// read all the missiles of the current id launcher
protected void readMissilesForGivenLauncher(NodeList missiles, String idLauncher) {
int launchTime, flyTime, damage;
for (int i = 0; i < missiles.getLength(); i++) {
Element missile = (Element) missiles.item(i);
String id = missile.getAttribute("id");
String destination = missile.getAttribute("destination");
try {
launchTime = Integer.parseInt(missile.getAttribute("launchTime"));
flyTime = Integer.parseInt(missile.getAttribute("flyTime"));
damage = Integer.parseInt(missile.getAttribute("damage"));
} catch (NumberFormatException e) {
launchTime = -1;
flyTime = -1;
damage = -1;
System.out.println("ERROR reading from XML");
// System.out.println(e.getStackTrace());
}
// create the thread of the missile
createEnemyMissile(id, destination, launchTime, flyTime, damage, idLauncher);
}
}
// read all defense missiles from given id
protected void readDefensDestructoreMissiles(NodeList missiles, String whoLaunchMeId) {
String targetId, destructTimeCheck;
int destructTime;
int size = missiles.getLength();
for (int i = 0; i < size; i++) {
Element missile = (Element) missiles.item(i);
targetId = missile.getAttribute("id");
destructTimeCheck = missile.getAttribute("destructAfterLaunch");
if (destructTimeCheck.equals("")) destructTimeCheck = missile.getAttribute("destructTime");
try {
destructTime = Integer.parseInt(destructTimeCheck);
} catch (NumberFormatException e) {
destructTime = -1;
// System.out.println(e.getStackTrace());
}
// create the thread of the missile
createDefenseMissile(whoLaunchMeId, targetId, destructTime);
}
}
/**
* Unmarshall a Genotype instance from a given XML Element representation. Its population of
* Chromosomes will be unmarshalled from the Chromosome sub-elements.
*
* @param a_activeConfiguration the current active Configuration object that is to be used during
* construction of the Genotype and Chromosome instances
* @param a_xmlElement the XML Element representation of the Genotype
* @return a new Genotype instance, complete with a population of Chromosomes, setup with the data
* from the XML Element representation
* @throws ImproperXMLException if the given Element is improperly structured or missing data
* @throws InvalidConfigurationException if the given Configuration is in an inconsistent state
* @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
* @author Klaus Meffert
* @since 1.0
*/
public static Genotype getGenotypeFromElement(
Configuration a_activeConfiguration, Element a_xmlElement)
throws ImproperXMLException, InvalidConfigurationException,
UnsupportedRepresentationException, GeneCreationException {
// Sanity check. Make sure the XML element isn't null and that it
// actually represents a genotype.
if (a_xmlElement == null || !(a_xmlElement.getTagName().equals(GENOTYPE_TAG))) {
throw new ImproperXMLException(
"Unable to build Genotype instance from XML Element: "
+ "given Element is not a 'genotype' element.");
}
// Fetch all of the nested chromosome elements and convert them
// into Chromosome instances.
// ------------------------------------------------------------
NodeList chromosomes = a_xmlElement.getElementsByTagName(CHROMOSOME_TAG);
int numChromosomes = chromosomes.getLength();
Population population = new Population(a_activeConfiguration, numChromosomes);
for (int i = 0; i < numChromosomes; i++) {
population.addChromosome(
getChromosomeFromElement(a_activeConfiguration, (Element) chromosomes.item(i)));
}
// Construct a new Genotype with the chromosomes and return it.
