cda/plugins/org.eclipse.mdht.api/src/org/eclipse/mdht/api/GenerateXMLAction.java - mdht/org.eclipse.mdht - Git at Google

 /**
  * Copyright: NEHTA 2015
  * Author: Joerg Kiegeland, Distributed Models Pty Ltd
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  */

 package org.eclipse.mdht.api;

 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;

 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.emf.common.util.URI;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.eclipse.emf.ecore.resource.ResourceSet;
 import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
 import org.eclipse.emf.ecore.util.BasicExtendedMetaData;
 import org.eclipse.emf.ecore.xmi.XMIResource;
 import org.eclipse.emf.ecore.xmi.XMLResource;
 import org.eclipse.emf.ecore.xmi.impl.XMLHelperImpl;
 import org.eclipse.mdht.transformation.ocl.OCLTransformation;
 import org.eclipse.mdht.uml.cda.core.util.CDACommonUtils;
 import org.eclipse.uml2.uml.Class;
 import org.eclipse.uml2.uml.Classifier;
 import org.eclipse.uml2.uml.Constraint;
 import org.eclipse.uml2.uml.Element;
 import org.eclipse.uml2.uml.NamedElement;
 import org.eclipse.uml2.uml.OpaqueExpression;
 import org.eclipse.uml2.uml.Package;
 import org.eclipse.uml2.uml.Property;
 import org.eclipse.uml2.uml.Type;

 /**
  * Action to generate XML files for the selected UML model
  */
 public class GenerateXMLAction extends GenerateAPIAction {

 	protected File xmlTestFolder;

 	/**
 	 * Stores the XML test files for a given UML model element
 	 */
 	private Map<Element, Collection<File>> testFilesFor = new HashMap<Element, Collection<File>>();

 	/**
 	 * Stores the test type of a given XML test file
 	 */
 	private Map<File, String> typeOfTestFile = new HashMap<File, String>();

 	@Override
 	protected String getTargetLanguage() {
 		return "Positive/Negative XML Samples";
 	}

 	@Override
 	protected String getRootFileExtension() {
 		return ".xml";
 	}

 	@Override
 	protected File genfolder(File modelFolder) {
 		return new File(modelFolder, "samples");
 	}

 	@Override
 	protected String toValidFileName(String filename) {
 		filename = filename.replace(".", "_").replace(" ", ""); // cosmetics
 		filename = filename.replaceAll("[:\\\\/*\"?|<>']", ""); // remove invalid characters
 		return filename;
 	}

 	/**
 	 * Generates positive and negative XML test files
 	 *
 	 * @param pack
 	 * @param monitor
 	 * @throws Exception
 	 */
 	protected void genAPICode(final Package pack, IProgressMonitor monitor) throws Exception {
 		xmlTestFolder = new File(genfolder, "xml");

 		monitor.setTaskName("Creating Min/Max Clinical Documents");
 		generateMinMaxXMLFiles(pack, monitor);

 		monitor.setTaskName("Creating XML test data for properties");
 		monitor = new SubProgressMonitor(monitor, 30);
 		monitor.beginTask("", CDACommonUtils.getAllContents(pack.eResource(), Constraint.class).size() + CDACommonUtils.getAllContents(pack.eResource(), Class.class).size() + CDACommonUtils.getAllContents(pack.eResource(), Property.class).size());

 		for (Constraint constraint : CDACommonUtils.getAllContents(pack.eResource(), Constraint.class)) {
 			monitor.worked(1);
 			if (constraint.getSpecification() instanceof OpaqueExpression && !constraint.getConstrainedElements().isEmpty() && constraint.getContext() instanceof Class) {
 				OpaqueExpression opaqueExpression = (OpaqueExpression) constraint.getSpecification();
 				if (!opaqueExpression.getLanguages().isEmpty() && "Analysis".equals(opaqueExpression.getLanguages().get(0))) {
 					Element ele = constraint.getConstrainedElements().get(0);
 					ele = CDACommonUtils.getMDHTRepresentative((NamedElement) ele);
 					EObject eObject = ele;
 					while (eObject != null) {
 						if (eObject instanceof Class) {
 							Class clazz = (Class) eObject;
 							List<Property> propertyPath = CDACommonUtils.getPropertyPath(clazz);
 							for (Element element : constraint.getConstrainedElements()) {
 								if (element instanceof Property) {
 									Property property = (Property) element;
 									propertyPath.add(property);
 								}
 							}
 							monitor.subTask(constraint.getName());
 							File placeholderFolder = new File(xmlTestFolder, "Placeholder");
 							creator.forgetLastFileContent();
 							creator.initialize(propertyPath);
 							creator.flushClinicalDocument(record((Class) constraint.getContext(), new File(placeholderFolder, "Positive"), constraint, "OK"));
 							creator.forgetLastFileContent();
 							creator.initialize(propertyPath);
 							creator.flushClinicalDocument(record((Class) constraint.getContext(), new File(placeholderFolder, "Negative"), constraint, "Fail"));
 							break;
 						}
 						eObject = eObject.eContainer();
 					}
 				}
 			}
 		}

