taverna-scufl2-wfdesc/src/main/java/org/apache/taverna/scufl2/wfdesc/WfdescSerialiser.java - incubator-taverna-language - Git at Google

 package org.apache.taverna.scufl2.wfdesc;

 /*
  *
  * Licensed to the Apache Software Foundation (ASF) under one
  * or more contributor license agreements.  See the NOTICE file
  * distributed with this work for additional information
  * regarding copyright ownership.  The ASF licenses this file
  * to you under the Apache License, Version 2.0 (the
  * "License"); you may not use this file except in compliance
  * with the License.  You may obtain a copy of the License at
  *
  *   http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing,
  * software distributed under the License is distributed on an
  * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  * KIND, either express or implied.  See the License for the
  * specific language governing permissions and limitations
  * under the License.
  *
 */

 import static org.apache.taverna.scufl2.api.common.Scufl2Tools.NESTED_WORKFLOW;

 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.util.logging.Level;
 import java.util.logging.Logger;

 import org.apache.jena.ontology.Individual;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.jena.riot.RiotException;
 import org.apache.jena.vocabulary.OWL;
 import org.apache.taverna.ro.vocabs.Prov_o;
 import org.apache.taverna.ro.vocabs.Roterms;
 import org.apache.taverna.ro.vocabs.Wf4ever;
 import org.apache.taverna.ro.vocabs.Wfdesc;
 import org.apache.taverna.scufl2.api.activity.Activity;
 import org.apache.taverna.scufl2.api.annotation.Annotation;
 import org.apache.taverna.scufl2.api.common.Child;
 import org.apache.taverna.scufl2.api.common.Named;
 import org.apache.taverna.scufl2.api.common.Scufl2Tools;
 import org.apache.taverna.scufl2.api.common.URITools;
 import org.apache.taverna.scufl2.api.common.Visitor.VisitorWithPath;
 import org.apache.taverna.scufl2.api.common.WorkflowBean;
 import org.apache.taverna.scufl2.api.configurations.Configuration;
 import org.apache.taverna.scufl2.api.container.WorkflowBundle;
 import org.apache.taverna.scufl2.api.core.DataLink;
 import org.apache.taverna.scufl2.api.core.Processor;
 import org.apache.taverna.scufl2.api.core.Workflow;
 import org.apache.taverna.scufl2.api.io.WriterException;
 import org.apache.taverna.scufl2.api.port.InputPort;
 import org.apache.taverna.scufl2.api.port.OutputPort;
 import org.apache.taverna.scufl2.api.port.WorkflowPort;
 import org.apache.taverna.scufl2.api.profiles.ProcessorBinding;
 import org.apache.taverna.scufl2.api.profiles.ProcessorPortBinding;
 import org.apache.taverna.scufl2.api.profiles.Profile;

 import com.fasterxml.jackson.databind.JsonNode;

 public class WfdescSerialiser {

 	private static Logger logger = Logger.getLogger(WfdescSerialiser.class.getCanonicalName());

 	public static URI REST = URI.create("http://ns.taverna.org.uk/2010/activity/rest");
 	public static URI WSDL = URI.create("http://ns.taverna.org.uk/2010/activity/wsdl");
 	public static URI SECURITY = WSDL.resolve("wsdl/security");
 	public static URI OPERATION = WSDL.resolve("wsdl/operation");
 	public static URI BEANSHELL = URI.create("http://ns.taverna.org.uk/2010/activity/beanshell");
 	public static URI RSHELL = URI.create("http://ns.taverna.org.uk/2010/activity/rshell");
 	public static URI TOOL = URI.create("http://ns.taverna.org.uk/2010/activity/tool");

 	private Scufl2Tools scufl2Tools = new Scufl2Tools();
 	private URITools uriTools = new URITools();

 	public Scufl2Tools getScufl2Tools() {
 		return scufl2Tools;
 	}

 	public URITools getUriTools() {
 		return uriTools;
 	}

 	private String uriForBean(WorkflowBean bean) {
 		return uriTools.uriForBean(bean).toASCIIString();
 	}

 	protected OntModel save(final WorkflowBundle bundle) {
 		final OntModel model = ModelFactory.createOntologyModel();
 		bundle.accept(new VisitorWithPath() {
 			Scufl2Tools scufl2Tools = new Scufl2Tools();

