Esempio n. 1
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  private static void validateXMLWithURL(File nmlFile, String schemaUrl) {

    try {
      Source schemaFileSource = new StreamSource(schemaUrl);

      SchemaFactory factory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);

      Schema schema = factory.newSchema(schemaFileSource);

      Validator validator = schema.newValidator();

      Source xmlFileSource = new StreamSource(nmlFile);

      validator.validate(xmlFileSource);

      System.out.println(
          "****   File: " + nmlFile + " is VALID according to " + schemaUrl + "!!!    ****");

    } catch (Exception ex) {
      System.err.println(
          "Problem validating xml file: "
              + nmlFile.getAbsolutePath()
              + " according to "
              + schemaUrl
              + "!!!");
      ex.printStackTrace();

      System.exit(1);
    }
  }
Esempio n. 2
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  public ArrayList<String> collectLinks(String p) {
    ArrayList<String> PageLinks = new ArrayList<String>();
    try {

      URL url = new URL(p);
      BufferedReader br3 = new BufferedReader(new InputStreamReader(url.openStream()));
      String str = "";
      while (null != (str = br3.readLine())) {
        Pattern link =
            Pattern.compile(
                "<a target=\"_top\" href=\"/m/.*", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
        Matcher match = link.matcher(str);
        while (match.find()) {
          String tmp = match.group();
          int start = tmp.indexOf('/');
          tmp = tmp.substring(start + 1, tmp.indexOf('\"', start + 1));
          if (Crawl.contains("http://www.rottentomatoes.com/" + tmp)
              || ToCrawl.contains("http://www.rottentomatoes.com/" + tmp)
              || PageLinks.contains("http://www.rottentomatoes.com/" + tmp)) continue;
          PageLinks.add("http://www.rottentomatoes.com/" + tmp);
          // bw4.write("http://www.rottentomatoes.com/"+tmp+"\r\n");
        }
      }

      br3.close();
    } catch (Exception ex) {
      ex.printStackTrace();
    }

    return PageLinks;
  }
Esempio n. 3
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  // ## operation runReactor()
  public void runReactor() {
    // #[ operation runReactor()
    // run reactor
    String dir = System.getProperty("RMG.workingDirectory");

    try {
      // system call for reactor
      String[] command = {dir + "/software/reactorModel/reactor.exe"};
      File runningDir = new File("chemkin");
      Process reactor = Runtime.getRuntime().exec(command, null, runningDir);
      InputStream ips = reactor.getInputStream();
      InputStreamReader is = new InputStreamReader(ips);
      BufferedReader br = new BufferedReader(is);
      String line = null;
      while ((line = br.readLine()) != null) {
        // System.out.println(line);
      }
      int exitValue = reactor.waitFor();
    } catch (Exception e) {
      System.out.println("Error in running reactor!");
      System.out.println(e.getMessage());
      System.exit(0);
    }

    // #]
  }
Esempio n. 4
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  // ## operation checkChemkinMessage()
  public void checkChemkinMessage() {
    // #[ operation checkChemkinMessage()
    try {
      String dir = System.getProperty("RMG.workingDirectory");
      String filename = "chemkin/chem.message";
      FileReader fr = new FileReader(filename);
      BufferedReader br = new BufferedReader(fr);

      String line = br.readLine().trim();
      if (line.startsWith("NO ERRORS FOUND ON INPUT")) {
        return;
      } else if (line.startsWith("WARNING...THERE IS AN ERROR IN THE LINKING FILE")) {
        System.out.println("Error in chemkin linking to reactor!");
        System.exit(0);
      } else {
        System.out.println("Unknown message in chem.message!");
        System.exit(0);
      }
    } catch (Exception e) {
      System.out.println("Can't read chem.message!");
      System.out.println(e.getMessage());
      System.exit(0);
    }

    // #]
  }
Esempio n. 5
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  public static void writeChemkinInputFile(ReactionSystem rs) {
    // #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)

    StringBuilder result = new StringBuilder();
    result.append(writeChemkinHeader());
    result.append(writeChemkinElement());
    double start = System.currentTimeMillis();
    result.append(writeChemkinSpecies(rs.reactionModel, rs.initialStatus));
    result.append(writeChemkinThermo(rs.reactionModel));
    Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
    start = System.currentTimeMillis();
    result.append(writeChemkinPdepReactions(rs));
    Global.chemkinReaction =
        Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;

    String dir = System.getProperty("RMG.workingDirectory");
    if (!dir.endsWith("/")) dir += "/";
    dir += "software/reactorModel/";
    String file = "chemkin/chem.inp";

    try {
      FileWriter fw = new FileWriter(file);
      fw.write(result.toString());
      fw.close();
    } catch (Exception e) {
      System.out.println("Error in writing chemkin input file chem.inp!");
      System.out.println(e.getMessage());
      System.exit(0);
    }

    // #]
  }
Esempio n. 6
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 private void deflate(String tmpDir, String path) {
   String tmpFile = "tmp-" + Utils.timestamp() + ".zip";
   try {
     ZipFile zipFile = new ZipFile(tmpFile);
     ZipParameters parameters = new ZipParameters();
     parameters.setCompressionMethod(Zip4jConstants.COMP_DEFLATE);
     parameters.setCompressionLevel(Zip4jConstants.DEFLATE_LEVEL_NORMAL);
     parameters.setIncludeRootFolder(false);
     zipFile.addFolder(tmpDir, parameters);
   } catch (Exception e) {
     e.printStackTrace();
     return;
   }
   File from = null;
   File to = null;
   try {
     File target = new File(path);
     if (target.exists()) FileUtils.forceDelete(target);
     from = new File(tmpFile);
     to = new File(path);
     FileUtils.moveFile(from, to);
   } catch (IOException e) {
     Utils.onError(new Error.FileMove(tmpFile, path));
   }
   try {
     FileUtils.deleteDirectory(new File(tmpDir));
   } catch (IOException e) {
     Utils.log("can't delete temporary folder");
   }
 }
Esempio n. 7
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  // ## operation writeChemkinInputFile(ReactionModel,SystemSnapshot)
  public static void writeChemkinInputFile(
      final ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
    // #[ operation writeChemkinInputFile(ReactionModel,SystemSnapshot)

    StringBuilder result = new StringBuilder();
    result.append(writeChemkinHeader());
    result.append(writeChemkinElement());
    double start = System.currentTimeMillis();
    result.append(writeChemkinSpecies(p_reactionModel, p_beginStatus));
    result.append(writeChemkinThermo(p_reactionModel));
    Global.chemkinThermo = Global.chemkinThermo + (System.currentTimeMillis() - start) / 1000 / 60;
    start = System.currentTimeMillis();
    result.append(
        writeChemkinPdepReactions(
            p_reactionModel, p_beginStatus)); // 10/26/07 gmagoon: changed to pass p_beginStatus
    // result.append(writeChemkinPdepReactions(p_reactionModel));
    Global.chemkinReaction =
        Global.chemkinReaction + (System.currentTimeMillis() - start) / 1000 / 60;

    String dir = System.getProperty("RMG.workingDirectory");
    if (!dir.endsWith("/")) dir += "/";
    dir += "software/reactorModel/";
    String file = "chemkin/chem.inp";

    try {
      FileWriter fw = new FileWriter(file);
      fw.write(result.toString());
      fw.close();
    } catch (Exception e) {
      System.out.println("Error in writing chemkin input file chem.inp!");
      System.out.println(e.getMessage());
      System.exit(0);
    }

    if (PDepRateConstant.getMode() == Mode.CHEBYSHEV
        || PDepRateConstant.getMode() == Mode.PDEPARRHENIUS
        || PDepRateConstant.getMode() == Mode.RATE) {
      StringBuilder gridOfRateCoeffs = new StringBuilder();
      gridOfRateCoeffs.append(writeGridOfRateCoeffs(p_reactionModel));
      String newFile = "chemkin/tableOfRateCoeffs.txt";
      try {
        FileWriter fw = new FileWriter(newFile);
        fw.write(gridOfRateCoeffs.toString());
        fw.close();
      } catch (Exception e) {
        System.out.println("Error in writing tableOfRateCoeffs.txt");
        System.out.println(e.getMessage());
        System.exit(0);
      }
    }

    // #]
  }
Esempio n. 8
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 private String inflate(String path) {
   if (!new File(path).canRead()) {
     Utils.onError(new Error.FileRead(path));
     return null;
   }
   String tmpDir = "tmp-" + Utils.timestamp();
   try {
     ZipFile zipFile = new ZipFile(path);
     zipFile.extractAll(tmpDir);
   } catch (Exception e) {
     e.printStackTrace();
     return null;
   }
   return tmpDir;
 }
Esempio n. 9
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  /**
   * Removes empty #text nodes from a document. From James Murty on this StackOverflow post:
   * http://stackoverflow.com/questions/978810/how-to-strip-whitespace-only-text-nodes-from-a-dom-before-serialization
   *
   * @param doc The document to remove empty text nodes from.
   */
  private static void removeEmptyTextNodes(Document doc) {
    try {
      XPathFactory xpathFactory = XPathFactory.newInstance();
      // XPath to find empty text nodes.
      XPathExpression xpathExp =
          xpathFactory.newXPath().compile("//text()[normalize-space(.) = '']");
      NodeList emptyTextNodes = (NodeList) xpathExp.evaluate(doc, XPathConstants.NODESET);

      // Remove each empty text node from document.
      for (int i = 0; i < emptyTextNodes.getLength(); i++) {
        Node emptyTextNode = emptyTextNodes.item(i);
        emptyTextNode.getParentNode().removeChild(emptyTextNode);
      }
    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }
Esempio n. 10
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  /**
   * Gets the string of an XML document containing multiple words for saving purposes.
   *
   * @param words The words to save.
   * @return String containing XML containing all words.
   */
  public static String getMultipleWordXML(Word[] words) {
    try {
      DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
      DocumentBuilder db = dbf.newDocumentBuilder();
      Document doc = db.newDocument();
      Element root = doc.createElement("Root");
      for (int i = 0; i < words.length; i++) {
        root.appendChild(words[i].getWordXMLNode(doc));
      }
      doc.appendChild(root);
      return getStringFromDocument(doc);

    } catch (Exception ex) {
      ex.printStackTrace();
      return null;
    }
  }
Esempio n. 11
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  public static void main(String[] args) {
    try {
      // open existing file
      File xmlFile = new File(userFile);
      DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
      DocumentBuilder dbuild = dbfac.newDocumentBuilder();
      Document doc = dbuild.parse(xmlFile);

