private static SAXParserFactory createFastSAXParserFactory()
throws ParserConfigurationException, SAXException {
if (fastParserFactoryClass == null) {
try {
fastParserFactoryClass =
Class.forName("org.apache.crimson.jaxp.SAXParserFactoryImpl"); // NOI18N
} catch (Exception ex) {
useFastSAXParserFactory = false;
if (System.getProperty("java.version").startsWith("1.4")) { // NOI18N
ErrorManager.getDefault().notify(ErrorManager.INFORMATIONAL, ex);
}
}
}
if (fastParserFactoryClass != null) {
try {
SAXParserFactory factory = (SAXParserFactory) fastParserFactoryClass.newInstance();
return factory;
} catch (Exception ex) {
useFastSAXParserFactory = false;
throw new ParserConfigurationException(ex.getMessage());
}
}
return SAXParserFactory.newInstance();
}
/**
* Examines a property's type to see which method should be used to parse the property's value.
*
* @param desc The description of the property
* @param value The value of the XML attribute containing the prop value
* @return The value stored in the element
* @throws IOException If there is an error reading the document
*/
public Object getObjectValue(PropertyDescriptor desc, String value) throws IOException {
// Find out what kind of property it is
Class type = desc.getPropertyType();
// If it's an array, get the base type
if (type.isArray()) {
type = type.getComponentType();
}
// For native types, object wrappers for natives, and strings, use the
// basic parse routine
if (type.equals(Integer.TYPE)
|| type.equals(Long.TYPE)
|| type.equals(Short.TYPE)
|| type.equals(Byte.TYPE)
|| type.equals(Boolean.TYPE)
|| type.equals(Float.TYPE)
|| type.equals(Double.TYPE)
|| Integer.class.isAssignableFrom(type)
|| Long.class.isAssignableFrom(type)
|| Short.class.isAssignableFrom(type)
|| Byte.class.isAssignableFrom(type)
|| Boolean.class.isAssignableFrom(type)
|| Float.class.isAssignableFrom(type)
|| Double.class.isAssignableFrom(type)) {
return parseBasicType(type, value);
} else if (String.class.isAssignableFrom(type)) {
return value;
} else if (java.util.Date.class.isAssignableFrom(type)) {
// If it's a date, use the date parser
return parseDate(value, JOXDateHandler.determineDateFormat());
} else {
return null;
}
}
Document parseDocument(String filename) throws Exception {
FileReader reader = new FileReader(filename);
String firstLine = new BufferedReader(reader).readLine();
reader.close();
Document document = null;
if (firstLine.startsWith("<?xml")) {
System.err.println("XML detected; using default XML parser.");
} else {
try {
Class nekoParserClass = Class.forName("org.cyberneko.html.parsers.DOMParser");
Object parser = nekoParserClass.newInstance();
Method parse = nekoParserClass.getMethod("parse", new Class[] {String.class});
Method getDocument = nekoParserClass.getMethod("getDocument", new Class[0]);
parse.invoke(parser, filename);
document = (Document) getDocument.invoke(parser);
} catch (Exception e) {
System.err.println("NekoHTML HTML parser not found; HTML4 support disabled.");
}
}
if (document == null) {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
try { // http://www.w3.org/blog/systeam/2008/02/08/w3c_s_excessive_dtd_traffic
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
} catch (ParserConfigurationException e) {
System.err.println("Warning: Could not disable external DTD loading");
}
DocumentBuilder builder = factory.newDocumentBuilder();
document = builder.parse(filename);
}
return document;
}
@SuppressWarnings("unchecked")
public void addDefaultValue(String className, JSONObject oper) throws Exception {
ObjectMapper defaultValueMapper = ObjectMapperFactory.getOperatorValueSerializer();
Class<? extends Operator> clazz = (Class<? extends Operator>) classLoader.loadClass(className);
if (clazz != null) {
Operator operIns = clazz.newInstance();
String s = defaultValueMapper.writeValueAsString(operIns);
oper.put("defaultValue", new JSONObject(s).get(className));
}
}
private static InputSource getConfigSource(Class pAppClass) throws DataNotFoundException {
URL resource = pAppClass.getResource(CONFIG_FILE_NAME);
String resourceFileName = resource.toExternalForm();
File resourceFile = new File(resourceFileName);
InputStream configResourceStream = pAppClass.getResourceAsStream(CONFIG_FILE_NAME);
if (null == configResourceStream) {
throw new DataNotFoundException(
"unable to find XML configuration file resource: "