 		for (Class clazz : CDACommonUtils.getAllContents(pack.eResource(), Class.class)) {
 			if (Boolean.parseBoolean(getStereotype(clazz, "noSchematronGen"))) {
 				continue;
 			}
 			monitor.worked(1);
 			String templateId = CDACommonUtils.getTemplateId(clazz);
 			Property templateIdProperty = creator.getTemplateIdProperty(clazz);
 			if (templateId != null && templateIdProperty != null) {
 				monitor.subTask(clazz.getName());
 				File templateIDsFolder = new File(xmlTestFolder, "TemplateIDs");
 				if (creator.initializePath(clazz, templateIdProperty, null, null) != null)
 					creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Positive"), templateIdProperty, "OK"));
 				if (creator.initializePath(clazz, templateIdProperty, null, templateIdProperty) != null)
 					creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Negative"), templateIdProperty, "AttributeValueTest"));
 				if (creator.initializePath(clazz, null, templateIdProperty, null) != null)
 					creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Negative"), templateIdProperty, "NodeExistenceTest"));
 			}

 		}

 		for (Property property : CDACommonUtils.getAllContents(pack.eResource(), Property.class)) {
 			monitor.worked(1);
 			if (property.eContainer() instanceof Class) {
 				Class clazz = (Class) property.eContainer();
 				monitor.subTask(CDACommonUtils.getUmlContext(property));
 				if (monitor.isCanceled())
 					throw new RuntimeException("Canceled by user");

 				if (Boolean.parseBoolean(getStereotype(property, "noSchematronGen"))) {
 					continue;
 				}
 				Property baseProperty = CDACommonUtils.getCDAProperty(property);
 				creator.forgetLastFileContent();
 				{
 					if (creator.initializePath(clazz, property, null, null) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "OK"));
 				}
 				if (property.getLower() >= 1 && CDACommonUtils.getPropertyForTypeCheck(clazz) != property && CDACommonUtils.getPropertyForCodeOrClasscodeCheck(clazz) != property) {
 					if (creator.initializePath(clazz, null, property, null) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "NodeExistenceTest"));
 				}
 				if ((CDACommonUtils.getDefault(property) != null || CDACommonUtils.getTextValue(property) != null) && CDACommonUtils.getPropertyForTypeCheck(clazz) != property && CDACommonUtils.getPropertyForCodeOrClasscodeCheck(clazz) != property) {
 					if (creator.initializePath(clazz, property, null, property) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "NodeValueTest"));
 				}
 				Property propertyForTypeCheck;
 				if (property.getLower() >= 1 && property.getType() instanceof Class && (propertyForTypeCheck = CDACommonUtils.getLeafPropertyForTypeCheck((Class) property.getType())) != null) {
 					if (creator.initializePath(clazz, property, null, propertyForTypeCheck) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "Predicated_NodeExistenceTest"));
 				}
 				if (property.getLower() >= 1 && property.getType() instanceof Class && CDACommonUtils.isDatatypeModel(property.getType()) && baseProperty != null && baseProperty.getType() != property.getType()) {
 					if (creator.initializePath(clazz, property, null, property) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "NodeTypeTest"));
 				}
 				if (property.getUpper() == 0) {
 					if (creator.initializePath(clazz, property, null, null) != null)
 						creator.flushClinicalDocument(getXMLTestFile(property, "NodeNonExistenceTest"));
 				}
 				if (property.getUpper() == 1 && baseProperty != null && baseProperty.getUpper() != property.getUpper()) {
 					Object child1 = creator.initializePath(clazz, property, null, null);
 					if (child1 instanceof EObject) {
 						EObject eObject = (EObject) child1;
 						Object child2 = creator.repopulateProperty(property, eObject);
 						if (child2 instanceof EObject) {
 							creator.flushClinicalDocument(getXMLTestFile(property, "NodeNumberTest"));
 						} else {
 							CDACommonUtils.addStatus(statuses, IStatus.ERROR, getPlugin(), 16, "Cannot re-populate " + CDACommonUtils.getUmlContextDoubled(property), property);
 						}
 					}
 				}

