plugins/org.eclipse.epsilon.flexmi/src/org/eclipse/epsilon/flexmi/FlexmiResource.java - epsilon/org.eclipse.epsilon - Git at Google

 package org.eclipse.epsilon.flexmi;

 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.Stack;

 import org.eclipse.emf.common.util.URI;
 import org.eclipse.emf.ecore.EAttribute;
 import org.eclipse.emf.ecore.EClass;
 import org.eclipse.emf.ecore.EClassifier;
 import org.eclipse.emf.ecore.ENamedElement;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.EPackage;
 import org.eclipse.emf.ecore.EReference;
 import org.eclipse.emf.ecore.EStructuralFeature;
 import org.eclipse.emf.ecore.EcorePackage;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.eclipse.emf.ecore.resource.ResourceSet;
 import org.eclipse.emf.ecore.resource.impl.ResourceImpl;
 import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
 import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.emf.ecore.xmi.impl.XMIResourceFactoryImpl;
 import org.eclipse.epsilon.flexmi.xml.Location;
 import org.eclipse.epsilon.flexmi.xml.PseudoSAXParser;
 import org.eclipse.epsilon.flexmi.xml.PseudoSAXParser.Handler;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
 import org.w3c.dom.ProcessingInstruction;
 import org.w3c.dom.Text;

 public class FlexmiResource extends ResourceImpl implements Handler {

 	public static final String OPTION_FUZZY_CONTAINMENT_MATCHING = "fuzzyContainmentMatching";
 	public static final String OPTION_ORPHANS_AS_TOP_LEVEL = "orphansAsTopLevel";
 	public static final String OPTION_FUZZY_MATCHING_THRESHOLD = "fuzzyMatchingThreshold";

 	protected EObjectTraceManager eObjectTraceManager = new EObjectTraceManager();
 	protected List<UnresolvedReference> unresolvedReferences = new ArrayList<UnresolvedReference>();
 	protected Stack<Object> stack = new Stack<Object>();
 	protected Node currentNode = null;
 	protected List<String> scripts = new ArrayList<String>();
 	protected HashMap<String, EClass> eClassCache = new HashMap<String, EClass>();
 	protected HashMap<EClass, List<EClass>> allSubtypesCache = new HashMap<EClass, List<EClass>>();
 	protected StringSimilarityProvider stringSimilarityProvider = new CachedStringSimilarityProvider(new DefaultStringSimilarityProvider());
 	protected Stack<URI> parsedFragmentURIStack = new Stack<URI>();
 	protected Set<URI> parsedFragmentURIs = new HashSet<URI>();

 	protected boolean fuzzyContainmentSlotMatching = true;
 	protected boolean orphansAsTopLevel = true;
 	protected int fuzzyMatchingThreshold = 0;

 	public void startProcessingFragment(URI uri) {
 		parsedFragmentURIStack.push(uri);
 		parsedFragmentURIs.add(uri);
 	}

 	public void endProcessingFragment() {
 		parsedFragmentURIStack.pop();
 	}

 	public Set<URI> getParsedFragmentURIs() {
 		return parsedFragmentURIs;
 	}

 	public static void main(String[] args) throws Exception {

 		// Load the metamodel
 		ResourceSet metamodelResourceSet = new ResourceSetImpl();
 		metamodelResourceSet.getPackageRegistry().put(EcorePackage.eINSTANCE.getNsURI(), EcorePackage.eINSTANCE);
 		metamodelResourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("*", new XMIResourceFactoryImpl());
 		Resource metamodelResource = metamodelResourceSet.createResource(URI.createFileURI(new File("models/messaging.ecore").getAbsolutePath()));
 		metamodelResource.load(null);

 		EPackage metamodel = (EPackage) metamodelResource.getContents().get(0);

 		// Load the model
 		ResourceSet modelResourceSet = new ResourceSetImpl();
 		modelResourceSet.getPackageRegistry().put(metamodel.getNsURI(), metamodel);
 		modelResourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("*", new FlexmiResourceFactory());
 		Resource modelResource = modelResourceSet.createResource(URI.createFileURI(new File("models/messaging.flexmi").getAbsolutePath()));
 		modelResource.load(null);

 		System.out.println(modelResource.getEObject("tom"));

 	}

 	public FlexmiResource(URI uri) {
 		super(uri);
 	}

 	@Override
 	protected void doLoad(InputStream inputStream, Map<?, ?> options)
 			throws IOException {
 		try {
 			doLoadImpl(inputStream, options);
 		}
 		catch (IOException ioException) {
 			ioException.printStackTrace();
 			throw ioException;
 		}
 		catch (Exception ex) {
 			ex.printStackTrace();
 			throw new RuntimeException(ex);
 		}
 	}

 	protected void processOption(String key, String value) {
 		try {
 			if (OPTION_FUZZY_CONTAINMENT_MATCHING.equalsIgnoreCase(key)) {
 				fuzzyContainmentSlotMatching = Boolean.parseBoolean(value);
 			}
 			else if (OPTION_ORPHANS_AS_TOP_LEVEL.equalsIgnoreCase(key)) {
 				orphansAsTopLevel = Boolean.parseBoolean(value);
 			}
 			else if (OPTION_FUZZY_MATCHING_THRESHOLD.equalsIgnoreCase(key)) {
 				fuzzyMatchingThreshold = Integer.parseInt(value);
 			}
 			else throw new Exception("Unknown option");
 		}
 		catch (Exception ex) {
 			addParseWarning("Could not process option " + key + ": " + ex.getMessage());
 		}
 	}

