[06/51] [partial] incubator-taverna-engine git commit:

[re...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationAssertionImpl.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationAssertionImpl.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationAssertionImpl.java
deleted file mode 100644
index cb63cd6..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationAssertionImpl.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-
-import net.sf.taverna.t2.annotation.AnnotationAssertion;
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AnnotationRole;
-import net.sf.taverna.t2.annotation.AnnotationSourceSPI;
-import net.sf.taverna.t2.annotation.CurationEvent;
-import net.sf.taverna.t2.annotation.Person;
-
-public class AnnotationAssertionImpl implements AnnotationAssertion<AnnotationBeanSPI> {
-	
-	private AnnotationBeanSPI annotationBean;
-	private AnnotationRole annotationRole;
-	private Date date;
-	private List<Person> creators;
-	private AnnotationSourceSPI annotationSource;
-	private List<CurationEvent<?>> curationEventList;
-
-	public AnnotationAssertionImpl(){
-		date = new Date();
-		curationEventList = new ArrayList<CurationEvent<?>>();
-		creators = new ArrayList<Person>();
-		
-	}
-	
-	public AnnotationAssertionImpl(AnnotationBeanSPI freeTextDescription, AnnotationRole annotationRole, List<Person> creators, AnnotationSourceSPI annotationSource) {
-		this.annotationBean = freeTextDescription;
-		this.annotationRole = annotationRole;
-		this.creators = creators;
-		this.annotationSource = annotationSource;
-	}
-
-	@Override
-	public AnnotationBeanSPI getDetail() {
-		return annotationBean;
-	}
-
-	@Override
-	public AnnotationRole getRole() {
-		return annotationRole;
-	}
-
-	@Override
-	public Date getCreationDate() {
-		return date;
-	}
-
-	@Override
-	public List<? extends Person> getCreators() {
-		return creators;
-	}
-	
-	public void addCreator(Person person) {
-		creators.add(person);
-	}
-	
-	public void removeCreator(Person person) {
-		creators.remove(person);
-	}
-
-	@Override
-	public List<CurationEvent<?>> getCurationAssertions() {
-		return curationEventList;
-	}
-
-	@Override
-	public AnnotationSourceSPI getSource() {
-		return annotationSource;
-	}
-
-	public void setAnnotationBean(AnnotationBeanSPI annotationBean) {
-		this.annotationBean = annotationBean;
-	}
-
-	public void setAnnotationRole(AnnotationRole annotationRole) {
-		this.annotationRole = annotationRole;
-	}
-	
-	public void removeAnnotationRole() {
-		this.annotationRole = null;
-	}
-
-	public void setDate(Date date) {
-		this.date = date;
-	}
-
-	public void setCreators(List<Person> creators) {
-		this.creators = creators;
-	}
-
-	public void setAnnotationSource(AnnotationSourceSPI annotationSource) {
-		this.annotationSource = annotationSource;
-	}
-	
-	public void removeAnnotationSource() {
-		this.annotationSource = null;
-	}
-
-	public void removeAnnotationBean() {
-		annotationBean = null;
-	}
-	
-	public void addCurationEvent(CurationEvent<?> curationEvent) {
-		curationEventList.add(curationEvent);
-	}
-
-	public void removeCurationEvent(CurationEvent<?> curationEvent) {
-		curationEventList.remove(curationEvent);
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationChainImpl.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationChainImpl.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationChainImpl.java
deleted file mode 100644
index 452044d..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/AnnotationChainImpl.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.annotation.AnnotationAssertion;
-import net.sf.taverna.t2.annotation.AnnotationChain;
-
-public class AnnotationChainImpl implements AnnotationChain{
-	private List<AnnotationAssertion<?>> annotationAssertions = new ArrayList<>();
-
-	@Override
-	public List<AnnotationAssertion<?>> getAssertions() {
-		return new ArrayList<>(annotationAssertions);
-	}
-	
-	/**
-	 * Add an annotation to the chain Added because without the edits stuff how
-	 * else can we do it?
-	 * 
-	 * @param annotationAssertion
-	 */
-	public void addAnnotationAssertion(AnnotationAssertion<?> annotationAssertion) {
-		annotationAssertions.add(annotationAssertion);
-	}
-	
-	public void removeAnnotationAssertion(AnnotationAssertion<?> annotationAssertion) {
-		annotationAssertions.remove(annotationAssertion);
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEvent.java
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diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEvent.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEvent.java
deleted file mode 100644
index 151768f..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEvent.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import net.sf.taverna.t2.annotation.Curateable;
-import net.sf.taverna.t2.annotation.CurationEvent;
-import net.sf.taverna.t2.annotation.CurationEventType;
-
-public class DisputeEvent implements CurationEvent<DisputeEventDetails> {
-	private DisputeEventDetails disputeEventDetails;
-	private CurationEventType curationEventType;
-	private Curateable targetEvent;
-
-	public DisputeEvent() {
-	}
-
-	public DisputeEvent(DisputeEventDetails disputeEventDetails,
-			CurationEventType curationEventType, Curateable targetEvent) {
-		this.disputeEventDetails = disputeEventDetails;
-		this.curationEventType = curationEventType;
-		this.targetEvent = targetEvent;
-	}
-
-	@Override
-	public DisputeEventDetails getDetail() {
-		return disputeEventDetails;
-	}
-
-	@Override
-	public Curateable getTarget() {
-		return targetEvent;
-	}
-
-	@Override
-	public CurationEventType getType() {
-		return curationEventType;
-	}
-
-	public void setDisputeEventDetails(DisputeEventDetails disputeEventDetails) {
-//		if (disputeEventDetails != null)
-//			throw new RuntimeException("Dispute event details have already been set");
-		this.disputeEventDetails = disputeEventDetails;
-	}
-
-	public void setCurationEventType(CurationEventType curationEventType) {
-//		if (curationEventType != null)
-//			throw new RuntimeException("Curation event details have already been set");
-		this.curationEventType = curationEventType;
-	}
-
-	public void setTargetEvent(Curateable targetEvent) {
-//		if (targetEvent!= null)
-//			throw new RuntimeException("Target event details have already been set");
-		this.targetEvent = targetEvent;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEventDetails.java
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diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEventDetails.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEventDetails.java
deleted file mode 100644
index 55aed16..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/DisputeEventDetails.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import net.sf.taverna.t2.annotation.CurationEventBeanSPI;
-
-public class DisputeEventDetails implements CurationEventBeanSPI {
-	public DisputeEventDetails() {
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/PersonImpl.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/PersonImpl.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/PersonImpl.java
deleted file mode 100644
index 8a80e81..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/PersonImpl.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import net.sf.taverna.t2.annotation.Person;
-
-public class PersonImpl implements Person {
-	@SuppressWarnings("unused")
-	private String name;
-
-	public PersonImpl(String name) {
-		this.name = name;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/URISource.java
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diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/URISource.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/URISource.java
deleted file mode 100644
index 7cee476..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/annotation/impl/URISource.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.annotation.impl;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.annotation.AnnotationSourceSPI;
-
-public class URISource implements AnnotationSourceSPI{
-	private URI uri;
-
-	public URISource() {
-	}
-
-	public URISource(URI uri) {
-		this.uri = uri;
-	}
-
-	public void setUri(URI uri) {
-//		if (uri != null)
-//			throw new RuntimeException("URI has already been set");
-		this.uri = uri;
-	}
-
-	public URI getUri() {