      //			DocumentBuilderFactory dbfac2 = DocumentBuilderFactory.newInstance();
      //			DocumentBuilder docBuilder = dbfac2.newDocumentBuilder();
      //			Document doc2 = docBuilder.parse(xmlFile);
      //			doc.getDocumentElement().normalize();

    } catch (Exception e) {
      System.err.println(e.getMessage());
    }
  }
Esempio n. 12
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 /**
  * Gets the definitions of a word, sets the main one if necessary, and returns it.
  *
  * @param overwrite if true, then function will attempt to retrieve from online even if the
  *     definition is already set.
  * @return String containing the main definition of the word.
  */
 public static Word[] getWordsFromFile(ByteArrayInputStream inputStream) {
   try {
     // now to parse the XML
     DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
     DocumentBuilder db = dbf.newDocumentBuilder();
     Document doc = db.parse(inputStream);
     removeEmptyTextNodes(doc);
     NodeList wordList = doc.getElementsByTagName("WordDefinitions");
     int wordCount = wordList.getLength();
     Word[] returnWords = new Word[wordCount];
     for (int wordi = 0; wordi < wordCount; wordi++) {
       NodeList list = ((Element) wordList.item(wordi)).getElementsByTagName("Definition");
       Element wordElement = (Element) wordList.item(wordi);
       String word = wordElement.getAttribute("word");
       String mainDefinition = wordElement.getAttribute("mainDefinition");
       int numDefinitions = list.getLength();
       Definition[] wordOtherDefinitions = new Definition[numDefinitions];
       for (int i = 0; i < numDefinitions; i++) {
         Node node = list.item(i);
         NodeList children = node.getChildNodes(); // gets each child node of the definition
         // get all data
         String definition = children.item(XML_DEFINITION_LOC).getTextContent();
         String theWord = children.item(XML_WORD_LOC).getTextContent();
         NodeList dictionaryNode = children.item(XML_DICTIONARY_BRANCH_LOC).getChildNodes();
         String dictionaryId = dictionaryNode.item(XML_DICTIONARY_ID_LOC).getTextContent();
         String dictionaryName = dictionaryNode.item(XML_DICTIONARY_NAME_LOC).getTextContent();
         // now we've got all the data lets add it to the array
         wordOtherDefinitions[i] =
             new Definition(dictionaryName, dictionaryId, definition, theWord);
       }
       if (wordOtherDefinitions.length == 0) {
         wordOtherDefinitions =
             new Definition[] {new Definition("nil", "nil", "NO DEFINITION FOUND", word)};
       }
       Word currentWord = new Word(word, mainDefinition);
       currentWord.setOtherDefinitions(wordOtherDefinitions);
       returnWords[wordi] = currentWord;
     }
     return returnWords;
   } catch (Exception ex) {
     ex.printStackTrace();
     return null;
   }
 }
Esempio n. 13
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  /** used for cut and paste. */
  public void addObjectFromClipboard(String a_value) throws CircularIncludeException {
    Reader reader = new StringReader(a_value);
    Document document = null;
    try {
      document = UJAXP.getDocument(reader);
    } catch (Exception e) {
      e.printStackTrace();
      return;
    } // try-catch

    Element root = document.getDocumentElement();
    if (!root.getNodeName().equals("clipboard")) {
      return;
    } // if

    Node child;
    for (child = root.getFirstChild(); child != null; child = child.getNextSibling()) {
      if (!(child instanceof Element)) {
        continue;
      } // if
      Element element = (Element) child;

      IGlyphFactory factory = GlyphFactory.getFactory();

      if (XModule.isMatch(element)) {
        EModuleInvoke module = (EModuleInvoke) factory.createXModule(element);
        addModule(module);
        continue;
      } // if

      if (XContour.isMatch(element)) {
        EContour contour = (EContour) factory.createXContour(element);
        addContour(contour);
        continue;
      } // if

      if (XInclude.isMatch(element)) {
        EIncludeInvoke include = (EIncludeInvoke) factory.createXInclude(element);
        addInclude(include);
        continue;
      } // if
    } // while
  }
Esempio n. 14
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  public static String errorMessage(Exception exception) {
    String message = "";
    try {
      String addErrorMessage = getErrorStackString(exception.getStackTrace());

      message = exception.toString();

      return "<errortext>"
          + message
          + "</errortext>".replaceAll("\"", "'")
          + "<stack>"
          + addErrorMessage.replaceAll(">", "-").replaceAll("<", "-")
          + "</stack>\n\r";
    } catch (Exception e) {
      System.out.println(e);
      e.printStackTrace();
      return "";
    }
  }
Esempio n. 15
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  /**
   * Gets XML string for this definition so that it may be printed.
   *
   * @return XML node that can be saved of this word.
   */
  public Element getWordXMLNode(Document doc) {
    try {
      Element rootWordElement = doc.createElement("WordDefinitions");
      rootWordElement.setAttribute("word", this.word);
      rootWordElement.setAttribute("mainDefinition", this.getMainDefinition());
      if (this.otherDefinitions == null) {
        this.getDefinitions();
      }
      for (int i = 0; i < this.otherDefinitions.length; i++) {
        // main definition node
        Element definition = doc.createElement("Definition");

        // word
        Element word = doc.createElement("Word");
        word.setTextContent(otherDefinitions[i].getWord());

        // dictionary
        Element dictionary = doc.createElement("Dictionary");
        Element id = doc.createElement("Id");
        id.setTextContent(otherDefinitions[i].getId());
        Element source = doc.createElement("Name");
        source.setTextContent(otherDefinitions[i].getSource());
        dictionary.appendChild(id);
        dictionary.appendChild(source);

        // definition
        Element wordDefinition = doc.createElement("WordDefinition");
        wordDefinition.setTextContent(otherDefinitions[i].getDefinition());

        // append all the children
        definition.appendChild(word);
        definition.appendChild(dictionary);
        definition.appendChild(wordDefinition);
        rootWordElement.appendChild(definition);
      }
      return rootWordElement;
    } catch (Exception ex) {
      ex.printStackTrace();
      return null;
    }
  }
Esempio n. 16
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 /**
  * Gets a ByteArrayInputStream to parse a word from the definition API.
  *
  * @return ByteArrayInputStream containing definition XML, null if trouble parsing or getting the
  *     definition.
  */
 public ByteArrayInputStream getStreamFromOnlineXML() {
   try {
     // download the xml definition page of the word
     String urlSafeWord = URLEncoder.encode(this.word, "UTF-8");
     InputStream response = new URL(SERVICE_URL + urlSafeWord).openStream();
     Scanner responseReader = new Scanner(response).useDelimiter("\\A");
     if (responseReader.hasNext()) {
       // gets a clean version of xml the document can parse
       String xml = responseReader.next();
       response.close();
       xml = xml.trim().replaceFirst("^([\\W]+)<", "<");
       ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("utf-8"));
       return stream;
     } else {
       return null;
     }
   } catch (Exception ex) {
     ex.printStackTrace();
     return null;
   }
 }
Esempio n. 17
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 /**
  * Gets the definitions of a word, sets the main one if necessary, and returns it.
  *
  * @param overwrite if true, then function will attempt to retrieve from online even if the
  *     definition is already set.
  * @return String containing the main definition of the word.
  */
 public String getDefinitions(ByteArrayInputStream inputStream, boolean overwrite) {
   if (overwrite || (definition == null || definition.isEmpty())) {
     // get definition from online service
     // if not able to access internet, then do something
     try {
       // now to parse the XML
       DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
       DocumentBuilder db = dbf.newDocumentBuilder();
       Document doc = db.parse(inputStream);
       removeEmptyTextNodes(doc);
       NodeList list = doc.getElementsByTagName("Definition");
       int numDefinitions = list.getLength();
       otherDefinitions = new Definition[numDefinitions];
       for (int i = 0; i < numDefinitions; i++) {
         Node node = list.item(i);
         NodeList children = node.getChildNodes(); // gets each child node of the definition
         // get all data
         String definition = children.item(XML_DEFINITION_LOC).getTextContent();
         String word = children.item(XML_WORD_LOC).getTextContent();
         NodeList dictionaryNode = children.item(XML_DICTIONARY_BRANCH_LOC).getChildNodes();
         String dictionaryId = dictionaryNode.item(XML_DICTIONARY_ID_LOC).getTextContent();
         String dictionaryName = dictionaryNode.item(XML_DICTIONARY_NAME_LOC).getTextContent();
         // now we've got all the data lets add it to the array
         otherDefinitions[i] = new Definition(dictionaryName, dictionaryId, definition, word);
       }
       if (otherDefinitions.length == 0) {
         otherDefinitions =
             new Definition[] {new Definition("nil", "nil", "NO DEFINITION FOUND", word)};
       }
       this.setMainDefinition(otherDefinitions[0].getDefinition());
       return otherDefinitions[0].getDefinition();
     } catch (Exception ex) {
       ex.printStackTrace();
       return "ERROR! " + ex;
     }
   } else {
     return this.definition;
   }
 }
 public Command executeStep(Element stepRow) throws Exception {
   Command command = new Command();
   NodeList stepFields = stepRow.getElementsByTagName("td");
   String cmd = stepFields.item(0).getTextContent().trim();
   command.cmd = cmd;
   ArrayList<String> argList = new ArrayList<String>();
   if (stepFields.getLength() == 1) {
     // skip comments
     command.result = "OK";
     return command;
   }
   for (int i = 1; i < stepFields.getLength(); i++) {
     String content = stepFields.item(i).getTextContent();
     content = content.replaceAll(" +", " ");
     content = content.replace('\u00A0', ' ');
     content = content.trim();
     argList.add(content);
   }
   String args[] = argList.toArray(new String[0]);
   command.args = args;
   if (this.verbose) {
     System.out.println(cmd + " " + Arrays.asList(args));
   }
   try {
     command.result = this.commandProcessor.doCommand(cmd, args);
     command.error = false;
   } catch (Exception e) {
     command.result = e.getMessage();
     command.error = true;
   }
   command.failure = command.error && !cmd.startsWith("verify");
   if (this.verbose) {
     System.out.println(command.result);
   }
   return command;
 }
Esempio n. 19
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  /** @param args the command line arguments */
  public static void main(String[] args) {
    // TODO code application logic here
    Model model;
    String insertstmt;
    String insertmodel = "",
        insertspecies = "",
        insertcompartment = "",
        insertfunction = "",
        insertunitdef = "",
        insertunits = "",
        insertreaction = "",
        insertreactant = "",
        insertproduct = "";
    String insertmodifier = "",
        insertklaw = "",
        insertrules = "",
        insertconstraint = "",
        insertdelay = "",
        inserttrigger = "",
        insertevent = "",
        inserteventassign = "",
        insertparameter = "";
    String insertstatement = "";
    String server, user, password, dbname, filepath;

