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A

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
the current plan for the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean)
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.
Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
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
Add a RegisterServiceCleanupMessage to the current thread for cleanup by the ServiceHandler on exit.
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.
Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the IEnum value which should be added to the index, and adds two fields.
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.
Helper method which takes the parameters from the BridgeHelper.set(String, Object, Document, LuceneOptions) method (possibly modified) as well as the parsed String value which should be added to the index, and adds two fields.
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
Called during the creation of instances if a particular file should be handled by AbstractFileDeletions.deleteLocal().
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
Assert that GraphTraversal.unlinkTargets(boolean) need not be called.
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
 

B

background(Callable<T>) - Method in class ome.services.scheduler.ThreadPool
Schedule a task in one of the limited background slots.
BASE_SCRIPT_FILTER - Static variable in class ome.services.scripts.ScriptRepoHelper
IOFileFilter instance used during ScriptRepoHelper.iterate() to find the matching scripts in the given directory.
basename() - Method in class ome.services.scripts.RepoFile
 
BasePolicy - Class in ome.security.policy
Simple base class for Policy implementations which always returns true for BasePolicy.isRestricted(IObject) and always fails on BasePolicy.checkRestriction(IObject).
BasePolicy(Set<Class<IObject>>) - Constructor for class ome.security.policy.BasePolicy
 
basic - Variable in class ome.security.SecuritySystemHolder
 
BasicACLVoter - Class in ome.security.basic
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, SessionProvider, ReadOnlyStatus) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService) - Constructor for class ome.security.basic.BasicACLVoter
Deprecated.
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles, SessionProvider, ReadOnlyStatus) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicACLVoter(CurrentDetails, SystemTypes, TokenHolder, SecurityFilter, PolicyService, Roles, LightAdminPrivileges, SessionProvider, ReadOnlyStatus, Set<String>, Set<String>, String) - Constructor for class ome.security.basic.BasicACLVoter
 
BasicEventContext - Class in ome.security.basic
EventContext implementation for use within the security system.
BasicEventContext(Principal, SessionStats) - Constructor for class ome.security.basic.BasicEventContext
 
BasicEventContext(Principal, SessionStats, EventContext) - Constructor for class ome.security.basic.BasicEventContext
Copy-constructor to not have to allow the mutator SimpleEventContext.copy(EventContext) or copyContext(EventContext) out of the EventContext hierarchy.
BasicMethodSecurity - Class in ome.security.basic
Implementation of MethodSecurity which checks method security based on the RolesAllowed annotations of our implementation methods.
BasicMethodSecurity() - Constructor for class ome.security.basic.BasicMethodSecurity
 
BasicMethodSecurity(boolean) - Constructor for class ome.security.basic.BasicMethodSecurity
 
BasicSecuritySystem - Class in ome.security.basic
simplest implementation of SecuritySystem.
BasicSecuritySystem(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, SessionProvider, EventProvider, Roles, ServiceFactory, TokenHolder, List<SecurityFilter>, PolicyService, ACLVoter) - Constructor for class ome.security.basic.BasicSecuritySystem
Main public constructor for this SecuritySystem implementation.
BasicSecuritySystemReadOnly - Class in ome.security.basic
Provides a group context check that does not rely on SQL to bypass interception by Hibernate.
BasicSecuritySystemReadOnly(OmeroInterceptor, SystemTypes, CurrentDetails, SessionManager, SessionProvider, EventProvider, Roles, ServiceFactory, TokenHolder, List<SecurityFilter>, PolicyService, ACLVoter) - Constructor for class ome.security.basic.BasicSecuritySystemReadOnly
 
BasicSecurityWiring - Class in ome.security.basic
Responsible for logging users in and out via the Principal before and after the actual invocation of OMERO methods.
BasicSecurityWiring() - Constructor for class ome.security.basic.BasicSecurityWiring
 
BasicSecurityWiring.CloseOnNoSessionContext - Class in ome.security.basic
 
batch - Variable in class ome.services.fulltext.FullTextIndexer
Deprecated.
 
batchSize - Variable in class ome.services.eventlogs.EventLogLoader
 
batchSize - Variable in class ome.services.search.SearchValues
 
batchTimer - Variable in class ome.services.fulltext.FullTextIndexer
Deprecated.
 
BeanHelper - Class in ome.services.util
Helper for all bean implementations.
BeanHelper(Class) - Constructor for class ome.services.util.BeanHelper
 
BeanInstantiationGuard - Class in ome.services.util
Prevents creation of Spring beans based on read-only status.
BeanInstantiationGuard(ReadOnlyStatus, String) - Constructor for class ome.services.util.BeanInstantiationGuard
Construct a bean instantiation guard.
BeanInstantiationSubstituter - Class in ome.services.util
Adjusts instantiation class of Spring beans based on read-only status.
BeanInstantiationSubstituter(ReadOnlyStatus, String, String) - Constructor for class ome.services.util.BeanInstantiationSubstituter
Construct a bean instantiation substituter.
beforeTransactionCompletion(Transaction) - Method in class ome.security.basic.OmeroInterceptor
 
BinaryAccessPolicy - Class in ome.security.policy
Policy which should be checked anytime access to original binary files in OMERO is being attempted.
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter) - Constructor for class ome.security.policy.BinaryAccessPolicy
 
BinaryAccessPolicy(Set<Class<IObject>>, ACLVoter, String[]) - Constructor for class ome.security.policy.BinaryAccessPolicy
 
BlobShareStore - Class in ome.services.sharing
Implements ShareStore and provides functionality to work with binary Ice data from the share.
BlobShareStore() - Constructor for class ome.services.sharing.BlobShareStore
 
BOOLEAN(Connection, List<Boolean>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
BOOLEAN() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.BOOLEAN
 
BOOLEAN(List<Boolean>) - Constructor for class ome.tools.hibernate.SqlArray.BOOLEAN
 
bridge - Variable in class ome.services.fulltext.FullTextThread
Deprecated.
 
BridgeHelper - Class in ome.services.fulltext
Deprecated.
BridgeHelper() - Constructor for class ome.services.fulltext.BridgeHelper
Deprecated.
 
Builder(AbstractFileSystemService, ExtendedMetadata) - Constructor for class ome.services.delete.Deletion.Builder
 
buildOrObtainSession() - Method in class ome.tools.hibernate.CurrentSessionContext
 
buildQuery(Session) - Method in class ome.services.query.CollectionCountQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.IObjectClassQuery
 
buildQuery(Session) - Method in class ome.services.query.PojosFindAnnotationsQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosFindHierarchiesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesByOptionsQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetImagesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosGetUserImagesQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.PojosLoadHierarchyQueryDefinition
 
buildQuery(Session) - Method in class ome.services.query.Query
main point of entry for subclasses.
buildQuery(Session) - Method in class ome.services.query.StringQuery
 
buildQuery(QueryBuilder) - Method in class ome.services.scripts.ScriptRepoHelper
Adds a single clause of the form "AND (A OR B ...)" where each ScriptFileType A, B, etc.
byAnnotatedWith(Annotation...) - Method in class ome.services.SearchBean
 
byFullText(String) - Method in class ome.services.SearchBean
 
byGroupForTags(String) - Method in class ome.services.SearchBean
 
byHqlQuery(String, Parameters) - Method in class ome.services.SearchBean
 
byLuceneQueryBuilder(String, String, String, String, String) - Method in class ome.services.SearchBean
 
bySimilarTerms(String...) - Method in class ome.services.SearchBean
 
bySomeMustNone(String[], String[], String[]) - Method in class ome.services.SearchBean
 
byTagForGroups(String) - Method in class ome.services.SearchBean
 
byUUID(String[]) - Method in class ome.services.SearchBean
 

C

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
Calls PasswordUtil.changeUserPasswordById(Long, String, METHOD) with "false" as the value of the salt argument in order to provide backwards compatibility.
changeUserPasswordById(Long, String, PasswordUtil.METHOD) - Method in class ome.security.auth.PasswordUtil
Calls either PasswordUtil.preparePassword(String) or PasswordUtil.prepareSaltedPassword(Long, String) and passes the resulting value to SqlAction.setUserPassword(Long, String).
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
Performs one of the checks returned by ChmodStrategy.getChecks(IObject obj, String permissions).
check(String) - Method in class ome.services.query.Query
check that there is a definition for this Query with the provided argument as its name.
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
Like OmeroInterceptor.checkManagedDetails(IObject, Details, Details) but allows passing in a specific Details instance.
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
Retrieves password from the database and calls ConfigurablePasswordProvider.comparePasswords(String, String).
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
calls BasicSecuritySystem.isReady() and if not throws an ApiUsageException.
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
Like Policy.isRestricted(IObject) but throws an appropriate SecurityViolation subclass if the restriction is active.
checkRestriction(String, IObject) - Method in interface ome.security.policy.PolicyService
Give each configured Policy instance the chance to throw a SecurityViolation from its Policy.checkRestriction(IObject) method.
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
Returns the SessionContext.Count instance held by this context.
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
Takes the lock checks returned by ExtendedMetadata.getLockChecks(Class) and performs the actual check returning a map from class to total number of locks.
countLocks(Session, Long, String[][], String) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
countOnDisk() - Method in class ome.services.scripts.ScriptRepoHelper
Returns the number of files which match ScriptRepoHelper.scriptFilter in ScriptRepoHelper.dir.
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
Percentage (100.0 - 0.0) of disk use which will cause an exception during RepositoryInfoImpl.sanityCheckRepository()
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
 

D

DatabaseIdentity - Class in ome.services.db
Represents the unique identity of this database, consisting of the omero.db.authority and omero.db.uuid properties.
DatabaseIdentity(String, SqlAction) - Constructor for class ome.services.db.DatabaseIdentity
 
DatabaseIdentity(String, String) - Constructor for class ome.services.db.DatabaseIdentity
 
dataPerUser - Variable in class ome.services.pixeldata.PersistentEventLogLoader
 
DATE(Connection, List<Date>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
DATE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DATE
 
DATE(List<Date>) - Constructor for class ome.tools.hibernate.SqlArray.DATE
 
DBEnumCheck - Class in ome.services.util
Hook run by the context to guarantee that various enumerations are up to date.
DBEnumCheck(Executor, PreferenceContext, EnsureEnum, ReadOnlyStatus) - Constructor for class ome.services.util.DBEnumCheck
 
DBMappedEnumCheck - Class in ome.services.util
When a new version of the OMERO server starts up check that the database includes an enumeration instance for every value mapped for code generation.
DBMappedEnumCheck(Executor, PreferenceContext, EnsureEnum, ReadOnlyStatus) - Constructor for class ome.services.util.DBMappedEnumCheck
 
DBPatchCheck - Class in ome.services.util
Hook run by the context.
DBPatchCheck(SqlAction, PreferenceContext) - Constructor for class ome.services.util.DBPatchCheck
 
DBUnicodeUnitsCheck - Class in ome.services.util
Checks that the database contains correctly encoded enumerations for units of measure.
DBUnicodeUnitsCheck(Executor, PreferenceContext, ReadOnlyStatus) - Constructor for class ome.services.util.DBUnicodeUnitsCheck
 
