Esempio n. 1
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  /**
   * Create from factory a DocumentBuilder and let it create a org.w3c.dom.Document. This method
   * takes InputSource. After successful finish the document tree is returned.
   *
   * @param input a parser input (for URL users use: <code>new InputSource(url.toExternalForm())
   *     </code>
   * @param validate if true validating parser is used
   * @param namespaceAware if true DOM is created by namespace aware parser
   * @param errorHandler a error handler to notify about exception or <code>null</code>
   * @param entityResolver SAX entity resolver or <code>null</code>; see class Javadoc for hints
   * @throws IOException if an I/O problem during parsing occurs
   * @throws SAXException is thrown if a parser error occurs
   * @throws FactoryConfigurationError Application developers should never need to directly catch
   *     errors of this type.
   * @return document representing given input, or null if a parsing error occurs
   */
  public static Document parse(
      InputSource input,
      boolean validate,
      boolean namespaceAware,
      ErrorHandler errorHandler,
      EntityResolver entityResolver)
      throws IOException, SAXException {

    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setValidating(validate);
    factory.setNamespaceAware(namespaceAware);

    DocumentBuilder builder = null;
    try {
      builder = factory.newDocumentBuilder();
    } catch (ParserConfigurationException ex) {
      throw new SAXException(
          "Cannot create parser satisfying configuration parameters", ex); // NOI18N
    }

    if (errorHandler != null) {
      builder.setErrorHandler(errorHandler);
    }

    if (entityResolver != null) {
      builder.setEntityResolver(entityResolver);
    }

    return builder.parse(input);
  }
Esempio n. 2
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 public static Document readXMLData(String dataXML) throws Exception {
   if (dataXML == null) return null;
   ByteArrayInputStream xmlSrcStream = new ByteArrayInputStream(dataXML.getBytes());
   DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
   dbf.setValidating(false);
   return dbf.newDocumentBuilder().parse(xmlSrcStream);
 }
Esempio n. 3
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 public static Document readXML(String uriXML) throws Exception {
   DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
   dbf.setValidating(false);
   if (uriXML.toUpperCase().trim().indexOf("HTTP:") == -1) {
     return dbf.newDocumentBuilder().parse(new File(uriXML));
   } else return DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(uriXML);
 }
Esempio n. 4
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  /** Create DOM builder using JAXP libraries. */
  static DocumentBuilder makeBuilder(boolean validate) throws IOException, SAXException {

    DocumentBuilder builder;
    DocumentBuilderFactory factory;

    // create factory according to javax.xml.parsers.SAXParserFactory property
    // or platform default (i.e. com.sun...)
    try {
      factory = DocumentBuilderFactory.newInstance();
      factory.setValidating(validate);
      factory.setNamespaceAware(false);
    } catch (FactoryConfigurationError err) {
      notifyFactoryErr(err, "javax.xml.parsers.DocumentBuilderFactory"); // NOI18N
      throw err;
    }

    try {
      builder = factory.newDocumentBuilder();
    } catch (ParserConfigurationException ex) {
      SAXException sex = new SAXException("Configuration exception."); // NOI18N
      ErrorManager emgr = ErrorManager.getDefault();
      emgr.annotate(sex, ex);
      emgr.annotate(
          sex,
          "Can not create a DOM builder!\nCheck javax.xml.parsers.DocumentBuilderFactory property and the builder library presence on classpath."); // NOI18N
      throw sex;
    }

