stragglers...

src/main/java/org/mitre/stix/Utilities.java

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+/**
+ * Copyright (c) 2015, The MITRE Corporation. All rights reserved.
+ * See LICENSE for complete terms.
+ */
+package org.mitre.stix;
+
+import java.io.ByteArrayOutputStream;
+import java.io.UnsupportedEncodingException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.logging.Logger;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.annotation.XmlSchema;
+import javax.xml.namespace.QName;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.w3c.dom.bootstrap.DOMImplementationRegistry;
+import org.w3c.dom.ls.DOMImplementationLS;
+import org.w3c.dom.ls.LSOutput;
+import org.w3c.dom.ls.LSSerializer;
+
+/**
+ * A collection of utility helper methods.
+ * 
+ * @author nemonik (Michael Joseph Walsh <github.com@nemonik.com>)
+ */
+public class Utilities {
+
+	@SuppressWarnings("unused")
+	private static final Logger LOGGER = Logger.getLogger(Utilities.class
+			.getName());
+
+	private static final String XML_SCHEMA_INSTANCE = "http://www.w3.org/2001/XMLSchema-instance";
+	private static final String XML_NAMESPACE = "http://www.w3.org/2000/xmlns/";
+
+	private interface ElementVisitor {
+
+		void visit(Element element);
+
+	}
+
+	/**
+	 * Used to transverse an XML document.
+	 * 
+	 * @param element
+	 * @param visitor
+	 */
+	private final static void traverse(Element element, ElementVisitor visitor) {
+
+		visitor.visit(element);
+
+		NodeList children = element.getChildNodes();
+
+		for (int i = 0; i < children.getLength(); i++) {
+			Node node = children.item(i);
+
+			if (node.getNodeType() != Node.ELEMENT_NODE)
+				continue;
+
+			traverse((Element) node, visitor);
+		}
+	}
+
+	/**
+	 * Returns a String for a JAXBElement
+	 * 
+	 * @param jaxbElement
+	 * @return
+	 */
+	public static String getXMLString(JAXBElement<?> jaxbElement) {
+		return getXMLString(jaxbElement, true);
+	}
+
+	/**
+	 * Returns a String for a JAXBElement
+	 * 
+	 * @param jaxbElement
+	 * @param prettyPrint
+	 * @return
+	 */
+	public static String getXMLString(JAXBElement<?> jaxbElement, boolean prettyPrint) {
+
+		try {
+	        Document document = DocumentBuilderFactory
+	                .newInstance().newDocumentBuilder().newDocument();
+
+	        JAXBContext jaxbContext = JAXBContext
+	                .newInstance(jaxbElement.getDeclaredType().getPackage().getName());
+
+	        Marshaller marshaller = jaxbContext.createMarshaller();
+
+	        marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT,
+	                true);
+
+	        marshaller
+	                .setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
+
+	        try {
+	            marshaller.marshal(jaxbElement, document);
+	        } catch (JAXBException e) {
+	            // otherwise handle non-XMLRootElements
+	            QName qualifiedName = new QName(
+	                    Utilities.getnamespaceURI(jaxbElement), jaxbElement.getClass().getSimpleName());
+
+	            @SuppressWarnings({ "rawtypes", "unchecked" })
+	            JAXBElement root = new JAXBElement(
+	                    qualifiedName, jaxbElement.getClass(), jaxbElement);
+
+	            marshaller.marshal(root, document);
+	        }
+
+	        Utilities.removeUnusedNamespaces(document);
+
+	        return Utilities.getXMLString(document, prettyPrint);
+
+		} catch (ParserConfigurationException e) {
+			throw new RuntimeException(e);
+		} catch (JAXBException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	/**
+	 * Returns a String for a Document.
+	 * 
+	 * @param document
+	 * @return
+	 */
+	public static String getXMLString(Document document) {
+		return getXMLString(document, true);
+	}
+
+	/**
+	 * Returns a String for a Document.
+	 * 
+	 * @param document
+	 * @param prettyPrint
+	 * @return
+	 */
+	public static String getXMLString(Document document, boolean prettyPrint) {
+
+		try {
+			DOMImplementationRegistry registry = DOMImplementationRegistry
+					.newInstance();
+			DOMImplementationLS domImplementationLS = (DOMImplementationLS) registry
+					.getDOMImplementation("LS");
+			LSSerializer serializaer = domImplementationLS.createLSSerializer();
+
+			if (prettyPrint) {
+				serializaer.getDomConfig().setParameter("format-pretty-print",
+						Boolean.TRUE);
+				serializaer.getDomConfig().setParameter("xml-declaration",
+						Boolean.TRUE);
+			}
+
+			// otherwise UTF-16 is used by default
+			LSOutput lsOutput = domImplementationLS.createLSOutput();
+			lsOutput.setEncoding("UTF-8");
+			ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
+			lsOutput.setByteStream(byteStream);
+
+			serializaer.write(document, lsOutput);
+
+			return new String(byteStream.toByteArray(), "UTF-8");
+
+		} catch (ClassNotFoundException e) {
+			throw new RuntimeException(e);
+		} catch (InstantiationException e) {
+			throw new RuntimeException(e);
+		} catch (IllegalAccessException e) {
+			throw new RuntimeException(e);
+		} catch (ClassCastException e) {
+			throw new RuntimeException(e);
+		} catch (UnsupportedEncodingException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	/**
+	 * JAXB adds all namespaces known by the JAXBContext to the root element of
+	 * the XML document for performance reasons as per JAXB-103
+	 * (http://java.net/
+	 * jira/browse/JAXB-103?focusedCommentId=64411&page=com.atlassian
+	 * .jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_64411).
+	 * 
+	 * This helper method based on Reboot's
+	 * (http://stackoverflow.com/users/392730/reboot) response to a
+	 * stackoverflow question on the subject will prune down the namespaces to
+	 * only those used.
+	 * 
+	 * @param document
+	 * @param class1 
+	 * @param string 
+	 */
+	public static void removeUnusedNamespaces(Document document) {
+
+		final Set<String> namespaces = new HashSet<String>();
+
+		Element element = document.getDocumentElement();
+
+		traverse(element, new ElementVisitor() {
+
+			public void visit(Element element) {
+
+				String namespace = element.getNamespaceURI();
+
+				if (namespace == null)
+					namespace = "";
+
+				namespaces.add(namespace);
+
+				NamedNodeMap attributes = element.getAttributes();
+
+				for (int i = 0; i < attributes.getLength(); i++) {
+					Node attribute = attributes.item(i);
+
+					if (XML_NAMESPACE.equals(attribute.getNamespaceURI())) {
+						continue;
+					}
+
+					String prefix;
+
+					if (XML_SCHEMA_INSTANCE.equals(attribute.getNamespaceURI())) {
+						if ("type".equals(attribute.getLocalName())) {
+							String value = attribute.getNodeValue();
+
+							if (value.contains(":")) {
+								prefix = value.substring(0, value.indexOf(":"));
+							} else {
+								prefix = null;
+							}
+						} else {
+							continue;
+						}
+					} else {
+						String value = attribute.getNodeValue();
+
+						if (value.contains(":")) {
+							prefix = value.substring(0, value.indexOf(":"));
+						} else {
+							prefix = attribute.getPrefix();
+						}
+					}
+
+					namespace = element.lookupNamespaceURI(prefix);
+
+					if (namespace == null) {
+						continue;
+					}
+
+					namespaces.add(namespace);
+				}
+			}
+
+		});
+
+		traverse(element, new ElementVisitor() {
+
+			public void visit(Element element) {
+
+				Set<String> removeLocalNames = new HashSet<String>();
+
+				NamedNodeMap attributes = element.getAttributes();
+
+				for (int i = 0; i < attributes.getLength(); i++) {
+					Node attribute = attributes.item(i);
+
+					if (!XML_NAMESPACE.equals(attribute.getNamespaceURI())) {
+						continue;
+					}
+
+					if (namespaces.contains(attribute.getNodeValue())) {
+						continue;
+					}
+
+					removeLocalNames.add(attribute.getLocalName());
+				}
+
+				for (String localName : removeLocalNames) {
+					element.removeAttributeNS(XML_NAMESPACE, localName);
+				}
+			}
+
+		});
+	}
+
+	/**
+	 * Pull the namespace URI from the package for the class of the object.
+	 * 
+	 * @param obj
+	 * @return
+	 */
+	public static String getnamespaceURI(Object obj) {
+
+		Package pkg = obj.getClass().getPackage();
+
+		XmlSchema xmlSchemaAnnotation = pkg.getAnnotation(XmlSchema.class);
+
+		return xmlSchemaAnnotation.namespace();
+	}
+}