DBUserCheck - Class in ome.services.util
Hook run by the context.
DBUserCheck(SqlAction, PreferenceContext, ReadOnlyStatus) - Constructor for class ome.services.util.DBUserCheck
 
deactivate() - Method in class ome.services.sharing.ShareBean
 
debugAll - Variable in class ome.security.basic.EventListenersFactoryBean
 
decrement() - Method in class ome.services.sessions.SessionContext.Count
Decrement the current reference count and return the new value atomically.
deepCopy(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
DEFAULT_BATCH_SIZE - Static variable in class ome.services.eventlogs.EventLogLoader
Currently 100.
DEFAULT_COMPRESSION_QUALITY - Static variable in class ome.services.ThumbnailBean
The default compression quality in fractional percent.
DEFAULT_ENCODING - Static variable in class ome.security.auth.PasswordUtil
The default encoding for converting plain text passwords to byte arrays (UTF-8)
DEFAULT_MAX - Static variable in class ome.services.eventlogs.EventLogQueue
Default maximum for the number of rows that will be loaded in a single call to SqlAction.getEventLogPartitions(java.util.Collection, java.util.Collection, long, long) .
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailBean
The default MIME type.
DEFAULT_MIME_TYPE - Static variable in class ome.services.ThumbnailCtx
Default thumbnail MIME type.
DEFAULT_PORT - Static variable in class ome.services.mail.SubethaSMTP
 
DEFAULT_REPORTING_LOOPS - Static variable in class ome.services.fulltext.FullTextIndexer
Deprecated.
Default number of loops to wait if no external value is set.
DEFAULT_X_WIDTH - Static variable in class ome.services.ThumbnailBean
The default X-width for a thumbnail.
DEFAULT_Y_WIDTH - Static variable in class ome.services.ThumbnailBean
The default Y-width for a thumbnail.
DefaultPolicyService - Class in ome.security.policy
PolicyService which is configured with all Policy instances which are discovered in the Spring context and only focuses on a small subset of IObject types as specified by DefaultPolicyService.filterObject(IObject).
DefaultPolicyService() - Constructor for class ome.security.policy.DefaultPolicyService
 
defaultTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
 
defaultTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
 
define(Session, String, String, long, SessionManager.CreationRequest) - Method in class ome.services.sessions.SessionManagerImpl
 
define(Session, String, String, long, long, long, String, String, String) - Method in class ome.services.sessions.SessionManagerImpl
 
Definitions - Class in ome.services.query
container for QueryParameterDef instances.
Definitions(QueryParameterDef...) - Constructor for class ome.services.query.Definitions
 
defs - Variable in class ome.services.query.Query
container of QueryParameterDef instances.
DelegatingStats - Class in ome.services.sessions.stats
Delegates to a SessionStats which is acquired from DelegatingStats.stats().
DelegatingStats() - Constructor for class ome.services.sessions.stats.DelegatingStats
 
DelegatingStats(SessionStats[]) - Constructor for class ome.services.sessions.stats.DelegatingStats
 
delete(long) - Method in class ome.services.scripts.ScriptRepoHelper
 
delete(String) - Method in class ome.tools.hibernate.QueryBuilder
 
DeleteBean - Class in ome.services.delete
Strict implementation of the IDelete service interface which will use the SecuritySystem via SecuritySystem.runAsAdmin(AdminAction) to forcibly delete instances.
DeleteBean(LocalAdmin, SessionFactory) - Constructor for class ome.services.delete.DeleteBean
 
deleteChannels(long) - Method in class ome.services.delete.DeleteBean
 
deleteComment(Annotation) - Method in class ome.services.sharing.ShareBean
 
deleteCurrentId() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
deletedIds - Variable in class ome.services.delete.files.AbstractFileDeletions
 
deleteEnumeration(T) - Method in class ome.logic.TypesImpl
 
deleteExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
 
deleteFiles(SetMultimap<String, Long>) - Method in class ome.services.delete.Deletion
For each Report use the map of tables to deleted ids to remove the files under Files, Pixels and Thumbnails if the ids no longer exist in the db.
deleteGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
deleteImage(long, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteImages(Set<Long>, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteImagesByDataset(long, boolean) - Method in class ome.services.delete.DeleteBean
 
deleteInstances(String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
Delete the given instances.
deleteLocal() - Method in class ome.services.delete.files.AbstractFileDeletions
Helper to delete and log.
DeleteLogMessage - Class in ome.services.messages
 
DeleteLogMessage(Object, long) - Constructor for class ome.services.messages.DeleteLogMessage
 
DeleteLogsMessage - Class in ome.services.messages
 
DeleteLogsMessage(Object, List<Long>) - Constructor for class ome.services.messages.DeleteLogsMessage
 
deleteObject(IObject) - Method in class ome.logic.UpdateImpl
 
deletePlate(long) - Method in class ome.services.delete.DeleteBean
 
deleteSettings(long) - Method in class ome.services.delete.DeleteBean
 
Deletion - Class in ome.services.delete
Maintain state about a delete itself.
Deletion(AbstractFileSystemService, OmeroContext) - Constructor for class ome.services.delete.Deletion
 
Deletion.Builder - Class in ome.services.delete
Inner class which can be used to generate a Deletion.
deliver(String, String, InputStream) - Method in class ome.services.mail.MapAnnotationSubethaListener
Stores each email as a map annotation with MapAnnotationSubethaListener.NAMESPACE set.
description() - Method in class ome.services.procs.ProcessManager.Work
 
description() - Method in class ome.services.search.SearchAction
Returns the SearchAction subclass as the description.
description - Variable in class ome.services.util.Executor.Descriptive
 
description() - Method in class ome.services.util.Executor.Descriptive
 
description() - Method in interface ome.services.util.Executor.LoggedWork
Returns a description of what this work will be doing for logging purposes.
description() - Method in interface ome.services.util.Executor.SqlWork
Return a description of what this work will be doing for logging purposes.
Descriptive(Object, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
 
Descriptive(String, String, Object...) - Constructor for class ome.services.util.Executor.Descriptive
 
destroy() - Method in class ome.services.util.SleepTimer
This method is called by Spring during server shut-down.
destroy() - Method in class ome.tools.spring.ShutdownSafeEhcacheManagerFactoryBean
 
DestroySessionMessage - Class in ome.services.messages
Published before a session destruction.
DestroySessionMessage(Object, String) - Constructor for class ome.services.messages.DestroySessionMessage
 
detach(String) - Method in interface ome.services.sessions.SessionManager
Allows decrementing the reference count for a session without calling the actual SessionManager.close(String) logic.
detach(String) - Method in class ome.services.sessions.SessionManagerImpl
 
detailsIndex(String[]) - Static method in class ome.tools.hibernate.HibernateUtils
 
dirname() - Method in class ome.services.scripts.RepoFile
 
dirtyMetadata(long) - Method in class ome.services.ThumbnailCtx
Whether or not the thumbnail metadata for a given Pixels ID is dirty (the RenderingDef has been updated since the Thumbnail was).
disable(Session) - Method in class ome.security.basic.AbstractSecurityFilter
 
disable(String...) - Method in class ome.security.basic.BasicSecuritySystem
 
disable(Session) - Method in interface ome.security.SecurityFilter
disable(Session) - Method in class ome.security.SecurityFilterHolder
 
disable(String...) - Method in interface ome.security.SecuritySystem
disables components of the backend for the current Thread.
disable(String...) - Method in class ome.security.SecuritySystemHolder
 
disable(String...) - Method in class ome.security.sharing.SharingSecuritySystem
 
DisableAction() - Constructor for class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
disableBaseFilters(Session) - Method in class ome.security.basic.AbstractSecurityFilter
 
disabled(MethodInvocation) - Method in class ome.tools.hibernate.EventMethodInterceptor.DisableAction
 
disableFilters(Session) - Method in class ome.services.query.Query
turns the filters off that are listed in Query.newlyEnabledFilters
disableQueryCache() - Method in class ome.services.query.Query
Disable the Hibernate level 2 cache for this query.
disableReadFilter(Object) - Method in class ome.security.basic.BasicSecuritySystem
disable this filer.
disassemble(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
discover() - Method in class ome.logic.LdapImpl
 
discoverGroups() - Method in class ome.logic.LdapImpl
 
dispose() - Method in class ome.services.sessions.state.CacheListener
 
doAction(SecureAction, T...) - Method in class ome.security.basic.BasicSecuritySystem
It would be better to catch the SecureAction.updateObject(IObject...) method in a try/finally block, but since flush can be so poorly controlled that's not possible.
doAction(SecureAction, T...) - Method in interface ome.security.SecuritySystem
 
doAction(SecureAction, T...) - Method in class ome.security.SecuritySystemHolder
 
doAction(SecureAction, T...) - Method in class ome.security.sharing.SharingSecuritySystem
 
doCheck() - Method in class ome.services.util.DBEnumCheck
 
doCheck() - Method in class ome.services.util.DBMappedEnumCheck
 
doCheck() - Method in class ome.services.util.DBUnicodeUnitsCheck
 
doCheckPassword(String, String, Properties, boolean) - Method in class ome.security.auth.FilePasswordProvider
 
doClose() - Method in class ome.services.sharing.BlobShareStore
 
doClose() - Method in class ome.services.sharing.ShareStore
 
doContains(long, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
 
doContains(ShareData, Class<T>, long) - Method in class ome.services.sharing.BlobShareStore
 
doContains(long, Class<T>, long) - Method in class ome.services.sharing.ShareStore
 
doFilter(String, Object) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
doFilter(String, Filterable) - Method in class ome.tools.hibernate.ProxySafeFilter
 
doFilter(String, Collection) - Method in class ome.tools.hibernate.ProxySafeFilter
 
doImport() - Method in class ome.formats.importer.util.TinyImportFixture
Deprecated.
 
doIndexing(FullTextSession) - Method in class ome.services.fulltext.FullTextIndexer
Deprecated.
 
doInHibernate(Session) - Method in class ome.services.query.Query
template method defined by HibernateTemplate.
doInit() - Method in class ome.services.sharing.BlobShareStore
 
doInit() - Method in class ome.services.sharing.ShareStore
 
doLogin(boolean, boolean) - Method in class ome.security.basic.EventHandler
 
doLookup(String, String, Long) - Method in class ome.services.query.HierarchyNavigator
Look up which objects of a given type relate to the given query object.
doLookup(T, E) - Method in class ome.services.query.HierarchyNavigatorWrap
Look up which objects of a given type relate to the given query object.
doMore(int) - Method in class ome.services.fulltext.FullTextIndexer
Deprecated.
Default implementation suggests doing more if fewer than FullTextIndexer.reps runs have been made and if there are still more than EventLogLoader.batchSize x 100 backlog entries.
doParse(File) - Method in class ome.services.fulltext.FileParser
Template method to parse a File into manageable chunks.
doParse(File) - Method in class ome.services.fulltext.PdfParser
 
doRun() - Method in class ome.services.fulltext.FullTextThread
Deprecated.
Passes the FullTextIndexer instance to Executor.Work.doWork(Session, ServiceFactory) between calls to DetailsFieldBridge.lock() and DetailsFieldBridge.unlock() in order to guarantee that no other FieldBridge can edit the property.
doRun() - Method in class ome.services.pixeldata.PixelDataThread
Loads event logs from the PixelDataHandler processing them all then in a background thread via a ExecutorCompletionService.
doRun() - Method in class ome.services.procs.ProcessManager
 
doRun() - Method in class ome.services.util.ExecutionThread
 
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.BlobShareStore
 
doSet(Share, ShareData, List<ShareItem>) - Method in class ome.services.sharing.ShareStore
 
