- accept(T) - Method in class ome.smuggler.core.msg.OnceOffRepeatConsumer
-
- accept(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.FinaliserFailureHandler
-
Called when a finalisation task failed permanently, i.e.
- accept(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportFailureHandler
-
- accept(QueuedMail) - Method in class ome.smuggler.core.service.mail.impl.MailFailureHandler
-
- ActuatorEndPointName - Enum in ome.smuggler.config.items
-
The names of Spring Boot Actuator's available end points.
- add(T, ConsumerE<OutputStream>) - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- add(T, Path) - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- add(T, ConsumerE<OutputStream>) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Writes a file associated to the specified task.
- add(T, String) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Writes a file associated to the specified task.
- add(T, Path) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Writes a file associated to the specified task by taking the contents
from a source file.
- addAnnotationId(PositiveN...) - Method in class ome.smuggler.core.types.ImportInput
-
- addAnnotationIds(Stream<PositiveN>) - Method in class ome.smuggler.core.types.ImportInput
-
- addTextAnnotation(TextAnnotation...) - Method in class ome.smuggler.core.types.ImportInput
-
- addTextAnnotations(Stream<TextAnnotation>) - Method in class ome.smuggler.core.types.ImportInput
-
- addToCompleted(ProcessedImport) - Method in class ome.smuggler.core.types.ImportBatchStatus
-
Updates the batch status to reflect that the specified import has
completed either successfully or with a failure depending on the
value returned by
ProcessedImport.succeeded().
- adminPassword() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- adminServerUrl() - Static method in class ome.smuggler.config.items.SpringBootAdminConfigProps
-
- adminUserName() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- afterRequest(HttpServletRequest, String) - Method in class ome.smuggler.web.RequestLoggingFilter
-
- allProcessed() - Method in class ome.smuggler.core.types.ImportBatchStatus
-
Have all the imports in this batch been processed?
- allSucceeded() - Method in class ome.smuggler.core.types.ImportBatchStatus
-
Have all the imports in this batch been processed successfully?
- annotationIds - Variable in class ome.smuggler.web.imports.ImportRequest
-
Any optional annotation ID's to attach to the image being imported.
- appDescription() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- AppInfoPrefix - Static variable in class ome.smuggler.config.items.SpringBootConfigProps
-
- appName() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- AppRunner - Class in ome.smuggler.run
-
Runs one of our applications in this package.
- AppRunner() - Constructor for class ome.smuggler.run.AppRunner
-
- appVersion() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- arg(String...) - Static method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- ArtemisConfigBeans - Class in ome.smuggler.config.wiring
-
Spring bean wiring of configuration items.
- ArtemisConfigBeans() - Constructor for class ome.smuggler.config.wiring.ArtemisConfigBeans
-
- ArtemisPersistenceConfig - Class in ome.smuggler.config.items
-
Specifies operational parameters for the embedded Artemis server.
- ArtemisPersistenceConfig() - Constructor for class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- artemisPersistenceConfig(ConfigProvider<ArtemisPersistenceConfig>) - Method in class ome.smuggler.config.wiring.ArtemisConfigBeans
-
- ArtemisPersistenceConfigProvider - Class in ome.smuggler.config.providers
-
The Artemis operational parameters.
- ArtemisPersistenceConfigProvider() - Constructor for class ome.smuggler.config.providers.ArtemisPersistenceConfigProvider
-
- ArtemisServerCfgCustomizer - Class in ome.smuggler.config.wiring
-
Implements the Spring Boot auto-configuration hook to customize the Artemis
server configuration created by Spring Boot.
- ArtemisServerCfgCustomizer() - Constructor for class ome.smuggler.config.wiring.ArtemisServerCfgCustomizer
-
- artemisServerConnector(ConnectionFactory) - Method in class ome.smuggler.config.wiring.ArtemisWiring
-
- ArtemisWiring - Class in ome.smuggler.config.wiring
-
Singleton beans for Artemis client resources that have to be shared and
reused.
- ArtemisWiring() - Constructor for class ome.smuggler.config.wiring.ArtemisWiring
-
- asDataSink() - Method in interface ome.smuggler.core.msg.MessageSink
-
Builds a channel sink that uses this message sink to consume data items
D.
- asDataSource() - Method in interface ome.smuggler.core.msg.MessageSource
-
Builds a channel source that uses this message source to send data items
D.
- assembleArguments(JvmCmdBuilder) - Method in class ome.smuggler.core.service.omero.impl.CloseCommandBuilder
-
- assembleArguments(JvmCmdBuilder) - Method in class ome.smuggler.core.service.omero.impl.CreateCommandBuilder
-
- assembleArguments(JvmCmdBuilder) - Method in class ome.smuggler.core.service.omero.impl.ImporterCommandBuilder
-
- assembleArguments(JvmCmdBuilder) - Method in class ome.smuggler.core.service.omero.impl.KeepAliveCommandBuilder
-
- assembleArguments(JvmCmdBuilder) - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- assembleCommand() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- authenticate(MailProtocol) - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- BaseConfigDir - Class in ome.smuggler.config
-
The base directory where to look for configuration files.
- BaseConfigDir() - Constructor for class ome.smuggler.config.BaseConfigDir
-
Creates a new instance to read the directory value from the system
properties or environment, defaulting to the current working directory
if no value is found.
- BaseDataDir - Class in ome.smuggler.config
-
The base directory where we keep all the import, mail, and HornetQ data.
- BaseDataDir() - Constructor for class ome.smuggler.config.BaseDataDir
-
Creates a new instance to read the directory value from the system
properties or environment, defaulting to the current working directory
if no value is found.
- BaseDir - Class in ome.smuggler.config
-
Path to a directory used as a base for
resolving
paths in configuration files.
- BaseDir(String, String) - Constructor for class ome.smuggler.config.BaseDir
-
Creates a new instance using the path returned by the
lookup method.
- BaseLogger - Class in ome.smuggler.core.service.log
-
Base class for loggers that extend the basic functionality of the
LogService to provide logging tailored to a particular service.
- BaseLogger(LogService) - Constructor for class ome.smuggler.core.service.log.BaseLogger
-
Creates a new instance.
- BaseStringId - Class in ome.smuggler.core.types
-
Base class for Identifiable's whose ID is an UUID string.
- BaseStringId(String) - Constructor for class ome.smuggler.core.types.BaseStringId
-
- BaseStringId() - Constructor for class ome.smuggler.core.types.BaseStringId
-
- batch() - Method in class ome.smuggler.core.types.ImportBatchStatus
-
- batchCanBeDiscarded(ProcessedImport) - Static method in class ome.smuggler.core.types.ProcessedImport
-
Creates a new instance to signal that the batch the specified import is
in has been completed and can be discarded.
- batchCompleted(ProcessedImport) - Static method in class ome.smuggler.core.types.ProcessedImport
-
Creates a new instance to signal that the batch the specified import is
in has been completed.
- BatchCompletedHandler - Class in ome.smuggler.core.service.imports.impl
-
Finalisation task to run when an import batch has completed, i.e.
- BatchCompletedHandler(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.BatchCompletedHandler
-
Creates a new instance.
- BatchDisposalHandler - Class in ome.smuggler.core.service.imports.impl
-
Finalisation task to run after
batch completion
to get rid of any resources still associated with the batch, such as import
logs and the batch store file.
- BatchDisposalHandler(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.BatchDisposalHandler
-
Creates a new instance.
- batchId() - Method in class ome.smuggler.core.types.ImportBatch
-
- batchId() - Method in class ome.smuggler.core.types.ImportId
-
- batchId() - Method in class ome.smuggler.core.types.ProcessedImport
-
- BatchManager - Class in ome.smuggler.core.service.imports.impl
-
- BatchManager(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.BatchManager
-
Creates a new instance.
- batchManager() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- BatchSessionsReaper - Class in ome.smuggler.core.service.imports.impl
-
Closes all the OMERO sessions in an import batch.
- BatchSessionsReaper(SessionService) - Constructor for class ome.smuggler.core.service.imports.impl.BatchSessionsReaper
-
Creates a new instance.
- batchStatusDbDir() - Method in class ome.smuggler.config.data.DevImportConfigSource
-
- batchStatusDbDir() - Method in class ome.smuggler.core.types.ImportConfigReader
-
- batchStatusDbDir() - Method in interface ome.smuggler.core.types.ImportConfigSource
-
- batchStatusDbLockStripes() - Method in class ome.smuggler.config.data.DevImportConfigSource
-
- batchStatusDbLockStripes() - Method in class ome.smuggler.core.types.ImportConfigReader
-
- batchStatusDbLockStripes() - Method in interface ome.smuggler.core.types.ImportConfigSource
-
Optional number of lock stripes to use with the import batch status
key-value store.
- batchStore(ImportConfigSource) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- batchStore() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- BatchUpdateHandler - Class in ome.smuggler.core.service.imports.impl
-
Finalisation task to update an import batch to reflect one of its imports
has completed.
- BatchUpdateHandler(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.BatchUpdateHandler
-
Creates a new instance.
- beforeRequest(HttpServletRequest, String) - Method in class ome.smuggler.web.RequestLoggingFilter
-
- build(ImportRequest...) - Method in class ome.smuggler.web.imports.ImportBatchBuilder
-
- build(ImportBatch) - Method in class ome.smuggler.web.imports.ImportResponseBuilder
-
Builds an
ImportResponse for each import request found in the
given batch.
- buildCountedScheduleSink(MessageSink<CountedSchedule, T>, SourceReader<InputStream, T>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildCountedScheduleSink(MessageSink<CountedSchedule, T>, SourceReader<InputStream, T>, boolean) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildCountedScheduleSource(SinkWriter<T, OutputStream>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildForRepeatConsumer(RepeatConsumer<T>, List<Duration>, Consumer<T>) - Static method in class ome.smuggler.core.msg.ReschedulableFactory
-
- buildMailMessage(Email) - Method in class ome.smuggler.core.service.imports.impl.ImportErrorMailFormatter
-
Builds an email messages to notify the specified recipient that the
import failed but will be retried.
- buildMailMessage(boolean, Email) - Method in class ome.smuggler.core.service.imports.impl.ImportMailFormatter
-
Builds an email messages to notify the specified recipient of the
processing outcome of the import batch.
- buildMimeMessage(PlainTextMail) - Method in class ome.smuggler.providers.mail.MessageBuilder
-
- buildOnceOffSchedule(RepeatConsumer<T>, Consumer<T>) - Static method in class ome.smuggler.core.msg.ReschedulableFactory
-
- buildReschedulableSink(Reschedulable<T>, SinkWriter<T, OutputStream>, SourceReader<InputStream, T>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildReschedulableSink(Reschedulable<T>, SinkWriter<T, OutputStream>, SourceReader<InputStream, T>, boolean) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildSchedulingSource(SinkWriter<T, OutputStream>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildSink(ChannelSink<T>, SourceReader<InputStream, T>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildSink(ChannelSink<T>, SourceReader<InputStream, T>, boolean) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- buildSource(SinkWriter<T, OutputStream>) - Method in class ome.smuggler.providers.q.QChannelFactory
-
- byteLength(Path) - Static method in class ome.smuggler.core.io.FileOps
-
Queries the size of the given file.
- cacheStrategy() - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
- CannotCreateSessionErrorMsg - Static variable in class ome.smuggler.web.omero.CreateSessionSubmitter
-
- canonicalName() - Method in enum ome.smuggler.core.io.crypto.CryptoAlgoSpec
-
- ChannelMessage<M,D> - Class in ome.smuggler.core.msg
-
Imposes a minimal structure to a message exchanged on a channel.
- ChannelMessage(Optional<M>, D) - Constructor for class ome.smuggler.core.msg.ChannelMessage
-
Creates a new instance.
- ChannelMessage(M, D) - Constructor for class ome.smuggler.core.msg.ChannelMessage
-
Creates a new instance.
- ChannelMessage(D) - Constructor for class ome.smuggler.core.msg.ChannelMessage
-
Creates a new instance with no metadata.
- ChannelSink<T> - Interface in ome.smuggler.core.msg
-
Encapsulates the consumption of an asynchronous message received from a
channel.
- ChannelSource<T> - Interface in ome.smuggler.core.msg
-
Encapsulates the sending of an asynchronous message along a channel.
- CipherFactory - Class in ome.smuggler.core.io.crypto
-
Factory to instantiate fresh Ciphers for a given algorithm and key.
- CipherFactory(CryptoAlgoSpec, Key) - Constructor for class ome.smuggler.core.io.crypto.CipherFactory
-
Creates a new instance.
- close(Closeable) - Static method in class ome.smuggler.core.io.StreamOps
-
Closes the given stream, silently swallowing any IOException.
- close(URI, String) - Method in class ome.smuggler.core.service.omero.impl.SessionManager
-
- close(URI, String) - Method in interface ome.smuggler.core.service.omero.SessionService
-
Closes the specified session.
- CloseCommandBuilder - Class in ome.smuggler.core.service.omero.impl
-
Builds the command line to call the OMERO close session command.
