which may contain an
IObject instance
- increment() - Method in class ome.services.sessions.SessionContext.Count
-
- increment(int) - Method in class ome.services.sessions.stats.LongCounter
-
- index() - Method in class ome.services.fulltext.FullTextIndexer2
-
Index a batch of model objects all at once.
- index(String, String[]) - Static method in class ome.tools.hibernate.HibernateUtils
-
- indexAllEvents() - Static method in class ome.services.fulltext.Main
-
- indexByClass(Set<String>) - Static method in class ome.services.fulltext.Main
-
- indexer - Variable in class ome.services.fulltext.FullTextThread
-
Deprecated.
- indexFullDb() - Static method in class ome.services.fulltext.Main
-
- indexNullAs() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- indexObject(IObject) - Method in class ome.logic.UpdateImpl
-
- indexObject(IObject, long, long, long) - Method in class ome.services.search.IndexWatcher
-
Index the given object.
- indexRetry() - Method in class ome.services.fulltext.FullTextIndexer2
-
Index a batch of model objects one by one.
- indexWatcher - Variable in class ome.logic.UpdateImpl
-
- IndexWatcher - Class in ome.services.search
-
The index watcher writes REINDEX entries to the event log and waits for the indexing thread to process them.
- IndexWatcher(DataSource, String) - Constructor for class ome.services.search.IndexWatcher
-
Construct a new index watcher.
- init() - Static method in class ome.services.fulltext.Main
-
- init() - Method in class ome.services.sessions.SessionManagerImpl
-
Initialization method called by the Spring run-time to acquire an initial
Session.
- init() - Method in class ome.services.sharing.ShareStore
-
Calls
ShareStore.doInit() within a transaction with a session available to
all
HibernateTemplate callbacks.
- INITIAL_DELAY - Static variable in class ome.logic.RepositoryInfoImpl
-
- INITIAL_FREE_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck
-
FreePhysicalMemorySize value from the OperatingSystem JMX bean
at startup.
- initialize(Object) - Method in interface ome.api.local.LocalQuery
-
Uses the Hibernate static method initialize to prepare an
object for shipping over the wire.
- initialize(Object) - Method in class ome.logic.QueryImpl
-
- initialize() - Method in class ome.services.eventlogs.EventLogQueue
-
Do nothing.
- initialize() - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
Called when the configuration database does not contain a valid
current_id.
- initialize() - Method in class ome.services.fulltext.PersistentEventLogLoader
-
Deprecated.
Called when the configuration database does not contain a valid
current_id.
- initialize() - Method in class ome.services.pixeldata.PersistentEventLogLoader
-
- initializeQuery(FullTextQuery) - Method in class ome.services.search.FullText
-
Allows settings offset and limit on the query.
- initializeUserAttributes(MethodInvocation, ServiceFactory, Principal, AtomicBoolean) - Static method in class ome.logic.HardWiredInterceptor
-
Adds the given environment context objects to the
ReflectiveMethodInvocation.getUserAttributes()
Map for lookup in subclasses
- inMemoryCache(String) - Method in interface ome.services.sessions.SessionManager
-
Returns after possibly creating an in-memory cache which
can be used throughout the session.
- inMemoryCache(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- inMemoryCache(String) - Method in class ome.services.sessions.state.SessionCache
-
- INNER_JOIN - Static variable in class ome.services.query.Query
-
imported constant for ease of use
- input - Variable in class ome.services.SVGRasterizer
-
The transcoder input.
- inputEnvironment(String) - Method in interface ome.services.sessions.SessionManager
-
Returns a copy of the input environment.
- inputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- instantiate(String, EntityMode, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
default logic, but we may want to use them eventually for
dependency-injection.
- INTEGER(Connection, List<Integer>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
-
- INTEGER() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.INTEGER
-
- INTEGER(List<Integer>) - Constructor for class ome.tools.hibernate.SqlArray.INTEGER
-
- interceptor - Variable in class ome.security.basic.BasicSecuritySystem
-
- Interceptor(ACLVoter, SessionHandler, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
-
- internalDelete(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
-
- internalMerge(IObject, UpdateFilter, Session) - Method in class ome.logic.UpdateImpl
-
- internalMoveToCommonSpace(IObject) - Method in interface ome.api.local.LocalAdmin
-
Unconditionally move an object into the user group (usually id=1).
- internalMoveToCommonSpace(IObject) - Method in class ome.logic.AdminImpl
-
Helpers which unconditionally moves the object to the common space.
- internalSave(IObject, ReloadFilter, Session) - Method in class ome.logic.UpdateImpl
-
- InternalServiceFactory - Class in ome.tools.spring
-
subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal")
service-instances.
- InternalServiceFactory() - Constructor for class ome.tools.spring.InternalServiceFactory
-
default construtor
- InternalServiceFactory(OmeroContext) - Constructor for class ome.tools.spring.InternalServiceFactory
-
- internalSession - Variable in class ome.services.sessions.SessionManagerImpl
-
- Intersection - Class in ome.services.search
-
Intersection
SearchAction which combines two other search actions
into one logical unit, e.g.
- Intersection(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Intersection
-
- invalidateConnection(long, Experimenter) - Method in class ome.services.sharing.ShareBean
-
- invalidateCurrentEventContext() - Method in class ome.security.basic.CurrentDetails
-
It suffices to set the Details to a new instance to make this
context unusable.
- invalidateEventContext() - Method in class ome.security.basic.BasicSecuritySystem
-
- invalidateEventContext() - Method in interface ome.security.SecuritySystem
-
- invalidateEventContext() - Method in class ome.security.SecuritySystemHolder
-
- invalidateEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- invertPDI(Set<Image>, CBlock<T>) - Static method in class ome.tools.HierarchyTransformations
-
- invoke(MethodInvocation) - Method in class ome.security.basic.BasicSecurityWiring
-
Wraps all OMERO invocations with login/logout semantics.
- invoke(MethodInvocation) - Method in class ome.security.basic.EventHandler
-
Invocation interceptor for preparing this Thread for execution
and subsequently resetting it.
- invoke(MethodInvocation) - Method in class ome.security.basic.NullEventHandler
-
- invoke(MethodInvocation) - Method in class ome.services.util.ServiceHandler
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.ProxyCleanupFilter.Interceptor
-
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionFactory
-
Wraps all invocations to Session to prevent certain usages.
- invoke(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
-
delegates to HibernateInterceptor or manages sessions internally,
based on the type of service.
- IObjectClassQuery - Class in ome.services.query
-
simple query subclass which uses the Parameters.CLASS
parameter value to create a Criteria and then adds
Expression instances based on all other
parameter names.
- IObjectClassQuery(Parameters) - Constructor for class ome.services.query.IObjectClassQuery
-
- ip - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- iPixels - Variable in class ome.services.projection.ProjectionBean
-
Reference to the service used to retrieve the pixels metadata.
- IProcessManager - Interface in ome.services.procs
-
Manages asynchronous processing logic for all Job
instances created.
- iQuery - Variable in class ome.logic.AbstractLevel2Service
-
- iQuery - Variable in class ome.services.AbstractStatefulBean
-
- iQuery - Variable in class ome.services.query.HierarchyNavigator
-
available query service
- is_admin - Static variable in class ome.security.basic.AllGroupsSecurityFilter
-
- is_adminorpi - Static variable in interface ome.security.SecurityFilter
-
- is_nonprivate - Static variable in interface ome.security.SecurityFilter
-
- is_share - Static variable in interface ome.security.SecurityFilter
-
- isActive() - Method in class ome.security.basic.BasicMethodSecurity
-
- isActive() - Method in interface ome.security.MethodSecurity
-
Indicates whether or not method security is active.
- isActive() - Method in interface ome.services.procs.Process
-
- isActive() - Method in class ome.services.procs.ProcessSkeleton
-
- isActive(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- isAdminOrPi(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isAllowLeadingWildcard() - Method in class ome.services.SearchBean
-
- isAutoCloseEnabled() - Method in class ome.tools.hibernate.CurrentSessionContext
-
- isCaseSensitive() - Method in class ome.services.SearchBean
-
- isCheckPermissions - Variable in class ome.services.graphs.GraphPolicy.Details
-
- isCompressed() - Method in class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- isCondition(String) - Method in class ome.services.graphs.GraphPolicy
-
Check if a condition has been set.
- isCurrentUserAdmin() - Method in class ome.services.sessions.SessionContextImpl
-
- isCurrentUserGuest() - Method in class ome.security.basic.CurrentDetails
-
- isDisabled(String) - Method in class ome.security.basic.BasicSecuritySystem
-
- isDisabled(String) - Method in class ome.security.basic.CurrentDetails
-
- isDisabled(String) - Method in interface ome.security.SecuritySystem
-
checks if the listed id is disabled for the current Thread.
- isDisabled(String) - Method in class ome.security.SecuritySystemHolder
-
- isDisabled(String) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isDiskSpaceChecking() - Method in class ome.services.RawFileBean
-
getter disk overflow checking
- isDiskSpaceChecking() - Method in class ome.services.RawPixelsBean
-
- isDiskSpaceChecking() - Method in class ome.services.ThumbnailBean
-
- isEmpty() - Method in class ome.services.query.Definitions
-
- isEmptyEventContext() - Method in class ome.security.sharing.SharingSecuritySystem
-
- isEnabled() - Method in class ome.security.auth.LdapConfig
-
- isEnabled() - Method in class ome.services.mail.MailSender
-
- isError(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
-
- isExtendedGraphCritical(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Whether or not we're extended graph critical for a given set of
dimension pools.
- isf - Variable in class ome.services.util.Executor.Impl
-
- isFloat() - Method in class ome.services.RawPixelsBean
-
- isGranted(Permissions.Role, Permissions.Right) - Static method in class ome.security.basic.AllGroupsSecurityFilter
-
- isGraphCritical(Details) - Method in class ome.security.basic.BasicSecuritySystem
-
- isGraphCritical(Details) - Method in class ome.security.basic.CurrentDetails
-
- isGraphCritical(Details) - Method in interface ome.security.SecuritySystem
-
Determines if the current security context has the possibility of
corrupting consistent graphs.
- isGraphCritical(Details) - Method in class ome.security.SecuritySystemHolder
-
- isGraphCritical(Details) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isGroupContextPermitted(long, long) - Method in class ome.security.basic.BasicSecuritySystem
-
Check the given group context.
- isGroupContextPermitted(long, String) - Method in class ome.security.basic.BasicSecuritySystem
-
- isGroupContextPermitted(long, long) - Method in class ome.security.basic.BasicSecuritySystemReadOnly
-
- isHard() - Method in class ome.services.messages.stats.AbstractStatsMessage
-
- isIgnoreCaseLookup() - Method in interface ome.security.auth.RoleProvider
-
- isIgnoreCaseLookup() - Method in class ome.security.auth.SimpleRoleProvider
-
- isInert() - Method in class ome.services.scripts.ScriptFileType
-
Returns true if the script type cannot be executed,
false otherwise.
- isInert(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper
-
Returns true if the file is an "inert" file e.g.
- isInProgress() - Method in class ome.services.ThumbnailBean
-
- isInRepo(long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- isInRepo(SqlAction, long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- isInSystemGroup(Long) - Method in class ome.security.SystemTypes
-
- isInSystemGroup(Details) - Method in class ome.security.SystemTypes
-
- isInUserGroup(Long) - Method in class ome.security.SystemTypes
-
- isInUserGroup(Details) - Method in class ome.security.SystemTypes
-
- isMatch(GraphPolicy.Details, String) - Method in interface ome.services.graphs.GraphPolicyRulePredicate
-
If this predicate is satisfied by the given object.
- isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.GroupPredicate
-
- isMatch(GraphPolicy.Details, String) - Method in class ome.services.graphs.PermissionsPredicate
-
- isMergedBatches() - Method in class ome.services.SearchBean
-
- isModified() - Method in class ome.services.AbstractStatefulBean
-
- isModified() - Method in class ome.services.RawFileBean
-
Extends the check of the
AbstractStatefulBean.modified flag performed by super
with an additional check of the actual file size against the value
stored in the database
- isMutable() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- isNonPrivate(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.BasicSecuritySystem
-
tests whether or not the current user is either the owner of this entity,
or the supervisor of this entity, for example as root or as group owner.
- isOwnerOrSupervisor(IObject) - Method in class ome.security.basic.CurrentDetails
-
- isPasswordRequired(Long) - Method in class ome.security.auth.PasswordUtil
-
Returns a boolean based on the supplied user ID and system property setting.
- isPixelsTypeSigned() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- isProbablyTimeout(DataAccessResourceFailureException) - Static method in class ome.logic.QueryImpl
-
- isPropertyAccessible(String, String) - Method in class ome.services.graphs.GraphPathBean
-
Find if the given property can be accessed.
- isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.EventProviderInDb
-
- isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.EventProviderInMemory
-
- isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.NodeProviderInDb
-
- isReadOnly(ReadOnlyStatus) - Method in class ome.security.basic.NodeProviderInMemory
-
- isReadOnly() - Method in class ome.services.sessions.SessionContextImpl
-
- isReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionProviderInDb
-
- isReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionProviderInMemory
-
- isReadOnly(ReadOnlyStatus) - Method in interface ome.services.util.ReadOnlyStatus.IsAware
-
- isReadOnlyDb() - Method in class ome.services.util.ReadOnlyStatus
-
- isReadOnlyRepo() - Method in class ome.services.util.ReadOnlyStatus
-
- isReady() - Method in class ome.security.basic.BasicSecuritySystem
-
- isReady() - Method in class ome.security.basic.CurrentDetails
-
Checks if the current Thread has non-null Experimenter,
Event, and ExperimenterGroup, required for proper
functioning of the security system.
- isReady() - Method in interface ome.security.SecuritySystem
-
- isReady() - Method in class ome.security.SecuritySystemHolder
-
- isReady() - Method in class ome.security.sharing.SharingSecuritySystem
-
- isRestricted(IObject) - Method in class ome.security.policy.BasePolicy
-
- isRestricted(IObject) - Method in class ome.security.policy.BinaryAccessPolicy
-
- isRestricted(String, IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- isRestricted(IObject) - Method in interface ome.security.policy.Policy
-
- isRestricted(String, IObject) - Method in interface ome.security.policy.PolicyService
-
Ask each configured
Policy instance with the given name argument
if it considers the restriction active for the given
IObject
argument.
- isReturnUnloaded() - Method in class ome.services.SearchBean
-
- isShare(EventContext) - Method in class ome.security.basic.AbstractSecurityFilter
-
- isSigned() - Method in class ome.services.RawPixelsBean
-
- isSingleton() - Method in class ome.security.basic.EventListenersFactoryBean
-
being a singleton implies that this FactoryBean will only ever
create one instance.
- isStopSet() - Method in class ome.services.eventlogs.EventLogLoader
-
Returns true if the stop flag has been set on this instance.
- isSyncOnLogin() - Method in class ome.security.auth.LdapConfig
-
- isSystemType(Class<? extends IObject>) - Method in class ome.security.basic.BasicSecuritySystem
-
classes which cannot be created by regular users.
- isSystemType(Class<? extends IObject>) - Method in interface ome.security.SecuritySystem
-
checks if instances of the given type are "System-Types".
- isSystemType(Class<? extends IObject>) - Method in class ome.security.SecuritySystemHolder
-
- isSystemType(Class<? extends IObject>) - Method in class ome.security.sharing.SharingSecuritySystem
-
- isSystemType(Class<?>) - Method in class ome.security.SystemTypes
-
classes which cannot be created by regular users.
- isThreadSafe() - Method in class ome.services.messages.AbstractSessionMessage
-
- isThumbnailCached(long) - Method in class ome.services.ThumbnailCtx
-
Checks to see if a thumbnail is in the on disk cache or not.
- isTransient(Object) - Method in class ome.security.basic.OmeroInterceptor
-
- isUnloaded(Object) - Static method in class ome.tools.hibernate.HibernateUtils
-
- isUseProjections() - Method in class ome.services.SearchBean
-
- iterate() - Method in class ome.services.scripts.ScriptRepoHelper
-
- iterator() - Method in class ome.services.eventlogs.EventLogLoader
-
- iUpdate - Variable in class ome.logic.AbstractLevel2Service
-
- iUpdate - Variable in class ome.services.AbstractStatefulBean
-
- lastEventLog() - Method in class ome.services.eventlogs.EventLogLoader
-
- lastresultsAsWorkingGroup() - Method in class ome.services.SearchBean
-
- LdapConfig - Class in ome.security.auth
-
Static methods for dealing with LDAP (DN) and the "password" table.
- LdapConfig(boolean, String, String, String, String, String) - Constructor for class ome.security.auth.LdapConfig
-
- LdapConfig(boolean, String, String, String, String, String, boolean) - Constructor for class ome.security.auth.LdapConfig
-
- LdapConfig(boolean, String, String, String, String, String, boolean, String) - Constructor for class ome.security.auth.LdapConfig
-
- LdapConfig(boolean, String, String, String, String, String, boolean, String, String) - Constructor for class ome.security.auth.LdapConfig
-
- LdapImpl - Class in ome.logic
-
Provides methods for administering user accounts, passwords, as well as
methods which require special privileges.