DOUBLE(Connection, List<Double>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
DOUBLE() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.DOUBLE
 
DOUBLE(List<Double>) - Constructor for class ome.tools.hibernate.SqlArray.DOUBLE
 
doUpdate() - Method in class ome.services.sessions.state.SessionCache
Will only ever be accessed by a single thread.
doWork(Session, ServiceFactory) - Method in class ome.services.fulltext.FullTextIndexer
Deprecated.
Runs FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction.
doWork(Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
Loads PixelDataHandler.reps EventLog instances and returns them.
doWork(Session, ServiceFactory) - Method in class ome.services.procs.ProcessManager.Work
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.AnnotatedWith
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Complement
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.FullText
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.HqlQuery
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Intersection
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.SimilarTerms
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.TagsAndGroups
 
doWork(Session, ServiceFactory) - Method in class ome.services.search.Union
 
doWork(SqlAction) - Method in interface ome.services.util.Executor.SqlWork
 
doWork(Session, ServiceFactory) - Method in interface ome.services.util.Executor.Work
Work method.
dryRun - Variable in class ome.services.fulltext.FullTextIndexer
Deprecated.
 
dsAllQuery - Static variable in class ome.services.delete.QueryConstraints
 
dsNotOwnQuery - Static variable in class ome.services.delete.QueryConstraints
 

E

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
Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String)
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
Encodes the password as it would be encoded for a check by ConfigurablePasswordProvider.comparePasswords(String, String) salting the password with the given userId if it's provided.
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
Convert a model object to the type string and database ID expected by HierarchyNavigator.
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
validation method called by Query.checkParameters().
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
Main public constructor for this EventProvider implementation.
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
Call Executor.execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work<T>) - Method in interface ome.services.util.Executor
Executes a Executor.Work instance wrapped in two layers of AOP.
execute(Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl
Call Executor.execute(Map, Principal, Work) with a null call context.
execute(Map<String, String>, Principal, Executor.Work<T>) - Method in class ome.services.util.Executor.Impl
Executes a Executor.Work instance wrapped in two layers of AOP.
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
Executes a Executor.SqlWork wrapped with a transaction.
executeSql(Executor.SqlWork) - Method in class ome.services.util.Executor.Impl
Executes a Executor.SqlWork in transaction.
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
Simple adapter which takes a String for Executor.Descriptive.description
Executor.SimpleWork<T> - Class in ome.services.util
Simple adapter which takes a String for Executor.Descriptive.description
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
extension of the model metadata provided by SessionFactory.
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

F

factory - Variable in class ome.security.basic.EventHandler
 
factory - Variable in class ome.services.sessions.SessionManagerImpl
 
factory - Variable in class ome.services.util.Executor.Impl
 
factory - Variable in class ome.tools.hibernate.ListAsSQLArrayUserType
 
FACTORY - Static variable in class ome.tools.hibernate.SqlArray
 
fail(File, Long, Long) - Method in class ome.services.delete.files.AbstractFileDeletions
 
FailedLoginMailSender - Class in ome.services.mail
On an LoginAttemptMessage potentially send an email to administrators or the user herself to alert of possible security issues.
FailedLoginMailSender() - Constructor for class ome.services.mail.FailedLoginMailSender
 
FETCH - Static variable in class ome.services.query.Query
imported constant for ease of use
fetchAlso(Map<T, String>) - Method in class ome.services.SearchBean
 
fetchAlso(String...) - Method in class ome.services.SearchBean
 
fetchAnnotations - Variable in class ome.services.search.SearchValues
 
fetchAnnotations(Class...) - Method in class ome.services.SearchBean
 
fetchChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
fetches - Variable in class ome.services.search.SearchValues
 
fetchParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
file - Variable in class ome.security.auth.FilePasswordProvider
Flat file read on each invocation with name, value pairs in Java Properties notation.
file() - Method in class ome.services.scripts.RepoFile
 
FileDeleter - Class in ome.services.delete.files
Helper class which sorts through a number of file-based deletions before processing them.
FileDeleter(OmeroContext, AbstractFileSystemService, SetMultimap<String, Long>) - Constructor for class ome.services.delete.files.FileDeleter
 
FILENAME - Static variable in class ome.formats.importer.util.TinyImportFixture
Deprecated.
Hard-coded filename of the image to be imported
FileParser - Class in ome.services.fulltext
Object which attempts to parse any file given to it.
FileParser() - Constructor for class ome.services.fulltext.FileParser
 
FilePasswordProvider - Class in ome.security.auth
Example password provider which uses the given file as password lookup.
FilePasswordProvider(PasswordUtil, File) - Constructor for class ome.security.auth.FilePasswordProvider
 
FilePasswordProvider(PasswordUtil, File, boolean) - Constructor for class ome.security.auth.FilePasswordProvider
 
files - Variable in class ome.services.fulltext.FullTextBridge
Deprecated.
 
fillRelationships(SessionFactoryImplementor, Map<String, ExtendedMetadata.Relationship>) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
For each of the fields contained in this ExtendedMetadata.Locks object, parse out the type and the field name and store those as the key and value in the "value" argument.
fillReplacement(MergeEvent) - Method in class ome.security.basic.MergeEventListener
 
filter(String, Filterable) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Collection) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Map) - Method in class ome.tools.hibernate.ProxyCleanupFilter
 
filter(String, Filter) - Method in class ome.tools.hibernate.QueryBuilder
 
filter(String, Filterable) - Method in class ome.tools.hibernate.ReloadFilter
 
filter(String, Object) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Object) to allow only certain types to enter the Hibernate system
filter(String, Filterable) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Filterable) to return previously merged or previously checked items.
filter(String, Collection) - Method in class ome.tools.hibernate.UpdateFilter
overrides ContextFilter.filter(String, Collection) to return previously checked collections.
filter(String, Map) - Method in class ome.tools.hibernate.UpdateFilter
Prevents CountPerOwner from being loaded unnecessarily.
filterName - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
filterNow() - Method in class ome.tools.hibernate.QueryBuilder
In order to support the order() method in addition to a filter, we allow applying the filter and nulling the instance eagerly before the user calls order.
filterObject(IObject) - Method in class ome.security.policy.DefaultPolicyService
Limit the objects to which Policy instances are applied.
filters - Variable in class ome.security.basic.BasicSecuritySystem
 
find(Class, long) - Method in class ome.logic.QueryImpl
 
find(String) - Method in interface ome.services.sessions.SessionManager
Finds a Session and update the last access time.
find(String) - Method in class ome.services.sessions.SessionManagerImpl
 
findAll(Class<T>, Filter) - Method in class ome.logic.QueryImpl
 
findAllByExample(T, Filter) - Method in class ome.logic.QueryImpl
 
findAllByFullText(Class<T>, String, Parameters) - Method in class ome.logic.QueryImpl
 
findAllByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
 
findAllByString(Class<T>, String, String, boolean, Filter) - Method in class ome.logic.QueryImpl
 
findByExample(T) - Method in class ome.logic.QueryImpl
 
findByMimetype(String) - Method in class ome.services.scripts.ScriptRepoHelper
Search through all ScriptFileType instances and find one with a matching mimetype string.
findByQuery(String, Parameters) - Method in class ome.logic.QueryImpl
 
findByString(Class<T>, String, String) - Method in class ome.logic.QueryImpl
 
findContainerHierarchies(Class, Set, Parameters) - Method in class ome.logic.PojosImpl
 
findDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class ome.security.basic.OmeroInterceptor
default logic
findDN(String) - Method in class ome.logic.LdapImpl
 
findExperimenter(String) - Method in class ome.logic.LdapImpl
 
findGroup(String) - Method in class ome.logic.LdapImpl
 
findGroupDN(String) - Method in class ome.logic.LdapImpl
 
findInDb(String, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
findInDb(RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
 
findInDb(SqlAction, RepoFile, boolean) - Method in class ome.services.scripts.ScriptRepoHelper
Looks to see if a path is contained in the repository.
findMinMax(int[]) - Method in class ome.services.RawPixelsBean
 
findQuietly(String) - Method in interface ome.services.sessions.SessionManager
Finds a Session without updating the last access time.
findQuietly(String) - Method in class ome.services.sessions.SessionManagerImpl
 
findSameUser(String, String...) - Method in interface ome.services.sessions.SessionManager
Returns a non-null, possibly empty list of session instances belonging to the same user as the given session with one of the given agents.
findSameUser(String, String...) - Method in class ome.services.sessions.SessionManagerImpl
 
findSessionById(long, Session) - Method in interface ome.services.sessions.SessionProvider
Retrieves a session by ID.
findSessionById(long, ServiceFactory) - Method in interface ome.services.sessions.SessionProvider
Retrieves a session by ID.
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderInDb
 
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInDb
 
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderInMemory
 
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInMemory
 
findSessionById(long, Session) - Method in class ome.services.sessions.SessionProviderWrapper
 
findSessionById(long, ServiceFactory) - Method in class ome.services.sessions.SessionProviderWrapper
 
findSessionIdByUuid(String, ServiceFactory) - Method in interface ome.services.sessions.SessionProvider
 
findSessionIdByUuid(String) - Method in interface ome.services.sessions.SessionProvider
 
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInDb
 
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderInDb
 
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderInMemory
 
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderInMemory
 
findSessionIdByUuid(String, ServiceFactory) - Method in class ome.services.sessions.SessionProviderWrapper
 
findSessionIdByUuid(String) - Method in class ome.services.sessions.SessionProviderWrapper
 
finish() - Method in interface ome.services.procs.Process
 
finish() - Method in class ome.services.procs.ProcessSkeleton
 
fixNulledOrFilteredCollections(IObject, IObject, EntityPersister, SessionImplementor) - Static method in class ome.tools.hibernate.HibernateUtils
loads collections which have been filtered or nulled by the user
flipState() - Method in class ome.services.eventlogs.EventBacklog
Flips the EventBacklog to the "adding" state if it is empty, otherwise to the "removing" state.
FLOAT(Connection, List<Float>) - Method in interface ome.tools.hibernate.ListAsSQLArrayUserType.ArrayFactory
 
FLOAT() - Constructor for class ome.tools.hibernate.ListAsSQLArrayUserType.FLOAT
 
FLOAT(List<Float>) - Constructor for class ome.tools.hibernate.SqlArray.FLOAT
 
flush() - Method in interface ome.api.local.LocalUpdate
 
flush() - Method in class ome.logic.UpdateImpl
 
ForceTransactionAttributeSource - Class in ome.tools.spring
Requires that all method calls have some other form of attribute source by throwing an exception if accessed;
ForceTransactionAttributeSource() - Constructor for class ome.tools.spring.ForceTransactionAttributeSource
 
foreground(boolean, String[]) - Static method in class ome.services.fulltext.Main
Uses a PersistentEventLogLoader and cycles through all the remaining logs.
free() - Method in class ome.tools.hibernate.SqlArray
 
FROM - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
from(String, String) - Method in class ome.tools.hibernate.QueryBuilder
 
fullname() - Method in class ome.services.scripts.RepoFile
 
FullText - Class in ome.services.search
Search based on Lucene's Query class.
FullText(SearchValues, String, String, String, String, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText
Constructs a new instance; Builds a Lucence query with the provided arguments and passes it on the Lucene parser
FullText(SearchValues, String, Class<? extends Analyzer>) - Constructor for class ome.services.search.FullText
Creates a new instance; Passes the query directly on to the Lucene parser.
FullTextAnalyzer - Class in ome.services.fulltext
Deprecated.
FullTextAnalyzer() - Constructor for class ome.services.fulltext.FullTextAnalyzer
Deprecated.
 
fullTextBridge - Variable in class ome.logic.UpdateImpl
 
FullTextBridge - Class in ome.services.fulltext
Deprecated.
FullTextBridge() - Constructor for class ome.services.fulltext.FullTextBridge
Deprecated.
Since this constructor provides the instance with no way of parsing OriginalFile binaries, all files will be assumed to have blank content.
FullTextBridge(OriginalFilesService, Map<String, FileParser>) - Constructor for class ome.services.fulltext.FullTextBridge
Deprecated.
Constructor which provides an empty set of custom bridges.
FullTextBridge(OriginalFilesService, Map<String, FileParser>, Class<FieldBridge>[]) - Constructor for class ome.services.fulltext.FullTextBridge
Deprecated.
Main constructor.
FullTextIndexer - Class in ome.services.fulltext
Deprecated.
FullTextIndexer(EventLogLoader) - Constructor for class ome.services.fulltext.FullTextIndexer
Deprecated.
 
