Example #1
0
  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();
    }
  }
Example #3
0
  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;
  }
Example #4
0
  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;
  }
Example #5
0
  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")
              + "&amp;xsl=metadata_to_html_full</query>");
    } else {
      out.println(
          "<query>owner=" + e.getAttribute("query") + "&amp;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;
 }
Example #12
0
  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;
  }
Example #13
0
  /**
   * 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);
    }
  }
Example #14
0
 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);
 }
Example #15
0
  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;
  }
Example #16
0
  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.");
  }
Example #17
0
  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;
  }
Example #18
0
  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;
  }
Example #20
0
  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) {

    }
  }
Example #21
0
  /**
   * 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;
  }
Example #22
0
  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;
  }
Example #23
0
  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;
  }
Example #24
0
  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];
  }
Example #26
0
    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;
    }
Example #27
0
    /** 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;
    }
Example #28
0
  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());
    }
  }
Example #29
0
  @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;
  }
Example #30
0
  // -----------------------------------------------------
  // 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();
    }
  }