- CloseCommandBuilder(OmeCliConfigSource, URI, String) - Constructor for class ome.smuggler.core.service.omero.impl.CloseCommandBuilder
-
Creates a new instance to build a command line from the given data.
- closeSessions(ImportBatch) - Method in class ome.smuggler.core.service.imports.impl.BatchSessionsReaper
-
Closes all the OMERO sessions in the specified import batch.
- commandName() - Method in class ome.smuggler.core.service.omero.impl.CloseCommandBuilder
-
- commandName() - Method in class ome.smuggler.core.service.omero.impl.CreateCommandBuilder
-
- commandName() - Method in class ome.smuggler.core.service.omero.impl.ImporterCommandBuilder
-
- commandName() - Method in class ome.smuggler.core.service.omero.impl.KeepAliveCommandBuilder
-
- commandName() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- CommandRunner - Class in ome.smuggler.core.io
-
Utility to run an external process redirecting both its error and output
streams to a file.
- CommandRunner(CommandBuilder) - Constructor for class ome.smuggler.core.io.CommandRunner
-
Creates a new instance to run a given process.
- config() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- config() - Method in class ome.smuggler.core.service.mail.impl.MailEnv
-
- config - Variable in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- config() - Method in class ome.smuggler.core.service.omero.impl.OmeroEnv
-
- configureContentNegotiation(ContentNegotiationConfigurer) - Method in class ome.smuggler.config.wiring.WebWiring
-
- connectionTimeoutFor(MailProtocol) - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- consume(T) - Method in interface ome.smuggler.core.msg.ChannelSink
-
Consumes a message.
- consume(CountedSchedule, T) - Method in class ome.smuggler.core.msg.MessageRepeater
-
- consume(CountedSchedule, T) - Method in class ome.smuggler.core.msg.OnceOffSchedule
-
- consume(T) - Method in interface ome.smuggler.core.msg.RepeatConsumer
-
Consumes the message data and returns an indication of whether the same
data should be delivered again.
- consume(CountedSchedule, T) - Method in interface ome.smuggler.core.msg.Reschedulable
-
Consumes the output of the channel this instance is bound to.
- consume(ChannelMessage<CountedSchedule, T>) - Method in class ome.smuggler.core.msg.ReschedulingSink
-
- consume(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.BatchCompletedHandler
-
- consume(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.BatchDisposalHandler
-
- consume(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.BatchUpdateHandler
-
- consume(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.Finaliser
-
Processes messages from the GC queue to carry out each step in the batch
finalisation procedure.
- consume(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportRunner
-
- consume(QueuedMail) - Method in class ome.smuggler.core.service.mail.impl.Mailer
-
- consume(CountedSchedule, QueuedOmeroKeepAlive) - Method in class ome.smuggler.core.service.omero.impl.SessionKeepAliveHandler
-
- consume(ChannelMessage<ClientMessage, T>) - Method in class ome.smuggler.providers.q.CountedScheduleSink
-
- convert(InputStream) - Method in class ome.smuggler.config.providers.YmlResourceReader
-
- copy(Path, Path) - Static method in class ome.smuggler.core.io.FileOps
-
Copies the source file to the destination path, overriding it if it
exists already.
- count() - Method in class ome.smuggler.core.msg.CountedSchedule
-
- CountedSchedule - Class in ome.smuggler.core.msg
-
Channel metadata to request the scheduling of a message and the sending of
a counter to indicate how many times the message has been scheduled for
delivery.
- CountedSchedule(FutureTimepoint, PositiveN) - Constructor for class ome.smuggler.core.msg.CountedSchedule
-
Creates a new instance.
- CountedScheduleSink<T> - Class in ome.smuggler.providers.q
-
DequeueTask consumer to convert raw Artemis metadata into a
CountedSchedule and forward it, along with the received data
T to a target message sink.
- CountedScheduleSink(MessageSink<CountedSchedule, T>) - Constructor for class ome.smuggler.providers.q.CountedScheduleSink
-
Creates a new instance.
- CountedScheduleTask<T> - Class in ome.smuggler.providers.q
-
Enqueues a message that will only be delivered to consumers at a specified
time in the future and makes a sender-specified delivery count available in
the metadata.
- CountedScheduleTask(QueueConnector, SinkWriter<T, OutputStream>) - Constructor for class ome.smuggler.providers.q.CountedScheduleTask
-
Creates a new instance.
- create(URI, String, String) - Method in class ome.smuggler.core.service.omero.impl.SessionManager
-
- create(URI, String, String) - Method in interface ome.smuggler.core.service.omero.SessionService
-
Starts a new session for the specified user.
- create(CreateSessionRequest) - Method in class ome.smuggler.web.omero.SessionController
-
Opens a new OMERO session.
- createAndKeepAlive(URI, String, String, Duration) - Method in class ome.smuggler.core.service.omero.impl.SessionManager
-
- createAndKeepAlive(URI, String, String, Duration) - Method in interface ome.smuggler.core.service.omero.SessionService
-
Starts a new session for the specified user and keeps it alive for a
given amount of time.
- createBatchFor(Stream<ImportInput>) - Method in class ome.smuggler.core.service.imports.impl.BatchManager
-
Creates a new batch containing the specified import requests.
- CreateCommandBuilder - Class in ome.smuggler.core.service.omero.impl
-
Builds the command line to call the OMERO create session command.
- CreateCommandBuilder(OmeCliConfigSource, URI, String, String) - Constructor for class ome.smuggler.core.service.omero.impl.CreateCommandBuilder
-
Creates a new instance to build a command line from the given data.
- CreateSessionRequest - Class in ome.smuggler.web.omero
-
Web clients use instances of this class to open a new OMERO session.
- CreateSessionRequest() - Constructor for class ome.smuggler.web.omero.CreateSessionRequest
-
- CreateSessionRequestValidator - Class in ome.smuggler.web.omero
-
- CreateSessionRequestValidator() - Constructor for class ome.smuggler.web.omero.CreateSessionRequestValidator
-
- CreateSessionResponse - Class in ome.smuggler.web.omero
-
Web clients receive instances of this class in response to a request to
open a new OMERO session.
- CreateSessionResponse() - Constructor for class ome.smuggler.web.omero.CreateSessionResponse
-
- CreateSessionSubmitter - Class in ome.smuggler.web.omero
-
- CreateSessionSubmitter(SessionService) - Constructor for class ome.smuggler.web.omero.CreateSessionSubmitter
-
Creates a new instance.
- CreateUrl - Static variable in class ome.smuggler.web.omero.SessionController
-
- CRLF - Static variable in class ome.smuggler.core.service.imports.impl.ImportMailFormatter
-
- CryptoAlgoSpec - Enum in ome.smuggler.core.io.crypto
-
Enumerates the JCA algorithms we use.
- CryptoConfig - Class in ome.smuggler.config.items
-
Specifies how to configure encryption of sensitive data.
- CryptoConfig() - Constructor for class ome.smuggler.config.items.CryptoConfig
-
- cryptoConfig(ConfigProvider<CryptoConfig>) - Method in class ome.smuggler.config.wiring.crypto.CryptoConfigBeans
-
- cryptoConfig() - Method in class ome.smuggler.config.wiring.crypto.CryptoDevConfigBeans
-
- CryptoConfigBeans - Class in ome.smuggler.config.wiring.crypto
-
Spring bean wiring of crypto configuration items for the
Prod profile.
- CryptoConfigBeans() - Constructor for class ome.smuggler.config.wiring.crypto.CryptoConfigBeans
-
- CryptoConfigProvider - Class in ome.smuggler.config.providers
-
Reads crypto configuration from a YAML file, falling back to hard-coded
configuration if no file is available.
- CryptoConfigProvider() - Constructor for class ome.smuggler.config.providers.CryptoConfigProvider
-
- CryptoConfigReader - Class in ome.smuggler.core.types
-
- CryptoConfigReader(CryptoConfig) - Constructor for class ome.smuggler.core.types.CryptoConfigReader
-
Creates a new instance.
- CryptoConfigSource - Interface in ome.smuggler.core.types
-
Provides read-only, type-safe access to the crypto configuration.
- CryptoDevConfigBeans - Class in ome.smuggler.config.wiring.crypto
-
Spring bean wiring of crypto configuration items for the
Dev profile.
- CryptoDevConfigBeans() - Constructor for class ome.smuggler.config.wiring.crypto.CryptoDevConfigBeans
-
- CryptoKeyFactory - Class in ome.smuggler.core.io.crypto
-
Factory methods for security Keys.
- CryptoKeyFactory() - Constructor for class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
- CryptoSerializationBeans - Class in ome.smuggler.config.wiring.crypto
-
Spring bean wiring configuration for serialization.
- CryptoSerializationBeans() - Constructor for class ome.smuggler.config.wiring.crypto.CryptoSerializationBeans
-
- CryptoSinkWriter<T> - Class in ome.smuggler.core.io.crypto
-
An encryption filter that wraps an underlying
SinkWriter w
to encrypt whatever
w writes to the sink
OutputStream.
- CryptoSinkWriter(CipherFactory, SinkWriter<T, OutputStream>) - Constructor for class ome.smuggler.core.io.crypto.CryptoSinkWriter
-
Creates a new instance.
- CryptoSourceReader<T> - Class in ome.smuggler.core.io.crypto
-
An encryption filter that wraps an underlying
SourceReader r
to decrypt whatever
r reads from the source
InputStream.
- CryptoSourceReader(CipherFactory, SourceReader<InputStream, T>) - Constructor for class ome.smuggler.core.io.crypto.CryptoSourceReader
-
Creates a new instance.
- CryptoYmlFile - Class in ome.smuggler.config.data
-
Default configuration for encryption of sensitive data, i.e.
- CryptoYmlFile() - Constructor for class ome.smuggler.config.data.CryptoYmlFile
-
- CryptoYmlGen - Class in ome.smuggler.run
-
Run this class redirecting stdout to config/crypto.yml to
generate the file.
- CryptoYmlGen() - Constructor for class ome.smuggler.run.CryptoYmlGen
-
- customize(Configuration) - Method in class ome.smuggler.config.wiring.ArtemisServerCfgCustomizer
-
- data() - Method in class ome.smuggler.core.msg.ChannelMessage
-
- DatasetId - Class in ome.smuggler.core.types
-
An OME dataset ID.
- DatasetId(Long) - Constructor for class ome.smuggler.core.types.DatasetId
-
- datasetId(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a dataset ID from a positive integer.
- datasetId - Variable in class ome.smuggler.web.imports.ImportRequest
-
If the image is to be imported into an existing OMERO dataset, then this
field specifies its ID; leave out otherwise.
- deadMailDir() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- deadMailDir() - Method in class ome.smuggler.core.types.MailConfigReader
-
- deadMailDir() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- DeadMailDirRelPath - Static variable in class ome.smuggler.config.data.MailYmlFile
-
- debug() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- debug(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.core.service.log.BaseLogger
-
- debug(Object, Consumer<PrintWriter>) - Method in interface ome.smuggler.core.service.log.LogService
-
Logs a debug message.
- debug(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.providers.log.LogAdapter
-
- decryptionChipher() - Method in class ome.smuggler.core.io.crypto.CipherFactory
-
- DefaultArtemisPersistenceConfig - Class in ome.smuggler.config.data
-
Hard-coded operational parameters for the embedded Artemis server.
- DefaultArtemisPersistenceConfig() - Constructor for class ome.smuggler.config.data.DefaultArtemisPersistenceConfig
-
- DefaultBatchStatusDbLockStripes - Static variable in interface ome.smuggler.core.types.ImportConfigSource
-
Default number of lock stripes to use with the import batch status
key-value store.
- DefaultImportGcQConfig - Class in ome.smuggler.config.data
-
Hard-coded configuration for the import garbage collection queue.
- DefaultImportGcQConfig() - Constructor for class ome.smuggler.config.data.DefaultImportGcQConfig
-
- DefaultImportQConfig - Class in ome.smuggler.config.data
-
Hard-coded import queue configuration.
- DefaultImportQConfig() - Constructor for class ome.smuggler.config.data.DefaultImportQConfig
-
- DefaultMailQConfig - Class in ome.smuggler.config.data
-
Hard-coded mail queue configuration.
- DefaultMailQConfig() - Constructor for class ome.smuggler.config.data.DefaultMailQConfig
-
- DefaultOmeCliConfig - Class in ome.smuggler.config.data
-
Hard-coded configuration for launching the OMERO CLI commands.
- DefaultOmeCliConfig() - Constructor for class ome.smuggler.config.data.DefaultOmeCliConfig
-
- DefaultOmeCliJarPrefix - Static variable in class ome.smuggler.config.items.OmeCliConfig
-
- DefaultOmeroSessionQConfig - Class in ome.smuggler.config.data
-
Hard-coded OMERO session queue configuration.
- DefaultOmeroSessionQConfig() - Constructor for class ome.smuggler.config.data.DefaultOmeroSessionQConfig
-
- delete(Path) - Static method in class ome.smuggler.core.io.FileOps
-
Deletes the specified file if it exists; does nothing otherwise.
- deleteBatch(ImportBatchId) - Method in class ome.smuggler.core.service.imports.impl.BatchManager
-
Removes the specified batch from permanent storage.