 	public void doLoadImpl(InputStream inputStream, Map<?, ?> options) throws Exception {
 		getContents().clear();
 		unresolvedReferences.clear();
 		stack.clear();
 		scripts.clear();
 		eClassCache.clear();
 		allSubtypesCache.clear();
 		setIntrinsicIDToEObjectMap(new HashMap<String, EObject>());

 		if (options != null) {
 			for (Object key : options.keySet()) {
 				processOption(key + "", options.get(key) + "");
 			}
 		}

 		new PseudoSAXParser().parse(this, inputStream, this);
 	}

 	@Override
 	public void startDocument(Document document) {}

 	@Override
 	public void startElement(Element element) {
 		currentNode = element;
 		String name = element.getNodeName();

 		//Remove prefixes
 		//TODO: Add option to disable this
 		if (name.indexOf(":") > -1) {
 			name = name.substring(name.indexOf(":")+1);
 		}

 		EObject eObject = null;
 		EClass eClass = null;

 		// We're at the root or we treat orphan elements as top-level
 		if (stack.isEmpty() || (stack.peek() == null && orphansAsTopLevel)) {
 			eClass = eClassForName(name);
 			if (eClass != null) {
 				eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
 				getContents().add(eObject);
 				setAttributes(eObject, element);
 			}
 			else {
 				addParseWarning("Could not map element " + name + " to an EObject");
 			}
 			stack.push(eObject);
 		}
 		else {
 			Object peek = stack.peek();

 			// We find an orphan element but don't treat it as top-level
 			if (peek == null) {
 				stack.push(null);
 				addParseWarning("Could not map element " + name + " to an EObject");
 				return;
 			}
 			// The parent is an already-established containment slot
 			else if (peek instanceof EReferenceSlot) {
 				EReferenceSlot containmentSlot = (EReferenceSlot) peek;
 				eClass = (EClass) eNamedElementForName(name, getAllSubtypes(containmentSlot.getEReference().getEReferenceType()));

 				if (eClass != null) {
 					eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
 					containmentSlot.newValue(eObject);
 					stack.push(eObject);
 					setAttributes(eObject, element);
 				}
 				else {
 					stack.push(null);
 					addParseWarning("Could not map element " + name + " to an EObject");
 				}
 			}
 			// The parent is an EObject
 			else if (peek instanceof EObject) {
 				EObject parent = (EObject) peek;

 				if (element.getAttributes().getLength() == 0 && element.getChildNodes().getLength() == 1 && element.getFirstChild() instanceof Text) {
 					EAttribute eAttribute = (EAttribute) eNamedElementForName(name, parent.eClass().getEAllAttributes());

 					if (eAttribute != null) {
 						setEAttributeValue(parent, eAttribute, name, element.getTextContent().trim());
 						eObjectTraceManager.trace(parent, getCurrentURI(), getLineNumber(element));
 						stack.push(null);
 						return;
 					}
 				}

 				EReference containment = null;

 				// No attributes -> Check whether there is a containment reference with that name
 				if (element.getAttributes().getLength() == 0) {
 					if (fuzzyContainmentSlotMatching) {
 						containment = (EReference) eNamedElementForName(name, parent.eClass().getEAllContainments());
 					}
 					else {
 						containment = (EReference) eNamedElementForName(name, parent.eClass().getEAllContainments(), false);
 					}
 					if (containment != null) {
 						EReferenceSlot containmentSlot = new EReferenceSlot(containment, parent);
 						eObjectTraceManager.trace(parent, getCurrentURI(), getLineNumber(element));
 						stack.push(containmentSlot);
 						return;
 					}
 				}

 				// No containment references found
 				// Find potential types for the element
 				Set<EClass> candidates = new HashSet<EClass>();
 				for (EReference eReference : parent.eClass().getEAllContainments()) {
 					candidates.addAll(getAllSubtypes(eReference.getEReferenceType()));
 				}

 				// Get the best match and an appropriate containment reference
 				eClass = (EClass) eNamedElementForName(name, candidates);
 				if (eClass != null) {
 					for (EReference eReference : parent.eClass().getEAllContainments()) {
 						if (getAllSubtypes(eReference.getEReferenceType()).contains(eClass)) {
 							containment = eReference;
 							break;
 						}
 					}
 				}

 				// Found an appropriate containment reference
 				if (containment != null) {
 					eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
 					if (containment.isMany()) {
 						((List<EObject>) parent.eGet(containment)).add(eObject);
 					}
 					else {
 						parent.eSet(containment, eObject);
 					}
 					setAttributes(eObject, element);
 					stack.push(eObject);
 				}
 				// No luck - add warning
 				else {
 					stack.push(null);
 					addParseWarning("Could not map element " + name + " to an EObject");
 				}
 			}
 		}
 	}

 	@Override
 	public void endElement(Element element) {
 		Object object = stack.pop();
 		if (object != null && object instanceof EObject) {
 			EObject eObject = (EObject) object;
 			eObjectTraceManager.trace(eObject, getCurrentURI(), getLineNumber(element));
 		}
 	}