- LdapImpl(ContextSource, LdapOperations, Roles, LdapConfig, RoleProvider, SqlAction) - Constructor for class ome.logic.LdapImpl
-
- LdapImpl.GroupLoader - Class in ome.logic
-
- LdapPasswordProvider - Class in ome.security.auth
-
- LdapPasswordProvider(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.LdapPasswordProvider
-
- LdapPasswordProvider(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.LdapPasswordProvider
-
- LdapPasswordProvider431 - Class in ome.security.auth.providers
-
- LdapPasswordProvider431(PasswordUtil, LdapImpl) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
-
- LdapPasswordProvider431(PasswordUtil, LdapImpl, boolean) - Constructor for class ome.security.auth.providers.LdapPasswordProvider431
-
- ldapUtil - Variable in class ome.logic.AdminImpl
-
- ldapUtil - Variable in class ome.security.auth.LdapPasswordProvider
-
- ldapUtil - Variable in class ome.security.auth.providers.LdapPasswordProvider431
-
- leader_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
-
- leadingWildcard - Variable in class ome.services.search.SearchValues
-
- LEFT_JOIN - Static variable in class ome.services.query.Query
-
imported constant for ease of use
- legacyUtil - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
- length() - Method in class ome.services.scripts.RepoFile.FsFile
-
- length() - Method in class ome.services.scripts.RepoFile
-
- LightAdminPrivileges - Class in ome.security.basic
-
Report the light administrator privileges associated with a given session.
- LightAdminPrivileges(Roles) - Constructor for class ome.security.basic.LightAdminPrivileges
-
- LightAdminPrivilegesCleanup - Class in ome.security.basic
-
Periodically clean up old entries from the _current_admin_privileges database table.
- LightAdminPrivilegesCleanup(SqlAction, int) - Constructor for class ome.security.basic.LightAdminPrivilegesCleanup
-
Start a new scheduled repeating task for cleaning up the _current_admin_privileges database table.
- LightAdminPrivilegesSecurityFilter - Class in ome.security.basic
-
- LightAdminPrivilegesSecurityFilter(Roles) - Constructor for class ome.security.basic.LightAdminPrivilegesSecurityFilter
-
Deprecated.
Construct a new light administrator filter.
- link(ILink[], Parameters) - Method in class ome.logic.PojosImpl
-
- linkGroupAndUser(ExperimenterGroup, Experimenter, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- list(List<Obj>) - Method in class ome.services.sharing.ShareBean
-
- listActiveRestrictions(IObject) - Method in class ome.security.policy.DefaultPolicyService
-
- listActiveRestrictions(IObject) - Method in interface ome.security.policy.PolicyService
-
- listAllRestrictions() - Method in class ome.security.policy.DefaultPolicyService
-
- listAllRestrictions() - Method in interface ome.security.policy.PolicyService
-
- ListAsSQLArrayUserType<T> - Class in ome.tools.hibernate
-
Hibernate type to store Lists of primitives using SQL ARRAY.
- ListAsSQLArrayUserType() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType
-
- ListAsSQLArrayUserType.ArrayFactory - Interface in ome.tools.hibernate
-
- ListAsSQLArrayUserType.BOOLEAN - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$BOOLEAN"
hibernate.column name="fieldName" sql-type="bool[]"
- ListAsSQLArrayUserType.DATE - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$DATE"
hibernate.column name="fieldName" sql-type="timestamp[]"
- ListAsSQLArrayUserType.DOUBLE - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$DOUBLE"
hibernate.column name="fieldName" sql-type="float8[]"
- ListAsSQLArrayUserType.ENUM<E extends java.lang.Enum<E>> - Class in ome.tools.hibernate
-
Warning, this one is special.
- ListAsSQLArrayUserType.FLOAT - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$FLOAT"
hibernate.column name="fieldName" sql-type="real[]"
- ListAsSQLArrayUserType.INTEGER - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$INTEGER"
hibernate.column name="fieldName" sql-type="int[]"
- ListAsSQLArrayUserType.STRING - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING"
hibernate.column name="fieldName" sql-type="text[]"
- ListAsSQLArrayUserType.STRING2 - Class in ome.tools.hibernate
-
To use, define : hibernate.property
type="ome.tools.hibernate.ListAsSQLArrayUserType$STRING2"
hibernate.column name="fieldName" sql-type="text[]"
Added by Josh
- load(FileDeleter.Type) - Method in class ome.services.delete.files.FileDeleter
-
Lookup the ids which are scheduled for deletion.
- load(List<Object[]>) - Method in class ome.services.eventlogs.EventLogQueue
-
- load(Long, String, Long, String, Integer) - Method in class ome.services.eventlogs.EventLogQueue
-
Guarantees that the given arguments are available somewhere in the queue
returning true if they were newly added.
- load() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- load(long, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
-
- load(long, Session, SqlAction, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
-
- load() - Method in class ome.services.util.DBUserCheck
-
- loadAll(boolean, String) - Method in class ome.services.scripts.ScriptRepoHelper
-
- loadAll(boolean, String, Principal) - Method in class ome.services.scripts.ScriptRepoHelper
-
- loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper
-
- loadAllMetadata(long) - Method in class ome.services.ThumbnailCtx
-
Retrieves all thumbnail metadata available in the database for a given
Pixels ID.
- loadAndPrepareMetadata(Set<Long>, int) - Method in class ome.services.ThumbnailCtx
-
Bulk loads and prepares metadata for a group of pixels sets.
- loadAndPrepareMetadata(Set<Long>, Dimension) - Method in class ome.services.ThumbnailCtx
-
Bulk loads and prepares metadata for a group of pixels sets.
- loadAndPrepareMetadata(Set<Long>, Dimension, boolean) - Method in class ome.services.ThumbnailCtx
-
Bulk loads and prepares metadata for a group of pixels sets.
- loadAndPrepareRenderingSettings(Set<Long>) - Method in class ome.services.ThumbnailCtx
-
Bulk loads a set of rendering settings for a group of pixels sets and
prepares our internal data structures.
- loadAndPrepareRenderingSettings(long, long) - Method in class ome.services.ThumbnailCtx
-
Loads and prepares a rendering settings for a Pixels ID and RenderingDef
ID.
- loadAnnotation(Set<Long>) - Method in class ome.logic.MetadataImpl
-
- loadAnnotations(Class<T>, Set<Long>, Set<String>, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
-
- loadAnnotationsUsedNotOwned(Class, long) - Method in class ome.logic.MetadataImpl
-
- loadChannelAcquisitionData(Set<Long>) - Method in class ome.logic.MetadataImpl
-
- loadContainerHierarchy(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
-
- loadedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
-
- loadedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
-
- loadedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
-
- loadedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
-
- loader - Variable in class ome.services.eventlogs.EventLogFailure
-
- loader - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- loader - Variable in class ome.services.pixeldata.PixelDataHandler
-
- loadEventContext(boolean) - Method in class ome.security.basic.BasicSecuritySystem
-
- loadEventContext(boolean, boolean) - Method in class ome.security.basic.BasicSecuritySystem
-
- loadEventContext(boolean) - Method in interface ome.security.SecuritySystem
-
Prepares the current EventContext instance with the current
Principal.
- loadEventContext(boolean) - Method in class ome.security.SecuritySystemHolder
-
- loadEventContext(boolean) - Method in class ome.security.sharing.SharingSecuritySystem
-
- loadInstrument(long) - Method in class ome.logic.MetadataImpl
-
- loadLdapGroups(String, DistinguishedName) - Method in class ome.logic.LdapImpl
-
Deprecated.
- loadLogFiles(Class<? extends IObject>, Set<Long>) - Method in class ome.logic.MetadataImpl
-
- loadMembers(ShareData) - Method in class ome.services.sharing.ShareBean
-
- loadPermissions(Session) - Method in class ome.security.basic.BasicEventContext
-
- loadPermissions(Session) - Method in class ome.security.basic.CurrentDetails
-
- loadRenderingDef(long) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- loadRndSettings(long) - Method in class ome.logic.PixelsImpl
-
- loadSpecifiedAnnotations(Class, Set<String>, Set<String>, Parameters) - Method in class ome.logic.MetadataImpl
-
- loadSpecifiedAnnotationsLinkedTo(Class, Set<String>, Set<String>, Class, Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
-
- loadTagContent(Set<Long>, Parameters) - Method in class ome.logic.MetadataImpl
-
- loadTagSets(Parameters) - Method in class ome.logic.MetadataImpl
-
- LocalAdmin - Interface in ome.api.local
-
Provides local (internal) extensions for administration
- localAdmin - Variable in class ome.logic.UpdateImpl
-
- LocalCompress - Interface in ome.api.local
-
Provides methods for performing scaling (change of the image size through
interpolation or other means) on BufferedImages.
- LocalConfig - Interface in ome.api.local
-
Provides local (internal) extensions for configuration.
- LocalQuery - Interface in ome.api.local
-
Provides local (internal) extensions for querying
- localQuery - Variable in class ome.logic.UpdateImpl
-
- LocalSession - Interface in ome.api.local
-
Provides local (internal) extensions for session management
- LocalShare - Interface in ome.api.local
-
Provides local (internal) extensions for shares
- LocalUpdate - Interface in ome.api.local
-
Provides local (internal) extensions for updating
- log - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
- log - Variable in class ome.security.basic.AbstractSecurityFilter
-
- log(String) - Method in class ome.security.basic.OmeroInterceptor
-
- log - Static variable in class ome.services.delete.DeleteBean
-
- log - Variable in class ome.services.eventlogs.EventLogFailure
-
- log - Variable in class ome.services.eventlogs.EventLogLoader
-
- log - Variable in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- log - Variable in class ome.services.mail.MailSender
-
- log - Variable in class ome.services.scripts.ScriptRepoHelper
-
- log - Static variable in class ome.services.sharing.ShareBean
-
- log - Variable in class ome.services.sharing.ShareStore
-
- log - Static variable in class ome.services.util.DBEnumCheck
-
- log - Static variable in class ome.services.util.DBPatchCheck
-
- log - Static variable in class ome.services.util.DBUserCheck
-
- log - Static variable in class ome.services.util.JvmSettingsCheck
-
- log - Static variable in class ome.services.util.ServerDirectoryCheck
-
- log - Static variable in class ome.services.util.ServerVersionCheck
-
- log(String) - Method in class ome.tools.hibernate.EventMethodInterceptor
-
- logger() - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- LOGGER - Static variable in class ome.services.util.DBUnicodeUnitsCheck
-
- login(Principal) - Method in class ome.security.basic.BasicSecuritySystem
-
- login(Principal) - Method in class ome.security.basic.CurrentDetails
-
- login(BasicEventContext) - Method in class ome.security.basic.CurrentDetails
-
Login method which can be used by the security system to replace the
existing
BasicEventContext.
- login(Principal) - Method in interface ome.security.basic.PrincipalHolder
-
Add a new principal context to the stack.
- login(BasicEventContext) - Method in interface ome.security.basic.PrincipalHolder
-
Allow logging in directly with an event context.
- login(Principal) - Method in interface ome.security.SecuritySystem
-
stores this Principal instance in the current thread context for
authenticating and authorizing all actions.
- login(Principal) - Method in class ome.security.SecuritySystemHolder
-
- login(Principal) - Method in class ome.security.sharing.SharingSecuritySystem
-
- loginAttempt(String, Boolean) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- LoginAttemptListener - Class in ome.security.auth
-
- LoginAttemptListener(int, long) - Constructor for class ome.security.auth.LoginAttemptListener
-
- LoginAttemptMessage - Class in ome.services.messages
-
Published when any check is performed against a password.
- LoginAttemptMessage(Object, String, Boolean) - Constructor for class ome.services.messages.LoginAttemptMessage
-
- logout() - Method in class ome.security.basic.BasicSecuritySystem
-
- logout() - Method in class ome.security.basic.CurrentDetails
-
- logout() - Method in interface ome.security.basic.PrincipalHolder
-
Pop the last created principal context and return the number of active
contexts remaining.
- logout() - Method in interface ome.security.SecuritySystem
-
clears the top Principal instance from the current thread
context.
- logout() - Method in class ome.security.SecuritySystemHolder
-
- logout() - Method in class ome.security.sharing.SharingSecuritySystem
-
- LongCounter - Class in ome.services.sessions.stats
-
Counter object which increments an internal long by some integer value,
and according to some strategy publishes an InternalMessage subclass.
- LongCounter(int) - Constructor for class ome.services.sessions.stats.LongCounter
-
- LongSeqHelper - Class in ome.services.sharing.data
-
- LongSeqHelper() - Constructor for class ome.services.sharing.data.LongSeqHelper
-
- LongSeqHolder - Class in ome.services.sharing.data
-
- LongSeqHolder() - Constructor for class ome.services.sharing.data.LongSeqHolder
-
- LongSeqHolder(List<Long>) - Constructor for class ome.services.sharing.data.LongSeqHolder
-
- lookup() - Method in class ome.services.eventlogs.EventLogQueue
-
- lookup(long) - Method in class ome.services.procs.ProcessorSkeleton
-
- lookup(String, Parameters) - Method in class ome.services.query.ClassQuerySource
-
- lookup(String, Parameters) - Method in class ome.services.query.NullQuerySource
-
- lookup(String, Parameters) - Method in class ome.services.query.QueryFactory
-
- lookup(String, Parameters) - Method in class ome.services.query.QuerySource
-
map the queryID argument to some Query instance (including null).
- lookup(String, Parameters) - Method in class ome.services.query.StringQuerySource
-
- lookupExperimenter(String) - Method in class ome.logic.AdminImpl
-
- lookupExperimenters() - Method in class ome.logic.AdminImpl
-
- lookupGroup(String) - Method in class ome.logic.AdminImpl
-
- lookupGroups() - Method in class ome.logic.AdminImpl
-
- lookupLdapAuthExperimenter(long) - Method in class ome.logic.AdminImpl
-
- lookupLdapAuthExperimenter(Long) - Method in class ome.logic.LdapImpl
-
Queries the LDAP server and returns the DN for the specified OMERO user
ID.
- lookupLdapAuthExperimenters() - Method in class ome.logic.AdminImpl
-
- lookupLdapAuthExperimenters() - Method in class ome.logic.LdapImpl
-
Queries the LDAP server and returns the DN for all OMERO users that have
the ldap flag enabled.
- lookupPixels(long) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- lookupRenderingDef(long) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- lowestEntityId - Variable in class ome.services.pixeldata.PersistentEventLogLoader
-
The lowest entity id from a single dataPerUser set.
- lsid(Class, long) - Method in class ome.services.db.DatabaseIdentity
-
- lsid(Class, long, long) - Method in class ome.services.db.DatabaseIdentity
-
- lsid(String, String) - Method in class ome.services.db.DatabaseIdentity
-
- lsid(String, String, String) - Method in class ome.services.db.DatabaseIdentity
-
- LsidUtils - Class in ome.tools.lsid
-
- LsidUtils() - Constructor for class ome.tools.lsid.LsidUtils
-
- LutProviderImpl - Class in ome.logic
-
Lookup table provider implementation.
- LutProviderImpl(ScriptRepoHelper, ScriptFileType) - Constructor for class ome.logic.LutProviderImpl
-
- lutReaders - Variable in class ome.logic.LutProviderImpl
-
Available readers, keyed off name.
- Obj - Class in ome.services.sharing.data
-
- Obj() - Constructor for class ome.services.sharing.data.Obj
-
- Obj(String, long) - Constructor for class ome.services.sharing.data.Obj
-
- objectList - Variable in class ome.services.sharing.data.ShareData
-
- ObjectMailSender - Class in ome.services.mail
-
When an
EventLogMessage of the specified type and kind is received,
an email is sent to all users which are returned by a given query.
- ObjectMailSender() - Constructor for class ome.services.mail.ObjectMailSender
-
- objectMap - Variable in class ome.services.sharing.data.ShareData
-
- objects - Variable in class ome.services.messages.ReindexMessage
-
- ObjectsReadCounter - Class in ome.services.sessions.stats
-
Counter for all the objects read in a session.
- ObjectsReadCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsReadCounter
-
- objectsReadHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
-
- ObjectsReadStatsMessage - Class in ome.services.messages.stats
-
Published when some limit in user/group/session activity has been reached.
- ObjectsReadStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsReadStatsMessage
-
- ObjectsWrittenCounter - Class in ome.services.sessions.stats
-
Counter for all the objects read in a session.
- ObjectsWrittenCounter(int) - Constructor for class ome.services.sessions.stats.ObjectsWrittenCounter
-
- objectsWrittenHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
-
- ObjectsWrittenStatsMessage - Class in ome.services.messages.stats
-
- ObjectsWrittenStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.ObjectsWrittenStatsMessage
-
- ObjHolder - Class in ome.services.sharing.data
-
- ObjHolder() - Constructor for class ome.services.sharing.data.ObjHolder
-
- ObjHolder(Obj) - Constructor for class ome.services.sharing.data.ObjHolder
-
- ObjPrx - Interface in ome.services.sharing.data
-
- ObjPrxHelper - Class in ome.services.sharing.data
-
Provides type-specific helper functions.
- ObjPrxHelper() - Constructor for class ome.services.sharing.data.ObjPrxHelper
-
- ObjPrxHolder - Class in ome.services.sharing.data
-
- ObjPrxHolder() - Constructor for class ome.services.sharing.data.ObjPrxHolder
-
- ObjPrxHolder(ObjPrx) - Constructor for class ome.services.sharing.data.ObjPrxHolder
-
- ObjSeqHelper - Class in ome.services.sharing.data
-
- ObjSeqHelper() - Constructor for class ome.services.sharing.data.ObjSeqHelper
-
- ObjSeqHolder - Class in ome.services.sharing.data
-
- ObjSeqHolder() - Constructor for class ome.services.sharing.data.ObjSeqHolder
-
- ObjSeqHolder(List<Obj>) - Constructor for class ome.services.sharing.data.ObjSeqHolder
-
- obToImageCache - Variable in class ome.services.sharing.BlobShareStore
-
- ome.api.local - package ome.api.local
-
Non-client service API for OMERO
- ome.formats - package ome.formats
-
- ome.formats.importer.util - package ome.formats.importer.util
-
- ome.logic - package ome.logic
-
The central repository of implementations which will be accessible through this server.
