uk.org.taverna.scufl2.api.core

Class Processor

java.lang.Object

uk.org.taverna.scufl2.api.common.AbstractCloneable

uk.org.taverna.scufl2.api.common.AbstractNamed

uk.org.taverna.scufl2.api.core.Processor

All Implemented Interfaces:

Cloneable, Comparable, Child<Workflow>, Configurable, Named, Ported, Typed, WorkflowBean

public class Processor
extends AbstractNamed
implements Child<Workflow>, Ported, Configurable

A Processor is a Workflow component that controls the invocation of activities.

When a Workflow is run, a particular Activity will be specified as bound to the Processor by the Profile.

A Processor contains an IterationStrategyStack to describe iterations, and may have input and output ports. The Processor can be configured with a Configuration within a Profile to specify execution details such as retries or parallel jobs.

The getType() of a Processor is normally fixed to the value given by . The configuration of a processor should correspondingly be of the type given by the constant .

The default (implied) configuration of a Processor is as of Taverna 3.0 alpha 2:

 { 
  "retry": {
     "maxRetries": 0,
     "initialDelay": 1000,
     "maxDelay": 5000,
     "backoffFactor": 1.0
  }, 
  "parallelize": {
      "maxJobs": 1
  }
 

These defaults mean that the processor would not retry the operation, and would only perform one concurrent invocation within a given workflow run.

You can provide a partial configuration, e.g. to activate 5 retries using the default initialDelay, add a Configuration of this Processor to the Profile with the keys:

 { 
   "retry": {
     "maxRetries": 5
   }
 }
 

Additionally, do..while-style looping can be configured using the key "loop":

 {
   "loop": {
     "comparePort": "outputB",
     "comparison": "EqualTo",
     "compareValue": "15",
     "delay": 0.5,
     "runFirst": true,
     "isFeedBack": false,
     "conditionActivity": "looping-loop"
   }
 }
 

Note that this is different from looping over incoming values, which happens according to the getIterationStrategyStack()..

The above loop configuration would repeat calling of the activity bound to this processor until its output "outputB" is equal to the string value "15" - with a delay of 0.5 seconds between each try.

if "isFeedBack": true, then outputs from the processor will on repeated invocations replace the original input values where the port names match. Note that the processor ports should be connected in the containing workflow.

"runFirst": true means that the activity is called at least once, which is generally needed to get a port value to compare.

The "conditionActivity" indicates the name of an Activity within the Profile, here called "looping-loop". This activity is invoked with the current processor output values as input ports, and if its output port "loop" contains the string value "true", then the processor is invoked again. If the condition output port matches a processor input port, then the returned values are used instead of the original processor inputs. The conditionActivity is then repeated on the new output values, repeated until "loop" no longer is "true".

As of Taverna 3 alpha 2, the "conditionActivity" is called directly without consideration of the other parameters. This typically contains a beanshell script generated from the above parameters and performs the actual comparisons.

FIXME: This conditionActivity currently has to be regenerated when the other parameters have changed. This now happens within the Taverna 3 workbench user interface when configuring looping. The ideal SCUFL2 behaviour would be to EITHER provide a custom conditionActivity OR the parameters.

Author:

Alan R Williams, Stian Soiland-Reyes

Nested Class Summary

Nested classes/interfaces inherited from class uk.org.taverna.scufl2.api.common.AbstractCloneable

AbstractCloneable.Cloning, AbstractCloneable.CopyVisitor

Field Summary

Fields

Modifier and Type	Field and Description
static URI	CONFIG_TYPE
static URI	PROCESSOR_TYPE

Constructor Summary

Constructors

Constructor and Description
Processor() Constructs a Processor with a random UUID as the name and no parent Workflow.
Processor(Workflow parent, String name) Constructs a Processor with the specified parent Workflow and name.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(Visitor visitor) Accepts a Visitor to this WorkflowBean.
NamedSet<InputProcessorPort>	getInputPorts() Returns the NamedSet of input ports.
IterationStrategyStack	getIterationStrategyStack() Returns the IterationStrategyStack or null if there is no IterationStrategyStack.
NamedSet<OutputProcessorPort>	getOutputPorts() Returns the NamedSet of output ports.
Workflow	getParent() Returns the parent Workflow of null if this Processor is an orphan.
URI	getType() Returns the type of the WorkflowBean.
void	setInputPorts(Set<InputProcessorPort> inputPorts) Sets the input ports.
void	setIterationStrategyStack(IterationStrategyStack iterationStrategyStack) Sets the IterationStrategyStack.
void	setOutputPorts(Set<OutputProcessorPort> outputPorts) Sets the output ports.
void	setParent(Workflow parent) Sets the parent of this workflow bean.
void	setType(URI type) Sets the type of the WorkflowBean.