 	@Override
 	public void processingInstruction(ProcessingInstruction processingInstruction) {
 		currentNode = processingInstruction;

 		String key = processingInstruction.getTarget();
 		String value = processingInstruction.getData();

 		if ("nsuri".equalsIgnoreCase(key)) {
 			EPackage ePackage = EPackage.Registry.INSTANCE.getEPackage(value);
 			if (ePackage != null) getResourceSet().getPackageRegistry().put(ePackage.getNsURI(), ePackage);
 			else addParseWarning("Failed to locate EPackage for nsURI " + value + " ");
 		}
 		else if ("eol".equalsIgnoreCase(key)) {
 			scripts.add(value);
 		}
 		else processOption(key, value);
 	}

 	@Override
 	public void endDocument(Document document) {
 		resolveReferences();
 	}

 	public List<UnresolvedReference> getUnresolvedReferences() {
 		return unresolvedReferences;
 	}

 	protected void addParseWarning(String message) {
 		addParseWarning(message, getLineNumber(currentNode));
 	}

 	protected void addParseWarning(String message, int line) {
 		addParseWarning(message, getCurrentURI(), line);
 	}

 	protected void addParseWarning(String message, URI uri, int line) {
 		getWarnings().add(new FlexmiDiagnostic(message, uri, line));
 	}

 	@SuppressWarnings("unchecked")
 	protected void resolveReferences() {
 		List<UnresolvedReference> unresolvableReferences = new ArrayList<UnresolvedReference>();

 		for (UnresolvedReference unresolvedReference : unresolvedReferences) {
 			EReference eReference = unresolvedReference.getEReference();
 			if (eReference.isMany()) {

 				if ("*".equals(unresolvedReference.getValue())) {
 					Iterator<EObject> it = this.getAllContents();
 					while (it.hasNext()) {
 						EObject candidate = it.next();
 						if (eReference.getEReferenceType().isInstance(candidate)) {
 							new EReferenceSlot(eReference, unresolvedReference.getEObject()).newValue(candidate);
 						}
 					}
 				}
 				else {
 					if (!resolveReference(unresolvedReference)) unresolvableReferences.add(unresolvedReference);
 				}
 			}
 			else {
 				if (!resolveReference(unresolvedReference)) unresolvableReferences.add(unresolvedReference);
 			}
 		}

 		for (UnresolvedReference reference : unresolvableReferences) {
 			addParseWarning("Could not resolve target " + reference.getValue() + " for reference " + reference.getAttributeName() + " (" + reference.getEReference().getName() + ")", reference.getUri(), reference.getLine());
 		}
 	}

 	protected boolean resolveReference(UnresolvedReference unresolvedReference) {
 		List<EObject> candidates = Arrays.asList(getIntrinsicIDToEObjectMap().get(unresolvedReference.getValue()));
 		if (!unresolvedReference.resolve(candidates)) {
 			System.out.println("Failed");
 			for (Resource resource : getResourceSet().getResources()) {
 				if (resource != this) {
 					candidates = Arrays.asList(resource.getEObject(unresolvedReference.getValue()));
 					if (unresolvedReference.resolve(candidates)) return true;
 				}
 			}
 			return false;
 		}
 		return true;
 	}

 	public int getLineNumber(Node node) {
 		Location location = (Location) node.getUserData(Location.ID);
 		if (location != null) {
 			return location.getStartLine();
 		}
 		return 0;
 	}


 	protected void setAttributes(EObject eObject, Element element) {

 		NamedNodeMap attributes = element.getAttributes();
 		List<EStructuralFeature> eStructuralFeatures = getCandidateStructuralFeaturesForAttribute(eObject.eClass());

 		if (attributes.getLength() == 0 || eStructuralFeatures.size() == 0) return;

 		if (!(eObject.eClass().getEStructuralFeature("id") instanceof EAttribute)) {
 			if (attributes.getNamedItem("id") != null) {
 				String value = attributes.getNamedItem("id").getNodeValue();
 				attributes.removeNamedItem("id");
 				getIntrinsicIDToEObjectMap().put(value, eObject);
 			}
 		}

 		if (attributes.getLength() == 0) return;

 		double[][] inverseSimilarities = new double[attributes.getLength()][eStructuralFeatures.size()];

 		for (int i=0;i<attributes.getLength();i++) {
 			int j=0;
 			String attributeName = attributes.item(i).getNodeName();
 			for (EStructuralFeature sf : eStructuralFeatures) {
 				int similarity = stringSimilarityProvider.getSimilarity(attributeName, sf.getName());
 				double inverseSimilarity = 2;
 				if (similarity != 0) inverseSimilarity = 1/(double)similarity;
 				inverseSimilarities[i][j] = inverseSimilarity;
 				j++;
 			}
 		}

 		int[] assignment = new HungarianAlgorithm(inverseSimilarities).execute();

 		for (int i=0;i<assignment.length;i++) {
 			String name = attributes.item(i).getNodeName();
 			String value = attributes.item(i).getNodeValue();

 			if (assignment[i]>=eStructuralFeatures.size() || assignment[i]<0) continue;