- deleteFile(String) - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
Removes the file associated to a task if it is in the store; does nothing
otherwise.
- dequeue() - Method in class ome.smuggler.core.msg.SourceQueue
-
Removes all the items currently in the queue, returning them in FIFO
order.
- dequeueData() - Method in class ome.smuggler.core.msg.SourceQueue
-
- dequeueImportFinaliserTask(QChannelFactory<ProcessedImport>, ImportConfigSource, ImportFinaliser, FailedFinalisationHandler) - Method in class ome.smuggler.config.wiring.imports.ImportGcQBeans
-
- dequeueImportTask(QChannelFactory<QueuedImport>, ImportConfigSource, ImportProcessor, FailedImportHandler) - Method in class ome.smuggler.config.wiring.imports.ImportQBeans
-
- dequeueMailTask(QChannelFactory<QueuedMail>, MailConfigSource, MailProcessor, FailedMailHandler) - Method in class ome.smuggler.config.wiring.mail.MailQBeans
-
- dequeueSessionTask(QChannelFactory<QueuedOmeroKeepAlive>, OmeroEnv, SessionService) - Method in class ome.smuggler.config.wiring.omero.SessionQBeans
-
- DequeueTask<T> - Class in ome.smuggler.providers.q
-
Receives messages asynchronously from a queue and dispatches them to a
consumer.
- DequeueTask(QueueConnector, ChannelSink<T>, SourceReader<InputStream, T>, boolean) - Constructor for class ome.smuggler.providers.q.DequeueTask
-
Creates a new instance.
- DequeueTask(QueueConnector, MessageSink<ClientMessage, T>, SourceReader<InputStream, T>, boolean) - Constructor for class ome.smuggler.providers.q.DequeueTask
-
Creates a new instance.
- description - Variable in class ome.smuggler.web.imports.ImportRequest
-
Optional field for the image or plate description to use.
- deserializer(Class<T>) - Method in class ome.smuggler.config.wiring.crypto.SerializationFactory
-
Instantiates a de-serializer for T-values.
- Dev - Static variable in class ome.smuggler.config.Profiles
-
Configuration for the development environment.
- DevCryptoConfigSource - Class in ome.smuggler.config.data
-
Dev crypto settings.
- DevCryptoConfigSource() - Constructor for class ome.smuggler.config.data.DevCryptoConfigSource
-
- DevImportConfigSource - Class in ome.smuggler.config.data
-
Dev import settings.
- DevImportConfigSource() - Constructor for class ome.smuggler.config.data.DevImportConfigSource
-
- DevMailConfigSource - Class in ome.smuggler.config.data
-
Dev mail settings.
- DevMailConfigSource() - Constructor for class ome.smuggler.config.data.DevMailConfigSource
-
- durableMessage() - Static method in class ome.smuggler.providers.q.Messages
-
- Email - Class in ome.smuggler.core.types
-
An email address.
- Email(String) - Constructor for class ome.smuggler.core.types.Email
-
- email(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates an email from its string representation.
- embeddedServletContainerFactory(ConfigProvider<UndertowConfig>) - Method in class ome.smuggler.config.wiring.WebWiring
-
- enableTranslation() - Method in class ome.smuggler.core.types.RemoteMountConfigReader
-
- enableTranslation() - Method in interface ome.smuggler.core.types.RemoteMountConfigSource
-
- encrypt() - Method in class ome.smuggler.config.data.DevCryptoConfigSource
-
- encrypt() - Method in class ome.smuggler.core.types.CryptoConfigReader
-
- encrypt() - Method in interface ome.smuggler.core.types.CryptoConfigSource
-
- encryptionChipher() - Method in class ome.smuggler.core.io.crypto.CipherFactory
-
- endpointEnabled(ActuatorEndPointName) - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- endpointId(ActuatorEndPointName) - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- endpointsEnabled() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- endpointSensitive(ActuatorEndPointName) - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- EndPointsPrefix - Static variable in class ome.smuggler.config.items.SpringBootConfigProps
-
- endpointsSensitive() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- enqueue(Stream<ImportInput>) - Method in class ome.smuggler.core.service.imports.impl.ImportTrigger
-
- enqueue(ImportInput) - Method in interface ome.smuggler.core.service.imports.ImportRequestor
-
Adds the import request to the queue and returns immediately.
- enqueue(Stream<ImportInput>) - Method in interface ome.smuggler.core.service.imports.ImportRequestor
-
Adds the import requests to the queue and returns immediately.
- enqueue(PlainTextMail) - Method in class ome.smuggler.core.service.mail.impl.MailTrigger
-
- enqueue(PlainTextMail) - Method in interface ome.smuggler.core.service.mail.MailRequestor
-
Adds the email request to the queue and returns immediately.
- enqueue(ImportRequest[]) - Method in class ome.smuggler.web.imports.ImportController
-
Adds the given requests to the import queue.
- EnqueueTask<T> - Class in ome.smuggler.providers.q
-
Puts messages on a queue, asynchronously.
- EnqueueTask(QueueConnector, SinkWriter<T, OutputStream>) - Constructor for class ome.smuggler.providers.q.EnqueueTask
-
Creates a new instance.
- ensureDirectories() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- ensureDirectories() - Method in class ome.smuggler.core.service.mail.impl.MailEnv
-
- ensureDirectory(Path) - Static method in class ome.smuggler.core.io.FileOps
-
Calls Files.createDirectories() re-throwing any exception without wrapping.
- EnvVarName - Static variable in class ome.smuggler.config.BaseConfigDir
-
- EnvVarName - Static variable in class ome.smuggler.config.BaseDataDir
-
- equals(Object) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- equals(Object) - Method in class ome.smuggler.config.items.CryptoConfig
-
- equals(Object) - Method in class ome.smuggler.config.items.ImportConfig
-
- equals(Object) - Method in class ome.smuggler.config.items.MailConfig
-
- equals(Object) - Method in class ome.smuggler.config.items.MountPointsConfig
-
- equals(Object) - Method in class ome.smuggler.config.items.MountPointsConfig.RemoteToLocalMapping
-
- equals(Object) - Method in class ome.smuggler.config.items.UndertowConfig
-
- equals(Object) - Method in class ome.smuggler.core.msg.ChannelMessage
-
- equals(Object) - Method in class ome.smuggler.core.msg.CountedSchedule
-
- equals(Object) - Method in class ome.smuggler.core.types.ImportBatch
-
- equals(Object) - Method in class ome.smuggler.core.types.ImportBatchStatus
-
- equals(Object) - Method in class ome.smuggler.core.types.ImportInput
-
- equals(Object) - Method in class ome.smuggler.core.types.PlainTextMail
-
- equals(Object) - Method in class ome.smuggler.core.types.ProcessedImport
-
- equals(Object) - Method in class ome.smuggler.core.types.QueuedImport
-
- equals(Object) - Method in class ome.smuggler.core.types.QueuedMail
-
- equals(Object) - Method in class ome.smuggler.core.types.QueuedOmeroKeepAlive
-
- equals(Object) - Method in class ome.smuggler.core.types.Schedule
-
- error(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.core.service.log.BaseLogger
-
- error(Object, Consumer<PrintWriter>) - Method in interface ome.smuggler.core.service.log.LogService
-
Logs an error.
- error(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.providers.log.LogAdapter
-
- Error - Class in ome.smuggler.web
-
Web clients receive instances of this class if their request results in an
error.
- Error() - Constructor for class ome.smuggler.web.Error
-
Empty constructor for (de-)serialisation.
- Error(String) - Constructor for class ome.smuggler.web.Error
-
Convenience constructor to set the reason for the error.
- error(String) - Static method in class ome.smuggler.web.Error
-
Utility method to create a left
Either with an
Error.
- exec(Path) - Method in class ome.smuggler.core.io.CommandRunner
-
Runs the process redirecting both its error and output streams to the
specified file.
- exec(Function<InputStream, T>) - Method in class ome.smuggler.core.io.CommandRunner
-
Runs the process redirecting both its error and output streams to an
input stream that is given to a consumer to read.
- experimenterEmail - Variable in class ome.smuggler.web.imports.ImportRequest
-
The email address to send an outcome notification to.
- exportKey(Key, OutputStream) - Static method in class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
Serialises a key into a given stream using Base64 encoding.
- exportKey(Key) - Static method in class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
Serialises a key into a string using Base64 encoding.
- exportNewKey(CryptoAlgoSpec) - Static method in class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
Generates a new key and serialises it using Base64 encoding.
- extendMessageConverters(List<HttpMessageConverter<?>>) - Method in class ome.smuggler.config.wiring.WebWiring
-
- id() - Method in class ome.smuggler.core.types.BaseStringId
-
- id() - Method in class ome.smuggler.core.types.ImportId
-
- identifyTargets() - Method in class ome.smuggler.core.types.ImportBatch
-
Associates each import target URI to the corresponding import ID.
- ImportBatch - Class in ome.smuggler.core.types
-
Groups multiple import runs into a single batch.
- ImportBatch(Stream<ImportInput>) - Constructor for class ome.smuggler.core.types.ImportBatch
-
Creates a new batch consisting of the specified imports.
- ImportBatchBuilder - Class in ome.smuggler.web.imports
-
- ImportBatchBuilder() - Constructor for class ome.smuggler.web.imports.ImportBatchBuilder
-
- importBatchCompleted(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- importBatchCompletionFinalisationFailed(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- importBatchDisposalFinalisationFailed(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- ImportBatchId - Class in ome.smuggler.core.types
-
Identifies an import batch.
- ImportBatchId(String) - Constructor for class ome.smuggler.core.types.ImportBatchId
-
- ImportBatchId() - Constructor for class ome.smuggler.core.types.ImportBatchId
-
- ImportBatchStatus - Class in ome.smuggler.core.types
-
- ImportBatchStatus(ImportBatch) - Constructor for class ome.smuggler.core.types.ImportBatchStatus
-
Creates a new instance.
- ImportBatchSubmitter - Class in ome.smuggler.web.imports
-
Submits a batch of import requests to the import service.
- ImportBatchSubmitter(ImportRequestor) - Constructor for class ome.smuggler.web.imports.ImportBatchSubmitter
-
Creates a new instance.
- importBatchUpdateFinalisationFailed(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- importChannelFactory(ServerConnector, ImportQConfig) - Method in class ome.smuggler.config.wiring.imports.ImportQBeans
-
- ImportConfig - Class in ome.smuggler.config.items
-
Specifies how to configure import logs.
- ImportConfig() - Constructor for class ome.smuggler.config.items.ImportConfig
-
- importConfig(ConfigProvider<ImportConfig>) - Method in class ome.smuggler.config.wiring.imports.ImportConfigBeans
-
- importConfig() - Method in class ome.smuggler.config.wiring.imports.ImportDevConfigBeans
-
- ImportConfigBeans - Class in ome.smuggler.config.wiring.imports
-
Spring bean wiring of import configuration items for the
Prod profile.
- ImportConfigBeans() - Constructor for class ome.smuggler.config.wiring.imports.ImportConfigBeans
-
- ImportConfigProvider - Class in ome.smuggler.config.providers
-
Reads import configuration from a YAML file, falling back to hard-coded
configuration if no file is available.
- ImportConfigProvider() - Constructor for class ome.smuggler.config.providers.ImportConfigProvider
-
- ImportConfigReader - Class in ome.smuggler.core.types
-
- ImportConfigReader(ImportConfig) - Constructor for class ome.smuggler.core.types.ImportConfigReader
-
Creates a new instance.
- ImportConfigSource - Interface in ome.smuggler.core.types
-
Provides read-only, type-safe access to the import configuration.
- ImportController - Class in ome.smuggler.web.imports
-
Enqueues a message to request OMERO imports.
- ImportController() - Constructor for class ome.smuggler.web.imports.ImportController
-
- ImportDevConfigBeans - Class in ome.smuggler.config.wiring.imports
-
Spring bean wiring of import configuration items for the
Dev profile.
- ImportDevConfigBeans() - Constructor for class ome.smuggler.config.wiring.imports.ImportDevConfigBeans
-
- importEnv(ImportConfigSource, SessionService, ImportService, ChannelSource<QueuedImport>, SchedulingSource<ProcessedImport>, KeyValueStore<ImportBatchId, ImportBatchStatus>, TaskFileStore<ImportId>, MailRequestor, MailConfigSource) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- ImportEnv - Class in ome.smuggler.core.service.imports.impl
-
Provides access to import configuration and queues.
- ImportEnv(ImportConfigSource, SessionService, ImportService, ChannelSource<QueuedImport>, SchedulingSource<ProcessedImport>, KeyValueStore<ImportBatchId, ImportBatchStatus>, TaskFileStore<ImportId>, MailRequestor, Optional<Email>, LogService) - Constructor for class ome.smuggler.core.service.imports.impl.ImportEnv
-
- importer() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- Importer - Class in ome.smuggler.core.service.omero.impl
-
OMERO import service implementation.
- Importer(OmeroEnv, ImportConfigSource) - Constructor for class ome.smuggler.core.service.omero.impl.Importer
-
Creates a new instance.