// ------------------------------------------------------------
return new Genotype(a_activeConfiguration, population);
}
// Gets the specified XML Schema doc if one is mentioned in the file
public static File getSchemaFile(Document xmlDoc) {
/** @todo Must be an easier way of doing this... */
logger.logComment("Getting schema file for: " + xmlDoc.getDocumentURI());
NodeList nl = xmlDoc.getChildNodes();
for (int j = 0; j < nl.getLength(); j++) {
Node node = nl.item(j);
logger.logComment("Type: " + node.getNodeType() + "Name: " + node.getNodeName());
if (node.getNodeName().equals(XML_STYLESHEET_NODE)) {
String nodeVal = node.getNodeValue();
logger.logComment("Looking at: " + nodeVal);
String xslFileName =
nodeVal.substring(nodeVal.indexOf("href=\"") + 6, nodeVal.length() - 1);
File xslFile = new File(xslFileName);
return xslFile;
}
if (node.getAttributes().getLength() > 0) {
logger.logComment("Attributes: " + node.getAttributes());
if (node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR) != null) {
String locString = node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR).getNodeValue();
logger.logComment("Loc string: " + locString);
String file = locString.split("\\s")[1];
return new File(file);
}
}
}
logger.logError("No node found with name: " + XML_STYLESHEET_NODE);
return null;
}
/*
* Output this item. Then, if the element has child elements, output each.
*/
private void outputItem(Element e, PrintWriter out) {
int chk = 0;
HashMap collection = new HashMap();
String key = null;
Element collectionElement = null;
log.fine("outputing item for " + e.getAttribute("name") + ": " + e.getAttribute("query"));
out.println("<item>");
out.println("<name>" + e.getAttribute("name") + "</name>");
if (e.getTagName().equalsIgnoreCase("collection")) {
// change made by NETTY (change collectionlist to collection)
out.println(
"<query>collection="
+ e.getAttribute("col_id")
+ "&xsl=metadata_to_html_full</query>");
} else {
out.println(
"<query>owner=" + e.getAttribute("query") + "&xsl=metadata_to_html_full</query>");
}
// now output children
NodeList children = e.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
chk++;
outputItem((Element) child, out);
}
}
out.println("</item>");
}
public ArrayList<String> parseXML() throws Exception {
ArrayList<String> ret = new ArrayList<String>();
handshake();
URL url =
new URL(
"http://mangaonweb.com/page.do?cdn="
+ cdn
+ "&cpn=book.xml&crcod="
+ crcod
+ "&rid="
+ (int) (Math.random() * 10000));
String page = DownloaderUtils.getPage(url.toString(), "UTF-8", cookies);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
InputSource is = new InputSource(new StringReader(page));
Document d = builder.parse(is);
Element doc = d.getDocumentElement();
NodeList pages = doc.getElementsByTagName("page");
total = pages.getLength();
for (int i = 0; i < pages.getLength(); i++) {
Element e = (Element) pages.item(i);
ret.add(e.getAttribute("path"));
}
return (ret);
}
public static Element[] filterChildElements(Element parent, String ns, String lname) {
/*
way too noisy
if (LOGGER.isDebugEnabled()) {
StringBuilder buf = new StringBuilder(100);
buf.append("XmlaUtil.filterChildElements: ");
buf.append(" ns=\"");
buf.append(ns);
buf.append("\", lname=\"");
buf.append(lname);
buf.append("\"");
LOGGER.debug(buf.toString());
}
*/
List<Element> elems = new ArrayList<Element>();
NodeList nlst = parent.getChildNodes();
for (int i = 0, nlen = nlst.getLength(); i < nlen; i++) {
Node n = nlst.item(i);
if (n instanceof Element) {
Element e = (Element) n;
if ((ns == null || ns.equals(e.getNamespaceURI()))