 			EStructuralFeature sf = eStructuralFeatures.get(assignment[i]);

 			if (sf instanceof EAttribute) {
 				setEAttributeValue(eObject, (EAttribute) sf, name, value);
 			}
 			else if (sf instanceof EReference) {
 				EReference eReference = (EReference) sf;
 				if (eReference.isMany()) {
 					for (String valuePart : value.split(",")) {
 						unresolvedReferences.add(new UnresolvedReference(eObject, getCurrentURI(), eReference, name, valuePart.trim(), getLineNumber(element)));
 					}
 				}
 				else {
 					unresolvedReferences.add(new UnresolvedReference(eObject, getCurrentURI(), eReference, name, value, getLineNumber(element)));
 				}
 			}
 		}

 	}

 	public URI getCurrentURI() {
 		return parsedFragmentURIStack.isEmpty() ? this.getURI() : parsedFragmentURIStack.peek();
 	}

 	@SuppressWarnings("unchecked")
 	protected void setEAttributeValue(EObject eObject, EAttribute eAttribute, String attributeName, String value) {
 		if (eAttribute.isMany()) {
 			for (String valuePart : value.split(",")) {
 				Object eValue = getEValue(eAttribute, attributeName, valuePart.trim());
 				if (eValue == null) continue;
 				((List<Object>) eObject.eGet(eAttribute)).add(eValue);
 			}
 		}
 		else {
 			Object eValue = getEValue(eAttribute, attributeName, value);
 			if (eValue == null) return;
 			eObject.eSet(eAttribute, eValue);
 			if (eAttribute.isID() || "name".equalsIgnoreCase(eAttribute.getName())) {
 				getIntrinsicIDToEObjectMap().put(value, eObject);
 			}
 		}
 	}

 	protected Object getEValue(EAttribute eAttribute, String attributeName, String value) {
 		try {
 			return eAttribute.getEAttributeType().getEPackage().getEFactoryInstance().createFromString(eAttribute.getEAttributeType(), value);
 		}
 		catch (Exception ex) {
 			ex.printStackTrace();
 			addParseWarning(ex.getMessage() + " in the value of " + attributeName);
 			return null;
 		}
 	}

 	protected List<EStructuralFeature> getCandidateStructuralFeaturesForAttribute(EClass eClass) {
 		List<EStructuralFeature> eStructuralFeatures = new ArrayList<EStructuralFeature>();
 		for (EStructuralFeature sf : eClass.getEAllStructuralFeatures()) {
 			if (sf.isChangeable() && (sf instanceof EAttribute || ((sf instanceof EReference) && !((EReference) sf).isContainment()))) {
 				eStructuralFeatures.add(sf);
 			}
 		}
 		return eStructuralFeatures;
 	}

 	protected List<EClass> getAllConcreteEClasses() {
 		List<EClass> eClasses = new ArrayList<EClass>();
 		Iterator<Object> it = getResourceSet().getPackageRegistry().values().iterator();
 		while (it.hasNext()) {
 			EPackage ePackage = (EPackage) it.next();
 			for (EClassifier eClassifier : ePackage.getEClassifiers()) {
 				if (eClassifier instanceof EClass && !((EClass) eClassifier).isAbstract()) {
 					eClasses.add((EClass) eClassifier);
 				}
 			}
 		}
 		return eClasses;
 	}

 	protected List<EClass> getAllSubtypes(EClass eClass) {
 		List<EClass> allSubtypes = allSubtypesCache.get(eClass);
 		if (allSubtypes == null) {
 			allSubtypes = new ArrayList<EClass>();
 			for (EClass candidate : getAllConcreteEClasses()) {
 				if (candidate.getEAllSuperTypes().contains(eClass)) {
 					allSubtypes.add(candidate);
 				}
 			}
 			if (!eClass.isAbstract()) allSubtypes.add(eClass);
 			allSubtypesCache.put(eClass, allSubtypes);
 		}
 		return allSubtypes;
 	}

 	protected EClass eClassForName(String name) {
 		EClass eClass = eClassCache.get(name);
 		if (eClass == null) {
 			eClass = (EClass) eNamedElementForName(name, getAllConcreteEClasses());
 			eClassCache.put(name, eClass);
 		}
 		return eClass;

 	}

 	protected ENamedElement eNamedElementForName(String name, Collection<? extends ENamedElement> candidates) {
 		ENamedElement eNamedElement = eNamedElementForName(name, candidates, false);
 		if (eNamedElement == null) eNamedElement = eNamedElementForName(name, candidates, true);
 		return eNamedElement;
 	}

 	public EObjectTraceManager getEObjectTraceManager() {
 		return eObjectTraceManager;
 	}

 	protected ENamedElement eNamedElementForName(String name, Collection<? extends ENamedElement> candidates, boolean fuzzy) {

 		if (fuzzy) {
 			int maxSimilarity = 0;
 			ENamedElement bestMatch = null;
 			for (ENamedElement candidate : candidates) {
 				int similarity = stringSimilarityProvider.getSimilarity(candidate.getName().toLowerCase(), name.toLowerCase());
 				if (similarity > maxSimilarity) {
 					maxSimilarity = similarity;
 					bestMatch = candidate;
 				}
 			}

 			if (maxSimilarity == 0 && candidates.size() == 1) {
 				return candidates.iterator().next();
 			}

