- AbstractActivity<ConfigType> - Class in org.apache.taverna.workflowmodel.processor.activity
-
Convenience abstract superclass for generic Activity instances.
- AbstractActivity() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- AbstractActivityEdit<T> - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a Activity instance.
- AbstractActivityEdit(Activity<T>) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
-
- AbstractAnnotatedThing<T> - Class in org.apache.taverna.annotation
-
Convenient abstract superclass for annotated things, manages edits.
- AbstractAnnotatedThing() - Constructor for class org.apache.taverna.annotation.AbstractAnnotatedThing
-
- AbstractAsynchronousActivity<ConfigType> - Class in org.apache.taverna.workflowmodel.processor.activity
-
Abstract superclass for asynchronous activities.
- AbstractAsynchronousActivity() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity
-
- AbstractCrystalizer - Class in org.apache.taverna.workflowmodel.impl
-
Receives Job and Completion events and emits Jobs unaltered.
- AbstractCrystalizer() - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer
-
- AbstractCrystalizer.CompletionAwareTreeCache - Class in org.apache.taverna.workflowmodel.impl
-
- AbstractDataflowEdit - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a Dataflow instance.
- AbstractDataflowEdit(Dataflow) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
-
- AbstractDataflowInputPortEdit - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a DataflowInputPort instance.
- AbstractDataflowInputPortEdit(DataflowInputPort) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
-
- AbstractDataflowOutputPortEdit - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a DataflowOutputPort instance.
- AbstractDataflowOutputPortEdit(DataflowOutputPort) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
-
- AbstractDatalinkEdit - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a Datalink instance.
- AbstractDatalinkEdit(Datalink) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
-
- AbstractDispatchEvent<EventType extends AbstractDispatchEvent<EventType>> - Class in org.apache.taverna.workflowmodel.processor.dispatch.events
-
Superclass of events within the dispatch stack
- AbstractDispatchEvent(String, int[], InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.events.AbstractDispatchEvent
-
- AbstractDispatchLayer<ConfigurationType> - Class in org.apache.taverna.workflowmodel.processor.dispatch
-
Convenience abstract implementation of DispatchLayer
- AbstractDispatchLayer() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- AbstractDispatchLayerEdit - Class in org.apache.taverna.workflowmodel.processor.dispatch.impl
-
Abstraction of an edit acting on a DispatchLayer instance.
- AbstractDispatchLayerEdit(DispatchStack) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
-
- AbstractEntityImpl - Class in org.apache.taverna.reference.impl
-
Abstract superclass of ReferenceSetImpl, IdentifiedArrayList and
ErrorDocumentImpl, manages the T2Reference field for these types and their
hibernate backing.
- AbstractEntityImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractEntityImpl
-
- AbstractErrorDocumentServiceImpl - Class in org.apache.taverna.reference.impl
-
Abstract implementation of ErrorDocumentService, inject with an appropriate
ErrorDocumentDao and T2ReferenceGenerator to enable.
- AbstractErrorDocumentServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
- AbstractErrorHandlerLayer<ConfigurationType> - Class in org.apache.taverna.workflowmodel.processor.dispatch
-
Superclass of error handling dispatch layers (for example retry and
failover).
- AbstractErrorHandlerLayer() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
- AbstractErrorHandlerLayer.JobState - Class in org.apache.taverna.workflowmodel.processor.dispatch
-
Abstract superclass of all state models for pending failure handlers.
- AbstractEventHandlingInputPort - Class in org.apache.taverna.workflowmodel.impl
-
Extends AbstractPort with the getIncomingLink method and an additional
implementation method to set the incoming data link
- AbstractEventHandlingInputPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
-
- AbstractExecution - Class in org.apache.taverna.platform.execution.api
-
- AbstractExecution(WorkflowBundle, Workflow, Profile, Bundle) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecution
-
Constructs an abstract implementation of an Execution.
- AbstractExecutionEnvironment - Class in org.apache.taverna.platform.execution.api
-
A common super type for concrete implementations of ExecutionEnvironment
s.
- AbstractExecutionEnvironment(String, String, String, ExecutionService) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
-
- AbstractExecutionService - Class in org.apache.taverna.platform.execution.api
-
A common super type for concrete implementations of ExecutionService
s.
- AbstractExecutionService(String, String, String) - Constructor for class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- AbstractExternalReference - Class in org.apache.taverna.reference
-
A trivial implementation of ExternalReference.
- AbstractExternalReference() - Constructor for class org.apache.taverna.reference.AbstractExternalReference
-
- AbstractFilteringInputPort - Class in org.apache.taverna.workflowmodel.impl
-
Abstract superclass for filtering input ports, extend and implement the
pushXXX methods to configure behaviour
- AbstractFilteringInputPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
-
- AbstractIterationStrategyNode - Class in org.apache.taverna.workflowmodel.processor.iteration
-
Abstract superclass for implementations of IterationStrategyNode, adds logic
to connect nodes together and convenience methods to push jobs and completion
events up to the parent node.
- AbstractIterationStrategyNode() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
- AbstractListServiceImpl - Class in org.apache.taverna.reference.impl
-
Abstract implementation of ListService, inject with an appropriate ListDao
and T2ReferenceGenerator to enable.
- AbstractListServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
- AbstractMergeEdit - Class in org.apache.taverna.workflowmodel.impl
-
- AbstractMergeEdit(Merge) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
-
- AbstractNumericRangeAssertion<NumericType extends Number> - Class in org.apache.taverna.annotation.annotationbeans
-
Generic annotation containing a pair of numeric values with precision
determined by the type parameter which form a bound.
- AbstractNumericRangeAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
-
Default constructor as mandated by java bean specification
- AbstractNumericValueAssertion<NumericType extends Number> - Class in org.apache.taverna.annotation.annotationbeans
-
Generic annotation containing a single number of precision specified by the
type variable
- AbstractNumericValueAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion
-
Default constructor as mandated by java bean specification
- AbstractOutputPort - Class in org.apache.taverna.workflowmodel
-
Simple implementation of OutputPort, extends AbstractPort and adds the
granular depth bean getter.
- AbstractOutputPort(String, int, int) - Constructor for class org.apache.taverna.workflowmodel.AbstractOutputPort
-
- AbstractPort - Class in org.apache.taverna.workflowmodel
-
Port definition with depth and name
- AbstractPort(String, int) - Constructor for class org.apache.taverna.workflowmodel.AbstractPort
-
- AbstractProcessorEdit - Class in org.apache.taverna.workflowmodel.impl
-
Abstraction of an edit acting on a Processor instance.
- AbstractProcessorEdit(Processor) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
-
- AbstractProvenanceItem - Class in org.apache.taverna.provenance.item
-
- AbstractProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- AbstractReferenceServiceImpl - Class in org.apache.taverna.reference.impl
-
Implementation of ReferenceService, inject with ReferenceSetService,
ErrorDocumentService and ListService to enable.
- AbstractReferenceServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- AbstractReferenceSetServiceImpl - Class in org.apache.taverna.reference.impl
-
Abstract implementation of ReferenceSetService, inject with an appropriate
ReferenceSetDao to enable.
- AbstractReferenceSetServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
- AbstractServiceImpl - Class in org.apache.taverna.reference.impl
-
Abstract superclass for all service implementation objects, will be used to
allow injection of thread pooling logic as and when we implement it.
- AbstractServiceImpl() - Constructor for class org.apache.taverna.reference.impl.AbstractServiceImpl
-
- AbstractT2ReferenceGenerator - Class in org.apache.taverna.reference.impl
-
- AbstractT2ReferenceGenerator() - Constructor for class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
-
- AbstractTextualValueAssertion - Class in org.apache.taverna.annotation.annotationbeans
-
Generic bit of free text that can be stuck to anything, subclass for more
specific uses
- AbstractTextualValueAssertion() - Constructor for class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion
-
Default constructor as mandated by java bean specification
- Activity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity
-
Defines a single abstract or concrete invokable activity.
- activity - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- ActivityAndBeanWrapper - Class in org.apache.taverna.workflowmodel.processor.activity
-
Used when dragging activities from the palette onto "something".
- ActivityAndBeanWrapper() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- ActivityConfigurationException - Exception in org.apache.taverna.platform.capability.api
-
Thrown when an activity's configuration is incorrect.
- ActivityConfigurationException() - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
-
- ActivityConfigurationException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
-
- ActivityConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
-
- ActivityConfigurationException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityConfigurationException
-
- ActivityConfigurationException - Exception in org.apache.taverna.workflowmodel.processor.activity
-
Thrown when attempting to configure an Activity instance with an invalid
configuration.
- ActivityConfigurationException(String) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
-
- ActivityConfigurationException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
-
- ActivityConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException
-
- activityExists(URI) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- activityExists(URI) - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns true if and only if the activity type exists.
- activityExists(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns true iff an activity exists for the specified URI in this ExecutionEnvironment.
- activityExists(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
-
- ActivityFactory - Interface in org.apache.taverna.workflowmodel.processor.activity
-
Factory for creating
Activity
instances.
- ActivityInputPort - Interface in org.apache.taverna.workflowmodel.processor.activity
-
Specialisation of InputPort to capture the extra information required by
Activity instances.
- ActivityInputPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config
-
A bean that describes properties of an Input port.
- ActivityInputPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- ActivityInputPortImpl - Class in org.apache.taverna.workflowmodel.processor.activity.impl
-
An input port on an Activity instance.
- ActivityInputPortImpl(String, int) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
-
Constructs an Activity input port instance with the provided name and
depth.
- ActivityInputPortImpl(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
-
Constructs an Activity input port with the provided name and depth,
together with a list of predetermined annotations.
- ActivityInvoker - Class in org.apache.taverna.activities.testutils
-
Helper class to facilitate in executing Activities in isolation.
- ActivityInvoker() - Constructor for class org.apache.taverna.activities.testutils.ActivityInvoker
-
- activityList - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- ActivityNotFoundException - Exception in org.apache.taverna.platform.capability.api
-
Thrown when an activity is not found.
- ActivityNotFoundException() - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
-
- ActivityNotFoundException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
-
- ActivityNotFoundException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
-
- ActivityNotFoundException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ActivityNotFoundException
-
- ActivityOutputPort - Interface in org.apache.taverna.workflowmodel.processor.activity
-
- ActivityOutputPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config
-
A bean that describes properties of an Output port.
- ActivityOutputPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
-
- ActivityOutputPortImpl - Class in org.apache.taverna.workflowmodel.processor.activity.impl
-
An output port on an Activity instance, used as a bean to hold port name,
depth and granular depth properties.
- ActivityOutputPortImpl(String, int, int) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityOutputPortImpl
-
Constructs an Activity output port instance with the provided name,depth
and granular depth.
- ActivityOutputPortImpl(String, int, int, Set<AnnotationChain>) - Constructor for class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityOutputPortImpl
-
Constructs an Activity input port with the provided name, depth and
granularDepth together with a list of predetermined annotations.
- ActivityPort - Interface in org.apache.taverna.workflowmodel.processor.activity
-
The input or output port of an
Activity
.
- ActivityPortDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config
-
A generic bean that describes the shared properties of input and output
ports.
- ActivityPortDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- ActivityPortsDefinitionBean - Class in org.apache.taverna.workflowmodel.processor.activity.config
-
Defines a configuration type that relates directly to an
Activity
and
in particular defines details its input and output ports.
An Activity that has its ports implicitly defined may define a ConfigType
that extends this class, but this is not enforced.
- ActivityPortsDefinitionBean() - Constructor for class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
-
- ActivityProvenanceItem - Class in org.apache.taverna.provenance.item
-
Contains details for an enacted Activity.
- ActivityProvenanceItem() - Constructor for class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- ActivityReport - Class in org.apache.taverna.platform.report
-
- ActivityReport(Activity) - Constructor for class org.apache.taverna.platform.report.ActivityReport
-
Constructs a new ActivityReport
.
- ActivityService - Interface in org.apache.taverna.platform.capability.api
-
Service for discovering available activities and the properties required to
configure the activities.
- ActivityServiceImpl - Class in org.apache.taverna.platform.capability.activity.impl
-
- ActivityServiceImpl() - Constructor for class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- ActivityTypeNotFoundException - Exception in org.apache.taverna.services
-
Thrown when an activity type is not found.
- ActivityTypeNotFoundException() - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
-
- ActivityTypeNotFoundException(String) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
-
- ActivityTypeNotFoundException(String, Throwable) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
-
- ActivityTypeNotFoundException(Throwable) - Constructor for exception org.apache.taverna.services.ActivityTypeNotFoundException
-
- add(T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- add(int, T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- addActivityReport(ActivityReport) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
- addAll(Collection<? extends T>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- addAll(int, Collection<? extends T>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- addAnnotation(Annotated<?>, AnnotationBeanSPI, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- addAnnotationAssertion(AnnotationAssertion<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl
-
Add an annotation to the chain Added because without the edits stuff how
else can we do it?
- addCreator(Person) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- addCurationEvent(CurationEvent<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- addDataflowIdentification(Dataflow, String, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Add the identification of a Dataflow into its identification annotation
chain (if necessary)
- addEntity(Object) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
-
- addEntity(Object) - Method in class org.apache.taverna.reference.impl.EmptyReferenceContext
-
- addEntity(Object) - Method in interface org.apache.taverna.reference.ReferenceContext
-
Add an entity to the context.
- addFacadeListener(FacadeListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- addFacadeListener(FacadeListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
A failure listener reports on overall workflow failure.
- addFragmentedURI(LinkedHashSet<URI>, URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- addInput(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
Creates and adds a new input port with the provided properties.
- addInput(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- addInputPort(DataflowInputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Adds an input port to the DataFlow.
- addInputPortDirectory(Path) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
-
- addInvocation(Invocation) - Method in class org.apache.taverna.platform.report.StatusReport
-
- addIterable(Iterable<E>) - Method in class org.pingel.util.CrossProduct
-
- addJobToStateList(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
- addKeyPair(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Insert a new key entry containing private key and the corresponding
public key certificate chain in the Keystore.
- addKeyPair(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Insert a new key entry containing private key and the corresponding
public key certificate chain in the Keystore.
- addLayer(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
- addLayer(DispatchLayer<?>, int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
- addMerge(MergeImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Adds a processor on the DataFlow.
- addMonitorableProperty(MonitorableProperty<?>) - Method in interface org.apache.taverna.monitor.MonitorNode
-
Properties can be added to the monitor node after creation if required,
although this should be used only when necessary to avoid race conditions
- addObserver(Observer<Message>) - Method in class org.apache.taverna.lang.observer.MultiCaster
-
Register an observer ie.
- addObserver(Observer<Message>) - Method in interface org.apache.taverna.lang.observer.Observable
-
- addObserver(Observer<MonitorManager.MonitorMessage>) - Method in class org.apache.taverna.monitor.MonitorManager
-
- addObserver(Observer<KeystoreChangedEvent>) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Add an observer of the changes to the Keystore or Truststore.
- addObserver(Observer<KeystoreChangedEvent>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Add an observer of the changes to the Keystore or Truststore.
- addObserver(Observer<ProcessorFinishedEvent>) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- addOutgoingLink(DatalinkImpl) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
- addOutput(String, int, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
Creates and adds a new output port with the provided properties.
- addOutput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
Convenience method, creates a new output port with depth and granular
depth both set to the value for depth, i.e.
- addOutputPort(DataflowOutputPortImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Adds an output port to the DataFlow.
- addProcessor(ProcessorImpl) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Adds a processor on the DataFlow.
- addProcessorReport(ProcessorReport) - Method in class org.apache.taverna.platform.report.WorkflowReport
-
- addProperties(Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- AddPropertiesMessage(String[], Set<MonitorableProperty<?>>) - Constructor for class org.apache.taverna.monitor.MonitorManager.AddPropertiesMessage
-
- addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Inject properties into an existing node
- addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager
-
Push new property get / set methods into the specified node.
- addPropertiesToNode(String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
-
- addProvenanceItem(ProvenanceItem) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
- addProxyInput(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity
-
Add an input to the NonExecutableActivity with the specified name.
- addProxyInput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity
-
Add an input to the NonExecutableActivity with the specified name and
depth.
- addProxyOutput(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity
-
Add an output to the NonExecutableActivity with the specified name
- addProxyOutput(String, int) - Method in class org.apache.taverna.workflowmodel.processor.activity.NonExecutableActivity
-
Add an output to the NonExecutableActivity with the specified name and
depth
- addReportListener(ReportListener) - Method in class org.apache.taverna.platform.report.StatusReport
-
- addResultListener(ResultListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- addResultListener(ResultListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
The result listener is used to handle data tokens produced by the
workflow.
- addResultListener(ResultListener) - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort
-
Add a ResultListener, capable of listening to results being received by
the output port
- addStrategy(IterationStrategy) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- addTreeModelListener(TypedTreeModelListener<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Adds a listener for the TreeModelEvent posted after the tree changes.
- addTrustedCertificate(X509Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Insert a trusted certificate entry in the Truststore with an alias
constructed as:
"trustedcert#"#""#
"
- addTrustedCertificate(X509Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Insert a trusted certificate entry in the Truststore with an alias
constructed as:
"trustedcert#"#""#
"
- addUsernameAndPasswordForService(UsernamePassword, URI) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Insert a username and password pair for the given service URI in the
Keystore.
- addUsernameAndPasswordForService(UsernamePassword, URI) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Insert a username and password pair for the given service URI in the
Keystore.
- allowsLiteralValues() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort
-
Literal values are a special case as they are not represented by
reference schemes - in rare cases activities may choose to deny literal
values, forcing *all* their inputs to be in a particular reference
scheme.
- allowsLiteralValues() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
-
- Annotated<TargetType> - Interface in org.apache.taverna.annotation
-
Denotes that the object carries workflow object level annotation.
- AnnotationAssertion<AnnotationBeanType extends AnnotationBeanSPI> - Interface in org.apache.taverna.annotation
-
Represents a single assertion of information, providing access to a bean
containing the information in the assertion and one specifying the source of
the information contained.
- AnnotationAssertionImpl - Class in org.apache.taverna.annotation.impl
-
- AnnotationAssertionImpl() - Constructor for class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- AnnotationAssertionImpl(AnnotationBeanSPI, AnnotationRole, List<Person>, AnnotationSourceSPI) - Constructor for class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- AnnotationBeanSPI - Interface in org.apache.taverna.annotation
-
Marker interface to denote that a bean class is a container for the
information encapsulated by an InformationAssertion object
- AnnotationChain - Interface in org.apache.taverna.annotation
-
A fact about an annotated entity is expressed in terms of an annotation
chain.
- AnnotationChainImpl - Class in org.apache.taverna.annotation.impl
-
- AnnotationChainImpl() - Constructor for class org.apache.taverna.annotation.impl.AnnotationChainImpl
-
- AnnotationPerspective - Interface in org.apache.taverna.annotation
-
Responsible for the interpretation of an AnnotationChain (which may contain
conflicting or disputed information) into a set of AnnotationAssertion
instances from that chain which are valid given the chain and some
interpretation rule.
- AnnotationRole - Enum in org.apache.taverna.annotation
-
Specifies the role of an AnnotationAssertion within an AnnotationChain
- AnnotationSourceSPI - Interface in org.apache.taverna.annotation
-
A marker interface that specified that the implementation is a bean
containing information about a source of annotations.
- AnnotationTools - Class in org.apache.taverna.workflowmodel.utils
-
- AnnotationTools() - Constructor for class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- AppliesTo - Annotation Type in org.apache.taverna.annotation
-
Annotation to be used on metadata objects to denote which workflow objects
they apply to
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
-
- applyEdit() - Method in class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
-
- AsynchronousActivity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity
-
A concrete invokable activity with an asynchronous invocation API and no
knowledge of invocation context.
- AsynchronousActivityCallback - Interface in org.apache.taverna.workflowmodel.processor.activity
-
The callback interface used by instances of AsynchronousActivity to push
results and failure messages back to the invocation layer.
- augmentationCompleted(Set<ExternalReferenceSPI>) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentorCallback
-
Called when the augmentation has succeeded
- augmentationFailed(ReferenceSetAugmentationException) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentorCallback
-
Called when the augmentation has failed for some reason
- augmentReferenceSet(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
-
- augmentReferenceSet(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentor
-
Attempts to modify the supplied ReferenceSet such that it contains an
implementation of at least one of the ExternalReferenceSPI classes
specified.