FullTextIndexer(EventLogLoader, Metrics) - Constructor for class ome.services.fulltext.FullTextIndexer
Deprecated.
 
FullTextIndexer2 - Class in ome.services.fulltext
An indexer bean replacing the 5.4 full-text thread FullTextIndexer with adequate functionality.
FullTextIndexer2(Scheduler, SessionFactory, FieldBridge, String, String, String) - Constructor for class ome.services.fulltext.FullTextIndexer2
Construct a new indexer.
FullTextThread - Class in ome.services.fulltext
Deprecated.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge) - Constructor for class ome.services.fulltext.FullTextThread
Deprecated.
Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, boolean) - Constructor for class ome.services.fulltext.FullTextThread
Deprecated.
Uses default Principal for indexing
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal) - Constructor for class ome.services.fulltext.FullTextThread
Deprecated.
Main constructor.
FullTextThread(SessionManager, Executor, FullTextIndexer, FullTextBridge, Principal, boolean) - Constructor for class ome.services.fulltext.FullTextThread
Deprecated.
Main constructor.

G

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
Calls SecuritySystem.getEventContext(boolean) with a false as "refresh".
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
Uses the locally defined query to load an Image and calls DeleteBean.collect(UnloadedCollector, Image) in order to define a list of what will be deleted.
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
Rather than iterating over an IObject like ExtendedMetadata.getLockCandidates(IObject) this method returns type/field name pairs (like ExtendedMetadata.getLockChecks(Class)) to allow performing the queries manually.
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
Can be implemented by all subclasses, so that they can configure themselves in HardWiredInterceptor.selfConfigure(OmeroContext).
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
Deprecated.
instead use GraphPathBean.getSimpleProperties(String, boolean) setting isNested to false
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
provides the link between two tables similar to {link ExtendedMetadata.getRelationship(String, String).
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
uses the ClassMetadata for this ExtendedMetadata.Locks tp retrieve the component value.
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
Each Policy should tell the PolicyService which types of IObject instances it cares about.
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
If an object instance has any GraphPolicy.Action.EXCLUDEd parents that would prevent it from being orphaned.
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
 

H

handleAnnotated(IAnnotated, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
Deprecated.
Responsible for iterating over any attached OMERO.tables and registering all appropriate row objects for later processing.
handleAnnotation(Annotation, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge
Deprecated.
Detects if the given annotation contains an OMERO.table and if so, passes it off for further processing.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.security.policy.DefaultPolicyService
Loads all Policy instances from the context, and uses them to initialize this PolicyService.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.graphs.GraphPathBean
The application context after refresh should contain a usable Hibernate session factory.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.mail.ServerUpMailSender
 
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.services.scripts.ScriptRepoHelper
Loads all ScriptFileType instances from the context, and uses them to initialize all scripts in the repo.
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
Listener method which waits for a ContextRefreshedEvent and then extracts the SessionFactory from the ApplicationContext and pases it to ExtendedMetadata.Impl.setSessionFactory(SessionFactory).
handleContextRefreshedEvent(ContextRefreshedEvent) - Method in class ome.tools.spring.OnContextRefreshedEventListener
 
handleEventLog(FullTextSession, EventLog) - Method in class ome.services.fulltext.FullTextIndexer
Deprecated.
 
handleEventLog(EventLog, Session, ServiceFactory) - Method in class ome.services.pixeldata.PixelDataHandler
Handles only single elements from the PersistentEventLogLoader in order to keep transactions short and safe.
handleHdf5(String, TablesBridge.RowProcessor) - Method in class ome.services.fulltext.bridges.TablesBridge
Deprecated.
Process a single OMERO.tables file.
handleImage(Image, Document, LuceneOptions) - Method in class ome.services.fulltext.bridges.TablesBridge
Deprecated.
Processes any annotations attached to the following types which contain this image: Plate, Dataset
HardWiredInterceptor - Class in ome.logic
Extension point for interceptors which should be compiled in from third-party code.
HardWiredInterceptor() - Constructor for class ome.logic.HardWiredInterceptor
 
hash - Variable in class ome.security.auth.ConfigurablePasswordProvider
Hash implementation to use for encoding passwords to check and changed passwords.
hash() - Method in class ome.services.scripts.RepoFile.FsFile
 
hash() - Method in class ome.services.scripts.RepoFile
 
hashCode(Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
hasher() - Method in class ome.services.scripts.RepoFile.FsFile
 
hasher() - Method in class ome.services.scripts.RepoFile
 
hasMetadata(long) - Method in class ome.services.ThumbnailCtx
Whether or not thumbnail metadata is available for a given Pixels ID.
hasNext() - Method in class ome.services.eventlogs.EventLogLoader
Tests for available objects.
hasNext() - Method in class ome.services.eventlogs.EventLogQueue
Checks if either any EventLogQueue.Entry instances are available or tries to load them if not.
hasNext() - Method in class ome.services.SearchBean
 
hasPassword(MethodInvocation) - Method in class ome.logic.HardWiredInterceptor
 
hasPassword(String) - Method in class ome.security.auth.ConfigurablePasswordProvider
Always returns false, override with specific logic.
hasPassword(String) - Method in class ome.security.auth.FilePasswordProvider
 
hasPassword(String) - Method in class ome.security.auth.JdbcPasswordProvider
 
hasPassword(String) - Method in class ome.security.auth.LdapPasswordProvider
Only returns if the user is already in the database and has a DN value in the password table.
hasPassword(String) - Method in interface ome.security.auth.PasswordProvider
Returns true if this provider considers itself responsible for the given user name.
hasPassword(String) - Method in class ome.security.auth.PasswordProviders
 
hasPassword(String) - Method in class ome.security.auth.providers.LdapPasswordProvider431
Only returns if the user is already in the database and has a DN value in the password table.
hasPrivilegedToken(IObject) - Method in class ome.security.basic.BasicSecuritySystem
 
hasPrivilegedToken(IObject) - Method in class ome.security.basic.TokenHolder
 
hasPrivilegedToken(IObject) - Method in interface ome.security.SecuritySystem
checks that the IObject argument has been granted a Token by the SecuritySystem.
hasPrivilegedToken(IObject) - Method in class ome.security.SecuritySystemHolder
 
hasPrivilegedToken(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
 
hasReplacement(Object) - Method in class ome.tools.hibernate.UpdateFilter
 
hasSettings(long) - Method in class ome.services.ThumbnailCtx
Whether or not settings are available for a given Pixels ID.
hasSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns true if this offset points to a field which is an embedded component.
HibernateUtils - Class in ome.tools.hibernate
contains methods for reloading unloaded entities and nulled collections as well as determining the index of certain properties in a dehydrated Hibernate array.
HibernateUtils() - Constructor for class ome.tools.hibernate.HibernateUtils
 
Hierarchy - Class in ome.services.query
single-point of entry for walking of OME container hierarchies.
Hierarchy() - Constructor for class ome.services.query.Hierarchy
 
HierarchyNavigator - Class in ome.services.query
Query the database for relationships between model objects.
HierarchyNavigator(IQuery) - Constructor for class ome.services.query.HierarchyNavigator
Construct a new hierarchy navigator.
HierarchyNavigatorWrap<T,E> - Class in ome.services.query
Convenience class for creating versions of HierarchyNavigator with different model object representations.
HierarchyNavigatorWrap(IQuery) - Constructor for class ome.services.query.HierarchyNavigatorWrap
 
HierarchyTransformations - Class in ome.tools
 
HierarchyTransformations() - Constructor for class ome.tools.HierarchyTransformations
 
hints - Variable in class ome.services.SVGRasterizer
The transcoder hints.
HqlQuery - Class in ome.services.search
Delegate to IQuery.findAllByQuery(String, Parameters).
HqlQuery(SearchValues, String, Parameters) - Constructor for class ome.services.search.HqlQuery
 

I

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
If true, this implementation should return a null on ConfigurablePasswordProvider.checkPassword(String, String, boolean) if the user is unknown, otherwise a Boolean.FALSE.
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 the current reference count and return the new value atomically.
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
Time (2 minutes) between successive calls to RepositoryInfoImpl.sanityCheckRepository() needed to trigger an actual call to RepositoryInfoImpl.getUsageFraction()
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
Note if we use anything other than merge here, functionality from MergeEventListener needs to be moved to UpdateFilter or to another event listener.
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
Note if we use anything other than merge here, functionality from MergeEventListener needs to be moved to UpdateFilter or to another event listener.
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
Internal SessionContext created during SessionManagerImpl.init() which is used for all method calls internal to the session manager (see execute* methods)
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
Clears the content of the EventContextso that the SecuritySystem will no longer return true for SecuritySystem.isReady().
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
if the user's permissions for the object should be checked before the GraphTraversal.Processor acts upon it
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
checks if this SecuritySystem instance is in a valid state.
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
Checks whether or not this instance would throw a SecurityViolation if the same instance were passed to Policy.checkRestriction(IObject).
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
 

J

JavaImageScalingService - Class in ome.logic
Provides methods for scaling buffered images using Java Image Scaling.
JavaImageScalingService() - Constructor for class ome.logic.JavaImageScalingService
 
JdbcHashedPasswordProvider - Class in ome.security.auth
Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcHashedPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
 
JdbcHashedPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcHashedPasswordProvider
 
JdbcPasswordProvider - Class in ome.security.auth
Central PasswordProvider which uses the "password" table in the central OMERO database.
JdbcPasswordProvider(PasswordUtil) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
JdbcPasswordProvider(PasswordUtil, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
JdbcPasswordProvider(PasswordUtil, boolean, boolean) - Constructor for class ome.security.auth.JdbcPasswordProvider
 
job(ServiceFactory, long) - Method in class ome.services.procs.ProcessManager.Work
 