- ImporterCommandBuilder - Class in ome.smuggler.core.service.omero.impl
-
Build the command line to call the OMERO importer.
- ImporterCommandBuilder(OmeCliConfigSource, ImportInput, Path, CommandBuilder) - Constructor for class ome.smuggler.core.service.omero.impl.ImporterCommandBuilder
-
Creates a new instance to build a command line from the given data.
- ImportErrorMailFormatter - Class in ome.smuggler.core.service.imports.impl
-
Formats email messages to send out to sys admins when an import within a
batch fails.
- ImportErrorMailFormatter(QueuedImport) - Constructor for class ome.smuggler.core.service.imports.impl.ImportErrorMailFormatter
-
Creates a new instance.
- ImportErrorMailFormatter(QueuedImport, Exception) - Constructor for class ome.smuggler.core.service.imports.impl.ImportErrorMailFormatter
-
Creates a new instance.
- ImportErrorNotifier - Class in ome.smuggler.core.service.imports.impl
-
Triggers the sending of an import error notification email.
- ImportErrorNotifier(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.ImportErrorNotifier
-
Creates a new instance.
- ImportFailureController - Class in ome.smuggler.web.imports
-
Exposes the functionality of the failed import log store to Web clients.
- ImportFailureController() - Constructor for class ome.smuggler.web.imports.ImportFailureController
-
- ImportFailureHandler - Class in ome.smuggler.core.service.imports.impl
-
Handles an import that failed permanently, i.e.
- ImportFailureHandler(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.ImportFailureHandler
-
- ImportFinalisationPhase - Enum in ome.smuggler.core.types
-
Enumerates the phases an import batch goes through from the moment we start
running the imports contained in the batch.
- importFinaliser(ImportEnv) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- ImportFinaliser - Interface in ome.smuggler.core.service.imports
-
- importGcChannelFactory(ServerConnector, ImportGcQConfig) - Method in class ome.smuggler.config.wiring.imports.ImportGcQBeans
-
- ImportGcQBeans - Class in ome.smuggler.config.wiring.imports
-
Singleton beans for HornetQ client resources that have to be shared and
reused.
- ImportGcQBeans() - Constructor for class ome.smuggler.config.wiring.imports.ImportGcQBeans
-
- ImportGcQConfig - Class in ome.smuggler.config.items
-
Holds the configuration for the import garbage collection queue.
- ImportGcQConfig() - Constructor for class ome.smuggler.config.items.ImportGcQConfig
-
- ImportGcQConfig(String, String, String, boolean) - Constructor for class ome.smuggler.config.items.ImportGcQConfig
-
- importGcQConfig(ConfigProvider<ImportGcQConfig>) - Method in class ome.smuggler.config.wiring.imports.ImportConfigBeans
-
- importGcQConfig(ConfigProvider<ImportGcQConfig>) - Method in class ome.smuggler.config.wiring.imports.ImportDevConfigBeans
-
- ImportGcQConfigProvider - Class in ome.smuggler.config.providers
-
The import garbage collection queue configuration as required by HornetQ.
- ImportGcQConfigProvider() - Constructor for class ome.smuggler.config.providers.ImportGcQConfigProvider
-
- importGcSourceChannel(QChannelFactory<ProcessedImport>) - Method in class ome.smuggler.config.wiring.imports.ImportGcQBeans
-
- ImportId - Class in ome.smuggler.core.types
-
Identifies an import run.
- ImportId(String) - Constructor for class ome.smuggler.core.types.ImportId
-
- ImportId(ImportBatchId) - Constructor for class ome.smuggler.core.types.ImportId
-
- ImportInput - Class in ome.smuggler.core.types
-
Details what an import task must do.
- ImportInput(Email, URI, URI, String) - Constructor for class ome.smuggler.core.types.ImportInput
-
- importKey(InputStream) - Static method in class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
De-serialises a key from a given Base64-encoded stream.
- importKey(String) - Static method in class ome.smuggler.core.io.crypto.CryptoKeyFactory
-
De-serialises a key from a given Base64-encoded string.
- importLogDir() - Method in class ome.smuggler.config.data.DevImportConfigSource
-
- importLogDir() - Method in class ome.smuggler.core.types.ImportConfigReader
-
- importLogDir() - Method in interface ome.smuggler.core.types.ImportConfigSource
-
- ImportLogger - Class in ome.smuggler.core.service.imports.impl
-
Logging methods for the import service.
- ImportLogger(LogService) - Constructor for class ome.smuggler.core.service.imports.impl.ImportLogger
-
- ImportLogPath - Class in ome.smuggler.core.types
-
A path to the log file of an import run.
- ImportLogPath(Path, ImportId) - Constructor for class ome.smuggler.core.types.ImportLogPath
-
Creates a new import log path where to store the output of the specified
import run.
- importLogPathFor(ImportId) - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- importLogPathFor(ImportId) - Method in class ome.smuggler.core.service.imports.impl.ImportMonitor
-
- importLogPathFor(ImportId) - Method in interface ome.smuggler.core.service.imports.ImportTracker
-
Determines the path to the import log for a given import.
- importLogRetentionFromNow() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- ImportMailFormatter - Class in ome.smuggler.core.service.imports.impl
-
Builds email messages to notify users and sys admins of the processing
outcome of an import batch.
- ImportMailFormatter(ImportBatchStatus) - Constructor for class ome.smuggler.core.service.imports.impl.ImportMailFormatter
-
Creates a new instance.
- ImportMonitor - Class in ome.smuggler.core.service.imports.impl
-
- ImportMonitor(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.ImportMonitor
-
Creates a new instance.
- ImportOutcomeNotifier - Class in ome.smuggler.core.service.imports.impl
-
Triggers the sending of import outcome notification emails.
- ImportOutcomeNotifier(ImportEnv, ImportBatchStatus) - Constructor for class ome.smuggler.core.service.imports.impl.ImportOutcomeNotifier
-
Creates a new instance.
- ImportOutput - Class in ome.smuggler.core.service.imports.impl
-
- ImportOutput(ImportLogPath, QueuedImport) - Constructor for class ome.smuggler.core.service.imports.impl.ImportOutput
-
- ImportOutputFormatter - Class in ome.smuggler.core.service.imports.impl
-
- ImportOutputFormatter() - Constructor for class ome.smuggler.core.service.imports.impl.ImportOutputFormatter
-
- importPermanentFailure(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
Logs an error when an import fails permanently, after having been
retried.
- importProcessor(ImportEnv) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- ImportProcessor - Interface in ome.smuggler.core.service.imports
-
Carries out an OMERO import.
- ImportQBeans - Class in ome.smuggler.config.wiring.imports
-
Singleton beans for HornetQ client resources that have to be shared and
reused.
- ImportQBeans() - Constructor for class ome.smuggler.config.wiring.imports.ImportQBeans
-
- ImportQConfig - Class in ome.smuggler.config.items
-
Holds the import queue configuration.
- ImportQConfig() - Constructor for class ome.smuggler.config.items.ImportQConfig
-
- ImportQConfig(String, String, String, boolean) - Constructor for class ome.smuggler.config.items.ImportQConfig
-
- importQConfig(ConfigProvider<ImportQConfig>) - Method in class ome.smuggler.config.wiring.imports.ImportConfigBeans
-
- importQConfig(ConfigProvider<ImportQConfig>) - Method in class ome.smuggler.config.wiring.imports.ImportDevConfigBeans
-
- ImportQConfigProvider - Class in ome.smuggler.config.providers
-
The import queue configuration as required by HornetQ.
- ImportQConfigProvider() - Constructor for class ome.smuggler.config.providers.ImportQConfigProvider
-
- importQueued(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- ImportRequest - Class in ome.smuggler.web.imports
-
Web clients use instances of this class to request an import.
- ImportRequest() - Constructor for class ome.smuggler.web.imports.ImportRequest
-
- importRequestor(ImportEnv) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- ImportRequestor - Interface in ome.smuggler.core.service.imports
-
Triggers an OMERO import.
- ImportRequestValidator - Class in ome.smuggler.web.imports
-
- ImportRequestValidator() - Constructor for class ome.smuggler.web.imports.ImportRequestValidator
-
- ImportResponse - Class in ome.smuggler.web.imports
-
Web clients receive instances of this class in response to an import request.
- ImportResponse() - Constructor for class ome.smuggler.web.imports.ImportResponse
-
- ImportResponseBuilder - Class in ome.smuggler.web.imports
-
- ImportResponseBuilder() - Constructor for class ome.smuggler.web.imports.ImportResponseBuilder
-
- ImportRunner - Class in ome.smuggler.core.service.imports.impl
-
- ImportRunner(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.ImportRunner
-
Creates a new instance.
- imports() - Method in class ome.smuggler.core.types.ImportBatch
-
- ImportServer - Class in ome.smuggler.run
-
Import sever entry point.
- ImportServer() - Constructor for class ome.smuggler.run.ImportServer
-
- importService(OmeroEnv, ImportConfigSource) - Method in class ome.smuggler.config.wiring.omero.OmeroServiceBeans
-
- ImportService - Interface in ome.smuggler.core.service.omero
-
Provides access to OMERO import functionality.
- ImportServiceBeans - Class in ome.smuggler.config.wiring.imports
-
Spring bean wiring configuration for the import service interfaces.
- ImportServiceBeans() - Constructor for class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- importSourceChannel(QChannelFactory<QueuedImport>) - Method in class ome.smuggler.config.wiring.imports.ImportQBeans
-
- importStart(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- ImportStatusController - Class in ome.smuggler.web.imports
-
- ImportStatusController() - Constructor for class ome.smuggler.web.imports.ImportStatusController
-
- importSuccessful(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.ImportLogger
-
- importTracker(ImportEnv) - Method in class ome.smuggler.config.wiring.imports.ImportServiceBeans
-
- ImportTracker - Interface in ome.smuggler.core.service.imports
-
Tracking of OMERO imports.
- ImportTrigger - Class in ome.smuggler.core.service.imports.impl
-
- ImportTrigger(ImportEnv) - Constructor for class ome.smuggler.core.service.imports.impl.ImportTrigger
-
- ImportUrl - Static variable in class ome.smuggler.web.imports.ImportController
-
- ImportYmlFile - Class in ome.smuggler.config.data
-
Default configuration for the import, i.e.
- ImportYmlFile() - Constructor for class ome.smuggler.config.data.ImportYmlFile
-
- ImportYmlGen - Class in ome.smuggler.run
-
Run this class redirecting stdout to config/import.yml to
generate the file.
- ImportYmlGen() - Constructor for class ome.smuggler.run.ImportYmlGen
-
- info(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.core.service.log.BaseLogger
-
- info(Object, Consumer<PrintWriter>) - Method in interface ome.smuggler.core.service.log.LogService
-
Logs an informational message.
- info(Object, Consumer<PrintWriter>) - Method in class ome.smuggler.providers.log.LogAdapter
-
- isEnableTranslation() - Method in class ome.smuggler.config.items.MountPointsConfig
-
- isPersistenceEnabled() - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- isRemoteFilePath(URI) - Static method in class ome.smuggler.core.types.RemoteMount
-
Is the given URI that of a file path on a remote host?
- isStillInTheFuture() - Method in class ome.smuggler.core.types.FutureTimepoint
-
Is this time point still in the future?
An instance of this class is always instantiated with a future time
point, but the passing of time will eventually make the initial time
point in the past.
- isValid - Static variable in class ome.smuggler.core.types.Nat
-
Test to check if a
long can be used to instantiate a
Nat.
- isValidEmail(String) - Static method in class ome.smuggler.core.types.Email
-
Does the given sequence of characters form a valid email address?
The test is done using RFC 822's regex.
- mail() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- mailChannelFactory(ServerConnector, MailQConfig) - Method in class ome.smuggler.config.wiring.mail.MailQBeans
-
- mailClient() - Method in class ome.smuggler.core.service.mail.impl.MailEnv
-
- MailClient - Interface in ome.smuggler.core.service.mail
-
Defines the functionality our services need to send mail.
- MailClientAdapter - Class in ome.smuggler.providers.mail
-
- MailClientAdapter(MailConfigSource) - Constructor for class ome.smuggler.providers.mail.MailClientAdapter
-
- MailClientException - Exception in ome.smuggler.core.service.mail
-
- MailClientException(Exception) - Constructor for exception ome.smuggler.core.service.mail.MailClientException
-
- MailConfig - Class in ome.smuggler.config.items
-
Specifies how to configure the mail service.
- MailConfig() - Constructor for class ome.smuggler.config.items.MailConfig
-
- mailConfig(ConfigProvider<MailConfig>) - Method in class ome.smuggler.config.wiring.mail.MailConfigBeans
-
- mailConfig() - Method in class ome.smuggler.config.wiring.mail.MailDevConfigBeans
-
- MailConfigBeans - Class in ome.smuggler.config.wiring.mail
-
Spring bean wiring of configuration items.
- MailConfigBeans() - Constructor for class ome.smuggler.config.wiring.mail.MailConfigBeans
-
- MailConfigProvider - Class in ome.smuggler.config.providers
-
Reads mail server configuration from a YAML file, falling back to hard-coded
configuration if no file is available.
