import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public String open(Path runFile) throws IOException {
	try {
		String runID = runFile.getFileName().toString();
		int dot = runID.indexOf('.');
		if (dot > 0)
			runID = runID.substring(0, dot);
		if (!runMap.containsKey(runID)) {
			Bundle bundle = DataBundles.openBundle(runFile);
			Run run = new Run(runID, bundle);
			runMap.put(run.getID(), run);
		}
		postEvent(RUN_OPENED, runID);
		return runID;
	} catch (ReaderException | ParseException e) {
		throw new IOException("Error opening file " + runFile, e);
	}
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public Configuration parseConfiguration(T2FlowParser t2FlowParser,
		ConfigBean configBean, ParserState parserState)
		throws ReaderException {
	ParallelizeConfig parallelConfig = unmarshallConfig(t2FlowParser,
			configBean, "xstream", ParallelizeConfig.class);
	Configuration c = new Configuration();
	c.setType(scufl2Uri.resolve("#Config"));

	BigInteger maxJobs = parallelConfig.getMaxJobs();
	if (maxJobs != null && maxJobs.intValue() > 0
			&& maxJobs.intValue() != Defaults.maxJobs) {
		ObjectNode json = (ObjectNode) c.getJson();
		json.put("maxJobs", maxJobs.intValue());
	}
	return c;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public WorkflowBundle readBundle(File bundleFile, String mediaType)
		throws ReaderException, IOException {
	try {
		WorkflowBundle bundle = getParser().parseT2Flow(bundleFile);
		scufl2Tools.setParents(bundle);
		preserveOriginal(bundle, new FileInputStream(bundleFile));
		return bundle;
	} catch (JAXBException e) {
		if (e.getCause() instanceof IOException) {
			IOException ioException = (IOException) e.getCause();
			throw ioException;
		}
		throw new ReaderException("Can't parse t2flow " + bundleFile, e);
	}
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public Configuration parseConfiguration(T2FlowParser t2FlowParser,
		ConfigBean configBean, ParserState parserState) throws ReaderException {
	StringConstantConfig strConfig = unmarshallConfig(t2FlowParser,
			configBean, "xstream", StringConstantConfig.class);
	String value = strConfig.getValue();
	if (value == null)
		throw new ReaderException("String constant configuration has no value set");
	Configuration configuration = new Configuration();
	ObjectNode json = (ObjectNode) configuration.getJson();
	configuration.setType(CONSTANT.resolve("#Config"));
	json.put("string", value);
	
	Activity activity = parserState.getCurrentActivity();
	OutputActivityPort valuePort = new OutputActivityPort(activity, VALUE);
	valuePort.setDepth(0);
	valuePort.setGranularDepth(0);
	return configuration;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
public <ConfigType> ConfigType unmarshallConfig(T2FlowParser t2FlowParser,
		ConfigBean configBean, String encoding, Class<ConfigType> configType)
		throws ReaderException {
	Object config = configBean.getAny();
	if (config instanceof JAXBElement) {
		JAXBElement<?> jaxbElement = (JAXBElement<?>) config;
		if (!configType.isInstance((jaxbElement.getValue())))
			throw new ReaderException("Unexpected config type: "
					+ jaxbElement.getValue().getClass() + ", expected "
					+ configType);
		return configType.cast(jaxbElement.getValue());
	}
	if (!(config instanceof Element)
			|| !configBean.getEncoding().equals(encoding))
		throw new ReaderException("Unsupported config bean " + configBean);
	return unmarshallElement(t2FlowParser, (Element) config, configType);
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public Configuration parseConfiguration(T2FlowParser t2FlowParser,
		ConfigBean configBean, ParserState parserState) throws ReaderException {
	DataflowConfig dataflowConfig = unmarshallConfig(t2FlowParser,
			configBean, "dataflow", DataflowConfig.class);
	Configuration configuration = new Configuration();
	configuration.setType(nestedUri.resolve("#Config"));		

	String wfId = dataflowConfig.getRef();
	URI wfUri = WORKFLOW_ROOT.resolve(wfId + "/");
	Workflow wf = (Workflow) getUriTools().resolveUri(wfUri, parserState.getCurrentWorkflowBundle());		
	if (wf == null)
        throw new ReaderException("Can't find nested workflow with id " + wfId);
	ObjectNode json = configuration.getJsonAsObjectNode();
	json.put("nestedWorkflow", wf.getName());
	return configuration;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public Configuration parseConfiguration(T2FlowParser t2FlowParser,
		ConfigBean configBean, ParserState parserState)
		throws ReaderException {
	ComponentConfig config = unmarshallConfig(t2FlowParser, configBean,
			"xstream", ComponentConfig.class);

	Configuration configuration = new Configuration();
	configuration.setParent(parserState.getCurrentProfile());