+ CONFIG_FILE_NAME
+ " for class: "
+ pAppClass.getName());
}
InputSource inputSource = new InputSource(configResourceStream);
if (!resourceFile.exists()) {
inputSource.setSystemId(resourceFileName);
}
return (inputSource);
}
static <T> T set(Class<T> interf, Object value) {
Properties p = new Properties();
Method ms[] = interf.getMethods();
for (Method m : ms) {
p.put(m.getName(), value);
}
return Configurable.createConfigurable(interf, (Map<Object, Object>) p);
}
public JSONObject describeClass(Class<?> clazz) throws Exception {
JSONObject desc = new JSONObject();
desc.put("name", clazz.getName());
if (clazz.isEnum()) {
@SuppressWarnings("unchecked")
Class<Enum<?>> enumClass = (Class<Enum<?>>) clazz;
ArrayList<String> enumNames = Lists.newArrayList();
for (Enum<?> e : enumClass.getEnumConstants()) {
enumNames.add(e.name());
}
desc.put("enum", enumNames);
}
UI_TYPE ui_type = UI_TYPE.getEnumFor(clazz);
if (ui_type != null) {
desc.put("uiType", ui_type.getName());
}
desc.put("properties", getClassProperties(clazz, 0));
return desc;
}
static {
try {
// Create factory
documentBuilderFactory =
(DocumentBuilderFactory)
Class.forName("orbeon.apache.xerces.jaxp.DocumentBuilderFactoryImpl").newInstance();
// Configure factory
documentBuilderFactory.setNamespaceAware(true);
} catch (Exception e) {
throw new OXFException(e);
}
}
/**
* Reads an string into a basic type
*
* @param type The type of the string to read
* @param str The string containing the value
* @return The parsed value of the string
*/
public static Object parseBasicType(Class type, String str) {
// Parse the text based on the property type
if (type.equals(Integer.TYPE) || Integer.class.isAssignableFrom(type)) {
return new Integer(str);
} else if (type.equals(Long.TYPE) || Long.class.isAssignableFrom(type)) {
return new Long(str);
} else if (type.equals(Short.TYPE) || Short.class.isAssignableFrom(type)) {
return new Short(str);
} else if (type.equals(Byte.TYPE) || Byte.class.isAssignableFrom(type)) {
return new Byte(str);
} else if (type.equals(Boolean.TYPE) || Boolean.class.isAssignableFrom(type)) {
return new Boolean(str);
} else if (type.equals(Float.TYPE) || Float.class.isAssignableFrom(type)) {
return new Float(str);
} else if (type.equals(Double.TYPE) || Double.class.isAssignableFrom(type)) {
return new Double(str);
}
return null;
}
/**
* XML Circuit constructor
*
* @param file the file that contains the XML description of the circuit
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
this("");
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
Document doc;
Element root;
Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();
try {
builder = factory.newDocumentBuilder();
doc = builder.parse(file);
} catch (SAXException sxe) {
throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
} catch (ParserConfigurationException pce) {
throw new CircuitLoadingException(
"Parser exception raised, parser configuration is invalid.");
} catch (IOException ioe) {
throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
}
root = (Element) doc.getElementsByTagName("Circuit").item(0);
this.setName(root.getAttribute("name"));
NodeList nl = root.getElementsByTagName("Node");
Element e;
Node n;
Class cl;
for (int i = 0; i < nl.getLength(); ++i) {
e = (Element) nl.item(i);
try {
cl = Class.forName(e.getAttribute("class"));
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
try {
n = ((Node) cl.newInstance());
} catch (Exception exc) {
System.err.println(exc.getMessage());
throw new RuntimeException("Circuit creation from xml.");
}
this.nodes.add(n);
n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));
if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));
if (n instanceof giraffe.ui.CompositeNode) {
try {
((CompositeNode) n)
.load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
} catch (Exception exc) {
/* try to load from the lib */
((CompositeNode) n)
.load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
}
}
NodeList nlist = e.getElementsByTagName("Anchor");
Element el;
for (int j = 0; j < nlist.getLength(); ++j) {
el = (Element) nlist.item(j);
Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
NodeList linklist = el.getElementsByTagName("Link");
Element link;
Link l;
for (int k = 0; k < linklist.getLength(); ++k) {
link = (Element) linklist.item(k);