- MailConfigProvider() - Constructor for class ome.smuggler.config.providers.MailConfigProvider
-
- MailConfigReader - Class in ome.smuggler.core.types
-
- MailConfigReader(MailConfig) - Constructor for class ome.smuggler.core.types.MailConfigReader
-
Creates a new instance.
- MailConfigSource - Interface in ome.smuggler.core.types
-
Provides read-only, type-safe access to mail configuration.
- MailDevConfigBeans - Class in ome.smuggler.config.wiring.mail
-
Spring bean wiring of configuration items for the
Dev
profile.
- MailDevConfigBeans() - Constructor for class ome.smuggler.config.wiring.mail.MailDevConfigBeans
-
- mailEnv(MailConfigSource, ChannelSource<QueuedMail>, TaskFileStore<MailId>) - Method in class ome.smuggler.config.wiring.mail.MailServiceBeans
-
- MailEnv - Class in ome.smuggler.core.service.mail.impl
-
Provides access to mail configuration and queue.
- MailEnv(MailConfigSource, ChannelSource<QueuedMail>, MailClient, TaskFileStore<MailId>, LogService) - Constructor for class ome.smuggler.core.service.mail.impl.MailEnv
-
- Mailer - Class in ome.smuggler.core.service.mail.impl
-
- Mailer(MailEnv) - Constructor for class ome.smuggler.core.service.mail.impl.Mailer
-
- MailFailureController - Class in ome.smuggler.web.mail
-
- MailFailureController() - Constructor for class ome.smuggler.web.mail.MailFailureController
-
- MailFailureHandler - Class in ome.smuggler.core.service.mail.impl
-
- MailFailureHandler(MailEnv) - Constructor for class ome.smuggler.core.service.mail.impl.MailFailureHandler
-
- MailId - Class in ome.smuggler.core.types
-
Identifies a mail delivery.
- MailId(String) - Constructor for class ome.smuggler.core.types.MailId
-
- MailId() - Constructor for class ome.smuggler.core.types.MailId
-
- MailLogger - Class in ome.smuggler.core.service.mail.impl
-
Logging methods for the mail service.
- MailLogger(LogService) - Constructor for class ome.smuggler.core.service.mail.impl.MailLogger
-
- mailProcessor(MailEnv) - Method in class ome.smuggler.config.wiring.mail.MailServiceBeans
-
- MailProcessor - Interface in ome.smuggler.core.service.mail
-
Carries out a request to send an email.
- MailProtocol - Enum in ome.smuggler.core.types
-
- MailQBeans - Class in ome.smuggler.config.wiring.mail
-
Singleton beans for HornetQ client resources that have to be shared and
reused.
- MailQBeans() - Constructor for class ome.smuggler.config.wiring.mail.MailQBeans
-
- MailQConfig - Class in ome.smuggler.config.items
-
Holds the mail queue configuration.
- MailQConfig() - Constructor for class ome.smuggler.config.items.MailQConfig
-
- MailQConfig(String, String, String, boolean) - Constructor for class ome.smuggler.config.items.MailQConfig
-
- mailQConfig(ConfigProvider<MailQConfig>) - Method in class ome.smuggler.config.wiring.mail.MailConfigBeans
-
- mailQConfig(ConfigProvider<MailQConfig>) - Method in class ome.smuggler.config.wiring.mail.MailDevConfigBeans
-
- MailQConfigProvider - Class in ome.smuggler.config.providers
-
The mail queue configuration as required by HornetQ.
- MailQConfigProvider() - Constructor for class ome.smuggler.config.providers.MailQConfigProvider
-
- mailRequestor(MailEnv) - Method in class ome.smuggler.config.wiring.mail.MailServiceBeans
-
- MailRequestor - Interface in ome.smuggler.core.service.mail
-
Requests the sending of an email.
- mailSent(QueuedMail) - Method in class ome.smuggler.core.service.mail.impl.MailLogger
-
- mailServer() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- mailServer() - Method in class ome.smuggler.core.types.MailConfigReader
-
- mailServer() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- MailServiceBeans - Class in ome.smuggler.config.wiring.mail
-
Spring bean wiring configuration for the mail service interfaces.
- MailServiceBeans() - Constructor for class ome.smuggler.config.wiring.mail.MailServiceBeans
-
- mailSourceChannel(QChannelFactory<QueuedMail>) - Method in class ome.smuggler.config.wiring.mail.MailQBeans
-
- MailTrigger - Class in ome.smuggler.core.service.mail.impl
-
- MailTrigger(MailEnv) - Constructor for class ome.smuggler.core.service.mail.impl.MailTrigger
-
- MailYmlFile - Class in ome.smuggler.config.data
-
The data that goes into 'config/mail.yml'.
- MailYmlFile() - Constructor for class ome.smuggler.config.data.MailYmlFile
-
- MailYmlGen - Class in ome.smuggler.run
-
Run this class redirecting stdout to config/mail.yml to
generate the file.
- MailYmlGen() - Constructor for class ome.smuggler.run.MailYmlGen
-
- Main - Class in ome.smuggler
-
Program's entry point; delegates all the work to
AppRunner.
- Main() - Constructor for class ome.smuggler.Main
-
- main(String[]) - Static method in class ome.smuggler.Main
-
- managementAddress() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- managementContextPath() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- managementPort() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- ManagementPrefix - Static variable in class ome.smuggler.config.items.SpringBootConfigProps
-
- mask - Static variable in class ome.smuggler.core.service.omero.impl.OmeCliCommandPrinter
-
The string used to replace the value of an option to mask.
- MemoryKeyValueStore<K extends util.object.Identifiable,V> - Class in ome.smuggler.core.service.file.impl
-
A
KeyValueStore backed by an in-memory map; mainly useful for
testing.
- MemoryKeyValueStore() - Constructor for class ome.smuggler.core.service.file.impl.MemoryKeyValueStore
-
Creates a new instance.
- message(Optional<M>, D) - Static method in class ome.smuggler.core.msg.ChannelMessage
-
- message(M, D) - Static method in class ome.smuggler.core.msg.ChannelMessage
-
- message(D) - Static method in class ome.smuggler.core.msg.ChannelMessage
-
- MessageBodyReader<T> - Class in ome.smuggler.providers.q
-
Reads the body of a message from the underlying Artemis buffer.
- MessageBodyReader(SourceReader<InputStream, T>) - Constructor for class ome.smuggler.providers.q.MessageBodyReader
-
Creates a new instance.
- MessageBodyWriter<T> - Class in ome.smuggler.providers.q
-
Writes the body of a message to the underlying Artemis buffer.
- MessageBodyWriter(SinkWriter<T, OutputStream>) - Constructor for class ome.smuggler.providers.q.MessageBodyWriter
-
Creates a new instance.
- MessageBuilder - Class in ome.smuggler.providers.mail
-
- MessageBuilder(MailConfigSource, JavaMailSender) - Constructor for class ome.smuggler.providers.mail.MessageBuilder
-
- MessageRepeater<T> - Class in ome.smuggler.core.msg
-
Plugs into a
ReschedulingSink to deliver the same message to sink's
consumers multiple times at predefined intervals for a finite number of
times.
- MessageRepeater(RepeatConsumer<T>, Stream<Duration>, Consumer<T>) - Constructor for class ome.smuggler.core.msg.MessageRepeater
-
Creates a new instance.
- Messages - Class in ome.smuggler.providers.q
-
- Messages() - Constructor for class ome.smuggler.providers.q.Messages
-
- MessageSink<M,D> - Interface in ome.smuggler.core.msg
-
Encapsulates the consumption of an asynchronous message received from a
channel.
- MessageSource<M,D> - Interface in ome.smuggler.core.msg
-
Encapsulates the sending of an asynchronous message along a channel that
supports metadata.
- metadata() - Method in class ome.smuggler.core.msg.ChannelMessage
-
- millis(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Parses the string representation of a positive integer as a Duration in milliseconds.
- modify(K, Function<V, V>) - Method in class ome.smuggler.core.service.file.impl.KeyValueFileStore
-
- modify(K, Function<V, V>) - Method in class ome.smuggler.core.service.file.impl.MemoryKeyValueStore
-
- modify(K, Function<V, V>) - Method in class ome.smuggler.core.service.file.impl.TSafeKeyValueStore
-
- modify(K, Function<V, V>) - Method in interface ome.smuggler.core.service.file.KeyValueStore
-
Updates the value associated to the specified key.
- MountPointsConfig - Class in ome.smuggler.config.items
-
Specifies how to configure remote-to-local translation file paths.
- MountPointsConfig() - Constructor for class ome.smuggler.config.items.MountPointsConfig
-
- MountPointsConfig.RemoteToLocalMapping - Class in ome.smuggler.config.items
-
Specifies how to map a remote file path into a local one.
- MountPointsConfigProvider - Class in ome.smuggler.config.providers
-
Reads mount points configuration from a YAML file, falling back to hard-coded
configuration if no file is available.
- MountPointsConfigProvider() - Constructor for class ome.smuggler.config.providers.MountPointsConfigProvider
-
- MountPointsYmlFile - Class in ome.smuggler.config.data
-
Default configuration for mount points mapping, i.e.
- MountPointsYmlFile() - Constructor for class ome.smuggler.config.data.MountPointsYmlFile
-
- MountPointsYmlGen - Class in ome.smuggler.run
-
Run this class redirecting stdout to config/mount-points.yml
to generate the file.
- MountPointsYmlGen() - Constructor for class ome.smuggler.run.MountPointsYmlGen
-
- of(long) - Static method in class ome.smuggler.core.types.Nat
-
Instantiate a
Nat from a non-negative value.
- of(long) - Static method in class ome.smuggler.core.types.PositiveN
-
- ome.smuggler - package ome.smuggler
-
- ome.smuggler.config - package ome.smuggler.config
-
- ome.smuggler.config.data - package ome.smuggler.config.data
-
- ome.smuggler.config.items - package ome.smuggler.config.items
-
- ome.smuggler.config.providers - package ome.smuggler.config.providers
-
- ome.smuggler.config.wiring - package ome.smuggler.config.wiring
-
- ome.smuggler.config.wiring.crypto - package ome.smuggler.config.wiring.crypto
-
- ome.smuggler.config.wiring.imports - package ome.smuggler.config.wiring.imports
-
- ome.smuggler.config.wiring.mail - package ome.smuggler.config.wiring.mail
-
- ome.smuggler.config.wiring.omero - package ome.smuggler.config.wiring.omero
-
- ome.smuggler.core.convert - package ome.smuggler.core.convert
-
- ome.smuggler.core.io - package ome.smuggler.core.io
-
- ome.smuggler.core.io.crypto - package ome.smuggler.core.io.crypto
-
- ome.smuggler.core.msg - package ome.smuggler.core.msg
-
- ome.smuggler.core.service.file - package ome.smuggler.core.service.file
-
- ome.smuggler.core.service.file.impl - package ome.smuggler.core.service.file.impl
-
- ome.smuggler.core.service.imports - package ome.smuggler.core.service.imports
-
- ome.smuggler.core.service.imports.impl - package ome.smuggler.core.service.imports.impl
-
- ome.smuggler.core.service.log - package ome.smuggler.core.service.log
-
- ome.smuggler.core.service.mail - package ome.smuggler.core.service.mail
-
- ome.smuggler.core.service.mail.impl - package ome.smuggler.core.service.mail.impl
-
- ome.smuggler.core.service.omero - package ome.smuggler.core.service.omero
-
- ome.smuggler.core.service.omero.impl - package ome.smuggler.core.service.omero.impl
-
- ome.smuggler.core.types - package ome.smuggler.core.types
-
- ome.smuggler.providers.json - package ome.smuggler.providers.json
-
- ome.smuggler.providers.log - package ome.smuggler.providers.log
-
- ome.smuggler.providers.mail - package ome.smuggler.providers.mail
-
- ome.smuggler.providers.q - package ome.smuggler.providers.q
-
- ome.smuggler.run - package ome.smuggler.run
-
- ome.smuggler.web - package ome.smuggler.web
-
- ome.smuggler.web.imports - package ome.smuggler.web.imports
-
- ome.smuggler.web.mail - package ome.smuggler.web.mail
-
- ome.smuggler.web.omero - package ome.smuggler.web.omero
-
- OmeCliCommandBuilder - Class in ome.smuggler.core.service.omero.impl
-
Template class for OMERO CLI command builders.
- OmeCliCommandBuilder(OmeCliConfigSource) - Constructor for class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- OmeCliCommandPrinter - Class in ome.smuggler.core.service.omero.impl
-
Pretty-prints an
OME CLI command, masking the
values of selected options if desired.
- OmeCliCommandPrinter(CommandBuilder) - Constructor for class ome.smuggler.core.service.omero.impl.OmeCliCommandPrinter
-
Creates a new instance.
- OmeCliCommandRunner - Class in ome.smuggler.core.service.omero.impl
-
Spawns a separate JVM process to run an OME CLI command.
- OmeCliCommandRunner(OmeroEnv, OmeCliCommandBuilder) - Constructor for class ome.smuggler.core.service.omero.impl.OmeCliCommandRunner
-
Creates a new instance to run the specified command.