 			public boolean visit() {
 				WorkflowBean node = getCurrentNode();
 				// System.out.println(node);
 				if (node instanceof WorkflowBundle) {
 					return true;
 				}
 				// @SuppressWarnings("rawtypes")

 				if (node instanceof org.apache.taverna.scufl2.api.core.Workflow) {
 					entityForBean(node, Wfdesc.Workflow);
 				} else if (node instanceof Processor) {
 					Processor processor = (Processor) node;
 					Individual process = entityForBean(processor, Wfdesc.Process);
 					Individual wf = entityForBean(processor.getParent(), Wfdesc.Workflow);
 					wf.addProperty(Wfdesc.hasSubProcess, process);
 				} else if (node instanceof InputPort) {
 					WorkflowBean parent = ((Child) node).getParent();
 					Individual input = entityForBean(node, Wfdesc.Input);
 					Individual process = entityForBean(parent, Wfdesc.Process);
 					process.addProperty(Wfdesc.hasInput, input);

 				} else if (node instanceof OutputPort) {
 					WorkflowBean parent = ((Child) node).getParent();
 					Individual output = entityForBean(node, Wfdesc.Output);
 					Individual process = entityForBean(parent, Wfdesc.Process);
 					process.addProperty(Wfdesc.hasOutput, output);
 				} else if (node instanceof DataLink) {
 					WorkflowBean parent = ((Child) node).getParent();
 					DataLink link = (DataLink) node;
 					Individual dl = entityForBean(link, Wfdesc.DataLink);

 					Individual source = entityForBean(link.getReceivesFrom(), Wfdesc.Output);
 					dl.addProperty(Wfdesc.hasSource, source);

 					Individual sink = entityForBean(link.getSendsTo(), Wfdesc.Input);
 					dl.addProperty(Wfdesc.hasSink, sink);
 					Individual wf = entityForBean(parent, Wfdesc.Workflow);
 					wf.addProperty(Wfdesc.hasDataLink, dl);
 				} else if (node instanceof Profile) {
 					// So that we can get at the ProcessorBinding - buy only if
 					// it is the main Profile
 					return node == bundle.getMainProfile();
 				} else if (node instanceof ProcessorBinding) {
 					ProcessorBinding b = (ProcessorBinding) node;
 					Activity a = b.getBoundActivity();
 					Processor boundProcessor = b.getBoundProcessor();
 					Individual process = entityForBean(boundProcessor, Wfdesc.Process);

 					// Note: We don't describe the activity and processor
 					// binding in wfdesc. Instead we
 					// assign additional types and attributes to the parent
 					// processor

 					try {
 						URI type = a.getType();
 						Configuration c = scufl2Tools.configurationFor(a, b.getParent());
 						JsonNode json = c.getJson();
 						if (type.equals(BEANSHELL)) {
 							process.addRDFType(Wf4ever.BeanshellScript);
 							String s = json.get("script").asText();
 							process.addProperty(Wf4ever.script, s);
 							JsonNode localDep = json.get("localDependency");
 							if (localDep != null && localDep.isArray()) {
 								for (int i = 0; i < localDep.size(); i++) {
 									String depStr = localDep.get(i).asText();
 									// FIXME: Better class for dependency?
 									Individual dep = model.createIndividual(OWL.Thing);
 									dep.addLabel(depStr, null);
 									dep.addComment("JAR dependency", "en");
 									process.addProperty(Roterms.requiresSoftware, dep);
 									// Somehow this gets the whole thing to fall
 									// out of the graph!
 									// QName depQ = new
 									// QName("http://google.com/", ""+
 									// UUID.randomUUID());
 									// sesameManager.rename(dep, depQ);