JobBean - Class in ome.services
Provides methods for submitting asynchronous tasks.
JobBean() - Constructor for class ome.services.JobBean
default constructor
jobError() - Method in class ome.services.JobBean
 
jobFinished() - Method in class ome.services.JobBean
 
jobMessage() - Method in class ome.services.JobBean
 
jobRunning() - Method in class ome.services.JobBean
 
jobStatus() - Method in class ome.services.JobBean
 
join(String) - Method in interface ome.services.sessions.SessionCallback
 
join(String) - Method in class ome.services.sessions.SessionCallback.SimpleCloseCallback
 
join(String, String, boolean, boolean) - Method in class ome.tools.hibernate.QueryBuilder
 
joinChildren(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
joinParents(Criteria, Class, int) - Static method in class ome.services.query.Hierarchy
 
JvmSettingsCheck - Class in ome.services.util
Hook run by the context which prints out JVM-related information, primarily Java version, max heap size and available processors.
JvmSettingsCheck() - Constructor for class ome.services.util.JvmSettingsCheck
 

K

key(String) - Method in class ome.security.auth.AttributeSet
 
key - Variable in class ome.services.eventlogs.PersistentEventLogLoader
Key used to look configuration value; 'name'
KeyAndTrustStoreConfiguration - Class in ome.security
Calls System.setProperty(String, String) for the "javax.net.ssl" properties needed to configure a trust store and a keystore for the Java process.
KeyAndTrustStoreConfiguration() - Constructor for class ome.security.KeyAndTrustStoreConfiguration
 
keys() - Method in class ome.services.sharing.BlobShareStore
 
keys() - Method in class ome.services.sharing.ShareStore
 
keySet() - Method in class ome.services.query.Definitions
 

L

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
Base constructor which stores all LdapConfig.parse(String) and stores all values for later lookup.
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
Data class which stores the state of the NewUserGroupBean and NewUserGroupOwnerBean operations.
LdapPasswordProvider - Class in ome.security.auth
LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
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
LDAP PasswordProvider which can create users on request to synchronize with an LDAP directory.
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
Possibly null PasswordUtil instance which will be used as a fallback for password checks if the ConfigurablePasswordProvider.util instance fails.
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
Deprecated.
because the 2019-SV5 fix addresses Session privacy no less than this, see PrivilegedStringType
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
Return all identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject) which considers itself active for the given argument.
listAllRestrictions() - Method in class ome.security.policy.DefaultPolicyService
 
listAllRestrictions() - Method in interface ome.security.policy.PolicyService
Return all configured identifier strings as would be passed as the first argument to PolicyService.isRestricted(String, IObject) or PolicyService.checkRestriction(String, IObject).
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
Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
loadAll(boolean, String, Principal) - Method in class ome.services.scripts.ScriptRepoHelper
 
loadAll(boolean) - Method in class ome.services.scripts.ScriptRepoHelper
Walks all files in the repository (via ScriptRepoHelper.iterate() and adds them if not found in the database.
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
Listens for any LoginAttemptMessage.
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.

M

mailSender - Variable in class ome.logic.AdminImpl
 
MailSender - Class in ome.services.mail
Basic bean with setter injection that can be used as a base class for other senders.
MailSender() - Constructor for class ome.services.mail.MailSender
 
mailSender - Variable in class ome.services.mail.MailUtil
 
MailUtil - Class in ome.services.mail
Methods for dealing with the preparation of JavaMail MIME messages.
MailUtil(String, JavaMailSender) - Constructor for class ome.services.mail.MailUtil
 
mailUtil - Variable in class ome.services.sharing.ShareBean
 
main(String[]) - Static method in class ome.security.auth.PasswordUtil
Main method which takes exactly one argument, passes it to PasswordUtil.preparePassword(String) and prints the results on System.out.
Main - Class in ome.services.fulltext
Commandline entry-point for various full text actions.
Main() - Constructor for class ome.services.fulltext.Main
 
main(String[]) - Static method in class ome.services.fulltext.Main
 
main(String[]) - Static method in class ome.services.graphs.GraphPathReport
Generate a Sphinx report of OMERO Hibernate entities.
main(String[]) - Static method in class ome.services.sharing.BlobShareStore
 
main(String[]) - Static method in class ome.services.util.JvmSettingsCheck
 
managedEvent(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
 
managedExternalInfo(boolean, IObject, Details, Details, Details) - Method in class ome.security.basic.OmeroInterceptor
Deprecated.
managedGroup(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
 
managedOwner(boolean, IObject, Details, Details, Details, BasicEventContext) - Method in class ome.security.basic.OmeroInterceptor
 
ManagedServiceFactory - Class in ome.tools.spring
subclass of ome.system.ServiceFactory which retrieves managed service-instances.
ManagedServiceFactory() - Constructor for class ome.tools.spring.ManagedServiceFactory
 
manager - Variable in class ome.services.util.ExecutionThread
 
ManualFlushHibernateTemplate - Class in ome.tools.spring
 
ManualFlushHibernateTemplate() - Constructor for class ome.tools.spring.ManualFlushHibernateTemplate
 
map(Map<String, List<Long>>) - Method in class ome.services.sharing.ShareBean
 
MapAnnotationSubethaListener - Class in ome.services.mail
Basic SimpleMessageListener which stores all received emails as MapAnnotation instances belong to root with the namespace MapAnnotationSubethaListener.NAMESPACE.
MapAnnotationSubethaListener(Executor, Principal) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
 
MapAnnotationSubethaListener(Executor, String) - Constructor for class ome.services.mail.MapAnnotationSubethaListener
 
mapFromAttributes(Attributes) - Method in class ome.security.auth.GroupAttributeMapper
 
mapFromContext(Object) - Method in class ome.security.auth.GroupContextMapper
 
mapFromContext(Object) - Method in class ome.security.auth.OmeroModelContextMapper
 
mapFromContext(Object) - Method in class ome.security.auth.PersonContextMapper
 
markAndSweep() - Method in class ome.services.db.SelfCorrectingDataSource
First removes all entries in SelfCorrectingDataSource.errorTimes that are older than some given time and then uses the remaining number of errors to determine the backoff : (#^1/2)*1000 milliseconds.
matches(String, String) - Method in class ome.services.messages.EventLogsMessage
 
matches(File) - Method in class ome.services.scripts.RepoFile
 
maxFileSize - Variable in class ome.services.fulltext.FileParser
 
maxUserTimeToIdle - Variable in class ome.services.sessions.SessionManagerImpl
 
maxUserTimeToLive - Variable in class ome.services.sessions.SessionManagerImpl
 
mayHaveMapProperties(Class<? extends IObject>) - Method in class ome.tools.hibernate.ExtendedMetadata.Impl
 
mayHaveMapProperties(Class<? extends IObject>) - Method in interface ome.tools.hibernate.ExtendedMetadata
Check if an object of this class may have map properties.
member_of_groups - Static variable in class ome.security.basic.AllGroupsSecurityFilter
 
members - Variable in class ome.services.sharing.data.ShareData
 
members - Variable in class ome.services.sharing.data.ShareItem
 
MERGE_EVENT - Static variable in class ome.security.basic.MergeEventListener
 
mergedBatches - Variable in class ome.services.search.SearchValues
 
MergeEventListener - Class in ome.security.basic
responsible for responding to merge events.
MergeEventListener(CurrentDetails, TokenHolder) - Constructor for class ome.security.basic.MergeEventListener
main constructor.
message - Variable in exception ome.services.graphs.GraphException
 
message() - Method in class ome.services.sessions.stats.LongCounter
 
message() - Method in class ome.services.sessions.stats.MethodCounter
 
message() - Method in class ome.services.sessions.stats.ObjectsReadCounter
 
message() - Method in class ome.services.sessions.stats.ObjectsWrittenCounter
 
message() - Method in class ome.services.sessions.stats.SessionsCreatedCounter
 
metadata - Variable in class ome.logic.AbstractLevel2Service
 
MetadataImpl - Class in ome.logic
Implement the IMetadata I/F.
MetadataImpl() - Constructor for class ome.logic.MetadataImpl
 
methodCount() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodCount() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodCount() - Method in interface ome.services.sessions.stats.SessionStats
 
methodCount() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
MethodCounter - Class in ome.services.sessions.stats
Counter for active methods for a given session.
MethodCounter(int) - Constructor for class ome.services.sessions.stats.MethodCounter
 
methodHardLimit - Variable in class ome.services.sessions.stats.CounterFactory
 
methodIn() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodIn() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodIn() - Method in interface ome.services.sessions.stats.SessionStats
 
methodIn() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
methodOut() - Method in class ome.services.sessions.stats.DelegatingStats
 
methodOut() - Method in class ome.services.sessions.stats.NullSessionStats
 
methodOut() - Method in interface ome.services.sessions.stats.SessionStats
 
methodOut() - Method in class ome.services.sessions.stats.SimpleSessionStats
 
methodSecurity - Variable in class ome.security.basic.BasicSecurityWiring
 
MethodSecurity - Interface in ome.security
Interface which allows security interceptors to check if a method should be executable for a given user.
MethodStatsMessage - Class in ome.services.messages.stats
Published when more than the specified number of active method calls is reached.
MethodStatsMessage(Object, long) - Constructor for class ome.services.messages.stats.MethodStatsMessage
 
ModelObjectSequencer - Class in ome.services.graphs
Deprecated.
no longer used internally, replaced by GraphTraversal.orderFileDeletion()
ModelObjectSequencer() - Constructor for class ome.services.graphs.ModelObjectSequencer
Deprecated.
 
modificationCheck() - Method in class ome.services.scripts.ScriptRepoHelper
Checks if
modified - Variable in class ome.services.AbstractStatefulBean
True if any write operation took place on this bean.
modified() - Method in class ome.services.AbstractStatefulBean
 
modifiedStart - Variable in class ome.services.search.SearchValues
 
modifiedStop - Variable in class ome.services.search.SearchValues
 
more() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
Returns the number of classes which are still unprocessed as a proxy for how much is left to process.
more() - Method in class ome.services.eventlogs.AllEventsLogLoader
 
more() - Method in class ome.services.eventlogs.EventLogLoader
Should return an estimate of how many more EventLog instances are available for processing.
more() - Method in class ome.services.eventlogs.EventLogQueue
In general, EventLogQueue will intend to use much larger batch sizes, and so further loops should likely not be attempted.
more() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
moveToCommonSpace(IObject...) - Method in class ome.logic.AdminImpl
 
multicastEvent(ApplicationEvent) - Method in class ome.services.messages.GlobalMulticaster
Multicast only if this instance was the first created.
multicastEvent(ApplicationEvent, ResolvableType) - Method in class ome.services.messages.GlobalMulticaster
 
myFilterCondition() - Method in class ome.security.basic.AllGroupsSecurityFilter
 
myFilterCondition() - Method in class ome.security.basic.OneGroupSecurityFilter
 
MySeqGenerator - Class in ome.tools.hibernate
http://www.hibernate.org/296.html
MySeqGenerator() - Constructor for class ome.tools.hibernate.MySeqGenerator
 