&& (lname == null || lname.equals(e.getLocalName()))) {
elems.add(e);
}
}
}
return elems.toArray(new Element[elems.size()]);
}
// Lee la configuracion que se encuentra en conf/RegistryConf
private void readConfXml() {
try {
File inputFile = new File("src/java/Conf/RegistryConf.xml");
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(inputFile);
doc.getDocumentElement().normalize();
NodeList nList = doc.getElementsByTagName("RegistryConf");
for (int i = 0; i < nList.getLength(); i++) {
Node nNode = nList.item(i);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
RegistryConf reg = new RegistryConf();
String aux;
int idSensor;
int value;
aux = eElement.getElementsByTagName("idSensor").item(0).getTextContent();
idSensor = Integer.parseInt(aux);
reg.setIdSensor(idSensor);
aux = eElement.getElementsByTagName("saveType").item(0).getTextContent();
reg.setSaveTypeString(aux);
aux = eElement.getElementsByTagName("value").item(0).getTextContent();
value = Integer.parseInt(aux);
reg.setValue(value);
registryConf.add(reg);
lastRead.put(idSensor, 0);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
private void buildHierarchyDOM() {
TransformerFactory factory = TransformerFactory.newInstance();
StreamSource src =
new StreamSource(
this.getServletContext()
.getResourceAsStream("/WEB-INF/classes/gpt/search/browse/ownerHierarchy.xml"));
log.info("initializing src from stream " + src);
try {
Transformer t = factory.newTransformer();
dom = new DOMResult();
t.transform(src, dom);
// now go thru tree, setting up the query attribute for each node
Node tree = dom.getNode();
NodeList children = tree.getChildNodes();
log.info("dom tree contains " + children.getLength() + " nodes");
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
Element e = (Element) child;
String query = computeQuery(e);
e.setAttribute("query", query);
}
}
} catch (Exception e) {
log.severe("Could not init ownerHierarchy because exception thrown:");
StringWriter sw = new StringWriter();
e.printStackTrace(new PrintWriter(sw));
log.severe(sw.toString());
}
}
private static Header parseHeader(Node parent) throws XmlParserException {
Header header = new Header();
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
try {
if (element.getTagName().equals("nrpeaks"))
header.setNrPeaks(Integer.parseInt(element.getTextContent()));
else if (element.getTagName().equals("date")) header.setDate(element.getTextContent());
else if (element.getTagName().equals("owner")) header.setOwner(element.getTextContent());
else if (element.getTagName().equals("description"))
header.setDescription(element.getTextContent());
else if (element.getTagName().equals("sets")) header.addSetInfos(parseSets(element));
else if (element.getTagName().equals("measurements"))
header.addMeasurementInfos(parseMeasurements(element));
else if (element.getTagName().equals("annotations")) {
Vector<Annotation> annotations = parseAnnotations(element);
if (annotations != null)
for (Annotation annotation : annotations) header.addAnnotation(annotation);
}
} catch (Exception e) {
throw new XmlParserException(
"Invalid value in header (" + element.getTagName() + "): '" + e.getMessage() + "'.");
}
}
return header;
}
/*
* If the element contains an attribute 'makeOnly' with a value of 'true',
* create a child element before any existing children which will display a node
* which will display only the elements records.
* Compute the query attribute, which is the appended result of all of the children
* appended to this element name. If noQuery=true. then do not generate a query term
* for this element.
