private static IPeakSet<? extends IPeak> parsePeakSet(Node parent) throws XmlParserException {
// retrieve all the properties
Vector<IPeak> peaks = new Vector<IPeak>();
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("peaks")) {
NodeList nodes2 = node.getChildNodes();
for (int nodeid2 = 0; nodeid2 < nodes2.getLength(); ++nodeid2) {
Node node2 = nodes2.item(nodeid2);
if (node2.getNodeType() != Node.ELEMENT_NODE) continue;
IPeak peak = parseIPeak(node2);
if (peak != null) peaks.add(peak);
}
}
}
// create the bugger
IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(peaks);
parseIPeak(parent, peakset);
return peakset;
}
// 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 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 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;
}
/*
* 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>");
}
// 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;
}
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());
}
}
/*
* 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;
}
/* return the value of the XML text node (never null) */
protected static String GetNodeText(Node root) {
StringBuffer sb = new StringBuffer();
if (root != null) {
NodeList list = root.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node n = list.item(i);
if (n.getNodeType() == Node.CDATA_SECTION_NODE) { // CDATA Section
sb.append(n.getNodeValue());
} else if (n.getNodeType() == Node.TEXT_NODE) {
sb.append(n.getNodeValue());
} else {
// Print.logWarn("Unrecognized node type: " + n.getNodeType());
}
}
}
return sb.toString();
}
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;
}
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;
}
/**
* 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);
}
}
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);
}
private static Vector<Annotation> parseAnnotations(Node parent) throws XmlParserException {
Vector<Annotation> annotations = new Vector<Annotation>();
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("annotation")) {
String label = null, value = null, valuetype = null, unit = null;
NodeList annotation_nodes = element.getChildNodes();
for (int annotationid = 0; annotationid < annotation_nodes.getLength(); ++annotationid) {
Node annotation_node = annotation_nodes.item(annotationid);
if (annotation_node.getNodeType() != Node.ELEMENT_NODE) continue;
Element annotation_element = (Element) annotation_node;
if (annotation_element.getTagName().equals("label"))
label = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("value"))
value = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("valuetype"))
valuetype = annotation_element.getTextContent();
}
if (label == null || value == null || valuetype == null)
throw new XmlParserException("Annotation is missing either: label, value or valuetype");
Annotation annotation =
new Annotation(label, value, Annotation.ValueType.valueOf(valuetype));
annotation.setUnit(unit);
if (annotation.getValueType() == Annotation.ValueType.ONTOLOGY)
annotation.setOntologyRef(element.getAttribute("ontologyref"));
if (element.getAttribute("unit") != null) annotation.setUnit(element.getAttribute("unit"));
annotations.add(annotation);
}
}
return annotations;
}
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.");
}
private static String getTextContent(Node n) {
NodeList nodeList = n.getChildNodes();
String textContent = "";
for (int j = 0; j < nodeList.getLength(); j++) {
Node k = nodeList.item(j);
if (k.getNodeType() == Node.TEXT_NODE) {
textContent = k.getNodeValue();
break;
}
}
return textContent;
}
private static Vector<FileInfo> parseFiles(Node parent) throws XmlParserException {
Vector<FileInfo> files = new Vector<FileInfo>();
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("file")) files.add(parseFile(node));
}
return files;
}
/**
* Get all the properties of this resource. This implementation stores properties in an XML
* document containing a properties root element. The properties file name is derived from the URI
* by adding the extension PropertiesManager.propertiesSuffix. This applies to collections as well
* as other resources.
*
* <p>Since the properties are stored in a file, and all methods that query and update the
* properties must read the XML file into memory and parse it, many of the other property methods
* are implemented by calling this method. Subclasses of ResourceImpl may want to use other
* techniques depending on how the properties are stored.
*
* @return a MultiStatus containing response elements with prop elements containing the properties
* and their statuses.
* @exception com.ibm.webdav.WebDAVException
*/
public MultiStatus getProperties() throws WebDAVException {
Document propertiesDocument = resource.loadProperties();
// create a MultiStatus to hold the results
MultiStatus results = new MultiStatus();
// create a response element to hold the properties for this resource
PropertyResponse response = null;
String urlstring;
if (false) {
// I consider this to be the more correct way and the
// way used in the examples in the spec... but it is
// redundant and creates the possibility of the two
// redundant parts being out of synch.
urlstring = resource.getURL().toString();
} else {
// this is the way that mod_dav and a few others do it. This
// way also makes it easier to debug clients even if
// redirecting through a dedicated proxy. Without this
// it's inconvenient to debug IE5. It gets confused if
// the host:port (if provided) don't match who it thinks
// it's connecting to.