- OmeCliConfig - Class in ome.smuggler.config.items
-
Holds the data needed to call the various OMERO CLI commands.
- OmeCliConfig() - Constructor for class ome.smuggler.config.items.OmeCliConfig
-
- omeCliConfig(ConfigProvider<OmeCliConfig>) - Method in class ome.smuggler.config.wiring.omero.OmeroConfigBeans
-
- omeCliConfig(ConfigProvider<OmeCliConfig>) - Method in class ome.smuggler.config.wiring.omero.OmeroDevConfigBeans
-
- OmeCliConfigProvider - Class in ome.smuggler.config.providers
-
The data needed to configure the OMERO CLI commands.
- OmeCliConfigProvider() - Constructor for class ome.smuggler.config.providers.OmeCliConfigProvider
-
- OmeCliConfigReader - Class in ome.smuggler.core.types
-
- OmeCliConfigReader(OmeCliConfig) - Constructor for class ome.smuggler.core.types.OmeCliConfigReader
-
Creates a new instance to read the given configuration.
- OmeCliConfigSource - Interface in ome.smuggler.core.types
-
Provides read-only, type-safe access to the OME CLI configuration.
- omeCliJar() - Method in class ome.smuggler.core.types.OmeCliConfigReader
-
- omeCliJar() - Method in interface ome.smuggler.core.types.OmeCliConfigSource
-
- OmeroConfigBeans - Class in ome.smuggler.config.wiring.omero
-
Spring bean wiring of OMERO configuration items for the
Prod profile.
- OmeroConfigBeans() - Constructor for class ome.smuggler.config.wiring.omero.OmeroConfigBeans
-
- OmeroDefault - Class in ome.smuggler.core.types
-
Default values for OMERO configuration items.
- OmeroDefault() - Constructor for class ome.smuggler.core.types.OmeroDefault
-
- OmeroDevConfigBeans - Class in ome.smuggler.config.wiring.omero
-
Spring bean wiring of OMERO configuration items for the
Dev profile.
- OmeroDevConfigBeans() - Constructor for class ome.smuggler.config.wiring.omero.OmeroDevConfigBeans
-
- omeroEnv(OmeCliConfigSource, ChannelSource<QueuedOmeroKeepAlive>, ConfigProvider<MountPointsConfig>) - Method in class ome.smuggler.config.wiring.omero.OmeroServiceBeans
-
- OmeroEnv - Class in ome.smuggler.core.service.omero.impl
-
Provides access to service configuration and auxiliary services such as
logging.
- OmeroEnv(OmeCliConfigSource, ChannelSource<QueuedOmeroKeepAlive>, RemotePathResolver, LogService) - Constructor for class ome.smuggler.core.service.omero.impl.OmeroEnv
-
Creates a new instance.
- omeroHost - Variable in class ome.smuggler.web.imports.ImportRequest
-
The hostname or IP address of the machine running the OMERO server in
which the data will be imported.
- omeroHost - Variable in class ome.smuggler.web.omero.CreateSessionRequest
-
The hostname or IP address of the machine running the OMERO server.
- OmeroLogger - Class in ome.smuggler.core.service.omero.impl
-
Logging methods for the OMERO services.
- OmeroLogger(LogService) - Constructor for class ome.smuggler.core.service.omero.impl.OmeroLogger
-
- omeroPort - Variable in class ome.smuggler.web.imports.ImportRequest
-
The port of the OMERO server.
- omeroPort - Variable in class ome.smuggler.web.omero.CreateSessionRequest
-
The port of the OMERO server.
- OmeroServiceBeans - Class in ome.smuggler.config.wiring.omero
-
Spring bean wiring configuration for the OMERO service interfaces.
- OmeroServiceBeans() - Constructor for class ome.smuggler.config.wiring.omero.OmeroServiceBeans
-
- OmeroSessionQConfig - Class in ome.smuggler.config.items
-
Holds the OMERO session queue configuration.
- OmeroSessionQConfig() - Constructor for class ome.smuggler.config.items.OmeroSessionQConfig
-
- OmeroSessionQConfig(String, String, String, boolean) - Constructor for class ome.smuggler.config.items.OmeroSessionQConfig
-
- omeroSessionQConfig(ConfigProvider<OmeroSessionQConfig>) - Method in class ome.smuggler.config.wiring.omero.OmeroConfigBeans
-
- omeroSessionQConfig(ConfigProvider<OmeroSessionQConfig>) - Method in class ome.smuggler.config.wiring.omero.OmeroDevConfigBeans
-
- OmeroSessionQConfigProvider - Class in ome.smuggler.config.providers
-
The OMERO session queue configuration as required by HornetQ.
- OmeroSessionQConfigProvider() - Constructor for class ome.smuggler.config.providers.OmeroSessionQConfigProvider
-
- omeroUri(String, String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a URI from host and port components: the returned URI will be of
the form omero://host:port/.
- onBatchCompletion(ProcessedImport) - Method in class ome.smuggler.core.service.imports.impl.Finaliser
-
Triggers the procedure to finalise the import batch after all import
tasks within it have run.
- OnceOffRepeatConsumer<T> - Class in ome.smuggler.core.msg
-
Makes message consumers returning
RepeatActions work well when used
for once-off schedules.
- OnceOffRepeatConsumer(RepeatConsumer<T>, Consumer<T>) - Constructor for class ome.smuggler.core.msg.OnceOffRepeatConsumer
-
Creates a new instance.
- OnceOffSchedule<T> - Class in ome.smuggler.core.msg
-
Plugs into a
ReschedulingSink to deliver messages to sink's consumers
exactly once.
- OnceOffSchedule(Consumer<T>) - Constructor for class ome.smuggler.core.msg.OnceOffSchedule
-
Creates a new instance.
- onFailure(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.Finaliser
-
Triggers the completion of an import task when the OMERO import has
failed.
- onMessage(ClientMessage) - Method in class ome.smuggler.providers.q.DequeueTask
-
- onSuccess(QueuedImport) - Method in class ome.smuggler.core.service.imports.impl.Finaliser
-
Triggers the completion of an import task when the OMERO import has run
successfully.
- OpTimeout - Static variable in class ome.smuggler.providers.mail.MailClientAdapter
-
- optionalArg(String, Optional<T>) - Static method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- password() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- password() - Method in class ome.smuggler.core.types.MailConfigReader
-
- password() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- password - Variable in class ome.smuggler.web.omero.CreateSessionRequest
-
The password of the user for whom to open the session.
- pathFor(T) - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- pathFor(T) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Builds the path to the file associated to the given task ID.
- PlainTextMail - Class in ome.smuggler.core.types
-
A plain text email message.
- PlainTextMail(Email, String, String) - Constructor for class ome.smuggler.core.types.PlainTextMail
-
Creates a new instance.
- Port - Static variable in class ome.smuggler.core.types.OmeroDefault
-
Default OMERO server port: 4064.
- positiveInt(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a positive natural from its string representation.
- PositiveN - Class in ome.smuggler.core.types
-
A positive natural number, i.e.
- PositiveN(Long) - Constructor for class ome.smuggler.core.types.PositiveN
-
- print() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandPrinter
-
Pretty-prints the command to a string.
- printMasking(String...) - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandPrinter
-
Pretty-prints the command to a string, masking the value of each
specified option.
- printMasking(Integer...) - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandPrinter
-
Pretty-prints the command to a string, masking the token at the
specified index.
- PriorityConfigProvider<T> - Class in ome.smuggler.config.providers
-
Base class for ConfigProvider beans that prioritize where
configuration is read from.
- PriorityConfigProvider() - Constructor for class ome.smuggler.config.providers.PriorityConfigProvider
-
- process(InputStream, OutputStream) - Method in interface ome.smuggler.core.io.StreamFilter
-
Same as
processE but masks
any exception into a runtime exception so we can use this interface as
a functional interface.
- processE(InputStream, OutputStream) - Method in interface ome.smuggler.core.io.StreamFilter
-
Reads from the input stream and writes to the output stream.
- processE(InputStream, OutputStream) - Method in class ome.smuggler.core.io.ValueFilter
-
- ProcessedImport - Class in ome.smuggler.core.types
-
Same as a
QueuedImport but only used after the import task has
completed and needs to be garbage-collected.
- Prod - Static variable in class ome.smuggler.config.Profiles
-
Configuration for the production environment.
- Profiles - Class in ome.smuggler.config
-
Enumerates the profile constants used to select configuration profiles.
- Profiles() - Constructor for class ome.smuggler.config.Profiles
-
- protocol() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- protocol() - Method in class ome.smuggler.core.types.MailConfigReader
-
- protocol() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- put(K, V) - Method in class ome.smuggler.core.service.file.impl.KeyValueFileStore
-
- put(K, V) - Method in class ome.smuggler.core.service.file.impl.MemoryKeyValueStore
-
- put(K, V) - Method in class ome.smuggler.core.service.file.impl.TSafeKeyValueStore
-
- put(K, V) - Method in interface ome.smuggler.core.service.file.KeyValueStore
-
Maps a key to a value.
- RawConfigValues - Class in ome.smuggler.core.convert
-
Utility methods to convert raw config values to values of more suitable
types.
- RawConfigValues() - Constructor for class ome.smuggler.core.convert.RawConfigValues
-
- read(S) - Method in interface ome.smuggler.core.convert.SourceReader
-
Reads a T-value from the data source.
- read(InputStream) - Method in class ome.smuggler.core.io.crypto.CryptoSourceReader
-
- read(Reader) - Method in class ome.smuggler.providers.json.JsonSourceReader
-
- read(S) - Method in class ome.smuggler.providers.json.JsonStreamReader
-
Reads JSON from the input stream and de-serialises it into a
T-value.
- read(ClientMessage) - Method in class ome.smuggler.providers.q.MessageBodyReader
-
- readAll(InputStream) - Static method in class ome.smuggler.core.io.StreamOps
-
Reads the whole input stream into a byte array.
- readConfig() - Method in class ome.smuggler.config.data.CryptoYmlFile
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultArtemisPersistenceConfig
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultImportGcQConfig
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultImportQConfig
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultMailQConfig
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultOmeCliConfig
-
- readConfig() - Method in class ome.smuggler.config.data.DefaultOmeroSessionQConfig
-
- readConfig() - Method in class ome.smuggler.config.data.ImportYmlFile
-
- readConfig() - Method in class ome.smuggler.config.data.MailYmlFile
-
- readConfig() - Method in class ome.smuggler.config.data.MountPointsYmlFile
-
- readConfig() - Method in class ome.smuggler.config.data.SpringBootAppPropsFile
-
- readConfig() - Method in class ome.smuggler.config.data.UndertowYmlFile
-
- readConfig() - Method in class ome.smuggler.config.providers.PriorityConfigProvider
-
Reads all the objects in the configuration file.
- readConfig(ResourceLocation...) - Method in class ome.smuggler.config.providers.PriorityConfigProvider
-
Reads configuration from the first available out of the specified
locations, falling back to hard-coded configuration if no file is
available.
- readLines(InputStream, FunctionE<Stream<String>, T>, Charset...) - Static method in class ome.smuggler.core.io.StreamOps
-
Builds a stream of lines out of the input data and passes the stream on
to the given reader to convert them into a value of type T.
- readLinesIntoString(InputStream) - Static method in class ome.smuggler.core.io.StreamOps
-
Reads the whole input stream into a string using the default character
encoding.
- readTimeoutFor(MailProtocol) - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- reason - Variable in class ome.smuggler.web.Error
-
Details what went wrong.
- RelBatchStatusDbDirPath - Static variable in class ome.smuggler.config.data.ImportYmlFile
-
- RelFailedImportLogDirPath - Static variable in class ome.smuggler.config.data.ImportYmlFile
-
- RelImportLogDirPath - Static variable in class ome.smuggler.config.data.ImportYmlFile
-
- RemoteMount - Class in ome.smuggler.core.types
-
Provides a way to translate a file path on a remote device into a local
path.
- RemoteMount(URI, Path) - Constructor for class ome.smuggler.core.types.RemoteMount
-
Creates a new instance.
- RemoteMountConfigReader - Class in ome.smuggler.core.types
-
- RemoteMountConfigReader(MountPointsConfig) - Constructor for class ome.smuggler.core.types.RemoteMountConfigReader
-
Creates a new instance.
- RemoteMountConfigSource - Interface in ome.smuggler.core.types
-
Provides read-only, type-safe access to remote mount point configuration.
- RemotePathMapper - Class in ome.smuggler.core.service.file.impl
-
- RemotePathMapper(List<RemoteMount>) - Constructor for class ome.smuggler.core.service.file.impl.RemotePathMapper
-
Creates a new instance.
- RemotePathResolver - Interface in ome.smuggler.core.service.file
-
Remote-to-local path translation.
- remoteToLocalMap() - Method in class ome.smuggler.core.types.RemoteMountConfigReader
-
- remoteToLocalMap() - Method in interface ome.smuggler.core.types.RemoteMountConfigSource
-
Lists the configured remote-to-local mappings.
