taverna-scufl2-wfbundle/src/test/java/org/apache/taverna/scufl2/rdfxml/TestRDFXMLSerializer.java - incubator-taverna-language - Git at Google

 package org.apache.taverna.scufl2.rdfxml;
 /*
  *
  * 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.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.fail;

 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.net.URI;
 import java.net.URL;

 import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.apache.commons.io.output.NullOutputStream;
 import org.apache.taverna.scufl2.api.ExampleWorkflow;
 import org.apache.taverna.scufl2.api.container.WorkflowBundle;
 import org.apache.taverna.scufl2.rdfxml.RDFXMLSerializer;
 import org.jdom.Attribute;
 import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.JDOMException;
 import org.jdom.Namespace;
 import org.jdom.input.SAXBuilder;
 import org.jdom.xpath.XPath;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;


 public class TestRDFXMLSerializer {
 	protected static final String TAVERNAWORKBENCH_RDF = "profile/tavernaWorkbench.rdf";
 	protected static final String TAVERNASERVER_RDF = "profile/tavernaServer.rdf";
 	protected static final String HELLOWORLD_RDF = "workflow/HelloWorld.rdf";
 	RDFXMLSerializer serializer = new RDFXMLSerializer();
 	ExampleWorkflow exampleWf = new ExampleWorkflow();
 	WorkflowBundle workflowBundle;

 	Namespace XSI_NS = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
 	Namespace RDF_NS = Namespace.getNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
 	Namespace RDSF_NS = Namespace.getNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
 	Namespace SCUFL2_NS = Namespace.getNamespace("s", "http://ns.taverna.org.uk/2010/scufl2#");
 	Namespace BEANSHELL_NS = Namespace.getNamespace("beanshell",
 			"http://ns.taverna.org.uk/2010/activity/beanshell#");


 	protected void assertXpathEquals(String expected, Element element,
 			String xpath) throws JDOMException {
 		Object o = xpathSelectElement(element, xpath);
 		if (o == null) {
 			fail("Can't find " + xpath  + " in " + element);
 			return;
 		}
 		String text;
 		if (o instanceof Attribute) {
 			text = ((Attribute)o).getValue();
 		} else {
 			text = ((Element)o).getValue();
 		}
 		assertEquals(expected, text);
 	}


 	protected void checkProfileDocument(Element root, boolean isWorkbench) throws JDOMException {

 		assertEquals("ProfileDocument", root.getAttributeValue("type", XSI_NS));
 		assertXpathEquals(isWorkbench ? "tavernaWorkbench/" : "tavernaServer/", root, "./@xml:base");

 		Element profile = (Element) root.getChildren().get(0);
 		Element activity = (Element) root.getChildren().get(1);
 		Element binding = (Element) root.getChildren().get(2);
 		Element configuration = (Element) root.getChildren().get(3);


 		assertSame(xpathSelectElement(root, "./s:Profile"), profile);
 		assertSame(xpathSelectElement(root, "./s:Activity"), activity);
 		assertSame(xpathSelectElement(root, "./s:ProcessorBinding"), binding);
 		assertSame(xpathSelectElement(root, "./s:Configuration"), configuration);

 		assertXpathEquals("", profile, "./@rdf:about");
 		assertXpathEquals(isWorkbench ? "tavernaWorkbench" : "tavernaServer", profile, "./s:name");
 		assertXpathEquals("processorbinding/Hello/", profile, "./s:processorBinding/@rdf:resource");
 		assertXpathEquals("configuration/Hello/", profile, "./s:activateConfiguration/@rdf:resource");

 		// activity
 		assertXpathEquals("activity/HelloScript/", activity, "./@rdf:about");
 		assertXpathEquals("HelloScript", activity, "./s:name");
 		assertXpathEquals("http://ns.taverna.org.uk/2010/activity/beanshell",
 				activity, "./rdf:type/@rdf:resource");
 		// activity input
 		assertXpathEquals("activity/HelloScript/in/personName", activity, "./s:inputActivityPort/s:InputActivityPort/@rdf:about");
 		assertXpathEquals("personName", activity, "./s:inputActivityPort/s:InputActivityPort/s:name");
 		assertXpathEquals("0", activity, "./s:inputActivityPort/s:InputActivityPort/s:portDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:inputActivityPort/s:InputActivityPort/s:portDepth/@rdf:datatype");
 		// activity output
 		assertXpathEquals("activity/HelloScript/out/hello", activity, "./s:outputActivityPort/s:OutputActivityPort/@rdf:about");
 		assertXpathEquals("hello", activity, "./s:outputActivityPort/s:OutputActivityPort/s:name");
 		assertXpathEquals("0", activity, "./s:outputActivityPort/s:OutputActivityPort/s:portDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:outputActivityPort/s:OutputActivityPort/s:portDepth/@rdf:datatype");
 		assertXpathEquals("0", activity, "./s:outputActivityPort/s:OutputActivityPort/s:granularPortDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:outputActivityPort/s:OutputActivityPort/s:granularPortDepth/@rdf:datatype");