int id = new Integer(link.getAttribute("id"));
int index = new Integer(link.getAttribute("index"));
if (id >= this.linkID) linkID = id + 1;
if (linkstable.containsKey(id)) {
l = linkstable.get(id);
l.addLinkedAnchorAt(a, index);
a.addLink(l);
} else {
l = new Link(id);
l.addLinkedAnchorAt(a, index);
this.links.add(l);
linkstable.put(id, l);
a.addLink(l);
}
}
}
}
}
private JSONArray getClassProperties(Class<?> clazz, int level) throws IntrospectionException {
JSONArray arr = new JSONArray();
TypeDiscoverer td = new TypeDiscoverer();
try {
for (PropertyDescriptor pd : Introspector.getBeanInfo(clazz).getPropertyDescriptors()) {
Method readMethod = pd.getReadMethod();
if (readMethod != null) {
if (readMethod.getDeclaringClass() == java.lang.Enum.class) {
// skip getDeclaringClass
continue;
} else if ("class".equals(pd.getName())) {
// skip getClass
continue;
}
} else {
// yields com.datatorrent.api.Context on JDK6 and
// com.datatorrent.api.Context.OperatorContext with JDK7
if ("up".equals(pd.getName())
&& com.datatorrent.api.Context.class.isAssignableFrom(pd.getPropertyType())) {
continue;
}
}
// LOG.info("name: " + pd.getName() + " type: " + pd.getPropertyType());
Class<?> propertyType = pd.getPropertyType();
if (propertyType != null) {
JSONObject propertyObj = new JSONObject();
propertyObj.put("name", pd.getName());
propertyObj.put("canGet", readMethod != null);
propertyObj.put("canSet", pd.getWriteMethod() != null);
if (readMethod != null) {
for (Class<?> c = clazz; c != null; c = c.getSuperclass()) {
OperatorClassInfo oci = classInfo.get(c.getName());
if (oci != null) {
MethodInfo getMethodInfo = oci.getMethods.get(readMethod.getName());
if (getMethodInfo != null) {
addTagsToProperties(getMethodInfo, propertyObj);
break;
}
}
}
// type can be a type symbol or parameterized type
td.setTypeArguments(clazz, readMethod.getGenericReturnType(), propertyObj);
} else {
if (pd.getWriteMethod() != null) {
td.setTypeArguments(
clazz, pd.getWriteMethod().getGenericParameterTypes()[0], propertyObj);
}
}
// if (!propertyType.isPrimitive() && !propertyType.isEnum() && !propertyType.isArray() &&
// !propertyType.getName().startsWith("java.lang") && level < MAX_PROPERTY_LEVELS) {
// propertyObj.put("properties", getClassProperties(propertyType, level + 1));
// }
arr.put(propertyObj);
}
}
} catch (JSONException ex) {
throw new RuntimeException(ex);
}
return arr;
}
/**
* Examines a property's type to see which method should be used to parse the property's value.
*
* @param desc The description of the property
* @param element The XML element containing the property value
* @return The value stored in the element
* @throws IOException If there is an error reading the document
*/
public Object getObjectValue(PropertyDescriptor desc, Element element) throws IOException {
// Find out what kind of property it is
Class type = desc.getPropertyType();
// If it's an array, get the base type
if (type.isArray()) {
type = type.getComponentType();
}
// For native types, object wrappers for natives, and strings, use the
// basic parse routine
if (type.equals(Integer.TYPE)
|| type.equals(Long.TYPE)
|| type.equals(Short.TYPE)
|| type.equals(Byte.TYPE)
|| type.equals(Boolean.TYPE)
|| type.equals(Float.TYPE)
|| type.equals(Double.TYPE)
|| Integer.class.isAssignableFrom(type)
|| Long.class.isAssignableFrom(type)
|| Short.class.isAssignableFrom(type)
|| Byte.class.isAssignableFrom(type)
|| Boolean.class.isAssignableFrom(type)
|| Float.class.isAssignableFrom(type)
|| Double.class.isAssignableFrom(type)
|| String.class.isAssignableFrom(type)) {
return readBasicType(type, element);
} else if (java.util.Date.class.isAssignableFrom(type)) {
// If it's a date, use the date parser
return readDate(element);
} else {
try {
// If it's an object, create a new instance of the object (it should
// be a bean, or there will be trouble)
Object newOb = type.newInstance();
// Copy the XML element into the bean
readObject(newOb, element);
return newOb;
} catch (InstantiationException exc) {
throw new IOException(
"Error creating object for " + desc.getName() + ": " + exc.toString());
} catch (IllegalAccessException exc) {
throw new IOException(
"Error creating object for " + desc.getName() + ": " + exc.toString());
}
}
}
/**
* Unmarshall a Chromosome instance from a given XML Element representation.
