Ejemplo n.º 1
0
 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");
   }
 }
  /**
   * Transforms the given XML file using the specified XSL file.
   *
   * @param origXmlFile The file containg the XML to transform
   * @param xslFile The XML Stylesheet conntaining the transform instructions
   * @return String representation of the transformation
   */
  public static String transform(File origXmlFile, File xslFile) {
    if (!origXmlFile.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, XML file: " + origXmlFile + " doesn't exist", null, null);
      return null;
    }

    if (!xslFile.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
      return null;
    }

    try {
      logger.logComment("The xslFile is " + xslFile + " *************");

      TransformerFactory tFactory = TransformerFactory.newInstance();

      StreamSource xslFileSource = new StreamSource(xslFile);

      Transformer transformer = tFactory.newTransformer(xslFileSource);

      StringWriter writer = new StringWriter();

      transformer.transform(new StreamSource(origXmlFile), new StreamResult(writer));

      return writer.toString();
    } catch (Exception e) {
      GuiUtils.showErrorMessage(logger, "Error when loading the XML file: " + origXmlFile, e, null);
      return null;
    }
  }
Ejemplo n.º 3
0
 public void apply(String path, String[] scripts)
     throws ParserConfigurationException, TransformerConfigurationException {
   File target = new File(path);
   if (target.isDirectory()) {
     String callerDir = this.targetDir;
     this.targetDir = path;
     for (String script : scripts) call(script);
     this.targetDir = callerDir;
   } else {
     String tmpDir = inflate(path);
     if (tmpDir == null) return;
     apply(tmpDir, scripts);
     deflate(tmpDir, path);
   }
 }
Ejemplo n.º 4
0
  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);
    }
  }
Ejemplo n.º 5
0
 private void processDelete(Node operation) {
   String path = absolutePath(operation.getTextContent());
   File target = new File(path);
   if (!target.exists()) {
     Utils.onError(new Error.FileNotFound(target.getPath()));
     return;
   }
   try {
     if (target.isDirectory()) {
       FileUtils.deleteDirectory(target);
     } else {
       FileUtils.forceDelete(target);
     }
   } catch (IOException ex) {
     Utils.onError(new Error.FileDelete(target.getPath()));
   }
 }
Ejemplo n.º 6
0
 public void apply(String path, NodeList[] operations)
     throws ParserConfigurationException, TransformerConfigurationException {
   File target = new File(path);
   if (target.isDirectory()) {
     String callerDir = this.targetDir;
     this.targetDir = path;
     for (NodeList ops : operations) {
       for (int i = 0; i < ops.getLength(); i++) call(ops.item(i));
     }
     this.targetDir = callerDir;
   } else {
     String tmpDir = inflate(path);
     if (tmpDir == null) return;
     apply(tmpDir, operations);
     deflate(tmpDir, path);
   }
 }
Ejemplo n.º 7
0
  private void processXml(Node operation)
      throws ParserConfigurationException, TransformerConfigurationException {
    List<Node> targets = getChildNodes(operation, "target");
    List<Node> appendOpNodes = getChildNodes(operation, "append");
    List<Node> setOpNodes = getChildNodes(operation, "set");
    List<Node> replaceOpNodes = getChildNodes(operation, "replace");
    List<Node> removeOpNodes = getChildNodes(operation, "remove");
    if (targets.isEmpty()) {
      return;
    }
    for (int t = 0; t < targets.size(); t++) {
      File target = new File(absolutePath(targets.get(t).getTextContent()));
      if (!target.exists()) {
        Utils.onError(new Error.FileNotFound(target.getPath()));
        return;
      }
      DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
      Document doc = null;
      try {
        doc = db.parse(target);
      } catch (Exception ex) {
        Utils.onError(new Error.FileParse(target.getPath()));
        return;
      }
      for (int i = 0; i < removeOpNodes.size(); i++) removeXmlEntry(doc, removeOpNodes.get(i));
      for (int i = 0; i < replaceOpNodes.size(); i++) replaceXmlEntry(doc, replaceOpNodes.get(i));
      for (int i = 0; i < setOpNodes.size(); i++) setXmlEntry(doc, setOpNodes.get(i));
      for (int i = 0; i < appendOpNodes.size(); i++) appendXmlEntry(doc, appendOpNodes.get(i));