- augmentReferenceSetAsynch(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetAugmentorCallback) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
-
- augmentReferenceSetAsynch(ReferenceSet, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetAugmentorCallback) - Method in interface org.apache.taverna.reference.ReferenceSetAugmentor
-
- Author - Class in org.apache.taverna.annotation.annotationbeans
-
The name of an author of a dataflow held as a String
It should allow many but currently only allows one
- Author() - Constructor for class org.apache.taverna.annotation.annotationbeans.Author
-
Default constructor as mandated by java bean specification
- CacheAspect - Class in org.apache.taverna.reference.impl
-
An aspect used to intercept calls to the various data access objects and
divert through a write-through cache provider
- CacheAspect() - Constructor for class org.apache.taverna.reference.impl.CacheAspect
-
- cacheSize() - Method in class org.apache.taverna.reference.impl.WriteQueueAspect
-
- cancel(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- cancel() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Cancels the execution.
- cancel(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Cancels the execution of a workflow.
- cancel() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- cancel() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- cancel(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Cancels a running or paused run.
- cancel() - Method in class org.apache.taverna.platform.run.impl.Run
-
- cancel(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- cancelWorkflow(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
Cancel the workflow run with the specified id
- cancelWorkflowRun() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- cancelWorkflowRun() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Cancel the workflow run corresponding to this facade
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.file.FileToFileReference
-
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.http.UrlToHttpReference
-
Can convert if the object is an instance of java.net.URL and the protocol
is HTTP
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.BooleanToStringReference
-
Can convert if the object is an instance of java.lang.Boolean
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference
-
Can convert if the object is an instance of byte[]
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.CharacterToStringReference
-
Can convert if the object is an instance of java.lang.Character
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.NumberToStringReference
-
Can convert if the object is an instance of java.lang.Number
- canConvert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.StringToStringReference
-
Can convert if the object is an instance of java.lang.String
- canConvert(Object, ReferenceContext) - Method in interface org.apache.taverna.reference.ValueToReferenceConverterSPI
-
Can this SPI implementation convert the specified object to an
ExternalReferenceSPI? This test should be as lightweight as possible, and
will usually be based on the Class of the object supplied.
- canVisit(Object) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityHealthChecker
-
- canVisit(Object) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
-
- canVisit(Object) - Method in interface org.apache.taverna.visit.Visitor
-
Returns true if the visitor can visit the specified object.
- canVisit(Object) - Method in class org.apache.taverna.workflowmodel.health.DisabledActivityHealthChecker
-
The visitor can visit DisabledActivitys.
- canVisit(Object) - Method in class org.apache.taverna.workflowmodel.health.UnrecognizedActivityHealthChecker
-
- CERTIFICATES_REVOKED_INDICATOR_FILE_NAME - Static variable in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
- changeMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Change the Keystore and the Truststore's master password to the one
provided.
- changeMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Change the Keystore and the Truststore's master password to the one
provided.
- CharacterToStringReference - Class in org.apache.taverna.reference.impl.external.object
-
- CharacterToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.CharacterToStringReference
-
- checkAugmentor() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Check that the reference set augmentor is configured
- checkConverterRegistry() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Check whether the converter registry has been defined, throw a
ReferenceServiceException if not
- checkDao() - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
Check that the list dao is configured
- checkDao() - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
Check that the list dao is configured
- checkDao() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Check that the reference set dao is configured
- checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
Check that the t2reference generator is configured
- checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
Check that the t2reference generator is configured
- checkGenerator() - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Check that the t2reference generator is configured
- checkServices() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Throw a ReferenceServiceException if methods in ReferenceService are
called without the necessary sub-services configured.
- checkValidity() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Triggers a check for various basic potential problems with the workflow,
in particular ones related to type checking.
- checkValidity() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Run the type check algorithm and return a report on any problems found.
- checkValidityImpl() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Works out whether a dataflow is valid.
- checkWorkflowFinished(WorkflowInstanceFacadeImpl.WorkflowInstanceFacadeChange) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- childAt(int) - Method in class org.apache.taverna.invocation.TreeCache.NamedNode
-
- childIndices - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
-
- children - Variable in class org.apache.taverna.invocation.TreeCache.NamedNode
-
- children - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
-
- children() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- children() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
Specialised return type of TreeNode#children()
- cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
-
Called after a final completion event has been emited for a given owning
process, should be used by subclasses to do any tidying required,
removing state etc.
- cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
-
- cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
-
- cleanUp(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.PrefixDotProduct
-
- CLEANUP_DELAY_MS - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- cleanupTimer - Static variable in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- clear() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- clear() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Clear the child list and parent of this node
- clear() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- clear() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
Remove all children nodes and set the parent to null
.
- clearCachedEndpointStatus() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
Clear the cached endpoint statuses.
- ClearCachedServiceURIsObserver() - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl.ClearCachedServiceURIsObserver
-
- clone() - Method in class org.apache.taverna.reference.AbstractExternalReference
-
- clone() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
-
- clone() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- clone() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
- clone() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- clone() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
- clone() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
- clone() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- clone() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
- clone() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
- clone() - Method in class org.apache.taverna.t2referencetest.RedReference
-
- clone() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
- clone() - Method in class org.apache.taverna.visit.VisitReport
-
- clone() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- close() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
-
- close() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
-
- close(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Closes a run.
- close(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- CMException - Exception in org.apache.taverna.security.credentialmanager
-
Represents a (cryptographic or any other) exception thrown by Credential
Manager.
- CMException() - Constructor for exception org.apache.taverna.security.credentialmanager.CMException
-
Creates a new CMException.
- CMException(String) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException
-
Creates a new CMException with the specified message.
- CMException(String, Throwable) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException
-
Creates a new CMException with the specified message and cause.
- CMException(Throwable) - Constructor for exception org.apache.taverna.security.credentialmanager.CMException
-
Creates a new CMException with the specified cause throwable.
- CMNotInitialisedException - Exception in org.apache.taverna.security.credentialmanager
-
Represents an exception thrown by Credential Manager if an application tries
to invoke certain methods on it before it has been initialised.
- CMNotInitialisedException() - Constructor for exception org.apache.taverna.security.credentialmanager.CMNotInitialisedException
-
Creates a new CMNotInitialisedException.
- CMNotInitialisedException(String) - Constructor for exception org.apache.taverna.security.credentialmanager.CMNotInitialisedException
-
Creates a new CMNotInitialisedException with the specified message.
- compare(MasterPasswordProvider, MasterPasswordProvider) - Method in class org.apache.taverna.security.credentialmanager.MasterPasswordProvider.ProviderComparator
-
- compare(NamedWorkflowEntity, NamedWorkflowEntity) - Method in class org.apache.taverna.workflowmodel.utils.NamedWorkflowEntityComparator
-
- compare(Port, Port) - Method in class org.apache.taverna.workflowmodel.utils.PortComparator
-
- compareTo(Invocation) - Method in class org.apache.taverna.platform.report.Invocation
-
- compareTo(TranslationPath) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
Order by total path cost
- Completion - Class in org.apache.taverna.invocation
-
Contains a (possibly partial) completion event.
- Completion(String, int[], InvocationContext) - Constructor for class org.apache.taverna.invocation.Completion
-
Construct a new optionally partial completion event with the specified
owner and completion index
- Completion(String, InvocationContext) - Constructor for class org.apache.taverna.invocation.Completion
-
Construct a new final completion event, equivalent to calling new
Completion(owningProcess, new int[0]);
- CompletionAwareTreeCache(String, InvocationContext) - Constructor for class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer.CompletionAwareTreeCache
-
- completionCreated(Completion) - Method in interface org.apache.taverna.workflowmodel.impl.Crystalizer
-
Called whenever a completion not corresponding to a node in the cache is
generated.
- completionCreated(Completion) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl
-
- CompletionHandlingAbstractIterationStrategyNode - Class in org.apache.taverna.workflowmodel.processor.iteration
-
A superclass for all iteration strategy nodes which are required to propagate
final completion events formed from multiple inputs.
- CompletionHandlingAbstractIterationStrategyNode() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
-
- CompletionHandlingAbstractIterationStrategyNode.CompletionState - Class in org.apache.taverna.workflowmodel.processor.iteration
-
Container class for the state of completion for a given process
identifier
- CompletionState(int) - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState
-
- CompoundEdit - Class in org.apache.taverna.workflowmodel
-
Implementation of Edit which contains an ordered list of child edits.
- CompoundEdit() - Constructor for class org.apache.taverna.workflowmodel.CompoundEdit
-
Create a new compound edit with no existing Edit objects.
- CompoundEdit(List<Edit<?>>) - Constructor for class org.apache.taverna.workflowmodel.CompoundEdit
-
Create a new compound edit with the specified edits as children.
- Condition - Interface in org.apache.taverna.workflowmodel
-
Defines the base interface for a condition which must be satisfied before a
processor can commence invocation.
- ConditionCallBack(String) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- conditions - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- conditionsSatisfied(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
Called to determine whether all the preconditions for this dispatch stack
are satisfied.
- Configurable<ConfigurationType> - Interface in org.apache.taverna.workflowmodel
-
Interface for workflow items that can be configured from a bean.
- ConfigurationBean - Annotation Type in org.apache.taverna.workflowmodel.processor.config
-
- ConfigurationException - Exception in org.apache.taverna.platform.capability.api
-
- ConfigurationException() - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
-
- ConfigurationException(String) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
-
- ConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
-
- ConfigurationException(Throwable) - Constructor for exception org.apache.taverna.platform.capability.api.ConfigurationException
-
- ConfigurationException - Exception in org.apache.taverna.workflowmodel
-
Thrown when attempting to configure a
Configurable
with an invalid
configuration.
- ConfigurationException() - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
- ConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
- ConfigurationException(String) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
- ConfigurationException(Throwable) - Constructor for exception org.apache.taverna.workflowmodel.ConfigurationException
- ConfigurationProperty - Annotation Type in org.apache.taverna.workflowmodel.processor.config
-
- ConfigurationProperty.OrderPolicy - Enum in org.apache.taverna.workflowmodel.processor.config
-
- configurationWouldWork() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- configurationWouldWork(Object) - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- configure(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
-
- configure(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
-
- configure(ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.Configurable
-
When the item is built from the workflow definition XML the object is
first constructed with a default constructor then this method is called,
passing in the configuration bean returned by getConfiguration().
- configure(ConfigType) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- configure(ConfigType) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity
-
Called immediately after object construction by the deserialisation
framework with a configuration bean built from the auto-generated XML.
- configure(ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
- configure(ActivityAndBeanWrapper) - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- configure(Element) - Method in class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
-
- configure(Object) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
-
- configure(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
-
- configure(JsonNode) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
- configureFromXML(Element) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
Configure from an XML element
- configurePorts(ActivityPortsDefinitionBean) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- confirmMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Checks if Keystore's master password is the same as the one provided.
- confirmMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Checks if Keystore's master password is the same as the one provided.
- connectDefault(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
Connect up a new named input port node to the first child of the terminal
node.
- CONNECTION_PROBLEM - Static variable in class org.apache.taverna.workflowmodel.health.HealthCheck
-
- CONNECTOR_DERBY - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- CONNECTOR_MYSQL - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- CONNECTOR_TYPE - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- contactEndpoint(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
Try to contact the specified endpoint as part of the health-checking of
the Activity.
- contains(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- containsAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- containsErrors() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Return whether the identified entity either is or contains errors
- containsErrors() - Method in interface org.apache.taverna.reference.T2Reference
-
Error documents always return true, as do any lists where at least one
immediate child of the list returns true when this property is evaluated.
- containsLocation(int[]) - Method in class org.apache.taverna.invocation.TreeCache
-
Does the location exist?
- containsNestedWorkflow(Processor) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Returns true if processor contains a nested workflow.
- contents - Variable in class org.apache.taverna.invocation.TreeCache.NamedNode
-
- context - Variable in class org.apache.taverna.invocation.Event
-
- ContextualizedT2Reference - Interface in org.apache.taverna.reference
-
- ContextualizedT2ReferenceImpl - Class in org.apache.taverna.reference.impl
-
Simple implementation of ContextualizedT2Reference
- ContextualizedT2ReferenceImpl(T2Reference, int[]) - Constructor for class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
-
- ControlBoundary - Annotation Type in org.apache.taverna.workflowmodel
-
Denotes that the associated type creates a boundary of control within the
dataflow.
- controlledConditions - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.file.FileToFileReference
-
Return a FileReference
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.http.UrlToHttpReference
-
Return a new HttpReference constructed from
((URL)o).toExternalForm()
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.BooleanToStringReference
-
Return a new InlineStringReference wrapping the supplied String
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.ByteArrayToByteArrayReference
-
Return a new InlineByteArrayReference wrapping the supplied byte[]
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.CharacterToStringReference
-
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.NumberToStringReference
-
Return a new InlineStringReference wrapping the supplied String
- convert(Object, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.StringToStringReference
-
Return a new InlineStringReference wrapping the supplied String
- convert(Object, ReferenceContext) - Method in interface org.apache.taverna.reference.ValueToReferenceConverterSPI
-
Construct and return a new ExternalReferenceSPI implementation which is
in some way equivalent to the supplied object.
- convertCertificate(Certificate) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
-
Convert the certificate object into an X509Certificate object.
- convertCertificate(Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
- converters - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- convertPathToObject(Path) - Static method in class org.apache.taverna.platform.execution.impl.local.T2ReferenceConverter
-
- convertReferenceToPath(Path, T2Reference, InvocationContext) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
-
- CoreDispatchLayerFactory - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
-
Factory for creating core dispatch layers.
- CoreDispatchLayerFactory() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
-
- createActivity() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- createActivity() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- createActivity(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- createActivity(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns the activity for the specified activity type.
- createActivity() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory
-
Creates a new Activity
instance.
- createActivityInputPort(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds an instance of an
InputPort
for an Activity.
- createActivityInputPort(String, int, boolean, List<Class<? extends ExternalReferenceSPI>>, Class<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createActivityOutputPort(String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- createActivityOutputPort(String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- createActivityReport(Activity) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- createAnnotationChain() - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new AnnotationChain.
- createAnnotationChain() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- createDataflow() - Method in interface org.apache.taverna.workflowmodel.Edits
-
Build a new Dataflow workflow
- createDataflow() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createDataflowInputPort(String, int, int, Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new DataflowInputPort.
- createDataflowInputPort(String, int, int, Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createDataflowOutputPort(String, Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new DataflowOutputPort.
- createDataflowOutputPort(String, Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createDatalink(EventForwardingOutputPort, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new Datalink with the given source and sink ports
- createDatalink(EventForwardingOutputPort, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createDispatchLayer(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService
-
Returns the dispatch layer for the specified URI.
- createDispatchLayer(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
-
- createDispatchLayer(URI) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory
-
- createDispatchLayer(URI) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
-
- createExecution(ExecutionEnvironment, WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- createExecution(ExecutionEnvironment, WorkflowBundle, Workflow, Profile, Bundle) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Creates a workflow execution and returns its ID.
- createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
Creates an implementation of an Execution.
- createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
- createExecutionImpl(WorkflowBundle, Workflow, Profile, Bundle) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
-
- createInputPort(String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Build a new dataflow input port, the granular depth is set for the input
port so it can be copied onto the internal output port
- createIterationStrategy() - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new instance of a IterationStrategy.
- createIterationStrategy() - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createKeyPairAlias(Key, Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Create a Keystore alias that would be used for adding the given key pair
(private and public key) entry to the Keystore.
- createKeyPairAlias(Key, Certificate[]) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Create a Keystore alias that would be used for adding the given key pair
(private and public key) entry to the Keystore.
- createMerge(Dataflow) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- createMerge(Dataflow) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
Creates a MergeImpl instance.
- createMergeInputPort(Merge, String, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new MergeOutputPort.
- createMergeInputPort(Merge, String, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createOutputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Create and return a new DataflowOutputPort in this dataflow
- createProcessor(String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Builds a new instance of a Processor with the given name.
- createProcessor(String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createProcessorInputPort(Processor, String, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Creates a new ProcessorInputPort
- createProcessorInputPort(Processor, String, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createProcessorOutputPort(Processor, String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Creates a new ProcessorOutputPort
- createProcessorOutputPort(Processor, String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- createProcessorReport(Processor) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
-
- createRecordReader(InputSplit, TaskAttemptContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputFormat
-
- createReference(InputStream, ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI
-
Given a stream of bytes, build the appropriate target
ExternalReferenceSPI implementation which would de-reference to the value
of that stream and return it.
- createReference(SourceType, ReferenceContext) - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI
-
Given an existing ExternalReferenceSPI, build the appropriate target
ExternalReferenceSPI implementation and return it.
- createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
-
- createReference(InlineByteArrayReference, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
-
- createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
-
- createReference(InlineStringReference, ReferenceContext) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
-
- createReference(InputStream, ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenBuilder
-
Construct a new GreenReference from the given input stream, ignoring the
otherwise helpful context as we don't need any resources from it.
- createReference(GreenReference, ReferenceContext) - Method in class org.apache.taverna.t2referencetest.GreenToRed
-
- createRun(RunProfile) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Creates a new run and returns the ID for the run.
- createRun(RunProfile) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- createTrustedCertificateAlias(X509Certificate) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Create a Truststore alias that would be used for adding the given trusted
X509 certificate to the Truststore.
- createTrustedCertificateAlias(X509Certificate) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Create a Truststore alias that would be used for adding the given trusted
X509 certificate to the Truststore.
- createWorkflowInstanceFacade(Dataflow, InvocationContext, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Build a new WorkflowInstanceFacade using the supplied Dataflow
- createWorkflowInstanceFacade(Dataflow, InvocationContext, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- createWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- CredentialManager - Interface in org.apache.taverna.security.credentialmanager
-
Provides a wrapper for Taverna's Keystore and Truststore and implements
methods for managing user's credentials (passwords, private/proxy key pairs)
and credentials of trusted services and CAs' (i.e.
- CredentialManager.KeystoreType - Enum in org.apache.taverna.security.credentialmanager
-
- CredentialManagerAuthenticator - Class in org.apache.taverna.security.credentialmanager.impl
-
- CredentialManagerAuthenticator(CredentialManager) - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
-
- CredentialManagerImpl - Class in org.apache.taverna.security.credentialmanager.impl
-
Provides an implementation of #CredentialManagerService
.
- CredentialManagerImpl() - Constructor for class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- CredentialManagerImpl.ClearCachedServiceURIsObserver - Class in org.apache.taverna.security.credentialmanager.impl
-
Clear the cached service URIs that have username and password associated
with them.
- CredentialManagerImpl.KeystoreChangedObserver - Class in org.apache.taverna.security.credentialmanager.impl
-
If any change to the Keystore or Truststore occurs - create the new
SSLSocketFactory and set the new default SSLContext which is initialised
with the updated Keystore and Truststore material
- CrossProduct - Class in org.apache.taverna.workflowmodel.processor.iteration
-
A cross product node combines its inputs in an 'all against all' manner.
- CrossProduct() - Constructor for class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
-
- CrossProduct<E> - Class in org.pingel.util
-
- CrossProduct(List<? extends Iterable<E>>) - Constructor for class org.pingel.util.CrossProduct
-
- CrossProduct(Iterable<E>...) - Constructor for class org.pingel.util.CrossProduct
-
- CrossProductInputFormat - Class in org.apache.taverna.platform.execution.impl.hadoop
-
An input format that receives an input directory containing a number of directories with input files
for each input port to a Taverna processor/activity that will be executed as part of this
MapReduce job.
- CrossProductInputFormat() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
-
- CrossProductInputSplit - Class in org.apache.taverna.platform.execution.impl.hadoop
-
- CrossProductInputSplit() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
-
- CrossProductInputSplit(Path, List<Path>) - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
-
- CrossProductRecordReader - Class in org.apache.taverna.platform.execution.impl.hadoop
-
- CrossProductRecordReader() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
-
- CrossProductTest - Class in org.apache.taverna.platform.execution.impl.hadoop
-
- CrossProductTest() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest
-
- CrossProductTest.Map - Class in org.apache.taverna.platform.execution.impl.hadoop
-
- CrossProductTest.Reduce - Class in org.apache.taverna.platform.execution.impl.hadoop
-
- Crystalizer - Interface in org.apache.taverna.workflowmodel.impl
-
Recieves Job and Completion events and emits Jobs unaltered.
- crystalizer - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- Curateable - Interface in org.apache.taverna.annotation
-
Implemented by objects which can have curation assertions attached to them.
- CurationEvent<CurationType extends CurationEventBeanSPI> - Interface in org.apache.taverna.annotation
-
Represents a single act of curation, parameterized on a bean encapsulating
the necessary and sufficient information to describe the specifics of the
curation event.