    return builder;
  }
Esempio n. 5
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 /** Возвращает объект Document, который является объектным представлением XML документа. */
 private static Document getDocument() throws Exception {
   try {
     DocumentBuilderFactory f = DocumentBuilderFactory.newInstance();
     f.setValidating(false);
     DocumentBuilder builder = f.newDocumentBuilder();
     return builder.parse(new File("app.xml"));
   } catch (Exception exception) {
     String message = "XML parsing error!";
     throw new Exception(message);
   }
 }
Esempio n. 6
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 public static void main(String args[]) {
   try {
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setNamespaceAware(true);
     factory.setValidating(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
     Document doc = builder.parse(args[0]);
   } catch (SAXException e) {
     // e.printStackTrace();
     System.out.println(e.getMessage());
   } catch (Exception e) {
     // e.printStackTrace();
   }
 }
Esempio n. 7
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 public static final Skeleton loadSkeleton(File file) {
   try {
     FileInputStream input_stream = new FileInputStream(file);
     DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
     factory.setValidating(true);
     DocumentBuilder builder = factory.newDocumentBuilder();
     builder.setErrorHandler(new GeometryErrorHandler());
     Document document = builder.parse(input_stream);
     Element root = document.getDocumentElement();
     return parseSkeleton(root);
   } catch (Exception e) {
     throw new RuntimeException(e);
   }
 }
Esempio n. 8
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  static {
    try {
      URL url = SpellCheckActivator.bundleContext.getBundle().getResource(RESOURCE_LOC);

      InputStream stream = url.openStream();

      if (stream == null) throw new IOException();

      // strict parsing options
      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();

      factory.setValidating(false);
      factory.setIgnoringComments(true);
      factory.setIgnoringElementContentWhitespace(true);

      // parses configuration xml
      /*-
       * Warning: Felix is unable to import the com.sun.rowset.internal
       * package, meaning this can't use the XmlErrorHandler. This causes
       * a warning and a default handler to be attached. Otherwise this
       * should have: builder.setErrorHandler(new XmlErrorHandler());
       */
      DocumentBuilder builder = factory.newDocumentBuilder();
      Document doc = builder.parse(stream);

      // iterates over nodes, parsing contents
      Node root = doc.getChildNodes().item(1);

      NodeList categories = root.getChildNodes();

      for (int i = 0; i < categories.getLength(); ++i) {
        Node node = categories.item(i);
        if (node.getNodeName().equals(NODE_DEFAULTS)) {
          parseDefaults(node.getChildNodes());
        } else if (node.getNodeName().equals(NODE_LOCALES)) {
          parseLocales(node.getChildNodes());
        } else {
          logger.warn("Unrecognized category: " + node.getNodeName());
        }
      }
    } catch (IOException exc) {
      logger.error("Unable to load spell checker parameters", exc);
    } catch (SAXException exc) {
      logger.error("Unable to parse spell checker parameters", exc);
    } catch (ParserConfigurationException exc) {
      logger.error("Unable to parse spell checker parameters", exc);
    }
  }
Esempio n. 9
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  // ## operation readReactorOutputFile(ReactionModel)
  public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
    // #[ operation readReactorOutputFile(ReactionModel)
    try {
      // open output file and build the DOM tree
      String dir = System.getProperty("RMG.workingDirectory");
      String filename = "chemkin/reactorOutput.xml";
      File inputFile = new File(filename);

      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
      factory.setValidating(true); // validate the document with the DTD
      factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
      DocumentBuilder builder = factory.newDocumentBuilder();
      Document doc = builder.parse(inputFile);

      // get root element and its children
      Element root = doc.getDocumentElement();
      NodeList rootchildren = root.getChildNodes();

      // header is rootchildren.item(0)

      // get return message and check for successful run
      Element returnmessageElement = (Element) rootchildren.item(1);
      Text returnmessageText = (Text) returnmessageElement.getFirstChild();
      String returnmessage = returnmessageText.toString();
      returnmessage = returnmessage.trim();
      if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
        System.out.println("External reactor model failed!");
        System.out.println("Reactor model error message: " + returnmessage);
        System.exit(0);
      }

      // get outputvalues element and its children
      Element outputvaluesElement = (Element) rootchildren.item(2);
      NodeList children = outputvaluesElement.getChildNodes();