 			}
 		}

 		monitor.done();

 	}

 	/**
 	 * Removes trailing digits from the name
 	 *
 	 * @param name
 	 * @return
 	 */
 	private static String withoutDigits(String name) {
 		while (!"".equals(name) && Character.isDigit(name.charAt(name.length() - 1))) {
 			name = name.substring(0, name.length() - 1);
 		}
 		return name;
 	}

 	/**
 	 * Copied from ClinicalDocumentCreator.toXMLString() TODO: remove this method
 	 *
 	 * @param eObject
 	 * @param clazz
 	 * @param options
 	 * @return
 	 */
 	public String toXMLString(EObject eObject, Class clazz, Map<String, Object> options) {
 		// generate no indentation in e.g. "<title>Adverse Reactions</title>", i.e. keep it in one line
 		options.put(XMLResource.OPTION_EXTENDED_META_DATA, BasicExtendedMetaData.INSTANCE);
 		options.put(XMLResource.OPTION_ENCODING, "UTF-8");
 		String xml;
 		try {
 			xml = XMLHelperImpl.saveString(options, Arrays.asList(eObject), null, null);
 		} catch (Exception e1) {
 			e1.printStackTrace();
 			return null;
 		}

 		xml = xml.replace("\"datatypes:", "\"");
 		xml = xml.replace("<cda:", "<");
 		xml = xml.replace("</cda:", "</");
 		xml = xml.replace("Extensions_3.0", "ext");
 		xml = xml.replace("xmlns:cda=\"urn:hl7-org:v3\"", "xmlns=\"urn:hl7-org:v3\"");
 		String eName = eObject.eClass().getName();
 		if (!"ClinicalDocument".equals(eName)) {
 			String rootTag = withoutDigits(eName.substring(0, 1).toLowerCase() + eName.substring(1));
 			if (eObject.eContainmentFeature() != null) {
 				rootTag = eObject.eContainingFeature().getName();
 			} else if (clazz != null && CDACommonUtils.getOverallPropertyReference(clazz) != null) {
 				Property cdaProperty = CDACommonUtils.getCDAProperty(CDACommonUtils.getOverallPropertyReference(clazz));
 				if (cdaProperty != null)
 					rootTag = cdaProperty.getName();
 			}
 			xml = xml.replace("<" + eName, "<" + rootTag);
 			xml = xml.replace("</" + eName, "</" + rootTag);

 			xml = xml.replace(" xmlns=\"urn:hl7-org:v3\"", "");
 			xml = xml.replace(" xmi:version=\"2.0\"", "");
 			xml = xml.replace(" xmlns:xmi=\"http://www.omg.org/XMI\"", "");
 			xml = xml.replace(" xmlns:datatypes=\"http://www.openhealthtools.org/mdht/uml/hl7/datatypes\"", "");
 			xml = xml.replace(" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"", "");
 		} else {
 			xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + xml;
 		}
 		// int index = xml.indexOf("<"+eName);
 		// xml = xml.substring(0, index) +
 		// "<ClinicalDocument xmlns:ext=\"http://ns.electronichealth.net.au/Ci/Cda/Extensions/3.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns=\"urn:hl7-org:v3\">"
 		// + xml.substring(xml.indexOf(">", index) + 1);

 		return xml;
 	}

 	/**
 	 * Generates a minimum XML test file, a maximum
 	 *
 	 * @param pack
 	 * @param monitor
 	 * @throws Exception
 	 */
 	protected void generateMinMaxXMLFiles(final Package pack, IProgressMonitor monitor) throws Exception {

 		String uriMap = "";
 		// resolve pathmap URIs
 		for (Resource res : pack.eResource().getResourceSet().getResources()) {
 			URI normURI = res.getResourceSet().getURIConverter().normalize(res.getURI());
 			if (!res.getURI().equals(normURI)) {
 				uriMap += " " + res.getURI() + " " + normURI;
 				// res.setURI(normURI);
 			}
 		}
 		currentCategory.setUriMap(uriMap.trim());

 		Collection<Property> propertyPath = new HashSet<Property>();
 		for (Class clazz : classes) {
 			propertyPath.addAll(CDACommonUtils.getPropertyPath(clazz));
 		}

 		String pref = specContractedName + "_";

 		creator.initialize(Collections.<Property> emptyList());
 		creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Min_mdht.xml"));

 		creator.initialize(propertyPath);
 		creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Max(All_Classes)_mdht.xml"));