- CurationEventBeanSPI - Interface in org.apache.taverna.annotation
-
Contains the detail for a single curation event.
- CurationEventType - Enum in org.apache.taverna.annotation
-
- CURRENT_PORT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- cut(int[]) - Method in class org.apache.taverna.invocation.TreeCache
-
Chop the cache off at the specified index
- generateWorkflowReport(Workflow) - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- get(int[]) - Method in class org.apache.taverna.invocation.TreeCache
-
Get the job object at the specified index array
- get(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentDao
-
Retrieves a named and populated ErrorDocument
- get(int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
-
- get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
-
- get(T2Reference) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
-
- get(T2Reference) - Method in class org.apache.taverna.reference.impl.SimpleCacheProviderImpl
-
- get(T2Reference) - Method in interface org.apache.taverna.reference.ListDao
-
Retrieves a named and populated IdentifiedList of T2Reference from the
database by T2Reference
- get(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceServiceCacheProvider
-
Called before an attempt is made to retrieve an item from the backing
store
- get(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceSetDao
-
Fetch a reference set by id
- getA() - Method in class org.apache.taverna.workflowmodel.OrderedPair
-
Return object a
- getAbove() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
-
Returns a list of activity instances which can be applied to the data
contained by this job event.
- getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
-
- getActivities() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
Override to return the list of activities to be used by this dispatch
stack.
- getActivity() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- getActivity() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- getActivity() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- getActivity() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- getActivityConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- getActivityConfigurationSchema() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- getActivityConfigurationSchema() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns the JSON Schema for the configuration required by an activity.
- getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns a JSON Schema for the configuration required by an activity.
- getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
-
- getActivityConfigurationSchema(URI) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- getActivityConfigurationSchema(URI) - Method in interface org.apache.taverna.services.ServiceRegistry
-
Returns the JSON Schema for the configuration required by an activity.
- getActivityConfigurationSchema() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory
-
Returns the JSON Schema for the configuration required by the
Activity
.
- getActivityInputPort(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getActivityInputPorts(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- getActivityInputPorts(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns the input ports that the activity type requires to be present in
order to execute with the specified configuration.
- getActivityInputPorts(URI, JsonNode) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- getActivityInputPorts(URI, JsonNode) - Method in interface org.apache.taverna.services.ServiceRegistry
-
Returns the input ports that the activity type requires to be present in order to execute
with the specified configuration.
- getActivityList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getActivityList() - Method in interface org.apache.taverna.workflowmodel.Processor
-
A processor contains zero or more activities in an ordered list.
- getActivityOutputPort(Activity<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getActivityOutputPorts(URI, JsonNode) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- getActivityOutputPorts(URI, JsonNode) - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns the output ports that the activity type requires to be present in
order to execute with the specified configuration.
- getActivityOutputPorts(URI, JsonNode) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- getActivityOutputPorts(URI, JsonNode) - Method in interface org.apache.taverna.services.ServiceRegistry
-
Returns the output ports that the activity type requires to be present in order to execute
with the specified configuration.
- getActivityProvenanceItem() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
-
- getActivityReports() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
- getActivityType() - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- getActivityType() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- getActivityType() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory
-
What type of Activity
s can this factory create?
- getActivityTypes() - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
- getActivityTypes() - Method in interface org.apache.taverna.platform.capability.api.ActivityService
-
Returns the available activity types.
- getActivityTypes() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns the activity types available in this ExecutionEnvironment.
- getActivityTypes() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
-
- getActivityTypes() - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- getActivityTypes() - Method in interface org.apache.taverna.services.ServiceRegistry
-
Returns the activity types in the registry.
- getAddActivityEdit(Processor, Activity<?>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Add an Activity implementation to the set of activities within a
Processor
- getAddActivityEdit(Processor, Activity<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add an ActivityInputPort to an Activity.
- getAddActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddActivityInputPortMappingEdit(Activity<?>, String, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add a ProcessorInputPort to ActivityInputPort mapping
to an Activity.
- getAddActivityInputPortMappingEdit(Activity<?>, String, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add an ActivityOutputPort to an Activity.
- getAddActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddActivityOutputPortMappingEdit(Activity<?>, String, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add a ProcessorOutputPort to OutputPort mapping to an
Activity.
- getAddActivityOutputPortMappingEdit(Activity<?>, String, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddAnnotationAssertionEdit(AnnotationChain, AnnotationAssertion<?>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddAnnotationAssertionEdit(AnnotationChain, AnnotationAssertion<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddAnnotationBean(AnnotationAssertion<T>, AnnotationBeanSPI) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddAnnotationBean(AnnotationAssertion, AnnotationBeanSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddAnnotationChainEdit(Annotated<?>, AnnotationBeanSPI) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returnes an edit that creates an AnnotationAssertion, adds the
AnnotationAssertion to an AnnotationChain and adds the AnnotationChain to
the Annotated.
- getAddAnnotationChainEdit(Annotated<?>, AnnotationBeanSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddAnnotationEdit(AnnotationChain) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
-
- getAddAnnotationEdit(AnnotationChain) - Method in interface org.apache.taverna.annotation.Annotated
-
Add new workflow object metadata to this annotated entity
- getAddAnnotationRole(AnnotationAssertion<T>, AnnotationRole) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddAnnotationRole(AnnotationAssertion, AnnotationRole) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddAnnotationSource(AnnotationAssertion<T>, AnnotationSourceSPI) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddAnnotationSource(AnnotationAssertion, AnnotationSourceSPI) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddCreator(AnnotationAssertion<T>, Person) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddCreator(AnnotationAssertion, Person) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddCurationEvent(AnnotationAssertion<T>, CurationEvent<S>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddCurationEvent(AnnotationAssertion, CurationEvent) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add a DataflowInputPort to a Dataflow.
- getAddDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add a DataflowOutputPort to a Dataflow.
- getAddDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddDispatchLayerEdit(DispatchStack, DispatchLayer<?>, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Add a new layer to the specified dispatch stack
- getAddDispatchLayerEdit(DispatchStack, DispatchLayer<?>, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddIterationStrategyEdit(IterationStrategyStack, IterationStrategy) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddIterationStrategyEdit(IterationStrategyStack, IterationStrategy) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddIterationStrategyInputNodeEdit(IterationStrategy, NamedInputPortNode) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddIterationStrategyInputNodeEdit(IterationStrategy, NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddMergeEdit(Dataflow, Merge) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getAddMergeEdit(Dataflow, Merge) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddMergeInputPortEdit(Merge, MergeInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to add a MergeInputPort to a Merge.
- getAddMergeInputPortEdit(Merge, MergeInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddProcessorEdit(Dataflow, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provides an edit object responsible for adding a Processor to a Dataflow
- getAddProcessorEdit(Dataflow, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provides an Edit to add an input port a processor, creating matching
ports in the iteration strategy or strategies as a side effect.
- getAddProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAddProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provides an Edit to add a new output port on a processor
- getAddProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getAliases(CredentialManager.KeystoreType) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get all the aliases from the Keystore/Truststore or null if there was
some error while accessing it.
- getAliases(CredentialManager.KeystoreType) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get all the aliases from the Keystore/Truststore or null if there was
some error while accessing it.
- getAllowsChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- getAllowsChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
These nodes can never have children
- getAllowsLiteralValues() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- getAnnotatingClasses(List<AnnotationBeanSPI>, Annotated<?>) - Method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- getAnnotation(Annotated<?>, Class<?>) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- getAnnotationBeanClasses(List<AnnotationBeanSPI>, Class<T>) - Method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- getAnnotations() - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
-
Return the set of annotations bound to this annotated object, the set
returned is an unmodifiable copy of the internal annotation set, if you
need to modify the annotations you should use the get methods for Edit
objects to do so.
- getAnnotations() - Method in interface org.apache.taverna.annotation.Annotated
-
Each annotated object contains a bag of metadata object instances
- getAnnotations(AnnotationChain) - Method in interface org.apache.taverna.annotation.AnnotationPerspective
-
Evaluate the annotations and their curation events in the specified
chain, resolve conflicts if possible and return the resultant set of
annotations
- getAnnotationString(Annotated<?>, Class<?>, String) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- getApproximateSizeInBytes() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
-
Approximate size of the stored data or -1 if we do not know.
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
-
- getApproximateSizeInBytes() - Method in interface org.apache.taverna.reference.ReferenceSet
-
Get approximate size of the data pointed to by this ReferenceSet.
- getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.RedReference
-
- getApproximateSizeInBytes() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
- getAsImpl(T2Reference) - Static method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
- getAssertions() - Method in interface org.apache.taverna.annotation.AnnotationChain
-
Returns the ordered list of AnnotationAssertions.
- getAssertions() - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl
-
- getAuthenticator() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
- getAuthenticator() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- getB() - Method in class org.apache.taverna.workflowmodel.OrderedPair
-
Return object b
- getBackoffFactor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
Factor by which the initial delay is multiplied for each retry after the
first, this allows for exponential backoff of retry times up to a certain
ceiling
- getBean() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- getBelow() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- getBuilders() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getC() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getC() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getCancelledDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status changed to CANCELLED.
- getCancelledWorkflowRunId() - Method in class org.apache.taverna.facade.WorkflowRunCancellation
-
- getCardinality() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
Each node defines the level of collection depth for that input port
- getCategory() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getCategory() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getCause() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- getCause() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
-
Return the throwable behind this error, or null if there was no exception
raised to create it.
- getCertificate(CredentialManager.KeystoreType, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get certificate entry from the Keystore or Truststore.
- getCertificate(CredentialManager.KeystoreType, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get certificate entry from the Keystore or Truststore.
- getChangeDataflowInputPortDepthEdit(DataflowInputPort, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to change the depth of a DataflowInputPort.
- getChangeDataflowInputPortDepthEdit(DataflowInputPort, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getChangeDataflowInputPortGranularDepthEdit(DataflowInputPort, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to change the granular depth of a DataflowInputPort.
- getChangeDataflowInputPortGranularDepthEdit(DataflowInputPort, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getCharset() - Method in class org.apache.taverna.reference.AbstractExternalReference
-
Default to returning null for charset
- getCharset() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
-
For textual data return the character set that should be used to pull
data into a java String object.
- getCharset() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
Default to returning null for charset
- getCharset() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
- getCharset() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
Character encoding set to 'UTF-8' by default
- getCharset() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
Character encoding set to 'UTF-8'
- getCharset() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
Character encoding set to 'UTF-8'
- getCharset() - Method in class org.apache.taverna.t2referencetest.RedReference
-
Character encoding set to 'UTF-8'
- getCharset() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
Character encoding set to 'UTF-8'
- getCheckTime() - Method in class org.apache.taverna.visit.VisitReport
-
- getChild(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Return the T2Reference for the sole child of an error document
identifier.
- getChild(T2Reference) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
-
- getChild(NodeType, int) - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Returns the child of parent at index 'index' in the parent's child array.
- getChildAt(int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- getChildAt(int) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
Specialised return type of TreeNode#getChildAt(int)
- getChildCount(NodeType) - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Returns the number of children of parent.
- getChildCount() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- getChildEdits() - Method in class org.apache.taverna.workflowmodel.CompoundEdit
-
- getChildIndices() - Method in class org.apache.taverna.utility.TypedTreeModelEvent
-
Returns the values of the child indexes.
- getChildren() - Method in class org.apache.taverna.utility.TypedTreeModelEvent
-
Returns the objects that are children of the node identified by getPath
at the locations specified by getChildIndices.
- getChildren() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implements IterationStrategyNode
- getChildren() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
- getClassName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- getClassName() - Method in interface org.apache.taverna.reference.StackTraceElementBean
-
Returns the fully qualified name of the class containing the execution
point represented by this stack trace element.
- getClearIterationStrategyStackEdit(IterationStrategyStack) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getClearIterationStrategyStackEdit(IterationStrategyStack) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getCN() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getCN() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getCollections() - Method in class org.pingel.util.CrossProduct
-
- getCompactForm() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
- getCompletedDate() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the date that the status changed to COMPLETED.
- getCompletedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status changed to COMPLETED.
- getCompletionState(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
-
- getCondition() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- getConfiguration() - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
-
- getConfiguration() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
-
- getConfiguration() - Method in interface org.apache.taverna.workflowmodel.Configurable
-
Each item stores configuration within a bean of type ConfigurationType,
this method returns the configuration.
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity
-
Get a configuration bean representing the definition of the activity.
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.UnrecognizedActivity
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
-
- getConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
- getConfigureActivityEdit(Activity<ConfigurationBean>, ConfigurationBean) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an Edit that is responsible for configuring an Activity with a
given configuration bean.
- getConfigureActivityEdit(Activity<T>, T) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getConfigureEdit(Configurable<ConfigurationType>, ConfigurationType) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getConfigureEdit(Configurable<T>, T) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getConnectDatalinkEdit(Datalink) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Connect a datalink to its source and sink.
- getConnectDatalinkEdit(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getConnection() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
-
- getConnection() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
- getConnectMergedDatalinkEdit(Merge, EventForwardingOutputPort, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Creates and returns an instance of an Edit that is responsible for
generating the links to an from the Merge instance to link together the
source and sink port via the merge instance.
- getConnectMergedDatalinkEdit(Merge, EventForwardingOutputPort, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getConnectorType() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getConnectorType() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getConnectProcessorOutputEdit(Processor, String, EventHandlingInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Connect the output port of the specified processor to a target input
port.
- getConnectProcessorOutputEdit(Processor, String, EventHandlingInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getConstructionCost() - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI
-
Return an approximate complexity cost of the reference construction.
- getConstructionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
-
- getConstructionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
-
- getConstructionCost() - Method in class org.apache.taverna.t2referencetest.GreenBuilder
-
Construction cost fixed at 1.5f
- getContainsErrors() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Property accessor for Hibernate, complies with java bean spec
- getContent() - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
-
- getContents() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- getContents() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
Get the 'value' of this reference as a string, really just returns the
internal string representation.
- getContents() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
Get the 'value' of this reference as a string, really just returns the
internal string representation.
- getContents() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
Get the 'value' of this reference as a string, really just returns the
internal string representation.
- getContents() - Method in class org.apache.taverna.t2referencetest.RedReference
-
Get the 'value' of this reference as a string, really just returns the
internal string representation.
- getContents() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
Get the 'value' of this reference as a string, really just returns the
internal string representation.
- getContext() - Method in class org.apache.taverna.activities.testutils.DummyCallback
-
- getContext() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getContext() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Return the invocation context used by this facade
- getContext() - Method in class org.apache.taverna.invocation.Event
-
- getContext() - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback
-
The invocation context contains resources such as data managers, security
agents and provenance consumers to be used by the Activity as it runs.
- getContext() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- getContext() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- getControl() - Method in interface org.apache.taverna.workflowmodel.Condition
-
- getControlledPreconditionList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getControlledPreconditionList() - Method in interface org.apache.taverna.workflowmodel.Processor
-
A processor may control zero or more other processors within the same
level of the workflow through preconditions.
- getCreateAndConnectDatalinkEdit(Dataflow, EventForwardingOutputPort, EventHandlingInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Creates an Edit that creates a Datalink between a source and sink port
and connects the Datalink.
- getCreateAndConnectDatalinkEdit(Dataflow, OutputPort, InputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Get an
Edit
that will link the given output port to the given
input port.
- getCreateConditionEdit(Processor, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Create a condition governing execution of the target processor.
- getCreateConditionEdit(Processor, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getCreateDataflowInputPortEdit(Dataflow, String, int, int) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Add an input port to a dataflow.
- getCreateDataflowInputPortEdit(Dataflow, String, int, int) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getCreateDataflowOutputPortEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Add an output port to a dataflow.
- getCreateDataflowOutputPortEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getCreatedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status was set to CREATED.
- getCreationDate() - Method in interface org.apache.taverna.annotation.Curateable
-
All curation events are marked with their creation date, this is the date
at which the curation event was associated with its target.
- getCreationDate() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getCreationDate() - Method in interface org.apache.taverna.monitor.MonitorNode
-
Each node has a creation date
- getCreators() - Method in interface org.apache.taverna.annotation.Curateable
-
Each curateable has a list of people associated with it, frequently one
person and in some cases none, although this should be avoided if
possible.
- getCreators() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getCredentialManagerDefaultDirectory(ApplicationConfiguration) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
-
Get the configuration directory where the security stuff will be/is saved
to.
- getCredentialManagerDefaultDirectory(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
- getCurationAssertions() - Method in interface org.apache.taverna.annotation.Curateable
-
Curateable instances have a list of curation events which are used to
determine whether the implementing object is valid given a particular
interpretive context.
- getCurationAssertions() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getCurrentKey() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
-
- getCurrentKey() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
-
- getCurrentPort() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getCurrentPort() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getCurrentValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
-
- getCurrentValue() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
-
- getData() - Method in class org.apache.taverna.invocation.WorkflowDataToken
-
Return the ID of the data this event represents
- getData() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- getData() - Method in class org.apache.taverna.workflowmodel.processor.activity.Job
-
The actual data carried by this (partial) Job object is in the form of a
map, where the keys of the map are Strings identifying the named input
and the values are Strings containing valid data identifiers within the
context of a visible DataManager object (see CloudOne specification for
further information on the DataManager system)
- getData() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
-
The actual data carried by this dispatch job event object is in the form
of a map, where the keys of the map are Strings identifying the named
input and the values are Strings containing valid data identifiers within
the context of a visible DataManager object (see CloudOne specification
for further information on the DataManager system)
- getData() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent
-
The result contains a map of named EntityIdentifier instances
corresponding to the result data.
- getDatabaseContext() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getDatabaseContext() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getDataBundle() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getDataBundle() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the Bundle
containing the data values for the Workflow
.
- getDataBundle() - Method in class org.apache.taverna.platform.report.WorkflowReport
-
- getDataBundle() - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Returns the Bundle
containing the data values for the
Workflow
.
- getDataBundle(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the Bundle
containing the data values of the run.
- getDataBundle() - Method in class org.apache.taverna.platform.run.impl.Run
-
Returns the Bundle
containing the data values of the run.
- getDataBundle(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getDataflow() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getDataflow() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Return the dataflow this facade facades
- getDataflow(Workflow) - Method in interface org.apache.taverna.platform.execution.api.WorkflowCompiler
-
Convert a workflow into a dataflow.
- getDataflow(WorkflowBundle) - Method in interface org.apache.taverna.platform.execution.api.WorkflowCompiler
-
Convert a workflow bundle into a dataflow.
- getDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
- getDataflow(WorkflowBundle) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
- getDataflow(Workflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getDataflow() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- getDataflow() - Method in interface org.apache.taverna.workflowmodel.DataflowPort
-
Get the parent DataFlow to which this port belongs
- getDataflow() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
-
- getDataflow() - Method in exception org.apache.taverna.workflowmodel.InvalidDataflowException
-
- getDataflowActivity(Activity) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getDataflowID() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- getDataflowProcessor(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getDataflowValidationReport() - Method in exception org.apache.taverna.workflowmodel.InvalidDataflowException
-
- getDataMap() - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
-
- getDataNature() - Method in class org.apache.taverna.reference.AbstractExternalReference
-
Default to returning DataReferenceNature.UNKNOWN
- getDataNature() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
-
Determine, if possible, whether the data this reference refers to is
textual or binary in nature.
- getDataNature() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- getDataNature() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
Data nature set to 'ReferencedDataNature.TEXT'
- getDataNature() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
Data nature set to 'ReferencedDataNature.TEXT'
- getDataNature() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
Data nature set to 'ReferencedDataNature.TEXT'
- getDataNature() - Method in class org.apache.taverna.t2referencetest.RedReference
-
Data nature set to 'ReferencedDataNature.TEXT'
- getDataNature() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
Data nature set to 'ReferencedDataNature.TEXT'
- getDataNatureName() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- getDataSource() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
-
- getDataSource() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
- getDate(JsonNode, String) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
-
- getDefaultDispatchStackEdit(Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provides an edit that setup the default dispatch stack on a raw
processor.
- getDefaultDispatchStackEdit(Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getDefaultPropertyMap() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getDefaultPropertyMap() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getDeleteDispatchLayerEdit(DispatchStack, DispatchLayer<?>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Remove a dispatch layer from its dispatch stack
- getDeleteDispatchLayerEdit(DispatchStack, DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getDepth() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Get the depth of the entity referred to by this reference
- getDepth() - Method in interface org.apache.taverna.reference.T2Reference
-
All entities identified by a T2Reference have a conceptual depth.