src/main/java/org/mitre/stix/ValidationErrorHandler.java

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+/**
+ * Copyright (c) 2015, The MITRE Corporation. All rights reserved.
+ * See LICENSE for complete terms.
+ */
+package org.mitre.stix;
+
+import org.xml.sax.ErrorHandler;
+import org.xml.sax.SAXParseException;
+import org.xml.sax.SAXException;
+
+/**
+ * Parsing and validating error handler
+ * 
+ * @author nemonik (Michael Joseph Walsh <github.com@nemonik.com>) *
+ */
+public class ValidationErrorHandler implements ErrorHandler {
+
+	private void log(String type, SAXParseException e) {
+		System.err.println("SAXParseException " + type);
+		System.err.println("  Public ID: " + e.getPublicId());
+		System.err.println("  System ID: " + e.getSystemId());
+		System.err.println("  Line     : " + e.getLineNumber());
+		System.err.println("  Column   : " + e.getColumnNumber());
+		System.err.println("  Message  : " + e.getMessage());
+	}
+
+	/* (non-Javadoc)
+	 * @see org.xml.sax.ErrorHandler#error(org.xml.sax.SAXParseException)
+	 */
+	@Override
+	public void error(SAXParseException e) throws SAXException {
+		log("ERROR", e);
+		throw e;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.xml.sax.ErrorHandler#fatalError(org.xml.sax.SAXParseException)
+	 */
+	@Override
+	public void fatalError(SAXParseException e) throws SAXException {
+		log("FATAL ERROR", e);
+		throw e;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.xml.sax.ErrorHandler#warning(org.xml.sax.SAXParseException)
+	 */
+	@Override
+	public void warning(SAXParseException e) throws SAXException {
+		log("WARNING", e);
+		throw e;
+	}
+}

src/main/java/org/mitre/stix/package-info.java

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+/**
+ * Contains convenience and utility classes.
+
+ * @author nemonik (Michael Joseph Walsh <github.com@nemonik.com>)
+ */
+package org.mitre.stix;