    String Filedata = "";

    String cwd = System.getProperty("user.dir");

    if (args.length == 0) {
      server = "localhost";
      user = "******";
      password = "******";
      dbname = "sbmldb2";

      /**
       * Path to extract the SBML files from database, where cwd is
       * "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
       * mention folder name instead of extractedbm folder
       */
      filepath = cwd + "\\extractedbm\\";
    } else {
      server = args[0];
      user = args[1];
      password = args[2];
      dbname = args[3];
      filepath = args[4];
    }

    try {
      Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
    } catch (Exception e) {
      e.printStackTrace();
    }

    Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
    // String modelids.getId() = "MorrisonAllegra" ;

    ASTNode math = null;
    int level = 0, version = 0;

    ArrayList<modellist> modelidlist = sql.getmodels();
    insertstatement =
        "LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
    insertstatement =
        insertstatement
            + "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
    insertstatement =
        insertstatement
            + "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
    insertstatement =
        insertstatement
            + "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
            + ";";

    for (modellist modelids : modelidlist) {

      ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());

      for (modellist modellv : modellevel) {
        level = modellv.getlevel();
        version = modellv.getversion();
      }

      SBMLDocument doc = new SBMLDocument(level, version);

      ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());

      if (!modellists.isEmpty())
        insertmodel =
            insertmodel
                + "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
      for (modellist models : modellists) {
        insertmodel =
            insertmodel
                + "(\'"
                + models.getId()
                + "\',\'"
                + models.getName()
                + "\',"
                + models.getlevel()
                + ","
                + models.getversion()
                + ",\'"
                + models.getnotes()
                + "\',\'"
                + models.getannotation().toString()
                + "\'),";
        model = doc.createModel(models.getId());
        model.setName(models.getName());
        // System.out.println("model : " + models.getId());
        // model.setNotes(models.getnotes());  // there is some null exception is command line run
        // but run perfectly from netbeans so ommented out
        if (!models.getannotation().equals("")) {
          Annotation annot = new Annotation(models.getannotation().toString());
          model.setAnnotation(annot);
        }
        doc.setModel(model);
      }
      if (!modellists.isEmpty()) {
        insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
        insertmodel = insertmodel + ';';
      }
      //   insertmodel = insertmodel + "\nUNLOCK TABLES;";
      //  System.out.println(insertmodel);

      ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());

      if (!specieslist.isEmpty())
        insertspecies =
            insertspecies
                + "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
      for (SpeciesList species : specieslist) {
        insertspecies =
            insertspecies
                + "(\'"
                + species.getId()
                + "\',\'"
                + species.getName()
                + "\',\'"
                + species.getcompartment()
                + "\',"
                + species.getia()
                + ","
                + species.getic()
                + ",\'"
                + species.getsu()
                + "\',"
                + species.gethosu()
                + ","
                + species.getbc()
                + ","
                + species.getconstant()
                + ","
                + species.getcf()
                + ",\'"
                + modelids.getId()
                + "\',\'"
                + species.getannotation()
                + "\'),";
        Species sp = doc.getModel().createSpecies(species.getId());
        sp.setName(species.getName());
        sp.setCompartment(species.getcompartment());
        sp.setConstant(species.getconstant());
        sp.setInitialAmount(species.getia());
        sp.setInitialConcentration(species.getic());
        sp.setHasOnlySubstanceUnits(species.gethosu());
        if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
        sp.setBoundaryCondition(species.getbc());
        sp.setSubstanceUnits(species.getsu());
        if (!species.getannotation().equals("")) {
          Annotation annot = new Annotation(species.getannotation().toString());
          sp.setAnnotation(annot);
        }
        // doc.getModel().addSpecies(sp) ;
      }
      if (!specieslist.isEmpty()) {
        insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
        insertspecies = insertspecies + ';';
      }

      ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());

      if (!complist.isEmpty())
        insertcompartment =
            insertcompartment
                + "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";

      for (CompartmentList comp : complist) {
        insertcompartment =
            insertcompartment
                + "(\'"
                + comp.getId()
                + "\',\'"
                + comp.getName()
                + "\',"
                + comp.getconstant()
                + ",\'"
                + modelids.getId()
                + "\',"
                + comp.getspatialdimensions()
                + ","
                + comp.getsize()
                + ","
                + comp.getunits()
                + "\'),";
        Compartment c = doc.getModel().createCompartment(comp.getId());
        c.setName(comp.getName());
        c.setConstant(comp.getconstant());
        c.setSize(comp.getsize());
        c.setSpatialDimensions(comp.getspatialdimensions());
        if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
        // doc.getModel().addSpecies(sp) ;
      }
      if (!complist.isEmpty()) {
        insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
        insertcompartment = insertcompartment + ';';
      }

      ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());

      if (!funclist.isEmpty())
        insertfunction =
            insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";

      for (functionList func : funclist) {
        insertfunction =
            insertfunction
                + "(\'"
                + func.getId()
                + "\',\'"
                + func.getxmlns()
                + "\',\'"
                + modelids.getId()
                + "\'),";
        FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());

        try {
          math = ASTNode.parseFormula(func.getxmlns());
          fd.setMath(math);
        } catch (Exception e) {
          e.printStackTrace();
        }
      }
      if (!funclist.isEmpty()) {
        insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
        insertfunction = insertfunction + ';';
      }

      ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());

      if (!unitlist.isEmpty())
        insertunitdef =
            insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";

      for (unitList units : unitlist) {
        insertunitdef =
            insertunitdef
                + "(\'"
                + units.getId()
                + "\',\'"
                + units.getName()
                + "\',\'"
                + modelids.getId()
                + "\'),";

        UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
        ud.setName(units.getName());
        ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());

        if (!unitdeflist.isEmpty())
          insertunits =
              insertunits
                  + "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";

        for (unitList unitdef : unitdeflist) {
          insertunits =
              insertunits
                  + "(\'"
                  + units.getId()
                  + "\',\'"
                  + unitdef.getkind()
                  + "\',"
                  + unitdef.getscale()
                  + ","
                  + unitdef.getexponent()
                  + ","
                  + unitdef.getmultiplier()
                  + "),";
          Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
          u.setScale(unitdef.getscale());
          u.setExponent(unitdef.getexponent());
          u.setMultiplier(unitdef.getmultiplier());
        }
        // doc.getModel().addSpecies(sp) ;
        if (!unitdeflist.isEmpty()) {
          insertunits = insertunits.substring(0, insertunits.length() - 1);
          insertunits = insertunits + ';';
        }
      }
      if (!unitlist.isEmpty()) {
        insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
        insertunitdef = insertunitdef + ';';
      }

      ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());

      if (!reactionlist.isEmpty())
        insertreaction =
            insertreaction
                + "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";

      for (reactionList reaction : reactionlist) {
        insertreaction =
            insertreaction
                + "(\'"
                + reaction.getId()
                + "\',\'"
                + reaction.getName()
                + "\',"
                + reaction.getreversible()
                + ","
                + reaction.getfast()
                + ",\'"
                + modelids.getId()
                + "\',\'"
                + reaction.getcompartment()
                + "\',\'"
                + reaction.getannotation()
                + "\'),";
        Reaction rn = doc.getModel().createReaction(reaction.getId());
        rn.setName(reaction.getName());
        if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
        rn.setFast(reaction.getfast());
        rn.setReversible(reaction.getreversible());
        if (!reaction.getannotation().equals("")) {
          Annotation annot = new Annotation(reaction.getannotation().toString());
          rn.setAnnotation(annot);
        }

        ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());

        if (!reactantlist.isEmpty())
          insertreactant =
              insertreactant
                  + "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
        for (reactionList reactant : reactantlist) {
          insertreactant =
              insertreactant
                  + "(\'"
                  + reaction.getId()
                  + "\',\'"
                  + reactant.getspecies()
                  + "\',\'"
                  + reactant.getsboTerm()
                  + "\',"
                  + reactant.getstoichometry()
                  + ","
                  + reactant.getconstant()
                  + ",\'reactants\'),";
          SpeciesReference rt = new SpeciesReference();
          rt.setName(reactant.getspecies());
          rt.setSpecies(reactant.getspecies());
          // rt.setSBOTerm(reactant.getsboTerm());
          rt.setStoichiometry(reactant.getstoichometry());
          //    rt.setConstant(reactant.getconstant());
          rn.addReactant(rt);
        }
        if (!reactantlist.isEmpty()) {
          insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
          insertreactant = insertreactant + ';';
        }

        ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());

        if (!productlist.isEmpty())
          insertproduct =
              insertproduct
                  + "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
        for (reactionList product : productlist) {
          insertproduct =
              insertproduct
                  + "(\'"
                  + reaction.getId()
                  + "\',\'"
                  + product.getspecies()
                  + "\',\'"
                  + product.getsboTerm()
                  + "\',"
                  + product.getstoichometry()
                  + ","
                  + product.getconstant()
                  + ",\'products\'),";
          SpeciesReference pr = new SpeciesReference();
          pr.setName(product.getspecies());
          pr.setSpecies(product.getspecies());
          //   pr.setSBOTerm(product.getsboTerm());
          pr.setStoichiometry(product.getstoichometry());
          //    pr.setConstant(product.getconstant());
          rn.addProduct(pr);
        }
        if (!productlist.isEmpty()) {
          insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
          insertproduct = insertproduct + ';';
        }

        ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());

        if (!modifierlist.isEmpty())
          insertmodifier =
              insertmodifier
                  + "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
        for (reactionList modifier : modifierlist) {
          insertmodifier =
              insertmodifier
                  + "(\'"
                  + reaction.getId()
                  + "\',\'"
                  + modifier.getspecies()
                  + "\',\'"
                  + modifier.getsboTerm()
                  + "\',\'modifiers\'),";
          ModifierSpeciesReference m = new ModifierSpeciesReference();
          m.setName(modifier.getspecies());
          m.setSpecies(modifier.getspecies());
          //    m.setSBOTerm(modifier.getsboTerm());
          rn.addModifier(m);
        }
        if (!modifierlist.isEmpty()) {
          insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
          insertmodifier = insertmodifier + ';';
        }

        ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());

        if (!klawlist.isEmpty())
          insertklaw =
              insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
        for (reactionList klaw : klawlist) {
          insertklaw =
              insertklaw
                  + "(\'"
                  + reaction.getId()
                  + "\',\'"
                  + klaw.getId()
                  + "\',\'"
                  + klaw.getmath()
                  + "\',\'"
                  + klaw.getannotation()
                  + "\'),";
          KineticLaw kl = rn.createKineticLaw();
          try {
            math = ASTNode.parseFormula(klaw.getmath());
            kl.setMath(math);
            if (!klaw.getannotation().equals("")) {
              Annotation annot = new Annotation(klaw.getannotation().toString());
              kl.setAnnotation(annot);
            }
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
        if (!klawlist.isEmpty()) {
          insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
          insertklaw = insertklaw + ';';
        }
      }
      if (!reactionlist.isEmpty()) {
        insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
        insertreaction = insertreaction + ';';
      }

      ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());

      if (!paralist.isEmpty())
        insertparameter =
            insertparameter
                + "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";

      for (parameterList para : paralist) {
        insertparameter =
            insertparameter
                + "(\'"
                + para.getId()
                + "\',\'"
                + para.getName()
                + "\',"
                + para.getvalue()
                + ","
                + para.getunits()
                + ","
                + para.getconstant()
                + ",\'"
                + modelids.getId()
                + "\'),";
        Parameter par = doc.getModel().createParameter(para.getId());
        par.setName(para.getId());
        par.setConstant(para.getconstant());
        par.setUnits(para.getunits());
        par.setValue(para.getvalue());
      }
      if (!paralist.isEmpty()) {
        insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
        insertparameter = insertparameter + ';';
      }

      ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());

      if (!conslist.isEmpty())
        insertconstraint =
            insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";

      for (constraintList constraint : conslist) {
        insertconstraint =
            insertconstraint
                + "(\'"
                + constraint.getmath()
                + "\',\'"
                + constraint.getmessage()
                + "\',\'"
                + modelids.getId()
                + "\'),";
        Constraint cons = doc.getModel().createConstraint();
        try {
          math = ASTNode.parseFormula(constraint.getmath());
          cons.setMath(math);
          cons.setMessage(constraint.getmessage());
        } catch (Exception e) {
          e.printStackTrace();
        }
      }
      if (!conslist.isEmpty()) {
        insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
        insertconstraint = insertconstraint + ';';
      }

      ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());

      if (!eventlist.isEmpty())
        insertevent =
            insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";

      for (eventsList events : eventlist) {
        insertevent =
            insertevent
                + "(\'"
                + events.getId()
                + "\',\'"
                + events.getName()
                + "\',"
                + events.getuservalues()
                + ",\'"
                + modelids.getId()
                + "\'),";
        Event ev = doc.getModel().createEvent(events.getId());
        ev.setName(events.getName());
        // ev.setUseValuesFromTriggerTime(events.getuservalues());

        ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());

        if (!triggerlist.isEmpty())
          inserttrigger =
              inserttrigger
                  + "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
        for (eventsList triggers : triggerlist) {
          Trigger tr = doc.getModel().createTrigger();
          try {
            math = ASTNode.parseFormula(triggers.getmath());
            tr.setMath(math);
            tr.setInitialValue(triggers.getinitialval());
            tr.setPersistent(triggers.getpersistent());
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
        if (!triggerlist.isEmpty()) {
          inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
          inserttrigger = inserttrigger + ';';
        }

        ArrayList<eventsList> delaylist = sql.getdelays(events.getId());

        if (!delaylist.isEmpty())
          insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
        for (eventsList delays : delaylist) {
          Delay d = doc.getModel().createDelay();
          try {
            math = ASTNode.parseFormula(delays.getmath());
            d.setMath(math);
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
        if (!delaylist.isEmpty()) {
          insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
          insertdelay = insertdelay + ';';
        }

        ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());

        if (!evasslist.isEmpty())
          inserteventassign =
              inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
        for (eventsList evassign : evasslist) {
          EventAssignment ea = doc.getModel().createEventAssignment();
          try {
            math = ASTNode.parseFormula(evassign.getmath());
            ea.setMath(math);
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
        if (!evasslist.isEmpty()) {
          inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
          inserteventassign = inserteventassign + ';';
        }
      }
      if (!eventlist.isEmpty()) {
        insertevent = insertevent.substring(0, insertevent.length() - 1);
        insertevent = insertevent + ';';
      }

      ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());

      if (!rulelist.isEmpty())
        insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
      for (ruleslist rules : rulelist) {
        insertrules =
            insertrules
                + "(\'"
                + rules.getId()
                + "\',\'"
                + rules.getmath()
                + "\',\'"
                + rules.getruletype()
                + "\',\'"
                + modelids.getId()
                + "\'),";
        if (rules.getruletype().equals("assignmentrule")) {
          Rule r = doc.getModel().createAssignmentRule();
          r.setMetaId(rules.getId());
          try {
            math = ASTNode.parseFormula(rules.getmath());
            r.setMath(math);
          } catch (Exception e) {
            e.printStackTrace();
          }
        }
      }
      if (!rulelist.isEmpty()) {
        insertrules = insertrules.substring(0, insertrules.length() - 1);
        insertrules = insertrules + ';';
      }

      SBMLWriter writer = new SBMLWriter();
      try {
        String Path = filepath + modelids.getId() + ".xml";
        writer.write(doc, Path);

        DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
        DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
        Document document = documentBuilder.parse(Path);
        Element root = document.getDocumentElement();
        Element newdataset = document.createElement("dataset");
        root.appendChild(newdataset);

        ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
        for (dataset ds : datasetlist) {
          // System.out.println(ds.getexpcond());

          Element name = document.createElement("experimentalcondition");
          name.setAttribute("bioelement", ds.getbioel());
          name.setAttribute("name", ds.getName());
          name.setAttribute("descr", ds.getdescr());
          name.setAttribute("expcond", ds.getexpcond());
          name.setAttribute("value", String.valueOf(ds.getvalue()));
          name.setAttribute("type", ds.gettype());
          name.setAttribute("uri", ds.geturi());
          newdataset.appendChild(name);
        }

        root.appendChild(newdataset);
        DOMSource source = new DOMSource(document);

        TransformerFactory transformerFactory = TransformerFactory.newInstance();
        Transformer transformer = transformerFactory.newTransformer();
        transformer.setOutputProperty(OutputKeys.INDENT, "yes");
        transformer.setOutputProperty(OutputKeys.METHOD, "xml");
        transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
        StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
        transformer.transform(source, result);
        System.out.println(
            "Files : "
                + modelids.getId()
                + ".xml and "
                + modelids.getId()
                + "d.xml have been generated successfully !!!");

      } catch (Exception e) {
        e.printStackTrace();
      }

      insertstatement =
          insertstatement
              + "\n\n"
              + insertmodel
              + "\n"
              + insertspecies
              + "\n"
              + insertcompartment
              + "\n"
              + insertfunction;
      insertstatement =
          insertstatement
              + "\n"
              + insertparameter
              + "\n"
              + insertreaction
              + "\n"
              + insertreactant
              + "\n"
              + insertproduct;
      insertstatement =
          insertstatement
              + "\n"
              + insertmodifier
              + "\n"
              + insertklaw
              + "\n"
              + insertunitdef
              + "\n"
              + insertunits;
      insertstatement =
          insertstatement
              + "\n"
              + insertrules
              + "\n"
              + insertconstraint
              + "\n"
              + insertevent
              + "\n"
              + inserttrigger
              + "\n"
              + insertdelay
              + "\n"
              + inserteventassign;

      insertcompartment = "";
      insertmodel = "";
      insertspecies = "";

      // System.out.println("document : " + doc);
    }
    insertstatement = insertstatement + "\nUNLOCK TABLES;";
    Filedata = Filedata + "\n\n\n" + insertstatement;

    try {
      wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
    } catch (IOException e) {
      e.printStackTrace();
    }
    // System.out.println(insertstatement);
  }
Esempio n. 20
0
  /**
   * XML Circuit constructor
   *
   * @param file the file that contains the XML description of the circuit
   * @param g the graphics that will paint the node
   * @throws CircuitLoadingException if the internal circuit can not be loaded
   */
  public CircuitUI(File file, Graphics g) throws CircuitLoadingException {
    this("");

    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    DocumentBuilder builder;
    Document doc;
    Element root;

    Hashtable<Integer, Link> linkstable = new Hashtable<Integer, Link>();

    try {
      builder = factory.newDocumentBuilder();
      doc = builder.parse(file);
    } catch (SAXException sxe) {
      throw new CircuitLoadingException("SAX exception raised, invalid XML file.");
    } catch (ParserConfigurationException pce) {
      throw new CircuitLoadingException(
          "Parser exception raised, parser configuration is invalid.");
    } catch (IOException ioe) {
      throw new CircuitLoadingException("I/O exception, file cannot be loaded.");
    }

    root = (Element) doc.getElementsByTagName("Circuit").item(0);
    this.setName(root.getAttribute("name"));

    NodeList nl = root.getElementsByTagName("Node");
    Element e;
    Node n;
    Class cl;

    for (int i = 0; i < nl.getLength(); ++i) {
      e = (Element) nl.item(i);

      try {
        cl = Class.forName(e.getAttribute("class"));
      } catch (Exception exc) {
        System.err.println(exc.getMessage());
        throw new RuntimeException("Circuit creation from xml.");
      }

      try {
        n = ((Node) cl.newInstance());
      } catch (Exception exc) {
        System.err.println(exc.getMessage());
        throw new RuntimeException("Circuit creation from xml.");
      }

      this.nodes.add(n);
      n.setLocation(new Integer(e.getAttribute("x")), new Integer(e.getAttribute("y")));

      if (n instanceof giraffe.ui.Nameable) ((Nameable) n).setNodeName(e.getAttribute("node_name"));

      if (n instanceof giraffe.ui.CompositeNode) {
        try {
          ((CompositeNode) n)
              .load(new File(file.getParent() + "/" + e.getAttribute("file_name")), g);
        } catch (Exception exc) {
          /* try to load from the lib */
          ((CompositeNode) n)
              .load(new File(giraffe.Giraffe.PATH + "/lib/" + e.getAttribute("file_name")), g);
        }
      }