 		EObject aClinicalDocument = creator.initializeSnippet(this.umlClinicalDocument, CDACommonUtils.getAllContents(irResources, Property.class));
 		traceCreatedInstances(pref + "Max(All_Properties)_mdht", aClinicalDocument);

 		creator.enableSampleData(true);
 		creator.enableSampleDataExpansion(true);
 		creator.initialize(Collections.<Property> emptyList());
 		creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Sample_mdht.xml"));
 		creator.enableSampleData(false);

 	}

 	/**
 	 *
 	 *
 	 * @param fileName
 	 *            file name without extension - .xmi is appended automatically as it doesn't work with .xml
 	 * @param aClinicalDocument
 	 * @throws IOException
 	 */
 	private void traceCreatedInstances(String fileName, EObject aClinicalDocument) throws IOException {
 		trace("Clinical Document instance", umlClinicalDocument, aClinicalDocument);
 		currentCategory.setTargetModel(aClinicalDocument);
 		for (EObject eObject : CDACommonUtils.getAllContents(Arrays.asList(aClinicalDocument), EObject.class)) {
 			Property property = creator.getInitializedByProperty(eObject);
 			if (property != null) {
 				trace("Property instance", property, eObject);
 			}
 			Type clazz = creator.getInitializedByClass(eObject);
 			if (clazz != null) {
 				trace("Class instance", clazz, eObject);
 			}
 		}
 		File file = new File(xmlTestFolder, fileName + ".xmi");
 		Map<String, Object> options = new HashMap<String, Object>();
 		options.put(XMIResource.OPTION_SCHEMA_LOCATION_IMPLEMENTATION, true);
 		String xml = toXMLString(aClinicalDocument, this.umlClinicalDocument, options);
 		creator.writeFile(xml, file);
 		ResourceSet rSet = new ResourceSetImpl();
 		Resource res = rSet.createResource(URI.createFileURI(file.toString()));
 		res.getContents().add(aClinicalDocument);
 		// options.put(XMIResource.OPTION_SCHEMA_LOCATION, true);
 		// options.put(XMLResource.OPTION_EXTENDED_META_DATA, BasicExtendedMetaData.INSTANCE);
 		// // options.put(XMLResource.OPTION_ENCODING, "UTF-8");
 		// res.save(options);
 	}

 	private File getXMLTestFile(Property property, String testType) {
 		if (!(property.getType() instanceof Class))
 			testType = testType.replace("Node", "Attribute");
 		Class clazz = (Class) property.eContainer();
 		if (testType.contains("OK"))
 			return record(clazz, new File(new File(xmlTestFolder, "Properties"), "Positive"), property, testType);
 		else
 			return record(clazz, new File(new File(xmlTestFolder, "Properties"), "Negative"), property, testType);
 	}

 	/**
 	 * Records a XML test file for the given UML element
 	 *
 	 * @param element
 	 * @param result
 	 * @return
 	 */
 	private File record(Class context, File parent, NamedElement constrainedElement, String testType) {
 		NamedElement element = constrainedElement instanceof Constraint || isTemplateId(constrainedElement) ? context : constrainedElement;
 		Collection<File> testTypes = testFilesFor.get(element);
 		if (testTypes == null) {
 			testFilesFor.put(element, testTypes = new ArrayList<File>());
 		}
 		String xmlTestFilenameTemplate = getStereotype(constrainedElement.getNearestPackage(), "xmlTestFilenameTemplate");
 		String filename = toValidFileName(resolve(xmlTestFilenameTemplate, context, constrainedElement, testType));

 		File result = new File(parent, filename + ".xml");
 		testTypes.add(result);
 		typeOfTestFile.put(result, testType);
 		return result;
 	}

 	private String getTestTypes(Class clazz, NamedElement element, boolean anchor) {
 		String result = "";
 		Collection<File> testTypes = testFilesFor.get(isTemplateId(element) ? clazz : element);
 		if (testTypes != null) {
 			for (File file : testTypes) {
 				if (anchor)
 					result += getAnchor(file, typeOfTestFile.get(file), getEntityMimeType());
 				else
 					result += " " + typeOfTestFile.get(file);
 			}
 		}
 		return result;
 	}

 	protected String resolve(String template, Class clazz, NamedElement element) {
 		this.template = template;

 		if (needResolve("{test-types-covered}", clazz, element))
 			resolve(getTestTypes(clazz, element, false));
 		if (needResolve("{test-file-anchors}", clazz, element))
 			resolve(getTestTypes(clazz, element, true));

 		return super.resolve(this.template, clazz, element);
 	}

 	@Override
 	protected OCLTransformation<Package, Classifier, ?, Property, ?, ?, ?, ?, ?, ?, ?, ?> createTrafo(ResourceSet resourceSet) {
 		return null;