N

NAME - Static variable in class ome.security.policy.BinaryAccessPolicy
This string can also be found in the Constants.ice file in the blitz package.
name - Variable in class ome.services.query.QueryParameterDef
name of this parameter.
name - Variable in class ome.services.scripts.RepoFile.FsFile
 
nameById(long) - Method in interface ome.security.auth.RoleProvider
 
nameById(long) - Method in class ome.security.auth.SimpleRoleProvider
 
NAMESPACE - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
neededRight(Class<?>, Class<?>) - Method in class ome.security.basic.OmeroInterceptor
The default right need for a linkage is Permissions.Right.WRITE.
needsSanityCheck() - Method in class ome.logic.RepositoryInfoImpl
Calculates based on the cached usage and the elapsed time whether or not a real RepositoryInfoImpl.sanityCheckRepository() should be calculated.
newEvent(Session, EventType, TokenHolder) - Method in class ome.security.basic.CurrentDetails
 
newlyEnabledFilters - Variable in class ome.services.query.Query
the set of filters that is being or has been enabled for this Query.
newTaskFor(Callable<T>) - Method in class ome.services.scheduler.ThreadPool
Overrides ThreadPoolExecutor to return our own instance of FutureTask so that we have a marker for when the background activity is completed in ThreadPool.afterExecute(Runnable, Throwable).
newTransientDetails(IObject) - Method in class ome.security.basic.BasicSecuritySystem
 
newTransientDetails(IObject) - Method in class ome.security.basic.OmeroInterceptor
 
newTransientDetails(IObject, Details) - Method in class ome.security.basic.OmeroInterceptor
Like OmeroInterceptor.newTransientDetails(IObject) but allows passing in a newDetails object with possibly preset values.
newTransientDetails(IObject) - Method in interface ome.security.SecuritySystem
creates a new secure details for transient entities.
newTransientDetails(IObject) - Method in class ome.security.SecuritySystemHolder
 
newTransientDetails(IObject) - Method in class ome.security.sharing.SharingSecuritySystem
 
NewUserGroupBean - Interface in ome.security.auth
Strategy for finding the appropriate groups for a given user in LDAP.
NewUserGroupOwnerBean - Interface in ome.security.auth
Strategy for finding the appropriate group owners for a given user in LDAP.
next() - Method in class ome.services.eventlogs.EventLogLoader
Returns the current EventLogLoader.log instance which may be loaded by a call to EventLogLoader.hasNext() if necessary.
next() - Method in class ome.services.eventlogs.EventLogQueue
Return a wrapped version of EventLogQueue.Data.next() which could possibly be null.
next() - Method in class ome.services.SearchBean
 
nextEventLog(long) - Method in class ome.services.eventlogs.EventLogLoader
Returns the EventLog with the next id after the given argument or null if none exists.
NodeProvider - Interface in ome.security
Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInDb - Class in ome.security.basic
Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInDb(String, Executor) - Constructor for class ome.security.basic.NodeProviderInDb
 
NodeProviderInMemory - Class in ome.security.basic
Provider for Node objects which is responsible for persisting and populating such entities.
NodeProviderInMemory(String) - Constructor for class ome.security.basic.NodeProviderInMemory
 
NodeProviderWrapper<P extends NodeProvider & ReadOnlyStatus.IsAware> - Class in ome.security.basic
A node provider that offers a unified view of multiple underlying node providers.
NodeProviderWrapper(ReadOnlyStatus, List<P>) - Constructor for class ome.security.basic.NodeProviderWrapper
Construct a new node provider.
norm(String) - Static method in class ome.services.scripts.RepoFile
Somewhat complicated method to turn any path into a unique like path rooted at "/".
not() - Method in class ome.services.SearchBean
 
notAnnotatedBy - Variable in class ome.services.search.SearchValues
 
notAnnotatedBy(Details) - Method in class ome.services.SearchBean
 
note() - Method in class ome.services.fulltext.FullTextIndexer2
Note which event log entries were processed.
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GraphPolicy
Any model object about which policy may be asked is first passed to GraphPolicy.noteDetails(Session, IObject, String, long) before GraphPolicy.review(Map, Details, Map, Set, boolean).
noteDetails(Session, IObject, String, long) - Method in interface ome.services.graphs.GraphPolicyRulePredicate
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.GroupPredicate
 
noteDetails(Session, IObject, String, long) - Method in class ome.services.graphs.PermissionsPredicate
 
NoThumbnail(String) - Constructor for exception ome.services.ThumbnailCtx.NoThumbnail
 
notifications(String) - Method in class ome.services.sessions.SessionManagerImpl
 
notifyElementEvicted(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementExpired(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementPut(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementRemoved(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyElementUpdated(Ehcache, Element) - Method in class ome.services.sessions.state.CacheListener
 
notifyMembersOfShare(long, String, String, boolean) - Method in class ome.services.sharing.ShareBean
 
notifyRemoveAll(Ehcache) - Method in class ome.services.sessions.state.CacheListener
 
notNullOrLikeOrEqual(QueryBuilder, String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
 
notNullOrLikeOrEqual(String, Class, Object, boolean, boolean) - Static method in class ome.services.search.SearchAction
 
notOwnedBy - Variable in class ome.services.search.SearchValues
 
notOwnedBy(Details) - Method in class ome.services.SearchBean
 
NS_COMMENT - Static variable in class ome.services.sharing.ShareBean
 
NS_ENABLED - Static variable in class ome.services.sharing.ShareBean
 
NSEXPERIMENTERPHOTO - Static variable in class ome.logic.AdminImpl
 
NULL_RENDERER - Static variable in class ome.services.RenderingBean
Message if the rendering engine is not ready.
NullEventHandler - Class in ome.security.basic
Provides only the bare minimum of functionality to allow methods to succeed.
NullEventHandler(SecuritySystem, SessionFactory) - Constructor for class ome.security.basic.NullEventHandler
 
nullProperties(String, String, Collection<Long>) - Method in interface ome.services.graphs.GraphTraversal.Processor
Null the given property of the indicated instances.
NullQuerySource - Class in ome.services.query
always returns null for any id.
NullQuerySource() - Constructor for class ome.services.query.NullQuerySource
 
nullSafeGet(ResultSet, String[], Object) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
nullSafeGroupId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils
returns the id of the group of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the group is null.
nullSafeOwnerId(IObject) - Static method in class ome.tools.hibernate.HibernateUtils
returns the id of the owner of this entity, or null if: (1) the object is null, (2) the Details is null, (3) the owner is null.
nullSafeSet(PreparedStatement, Object, int) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
NullSessionStats - Class in ome.services.sessions.stats
Implementation of SessionStats which does nothing.
NullSessionStats() - Constructor for class ome.services.sessions.stats.NullSessionStats
 
numberOfSubtypes(int) - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
returns the number of subtypes for iterating over this secondary array.
numThreads - Variable in class ome.services.pixeldata.PersistentEventLogLoader
 

O

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
If a ContextMessage is received then we need to either add a ContextMessage.Push login to the stack or ContextMessage.Pop remove one.
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
calls back to BasicSecuritySystem.checkManagedDetails(IObject, Details) for properly setting Details.
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
calls back to BasicSecuritySystem.newTransientDetails(IObject) for properly setting Details
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
the current orphan state of the object, may be mutated by GraphPolicy.review(Map, Details, Map, Set, boolean); applies only if GraphPolicy.Details.action is GraphPolicy.Action.EXCLUDE
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.

P

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
Produces a List of instantiated interceptors from a list of HardWiredInterceptor subclass names.
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
Uses FileParser.doParse(File) to create manageable chunks of a file for indexing.
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
Caught exception thrown from PasswordProvider.changePassword(String, String) to allow read-only implementations to refuse an action.
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
FileParser for "application/pdf" files using PDFBox.
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
Calculates PixelDataThread.performProcessing based on the existence of the "pixelDataTrigger" and passes all parameters to the main ctor.
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
Registers the given file paths as well as other Pixel-related files like Pyramids for later deletion via AbstractFileDeletions.deleteLocal().
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
The predicates that have been registered with GraphPolicy.registerPredicate(GraphPolicyRulePredicate).
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
Batch bulk database queries to prime the cache for HierarchyNavigator.doLookup(String, String, Long).
prepareLookups(T, Collection<E>) - Method in class ome.services.query.HierarchyNavigatorWrap
Batch bulk database queries to prime the cache for HierarchyNavigatorWrap.doLookup(Object, Object).
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
This uses DeleteBean.IMAGE_QUERY to load all the subordinate metadata of the Image which will be deleted.
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
Task performed by the ProcessManager on each invocation of ExecutionThread.run().
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
Map of all active processes.
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
Passes nulls to ProxyCleanupFilter.ProxyCleanupFilter(ACLVoter, CurrentDetails) such that all restricted objects will be unloaded.
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
 

Q

query() - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
query() - Method in class ome.services.eventlogs.AllEventsLogLoader
 
query - Variable in class ome.services.eventlogs.EventLogLoader
Query string to be kept in sync with EventLogLoader.excludes.
query() - Method in class ome.services.eventlogs.EventLogLoader
 
query() - Method in class ome.services.eventlogs.EventLogQueue
 
query() - Method in class ome.services.eventlogs.PersistentEventLogLoader
 
query() - Method in class ome.services.pixeldata.PersistentEventLogLoader
Uses data from the PersistentEventLogLoader.dataPerUser "queue" to allow new requests to be processed even if one user adds a large number of PIXELDATA events.
Query<T> - Class in ome.services.query
base Query type to facilitate the creation of ORM queries.
Query(Definitions, Parameters) - Constructor for class ome.services.query.Query
main constructor used by subclasses.
query(Session) - Method in class ome.tools.hibernate.QueryBuilder
 
QueryBuilder - Class in ome.tools.hibernate
Very thin wrapper around a StringBuilder to generate HQL queries.
QueryBuilder() - Constructor for class ome.tools.hibernate.QueryBuilder
 
QueryBuilder(boolean) - Constructor for class ome.tools.hibernate.QueryBuilder
Whether Session.createSQLQuery(String) should be used or not during QueryBuilder.query(Session) and similar.
QueryBuilder(int) - Constructor for class ome.tools.hibernate.QueryBuilder
 
QueryConstraints - Class in ome.services.delete
AdminAction which queries all datasets and retrieve images linked to the datasets.
QueryConstraints(LocalAdmin, LocalQuery, long, boolean) - Constructor for class ome.services.delete.QueryConstraints
 
QueryException - Exception in ome.services.query
something failed in looking up a query
QueryException(String) - Constructor for exception ome.services.query.QueryException
 
queryFactory - Variable in class ome.logic.AbstractLevel1Service
 
queryFactory - Variable in class ome.logic.AbstractLevel2Service
 
QueryFactory - Class in ome.services.query
query locator which is configured by Spring.
QueryFactory(QuerySource...) - Constructor for class ome.services.query.QueryFactory
main constructor which takes a non-null array of query sources as its only argument.
QueryImpl - Class in ome.logic
Provides methods for directly querying object graphs.
QueryImpl() - Constructor for class ome.logic.QueryImpl
 
QueryNewUserGroupBean - Class in ome.security.auth
Handles the ":query:" specifier from omero-server.properties.
QueryNewUserGroupBean(String) - Constructor for class ome.security.auth.QueryNewUserGroupBean
 