- ome.security - package ome.security
-
JBoss and OMERO security handling
- ome.security.auth - package ome.security.auth
-
- ome.security.auth.providers - package ome.security.auth.providers
-
- ome.security.basic - package ome.security.basic
-
Basic OMERO security contextual classes
- ome.security.policy - package ome.security.policy
-
Extensible service and security policies which can influence
whether a user, group, or other agent can perform a certain
action.
- ome.security.sharing - package ome.security.sharing
-
- ome.services - package ome.services
-
Base services package for OMERO API services
- ome.services.db - package ome.services.db
-
- ome.services.delete - package ome.services.delete
-
Implementations of the ome.api.IDelete service.
- ome.services.delete.files - package ome.services.delete.files
-
- ome.services.eventlogs - package ome.services.eventlogs
-
- ome.services.fulltext - package ome.services.fulltext
-
All necessary classes for background indexing of metadata and attached binary
files.
- ome.services.fulltext.bridges - package ome.services.fulltext.bridges
-
Custom FieldBridge implementations which can be configured to be run on each
indexing activity.
- ome.services.graphs - package ome.services.graphs
-
Server classes for handling complicated graphs of model objects.
- ome.services.mail - package ome.services.mail
-
General mail services.
- ome.services.messages - package ome.services.messages
-
Message implementations used throughout the server for internal communication.
- ome.services.messages.stats - package ome.services.messages.stats
-
- ome.services.pixeldata - package ome.services.pixeldata
-
- ome.services.procs - package ome.services.procs
-
Internal process and process management
- ome.services.procs.scripts - package ome.services.procs.scripts
-
Script processor infrastructure.
- ome.services.projection - package ome.services.projection
-
- ome.services.query - package ome.services.query
-
facilitates the creation of Hibernate Queries and Criteria.
- ome.services.scheduler - package ome.services.scheduler
-
- ome.services.scripts - package ome.services.scripts
-
- ome.services.search - package ome.services.search
-
Internal search implementation classes.
- ome.services.sessions - package ome.services.sessions
-
- ome.services.sessions.events - package ome.services.sessions.events
-
- ome.services.sessions.state - package ome.services.sessions.state
-
- ome.services.sessions.stats - package ome.services.sessions.stats
-
- ome.services.sharing - package ome.services.sharing
-
- ome.services.sharing.data - package ome.services.sharing.data
-
- ome.services.util - package ome.services.util
-
Helper classes to support OMERO service beans
- ome.tools - package ome.tools
-
OMERO Server Utility and Spring/Hibernate Tools
- ome.tools.hibernate - package ome.tools.hibernate
-
Hibernate specific tools for the OMERO Server
- ome.tools.lsid - package ome.tools.lsid
-
Life Science Identifier (LSID) tools
- ome.tools.spring - package ome.tools.spring
-
OMERO Server tools specific to Spring
- OMERO_TABLE - Variable in class ome.services.fulltext.bridges.TablesBridge
-
Deprecated.
Mimetype set on OriginalFile.mimetype (or in previous version,
OriginalFile.format.value).
- omeroDataDir - Variable in class ome.services.OmeroFilePathResolver
-
The server's OMERO data directory.
- OmeroFilePathResolver - Class in ome.services
-
OMERO server based resolver for file paths.
- OmeroFilePathResolver(SqlAction, String) - Constructor for class ome.services.OmeroFilePathResolver
-
Constructor.
- OmeroInterceptor - Class in ome.security.basic
-
implements Interceptor for controlling various aspects
of the Hibernate runtime.
- OmeroInterceptor(Roles, SystemTypes, ExtendedMetadata, CurrentDetails, TokenHolder, SessionStats, LightAdminPrivileges, SqlAction, SqlQueryTransformer, Set<String>, Set<String>) - Constructor for class ome.security.basic.OmeroInterceptor
-
- OMEROMetadataStore - Class in ome.formats
-
An OMERO metadata store.
- OMEROMetadataStore() - Constructor for class ome.formats.OMEROMetadataStore
-
Empty constructor for testing purposes.
- OMEROMetadataStore(ServiceFactory, SqlAction) - Constructor for class ome.formats.OMEROMetadataStore
-
Creates a new instance.
- OmeroModelContextMapper - Class in ome.security.auth
-
Parent class for any OMERO model-to-LDAP mappers.
- OmeroModelContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.OmeroModelContextMapper
-
- onApplicationEvent(LoginAttemptMessage) - Method in class ome.security.auth.LoginAttemptListener
-
- onApplicationEvent(EventLogMessage) - Method in class ome.security.basic.BasicSecuritySystem
-
- onApplicationEvent(ContextMessage) - Method in class ome.security.basic.EventHandler
-
- onApplicationEvent(UserSignalMessage) - Method in class ome.services.db.SelfCorrectingDataSource
-
Handles the USR1 posix signal by calling close on the underlying
data source via reflection.
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogLoader
-
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.eventlogs.EventLogQueue
-
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.ParserSession
-
Deprecated.
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.fulltext.PersistentEventLogLoader
-
Deprecated.
- onApplicationEvent(LoginAttemptMessage) - Method in class ome.services.mail.FailedLoginMailSender
-
- onApplicationEvent(EventLogsMessage) - Method in class ome.services.mail.ObjectMailSender
-
- onApplicationEvent(ShutdownMessage) - Method in class ome.services.mail.ServerDownMailSender
-
- onApplicationEvent(MissingPyramidMessage) - Method in class ome.services.pixeldata.PixelDataThread
-
Called in the main server (Blitz-0) in order to create a PIXELDATA
EventLog which will get processed by PixelData-0.
- onApplicationEvent(ContextRefreshedEvent) - Method in class ome.services.scheduler.SchedulerFactoryBean
-
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.sessions.SessionManagerImpl
-
- onApplicationEvent(ApplicationEvent) - Method in class ome.services.util.ServiceHandler
-
- onApplicationEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
-
- onCollectionRecreate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
- onCollectionRemove(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
- onCollectionUpdate(Object, Serializable) - Method in class ome.security.basic.OmeroInterceptor
-
- OnContextRefreshedEventListener - Class in ome.tools.spring
-
ApplicationListener which only listens for
ContextRefreshedEvent and only responds to the first one.
- OnContextRefreshedEventListener() - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
-
- OnContextRefreshedEventListener(boolean, int) - Constructor for class ome.tools.spring.OnContextRefreshedEventListener
-
- onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
-
default logic
- onDiskCache(String) - Method in interface ome.services.sessions.SessionManager
-
Returns after possibly creating an on-disk cache which
can be used throughout the session.
- onDiskCache(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- onDiskCache(String) - Method in class ome.services.sessions.state.SessionCache
-
- onegroup - Variable in class ome.security.SecurityFilterHolder
-
- OneGroupSecurityFilter - Class in ome.security.basic
-
overrides FilterDefinitionFactoryBean in order to construct our
security filter in code and not in XML.
- OneGroupSecurityFilter() - Constructor for class ome.security.basic.OneGroupSecurityFilter
-
Default constructor which calls all the necessary setters for this
FactoryBean.
- OneGroupSecurityFilter(Roles) - Constructor for class ome.security.basic.OneGroupSecurityFilter
-
- onExecutionException(ExecutionException) - Method in class ome.services.pixeldata.PixelDataThread
-
Basic handling just logs at ERROR level.
- onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
-
- onLoad(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
-
default logic.
- onlyAnnotatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
-
- onlyAnnotatedBy(Details) - Method in class ome.services.SearchBean
-
- onlyAnnotatedWith - Variable in class ome.services.search.SearchValues
-
- onlyAnnotatedWith(Class...) - Method in class ome.services.SearchBean
-
- onlyCreatedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
-
- onlyIds - Variable in class ome.services.search.SearchValues
-
- onlyIds(Long...) - Method in class ome.services.SearchBean
-
- onlyModifiedBetween(Timestamp, Timestamp) - Method in class ome.services.SearchBean
-
- onlyOwnedBy(Details) - Method in class ome.services.SearchBean
-
- onlyPermissionsChanged(Details, Details) - Static method in class ome.tools.hibernate.HibernateUtils
-
- onlyType(Class<T>) - Method in class ome.services.SearchBean
-
- onlyTypes - Variable in class ome.services.search.SearchValues
-
- onlyTypes(Class<T>...) - Method in class ome.services.SearchBean
-
- onMerge(MergeEvent) - Method in class ome.security.basic.MergeEventListener
-
- onMerge(MergeEvent, Map) - Method in class ome.security.basic.MergeEventListener
-
- onPostDelete(PostDeleteEvent) - Method in class ome.security.ACLEventListener
-
unused
- onPostDelete(PostDeleteEvent) - Method in class ome.security.basic.EventLogListener
-
- onPostInsert(PostInsertEvent) - Method in class ome.security.ACLEventListener
-
unused
- onPostInsert(PostInsertEvent) - Method in class ome.security.basic.EventLogListener
-
- onPostLoad(PostLoadEvent) - Method in class ome.security.ACLEventListener
-
catches all load events after the fact, and tests the current users
permissions to read that object.
- onPostUpdate(PostUpdateEvent) - Method in class ome.security.ACLEventListener
-
unused
- onPostUpdate(PostUpdateEvent) - Method in class ome.security.basic.EventLogListener
-
- onPreDelete(PreDeleteEvent) - Method in class ome.security.ACLEventListener
-
- onPreInsert(PreInsertEvent) - Method in class ome.security.ACLEventListener
-
- onPreLoad(PreLoadEvent) - Method in class ome.security.ACLEventListener
-
unused
- onPrepareStatement(String) - Method in class ome.security.basic.OmeroInterceptor
-
- onPrepareStatement(String) - Method in class ome.security.basic.SqlQueryInterceptor
-
- onPreUpdate(PreUpdateEvent) - Method in class ome.security.ACLEventListener
-
- onPreUpdate(PreUpdateEvent) - Method in class ome.security.basic.UpdateEventListener
-
updates the update event field of an IObject instance.
- onRefresh(RefreshEvent) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
-
- onRefresh(RefreshEvent, Map) - Method in class ome.tools.hibernate.ReloadingRefreshEventListener
-
- onSave(Object, Serializable, Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
-
- onSaveOrUpdate(SaveOrUpdateEvent) - Method in class ome.security.basic.SaveEventListener
-
- optimize() - Method in class ome.services.fulltext.FullTextIndexer2
-
Defragment the search index.
- optional - Variable in class ome.services.query.QueryParameterDef
-
whether or not this QueryParameter can be omitted or its
value null.
- optlock - Variable in class ome.services.sharing.data.ShareData
-
- or() - Method in class ome.services.SearchBean
-
- or(String) - Method in class ome.tools.hibernate.QueryBuilder
-
Appends "or" plus your string unless this is the first where-spec in
which case it is simply appended.
- order(String, boolean) - Method in class ome.tools.hibernate.QueryBuilder
-
- orderBy - Variable in class ome.services.search.SearchValues
-
- orderByAscending(String) - Static method in class ome.services.search.SearchAction
-
- orderByPath(String) - Static method in class ome.services.search.SearchAction
-
- OrgUnitNewUserGroupBean - Class in ome.security.auth
-
Handles the ":ou:" specifier from omero-server.properties by adding the user
to a group named by the final organizational unit.
- OrgUnitNewUserGroupBean(DistinguishedName) - Constructor for class ome.security.auth.OrgUnitNewUserGroupBean
-
- OriginalFileDeletions - Class in ome.services.delete.files
-
Deletes all repository files immediately.
- OriginalFileDeletions(AbstractFileSystemService, Set<Long>, OmeroContext) - Constructor for class ome.services.delete.files.OriginalFileDeletions
-
- orphan - Variable in class ome.services.graphs.GraphPolicy.Details
-
- osf - Variable in class ome.logic.AdminImpl
-
- outputEnvironment(String) - Method in interface ome.services.sessions.SessionManager
-
Returns a copy of the output environment.
- outputEnvironment(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- override(String[], Object) - Method in class ome.security.basic.EventListenersFactoryBean
-
calls override for each key
- override(String, Object) - Method in class ome.security.basic.EventListenersFactoryBean
-
first re-initializes the list for key, and then adds object
- overrides() - Method in class ome.security.basic.EventListenersFactoryBean
-
- own(String) - Method in class ome.services.db.DatabaseIdentity
-
- ownedBy - Variable in class ome.services.search.SearchValues
-
- owner - Variable in class ome.services.sharing.data.ShareData
-
- ownerId - Variable in class ome.services.graphs.GraphPolicy.Details
-
the ID of the object's Experimenter,
or null if the object does not have an owner
- ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in interface ome.security.auth.NewUserGroupOwnerBean
-
- ownerOfGroups(String, LdapConfig, LdapOperations, RoleProvider, AttributeSet) - Method in class ome.security.auth.QueryNewUserGroupBean
-
- ownerOrGroup(Class, Criteria) - Method in class ome.services.search.SearchAction
-
- ownerOrGroup(Class, QueryBuilder, String) - Method in class ome.services.search.SearchAction
-
- ownerOrGroupFilters(Session, String[], String[]) - Method in class ome.services.query.Query
-
standard filter used by many subclasses which uses the
Parameters.isExperimenter() and Parameters.isGroup()
booleans to see if a filter should be turned on.
- param(int, Object) - Method in class ome.tools.hibernate.QueryBuilder
-
- param(String, Object) - Method in class ome.tools.hibernate.QueryBuilder
-
- paramList(String, Collection) - Method in class ome.tools.hibernate.QueryBuilder
-
- params - Variable in class ome.services.query.Query
-
container of QueryParameter instances.
- params(Parameters) - Method in class ome.tools.hibernate.QueryBuilder
-
- parse(String[]) - Static method in class ome.logic.HardWiredInterceptor
-
- parse(String) - Method in class ome.security.auth.LdapConfig
-
- parse(OriginalFile, OriginalFilesService, Map<String, FileParser>) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
Attempts to parse the given OriginalFile.
- parse(File) - Method in class ome.services.fulltext.FileParser
-
- parse(String[], String[], String[]) - Static method in class ome.services.search.SomeMustNone
-
- parse(ShareData) - Method in class ome.services.sharing.ShareStore
-
- parse(long, byte[]) - Method in class ome.services.sharing.ShareStore
-
- parseField(String) - Static method in class ome.tools.lsid.LsidUtils
-
takes a field identifier as code-generated in each IObject class and
produces a back-end useable name.
- parseFilter(Criteria, Filter) - Method in class ome.logic.QueryImpl
-
Responsible for applying the information provided in a
Filter to a Criteria
instance.
- ParserOpenFileMessage - Class in ome.services.messages
-
A trivial copy of RegisterServiceCleanupMessage with a different name so that
we can catch files opened during search indexing and close them at the end of
parsing.
- ParserOpenFileMessage(Object, Object) - Constructor for class ome.services.messages.ParserOpenFileMessage
-
- parsers - Variable in class ome.services.fulltext.FullTextBridge
-
Deprecated.
- parserSession - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- ParserSession - Class in ome.services.fulltext
-
Deprecated.
- ParserSession() - Constructor for class ome.services.fulltext.ParserSession
-
Deprecated.
- parseRules(GraphPathBean, Collection<GraphPolicyRule>) - Static method in class ome.services.graphs.GraphPolicyRule
-
Convert the text-based rules as specified in the configuration metadata into a policy applicable in
model object graph traversal.
- parseStream(InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
-
- parseType(String) - Static method in class ome.tools.lsid.LsidUtils
-
takes a field identifier as code-generated in each IObject class and
produces a back-end useable type name.
- passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.AllGroupsSecurityFilter
-
tests that the Details argument passes the security test that
this filter defines.
- passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.LightAdminPrivilegesSecurityFilter
-
Deprecated.
- passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.OneGroupSecurityFilter
-
tests that the Details argument passes the security test that
this filter defines.
- passesFilter(Session, Details, EventContext) - Method in class ome.security.basic.SharingSecurityFilter
-
- passesFilter(Session, Details, EventContext) - Method in interface ome.security.SecurityFilter
-
tests that the Details argument passes the security test that
this filter defines.
- passesFilter(Session, Details, EventContext) - Method in class ome.security.SecurityFilterHolder
-
- passivate() - Method in class ome.services.JobBean
-
Does nothing.
- passivate() - Method in class ome.services.RawFileBean
-
- passivate() - Method in class ome.services.RawPixelsBean
-
- passivate() - Method in class ome.services.RenderingBean
-
- passivate() - Method in class ome.services.SearchBean
-
- passivate() - Method in class ome.services.ThumbnailBean
-
- passivationNotAllowed() - Method in class ome.services.util.BeanHelper
-
- PasswordChangeException - Exception in ome.security.auth
-
- PasswordChangeException(String) - Constructor for exception ome.security.auth.PasswordChangeException
-
- passwordDigest(String) - Method in class ome.security.auth.PasswordUtil
-
Creates an MD5 hash of the given clear text and base64 encodes it.