 			return bestMatch;
 		}
 		else {
 			for (ENamedElement candidate : candidates) {
 				if (candidate.getName().equalsIgnoreCase(name)) return candidate;
 			}
 		}

 		return null;
 	}

 }
	package org.eclipse.epsilon.flexmi;

	import java.io.File;
	import java.io.IOException;
	import java.io.InputStream;
	import java.util.ArrayList;
	import java.util.Arrays;
	import java.util.Collection;
	import java.util.HashMap;
	import java.util.HashSet;
	import java.util.Iterator;
	import java.util.List;
	import java.util.Map;
	import java.util.Set;
	import java.util.Stack;

	import org.eclipse.emf.common.util.URI;
	import org.eclipse.emf.ecore.EAttribute;
	import org.eclipse.emf.ecore.EClass;
	import org.eclipse.emf.ecore.EClassifier;
	import org.eclipse.emf.ecore.ENamedElement;
	import org.eclipse.emf.ecore.EObject;
	import org.eclipse.emf.ecore.EPackage;
	import org.eclipse.emf.ecore.EReference;
	import org.eclipse.emf.ecore.EStructuralFeature;
	import org.eclipse.emf.ecore.EcorePackage;
	import org.eclipse.emf.ecore.resource.Resource;
	import org.eclipse.emf.ecore.resource.ResourceSet;
	import org.eclipse.emf.ecore.resource.impl.ResourceImpl;
	import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
	import org.eclipse.emf.ecore.util.EcoreUtil;
	import org.eclipse.emf.ecore.xmi.impl.XMIResourceFactoryImpl;
	import org.eclipse.epsilon.flexmi.xml.Location;
	import org.eclipse.epsilon.flexmi.xml.PseudoSAXParser;
	import org.eclipse.epsilon.flexmi.xml.PseudoSAXParser.Handler;
	import org.w3c.dom.Document;
	import org.w3c.dom.Element;
	import org.w3c.dom.NamedNodeMap;
	import org.w3c.dom.Node;
	import org.w3c.dom.ProcessingInstruction;
	import org.w3c.dom.Text;

	public class FlexmiResource extends ResourceImpl implements Handler {

	public static final String OPTION_FUZZY_CONTAINMENT_MATCHING = "fuzzyContainmentMatching";
	public static final String OPTION_ORPHANS_AS_TOP_LEVEL = "orphansAsTopLevel";
	public static final String OPTION_FUZZY_MATCHING_THRESHOLD = "fuzzyMatchingThreshold";

	protected EObjectTraceManager eObjectTraceManager = new EObjectTraceManager();
	protected List<UnresolvedReference> unresolvedReferences = new ArrayList<UnresolvedReference>();
	protected Stack<Object> stack = new Stack<Object>();
	protected Node currentNode = null;
	protected List<String> scripts = new ArrayList<String>();
	protected HashMap<String, EClass> eClassCache = new HashMap<String, EClass>();
	protected HashMap<EClass, List<EClass>> allSubtypesCache = new HashMap<EClass, List<EClass>>();
	protected StringSimilarityProvider stringSimilarityProvider = new CachedStringSimilarityProvider(new DefaultStringSimilarityProvider());
	protected Stack<URI> parsedFragmentURIStack = new Stack<URI>();
	protected Set<URI> parsedFragmentURIs = new HashSet<URI>();

	protected boolean fuzzyContainmentSlotMatching = true;
	protected boolean orphansAsTopLevel = true;
	protected int fuzzyMatchingThreshold = 0;

	public void startProcessingFragment(URI uri) {
	parsedFragmentURIStack.push(uri);
	parsedFragmentURIs.add(uri);
	}

	public void endProcessingFragment() {
	parsedFragmentURIStack.pop();
	}

	public Set<URI> getParsedFragmentURIs() {
	return parsedFragmentURIs;
	}

	public static void main(String[] args) throws Exception {

	// Load the metamodel
	ResourceSet metamodelResourceSet = new ResourceSetImpl();
	metamodelResourceSet.getPackageRegistry().put(EcorePackage.eINSTANCE.getNsURI(), EcorePackage.eINSTANCE);
	metamodelResourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("*", new XMIResourceFactoryImpl());
	Resource metamodelResource = metamodelResourceSet.createResource(URI.createFileURI(new File("models/messaging.ecore").getAbsolutePath()));
	metamodelResource.load(null);

	EPackage metamodel = (EPackage) metamodelResource.getContents().get(0);

	// Load the model
	ResourceSet modelResourceSet = new ResourceSetImpl();
	modelResourceSet.getPackageRegistry().put(metamodel.getNsURI(), metamodel);
	modelResourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("*", new FlexmiResourceFactory());
	Resource modelResource = modelResourceSet.createResource(URI.createFileURI(new File("models/messaging.flexmi").getAbsolutePath()));
	modelResource.load(null);

	System.out.println(modelResource.getEObject("tom"));