*/
String computeQuery(Element e) {
String query = "";
if (!(e.getAttribute("noQuery").equalsIgnoreCase("true"))) {
query = e.getAttribute("name");
}
String makeOnly = e.getAttribute("makeOnly");
boolean madeOnly = false;
NodeList children = e.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (child.getNodeType() == Node.ELEMENT_NODE) {
if (makeOnly.equalsIgnoreCase("true") && !madeOnly) {
// need to make an ...-Only node and populate it
String onlyTagName = e.getTagName() + "-Only";
Element only = ((Document) dom.getNode()).createElement(onlyTagName);
only.setAttribute("name", e.getAttribute("name") + "-Only");
only.setAttribute("query", e.getAttribute("name"));
e.insertBefore(only, child);
i++;
madeOnly = true;
}
if (query.length() > 0) {
query += ",";
}
query += computeQuery((Element) child);
}
}
log.info("setting query for " + e.getNodeName() + " " + query);
e.setAttribute("query", query);
return query;
}
private static MeasurementInfo parseMeasurement(Node parent) throws XmlParserException {
String id = "";
String label = "";
String sampleid = "";
Vector<FileInfo> files = null;
Vector<ScanInfo> scans = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("id")) id = element.getTextContent();
else if (element.getTagName().equals("label")) label = element.getTextContent();
else if (element.getTagName().equals("sampleid")) sampleid = element.getTextContent();
else if (element.getTagName().equals("scans")) scans = parseScans(node);
else if (element.getTagName().equals("files")) files = parseFiles(node);
}
MeasurementInfo measurement = new MeasurementInfo(Integer.parseInt(id), sampleid);
measurement.setLabel(label);
measurement.addFileInfos(files);
if (scans != null) measurement.addScanInfos(scans);
return measurement;
}
private static SetInfo parseSet(Node parent) throws XmlParserException {
String id = "";
String type = "";
String measurementids = null;
NodeList nodes = parent.getChildNodes();
Vector<SetInfo> sets = new Vector<SetInfo>();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("id")) id = element.getTextContent();
else if (element.getTagName().equals("set")) sets.add(parseSet(element));
else if (element.getTagName().equals("type")) type = element.getTextContent();
else if (element.getTagName().equals("measurementids"))
measurementids = element.getTextContent();
}
// create the set
SetInfo set = new SetInfo(id, Integer.parseInt(type));
if (measurementids != null) {
int mids[] = ByteArray.toIntArray(Base64.decode(measurementids), ByteArray.ENDIAN_LITTLE, 32);
for (int mid : mids) set.addMeasurementID(mid);
}
// add the children
for (SetInfo s : sets) set.addChild(s);
return set;
}
private LinkedHashMap[] obtenerMapeos(CliGol cliGol, NodeList variables, String[] excluye) {
LinkedHashMap<String, Object> mapa = new LinkedHashMap<String, Object>();
LinkedHashMap<String, String> puntos = new LinkedHashMap<String, String>();
List<String> ex = Arrays.asList(excluye);
for (int i = 0; i < variables.getLength(); i++) {
String nom = variables.item(i).getNodeName();
if (!ex.contains(nom)) {
String golMapdijo = GolMap.xmlGol(nom);
String val = null;
if (golMapdijo != null) {
val = buscaValEnCli(golMapdijo, cliGol);
mapa.put(nom, val);
puntos.put(nom, variables.item(i).getTextContent());
}
}
}
return new LinkedHashMap[] {mapa, puntos};
}
public static final Map parseFrame(Node node) {
NodeList bones = node.getChildNodes();
Map bone_infos = new HashMap();
for (int i = 0; i < bones.getLength(); i++) {
Node bone = bones.item(i);
if (bone.getNodeName().equals("transform")) {
String name = bone.getAttributes().getNamedItem("name").getNodeValue();
float[] matrix = new float[16];
matrix[0 * 4 + 0] = getAttrFloat(bone, "m00");
matrix[0 * 4 + 1] = getAttrFloat(bone, "m01");
matrix[0 * 4 + 2] = getAttrFloat(bone, "m02");
matrix[0 * 4 + 3] = getAttrFloat(bone, "m03");
matrix[1 * 4 + 0] = getAttrFloat(bone, "m10");