-		return uri;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/facade/impl/WorkflowInstanceFacadeImpl.java
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diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/facade/impl/WorkflowInstanceFacadeImpl.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/facade/impl/WorkflowInstanceFacadeImpl.java
deleted file mode 100644
index a21fae6..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/facade/impl/WorkflowInstanceFacadeImpl.java
+++ /dev/null
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-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.facade.impl;
-
-import static java.lang.System.currentTimeMillis;
-import static java.util.Collections.synchronizedList;
-import static java.util.UUID.randomUUID;
-
-import java.lang.ref.WeakReference;
-import java.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.UUID;
-import java.util.WeakHashMap;
-import java.util.concurrent.atomic.AtomicLong;
-
-import net.sf.taverna.t2.facade.FacadeListener;
-import net.sf.taverna.t2.facade.ResultListener;
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
-import net.sf.taverna.t2.facade.WorkflowRunCancellation;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.TokenOrderException;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.lang.observer.Observable;
-import net.sf.taverna.t2.lang.observer.Observer;
-import net.sf.taverna.t2.monitor.MonitorManager;
-import net.sf.taverna.t2.monitor.MonitorNode;
-import net.sf.taverna.t2.monitor.MonitorableProperty;
-import net.sf.taverna.t2.monitor.NoSuchPropertyException;
-import net.sf.taverna.t2.provenance.item.DataflowRunComplete;
-import net.sf.taverna.t2.provenance.item.WorkflowDataProvenanceItem;
-import net.sf.taverna.t2.provenance.item.WorkflowProvenanceItem;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.WorkflowRunIdEntity;
-import net.sf.taverna.t2.utility.TypedTreeModel;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowValidationReport;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.InvalidDataflowException;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.ProcessorFinishedEvent;
-import net.sf.taverna.t2.workflowmodel.impl.EditsImpl;
-import net.sf.taverna.t2.workflowmodel.impl.ProcessorImpl;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayer;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchStack;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.IntermediateProvenance;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Stop;
-
-import org.apache.log4j.Logger;
-
-/**
- * Implementation of {@link WorkflowInstanceFacade}
- * 
- * @author Tom Oinn
- * @author Stian Soiland-Reyes
- * @author Ian Dunlop
- * @author Alex Nenadic
- */
-public class WorkflowInstanceFacadeImpl implements WorkflowInstanceFacade {
-	private static Logger logger = Logger
-			.getLogger(WorkflowInstanceFacadeImpl.class);
-
-	protected static AtomicLong owningProcessId = new AtomicLong(0);
-	private InvocationContext context;	
-	private State state = State.prepared;
-	public Date stateLastModified = new Date();
-
-	@Override
-	public InvocationContext getContext() {
-		return context;
-	}
-
-	private Dataflow dataflow;
-	private FacadeResultListener facadeResultListener;
-	/** How many processors have finished so far */
-	private int processorsToComplete;
-	private String instanceOwningProcessId;
-	private String localName;
-	private MonitorManager monitorManager = MonitorManager.getInstance();
-	protected List<FacadeListener> facadeListeners = synchronizedList(new ArrayList<FacadeListener>());
-	protected List<ResultListener> resultListeners = synchronizedList(new ArrayList<ResultListener>());
-	private boolean provEnabled = false;
-	private WeakHashMap<String, T2Reference> pushedDataMap = new WeakHashMap<>();
-	/** Id of this run */
-	private String workflowRunId;
-	private Timestamp workflowStarted;
-	private WorkflowProvenanceItem workflowItem = null;
-	private int portsToComplete;
-	
-	private enum WorkflowInstanceFacadeChange {
-		CANCELLATION, PORT_DECREMENT, PROCESSOR_DECREMENT
-	};
-
-	public WorkflowInstanceFacadeImpl(Dataflow dataflow,
-			InvocationContext context, String parentProcess)
-			throws InvalidDataflowException {
-		if (dataflow == null) {
-			logger.error("Dataflow is null");
-			throw new IllegalArgumentException("Dataflow is null");
-		}
-		DataflowValidationReport report = dataflow.checkValidity();
-		if (!report.isValid())
-			throw new InvalidDataflowException(dataflow, report);
-
-		this.dataflow = dataflow;
-		this.context = context;
-		this.portsToComplete = dataflow.getOutputPorts().size();
-		this.processorsToComplete = dataflow.getProcessors().size();
-		this.localName = "facade" + owningProcessId.getAndIncrement();
-		// Set the wf run id
-		workflowRunId = UUID.randomUUID().toString();
-		if (parentProcess.isEmpty()) {
-			// Top-level workflow
-			
-			/*
-			 * add top level workflow run so that reference service can generate
-			 * identifiers linked to our run
-			 */
-			context.addEntity(new WorkflowRunIdEntity(workflowRunId));
-			this.instanceOwningProcessId = localName;
-			
-			/*
-			 * Add this WorkflowInstanceFacade to the map of all workflow run
-			 * IDs against the corresponding WorkflowInstanceFacadeS/ - to be
-			 * used by DependencyActivity's such as API consumer and Beanshell
-			 */
-			workflowRunFacades.put(localName, new WeakReference<WorkflowInstanceFacade>(this));
-			/*
-			 * Note that we do not put the IDs for nested workflows, just for
-			 * the main ones!
-			 */
-		} else {
-			// Nested workflow
-			this.instanceOwningProcessId = parentProcess + ":" + localName;
-		}		
-				
-		if (context.getProvenanceReporter() != null) {
-			provEnabled = true;
-			workflowItem = new WorkflowProvenanceItem();
-			workflowItem.setDataflow(dataflow);
-			workflowItem.setProcessId(instanceOwningProcessId);
-			workflowItem.setIdentifier(workflowRunId);
-			workflowItem.setParentId(dataflow.getIdentifier());
-			workflowItem.setWorkflowId(dataflow.getIdentifier());
-			
-			/*
-			 * FIXME: workflowItem is local to each instanceOwningProcessId, but
-			 * might be added to the Processor within different concurrent runs.
-			 * (T3-930)
-			 */
-			addProvenanceLayerToProcessors(workflowItem);
-			context.getProvenanceReporter().setSessionID(workflowRunId);
-		}
-		facadeResultListener = new FacadeResultListener(dataflow, workflowItem);
-		
-		// Register an observer with each of the processors
-		for (Processor processor : dataflow.getProcessors()) {
-			String expectedProcessId = instanceOwningProcessId + ":"
-					+ dataflow.getLocalName() + ":" + processor.getLocalName();
-			ProcessorFinishedObserver observer = new ProcessorFinishedObserver(
-					workflowItem, expectedProcessId);
-			((ProcessorImpl) processor).addObserver(observer);
-		}
-	}
-
-	private void addProvenanceLayerToProcessors(WorkflowProvenanceItem workflowItem) {
-		// TODO Shouldn't we use a bean for this? 
-		Edits edits = new EditsImpl();
-		for (Processor processor : dataflow.getProcessors())
-			/*
-			 * Synchronized per processor as we might be modifying its dispatch
-			 * stack (fixes T3-929)
-			 */
-		    synchronized (processor) {               
-		        DispatchStack dispatchStack = processor.getDispatchStack();
-    			List<DispatchLayer<?>> layers = dispatchStack.getLayers();
-    			if (isProvenanceAlreadyAdded(layers))
-    				continue;
-    			IntermediateProvenance provenance = new IntermediateProvenance();
-				provenance.setWorkflow(workflowItem);
-				provenance.setReporter(context.getProvenanceReporter());
-
-				try {
-					edits.getAddDispatchLayerEdit(dispatchStack, provenance,
-					        provenancePosition(layers)).doEdit();
-					break;
-				} catch (EditException e) {
-					logger.warn("adding provenance layer to dispatch stack failed "
-									+ e.toString());
-				}
-		    }
-	}
-
-    private boolean isProvenanceAlreadyAdded(List<DispatchLayer<?>> layers) {
-        for (DispatchLayer<?> layer : layers)
-        	if (layer instanceof IntermediateProvenance)
-        		return true;
-        return false;
-    }
-
-    private int provenancePosition(List<DispatchLayer<?>> layers) {
-        int position=0; // fallback - beginning of list
-        for (int i = 0; i < layers.size(); i++) {
-            DispatchLayer<?> layer = layers.get(i);
-        	if (layer instanceof Parallelize)
-        	    // Below Parallelize (should be there!)