QueryParameterDef - Class in ome.services.query
definition of a slot into which a QueryParameter must fit.
QueryParameterDef(String, Class, boolean) - Constructor for class ome.services.query.QueryParameterDef
main constructor.
queryService - Variable in class ome.services.eventlogs.EventLogLoader
 
QuerySource - Class in ome.services.query
contract for any source of queries.
QuerySource() - Constructor for class ome.services.query.QuerySource
 
queryString() - Method in class ome.tools.hibernate.QueryBuilder
Returns the current query as a String.
queryWithoutFilter(Session) - Method in class ome.tools.hibernate.QueryBuilder
 

R

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.
Publishes a ReindexMessage which will get processed asynchronously.
reindexAll(List<T>) - Method in class ome.services.fulltext.BridgeHelper
Deprecated.
Publishes a ReindexMessage which will get processed asynchronously.
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
Similar to SessionManager.getEventContext(Principal) but uses the internal reload logic to get a fresh representation of the context.
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
Provides the reloading logic of the SessionCache for the SessionManagerImpl to use.
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
Given the current files on disk, ScriptRepoHelper.unregister(Long, SqlAction) all files which have been removed from disk.
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
Check the current state of the 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
Assumes that path is relative under root, and constructs a new File and calls RepoFile.RepoFile(File, File)
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
Can be used to reset the value that the PersistentEventLogLoader would read if started now.
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
Initializes the Session for this Thread if necessary, then calls ExecutionThread.doRun().
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
executes with special privileges within the SecuritySystem.
runAsAdmin(AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
runAsAdmin(ExperimenterGroup, AdminAction) - Method in class ome.security.basic.BasicSecuritySystem
merge event is disabled for BasicSecuritySystem.runAsAdmin(AdminAction) because passing detached (client-side) entities to this method is particularly dangerous.
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
 

S

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
Values used by SearchBean to store user requests.
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
SecuritySystem in order to perform a secure save on the Job instance.
secSys - Variable in class ome.security.basic.EventHandler
 
SecureAction - Interface in ome.security
SecureMerge - Class in ome.tools.hibernate
Helper originally from SimpleRoleProvider for merging admin objects.
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
Synchronized and lockable state for the SessionManager.
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
Constructor taking a SessionFactory.
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
Provides SessionManagerImpl with wrapper around session storage backends.
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
In-memory implementation of SessionProviderInDb.
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.
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
Injection method, also performs the creation of SessionCache.sessions
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
CurrentDetails setter for dependency injection.
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
Deprecated.
As of release 5.1.0, replaced by PlaneDef.setShapeIds(List).
setOwner(Experimenter) - Method in class ome.security.basic.BasicEventContext
 
setOwnsAll() - Method in class ome.services.graphs.GraphTraversal
Deprecated.
An ugly expedient hack that requires review and may be removed without notice.
setParameterValues(Properties) - Method in class ome.tools.hibernate.ListAsSQLArrayUserType
 
setPermissionsForGroup(Long, Permissions) - Method in class ome.security.basic.BasicEventContext
Called during BasicACLVoter.allowLoad(org.hibernate.Session, Class, ome.model.internal.Details, long) to track groups that will need resolving later.
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
The Share id is the only mutable bit in the 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
Unlike ScriptRepoHelper.delete(long) this method simply performs the DB delete on the given original file id.
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
Implements RoleProvider.
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
Return a SessionStats implementation for this session.
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
Call Executor.submit(Map, Callable) with a null callContext.
submit(Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
Simple submission method which can be used in conjunction with a call to Executor.execute(Principal, Work) to overcome the no-multiple-login rule.
submit(Executor.Priority, Callable<T>) - Method in interface ome.services.util.Executor
Simple submission method with a Executor.Priority.
submit(Executor.Priority, Map<String, String>, Callable<T>) - Method in interface ome.services.util.Executor
Like Executor.submit(Map, Callable) but provide info to which priority queue should be used.
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
 

T

TablesBridge - Class in ome.services.fulltext.bridges
Deprecated.
TablesBridge() - Constructor for class ome.services.fulltext.bridges.TablesBridge
Deprecated.
 
TagsAndGroups - Class in ome.services.search
Query template used by SearchBean to store user requests.
TagsAndGroups(SearchValues, String, boolean) - Constructor for class ome.services.search.TagsAndGroups
 
targetName - Variable in class ome.services.util.BeanInstantiationGuard
 
tearDown() - Method in class ome.formats.importer.util.TinyImportFixture
Deprecated.
 
templateMessage - Variable in class ome.logic.AdminImpl
 
ThreadPool - Class in ome.services.scheduler
An internal implementation of ThreadPoolExecutor that additionally handles the submission of ThreadPool.background(Callable) tasks at a lower priority and with more limited slots.
ThreadPool() - Constructor for class ome.services.scheduler.ThreadPool
 
ThreadPool(int, int, long, int, long) - Constructor for class ome.services.scheduler.ThreadPool
 
throwable - Variable in class ome.services.eventlogs.EventLogFailure
 
throwCreationViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwCreationViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwCreationViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwCreationViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwDeleteViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwDeleteViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwDeleteViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwDeleteViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwDisabled(String) - Method in class ome.security.sharing.SharingACLVoter
 
throwIfAlreadySet(Object, Object) - Method in class ome.services.util.BeanHelper
 
throwIfCancelled() - Method in class ome.services.sessions.events.ChangeSecurityContextEvent
 
throwLoadViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwLoadViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwLoadViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwLoadViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
throwOnNullData(long, ShareData) - Method in class ome.services.sharing.ShareBean
 
throwUpdateViolation(IObject) - Method in interface ome.security.ACLVoter
throws a SecurityViolation based on the given IObject and the context of the current user.
throwUpdateViolation(IObject) - Method in class ome.security.basic.BasicACLVoter
 
throwUpdateViolation(IObject) - Method in class ome.security.CompositeACLVoter
 
throwUpdateViolation(IObject) - Method in class ome.security.sharing.SharingACLVoter
 
ThumbnailBean - Class in ome.services
Provides methods for directly querying object graphs.
ThumbnailBean(boolean) - Constructor for class ome.services.ThumbnailBean
overridden to allow Spring to set boolean
ThumbnailBeanReadOnly - Class in ome.services
Provides methods for directly querying object graphs.
ThumbnailBeanReadOnly(boolean) - Constructor for class ome.services.ThumbnailBeanReadOnly
overridden to allow Spring to set boolean
ThumbnailCtx - Class in ome.services
 
ThumbnailCtx(IQuery, IUpdate, IPixels, IRenderingSettings, ThumbnailService, OmeroContext, SecuritySystem, long) - Constructor for class ome.services.ThumbnailCtx
Default constructor.
ThumbnailCtx.NoThumbnail - Exception in ome.services
Marker exception which is thrown by all methods which wish to tell their callers that for whatever reason the desired Thumbnail is not available, in which case the caller can use a *Direct method instead.
thumbnailExists(Integer, Integer) - Method in class ome.services.ThumbnailBean
 
ThumbnailFileDeletions - Class in ome.services.delete.files
Helper class which sorts through a number of file-based deletions before processing them.
ThumbnailFileDeletions(AbstractFileSystemService, Set<Long>) - Constructor for class ome.services.delete.files.ThumbnailFileDeletions
 
timeout - Variable in class ome.services.search.SearchAction
 
timeoutSetter - Variable in class ome.logic.QueryImpl
 
TimeoutSetter - Class in ome.services.util
Sets timeouts for queries according to event context.
TimeoutSetter(SecuritySystem, int, int) - Constructor for class ome.services.util.TimeoutSetter
Construct the timeout setter.
timeToIdle - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
timeToLive - Variable in class ome.services.sessions.SessionManager.CreationRequest
 
TinyImportFixture - Class in ome.formats.importer.util
Deprecated.
TinyImportFixture(ServiceFactory) - Constructor for class ome.formats.importer.util.TinyImportFixture
Deprecated.
 
TO - Static variable in class ome.services.mail.MapAnnotationSubethaListener
 
tokenHolder - Variable in class ome.security.basic.BasicACLVoter
 
tokenHolder - Variable in class ome.security.basic.BasicSecuritySystem
 
TokenHolder - Class in ome.security.basic
Manages a special token (a unique object) which can be inserted into IObject instances for special almost-administrative handling.
TokenHolder() - Constructor for class ome.security.basic.TokenHolder
 
tokenStream(String, Reader) - Method in class ome.services.fulltext.FullTextAnalyzer
Deprecated.
Returns a FullTextAnalyzer.LowercaseAlphaNumericTokenizer
toString() - Method in class ome.security.basic.BasicEventContext
 
toString() - Method in exception ome.services.graphs.GraphException
 
toString() - Method in class ome.services.graphs.GraphPolicyRule
 
toString() - Method in class ome.services.scripts.RepoFile.FsFile
 
toString() - Method in class ome.services.scripts.RepoFile
 
toString() - Method in class ome.tools.hibernate.QueryBuilder
 
toString() - Method in class ome.tools.hibernate.SqlArray
 
toString() - Method in class ome.tools.spring.InternalServiceFactory
 
total() - Method in class ome.tools.hibernate.ExtendedMetadata.Locks
as opposed to ExtendedMetadata.Locks.size(), the returns the actual number of fields that will need to be checked.
TOTAL_PHYSICAL_MEMORY - Static variable in class ome.services.util.JvmSettingsCheck
TotalPhysicalMemorySize value from the OperatingSystem JMX bean at startup.
TOTAL_SIZE - Static variable in class ome.services.search.FullText
 
totalSharedItems() - Method in class ome.services.sharing.BlobShareStore
 
totalSharedItems() - Method in class ome.services.sharing.ShareStore
 
totalShares() - Method in class ome.services.sharing.BlobShareStore
 
totalShares() - Method in class ome.services.sharing.ShareStore
 
transformQuery(String) - Method in class ome.tools.hibernate.SqlQueryTransformer
Reverse the effects of @ColumnTransformer annotations in WHERE clauses.
translateException(Throwable) - Method in class ome.services.util.BeanHelper
 
truncate(long) - Method in class ome.services.RawFileBean
 
txSource - Variable in class ome.security.basic.EventHandler
 
type - Variable in class ome.services.query.QueryParameterDef
type of this parameter.
type - Variable in class ome.services.sharing.data.Obj
 
type() - Method in class ome.services.sharing.data.ObjHolder
 
type() - Method in class ome.services.sharing.data.ShareDataHolder
 
type - Variable in class ome.services.sharing.data.ShareItem
 
type() - Method in class ome.services.sharing.data.ShareItemHolder
 
types - Variable in class ome.security.policy.BasePolicy
 
types - Variable in class ome.services.eventlogs.PersistentEventLogLoader
 
TypesImpl - Class in ome.logic
implementation of the ITypes service interface.
TypesImpl() - Constructor for class ome.logic.TypesImpl
 
typeToString(T) - Method in class ome.services.query.HierarchyNavigatorWrap
Convert the given object type to the type strings expected by HierarchyNavigator.