matrix[1 * 4 + 1] = getAttrFloat(bone, "m11");
matrix[1 * 4 + 2] = getAttrFloat(bone, "m12");
matrix[1 * 4 + 3] = getAttrFloat(bone, "m13");
matrix[2 * 4 + 0] = getAttrFloat(bone, "m20");
matrix[2 * 4 + 1] = getAttrFloat(bone, "m21");
matrix[2 * 4 + 2] = getAttrFloat(bone, "m22");
matrix[2 * 4 + 3] = getAttrFloat(bone, "m23");
matrix[3 * 4 + 0] = getAttrFloat(bone, "m30");
matrix[3 * 4 + 1] = getAttrFloat(bone, "m31");
matrix[3 * 4 + 2] = getAttrFloat(bone, "m32");
matrix[3 * 4 + 3] = getAttrFloat(bone, "m33");
bone_infos.put(name, matrix);
}
}
return bone_infos;
}
public static void traverseAMLforObjectNames(
HashMap partialMap, Node currentNode, HashMap ObjDef_LinkId, HashMap ModelId_ModelType) {
if (currentNode.hasChildNodes()) {
for (int i = 0; i < currentNode.getChildNodes().getLength(); i++) {
Node currentChild = currentNode.getChildNodes().item(i);
if (currentChild.getNodeName().equals("Group")) {
traverseAMLforObjectNames(partialMap, currentChild, ObjDef_LinkId, ModelId_ModelType);
}
if (currentChild.getNodeName().equals("Model")) {
if (currentChild.hasAttributes()) {
String mid = currentChild.getAttributes().getNamedItem("Model.ID").getNodeValue();
String type = currentChild.getAttributes().getNamedItem("Model.Type").getNodeValue();
ModelId_ModelType.put(mid, type);
}
// traverseAMLforObjectNames(partialMap, currentChild,
// ObjDef_LinkId);
}
if (currentChild.getNodeName().equals("ObjDef")) {
String id = currentChild.getAttributes().getNamedItem("ObjDef.ID").getNodeValue();
NodeList currentChildren = currentChild.getChildNodes();
String ObjName = "";
for (int k = 0; k < currentChildren.getLength(); k++) {
Node Child = currentChildren.item(k);
if (!Child.getNodeName().equals("AttrDef")) {
continue;
} else if (!Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
continue;
} else if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
ObjName = getTextContent(Child.getChildNodes().item(l));
ObjName = ObjName.replaceAll("\n", "\\\\n");
break;
}
}
}
}
partialMap.put(id, ObjName);
for (int j = 0; j < currentChild.getAttributes().getLength(); j++) {
if (currentChild.getAttributes().item(j).getNodeName().equals("LinkedModels.IdRefs")) {
String links =
currentChild.getAttributes().getNamedItem("LinkedModels.IdRefs").getNodeValue();
/*
* if (links.indexOf(" ") > -1) {
* Message.add("yes, yes, yes"); links =
* links.substring(0, links.indexOf(" ")); }
*/
ObjDef_LinkId.put(id, links);
}
}
}
}
}
}
private Element getElement(String eltName) {
NodeList nodeList = docElt.getElementsByTagName(eltName);
if (nodeList.getLength() != 0) {
Node node = nodeList.item(0);
if (node instanceof Element) return (Element) node;
}
return null;
}
public static Element recuperarHijo(Element esteNodo, String tag) {
Element xmlElement = null;
if (esteNodo != null) {
NodeList listaElem = esteNodo.getElementsByTagName(tag);
if (listaElem != null) xmlElement = (Element) listaElem.item(0);
}
return xmlElement;
}
void lookup(String text) {
NodeList nl = DOMInfoExtractor.locateNodes(document, ".//text()[contains(.,'" + text + "')]");
System.out.println("find " + nl.getLength() + " items");
FoundItem[] fis = new FoundItem[nl.getLength()];
for (int i = 0; i < nl.getLength(); i++) {
fis[i] = getFoundItem(nl.item(i), text);
}
foundList.setListData(fis);
}
private void removeNodes(NodeList nl) {
int count = nl.getLength();
for (int i = 0; i < count; i++) {
Node node = nl.item(i);
Node parent = node.getParentNode();
if (parent == null) continue;
parent.removeChild(node);
}
}
public Vector getNodes(Element padre) {
Vector vectorNode = new Vector();
NodeList nodeList = padre.getChildNodes();
for (int i = 0; i < nodeList.getLength(); i++) {
Node node = nodeList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) vectorNode.add(node);
}
return vectorNode;
}
/**
* Honey, can you just check on the kids? Thanks.
*
* <p>Internal function; not included in reference.