	ObjectNode json = (ObjectNode) configuration.getJson();
	configuration.setType(ACTIVITY_URI.resolve("#Config"));

	json.put("registryBase", config.getRegistryBase());
	json.put("familyName", config.getFamilyName());
	json.put("componentName", config.getComponentName());
	if (config.getComponentVersion() != null)
		json.put("componentVersion", (int) config.getComponentVersion());

	return configuration;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
private URI mapTypeFromRaven(Raven raven, String activityClass)
		throws ReaderException {
	URI classURI = makeRavenURI(raven, activityClass);
	parserState.get().setCurrentT2Parser(null);
	T2Parser t2Parser = getT2Parser(classURI);
	if (t2Parser == null) {
		String message = "Unknown T2 activity or dispatch layer "
				+ classURI + ", install supporting T2Parser";
		if (isStrict())
			throw new ReaderException(message);
		logger.warning(message);
		return classURI;
	}
	parserState.get().setCurrentT2Parser(t2Parser);
	return t2Parser.mapT2flowRavenIdToScufl2URI(classURI);
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected Workflow parseDataflow(Dataflow df, Workflow wf)
		throws ReaderException, JAXBException {
	parserState.get().setCurrentWorkflow(wf);
	wf.setInputPorts(parseInputPorts(df.getInputPorts()));
	wf.setOutputPorts(parseOutputPorts(df.getOutputPorts()));
	wf.setProcessors(parseProcessors(df.getProcessors()));
	wf.setDataLinks(parseDatalinks(df.getDatalinks()));
	wf.setControlLinks(parseControlLinks(df.getConditions()));		
	Revision revision = parseIdentificationAnnotations(df.getAnnotations());
	if (revision != null)
		wf.setCurrentRevision(revision);
	parseAnnotations(wf, df.getAnnotations());

	parserState.get().setCurrentWorkflow(null);
	return wf;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected void parseDispatchStack(DispatchStack dispatchStack)
		throws ReaderException {
	Processor processor = parserState.get().getCurrentProcessor();
	Configuration procConfig = scufl2Tools.createConfigurationFor(
			processor, parserState.get().getCurrentProfile());
	parserState.get().setCurrentConfigurable(processor);
	parserState.get().setCurrentConfiguration(procConfig);
	parserState.get().setPreviousDispatchLayerName(null);
	try {
		for (DispatchLayer dispatchLayer : dispatchStack.getDispatchLayer())
			parseDispatchStack(dispatchLayer);
	} finally {
		parserState.get().setCurrentConfigurable(null);
		parserState.get().setCurrentConfiguration(null);
		parserState.get().setPreviousDispatchLayerName(null);
	}
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected Set<InputWorkflowPort> parseInputPorts(
		AnnotatedGranularDepthPorts originalPorts) throws ReaderException {
	Set<InputWorkflowPort> createdPorts = new HashSet<>();
	for (AnnotatedGranularDepthPort originalPort : originalPorts.getPort()) {
		InputWorkflowPort newPort = new InputWorkflowPort(parserState.get()
				.getCurrentWorkflow(), originalPort.getName());
		newPort.setDepth(originalPort.getDepth().intValue());
		if (!originalPort.getGranularDepth()
				.equals(originalPort.getDepth())) {
			String message = "Specific input port granular depth not "
					+ "supported in scufl2, port " + originalPort.getName()
					+ " has depth " + originalPort.getDepth()
					+ " and granular depth "
					+ originalPort.getGranularDepth();
			if (isStrict())
				throw new ReaderException(message);
			logger.warning(message);
		}
		parseAnnotations(newPort, originalPort.getAnnotations());

		createdPorts.add(newPort);
	}
	return createdPorts;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected IterationStrategyStack parseIterationStrategyStack(
		org.apache.taverna.scufl2.xml.t2flow.jaxb.IterationStrategyStack originalStack)
		throws ReaderException {
	IterationStrategyStack newStack = new IterationStrategyStack();

	for (TopIterationNode strategy : originalStack.getIteration()
			.getStrategy()) {
		IterationNode topNode = strategy.getCross();
		if (topNode == null)
			topNode = strategy.getDot();
		if (topNode == null)
			continue;
		IterationNodeParent parent = (IterationNodeParent) topNode;
		if (parent.getCrossOrDotOrPort().isEmpty())
			continue;
		try {
			newStack.add((IterationStrategyTopNode) parseIterationStrategyNode(topNode));
		} catch (ReaderException e) {
			if (isStrict())
				throw e;
			logger.warning(e.getMessage());
		}
	}

	return newStack;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected Set<Processor> parseProcessors(Processors originalProcessors)
		throws ReaderException, JAXBException {
	HashSet<Processor> newProcessors = new HashSet<>();
	for (org.apache.taverna.scufl2.xml.t2flow.jaxb.Processor origProc : originalProcessors
			.getProcessor()) {
		Processor newProc = new Processor(parserState.get()
				.getCurrentWorkflow(), origProc.getName());
		parserState.get().setCurrentProcessor(newProc);
		newProc.setInputPorts(parseProcessorInputPorts(newProc,
				origProc.getInputPorts()));
		newProc.setOutputPorts(parseProcessorOutputPorts(newProc,
				origProc.getOutputPorts()));
		parseDispatchStack(origProc
				.getDispatchStack());
		newProc.setIterationStrategyStack(parseIterationStrategyStack(origProc
				.getIterationStrategyStack()));
		parseAnnotations(newProc, origProc.getAnnotations());

		newProcessors.add(newProc);
		int i = 0;
		for (Activity origActivity : origProc.getActivities().getActivity())
			parseActivityBinding(origActivity, i++);
	}
	parserState.get().setCurrentProcessor(null);
	return newProcessors;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@Override
public OutputStream getOutputStream() throws IOException {
	final PipedInputStream is = new PipedInputStream();
	OutputStream os = new PipedOutputStream(is);
	new Worker() {
		@Override
		public void doWork() throws IOException, ReaderException {
			wf = new Workflow(io.readBundle(is, null));
		}