 	}

 	@Override
 	protected String getEntityMimeType() {
 		return "text/xml";
 	}

 }
	/**
	* Copyright: NEHTA 2015
	* Author: Joerg Kiegeland, Distributed Models Pty Ltd
	*
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*/

	package org.eclipse.mdht.api;

	import java.io.File;
	import java.io.IOException;
	import java.util.ArrayList;
	import java.util.Arrays;
	import java.util.Collection;
	import java.util.Collections;
	import java.util.HashMap;
	import java.util.HashSet;
	import java.util.List;
	import java.util.Map;

	import org.eclipse.core.runtime.IProgressMonitor;
	import org.eclipse.core.runtime.IStatus;
	import org.eclipse.core.runtime.SubProgressMonitor;
	import org.eclipse.emf.common.util.URI;
	import org.eclipse.emf.ecore.EObject;
	import org.eclipse.emf.ecore.resource.Resource;
	import org.eclipse.emf.ecore.resource.ResourceSet;
	import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
	import org.eclipse.emf.ecore.util.BasicExtendedMetaData;
	import org.eclipse.emf.ecore.xmi.XMIResource;
	import org.eclipse.emf.ecore.xmi.XMLResource;
	import org.eclipse.emf.ecore.xmi.impl.XMLHelperImpl;
	import org.eclipse.mdht.transformation.ocl.OCLTransformation;
	import org.eclipse.mdht.uml.cda.core.util.CDACommonUtils;
	import org.eclipse.uml2.uml.Class;
	import org.eclipse.uml2.uml.Classifier;
	import org.eclipse.uml2.uml.Constraint;
	import org.eclipse.uml2.uml.Element;
	import org.eclipse.uml2.uml.NamedElement;
	import org.eclipse.uml2.uml.OpaqueExpression;
	import org.eclipse.uml2.uml.Package;
	import org.eclipse.uml2.uml.Property;
	import org.eclipse.uml2.uml.Type;

	/**
	* Action to generate XML files for the selected UML model
	*/
	public class GenerateXMLAction extends GenerateAPIAction {

	protected File xmlTestFolder;

	/**
	* Stores the XML test files for a given UML model element
	*/
	private Map<Element, Collection<File>> testFilesFor = new HashMap<Element, Collection<File>>();

	/**
	* Stores the test type of a given XML test file
	*/
	private Map<File, String> typeOfTestFile = new HashMap<File, String>();

	@Override
	protected String getTargetLanguage() {
	return "Positive/Negative XML Samples";
	}

	@Override
	protected String getRootFileExtension() {
	return ".xml";
	}

	@Override
	protected File genfolder(File modelFolder) {
	return new File(modelFolder, "samples");
	}

	@Override
	protected String toValidFileName(String filename) {
	filename = filename.replace(".", "_").replace(" ", ""); // cosmetics
	filename = filename.replaceAll("[:\\\\/*\"?\|<>']", ""); // remove invalid characters
	return filename;
	}

	/**
	* Generates positive and negative XML test files
	*
	* @param pack
	* @param monitor
	* @throws Exception
	*/
	protected void genAPICode(final Package pack, IProgressMonitor monitor) throws Exception {
	xmlTestFolder = new File(genfolder, "xml");

	monitor.setTaskName("Creating Min/Max Clinical Documents");
	generateMinMaxXMLFiles(pack, monitor);

	monitor.setTaskName("Creating XML test data for properties");
	monitor = new SubProgressMonitor(monitor, 30);
	monitor.beginTask("", CDACommonUtils.getAllContents(pack.eResource(), Constraint.class).size() + CDACommonUtils.getAllContents(pack.eResource(), Class.class).size() + CDACommonUtils.getAllContents(pack.eResource(), Property.class).size());