 		// processor binding
 		assertXpathEquals("processorbinding/Hello/", binding, "./@rdf:about");
 		assertXpathEquals("Hello", binding, "./s:name");
 		assertXpathEquals("activity/HelloScript/", binding, "./s:bindActivity/@rdf:resource");
 		assertXpathEquals("../../workflow/HelloWorld/processor/Hello/", binding, "./s:bindProcessor/@rdf:resource");
 		// input port binding
 		assertXpathEquals("processorbinding/Hello/in/name", binding, "./s:inputPortBinding/s:InputPortBinding/@rdf:about");
 		assertXpathEquals("activity/HelloScript/in/personName", binding, "./s:inputPortBinding/s:InputPortBinding/s:bindInputActivityPort/@rdf:resource");
 		assertXpathEquals("../../workflow/HelloWorld/processor/Hello/in/name", binding, "./s:inputPortBinding/s:InputPortBinding/s:bindInputProcessorPort/@rdf:resource");
 		// output port binding
 		assertXpathEquals("processorbinding/Hello/out/greeting", binding, "./s:outputPortBinding/s:OutputPortBinding/@rdf:about");
 		assertXpathEquals("activity/HelloScript/out/hello", binding, "./s:outputPortBinding/s:OutputPortBinding/s:bindOutputActivityPort/@rdf:resource");
 		assertXpathEquals("../../workflow/HelloWorld/processor/Hello/out/greeting", binding, "./s:outputPortBinding/s:OutputPortBinding/s:bindOutputProcessorPort/@rdf:resource");


 		assertXpathEquals("configuration/Hello/", configuration, "./@rdf:about");
 		assertXpathEquals("configuration/Hello.json", configuration, "./rdfs:seeAlso/@rdf:resource");

 		assertXpathEquals(
 				"http://ns.taverna.org.uk/2010/activity/beanshell#Config",
 				configuration, "./rdf:type/@rdf:resource");
 		assertXpathEquals("Hello", configuration, "./s:name");
 		assertXpathEquals("activity/HelloScript/", configuration, "./s:configure/@rdf:resource");
 //		assertXpathEquals("hello = \"Hello, \" + personName;\n" +
 //				(isWorkbench ? "JOptionPane.showMessageDialog(null, hello);" : "System.out.println(\"Server says: \" + hello);"), configuration, "./beanshell:script");

 	}

 	protected void checkRoot(Element root) {
 		assertEquals(RDF_NS, root.getNamespace());
 		assertEquals("rdf", root.getNamespacePrefix());
 		assertEquals("RDF", root.getName());
 		assertEquals(SCUFL2_NS, root.getNamespace(""));
 		String schemaLocation = root.getAttributeValue("schemaLocation", XSI_NS);
 		schemaLocation = schemaLocation.replaceAll("\\s+", " ");
 		String[] schemaLocations = schemaLocation.split(" ");
 		String[] expectedSchemaLocations = {
 				"http://ns.taverna.org.uk/2010/scufl2#","http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd",
 				"http://www.w3.org/1999/02/22-rdf-syntax-ns#","http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"
 		};
 		assertArrayEquals(expectedSchemaLocations, schemaLocations);
 	}


 	protected void checkWorkflowBundleDocument(Element root) throws JDOMException {
 		assertEquals("WorkflowBundleDocument", root.getAttributeValue("type", XSI_NS));

 		assertXpathEquals("./", root, "./@xml:base");

 		Element wbundle = root.getChild("WorkflowBundle", SCUFL2_NS);
 		assertSame(wbundle, root.getChildren().get(0));


 		assertXpathEquals("", wbundle, "./@rdf:about");

 		assertXpathEquals("HelloWorld", wbundle, "./s:name");
 		assertXpathEquals("http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/",
 				wbundle, "./s:globalBaseURI/@rdf:resource");

 		assertXpathEquals("workflow/HelloWorld/",
 				wbundle, "./s:mainWorkflow/@rdf:resource");
 		assertXpathEquals("workflow/HelloWorld/",
 				wbundle, "./s:workflow/s:Workflow/@rdf:about");
 		assertXpathEquals(HELLOWORLD_RDF,
 				wbundle, "./s:workflow/s:Workflow/rdfs:seeAlso/@rdf:resource");

 		assertXpathEquals("profile/tavernaWorkbench/",
 				wbundle, "./s:mainProfile/@rdf:resource");


 		assertXpathEquals("profile/tavernaServer/",
 				wbundle, "./s:profile[1]/s:Profile/@rdf:about");
 		assertXpathEquals("profile/tavernaServer.rdf", wbundle, "./s:profile[1]/s:Profile/rdfs:seeAlso/@rdf:resource");

 		assertXpathEquals("profile/tavernaWorkbench/",
 				wbundle, "./s:profile[2]/s:Profile/@rdf:about");
 		assertXpathEquals(TAVERNAWORKBENCH_RDF,
 				wbundle, "./s:profile[2]/s:Profile/rdfs:seeAlso/@rdf:resource");


 	}


 	protected void checkWorkflowDocument(Element root) throws JDOMException {
 		assertEquals("WorkflowDocument", root.getAttributeValue("type", XSI_NS));


 		assertXpathEquals("HelloWorld/", root, "./@xml:base");