- getDepth() - Method in class org.apache.taverna.workflowmodel.AbstractPort
-
- getDepth() - Method in interface org.apache.taverna.workflowmodel.Port
-
- getDepth() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- getDereferenceBasedPaths(ReferenceSet) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
Return a list of translation paths based on this one but which start at
an existing reference within the supplied reference set.
- getDescription() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
-
- getDescription() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- getDescription() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns a description of this ExecutionEnvironment.
- getDescription() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Returns a description of this ExecutionService.
- getDesiredCardinalities() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- getDesiredCardinalities() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy
-
Return a map of port name -> desired cardinality for this iteration
strategy
- getDetail() - Method in interface org.apache.taverna.annotation.AnnotationAssertion
-
Each annotation assertion contains a bean specifying the actual
annotation, varying from a simple string for a free text description to
more sophisticated semantic annotations or controlled vocabularies.
- getDetail() - Method in interface org.apache.taverna.annotation.CurationEvent
-
- getDetail() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getDetail() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- getDisconnectDatalinkAndRemovePortsEdit(Datalink, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getDisconnectDatalinkEdit(Datalink) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Disconnect a datalink from its source and sink.
- getDisconnectDatalinkEdit(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService
-
Returns the JSON Schema for the configuration required by a dispatch
layer.
- getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
-
- getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns a JSON Schema for the configuration required by a dispatch layer.
- getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
-
- getDispatchLayerConfigurationSchema(URI) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory
-
Returns the JSON Schema for the configuration required by the
DispatchLayer
.
- getDispatchLayerConfigurationSchema(URI) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
-
- getDispatchLayerTypes() - Method in interface org.apache.taverna.platform.capability.api.DispatchLayerService
-
Returns the available dispatch layer types.
- getDispatchLayerTypes() - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
-
- getDispatchLayerTypes() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns the dispatch layer types available in this ExecutionEnvironment.
- getDispatchLayerTypes() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionEnvironment
-
- getDispatchLayerTypes() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayerFactory
-
Returns the types of the
DispatchLayer
s that this factory
can create.
- getDispatchLayerTypes() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.CoreDispatchLayerFactory
-
- getDispatchStack() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getDispatchStack() - Method in interface org.apache.taverna.workflowmodel.Processor
-
The dispatch stack pulls jobs from the queue generated by the iteration
system and handles the dispatch of these jobs to appropriate activity
workers
- getDisplayName() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getDisplayName() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getDocumentationURL() - Method in class org.apache.taverna.annotation.annotationbeans.DocumentationUrl
-
- getDriverClassName() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getDriverClassName() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getEdits() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getEmailAddress() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getEmailAddress() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getEmptyJob(String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer
-
- getEmptyJob(String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorCrystalizerImpl
-
- getEnableDisabledActivityEdit(Processor, DisabledActivity, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getEnactmentEnded() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getEnactmentStarted() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getEndpointExpiryInMilliseconds() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
- getEntities(Class<T>) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
-
- getEntities(Class<T>) - Method in class org.apache.taverna.reference.impl.EmptyReferenceContext
-
Return an empty entity set for all queries.
- getEntities(Class<T>) - Method in interface org.apache.taverna.reference.ReferenceContext
-
Return a list of all entities in the resolution context which match the
supplied entity type argument.
- getEntities(Class<T>) - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Get all workflow entities with the specified type restriction, this
allows retrieval of Processor, Merge, a mix of the two or any other
future entity to be added to the workflow model without a significant
change in this part of the API.
- getEntities(Class<T>) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Gets all workflow entities of the specified type and returns as an
unmodifiable list of that type
- getError(T2Reference) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Retrieve a previously named and registered ErrorDocument from the backing
store
- getError(T2Reference) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
-
- getErrorAsynch(T2Reference, ErrorDocumentServiceCallback) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Functionality the same as
getError
but in
asynchronous mode, returning immediately and using the supplied callback
to communicate its results.
- getErrorAsynch(T2Reference, ErrorDocumentServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
- getErrorDocumentService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- getErrorDocumentService() - Method in interface org.apache.taverna.reference.ReferenceService
-
Returns the
ErrorDocumentService
this ReferenceService uses, use
this when you need functionality from that service explicitly.
- getErrorItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getErrorReferences() - Method in interface org.apache.taverna.reference.ErrorDocument
-
If the error document is created from set of references that contain
error documents, this method returns them.
- getErrorReferences() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
- getErrorReferenceSet() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
Used by Hibernate to bodge around problems with interface types in the
API
- getErrorType() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
-
- getEventType() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.InputDataProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.OutputDataProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- getEventType() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
What type of information does the item contain.
- getEventType() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- getEventType() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- getExceptionMessage() - Method in interface org.apache.taverna.reference.ErrorDocument
-
If the error document is created from a
Throwable
, this contains
the message part of the
Throwable
.
- getExceptionMessage() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
- getExecution(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- getExecutionEnvironment() - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Returns the ExecutionEnvironment
used to execute the
Workflow
.
- getExecutionEnvironments() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironmentService
-
Returns the available ExecutionEnvironment
s.
- getExecutionEnvironments(Profile) - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironmentService
-
Returns the ExecutionEnvironment
s that can execute the specified
Profile
.
- getExecutionEnvironments() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Returns the ExecutionEnvironments available for this ExecutionService.
- getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
-
- getExecutionEnvironments(Profile) - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
-
- getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
- getExecutionEnvironments() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
-
- getExecutionEnvironments() - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the available ExecutionEnvironment
s.
- getExecutionEnvironments(WorkflowBundle) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the ExecutionEnvironment
s that can execute the
specified WorkflowBundle
using its default
Profile
.
- getExecutionEnvironments(Profile) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the ExecutionEnvironment
s that can execute the
specified Profile
.
- getExecutionEnvironments() - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getExecutionEnvironments(WorkflowBundle) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getExecutionEnvironments(Profile) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getExecutionService() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
-
- getExecutionService() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns the ExecutionService that provides this ExecutionEnvironment.
- getExternalReferences() - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
-
- getExternalReferences() - Method in interface org.apache.taverna.reference.ReferenceSet
-
The reference set contains a set of ExternalReferenceSPI instances, all
of which point to byte equivalent data.
- getExternalReferences() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
-
- getExtraDescription() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
-
- getFacadeID() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
As WorkflowInstanceFacade
s are created for a Processor the
details are appended to the owning process identifier.
- getFailedActivity() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
-
Return the Activity instance which failed to produce this error message
- getFailedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status changed to FAILED.
- getFailedEntities() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport
-
The workflow will be marked as invalid if any entity fails to type check.
- getFailedEntities() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
-
- getFailureTransmitter() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
The failure transmitter contains event listeners to be notified of
workflow level failures - these occur when an error bubbles up to the top
of the dispatch stack in a processor and is not handled by conversion to
an error token within the data stream.
- getFailureTransmitter() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- getFailureType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
-
Return the type of failure, this is used by upstream dispatch layers to
determine whether they can reasonably handle the error message
- getFile() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- getFileName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- getFileName() - Method in interface org.apache.taverna.reference.StackTraceElementBean
-
Returns the name of the source file containing the execution point
represented by this stack trace element.
- getFilePath() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
Getter used by hibernate to retrieve the file path string property
- getFilePrefix() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getFilePrefix() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getFilterDepth() - Method in interface org.apache.taverna.workflowmodel.FilteringInputPort
-
Set the depth at which to filter events.
- getFilterDepth() - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
-
- getFirstProcessorWithActivityInputPort(Dataflow, ActivityInputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Find the first processor that contains an activity that has the given
activity input port.
- getFirstProcessorWithActivityOutputPort(Dataflow, ActivityOutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getFragmentMappedURIsForAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- getGranularDepth() - Method in class org.apache.taverna.workflowmodel.AbstractOutputPort
-
- getGranularDepth() - Method in interface org.apache.taverna.workflowmodel.OutputPort
-
The granular depth is the depth of the finest grained item that can be
emitted from this output port.
- getGranularDepth() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
-
- getGranularInputDepth() - Method in interface org.apache.taverna.workflowmodel.DataflowInputPort
-
Define the finest grained item that will be sent to this input port.
- getGranularInputDepth() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
-
- getHandledReferenceSchemes() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort
-
Declares that the DataDocument instances fed as input data (either
directly or as elements of a collection) to this input port must contain
at least one of the specified ReferenceScheme types.
- getHandledReferenceSchemes() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- getHandledReferenceSchemes() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
-
- getHibernateDialect() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getHibernateDialect() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getHttpUrl() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
- getHttpUrlString() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
Getter used by hibernate to retrieve the file path string property
- getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
-
- getID() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- getID() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the identifier for this execution.
- getID() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns the identifier for this ExecutionEnvironment.
- getID() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Returns the identifier for this ExecutionService.
- getId() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the identifier for this invocation by prepending the identifier of the parent
invocation.
- getID() - Method in class org.apache.taverna.platform.run.impl.Run
-
Returns the identifier for this Run
.
- getId() - Method in interface org.apache.taverna.reference.Identified
-
Return an appropriately configured instance of T2Reference for this
identified object.
- getId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
-
- getId() - Method in class org.apache.taverna.t2referencetest.DummyReferenceSet
-
- getIdentification() - Method in class org.apache.taverna.annotation.annotationbeans.IdentificationAssertion
-
- GetIdentifiedOperation - Annotation Type in org.apache.taverna.reference.annotations
-
Applied to methods in Dao implementations which fetch data from the backing
store by ID
- getIdentifier() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getIdentifier() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
An identifier that is unique to this facade.
- getIdentifier() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- getIdentifier() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
The unique identifier for this item
- getIdentifier() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
An identifier that is unique to this dataflow and its current state.
- getIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- getIncomingLink() - Method in interface org.apache.taverna.workflowmodel.EventHandlingInputPort
-
If this port is connected to a Datalink return the link, otherwise return
null
- getIncomingLink() - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
-
- getIndex() - Method in class org.apache.taverna.invocation.Event
-
Events have an index placing them in a conceptual tree structure.
- getIndex() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
-
- getIndex() - Method in class org.apache.taverna.platform.report.Invocation
-
- getIndex() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- getIndex() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- getIndex() - Method in interface org.apache.taverna.reference.ContextualizedT2Reference
-
- getIndex() - Method in class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
-
- getIndex(TreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- getIndexesByProcess(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- getIndexLength() - Method in class org.apache.taverna.invocation.TreeCache
-
The length of index arrays of jobs within the TreeCache.
- getIndexOfChild(NodeType, NodeType) - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Returns the index of child in parent.
- getInitialBuilder() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getInitialDelay() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
Delay in milliseconds between the initial failure message and the first
attempt to retry the failed job
- getInputDataItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getInputPortDefinitions() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
-
- getInputPortDirectories() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
-
- getInputPortMapping() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getInputPortMapping() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
A processor may have different input port names to the activity or
activities it contains.
- getInputPorts(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- getInputPorts(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Dataflows have a list of input ports.
- getInputPorts() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Return a copy of the list of dataflow input ports for this dataflow
- getInputPorts() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Merge
-
The Merge object contains an ordered list of InputPort objects.
- getInputPorts() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getInputPorts() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
An Activity contains a set of named input ports.
- getInputPorts(JsonNode) - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory
-
Returns the ActivityInputPort
s that the
Activity
requires to be present in order to execute with the
specified configuration.
- getInputPorts() - Method in interface org.apache.taverna.workflowmodel.Processor
-
Each processor has a list of zero or more input ports.
- getInputPorts() - Method in interface org.apache.taverna.workflowmodel.TokenProcessingEntity
-
- getInputPortWithName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getInputs() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
-
- getInputs() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns a map of input port names to values.
- getInstance() - Static method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Get the MonitorImpl singleton
- getInstance() - Static method in class org.apache.taverna.monitor.MonitorManager
-
Get the MonitorManager singleton instance.
- getInstance() - Static method in class org.apache.taverna.visit.DataflowCollation
-
- getInstance() - Static method in class org.apache.taverna.workflowmodel.health.HealthCheck
-
- getInternalId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
-
- getInternalInputPort() - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort
-
Get the internal input port for this workflow output
- getInternalOutputPort() - Method in interface org.apache.taverna.workflowmodel.DataflowInputPort
-
Return the internal output port.
- getInternalOutputPort() - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
-
- getInvalidDataflows() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport
-
An entity will be marked invalid if it depends on a nested dataflow which
itself is invalid.
- getInvalidDataflows() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
-
- getInvocation(String) - Method in class org.apache.taverna.platform.report.StatusReport
-
Get an invocation with a given name.
- getInvocationContext() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
Get the
InvocationContext
that this reporter should be using if
it needs to dereference any data
- getInvocationEnded() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
-
- getInvocationProcessId() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- getInvocations() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the child invocations.
- getInvocations() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the invocations.
- getInvocationStarted() - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- getInvocationStarted() - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- getIteration() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CrossProduct
-
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.DotProduct
-
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
-
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
The iteration depth here is calculated by taking first the top iteration
strategy and applying the actual input types to it, then for each
subsequent strategy in the stack using the 'desired cardinality' of the
input nodes for each layer to work out the increase in index array
length.
- getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy
-
The iteration strategy results in a set of job objects with a particular
job index.
- getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
In the context of an enclosing iteration strategy each node should be
able to return the iteration depth, i.e.
- getIterationDepth(Map<String, Integer>) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyStack
-
Calculate the depth of the iteration strategy stack as a whole given a
set of named inputs and their cardinalities.
- getIterationDepth(Map<String, Integer>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
Iteration depth is the difference between the supplied input depth and
the desired one.
- getIterationProvenanceItem() - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- getIterationProvItem(Event<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- getIterationStrategy() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getIterationStrategy() - Method in interface org.apache.taverna.workflowmodel.Processor
-
The iteration strategy is responsible for combining input data events
into jobs which are then queued for execution through the dispatch stack
- getJavaTruststorePassword() - Method in interface org.apache.taverna.security.credentialmanager.JavaTruststorePasswordProvider
-
Get the Java truststore password.
- getJavaTruststorePasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get the Java truststore password providers for providing the password to
encrypt/decrypt the Java's default truststore.
- getJDBCUri() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getJDBCUri() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getJobsCompleted() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getJobsCompleted() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Returns the number of jobs that the processor has completed.
- getJobsCompletedWithErrors() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getJobsCompletedWithErrors() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Returns the number of jobs that completed with an error.
- getJobsCopy(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
- getJobsDefault(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
- getJobsQueued() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getJobsQueued() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Returns the number of jobs queued by the processor.
- getJobsStarted() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getJobsStarted() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Returns the number of jobs that the processor has started processing.
- getJTree() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Returns a tree view over the monitor.
- getKeyPairsCertificateChain(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get certificate chain for the key pair entry from the Keystore given its
alias.
- getKeyPairsCertificateChain(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get certificate chain for the key pair entry from the Keystore.
- getKeyPairsPrivateKey(String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get the private key part of a key pair entry from the Keystore given its
alias.
- getKeyPairsPrivateKey(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get the private key part of a key pair entry from the Keystore given its
alias.
- getKind() - Method in class org.apache.taverna.visit.VisitReport
-
- getL() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getL() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getLastModified() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
-
- getLastModified() - Method in interface org.apache.taverna.monitor.MonitorableProperty
-
Get the last update date for this property, if the property is immutable
then this should be set to the date at which the implementation is
created.
- getLastModified() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
-
- getLastWorkingConfiguration() - Method in class org.apache.taverna.workflowmodel.processor.activity.DisabledActivity
-
- getLayers() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack
-
The DispatchStack consists of an ordered list of DispatchLayer instances
where the DispatchLayer at index zero is at the bottom of the stack and
is almost always an invocation layer of some kind (in any working
dispatch stack configuration)
- getLayers() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
- getLength() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
-
- getLineNumber() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- getLineNumber() - Method in interface org.apache.taverna.reference.StackTraceElementBean
-
Returns the line number of the source line containing the execution point
represented by this stack trace element.
- getLinks() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
The dataflow is largely defined by the links between processors and other
entities within its scope.
- getLinks() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
For each processor input, merge input and workflow output get the
incoming link and, if non null, add to a list and return the entire list.
- getList(T2Reference) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
-
- getList(T2Reference) - Method in interface org.apache.taverna.reference.ListService
-
Retrieve a previously named and registered list of T2Reference instances
identified by the specified T2Reference (which must be of type
T2ReferenceType.IdentifiedList)
- getListAsynch(T2Reference, ListServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
- getListAsynch(T2Reference, ListServiceCallback) - Method in interface org.apache.taverna.reference.ListService
-
Functionality the same as
getList
but in
asynchronous mode, returning immediately and using the supplied callback
to communicate its results.
- getListContents() - Method in class org.apache.taverna.reference.impl.T2ReferenceListImpl
-
This is only called from Hibernate, outside of test code, so is
relatively safe to leave unchecked.
- getListService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- getListService() - Method in interface org.apache.taverna.reference.ReferenceService
-
Returns the
ListService
this ReferenceService uses, use this when
you need functionality from that service explicitly.
- getLocalName() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Return the local name of this workflow
- getLocalName() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getLocalName() - Method in interface org.apache.taverna.workflowmodel.NamedWorkflowEntity
-
Every workflow level entity has a name which is unique within the
workflow in which it exists.
- getLocalPart() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Get the local part of the URI for this reference
- getLocalPart() - Method in interface org.apache.taverna.reference.T2Reference
-
In addition to the namespace the T2Reference contains a local identifier.
- getLocations() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaInputSplit
-
- getLowerNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
-
- getMapProcessorPortsForActivityEdit(Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provides an edit that will configure the processors ports to map to those
of its internal Activity.
- getMapProcessorPortsForActivityEdit(Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getMasterPassword(boolean) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
-
- getMasterPassword(boolean) - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider
-
Get the master password for the Credential Manager.
- getMasterPasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get the master password providers for providing the master password to
encrypt/decrypt the Credential Maager's Keystore and Truststore.
- getMaxDelay() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
Maximum delay in milliseconds between failure reception and retry.
- getMaximumJobs() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ParallelizeConfig
-
- getMaxRetries() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
Maximum number of retries for a failing process
- getMerge() - Method in interface org.apache.taverna.workflowmodel.MergePort
-
- getMerges() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Dataflows also contain a set of merge operations, this method returns an
unmodifiable copy of the set.
- getMerges() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Return the list of all merge operations within the dataflow
- getMessage() - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- getMessage() - Method in interface org.apache.taverna.reference.ErrorDocument
-
Error documents can carry an arbitrary string message, this returns it.
- getMessage() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
- getMessage() - Method in class org.apache.taverna.visit.VisitReport
-
- getMessage() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
-
Return the textual message representing this error
- getMessageDigestAsFormattedString(byte[], String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
-
- getMessageDigestAsFormattedString(byte[], String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
Get the message digest of the given byte array as a string of hexadecimal
characters in the form XX:XX:XX...
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.AbstractDispatchEvent
-
Return the DispatchMessageType for this event object
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchCompletionEvent
-
DispatchMessageType.RESULT_COMPLETION
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorEvent
-
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobEvent
-
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
-
- getMessageType() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchResultEvent
-
- getMethodName() - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- getMethodName() - Method in interface org.apache.taverna.reference.StackTraceElementBean
-
Returns the name of the method containing the execution point represented
by this stack trace element.
- getMimeType() - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
-
- getMimeTypes() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- getMonitorTree() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
- getMoveDatalinkSinkEdit(Dataflow, Datalink, EventHandlingInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getName() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
-
- getName() - Method in interface org.apache.taverna.monitor.MonitorableProperty
-
Return the name of this property, names are heirarchical in nature and
are defined as an array of String objects.
- getName() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionEnvironment
-
- getName() - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- getName() - Method in interface org.apache.taverna.platform.execution.api.ExecutionEnvironment
-
Returns the name of this ExecutionEnvironment.
- getName() - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Returns the name of this ExecutionService.
- getName() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
-
- getName() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the name for this invocation.
- getName() - Method in class org.apache.taverna.workflowmodel.AbstractPort
-
- getName() - Method in interface org.apache.taverna.workflowmodel.Port
-
- getName() - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- getName() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- getNamespace() - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
-
Get the namespace for identifiers generated by this class
- getNamespace() - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator
-
- getNamespace() - Method in interface org.apache.taverna.reference.T2ReferenceGenerator
-
All T2Reference objects will have this namespace
- getNamespacePart() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Get the namespace part of the URI for this reference
- getNamespacePart() - Method in interface org.apache.taverna.reference.T2Reference
-
T2Reference instances retain a reference to the reference manager which
created them in the form of a namespace.