	for (Constraint constraint : CDACommonUtils.getAllContents(pack.eResource(), Constraint.class)) {
	monitor.worked(1);
	if (constraint.getSpecification() instanceof OpaqueExpression && !constraint.getConstrainedElements().isEmpty() && constraint.getContext() instanceof Class) {
	OpaqueExpression opaqueExpression = (OpaqueExpression) constraint.getSpecification();
	if (!opaqueExpression.getLanguages().isEmpty() && "Analysis".equals(opaqueExpression.getLanguages().get(0))) {
	Element ele = constraint.getConstrainedElements().get(0);
	ele = CDACommonUtils.getMDHTRepresentative((NamedElement) ele);
	EObject eObject = ele;
	while (eObject != null) {
	if (eObject instanceof Class) {
	Class clazz = (Class) eObject;
	List<Property> propertyPath = CDACommonUtils.getPropertyPath(clazz);
	for (Element element : constraint.getConstrainedElements()) {
	if (element instanceof Property) {
	Property property = (Property) element;
	propertyPath.add(property);
	}
	}
	monitor.subTask(constraint.getName());
	File placeholderFolder = new File(xmlTestFolder, "Placeholder");
	creator.forgetLastFileContent();
	creator.initialize(propertyPath);
	creator.flushClinicalDocument(record((Class) constraint.getContext(), new File(placeholderFolder, "Positive"), constraint, "OK"));
	creator.forgetLastFileContent();
	creator.initialize(propertyPath);
	creator.flushClinicalDocument(record((Class) constraint.getContext(), new File(placeholderFolder, "Negative"), constraint, "Fail"));
	break;
	}
	eObject = eObject.eContainer();
	}
	}
	}
	}

	for (Class clazz : CDACommonUtils.getAllContents(pack.eResource(), Class.class)) {
	if (Boolean.parseBoolean(getStereotype(clazz, "noSchematronGen"))) {
	continue;
	}
	monitor.worked(1);
	String templateId = CDACommonUtils.getTemplateId(clazz);
	Property templateIdProperty = creator.getTemplateIdProperty(clazz);
	if (templateId != null && templateIdProperty != null) {
	monitor.subTask(clazz.getName());
	File templateIDsFolder = new File(xmlTestFolder, "TemplateIDs");
	if (creator.initializePath(clazz, templateIdProperty, null, null) != null)
	creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Positive"), templateIdProperty, "OK"));
	if (creator.initializePath(clazz, templateIdProperty, null, templateIdProperty) != null)
	creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Negative"), templateIdProperty, "AttributeValueTest"));
	if (creator.initializePath(clazz, null, templateIdProperty, null) != null)
	creator.flushClinicalDocument(record(clazz, new File(templateIDsFolder, "Negative"), templateIdProperty, "NodeExistenceTest"));
	}

	}

	for (Property property : CDACommonUtils.getAllContents(pack.eResource(), Property.class)) {
	monitor.worked(1);
	if (property.eContainer() instanceof Class) {
	Class clazz = (Class) property.eContainer();
	monitor.subTask(CDACommonUtils.getUmlContext(property));
	if (monitor.isCanceled())
	throw new RuntimeException("Canceled by user");

	if (Boolean.parseBoolean(getStereotype(property, "noSchematronGen"))) {
	continue;
	}
	Property baseProperty = CDACommonUtils.getCDAProperty(property);
	creator.forgetLastFileContent();
	{
	if (creator.initializePath(clazz, property, null, null) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "OK"));
	}
	if (property.getLower() >= 1 && CDACommonUtils.getPropertyForTypeCheck(clazz) != property && CDACommonUtils.getPropertyForCodeOrClasscodeCheck(clazz) != property) {
	if (creator.initializePath(clazz, null, property, null) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "NodeExistenceTest"));
	}
	if ((CDACommonUtils.getDefault(property) != null \|\| CDACommonUtils.getTextValue(property) != null) && CDACommonUtils.getPropertyForTypeCheck(clazz) != property && CDACommonUtils.getPropertyForCodeOrClasscodeCheck(clazz) != property) {
	if (creator.initializePath(clazz, property, null, property) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "NodeValueTest"));
	}
	Property propertyForTypeCheck;
	if (property.getLower() >= 1 && property.getType() instanceof Class && (propertyForTypeCheck = CDACommonUtils.getLeafPropertyForTypeCheck((Class) property.getType())) != null) {
	if (creator.initializePath(clazz, property, null, propertyForTypeCheck) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "Predicated_NodeExistenceTest"));
	}
	if (property.getLower() >= 1 && property.getType() instanceof Class && CDACommonUtils.isDatatypeModel(property.getType()) && baseProperty != null && baseProperty.getType() != property.getType()) {
	if (creator.initializePath(clazz, property, null, property) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "NodeTypeTest"));
	}
	if (property.getUpper() == 0) {
	if (creator.initializePath(clazz, property, null, null) != null)
	creator.flushClinicalDocument(getXMLTestFile(property, "NodeNonExistenceTest"));
	}
	if (property.getUpper() == 1 && baseProperty != null && baseProperty.getUpper() != property.getUpper()) {
	Object child1 = creator.initializePath(clazz, property, null, null);
	if (child1 instanceof EObject) {
	EObject eObject = (EObject) child1;
	Object child2 = creator.repopulateProperty(property, eObject);
	if (child2 instanceof EObject) {
	creator.flushClinicalDocument(getXMLTestFile(property, "NodeNumberTest"));
	} else {
	CDACommonUtils.addStatus(statuses, IStatus.ERROR, getPlugin(), 16, "Cannot re-populate " + CDACommonUtils.getUmlContextDoubled(property), property);
	}
	}
	}