- passwordDigest(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
-
- passwordProvider - Variable in class ome.logic.AdminImpl
-
- PasswordProvider - Interface in ome.security.auth
-
Authentication interface responsible for checking and changing passwords.
- PasswordProviders - Class in ome.security.auth
-
Composite class which delegates to each of the configured providers in turn.
- PasswordProviders(PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
-
- PasswordProviders(AtomicBoolean, PasswordProvider...) - Constructor for class ome.security.auth.PasswordProviders
-
- passwordUtil - Variable in class ome.logic.AdminImpl
-
- PasswordUtil - Class in ome.security.auth
-
Static methods for dealing with password hashes and the "password" table.
- PasswordUtil(SqlAction) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil(SqlAction, boolean) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil(SqlAction, Charset) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil(SqlAction, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil(SqlAction, Roles, boolean) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil(SqlAction, Roles, boolean, Charset) - Constructor for class ome.security.auth.PasswordUtil
-
- PasswordUtil.METHOD - Enum in ome.security.auth
-
- PasswordUtility - Interface in ome.security.auth
-
Extension interface to
PasswordProvider for methods which may or may
not be available from a provider implementation.
- patch(Object) - Method in class ome.services.sharing.data.ObjHolder
-
- patch(Object) - Method in class ome.services.sharing.data.ShareDataHolder
-
- patch(Object) - Method in class ome.services.sharing.data.ShareItemHolder
-
- path - Variable in class ome.services.scripts.RepoFile.FsFile
-
- PdfParser - Class in ome.services.fulltext
-
- PdfParser() - Constructor for class ome.services.fulltext.PdfParser
-
- permissions(Class<T>) - Method in class ome.logic.TypesImpl
-
- permissions - Variable in class ome.services.graphs.GraphPolicy.Details
-
the current permissions on the object
- PermissionsPredicate - Class in ome.services.graphs
-
A predicate that allows perms=rwr--- and similar to be used in graph policy rule matches.
- PermissionsPredicate() - Constructor for class ome.services.graphs.PermissionsPredicate
-
- PerSessionStats - Class in ome.services.sessions.stats
-
Delegates to a
SessionStats which is acquired on every method
invocation.
- PerSessionStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerSessionStats
-
- PersistentEventLogLoader - Class in ome.services.eventlogs
-
EventLogLoader implementation which keeps tracks of the last
EventLog instance, and always provides the next unindexed instance.
- PersistentEventLogLoader() - Constructor for class ome.services.eventlogs.PersistentEventLogLoader
-
- PersistentEventLogLoader - Class in ome.services.fulltext
-
Deprecated.
- PersistentEventLogLoader() - Constructor for class ome.services.fulltext.PersistentEventLogLoader
-
Deprecated.
- PersistentEventLogLoader - Class in ome.services.pixeldata
-
EventLogLoader implementation which keeps tracks of the last
EventLog instance, and always provides the next unindexed instance.
- PersistentEventLogLoader(String, int) - Constructor for class ome.services.pixeldata.PersistentEventLogLoader
-
- PersonContextMapper - Class in ome.security.auth
-
Specialized OME Experimenter context mapper.
- PersonContextMapper(LdapConfig, String) - Constructor for class ome.security.auth.PersonContextMapper
-
- PersonContextMapper(LdapConfig, String, String) - Constructor for class ome.security.auth.PersonContextMapper
-
- PerThreadStats - Class in ome.services.sessions.stats
-
Delegates to a
SessionStats which is acquired on every method
invocation.
- PerThreadStats(CurrentDetails) - Constructor for class ome.services.sessions.stats.PerThreadStats
-
- PixelDataHandler - Class in ome.services.pixeldata
-
Simple action which can be done in an asynchronous thread in order to process
PIXELDATA event logs.
- PixelDataHandler(EventLogLoader, PixelsService) - Constructor for class ome.services.pixeldata.PixelDataHandler
-
- PixelDataThread - Class in ome.services.pixeldata
-
- PixelDataThread(SessionManager, Executor, PixelDataHandler, String) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(SessionManager, Executor, PixelDataHandler, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread
-
- PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Deprecated.
- PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Calls main constructor with NullMetrics.
- PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Calls main constructor with read-only status being all read-write.
- PixelDataThread(boolean, SessionManager, Executor, PixelDataHandler, Principal, String, int, Metrics, ReadOnlyStatus) - Constructor for class ome.services.pixeldata.PixelDataThread
-
Main constructor.
- pixelsData - Variable in class ome.logic.RenderingSettingsImpl
-
Reference to the service used to retrieve the pixels data.
- PixelsFileDeletions - Class in ome.services.delete.files
-
- PixelsFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.PixelsFileDeletions
-
- PixelsImpl - Class in ome.logic
-
implementation of the Pixels service interface.
- PixelsImpl() - Constructor for class ome.logic.PixelsImpl
-
- pixelsMetadata - Variable in class ome.logic.RenderingSettingsImpl
-
Reference to the service used to retrieve the pixels metadata.
- pixelsService - Variable in class ome.services.pixeldata.PixelDataHandler
-
- pixelsService - Variable in class ome.services.projection.ProjectionBean
-
Reference to the service used to retrieve the pixels data.
- pixToImageCache - Variable in class ome.services.sharing.BlobShareStore
-
- planOperation(SetMultimap<String, Long>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal
-
Traverse model object graph to determine steps for the proposed operation.
- planOperation(Collection<? extends IObject>, boolean, boolean) - Method in class ome.services.graphs.GraphTraversal
-
Traverse model object graph to determine steps for the proposed operation.
- PLATEIMAGES_QUERY - Static variable in class ome.services.delete.DeleteBean
-
- PojosFindAnnotationsQueryDefinition - Class in ome.services.query
-
- PojosFindAnnotationsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindAnnotationsQueryDefinition
-
- PojosFindHierarchiesQueryDefinition - Class in ome.services.query
-
walks up the hierarchy tree starting at Image nodes
while fetching various information.
- PojosFindHierarchiesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosFindHierarchiesQueryDefinition
-
- PojosGetImagesByOptionsQueryDefinition - Class in ome.services.query
-
- PojosGetImagesByOptionsQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesByOptionsQueryDefinition
-
- PojosGetImagesQueryDefinition - Class in ome.services.query
-
- PojosGetImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetImagesQueryDefinition
-
- PojosGetUserImagesQueryDefinition - Class in ome.services.query
-
- PojosGetUserImagesQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosGetUserImagesQueryDefinition
-
- PojosImpl - Class in ome.logic
-
implementation of the Pojos service interface.
- PojosImpl() - Constructor for class ome.logic.PojosImpl
-
- PojosLoadHierarchyQueryDefinition - Class in ome.services.query
-
- PojosLoadHierarchyQueryDefinition(Parameters) - Constructor for class ome.services.query.PojosLoadHierarchyQueryDefinition
-
- Policy - Interface in ome.security.policy
-
Strategy to permit the flexible restriction of certain actions
throughout OMERO.
- policyService - Variable in class ome.security.basic.BasicACLVoter
-
- policyService - Variable in class ome.security.basic.BasicSecuritySystem
-
- PolicyService - Interface in ome.security.policy
-
Internal service containing a number of configured
Policy instances.
- poll() - Method in class ome.services.search.IndexWatcher
-
Check for new objects to index and for progress with indexing past objects.
- Pop(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Pop
-
- pop() - Method in class ome.services.pixeldata.PersistentEventLogLoader
-
- pop(List<IObject>) - Method in class ome.services.SearchBean
-
Wrapper method which should be called on all results for the user.
- populateMinMax(double[][][]) - Method in class ome.formats.OMEROMetadataStore
-
Synchronize the minimum and maximum intensity values with those
specified by the client and save them in the DB.
- postFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
-
- postProcess(IObject) - Method in interface ome.security.ACLVoter
-
Gives the
ACLVoter instance a chance to act on the
IObject
after the transaction but before finishing the AOP stack.
- postProcess(IObject) - Method in class ome.security.basic.BasicACLVoter
-
- postProcess(IObject) - Method in class ome.security.CompositeACLVoter
-
- postProcess(IObject) - Method in class ome.security.sharing.SharingACLVoter
-
- postProcessBeanFactory(ConfigurableListableBeanFactory) - Method in class ome.services.util.BeanInstantiationGuard
-
- predicates - Variable in class ome.services.graphs.GraphPolicy
-
- preFlush(Iterator) - Method in class ome.security.basic.OmeroInterceptor
-
- prepare() - Method in class ome.services.fulltext.FullTextIndexer2
-
Query the database for new event log entries indicating model objects to process.
- prepare(Set<Long>) - Method in class ome.services.RawPixelsBean
-
- prepareLookups(String, String, Collection<Long>) - Method in class ome.services.query.HierarchyNavigator
-
- prepareLookups(T, Collection<E>) - Method in class ome.services.query.HierarchyNavigatorWrap
-
- preparePassword(String) - Method in class ome.security.auth.PasswordUtil
-
- preparePassword(Long, String, boolean) - Method in class ome.security.auth.PasswordUtil
-
- prepareReload() - Method in class ome.services.sessions.SessionManagerImpl
-
- prepareSaltedPassword(Long, String) - Method in class ome.security.auth.PasswordUtil
-
- prepend(String, Object...) - Method in class ome.security.basic.EventListenersFactoryBean
-
adds the objects to the existing list identified by key.
- previewImageDelete(long, boolean) - Method in class ome.services.delete.DeleteBean
-
- principal() - Method in class ome.security.basic.NodeProviderInDb
-
- principal() - Method in class ome.security.basic.NodeProviderInMemory
-
- principal() - Method in class ome.security.basic.NodeProviderWrapper
-
- principal() - Method in interface ome.security.NodeProvider
-
Retrieves the current active principal.
- principal - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- principal - Variable in class ome.services.util.ExecutionThread
-
- principal() - Method in class ome.services.util.Executor.Impl
-
- principal() - Method in interface ome.services.util.Executor
-
Returns a Principal representing your current session or null,
if none is active.
- principalHolder - Variable in class ome.security.basic.BasicSecurityWiring
-
- PrincipalHolder - Interface in ome.security.basic
-
Stack of active Principal instances.
- principalHolder - Variable in class ome.services.sessions.SessionManagerImpl
-
- principalHolder - Variable in class ome.services.util.Executor.Impl
-
- process(Long, ServiceFactory, Session) - Method in class ome.services.pixeldata.PixelDataHandler
-
Here we assume that our log loader will only return
us the proper types, since we are using the specific
type defined in this package.
- Process - Interface in ome.services.procs
-
- process(long) - Method in interface ome.services.procs.Processor
-
- process(long) - Method in class ome.services.procs.ProcessorSkeleton
-
- process(Job) - Method in class ome.services.procs.ProcessorSkeleton
-
- ProcessCallback - Interface in ome.services.procs
-
- processCancelled(Process) - Method in class ome.services.JobBean
-
- processCancelled(Process) - Method in interface ome.services.procs.ProcessCallback
-
- processFinished(Process) - Method in class ome.services.JobBean
-
- processFinished(Process) - Method in interface ome.services.procs.ProcessCallback
-
- processInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
-
Process the given instances.
- ProcessManager - Class in ome.services.procs
-
- ProcessManager(SessionManager, SecuritySystem, Executor, Processor...) - Constructor for class ome.services.procs.ProcessManager
-
main constructor which takes a non-null array of
Processor
instances as its only argument.
- ProcessManager.Work - Class in ome.services.procs
-
- processor() - Method in interface ome.services.procs.Process
-
- Processor - Interface in ome.services.procs
-
- processor() - Method in class ome.services.procs.ProcessSkeleton
-
- processors - Variable in class ome.services.procs.ProcessManager.Work
-
processors available for processing.
- ProcessorSkeleton - Class in ome.services.procs
-
- ProcessorSkeleton() - Constructor for class ome.services.procs.ProcessorSkeleton
-
- ProcessSkeleton - Class in ome.services.procs
-
- ProcessSkeleton(Processor) - Constructor for class ome.services.procs.ProcessSkeleton
-
- processTargets() - Method in class ome.services.graphs.GraphTraversal
-
Prepare to process the targeted model objects.
- procMap - Variable in class ome.services.procs.ProcessManager.Work
-
- projection(String, Parameters) - Method in class ome.logic.QueryImpl
-
- ProjectionBean - Class in ome.services.projection
-
Implements projection functionality for Pixels sets as declared in IProjection.
- ProjectionBean() - Constructor for class ome.services.projection.ProjectionBean
-
- projectPixels(long, PixelsType, int, int, int, List<Integer>, int, int, int, String) - Method in class ome.services.projection.ProjectionBean
-
- projectStack(long, PixelsType, int, int, int, int, int, int) - Method in class ome.services.projection.ProjectionBean
-
- ProjectWithImageNameBridge - Class in ome.services.fulltext.bridges
-
Deprecated.
- ProjectWithImageNameBridge() - Constructor for class ome.services.fulltext.bridges.ProjectWithImageNameBridge
-
Deprecated.
- propagateHiddenValues(IObject, IObject) - Method in class ome.security.basic.MergeEventListener
-
- PropertyFilterInitializer - Class in ome.security.basic
-
Initialize the filters for the subclasses of PrivilegedStringType.
- PropertyFilterInitializer(LightAdminPrivileges, CurrentDetails, DataSource, Roles) - Constructor for class ome.security.basic.PropertyFilterInitializer
-
Provide the property filter implementations for PrivilegedStringType.
- ProxyCleanupFilter - Class in ome.tools.hibernate
-
removes all proxies from a return graph to prevent ClassCastExceptions and
Session Closed exceptions.
- ProxyCleanupFilter() - Constructor for class ome.tools.hibernate.ProxyCleanupFilter
-
- ProxyCleanupFilter(ACLVoter, CurrentDetails) - Constructor for class ome.tools.hibernate.ProxyCleanupFilter
-
Construct a proxy cleanup filter that checks
the security restrictions on certain objects.
- ProxyCleanupFilter.Interceptor - Class in ome.tools.hibernate
-
wraps a filter for each invocation
- proxyNames - Variable in class ome.services.util.Executor.Impl
-
- ProxySafeFilter - Class in ome.tools.hibernate
-
extension to ContextFilter to check for uninitialized
Hibernate proxies before stepping into an entity or collection.
- ProxySafeFilter() - Constructor for class ome.tools.hibernate.ProxySafeFilter
-
- publisher - Variable in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- publisher - Variable in class ome.services.sessions.stats.CounterFactory
-
- purge() - Method in class ome.services.fulltext.FullTextIndexer2
-
Purge a batch of model objects.
- Push(Object, Map<String, String>) - Constructor for class ome.services.messages.ContextMessage.Push
-
- put(String, String) - Method in class ome.security.auth.AttributeSet
-
- put(String, Object[]) - Method in class ome.security.basic.EventListenersFactoryBean
-
replaces the key with the provided objects or an empty list if none
provided
- putSession(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache
-
Puts a session blindly into the context.
- putStatus(MethodInvocation, SessionStatus) - Method in class ome.tools.hibernate.SessionHandler
-
- Rasterizer() - Constructor for class ome.services.SVGRasterizer.Rasterizer
-
- RawFileBean - Class in ome.services
-
Raw file gateway which provides access to the OMERO file repository.
- RawFileBean() - Constructor for class ome.services.RawFileBean
-
default constructor
- RawFileBean(boolean) - Constructor for class ome.services.RawFileBean
-
overridden to allow Spring to set boolean
- RawFileBeanReadOnly - Class in ome.services
-
Raw file gateway which provides access to the OMERO file repository.
- RawFileBeanReadOnly() - Constructor for class ome.services.RawFileBeanReadOnly
-
default constructor
- RawFileBeanReadOnly(boolean) - Constructor for class ome.services.RawFileBeanReadOnly
-
overridden to allow Spring to set boolean
- RawPixelsBean - Class in ome.services
-
Implementation of the RawPixelsStore stateful service.
- RawPixelsBean() - Constructor for class ome.services.RawPixelsBean
-
default constructor
- RawPixelsBean(boolean, String) - Constructor for class ome.services.RawPixelsBean
-
overridden to allow Spring to set boolean
- RawPixelsBeanReadOnly - Class in ome.services
-
Implementation of the RawPixelsStore stateful service.
- RawPixelsBeanReadOnly() - Constructor for class ome.services.RawPixelsBeanReadOnly
-
default constructor
- RawPixelsBeanReadOnly(boolean, String) - Constructor for class ome.services.RawPixelsBeanReadOnly
-
overridden to allow Spring to set boolean
- read(long, int) - Method in class ome.services.RawFileBean
-
- read(String) - Method in class ome.services.scripts.ScriptRepoHelper
-
- read(BasicStream) - Static method in class ome.services.sharing.data.IdMapHelper
-
- read(BasicStream) - Static method in class ome.services.sharing.data.LongSeqHelper
-
- read(BasicStream) - Static method in class ome.services.sharing.data.ObjSeqHelper
-
- read(BasicStream) - Static method in class ome.services.sharing.data.StringSeqHelper
-
- readBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
-
- readBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
-
- readBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
-
- readBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
-
- readOnly - Variable in class ome.security.basic.EventHandler
-
- readOnly - Variable in class ome.services.sessions.SessionManagerImpl
-
- ReadOnlyConfigInit - Class in ome.services.util
-
Propagate the server's read-only status into corresponding keys in the configuration service.