U

uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ObjPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
uncheckedCast(ObjectPrx, String) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
Downcasts the given proxy to this type without contacting the remote server.
Union - Class in ome.services.search
Union SearchAction which combines two other search actions into one logical unit, e.g.
Union(SearchValues, SearchAction, SearchAction) - Constructor for class ome.services.search.Union
 
unique_alias(String) - Method in class ome.tools.hibernate.QueryBuilder
Obtain a unique alias to be used in the SQL.
unlink(ILink[], Parameters) - Method in class ome.logic.PojosImpl
 
unlinkTargets(boolean) - Method in class ome.services.graphs.GraphTraversal
Prepare to remove links between the targeted model objects and the remainder of the model object graph.
unloadedObjectCache - Variable in class ome.tools.hibernate.ProxyCleanupFilter
 
unloadReplacedObjects() - Method in class ome.tools.hibernate.UpdateFilter
provides an external hook to unload all files which have already been merged.
unordered() - Method in class ome.services.SearchBean
 
unregister(Long, SqlAction) - Method in class ome.services.scripts.ScriptRepoHelper
Unregisters a given file from the script repository by setting its Repo uuid to null.
unregisterCallback(ProcessCallback) - Method in interface ome.services.procs.Process
 
unregisterCallback(ProcessCallback) - Method in class ome.services.procs.ProcessSkeleton
 
unsetGroupOwner(ExperimenterGroup, Experimenter) - Method in class ome.logic.AdminImpl
 
update(RepoFile, Long, Map<String, String>) - Method in class ome.services.scripts.ScriptRepoHelper
 
update(Session) - Method in interface ome.services.sessions.SessionManager
Certain fields from the Session instance will be copied and then saved to the db, as well as a new SessionContext created.
update(Session, boolean) - Method in interface ome.services.sessions.SessionManager
Same as SessionManager.update(Session) but some security checks can be overridden.
update(Session) - Method in class ome.services.sessions.SessionManagerImpl
 
update(Session, boolean) - Method in class ome.services.sessions.SessionManagerImpl
 
update(Share, ShareData) - Method in class ome.services.sharing.ShareStore
 
update(String) - Method in class ome.tools.hibernate.QueryBuilder
 
UPDATE_EVENT - Static variable in class ome.security.basic.UpdateEventListener
 
updateCodomainMap(CodomainMapContext) - Method in class ome.services.RenderingBean
Deprecated.
updateDataObject(IObject, Parameters) - Method in class ome.logic.PojosImpl
 
updateDataObjects(IObject[], Parameters) - Method in class ome.logic.PojosImpl
 
updatedObjects(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
updatedObjects(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
updatedObjects(int) - Method in interface ome.services.sessions.stats.SessionStats
 
updatedObjects(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 
updateEnumeration(T) - Method in class ome.logic.TypesImpl
 
updateEnumerations(List<T>) - Method in class ome.logic.TypesImpl
 
updateEvent(Event) - Method in class ome.security.basic.EventProviderInDb
Persists a given Event.
updateEvent(Event) - Method in class ome.security.basic.EventProviderInMemory
Persists a given Event.
updateEvent(Event) - Method in class ome.security.basic.EventProviderWrapper
 
updateEvent(Event) - Method in interface ome.security.EventProvider
Persists a given Event.
updateEvent(UserGroupUpdateEvent) - Method in class ome.services.sessions.state.SessionCache
Adds a new entry to SessionCache.state.
UpdateEventListener - Class in ome.security.basic
responsible for setting the updat event on all events shortly before being saved.
UpdateEventListener(CurrentDetails) - Constructor for class ome.security.basic.UpdateEventListener
main constructor.
updateExperimenter(Experimenter) - Method in class ome.logic.AdminImpl
 
updateExperimenterWithPassword(Experimenter, String) - Method in class ome.logic.AdminImpl
 
UpdateFilter - Class in ome.tools.hibernate
responsible for correlating entity identities during multiple calls to merge.
UpdateFilter() - Constructor for class ome.tools.hibernate.UpdateFilter
 
updateGroup(ExperimenterGroup) - Method in class ome.logic.AdminImpl
 
UpdateImpl - Class in ome.logic
implementation of the IUpdate service interface
UpdateImpl() - Constructor for class ome.logic.UpdateImpl
 
updateObject(String, IObject, Map<String, Integer>) - Method in class ome.formats.OMEROMetadataStore
Updates a given model object in our object graph.
updateObject(T...) - Method in interface ome.security.SecureAction
executes with special privileges within the SecuritySystem.
updateObject(T...) - Method in class ome.tools.hibernate.SecureMerge
 
updateReadFilter(Session) - Method in class ome.security.basic.BasicSecuritySystem
 
updateReferences(Map<String, String[]>) - Method in class ome.formats.OMEROMetadataStore
Updates our object graph references.
updateSelf(Experimenter) - Method in class ome.logic.AdminImpl
 
updateSession(Session) - Method in class ome.services.sessions.SessionBean
 
updateSettings(RenderingDef) - Method in class ome.services.RenderingBean
Implemented as specified by the RenderingEngine interface.
uploadMyUserPhoto(String, String, byte[]) - Method in class ome.logic.AdminImpl
 
usage() - Static method in class ome.services.fulltext.Main
 
useProjections - Variable in class ome.services.search.SearchValues
 
user - Variable in class ome.services.messages.LoginAttemptMessage
 
userGroups(String) - Method in class ome.security.auth.PasswordUtil
 
UserGroupUpdateEvent - Class in ome.services.sessions.events
InternalMessage published by the SecuritySystem when an Experimenter, ExperimenterGroup, or GroupExperimenterMap is inserted or updated.
UserGroupUpdateEvent(Object) - Constructor for class ome.services.sessions.events.UserGroupUpdateEvent
 
userId(String) - Method in class ome.security.auth.PasswordUtil
Get the user's ID
userName(long) - Method in class ome.security.auth.PasswordUtil
Get the user's name
usernameFilter(String) - Method in class ome.security.auth.LdapConfig
 
userProxy(String) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given user name.
userProxy(Long) - Method in interface ome.api.local.LocalAdmin
returns a possibly uninitialized proxy for the given user id.
userProxy(Long) - Method in class ome.logic.AdminImpl
 
userProxy(String) - Method in class ome.logic.AdminImpl
 
util - Variable in class ome.security.auth.ConfigurablePasswordProvider
 
uuid - Variable in class ome.security.basic.NodeProviderInDb
UUID for this cluster node.
uuid - Variable in class ome.security.basic.NodeProviderInMemory
UUID for this cluster node.

V

valid(String) - Method in class ome.services.db.DatabaseIdentity
 
validateEmail(String) - Method in class ome.services.mail.MailUtil
Helper Validate that this address conforms to the syntax rules of RFC 822.
validatePassword(String, String) - Method in class ome.logic.LdapImpl
Validates password for base.
value(String) - Method in class ome.services.query.Query
get the Object value for this name argument.
value - Variable in class ome.services.sharing.data.ObjPrxHolder
 
value - Variable in class ome.services.sharing.data.ShareDataPrxHolder
 
value - Variable in class ome.services.sharing.data.ShareItemPrxHolder
 
valueOf(String) - Static method in enum ome.security.auth.PasswordUtil.METHOD
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Ability
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.graphs.GraphPolicy.Orphan
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum ome.services.util.Executor.Priority
Returns the enum constant of this type with the specified name.
values() - Static method in enum ome.security.auth.PasswordUtil.METHOD
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Ability
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum ome.services.graphs.GraphPolicy.Orphan
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class ome.services.search.SearchAction
 
values() - Static method in enum ome.services.util.Executor.Priority
Returns an array containing the constants of this enum type, in the order they are declared.
verbose - Variable in class ome.tools.hibernate.EventMethodInterceptor
 

W

waitForLock - Variable in class ome.services.fulltext.FullTextThread
Deprecated.
 
wasSource(EventLogLoader) - Method in class ome.services.eventlogs.EventLogFailure
 
where() - Method in class ome.tools.hibernate.QueryBuilder
Marks the end of all fetches by adding a "where" clause to the string.
whereClause() - Method in class ome.tools.hibernate.QueryBuilder
Similar to how skipFrom and skipWhere were previously used, this sets the current builder to QueryBuilder.where() but without prefacing the "where " string.
Work(SecuritySystem, Processor...) - Constructor for class ome.services.procs.ProcessManager.Work
 
work - Variable in class ome.services.util.ExecutionThread
 
wrap(String, IObject) - Method in class ome.services.eventlogs.AllEntitiesPseudoLogLoader
 
wrap(Iterator<Reader>) - Method in class ome.services.fulltext.FileParser
Wraps an Iterator with an Iterable instance.
wrap(Reader) - Method in class ome.services.fulltext.FileParser
 
write(byte[], long, int) - Method in class ome.services.RawFileBean
 
write(String, String) - Method in class ome.services.scripts.ScriptRepoHelper
 
write(RepoFile, String) - Method in class ome.services.scripts.ScriptRepoHelper
 
write(BasicStream, Map<String, List<Long>>) - Static method in class ome.services.sharing.data.IdMapHelper
 
write(BasicStream, List<Long>) - Static method in class ome.services.sharing.data.LongSeqHelper
 
write(BasicStream, List<Obj>) - Static method in class ome.services.sharing.data.ObjSeqHelper
 
write(BasicStream, List<String>) - Static method in class ome.services.sharing.data.StringSeqHelper
 
writeImage(BufferedImage, TranscoderOutput) - Method in class ome.services.SVGRasterizer.Rasterizer
 
WriteStrategy - Interface in ome.security
Responsible for determining which users can modify which objects in which contexts.
writtenBytes(int) - Method in class ome.services.sessions.stats.DelegatingStats
 
writtenBytes(int) - Method in class ome.services.sessions.stats.NullSessionStats
 
writtenBytes(int) - Method in interface ome.services.sessions.stats.SessionStats
 
writtenBytes(int) - Method in class ome.services.sessions.stats.SimpleSessionStats
 

_

__dont_use_me_factory - Variable in class ome.services.sharing.BlobShareStore
Used indirectly to obtain sessions for querying and updating the store during normal operation.
__ids - Static variable in class ome.services.sharing.data.Obj
 
__ids - Static variable in class ome.services.sharing.data.ObjPrxHelper
 
__ids - Static variable in class ome.services.sharing.data.ShareData
 
__ids - Static variable in class ome.services.sharing.data.ShareDataPrxHelper
 
__ids - Static variable in class ome.services.sharing.data.ShareItem
 
__ids - Static variable in class ome.services.sharing.data.ShareItemPrxHelper
 
__read(BasicStream) - Static method in class ome.services.sharing.data.ObjPrxHelper
 
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
 
__read(BasicStream) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
 
__readImpl(BasicStream) - Method in class ome.services.sharing.data.Obj
 
__readImpl(BasicStream) - Method in class ome.services.sharing.data.ShareData
 
__readImpl(BasicStream) - Method in class ome.services.sharing.data.ShareItem
 
__write(BasicStream, ObjPrx) - Static method in class ome.services.sharing.data.ObjPrxHelper
 
__write(BasicStream, ShareDataPrx) - Static method in class ome.services.sharing.data.ShareDataPrxHelper
 
__write(BasicStream, ShareItemPrx) - Static method in class ome.services.sharing.data.ShareItemPrxHelper
 
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.Obj
 
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.ShareData
 
__writeImpl(BasicStream) - Method in class ome.services.sharing.data.ShareItem
 
_addGraph(ShareData, ShareBean.Graph) - Method in class ome.services.sharing.ShareBean
 
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