-        	    position = i+1;
-        	else if (layer instanceof ErrorBounce)
-        	    // and inserted just above ErrorBounce (if it's there)
-        		position = i;
-        }
-        return position;
-    }
-
-	@Override
-	public void addFacadeListener(FacadeListener listener) {
-		facadeListeners.add(listener);
-	}
-
-	@Override
-	public void addResultListener(ResultListener listener) {
-		synchronized (resultListeners) {
-			if (resultListeners.isEmpty())
-				for (DataflowOutputPort port : dataflow.getOutputPorts())
-					port.addResultListener(facadeResultListener);
-			resultListeners.add(listener); 
-		}		
-	}
-
-	@Override
-	public synchronized void fire() throws IllegalStateException {
-		if (getState().equals(State.running))
-			throw new IllegalStateException("Workflow is already running!");
-		workflowStarted = new Timestamp(currentTimeMillis());
-		setState(State.running);
-		if (provEnabled) {
-			workflowItem.setInvocationStarted(workflowStarted);
-			context.getProvenanceReporter().addProvenanceItem(workflowItem);
-		}
-		
-		HashSet<MonitorableProperty<?>> properties = new HashSet<>();
-		properties.add(new StateProperty());
-		monitorManager.registerNode(this, instanceOwningProcessId.split(":"),				
-				properties);
-		dataflow.fire(instanceOwningProcessId, context);		
-	}
-
-	public final class StateProperty implements MonitorableProperty<State> {
-		@Override
-		public Date getLastModified() {
-			return stateLastModified;
-		}
-
-		@Override
-		public String[] getName() {
-			return new String[] { "facade", "state" };
-		}
-
-		@Override
-		public State getValue() throws NoSuchPropertyException {
-			return getState();
-		}
-	}
-	
-	@Override
-	public Dataflow getDataflow() {
-		return dataflow;
-	}
-
-	@Override
-	public TypedTreeModel<MonitorNode> getStateModel() {
-		// TODO WorkflowInstanceFacade.getStateModel not yet implemented
-		return null;
-	}
-
-	@Override
-	public void pushData(WorkflowDataToken token, String portName)
-			throws TokenOrderException {
-		State currentState = getState();
-		if (! currentState.equals(State.running))
-			throw new IllegalStateException(
-					"Can't push data, current state is not running, but "
-							+ currentState);
-		/*
-		 * TODO: throw TokenOrderException when token stream is violates order
-		 * constraints.
-		 */
-		for (DataflowInputPort port : dataflow.getInputPorts()) {
-			if (!portName.equals(port.getName()))
-				continue;
-			if (token.getIndex().length == 0) {
-				if (pushedDataMap.containsKey(portName))
-					throw new IllegalStateException("Already pushed for port " + portName);
-				pushedDataMap.put(portName, token.getData());					
-			}
-			if (provEnabled) {
-				WorkflowDataProvenanceItem provItem = new WorkflowDataProvenanceItem();
-				provItem.setPortName(portName);
-				provItem.setInputPort(true);
-				provItem.setData(token.getData());
-				provItem.setReferenceService(context.getReferenceService());
-				provItem.setParentId(workflowItem.getIdentifier());
-				provItem.setWorkflowId(workflowItem.getParentId());
-				provItem.setIdentifier(randomUUID().toString());
-				provItem.setParentId(instanceOwningProcessId);
-				provItem.setProcessId(instanceOwningProcessId);
-				provItem.setIndex(token.getIndex());
-				provItem.setFinal(token.isFinal());
-				context.getProvenanceReporter().addProvenanceItem(provItem);
-			}
-			port.receiveEvent(token.pushOwningProcess(localName));
-		}
-	}
-
-	@Override
-	public void removeFacadeListener(FacadeListener listener) {
-		facadeListeners.remove(listener);
-	}
-
-	private <T> ArrayList<T> copyList(List<T> listenerList) {
-		synchronized (listenerList) {
-			return new ArrayList<>(listenerList);
-		}
-	}
-
-	@Override
-	public void removeResultListener(ResultListener listener) {
-		synchronized (resultListeners) {
-			resultListeners.remove(listener);
-			if (resultListeners.isEmpty())
-				for (DataflowOutputPort port : dataflow.getOutputPorts())
-					port.removeResultListener(facadeResultListener);
-		}
-	}
-
-	protected class FacadeResultListener implements ResultListener {
-		private final WorkflowProvenanceItem workflowItem;
-
-		public FacadeResultListener(Dataflow dataflow,
-				WorkflowProvenanceItem workflowItem) {
-			this.workflowItem = workflowItem;
-		}
-
-		@Override
-		public void resultTokenProduced(WorkflowDataToken token, String portName) {			
-			if (!instanceOwningProcessId.equals(token.getOwningProcess()))
-				return;
-			if (getState().equals(State.cancelled))
-				// Throw the token away
-				return;
-
-			if (provEnabled) {
-				WorkflowDataProvenanceItem provItem = new WorkflowDataProvenanceItem();
-				provItem.setPortName(portName);
-				provItem.setInputPort(false);
-				provItem.setData(token.getData());
-				provItem.setReferenceService(context.getReferenceService());
-				provItem.setParentId(workflowItem.getIdentifier());
-				provItem.setWorkflowId(workflowItem.getParentId());
-				provItem.setIdentifier(randomUUID().toString());
-				provItem.setParentId(instanceOwningProcessId);
-				provItem.setProcessId(instanceOwningProcessId);
-				provItem.setIndex(token.getIndex());
-				provItem.setFinal(token.isFinal());
-				context.getProvenanceReporter().addProvenanceItem(provItem);
-			}
-			
-			for (ResultListener resultListener : copyList(resultListeners))
-				try {
-					resultListener.resultTokenProduced(
-							token.popOwningProcess(), portName);
-				} catch (RuntimeException ex) {
-					logger.warn("Could not notify result listener "
-							+ resultListener, ex);
-				}
-			if (token.getIndex().length == 0)
-				checkWorkflowFinished(WorkflowInstanceFacadeChange.PORT_DECREMENT);
-		}
-	}
-	
-
-	/**
-	 * An observer of events that occur when a processor finishes with execution.