      NodeList nlist = e.getElementsByTagName("Anchor");
      Element el;

      for (int j = 0; j < nlist.getLength(); ++j) {
        el = (Element) nlist.item(j);

        Anchor a = n.getAnchor(new Integer(el.getAttribute("id")));
        NodeList linklist = el.getElementsByTagName("Link");
        Element link;
        Link l;

        for (int k = 0; k < linklist.getLength(); ++k) {
          link = (Element) linklist.item(k);
          int id = new Integer(link.getAttribute("id"));
          int index = new Integer(link.getAttribute("index"));

          if (id >= this.linkID) linkID = id + 1;

          if (linkstable.containsKey(id)) {
            l = linkstable.get(id);
            l.addLinkedAnchorAt(a, index);
            a.addLink(l);
          } else {
            l = new Link(id);
            l.addLinkedAnchorAt(a, index);
            this.links.add(l);
            linkstable.put(id, l);
            a.addLink(l);
          }
        }
      }
    }
  }
Esempio n. 21
0
  public StartProcess() {
    super();

    Hashtable jndiProps = new Hashtable();
    jndiProps.put(Context.PROVIDER_URL, "t3://soaps3.alfa.local:8001/soa-infra");
    jndiProps.put(Context.INITIAL_CONTEXT_FACTORY, "weblogic.jndi.WLInitialContextFactory");
    jndiProps.put(Context.SECURITY_PRINCIPAL, "weblogic");
    jndiProps.put(Context.SECURITY_CREDENTIALS, "weblogic1");
    jndiProps.put("dedicated.connection", "true");

    String inputPayload =
        "<process xmlns=\"http://xmlns.oracle.com/HelloWorld/Helloworld/BPELProcess1\">"
            + "   <input>hello</input>"
            + "</process>";

    Locator locator = null;
    try {
      // connect to the soa server
      locator = LocatorFactory.createLocator(jndiProps);
      String compositeDN = "default/Helloworld!1.0";

      // find composite
      Composite composite = locator.lookupComposite("default/Helloworld!1.0");

      System.out.println("Got Composite : " + composite.toString());

      // find exposed service of the composite
      Service service = composite.getService("ADFBindingService");
      System.out.println("Got serviceName : " + service.toString());

      // make the input request and add this to a operation of the service
      NormalizedMessage input = new NormalizedMessageImpl();
      String uuid = "uuid:" + UUID.randomUUID();
      input.addProperty(NormalizedMessage.PROPERTY_CONVERSATION_ID, uuid);

      // payload is the partname of the process operation
      input.getPayload().put("payload", inputPayload);

      // process is the operation of the employee service
      NormalizedMessage res = null;
      try {
        res = service.request("process", input);
      } catch (Exception e) {
        e.printStackTrace();
      }

      Map payload = res.getPayload();
      Element element = (Element) payload.get("payload");

      TransformerFactory tFactory = TransformerFactory.newInstance();
      Transformer transformer = tFactory.newTransformer();
      transformer.setOutputProperty("indent", "yes");
      StringWriter sw = new StringWriter();
      StreamResult result = new StreamResult(sw);

      DOMSource source = new DOMSource(element);

      transformer.transform(source, result);
      System.out.println("Result\n" + sw.toString());

      System.out.println("instances");

      CompositeInstanceFilter filter = new CompositeInstanceFilter();
      filter.setMinCreationDate(new java.util.Date((System.currentTimeMillis() - 2000000)));
      // get composite instances by filter ..
      List<CompositeInstance> obInstances = composite.getInstances(filter);
      // for each of the returned composite instances..
      for (CompositeInstance instance : obInstances) {
        System.out.println(
            " DN: "
                + instance.getCompositeDN()
                + " Instance: "
                + instance.getId()
                + " creation-date: "
                + instance.getCreationDate()
                + " state ("
                + instance.getState()
                + "): "
                + getStateAsString(instance.getState()));

        // setup a component filter
        ComponentInstanceFilter cInstanceFilter = new ComponentInstanceFilter();
        // get child component instances ..
        List<ComponentInstance> childComponentInstances =
            instance.getChildComponentInstances(cInstanceFilter);

        // for each child component instance (e.g. a bpel process)
        for (ComponentInstance cInstance : childComponentInstances) {
          System.out.println(
              "  -> componentinstance: "
                  + cInstance.getComponentName()
                  + " type: "
                  + cInstance.getServiceEngine().getEngineType()
                  + " state: "
                  + getStateAsString(cInstance.getState()));
          System.out.println("State: " + cInstance.getNormalizedStateAsString());
        }
      }

    } catch (Exception e) {
      e.printStackTrace();
    }
  }
Esempio n. 22
0
  // ## operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
  public boolean writeReactorInputFile(
      ReactionModel p_reactionModel,
      ReactionTime p_beginTime,
      ReactionTime p_endTime,
      SystemSnapshot p_beginStatus) {
    // #[ operation writeReactorInputFile(ReactionModel,ReactionTime,ReactionTime,SystemSnapshot)
    // construct "input" string
    String input = "<?xml version=\"1.0\" standalone=\"no\"?>" + "\n";

    String dir = System.getProperty("RMG.workingDirectory");
    if (!dir.endsWith("/")) dir += "/";
    String dtd = dir + "software/reactorModel/documentTypeDefinitions/reactorInput.dtd";
    input += "<!DOCTYPE reactorinput SYSTEM \"" + dtd + "\">" + "\n";

    input += "<reactorinput>" + "\n";
    input += "<header>" + "\n";
    input += "<title>Reactor Input File</title>" + "\n";
    input +=
        "<description>RMG-generated file used to call an external reactor model</description>"
            + "\n";
    input += "</header>" + "\n";
    input += "<inputvalues>" + "\n";
    input += "<integrationparameters>" + "\n";
    input += "<reactortype>" + reactorType + "</reactortype>" + "\n";
    input +=
        "<starttime units=\""
            + p_beginTime.getUnit()
            + "\">"
            + MathTool.formatDouble(p_beginTime.getTime(), 15, 6)
            + "</starttime>"
            + "\n";
    input +=
        "<endtime units=\""
            + p_endTime.getUnit()
            + "\">"
            + MathTool.formatDouble(p_endTime.getTime(), 15, 6)
            + "</endtime>"
            + "\n";
    //      input += "<starttime units=\"" + p_beginTime.unit + "\">" +
    // MathTool.formatDouble(p_beginTime.time,15,6) +  "</starttime>" + "\n";
    //      input += "<endtime units=\"" + p_endTime.unit + "\">" +
    // MathTool.formatDouble(p_endTime.time,15,6) +  "</endtime>" + "\n";
    input += "<rtol>" + rtol + "</rtol>" + "\n";
    input += "<atol>" + atol + "</atol>" + "\n";
    input += "</integrationparameters>" + "\n";
    input += "<chemistry>" + "\n";
    input += "</chemistry>" + "\n";
    input += "<systemstate>" + "\n";
    input +=
        "<temperature units=\"K\">"
            + MathTool.formatDouble(p_beginStatus.getTemperature().getK(), 15, 6)
            + "</temperature>"
            + "\n";
    input +=
        "<pressure units=\"Pa\">"
            + MathTool.formatDouble(p_beginStatus.getPressure().getPa(), 15, 6)
            + "</pressure>"
            + "\n";
    for (Iterator iter = p_beginStatus.getSpeciesStatus(); iter.hasNext(); ) {
      SpeciesStatus spcStatus = (SpeciesStatus) iter.next();
      Species thisSpecies = spcStatus.getSpecies();
      CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
      if (cerm.containsAsReactedSpecies(thisSpecies)) {
        String spcChemkinName = thisSpecies.getChemkinName();
        double concentration = spcStatus.getConcentration();
        input +=
            "<amount units=\"molPerCm3\" speciesid=\""
                + spcChemkinName
                + "\">"
                + concentration
                + "</amount>"
                + "\n";
      }
    }
    for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
      String name = (String) iter.next();
      double conc = p_beginStatus.getInertGas(name);
      if (conc != 0.0)
        input +=
            "<amount units=\"molPerCm3\" speciesid=\"" + name + "\">" + conc + "</amount>" + "\n";
    }
    input += "</systemstate>" + "\n";
    input += "</inputvalues>" + "\n";
    input += "</reactorinput>" + "\n";

    // write "input" string to file
    try {
      String file = "chemkin/reactorInput.xml";
      FileWriter fw = new FileWriter(file);
      fw.write(input);
      fw.close();
      return true;
    } catch (Exception e) {
      System.out.println("Error in writing reactorInput.xml!");
      System.out.println(e.getMessage());
      return false;
    }

    // #]
  }
Esempio n. 23
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  private void importItemActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_importItemActionPerformed
    // Display a file chooser

    File selectedFile;
    Model m = null;

    JFileChooser jfc = new JFileChooser(workingDirectory);
    jfc.setFileFilter(
        new FileFilter() {
          public boolean accept(File f) {
            return f.isDirectory() || f.getName().endsWith(".xmi");
          }

          public String getDescription() {
            return "XMI UML files (*.xmi)";
          }
        });

    jfc.setCurrentDirectory(workingDirectory);

    jfc.showDialog(this, "Import");

    selectedFile = jfc.getSelectedFile();
    if (selectedFile != null) {
      try {
        m = importModel(selectedFile);
        if (m != null) {
          models.add(m);
          JOptionPane.showMessageDialog(
              this, "Model loaded successfully.", "Success!", JOptionPane.INFORMATION_MESSAGE);
          workingDirectory = jfc.getSelectedFile().getParentFile();
          getContentPane().remove(MTP);
          MTP = new ModelTreePanel(m);
          getContentPane().add(MTP, BorderLayout.CENTER);
          try {
            ObjectOutputStream Out =
                new ObjectOutputStream(
                    new FileOutputStream(System.getProperty("user.home") + "/" + "WorkSpace.dat"));
            Out.writeObject(new WorkSpace(workingDirectory.getAbsolutePath()));
            Out.close();
          } catch (Exception ex) {
            ex.printStackTrace();
          }
        }
      } catch (FileNotFoundException fnfe) {
        JOptionPane.showMessageDialog(
            this,
            "Could not open the model file: " + fnfe.getMessage(),
            "File not found",
            JOptionPane.ERROR_MESSAGE);
      } catch (ParseException pe) {
        JOptionPane.showMessageDialog(
            this,
            "There was an error in parsing the given model: " + pe.getMessage(),
            "Parse error",
            JOptionPane.ERROR_MESSAGE);