- getNestedDataflow() - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
-
- getNestedDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflow
-
- getNestedDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflowSource
-
- getNestedPathForProcessor(Processor, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Return a path of processors where the last element is this processor and
previous ones are nested processors that contain this one all the way to
the top but excluding the top level workflow as this is only a list of
processors.
- getNestedWorkflowReport() - Method in class org.apache.taverna.platform.report.ActivityReport
-
- getNewProperties() - Method in class org.apache.taverna.monitor.MonitorManager.AddPropertiesMessage
-
- getNextLocalPart() - Method in class org.apache.taverna.reference.impl.AbstractT2ReferenceGenerator
-
Generate a new local part for a new
reference
.
- getNextLocalPart() - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
-
- getNextLocalPart() - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator
-
- getNodeRemovalDelay() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
- getNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion
-
- getO() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getO() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.CacheAspect
-
Handle a 'get by T2Reference' operation on a Dao
- getObject() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
- getObject(ProceedingJoinPoint) - Method in class org.apache.taverna.reference.impl.WriteQueueAspect
-
Handle a 'get by T2Reference' operation on a Dao
- getObservers() - Method in class org.apache.taverna.lang.observer.MultiCaster
-
A list of all the classes currently registered with this
MultiCaster
- getObservers() - Method in interface org.apache.taverna.lang.observer.Observable
-
A list of all the currently registered
Observer
s
- getObservers() - Method in class org.apache.taverna.monitor.MonitorManager
-
A list of all the currently registered
Observer
s
- getObservers() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get all current observers of changes to the Keystore or Truststore.
- getObservers() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get all current observers of changes to the Keystore or Truststore.
- getObservers() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getOU() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getOU() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getOutgoingLinks() - Method in interface org.apache.taverna.workflowmodel.EventForwardingOutputPort
-
The set of datalinks for which this output port is the source of events
- getOutgoingLinks() - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
Implements EventForwardingOutputPort
- getOutputDataItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getOutputPort() - Method in interface org.apache.taverna.workflowmodel.Merge
-
The Merge object has a single output port through which modified events
are emitted as described in the javadoc for getInputPorts
- getOutputPortDefinitions() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
-
- getOutputPortMapping() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getOutputPortMapping() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
Outputs of the activity may be named differently to those of the
processor.
- getOutputPorts(JsonNode) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- getOutputPorts(JsonNode) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Dataflows have a list of output ports.
- getOutputPorts() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Return all dataflow output ports
- getOutputPorts() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getOutputPorts() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
An Activity contains a set of named output ports.
- getOutputPorts(JsonNode) - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityFactory
-
Returns the ActivityOutputPort
s that the
Activity
requires to be present in order to execute with the
specified configuration.
- getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.Processor
-
Each processor has a list of zero or more output ports.
- getOutputPorts() - Method in interface org.apache.taverna.workflowmodel.TokenProcessingEntity
-
- getOutputPortWithName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getOutputs() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns a map of output port names to values.
- getOwningProcess() - Method in class org.apache.taverna.invocation.Event
-
The event has an owner, this is represented as a String object but the
ownership is hierarchical in nature.
- getOwningProcess() - Method in class org.apache.taverna.monitor.MonitorManager.MonitorMessage
-
- getOwningProcess() - Method in interface org.apache.taverna.monitor.MonitorNode
-
Each monitor node has an identity corresponding to the identifier stack
of the data flowing through the workflow object that created it.
- getOwningProcess() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- getOwningProcess() - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
-
- getParent() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the parent invocation.
- getParent() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implement TreeNode
- getParent() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
Specialised return type of TreeNode#getParent()
- getParentDataflow() - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflowSource
-
- getParentId() - Method in class org.apache.taverna.platform.report.Invocation
-
- getParentId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- getParentId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
Who is the parent of this item?
- getParentIterationItem() - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- getParentProcessIdentifier() - Method in class org.apache.taverna.activities.testutils.DummyCallback
-
- getParentProcessIdentifier() - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback
-
For activities which are going to establish state below the invoke node
in the monitor tree this method returns the owning process identifier
allocated to the invoke node.
- getParentProcessIdentifier() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- getParentProcessIdentifier() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- getParentReport() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the parent report.
- getPassword() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getPassword() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getPassword() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- getPasswordAsString() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- getPasswordAuthentication() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
-
- getPathCost() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
Sum of translation costs of all translators in path
- getPausedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status last changed to PAUSED.
- getPausedDates() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the dates that the status changed to PAUSED.
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
-
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
-
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
-
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
-
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
-
- getPojoClass() - Method in class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
-
- getPojoClass() - Method in interface org.apache.taverna.reference.StreamToValueConverterSPI
-
The class of objects which this builder can construct from a stream
- getPoolMaxActive() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getPoolMaxActive() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getPoolMaxIdle() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getPoolMaxIdle() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getPoolMinIdle() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getPoolMinIdle() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getPoppedIndex() - Method in class org.apache.taverna.invocation.IterationInternalEvent
-
Helper method for the popIndex operation, returns the modified index
array.
- getPort() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getPort() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getPortName() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- getPortName() - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
Each node maps to a single named input port within the processor
- getPossibleServiceURIsToLookup(URI, boolean) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- getPreconditionList() - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- getPreconditionList() - Method in interface org.apache.taverna.workflowmodel.Processor
-
A processor has zero or more preconditions explicitly declared.
- getPrimaryKey() - Method in class org.apache.taverna.reference.AbstractExternalReference
-
Used by Hibernate internally to establish a foreign key relationship
between this abstract superclass and tables corresponding to
implementations of the ExternalReference interface.
- getProcessId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- getProcessId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
Get the enactor supplie identifier
- getProcessName() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
Defines the enclosing process name, usually Processor.getName() on the
parent
- getProcessor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- getProcessor() - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack
-
The dispatch stack is contained within a processor, this can be null if
the stack is being used out of this context but layers may be relying on
this link to get information about the processor input ports and their
annotations for various reasons.
- getProcessor() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- getProcessor() - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
-
- getProcessor() - Method in interface org.apache.taverna.workflowmodel.ProcessorPort
-
Get the Processor to which this port belongs
- getProcessorId(String[]) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
-
- getProcessorID() - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
-
- getProcessorInputPort(Processor, Activity<?>, InputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getProcessorOutputPort(Processor, Activity<?>, OutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getProcessorProvenanceItem() - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- getProcessorReports() - Method in class org.apache.taverna.platform.report.WorkflowReport
-
- getProcessors() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
A Dataflow consists of a set of named Processor instances.
- getProcessors() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Return the list of all processors within the dataflow
- getProcessorsWithActivity(Dataflow, Activity<?>) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getProcessorsWithActivityInputPort(Dataflow, ActivityInputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getProcessorsWithActivityOutputPort(Dataflow, OutputPort) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getProfile() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getProfile() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the Profile
to use when executing the Workflow
.
- getProfile(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
- getProfile() - Method in class org.apache.taverna.platform.run.impl.Run
-
- getProfile(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getProfileName() - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Returns the name of the Profile
to use when running the
Workflow
.
- getProgress() - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductRecordReader
-
- getProgress() - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaRecordReader
-
- getProperties() - Method in class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
-
- getProperties() - Method in interface org.apache.taverna.monitor.MonitorNode
-
Each monitor node exposes a set of properties, which may or may not be
mutable
- getProperties() - Method in class org.apache.taverna.visit.VisitReport
-
- getProperties() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- getProperty(String) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getProperty(String) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
- getProperty(String) - Method in class org.apache.taverna.visit.VisitReport
-
- getPropertyKeys() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- getPropertyKeys() - Method in class org.apache.taverna.platform.report.ProcessorReport
-
- getProvenanceCollection() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
- getProvenanceReporter() - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
-
- getProvenanceReporter() - Method in interface org.apache.taverna.invocation.InvocationContext
-
- getProviderPriority() - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
-
- getProviderPriority() - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider
-
Get the priority of this provider.
- getPushedDataMap() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getPushedDataMap() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Return a map of the data pushed on the named port
- getPushedOwningProcess() - Method in class org.apache.taverna.invocation.IterationInternalEvent
-
Helper method for the pushIndex operation
- getQueue() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchJobQueueEvent
-
- getReference() - Method in interface org.apache.taverna.reference.ContextualizedT2Reference
-
- getReference() - Method in class org.apache.taverna.reference.impl.ContextualizedT2ReferenceImpl
-
- getReferenceService() - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
-
- getReferenceService() - Method in interface org.apache.taverna.invocation.InvocationContext
-
Return the reference service to be used within this invocation context
- getReferenceService() - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
-
- getReferenceService() - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- getReferenceService() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
- getReferenceSet(T2Reference) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
-
- getReferenceSet(T2Reference) - Method in interface org.apache.taverna.reference.ReferenceSetService
-
- getReferenceSetAsynch(T2Reference, ReferenceSetServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
- getReferenceSetAsynch(T2Reference, ReferenceSetServiceCallback) - Method in interface org.apache.taverna.reference.ReferenceSetService
-
Functionality the same as
getReferenceSet
but in asynchronous mode, returning immediately and
using the supplied callback to communicate its results.
- getReferenceSetService() - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- getReferenceSetService() - Method in interface org.apache.taverna.reference.ReferenceService
-
Returns the
ReferenceSetService
this ReferenceService uses, use
this when you need functionality from that service explicitly.
- getReferenceSetWithAugmentation(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
-
- getReferenceSetWithAugmentation(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetService
-
- getReferenceSetWithAugmentationAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetServiceCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
- getReferenceSetWithAugmentationAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceSetServiceCallback) - Method in interface org.apache.taverna.reference.ReferenceSetService
-
- getReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceBuilderSPI
-
Expose the type of the ExternalReferenceSPI that this builder can
construct
- getReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder
-
- getReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder
-
- getReferenceType() - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
Get the type of the entity to which this reference refers
- getReferenceType() - Method in interface org.apache.taverna.reference.T2Reference
-
To determine the entity that this reference points to we use an
enumeration of possible entity types
- getReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenBuilder
-
- getRemoveActivityEdit(Processor, Activity<?>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove an Activity from a Processor
- getRemoveActivityEdit(Processor, Activity<?>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove an ActivityInputPort from an Activity.
- getRemoveActivityInputPortEdit(Activity<?>, ActivityInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveActivityInputPortMappingEdit(Activity<?>, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove a ProcessorInputPort to ActivityInputPort
mapping from an Activity.
- getRemoveActivityInputPortMappingEdit(Activity<?>, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove an OutputPort from an Activity.
- getRemoveActivityOutputPortEdit(Activity<?>, ActivityOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveActivityOutputPortMappingEdit(Activity<?>, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove a ProcessorOutputPort to OutputPort mapping
from an Activity.
- getRemoveActivityOutputPortMappingEdit(Activity<?>, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveAnnotationEdit(AnnotationChain) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
-
- getRemoveAnnotationEdit(AnnotationChain) - Method in interface org.apache.taverna.annotation.Annotated
-
Remove an annotation object from the this annotated entity
- getRemoveConditionEdit(Processor, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Remove a condition previously applied to the specified pair of Processor
instances
- getRemoveConditionEdit(Processor, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove a DataflowInputPort from a Dataflow.
- getRemoveDataflowInputPortEdit(Dataflow, DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove a DataflowOutputPort from a Dataflow.
- getRemoveDataflowOutputPortEdit(Dataflow, DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveMergeEdit(Dataflow, Merge) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Removes a merge from the dataflow.
- getRemoveMergeEdit(Dataflow, Merge) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveProcessorEdit(Dataflow, Processor) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to remove a Processor from a Dataflow.
- getRemoveProcessorEdit(Dataflow, Processor) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Removes a Processor input port.
- getRemoveProcessorInputPortEdit(Processor, ProcessorInputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveProcessorInputPortEdit(ProcessorInputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getRemoveProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getRemoveProcessorOutputPortEdit(Processor, ProcessorOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRemoveProcessorOutputPortEdit(ProcessorOutputPort, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getRenameDataflowInputPortEdit(DataflowInputPort, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Rename a dataflow input port
- getRenameDataflowInputPortEdit(DataflowInputPort, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRenameDataflowOutputPortEdit(DataflowOutputPort, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Rename a dataflow output port
- getRenameDataflowOutputPortEdit(DataflowOutputPort, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRenameMergeEdit(Merge, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Rename a merge
- getRenameMergeEdit(Merge, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getRenameProcessorEdit(Processor, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Rename a processor
- getRenameProcessorEdit(Processor, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getReorderMergeInputPortsEdit(Merge, List<MergeInputPort>) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Returns an edit to reorder the list of MergeInputPortS in a Merge.
- getReorderMergeInputPortsEdit(Merge, List<MergeInputPort>) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getReplacementActivity() - Method in interface org.apache.taverna.workflowmodel.processor.activity.SupersededActivity
-
- getReport() - Method in class org.apache.taverna.platform.report.Invocation
-
- getReporter() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- getResolutionCost() - Method in class org.apache.taverna.reference.AbstractExternalReference
-
Default to a value of 0.0f for the resolution cost, but implementations
should at least attempt to set this to a more sensible level!
- getResolutionCost() - Method in interface org.apache.taverna.reference.ExternalReferenceSPI
-
Resolution cost is an informal guide to how costly the process of
de-referencing this reference would be.
- getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
- getResolutionCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
Default resolution cost of 0.0f whatever the contents
- getResolutionCost() - Method in class org.apache.taverna.t2referencetest.BlueReference
-
Default resolution cost of 1.0f whatever the contents
- getResolutionCost() - Method in class org.apache.taverna.t2referencetest.GreenReference
-
Default resolution cost of 1.0f whatever the contents
- getResolutionCost() - Method in class org.apache.taverna.t2referencetest.RedReference
-
Default resolution cost of 1.0f whatever the contents
- getResolutionCost() - Method in class org.apache.taverna.t2referencetest.YellowReference
-
Default resolution cost of 1.0f whatever the contents
- getResolvedDepth() - Method in interface org.apache.taverna.workflowmodel.Datalink
-
Each datalink has a resolved depth, this being the constant sum of index
array length + item depth for all tokens exchanged along this link.
- getResultId() - Method in class org.apache.taverna.visit.VisitReport
-
- getResumedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status last changed form PAUSED to RUNNING.
- getResumedDates() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the dates that the status changed from PAUSED to RUNNING.
- getRole() - Method in interface org.apache.taverna.annotation.AnnotationAssertion
-
The annotation assertion plays one of several roles within the annotation
chain, either an initial assertion, a refinement of a previous assertion
or a replacement of a previous assertion.
- getRole() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getRoot() - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Returns the root of the tree.
- getRunName(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
- getRunName(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getRuns() - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the list of runs that this service is managing.
- getRuns() - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getServiceURIsForAllUsernameAndPasswordPairs() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get service URIs associated with all username/password pairs currently in
the Keystore.
- getServiceURIsForAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get service URIs associated with all username/password pairs currently in
the Keystore.
- getServiceURLsforAllUsernameAndPasswordPairs() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Deprecated.
- getServiceUsernameAndPassword(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.ServiceUsernameAndPasswordProvider
-
Get the username and password pair for the given service URI.
- getServiceUsernameAndPasswordProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get the providers of username and passwords for services.
- getSessionID() - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
What is the unique identifier used by this connector
- getSetIterationStrategyStackEdit(Processor, IterationStrategyStack) - Method in interface org.apache.taverna.workflowmodel.Edits
-
Provide an edit that will configure a processors's iteration strategy
stack to the one provided.
- getSetIterationStrategyStackEdit(Processor, IterationStrategyStack) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getSink() - Method in interface org.apache.taverna.workflowmodel.Datalink
-
Get the sink for events flowing through this link
- getSource() - Method in interface org.apache.taverna.annotation.Curateable
-
Each annotation or curation has a resource from which the event is
inherently derived, for example if the annotation was created manually
after reading a paper the source would unambiguously specify the
publication.
- getSource() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- getSource() - Method in class org.apache.taverna.utility.TypedTreeModelEvent
-
The object on which the Event initially occurred.
- getSource() - Method in interface org.apache.taverna.workflowmodel.Datalink
-
Get the source for events flowing through this link
- getSourceReference() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getSourceReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI
-
Return the type of external reference that this translator consumes.
- getSourceReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
-
- getSourceReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
-
- getSourceReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenToRed
-
- getSourceType() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getSplits(JobContext) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputFormat
-
- getST() - Method in class org.apache.taverna.security.credentialmanager.impl.ParsedDistinguishedNameImpl
-
- getST() - Method in interface org.apache.taverna.security.credentialmanager.ParsedDistinguishedName
-
- getStackTraceElementString(StackTraceElementBean) - Static method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
-
- getStackTraceList() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
Used by Hibernate to bodge around problems with interface types in the
API
- getStackTraceStrings() - Method in interface org.apache.taverna.reference.ErrorDocument
-
If the error document is created from a
Throwable
it will have a
stack trace, in this case the stack trace is represented as a list of
StackTraceElement
beans
- getStackTraceStrings() - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
From interface, not used by hibernate internally
- getStartedDate() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the date that the status changed to RUNNING.
- getStartedDate() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the date that the status changed to RUNNING.
- getStartInternalDerbyServer() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getStartInternalDerbyServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getState() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getState() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
- getState() - Method in class org.apache.taverna.platform.report.Invocation
-
Returns the current
State
of the invocation.
- getState() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the current
State
.
- getState(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the current state of the run.
- getState() - Method in class org.apache.taverna.platform.run.impl.Run
-
Returns the current
State
of the
Run
.
- getState(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getState() - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
-
- getStateModel() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getStateModel() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Workflow state is available through a sub-tree of the monitor tree.
- getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
Generate an appropriate state object from the specified job event.
- getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
-
- getStateObject(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
-
- getStatus() - Method in class org.apache.taverna.visit.VisitReport
-
Determines the overall Status.
- getStrategies() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- getStrategies() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyStack
-
The iteration strategy stack consists of an ordered list of iteration
strategies.
- getStringValue() - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivity
-
- getSubject() - Method in class org.apache.taverna.platform.report.StatusReport
-
Returns the subject of this report.
- getSubject() - Method in class org.apache.taverna.visit.VisitReport
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.CompoundEdit
-
There is no explicit subject for a compound edit, so this method always
returns null.
- getSubject() - Method in interface org.apache.taverna.workflowmodel.Edit
-
Return the object to which this edit applies
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractActivityEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowInputPortEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDataflowOutputPortEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractDatalinkEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractMergeEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.impl.AbstractProcessorEdit
-
- getSubject() - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.AbstractDispatchLayerEdit
-
- getSubjectURI() - Method in class org.apache.taverna.platform.report.StatusReport
-
- getSubReports() - Method in class org.apache.taverna.visit.VisitReport
-
Provides a list of sub reports.
- getTarget() - Method in interface org.apache.taverna.annotation.CurationEvent
-
The curation event applies to a specific other event, either another
curation event or an annotation assertion.
- getTarget() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- getTarget() - Method in interface org.apache.taverna.workflowmodel.Condition
-
- getTargetReferenceType() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI
-
Return the type of external reference this translator constructs.
- getTargetReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
-
- getTargetReferenceType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
-
- getTargetReferenceType() - Method in class org.apache.taverna.t2referencetest.GreenToRed
-
- getTargetType() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getTavernaSSLSocketFactory() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get Taverna's SSLSocketFactory backed by Credential Manager's Keystore
and Truststore.
- getTavernaSSLSocketFactory() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- getTemporaryDerbyJDBC() - Method in class org.apache.taverna.platform.spring.jdbc.TemporaryJDBC
-
- getTerminalNode() - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- getTerminalNode() - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategy
-
- getText() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion
-
- getText() - Method in class org.apache.taverna.annotation.annotationbeans.MimeType
-
Return the MIME type as a string, mime types look like 'part/part'.
- getTheCredentialManagerDefaultDirectory(ApplicationConfiguration) - Static method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
Get the configuration directory where the security stuff will be/is saved
to.
- getTimeoutInSeconds() - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
- getTokenProcessingEntityWithEventForwardingOutputPort(EventForwardingOutputPort, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Get the TokenProcessingEntity (Processor, Merge or Dataflow) from the
workflow that contains the given EventForwardingOutputPort.