-	 *
-	 */
-	private class ProcessorFinishedObserver implements Observer<ProcessorFinishedEvent>{
-		private final String expectedProcessId;
-
-		public ProcessorFinishedObserver(WorkflowProvenanceItem workflowItem, String expectedProcessId) {
-			this.expectedProcessId = expectedProcessId;
-		}
-
-		@Override
-		public void notify(Observable<ProcessorFinishedEvent> sender,
-				ProcessorFinishedEvent message) throws Exception {
-			if (! message.getOwningProcess().equals(expectedProcessId))
-				return;
-			
-			// De-register the processor node from the monitor as it has finished
-			monitorManager.deregisterNode(message.getOwningProcess());
-			
-			// De-register this observer from the processor
-			message.getProcessor().removeObserver(this);
-			
-			// All processors have finished => the workflow run has finished
-			checkWorkflowFinished(WorkflowInstanceFacadeChange.PROCESSOR_DECREMENT);
-		}
-	}
-
-	private void applyChange(WorkflowInstanceFacadeChange change) {
-		switch (change) {
-		case CANCELLATION:
-			processorsToComplete = 0;
-			portsToComplete = 0;
-			break;
-		case PORT_DECREMENT:
-			portsToComplete--;
-			break;
-		case PROCESSOR_DECREMENT:
-			processorsToComplete--;
-			break;
-		}
-	}
-	protected void checkWorkflowFinished(WorkflowInstanceFacadeChange change) {
-		synchronized (this) {
-			applyChange(change);
-			if (getState().equals(State.cancelled) && processorsToComplete < 0) {
-				logger.error("Already cancelled workflow run "
-						+ instanceOwningProcessId);
-				return;
-			}
-			if (getState().equals(State.completed)) {
-				logger.error("Already finished workflow run "
-						+ instanceOwningProcessId, new IllegalStateException());
-				return;
-			}
-			if (processorsToComplete > 0 || portsToComplete > 0)
-				// Not yet finished
-				return;
-			if (processorsToComplete < 0 || portsToComplete < 0) {
-				logger.error("Already finished workflow run "
-						+ instanceOwningProcessId, new IllegalStateException());
-				return;
-			}
-			if (!getState().equals(State.cancelled))
-				setState(State.completed);
-			processorsToComplete = -1;
-			portsToComplete = -1;
-		}	
-		// De-register the workflow node from the monitor
-		monitorManager.deregisterNode(instanceOwningProcessId + ":" + dataflow.getLocalName());
-
-		/*
-		 * De-register this facade node from the monitor - this will effectively
-		 * tell the monitor that the workflow run has finished
-		 */
-		monitorManager.deregisterNode(instanceOwningProcessId);
-
-		if (provEnabled) {
-			DataflowRunComplete provItem = new DataflowRunComplete();
-			provItem.setInvocationEnded(new Timestamp(currentTimeMillis()));
-			provItem.setParentId(workflowItem.getIdentifier());
-			provItem.setWorkflowId(workflowItem.getParentId());
-			provItem.setProcessId(instanceOwningProcessId);
-			provItem.setIdentifier(randomUUID().toString());
-			provItem.setState(getState());
-			context.getProvenanceReporter().addProvenanceItem(provItem);
-		}
-	}
-
-	@Override
-	public WeakHashMap<String, T2Reference> getPushedDataMap() {
-		return pushedDataMap;
-	}
-
-	public void setWorkflowRunId(String workflowRunId) {
-		this.workflowRunId = workflowRunId;
-	}
-
-	@Override
-	public String getWorkflowRunId() {
-		return workflowRunId;
-	}
-	
-	@Override
-	public synchronized State getState() {
-		return state;
-	}
-	
-	public synchronized void setState(State newState) throws IllegalStateException {
-		State oldState = state;
-		if (newState.equals(state))
-			return;
-		switch (newState) {
-		case running:
-			switch (state) {
-			case prepared:
-			case paused:
-				stateLastModified = new Date();
-				state = newState;
-				notifyFacadeListeners(oldState, newState);
-				return;
-			default:
-				throw new IllegalStateException("Can't change state from "
-						+ state + " to " + newState);
-			}
-		case paused:
-			switch (state) {
-			case running:
-				stateLastModified = new Date();
-				state = newState;
-				notifyFacadeListeners(oldState, newState);
-				return;
-			default:
-				throw new IllegalStateException("Can't change state from "
-						+ state + " to " + newState);
-			}
-		case completed:
-			switch (state) {
-			case running:
-				stateLastModified = new Date();
-				state = newState;
-				notifyFacadeListeners(oldState, newState);
-				return;
-			case cancelled:
-				// Keep as cancelled
-				return;
-			default:
-				throw new IllegalStateException("Can't change state from "
-						+ state + " to " + newState);
-			}
-		case cancelled:
-			switch (state) {
-			case completed:
-				throw new IllegalStateException("Can't change state from "
-						+ state + " to " + newState);
-			default:
-				stateLastModified = new Date();
-				state = newState;
-				notifyFacadeListeners(oldState, newState);
-				return;
-			}
-		default:
-			throw new IllegalStateException("Can't change state from " + state  + " to " + newState);		
-		}		
-	}
-
-	private void notifyFacadeListeners(State oldState, State newState) {
-		for (FacadeListener facadeListener : copyList(facadeListeners))
-			try {
-				facadeListener.stateChange(this, oldState, newState);
-			} catch (RuntimeException ex) {
-				logger.warn("Could not notify facade listener "
-						+ facadeListener, ex);
-			}
-	}
-
-	@Override
-	public synchronized boolean cancelWorkflowRun() {
-		if (getState().equals(State.completed))
-			return false;
-		boolean result = Stop.cancelWorkflow(getWorkflowRunId());
-		if (result) {
-			setState(State.cancelled);
-			logger.info("Cancelled workflow runId=" + getWorkflowRunId()
-					+ " processId=" + instanceOwningProcessId);
-			for (FacadeListener facadeListener : copyList(facadeListeners))
-				try {
-					facadeListener.workflowFailed(this, "Workflow was cancelled",
-							new WorkflowRunCancellation(getWorkflowRunId()));
-				} catch (RuntimeException ex) {
-					logger.warn("Could not notify failure listener "
-							+ facadeListener, ex);
-				}
-			checkWorkflowFinished(WorkflowInstanceFacadeChange.CANCELLATION);		
-		}
-		return result;
-	}
-
-	@Override
-	public boolean pauseWorkflowRun() {
-		setState(State.paused);
-		if (Stop.pauseWorkflow(getWorkflowRunId())) {
-			logger.info("Paused workflow runId=" + getWorkflowRunId()
-					+ " processId=" + instanceOwningProcessId);
-			return true;
-		}
-		return false;
-	}
-
-	@Override
-	public boolean resumeWorkflowRun() {
-		setState(State.running);
-		if (Stop.resumeWorkflow(getWorkflowRunId())) {
-			logger.info("Resumed paused workflow runId=" + getWorkflowRunId()
-					+ " processId=" + instanceOwningProcessId);
-			return true;
-		}
-		return false;
-	}
-
-	@Override
-	public String getIdentifier() {
-		return localName;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/invocation/impl/InvocationContextImpl.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/invocation/impl/InvocationContextImpl.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/invocation/impl/InvocationContextImpl.java
deleted file mode 100644
index de4abe4..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/invocation/impl/InvocationContextImpl.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.invocation.impl;
-
-import static java.util.Collections.synchronizedList;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.provenance.reporter.ProvenanceReporter;
-import net.sf.taverna.t2.reference.ReferenceService;
-
-public class InvocationContextImpl implements InvocationContext {
-	private final ReferenceService referenceService;
-	private final ProvenanceReporter provenanceReporter;
-	private List<Object> entities = synchronizedList(new ArrayList<Object>());
-
-	public InvocationContextImpl(ReferenceService referenceService,
-			ProvenanceReporter provenanceReporter) {
-		this.referenceService = referenceService;
-		this.provenanceReporter = provenanceReporter;
-	}
-
-	@Override
-	public ReferenceService getReferenceService() {
-		return referenceService;
-	}
-
-	@Override
-	public ProvenanceReporter getProvenanceReporter() {
-		return provenanceReporter;
-	}
-
-	@Override
-	public <T extends Object> List<T> getEntities(Class<T> entityType) {
-		List<T> entitiesOfType = new ArrayList<>();
-		synchronized (entities) {
-			for (Object entity : entities)
-				if (entityType.isInstance(entity))
-					entitiesOfType.add(entityType.cast(entity));
-		}
-		return entitiesOfType;
-	}
-
-	@Override
-	public void addEntity(Object entity) {
-		entities.add(entity);
-	}
-
-	public void removeEntity(Object entity) {
-		entities.remove(entity);
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/monitor/impl/MonitorTreeModel.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/monitor/impl/MonitorTreeModel.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/monitor/impl/MonitorTreeModel.java
deleted file mode 100644
index 2709164..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/monitor/impl/MonitorTreeModel.java
+++ /dev/null
@@ -1,423 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.monitor.impl;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Collections;
-import java.util.Date;
-import java.util.Set;
-import java.util.Timer;
-import java.util.TimerTask;
-
-import javax.swing.JFrame;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-import javax.swing.SwingUtilities;
-import javax.swing.event.TreeModelEvent;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.MutableTreeNode;
-import javax.swing.tree.TreeModel;
-import javax.swing.tree.TreePath;
-
-import net.sf.taverna.t2.lang.observer.Observable;
-import net.sf.taverna.t2.lang.observer.Observer;
-import net.sf.taverna.t2.monitor.MonitorNode;
-import net.sf.taverna.t2.monitor.MonitorableProperty;
-import net.sf.taverna.t2.monitor.NoSuchPropertyException;
-import net.sf.taverna.t2.monitor.MonitorManager.AddPropertiesMessage;
-import net.sf.taverna.t2.monitor.MonitorManager.DeregisterNodeMessage;
-import net.sf.taverna.t2.monitor.MonitorManager.MonitorMessage;
-import net.sf.taverna.t2.monitor.MonitorManager.RegisterNodeMessage;
-
-import org.apache.log4j.Logger;
-
-/**
- * A relatively naive Monitor interface which holds all
- * state in a tree model. Use getMonitor() to get the monitor singleton, all
- * workflows under a given JVM use the same instance in this implementation with
- * the root node of the monitor tree corresponding to the monitor itself.
