private List<Node> getChildNodes(Node parentNode, String tagName) {
List<Node> nodeList = new ArrayList<Node>();
for (Node child = parentNode.getFirstChild(); child != null; child = child.getNextSibling()) {
if (child.getNodeType() == Node.ELEMENT_NODE && tagName.equals(child.getNodeName())) {
nodeList.add(child);
}
}
return nodeList;
}
public InputStream invokeServerInbound(HttpServletRequest request, OutputStream os)
throws IOException {
Map<String, DataHandler> attachments = new HashMap<String, DataHandler>();
Map<String, Object> httpProperties = new HashMap<String, Object>();
httpProperties.put(HTTP_REQUEST_METHOD, request.getMethod());
Map<String, List<String>> headers = new HashMap<String, List<String>>();
Enumeration headerNames = request.getHeaderNames();
while (headerNames.hasMoreElements()) {
String name = (String) headerNames.nextElement();
List<String> values = new ArrayList<String>();
Enumeration headerValues = request.getHeaders(name);
while (headerValues.hasMoreElements()) {
String value = (String) headerValues.nextElement();
values.add(value);
}
headers.put(name, values);
}
httpProperties.put(HTTP_REQUEST_HEADERS, headers);
prepare(httpProperties, /*request=*/ true);
if (!invokeInbound(request.getInputStream(), attachments)) {
if (getProtocolException() != null) {
reverseDirection();
invokeInboundFaultHandlers();
} else if (getRuntimeException() == null) uninvokeInbound();
closeServer();
finish(os);
return null;
}
return finish();
}
/**
* 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()]);
}