- ReadOnlyConfigInit(IConfig, ReadOnlyStatus) - Constructor for class ome.services.util.ReadOnlyConfigInit
-
Set read-only status in the current configuration.
- readOnlyStatus - Variable in class ome.logic.AbstractLevel2Service
-
- ReadOnlyStatus - Class in ome.services.util
-
Hook run by the context as early as possible to detect if the DB
connection is read-only.
- ReadOnlyStatus(boolean, boolean) - Constructor for class ome.services.util.ReadOnlyStatus
-
- ReadOnlyStatus(boolean, boolean, boolean, SqlAction, String, String) - Constructor for class ome.services.util.ReadOnlyStatus
-
- ReadOnlyStatus.IsAware - Interface in ome.services.util
-
Implemented by classes that can report if a given read-only status would cause them to be in read-only mode.
- refresh(T) - Method in class ome.logic.QueryImpl
-
- refresh(String, SessionContext) - Method in class ome.services.sessions.state.SessionCache
-
Used externally to refresh the
SessionContext instance
associated with the session uuid
- registerAll(Ehcache, CacheEventListener...) - Method in class ome.services.sessions.state.CacheFactory
-
- registerCallback(ProcessCallback) - Method in interface ome.services.procs.Process
-
- registerCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
-
- registerPredicate(GraphPolicyRulePredicate) - Method in class ome.services.graphs.GraphPolicy
-
Use the given predicate in executing this graph policy.
- RegisterServiceCleanupMessage - Class in ome.services.messages
-
Published when some resource must be cleaned up after method execution.
- RegisterServiceCleanupMessage(Object, Object) - Constructor for class ome.services.messages.RegisterServiceCleanupMessage
-
- registerTrigger(String, Trigger) - Method in class ome.services.scheduler.SchedulerFactoryBean
-
Registers a Trigger.
- reindex(T) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- ReindexMessage<T extends ome.model.IObject> - Class in ome.services.messages
-
Published when one or more IObject instances must be re-indexed.
- ReindexMessage(Object, List<T>) - Constructor for class ome.services.messages.ReindexMessage
-
- relativeDN(String) - Method in class ome.security.auth.LdapConfig
-
Calculate the relative DN based on the current base.
- reload(String) - Method in interface ome.services.sessions.SessionManager
-
- reload(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- reload(SessionContext) - Method in class ome.services.sessions.SessionManagerImpl
-
Will be called in a synchronized block by
SessionCache in order
to allow for an update.
- reload(String) - Method in class ome.services.sessions.state.SessionCache
-
- reload(SessionContext) - Method in interface ome.services.sessions.state.SessionCache.StaleCacheListener
-
Method called for every active session in the cache.
- ReloadFilter - Class in ome.tools.hibernate
-
UpdateFilter subclass specialized for use with the
Session.save(Object) (as opposed to
Session.merge(Object))
method.
- ReloadFilter(Session) - Constructor for class ome.tools.hibernate.ReloadFilter
-
- ReloadingRefreshEventListener - Class in ome.tools.hibernate
-
responsible for responding to RefreshEvent.
- ReloadingRefreshEventListener() - Constructor for class ome.tools.hibernate.ReloadingRefreshEventListener
-
- remove() - Method in class ome.services.eventlogs.EventBacklog
-
Removes and returns the next EventLog instance or null if none is
present.
- remove() - Method in class ome.services.eventlogs.EventLogLoader
-
- remove() - Method in class ome.services.SearchBean
-
- removeAllDisabled(String...) - Method in class ome.security.basic.CurrentDetails
-
- removeAllListeners() - Method in class ome.services.messages.GlobalMulticaster
-
- removeApplicationListener(ApplicationListener) - Method in class ome.services.messages.GlobalMulticaster
-
- removeApplicationListenerBean(String) - Method in class ome.services.messages.GlobalMulticaster
-
- removeCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
-
Deprecated.
- removeCodomainMapFromChannel(CodomainMapContext, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- removeDisabled(String) - Method in class ome.security.basic.CurrentDetails
-
- removeGroupOwners(ExperimenterGroup, Experimenter...) - Method in class ome.logic.AdminImpl
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.logic.AdminImpl
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in interface ome.security.auth.RoleProvider
-
- removeGroups(Experimenter, ExperimenterGroup...) - Method in class ome.security.auth.SimpleRoleProvider
-
- removeGuest(long, String) - Method in class ome.services.sharing.ShareBean
-
- removeGuests(long, String...) - Method in class ome.services.sharing.ShareBean
-
- removeMissingFilesFromDb(SqlAction, Session, List<OriginalFile>) - Method in class ome.services.scripts.ScriptRepoHelper
-
- removeObject(long, T) - Method in class ome.services.sharing.ShareBean
-
- removeObjects(long, T...) - Method in class ome.services.sharing.ShareBean
-
- removeSession(String) - Method in class ome.services.sessions.state.SessionCache
-
- removeSessionCallback(String, SessionCallback) - Method in class ome.services.sessions.state.SessionCache
-
- removeStatus(MethodInvocation) - Method in class ome.tools.hibernate.SessionHandler
-
- removeUnusedFiles() - Method in class ome.logic.RepositoryInfoImpl
-
- removeUser(long, Experimenter) - Method in class ome.services.sharing.ShareBean
-
- removeUsers(long, List<Experimenter>) - Method in class ome.services.sharing.ShareBean
-
- removingOnly() - Method in class ome.services.eventlogs.EventBacklog
-
- render(PlaneDef) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- renderAsPackedInt(PlaneDef) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- renderCompressed(PlaneDef) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- RENDERING_DEF_QUERY_PREFIX - Static variable in class ome.logic.PixelsImpl
-
Standard rendering definition HQL query prefix
- RenderingBean - Class in ome.services
-
Provides the RenderingEngine service.
- RenderingBean(PixelsService, LocalCompress, Executor, SecuritySystem, LutProvider) - Constructor for class ome.services.RenderingBean
-
Compression service Bean injector.
- RenderingSettingsImpl - Class in ome.logic
-
Implementation of the IRenderingSettings I/F.
- RenderingSettingsImpl() - Constructor for class ome.logic.RenderingSettingsImpl
-
- renderProjectedAsPackedInt(int, int, int, int, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- renderProjectedCompressed(int, int, int, int, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- replace(Object, Object, Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- repo - Variable in class ome.services.pixeldata.PersistentEventLogLoader
-
- RepoFile - Class in ome.services.scripts
-
File type wrapper for paths which are intended for being stored in the
database as a part of this repository.
- RepoFile(File, String) - Constructor for class ome.services.scripts.RepoFile
-
- RepoFile(File, File) - Constructor for class ome.services.scripts.RepoFile
-
Both root and file are absolute paths to files.
- RepoFile.FsFile - Class in ome.services.scripts
-
File type wrapper for actual OS files.
- reportForgottenPassword(String, String) - Method in class ome.logic.AdminImpl
-
- reportingLoops - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
Frequency with which the percentage done should be calculated.
- RepositoryInfoImpl - Class in ome.logic
-
Class implementation of the IRepositoryInfo service interface.
- RepositoryInfoImpl() - Constructor for class ome.logic.RepositoryInfoImpl
-
- RepositoryTask - Class in ome.tools
-
Class implementation of various mechanized tasks, database queries, file I/O,
etc.
- RepositoryTask(SqlAction) - Constructor for class ome.tools.RepositoryTask
-
- reps - Variable in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- reps - Variable in class ome.services.pixeldata.PixelDataHandler
-
- requiresPixelsPyramid() - Method in class ome.services.RawPixelsBean
-
- requiresPixelsPyramid() - Method in class ome.services.RenderingBean
-
- reset(String[]) - Static method in class ome.services.fulltext.Main
-
- resetDefaults(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- resetDefaults() - Method in class ome.services.SearchBean
-
- resetDefaults() - Method in class ome.services.ThumbnailBean
-
- resetDefaultsByOwnerInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetDefaultSettings(boolean) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- resetDefaultsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetDefaultsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetDefaultsInImage(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetDefaultsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetDefaultsNoSave(RenderingDef, Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- resetDetails(IObject, Object[], Object[], int, Details) - Method in class ome.security.basic.OmeroInterceptor
-
asks
BasicSecuritySystem to create a new managed
Details
based on the previous state of this entity.
- resetEnumerations(Class<T>) - Method in class ome.logic.TypesImpl
-
- resetMinMaxInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- resetReadFilter(Session) - Method in interface ome.api.local.LocalShare
-
- resetReadFilter(Session) - Method in class ome.services.sharing.ShareBean
-
- resource - Variable in class ome.services.messages.ParserOpenFileMessage
-
- resource - Variable in class ome.services.messages.RegisterServiceCleanupMessage
-
- restartIfNeeded() - Method in class ome.services.scheduler.SchedulerFactoryBean
-
Similar to the SchedulerFactoryBean.isRunning() method, but properly handles the
situation where the Scheduler has been completely shutdown and
therefore must be replaced.
- restrictions(IObject) - Method in interface ome.security.ACLVoter
-
Provide the active restrictions for this IObject.
- restrictions(IObject) - Method in class ome.security.basic.BasicACLVoter
-
- restrictions(IObject) - Method in class ome.security.CompositeACLVoter
-
- restrictions(IObject) - Method in class ome.security.sharing.SharingACLVoter
-
- results() - Method in class ome.services.SearchBean
-
- retrieveAllRndSettings(long, long) - Method in class ome.logic.PixelsImpl
-
- retrieveCollection(IObject, String, Parameters) - Method in class ome.logic.PojosImpl
-
- retrievePixDescription(long) - Method in class ome.logic.PixelsImpl
-
- retrieveRndSettings(long) - Method in class ome.logic.PixelsImpl
-
- retrieveRndSettingsFor(long, long) - Method in class ome.logic.PixelsImpl
-
- returnedClass() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- returnSeen(Object) - Method in class ome.tools.hibernate.UpdateFilter
-
- returnUnloaded - Variable in class ome.services.search.SearchValues
-
- review(Map<String, Set<GraphPolicy.Details>>, GraphPolicy.Details, Map<String, Set<GraphPolicy.Details>>, Set<String>, boolean) - Method in class ome.services.graphs.GraphPolicy
-
The action to take about the link between the mapped objects.
- roleProvider - Variable in class ome.logic.AdminImpl
-
- RoleProvider - Interface in ome.security.auth
-
Provides user and group
creation, deletion, and modification for use by services.
- roles - Variable in class ome.security.basic.AbstractSecurityFilter
-
- roles - Variable in class ome.security.basic.BasicACLVoter
-
- roles - Variable in class ome.security.basic.BasicSecuritySystem
-
- roles - Variable in class ome.services.sessions.SessionManagerImpl
-
- rollback(EventLog) - Method in class ome.services.eventlogs.EventLogLoader
-
- run() - Method in class ome.security.basic.LightAdminPrivilegesCleanup
-
- run() - Method in class ome.services.delete.files.FileDeleter
-
- run() - Method in interface ome.services.procs.IProcessManager
-
Runs the processing phase as root.
- run() - Method in class ome.services.util.ExecutionThread
-
- run() - Method in class ome.services.util.ServerDirectoryCheck
-
Ensures that directories exist corresponding to,
${omero.data.dir}/FullText
${omero.managed.dir}
- runAsAdmin() - Method in interface ome.security.AdminAction
-
- runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in interface ome.security.SecuritySystem
-
Allows actions to be performed with the
EventContext.isCurrentUserAdmin() flag enabled but
without changing the value of
EventContext.getCurrentUserId(), so that ownerships are properly
handled.
- runAsAdmin(AdminAction) - Method in interface ome.security.SecuritySystem
-
- runAsAdmin(AdminAction) - Method in class ome.security.SecuritySystemHolder
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.SecuritySystemHolder
-
- runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
-
- runAsAdmin(AdminAction) - Method in class ome.security.sharing.SharingSecuritySystem
-
- runAsAdmin() - Method in class ome.services.delete.QueryConstraints
-
- runningProcess(long) - Method in interface ome.services.procs.IProcessManager
-
Returns a running
Process for the
id
or null.
- runningProcess(long) - Method in class ome.services.procs.ProcessManager
-
- salt - Variable in class ome.security.auth.ConfigurablePasswordProvider
-
Whether or not salting based on the user ID should be attempted.
- saltedPasswordDigest(Long, String) - Method in class ome.security.auth.PasswordUtil
-
Creates an MD5 hash of the given clear text and base64 encodes it.
- sanityCheckPixels(Pixels, Pixels) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F
- sanityCheckRepository() - Method in class ome.logic.RepositoryInfoImpl
-
- save() - Method in class ome.services.RawFileBean
-
- save() - Method in class ome.services.RawPixelsBean
-
- SAVE_EVENT - Static variable in class ome.security.basic.SaveEventListener
-
- saveAndReturnArray(IObject[]) - Method in class ome.logic.UpdateImpl
-
- saveAndReturnIds(IObject[]) - Method in class ome.logic.UpdateImpl
-
- saveAndReturnObject(IObject) - Method in class ome.logic.UpdateImpl
-
- saveArray(IObject[]) - Method in class ome.logic.UpdateImpl
-
- saveAsNewSettings() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- saveCollection(Collection) - Method in class ome.logic.UpdateImpl
-
- saveCurrentSettings() - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- SaveEventListener - Class in ome.security.basic
-
event listener which will only handle newly created (transient) objects in
a given graph.
- SaveEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.SaveEventListener
-
main constructor.
- saveObject(IObject) - Method in class ome.logic.UpdateImpl
-
- saveRndSettings(RenderingDef) - Method in class ome.logic.PixelsImpl
-
- saveToDB(FilesetJobLink) - Method in class ome.formats.OMEROMetadataStore
-
Saves the current object graph to the database.
- scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.AWTScaleService
-
- scaleBufferedImage(BufferedImage, float, float) - Method in class ome.logic.JavaImageScalingService
-
- SchedulerFactoryBean - Class in ome.services.scheduler
-
Produces a
Scheduler which automatically loads all the triggers it can find.
- SchedulerFactoryBean() - Constructor for class ome.services.scheduler.SchedulerFactoryBean
-
- SCRIPT_REPO - Static variable in class ome.services.scripts.ScriptRepoHelper
-
Id used by all script repositories.
- ScriptFileType - Class in ome.services.scripts
-
Definition of the script types that will be accepted by the server.
- ScriptFileType(String, String) - Constructor for class ome.services.scripts.ScriptFileType
-
- ScriptFileType(String, String, String, String) - Constructor for class ome.services.scripts.ScriptFileType
-
- ScriptProcess - Class in ome.services.procs.scripts
-
- ScriptProcess(Processor) - Constructor for class ome.services.procs.scripts.ScriptProcess
-
- ScriptProcessor - Class in ome.services.procs.scripts
-
- ScriptProcessor() - Constructor for class ome.services.procs.scripts.ScriptProcessor
-
- ScriptRepoHelper - Class in ome.services.scripts
-
Strategy used by the ScriptRepository for registering, loading, and saving
files.
- ScriptRepoHelper(Executor, String, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
Deprecated.
- ScriptRepoHelper(Executor, String, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
- ScriptRepoHelper(File, Executor, String, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
Deprecated.
- ScriptRepoHelper(String, File, Executor, String, Principal, Roles) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
Deprecated.
- ScriptRepoHelper(File, Executor, String, Principal, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
Deprecated.
- ScriptRepoHelper(String, File, Executor, String, Principal, Roles, ReadOnlyStatus) - Constructor for class ome.services.scripts.ScriptRepoHelper
-
- SearchAction - Class in ome.services.search
-
Serializable action used by
SearchBean to generate results lazily.
- SearchAction(SearchValues) - Constructor for class ome.services.search.SearchAction
-
- searchAll() - Method in class ome.logic.LdapImpl
-
- SearchBean - Class in ome.services
-
Implements the Search interface.
- SearchBean(Executor, Class<? extends Analyzer>) - Constructor for class ome.services.SearchBean
-
- SearchBean() - Constructor for class ome.services.SearchBean
-
Empty constructor required by EJB and
self configuration.
- searchByAttribute(String, String, String) - Method in class ome.logic.LdapImpl
-
- searchByAttributes(String, String[], String[]) - Method in class ome.logic.LdapImpl
-
- searchByDN(String) - Method in class ome.logic.LdapImpl
-
- searchDnInGroups(String, String) - Method in class ome.logic.LdapImpl
-
- SearchValues - Class in ome.services.search
-
- SearchValues() - Constructor for class ome.services.search.SearchValues
-
- sec - Variable in class ome.logic.AbstractLevel2Service
-
- sec - Variable in class ome.security.auth.SimpleRoleProvider
-
- sec - Variable in class ome.services.AbstractStatefulBean
-
- sec - Variable in class ome.services.procs.ProcessManager.Work
-
- secSys - Variable in class ome.security.basic.EventHandler
-
- SecureAction - Interface in ome.security
-
- SecureMerge - Class in ome.tools.hibernate
-
- SecureMerge(Session) - Constructor for class ome.tools.hibernate.SecureMerge
-
- SecureMerge(Session, boolean) - Constructor for class ome.tools.hibernate.SecureMerge
-
- securityFilter - Variable in class ome.security.basic.BasicACLVoter
-
- SecurityFilter - Interface in ome.security
-
Base filter interface ...
- SecurityFilterHolder - Class in ome.security
-
Security dispatcher holding each currently active
SecurityFilter
instance and allowing dispatching between them.