*
* @param a_activeConfiguration current Configuration object
* @param a_xmlElement the XML Element representation of the Chromosome
* @return a new Chromosome instance setup with the data from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws UnsupportedRepresentationException if the actively configured Gene implementation does
* not support the string representation of the alleles used in the given XML document
* @throws GeneCreationException if there is a problem creating or populating a Gene instance
* @author Neil Rotstan
* @since 1.0
*/
public static Gene[] getGenesFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, UnsupportedRepresentationException, GeneCreationException {
// Do some sanity checking. Make sure the XML Element isn't null and
// that it in fact represents a set of genes.
// -----------------------------------------------------------------
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENES_TAG))) {
throw new ImproperXMLException(
"Unable to build Chromosome instance from XML Element: "
+ "given Element is not a 'genes' element.");
}
List genes = Collections.synchronizedList(new ArrayList());
// Extract the nested gene elements.
// ---------------------------------
NodeList geneElements = a_xmlElement.getElementsByTagName(GENE_TAG);
if (geneElements == null) {
throw new ImproperXMLException(
"Unable to build Gene instances from XML Element: "
+ "'"
+ GENE_TAG
+ "'"
+ " sub-elements not found.");
}
// For each gene, get the class attribute so we know what class
// to instantiate to represent the gene instance, and then find
// the child text node, which is where the string representation
// of the allele is located, and extract the representation.
// -------------------------------------------------------------
int numberOfGeneNodes = geneElements.getLength();
for (int i = 0; i < numberOfGeneNodes; i++) {
Element thisGeneElement = (Element) geneElements.item(i);
thisGeneElement.normalize();
// Fetch the class attribute and create an instance of that
// class to represent the current gene.
// --------------------------------------------------------
String geneClassName = thisGeneElement.getAttribute(CLASS_ATTRIBUTE);
Gene thisGeneObject;
Class geneClass = null;
try {
geneClass = Class.forName(geneClassName);
try {
Constructor constr = geneClass.getConstructor(new Class[] {Configuration.class});
thisGeneObject = (Gene) constr.newInstance(new Object[] {a_activeConfiguration});
} catch (NoSuchMethodException nsme) {
// Try it by calling method newGeneInternal.
// -----------------------------------------
Constructor constr = geneClass.getConstructor(new Class[] {});
thisGeneObject = (Gene) constr.newInstance(new Object[] {});
thisGeneObject =
(Gene)
PrivateAccessor.invoke(
thisGeneObject, "newGeneInternal", new Class[] {}, new Object[] {});
}
} catch (Throwable e) {
throw new GeneCreationException(geneClass, e);
}
// Find the text node and fetch the string representation of
// the allele.
// ---------------------------------------------------------
NodeList children = thisGeneElement.getChildNodes();
int childrenSize = children.getLength();
String alleleRepresentation = null;
for (int j = 0; j < childrenSize; j++) {
Element alleleElem = (Element) children.item(j);
if (alleleElem.getTagName().equals(ALLELE_TAG)) {
alleleRepresentation = alleleElem.getAttribute("value");
}
if (children.item(j).getNodeType() == Node.TEXT_NODE) {
// We found the text node. Extract the representation.
// ---------------------------------------------------
alleleRepresentation = children.item(j).getNodeValue();
break;
}
}
// Sanity check: Make sure the representation isn't null.
// ------------------------------------------------------
if (alleleRepresentation == null) {
throw new ImproperXMLException(
"Unable to build Gene instance from XML Element: "
+ "value (allele) is missing representation.");
}
// Now set the value of the gene to that reflect the
// string representation.
// -------------------------------------------------
try {
thisGeneObject.setValueFromPersistentRepresentation(alleleRepresentation);
} catch (UnsupportedOperationException e) {
throw new GeneCreationException(
"Unable to build Gene because it does not support the "
+ "setValueFromPersistentRepresentation() method.");
}
// Finally, add the current gene object to the list of genes.
// ----------------------------------------------------------
genes.add(thisGeneObject);
}
return (Gene[]) genes.toArray(new Gene[genes.size()]);
}