	}

	public FlexmiResource(URI uri) {
	super(uri);
	}

	@Override
	protected void doLoad(InputStream inputStream, Map<?, ?> options)
	throws IOException {
	try {
	doLoadImpl(inputStream, options);
	}
	catch (IOException ioException) {
	ioException.printStackTrace();
	throw ioException;
	}
	catch (Exception ex) {
	ex.printStackTrace();
	throw new RuntimeException(ex);
	}
	}

	protected void processOption(String key, String value) {
	try {
	if (OPTION_FUZZY_CONTAINMENT_MATCHING.equalsIgnoreCase(key)) {
	fuzzyContainmentSlotMatching = Boolean.parseBoolean(value);
	}
	else if (OPTION_ORPHANS_AS_TOP_LEVEL.equalsIgnoreCase(key)) {
	orphansAsTopLevel = Boolean.parseBoolean(value);
	}
	else if (OPTION_FUZZY_MATCHING_THRESHOLD.equalsIgnoreCase(key)) {
	fuzzyMatchingThreshold = Integer.parseInt(value);
	}
	else throw new Exception("Unknown option");
	}
	catch (Exception ex) {
	addParseWarning("Could not process option " + key + ": " + ex.getMessage());
	}
	}

	public void doLoadImpl(InputStream inputStream, Map<?, ?> options) throws Exception {
	getContents().clear();
	unresolvedReferences.clear();
	stack.clear();
	scripts.clear();
	eClassCache.clear();
	allSubtypesCache.clear();
	setIntrinsicIDToEObjectMap(new HashMap<String, EObject>());

	if (options != null) {
	for (Object key : options.keySet()) {
	processOption(key + "", options.get(key) + "");
	}
	}

	new PseudoSAXParser().parse(this, inputStream, this);
	}

	@Override
	public void startDocument(Document document) {}

	@Override
	public void startElement(Element element) {
	currentNode = element;
	String name = element.getNodeName();

	//Remove prefixes
	//TODO: Add option to disable this
	if (name.indexOf(":") > -1) {
	name = name.substring(name.indexOf(":")+1);
	}

	EObject eObject = null;
	EClass eClass = null;

	// We're at the root or we treat orphan elements as top-level
	if (stack.isEmpty() \|\| (stack.peek() == null && orphansAsTopLevel)) {
	eClass = eClassForName(name);
	if (eClass != null) {
	eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
	getContents().add(eObject);
	setAttributes(eObject, element);
	}
	else {
	addParseWarning("Could not map element " + name + " to an EObject");
	}
	stack.push(eObject);
	}
	else {
	Object peek = stack.peek();

	// We find an orphan element but don't treat it as top-level
	if (peek == null) {
	stack.push(null);
	addParseWarning("Could not map element " + name + " to an EObject");
	return;
	}
	// The parent is an already-established containment slot
	else if (peek instanceof EReferenceSlot) {
	EReferenceSlot containmentSlot = (EReferenceSlot) peek;
	eClass = (EClass) eNamedElementForName(name, getAllSubtypes(containmentSlot.getEReference().getEReferenceType()));

	if (eClass != null) {
	eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
	containmentSlot.newValue(eObject);
	stack.push(eObject);
	setAttributes(eObject, element);
	}
	else {
	stack.push(null);
	addParseWarning("Could not map element " + name + " to an EObject");
	}
	}
	// The parent is an EObject
	else if (peek instanceof EObject) {
	EObject parent = (EObject) peek;

	if (element.getAttributes().getLength() == 0 && element.getChildNodes().getLength() == 1 && element.getFirstChild() instanceof Text) {
	EAttribute eAttribute = (EAttribute) eNamedElementForName(name, parent.eClass().getEAllAttributes());

	if (eAttribute != null) {
	setEAttributeValue(parent, eAttribute, name, element.getTextContent().trim());
	eObjectTraceManager.trace(parent, getCurrentURI(), getLineNumber(element));
	stack.push(null);
	return;
	}
	}

	EReference containment = null;

	// No attributes -> Check whether there is a containment reference with that name
	if (element.getAttributes().getLength() == 0) {
	if (fuzzyContainmentSlotMatching) {
	containment = (EReference) eNamedElementForName(name, parent.eClass().getEAllContainments());
	}
	else {
	containment = (EReference) eNamedElementForName(name, parent.eClass().getEAllContainments(), false);
	}
	if (containment != null) {
	EReferenceSlot containmentSlot = new EReferenceSlot(containment, parent);
	eObjectTraceManager.trace(parent, getCurrentURI(), getLineNumber(element));
	stack.push(containmentSlot);
	return;
	}
	}

	// No containment references found
	// Find potential types for the element
	Set<EClass> candidates = new HashSet<EClass>();
	for (EReference eReference : parent.eClass().getEAllContainments()) {
	candidates.addAll(getAllSubtypes(eReference.getEReferenceType()));
	}

	// Get the best match and an appropriate containment reference
	eClass = (EClass) eNamedElementForName(name, candidates);
	if (eClass != null) {
	for (EReference eReference : parent.eClass().getEAllContainments()) {
	if (getAllSubtypes(eReference.getEReferenceType()).contains(eClass)) {
	containment = eReference;
	break;
	}
	}
	}

	// Found an appropriate containment reference
	if (containment != null) {
	eObject = eClass.getEPackage().getEFactoryInstance().create(eClass);
	if (containment.isMany()) {
	((List<EObject>) parent.eGet(containment)).add(eObject);
	}
	else {
	parent.eSet(containment, eObject);
	}
	setAttributes(eObject, element);
	stack.push(eObject);
	}
	// No luck - add warning
	else {
	stack.push(null);
	addParseWarning("Could not map element " + name + " to an EObject");
	}
	}
	}
	}