- SecurityFilterHolder(CurrentDetails, OneGroupSecurityFilter, AllGroupsSecurityFilter, SharingSecurityFilter) - Constructor for class ome.security.SecurityFilterHolder
-
- SecuritySystem - Interface in ome.security
-
central security interface.
- SecuritySystemHolder - Class in ome.security
-
Security dispatcher holding each currently active
SecuritySystem
instance and allowing dispatching between them.
- SecuritySystemHolder(BasicSecuritySystem, SharingSecuritySystem) - Constructor for class ome.security.SecuritySystemHolder
-
- select(String...) - Method in class ome.tools.hibernate.QueryBuilder
-
- selfConfigure() - Method in class ome.logic.AbstractLevel1Service
-
This method was previously called by the EJB container, but is no longer
needed.
- selfConfigure() - Method in class ome.logic.AbstractLevel2Service
-
This method was previously called by the EJB container,
but is no longer needed.
- selfConfigure(OmeroContext) - Method in class ome.logic.HardWiredInterceptor
-
Calls OmeroContext.applyBeanPropertyValues(Object, String) to
have properties injected.
- selfConfigure(SessionManager, ServiceFactory, SessionCache) - Static method in class ome.security.basic.BasicSecuritySystem
-
Simplified factory method which generates all the security primitives
internally.
- selfConfigure() - Method in class ome.services.AbstractStatefulBean
-
- SelfCorrectingDataSource - Class in ome.services.db
-
DataSource delegate which wraps the
- SelfCorrectingDataSource(DataSource, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
-
- SelfCorrectingDataSource(DataSource, long, int, long) - Constructor for class ome.services.db.SelfCorrectingDataSource
-
- sendBlind(Set<String>, String) - Method in class ome.services.mail.MailSender
-
- sendBlind(Set<String>, String, String) - Method in class ome.services.mail.MailSender
-
- sendEmail(String, String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil
-
Main method which takes typical email fields as arguments, to prepare and
populate the given new MimeMessage instance and send.
- sendEmail(String, String, String, boolean, List<String>, List<String>) - Method in class ome.services.mail.MailUtil
-
Overloaded method which takes typical email fields as arguments, to
prepare and populate the given new MimeMessage instance and send.
- sendEmail(Collection<EventLog>) - Method in class ome.services.mail.ObjectMailSender
-
- sender - Variable in class ome.services.mail.MailUtil
-
- sender - Variable in class ome.services.mail.ServerUpMailSender
-
- serialVersionUID - Static variable in class ome.services.sharing.data.Obj
-
- serialVersionUID - Static variable in class ome.services.sharing.data.ObjPrxHelper
-
- serialVersionUID - Static variable in class ome.services.sharing.data.ShareData
-
- serialVersionUID - Static variable in class ome.services.sharing.data.ShareDataPrxHelper
-
- serialVersionUID - Static variable in class ome.services.sharing.data.ShareItem
-
- serialVersionUID - Static variable in class ome.services.sharing.data.ShareItemPrxHelper
-
- ServerDirectoryCheck - Class in ome.services.util
-
Hook run by the context at startup to create needed directories for the server.
- ServerDirectoryCheck(String, String, ReadOnlyStatus) - Constructor for class ome.services.util.ServerDirectoryCheck
-
- ServerDownMailSender - Class in ome.services.mail
-
Send an email to all members of the system group when the server is
shutting down.
- ServerDownMailSender() - Constructor for class ome.services.mail.ServerDownMailSender
-
- ServerUpMailSender - Class in ome.services.mail
-
Announces to all members of the system group that the server has come up.
- ServerUpMailSender(MailSender) - Constructor for class ome.services.mail.ServerUpMailSender
-
- ServerVersionCheck - Class in ome.services.util
-
Hook run by the context.
- ServerVersionCheck(String) - Constructor for class ome.services.util.ServerVersionCheck
-
- service - Variable in class ome.services.util.Executor.Impl
-
- ServiceHandler - Class in ome.services.util
-
- ServiceHandler(CurrentDetails) - Constructor for class ome.services.util.ServiceHandler
-
- ServiceHandler(CurrentDetails, long, long) - Constructor for class ome.services.util.ServiceHandler
-
- SessionBean - Class in ome.services.sessions
-
Implementation of ISession.
- SessionBean(SessionManager, Executor, CurrentDetails, LightAdminPrivileges) - Constructor for class ome.services.sessions.SessionBean
-
- SessionCache - Class in ome.services.sessions.state
-
- SessionCache() - Constructor for class ome.services.sessions.state.SessionCache
-
- SessionCache.StaleCacheListener - Interface in ome.services.sessions.state
-
Observer pattern used to refresh sessions in doUpdate.
- SessionCallback - Interface in ome.services.sessions
-
- SessionCallback.SimpleCloseCallback - Class in ome.services.sessions
-
Assumes that only close() will be called.
- SessionContext - Interface in ome.services.sessions
-
Extends EventContext to hold a Session.
- SessionContext.Count - Class in ome.services.sessions
-
Synchronized counter which can be passed between
SessionContext
instances as they are recreated.
- SessionContextImpl - Class in ome.services.sessions
-
- SessionContextImpl(Session, List<Long>, List<Long>, List<String>, SessionStats, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
-
- SessionContextImpl(Session, Set<AdminPrivilege>, List<Long>, List<Long>, List<String>, SessionStats, Roles, SessionContext) - Constructor for class ome.services.sessions.SessionContextImpl
-
- sessionFactory - Variable in class ome.logic.AbstractLevel1Service
-
- SessionFactory - Class in ome.tools.hibernate
-
Simple source of Thread-aware Session instances.
- SessionFactory(SessionFactory, SqlAction) - Constructor for class ome.tools.hibernate.SessionFactory
-
- SessionHandler - Class in ome.tools.hibernate
-
interceptor which delegates to
HibernateInterceptor for stateless
services but which keeps a WeakHashMap of sessions keyed by
the stateful service reference.
- SessionHandler(SessionFactory) - Constructor for class ome.tools.hibernate.SessionHandler
-
- sessionInit() - Method in class ome.services.util.ExecutionThread
-
- sessionManager - Variable in class ome.logic.UpdateImpl
-
- sessionManager - Variable in class ome.security.basic.BasicSecuritySystem
-
- SessionManager - Interface in ome.services.sessions
-
Responsible for holding onto Session instances for optimized login.
- sessionManager - Variable in class ome.services.sharing.ShareBean
-
- SessionManager.CreationRequest - Class in ome.services.sessions
-
Extensible data object which can be passed to create* methods to stop
the explosion of different methods.
- SessionManagerImpl - Class in ome.services.sessions
-
Is for ISession a cache and will be kept there in sync? OR Factors out the
logic from ISession and SessionManagerI
Therefore either called directly, or via synchronous messages.
- SessionManagerImpl() - Constructor for class ome.services.sessions.SessionManagerImpl
-
- sessionProvider - Variable in class ome.security.basic.BasicSecuritySystem
-
- sessionProvider - Variable in class ome.services.sessions.SessionManagerImpl
-
- SessionProvider - Interface in ome.services.sessions
-
- SessionProviderInDb - Class in ome.services.sessions
-
Is for ISession a cache and will be kept there in sync? OR Factors out the
logic from ISession and SessionManagerI
Therefore either called directly, or via synchronous messages.
- SessionProviderInDb(Roles, NodeProvider, Executor, SqlAction) - Constructor for class ome.services.sessions.SessionProviderInDb
-
- SessionProviderInMemory - Class in ome.services.sessions
-
- SessionProviderInMemory(Roles, NodeProvider, Executor) - Constructor for class ome.services.sessions.SessionProviderInMemory
-
- SessionProviderWrapper<P extends SessionProvider & ReadOnlyStatus.IsAware> - Class in ome.services.sessions
-
A session provider that offers a unified view of multiple underlying session providers.
- SessionProviderWrapper(ReadOnlyStatus, List<P>) - Constructor for class ome.services.sessions.SessionProviderWrapper
-
Construct a new Session provider.
- SessionsCreatedCounter - Class in ome.services.sessions.stats
-
Counter for all the objects read in a session.
- SessionsCreatedCounter(int) - Constructor for class ome.services.sessions.stats.SessionsCreatedCounter
-
- SessionsCreatedStatsMessage - Class in ome.services.messages.stats
-
Published when some limit in user/group/session activity has been reached.
- SessionsCreatedStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.SessionsCreatedStatsMessage
-
- SessionStats - Interface in ome.services.sessions.stats
-
Thread-safe counter for all
- set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
Method to be implemented by all bridges.
- set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.ProjectWithImageNameBridge
-
Deprecated.
If the "value" argument is a Project, this
bridge gathers all images and adds them to the index
with a slightly reduced boost value.
- set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
-
Deprecated.
Primary entry point for all bridges.
- set(String, Object, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Default implementation of the
FullTextBridge.set(String, Object, Document, LuceneOptions)
method which calls
FullTextBridge.set_file(String, IObject, Document, LuceneOptions)
FullTextBridge.set_annotations(String, IObject, Document, LuceneOptions),
FullTextBridge.set_acquisition(String, IObject, Document, LuceneOptions),
FullTextBridge.set_details(String, IObject, Document, LuceneOptions),
FullTextBridge.set_fileset(String, IObject, Document, LuceneOptions),
FullTextBridge.set_folders(String, IObject, Document, LuceneOptions),
and finally
FullTextBridge.set_custom(String, IObject, Document, LuceneOptions).
- set(Share, long, List<T>, List<Long>, List<String>, boolean) - Method in class ome.services.sharing.ShareStore
-
- set_acquisition(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Walks the acquisition related metadata including channel names.
- set_annotations(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Walks the various Annotation instances attached to the object
argument and adds various levels to the index.
- set_custom(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Loops over each
field bridge class and calls its
FieldBridge.set(String, Object, Document, LuceneOptions)
method.
- set_details(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Parses all ownership and time-based details to the index for the given
object.
- set_file(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
- set_fileset(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Walks the Fileset instances attached to an Image.
- set_folders(String, IObject, Document, LuceneOptions) - Method in class ome.services.fulltext.FullTextBridge
-
Deprecated.
Walks the various Folder instances attached to the object
argument so that it may be found via its immediate parent folder.
- setAction(String) - Method in class ome.services.mail.ObjectMailSender
-
- setActive(int, boolean) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setActive(long, boolean) - Method in class ome.services.sharing.ShareBean
-
- setAdmin(boolean) - Method in class ome.security.basic.BasicEventContext
-
- setAdminPrivileges(Experimenter, List<AdminPrivilege>) - Method in class ome.logic.AdminImpl
-
- setAdminPrivileges(Set<AdminPrivilege>) - Method in class ome.security.basic.BasicEventContext
-
- setAdminPrivileges(LightAdminPrivileges) - Method in class ome.services.sessions.SessionManagerImpl
-
- setAdminService(LocalAdmin) - Method in class ome.logic.UpdateImpl
-
- setAdminService(IAdmin) - Method in class ome.services.RawFileBean
-
- setAllowLeadingWildcard(boolean) - Method in class ome.services.SearchBean
-
- setAlternateStylesheet(String) - Method in class ome.services.SVGRasterizer
-
Sets the alternate stylesheet to use.
- setAnalyzer(Class<? extends Analyzer>) - Method in class ome.logic.QueryImpl
-
- setAnalyzer(Class<? extends Analyzer>) - Method in class ome.services.SearchBean
-
Injector used by Spring.
- setApplicationContext(ApplicationContext) - Method in class ome.logic.AdminImpl
-
- setApplicationContext(ApplicationContext) - Method in class ome.logic.ConfigImpl
-
- setApplicationContext(ApplicationContext) - Method in class ome.logic.LdapImpl
-
- setApplicationContext(ApplicationContext) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- setApplicationContext(ApplicationContext) - Method in class ome.security.basic.BasicSecuritySystem
-
- setApplicationContext(ApplicationContext) - Method in class ome.security.basic.GroupChmodStrategy
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.delete.Deletion.Builder
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FileParser
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- setApplicationContext(ApplicationContext) - Method in class ome.services.scheduler.SchedulerFactoryBean
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.SessionManagerImpl
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.CacheFactory
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.sessions.state.SessionCache
-
Context injector.
- setApplicationContext(ApplicationContext) - Method in class ome.services.sharing.BlobShareStore
-
Because there is a cyclic dependency (SF -> ACLVoter -> BlobStore -> SF), we
have to lazy-load the session factory via the context.
- setApplicationContext(ApplicationContext) - Method in class ome.services.ThumbnailBean
-
- setApplicationContext(ApplicationContext) - Method in class ome.services.util.Executor.Impl
-
- setApplicationContext(ApplicationContext) - Method in class ome.tools.hibernate.SessionHandler
-
- setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.InternalServiceFactory
-
simple injector for the ApplicationContext
- setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.ManagedServiceFactory
-
simple injector for the ApplicationContext
- setApplicationContext(ApplicationContext) - Method in class ome.tools.spring.OnContextRefreshedEventListener
-
- setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.BridgeHelper
-
Deprecated.
- setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.fulltext.bridges.TablesBridge
-
Deprecated.
- setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.CounterFactory
-
- setApplicationEventPublisher(ApplicationEventPublisher) - Method in class ome.services.sessions.stats.LongCounter
-
- setBackgroundColor(Paint) - Method in class ome.services.SVGRasterizer
-
Sets the Paint to use for the background of the image.
- setBatchSize(int) - Method in class ome.services.eventlogs.EventLogLoader
-
Set the number of EventLog instances will be loaded in a single
run.
- setBatchSize(int) - Method in class ome.services.SearchBean
-
- setBeanDefinitionForReadOnly(BeanDefinitionRegistry) - Method in class ome.services.util.BeanInstantiationGuard
-
Act on the bean definition registry to make the target bean suitable for read-only mode.
- setBeanDefinitionForReadOnly(BeanDefinitionRegistry) - Method in class ome.services.util.BeanInstantiationSubstituter
-
- setBeanFactory(BeanFactory) - Method in class ome.services.messages.GlobalMulticaster
-
- setCacheEventListeners(CacheEventListener[]) - Method in class ome.services.sessions.state.CacheFactory
-
- setCacheManager(CacheManager) - Method in class ome.services.sessions.state.SessionCache
-
- setCallContext(Map<String, String>) - Method in class ome.security.basic.BasicEventContext
-
- setCaseSensitive(boolean) - Method in class ome.services.SearchBean
-
- setCaseSentivice(boolean) - Method in class ome.services.SearchBean
-
- setChanges(String) - Method in class ome.services.graphs.GraphPolicyRule
-
- setChannelGlobalMinMax(long, int, double, double) - Method in class ome.logic.PixelsImpl
-
- setChannelLookupTable(int, String) - Method in class ome.services.RenderingBean
-
- setChannelWindow(int, double, double) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setChecksumProviderFactory(ChecksumProviderFactory) - Method in class ome.services.RawFileBean
-
ChecksumProviderFactory Bean injector
- setClasses(Set<String>) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
-
- setCodomainInterval(int, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setCompressionLevel(float) - Method in interface ome.api.local.LocalCompress
-
Sets the current compression level for the service.
- setCompressionLevel(float) - Method in class ome.logic.CompressImpl
-
- setCompressionLevel(float) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setCompressionService(LocalCompress) - Method in class ome.services.ThumbnailBean
-
Compression service Bean injector.
- setCondition(String) - Method in class ome.services.graphs.GraphPolicy
-
Set a named condition,
- setConfigValue(String, String) - Method in class ome.logic.ConfigImpl
-
see IConfig.setConfigValue(String, String)
- setConfigValueIfEquals(String, String, String) - Method in class ome.logic.ConfigImpl
-
see IConfig.setConfigValueIfEquals(String, String, String)
- setContactSystem(boolean) - Method in class ome.services.mail.FailedLoginMailSender
-
- setContactUser(boolean) - Method in class ome.services.mail.FailedLoginMailSender
-
- setContext(Map<String, String>) - Method in class ome.security.basic.CurrentDetails
-
- setCounterFactory(CounterFactory) - Method in class ome.services.sessions.SessionManagerImpl
-
- setCriteria(Criteria) - Method in class ome.services.query.Query
-
provide this Query instance with a Criteria to be
used for retrieving data.
- setCronExpression(String) - Method in class ome.services.fulltext.FullTextIndexer2
-
- setCurrentDetails(CurrentDetails) - Method in class ome.logic.ConfigImpl
-
- setCurrentId(long) - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- setDatabaseIdentity(DatabaseIdentity) - Method in class ome.logic.ConfigImpl
-
- setDatadir(String) - Method in class ome.logic.RepositoryInfoImpl
-
Bean injection setter for data repository directory
- setDebug(boolean) - Method in class ome.tools.hibernate.EventMethodInterceptor
-
- setDebugAll(boolean) - Method in class ome.security.basic.EventListenersFactoryBean
-
for setter injection
- setDefaultBody(String) - Method in class ome.services.mail.MailSender
-
- setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.logic.AdminImpl
-
- setDefaultGroup(Experimenter, ExperimenterGroup) - Method in interface ome.security.auth.RoleProvider
-
- setDefaultGroup(Experimenter, ExperimenterGroup) - Method in class ome.security.auth.SimpleRoleProvider
-
- setDefaultT(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setDefaultTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
-
- setDefaultTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
-
- setDefaultZ(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setDescription(long, String) - Method in class ome.services.sharing.ShareBean
-
- setDisabledSubsystems(Set<String>) - Method in class ome.security.basic.BasicEventContext
-
- setDiskSpaceChecking(boolean) - Method in class ome.services.RawFileBean
-
setter disk overflow checking
- setDiskSpaceChecking(boolean) - Method in class ome.services.RawPixelsBean
-
- setDiskSpaceChecking(boolean) - Method in class ome.services.ThumbnailBean
-
- setDN(Long, String) - Method in class ome.logic.LdapImpl
-
Deprecated.