      try {
        OutputFormat format = new OutputFormat(doc);
        format.setOmitXMLDeclaration(true);
        format.setLineWidth(65);
        format.setIndenting(true);
        format.setIndent(4);
        Writer out = new FileWriter(target);
        XMLSerializer serializer = new XMLSerializer(out, format);
        serializer.serialize(doc);
      } catch (IOException e) {
        Utils.onError(new Error.WriteXmlConfig(target.getPath()));
      }
    }
  }
Ejemplo n.º 8
0
  private Transformer buildTransformer(String name, File xslDir, TransformerFactory tf)
      throws Exception {

    Transformer tr =
        tf.newTransformer(
            new StreamSource(
                new FileReader(xslDir.getAbsolutePath() + File.separatorChar + name + ".xsl")));
    tr.setOutputProperty(OutputKeys.INDENT, "yes");
    tr.setOutputProperty(OutputKeys.METHOD, "html");
    tr.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");

    return tr;
  }
Ejemplo n.º 9
0
  // ## operation Chemkin(double,double,String)
  public Chemkin(double p_rtol, double p_atol, String p_reactorType) {
    // #[ operation Chemkin(double,double,String)
    if (p_rtol < 0 || p_atol < 0)
      throw new InvalidChemkinParameterException("Negative rtol or atol!");
    if (p_reactorType == null) throw new NullPointerException();

    String dir = System.getProperty("RMG.workingDirectory");

    // create the documentTypesDefinitions
    File docFile = new File("chemkin/documentTypeDefinitions");
    docFile.mkdir();
    copyFiles(
        dir + "/software/reactorModel/documentTypeDefinitions/reactorInput.dtd",
        "chemkin/documentTypeDefinitions/reactorInput.dtd");
    copyFiles(
        dir + "/software/reactorModel/documentTypeDefinitions/reactorOutput.dtd",
        "chemkin/documentTypeDefinitions/reactorOutput.dtd");

    rtol = p_rtol;
    atol = p_atol;
    reactorType = p_reactorType;
  }
  /**
   * Transforms the given XML string using the specified XSL file.
   *
   * @param xmlString The String containg the XML to transform
   * @param xslFile The XML Stylesheet conntaining the transform instructions
   * @return String representation of the transformation
   */
  public static String transform(String xmlString, File xslFile) {

    if (!xslFile.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
      return null;
    }

    String shortString = new String(xmlString);
    if (shortString.length() > 100) shortString = shortString.substring(0, 100) + "...";

    try {
      logger.logComment("The xslFile is " + xslFile.getAbsolutePath() + " *************");

      TransformerFactory tFactory = TransformerFactory.newInstance();

      logger.logComment("Transforming string: " + shortString);

      StreamSource xslFileSource = new StreamSource(xslFile);

      Transformer transformer = tFactory.newTransformer(xslFileSource);

      StringWriter writer = new StringWriter();

      transformer.transform(
          new StreamSource(new StringReader(xmlString)), new StreamResult(writer));

      String shortResult = writer.toString();
      if (shortResult.length() > 100) shortResult = shortResult.substring(0, 100) + "...";

      logger.logComment("Result: " + shortResult);

      return writer.toString();
    } catch (TransformerException e) {
      GuiUtils.showErrorMessage(logger, "Error when transforming the XML: " + shortString, e, null);
      return null;
    }
  }
Ejemplo n.º 11
0
  /**
   * opens existing file
   *
   * @param a_file
   */
  public GlyphFile(File a_file) {
    super();

    m_fileName = a_file;

