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();
}
/** For internal use only. */
private static Object makeDerivedWrapper(Element elt, String baseTypeName) {
synchronized (DOMUtils.getDOMLock(elt)) {
QName typeName = XArchUtils.getXSIType(elt);
if (typeName == null) {
return null;
} else {
if (!DOMUtils.hasXSIType(
elt, "http://www.ics.uci.edu/pub/arch/xArch/changesets.xsd", baseTypeName)) {
try {
String packageTitle = XArchUtils.getPackageTitle(typeName.getNamespaceURI());
String packageName = XArchUtils.getPackageName(packageTitle);
String implName = XArchUtils.getImplName(packageName, typeName.getName());
Class c = Class.forName(implName);
java.lang.reflect.Constructor con = c.getConstructor(new Class[] {Element.class});
Object o = con.newInstance(new Object[] {elt});
return o;
} catch (Exception e) {
// Lots of bad things could happen, but this
// is OK, because this is best-effort anyway.
}
}
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;
}
/**
* @param args 1. rddl description file name (can be directory), in RDDL format, with complete
* path 2. (optional) port number 3. (optional) random seed
*/
public static void main(String[] args) {
// StateViz state_viz = new GenericScreenDisplay(true);
StateViz state_viz = new NullScreenDisplay(false);
ArrayList<RDDL> rddls = new ArrayList<RDDL>();
int port = PORT_NUMBER;
if (args.length < 1) {
System.out.println(
"usage: rddlfilename (optional) portnumber random-seed state-viz-class-name");
System.out.println("\nexample 1: Server rddlfilename");
System.out.println("example 2: Server rddlfilename 2323");
System.out.println("example 3: Server rddlfilename 2323 0 rddl.viz.GenericScreenDisplay");
System.exit(1);
}
try {
// Load RDDL files
RDDL rddl = new RDDL();
File f = new File(args[0]);
if (f.isDirectory()) {
for (File f2 : f.listFiles())
if (f2.getName().endsWith(".rddl")) {
System.out.println("Loading: " + f2);
rddl.addOtherRDDL(parser.parse(f2));
}
} else rddl.addOtherRDDL(parser.parse(f));
if (args.length > 1) {
port = Integer.valueOf(args[1]);
}
ServerSocket socket1 = new ServerSocket(port);
if (args.length > 2) {
Server.rand = new Random(Integer.valueOf(args[2]));
} else {
Server.rand = new Random(DEFAULT_SEED);
}
if (args.length > 3) {
state_viz = (StateViz) Class.forName(args[3]).newInstance();
}
System.out.println("RDDL Server Initialized");
while (true) {
Socket connection = socket1.accept();
Runnable runnable = new Server(connection, ++ID, rddl, state_viz);
Thread thread = new Thread(runnable);
thread.start();
}
} catch (Exception e) {
// TODO Auto-generated catch block
System.out.println(e);
e.printStackTrace();
}
}
/** This method generates the output given a context and output stream */
public boolean generate(XPathContext context, ProgramWriter out) {
try {
String collectionName = Strings.firstUpper(collection.getName());
if (ejb) {
out.print(" \n\t/**\n\t * @ejb:interface-method\n\t */");
}
out.print(" \n\tpublic java.util.Collection get");
out.print(collectionName);
out.print("() {");
if (ejb) {
out.print(
" \n\t\tboolean cmtActivated = false;\n\t\tif (!org.openxava.hibernate.XHibernate.isCmt()) {\n\t\t\torg.openxava.hibernate.XHibernate.setCmt(true);\n\t\t\tcmtActivated = true;\n\t\t}");
}
out.print(" \n\t\ttry {");
MetaCalculator calculator = collection.getMetaCalculator();
String calculatorClass = calculator.getClassName();
out.print(" \t\t\n\t\t\t");
out.print(calculatorClass);
out.print(" ");
out.print(collection.getName());
out.print("Calculator= (");
out.print(calculatorClass);
out.print(")\n\t\t\t\tgetMetaModel().getMetaCollection(\"");
out.print(collection.getName());
out.print("\").getMetaCalculator().createCalculator();");
Iterator itSets = calculator.getMetaSetsWithoutValue().iterator();
while (itSets.hasNext()) {
MetaSet set = (MetaSet) itSets.next();
String propertyNameInCalculator = Strings.firstUpper(set.getPropertyName());
String propertyNameFrom = set.getPropertyNameFrom();
MetaProperty p = metaModel.getMetaProperty(propertyNameFrom);
if (propertyNameFrom.indexOf('.') >= 0) {
if (p.isKey() || p.getMetaModel() instanceof MetaAggregate) {
propertyNameFrom = Strings.firstUpper(Strings.change(propertyNameFrom, ".", "_"));
} else {
StringTokenizer st = new StringTokenizer(propertyNameFrom, ".");
String ref = st.nextToken();
String pro = st.nextToken();
propertyNameFrom = Strings.firstUpper(ref) + "().get" + Strings.firstUpper(pro);
}
} else {
propertyNameFrom = Strings.firstUpper(propertyNameFrom);
}
String getPropertyFrom = "boolean".equals(p.getTypeName()) ? "is" : "get";
String value = set.getValue();
if (set.hasValue()) {
out.print(" \n\t\t\t");
out.print(collection.getName());
out.print("Calculator.set");
out.print(propertyNameInCalculator);
out.print("(\"");
out.print(value);
out.print("\");");
} else {
out.print(" \t\n\t\t\t");
out.print(collection.getName());
out.print("Calculator.set");