- getTokenProcessingEntityWithEventHandlingInputPort(EventHandlingInputPort, Dataflow) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Get the TokenProcessingEntity (Processor, Merge or Dataflow) from the
workflow that contains the given target EventHandlingInputPort.
- getTranslatedElementClass() - Method in interface org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort
-
The Java object type desired when the input data reference is converted
to an object.
- getTranslatedElementClass() - Method in class org.apache.taverna.workflowmodel.processor.activity.impl.ActivityInputPortImpl
-
- getTranslatedElementType() - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- getTranslationCost() - Method in interface org.apache.taverna.reference.ExternalReferenceTranslatorSPI
-
Return an approximate complexity cost of the translation.
- getTranslationCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteToInlineStringTranslator
-
- getTranslationCost() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringToInlineByteTranslator
-
- getTranslationCost() - Method in class org.apache.taverna.t2referencetest.GreenToRed
-
- getTranslators() - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- getTreePath() - Method in class org.apache.taverna.utility.TypedTreeModelEvent
-
For all events, except treeStructureChanged, returns the parent of the
changed nodes.
- getTrustConfirmationProviders() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get the providers of trust confirmation for HTTPS connections to external
services/sites
- getType() - Method in interface org.apache.taverna.annotation.CurationEvent
-
The curation event type specifies whether this curation event is a
validation, repudiation or neither of its target.
- getType() - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- getTypedId() - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
-
Used because technically you can't accept and return implementation types
in the methods on a bean which implements an interface, but Hibernate
needs to construct concrete input and output types!
- getUniqueMergeInputPortName(Merge, String, int) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
- getUnresolvedOutputs() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport
-
The workflow will be marked as invalid if any of the dataflow output
ports can't be typed based on incoming links.
- getUnresolvedOutputs() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
-
- getUnsatisfiedEntities() - Method in interface org.apache.taverna.workflowmodel.DataflowValidationReport
-
The workflow will be marked as invalid if there are entities with
unlinked input ports or where there are cycles causing the type checking
algorithm to give up.
- getUnsatisfiedEntities() - Method in class org.apache.taverna.workflowmodel.impl.DataflowValidationReportImpl
-
- getUpdateDataflowInternalIdentifierEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getUpdateDataflowInternalIdentifierEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getUpdateDataflowNameEdit(Dataflow, String) - Method in interface org.apache.taverna.workflowmodel.Edits
-
- getUpdateDataflowNameEdit(Dataflow, String) - Method in class org.apache.taverna.workflowmodel.impl.EditsImpl
-
- getUpperNumericValue() - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
-
- getUri() - Method in class org.apache.taverna.annotation.impl.URISource
-
- getUsername() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getUsername() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getUsername() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- getUsernameAndPasswordForService(URI, boolean, String) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Get a username and password pair for the given service's URI, or null if
it does not exit.
- getUsernameAndPasswordForService(String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- getUsernameAndPasswordForService(URI, boolean, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Get a username and password pair for the given service's URI, or null if
it does not exit.
- getUUID() - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- getUUID() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- getUuid() - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
Getter used by hibernate to retrieve the object uuid property.
- getValue() - Method in class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
-
- getValue() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
-
- getValue() - Method in interface org.apache.taverna.monitor.MonitorableProperty
-
Return the value of this property
- getValue() - Method in class org.apache.taverna.platform.execution.impl.local.StaticProperty
-
- getValue() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- getValue() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
- getValue() - Method in interface org.apache.taverna.reference.ValueCarryingExternalReference
-
Returns the value
- getValueType() - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- getValueType() - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
- getValueType() - Method in interface org.apache.taverna.reference.ValueCarryingExternalReference
-
Returns the type of the inlined value
- getVisitorClass() - Method in class org.apache.taverna.visit.DataflowCollation
-
- getVisitorClass() - Method in class org.apache.taverna.visit.VisitKind
-
The class that all visitors that extend/implement if they make this type
of visit.
- getVisitorClass() - Method in class org.apache.taverna.workflowmodel.health.HealthCheck
-
Sub-classes of HealthChecker are used to perform HealthCheck visits.
- getWorkflow() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getWorkflow() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the Workflow
to execute.
- getWorkflow(Dataflow) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getWorkflow(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
- getWorkflow() - Method in class org.apache.taverna.platform.run.impl.Run
-
- getWorkflow(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getWorkflowActivity(Activity<?>) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getWorkflowBundle() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getWorkflowBundle() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the WorkflowBundle
containing the Workflow
s required for execution.
- getWorkflowBundle() - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Returns the WorkflowBundle
.
- getWorkflowId() - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- getWorkflowId() - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
The uuid that belongs to the actual dataflow
- getWorkflowName() - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Returns the name of the Workflow
to run.
- getWorkflowObject() - Method in class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
-
- getWorkflowObject() - Method in interface org.apache.taverna.monitor.MonitorNode
-
Each monitor node can reference zero or one workflow object.
- getWorkflowProcessor(Processor) - Method in class org.apache.taverna.platform.execution.impl.local.WorkflowToDataflowMapper
-
- getWorkflowReport() - Method in class org.apache.taverna.platform.execution.api.AbstractExecution
-
- getWorkflowReport(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- getWorkflowReport() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Returns the WorkflowReport
for the execution.
- getWorkflowReport(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Returns the workflow report for the specified execution.
- getWorkflowReport(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Returns the status report for the run.
- getWorkflowReport() - Method in class org.apache.taverna.platform.run.impl.Run
-
Returns the status report for the run.
- getWorkflowReport(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- getWorkflowRunId() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- getWorkflowRunId() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Get the unique id of the wf run inside the facede.
- getWorkflowRunId() - Method in class org.apache.taverna.reference.WorkflowRunIdEntity
-
- getWorstStatus(Collection<VisitReport>) - Static method in class org.apache.taverna.visit.VisitReport
-
Determine the worst status from a collection of reports
- granularDepth - Variable in class org.apache.taverna.workflowmodel.AbstractOutputPort
-
- GreenBuilder - Class in org.apache.taverna.t2referencetest
-
Trivially build a GreenReference from an InputStream, implementing the
ExternalReferenceBuilderSPI interface.
- GreenBuilder() - Constructor for class org.apache.taverna.t2referencetest.GreenBuilder
-
- GreenReference - Class in org.apache.taverna.t2referencetest
-
GreenReferences carry their data as an internal String and have a resolution
cost of 1.1f whatever the value of that string.
- GreenReference() - Constructor for class org.apache.taverna.t2referencetest.GreenReference
-
- GreenReference(String) - Constructor for class org.apache.taverna.t2referencetest.GreenReference
-
- GreenToRed - Class in org.apache.taverna.t2referencetest
-
- GreenToRed() - Constructor for class org.apache.taverna.t2referencetest.GreenToRed
-
- ReactionTo - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description
-
Describes the type of message to which the various DispatchLayerFooReaction
classes are referring
- readFields(DataInput) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductInputSplit
-
- receiveBypassCompletion(Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
-
- receiveCompletion(int[]) - Method in class org.apache.taverna.activities.testutils.DummyCallback
-
- receiveCompletion(int[]) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback
-
If (and only if) the activity is streaming data then this method can be
called to signal a (possibly partial) completion of the stream.
- receiveCompletion(int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- receiveCompletion(int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
-
- receiveCompletion(String, String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
-
- receiveCompletion(String, String, int[], InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- receiveCompletion(int, Completion) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
Nodes can also receive completion events, the simplest being one
declaring that no further input is expected on the given input, or
partial completion events which are interpreted as 'no event with an
index array prefixed by the specified completion index array will be
received on the specified index'
- receiveCompletion(int, Completion) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
Completion events are passed straight through the same as jobs
- receiveData(String, String, int[], T2Reference, InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
Receive a single data event from an upstream process.
- receiveData(String, String, int[], T2Reference, InvocationContext) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- receivedCompletion - Variable in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.CompletionState
-
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
If an error occurs we can either handle the error or send it to the layer
above for further processing.
- receiveError(DispatchErrorEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Receive a single error reference from the layer below
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
-
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
-
Always send the error document job result on receiving a failure, at
least for now! This should be configurable, in effect this is the part
that ensures the processor never sees a top level failure.
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- receiveError(DispatchErrorEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- receiveEvent(WorkflowDataToken) - Method in interface org.apache.taverna.workflowmodel.EventHandlingInputPort
-
Receive an arbitrary workflow event.
- receiveEvent(IterationInternalEvent<?>) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer
-
Receive a Job or Completion, Jobs are emitted unaltered and cached,
Completion events trigger registration of a corresponding list - this may
be recursive in nature if the completion event's index implies nested
lists which have not been registered.
- receiveEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
-
- receiveEvent(IterationInternalEvent<? extends IterationInternalEvent<?>>) - Method in interface org.apache.taverna.workflowmodel.impl.Crystalizer
-
Receive a Job or Completion, Jobs are emitted unaltered and cached,
Completion events trigger registration of a corresponding list - this may
be recursive in nature if the completion event's index implies nested
lists which have not been registered.
- receiveEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
-
Receive an input event, relay it through the internal output port to all
connected entities
- receiveEvent(WorkflowDataToken) - Method in interface org.apache.taverna.workflowmodel.MergeInputPort
-
Receive an arbitrary workflow event.
- receiveEvent(IterationInternalEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
Receive an event to be fed into the top layer of the dispatch stack for
processing.
- receiveEvent(IterationInternalEvent<?>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
Receive a single job from an upstream IterationStrategyImpl in the stack.
- receiveEventFromStrategy(IterationInternalEvent<? extends IterationInternalEvent<?>>) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
Called by the final iteration strategy to push events onto the
dispatcher's queue
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
Receive a job from the layer above, store it for later retries and pass
it down to the next layer
- receiveJob(DispatchJobEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Receive a single job and associated set of activities from the layer
above
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ErrorBounce
-
If the job contains errors, or collections which contain errors
themselves then bounce a result message with error documents in back up
to the layer above
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Failover
-
Receive a job from the layer above, store it in the state map then relay
it to the layer below with a modified activity list containing only the
activity at index 0
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
Create the
ProvenanceItem
s and send them all across to the
ProvenanceConnector
except for the
IterationProvenanceItem
, this one is told what it's inputs are
but has to wait until the results are received before being sent across.
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke
-
Receive a job from the layer above and pick the first concrete activity
from the list to invoke.
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- receiveJob(Job, List<? extends Activity<?>>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- receiveJob(DispatchJobEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
- receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode
-
- receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl.TerminalNodeImpl
-
- receiveJob(int, Job) - Method in interface org.apache.taverna.workflowmodel.processor.iteration.IterationStrategyNode
-
The nodes within the iteration strategy, a tree structure, are event
based.
- receiveJob(int, Job) - Method in class org.apache.taverna.workflowmodel.processor.iteration.NamedInputPortNode
-
If this node receives a job it will always be pushed without modification
up to the parent
- receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- receiveJobQueue(DispatchJobQueueEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Receive a pointer to the job queue along with a set of activities, this
is received from the layer above in the dispatch stack or from the
DispatchStackImpl object itself if this is the top layer.
- receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- receiveJobQueue(DispatchJobQueueEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
- receiveMonitorableProperty(MonitorableProperty<?>, String) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchStack
-
The dispatch stack acts as an aggregator for monitorable properties
exposed by the dispatch layers.
- receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.activities.testutils.DummyCallback
-
- receiveResult(Map<String, T2Reference>, int[]) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback
-
Push a map of named identifiers out to the invocation layer which is then
responsible for wrapping them up into an appropriate Job object and
sending it up the dispatch stack.
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
If we see a result with an index matching one of those in the current
retry state we can safely forget that state object
- receiveResult(DispatchResultEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Receive a result from the layer below
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
-
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- receiveResult(Map<String, T2Reference>, int[]) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- receiveResult(DispatchResultEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
If we see a completion event with an index matching one of those in the
current retry state we can safely forget that state object
- receiveResultCompletion(DispatchCompletionEvent) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Receive a (possibly partial) completion event from the layer below.
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl.TopLayer
-
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop
-
- receiveResultCompletion(DispatchCompletionEvent) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Parallelize
-
Only going to receive this if the activity invocation was streaming, in
which case we need to handle all completion events and pass them up the
stack.
- receiveToken(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
-
- recordIdentifier() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
- recordIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- RedReference - Class in org.apache.taverna.t2referencetest
-
RedReferences carry their data as an internal String and have a resolution
cost of 0.9f whatever the value of that string.
- RedReference() - Constructor for class org.apache.taverna.t2referencetest.RedReference
-
- RedReference(String) - Constructor for class org.apache.taverna.t2referencetest.RedReference
-
- Reduce() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Reduce
-
- reduce(Text, Iterable<TextArrayWritable>, Reducer<Text, TextArrayWritable, Text, Text>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest.Reduce
-
- Reduce() - Constructor for class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Reduce
-
- reduce(LongWritable, Iterable<MapWritable>, Reducer<LongWritable, MapWritable, LongWritable, Text>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest.Reduce
-
- reduce(int[], Iterable<Map<String, Path>>, Reducer<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaReducer
-
- REFERENCE_SERVICE_CONTEXT - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- ReferenceContext - Interface in org.apache.taverna.reference
-
Many operations over the reference manager require access to an appropriate
context.
- ReferencedDataNature - Enum in org.apache.taverna.reference
-
Where possible ExternalReferenceSPI implementations should be able to
determine whether the data they refer to is textual or binary in nature.
- referenceFromString(String) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
-
Parse the reference contained in the string and return a
T2Reference
with the correct properties
- referenceFromString(String) - Method in interface org.apache.taverna.reference.ReferenceService
-
Given a string representation of a T2Reference create a new T2Reference
with the correct depth etc.
- referenceService - Variable in class org.apache.taverna.activities.testutils.DummyCallback
-
- ReferenceService - Interface in org.apache.taverna.reference
-
Top level access point to the reference manager for client code which is
aware of references and error documents.
- ReferenceServiceCacheProvider - Interface in org.apache.taverna.reference
-
A simple interface to be implemented by data access object cache providers,
intended to be used to inject cache implementations through AoP
- ReferenceServiceException - Exception in org.apache.taverna.reference
-
Thrown by methods in the ReferenceService, used to wrap any underlying
exceptions from lower layers.
- ReferenceServiceException() - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
-
- ReferenceServiceException(String) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
-
- ReferenceServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
-
- ReferenceServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceServiceException
-
- ReferenceServiceImpl - Class in org.apache.taverna.reference.impl
-
Implementation of ReferenceService, inject with ReferenceSetService,
ErrorDocumentService and ListService to enable.
- ReferenceServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceServiceImpl
-
- ReferenceServiceResolutionCallback - Interface in org.apache.taverna.reference
-
Used by the asynchronous form of the resolveIdentifier method in
ReferenceService
- ReferenceSet - Interface in org.apache.taverna.reference
-
A set of ExternalReferenceSPI instances, all of which point to the same (byte
equivalent) data.
- ReferenceSetAugmentationException - Exception in org.apache.taverna.reference
-
Thrown when the reference set augmentor is unable to provide at least one of
the desired types for any reason.
- ReferenceSetAugmentationException() - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
-
- ReferenceSetAugmentationException(String) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
-
- ReferenceSetAugmentationException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
-
- ReferenceSetAugmentationException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetAugmentationException
-
- referenceSetAugmentor - Variable in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
- ReferenceSetAugmentor - Interface in org.apache.taverna.reference
-
- ReferenceSetAugmentorCallback - Interface in org.apache.taverna.reference
-
- ReferenceSetAugmentorImpl - Class in org.apache.taverna.reference.impl
-
Implementation of ReferenceSetAugmentor using Dijkstra's shortest path
algorithm over a type graph built from SPI instance registries of reference
builders and reference translators.
- ReferenceSetAugmentorImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
-
Default constructor to make life easier when using Spring.
- referenceSetDao - Variable in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
- ReferenceSetDao - Interface in org.apache.taverna.reference
-
- ReferenceSetImpl - Class in org.apache.taverna.reference.impl
-
An implementation of ReferenceSet with the additional methods and metadata
required by Hibernate3 to allow it to be persisted in a relational store.
- ReferenceSetImpl(Set<ExternalReferenceSPI>, T2ReferenceImpl) - Constructor for class org.apache.taverna.reference.impl.ReferenceSetImpl
-
Construct a new ReferenceSetImpl with the given set of external
references and identifier.
- ReferenceSetImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetImpl
-
Default constructor, used by Hibernate when reconstructing this bean from
the database.
- referenceSetRetrievalFailed(ReferenceSetServiceException) - Method in interface org.apache.taverna.reference.ReferenceSetServiceCallback
-
Called if the retrieval failed for some reason
- referenceSetRetrieved(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetServiceCallback
-
Called when the requested
ReferenceSet
has been successfully
retrieved.
- referenceSetService - Variable in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
- ReferenceSetService - Interface in org.apache.taverna.reference
-
Provides facilities to register sets of ExternalReferenceSPI implementations
within the reference manager and to retrieve these sets by T2Reference either
as stored or with translation support.
- ReferenceSetServiceCallback - Interface in org.apache.taverna.reference
-
- ReferenceSetServiceException - Exception in org.apache.taverna.reference
-
RuntimeException subclass thrown by the reference set service layer
interfaces.
- ReferenceSetServiceException() - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
-
- ReferenceSetServiceException(String) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
-
- ReferenceSetServiceException(Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
-
- ReferenceSetServiceException(String, Throwable) - Constructor for exception org.apache.taverna.reference.ReferenceSetServiceException
-
- ReferenceSetServiceImpl - Class in org.apache.taverna.reference.impl
-
Implementation of ReferenceSetService, inject with an appropriate
ReferenceSetDao to enable.
- ReferenceSetServiceImpl() - Constructor for class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
-
- refreshInternalIdentifier() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- refService - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- register(Object, int, boolean, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
-
The top level registration method is used to register either as yet
unregistered ErrorDocuments and ReferenceSets (if these are passed in and
already have an identifier this call does nothing) and arbitrarily nested
Lists of the same.
- register(Object, int, boolean, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService
-
The top level registration method is used to register either as yet
unregistered ErrorDocuments and ReferenceSets (if these are passed in and
already have an identifier this call does nothing) and arbitrarily nested
Lists of the same.
- registerEmptyList(int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
-
- registerEmptyList(int, ReferenceContext) - Method in interface org.apache.taverna.reference.ListService
-
Register a new empty list with the specified depth.
- registerError(String, Throwable, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Register a new error document.
- registerError(String, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Equivalent to registerError(message, null, depth, context)
.
- registerError(Throwable, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Equivalent to registerError("", t, depth, context)
.
- registerError(String, Set<T2Reference>, int, ReferenceContext) - Method in interface org.apache.taverna.reference.ErrorDocumentService
-
Register a new error document.
- registerError(String, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
- registerError(Throwable, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
- registerError(String, Throwable, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
-
Register the specified error and any child errors (which have the same
namespace and local part but a lower depth, down to depth of zero
- registerError(String, Set<T2Reference>, int, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ErrorDocumentServiceImpl
-
- registerList(List<T2Reference>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ListServiceImpl
-
- registerList(List<T2Reference>, ReferenceContext) - Method in interface org.apache.taverna.reference.ListService
-
Register a new list of T2References.
- registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Create a new node in the monitor
- registerNode(Object, String) - Method in class org.apache.taverna.monitor.MonitorManager
-
Register a new node with this monitor.
- registerNode(Object, String, Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager
-
Register a new node with this monitor.
- registerNode(Object, String[]) - Method in class org.apache.taverna.monitor.MonitorManager
-
Register a new node with this monitor.
- registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.monitor.MonitorManager
-
Register a new node with this monitor.
- registerNode(Object, String[], Set<MonitorableProperty<?>>) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionMonitor
-
- RegisterNodeMessage(Object, String[], Set<MonitorableProperty<?>>) - Constructor for class org.apache.taverna.monitor.MonitorManager.RegisterNodeMessage
-
- registerReferenceSet(Set<ExternalReferenceSPI>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceSetServiceImpl
-
- registerReferenceSet(Set<ExternalReferenceSPI>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceSetService
-
- RemoteExecution - Class in org.apache.taverna.platform.execution.impl.remote
-
An
Execution
for executing a Taverna workflow on a Taverna Server.
- RemoteExecution(WorkflowBundle, Workflow, Profile, Bundle) - Constructor for class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- RemoteExecutionService - Class in org.apache.taverna.platform.execution.impl.remote
-
Service for executing Taverna workflows on a Taverna Server.