      // get time
      Element timeElement = (Element) children.item(0);
      Text timeText = (Text) timeElement.getFirstChild();
      double time = Double.parseDouble(timeText.getData());
      String timeUnits = timeElement.getAttribute("units");

      // get systemstate element and its children
      Element systemstateElement = (Element) children.item(1);
      NodeList states = systemstateElement.getChildNodes();

      // get temperature and its units
      Element temperatureElement = (Element) states.item(0);
      String tempUnits = temperatureElement.getAttribute("units");
      Text temperatureText = (Text) temperatureElement.getFirstChild();
      double temp = Double.parseDouble(temperatureText.getData());
      Temperature T = new Temperature(temp, tempUnits);

      // get pressure and its units
      Element pressureElement = (Element) states.item(1);
      String presUnits = pressureElement.getAttribute("units");
      Text pressureText = (Text) pressureElement.getFirstChild();
      double pres = Double.parseDouble(pressureText.getData());
      Pressure P = new Pressure(pres, presUnits);

      // get species amounts (e.g. concentrations)
      ArrayList speciesIDs = new ArrayList();
      ArrayList amounts = new ArrayList();
      ArrayList fluxes = new ArrayList();
      String amountUnits = null;
      String fluxUnits = null;

      // loop thru all the species
      // begin at i=2, since T and P take already the first two position of states
      int nSpe = (states.getLength() - 2) / 2;
      int index = 0;
      LinkedHashMap inertGas = new LinkedHashMap();
      for (int i = 2; i < nSpe + 2; i++) {
        // get amount element and the units
        Element amountElement = (Element) states.item(i);
        amountUnits = amountElement.getAttribute("units");

        Element fluxElement = (Element) states.item(i + nSpe);
        fluxUnits = fluxElement.getAttribute("units");

        // get speciesid and store in an array list
        String thisSpeciesID = amountElement.getAttribute("speciesid");

        // get amount (e.g. concentraion) and store in an array list
        Text amountText = (Text) amountElement.getFirstChild();
        double thisAmount = Double.parseDouble(amountText.getData());
        if (thisAmount < 0) {
          double aTol = ReactionModelGenerator.getAtol();
          // if (Math.abs(thisAmount) < aTol) thisAmount = 0;
          // else throw new NegativeConcentrationException("Negative concentration in
          // reactorOutput.xml: " + thisSpeciesID);
          if (thisAmount < -100.0 * aTol)
            throw new NegativeConcentrationException(
                "Species "
                    + thisSpeciesID
                    + " has negative concentration: "
                    + String.valueOf(thisAmount));
        }

        // get amount (e.g. concentraion) and store in an array list
        Text fluxText = (Text) fluxElement.getFirstChild();
        double thisFlux = Double.parseDouble(fluxText.getData());

        if (thisSpeciesID.compareToIgnoreCase("N2") == 0
            || thisSpeciesID.compareToIgnoreCase("Ne") == 0
            || thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
          inertGas.put(thisSpeciesID, new Double(thisAmount));
        } else {
          speciesIDs.add(index, thisSpeciesID);
          amounts.add(index, new Double(thisAmount));
          fluxes.add(index, new Double(thisFlux));
          index++;
        }
      }

      // print results for debugging purposes
      /**
       * System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
       * System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
       * i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
       */
      ReactionTime rt = new ReactionTime(time, timeUnits);
      LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
      SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
      ss.inertGas = inertGas;
      return ss;
    } catch (Exception e) {
      System.out.println("Error reading reactor model output: " + e.getMessage());
      System.exit(0);
      return null;
    }

    // #]
  }
Esempio n. 10
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  public static MiningResult importFile(InputStream input) throws IOException {
    try {
      DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
      Document doc;
      // NodeList netNodes;
      dbf.setValidating(false);
      dbf.setIgnoringComments(true);
      dbf.setIgnoringElementContentWhitespace(true);
      // dbf.setExpandEntityReferences(false);
      // dbf.setNamespaceAware(false);