 								}
 							}
 						}
 						if (type.equals(RSHELL)) {
 							process.addRDFType(Wf4ever.RScript);
 							String s = json.get("script").asText();
 							process.addProperty(Wf4ever.script, s);
 						}
 						if (type.equals(WSDL)) {
 							process.addRDFType(Wf4ever.SOAPService);
 							JsonNode operation = json.get("operation");
 							URI wsdl = URI.create(operation.get("wsdl").asText());
 							process.addProperty(Wf4ever.wsdlURI, wsdl.toASCIIString());
 							process.addProperty(Wf4ever.wsdlOperationName, operation.get("name").asText());
 							process.addProperty(Wf4ever.rootURI, wsdl.resolve("/").toASCIIString());
 						}
 						if (type.equals(REST)) {
 							process.addRDFType(Wf4ever.RESTService);
 							// System.out.println(json);
 							JsonNode request = json.get("request");
 							String absoluteURITemplate = request.get("absoluteURITemplate").asText();
 							String uriTemplate = absoluteURITemplate.replace("{", "");
 							uriTemplate = uriTemplate.replace("}", "");
 							// TODO: Detect {}
 							try {
 								URI root = new URI(uriTemplate).resolve("/");
 								process.addProperty(Wf4ever.rootURI, root.toASCIIString());
 							} catch (URISyntaxException e) {
 								logger.warning("Potentially invalid URI template: " + absoluteURITemplate);
 								// Uncomment to temporarily break
 								// TestInvalidURITemplate:
 								// rest.getWfRootURI().add(URI.create("http://example.com/FRED"));
 							}
 						}
 						if (type.equals(TOOL)) {
 							process.addRDFType(Wf4ever.CommandLineTool);
 							JsonNode desc = json.get("toolDescription");
 							// System.out.println(json);
 							JsonNode command = desc.get("command");
 							if (command != null) {
 								process.addProperty(Wf4ever.command, command.asText());
 							}
 						}
 						if (type.equals(NESTED_WORKFLOW)) {
 							Workflow nestedWf = scufl2Tools.nestedWorkflowForProcessor(boundProcessor, b.getParent());
 							// The parent process is a specialization of the
 							// nested workflow
 							// (because the nested workflow could exist as
 							// several processors)
 							specializationOf(boundProcessor, nestedWf);
 							process.addRDFType(Wfdesc.Workflow);

 							// Just like the Processor specializes the nested
 							// workflow, the
 							// ProcessorPorts specialize the WorkflowPort
 							for (ProcessorPortBinding portBinding : b.getInputPortBindings()) {
 								// Map from activity port (not in wfdesc) to
 								// WorkflowPort
 								WorkflowPort wfPort = nestedWf.getInputPorts()
 										.getByName(portBinding.getBoundActivityPort().getName());
 								if (wfPort == null) {
 									continue;
 								}
 								specializationOf(portBinding.getBoundProcessorPort(), wfPort);
 							}
 							for (ProcessorPortBinding portBinding : b.getOutputPortBindings()) {
 								WorkflowPort wfPort = nestedWf.getOutputPorts()
 										.getByName(portBinding.getBoundActivityPort().getName());
 								if (wfPort == null) {
 									continue;
 								}
 								specializationOf(portBinding.getBoundProcessorPort(), wfPort);
 							}
 						}
 					} catch (IndexOutOfBoundsException ex) {
 					}
 					return false;
 				} else {
 					// System.out.println("--NO!");
 					return false;
 				}
 				for (Annotation ann : scufl2Tools.annotationsFor(node, bundle)) {
 					String annotationBody = ann.getBody().toASCIIString();
 					String baseURI = bundle.getGlobalBaseURI().resolve(ann.getBody()).toASCIIString();
 					InputStream annotationStream;
 					try {
 						annotationStream = bundle.getResources().getResourceAsInputStream(annotationBody);

 						try {
 							// FIXME: Don't just assume Lang.TURTLE
 							RDFDataMgr.read(model, annotationStream, baseURI, Lang.TURTLE);
 						} catch (RiotException e) {
 							logger.log(Level.WARNING, "Can't parse RDF Turtle from " + annotationBody, e);
 						} finally {
 							annotationStream.close();
 						}
 					} catch (IOException e) {
 						logger.log(Level.WARNING, "Can't read " + annotationBody, e);
 					}
 				}
 				if (node instanceof Named) {
 					Named named = (Named) node;
 					entityForBean(node, OWL.Thing).addLabel(named.getName(), null);
 				}
 				return true;
 			}

 			private void specializationOf(WorkflowBean special, WorkflowBean general) {
 				Individual specialEnt = entityForBean(special, Prov_o.Entity);
 				Individual generalEnt = entityForBean(general, Prov_o.Entity);
 				specialEnt.addProperty(Prov_o.specializationOf, generalEnt);
 			}

 			private Individual entityForBean(WorkflowBean bean, Resource thing) {
 				return model.createIndividual(uriForBean(bean), thing);
 			}