out.print(propertyNameInCalculator);
out.print("(");
out.print(getPropertyFrom);
out.print(propertyNameFrom);
out.print("());");
}
} // else/sets
if (IModelCalculator.class.isAssignableFrom(Class.forName(calculatorClass))) {
out.print(" \n\t\t\t\t");
out.print(collection.getName());
out.print("Calculator.setModel(this);");
}
if (IEntityCalculator.class.isAssignableFrom(Class.forName(calculatorClass))) {
out.print(" \n\t\t\t\t");
out.print(collection.getName());
out.print("Calculator.setEntity(this);");
}
if (IJDBCCalculator.class.isAssignableFrom(Class.forName(calculatorClass))) {
out.print(" \n\t\t\t\t");
out.print(collection.getName());
out.print("Calculator.setConnectionProvider(getPortableContext());");
}
String calculateValueSentence = collection.getName() + "Calculator.calculate()";
out.print(" \n\t\t\treturn ");
out.print(Generators.generateCast("java.util.Collection", calculateValueSentence));
out.print(
";\n\t\t}\n\t\tcatch (Exception ex) {\n\t\t\tex.printStackTrace();\n\t\t\tthrow new ");
out.print(getException());
out.print("(XavaResources.getString(\"generator.calculate_value_error\", \"");
out.print(collection.getName());
out.print("\", \"");
out.print(metaModel.getName());
out.print("\", ex.getLocalizedMessage()));\n\t\t}");
if (ejb) {
out.print(
" \n\t\tfinally {\n\t\t\tif (cmtActivated) {\n\t\t\t\torg.openxava.hibernate.XHibernate.setCmt(false);\n\t\t\t}\n\t\t}");
}
out.print(" \t\t\t\t\n\t}");
} catch (Exception e) {
System.out.println("Exception: " + e.getMessage());
e.printStackTrace();
return false;
}
return true;
}
/**
* 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);
}
}
}
}
}
/**
* Read a catalog from an input stream.
*
* <p>This class reads a catalog from an input stream:
*
* <ul>
* <li>Based on the QName of the root element, it determines which parser to instantiate for
* this catalog.
* <li>It constructs a DOM Document from the catalog and
* <li>For each child of the root node, it calls the parser's parseCatalogEntry method. This
* method is expected to make appropriate calls back into the catalog to add entries for the
* entries in the catalog. It is free to do this in whatever manner is appropriate (perhaps
* using just the node passed in, perhaps wandering arbitrarily throughout the tree).
* </ul>
*
* @param catalog The catalog for which this reader is called.
* @param is The input stream that is to be read.
* @throws IOException if the URL cannot be read.
* @throws UnknownCatalogFormatException if the catalog format is not recognized.
* @throws UnparseableCatalogException if the catalog cannot be parsed. (For example, if it is
* supposed to be XML and isn't well-formed or if the parser class cannot be instantiated.)
*/
public void readCatalog(Catalog catalog, InputStream is) throws IOException, CatalogException {
DocumentBuilderFactory factory = null;
DocumentBuilder builder = null;
factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(false);
factory.setValidating(false);
try {
builder = factory.newDocumentBuilder();
} catch (ParserConfigurationException pce) {
throw new CatalogException(CatalogException.UNPARSEABLE);
}
Document doc = null;
try {
doc = builder.parse(is);
} catch (SAXException se) {
throw new CatalogException(CatalogException.UNKNOWN_FORMAT);
}
Element root = doc.getDocumentElement();
String namespaceURI = Namespaces.getNamespaceURI(root);
String localName = Namespaces.getLocalName(root);
String domParserClass = getCatalogParser(namespaceURI, localName);
if (domParserClass == null) {
if (namespaceURI == null) {
catalog.getCatalogManager().debug.message(1, "No Catalog parser for " + localName);
} else {
catalog
.getCatalogManager()
.debug
.message(1, "No Catalog parser for " + "{" + namespaceURI + "}" + localName);
}
return;
}
DOMCatalogParser domParser = null;
try {
domParser = (DOMCatalogParser) Class.forName(domParserClass).newInstance();
} catch (ClassNotFoundException cnfe) {
catalog
.getCatalogManager()
.debug
.message(1, "Cannot load XML Catalog Parser class", domParserClass);
throw new CatalogException(CatalogException.UNPARSEABLE);
} catch (InstantiationException ie) {
catalog
.getCatalogManager()
.debug
.message(1, "Cannot instantiate XML Catalog Parser class", domParserClass);
throw new CatalogException(CatalogException.UNPARSEABLE);
} catch (IllegalAccessException iae) {
catalog
.getCatalogManager()
.debug
.message(1, "Cannot access XML Catalog Parser class", domParserClass);
throw new CatalogException(CatalogException.UNPARSEABLE);
} catch (ClassCastException cce) {
catalog
.getCatalogManager()
.debug
.message(1, "Cannot cast XML Catalog Parser class", domParserClass);
throw new CatalogException(CatalogException.UNPARSEABLE);
}
Node node = root.getFirstChild();
while (node != null) {
domParser.parseCatalogEntry(catalog, node);
node = node.getNextSibling();
}
}
/**
* 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()]);
}