- * <p>
- * Internally we use a default tree model with default mutable tree nodes where
- * the user object is set to instances of MonitorNode, with the exception of the
- * 'true' root of the tree in which it is set to the MonitorImpl itself
- * 
- * @author Tom Oinn
- * @author Stian Soiland-Reyes
- * 
- */
-public class MonitorTreeModel implements Observer<MonitorMessage> {
-	private static MonitorTreeModel instance = null;
-	private static Logger logger = Logger.getLogger(MonitorTreeModel.class);
-	
-	/**
-	 * Get the MonitorImpl singleton
-	 * 
-	 * @return The MonitorImpl singleton
-	 */
-	public synchronized static MonitorTreeModel getInstance() {
-		// TODO Convert to a bean?
-		if (instance == null)
-			instance = new MonitorTreeModel();
-		return instance;
-	}
-
-	private long nodeRemovalDelay = 1000;
-	private DefaultTreeModel monitorTree;
-	private Timer nodeRemovalTimer;
-
-	/**
-	 * Protected constructor, use singleton access {@link #getInstance()}
-	 * instead.
-	 * 
-	 */
-	protected MonitorTreeModel() {
-		monitorTree = new DefaultTreeModel(new DefaultMutableTreeNode(this));
-		// Create the node removal timer as a daemon thread
-		nodeRemovalTimer = new Timer(true);
-	}
-
-	/**
-	 * Returns a tree view over the monitor.
-	 * 
-	 * @return a tree view over the monitor
-	 */
-	public JTree getJTree() {
-		return new AlwaysOpenJTree(monitorTree);
-	}
-
-	/**
-	 * {@inheritDoc}
-	 */
-	@Override
-	public void notify(Observable<MonitorMessage> sender, MonitorMessage message)
-			throws Exception {
-		if (message instanceof RegisterNodeMessage) {
-			RegisterNodeMessage regMessage = (RegisterNodeMessage) message;
-			registerNode(regMessage.getWorkflowObject(), regMessage
-					.getOwningProcess(), regMessage.getProperties());
-		} else if (message instanceof DeregisterNodeMessage) {
-			deregisterNode(message.getOwningProcess());
-		} else if (message instanceof AddPropertiesMessage) {
-			AddPropertiesMessage addMessage = (AddPropertiesMessage) message;
-			addPropertiesToNode(addMessage.getOwningProcess(), addMessage
-					.getNewProperties());
-		} else {
-			logger.warn("Unknown message " + message + " from " + sender);
-		}
-	}
-
-	/**
-	 * 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.
-	 * 
-	 * @param delayTime
-	 *            time in milliseconds between the deregistration request and
-	 *            attempt to actually remove the node in question
-	 */
-	public void setNodeRemovalDelay(long delayTime) {
-		nodeRemovalDelay = delayTime;
-	}
-
-	/**
-	 * Very simple UI!
-	 */
-	public void showMonitorFrame() {
-		final JTree tree = new AlwaysOpenJTree(monitorTree);
-		final JScrollPane jsp = new JScrollPane(tree);
-		JFrame frame = new JFrame();
-		frame.getContentPane().setLayout(new BorderLayout());
-		frame.getContentPane().add(jsp);
-		frame.pack();
-		frame.setVisible(true);
-		new javax.swing.Timer(500, new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent ae) {
-				jsp.repaint();
-			}
-		}).start();
-	}
-
-	/**
-	 * Return the node pointed to by the first 'limit' number of elements in the
-	 * owning process string array. If limit is -1 then use owningProcess.length
-	 * 
-	 * @param owningProcess
-	 * @param limit
-	 * @return
-	 */
-	protected DefaultMutableTreeNode nodeAtProcessPath(String[] owningProcess,
-			int limit) throws IndexOutOfBoundsException {
-		if (limit == -1)
-			limit = owningProcess.length;
-		DefaultMutableTreeNode currentNode = (DefaultMutableTreeNode) monitorTree
-				.getRoot();
-		for (int index = 0; index < limit && index < owningProcess.length; index++) {
-			boolean found = false;
-			for (int childIndex = 0; childIndex < monitorTree
-					.getChildCount(currentNode)
-					&& !found; childIndex++) {
-				DefaultMutableTreeNode childNode = (DefaultMutableTreeNode) monitorTree
-						.getChild(currentNode, childIndex);
-				MonitorNode childMonitorNode = (MonitorNode) childNode
-						.getUserObject();
-				if (childMonitorNode.getOwningProcess()[index]
-						.equals(owningProcess[index])) {
-					currentNode = childNode;
-					found = true;
-					// break;
-				}
-			}
-			if (!found)
-				throw new IndexOutOfBoundsException(
-						"Cannot locate node with process ID "
-								+ printProcess(owningProcess));
-		}
-		return currentNode;
-	}
-
-	protected String printProcess(String[] process) {
-		StringBuffer sb = new StringBuffer();
-		for (String part : process)
-			sb.append("{").append(part).append("}");
-		return sb.toString();
-	}
-
-	/**
-	 * Inject properties into an existing node
-	 */
-	protected void addPropertiesToNode(String[] owningProcess,
-			Set<MonitorableProperty<?>> newProperties) {
-		try {
-			DefaultMutableTreeNode node = nodeAtProcessPath(owningProcess, -1);
-			MonitorNode mn = (MonitorNode) node.getUserObject();
-			for (MonitorableProperty<?> prop : newProperties)
-				mn.addMonitorableProperty(prop);
-		} catch (IndexOutOfBoundsException ioobe) {
-			// Fail silently here, the node wasn't found in the state tree
-			logger.warn("Could not add properties to unknown node "
-					+ printProcess(owningProcess));
-		}
-	}
-
-	/**
-	 * Request the removal of the specified node from the monitor tree. In this
-	 * particular case the removal task will be added to a timer and executed at
-	 * some (slightly) later time as determined by the removalDelay property.