 			// @Override
 			// public boolean visitEnter(WorkflowBean node) {
 			// if (node instanceof Processor
 			// || node instanceof org.apache.taverna.scufl2.api.core.Workflow
 			// || node instanceof Port || node instanceof DataLink) {
 			// visit(node);
 			// return true;
 			// }
 			// // The other node types (e.g. dispatch stack, configuration) are
 			// // not (directly) represented in wfdesc
 			//// System.out.println("Skipping " + node);
 			// return false;
 			// };
 		});
 		return model;
 	}

 	public void save(WorkflowBundle wfBundle, OutputStream output) throws WriterException {
 		OntModel model;

 		final URI baseURI;
 		if (wfBundle.getMainWorkflow() != null) {
 			Workflow mainWorkflow = wfBundle.getMainWorkflow();
 			baseURI = uriTools.uriForBean(mainWorkflow);
 			model = save(wfBundle);
 		} else {
 			throw new WriterException("wfdesc format requires a main workflow");
 		}

 		model.setNsPrefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
 		model.setNsPrefix("xsd", "http://www.w3.org/2001/XMLSchema#");
 		model.setNsPrefix("owl", "http://www.w3.org/2002/07/owl#");
 		model.setNsPrefix("prov", "http://www.w3.org/ns/prov#");
 		model.setNsPrefix("wfdesc", "http://purl.org/wf4ever/wfdesc#");
 		model.setNsPrefix("wf4ever", "http://purl.org/wf4ever/wf4ever#");
 		model.setNsPrefix("roterms", "http://purl.org/wf4ever/roterms#");
 		model.setNsPrefix("dc", "http://purl.org/dc/elements/1.1/");
 		model.setNsPrefix("dcterms", "http://purl.org/dc/terms/");
 		model.setNsPrefix("comp", "http://purl.org/DP/components#");
 		model.setNsPrefix("dep", "http://scape.keep.pt/vocab/dependencies#");
 		model.setNsPrefix("biocat", "http://biocatalogue.org/attribute/");

 		model.setNsPrefix("", "#");

 		try {
 			model.write(output, Lang.TURTLE.getName(), baseURI.toString());
 		} catch (RiotException e) {
 			throw new WriterException("Can't write to output", e);
 		}

 	}

 	public void setScufl2Tools(Scufl2Tools scufl2Tools) {
 		this.scufl2Tools = scufl2Tools;
 	}

 	public void setUriTools(URITools uriTools) {
 		this.uriTools = uriTools;
 	}

 }
	package org.apache.taverna.scufl2.wfdesc;

	/*
	*
	* Licensed to the Apache Software Foundation (ASF) under one
	* or more contributor license agreements. See the NOTICE file
	* distributed with this work for additional information
	* regarding copyright ownership. The ASF licenses this file
	* to you under the Apache License, Version 2.0 (the
	* "License"); you may not use this file except in compliance
	* with the License. You may obtain a copy of the License at
	*
	* http://www.apache.org/licenses/LICENSE-2.0
	*
	* Unless required by applicable law or agreed to in writing,
	* software distributed under the License is distributed on an
	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
	* KIND, either express or implied. See the License for the
	* specific language governing permissions and limitations
	* under the License.
	*
	*/

	import static org.apache.taverna.scufl2.api.common.Scufl2Tools.NESTED_WORKFLOW;

	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStream;
	import java.net.URI;
	import java.net.URISyntaxException;
	import java.util.logging.Level;
	import java.util.logging.Logger;