- setDryRun(boolean) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- setEnabled(boolean) - Method in class ome.services.mail.MailSender
-
- setError(String) - Method in class ome.services.graphs.GraphPolicyRule
-
- setEvent(Event) - Method in class ome.security.basic.BasicEventContext
-
- setExcludes(String[]) - Method in class ome.services.eventlogs.EventLogLoader
-
Spring injector
- setExecutor(Executor) - Method in class ome.logic.UpdateImpl
-
- setExecutor(Executor) - Method in class ome.services.mail.MailSender
-
- setExecutor(Executor) - Method in class ome.services.SearchBean
-
Injector used by Spring, currently, since
SelfConfigurableService.selfConfigure() requires it.
- setExecutor(Executor) - Method in class ome.services.sessions.SessionManagerImpl
-
- setExpiration(long, Timestamp) - Method in class ome.services.sharing.ShareBean
-
- setExtendedMetadata(ExtendedMetadata) - Method in class ome.logic.AbstractLevel2Service
-
- setFileId(long) - Method in class ome.services.RawFileBean
-
- setFileIdWithBuffer(long, FileBuffer) - Method in class ome.services.RawFileBean
-
- setFileService(OriginalFilesService) - Method in class ome.logic.RepositoryInfoImpl
-
Bean injection setter for ROMIO file service
- setFullTextBridge(FullTextBridge) - Method in class ome.logic.UpdateImpl
-
- setGroup(ExperimenterGroup, Permissions) - Method in class ome.security.basic.BasicEventContext
-
- setGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
-
- setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in interface ome.security.auth.RoleProvider
-
- setGroupOwner(Experimenter, ExperimenterGroup, boolean) - Method in class ome.security.auth.SimpleRoleProvider
-
- setIContainer(IContainer) - Method in class ome.logic.MetadataImpl
-
IContainer bean injector.
- setIdOnly() - Method in class ome.services.SearchBean
-
- setImageHeight(float) - Method in class ome.services.SVGRasterizer
-
Sets the height of the image to rasterize.
- setImageWidth(float) - Method in class ome.services.SVGRasterizer
-
Sets the width of the image to rasterize.
- setIndexWatcher(IndexWatcher) - Method in class ome.logic.UpdateImpl
-
- setInProgressImageResource(Resource) - Method in class ome.services.ThumbnailBean
-
In-progress image resource Bean injector.
- setInput(String, String, Object) - Method in class ome.services.sessions.SessionBean
-
- setInput(String, String, Object) - Method in interface ome.services.sessions.SessionManager
-
Places the argument in the input environment under the
given key, possibly initializing the Map Throws an exception if
there is no Session with the given identifier.
- setInput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
-
- setIoService(ThumbnailService) - Method in class ome.services.ThumbnailBean
-
I/O service (ThumbnailService) Bean injector.
- setIPixels(IPixels) - Method in class ome.services.projection.ProjectionBean
-
IPixels bean injector.
- setIPixels(IPixels) - Method in class ome.services.ThumbnailBean
-
Pixels service Bean injector.
- setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawFileBean
-
Disk Space Usage service Bean injector
- setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.RawPixelsBean
-
Disk Space Usage service Bean injector
- setIRepositoryInfo(IRepositoryInfo) - Method in class ome.services.ThumbnailBean
-
Disk Space Usage service Bean injector
- setIsWriteDb(boolean) - Method in class ome.services.util.BeanInstantiationGuard
-
- setIsWriteRepo(boolean) - Method in class ome.services.util.BeanInstantiationGuard
-
- setKey(String) - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- setKeyStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
-
- setKeyStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
-
- setLanguages(String) - Method in class ome.services.SVGRasterizer
-
Sets the preferred language to use.
- setLeaderOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
-
- setLegacyUtil(PasswordUtil) - Method in class ome.security.auth.ConfigurablePasswordProvider
-
- setLockCandidates(Set<IObject>) - Method in class ome.security.basic.BasicEventContext
-
- setLogs(List<EventLog>) - Method in class ome.security.basic.BasicEventContext
-
- setLutProvider(LutProvider) - Method in class ome.services.ThumbnailBean
-
Lookup table provider Bean injector.
- setMailUtil(MailUtil) - Method in class ome.services.mail.MailSender
-
- setManagerDown(String) - Method in class ome.security.basic.NodeProviderInDb
-
- setManagerDown(String) - Method in class ome.security.basic.NodeProviderInMemory
-
- setManagerDown(String) - Method in class ome.security.basic.NodeProviderWrapper
-
- setManagerDown(String) - Method in interface ome.security.NodeProvider
-
Sets a given manager node as down.
- setMatches(String) - Method in class ome.services.graphs.GraphPolicyRule
-
- setMaxClauseCount(Integer) - Method in class ome.services.SearchBean
-
Deprecated.
- setMaxFileSize(Long) - Method in class ome.services.fulltext.FileParser
-
- setMaxUserTimeToIdle(long) - Method in class ome.services.sessions.SessionManagerImpl
-
- setMaxUserTimeToLive(long) - Method in class ome.services.sessions.SessionManagerImpl
-
- setMedia(String) - Method in class ome.services.SVGRasterizer
-
Sets the media to rasterize.
- setMemberOfGroups(List<Long>) - Method in class ome.security.basic.BasicEventContext
-
- setMergedBatches(boolean) - Method in class ome.services.SearchBean
-
- setMessage(String) - Method in class ome.services.JobBean
-
- setMethodHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
-
- setMethodSecurity(MethodSecurity) - Method in class ome.security.basic.BasicSecurityWiring
-
Setter injection.
- setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptFileType
-
Sets the mimetype on the given
OriginalFile
if the name field matches the
wildcard pattern
for this instance.
- setMimetype(OriginalFile) - Method in class ome.services.scripts.ScriptRepoHelper
-
- setModel(RenderingModel) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setObjectClass(Class<IObject>) - Method in class ome.services.mail.ObjectMailSender
-
- setObjectsReadHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
-
- setObjectsWrittenHardLimit(int) - Method in class ome.services.sessions.stats.CounterFactory
-
- setOnAllUsers(boolean) - Method in class ome.services.mail.FailedLoginMailSender
-
- setOnSpecificUsers(Set<String>) - Method in class ome.services.mail.FailedLoginMailSender
-
- setOriginalFilesService(OriginalFilesService) - Method in class ome.services.RawFileBean
-
I/O service (OriginalFilesService) Bean injector.
- setOriginalSettingsForPixels(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- setOriginalSettingsInDataset(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- setOriginalSettingsInImage(long) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- setOriginalSettingsInSet(Class<T>, Set<Long>) - Method in class ome.logic.RenderingSettingsImpl
-
Implemented as specified by the IRenderingSettings I/F.
- setOutput(String, String, Object) - Method in class ome.services.sessions.SessionBean
-
- setOutput(String, String, Object) - Method in interface ome.services.sessions.SessionManager
-
Places the argument in the output environment under the
given key, possibly initializing the Map Throws an exception if
there is no Session with the given identifier.
- setOutput(String, String, Object) - Method in class ome.services.sessions.SessionManagerImpl
-
- setOverlays(Map<byte[], Integer>) - Method in class ome.services.RenderingBean
-
- setOwner(Experimenter) - Method in class ome.security.basic.BasicEventContext
-
- setOwnsAll() - Method in class ome.services.graphs.GraphTraversal
-
- setParameterValues(Properties) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- setPermissionsForGroup(Long, Permissions) - Method in class ome.security.basic.BasicEventContext
-
- setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in interface ome.security.ACLVoter
-
Specify object classes based on restriction constants in Permissions that do not always have those
restrictions.
- setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.basic.BasicACLVoter
-
- setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.CompositeACLVoter
-
- setPermittedClasses(Map<Integer, Set<Class<? extends IObject>>>) - Method in class ome.security.sharing.SharingACLVoter
-
- setPixelDataService(PixelsService) - Method in class ome.services.ThumbnailBean
-
Pixels data service Bean injector.
- setPixelsData(PixelsService) - Method in class ome.logic.RenderingSettingsImpl
-
Sets injector.
- setPixelsData(PixelsService) - Method in class ome.services.RawPixelsBean
-
- setPixelsId(long, boolean) - Method in class ome.services.RawPixelsBean
-
- setPixelsId(long) - Method in class ome.services.ThumbnailBean
-
- setPixelsId(long) - Method in class ome.services.ThumbnailBeanReadOnly
-
- setPixelsMetadata(IPixels) - Method in class ome.logic.RenderingSettingsImpl
-
Sets injector.
- setPixelsMetadata(IPixels) - Method in class ome.services.RawPixelsBean
-
- setPixelsService(PixelsService) - Method in class ome.logic.RepositoryInfoImpl
-
Bean injection setter for ROMIO pixels service
- setPixelsService(PixelsService) - Method in class ome.services.projection.ProjectionBean
-
PixelsService bean injector.
- setPixelToMMFactor(float) - Method in class ome.services.SVGRasterizer
-
Sets the unit conversion factor to the specified value.
- setPlane(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
-
- setPreferenceContext(PreferenceContext) - Method in class ome.logic.ConfigImpl
-
PreferenceContext setter for dependency injection.
- setPrincipalHolder(PrincipalHolder) - Method in class ome.security.basic.BasicSecurityWiring
-
Setter injection.
- setPrincipalHolder(PrincipalHolder) - Method in class ome.services.sessions.SessionManagerImpl
-
- setProcessManager(IProcessManager) - Method in class ome.services.JobBean
-
Process Manager Bean injector.
- setQuality(float) - Method in class ome.services.SVGRasterizer
-
Sets the quality of the image to rasterize when rasterizing to a JPEG.
- setQuantizationMap(int, Family, double, boolean) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setQuantumStrategy(int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setQuery(Query) - Method in class ome.services.query.Query
-
provide this Query instance with a Query to be used
for retrieving data.
- setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel1Service
-
- setQueryFactory(QueryFactory) - Method in class ome.logic.AbstractLevel2Service
-
- setQueryService(LocalQuery) - Method in class ome.logic.AbstractLevel2Service
-
- setQueryService(LocalQuery) - Method in class ome.logic.UpdateImpl
-
- setQueryService(IQuery) - Method in class ome.security.auth.PasswordUtil
-
- setQueryService(LocalQuery) - Method in class ome.services.AbstractStatefulBean
-
Query service Bean injector.
- setQueryService(IQuery) - Method in class ome.services.eventlogs.EventLogLoader
-
Spring injector
- setQueryService(IQuery) - Method in class ome.services.mail.MailSender
-
- setQueryService(IQuery) - Method in class ome.services.procs.ProcessorSkeleton
-
- setQueryString(String) - Method in class ome.services.mail.ObjectMailSender
-
- setRawPixelsStore(RawPixelsStore) - Method in class ome.logic.RenderingSettingsImpl
-
Sets injector.
- setReadOnly(boolean) - Method in class ome.security.basic.BasicEventContext
-
- setReadOnly(ReadOnlyStatus) - Method in class ome.services.sessions.SessionManagerImpl
-
- setReadOnlyStatus(ReadOnlyStatus) - Method in class ome.logic.AbstractLevel2Service
-
- setRegion(int, long, byte[]) - Method in class ome.services.RawPixelsBean
-
- setRenderingDefId(long) - Method in class ome.services.ThumbnailBean
-
- setRepetitions(int) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
Spring injector.
- setRepetitions(int) - Method in class ome.services.pixeldata.PixelDataHandler
-
Spring injector.
- setReportingLoops(int) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
- setResolutionLevel(int) - Method in class ome.services.RawPixelsBean
-
- setResolutionLevel(int) - Method in class ome.services.RenderingBean
-
- setReturnUnloaded(boolean) - Method in class ome.services.SearchBean
-
- setRGBA(int, int, int, int, int) - Method in class ome.services.RenderingBean
-
Implemented as specified by the RenderingEngine interface.
- setRoles(Roles) - Method in class ome.services.mail.MailSender
-
- setRoles(Roles) - Method in class ome.services.sessions.SessionManagerImpl
-
- setRow(byte[], int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- setScaleService(IScale) - Method in class ome.services.ThumbnailBean
-
Scale service Bean injector.
- setSecurityContext(Principal, IObject) - Method in interface ome.services.sessions.SessionManager
-
Sets the context for the current session to the given value.
- setSecurityContext(Principal, IObject) - Method in class ome.services.sessions.SessionManagerImpl
-
- setSecuritySystem(SecuritySystem) - Method in class ome.logic.AbstractLevel2Service
-
- setSecuritySystem(SecuritySystem) - Method in class ome.services.AbstractStatefulBean
-
- setServiceCleanups(Set<RegisterServiceCleanupMessage>) - Method in class ome.security.basic.BasicEventContext
-
- setSessionCache(SessionCache) - Method in class ome.services.sessions.SessionManagerImpl
-
- setSessionFactory(SessionFactory) - Method in class ome.logic.AbstractLevel1Service
-
delegates to HibernateDaoSupport.
- setSessionFactory(SessionFactory) - Method in class ome.logic.TypesImpl
-
injector for usage by the container.
- setSessionFactory(SessionFactory) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
-
Initializes the metadata needed by this instance.
- setSessionManager(SessionManager) - Method in class ome.logic.UpdateImpl
-
- setSessionManager(SessionManager) - Method in class ome.security.basic.BasicMethodSecurity
-
- setSessionProvider(SessionProvider) - Method in class ome.services.sessions.SessionManagerImpl
-
- setSettingsService(IRenderingSettings) - Method in class ome.services.ThumbnailBean
-
Rendering settings service Bean injector.
- setShareId(Long) - Method in class ome.security.basic.BasicEventContext
-
- setShareId(Long) - Method in interface ome.services.sessions.SessionContext
-
- setShareId(Long) - Method in class ome.services.sessions.SessionContextImpl
-
- setSqlAction(SqlAction) - Method in class ome.logic.ConfigImpl
-
SqlAction setter for dependency injection.
- setSqlAction(SqlAction) - Method in class ome.logic.RepositoryInfoImpl
-
Bean injection setter for SQL operations
- setSqlAction(SqlAction) - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- setSqlAction(SqlAction) - Method in class ome.services.fulltext.FullTextIndexer
-
Deprecated.
Since these instances are used repeatedly, we need to check for
already set SqlAction
- setSqlAction(SqlAction) - Method in class ome.services.pixeldata.PixelDataHandler
-
Since these instances are used repeatedly, we need to check for
already set SqlAction
- setSqlAction(SqlAction) - Method in class ome.services.RawPixelsBean
-
SQL action Bean injector
- setSqlAction(SqlAction) - Method in class ome.services.sharing.BlobShareStore
-
- setSqlAction(SqlAction) - Method in class ome.services.util.Executor.SimpleWork
-
- setStack(byte[], int, int, int) - Method in class ome.services.RawPixelsBean
-
- setStaleCacheListener(SessionCache.StaleCacheListener) - Method in class ome.services.sessions.state.SessionCache
-
- setStatus(String) - Method in class ome.services.JobBean
-
- setStatusAndMessage(String, String) - Method in class ome.services.JobBean
-
- setStop(boolean) - Method in class ome.services.eventlogs.EventLogLoader
-
Called by controlling objects (a worker thread) in order
to free up the thread.
- setSubjectPrefix(String) - Method in class ome.services.mail.MailSender
-
- setSudoer(Experimenter) - Method in class ome.security.basic.BasicEventContext
-
- setThumbnailService(ThumbnailService) - Method in class ome.logic.RepositoryInfoImpl
-
Bean injection setter for ROMIO thumbnail service
- setTile(byte[], int, int, int, int, int, int, int) - Method in class ome.services.RawPixelsBean
-
- setTimeout(int) - Method in class ome.services.query.Query
-
- setTimeout(int) - Method in class ome.services.search.SearchAction
-
- setTimeout(Consumer<Integer>) - Method in class ome.services.util.TimeoutSetter
-
Set the timeout on the given query.
- setTimeoutSetter(TimeoutSetter) - Method in class ome.logic.QueryImpl
-
- setTimeoutSetter(TimeoutSetter) - Method in class ome.services.SearchBean
-
- setTimepoint(byte[], int) - Method in class ome.services.RawPixelsBean
-
- SETTINGSID_QUERY - Static variable in class ome.services.delete.DeleteBean
-
- setToken(GraphHolder) - Method in class ome.security.basic.TokenHolder
-
- setTrustStore(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
-
- setTrustStorePassword(String) - Method in class ome.security.KeyAndTrustStoreConfiguration
-
- setTypes(ITypes) - Method in class ome.services.eventlogs.PersistentEventLogLoader
-
- setTypesService(ITypes) - Method in class ome.services.JobBean
-
Types service Bean injector.
- setTypesService(ITypes) - Method in class ome.services.procs.ProcessorSkeleton
-
- setUmask(Permissions) - Method in class ome.security.basic.BasicEventContext
-
- setUp() - Method in class ome.formats.importer.util.TinyImportFixture
-
Deprecated.
Creates a dataset and locates the test image file.
- setUpdateInterval(long) - Method in class ome.services.sessions.state.SessionCache
-
Inject time in milliseconds between updates.