	}
	}

	monitor.done();

	}

	/**
	* Removes trailing digits from the name
	*
	* @param name
	* @return
	*/
	private static String withoutDigits(String name) {
	while (!"".equals(name) && Character.isDigit(name.charAt(name.length() - 1))) {
	name = name.substring(0, name.length() - 1);
	}
	return name;
	}

	/**
	* Copied from ClinicalDocumentCreator.toXMLString() TODO: remove this method
	*
	* @param eObject
	* @param clazz
	* @param options
	* @return
	*/
	public String toXMLString(EObject eObject, Class clazz, Map<String, Object> options) {
	// generate no indentation in e.g. "<title>Adverse Reactions</title>", i.e. keep it in one line
	options.put(XMLResource.OPTION_EXTENDED_META_DATA, BasicExtendedMetaData.INSTANCE);
	options.put(XMLResource.OPTION_ENCODING, "UTF-8");
	String xml;
	try {
	xml = XMLHelperImpl.saveString(options, Arrays.asList(eObject), null, null);
	} catch (Exception e1) {
	e1.printStackTrace();
	return null;
	}

	xml = xml.replace("\"datatypes:", "\"");
	xml = xml.replace("<cda:", "<");
	xml = xml.replace("</cda:", "</");
	xml = xml.replace("Extensions_3.0", "ext");
	xml = xml.replace("xmlns:cda=\"urn:hl7-org:v3\"", "xmlns=\"urn:hl7-org:v3\"");
	String eName = eObject.eClass().getName();
	if (!"ClinicalDocument".equals(eName)) {
	String rootTag = withoutDigits(eName.substring(0, 1).toLowerCase() + eName.substring(1));
	if (eObject.eContainmentFeature() != null) {
	rootTag = eObject.eContainingFeature().getName();
	} else if (clazz != null && CDACommonUtils.getOverallPropertyReference(clazz) != null) {
	Property cdaProperty = CDACommonUtils.getCDAProperty(CDACommonUtils.getOverallPropertyReference(clazz));
	if (cdaProperty != null)
	rootTag = cdaProperty.getName();
	}
	xml = xml.replace("<" + eName, "<" + rootTag);
	xml = xml.replace("</" + eName, "</" + rootTag);

	xml = xml.replace(" xmlns=\"urn:hl7-org:v3\"", "");
	xml = xml.replace(" xmi:version=\"2.0\"", "");
	xml = xml.replace(" xmlns:xmi=\"http://www.omg.org/XMI\"", "");
	xml = xml.replace(" xmlns:datatypes=\"http://www.openhealthtools.org/mdht/uml/hl7/datatypes\"", "");
	xml = xml.replace(" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"", "");
	} else {
	xml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + xml;
	}
	// int index = xml.indexOf("<"+eName);
	// xml = xml.substring(0, index) +
	// "<ClinicalDocument xmlns:ext=\"http://ns.electronichealth.net.au/Ci/Cda/Extensions/3.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns=\"urn:hl7-org:v3\">"
	// + xml.substring(xml.indexOf(">", index) + 1);

	return xml;
	}

	/**
	* Generates a minimum XML test file, a maximum
	*
	* @param pack
	* @param monitor
	* @throws Exception
	*/
	protected void generateMinMaxXMLFiles(final Package pack, IProgressMonitor monitor) throws Exception {

	String uriMap = "";
	// resolve pathmap URIs
	for (Resource res : pack.eResource().getResourceSet().getResources()) {
	URI normURI = res.getResourceSet().getURIConverter().normalize(res.getURI());
	if (!res.getURI().equals(normURI)) {
	uriMap += " " + res.getURI() + " " + normURI;
	// res.setURI(normURI);
	}
	}
	currentCategory.setUriMap(uriMap.trim());

	Collection<Property> propertyPath = new HashSet<Property>();
	for (Class clazz : classes) {
	propertyPath.addAll(CDACommonUtils.getPropertyPath(clazz));
	}

	String pref = specContractedName + "_";

	creator.initialize(Collections.<Property> emptyList());
	creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Min_mdht.xml"));

	creator.initialize(propertyPath);
	creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Max(All_Classes)_mdht.xml"));