 		Element wf = root.getChild("Workflow", SCUFL2_NS);
 		assertSame(wf, root.getChildren().get(0));

 		assertXpathEquals("", wf, "./@rdf:about");


 		assertXpathEquals("HelloWorld", wf, "./s:name");
 		assertXpathEquals("http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/",
 				wf, "./s:workflowIdentifier/@rdf:resource");

 		assertXpathEquals("in/yourName",
 				wf, "./s:inputWorkflowPort/s:InputWorkflowPort/@rdf:about");
 		assertXpathEquals("yourName",
 				wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:name");
 		assertXpathEquals("0",
 				wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:portDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:portDepth/@rdf:datatype");


 		assertXpathEquals("out/results",
 				wf, "./s:outputWorkflowPort/s:OutputWorkflowPort/@rdf:about");
 		assertXpathEquals("results",
 				wf, "./s:outputWorkflowPort/s:OutputWorkflowPort/s:name");


 		assertXpathEquals("processor/Hello/",
 				wf, "./s:processor[1]/s:Processor/@rdf:about");
 		assertXpathEquals("Hello",
 				wf, "./s:processor[1]/s:Processor/s:name");

 		assertXpathEquals("processor/Hello/in/name",
 				wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/@rdf:about");
 		assertXpathEquals("name",
 				wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:name");
 		assertXpathEquals("0",
 				wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:portDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:portDepth/@rdf:datatype");


 		assertXpathEquals("processor/Hello/out/greeting",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/@rdf:about");

 		assertXpathEquals("greeting",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:name");
 		assertXpathEquals("0",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:portDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:portDepth/@rdf:datatype");
 		assertXpathEquals("0",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:granularPortDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:granularPortDepth/@rdf:datatype");

 		assertXpathEquals("processor/Hello/iterationstrategy/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/@rdf:about");
 		assertXpathEquals("Collection", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/@rdf:parseType");
 		assertXpathEquals("processor/Hello/iterationstrategy/0/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/@rdf:about");
 		assertXpathEquals("Collection", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/@rdf:parseType");
 		assertXpathEquals("processor/Hello/iterationstrategy/0/0/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/@rdf:about");
 		assertXpathEquals("processor/Hello/in/name", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:iterateOverInputPort/@rdf:resource");
 		assertXpathEquals("0", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:desiredDepth");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:desiredDepth/@rdf:datatype");


 		assertXpathEquals("processor/wait4me/",
 				wf, "./s:processor[2]/s:Processor/@rdf:about");
 		assertXpathEquals("wait4me",
 				wf, "./s:processor[2]/s:Processor/s:name");


 		assertXpathEquals("datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0",
 				wf, "./s:datalink[1]/s:DataLink/@rdf:about");

 		assertXpathEquals("datalink?from=in/yourName&to=processor/Hello/in/name",
 				wf, "./s:datalink[2]/s:DataLink/@rdf:about");

 		assertXpathEquals("datalink?from=in/yourName&to=out/results&mergePosition=1",
 				wf, "./s:datalink[3]/s:DataLink/@rdf:about");
 		assertXpathEquals("in/yourName",
 				wf, "./s:datalink[3]/s:DataLink/s:receiveFrom/@rdf:resource");
 		assertXpathEquals("out/results",
 				wf, "./s:datalink[3]/s:DataLink/s:sendTo/@rdf:resource");
 		assertXpathEquals("1",
 				wf, "./s:datalink[3]/s:DataLink/s:mergePosition");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:datalink[3]/s:DataLink/s:mergePosition/@rdf:datatype");

 		assertXpathEquals("control?block=processor/Hello/&untilFinished=processor/wait4me/",
 				wf, "./s:control/s:Blocking/@rdf:about");


 		assertXpathEquals("processor/Hello/",
 				wf, "./s:control/s:Blocking/s:block/@rdf:resource");
 		assertXpathEquals("processor/wait4me/",
 				wf, "./s:control/s:Blocking/s:untilFinished/@rdf:resource");

 		assertXpathEquals("datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0",
 				wf, "./s:datalink[1]/s:DataLink/@rdf:about");
 		assertXpathEquals("processor/Hello/out/greeting",
 				wf, "./s:datalink[1]/s:DataLink/s:receiveFrom/@rdf:resource");
 		assertXpathEquals("out/results",
 				wf, "./s:datalink[1]/s:DataLink/s:sendTo/@rdf:resource");
 		assertXpathEquals("0",
 				wf, "./s:datalink[1]/s:DataLink/s:mergePosition");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:datalink[1]/s:DataLink/s:mergePosition/@rdf:datatype");


 		assertXpathEquals("datalink?from=in/yourName&to=processor/Hello/in/name",
 				wf, "./s:datalink[2]/s:DataLink/@rdf:about");
 		assertXpathEquals("in/yourName",
 				wf, "./s:datalink[2]/s:DataLink/s:receiveFrom/@rdf:resource");
 		assertXpathEquals("processor/Hello/in/name",
 				wf, "./s:datalink[2]/s:DataLink/s:sendTo/@rdf:resource");
 		assertNull(xpathSelectElement(wf, "./s:datalink[2]/s:DataLink/s:mergePosition"));


 		assertXpathEquals("datalink?from=in/yourName&to=out/results&mergePosition=1",
 				wf, "./s:datalink[3]/s:DataLink/@rdf:about");
 		assertXpathEquals("in/yourName",
 				wf, "./s:datalink[3]/s:DataLink/s:receiveFrom/@rdf:resource");
 		assertXpathEquals("out/results",
 				wf, "./s:datalink[3]/s:DataLink/s:sendTo/@rdf:resource");
 		assertXpathEquals("1",
 				wf, "./s:datalink[3]/s:DataLink/s:mergePosition");
 		assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
 				wf, "./s:datalink[3]/s:DataLink/s:mergePosition/@rdf:datatype");

 		assertXpathEquals("control?block=processor/Hello/&untilFinished=processor/wait4me/",
 				wf, "./s:control/s:Blocking/@rdf:about");


 		assertXpathEquals("processor/Hello/",
 				wf, "./s:control/s:Blocking/s:block/@rdf:resource");
 		assertXpathEquals("processor/wait4me/",
 				wf, "./s:control/s:Blocking/s:untilFinished/@rdf:resource");