-	 */
-	protected void deregisterNode(String[] owningProcess) {
-		// logger.debug("Remove node @" + printProcess(owningProcess));
-		final DefaultMutableTreeNode nodeToRemove = nodeAtProcessPath(
-				owningProcess, -1);
-		((MonitorNodeImpl) nodeToRemove.getUserObject()).expire();
-		nodeRemovalTimer.schedule(new TimerTask() {
-			@Override
-			public void run() {
-				synchronized (monitorTree) {
-					monitorTree.removeNodeFromParent(nodeToRemove);
-				}
-			}
-		}, getNodeRemovalDelay());
-	}
-
-	/**
-	 * Create a new node in the monitor
-	 */
-	protected void registerNode(final Object workflowObject,
-			final String[] owningProcess,
-			final Set<MonitorableProperty<?>> properties) {
-		// logger.debug("Registering node " + printProcess(owningProcess));
-	
-		// Create a new MonitorNode
-		final DefaultMutableTreeNode newNode = new DefaultMutableTreeNode(
-				new MonitorNodeImpl(workflowObject, owningProcess, properties));
-		synchronized (monitorTree) {
-			final MutableTreeNode parentNode = nodeAtProcessPath(owningProcess,
-					owningProcess.length - 1);
-			monitorTree.insertNodeInto(newNode, parentNode, monitorTree
-					.getChildCount(parentNode));
-		}
-	}
-
-	class AlwaysOpenJTree extends JTree {
-		private static final long serialVersionUID = -3769998854485605447L;
-
-		public AlwaysOpenJTree(TreeModel newModel) {
-			super(newModel);
-			setRowHeight(18);
-			setLargeModel(true);
-			setEditable(false);
-			setExpandsSelectedPaths(false);
-			setDragEnabled(false);
-			setScrollsOnExpand(false);
-			setSelectionModel(EmptySelectionModel.sharedInstance());
-			setCellRenderer(new CellRenderer());
-		}
-
-		@Override
-		public void setModel(TreeModel model) {
-			if (treeModel == model)
-				return;
-			if (treeModelListener == null)
-				treeModelListener = new TreeModelListener();
-			if (model != null) {
-				model.addTreeModelListener(treeModelListener);
-			}
-			TreeModel oldValue = treeModel;
-			treeModel = model;
-			firePropertyChange(TREE_MODEL_PROPERTY, oldValue, model);
-		}
-
-		protected class CellRenderer extends DefaultTreeCellRenderer {
-			private static final long serialVersionUID = 7106767124654545039L;
-
-			@Override
-			public Component getTreeCellRendererComponent(JTree tree,
-					Object value, boolean sel, boolean expanded,
-					boolean leaf, int row, boolean hasFocus) {
-				super.getTreeCellRendererComponent(tree, value, sel,
-						expanded, leaf, row, hasFocus);
-				if (value instanceof DefaultMutableTreeNode) {
-					Object o = ((DefaultMutableTreeNode) value)
-							.getUserObject();
-					if (o instanceof MonitorNode)
-						if (((MonitorNode) o).hasExpired())
-							setEnabled(false);
-				}
-				return this;
-			}
-		}
-
-		protected class TreeModelListener extends TreeModelHandler {
-			@Override
-			public void treeNodesInserted(final TreeModelEvent ev) {
-				SwingUtilities.invokeLater(new Runnable() {
-					@Override
-					public void run() {
-						TreePath path = ev.getTreePath();
-						setExpandedState(path, true);
-						fireTreeExpanded(path);
-					}
-				});
-			}
-			@Override
-			public void treeStructureChanged(final TreeModelEvent ev) {
-				SwingUtilities.invokeLater(new Runnable() {
-					@Override
-					public void run() {
-						TreePath path = ev.getTreePath();
-						setExpandedState(path, true);
-						fireTreeExpanded(path);
-					}
-				});
-			}
-		}
-	}
-
-	class MonitorNodeImpl implements MonitorNode {
-		private boolean expired = false;
-		private String[] owningProcess;
-		private Set<MonitorableProperty<?>> properties;
-		private Object workflowObject;
-		Date creationDate = new Date();
-
-		MonitorNodeImpl(Object workflowObject, String[] owningProcess,
-				Set<MonitorableProperty<?>> properties) {
-			this.properties = properties;
-			this.workflowObject = workflowObject;
-			this.owningProcess = owningProcess;
-		}
-
-		@Override
-		public void addMonitorableProperty(MonitorableProperty<?> newProperty) {
-			properties.add(newProperty);
-		}
-
-		public void expire() {
-			expired = true;
-		}
-
-		@Override
-		public Date getCreationDate() {
-			return creationDate;
-		}
-
-		@Override
-		public String[] getOwningProcess() {
-			return owningProcess;
-		}
-
-		/**
-		 * Return an unmodifiable copy of the property set
-		 */
-		@Override
-		public Set<? extends MonitorableProperty<?>> getProperties() {
-			return Collections.unmodifiableSet(properties);
-		}
-
-		@Override
-		public Object getWorkflowObject() {
-			return workflowObject;
-		}
-
-		@Override
-		public boolean hasExpired() {
-			return this.expired;
-		}
-
-		@Override
-		public String toString() {
-			StringBuffer sb = new StringBuffer();
-			sb.append(getWorkflowObject().getClass().getSimpleName());
-			sb.append(", ");
-			sb.append(owningProcess[owningProcess.length - 1]);
-			sb.append(" : ");
-			for (MonitorableProperty<?> prop : getProperties()) {
-				String separator = "";
-				for (String nameElement : prop.getName()) {
-					sb.append(separator).append(nameElement);
-					separator = ".";
-				}
-				sb.append("=");
-				try {
-					sb.append(prop.getValue().toString());
-				} catch (NoSuchPropertyException nspe) {
-					sb.append("EXPIRED");
-				}
-				sb.append(" ");
-			}
-			return sb.toString();
-		}
-	}
-
-	public long getNodeRemovalDelay() {
-		return nodeRemovalDelay;
-	}
-
-	protected DefaultTreeModel getMonitorTree() {
-		return monitorTree;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractActivityEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractActivityEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractActivityEdit.java
deleted file mode 100644
index 2725d2f..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractActivityEdit.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007-2008 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * Abstraction of an edit acting on a Activity instance. Handles the check to
- * see that the Activity supplied is really a AbstractActivity.
- * 
- * @author David Withers
- * @author Stian Soiland-Reyes
- */
-public abstract class AbstractActivityEdit<T> extends EditSupport<Activity<T>> {
-	private final AbstractActivity<T> activity;
-
-	protected AbstractActivityEdit(Activity<T> activity) {
-		if (activity == null)
-			throw new RuntimeException(
-					"Cannot construct an activity edit with null activity");
-		if (!(activity instanceof AbstractActivity))
-			throw new RuntimeException(
-					"Edit cannot be applied to an Activity which isn't an instance of AbstractActivity");
-		this.activity = (AbstractActivity<T>) activity;
-	}
-
-	@Override
-	public final Activity<T> applyEdit() throws EditException {
-		synchronized (activity) {
-			doEditAction(activity);
-		}
-		return activity;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param processor
-	 *            The ProcessorImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(AbstractActivity<T> processor)
-			throws EditException;
-
-	@Override
-	public final Activity<T> getSubject() {
-		return activity;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractAnnotationEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractAnnotationEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractAnnotationEdit.java
deleted file mode 100644
index ff89988..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractAnnotationEdit.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007-2014 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.annotation.AnnotationAssertion;
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.impl.AnnotationAssertionImpl;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Abstraction of an edit acting on a AnnotationAssertion instance. Handles the
- * check to see that the AnnotationAssertion supplied is really an
- * AnnotationAssertionImpl.