*/
protected void checkChildren() {
if (children == null) {
NodeList kids = node.getChildNodes();
int childCount = kids.getLength();
children = new XML[childCount];
for (int i = 0; i < childCount; i++) {
children[i] = new XML(this, kids.item(i));
}
}
}
public static Vector recuperarHojasAsVector(Element esteNodo, String tag) {
NodeList listaElem = esteNodo.getElementsByTagName(tag);
Vector vector = new Vector();
for (int i = 0; i < listaElem.getLength(); i++) {
Element xmlElement = (Element) listaElem.item(i);
Node xmlHoja = (Node) xmlElement.getChildNodes().item(0);
vector.addElement(xmlHoja.getNodeValue());
}
return vector;
}
/**
* Carries out preprocessing that makes JEuclid handle the document better.
*
* @param doc Document
*/
static void preprocessForJEuclid(Document doc) {
// underbrace and overbrace
NodeList list = doc.getElementsByTagName("mo");
for (int i = 0; i < list.getLength(); i++) {
Element mo = (Element) list.item(i);
String parentName = ((Element) mo.getParentNode()).getTagName();
if (parentName == null) {
continue;
}
if (parentName.equals("munder") && isTextChild(mo, "\ufe38")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23df"));
} else if (parentName.equals("mover") && isTextChild(mo, "\ufe37")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23de"));
}
}
// menclose for long division doesn't allow enough top padding. Oh, and
// <mpadded> isn't implemented. And there isn't enough padding to left of
// the bar either. Solve by adding an <mover> with just an <mspace> over#
// the longdiv, contained within an mrow that adds a <mspace> before it.
list = doc.getElementsByTagName("menclose");
for (int i = 0; i < list.getLength(); i++) {
Element menclose = (Element) list.item(i);
// Only for longdiv
if (!"longdiv".equals(menclose.getAttribute("notation"))) {
continue;
}
Element mrow = doc.createElementNS(WebMathsService.NS, "mrow");
Element mover = doc.createElementNS(WebMathsService.NS, "mover");
Element mspace = doc.createElementNS(WebMathsService.NS, "mspace");
Element mspaceW = doc.createElementNS(WebMathsService.NS, "mspace");
boolean previousElement = false;
for (Node previous = menclose.getPreviousSibling();
previous != null;
previous = previous.getPreviousSibling()) {
if (previous.getNodeType() == Node.ELEMENT_NODE) {
previousElement = true;
break;
}
}
if (previousElement) {
mspaceW.setAttribute("width", "4px");
}
menclose.getParentNode().insertBefore(mrow, menclose);
menclose.getParentNode().removeChild(menclose);
mrow.appendChild(mspaceW);
mrow.appendChild(mover);
mover.appendChild(menclose);
mover.appendChild(mspace);
}
}
/**
* ** Gets a virtual DBRecord from the specified remote service ** @param servReq The remote web
* service ** @return The virtual DBRecord (cannot be saved or reloaded)
*/
@SuppressWarnings("unchecked")
public gDBR getVirtualDBRecord(final ServiceRequest servReq) throws DBException {
String CMD_dbget = DBFactory.CMD_dbget;
String TAG_Response = servReq.getTagResponse();
String TAG_Record = DBFactory.TAG_Record;
String ATTR_command = servReq.getAttrCommand();
String ATTR_result = servReq.getAttrResult();
/* send request / get response */
Document xmlDoc = null;
try {
xmlDoc =
servReq.sendRequest(
CMD_dbget,
new ServiceRequest.RequestBody() {
public StringBuffer appendRequestBody(StringBuffer sb, int indent) {
return DBRecordKey.this.toRequestXML(sb, indent);
}
});
} catch (IOException ioe) {
Print.logException("Error", ioe);
throw new DBException("Request read error", ioe);
}
/* parse 'GTSResponse' */
Element gtsResponse = xmlDoc.getDocumentElement();
if (!gtsResponse.getTagName().equalsIgnoreCase(TAG_Response)) {
Print.logError("Request XML does not start with '%s'", TAG_Response);
throw new DBException("Response XML does not begin eith '" + TAG_Response + "'");