 	}

 	// TODO: Update tests
 	@Ignore
 	@Test
 	public void exampleProfileTavernaServer() throws Exception {
 		URL tavernaWorkbenc = getClass().getResource("example/profile/tavernaServer.rdf");
 		SAXBuilder saxBuilder = new SAXBuilder();
 		Document doc = saxBuilder.build(tavernaWorkbenc);
 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkProfileDocument(root, false);

 	}


 	// TODO: Update tests
 	@Ignore
 	@Test
 	public void exampleProfileTavernaWorkbench() throws Exception {
 		URL tavernaWorkbenc = getClass().getResource("example/profile/tavernaWorkbench.rdf");
 		SAXBuilder saxBuilder = new SAXBuilder();
 		Document doc = saxBuilder.build(tavernaWorkbenc);
 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkProfileDocument(root, true);

 	}

 	@Test
 	public void exampleWorkflow() throws Exception {
 		URL workflowURL = getClass().getResource("example/workflow/HelloWorld.rdf");
 		SAXBuilder saxBuilder = new SAXBuilder();
 		Document doc = saxBuilder.build(workflowURL);

 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkWorkflowDocument(root);

 	}


 	@Test
 	public void exampleWorkflowBundle() throws Exception {
 		URL workflowBundleURL = getClass().getResource("example/workflowBundle.rdf");


 		SAXBuilder saxBuilder = new SAXBuilder();
 		Document doc = saxBuilder.build(workflowBundleURL);

 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkWorkflowBundleDocument(root);

 	}


 	@Before
 	public void makeExampleWorkflow() {
 		workflowBundle = new ExampleWorkflow().makeWorkflowBundle();
 		serializer.setWfBundle(workflowBundle);
 	}


 	protected Document parseXml(ByteArrayOutputStream outStream)
 			throws JDOMException, IOException {
 		SAXBuilder saxBuilder = new SAXBuilder();
 		return saxBuilder.build(new ByteArrayInputStream(outStream.toByteArray()));
 	}


 	@Test
 	public void profile() throws Exception {
 		ByteArrayOutputStream outStream = new ByteArrayOutputStream();
 		// To test that seeAlso URIs are stored
 		serializer.profileDoc(outStream, workflowBundle.getMainProfile(), URI.create(TAVERNAWORKBENCH_RDF));
 		//System.out.write(outStream.toByteArray());
 		Document doc = parseXml(outStream);
 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkProfileDocument(root, true);
 	}


 	@Test
 	public void workflow() throws Exception {
 		ByteArrayOutputStream outStream = new ByteArrayOutputStream();
 		// To test that seeAlso URIs are stored
 		serializer.workflowDoc(outStream, workflowBundle.getMainWorkflow(), URI.create(HELLOWORLD_RDF));
 //		System.out.write(outStream.toByteArray());
 		Document doc = parseXml(outStream);
 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkWorkflowDocument(root);
 	}

 	@Test
 	public void workflowBundle() throws Exception {
 		ByteArrayOutputStream outStream = new ByteArrayOutputStream();
 		// To test that seeAlso URIs are stored
 		serializer.workflowDoc(new NullOutputStream(), workflowBundle.getMainWorkflow(), URI.create(HELLOWORLD_RDF));
 		serializer.profileDoc(new NullOutputStream(), workflowBundle.getProfiles().getByName("tavernaWorkbench"), URI.create(TAVERNAWORKBENCH_RDF));
 		serializer.profileDoc(new NullOutputStream(), workflowBundle.getProfiles().getByName("tavernaServer"), URI.create(TAVERNASERVER_RDF));

 		serializer.workflowBundleDoc(outStream, URI.create("workflowBundle.rdf"));
 		//System.out.write(outStream.toByteArray());
 		Document doc = parseXml(outStream);
 		Element root = doc.getRootElement();

 		checkRoot(root);
 		checkWorkflowBundleDocument(root);

 	}


 	protected Object xpathSelectElement(Element element, String xpath) throws JDOMException {
 		XPath x = XPath.newInstance(xpath);
 		x.addNamespace(SCUFL2_NS);
 		x.addNamespace(RDF_NS);
 		x.addNamespace(RDSF_NS);
 		x.addNamespace(BEANSHELL_NS);
 		//x.addNamespace(XML_NS);

 		return x.selectSingleNode(element);
 	}
 }
	package org.apache.taverna.scufl2.rdfxml;
	/*
	*
	* 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.junit.Assert.assertArrayEquals;
	import static org.junit.Assert.assertEquals;
	import static org.junit.Assert.assertNull;
	import static org.junit.Assert.assertSame;
	import static org.junit.Assert.fail;

	import java.io.ByteArrayInputStream;
	import java.io.IOException;
	import java.net.URI;
	import java.net.URL;