    URL url = null;

    try {
      url = a_file.toURI().toURL();
    } catch (MalformedURLException e) {
      e.printStackTrace();
    }

    init(url);
  }
Ejemplo n.º 12
0
 private void processCopy(Node operation) {
   List<Node> fromNode = getChildNodes(operation, "from");
   List<Node> toNode = getChildNodes(operation, "to");
   if (fromNode.isEmpty() || toNode.isEmpty()) {
     return;
   }
   String path = fromNode.get(0).getTextContent();
   String fromPath = (new File(path).isAbsolute()) ? path : absolutePath(path);
   String toPath = absolutePath(toNode.get(0).getTextContent());
   Boolean copyContents = fromPath.endsWith(File.separator + "*");
   File from = new File((copyContents) ? fromPath.substring(0, fromPath.length() - 2) : fromPath);
   File to = new File(toPath);
   if (!from.exists()) {
     Utils.onError(new Error.FileNotFound(from.getPath()));
     return;
   }
   try {
     if (copyContents) {
       FileUtils.forceMkdir(to);
       FileUtils.copyDirectory(from, to);
     } else if (from.isDirectory()) {
       FileUtils.forceMkdir(to);
       FileUtils.copyDirectoryToDirectory(from, to);
     } else {
       if (to.isDirectory()) {
         FileUtils.forceMkdir(to);
         FileUtils.copyFileToDirectory(from, to);
       } else {
         File toDir = new File(Utils.getParentDir(to));
         FileUtils.forceMkdir(toDir);
         FileUtils.copyFile(from, to);
       }
     }
   } catch (IOException ex) {
     Utils.onError(new Error.FileCopy(from.getPath(), to.getPath()));
   }
 }
Ejemplo n.º 13
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);
          }
        }
      }
    }
  }
Ejemplo n.º 14
0
  public void init(ServletConfig config) throws ServletException {
    super.init(config);
    context = config.getServletContext();

    TextProcessor tp = new CaseFolder();

    try {
      wikipedia =
          new Wikipedia(
              context.getInitParameter("mysql_server"),
              context.getInitParameter("mysql_database"),
              context.getInitParameter("mysql_user"),
              context.getInitParameter("mysql_password"));
    } catch (Exception e) {
      throw new ServletException("Could not connect to wikipedia database.");
    }

    // Escaper escaper = new Escaper() ;

    definer = new Definer(this);
    comparer = new Comparer(this);
    searcher = new Searcher(this);

    try {
      wikifier = new Wikifier(this, tp);

    } catch (Exception e) {
      System.err.println("Could not initialize wikifier");
    }

    try {
      File dataDirectory = new File(context.getInitParameter("data_directory"));

      if (!dataDirectory.exists() || !dataDirectory.isDirectory()) {
        throw new Exception();
      }

      cachingThread = new CacherThread(dataDirectory, tp);
      cachingThread.start();
    } catch (Exception e) {
      throw new ServletException("Could not locate wikipedia data directory.");
    }

    try {
      TransformerFactory tf = TransformerFactory.newInstance();

      transformersByName = new HashMap<String, Transformer>();
      transformersByName.put(
          "help", buildTransformer("help", new File("/research/wikipediaminer/web/xsl"), tf));
      transformersByName.put(
          "loading", buildTransformer("loading", new File("/research/wikipediaminer/web/xsl"), tf));
      transformersByName.put(
          "search", buildTransformer("search", new File("/research/wikipediaminer/web/xsl"), tf));
      transformersByName.put(
          "compare", buildTransformer("compare", new File("/research/wikipediaminer/web/xsl"), tf));
      transformersByName.put(
          "wikify", buildTransformer("wikify", new File("/research/wikipediaminer/web/xsl"), tf));

      Transformer serializer = TransformerFactory.newInstance().newTransformer();
      serializer.setOutputProperty(OutputKeys.INDENT, "yes");
      serializer.setOutputProperty(OutputKeys.METHOD, "xml");
      serializer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
      transformersByName.put("serializer", serializer);