	@Override
	public void endElement(Element element) {
	Object object = stack.pop();
	if (object != null && object instanceof EObject) {
	EObject eObject = (EObject) object;
	eObjectTraceManager.trace(eObject, getCurrentURI(), getLineNumber(element));
	}
	}

	@Override
	public void processingInstruction(ProcessingInstruction processingInstruction) {
	currentNode = processingInstruction;

	String key = processingInstruction.getTarget();
	String value = processingInstruction.getData();

	if ("nsuri".equalsIgnoreCase(key)) {
	EPackage ePackage = EPackage.Registry.INSTANCE.getEPackage(value);
	if (ePackage != null) getResourceSet().getPackageRegistry().put(ePackage.getNsURI(), ePackage);
	else addParseWarning("Failed to locate EPackage for nsURI " + value + " ");
	}
	else if ("eol".equalsIgnoreCase(key)) {
	scripts.add(value);
	}
	else processOption(key, value);
	}

	@Override
	public void endDocument(Document document) {
	resolveReferences();
	}

	public List<UnresolvedReference> getUnresolvedReferences() {
	return unresolvedReferences;
	}

	protected void addParseWarning(String message) {
	addParseWarning(message, getLineNumber(currentNode));
	}

	protected void addParseWarning(String message, int line) {
	addParseWarning(message, getCurrentURI(), line);
	}

	protected void addParseWarning(String message, URI uri, int line) {
	getWarnings().add(new FlexmiDiagnostic(message, uri, line));
	}

	@SuppressWarnings("unchecked")
	protected void resolveReferences() {
	List<UnresolvedReference> unresolvableReferences = new ArrayList<UnresolvedReference>();

	for (UnresolvedReference unresolvedReference : unresolvedReferences) {
	EReference eReference = unresolvedReference.getEReference();
	if (eReference.isMany()) {

	if ("*".equals(unresolvedReference.getValue())) {
	Iterator<EObject> it = this.getAllContents();
	while (it.hasNext()) {
	EObject candidate = it.next();
	if (eReference.getEReferenceType().isInstance(candidate)) {
	new EReferenceSlot(eReference, unresolvedReference.getEObject()).newValue(candidate);
	}
	}
	}
	else {
	if (!resolveReference(unresolvedReference)) unresolvableReferences.add(unresolvedReference);
	}
	}
	else {
	if (!resolveReference(unresolvedReference)) unresolvableReferences.add(unresolvedReference);
	}
	}

	for (UnresolvedReference reference : unresolvableReferences) {
	addParseWarning("Could not resolve target " + reference.getValue() + " for reference " + reference.getAttributeName() + " (" + reference.getEReference().getName() + ")", reference.getUri(), reference.getLine());
	}
	}

	protected boolean resolveReference(UnresolvedReference unresolvedReference) {
	List<EObject> candidates = Arrays.asList(getIntrinsicIDToEObjectMap().get(unresolvedReference.getValue()));
	if (!unresolvedReference.resolve(candidates)) {
	System.out.println("Failed");
	for (Resource resource : getResourceSet().getResources()) {
	if (resource != this) {
	candidates = Arrays.asList(resource.getEObject(unresolvedReference.getValue()));
	if (unresolvedReference.resolve(candidates)) return true;
	}
	}
	return false;
	}
	return true;
	}

	public int getLineNumber(Node node) {
	Location location = (Location) node.getUserData(Location.ID);
	if (location != null) {
	return location.getStartLine();
	}
	return 0;
	}


	protected void setAttributes(EObject eObject, Element element) {

	NamedNodeMap attributes = element.getAttributes();
	List<EStructuralFeature> eStructuralFeatures = getCandidateStructuralFeaturesForAttribute(eObject.eClass());

	if (attributes.getLength() == 0 \|\| eStructuralFeatures.size() == 0) return;

	if (!(eObject.eClass().getEStructuralFeature("id") instanceof EAttribute)) {
	if (attributes.getNamedItem("id") != null) {
	String value = attributes.getNamedItem("id").getNodeValue();
	attributes.removeNamedItem("id");
	getIntrinsicIDToEObjectMap().put(value, eObject);
	}
	}

	if (attributes.getLength() == 0) return;

	double[][] inverseSimilarities = new double[attributes.getLength()][eStructuralFeatures.size()];

	for (int i=0;i<attributes.getLength();i++) {
	int j=0;
	String attributeName = attributes.item(i).getNodeName();
	for (EStructuralFeature sf : eStructuralFeatures) {
	int similarity = stringSimilarityProvider.getSimilarity(attributeName, sf.getName());
	double inverseSimilarity = 2;
	if (similarity != 0) inverseSimilarity = 1/(double)similarity;
	inverseSimilarities[i][j] = inverseSimilarity;
	j++;
	}
	}

	int[] assignment = new HungarianAlgorithm(inverseSimilarities).execute();

	for (int i=0;i<assignment.length;i++) {
	String name = attributes.item(i).getNodeName();
	String value = attributes.item(i).getNodeValue();

	if (assignment[i]>=eStructuralFeatures.size() \|\| assignment[i]<0) continue;