	import org.apache.commons.io.output.ByteArrayOutputStream;
	import org.apache.commons.io.output.NullOutputStream;
	import org.apache.taverna.scufl2.api.ExampleWorkflow;
	import org.apache.taverna.scufl2.api.container.WorkflowBundle;
	import org.apache.taverna.scufl2.rdfxml.RDFXMLSerializer;
	import org.jdom.Attribute;
	import org.jdom.Document;
	import org.jdom.Element;
	import org.jdom.JDOMException;
	import org.jdom.Namespace;
	import org.jdom.input.SAXBuilder;
	import org.jdom.xpath.XPath;
	import org.junit.Before;
	import org.junit.Ignore;
	import org.junit.Test;


	public class TestRDFXMLSerializer {
	protected static final String TAVERNAWORKBENCH_RDF = "profile/tavernaWorkbench.rdf";
	protected static final String TAVERNASERVER_RDF = "profile/tavernaServer.rdf";
	protected static final String HELLOWORLD_RDF = "workflow/HelloWorld.rdf";
	RDFXMLSerializer serializer = new RDFXMLSerializer();
	ExampleWorkflow exampleWf = new ExampleWorkflow();
	WorkflowBundle workflowBundle;

	Namespace XSI_NS = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
	Namespace RDF_NS = Namespace.getNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
	Namespace RDSF_NS = Namespace.getNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
	Namespace SCUFL2_NS = Namespace.getNamespace("s", "http://ns.taverna.org.uk/2010/scufl2#");
	Namespace BEANSHELL_NS = Namespace.getNamespace("beanshell",
	"http://ns.taverna.org.uk/2010/activity/beanshell#");


	protected void assertXpathEquals(String expected, Element element,
	String xpath) throws JDOMException {
	Object o = xpathSelectElement(element, xpath);
	if (o == null) {
	fail("Can't find " + xpath + " in " + element);
	return;
	}
	String text;
	if (o instanceof Attribute) {
	text = ((Attribute)o).getValue();
	} else {
	text = ((Element)o).getValue();
	}
	assertEquals(expected, text);
	}


	protected void checkProfileDocument(Element root, boolean isWorkbench) throws JDOMException {

	assertEquals("ProfileDocument", root.getAttributeValue("type", XSI_NS));
	assertXpathEquals(isWorkbench ? "tavernaWorkbench/" : "tavernaServer/", root, "./@xml:base");

	Element profile = (Element) root.getChildren().get(0);
	Element activity = (Element) root.getChildren().get(1);
	Element binding = (Element) root.getChildren().get(2);
	Element configuration = (Element) root.getChildren().get(3);


	assertSame(xpathSelectElement(root, "./s:Profile"), profile);
	assertSame(xpathSelectElement(root, "./s:Activity"), activity);
	assertSame(xpathSelectElement(root, "./s:ProcessorBinding"), binding);
	assertSame(xpathSelectElement(root, "./s:Configuration"), configuration);

	assertXpathEquals("", profile, "./@rdf:about");
	assertXpathEquals(isWorkbench ? "tavernaWorkbench" : "tavernaServer", profile, "./s:name");
	assertXpathEquals("processorbinding/Hello/", profile, "./s:processorBinding/@rdf:resource");
	assertXpathEquals("configuration/Hello/", profile, "./s:activateConfiguration/@rdf:resource");

	// activity
	assertXpathEquals("activity/HelloScript/", activity, "./@rdf:about");
	assertXpathEquals("HelloScript", activity, "./s:name");
	assertXpathEquals("http://ns.taverna.org.uk/2010/activity/beanshell",
	activity, "./rdf:type/@rdf:resource");
	// activity input
	assertXpathEquals("activity/HelloScript/in/personName", activity, "./s:inputActivityPort/s:InputActivityPort/@rdf:about");
	assertXpathEquals("personName", activity, "./s:inputActivityPort/s:InputActivityPort/s:name");
	assertXpathEquals("0", activity, "./s:inputActivityPort/s:InputActivityPort/s:portDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:inputActivityPort/s:InputActivityPort/s:portDepth/@rdf:datatype");
	// activity output
	assertXpathEquals("activity/HelloScript/out/hello", activity, "./s:outputActivityPort/s:OutputActivityPort/@rdf:about");
	assertXpathEquals("hello", activity, "./s:outputActivityPort/s:OutputActivityPort/s:name");
	assertXpathEquals("0", activity, "./s:outputActivityPort/s:OutputActivityPort/s:portDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:outputActivityPort/s:OutputActivityPort/s:portDepth/@rdf:datatype");
	assertXpathEquals("0", activity, "./s:outputActivityPort/s:OutputActivityPort/s:granularPortDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", activity, "./s:outputActivityPort/s:OutputActivityPort/s:granularPortDepth/@rdf:datatype");