		@Override
		public void doneWork() {
			closeQuietly(is);
		}
	};
	return os;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
public WorkflowBundle parseScufl(ScuflType wf) throws ReaderException,
		JAXBException {
	try {
		parserState.get().setCurrentParser(this);
		WorkflowBundle wfBundle = new WorkflowBundle();
		parserState.get().setCurrentWorkflowBundle(wfBundle);
		makeProfile(wf);
		Workflow w = parseWorkflow(wf);
		wfBundle.setMainWorkflow(w);

		scufl2Tools.setParents(wfBundle);

		return wfBundle;
	} finally {
		parserState.remove();
	}
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
@SuppressWarnings({ "unchecked" })
public Map<URI, Revision> readRevisionChain(
		InputStream revisionDocumentStream, URI base)
		throws ReaderException {
	JAXBElement<RoEvoDocument> roEvoDoc;
	try {
		Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
		roEvoDoc = (JAXBElement<RoEvoDocument>) unmarshaller
				.unmarshal(revisionDocumentStream);
	} catch (JAXBException e) {
		throw new ReaderException(e);
	}

	RoEvoDocument document = roEvoDoc.getValue();
	if (document.getBase() != null)
		base = base.resolve(document.getBase());
	Map<URI, Revision> revisions = new LinkedHashMap<>();
	// NOTE: Silly hack to iterate/cast in one go.. will it work?
	for (VersionableResource verResource : document.getAny().toArray(
			new VersionableResource[0]))
		parse(base, verResource, revisions);
	return revisions;
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
protected void parseIterationStrategyStack(IterationStrategyStack original)
		throws ReaderException {
	org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack iterationStrategyStack = new org.apache.taverna.scufl2.api.iterationstrategy.IterationStrategyStack();
	iterationStrategyStack.setParent(getParserState().getCurrent(
			Processor.class));

	mapBean(getParserState().getCurrentBase().resolve(original.getAbout()),
			iterationStrategyStack);
	if (original.getIterationStrategies() != null) {
		getParserState().push(iterationStrategyStack);
		try {
			parseCrossDotOrPortNodeList(original.getIterationStrategies()
					.getDotProductOrCrossProduct());
		} finally {
			getParserState().pop();
		}
	}
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
public void makeWorkflowBundle() throws IOException, WriterException,
		ReaderException {

	/** Top-level object is a Workflow Bundle */
	bundle = new WorkflowBundle();

	/** Generate the workflow structure **/
	makeWorkflow();
	
	/** Specify the implementations **/
	makeProfile();

	/**
	 * Before storing the workflow bundle, we'll make sure that everything
	 * we made has a parent included (so that for instance a configuration
	 * is stored together with its parent profile). The
	 * scufl2Tools.setParents method will traverse the WorkflowBundle from
	 * the top and fill in any blank parents.
	 */
	scufl2Tools.setParents(bundle);

	/** Write bundle to StdOut and a new file */
	writeBundleToFile();

}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
private void writeBundleToFile() throws IOException, WriterException,
		ReaderException {
	file = File.createTempFile("test", ".wfbundle");

	/**
	 * Bundle IO 
	 */
	bundleIO.writeBundle(bundle, file,
			"application/vnd.taverna.scufl2.workflow-bundle");
	System.out.println("Written to " + file + "\n");

	// Read it back in
	WorkflowBundle secondBundle = bundleIO.readBundle(file,
			"application/vnd.taverna.scufl2.workflow-bundle");

	// Write in a debug text format
	bundleIO.writeBundle(secondBundle, System.out,
			"text/vnd.taverna.scufl2.structure");
}
 

import org.apache.taverna.scufl2.api.io.ReaderException; //导入依赖的package包/类
public void convert(String[] filepaths) throws ReaderException, IOException, WriterException {

		WorkflowBundleIO io = new WorkflowBundleIO();
		for (String filepath : filepaths) {
			File t2File = new File(filepath);
			
			String filename = t2File.getName();			
			filename = filename.replaceFirst("\\..*", ".wfbundle");			
			File scufl2File = new File(t2File.getParentFile(), filename);
			
			WorkflowBundle wfBundle = io.readBundle(t2File,
					"application/vnd.taverna.t2flow+xml");
			io.writeBundle(wfBundle, scufl2File,
					"application/vnd.taverna.scufl2.workflow-bundle");
		}

	}