	import org.apache.jena.ontology.Individual;
	import org.apache.jena.ontology.OntModel;
	import org.apache.jena.rdf.model.ModelFactory;
	import org.apache.jena.rdf.model.Resource;
	import org.apache.jena.riot.Lang;
	import org.apache.jena.riot.RDFDataMgr;
	import org.apache.jena.riot.RiotException;
	import org.apache.jena.vocabulary.OWL;
	import org.apache.taverna.ro.vocabs.Prov_o;
	import org.apache.taverna.ro.vocabs.Roterms;
	import org.apache.taverna.ro.vocabs.Wf4ever;
	import org.apache.taverna.ro.vocabs.Wfdesc;
	import org.apache.taverna.scufl2.api.activity.Activity;
	import org.apache.taverna.scufl2.api.annotation.Annotation;
	import org.apache.taverna.scufl2.api.common.Child;
	import org.apache.taverna.scufl2.api.common.Named;
	import org.apache.taverna.scufl2.api.common.Scufl2Tools;
	import org.apache.taverna.scufl2.api.common.URITools;
	import org.apache.taverna.scufl2.api.common.Visitor.VisitorWithPath;
	import org.apache.taverna.scufl2.api.common.WorkflowBean;
	import org.apache.taverna.scufl2.api.configurations.Configuration;
	import org.apache.taverna.scufl2.api.container.WorkflowBundle;
	import org.apache.taverna.scufl2.api.core.DataLink;
	import org.apache.taverna.scufl2.api.core.Processor;
	import org.apache.taverna.scufl2.api.core.Workflow;
	import org.apache.taverna.scufl2.api.io.WriterException;
	import org.apache.taverna.scufl2.api.port.InputPort;
	import org.apache.taverna.scufl2.api.port.OutputPort;
	import org.apache.taverna.scufl2.api.port.WorkflowPort;
	import org.apache.taverna.scufl2.api.profiles.ProcessorBinding;
	import org.apache.taverna.scufl2.api.profiles.ProcessorPortBinding;
	import org.apache.taverna.scufl2.api.profiles.Profile;

	import com.fasterxml.jackson.databind.JsonNode;

	public class WfdescSerialiser {

	private static Logger logger = Logger.getLogger(WfdescSerialiser.class.getCanonicalName());

	public static URI REST = URI.create("http://ns.taverna.org.uk/2010/activity/rest");
	public static URI WSDL = URI.create("http://ns.taverna.org.uk/2010/activity/wsdl");
	public static URI SECURITY = WSDL.resolve("wsdl/security");
	public static URI OPERATION = WSDL.resolve("wsdl/operation");
	public static URI BEANSHELL = URI.create("http://ns.taverna.org.uk/2010/activity/beanshell");
	public static URI RSHELL = URI.create("http://ns.taverna.org.uk/2010/activity/rshell");
	public static URI TOOL = URI.create("http://ns.taverna.org.uk/2010/activity/tool");

	private Scufl2Tools scufl2Tools = new Scufl2Tools();
	private URITools uriTools = new URITools();

	public Scufl2Tools getScufl2Tools() {
	return scufl2Tools;
	}

	public URITools getUriTools() {
	return uriTools;
	}

	private String uriForBean(WorkflowBean bean) {
	return uriTools.uriForBean(bean).toASCIIString();
	}

	protected OntModel save(final WorkflowBundle bundle) {
	final OntModel model = ModelFactory.createOntologyModel();
	bundle.accept(new VisitorWithPath() {
	Scufl2Tools scufl2Tools = new Scufl2Tools();

	public boolean visit() {
	WorkflowBean node = getCurrentNode();
	// System.out.println(node);
	if (node instanceof WorkflowBundle) {
	return true;
	}
	// @SuppressWarnings("rawtypes")

	if (node instanceof org.apache.taverna.scufl2.api.core.Workflow) {
	entityForBean(node, Wfdesc.Workflow);
	} else if (node instanceof Processor) {
	Processor processor = (Processor) node;
	Individual process = entityForBean(processor, Wfdesc.Process);
	Individual wf = entityForBean(processor.getParent(), Wfdesc.Workflow);
	wf.addProperty(Wfdesc.hasSubProcess, process);
	} else if (node instanceof InputPort) {
	WorkflowBean parent = ((Child) node).getParent();
	Individual input = entityForBean(node, Wfdesc.Input);
	Individual process = entityForBean(parent, Wfdesc.Process);
	process.addProperty(Wfdesc.hasInput, input);

	} else if (node instanceof OutputPort) {
	WorkflowBean parent = ((Child) node).getParent();
	Individual output = entityForBean(node, Wfdesc.Output);
	Individual process = entityForBean(parent, Wfdesc.Process);
	process.addProperty(Wfdesc.hasOutput, output);
	} else if (node instanceof DataLink) {
	WorkflowBean parent = ((Child) node).getParent();
	DataLink link = (DataLink) node;
	Individual dl = entityForBean(link, Wfdesc.DataLink);

	Individual source = entityForBean(link.getReceivesFrom(), Wfdesc.Output);
	dl.addProperty(Wfdesc.hasSource, source);