urlstring = resource.getURL().getFile();
}
response = new PropertyResponse(urlstring);
// add the properties to the response
NodeList properties = propertiesDocument.getDocumentElement().getChildNodes();
Node temp = null;
for (int i = 0; i < properties.getLength(); i++) {
temp = properties.item(i);
// Skip ignorable TXText elements
if (!(temp.getNodeType() == Node.ELEMENT_NODE)) {
continue;
}
Element property = (Element) temp;
PropertyName pn = new PropertyName(property);
response.addProperty(pn, property, WebDAVStatus.SC_OK);
}
results.addResponse(response);
return results;
}
public void read(Document doc) {
try {
Element root = doc.getDocumentElement();
NodeList nList = doc.getElementsByTagName("user");
for (int i = 0; i < nList.getLength(); i++) {
Node node = nList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
Element element = (Element) node;
}
}
// Element e1 = (Element) nList.item(0);
} catch (Exception e) {
}
}
/**
* Method that reads a XML-file, and returns a Model that contains the information
*
* @param file
* @return
* @return
*/
public static Model readXML(String file) {
// initialize table to be filled with content of XML file
Model t = new Model();
try {
// Create file to be parsed by document parser
File xmlfile = new File(file);
// create parser
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// parse the file
Document parsedfile = parser.parse(xmlfile);
// normalize the parsed file (make it more user-friendly)
parsedfile.getDocumentElement().normalize();
NodeList cells = parsedfile.getElementsByTagName("CELL");
for (int i = 0; i < cells.getLength(); i++) {
// Get cell at list index i
Node currentcell = cells.item(i);
// read the elements "location" attributes row/column
if (Node.ELEMENT_NODE == currentcell.getNodeType()) {
Element cellinfo = (Element) currentcell;
// get the row number from node attribute
int row = Integer.parseInt(cellinfo.getAttribute("row")) - 1;
// get the column number from the node attribute
int col = Integer.parseInt(cellinfo.getAttribute("column")) - 1;
// get content from node
String content = cellinfo.getTextContent();
if (content != null) {
content = content.replace("\n", "");
}
// Make the content an Integer (if it is a number), easier
// for
// using it later on
// put content in table, with row/column inserted as x/y
t.setContent(row, col, (String) content);
}
}
} catch (ParserConfigurationException e) {
System.out.println("Fileparser could not be made");
} catch (IOException f) {
System.out.println("File could not be parsed, did you enter the correct file name?");
} catch (SAXException g) {
System.out.println("Something went wrong in parsing the file");
}
return t;
}
private static ScanInfo parseScan(Node parent) throws XmlParserException {
double retentiontime = 0;
Polarity polarity = Polarity.NEUTRAL;
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("polarity"))
polarity = Polarity.valueOf(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
}
ScanInfo scan = new ScanInfo(retentiontime, polarity);
if (annotations != null) scan.addAnnotations(annotations);
return scan;
}
private void call(String script)
throws ParserConfigurationException, TransformerConfigurationException {
File callerScript = this.currentScript;
Document doc = null;
try {
this.currentScript = new File(script);
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = db.parse(this.currentScript);
} catch (Exception ex) {
this.currentScript = callerScript;
Utils.onError(new Error.FileParse(script));
return;
}
NodeList operations = doc.getDocumentElement().getChildNodes();
for (int i = 0; i < operations.getLength(); i++) {
Node operation = operations.item(i);
if (operation.getNodeType() != Node.ELEMENT_NODE) continue;
call(operation);
}
this.currentScript = callerScript;
}
private static FileInfo parseFile(Node parent) throws XmlParserException {
String label = "";
String name = "";
String location = "";
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("label")) label = element.getTextContent();
else if (element.getTagName().equals("name")) name = element.getTextContent();
else if (element.getTagName().equals("location")) location = element.getTextContent();
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(node);
}
FileInfo file = new FileInfo(label, name, location);
if (annotations != null) file.addAnnotations(annotations);
return file;
}
// http://www.java-tips.org/java-se-tips/javax.xml.parsers/how-to-read-xml-file-in-java.html
private double my_ListParser(int itIs) {
double[] my_list = new double[3];
try {
File fXmlFile =
new File("/Users/alexiaKourfali/NetBeansProjects/mav_project3_part2/web/my_list.xml");
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(fXmlFile);
doc.getDocumentElement().normalize();
// System.out.println("Root element " + doc.getDocumentElement().getNodeName());
NodeList nodeLst = doc.getElementsByTagName("Entry");
for (int s = 0; s < nodeLst.getLength(); s++) {
Node fstNode = nodeLst.item(s);
if (fstNode.getNodeType() == Node.ELEMENT_NODE) {
Element fstElmnt = (Element) fstNode;
NodeList fstNmElmntLst = fstElmnt.getElementsByTagName("Price");
Element fstNmElmnt = (Element) fstNmElmntLst.item(0);
NodeList fstNm = fstNmElmnt.getChildNodes();
Node nV = (Node) fstNm.item(0);
/*not sureeeee*/
my_list[s] = Double.parseDouble(nV.getNodeValue());
}
}
} catch (Exception e) {
}
if (itIs == 0) return my_list[0];
if (itIs == 1) return my_list[1];
else return my_list[2];
}
public List<ClassNode> getClasses() {
ArrayList<ClassNode> classes = new ArrayList<ClassNode>();
/**
* Получаем список дочерних узлов для данного узла XML, который соответствует приложению
* application. Здесь будут располагаться все узлы Node, каждый из которых является объектным
* представлением тега class для текущего тега application.