      } catch (LemException le) {
        JOptionPane.showMessageDialog(
            this,
            "There was an error in parsing the given model: " + le.getMessage(),
            "Parse error",
            JOptionPane.ERROR_MESSAGE);
      } catch (IOException ioe) {
        JOptionPane.showMessageDialog(
            this,
            "An input/output error occured while trying to read the model: " + ioe.getMessage(),
            "Read error",
            JOptionPane.ERROR_MESSAGE);
      } catch (Exception e) {
        e.printStackTrace();
      }
    }

    setVisible(true);
  } // GEN-LAST:event_importItemActionPerformed
Esempio n. 24
0
  // ## 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;
    }

    // #]
  }
 public static void main(String args[]) {
   try {
     SeleniumHtmlClient client = new SeleniumHtmlClient();
     String testFile = null;
     String testSuite = null;
     String resultsFilename = null;
     for (int i = 0; i < args.length; i++) {
       if (args[i].equals("--host")) {
         i++;
         if (i < args.length) {
           client.setHost(args[i]);
         } else {
           throw new BadUsageException("--host must be followed by a hostname");
         }
       } else if (args[i].equals("--port")) {
         i++;
         if (i < args.length) {
           client.setPort(Integer.parseInt(args[i]));
         } else {
           throw new BadUsageException("--port must be followed by a port number");
         }
       } else if (args[i].equals("--browser")) {
         i++;
         if (i < args.length) {
           client.setBrowser(args[i]);
         } else {
           throw new BadUsageException("--browser must be followed by a browser spec");
         }
       } else if (args[i].equals("--out")) {
         i++;
         if (i < args.length) {
           resultsFilename = args[i];
         } else {
           throw new BadUsageException("--out must be followed by a filename");
         }
         /*
         } else if (args[i].equals("--outdir")) {
         	i++;
         	if (i < args.length) {
         		client.setResultsDir(new File(args[i]));
         	} else {
         		throw new BadUsageException("--outdir must be followed by a path");
         	}
         	*/
       } else if (args[i].equals("--baseurl")) {
         i++;
         if (i < args.length) {
           client.setBaseUrl(args[i]);
         } else {
           throw new BadUsageException("--baseurl must be followed by a URL");
         }
       } else if (args[i].equals("--test")) {
         i++;
         if (i < args.length) {
           if (testFile == null) {
             testFile = args[i];
           } else {
             throw new BadUsageException("only one test file permitted");
           }
         } else {
           throw new BadUsageException("--test must be followed by a test filepath");
         }
       } else if (args[i].equals("--testsuite")) {
         i++;
         if (i < args.length) {
           testSuite = args[i];
         } else {
           throw new BadUsageException("--testsuite must be followed by a testsuite filepath");
         }
       } else if (args[i].equals("--verbose") || args[i].equals("-v")) {
         client.setVerbose(true);
       } else if (args[i].equals("--help") || args[i].equals("-h")) {
         printUsage();
         System.exit(0);
       } else {
         throw new BadUsageException("Unknown parameter " + args[i]);
       }
     }
     if (testFile == null && testSuite == null) {
       throw new BadUsageException("No test or testsuite file specified");
     } else if (testFile != null && testSuite != null) {
       throw new BadUsageException("A test and testsuite file cannot both be specified");
     }
     Writer resultsWriter = null;
     if (resultsFilename != null) {
       resultsWriter = new FileWriter(resultsFilename);
     } else /* if (client.resultsDir == null) */ {
       resultsWriter = new OutputStreamWriter(System.out);
     }
     client.setResultsWriter(resultsWriter);
     if (testFile != null) {
       client.runTest(testFile);
     } else {
       client.runSuite(testSuite);
     }
     if (resultsWriter != null) resultsWriter.close();
   } catch (BadUsageException e) {
     System.err.println("Error: " + e.getMessage());
     System.err.println();
     printUsage();
     System.exit(1);
   } catch (Exception e) {
     e.printStackTrace();
     System.exit(1);
   }
 }
Esempio n. 26
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  public void doGet(HttpServletRequest request, HttpServletResponse response)
      throws IOException, ServletException {

    try {

      response.setHeader("Cache-Control", "no-cache");
      response.setCharacterEncoding("UTF-8");

      String task = request.getParameter("task");

      Element data = null;

      // process help request
      if (request.getParameter("help") != null) data = getDescription(task);

      // redirect to home page if there is no task
      if (data == null && task == null) {
        response.setContentType("text/html");
        response
            .getWriter()
            .append(
                "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\"><html><head><meta http-equiv=\"REFRESH\" content=\"0;url="
                    + context.getInitParameter("server_path")
                    + "></head><body></body></html>");
        return;
      }

      // process definition request
      if (data == null && task.equals("define")) {
        int id = resolveIntegerArg(request.getParameter("id"), -1);
        int length = resolveIntegerArg(request.getParameter("length"), definer.getDefaultLength());
        int format = resolveIntegerArg(request.getParameter("format"), definer.getDefaultFormat());
        int maxImageWidth =
            resolveIntegerArg(
                request.getParameter("maxImageWidth"), definer.getDefaultMaxImageWidth());
        int maxImageHeight =
            resolveIntegerArg(
                request.getParameter("maxImageHeight"), definer.getDefaultMaxImageHeight());
        int linkDestination =
            resolveIntegerArg(
                request.getParameter("linkDestination"), definer.getDefaultLinkDestination());
        boolean getImages = resolveBooleanArg(request.getParameter("getImages"), false);

        data =
            definer.getDefinition(
                id, length, format, linkDestination, getImages, maxImageWidth, maxImageHeight);
      }

      // all of the remaining tasks require data to be cached, so lets make sure that is finished
      // before continuing.
      if (!cachingThread.isOk()) throw new ServletException("Could not cache wikipedia data");

      double progress = cachingThread.getProgress();
      if (data == null && (progress < 1 || task.equals("progress"))) {
        // still caching up data, not ready to return a response yet.

        data = doc.createElement("loading");
        data.setAttribute("progress", df.format(progress));
        task = "loading";
      }

      // process search request
      if (data == null && task.equals("search")) {
        String term = request.getParameter("term");
        String id = request.getParameter("id");
        int linkLimit =
            resolveIntegerArg(request.getParameter("linkLimit"), searcher.getDefaultMaxLinkCount());
        int senseLimit =
            resolveIntegerArg(
                request.getParameter("senseLimit"), searcher.getDefaultMaxSenseCount());

        if (id == null) data = searcher.doSearch(term, linkLimit, senseLimit);
        else data = searcher.doSearch(Integer.parseInt(id), linkLimit);
      }

      // process compare request
      if (data == null && task.equals("compare")) {
        String term1 = request.getParameter("term1");
        String term2 = request.getParameter("term2");
        int linkLimit =
            resolveIntegerArg(request.getParameter("linkLimit"), comparer.getDefaultMaxLinkCount());
        boolean details =
            resolveBooleanArg(request.getParameter("details"), comparer.getDefaultShowDetails());

        data = comparer.getRelatedness(term1, term2, details, linkLimit);
      }

      // process wikify request
      if (data == null && task.equals("wikify")) {

        if (this.wikifier == null)
          throw new ServletException(
              "Wikifier is not available. You must configure the servlet so that it has access to link detection and disambiguation models.");

        String source = request.getParameter("source");
        int sourceMode =
            resolveIntegerArg(request.getParameter("sourceMode"), Wikifier.SOURCE_AUTODETECT);
        String linkColor = request.getParameter("linkColor");
        String baseColor = request.getParameter("baseColor");
        double minProb =
            resolveDoubleArg(
                request.getParameter("minProbability"), wikifier.getDefaultMinProbability());
        int repeatMode =
            resolveIntegerArg(request.getParameter("repeatMode"), wikifier.getDefaultRepeatMode());
        boolean showTooltips =
            resolveBooleanArg(
                request.getParameter("showTooltips"), wikifier.getDefaultShowTooltips());
        String bannedTopics = request.getParameter("bannedTopics");

        boolean wrapInXml = resolveBooleanArg(request.getParameter("wrapInXml"), true);

        if (wrapInXml) {
          data =
              wikifier.wikifyAndWrapInXML(
                  source,
                  sourceMode,
                  minProb,
                  repeatMode,
                  bannedTopics,
                  baseColor,
                  linkColor,
                  showTooltips);
        } else {
          response.setContentType("text/html");
          response
              .getWriter()
              .append(
                  wikifier.wikify(
                      source,
                      sourceMode,
                      minProb,
                      repeatMode,
                      bannedTopics,
                      baseColor,
                      linkColor,
                      showTooltips));
          return;
        }
      }

      if (data == null) throw new Exception("Unknown Task");

      // wrap data
      Element wrapper = doc.createElement("WikipediaMinerResponse");
      wrapper.setAttribute("server_path", context.getInitParameter("server_path"));
      wrapper.setAttribute("service_name", context.getInitParameter("service_name"));
      wrapper.appendChild(data);

      data = wrapper;

      // Transform or serialize xml data as appropriate

      Transformer tf = null;

      if (request.getParameter("xml") == null) {
        // we need to transform the data into html
        tf = transformersByName.get(task);

        if (request.getParameter("help") != null) tf = transformersByName.get("help");
      }

      if (tf == null) {
        // we need to serialize the data as xml
        tf = transformersByName.get("serializer");
        response.setContentType("application/xml");
      } else {
        // output will be transformed to html
        response.setContentType("text/html");
        response
            .getWriter()
            .append(
                "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">\n");
      }

      tf.transform(new DOMSource(data), new StreamResult(response.getWriter()));

    } catch (Exception error) {
      response.reset();
      response.setContentType("application/xml");
      response.setHeader("Cache-Control", "no-cache");
      response.setCharacterEncoding("UTF8");

      Element xmlError = doc.createElement("Error");
      if (error.getMessage() != null) xmlError.setAttribute("message", error.getMessage());

      Element xmlStackTrace = doc.createElement("StackTrace");
      xmlError.appendChild(xmlStackTrace);

      for (StackTraceElement ste : error.getStackTrace()) {

        Element xmlSte = doc.createElement("StackTraceElement");
        xmlSte.setAttribute("message", ste.toString());
        xmlStackTrace.appendChild(xmlSte);
      }
      try {
        transformersByName
            .get("serializer")
            .transform(new DOMSource(xmlError), new StreamResult(response.getWriter()));
      } catch (Exception e) {
        // TODO: something for when an error is thrown processing an error????