}
/* request command/argument */
String cmd = StringTools.trim(gtsResponse.getAttribute(ATTR_command));
String result = StringTools.trim(gtsResponse.getAttribute(ATTR_result));
if (StringTools.isBlank(result)) {
result = StringTools.trim(gtsResponse.getAttribute("type"));
}
if (!result.equalsIgnoreCase("success")) {
Print.logError("Response indicates failure");
throw new DBException("Response does not indicate 'success'");
}
/* Record */
NodeList rcdList = XMLTools.getChildElements(gtsResponse, TAG_Record);
if (rcdList.getLength() <= 0) {
Print.logError("No 'Record' tags");
throw new DBException("GTSResponse does not contain any 'Record' tags");
}
Element rcdElem = (Element) rcdList.item(0);
/* return DBRecord */
gDBR dbr = (gDBR) DBFactory.parseXML_DBRecord(rcdElem);
dbr.setVirtual(true);
return dbr;
}
private static Collection<Node> getNodeMatching(Node body, String regexp) {
final Collection<Node> nodes = new ArrayList<>();
if (body.getNodeName().matches(regexp)) nodes.add(body);
if (body.getChildNodes().getLength() == 0) return nodes;
NodeList returnList = body.getChildNodes();
for (int k = 0; k < returnList.getLength(); k++) {
final Node node = returnList.item(k);
nodes.addAll(getNodeMatching(node, regexp));
}
return nodes;
}
private static boolean isTextChild(Node parent, String text) {
NodeList list = parent.getChildNodes();
if (list.getLength() != 1) {
return false;
}
Node child = list.item(0);
if (child.getNodeType() != Node.TEXT_NODE) {
return false;
}
return child.getNodeValue().equals(text);
}
public String getProperty(String pPropertyName) {
String propertyValue = null;
NodeList nodeList = mConfigFileDocument.getElementsByTagName(pPropertyName);
int nodeListLength = nodeList.getLength();
if (nodeListLength > 0) {
Node firstChildNode = nodeList.item(nodeListLength - 1).getFirstChild();
if (null != firstChildNode) {
propertyValue = firstChildNode.getNodeValue();
}
}
return (propertyValue);
}
private void appendXmlEntry(Document doc, Node opAppend) {
NodeList targetNodes = findNodes(doc, opAppend);
NodeList valueNodes = getValueNodes(opAppend);
if (targetNodes == null) {
return;
}
int targetNodesCount = targetNodes.getLength();
for (int i = 0; i < targetNodesCount; i++) {
Node target = targetNodes.item(i);
appendNodes(doc, target, valueNodes);
}
}
private static void parseIPeak(Node parent, IPeak peak) throws XmlParserException {
// retrieve all the properties
int scan = -1;
double retentiontime = -1;
double mass = -1;
double intensity = -1;
int patternid = -1;
int measurementid = -1;
// String sha1 = null;
Vector<Annotation> annotations = null;
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("patternid"))
patternid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("measurementid"))
measurementid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
else if (element.getTagName().equals("scan"))
scan = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("mass"))
mass = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("intensity"))
intensity = Double.parseDouble(element.getTextContent());
// else if (element.getTagName().equals("sha1sum"))
// sha1 = element.getTextContent();
}
// check whether obligatory values are missing
if (mass == -1 || intensity == -1)
throw new XmlParserException("Mass and/or intensity information is missing for IPeak.");
peak.setScanID(scan);
peak.setRetentionTime(retentiontime);
peak.setMass(mass);
peak.setIntensity(intensity);
peak.setPatternID(patternid);
peak.setMeasurementID(measurementid);
if (annotations != null)
for (Annotation annotation : annotations) peak.addAnnotation(annotation);
// check whether
// if (sha1!=null && !sha1.equals(peak.sha1()))
// throw new XmlParserException("SHA1-sum for individual ipeak element does not match.");
}