- */
-abstract class AbstractAnnotationEdit extends
-		EditSupport<AnnotationAssertion<AnnotationBeanSPI>> {
-	private final AnnotationAssertionImpl annotation;
-
-	protected AbstractAnnotationEdit(AnnotationAssertion<AnnotationBeanSPI> annotation) {
-		if (annotation == null)
-			throw new RuntimeException(
-					"Cannot construct an annotation edit with null annotation");
-		if (!(annotation instanceof AnnotationAssertionImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to an AnnotationAssertion which isn't an instance of AnnotationAssertionImpl");
-		this.annotation = (AnnotationAssertionImpl) annotation;
-	}
-
-	@Override
-	public final AnnotationAssertion<AnnotationBeanSPI> applyEdit()
-			throws EditException {
-		synchronized (annotation) {
-			doEditAction(annotation);
-		}
-		return annotation;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param annotationAssertion
-	 *            The AnnotationAssertionImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(
-			AnnotationAssertionImpl annotationAssertion) throws EditException;
-
-	@Override
-	public final AnnotationAssertion<AnnotationBeanSPI> getSubject() {
-		return annotation;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractBinaryProcessorEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractBinaryProcessorEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractBinaryProcessorEdit.java
deleted file mode 100644
index ba1c505..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractBinaryProcessorEdit.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007-2014 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import static java.lang.System.identityHashCode;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OrderedPair;
-import net.sf.taverna.t2.workflowmodel.Processor;
-
-/**
- * Generalization over all operations acting on an ordered pair of ProcessorImpl
- * objects. These include most operations where a relationship is created,
- * modified or destroyed between two processors.
- * 
- * @author Tom Oinn
- * @author Donal Fellows
- */
-abstract class AbstractBinaryProcessorEdit extends
-		EditSupport<OrderedPair<Processor>> {
-	private final OrderedPair<Processor> processors;
-
-	public AbstractBinaryProcessorEdit(Processor a, Processor b) {
-		if (!(a instanceof ProcessorImpl) || !(b instanceof ProcessorImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to a Processor which isn't an instance of ProcessorImpl");
-		processors = new OrderedPair<>(a, b);
-	}
-
-	@Override
-	public final OrderedPair<Processor> applyEdit() throws EditException {
-		ProcessorImpl pia = (ProcessorImpl) processors.getA();
-		ProcessorImpl pib = (ProcessorImpl) processors.getB();
-
-		/*
-		 * Acquire both locks. Guarantee to acquire in a consistent order, based
-		 * on the system hash code (i.e., the object addresses, which we're not
-		 * supposed to know). This means that we should not deadlock, as we've
-		 * got a total order over all extant processors.
-		 * 
-		 * If someone is silly enough to use the same processor for both halves,
-		 * it doesn't matter which arm of the conditional we take.
-		 */
-		if (identityHashCode(pia) < identityHashCode(pib)) {
-			synchronized (pia) {
-				synchronized (pib) {
-					doEditAction(pia, pib);
-				}
-			}
-		} else {
-			synchronized (pib) {
-				synchronized (pia) {
-					doEditAction(pia, pib);
-				}
-			}
-		}
-		return processors;
-	}
-
-	@Override
-	public final OrderedPair<Processor> getSubject() {
-		return processors;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param processorA
-	 *            The ProcessorImpl which is in some sense the source of the
-	 *            relation between the two being asserted or operated on by this
-	 *            edit
-	 * @param processorB
-	 *            The ProcessorImpl at the other end of the relation. *
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(ProcessorImpl processorA,
-			ProcessorImpl processorB) throws EditException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractCrystalizer.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractCrystalizer.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractCrystalizer.java
deleted file mode 100644
index 7d519af..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractCrystalizer.java
+++ /dev/null
@@ -1,194 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.invocation.Completion;
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.IterationInternalEvent;
-import net.sf.taverna.t2.invocation.TreeCache;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Job;
-
-/**
- * Receives Job and Completion events and emits Jobs unaltered. Completion
- * events additionally cause registration of lists for each key in the datamap
- * of the jobs at immediate child locations in the index structure. These list
- * identifiers are sent in place of the Completion events.
- * <p>
- * State for a given process ID is purged when a final completion event is
- * received so there is no need for an explicit cache purge operation in the
- * public API (although for termination of partially complete workflows it may
- * be sensible for subclasses to provide one)
- * <p>
- * 
- * @author Tom Oinn
- * @author David Withers
- */
-public abstract class AbstractCrystalizer implements Crystalizer {
-	private Map<String, CompletionAwareTreeCache> cacheMap = new HashMap<>();
-
-	public abstract Job getEmptyJob(String owningProcess, int[] index,
-			InvocationContext context);
-
-	/**
-	 * 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.
-	 * <p>
-	 * If the baseListDepth property is defined then completion events on nodes
-	 * which don't already exist create empty jobs instead and emit those, if
-	 * undefined the completion event is emited intact.
-	 * 
-	 * @param e The event (a {@link Job} or a {@link Completion})
-	 */
-	@Override
-	public void receiveEvent(IterationInternalEvent<?> e) {
-		String owningProcess = e.getOwningProcess();
-		CompletionAwareTreeCache cache = null;
-		synchronized (cacheMap) {
-			if (!cacheMap.containsKey(owningProcess)) {
-				cache = new CompletionAwareTreeCache(owningProcess, e
-						.getContext());
-				cacheMap.put(owningProcess, cache);
-			} else
-				cache = cacheMap.get(owningProcess);
-		}
-		if (e instanceof Job) {
-			// Pass through Job after storing it in the cache
-			Job j = (Job) e;
-			synchronized (cache) {
-				cache.insertJob(new Job("", j.getIndex(), j.getData(), j
-						.getContext()));
-				jobCreated(j);
-				if (j.getIndex().length == 0)
-					cacheMap.remove(j.getOwningProcess());
-			}
-		} else if (e instanceof Completion) {
-			Completion c = (Completion) e;
-			synchronized (cache) {
-				cache.resolveAt(owningProcess, c.getIndex());
-				if (c.getIndex().length == 0)
-					cacheMap.remove(c.getOwningProcess());
-			}
-		}
-	}
-
-	protected class CompletionAwareTreeCache extends TreeCache {
-		private String owningProcess;
-		private InvocationContext context;
-
-		public CompletionAwareTreeCache(String owningProcess,
-				InvocationContext context) {
-			super();
-			this.context = context;
-			this.owningProcess = owningProcess;
-		}
-
-		public void resolveAt(String owningProcess, int[] completionIndex) {
-			NamedNode n = nodeAt(completionIndex);
-			if (n != null) {
-				assignNamesTo(n, completionIndex);
-				return;
-			}
-
-			/*
-			 * We know what the list depth should be, so we can construct
-			 * appropriate depth empty lists to fill in the gaps.
-			 */
-
-			Job j = getEmptyJob(owningProcess, completionIndex, context);
-			insertJob(j);
-			jobCreated(j);
-		}
-
-		private void assignNamesTo(NamedNode n, int[] index) {
-			/* Only act if contents of this node undefined */
-			if (n.contents != null)
-				return;
-
-			Map<String, List<T2Reference>> listItems = new HashMap<>();
-			int pos = 0;
-			for (NamedNode child : n.children) {
-				/*
-				 * If child doesn't have a defined name map yet then define it.