      }
      ;
    }
  }
Esempio n. 27
0
  /**
   * Format this XML data as a String.
   *
   * @webref xml:method
   * @brief Formats XML data as a String
   * @param indent -1 for a single line (and no declaration), >= 0 for indents and newlines
   * @return the content
   * @see XML#toString()
   */
  public String format(int indent) {
    try {
      // entities = doctype.getEntities()
      boolean useIndentAmount = false;
      TransformerFactory factory = TransformerFactory.newInstance();
      if (indent != -1) {
        try {
          factory.setAttribute("indent-number", indent);
        } catch (IllegalArgumentException e) {
          useIndentAmount = true;
        }
      }
      Transformer transformer = factory.newTransformer();

      // Add the XML declaration at the top if this node is the root and we're
      // not writing to a single line (indent = -1 means single line).
      if (indent == -1 || parent == null) {
        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
      } else {
        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
      }

      //      transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "sample.dtd");

      transformer.setOutputProperty(OutputKeys.METHOD, "xml");

      //      transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS, "yes");  // huh?

      //      transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC,
      //          "-//W3C//DTD XHTML 1.0 Transitional//EN");
      //      transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM,
      //          "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd");

      // For Android, because (at least 2.3.3) doesn't like indent-number
      if (useIndentAmount) {
        transformer.setOutputProperty(
            "{http://xml.apache.org/xslt}indent-amount", String.valueOf(indent));
      }

      //      transformer.setOutputProperty(OutputKeys.ENCODING,"ISO-8859-1");
      //      transformer.setOutputProperty(OutputKeys.ENCODING,"UTF8");
      transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
      //      transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS

      // Always indent, otherwise the XML declaration will just be jammed
      // onto the first line with the XML code as well.
      transformer.setOutputProperty(OutputKeys.INDENT, "yes");

      //      Properties p = transformer.getOutputProperties();
      //      for (Object key : p.keySet()) {
      //        System.out.println(key + " -> " + p.get(key));
      //      }

      // If you smell something, that's because this code stinks. No matter
      // the settings of the Transformer object, if the XML document already
      // has whitespace elements, it won't bother re-indenting/re-formatting.
      // So instead, transform the data once into a single line string.
      // If indent is -1, then we're done. Otherwise re-run and the settings
      // of the factory will kick in. If you know a better way to do this,
      // please contribute. I've wasted too much of my Sunday on it. But at
      // least the Giants are getting blown out by the Falcons.

      final String decl = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
      final String sep = System.getProperty("line.separator");

      StringWriter tempWriter = new StringWriter();
      StreamResult tempResult = new StreamResult(tempWriter);
      transformer.transform(new DOMSource(node), tempResult);
      String[] tempLines = PApplet.split(tempWriter.toString(), sep);
      //      PApplet.println(tempLines);
      if (tempLines[0].startsWith("<?xml")) {
        // Remove XML declaration from the top before slamming into one line
        int declEnd = tempLines[0].indexOf("?>") + 2;
        // if (tempLines[0].length() == decl.length()) {
        if (tempLines[0].length() == declEnd) {
          // If it's all the XML declaration, remove it
          //          PApplet.println("removing first line");
          tempLines = PApplet.subset(tempLines, 1);
        } else {
          //          PApplet.println("removing part of first line");
          // If the first node has been moved to this line, be more careful
          // tempLines[0] = tempLines[0].substring(decl.length());
          tempLines[0] = tempLines[0].substring(declEnd);
        }
      }
      String singleLine = PApplet.join(PApplet.trim(tempLines), "");
      if (indent == -1) {
        return singleLine;
      }

      // Might just be whitespace, which won't be valid XML for parsing below.
      // https://github.com/processing/processing/issues/1796
      // Since indent is not -1, that means they want valid XML,
      // so we'll give them the single line plus the decl... Lame? sure.
      if (singleLine.trim().length() == 0) {
        // You want whitespace? I've got your whitespace right here.
        return decl + sep + singleLine;
      }

      // Since the indent is not -1, bring back the XML declaration
      // transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");

      StringWriter stringWriter = new StringWriter();
      StreamResult xmlOutput = new StreamResult(stringWriter);
      //      DOMSource source = new DOMSource(node);
      Source source = new StreamSource(new StringReader(singleLine));
      transformer.transform(source, xmlOutput);
      String outgoing = stringWriter.toString();

      // Add the XML declaration to the top if it's not there already
      if (outgoing.startsWith(decl)) {
        int declen = decl.length();
        int seplen = sep.length();
        if (outgoing.length() > declen + seplen
            && !outgoing.substring(declen, declen + seplen).equals(sep)) {
          // make sure there's a line break between the XML decl and the code
          return outgoing.substring(0, decl.length()) + sep + outgoing.substring(decl.length());
        }
        return outgoing;
      } else {
        return decl + sep + outgoing;
      }

    } catch (Exception e) {
      e.printStackTrace();
    }
    return null;
  }
Esempio n. 28
0
  public void run() {

    // String a =
    // "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
    // For developer use

    if (myArgs.length == 0) {
      String usage =
          "\nError, missing SWC file containing morphology!\n\nUsage: \n    java -cp build cvapp.main swc_file [-test]"
              + "\n  or:\n    ./run.sh swc_file ["
              + TEST_FLAG
              + "|"
              + TEST_NOGUI_FLAG
              + "|"
              + NEUROML1_EXPORT_FLAG
              + "|"
              + NEUROML2_EXPORT_FLAG
              + "]\n\n"
              + "where swc_file is the file name or URL of the SWC morphology file\n";
      System.out.println(usage);
      System.exit(0);
    }

    String a = myArgs[0];
    File baseDir = new File(".");
    if ((new File(a)).exists()) {
      baseDir = (new File(a)).getParentFile();
    }

    try {

      File root =
          new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
              .getParentFile();

      if (!a.startsWith("http://") && !a.startsWith("file://")) {
        a = "file://" + (new File(a)).getCanonicalPath();
      }

      boolean supressGui = false;

      if (myArgs.length == 2
          && (myArgs[1].equals(TEST_NOGUI_FLAG)
              || myArgs[1].equals(NEUROML1_EXPORT_FLAG)
              || myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
        supressGui = true;
      }

      neuronEditorFrame nef = null;
      nef = new neuronEditorFrame(700, 600, supressGui);

      // nef.validate();
      nef.pack();
      centerWindow(nef);

      nef.setVisible(!supressGui);

      nef.setReadWrite(true, true);
      int indexof = a.lastIndexOf('/') + 1;
      String directory = a.substring(0, indexof);
      String fileName = a.substring(indexof, a.length());

      URL u = new URL(a);
      String sdata[] = readStringArrayFromURL(u);

      nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
      nef.loadFile(sdata, directory, fileName);
      System.out.println("Loaded: " + fileName);

      if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
        // Thread.sleep(1000);
        doTests(nef, fileName);
      } else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
        File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();

        String nml1FileName =
            rootFile.getName().endsWith(".swc")
                ? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
                : rootFile.getName() + ".xml";

        File nml1File = new File(rootFile.getParentFile(), nml1FileName);

        neuronEditorPanel nep = nef.getNeuronEditorPanel();

        nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());

        System.out.println(
            "Saved NeuroML representation of the file to: "
                + nml1File.getAbsolutePath()
                + ": "
                + nml1File.exists());

        File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");

        validateXML(nml1File, v1schemaFile);

        System.exit(0);
      } else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {

        File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();

        String nml2FileName =
            rootFile.getName().endsWith(".swc")
                ? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
                : rootFile.getName() + ".cell.nml";

        if (Character.isDigit(nml2FileName.charAt(0))) {
          nml2FileName = "Cell_" + nml2FileName;
        }

        File nml2File = new File(rootFile.getParentFile(), nml2FileName);

        neuronEditorPanel nep = nef.getNeuronEditorPanel();

        nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());

        System.out.println(
            "Saved the NeuroML representation of the file to: "
                + nml2File.getAbsolutePath()
                + ": "
                + nml2File.exists());

        validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));

        System.exit(0);
      } else if (myArgs.length == 2
          && (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
        // Thread.sleep(1000);
        doTests(nef, fileName);

        File exampleDir = new File("twoCylSwc");
        for (File f : exampleDir.listFiles()) {
          if (f.getName().endsWith(".swc")) {
            sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
            nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
            nef.loadFile(sdata, f.getParent(), f.getName());
            doTests(nef, f.getAbsolutePath());
          }
        }
        exampleDir = new File("spherSomaSwc");
        for (File f : exampleDir.listFiles()) {
          if (f.getName().endsWith(".swc")) {
            sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
            nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
            nef.loadFile(sdata, f.getParent(), f.getName());
            doTests(nef, f.getAbsolutePath());
          }
        }
        exampleDir = new File("caseExamples");
        for (File f : exampleDir.listFiles()) {
          if (f.getName().endsWith(".swc")) {
            sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
            nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
            nef.loadFile(sdata, f.getParent(), f.getName());
            doTests(nef, f.getAbsolutePath());
          }
        }

        if (supressGui) System.exit(0);
      }

    } catch (Exception exception) {
      System.err.println("Error while handling SWC file (" + a + ")");
      exception.printStackTrace();
    }
  }
  public boolean runTest(Test test) throws Exception {
    String filename = test.file.toString();
    if (this.verbose) {
      System.out.println(
          "Running "
              + filename
              + " against "
              + this.host
              + ":"
              + this.port
              + " with "
              + this.browser);
    }
    this.document = parseDocument(filename);

    if (this.baseUrl == null) {
      NodeList links = this.document.getElementsByTagName("link");
      if (links.getLength() != 0) {
        Element link = (Element) links.item(0);
        setBaseUrl(link.getAttribute("href"));
      }
    }
    if (this.verbose) {
      System.out.println("Base URL=" + this.baseUrl);
    }