    } catch (Exception e) {
      throw new ServletException("Could not load xslt library.");
    }
  }
Ejemplo n.º 15
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 static boolean transform(
      File origXmlFileOrDir, File xslFile, File targetDir, String extension) {
    logger.logComment(
        "Going to transform " + origXmlFileOrDir + " into dir " + targetDir + " using: " + xslFile,
        true);

    if (!origXmlFileOrDir.exists()) {
      GuiUtils.showErrorMessage(
          logger,
          "Warning, XML file/directory: " + origXmlFileOrDir + " doesn't exist",
          null,
          null);
      return false;
    }

    if (!xslFile.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, XSL file: " + xslFile + " doesn't exist", null, null);
      return false;
    }

    if (!targetDir.exists()) {
      GuiUtils.showErrorMessage(
          logger, "Warning, target directory: " + targetDir + " doesn't exist", null, null);
      return false;
    }

    if (origXmlFileOrDir.isDirectory()) {
      logger.logComment("That file is a directory. Converting all of the XML files in it");
      File[] files = origXmlFileOrDir.listFiles();

      boolean totalSuccess = true;
      for (int i = 0; i < files.length; i++) {
        if (!files[i].isDirectory()
            && (files[i].getName().endsWith(".xml") || files[i].getName().endsWith(".XML"))) {
          boolean partialSuccess = transform(files[i], xslFile, targetDir, extension);

          totalSuccess = totalSuccess || partialSuccess;
        } else if (files[i].isDirectory() && !GeneralUtils.isVersionControlDir(files[i])) {
          File newFolder = new File(targetDir, files[i].getName());
          newFolder.mkdir();

          logger.logComment(
              "Found a sub folder. Going to convert all there into: " + newFolder + "...");

          transform(files[i], xslFile, newFolder, extension);
        }
      }
      return totalSuccess;
    }

    String result = transform(origXmlFileOrDir, xslFile);

    String newName = origXmlFileOrDir.getName();

    if (newName.endsWith(".xml") || newName.endsWith(".XML")) {
      newName = newName.substring(0, newName.length() - 4) + extension;
    }
    File targetFile = new File(targetDir, newName);

    try {
      FileWriter fw = new FileWriter(targetFile);
      fw.write(result);
      fw.close();
    } catch (IOException ex) {
      GuiUtils.showErrorMessage(logger, "Exception writing to file: " + targetFile, ex, null);
      return false;
    }

    logger.logComment("The result is in " + targetFile + " *************");

    return result != null;
  }
Ejemplo n.º 17
0
  /*
   * Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
   */
  private static void doTests(neuronEditorFrame nef, String fileName) {
    System.out.println(
        "Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
            + fileName);
    File tempDir = new File("temp");
    if (!tempDir.exists()) tempDir.mkdir();

    neuronEditorPanel nep = nef.getNeuronEditorPanel();

    String rootFileName = fileName;
    if (rootFileName.toLowerCase().endsWith(".swc")) {
      rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
    }

    if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
      rootFileName =
          rootFileName.substring(
              rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
    }

    // NEURON save...

    String neuronFileName = rootFileName + ".hoc";
    File neuronFile = new File(tempDir, neuronFileName);
    File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");

    nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());

    StringBuilder sbNeuTest = new StringBuilder();
    sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
    sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
    sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
    sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
    sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
    sbNeuTest.append("forall morph()\n");
    System.out.println("--------------------------------------------------------------");
    nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());

    System.out.println(
        "Saved NEURON representation of the file to: "
            + neuronFile.getAbsolutePath()
            + ": "
            + neuronFile.exists());
    System.out.println("--------------------------------------------------------------");

    // GENESIS save...

    String genesisFileName = rootFileName + ".p";
    File genesisFile = new File(tempDir, genesisFileName);
    File genesisTestFile = new File(tempDir, rootFileName + "_test.g");

    nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());

    StringBuilder sbGenTest = new StringBuilder();

    sbGenTest.append("include compartments \n");
    sbGenTest.append("create neutral /library\n");
    sbGenTest.append("disable /library\n");
    sbGenTest.append("ce /library\n");
    sbGenTest.append("make_cylind_compartment\n");
    sbGenTest.append("make_cylind_symcompartment\n");
    sbGenTest.append("make_sphere_compartment\n");
    sbGenTest.append("ce /\n");
    sbGenTest.append(
        "echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
    sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");

    sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
    sbGenTest.append(
        "create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
    sbGenTest.append(
        "setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
    sbGenTest.append(
        "create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
    sbGenTest.append("xcolorscale hot\n");
    sbGenTest.append("xshow /form\n\n");
    sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");

    nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());

    System.out.println(
        "Saved GENESIS representation of the file to: "
            + genesisFile.getAbsolutePath()
            + ": "
            + genesisFile.exists());
    System.out.println("--------------------------------------------------------------");

    // NeuroML save...