- RemoteExecutionService() - Constructor for class org.apache.taverna.platform.execution.impl.remote.RemoteExecutionService
-
- RemoteHealthChecker - Class in org.apache.taverna.workflowmodel.health
-
A RemoteHealthChecker performs a visit to an Activity by trying to contact a
specific endpoint
- RemoteHealthChecker() - Constructor for class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
- remove(Object) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- remove(int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- remove(int) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
- remove(MutableTreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
- removeAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- removeAnnotationAssertion(AnnotationAssertion<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationChainImpl
-
- removeAnnotationBean() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- removeAnnotationRole() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- removeAnnotationSource() - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- removeCreator(Person) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- removeCurationEvent(CurationEvent<?>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- removeDataflowInputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Remove the named dataflow input port
- removeDataflowInputPort(DataflowInputPort) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Remove the specified input port from this dataflow
- removeDataflowOutputPort(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Remove the named dataflow output port
- removeDataflowOutputPort(DataflowOutputPort) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Remove the specified output port from this dataflow
- removeEntity(Object) - Method in class org.apache.taverna.invocation.impl.InvocationContextImpl
-
- removeFacadeListener(FacadeListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- removeFacadeListener(FacadeListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Remove a previously registered failure listener
- removeFromParent() - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
- removeInput(NamedInputPortNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- removeInputByName(String) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- removeInputs() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
Remove existing input ports
- removeJob(String, AbstractErrorHandlerLayer<ConfigurationType>.JobState) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer
-
- removeLayer(DispatchLayer<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
- removeMerge(Merge) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- removeObserver(Observer<Message>) - Method in class org.apache.taverna.lang.observer.MultiCaster
-
Remove the observer and no longer send out any notifications about it
- removeObserver(Observer<Message>) - Method in interface org.apache.taverna.lang.observer.Observable
-
Remove a class who is currently observing
- removeObserver(Observer<MonitorManager.MonitorMessage>) - Method in class org.apache.taverna.monitor.MonitorManager
-
Remove a class who is currently observing
- removeObserver(Observer<KeystoreChangedEvent>) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Remove an observer of the changes to the Keystore or Truststore.
- removeObserver(Observer<KeystoreChangedEvent>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Remove an observer of the changes to the Keystore or Truststore.
- removeObserver(Observer<ProcessorFinishedEvent>) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- removeOutgoingLink(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
- removeOutputs() - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
Remove existing output ports.
- removeProcessor(Processor) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- removeReportListener(ReportListener) - Method in class org.apache.taverna.platform.report.StatusReport
-
- removeResultListener(ResultListener) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- removeResultListener(ResultListener) - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Remove a previously registered result listener
- removeResultListener(ResultListener) - Method in interface org.apache.taverna.workflowmodel.DataflowOutputPort
-
Remove a ResultListener
- removeStrategy(IterationStrategy) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl
-
- removeTreeModelListener(TypedTreeModelListener<NodeType>) - Method in interface org.apache.taverna.utility.TypedTreeModel
-
Removes a listener previously added with addTreeModelListener.
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
-
- renderFrom(InputStream, ReferencedDataNature, String) - Method in interface org.apache.taverna.reference.StreamToValueConverterSPI
-
Render the stream to the target object type
- renderIdentifier(T2Reference, Class<?>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
-
- renderIdentifier(T2Reference, Class<?>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService
-
Resolve the given identifier, building a POJO structure where the
non-list items are of the desired class.
- ReportListener - Interface in org.apache.taverna.platform.report
-
- requestRun(Runnable) - Method in class org.apache.taverna.activities.testutils.DummyCallback
-
- requestRun(Runnable) - Method in interface org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback
-
If an activity proxy wants to create a new thread of activity it should
use this method unless there is a very good reason not to.
- requestRun(Runnable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- requestRun(Runnable) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Loop.ConditionCallBack
-
- resetAuthCache() - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Reset the JVMs cache for authentication like HTTP Basic Auth.
- resetAuthCache() - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Reset the JVMs cache for authentication like HTTP Basic Auth.
- resetPassword() - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- resolutionFailed(ReferenceServiceException) - Method in interface org.apache.taverna.reference.ReferenceServiceResolutionCallback
-
Called when the resolution process has failed
- resolveAt(String, int[]) - Method in class org.apache.taverna.workflowmodel.impl.AbstractCrystalizer.CompletionAwareTreeCache
-
- resolveIdentifier(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in class org.apache.taverna.reference.impl.ReferenceServiceImpl
-
Perform recursive identifier resolution, building a collection structure
of Identified objects, any collection elements being IdentifiedLists of
Identified subclasses.
- resolveIdentifier(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext) - Method in interface org.apache.taverna.reference.ReferenceService
-
Perform recursive identifier resolution, building a collection structure
of Identified objects, any collection elements being IdentifiedLists of
Identified subclasses.
- resolveIdentifierAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceServiceResolutionCallback) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Wraps the synchronous form, using the executeRunnable method to schedule
it.
- resolveIdentifierAsynch(T2Reference, Set<Class<ExternalReferenceSPI>>, ReferenceContext, ReferenceServiceResolutionCallback) - Method in interface org.apache.taverna.reference.ReferenceService
-
As resolveIdentifier but using a callback object and returning
immediately
- ResultListener - Interface in org.apache.taverna.facade
-
Implement and use with the WorkflowInstanceFacade to listen for data
production events from the underlying workflow instance
- resultListeners - Variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- resultTokenProduced(WorkflowDataToken, String) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.FacadeResultListener
-
- resultTokenProduced(WorkflowDataToken, String) - Method in interface org.apache.taverna.facade.ResultListener
-
Called when a new result token is produced by the workflow instance.
- resultTokenProduced(WorkflowDataToken, String) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- resultWrappingDepth - Variable in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- resume(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- resume() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Resumes a paused execution.
- resume(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Resumes the execution of a paused workflow.
- resume() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- resume() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- resume(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Resumes a paused run.
- resume() - Method in class org.apache.taverna.platform.run.impl.Run
-
- resume(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- resumeWorkflow(String) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
Resume the workflow run with the specified id
- resumeWorkflowRun() - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- resumeWorkflowRun() - Method in interface org.apache.taverna.facade.WorkflowInstanceFacade
-
Resume the workflow run corresponding to this facade
- retainAll(Collection<?>) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- Retry - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
-
Implements retry policy with delay between retries and exponential backoff
- Retry() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
-
- Retry(int, int, int, double) - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Retry
-
- RetryConfig - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
-
- RetryConfig() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
- run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.CrossProductTest
-
- run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.DotProductTest
-
- run(String[]) - Method in class org.apache.taverna.platform.execution.impl.hadoop.Test
-
- Run - Class in org.apache.taverna.platform.run.impl
-
- Run(RunProfile) - Constructor for class org.apache.taverna.platform.run.impl.Run
-
Constructs a Run
from the specified RunProfile
.
- Run(String, Bundle) - Constructor for class org.apache.taverna.platform.run.impl.Run
-
- RUN_CLOSED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_CREATED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_DELETED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_OPENED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_PAUSED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_RESUMED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_STARTED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RUN_STOPPED - Static variable in interface org.apache.taverna.platform.run.api.RunService
-
- RunDeletionListener - Interface in org.apache.taverna.workflowmodel
-
A RunDeletionListener is notified when a run is deleted.
- RunProfile - Class in org.apache.taverna.platform.run.api
-
A
RunProfile
specifies the parameters required to run a
Workflow
.
- RunProfile(ExecutionEnvironment, WorkflowBundle, Bundle) - Constructor for class org.apache.taverna.platform.run.api.RunProfile
-
Constructs a
RunProfile
that specifies the parameters
required to run a
Workflow
.
- RunProfile(ExecutionEnvironment, WorkflowBundle, String, String, Bundle) - Constructor for class org.apache.taverna.platform.run.api.RunProfile
-
Constructs a
RunProfile
that specifies the parameters
required to run a
Workflow
.
- RunProfileException - Exception in org.apache.taverna.platform.run.api
-
Thrown when a RunProfile
doesn't contain the correct components
to run a workflow.
- RunProfileException() - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
-
- RunProfileException(String, Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
-
- RunProfileException(String) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
-
- RunProfileException(Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunProfileException
-
- RunService - Interface in org.apache.taverna.platform.run.api
-
Service for managing runs of Taverna workflows.
- RunServiceImpl - Class in org.apache.taverna.platform.run.impl
-
Implementation of the RunService
.
- RunServiceImpl() - Constructor for class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- RunStateException - Exception in org.apache.taverna.platform.run.api
-
Thrown when an operation is attempted when a workflow is in the wrong state,
e.g., resuming a workflow that is not paused.
- RunStateException() - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
-
- RunStateException(String, Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
-
- RunStateException(String) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
-
- RunStateException(Throwable) - Constructor for exception org.apache.taverna.platform.run.api.RunStateException
-
- sanitiseName(String) - Static method in class org.apache.taverna.workflowmodel.utils.Tools
-
Checks that the name does not have any characters that are invalid for a
Taverna name.
- satisfyConditions(String) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.impl.DispatchStackImpl
-
Called when a set of conditions which were unsatisfied in the context of
a given owning process become satisfied.
- save(String, Path) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Saves a run.
- save(String, Path) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- save(WorkflowReport, Path) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
-
- save(WorkflowReport, Bundle) - Method in class org.apache.taverna.platform.run.impl.WorkflowReportJSON
-
- saveProperties() - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- saveUsernameAndPasswordForService(String, String, String) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
- SemanticAnnotation - Class in org.apache.taverna.annotation.annotationbeans
-
A SemanticAssertion holds a String which contains RDF about an Object
- SemanticAnnotation() - Constructor for class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
-
- sendEvent(WorkflowDataToken) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
Forward the specified event to all targets
- sentJob - Variable in class org.apache.taverna.workflowmodel.processor.dispatch.layers.Invoke.InvokeCallBack
-
- SerializationException - Exception in org.apache.taverna.workflowmodel.serialization
-
- SerializationException(String, Exception) - Constructor for exception org.apache.taverna.workflowmodel.serialization.SerializationException
-
- SerializationException(String) - Constructor for exception org.apache.taverna.workflowmodel.serialization.SerializationException
-
- SerializeParam(Object) - Static method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- ServiceRegistry - Interface in org.apache.taverna.services
-
Register of Taverna services.
- ServiceRegistryImpl - Class in org.apache.taverna.services.impl
-
Simple implementation of a ServiceRegistry that discovers available services from the
ActivityService.
- ServiceRegistryImpl() - Constructor for class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- ServiceUsernameAndPasswordProvider - Interface in org.apache.taverna.security.credentialmanager
-
Defines an interface for providing a username and password for a service to
be invoked as part of a workflow run.
- set(int, T) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- setActivity(Activity<?>) - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- setActivity(Activity<?>) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- setActivity(Activity<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- setActivityFactories(List<ActivityFactory>) - Method in class org.apache.taverna.platform.capability.activity.impl.ActivityServiceImpl
-
Sets the list of available ActivityFactory
s.
- setActivityProvenanceItem(ActivityProvenanceItem) - Method in class org.apache.taverna.provenance.item.ProcessorProvenanceItem
-
- setActivityService(ActivityService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
Sets the service for creating activities.
- setActivityService(ActivityService) - Method in class org.apache.taverna.services.impl.ServiceRegistryImpl
-
- setAllowsLiteralValues(boolean) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- setAnnotationBean(AnnotationBeanSPI) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- setAnnotationRole(AnnotationRole) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- setAnnotations(Set<AnnotationChain>) - Method in class org.apache.taverna.annotation.AbstractAnnotatedThing
-
Set the annotation chains associated with this annotated object.
- setAnnotations(Set<AnnotationChain>) - Method in interface org.apache.taverna.annotation.Annotated
-
- setAnnotationSource(AnnotationSourceSPI) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- setAnnotationString(Annotated<?>, Class<?>, String, Edits) - Static method in class org.apache.taverna.workflowmodel.utils.AnnotationTools
-
- setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
Sets the applicationConfiguration.
- setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Sets the applicationConfiguration.
- setApplicationConfiguration(ApplicationConfiguration) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
-
Sets the applicationConfiguration.
- setApproximateSizeInBytes(Long) - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
-
- setBackoffFactor(float) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
- setBean(Object) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- setBuilders(List<ExternalReferenceBuilderSPI<?>>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
-
Inject a list containing all known implementations of
ExternalReferenceBuilderSPI.
- setBuilders(List<ExternalReferenceBuilderSPI<?>>) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- setCacheProvider(ReferenceServiceCacheProvider) - Method in class org.apache.taverna.reference.impl.CacheAspect
-
Inject an instance of ReferenceServiceCacheProvider
- setCancelledDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status changed to CANCELLED.
- setCause(Throwable) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- setCharset(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
Setter used by hibernate to set the charset property of the file
reference
- setCheckTime(long) - Method in class org.apache.taverna.visit.VisitReport
-
- setClassName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- setCompletedDate(Date) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the date that the status changed to COMPLETED.
- setCompletedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status changed to COMPLETED.
- setCondition(Activity<?>) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- setConfigurationDirectoryPath(Path) - Method in interface org.apache.taverna.security.credentialmanager.CredentialManager
-
Set the directory where Credential Manager's Keystore and Truststore
files will be read from.
- setConfigurationDirectoryPath(Path) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Set the directory where Credential Manager's Keystore and Truststore
files will be read from.
- setContainsErrors(boolean) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
This method is only ever called from within Hibernate when
re-constructing the identifier component to set the error property of the
identifier.
- setContent(String) - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
-
- setContents(String) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- setContents(String) - Method in class org.apache.taverna.reference.impl.external.object.InlineStringReference
-
Set the 'value' of this reference as a string.
- setContents(String) - Method in class org.apache.taverna.t2referencetest.BlueReference
-
Set the 'value' of this reference as a string.
- setContents(String) - Method in class org.apache.taverna.t2referencetest.GreenReference
-
Set the 'value' of this reference as a string.
- setContents(String) - Method in class org.apache.taverna.t2referencetest.RedReference
-
Set the 'value' of this reference as a string.
- setContents(String) - Method in class org.apache.taverna.t2referencetest.YellowReference
-
Set the 'value' of this reference as a string.
- setConverters(List<ValueToReferenceConverterSPI>) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Inject value to reference convertor SPI
- setCreatedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status was set to CREATED.
- setCreators(List<Person>) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- setCredentialManager(CredentialManager) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerAuthenticator
-
- setCurationEventType(CurationEventType) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- setCurrentPort(int) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setCurrentPort(int) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setData(T2Reference) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setDatabaseConfiguration(DatabaseConfiguration) - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
Sets the databaseConfiguration.
- setDataBundle(Bundle) - Method in class org.apache.taverna.platform.report.WorkflowReport
-
- setDataBundle(Bundle) - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Sets the Bundle
containing the data values for the
Workflow
.
- setDataflow(Dataflow) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- setDataflowID(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- setDataMap(Map<String, T2Reference>) - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
-
- setDataNature(ReferencedDataNature) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- setDataNatureName(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
- setDate(Date) - Method in class org.apache.taverna.annotation.impl.AnnotationAssertionImpl
-
- setDepth(int) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
This method is only ever called from within Hibernate when
re-constructing the identifier component to set the depth of the
identifier.
- setDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
- setDepth(int) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- setDispatchLayerFactories(List<DispatchLayerFactory>) - Method in class org.apache.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl
-
Sets the list of available DispatchLayerFactory
s.
- setDispatchLayerService(DispatchLayerService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
Sets the service for creating dispatch layers.
- setDispatchStack(DispatchStack) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.AbstractDispatchLayer
-
- setDispatchStack(DispatchStack) - Method in interface org.apache.taverna.workflowmodel.processor.dispatch.DispatchLayer
-
Set the parent dispatch stack of this layer, this is called when a layer
is added to the dispatch stack and can be safely ignored by end users of
this API
- setDisputeEventDetails(DisputeEventDetails) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- setDocumentationURL(URL) - Method in class org.apache.taverna.annotation.annotationbeans.DocumentationUrl
-
- setDriverClassName(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setDriverClassName(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setEdits(Edits) - Method in class org.apache.taverna.activities.dataflow.DataflowActivityFactory
-
- setEdits(Edits) - Method in class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- setEdits(Edits) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
Sets the Edits Service for creating Taverna Dataflows.
- setEdits(Edits) - Method in class org.apache.taverna.workflowmodel.processor.activity.AbstractActivity
-
- setEdits(Edits) - Method in interface org.apache.taverna.workflowmodel.processor.activity.Activity
-
- setEnactmentEnded(Timestamp) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setEnactmentStarted(Timestamp) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setEndpointExpiryInMilliseconds(int) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
- setErrorDao(ErrorDocumentDao) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
Inject the error document data access object.
- setErrorDocumentService(ErrorDocumentService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Inject error document service
- setErrorItem(ErrorProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setErrorReferenceSet(Set) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
Used by Hibernate to bodge around problems with interface types in the
API
- setErrorType(String) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- setEventAdmin(EventAdmin) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- setExceptionMessage(String) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
- setExecutionEnvironment(ExecutionEnvironment) - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Sets the ExecutionEnvironment
used to execute the
Workflow
.
- setExecutionEnvironmentService(ExecutionEnvironmentService) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- setExecutionServices(Set<ExecutionService>) - Method in class org.apache.taverna.platform.execution.impl.ExecutionEnvironmentServiceImpl
-
Sets the ExecutionServices that will be used to find ExecutionEnvironments.
- setExposeDatanature(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setExposeDatanature(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setExternalReferences(Set<ExternalReferenceSPI>) - Method in class org.apache.taverna.reference.impl.ReferenceSetImpl
-
This method is only ever called from within Hibernate, and is used to
initialize the set of external references.
- setFacadeID(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- setFailedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status changed to FAILED.
- setFileName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- setFilePath(String) - Method in class org.apache.taverna.reference.impl.external.file.FileReference
-
Setter used by hibernate to set the file path property of the file
reference
- setFilterDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.AbstractFilteringInputPort
-
- setFinal(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setFinal(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- setFragmentForURI(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
-
- setFragmentForURI(URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
- setGranularDepth(int) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
- setGranularDepth(int) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean
-
- setHandledReferenceSchemes(List<Class<? extends ExternalReferenceSPI>>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- setHttpUrlString(String) - Method in class org.apache.taverna.reference.impl.external.http.HttpReference
-
Setter used by hibernate to set the file path property of the file
reference
- setIdentification(String) - Method in class org.apache.taverna.annotation.annotationbeans.IdentificationAssertion
-
- setIdentifier(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- setIdentifier(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
A unique id for this event.
- setImmutable() - Method in interface org.apache.taverna.workflowmodel.Dataflow
-
Mark this dataflow as immutable.
- setImmutable() - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
- setIncomingLink(Datalink) - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
-
- setIndex(int[]) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setIndex(int[]) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- setInitialBuilder(ExternalReferenceBuilderSPI<?>) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- setInitialDelay(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
- setInMemory(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setInMemory(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setInput(String, Path) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the value of an input port.
- setInputDataItem(InputDataProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setInputPort(boolean) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setInputPortDefinitions(List<ActivityInputPortDefinitionBean>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
-
- setInputs(Map<String, Path>) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the values of input ports.
- setInstance(MonitorManager) - Static method in class org.apache.taverna.monitor.MonitorManager
-
Set the MonitorManager singleton instance.
- setInternalId(String) - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
-
- setInvocationContext(InvocationContext) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
- setInvocationEnded(Timestamp) - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
-
- setInvocationProcessId(String) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- setInvocationStarted(Date) - Method in class org.apache.taverna.provenance.item.InvocationStartedProvenanceItem
-
- setInvocationStarted(Timestamp) - Method in class org.apache.taverna.provenance.item.WorkflowProvenanceItem
-
- setIteration(int[]) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setIterationProvenanceItem(IterationProvenanceItem) - Method in class org.apache.taverna.provenance.item.ActivityProvenanceItem
-
- setIterationStrategyStack(IterationStrategyStackImpl) - Method in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- setJavaTruststorePassword(String) - Method in interface org.apache.taverna.security.credentialmanager.JavaTruststorePasswordProvider
-
Set the Java truststore password.
- setJavaTruststorePasswordProviders(List<JavaTruststorePasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Set the Java truststore password providers for providing the password to
encrypt/decrypt the Java's default truststore.
- setJDBCUri(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setJDBCUri(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setJobsCompleted(int) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Set the number of completed jobs.
- setJobsCompletedWithErrors(int) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Set the number of jobs that have completed, but with errors.
- setJobsQueued(int) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Set the number of queued jobs.
- setJobsStarted(int) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Set the number of started jobs.