- setUpdateService(LocalUpdate) - Method in class ome.logic.AbstractLevel2Service
-
- setUpdateService(LocalUpdate) - Method in class ome.services.AbstractStatefulBean
-
- setUpdateService(IUpdate) - Method in class ome.services.procs.ProcessorSkeleton
-
- setUseProjections(boolean) - Method in class ome.services.SearchBean
-
- setUserId(long) - Method in class ome.services.ThumbnailCtx
-
Sets the user ID to use for queries.
- setUserStyleSheetURI(String) - Method in class ome.services.SVGRasterizer
-
Sets the uri of the user stylesheet.
- setUuid(String) - Method in class ome.services.sessions.SessionManagerImpl
-
- setXMLParserValidating(boolean) - Method in class ome.services.SVGRasterizer
-
Sets whether or not the XML parser used to parse SVG document should be
validating or not, depending on the specified parameter.
- sf - Variable in class ome.logic.TypesImpl
-
- sf - Variable in class ome.security.auth.SimpleRoleProvider
-
- sf - Variable in class ome.security.basic.BasicSecuritySystem
-
- sf - Variable in class ome.services.delete.DeleteBean
-
- share - Variable in class ome.security.SecurityFilterHolder
-
- share - Variable in class ome.services.sharing.data.ShareItem
-
- ShareBean - Class in ome.services.sharing
-
Note:
SessionManager should not be used to obtain the
Share
data since it may not be completely in sync.
- ShareBean(LocalAdmin, SessionManager, ShareStore, Executor, MailUtil) - Constructor for class ome.services.sharing.ShareBean
-
- ShareData - Class in ome.services.sharing.data
-
- ShareData() - Constructor for class ome.services.sharing.data.ShareData
-
- ShareData(long, long, List<Long>, List<String>, Map<String, List<Long>>, List<Obj>, boolean, long) - Constructor for class ome.services.sharing.data.ShareData
-
- ShareDataHolder - Class in ome.services.sharing.data
-
- ShareDataHolder() - Constructor for class ome.services.sharing.data.ShareDataHolder
-
- ShareDataHolder(ShareData) - Constructor for class ome.services.sharing.data.ShareDataHolder
-
- ShareDataPrx - Interface in ome.services.sharing.data
-
- ShareDataPrxHelper - Class in ome.services.sharing.data
-
Provides type-specific helper functions.
- ShareDataPrxHelper() - Constructor for class ome.services.sharing.data.ShareDataPrxHelper
-
- ShareDataPrxHolder - Class in ome.services.sharing.data
-
- ShareDataPrxHolder() - Constructor for class ome.services.sharing.data.ShareDataPrxHolder
-
- ShareDataPrxHolder(ShareDataPrx) - Constructor for class ome.services.sharing.data.ShareDataPrxHolder
-
- ShareItem - Class in ome.services.sharing.data
-
- ShareItem() - Constructor for class ome.services.sharing.data.ShareItem
-
- ShareItem(long, String, long, List<Long>, List<String>) - Constructor for class ome.services.sharing.data.ShareItem
-
- ShareItemHolder - Class in ome.services.sharing.data
-
- ShareItemHolder() - Constructor for class ome.services.sharing.data.ShareItemHolder
-
- ShareItemHolder(ShareItem) - Constructor for class ome.services.sharing.data.ShareItemHolder
-
- ShareItemPrx - Interface in ome.services.sharing.data
-
- ShareItemPrxHelper - Class in ome.services.sharing.data
-
Provides type-specific helper functions.
- ShareItemPrxHelper() - Constructor for class ome.services.sharing.data.ShareItemPrxHelper
-
- ShareItemPrxHolder - Class in ome.services.sharing.data
-
- ShareItemPrxHolder() - Constructor for class ome.services.sharing.data.ShareItemPrxHolder
-
- ShareItemPrxHolder(ShareItemPrx) - Constructor for class ome.services.sharing.data.ShareItemPrxHolder
-
- ShareRestrictionTransactionAttributeSource - Class in ome.services.sharing
-
Prevents methods from setting the transaction to readOnly = false when a
share is activated.
- ShareRestrictionTransactionAttributeSource(CurrentDetails, SessionCache) - Constructor for class ome.services.sharing.ShareRestrictionTransactionAttributeSource
-
- ShareStore - Class in ome.services.sharing
-
Entry to the Ice code generated data/ directory.
- ShareStore() - Constructor for class ome.services.sharing.ShareStore
-
- sharesToSessions(List<ShareData>) - Method in class ome.services.sharing.ShareBean
-
- shareToSession(ShareData) - Method in class ome.services.sharing.ShareBean
-
- sharing - Variable in class ome.security.SecuritySystemHolder
-
- SharingACLVoter - Class in ome.security.sharing
-
- SharingACLVoter(CurrentDetails, SystemTypes, ShareStore, TokenHolder) - Constructor for class ome.security.sharing.SharingACLVoter
-
- SharingSecurityFilter - Class in ome.security.basic
-
The sharing security filter provides database-level access protection for share contexts.
- SharingSecurityFilter(Roles, ShareStore) - Constructor for class ome.security.basic.SharingSecurityFilter
-
Construct a new sharing security filter.
- SharingSecuritySystem - Class in ome.security.sharing
-
central security interface.
- SharingSecuritySystem(BasicSecuritySystem) - Constructor for class ome.security.sharing.SharingSecuritySystem
-
- ShutdownSafeEhcacheManagerFactoryBean - Class in ome.tools.spring
-
Workaround for the Spring/EHCache shutdown sequence.
- ShutdownSafeEhcacheManagerFactoryBean() - Constructor for class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
-
- SimilarTerms - Class in ome.services.search
-
Search to find similar terms to some given terms.
- SimilarTerms(SearchValues, String...) - Constructor for class ome.services.search.SimilarTerms
-
- SimpleCloseCallback() - Constructor for class ome.services.sessions.SessionCallback.SimpleCloseCallback
-
- simpleDelete(Map<String, String>, Executor, Principal, long) - Method in class ome.services.scripts.ScriptRepoHelper
-
- SimpleLuceneOptions - Class in ome.services.fulltext
-
Deprecated.
- SimpleLuceneOptions(LuceneOptions, Float) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- SimpleLuceneOptions(LuceneOptions, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- SimpleLuceneOptions(LuceneOptions, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- SimpleLuceneOptions(LuceneOptions, Float, Field.Index, Field.Store) - Constructor for class ome.services.fulltext.SimpleLuceneOptions
-
Deprecated.
- SimpleRoleProvider - Class in ome.security.auth
-
- SimpleRoleProvider(SecuritySystem, SessionFactory) - Constructor for class ome.security.auth.SimpleRoleProvider
-
- SimpleRoleProvider(SecuritySystem, SessionFactory, AtomicBoolean) - Constructor for class ome.security.auth.SimpleRoleProvider
-
- SimpleSessionStats - Class in ome.services.sessions.stats
-
- SimpleSessionStats(ObjectsReadCounter, ObjectsWrittenCounter, MethodCounter) - Constructor for class ome.services.sessions.stats.SimpleSessionStats
-
- SimpleSqlWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleSqlWork
-
- SimpleWork(Object, String, Object...) - Constructor for class ome.services.util.Executor.SimpleWork
-
- size(String) - Method in class ome.security.auth.AttributeSet
-
- size() - Method in class ome.security.basic.CurrentDetails
-
- size() - Method in interface ome.security.basic.PrincipalHolder
-
Get the number of active principal contexts.
- size() - Method in class ome.services.query.Definitions
-
- size() - Method in class ome.services.RawFileBean
-
- size() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
the total number of fields for this entity.
- skipFrom() - Method in class ome.tools.hibernate.QueryBuilder
-
- skipWhere() - Method in class ome.tools.hibernate.QueryBuilder
-
- sleepFor(long) - Static method in class ome.services.util.SleepTimer
-
Sleep for the given number of milliseconds.
- SleepTimer - Class in ome.services.util
-
Provides a timer for having a thread sleep that prematurely awakens when the server is to shut down,
so the sleeping does not keep the server running.
- SleepTimer() - Constructor for class ome.services.util.SleepTimer
-
- SmtpAuthenticator - Class in ome.security
-
- SmtpAuthenticator(String, String) - Constructor for class ome.security.SmtpAuthenticator
-
- SomeMustNone - Class in ome.services.search
-
FullText subclass which
parses 3 arrays of strings into
into a single Lucene query.
- SomeMustNone(SearchValues, String[], String[], String[], Class<? extends Analyzer>) - Constructor for class ome.services.search.SomeMustNone
-
- sortOriginalFileIds(Session, Collection<Long>) - Static method in class ome.services.graphs.ModelObjectSequencer
-
Deprecated.
Sort a list of original file IDs such that files precede containing directories.
- sources - Variable in class ome.services.query.QueryFactory
-
sources available for lookups.
- sql - Variable in class ome.logic.AdminImpl
-
- sql - Variable in class ome.security.basic.EventHandler
-
- sql - Variable in class ome.services.eventlogs.PersistentEventLogLoader
-
- sql - Variable in class ome.services.OmeroFilePathResolver
-
SQL action instance for this class.
- sqlAction - Variable in class ome.services.sharing.BlobShareStore
-
- sqlAction - Variable in class ome.services.util.Executor.Impl
-
- SqlArray<T> - Class in ome.tools.hibernate
-
Hibernate type to store a java array using SQL ARRAY.
- SqlArray(List<T>, int) - Constructor for class ome.tools.hibernate.SqlArray
-
- SqlArray(List<T>, int, String) - Constructor for class ome.tools.hibernate.SqlArray
-
- SqlArray.BOOLEAN - Class in ome.tools.hibernate
-
- SqlArray.DATE - Class in ome.tools.hibernate
-
- SqlArray.DOUBLE - Class in ome.tools.hibernate
-
- SqlArray.FLOAT - Class in ome.tools.hibernate
-
- SqlArray.INTEGER - Class in ome.tools.hibernate
-
- SqlArray.STRING - Class in ome.tools.hibernate
-
- SqlArray.STRING2 - Class in ome.tools.hibernate
-
- SqlQueryInterceptor - Class in ome.security.basic
-
Pulls SQL query rewriting into a simple superclass of
OmeroInterceptor for use outside Blitz by other server threads.
- SqlQueryInterceptor(SqlQueryTransformer) - Constructor for class ome.security.basic.SqlQueryInterceptor
-
- SqlQueryTransformer - Class in ome.tools.hibernate
-
Rewrite SQL queries to reverse the effects of @ColumnTransformer annotations in WHERE clauses.
- SqlQueryTransformer() - Constructor for class ome.tools.hibernate.SqlQueryTransformer
-
Convenience constructor for unit testing so that it need not mock a data source.
- SqlQueryTransformer(DataSource) - Constructor for class ome.tools.hibernate.SqlQueryTransformer
-
Construct a SQL query transformer that parses the SQL dialect appropriate for the given data source.
- sqlTypes() - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
-
- standalone(String[]) - Static method in class ome.services.fulltext.Main
-
Starts up and simply waits until told by the grid to disconnect.
- start() - Method in class ome.services.fulltext.FullTextIndexer2
-
Start the indexer.
- start() - Method in class ome.services.fulltext.FullTextThread
-
Deprecated.
Called by Spring on creation.
- start() - Method in class ome.services.mail.SubethaSMTP
-
- start() - Method in class ome.services.pixeldata.PixelDataThread
-
Called by Spring on creation.
- start() - Method in class ome.services.util.DBPatchCheck
-
- start() - Method in class ome.services.util.ServerVersionCheck
-
Prints simple banner with OMERO version.
- startProcess(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
-
- stats() - Method in interface ome.services.sessions.SessionContext
-
- stats() - Method in class ome.services.sessions.SessionContextImpl
-
- stats() - Method in class ome.services.sessions.stats.CurrentSessionStats
-
- stats() - Method in class ome.services.sessions.stats.DelegatingStats
-
Intended to be overwritten by subclasses.
- stats() - Method in class ome.services.sessions.stats.PerSessionStats
-
- stats() - Method in class ome.services.sessions.stats.PerThreadStats
-
- stop() - Method in class ome.services.fulltext.FullTextIndexer2
-
Stop the indexer.
- stop() - Method in class ome.services.fulltext.FullTextThread
-
Deprecated.
Called by Spring on destruction.
- stop() - Method in class ome.services.mail.SubethaSMTP
-
- stop() - Method in class ome.services.pixeldata.PixelDataThread
-
Called by Spring on destruction.
- stop() - Method in class ome.services.util.ServerVersionCheck
-
Prints simple banner with "Stopping OMERO"
- store - Variable in class ome.security.basic.BasicSecuritySystem
-
- store - Variable in class ome.services.sharing.ShareBean
-
- storeShareData(long, ShareData) - Method in class ome.services.sharing.ShareBean
-
- STRING - Static variable in class ome.services.query.StringQuery
-
parameter name for the definition of the HQL string.
- STRING(Connection, List<String>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
-
- STRING() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING
-
- STRING(List<String>) - Constructor for class ome.tools.hibernate.SqlArray.STRING
-
- STRING2(Connection, List<String[]>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
-
- STRING2() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.STRING2
-
- STRING2(List<String[]>) - Constructor for class ome.tools.hibernate.SqlArray.STRING2
-
- stringLongToEntity(String, long) - Method in class ome.services.query.HierarchyNavigatorWrap
-
Convert the given type string and database ID to the model object.
- StringQuery - Class in ome.services.query
-
simple HQL query.
- StringQuery(Parameters) - Constructor for class ome.services.query.StringQuery
-
Default constructor, used primarily for testing.
- StringQuery(SqlAction, Parameters) - Constructor for class ome.services.query.StringQuery
-
- StringQuerySource - Class in ome.services.query
-
interprets the query id as an HQL query.
- StringQuerySource() - Constructor for class ome.services.query.StringQuerySource
-
Default constructor, used primarily for testing.
- StringQuerySource(SqlAction) - Constructor for class ome.services.query.StringQuerySource
-
- StringSeqHelper - Class in ome.services.sharing.data
-
- StringSeqHelper() - Constructor for class ome.services.sharing.data.StringSeqHelper
-
- StringSeqHolder - Class in ome.services.sharing.data
-
- StringSeqHolder() - Constructor for class ome.services.sharing.data.StringSeqHolder
-
- StringSeqHolder(List<String>) - Constructor for class ome.services.sharing.data.StringSeqHolder
-
- stringToType(String) - Method in class ome.services.query.HierarchyNavigatorWrap
-
Convert the given type string to the object type.
- SubethaSMTP - Class in ome.services.mail
-
Simple server bean which can be started on Spring context creation
and shutdown when the application is editing.
- SubethaSMTP(MessageHandlerFactory) - Constructor for class ome.services.mail.SubethaSMTP
-
- SubethaSMTP(MessageHandlerFactory, int) - Constructor for class ome.services.mail.SubethaSMTP
-
- subject - Variable in class ome.services.graphs.GraphPolicy.Details
-
the unloaded instance
- submit(Job) - Method in class ome.services.JobBean
-
- submit(Callable<T>) - Method in class ome.services.util.Executor.Impl
-
- submit(Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
-
- submit(Executor.Priority, Callable<T>) - Method in class ome.services.util.Executor.Impl
-
- submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in class ome.services.util.Executor.Impl
-
- submit(Callable<T>) - Method in interface ome.services.util.Executor
-
- submit(Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
-
- submit(Executor.Priority, Callable<T>) - Method in interface ome.services.util.Executor
-
- submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
-
- subselect(QueryBuilder) - Method in class ome.tools.hibernate.QueryBuilder
-
Appends the string representation of the
QueryBuilder argument
inside of parentheses.
- subtypeEquals(int, int, String) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
returns true is the indexed subtype returns the same class type as the
klass argument.
- subtypeName(int, int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
-
retrieves the full Hibernate path for this component field.
- success(SqlAction.DeleteLog) - Method in class ome.services.messages.DeleteLogMessage
-
- success - Variable in class ome.services.messages.LoginAttemptMessage
-
- sudoer - Variable in class ome.services.sessions.SessionManager.CreationRequest
-
- SVGRasterizer - Class in ome.services
-
This class provides a simple and method based API for converting a SVG
document fragment to a BufferedImage.
- SVGRasterizer(String) - Constructor for class ome.services.SVGRasterizer
-
Constructs a new SVGRasterizer.
- SVGRasterizer(URL) - Constructor for class ome.services.SVGRasterizer
-
Constructs a new SVGRasterizer.
- SVGRasterizer(InputStream) - Constructor for class ome.services.SVGRasterizer
-
Constructs a new SVGRasterizer converter.
- SVGRasterizer(Reader) - Constructor for class ome.services.SVGRasterizer
-
Constructs a new SVGRasterizer converter.
- SVGRasterizer.Rasterizer - Class in ome.services
-
An image transcoder that stores the resulting image.
- synchronizeLdapUser(String) - Method in class ome.logic.LdapImpl
-
- synchronizeLoginCache() - Method in class ome.logic.AdminImpl
-
- systemService - Variable in class ome.services.util.Executor.Impl
-
- SystemTypes - Class in ome.security
-
Defines what IObject classes are considered "system" types.
- SystemTypes() - Constructor for class ome.security.SystemTypes
-
- SystemTypes(Roles) - Constructor for class ome.security.SystemTypes
-
- sysTypes - Variable in class ome.security.basic.BasicACLVoter
-
- sysTypes - Variable in class ome.security.basic.BasicSecuritySystem
-