*/
NodeList classNodes = node.getChildNodes();
for (int i = 0; i < classNodes.getLength(); i++) {
Node node = classNodes.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
/** Создаем на основе Node узла своё объектное представление класса. */
ClassNode classNode = new ClassNode(node);
classes.add(classNode);
}
}
return classes;
}
/** Возвращает список методов класса. */
public List<MethodNode> getMethods() {
ArrayList<MethodNode> methods = new ArrayList<MethodNode>();
/**
* Получаем список дочерних узлов для данного узла XML, который соответствует классу class.
* Здесь будут располагаться все узлы Node, каждый из которых является объектным
* представлением тега method для текущего тега class.
*/
NodeList methodNodes = node.getChildNodes();
for (int i = 0; i < methodNodes.getLength(); i++) {
node = methodNodes.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
/** Создаем на основе Node узла своё объектное представление метода. */
MethodNode methodNode = new MethodNode(node);
methods.add(methodNode);
}
}
return methods;
}
public void outputOwners(PrintWriter out) {
// traverse doc, outputing nodes
log.info("inserting owners ");
try {
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) {
// check to see if there are collections under owner
Element e = (Element) child;
outputItem(e, out);
}
}
} 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());
}
}
@SuppressWarnings("unchecked")
private static BackgroundIon<? extends Peak> parseBackgroundIon(Node parent)
throws XmlParserException {
// retrieve the separate peaks
PeakData<? extends Peak> peakdata = 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("peakdata")) {
peakdata = parsePeakData(element);
}
}
// create the bugger
BackgroundIon<? extends Peak> backgroundion = null;
if (peakdata.getFactory().getPeakClass().equals(Centroid.class))
backgroundion = new BackgroundIon<Centroid>((PeakData<Centroid>) peakdata);
parseIPeak(parent, backgroundion);
return backgroundion;
}
// -----------------------------------------------------
// Description: Using the specified template, create
// csv records corresponding to the output xml criteria.
// -----------------------------------------------------
void transformWithTemplate(String templateName, String fileName, String destinationDirectory) {
System.out.println("fileName = " + fileName);
String fileName_woext = fileName.substring(0, fileName.lastIndexOf('.'));
try {
File fXmlFile = new File(templateLocation, templateName);
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
Document doc = dBuilder.parse(fXmlFile);
doc.getDocumentElement().normalize();
System.out.println("Root element :" + doc.getDocumentElement().getNodeName());
NodeList nList = doc.getElementsByTagName("output");
// loop through all the output nodes
for (int temp = 0; temp < nList.getLength(); temp++) {
Node nNode = nList.item(temp);
if (nNode.getNodeType() == Node.ELEMENT_NODE) {
Element eElement = (Element) nNode;
String outputLine = getTagValue("line", eElement);
FileWriter output =
new FileWriter(
destinationDirectory
+ File.separator
+ fileName_woext.substring(0, fileName.lastIndexOf('_'))
+ ".csv",
true);
BufferedWriter bufWrite = new BufferedWriter(output);
System.out.println(
destinationDirectory
+ File.separator
+ fileName_woext.substring(0, fileName.lastIndexOf("_"))
+ ".csv");
if (Settings.optionalIdentifier != null) {
bufWrite.write("\"" + Settings.optionalIdentifier + "\"");
}
String[] outputItems = outputLine.split("#");
for (String outputItem : outputItems) {
if ((temp == 0) && (Settings.optionalIdentifier == null)) {
bufWrite.write(
"\"" + interpretText(destinationDirectory, fileName_woext, outputItem) + "\"");
} else {
bufWrite.write(
",\"" + interpretText(destinationDirectory, fileName_woext, outputItem) + "\"");
}
}
bufWrite.write("\r\n");
bufWrite.close();
output.close();
}
}
} catch (Exception e) {
e.printStackTrace();
}
}