Пример #1
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);
    }
  }
Пример #2
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;
  }
  /**
   * 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;
    }
  }
Пример #4
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();
    }
  }
Пример #5
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");
  }