-				 */
-				Job j;
-				if (child == null) {
-					/*
-					 * happens if we're completing a partially empty collection
-					 * structure
-					 */
-					int[] newIndex = new int[index.length + 1];
-					for (int i = 0; i < index.length; i++)
-						newIndex[i] = index[i];
-					newIndex[index.length] = pos++;
-					j = getEmptyJob(owningProcess, newIndex, context);
-					jobCreated(j);
-				} else if (child.contents == null) {
-					int[] newIndex = new int[index.length + 1];
-					for (int i = 0; i < index.length; i++)
-						newIndex[i] = index[i];
-					newIndex[index.length] = pos++;
-					assignNamesTo(child, newIndex);
-					j = child.contents;
-				} else {
-					pos++;
-					j = child.contents;
-				}
-
-				/*
-				 * Now pull the names out of the child job map and push them
-				 * into lists to be registered
-				 */
-
-				for (String outputName : j.getData().keySet()) {
-					List<T2Reference> items = listItems.get(outputName);
-					if (items == null) {
-						items = new ArrayList<>();
-						listItems.put(outputName, items);
-					}
-					items.add(j.getData().get(outputName));
-				}
-			}
-			Map<String, T2Reference> newDataMap = new HashMap<>();
-			for (String outputName : listItems.keySet())
-				newDataMap.put(
-						outputName,
-						context.getReferenceService()
-								.getListService()
-								.registerList(listItems.get(outputName),
-										context).getId());
-			Job newJob = new Job(owningProcess, index, newDataMap, context);
-			n.contents = newJob;
-
-			/* Get rid of the children as we've now named this node */
-
-			n.children.clear();
-			jobCreated(n.contents);
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowEdit.java
deleted file mode 100644
index 9f8bc33..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowEdit.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007-2008 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Abstraction of an edit acting on a Dataflow instance. Handles the check to
- * see that the Dataflow supplied is really a DataflowImpl.
- * 
- * @author David Withers
- * 
- */
-public abstract class AbstractDataflowEdit extends EditSupport<Dataflow> {
-	private final DataflowImpl dataflow;
-
-	protected AbstractDataflowEdit(Dataflow dataflow) {
-		if (dataflow == null)
-			throw new RuntimeException(
-					"Cannot construct a dataflow edit with null dataflow");
-		if (!(dataflow instanceof DataflowImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to a Dataflow which isn't an instance of DataflowImpl");
-		this.dataflow = (DataflowImpl) dataflow;
-	}
-
-	@Override
-	public final Dataflow applyEdit() throws EditException {
-		synchronized (dataflow) {
-			doEditAction(dataflow);
-		}
-		return dataflow;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param dataflow
-	 *            The DataflowImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(DataflowImpl dataflow)
-			throws EditException;
-
-	@Override
-	public final Dataflow getSubject() {
-		return dataflow;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowInputPortEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowInputPortEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowInputPortEdit.java
deleted file mode 100644
index 8f90758..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowInputPortEdit.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Abstraction of an edit acting on a DataflowInputPort instance. Handles the check to
- * see that the DataflowInputPort supplied is really a DataflowInputPortImpl.
- * 
- * @author David Withers
- *
- */
-public abstract class AbstractDataflowInputPortEdit extends EditSupport<DataflowInputPort> {
-	private final DataflowInputPortImpl dataflowInputPort;
-
-	protected AbstractDataflowInputPortEdit(DataflowInputPort dataflowInputPort) {
-		if (dataflowInputPort == null)
-			throw new RuntimeException(
-					"Cannot construct a DataflowInputPort edit with null DataflowInputPort");
-		if (!(dataflowInputPort instanceof DataflowInputPortImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to a DataflowInputPort which isn't an instance of DataflowInputPortImpl");
-		this.dataflowInputPort = (DataflowInputPortImpl) dataflowInputPort;
-	}
-
-	@Override
-	public final DataflowInputPort applyEdit() throws EditException {
-		synchronized (dataflowInputPort) {
-			doEditAction(dataflowInputPort);
-		}
-		return dataflowInputPort;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param dataflowInputPort
-	 *            The DataflowInputPortImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(DataflowInputPortImpl dataflowInputPort)
-			throws EditException;
-
-	@Override
-	public final DataflowInputPort getSubject() {
-		return dataflowInputPort;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowOutputPortEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowOutputPortEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowOutputPortEdit.java
deleted file mode 100644
index 401faa5..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDataflowOutputPortEdit.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Abstraction of an edit acting on a DataflowOutputPort instance. Handles the
- * check to see that the DataflowOutputPort supplied is really a
- * DataflowOutputPortImpl.
- * 
- * @author David Withers
- */
-public abstract class AbstractDataflowOutputPortEdit extends
-		EditSupport<DataflowOutputPort> {
-	private final DataflowOutputPortImpl dataflowOutputPort;
-
-	protected AbstractDataflowOutputPortEdit(
-			DataflowOutputPort dataflowOutputPort) {
-		if (dataflowOutputPort == null)
-			throw new RuntimeException(
-					"Cannot construct a DataflowOutputPort edit with null DataflowOutputPort");
-		if (!(dataflowOutputPort instanceof DataflowOutputPortImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to a DataflowOutputPort which isn't an instance of DataflowOutputPortImpl");
-		this.dataflowOutputPort = (DataflowOutputPortImpl) dataflowOutputPort;
-	}
-
-	@Override
-	public final DataflowOutputPort applyEdit() throws EditException {
-		synchronized (dataflowOutputPort) {
-			doEditAction(dataflowOutputPort);
-		}
-		return dataflowOutputPort;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param dataflowOutputPort
-	 *            The DataflowOutputPortImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(
-			DataflowOutputPortImpl dataflowOutputPort) throws EditException;
-
-	@Override
-	public final DataflowOutputPort getSubject() {
-		return dataflowOutputPort;
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDatalinkEdit.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDatalinkEdit.java b/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDatalinkEdit.java
deleted file mode 100644
index 31b7480..0000000
--- a/taverna-workflowmodel-impl/src/main/java/net/sf/taverna/t2/workflowmodel/impl/AbstractDatalinkEdit.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester   
- * 
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- * 
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *    
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *    
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.workflowmodel.impl;
-
-import net.sf.taverna.t2.workflowmodel.Datalink;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Abstraction of an edit acting on a Datalink instance. Handles the check to
- * see that the Datalink supplied is really a DatalinkImpl.
- * 
- * @author David Withers
- */
-public abstract class AbstractDatalinkEdit extends EditSupport<Datalink> {
-	private final DatalinkImpl datalink;
-
-	protected AbstractDatalinkEdit(Datalink datalink) {
-		if (datalink == null)
-			throw new RuntimeException(
-					"Cannot construct a datalink edit with null datalink");
-		if (!(datalink instanceof DatalinkImpl))
-			throw new RuntimeException(
-					"Edit cannot be applied to a Datalink which isn't an instance of DatalinkImpl");
-		this.datalink = (DatalinkImpl) datalink;
-	}
-
-	@Override
-	public final Datalink applyEdit() throws EditException {
-		synchronized (datalink) {
-			doEditAction(datalink);
-		}
-		return datalink;
-	}
-
-	/**
-	 * Do the actual edit here
-	 * 
-	 * @param datalink
-	 *            The DatalinkImpl to which the edit applies
-	 * @throws EditException
-	 */
-	protected abstract void doEditAction(DatalinkImpl datalink)
-			throws EditException;
-
-	@Override
-	public final Datalink getSubject() {
-		return datalink;
-	}
-}