	Individual sink = entityForBean(link.getSendsTo(), Wfdesc.Input);
	dl.addProperty(Wfdesc.hasSink, sink);
	Individual wf = entityForBean(parent, Wfdesc.Workflow);
	wf.addProperty(Wfdesc.hasDataLink, dl);
	} else if (node instanceof Profile) {
	// So that we can get at the ProcessorBinding - buy only if
	// it is the main Profile
	return node == bundle.getMainProfile();
	} else if (node instanceof ProcessorBinding) {
	ProcessorBinding b = (ProcessorBinding) node;
	Activity a = b.getBoundActivity();
	Processor boundProcessor = b.getBoundProcessor();
	Individual process = entityForBean(boundProcessor, Wfdesc.Process);

	// Note: We don't describe the activity and processor
	// binding in wfdesc. Instead we
	// assign additional types and attributes to the parent
	// processor

	try {
	URI type = a.getType();
	Configuration c = scufl2Tools.configurationFor(a, b.getParent());
	JsonNode json = c.getJson();
	if (type.equals(BEANSHELL)) {
	process.addRDFType(Wf4ever.BeanshellScript);
	String s = json.get("script").asText();
	process.addProperty(Wf4ever.script, s);
	JsonNode localDep = json.get("localDependency");
	if (localDep != null && localDep.isArray()) {
	for (int i = 0; i < localDep.size(); i++) {
	String depStr = localDep.get(i).asText();
	// FIXME: Better class for dependency?
	Individual dep = model.createIndividual(OWL.Thing);
	dep.addLabel(depStr, null);
	dep.addComment("JAR dependency", "en");
	process.addProperty(Roterms.requiresSoftware, dep);
	// Somehow this gets the whole thing to fall
	// out of the graph!
	// QName depQ = new
	// QName("http://google.com/", ""+
	// UUID.randomUUID());
	// sesameManager.rename(dep, depQ);

	}
	}
	}
	if (type.equals(RSHELL)) {
	process.addRDFType(Wf4ever.RScript);
	String s = json.get("script").asText();
	process.addProperty(Wf4ever.script, s);
	}
	if (type.equals(WSDL)) {
	process.addRDFType(Wf4ever.SOAPService);
	JsonNode operation = json.get("operation");
	URI wsdl = URI.create(operation.get("wsdl").asText());
	process.addProperty(Wf4ever.wsdlURI, wsdl.toASCIIString());
	process.addProperty(Wf4ever.wsdlOperationName, operation.get("name").asText());
	process.addProperty(Wf4ever.rootURI, wsdl.resolve("/").toASCIIString());
	}
	if (type.equals(REST)) {
	process.addRDFType(Wf4ever.RESTService);
	// System.out.println(json);
	JsonNode request = json.get("request");
	String absoluteURITemplate = request.get("absoluteURITemplate").asText();
	String uriTemplate = absoluteURITemplate.replace("{", "");
	uriTemplate = uriTemplate.replace("}", "");
	// TODO: Detect {}
	try {
	URI root = new URI(uriTemplate).resolve("/");
	process.addProperty(Wf4ever.rootURI, root.toASCIIString());
	} catch (URISyntaxException e) {
	logger.warning("Potentially invalid URI template: " + absoluteURITemplate);
	// Uncomment to temporarily break
	// TestInvalidURITemplate:
	// rest.getWfRootURI().add(URI.create("http://example.com/FRED"));
	}
	}
	if (type.equals(TOOL)) {
	process.addRDFType(Wf4ever.CommandLineTool);
	JsonNode desc = json.get("toolDescription");
	// System.out.println(json);
	JsonNode command = desc.get("command");
	if (command != null) {
	process.addProperty(Wf4ever.command, command.asText());
	}
	}
	if (type.equals(NESTED_WORKFLOW)) {
	Workflow nestedWf = scufl2Tools.nestedWorkflowForProcessor(boundProcessor, b.getParent());
	// The parent process is a specialization of the
	// nested workflow
	// (because the nested workflow could exist as
	// several processors)
	specializationOf(boundProcessor, nestedWf);
	process.addRDFType(Wfdesc.Workflow);