	EStructuralFeature sf = eStructuralFeatures.get(assignment[i]);

	if (sf instanceof EAttribute) {
	setEAttributeValue(eObject, (EAttribute) sf, name, value);
	}
	else if (sf instanceof EReference) {
	EReference eReference = (EReference) sf;
	if (eReference.isMany()) {
	for (String valuePart : value.split(",")) {
	unresolvedReferences.add(new UnresolvedReference(eObject, getCurrentURI(), eReference, name, valuePart.trim(), getLineNumber(element)));
	}
	}
	else {
	unresolvedReferences.add(new UnresolvedReference(eObject, getCurrentURI(), eReference, name, value, getLineNumber(element)));
	}
	}
	}

	}

	public URI getCurrentURI() {
	return parsedFragmentURIStack.isEmpty() ? this.getURI() : parsedFragmentURIStack.peek();
	}

	@SuppressWarnings("unchecked")
	protected void setEAttributeValue(EObject eObject, EAttribute eAttribute, String attributeName, String value) {
	if (eAttribute.isMany()) {
	for (String valuePart : value.split(",")) {
	Object eValue = getEValue(eAttribute, attributeName, valuePart.trim());
	if (eValue == null) continue;
	((List<Object>) eObject.eGet(eAttribute)).add(eValue);
	}
	}
	else {
	Object eValue = getEValue(eAttribute, attributeName, value);
	if (eValue == null) return;
	eObject.eSet(eAttribute, eValue);
	if (eAttribute.isID() \|\| "name".equalsIgnoreCase(eAttribute.getName())) {
	getIntrinsicIDToEObjectMap().put(value, eObject);
	}
	}
	}

	protected Object getEValue(EAttribute eAttribute, String attributeName, String value) {
	try {
	return eAttribute.getEAttributeType().getEPackage().getEFactoryInstance().createFromString(eAttribute.getEAttributeType(), value);
	}
	catch (Exception ex) {
	ex.printStackTrace();
	addParseWarning(ex.getMessage() + " in the value of " + attributeName);
	return null;
	}
	}

	protected List<EStructuralFeature> getCandidateStructuralFeaturesForAttribute(EClass eClass) {
	List<EStructuralFeature> eStructuralFeatures = new ArrayList<EStructuralFeature>();
	for (EStructuralFeature sf : eClass.getEAllStructuralFeatures()) {
	if (sf.isChangeable() && (sf instanceof EAttribute \|\| ((sf instanceof EReference) && !((EReference) sf).isContainment()))) {
	eStructuralFeatures.add(sf);
	}
	}
	return eStructuralFeatures;
	}

	protected List<EClass> getAllConcreteEClasses() {
	List<EClass> eClasses = new ArrayList<EClass>();
	Iterator<Object> it = getResourceSet().getPackageRegistry().values().iterator();
	while (it.hasNext()) {
	EPackage ePackage = (EPackage) it.next();
	for (EClassifier eClassifier : ePackage.getEClassifiers()) {
	if (eClassifier instanceof EClass && !((EClass) eClassifier).isAbstract()) {
	eClasses.add((EClass) eClassifier);
	}
	}
	}
	return eClasses;
	}

	protected List<EClass> getAllSubtypes(EClass eClass) {
	List<EClass> allSubtypes = allSubtypesCache.get(eClass);
	if (allSubtypes == null) {
	allSubtypes = new ArrayList<EClass>();
	for (EClass candidate : getAllConcreteEClasses()) {
	if (candidate.getEAllSuperTypes().contains(eClass)) {
	allSubtypes.add(candidate);
	}
	}
	if (!eClass.isAbstract()) allSubtypes.add(eClass);
	allSubtypesCache.put(eClass, allSubtypes);
	}
	return allSubtypes;
	}

	protected EClass eClassForName(String name) {
	EClass eClass = eClassCache.get(name);
	if (eClass == null) {
	eClass = (EClass) eNamedElementForName(name, getAllConcreteEClasses());
	eClassCache.put(name, eClass);
	}
	return eClass;

	}

	protected ENamedElement eNamedElementForName(String name, Collection<? extends ENamedElement> candidates) {
	ENamedElement eNamedElement = eNamedElementForName(name, candidates, false);
	if (eNamedElement == null) eNamedElement = eNamedElementForName(name, candidates, true);
	return eNamedElement;
	}

	public EObjectTraceManager getEObjectTraceManager() {
	return eObjectTraceManager;
	}

	protected ENamedElement eNamedElementForName(String name, Collection<? extends ENamedElement> candidates, boolean fuzzy) {

	if (fuzzy) {
	int maxSimilarity = 0;
	ENamedElement bestMatch = null;
	for (ENamedElement candidate : candidates) {
	int similarity = stringSimilarityProvider.getSimilarity(candidate.getName().toLowerCase(), name.toLowerCase());
	if (similarity > maxSimilarity) {
	maxSimilarity = similarity;
	bestMatch = candidate;
	}
	}

	if (maxSimilarity == 0 && candidates.size() == 1) {
	return candidates.iterator().next();
	}

	return bestMatch;
	}
	else {
	for (ENamedElement candidate : candidates) {
	if (candidate.getName().equalsIgnoreCase(name)) return candidate;
	}
	}

	return null;
	}

	}