Methods inherited from class uk.org.taverna.scufl2.api.common.AbstractNamed

cloneInto, compareTo, equals, getName, hashCode, setName, toString

Methods inherited from class uk.org.taverna.scufl2.api.common.AbstractCloneable

clone, cloneWorkflowBean

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.org.taverna.scufl2.api.common.WorkflowBean

clone

Field Detail

PROCESSOR_TYPE

public static final URI PROCESSOR_TYPE

CONFIG_TYPE

public static final URI CONFIG_TYPE

Constructor Detail

Processor

public Processor()

Constructs a Processor with a random UUID as the name and no parent Workflow.

Processor

public Processor(Workflow parent,
         String name)

Constructs a Processor with the specified parent Workflow and name.

Parameters:

parent - the Workflow to set as the Processor's parent. Can be null.

name - the name of the Processor. Must not be null or an empty String.

Method Detail

accept

public boolean accept(Visitor visitor)

Description copied from interface: WorkflowBean

Accepts a Visitor to this WorkflowBean.

Specified by:

accept in interface WorkflowBean

Parameters:

visitor - the Visitor to accept

Returns:

true if this WorkflowBeans children should be visited.

getInputPorts

public NamedSet<InputProcessorPort> getInputPorts()

Returns the NamedSet of input ports. Returns an empty NamedSet if there are no input ports.

Specified by:

getInputPorts in interface Ported

Returns:

the input ports

getIterationStrategyStack

public IterationStrategyStack getIterationStrategyStack()

Returns the IterationStrategyStack or null if there is no IterationStrategyStack.

Returns:

the IterationStrategyStack or null if there is no IterationStrategyStack

getOutputPorts

public NamedSet<OutputProcessorPort> getOutputPorts()

Returns the NamedSet of output ports. Returns an empty NamedSet if there are no output ports.

Specified by:

getOutputPorts in interface Ported

Returns:

the output ports

getParent

public Workflow getParent()

Returns the parent Workflow of null if this Processor is an orphan.

Specified by:

getParent in interface Child<Workflow>

Returns:

the parent Workflow of null if this Processor is an orphan

setInputPorts

public void setInputPorts(Set<InputProcessorPort> inputPorts)

Sets the input ports.

setIterationStrategyStack

public void setIterationStrategyStack(IterationStrategyStack iterationStrategyStack)

Sets the IterationStrategyStack.

Parameters:

iterationStrategyStack - the IterationStrategyStack. Can be null

setOutputPorts

public void setOutputPorts(Set<OutputProcessorPort> outputPorts)

Sets the output ports.

setParent

public void setParent(Workflow parent)

Description copied from interface: Child

Sets the parent of this workflow bean.

Setting the parent would normally also add the object to the relevant collection in the parent if it does not already exist there.

If the child has an existing, object-identity different parent, the child will first be removed from the parent collection if it exists there.

Note:If the child is Named the parent collection will be a NamedSet. This implicit insertion would overwrite any conflicting sibling with the same Named.getName() - to avoid this, add the child to the parent collection by using NamedSet.addWithUniqueName(Named) before setting the parent.

Specified by:

setParent in interface Child<Workflow>

Parameters:

parent - the parent of this workflow bean

getType

public URI getType()

Description copied from interface: Typed

Returns the type of the WorkflowBean.

Specified by:

getType in interface Typed

Returns:

the type of the WorkflowBean

setType

public void setType(URI type)

Description copied from interface: Typed

Sets the type of the WorkflowBean.

Specified by:

setType in interface Typed

Parameters:

type - the type of the WorkflowBean.