	// Just like the Processor specializes the nested
	// workflow, the
	// ProcessorPorts specialize the WorkflowPort
	for (ProcessorPortBinding portBinding : b.getInputPortBindings()) {
	// Map from activity port (not in wfdesc) to
	// WorkflowPort
	WorkflowPort wfPort = nestedWf.getInputPorts()
	.getByName(portBinding.getBoundActivityPort().getName());
	if (wfPort == null) {
	continue;
	}
	specializationOf(portBinding.getBoundProcessorPort(), wfPort);
	}
	for (ProcessorPortBinding portBinding : b.getOutputPortBindings()) {
	WorkflowPort wfPort = nestedWf.getOutputPorts()
	.getByName(portBinding.getBoundActivityPort().getName());
	if (wfPort == null) {
	continue;
	}
	specializationOf(portBinding.getBoundProcessorPort(), wfPort);
	}
	}
	} catch (IndexOutOfBoundsException ex) {
	}
	return false;
	} else {
	// System.out.println("--NO!");
	return false;
	}
	for (Annotation ann : scufl2Tools.annotationsFor(node, bundle)) {
	String annotationBody = ann.getBody().toASCIIString();
	String baseURI = bundle.getGlobalBaseURI().resolve(ann.getBody()).toASCIIString();
	InputStream annotationStream;
	try {
	annotationStream = bundle.getResources().getResourceAsInputStream(annotationBody);

	try {
	// FIXME: Don't just assume Lang.TURTLE
	RDFDataMgr.read(model, annotationStream, baseURI, Lang.TURTLE);
	} catch (RiotException e) {
	logger.log(Level.WARNING, "Can't parse RDF Turtle from " + annotationBody, e);
	} finally {
	annotationStream.close();
	}
	} catch (IOException e) {
	logger.log(Level.WARNING, "Can't read " + annotationBody, e);
	}
	}
	if (node instanceof Named) {
	Named named = (Named) node;
	entityForBean(node, OWL.Thing).addLabel(named.getName(), null);
	}
	return true;
	}

	private void specializationOf(WorkflowBean special, WorkflowBean general) {
	Individual specialEnt = entityForBean(special, Prov_o.Entity);
	Individual generalEnt = entityForBean(general, Prov_o.Entity);
	specialEnt.addProperty(Prov_o.specializationOf, generalEnt);
	}

	private Individual entityForBean(WorkflowBean bean, Resource thing) {
	return model.createIndividual(uriForBean(bean), thing);
	}

	// @Override
	// public boolean visitEnter(WorkflowBean node) {
	// if (node instanceof Processor
	// \|\| node instanceof org.apache.taverna.scufl2.api.core.Workflow
	// \|\| node instanceof Port \|\| node instanceof DataLink) {
	// visit(node);
	// return true;
	// }
	// // The other node types (e.g. dispatch stack, configuration) are
	// // not (directly) represented in wfdesc
	//// System.out.println("Skipping " + node);
	// return false;
	// };
	});
	return model;
	}

	public void save(WorkflowBundle wfBundle, OutputStream output) throws WriterException {
	OntModel model;

	final URI baseURI;
	if (wfBundle.getMainWorkflow() != null) {
	Workflow mainWorkflow = wfBundle.getMainWorkflow();
	baseURI = uriTools.uriForBean(mainWorkflow);
	model = save(wfBundle);
	} else {
	throw new WriterException("wfdesc format requires a main workflow");
	}

	model.setNsPrefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
	model.setNsPrefix("xsd", "http://www.w3.org/2001/XMLSchema#");
	model.setNsPrefix("owl", "http://www.w3.org/2002/07/owl#");
	model.setNsPrefix("prov", "http://www.w3.org/ns/prov#");
	model.setNsPrefix("wfdesc", "http://purl.org/wf4ever/wfdesc#");
	model.setNsPrefix("wf4ever", "http://purl.org/wf4ever/wf4ever#");
	model.setNsPrefix("roterms", "http://purl.org/wf4ever/roterms#");
	model.setNsPrefix("dc", "http://purl.org/dc/elements/1.1/");
	model.setNsPrefix("dcterms", "http://purl.org/dc/terms/");
	model.setNsPrefix("comp", "http://purl.org/DP/components#");
	model.setNsPrefix("dep", "http://scape.keep.pt/vocab/dependencies#");
	model.setNsPrefix("biocat", "http://biocatalogue.org/attribute/");

	model.setNsPrefix("", "#");

	try {
	model.write(output, Lang.TURTLE.getName(), baseURI.toString());
	} catch (RiotException e) {
	throw new WriterException("Can't write to output", e);
	}

	}

	public void setScufl2Tools(Scufl2Tools scufl2Tools) {
	this.scufl2Tools = scufl2Tools;
	}

	public void setUriTools(URITools uriTools) {
	this.uriTools = uriTools;
	}

	}