      DocumentBuilder db = dbf.newDocumentBuilder();

      db.setEntityResolver(
          new EntityResolver() {
            public InputSource resolveEntity(String publicId, String systemId) {
              if (systemId.indexOf("ARIS-Export") != -1) {
                return new InputSource("file:" + About.EXTLIBLOCATION() + "ARIS-Export101.dtd");
              } else {
                return null;
              }
            }
          });

      InputSource inpStream = new InputSource(input);
      inpStream.setSystemId("file:" + System.getProperty("user.dir", ""));
      doc = db.parse(inpStream);

      // check if root element is a aml tag
      Message.add("parsing done" + doc, Message.DEBUG);
      if (!(doc.getDocumentElement().getNodeName().equals("AML"))) {
        Message.add("aml tag not found", Message.ERROR);
        throw new Exception("aml tag not found");
      } else {
        Message.add("aml root element found");
      }

      EPCResult result = new EPCResult(null, (EPC) null);
      HashMap ObjDef_LinkId = new HashMap();
      HashMap modelid_net = new HashMap();
      HashMap ObjDef_Name = new HashMap();
      HashMap function_LinkId = new HashMap();
      HashMap ModelId_ModelType = new HashMap();
      traverseAMLforObjectNames(
          ObjDef_Name, doc.getDocumentElement(), ObjDef_LinkId, ModelId_ModelType);
      Iterator findLinkToEpc = ObjDef_LinkId.keySet().iterator();
      while (findLinkToEpc.hasNext()) {
        String currentObjDef = (String) findLinkToEpc.next();
        String Links = (String) ObjDef_LinkId.get(currentObjDef);
        StringTokenizer linkSet = new StringTokenizer(Links);
        String realEpcLink = "";
        while (linkSet.hasMoreTokens()) {
          String currentLink = linkSet.nextToken();
          if (ModelId_ModelType.get(currentLink).equals("MT_EEPC")) {
            realEpcLink = currentLink;
            break;
          }
        }
        if (realEpcLink.equals(" ")) {
          ObjDef_LinkId.remove(currentObjDef);
        } else {
          ObjDef_LinkId.put(currentObjDef, realEpcLink);
        }
      }
      result =
          traverseAML(
              result,
              doc.getDocumentElement(),
              null,
              ObjDef_Name,
              ObjDef_LinkId,
              modelid_net,
              function_LinkId);
      Iterator hierarchicalFunctions = function_LinkId.keySet().iterator();
      while (hierarchicalFunctions.hasNext()) {
        EPCSubstFunction f = (EPCSubstFunction) hierarchicalFunctions.next();
        f.setSubstitutedEPC((EPC) modelid_net.get(function_LinkId.get(f)));
        // Message.add(f.getSubstitutedEPC().getName());
      }

      return result;

    } catch (Throwable x) {
      Message.add(x.toString());
      throw new IOException(x.getMessage());
    }
  }
Esempio n. 11
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  protected Document parse(InputStream inputStream) throws LibraryException {
    Map<Integer, SongBean> songMap = new HashMap<Integer, SongBean>();
    Map<Integer, AlbumBean> albumMap = new HashMap<Integer, AlbumBean>();
    Map<Integer, AlbumBean> secondaryAlbumMap = new HashMap<Integer, AlbumBean>();
    warningList.clear();

    try {
      // Create a builder factory
      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
      factory.setValidating(false);
      factory.setNamespaceAware(true);
      factory.setIgnoringElementContentWhitespace(true);
      factory.setIgnoringComments(true);

      // Create the builder and parse the file
      DocumentBuilder builder = factory.newDocumentBuilder();

      // Set an error listener and parse the document
      builder.setErrorHandler(new iTradeTunesLibraryErrorHandler());
      builder.setEntityResolver(new iTradeTunesLibraryResolver());
      Document document = builder.parse(inputStream);

      synchronized (libraryList) {
        // Query the library document and build the library list
        XPath xPath = XPathFactory.newInstance().newXPath();
        XPathExpression xPathExpression = xPath.compile(XPATH_LIBRARY_LIST);
        NodeList nodelist = (NodeList) xPathExpression.evaluate(document, XPathConstants.NODESET);