- RemoteToLocalMapping() - Constructor for class ome.smuggler.config.items.MountPointsConfig.RemoteToLocalMapping
-
- remove(K) - Method in class ome.smuggler.core.service.file.impl.KeyValueFileStore
-
- remove(K) - Method in class ome.smuggler.core.service.file.impl.MemoryKeyValueStore
-
- remove(T) - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- remove(K) - Method in class ome.smuggler.core.service.file.impl.TSafeKeyValueStore
-
- remove(K) - Method in interface ome.smuggler.core.service.file.KeyValueStore
-
Deletes the mapping identified by the specified key.
- remove(T) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Deletes the file associated to the specified task ID.
- RepeatAction - Enum in ome.smuggler.core.msg
-
Indicates whether a message should be re-delivered after being consumed.
- RepeatConsumer<T> - Interface in ome.smuggler.core.msg
-
Plugs into a channel sink to consume its data and optionally request that
the same data be delivered again.
- replace(T, StreamFilter) - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- replace(T, StreamFilter) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Uses a filter function to replace the content of the file
associated to the specified task.
- replace(T, FunctionE<String, String>) - Method in interface ome.smuggler.core.service.file.TaskFileStore
-
Uses a setter function to replace the content of the file
associated to the specified task.
- requestLoggingFilter() - Method in class ome.smuggler.config.wiring.WebWiring
-
- RequestLoggingFilter - Class in ome.smuggler.web
-
Logs every import request and, in addition, if the application was started
with the DEBUG log level then any other request will be logged too.
- RequestLoggingFilter() - Constructor for class ome.smuggler.web.RequestLoggingFilter
-
Creates a new instance.
- Reschedulable<T> - Interface in ome.smuggler.core.msg
-
A task that consumes a channel sink's output and optionally requests the
channel to deliver again some more data at a later point in time.
- ReschedulableFactory - Class in ome.smuggler.core.msg
-
- ReschedulableFactory() - Constructor for class ome.smuggler.core.msg.ReschedulableFactory
-
- ReschedulingSink<T> - Class in ome.smuggler.core.msg
-
A channel sink feeding the channel output to a task that may produce more
input to be delivered on the channel at a later point in time.
- ReschedulingSink(Reschedulable<T>, MessageSource<CountedSchedule, T>) - Constructor for class ome.smuggler.core.msg.ReschedulingSink
-
Creates a new instance.
- resolve(String) - Method in class ome.smuggler.config.BaseDir
-
Resolves the given path as follows.
- resolveRequiredPath(String) - Method in class ome.smuggler.config.BaseDir
-
Resolves the given path as follows.
- retryIntervals() - Method in class ome.smuggler.config.data.DevImportConfigSource
-
- retryIntervals() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- retryIntervals() - Method in class ome.smuggler.core.types.ImportConfigReader
-
- retryIntervals() - Method in interface ome.smuggler.core.types.ImportConfigSource
-
- retryIntervals() - Method in class ome.smuggler.core.types.MailConfigReader
-
- retryIntervals() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- rewrite(Path, StreamFilter) - Static method in class ome.smuggler.core.io.FileOps
-
Uses a filter to rewrite the content of the specified file.
- RootDir - Static variable in class ome.smuggler.config.data.DefaultArtemisPersistenceConfig
-
- rootLogLevel() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- RootPath - Static variable in class ome.smuggler.web.imports.ImportFailureController
-
- rootPath() - Method in class ome.smuggler.web.imports.ImportFailureController
-
- RootPath - Static variable in class ome.smuggler.web.mail.MailFailureController
-
- rootPath() - Method in class ome.smuggler.web.mail.MailFailureController
-
- rootPath() - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
- run(ImportInput, Path) - Method in class ome.smuggler.core.service.omero.impl.Importer
-
- run(Path) - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandRunner
-
Runs the command redirecting all output to the specified file.
- run() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandRunner
-
Runs the command discarding any output.
- run(ImportInput, Path) - Method in interface ome.smuggler.core.service.omero.ImportService
-
Runs an import.
- run(List<String>) - Method in class ome.smuggler.run.CryptoYmlGen
-
Dumps YAML config to stdout.
- run(List<String>) - Method in class ome.smuggler.run.ImportServer
-
- run(List<String>) - Method in class ome.smuggler.run.ImportYmlGen
-
Dumps YAML config to stdout.
- run(List<String>) - Method in class ome.smuggler.run.MailYmlGen
-
Dumps YAML config to stdout.
- run(List<String>) - Method in class ome.smuggler.run.MountPointsYmlGen
-
Dumps YAML config to stdout.
- run(List<String>) - Method in interface ome.smuggler.run.RunnableApp
-
Runs the app with the given command line arguments.
- run(List<String>) - Method in class ome.smuggler.run.SpringBootPropsGen
-
Dumps Java props to stdout.
- run(List<String>) - Method in class ome.smuggler.run.UndertowYmlGen
-
Dumps YAML config to stdout.
- runAndCollectOutput() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandRunner
-
Runs the command collecting any output in a result string.
- RunnableApp - Interface in ome.smuggler.run
-
All our apps in this package implement this interface so we can easily
run any of them; also they all are expected to have a parameter-less
constructor.
- Schedule<T> - Class in ome.smuggler.core.types
-
A plan for carrying out a task on an item T at a specified future
time.
- Schedule(FutureTimepoint, T) - Constructor for class ome.smuggler.core.types.Schedule
-
Creates a new instance.
- ScheduleCountKey - Static variable in class ome.smuggler.providers.q.Messages
-
- ScheduleTask<T> - Class in ome.smuggler.providers.q
-
Enqueues a message that will only be delivered to consumers at a specified
time in the future.
- ScheduleTask(QueueConnector, SinkWriter<T, OutputStream>) - Constructor for class ome.smuggler.providers.q.ScheduleTask
-
Creates a new instance.
- SchedulingSource<T> - Interface in ome.smuggler.core.msg
-
A channel source that allows the scheduling of messages to send.
- ScreenId - Class in ome.smuggler.core.types
-
An OME screen ID.
- ScreenId(Long) - Constructor for class ome.smuggler.core.types.ScreenId
-
- screenId(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a screen ID from a positive integer.
- screenId - Variable in class ome.smuggler.web.imports.ImportRequest
-
If the image is to be imported into an existing OMERO screen, then this
field specifies its ID; leave out otherwise.
- securityEnabled() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- SecurityPrefix - Static variable in class ome.smuggler.config.items.SpringBootConfigProps
-
- securityRole() - Static method in class ome.smuggler.config.items.SpringBootConfigProps
-
- send(T) - Method in interface ome.smuggler.core.msg.ChannelSource
-
Inputs data into the channel and returns immediately.
- send(ChannelMessage<M, D>) - Method in class ome.smuggler.core.msg.SourceQueue
-
- send(PlainTextMail) - Method in interface ome.smuggler.core.service.mail.MailClient
-
Relays a mail message to a server.
- send(PlainTextMail) - Method in class ome.smuggler.providers.mail.MailClientAdapter
-
- send(ChannelMessage<CountedSchedule, T>) - Method in class ome.smuggler.providers.q.CountedScheduleTask
-
- send(ChannelMessage<Function<QueueConnector, ClientMessage>, T>) - Method in class ome.smuggler.providers.q.EnqueueTask
-
- send(ChannelMessage<FutureTimepoint, T>) - Method in class ome.smuggler.providers.q.ScheduleTask
-
Sends the message so that the channel will only deliver it to consumers
at the specified time in the future.
- serializationFactory(CryptoConfigSource) - Method in class ome.smuggler.config.wiring.crypto.CryptoSerializationBeans
-
- SerializationFactory - Class in ome.smuggler.config.wiring.crypto
-
Builds serializers depending on the current crypto configuration.
- SerializationFactory(CryptoConfigSource) - Constructor for class ome.smuggler.config.wiring.crypto.SerializationFactory
-
Creates a new instance.
- serializer() - Method in class ome.smuggler.config.wiring.crypto.SerializationFactory
-
Instantiates a serializer for T-values.
- ServerConnector - Class in ome.smuggler.providers.q
-
Establishes a connection and client session with the Artemis server.
- ServerConnector(ServerLocator) - Constructor for class ome.smuggler.providers.q.ServerConnector
-
Connects to the Artemis server and starts a client session.
- service() - Method in class ome.smuggler.web.imports.ImportFailureController
-
- service() - Method in class ome.smuggler.web.mail.MailFailureController
-
- service() - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
- session() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- sessionChannelFactory(ServerConnector, OmeroSessionQConfig) - Method in class ome.smuggler.config.wiring.omero.SessionQBeans
-
- SessionController - Class in ome.smuggler.web.omero
-
Exposes OMERO session-related operations.
- SessionController() - Constructor for class ome.smuggler.web.omero.SessionController
-
- SessionKeepAliveHandler - Class in ome.smuggler.core.service.omero.impl
-
Consumes a message from the session keep-alive queue by pinging the
specified OMERO session.
- SessionKeepAliveHandler(OmeroEnv, SessionService) - Constructor for class ome.smuggler.core.service.omero.impl.SessionKeepAliveHandler
-
Creates a new instance.
- sessionKeepAliveInterval() - Method in class ome.smuggler.core.types.OmeCliConfigReader
-
- sessionKeepAliveInterval() - Method in interface ome.smuggler.core.types.OmeCliConfigSource
-
- SessionKeepAliveInterval - Static variable in class ome.smuggler.core.types.OmeroDefault
-
- sessionKey - Variable in class ome.smuggler.web.imports.ImportRequest
-
Mandatory field to identify the OMERO session to use for the import.
- sessionKey - Variable in class ome.smuggler.web.omero.CreateSessionResponse
-
The OMERO session key that identifies the newly opened session.
- SessionManager - Class in ome.smuggler.core.service.omero.impl
-
- SessionManager(OmeroEnv) - Constructor for class ome.smuggler.core.service.omero.impl.SessionManager
-
Creates a new instance.
- sessionQ() - Method in class ome.smuggler.core.service.omero.impl.OmeroEnv
-
- SessionQBeans - Class in ome.smuggler.config.wiring.omero
-
Singleton beans for HornetQ client resources that have to be shared and
reused.
- SessionQBeans() - Constructor for class ome.smuggler.config.wiring.omero.SessionQBeans
-
- sessionService(OmeroEnv) - Method in class ome.smuggler.config.wiring.omero.OmeroServiceBeans
-
- SessionService - Interface in ome.smuggler.core.service.omero
-
Provides access to OMERO sessions functionality.
- sessionSourceChannel(QChannelFactory<QueuedOmeroKeepAlive>) - Method in class ome.smuggler.config.wiring.omero.SessionQBeans
-
- SessionTimeout - Static variable in class ome.smuggler.core.types.OmeroDefault
-
Default OMERO session timeout: 10 minutes.
- setBatchStatusDbDir(String) - Method in class ome.smuggler.config.items.ImportConfig
-
- setBatchStatusDbLockStripes(Long) - Method in class ome.smuggler.config.items.ImportConfig
-
- setBindingsDirPath(String) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- setDatasetId(PositiveN) - Method in class ome.smuggler.core.types.ImportInput
-
- setDatasetId(Optional<DatasetId>) - Method in class ome.smuggler.core.types.ImportInput
-
- setDeadMailDir(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setDescription(String) - Method in class ome.smuggler.core.types.ImportInput
-
- setEnableTranslation(boolean) - Method in class ome.smuggler.config.items.MountPointsConfig
-
- setEncrypt(Boolean) - Method in class ome.smuggler.config.items.CryptoConfig
-
- setFailedImportLogDir(String) - Method in class ome.smuggler.config.items.ImportConfig
-
- setFromAddress(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setImportLogDir(String) - Method in class ome.smuggler.config.items.ImportConfig
-
- setJournalDirPath(String) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- setKey(String) - Method in class ome.smuggler.config.items.CryptoConfig
-
- setLargeMessagesDirPath(String) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- setLocalBasePath(String) - Method in class ome.smuggler.config.items.MountPointsConfig.RemoteToLocalMapping
-
- setLogRetentionMinutes(Long) - Method in class ome.smuggler.config.items.ImportConfig
-
- setMailServerHost(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setMailServerPort(int) - Method in class ome.smuggler.config.items.MailConfig
-
- setName(String) - Method in class ome.smuggler.core.types.ImportInput
-
- setNiceCommand(String) - Method in class ome.smuggler.config.items.ImportConfig
-
- setOmeCliJarPath(String) - Method in class ome.smuggler.config.items.OmeCliConfig
-
- setOmeCliJarPrefix(String) - Method in class ome.smuggler.config.items.OmeCliConfig
-
- setPagingDirPath(String) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- setPassword(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setPersistenceEnabled(boolean) - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- setPort(int) - Method in class ome.smuggler.config.items.UndertowConfig
-
- setProp(String, long) - Static method in class ome.smuggler.providers.q.Messages
-
- setRemoteBaseUri(String) - Method in class ome.smuggler.config.items.MountPointsConfig.RemoteToLocalMapping
-
- setRemoteToLocalMap(MountPointsConfig.RemoteToLocalMapping[]) - Method in class ome.smuggler.config.items.MountPointsConfig
-
- setRetryIntervals(Long[]) - Method in class ome.smuggler.config.items.ImportConfig
-
- setRetryIntervals(Long[]) - Method in class ome.smuggler.config.items.MailConfig
-
- setScheduleCount(PositiveN) - Static method in class ome.smuggler.providers.q.Messages
-
- setScheduledDeliveryTime(FutureTimepoint) - Static method in class ome.smuggler.providers.q.Messages
-
- setScreenId(PositiveN) - Method in class ome.smuggler.core.types.ImportInput
-
- setScreenId(Optional<ScreenId>) - Method in class ome.smuggler.core.types.ImportInput
-
- setSessionKeepAliveInterval(Long) - Method in class ome.smuggler.config.items.OmeCliConfig
-
- setSkipServerCertificateValidation(boolean) - Method in class ome.smuggler.config.items.MailConfig
-
- setSysAdminEmail(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setUsername(String) - Method in class ome.smuggler.config.items.MailConfig
-
- setUseSmtps(boolean) - Method in class ome.smuggler.config.items.MailConfig
-
- shouldLog(HttpServletRequest) - Method in class ome.smuggler.web.RequestLoggingFilter
-
- SinkWriter<T,S> - Interface in ome.smuggler.core.convert
-
Writes a value V to a data sink S.