    Node body = this.document.getElementsByTagName("body").item(0);
    Element resultContainer = document.createElement("div");
    resultContainer.setTextContent("Result: ");
    Element resultElt = document.createElement("span");
    resultElt.setAttribute("id", "result");
    resultElt.setIdAttribute("id", true);
    resultContainer.appendChild(resultElt);
    body.insertBefore(resultContainer, body.getFirstChild());

    Element executionLogContainer = document.createElement("div");
    executionLogContainer.setTextContent("Execution Log:");
    Element executionLog = document.createElement("div");
    executionLog.setAttribute("id", "log");
    executionLog.setIdAttribute("id", true);
    executionLog.setAttribute("style", "white-space: pre;");
    executionLogContainer.appendChild(executionLog);
    body.appendChild(executionLogContainer);

    NodeList tableRows = document.getElementsByTagName("tr");
    Element theadRow = (Element) tableRows.item(0);
    test.name = theadRow.getTextContent();
    appendCellToRow(theadRow, "Result");

    this.commandProcessor =
        new HtmlCommandProcessor(this.host, this.port, this.browser, this.baseUrl);
    String resultState;
    String resultLog;
    test.result = true;
    try {
      this.commandProcessor.start();
      test.commands = new Command[tableRows.getLength() - 1];
      for (int i = 1; i < tableRows.getLength(); i++) {
        Element stepRow = (Element) tableRows.item(i);
        Command command = executeStep(stepRow);
        appendCellToRow(stepRow, command.result);
        test.commands[i - 1] = command;
        if (command.error) {
          test.result = false;
        }
        if (command.failure) {
          test.result = false;
          // break;
        }
      }
      resultState = test.result ? "PASSED" : "FAILED";
      resultLog = (test.result ? "Test Complete" : "Error");
      this.commandProcessor.stop();
    } catch (Exception e) {
      test.result = false;
      resultState = "ERROR";
      resultLog = "Failed to initialize session\n" + e;
      e.printStackTrace();
    }
    document.getElementById("result").setTextContent(resultState);
    Element log = document.getElementById("log");
    log.setTextContent(log.getTextContent() + resultLog + "\n");
    return test.result;
  }
Esempio n. 30
0
  public void CollectData(String link) {

    try {
      // Creating an empty XML Document

      DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
      DocumentBuilder docBuilder = dbfac.newDocumentBuilder();
      Document doc = docBuilder.newDocument();
      int flag = 0;
      // create the root element and add it to the document
      Element movie = doc.createElement("movie");
      doc.appendChild(movie);
      movie.setAttribute("id", String.valueOf(n));
      n++;
      // create sub elements
      Element genres = doc.createElement("genres");
      Element actors = doc.createElement("actors");
      Element reviews = doc.createElement("reviews");

      URL movieUrl = new URL(link);
      URL reviewsURL = new URL(link + "reviews/#type=top_critics");
      BufferedWriter bw3 = new BufferedWriter(new FileWriter("movies.xml", true));
      int count = -1;
      String auth = "";
      BufferedReader br3 = new BufferedReader(new InputStreamReader(movieUrl.openStream()));
      String str2 = "";
      String info = "";
      while (null != (str2 = br3.readLine())) {
        // start reading the html document
        if (str2.isEmpty()) continue;
        if (count == 14) break;
        if (count == 12) {
          if (!str2.contains("<h3>Cast</h3>")) continue;
          else count++;
        }
        if (count == 13) {
          if (str2.contains(">ADVERTISEMENT</p>")) {
            count++;
            movie.appendChild(actors);
            continue;
          } else {
            if (str2.contains("itemprop=\"name\">")) {
              Element actor = doc.createElement("actor");
              actors.appendChild(actor);
              Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
              actor.appendChild(text);
            } else continue;
          }
        }

        if (count <= 11) {
          switch (count) {
            case -1:
              {
                if (!str2.contains("property=\"og:image\"")) continue;
                else {
                  Pattern image =
                      Pattern.compile("http://.*.jpg", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
                  Matcher match = image.matcher(str2);
                  while (match.find()) {

                    Element imageLink = doc.createElement("imageLink");
                    movie.appendChild(imageLink);
                    Text text = doc.createTextNode(match.group());
                    imageLink.appendChild(text);
                    count++;
                  }
                }
                break;
              }
            case 0:
              {
                if (str2.contains("<title>")) {

                  Element name = doc.createElement("name");
                  movie.appendChild(name);
                  Text text =
                      doc.createTextNode(
                          Jsoup.parse(str2.toString().replace(" - Rotten Tomatoes", "")).text());
                  name.appendChild(text);
                  count++;
                }
                break;
              }
            case 1:
              {
                if (!str2.contains("itemprop=\"ratingValue\"")) break;
                else {
                  Element score = doc.createElement("score");
                  movie.appendChild(score);
                  Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
                  score.appendChild(text);
                  count++;
                }
                break;
              }
            case 2:
              {
                if (!str2.contains("itemprop=\"description\">")) continue;
                else count++;
                break;
              }
            case 3:
              {
                if (!str2.contains("itemprop=\"duration\"")) info = info.concat(str2);
                else {
                  Element MovieInfo = doc.createElement("MovieInfo");
                  movie.appendChild(MovieInfo);
                  Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                  MovieInfo.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 4:
              {
                if (!str2.contains("itemprop=\"genre\"")) info = info.concat(str2);
                else {
                  Element duration = doc.createElement("duration");
                  movie.appendChild(duration);
                  Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                  duration.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 5:
              {
                if (info.contains("itemprop=\"genre\"")) {
                  Element genre = doc.createElement("genre");
                  genres.appendChild(genre);
                  Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                  genre.appendChild(text);
                  info = "";
                }
                if (str2.contains(">Directed By:<")) {
                  count++;
                  movie.appendChild(genres);
                  continue;
                } else {

                  if (str2.contains("itemprop=\"genre\"")) {
                    Element genre = doc.createElement("genre");
                    genres.appendChild(genre);
                    Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text());
                    genre.appendChild(text);
                  } else continue;
                }
                break;
              }
            case 6:
              {
                if (!str2.contains(">Written By:<")) {
                  if (str2.contains(">In Theaters:<")) {
                    Element director = doc.createElement("director");
                    movie.appendChild(director);
                    Text text =
                        doc.createTextNode(
                            Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
                    director.appendChild(text);
                    info = str2;
                    count += 2;
                    break;
                  }
                  info = info.concat(str2);
                } else {
                  Element director = doc.createElement("director");
                  movie.appendChild(director);
                  Text text =
                      doc.createTextNode(
                          Jsoup.parse(info.toString().replace("Directed By: ", "")).text());
                  director.appendChild(text);
                  info = "";
                  count++;
                }
                break;
              }
            case 7:
              {
                if (!str2.contains(">In Theaters:<")) {
                  if (str2.contains(">On DVD:<")) {
                    Element writer = doc.createElement("writer");
                    movie.appendChild(writer);
                    Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                    writer.appendChild(text);
                    info = str2;
                    count += 2;
                    break;
                  }
                  info = info.concat(str2);
                } else {
                  Element writer = doc.createElement("writer");
                  movie.appendChild(writer);
                  Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                  writer.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 8:
              {
                if (!str2.contains(">On DVD:<")) info = info.concat(str2);
                else {
                  Element TheatreRelease = doc.createElement("TheatreRelease");
                  movie.appendChild(TheatreRelease);
                  Text text =
                      doc.createTextNode(
                          Jsoup.parse(info.toString().replace("In Theaters:", "")).text());
                  TheatreRelease.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 9:
              {
                if (!str2.contains(">US Box Office:<")) {
                  if (str2.contains("itemprop=\"productionCompany\"")) {
                    Element DvdRelease = doc.createElement("DvdRelease");
                    movie.appendChild(DvdRelease);
                    Text text =
                        doc.createTextNode(
                            Jsoup.parse(info.toString().replace("On DVD:", "")).text());
                    DvdRelease.appendChild(text);
                    info = str2;
                    count += 2;
                    break;
                  }
                  info = info.concat(str2);
                } else {
                  Element DvdRelease = doc.createElement("DvdRelease");
                  movie.appendChild(DvdRelease);
                  Text text =
                      doc.createTextNode(
                          Jsoup.parse(info.toString().replace("On DVD:", "")).text());
                  DvdRelease.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 10:
              {
                if (!str2.contains("itemprop=\"productionCompany\"")) info = info.concat(str2);
                else {
                  Element BOCollection = doc.createElement("BOCollection");
                  movie.appendChild(BOCollection);
                  Text text =
                      doc.createTextNode(
                          Jsoup.parse(info.toString().replace("US Box Office:", "")).text());
                  BOCollection.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }
            case 11:
              {
                if (!str2.contains(">Official Site")) info = info.concat(str2);
                else {
                  Element Production = doc.createElement("Production");
                  movie.appendChild(Production);
                  Text text = doc.createTextNode(Jsoup.parse(info.toString()).text());
                  Production.appendChild(text);
                  info = str2;
                  count++;
                }
                break;
              }

            default:
              break;
          }
        }
      }
      BufferedReader br4 = new BufferedReader(new InputStreamReader(reviewsURL.openStream()));
      String str3 = "";
      String info2 = "";
      int count2 = 0;
      while (null != (str3 = br4.readLine())) {
        if (count2 == 0) {

          if (!str3.contains("<div class=\"reviewsnippet\">")) continue;
          else count2++;
        }
        if (count2 == 1) {
          if (!str3.contains("<p class=\"small subtle\">")) info2 = info2.concat(str3);
          else {
            Element review = doc.createElement("review");
            reviews.appendChild(review);
            Text text = doc.createTextNode(Jsoup.parse(info2.toString()).text());
            review.appendChild(text);
            info2 = "";
            count2 = 0;
          }
        }
      }
      movie.appendChild(reviews);
      TransformerFactory transfac = TransformerFactory.newInstance();
      Transformer trans = transfac.newTransformer();
      trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
      trans.setOutputProperty(OutputKeys.INDENT, "yes");

      // create string from xml tree
      StringWriter sw = new StringWriter();
      StreamResult result = new StreamResult(sw);
      DOMSource source = new DOMSource(doc);
      trans.transform(source, result);
      String xmlString = sw.toString();
      bw3.write(xmlString);
      br3.close();
      br4.close();
      bw3.close();
    } catch (Exception ex) {
      ex.printStackTrace();
    }
  }