        // Process the elements in the nodelist
        SongBean song = null;

        for (int i = 0; i < nodelist.getLength(); i++) {
          boolean isTrackID = false;

          // Get element and child nodes
          Element elem = (Element) nodelist.item(i);
          NodeList list = elem.getChildNodes();

          // Get node value
          Node childKey = list.item(0);
          String key = childKey.getNodeValue();

          // Check if we have to create a new bean
          if (SongBean.NAME_TRACK_ID.equals(key)) {
            isTrackID = true;
            SongBean previousSong = song;
            song = new SongBean();
            if (previousSong != null
                && !("AAC audio file".equals(previousSong.getKind())
                    || "MPEG audio file".equals(previousSong.getKind()))) {
              songMap.remove(previousSong.getTrack_ID());
            } else {
              // Add an album bean
              addOrUpdateAlbum(albumMap, previousSong, false);
            }
          }

          // The first parameter is the key
          String prop = childKey.getNodeValue().replace(' ', '_');

          // The second parameter is the value
          i++;

          // Get element and child nodes
          elem = (Element) nodelist.item(i);

          // Check for boolean properties
          Object value = null;
          // Get node value
          list = elem.getChildNodes();
          childKey = list.item(0);
          value = (childKey == null) ? elem.getNodeName() : childKey.getNodeValue();

          if (isTrackID) {
            isTrackID = false;
          }

          // Set the property of the song bean
          Statement stmt = new Statement(song, "set" + prop, new Object[] {value});
          try {
            stmt.execute();

          } catch (Exception e) {
            // Ignore that field, we do not have it in our bean
          }

          // If the property is the track ID, add the song to the hash
          // map
          if (SongBean.NAME_TRACK_ID.equals(key)) {
            int trackID = Integer.valueOf((String) value);
            songMap.put(trackID, song);
          }
        }

        // Update album for last song
        addOrUpdateAlbum(albumMap, song, false);

        // Check the album map for inconsistencies
        Iterator<AlbumBean> albums = albumMap.values().iterator();
        while (albums.hasNext()) {
          AlbumBean album = albums.next();
          if (album.checkConsistency()) {
            libraryList.add(album);
            album.setHashCode();
          } else {
            // Add an inconsistent album only using the album title
            SongBean[] songs = album.getSongs();
            for (int i = 0; i < songs.length; i++) {
              addOrUpdateAlbum(secondaryAlbumMap, songs[i], true);
            }
          }
        }

        // Check secondary album map for consistency
        albums = secondaryAlbumMap.values().iterator();
        while (albums.hasNext()) {
          AlbumBean album = albums.next();
          if (album.checkConsistency()) {
            libraryList.add(album);
            album.setHashCode();
          } else {
            // This album cannot be matched
            // TODO: Add to warning message
          }
        }

        setChanged();
      }

      return document;
    } catch (IOException ioe) {
      // Log an expected connect exception
      throw new LibraryException(ioe);
    } catch (SAXException se) {
      // Catch all other exceptions
      throw new LibraryException(se);
    } catch (ParserConfigurationException pce) {
      // Catch all other exceptions
      Utils.logSevere(pce);
      throw new LibraryException(pce);
    } catch (XPathExpressionException xpe) {
      // Catch all other exceptions
      Utils.logSevere(xpe);
      throw new LibraryException(xpe);
    } catch (NumberFormatException nfe) {
      // Catch all other exceptions
      throw new LibraryException(nfe);
    }
  }
Esempio n. 12
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 @Override
 protected DocumentBuilderFactory getDocBuilderFactory() {
   DocumentBuilderFactory factory = super.getDocBuilderFactory();
   factory.setValidating(true);
   return factory;
 }