    String nml1FileName = rootFileName + ".xml";
    File nml1File = new File(tempDir, nml1FileName);

    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("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");

    validateXML(nml1File, v1schemaFile);

    String nml2FileName = rootFileName + ".cell.nml";

    if (Character.isDigit(nml2FileName.charAt(0))) {
      nml2FileName = "Cell_" + nml2FileName;
    }
    File nml2File = new File(tempDir, nml2FileName);

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

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

    validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
  }
Ejemplo n.º 18
0
 public String getShortFileName() {
   return m_fileName.getName();
 }
Ejemplo n.º 19
0
  private void processTxt(Node operation) {
    List<Node> targets = getChildNodes(operation, "target");
    List<Node> optionNodes = getChildNodes(operation, "opt");
    List<Node> separatorNode = getChildNodes(operation, "separator");
    if (targets.isEmpty() || optionNodes.isEmpty()) {
      return;
    }
    String defaultSeparator = "=";
    String globalSeparator = defaultSeparator;
    if (!separatorNode.isEmpty()) {
      globalSeparator = separatorNode.get(0).getTextContent();
      if (globalSeparator.length() != 1) {
        globalSeparator = defaultSeparator;
      }
    }
    Map<String, String> options = new HashMap<String, String>();
    Map<String, String> processedOptions = new HashMap<String, String>();
    for (int i = 0; i < optionNodes.size(); i++) {
      Node option = optionNodes.get(i);
      String name = option.getAttributes().getNamedItem("name").getNodeValue();
      String value = option.getTextContent();
      if (options.containsKey(name)) {
        options.remove(name);
      }
      options.put(name, value);
    }
    for (int t = 0; t < targets.size(); t++) {
      File target = new File(absolutePath(targets.get(t).getTextContent()));
      File tmpFile = new File(Utils.timestamp());
      BufferedWriter bw = null;
      BufferedReader br = null;
      try {
        Node separatorAttr = targets.get(t).getAttributes().getNamedItem("separator");
        String separator = (separatorAttr == null) ? globalSeparator : separatorAttr.getNodeValue();
        if (separator.length() != 1) {
          separator = globalSeparator;
        }
        bw = new BufferedWriter(new FileWriter(tmpFile));
        if (target.exists()) {
          br = new BufferedReader(new FileReader(target));
          for (String line; (line = br.readLine()) != null; ) {
            String[] parts = line.split(separator);
            if (parts.length < 2) {
              bw.write(line);
              bw.newLine();
              continue;
            }

            String optName = parts[0].trim();
            if (options.containsKey(optName)) {
              String optValue = options.get(optName);
              bw.write(optName + " " + separator + " " + optValue);
              bw.newLine();
              processedOptions.put(optName, optValue);
              options.remove(optName);
            } else if (processedOptions.containsKey(optName)) {
              bw.write(optName + " " + separator + " " + processedOptions.get(optName));
              bw.newLine();
            } else {
              bw.write(line);
              bw.newLine();
            }
          }
          br.close();
        }
        for (Map.Entry<String, String> entry : options.entrySet()) {
          bw.write(entry.getKey() + " " + separator + " " + entry.getValue());
          bw.newLine();
        }
        bw.close();
        FileUtils.copyFile(tmpFile, target);
        FileUtils.forceDelete(tmpFile);
      } catch (IOException ex) {
        Utils.onError(new Error.WriteTxtConfig(target.getPath()));
      }
    }
  }