	// processor binding
	assertXpathEquals("processorbinding/Hello/", binding, "./@rdf:about");
	assertXpathEquals("Hello", binding, "./s:name");
	assertXpathEquals("activity/HelloScript/", binding, "./s:bindActivity/@rdf:resource");
	assertXpathEquals("../../workflow/HelloWorld/processor/Hello/", binding, "./s:bindProcessor/@rdf:resource");
	// input port binding
	assertXpathEquals("processorbinding/Hello/in/name", binding, "./s:inputPortBinding/s:InputPortBinding/@rdf:about");
	assertXpathEquals("activity/HelloScript/in/personName", binding, "./s:inputPortBinding/s:InputPortBinding/s:bindInputActivityPort/@rdf:resource");
	assertXpathEquals("../../workflow/HelloWorld/processor/Hello/in/name", binding, "./s:inputPortBinding/s:InputPortBinding/s:bindInputProcessorPort/@rdf:resource");
	// output port binding
	assertXpathEquals("processorbinding/Hello/out/greeting", binding, "./s:outputPortBinding/s:OutputPortBinding/@rdf:about");
	assertXpathEquals("activity/HelloScript/out/hello", binding, "./s:outputPortBinding/s:OutputPortBinding/s:bindOutputActivityPort/@rdf:resource");
	assertXpathEquals("../../workflow/HelloWorld/processor/Hello/out/greeting", binding, "./s:outputPortBinding/s:OutputPortBinding/s:bindOutputProcessorPort/@rdf:resource");


	assertXpathEquals("configuration/Hello/", configuration, "./@rdf:about");
	assertXpathEquals("configuration/Hello.json", configuration, "./rdfs:seeAlso/@rdf:resource");

	assertXpathEquals(
	"http://ns.taverna.org.uk/2010/activity/beanshell#Config",
	configuration, "./rdf:type/@rdf:resource");
	assertXpathEquals("Hello", configuration, "./s:name");
	assertXpathEquals("activity/HelloScript/", configuration, "./s:configure/@rdf:resource");
	// assertXpathEquals("hello = \"Hello, \" + personName;\n" +
	// (isWorkbench ? "JOptionPane.showMessageDialog(null, hello);" : "System.out.println(\"Server says: \" + hello);"), configuration, "./beanshell:script");

	}

	protected void checkRoot(Element root) {
	assertEquals(RDF_NS, root.getNamespace());
	assertEquals("rdf", root.getNamespacePrefix());
	assertEquals("RDF", root.getName());
	assertEquals(SCUFL2_NS, root.getNamespace(""));
	String schemaLocation = root.getAttributeValue("schemaLocation", XSI_NS);
	schemaLocation = schemaLocation.replaceAll("\\s+", " ");
	String[] schemaLocations = schemaLocation.split(" ");
	String[] expectedSchemaLocations = {
	"http://ns.taverna.org.uk/2010/scufl2#","http://ns.taverna.org.uk/2010/scufl2/scufl2.xsd",
	"http://www.w3.org/1999/02/22-rdf-syntax-ns#","http://ns.taverna.org.uk/2010/scufl2/rdf.xsd"
	};
	assertArrayEquals(expectedSchemaLocations, schemaLocations);
	}


	protected void checkWorkflowBundleDocument(Element root) throws JDOMException {
	assertEquals("WorkflowBundleDocument", root.getAttributeValue("type", XSI_NS));

	assertXpathEquals("./", root, "./@xml:base");

	Element wbundle = root.getChild("WorkflowBundle", SCUFL2_NS);
	assertSame(wbundle, root.getChildren().get(0));



	assertXpathEquals("", wbundle, "./@rdf:about");

	assertXpathEquals("HelloWorld", wbundle, "./s:name");
	assertXpathEquals("http://ns.taverna.org.uk/2010/workflowBundle/28f7c554-4f35-401f-b34b-516e9a0ef731/",
	wbundle, "./s:globalBaseURI/@rdf:resource");

	assertXpathEquals("workflow/HelloWorld/",
	wbundle, "./s:mainWorkflow/@rdf:resource");
	assertXpathEquals("workflow/HelloWorld/",
	wbundle, "./s:workflow/s:Workflow/@rdf:about");
	assertXpathEquals(HELLOWORLD_RDF,
	wbundle, "./s:workflow/s:Workflow/rdfs:seeAlso/@rdf:resource");

	assertXpathEquals("profile/tavernaWorkbench/",
	wbundle, "./s:mainProfile/@rdf:resource");



	assertXpathEquals("profile/tavernaServer/",
	wbundle, "./s:profile[1]/s:Profile/@rdf:about");
	assertXpathEquals("profile/tavernaServer.rdf", wbundle, "./s:profile[1]/s:Profile/rdfs:seeAlso/@rdf:resource");

	assertXpathEquals("profile/tavernaWorkbench/",
	wbundle, "./s:profile[2]/s:Profile/@rdf:about");
	assertXpathEquals(TAVERNAWORKBENCH_RDF,
	wbundle, "./s:profile[2]/s:Profile/rdfs:seeAlso/@rdf:resource");



	}


	protected void checkWorkflowDocument(Element root) throws JDOMException {
	assertEquals("WorkflowDocument", root.getAttributeValue("type", XSI_NS));



	assertXpathEquals("HelloWorld/", root, "./@xml:base");