- setKind(VisitKind) - Method in class org.apache.taverna.visit.VisitReport
-
- setLineNumber(int) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- setListContents(List) - Method in class org.apache.taverna.reference.impl.T2ReferenceListImpl
-
This is only called from Hibernate, outside of test code, so is
relatively safe to leave unchecked.
- setListDao(ListDao) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
Inject the list data access object.
- setListService(ListService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Inject list service
- setLocalName(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowImpl
-
Sets the local name for the dataflow
- setLocalPart(String) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
This method is only ever called from within Hibernate when
re-constructing the identifier component to set the local part of the
identifier.
- setLowerNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
-
- setMasterPassword(String) - Method in class org.apache.taverna.security.credentialmanager.impl.DefaultMasterPasswordProvider
-
- setMasterPassword(String) - Method in interface org.apache.taverna.security.credentialmanager.MasterPasswordProvider
-
Set the master password.
- setMasterPasswordProviders(List<MasterPasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Set the master password providers for providing the master password to
encrypt/decrypt the Credential Maager's Keystore and Truststore.
- setMaxDelay(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
- setMaximumJobs(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.ParallelizeConfig
-
- setMaxRetries(int) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.RetryConfig
-
- setMessage(String) - Method in class org.apache.taverna.provenance.item.ErrorProvenanceItem
-
- setMessage(String) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
- setMessage(String) - Method in class org.apache.taverna.visit.VisitReport
-
Sets the message
- setMethodName(String) - Method in class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- setMimeType(String) - Method in class org.apache.taverna.annotation.annotationbeans.SemanticAnnotation
-
- setMimeTypes(List<String>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- setMimeTypes(Set<URI>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.impl.AbstractEventHandlingInputPort
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.impl.BasicEventForwardingOutputPort
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.impl.DataflowInputPortImpl
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.impl.ProcessorImpl
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.ActivityAndBeanWrapper
-
- setName(String) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortDefinitionBean
-
- setNamespace(String) - Method in class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
-
Set the namespace for identifiers generated by this class as a string
- setNamespace(String) - Method in class org.apache.taverna.reference.impl.UUIDT2ReferenceGenerator
-
Set the namespace for identifiers generated by this class as a string
- setNamespacePart(String) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
This method is only ever called from within Hibernate when
re-constructing the identifier component to set the namespace part of the
identifier.
- setNestedDataflow(Dataflow) - Method in class org.apache.taverna.activities.dataflow.DataflowActivity
-
- setNestedDataflow(Dataflow) - Method in interface org.apache.taverna.workflowmodel.processor.activity.NestedDataflow
-
- setNestedWorkflowReport(WorkflowReport) - Method in class org.apache.taverna.platform.report.ActivityReport
-
- setNodeRemovalDelay(long) - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Nodes will be removed at least delayTime milliseconds after their initial
deregistration request, this allows UI components to show nodes which
would otherwise vanish almost instantaneously.
- setNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericValueAssertion
-
- setObject(Object) - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
- setOutput(String, Path) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the value of an output port.
- setOutputDataItem(OutputDataProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setOutputPortDefinitions(List<ActivityOutputPortDefinitionBean>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean
-
- setOutputs(Map<String, Path>) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the values of input ports.
- setOwningProcess(String) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- setOwningProcess(String) - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
-
- setParent(MutableTreeNode) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
Implements IterationStrategyNode
- setParentId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- setParentId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
The parent of this provenance Item.
- setParentIterationItem(IterationProvenanceItem) - Method in class org.apache.taverna.provenance.item.IterationProvenanceItem
-
- setParentReport(PARENT) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the parent report.
- setPassword(char[]) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- setPausedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status last changed to PAUSED.
- setPort(int) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setPort(String) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setPort(int) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setPort(String) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setPortName(String) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setPrimaryKey(int) - Method in class org.apache.taverna.reference.AbstractExternalReference
-
Used by Hibernate internally to establish a foreign key relationship
between this abstract superclass and tables corresponding to
implementations of the ExternalReference interface.
- setProcessId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- setProcessId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
The workflow model id that is supplied during enactment eg
facade0:dataflow2:processor1
- setProcessor(Processor) - Method in class org.apache.taverna.workflowmodel.ProcessorFinishedEvent
-
- setProcessorProvenanceItem(ProcessorProvenanceItem) - Method in class org.apache.taverna.provenance.item.ProcessProvenanceItem
-
- setProfileName(String) - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Sets the name of the Profile
to use when running the
Workflow
.
- setProperties(Properties) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- setProperty(T) - Method in interface org.apache.taverna.monitor.SteerableProperty
-
Set the property value
- setProperty(String, Object) - Method in class org.apache.taverna.platform.execution.impl.local.LocalProcessorReport
-
- setProperty(String, Object) - Method in class org.apache.taverna.platform.report.ProcessorReport
-
Set an additional property
- setProperty(String, Object) - Method in class org.apache.taverna.visit.VisitReport
-
- setProvenanceEnabled(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setProvenanceEnabled(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setReferenceService(ReferenceService) - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecutionService
-
Sets the reference service.
- setReferenceService(ReferenceService) - Method in class org.apache.taverna.provenance.item.DataProvenanceItem
-
- setReferenceService(ReferenceService) - Method in class org.apache.taverna.provenance.item.WorkflowDataProvenanceItem
-
- setReferenceService(ReferenceService) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
- setReferenceSetAugmentor(ReferenceSetAugmentor) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Inject the ReferenceSetAugmentor used to translate or construct new
ExternalReferenceSPI instances within a ReferenceSet
- setReferenceSetDao(ReferenceSetDao) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Inject the reference set data access object.
- setReferenceSetService(ReferenceSetService) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Inject reference set service
- setReferenceType(T2ReferenceType) - Method in class org.apache.taverna.reference.impl.T2ReferenceImpl
-
This method is only ever called from within Hibernate when
re-constructing the identifier component to set the reference type
property of the identifier.
- setReporter(ProvenanceReporter) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
Tell this layer what
ProvenanceConnector
implementation is being
used to capture the
ProvenanceItem
s.
- setResultId(int) - Method in class org.apache.taverna.visit.VisitReport
-
- setResumedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status last changed form PAUSED to RUNNING.
- setRunFirst(boolean) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.LoopConfiguration
-
- setServiceUsernameAndPassword(URI, UsernamePassword) - Method in interface org.apache.taverna.security.credentialmanager.ServiceUsernameAndPasswordProvider
-
Set the username and password pair for the given service URI.
- setServiceUsernameAndPasswordProviders(List<ServiceUsernameAndPasswordProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Set the providers of username and passwords for services.
- setSessionID(String) - Method in interface org.apache.taverna.provenance.reporter.ProvenanceReporter
-
A unique identifier for this run of provenance, should correspond to the
initial
WorkflowProvenanceItem
idenifier that gets sent through
- setShouldSave(boolean) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- setSourceReference(ExternalReferenceSPI) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- setStackTraceList(List) - Method in class org.apache.taverna.reference.impl.ErrorDocumentImpl
-
Used by Hibernate to bodge around problems with interface types in the
API
- setStartedDate(Date) - Method in class org.apache.taverna.platform.report.Invocation
-
Sets the date that the status changed to RUNNING.
- setStartedDate(Date) - Method in class org.apache.taverna.platform.report.StatusReport
-
Sets the date that the status changed to RUNNING.
- setStartInternalDerbyServer(boolean) - Method in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- setStartInternalDerbyServer(boolean) - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- setState(WorkflowInstanceFacade.State) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- setState(State) - Method in class org.apache.taverna.platform.report.StatusReport
-
- setState(WorkflowInstanceFacade.State) - Method in class org.apache.taverna.provenance.item.DataflowRunComplete
-
- setStatus(VisitReport.Status) - Method in class org.apache.taverna.visit.VisitReport
-
Sets the status of this report.
- setSubject(Object) - Method in class org.apache.taverna.visit.VisitReport
-
- setSubReports(Collection<VisitReport>) - Method in class org.apache.taverna.visit.VisitReport
-
Replaces the List of sub reports with those provided.
- setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractErrorDocumentServiceImpl
-
Inject the T2Reference generator used to allocate new IDs when
registering ErrorDocuments
- setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractListServiceImpl
-
Inject the T2Reference generator used to allocate new IDs when
registering lists of T2Reference
- setT2ReferenceGenerator(T2ReferenceGenerator) - Method in class org.apache.taverna.reference.impl.AbstractReferenceSetServiceImpl
-
Inject the T2Reference generator used to allocate new IDs when
registering sets of ExternalReferenceSPI
- setTargetEvent(Curateable) - Method in class org.apache.taverna.annotation.impl.DisputeEvent
-
- setText(String) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractTextualValueAssertion
-
- setTimeoutInSeconds(int) - Static method in class org.apache.taverna.workflowmodel.health.RemoteHealthChecker
-
- setTranslatedElementType(Class<?>) - Method in class org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean
-
- setTranslators(List<ExternalReferenceTranslatorSPI<?, ?>>) - Method in class org.apache.taverna.reference.impl.ReferenceSetAugmentorImpl
-
Inject a list containing all known implementations of
ExternalReferenceTranslatorSPI.
- setTranslators(List<ExternalReferenceTranslatorSPI<?, ?>>) - Method in class org.apache.taverna.reference.impl.TranslationPath
-
- setTrustConfirmationProviders(List<TrustConfirmationProvider>) - Method in class org.apache.taverna.security.credentialmanager.impl.CredentialManagerImpl
-
Set the providers of trust confirmation for HTTPS connections to external
services/sites.
- setTypedId(T2ReferenceImpl) - Method in class org.apache.taverna.reference.impl.AbstractEntityImpl
-
This method is only ever called from within Hibernate, and is used to
initialize the unique ID of this reference set.
- setup(Mapper<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaMapper
-
- setup(Reducer<int[], Map<String, Path>, Object, Object>.Context) - Method in class org.apache.taverna.platform.execution.impl.hadoop.TavernaReducer
-
- setUpperNumericValue(NumericType) - Method in class org.apache.taverna.annotation.annotationbeans.AbstractNumericRangeAssertion
-
- setUri(URI) - Method in class org.apache.taverna.annotation.impl.URISource
-
- setUserInfoForURI(URI, String) - Method in interface org.apache.taverna.security.credentialmanager.DistinguishedNameParser
-
- setUserInfoForURI(URI, String) - Method in class org.apache.taverna.security.credentialmanager.impl.DistinguishedNameParserImpl
-
- setUsername(String) - Method in class org.apache.taverna.security.credentialmanager.UsernamePassword
-
- setUserObject(Object) - Method in class org.apache.taverna.workflowmodel.processor.iteration.AbstractIterationStrategyNode
-
- setUuid(String) - Method in class org.apache.taverna.reference.impl.external.object.VMObjectReference
-
Setter used by hibernate to set the object uuid property.
- setValue(String) - Method in class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
-
- setValue(byte[]) - Method in class org.apache.taverna.reference.impl.external.object.InlineByteArrayReference
-
- setValueBuilders(List<StreamToValueConverterSPI>) - Method in class org.apache.taverna.reference.impl.AbstractReferenceServiceImpl
-
Inject stream to value converter SPI
- setWasTimeConsuming(boolean) - Method in class org.apache.taverna.visit.VisitReport
-
- setWorkflow(WorkflowProvenanceItem) - Method in class org.apache.taverna.workflowmodel.processor.dispatch.layers.IntermediateProvenance
-
- setWorkflowBundle(WorkflowBundle) - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Sets the WorkflowBundle
containing the Workflow
to run.
- setWorkflowBundleIO(WorkflowBundleIO) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- setWorkflowId(String) - Method in class org.apache.taverna.provenance.item.AbstractProvenanceItem
-
- setWorkflowId(String) - Method in interface org.apache.taverna.provenance.item.ProvenanceItem
-
The uuid that belongs to the actual dataflow
- setWorkflowName(String) - Method in class org.apache.taverna.platform.run.api.RunProfile
-
Sets the name of the Workflow
to run.
- setWorkflowRunId(String) - Method in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- setWorkflowRunId(String) - Method in class org.apache.taverna.reference.WorkflowRunIdEntity
-
- SharedVocabulary - Enum in org.apache.taverna.provenance.vocabulary
-
Static strings which identify all the
ProvenanceItem
s and
ProvenanceEventType
s
- shouldTrustCertificate(X509Certificate[]) - Method in interface org.apache.taverna.security.credentialmanager.TrustConfirmationProvider
-
If the given public key certificate should be trusted or not.
- showMonitorFrame() - Method in class org.apache.taverna.monitor.impl.MonitorTreeModel
-
Very simple UI!
- SimpleCacheProviderImpl - Class in org.apache.taverna.reference.impl
-
Completely naive cache provider that just stores everything in a map.
- SimpleCacheProviderImpl() - Constructor for class org.apache.taverna.reference.impl.SimpleCacheProviderImpl
-
- SimpleT2ReferenceGenerator - Class in org.apache.taverna.reference.impl
-
Simple implementation of T2ReferenceGenerator intended to be injected into
the service layers for integration testing.
- SimpleT2ReferenceGenerator() - Constructor for class org.apache.taverna.reference.impl.SimpleT2ReferenceGenerator
-
- size() - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- source - Variable in class org.apache.taverna.utility.TypedTreeModelEvent
-
- stack - Variable in class org.apache.taverna.workflowmodel.processor.iteration.impl.IterationStrategyImpl
-
- StackTraceElementBean - Interface in org.apache.taverna.reference
-
Used by the
ErrorDocument
interface to represent a frame within a
stack trace
- StackTraceElementBeanImpl - Class in org.apache.taverna.reference.impl
-
Simple bean implementation of StackTraceElement for Hibernate
- StackTraceElementBeanImpl() - Constructor for class org.apache.taverna.reference.impl.StackTraceElementBeanImpl
-
- start(String) - Method in class org.apache.taverna.platform.execution.api.AbstractExecutionService
-
- start() - Method in interface org.apache.taverna.platform.execution.api.Execution
-
Starts the execution.
- start(String) - Method in interface org.apache.taverna.platform.execution.api.ExecutionService
-
Starts the execution of a workflow.
- start() - Method in class org.apache.taverna.platform.execution.impl.local.LocalExecution
-
- start() - Method in class org.apache.taverna.platform.execution.impl.remote.RemoteExecution
-
- start(String) - Method in interface org.apache.taverna.platform.run.api.RunService
-
Starts a run.
- start() - Method in class org.apache.taverna.platform.run.impl.Run
-
- start(String) - Method in class org.apache.taverna.platform.run.impl.RunServiceImpl
-
- START_INTERNAL_DERBY - Static variable in interface org.apache.taverna.configuration.database.DatabaseConfiguration
-
- startDerbyNetworkServer() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
-
- startDerbyNetworkServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
- State - Enum in org.apache.taverna.platform.report
-
Valid states for status reports.
- stateChange(WorkflowInstanceFacade, WorkflowInstanceFacade.State, WorkflowInstanceFacade.State) - Method in interface org.apache.taverna.facade.FacadeListener
-
- stateChanged(State, State) - Method in interface org.apache.taverna.platform.report.ReportListener
-
- stateLastModified - Variable in class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl
-
- StateProperty() - Constructor for class org.apache.taverna.facade.impl.WorkflowInstanceFacadeImpl.StateProperty
-
- StaticProperty - Class in org.apache.taverna.platform.execution.impl.local
-
A MonitorableProperty with fixed values.
- StaticProperty(MonitorableProperty<?>) - Constructor for class org.apache.taverna.platform.execution.impl.local.StaticProperty
-
Records the state of the MonitorableProperty.
- StatusReport<SUBJECT extends Ported,PARENT extends StatusReport<?,?>> - Class in org.apache.taverna.platform.report
-
Report about the
State
of a workflow component.
- StatusReport(SUBJECT) - Constructor for class org.apache.taverna.platform.report.StatusReport
-
Constructs a new StatusReport
for the subject and sets the created date to the
current date.
- SteerableProperty<T> - Interface in org.apache.taverna.monitor
-
Some monitorable properties are mutable and can be written to by steering
agents or other clients.
- Stop - Class in org.apache.taverna.workflowmodel.processor.dispatch.layers
-
This layer allows for the cancellation, pausing and resuming of workflow
runs.
- Stop() - Constructor for class org.apache.taverna.workflowmodel.processor.dispatch.layers.Stop
-
- stopDerbyNetworkServer() - Method in interface org.apache.taverna.configuration.database.DatabaseManager
-
- stopDerbyNetworkServer() - Method in class org.apache.taverna.configuration.database.impl.DatabaseManagerImpl
-
- store() - Method in class org.apache.taverna.configuration.database.impl.DatabaseConfigurationImpl
-
- store(ErrorDocument) - Method in interface org.apache.taverna.reference.ErrorDocumentDao
-
Store a named ErrorDocument to the database.
- store(ErrorDocument) - Method in class org.apache.taverna.reference.impl.InMemoryErrorDocumentDao
-
- store(IdentifiedList<T2Reference>) - Method in class org.apache.taverna.reference.impl.InMemoryListDao
-
- store(ReferenceSet) - Method in class org.apache.taverna.reference.impl.InMemoryReferenceSetDao
-
- store(IdentifiedList<T2Reference>) - Method in interface org.apache.taverna.reference.ListDao
-
Store a named and populated IdentifiedList of T2Reference to the
database.
- store(ReferenceSet) - Method in interface org.apache.taverna.reference.ReferenceSetDao
-
Store the specified new reference set
- StreamToBooleanConverter - Class in org.apache.taverna.reference.impl.external.object
-
- StreamToBooleanConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToBooleanConverter
-
- StreamToByteArrayConverter - Class in org.apache.taverna.reference.impl.external.object
-
Build a byte[] from an InputStream
- StreamToByteArrayConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToByteArrayConverter
-
- StreamToDoubleConverter - Class in org.apache.taverna.reference.impl.external.object
-
- StreamToDoubleConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToDoubleConverter
-
- StreamToIntegerConverter - Class in org.apache.taverna.reference.impl.external.object
-
- StreamToIntegerConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToIntegerConverter
-
- StreamToStringConverter - Class in org.apache.taverna.reference.impl.external.object
-
Build a String from an InputStream
- StreamToStringConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToStringConverter
-
- StreamToValueConverterSPI<T> - Interface in org.apache.taverna.reference
-
SPI for objects that can render a POJO from an InputStream
- StreamToVMObjectReferenceConverter - Class in org.apache.taverna.reference.impl.external.object
-
Builds a VMObjectReference from an InputStream.
- StreamToVMObjectReferenceConverter() - Constructor for class org.apache.taverna.reference.impl.external.object.StreamToVMObjectReferenceConverter
-
- StringConstantActivity - Class in org.apache.taverna.activities.stringconstant
-
An Activity that holds a constant string value.
- StringConstantActivity() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivity
-
- StringConstantActivityFactory - Class in org.apache.taverna.activities.stringconstant
-
- StringConstantActivityFactory() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivityFactory
-
- StringConstantActivityHealthChecker - Class in org.apache.taverna.activities.stringconstant
-
- StringConstantActivityHealthChecker() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
-
- StringConstantConfigurationBean - Class in org.apache.taverna.activities.stringconstant
-
Configuration bean for setting up a StringConstantActivity.
The only thing to be configured is the string value, since the ports are fixed.
- StringConstantConfigurationBean() - Constructor for class org.apache.taverna.activities.stringconstant.StringConstantConfigurationBean
-
- StringToStringReference - Class in org.apache.taverna.reference.impl.external.object
-
Convert a String to a StringReference
- StringToStringReference() - Constructor for class org.apache.taverna.reference.impl.external.object.StringToStringReference
-
- subList(int, int) - Method in class org.apache.taverna.reference.impl.IdentifiedArrayList
-
- SupersededActivity<ConfigurationType> - Interface in org.apache.taverna.workflowmodel.processor.activity
-
A superseded activity is one which has been replaced be another activity type
of similar functionality but different configuration and name
- SupportsStreamedResult - Annotation Type in org.apache.taverna.workflowmodel.processor.dispatch.description
-
Declares that a dispatch layer can handle streamed result data correctly, if
this annotation is attached to a DispatchLayer implementation that
implementation must be able to correctly handle the result completion message
type.
- SwingAwareObserver<Message> - Class in org.apache.taverna.lang.observer
-
Implementation of an
Observer
that adds calls to notify to the AWT event dispatching
thread.
- SwingAwareObserver() - Constructor for class org.apache.taverna.lang.observer.SwingAwareObserver
-