results/src/main/java/net/sf/taverna/t2/lang/baclava/BaclavaDocumentHandler.java

package net.sf.taverna.t2.lang.baclava;

import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Map;

import net.sf.taverna.t2.invocation.InvocationContext;
import net.sf.taverna.t2.lang.results.ResultsUtils;
import net.sf.taverna.t2.reference.ReferenceService;
import net.sf.taverna.t2.reference.T2Reference;

import org.embl.ebi.escience.baclava.DataThing;
import org.embl.ebi.escience.baclava.factory.DataThingFactory;
import org.embl.ebi.escience.baclava.factory.DataThingXMLFactory;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.Namespace;
import org.jdom.input.SAXBuilder;
import org.jdom.output.Format;
import org.jdom.output.XMLOutputter;

/**
 * Handles the loading and saving of T2Reference data as Baclava documents
 * 
 * @author Stuart Owen
 * 
 */

public class BaclavaDocumentHandler {

	private Map<String, T2Reference> chosenReferences;

	private static Namespace namespace = Namespace.getNamespace("b",
			"http://org.embl.ebi.escience/baclava/0.1alpha");

	protected ReferenceService referenceService;

	protected InvocationContext context;

	// private static Logger logger =
	// Logger.getLogger(BaclavaDocumentHandler.class);
	
	
	/**
	 * Reads a baclava document from an InputStream and returns a map of DataThings mapped to the portName
	 * 
	 * @throws IOException, JDOMException
	 */
	public Map<String, DataThing> readData(InputStream inputStream)
			throws IOException, JDOMException {

		SAXBuilder builder = new SAXBuilder();
		Document inputDoc;
		inputDoc = builder.build(inputStream);
		
		return DataThingXMLFactory.parseDataDocument(inputDoc);
	}

	/**
	 * Saves the result data to an XML Baclava file.
	 * 
	 * @throws IOException
	 */
	public void saveData(File file) throws IOException {
		// Build the string containing the XML document from the result map
		Document doc = getDataDocument();
		XMLOutputter xo = new XMLOutputter(Format.getPrettyFormat());		
		PrintWriter out = new PrintWriter(new FileWriter(file));
		xo.output(doc, out);		
	}

	/**
	 * Returns a org.jdom.Document from a map of port named to DataThingS
	 * containing the port's results.
	 */
	public Document getDataDocument() {
		Element rootElement = new Element("dataThingMap", namespace);
		Document theDocument = new Document(rootElement);
		// Build the DataThing map from the chosenReferences
		// First convert map of references to objects into a map of real result
		// objects
		for (String portName : getChosenReferences().keySet()) {
			DataThing thing = DataThingFactory.bake(getObjectForName(portName));
			Element dataThingElement = new Element("dataThing", namespace);
			dataThingElement.setAttribute("key", portName);
			dataThingElement.addContent(thing.getElement());
			rootElement.addContent(dataThingElement);
		}
		return theDocument;
	}

	/**
	 * @param referenceService
	 *            the referenceService to set
	 */
	public void setReferenceService(ReferenceService referenceService) {
		this.referenceService = referenceService;
	}

	/**
	 * Sets the InvocationContext to be used to get the Reference Service to be
	 * used dereference the reference.
	 */
	public void setInvocationContext(InvocationContext context) {
		this.context = context;
	}

	protected Object getObjectForName(String name) {
		Object result = null;
		if (getChosenReferences().containsKey(name)) {
			result = ResultsUtils.convertReferenceToObject(
					getChosenReferences().get(name), referenceService, context);
		}
		if (result == null) {
			result = "null";
		}
		return result;
	}

	private Map<String, T2Reference> getChosenReferences() {
		return chosenReferences;
	}

	public void setChosenReferences(Map<String, T2Reference> chosenReferences) {
		this.chosenReferences = chosenReferences;
	}
}