- skipServerCertificateValidation() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- skipServerCertificateValidation() - Method in class ome.smuggler.core.types.MailConfigReader
-
- skipServerCertificateValidation() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- smtpEnableSsl() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- smtpEnableStartTls() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- smtpRequireStartTls() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- smtpsCheckServerIdentity() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- smtpsTrustedServers() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- SourceQueue<M,D> - Class in ome.smuggler.core.msg
-
A channel source that queues messages in memory and allows to retrieve the
head of the queue to consume messages or do a bulk retrieval of all queued
messages.
- SourceQueue() - Constructor for class ome.smuggler.core.msg.SourceQueue
-
Creates a new instance.
- SourceReader<S,T> - Interface in ome.smuggler.core.convert
-
Reads a value V from a data source S.
- spec() - Method in enum ome.smuggler.core.io.crypto.CryptoAlgoSpec
-
- SpringBootAdminConfigProps - Class in ome.smuggler.config.items
-
- SpringBootAdminConfigProps() - Constructor for class ome.smuggler.config.items.SpringBootAdminConfigProps
-
- SpringBootAdminPrefix - Static variable in class ome.smuggler.config.items.SpringBootAdminConfigProps
-
- SpringBootAppPropsFile - Class in ome.smuggler.config.data
-
The data that goes into 'config/application*.properties'.
- SpringBootAppPropsFile() - Constructor for class ome.smuggler.config.data.SpringBootAppPropsFile
-
- SpringBootConfigProps - Class in ome.smuggler.config.items
-
Accessors for Spring Boot application properties.
- SpringBootConfigProps() - Constructor for class ome.smuggler.config.items.SpringBootConfigProps
-
- SpringBootPropsGen - Class in ome.smuggler.run
-
Run this class redirecting stdout to
config/application.properties to generate the file.
- SpringBootPropsGen() - Constructor for class ome.smuggler.run.SpringBootPropsGen
-
- status() - Method in class ome.smuggler.core.types.ProcessedImport
-
- statusUri - Variable in class ome.smuggler.web.imports.ImportResponse
-
The location where the client can retrieve status updates to find out
what is the current state of the requested import.
- store(String, Path) - Static method in class ome.smuggler.config.BaseDir
-
Sets a system property with the specified key and value.
- store() - Method in class ome.smuggler.core.service.file.impl.MemoryKeyValueStore
-
- storeDir() - Method in class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
- storeTempDir(String, String) - Static method in class ome.smuggler.config.BaseDir
-
Creates a temporary directory and sets its path in the system properties
using the given key.
- stream(PlainTextMail, OutputStream) - Method in interface ome.smuggler.core.service.mail.MailClient
-
Writes a mail message to the given stream.
- stream(PlainTextMail, OutputStream) - Method in class ome.smuggler.providers.mail.MailClientAdapter
-
- streamFileOr404(String, HttpServletResponse) - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
Looks up the file associated to a task using the task ID and streams that
file to the client if found; otherwise outputs a 404 to the client.
- StreamFilter - Interface in ome.smuggler.core.io
-
Represents the process of reading from an InputStream to produce the
content of an OutputStream.
- StreamOps - Class in ome.smuggler.core.io
-
Utility methods for I/O steam operations.
- StreamOps() - Constructor for class ome.smuggler.core.io.StreamOps
-
- streamOr404(HttpServletResponse) - Method in class ome.smuggler.web.FileStreamer
-
Streams the file to the client or sends back a 404 if the file does not
exist.
- string(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Parses a string of length at least one.
- StringFilter - Class in ome.smuggler.core.io
-
A specialised
ValueFilter that reads and writes strings.
- StringFilter(Function<String, String>) - Constructor for class ome.smuggler.core.io.StringFilter
-
Creates a new instance.
- submit(ImportRequest...) - Method in class ome.smuggler.web.imports.ImportBatchSubmitter
-
Submits the given import requests as a batch to the underlying service.
- submit(CreateSessionRequest) - Method in class ome.smuggler.web.omero.CreateSessionSubmitter
-
Submits the given request to the underlying service.
- succeeded() - Method in class ome.smuggler.core.types.ImportBatchStatus
-
- succeeded(QueuedImport) - Static method in class ome.smuggler.core.types.ProcessedImport
-
Creates a new instance for an import that's completed successfully.
- succeeded() - Method in class ome.smuggler.core.types.ProcessedImport
-
- success(OmeCliCommandBuilder, int) - Method in class ome.smuggler.core.service.omero.impl.OmeroLogger
-
- sysAdminAddress() - Method in class ome.smuggler.config.data.DevMailConfigSource
-
- sysAdminAddress() - Method in class ome.smuggler.core.types.MailConfigReader
-
- sysAdminAddress() - Method in interface ome.smuggler.core.types.MailConfigSource
-
- sysAdminEmail() - Method in class ome.smuggler.core.service.imports.impl.ImportEnv
-
- SysPropKey - Static variable in class ome.smuggler.config.BaseConfigDir
-
- SysPropKey - Static variable in class ome.smuggler.config.BaseDataDir
-
- targetUri(String) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a URI from the target field in the import request.
- targetUri - Variable in class ome.smuggler.web.imports.ImportRequest
-
The URI of the file or directory containing the data to import.
- targetUri - Variable in class ome.smuggler.web.imports.ImportResponse
-
URI pointing to the data to import that was submitted in the
ImportRequest.
- TaskFileStore<T extends util.object.Identifiable> - Interface in ome.smuggler.core.service.file
-
Manages a directory containing files associated to Identifiable task
ID's.
- TaskFileStoreAdapter<T extends util.object.Identifiable> - Class in ome.smuggler.web
-
Provides the means to make the functionality of a
TaskFileStore
available to web clients.
- TaskFileStoreAdapter() - Constructor for class ome.smuggler.web.TaskFileStoreAdapter
-
- taskIdFromString() - Method in class ome.smuggler.web.imports.ImportFailureController
-
- taskIdFromString() - Method in class ome.smuggler.web.mail.MailFailureController
-
- taskIdFromString() - Method in class ome.smuggler.web.TaskFileStoreAdapter
-
- TaskIdPath - Class in ome.smuggler.core.types
-
A path which is the combination of a base path and a unique task identifier.
- TaskIdPath(Path, Identifiable) - Constructor for class ome.smuggler.core.types.TaskIdPath
-
Creates a new path by appending the given ID to the specified base path.
- TaskIdPathStore<T extends util.object.Identifiable> - Class in ome.smuggler.core.service.file.impl
-
- TaskIdPathStore(Path, Function<String, T>) - Constructor for class ome.smuggler.core.service.file.impl.TaskIdPathStore
-
Creates a new instance.
- text() - Method in class ome.smuggler.core.types.TextAnnotation
-
- TextAnnotation - Class in ome.smuggler.core.types
-
An OME textual annotation, i.e.
- TextAnnotation(Pair<String, String>) - Constructor for class ome.smuggler.core.types.TextAnnotation
-
- textAnnotation(String...) - Static method in class ome.smuggler.core.types.ValueParserFactory
-
Creates a text annotation from its string representation.
- textAnnotations - Variable in class ome.smuggler.web.imports.ImportRequest
-
Any optional image annotations to attach to the image being imported.
- toCommand(String) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- toDuration(Long) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- toDuration(Long, Duration) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- toDurationList(Long[]) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- tokens() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- toLocalPath(URI) - Method in class ome.smuggler.core.service.file.impl.RemotePathMapper
-
- toLocalPath(URI) - Method in interface ome.smuggler.core.service.file.RemotePathResolver
-
Resolves a remote path into a local one.
- toLocalPath(URI) - Method in class ome.smuggler.core.types.RemoteMount
-
Tries to translate a remote path into a local one using the remote and
local base paths of this instance.
- toPath(String) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- toPositiveN(Long, PositiveN) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- toString() - Method in class ome.smuggler.config.items.ArtemisPersistenceConfig
-
- toString() - Method in class ome.smuggler.config.items.CryptoConfig
-
- toString() - Method in class ome.smuggler.config.items.ImportConfig
-
- toString() - Method in class ome.smuggler.config.items.MailConfig
-
- toString() - Method in class ome.smuggler.config.items.MountPointsConfig.RemoteToLocalMapping
-
- toString() - Method in class ome.smuggler.config.items.MountPointsConfig
-
- toString() - Method in class ome.smuggler.config.items.UndertowConfig
-
- toString() - Method in class ome.smuggler.core.service.omero.impl.CloseCommandBuilder
-
- toString() - Method in class ome.smuggler.core.service.omero.impl.CreateCommandBuilder
-
- toString() - Method in class ome.smuggler.core.service.omero.impl.ImporterCommandBuilder
-
- toString() - Method in class ome.smuggler.core.service.omero.impl.KeepAliveCommandBuilder
-
- toString() - Method in class ome.smuggler.core.service.omero.impl.OmeCliCommandBuilder
-
- toString() - Method in class ome.smuggler.core.types.RemoteMount
-
- toString() - Method in class ome.smuggler.core.types.Schedule
-
- toURI(String, String, int) - Static method in class ome.smuggler.core.convert.RawConfigValues
-
- transfer(Path, Nat, OutputStream) - Static method in class ome.smuggler.core.io.FileOps
-
Efficiently copies an initial segment of a file into a target stream.
- transientError(Object, Throwable) - Method in class ome.smuggler.core.service.log.BaseLogger
-
Logs a warning containing a summary of the error and a debug message
with the entire exception's stack trace.
- transientError(Object, Optional<Throwable>...) - Method in class ome.smuggler.core.service.log.BaseLogger
-
Logs a warning containing a summary of the error and a debug message
with the entire exception's stack trace for each non-empty optional
in the list.
- transportProtocol() - Static method in class ome.smuggler.config.items.JavaMailConfigProps
-
- TSafeKeyValueStore<K extends util.object.Identifiable,V> - Class in ome.smuggler.core.service.file.impl
-
- TSafeKeyValueStore(KeyValueStore<K, V>, PositiveN) - Constructor for class ome.smuggler.core.service.file.impl.TSafeKeyValueStore
-
Creates a new instance to add thread-safety to the underlying
KeyValueStore.
- validate(String) - Method in class ome.smuggler.core.types.Email
-
- validate(ImportRequest) - Method in class ome.smuggler.web.imports.ImportRequestValidator
-
- validate(CreateSessionRequest) - Method in class ome.smuggler.web.omero.CreateSessionRequestValidator
-
- validator() - Static method in class ome.smuggler.core.types.Email
-
- ValueFilter<T> - Class in ome.smuggler.core.io
-
- ValueFilter(SourceReader<InputStream, T>, SinkWriter<T, OutputStream>, Function<T, T>) - Constructor for class ome.smuggler.core.io.ValueFilter
-
Creates a new instance.
- valueOf(String) - Static method in enum ome.smuggler.config.items.ActuatorEndPointName
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum ome.smuggler.config.items.LogLevel
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum ome.smuggler.core.io.crypto.CryptoAlgoSpec
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum ome.smuggler.core.msg.RepeatAction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum ome.smuggler.core.types.ImportFinalisationPhase
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum ome.smuggler.core.types.MailProtocol
-
Returns the enum constant of this type with the specified name.
- ValueParserFactory - Class in ome.smuggler.core.types
-
Methods to instantiate valid values of a certain type from their string
representation.
- ValueParserFactory() - Constructor for class ome.smuggler.core.types.ValueParserFactory
-
- values() - Static method in enum ome.smuggler.config.items.ActuatorEndPointName
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum ome.smuggler.config.items.LogLevel
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum ome.smuggler.core.io.crypto.CryptoAlgoSpec
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum ome.smuggler.core.msg.RepeatAction
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum ome.smuggler.core.types.ImportFinalisationPhase
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum ome.smuggler.core.types.MailProtocol
-
Returns an array containing the constants of this enum type, in
the order they are declared.