	EObject aClinicalDocument = creator.initializeSnippet(this.umlClinicalDocument, CDACommonUtils.getAllContents(irResources, Property.class));
	traceCreatedInstances(pref + "Max(All_Properties)_mdht", aClinicalDocument);

	creator.enableSampleData(true);
	creator.enableSampleDataExpansion(true);
	creator.initialize(Collections.<Property> emptyList());
	creator.flushClinicalDocument(new File(xmlTestFolder, pref + "Sample_mdht.xml"));
	creator.enableSampleData(false);

	}

	/**
	*
	*
	* @param fileName
	* file name without extension - .xmi is appended automatically as it doesn't work with .xml
	* @param aClinicalDocument
	* @throws IOException
	*/
	private void traceCreatedInstances(String fileName, EObject aClinicalDocument) throws IOException {
	trace("Clinical Document instance", umlClinicalDocument, aClinicalDocument);
	currentCategory.setTargetModel(aClinicalDocument);
	for (EObject eObject : CDACommonUtils.getAllContents(Arrays.asList(aClinicalDocument), EObject.class)) {
	Property property = creator.getInitializedByProperty(eObject);
	if (property != null) {
	trace("Property instance", property, eObject);
	}
	Type clazz = creator.getInitializedByClass(eObject);
	if (clazz != null) {
	trace("Class instance", clazz, eObject);
	}
	}
	File file = new File(xmlTestFolder, fileName + ".xmi");
	Map<String, Object> options = new HashMap<String, Object>();
	options.put(XMIResource.OPTION_SCHEMA_LOCATION_IMPLEMENTATION, true);
	String xml = toXMLString(aClinicalDocument, this.umlClinicalDocument, options);
	creator.writeFile(xml, file);
	ResourceSet rSet = new ResourceSetImpl();
	Resource res = rSet.createResource(URI.createFileURI(file.toString()));
	res.getContents().add(aClinicalDocument);
	// options.put(XMIResource.OPTION_SCHEMA_LOCATION, true);
	// options.put(XMLResource.OPTION_EXTENDED_META_DATA, BasicExtendedMetaData.INSTANCE);
	// // options.put(XMLResource.OPTION_ENCODING, "UTF-8");
	// res.save(options);
	}

	private File getXMLTestFile(Property property, String testType) {
	if (!(property.getType() instanceof Class))
	testType = testType.replace("Node", "Attribute");
	Class clazz = (Class) property.eContainer();
	if (testType.contains("OK"))
	return record(clazz, new File(new File(xmlTestFolder, "Properties"), "Positive"), property, testType);
	else
	return record(clazz, new File(new File(xmlTestFolder, "Properties"), "Negative"), property, testType);
	}

	/**
	* Records a XML test file for the given UML element
	*
	* @param element
	* @param result
	* @return
	*/
	private File record(Class context, File parent, NamedElement constrainedElement, String testType) {
	NamedElement element = constrainedElement instanceof Constraint \|\| isTemplateId(constrainedElement) ? context : constrainedElement;
	Collection<File> testTypes = testFilesFor.get(element);
	if (testTypes == null) {
	testFilesFor.put(element, testTypes = new ArrayList<File>());
	}
	String xmlTestFilenameTemplate = getStereotype(constrainedElement.getNearestPackage(), "xmlTestFilenameTemplate");
	String filename = toValidFileName(resolve(xmlTestFilenameTemplate, context, constrainedElement, testType));

	File result = new File(parent, filename + ".xml");
	testTypes.add(result);
	typeOfTestFile.put(result, testType);
	return result;
	}

	private String getTestTypes(Class clazz, NamedElement element, boolean anchor) {
	String result = "";
	Collection<File> testTypes = testFilesFor.get(isTemplateId(element) ? clazz : element);
	if (testTypes != null) {
	for (File file : testTypes) {
	if (anchor)
	result += getAnchor(file, typeOfTestFile.get(file), getEntityMimeType());
	else
	result += " " + typeOfTestFile.get(file);
	}
	}
	return result;
	}

	protected String resolve(String template, Class clazz, NamedElement element) {
	this.template = template;

	if (needResolve("{test-types-covered}", clazz, element))
	resolve(getTestTypes(clazz, element, false));
	if (needResolve("{test-file-anchors}", clazz, element))
	resolve(getTestTypes(clazz, element, true));

	return super.resolve(this.template, clazz, element);
	}

	@Override
	protected OCLTransformation<Package, Classifier, ?, Property, ?, ?, ?, ?, ?, ?, ?, ?> createTrafo(ResourceSet resourceSet) {
	return null;

	}

	@Override
	protected String getEntityMimeType() {
	return "text/xml";
	}

	}