	Element wf = root.getChild("Workflow", SCUFL2_NS);
	assertSame(wf, root.getChildren().get(0));

	assertXpathEquals("", wf, "./@rdf:about");


	assertXpathEquals("HelloWorld", wf, "./s:name");
	assertXpathEquals("http://ns.taverna.org.uk/2010/workflow/00626652-55ae-4a9e-80d4-c8e9ac84e2ca/",
	wf, "./s:workflowIdentifier/@rdf:resource");

	assertXpathEquals("in/yourName",
	wf, "./s:inputWorkflowPort/s:InputWorkflowPort/@rdf:about");
	assertXpathEquals("yourName",
	wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:name");
	assertXpathEquals("0",
	wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:portDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:inputWorkflowPort/s:InputWorkflowPort/s:portDepth/@rdf:datatype");


	assertXpathEquals("out/results",
	wf, "./s:outputWorkflowPort/s:OutputWorkflowPort/@rdf:about");
	assertXpathEquals("results",
	wf, "./s:outputWorkflowPort/s:OutputWorkflowPort/s:name");


	assertXpathEquals("processor/Hello/",
	wf, "./s:processor[1]/s:Processor/@rdf:about");
	assertXpathEquals("Hello",
	wf, "./s:processor[1]/s:Processor/s:name");

	assertXpathEquals("processor/Hello/in/name",
	wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/@rdf:about");
	assertXpathEquals("name",
	wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:name");
	assertXpathEquals("0",
	wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:portDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:processor[1]/s:Processor/s:inputProcessorPort/s:InputProcessorPort/s:portDepth/@rdf:datatype");



	assertXpathEquals("processor/Hello/out/greeting",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/@rdf:about");

	assertXpathEquals("greeting",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:name");
	assertXpathEquals("0",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:portDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:portDepth/@rdf:datatype");
	assertXpathEquals("0",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:granularPortDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:processor[1]/s:Processor/s:outputProcessorPort/s:OutputProcessorPort/s:granularPortDepth/@rdf:datatype");

	assertXpathEquals("processor/Hello/iterationstrategy/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/@rdf:about");
	assertXpathEquals("Collection", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/@rdf:parseType");
	assertXpathEquals("processor/Hello/iterationstrategy/0/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/@rdf:about");
	assertXpathEquals("Collection", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/@rdf:parseType");
	assertXpathEquals("processor/Hello/iterationstrategy/0/0/", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/@rdf:about");
	assertXpathEquals("processor/Hello/in/name", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:iterateOverInputPort/@rdf:resource");
	assertXpathEquals("0", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:desiredDepth");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer", wf, "./s:processor[1]/s:Processor/s:iterationStrategyStack/s:IterationStrategyStack/s:iterationStrategies/s:CrossProduct/s:productOf/s:PortNode/s:desiredDepth/@rdf:datatype");


	assertXpathEquals("processor/wait4me/",
	wf, "./s:processor[2]/s:Processor/@rdf:about");
	assertXpathEquals("wait4me",
	wf, "./s:processor[2]/s:Processor/s:name");


	assertXpathEquals("datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0",
	wf, "./s:datalink[1]/s:DataLink/@rdf:about");

	assertXpathEquals("datalink?from=in/yourName&to=processor/Hello/in/name",
	wf, "./s:datalink[2]/s:DataLink/@rdf:about");

	assertXpathEquals("datalink?from=in/yourName&to=out/results&mergePosition=1",
	wf, "./s:datalink[3]/s:DataLink/@rdf:about");
	assertXpathEquals("in/yourName",
	wf, "./s:datalink[3]/s:DataLink/s:receiveFrom/@rdf:resource");
	assertXpathEquals("out/results",
	wf, "./s:datalink[3]/s:DataLink/s:sendTo/@rdf:resource");
	assertXpathEquals("1",
	wf, "./s:datalink[3]/s:DataLink/s:mergePosition");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:datalink[3]/s:DataLink/s:mergePosition/@rdf:datatype");

	assertXpathEquals("control?block=processor/Hello/&untilFinished=processor/wait4me/",
	wf, "./s:control/s:Blocking/@rdf:about");


	assertXpathEquals("processor/Hello/",
	wf, "./s:control/s:Blocking/s:block/@rdf:resource");
	assertXpathEquals("processor/wait4me/",
	wf, "./s:control/s:Blocking/s:untilFinished/@rdf:resource");

	assertXpathEquals("datalink?from=processor/Hello/out/greeting&to=out/results&mergePosition=0",
	wf, "./s:datalink[1]/s:DataLink/@rdf:about");
	assertXpathEquals("processor/Hello/out/greeting",
	wf, "./s:datalink[1]/s:DataLink/s:receiveFrom/@rdf:resource");
	assertXpathEquals("out/results",
	wf, "./s:datalink[1]/s:DataLink/s:sendTo/@rdf:resource");
	assertXpathEquals("0",
	wf, "./s:datalink[1]/s:DataLink/s:mergePosition");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:datalink[1]/s:DataLink/s:mergePosition/@rdf:datatype");



	assertXpathEquals("datalink?from=in/yourName&to=processor/Hello/in/name",
	wf, "./s:datalink[2]/s:DataLink/@rdf:about");
	assertXpathEquals("in/yourName",
	wf, "./s:datalink[2]/s:DataLink/s:receiveFrom/@rdf:resource");
	assertXpathEquals("processor/Hello/in/name",
	wf, "./s:datalink[2]/s:DataLink/s:sendTo/@rdf:resource");
	assertNull(xpathSelectElement(wf, "./s:datalink[2]/s:DataLink/s:mergePosition"));



	assertXpathEquals("datalink?from=in/yourName&to=out/results&mergePosition=1",
	wf, "./s:datalink[3]/s:DataLink/@rdf:about");
	assertXpathEquals("in/yourName",
	wf, "./s:datalink[3]/s:DataLink/s:receiveFrom/@rdf:resource");
	assertXpathEquals("out/results",
	wf, "./s:datalink[3]/s:DataLink/s:sendTo/@rdf:resource");
	assertXpathEquals("1",
	wf, "./s:datalink[3]/s:DataLink/s:mergePosition");
	assertXpathEquals("http://www.w3.org/2001/XMLSchema#integer",
	wf, "./s:datalink[3]/s:DataLink/s:mergePosition/@rdf:datatype");

	assertXpathEquals("control?block=processor/Hello/&untilFinished=processor/wait4me/",
	wf, "./s:control/s:Blocking/@rdf:about");


	assertXpathEquals("processor/Hello/",
	wf, "./s:control/s:Blocking/s:block/@rdf:resource");
	assertXpathEquals("processor/wait4me/",
	wf, "./s:control/s:Blocking/s:untilFinished/@rdf:resource");

	}

	// TODO: Update tests
	@Ignore
	@Test
	public void exampleProfileTavernaServer() throws Exception {
	URL tavernaWorkbenc = getClass().getResource("example/profile/tavernaServer.rdf");
	SAXBuilder saxBuilder = new SAXBuilder();
	Document doc = saxBuilder.build(tavernaWorkbenc);
	Element root = doc.getRootElement();

	checkRoot(root);
	checkProfileDocument(root, false);

	}


	// TODO: Update tests
	@Ignore
	@Test
	public void exampleProfileTavernaWorkbench() throws Exception {
	URL tavernaWorkbenc = getClass().getResource("example/profile/tavernaWorkbench.rdf");
	SAXBuilder saxBuilder = new SAXBuilder();
	Document doc = saxBuilder.build(tavernaWorkbenc);
	Element root = doc.getRootElement();

	checkRoot(root);
	checkProfileDocument(root, true);

	}

	@Test
	public void exampleWorkflow() throws Exception {
	URL workflowURL = getClass().getResource("example/workflow/HelloWorld.rdf");
	SAXBuilder saxBuilder = new SAXBuilder();
	Document doc = saxBuilder.build(workflowURL);

	Element root = doc.getRootElement();

	checkRoot(root);
	checkWorkflowDocument(root);

	}


	@Test
	public void exampleWorkflowBundle() throws Exception {
	URL workflowBundleURL = getClass().getResource("example/workflowBundle.rdf");


	SAXBuilder saxBuilder = new SAXBuilder();
	Document doc = saxBuilder.build(workflowBundleURL);

	Element root = doc.getRootElement();

	checkRoot(root);
	checkWorkflowBundleDocument(root);

	}


	@Before
	public void makeExampleWorkflow() {
	workflowBundle = new ExampleWorkflow().makeWorkflowBundle();
	serializer.setWfBundle(workflowBundle);
	}


	protected Document parseXml(ByteArrayOutputStream outStream)
	throws JDOMException, IOException {
	SAXBuilder saxBuilder = new SAXBuilder();
	return saxBuilder.build(new ByteArrayInputStream(outStream.toByteArray()));
	}


	@Test
	public void profile() throws Exception {
	ByteArrayOutputStream outStream = new ByteArrayOutputStream();
	// To test that seeAlso URIs are stored
	serializer.profileDoc(outStream, workflowBundle.getMainProfile(), URI.create(TAVERNAWORKBENCH_RDF));
	//System.out.write(outStream.toByteArray());
	Document doc = parseXml(outStream);
	Element root = doc.getRootElement();

	checkRoot(root);
	checkProfileDocument(root, true);
	}


	@Test
	public void workflow() throws Exception {
	ByteArrayOutputStream outStream = new ByteArrayOutputStream();
	// To test that seeAlso URIs are stored
	serializer.workflowDoc(outStream, workflowBundle.getMainWorkflow(), URI.create(HELLOWORLD_RDF));
	// System.out.write(outStream.toByteArray());
	Document doc = parseXml(outStream);
	Element root = doc.getRootElement();

	checkRoot(root);
	checkWorkflowDocument(root);
	}

	@Test
	public void workflowBundle() throws Exception {
	ByteArrayOutputStream outStream = new ByteArrayOutputStream();
	// To test that seeAlso URIs are stored
	serializer.workflowDoc(new NullOutputStream(), workflowBundle.getMainWorkflow(), URI.create(HELLOWORLD_RDF));
	serializer.profileDoc(new NullOutputStream(), workflowBundle.getProfiles().getByName("tavernaWorkbench"), URI.create(TAVERNAWORKBENCH_RDF));
	serializer.profileDoc(new NullOutputStream(), workflowBundle.getProfiles().getByName("tavernaServer"), URI.create(TAVERNASERVER_RDF));

	serializer.workflowBundleDoc(outStream, URI.create("workflowBundle.rdf"));
	//System.out.write(outStream.toByteArray());
	Document doc = parseXml(outStream);
	Element root = doc.getRootElement();

	checkRoot(root);
	checkWorkflowBundleDocument(root);

	}


	protected Object xpathSelectElement(Element element, String xpath) throws JDOMException {
	XPath x = XPath.newInstance(xpath);
	x.addNamespace(SCUFL2_NS);
	x.addNamespace(RDF_NS);
	x.addNamespace(RDSF_NS);
	x.addNamespace(BEANSHELL_NS);
	//x.addNamespace(XML_NS);

	return x.selectSingleNode(element);
	}
	}