org.jdom.JDOMException Java Examples

public static Element readElementFromString(final String xmlData) {
  try {
    final StringReader sr = new StringReader(xmlData);
    final SAXBuilder builder = new SAXBuilder();
    builder.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
    final Document doc = builder.build(sr);

    if (doc == null) {
      return null;
    }

    final Element root = doc.getRootElement();
    return root;
  } catch (final IOException ioe) {
    LOGGER.info("read error", ioe);
    return null;
  } catch (final JDOMException jdome) {
    LOGGER.info("read error", jdome);
    return null;
  }
}
 

private void openFiles(String s) throws IOException, JDOMException, InterruptedException, ExecutionException {
  Document document = JDOMUtil.loadDocument(s);
  Element rootElement = document.getRootElement();
  ExpandMacroToPathMap map = new ExpandMacroToPathMap();
  map.addMacroExpand(PathMacroUtil.PROJECT_DIR_MACRO_NAME, getTestDataPath());
  map.substitute(rootElement, true, true);

  myManager.loadState(rootElement);

  UIAccess uiAccess = UIAccess.get();
  Future<?> future = ApplicationManager.getApplication().executeOnPooledThread(new Runnable() {
    @Override
    public void run() {
      myManager.getMainSplitters().openFiles(uiAccess);
    }
  });
  future.get();
}
 

@Nonnull
public Map<String, Couple<String>> getLastOutputRootsLayout() {
  File file = getOutputUrlsFile();

  Map<String, Couple<String>> map = new HashMap<>();
  if (file.exists()) {
    try {
      Element root = JDOMUtil.load(file);

      for (Element module : root.getChildren()) {
        String name = module.getAttributeValue("name");
        String outputUrl = module.getAttributeValue("output-url");
        String testOutputUrl = module.getAttributeValue("test-output-url");

        map.put(name, Couple.of(outputUrl, testOutputUrl));
      }
    }
    catch (IOException | JDOMException e) {
      LOG.error(e);
    }
  }

  return map;
}
 

@Deprecated
@SuppressWarnings("deprecation")
private void readDefTemplate(DefaultLiveTemplatesProvider provider, String defTemplate, boolean registerTemplate)
        throws JDOMException, InvalidDataException, IOException {
  InputStream inputStream = DecodeDefaultsUtil.getDefaultsInputStream(provider, defTemplate);
  if (inputStream != null) {
    TemplateGroup group =
            readTemplateFile(JDOMUtil.loadDocument(inputStream), defTemplate, true, registerTemplate, provider.getClass().getClassLoader());
    if (group != null && group.getReplace() != null) {
      Collection<TemplateImpl> templates = myTemplates.get(group.getReplace());
      for (TemplateImpl template : templates) {
        removeTemplate(template);
      }
    }
  }
}
 

/**
 * Creates an AnnotationSchema object from an XSchema file
 * 
 * @param anXSchemaURL the ResourceReference where to find the XSchema file
 */
public void fromXSchema(ResourceReference anXSchemaURL)
            throws ResourceInstantiationException {
  org.jdom.Document jDom = null;
  SAXBuilder saxBuilder = new SAXBuilder(false);
  try {
  try{
    jDom = saxBuilder.build(anXSchemaURL.toURL());
  }catch(JDOMException je){
    throw new ResourceInstantiationException(je);
  }
  } catch (java.io.IOException ex) {
    throw new ResourceInstantiationException(ex);
  }
  workWithJDom(jDom);
}
 

private void processFullCreoleXmlTree(Plugin plugin,
    Document jdomDoc, CreoleAnnotationHandler annotationHandler)
    throws GateException, IOException, JDOMException {
  // now we can process any annotations on the new classes
  // and augment the XML definition
  annotationHandler.processAnnotations(jdomDoc);

  // debugging
  if(DEBUG) {
    XMLOutputter xmlOut = new XMLOutputter(Format.getPrettyFormat());
    xmlOut.output(jdomDoc, System.out);
  }

  // finally, parse the augmented definition with the normal parser
  DefaultHandler handler =
      new CreoleXmlHandler(this, plugin);
  SAXOutputter outputter =
      new SAXOutputter(handler, handler, handler, handler);
  outputter.output(jdomDoc);
  if(DEBUG) {
    Out.prln("done parsing " + plugin);
  }
}
 

private synchronized void reloadConfiguration() throws JDOMException, IOException {
  LOG.info("Loading configuration file: " + configFile);
  Document document = JDOMUtil.loadDocument(configFile.toFile());

  Element root = document.getRootElement();

  TelegramSettings newSettings = new TelegramSettings();
  newSettings.setBotToken(unscramble(root.getAttributeValue(BOT_TOKEN_ATTR)));
  newSettings.setPaused(Boolean.parseBoolean(root.getAttributeValue(PAUSE_ATTR)));
  newSettings.setUseProxy(Boolean.parseBoolean(root.getAttributeValue(USE_PROXY_ATTR)));
  newSettings.setProxyServer(root.getAttributeValue(PROXY_SERVER_ATTR));
  newSettings.setProxyPort(restoreInteger(root.getAttributeValue(PROXY_PORT_ATTR)));
  newSettings.setProxyUsername(root.getAttributeValue(PROXY_PASSWORD_ATTR));
  newSettings.setProxyPassword(unscramble(root.getAttributeValue(PROXY_PASSWORD_ATTR)));

  settings = newSettings;
  botManager.reloadIfNeeded(settings);
}
 

/** Creates an AnnotationSchema object from an XSchema file
  * @param anXSchemaInputStream the Input Stream containing the XSchema file
  */
public void fromXSchema(InputStream anXSchemaInputStream)
            throws ResourceInstantiationException {
  org.jdom.Document jDom = null;
  SAXBuilder saxBuilder = new SAXBuilder(false);
  try {
  try{
    jDom = saxBuilder.build(anXSchemaInputStream);
  }catch(JDOMException je){
    throw new ResourceInstantiationException(je);
  }
  } catch (java.io.IOException ex) {
    throw new ResourceInstantiationException(ex);
  }
  workWithJDom(jDom);
}
 

public static void main(String[] args) throws JDOMException, IOException {
    //todo 存在xxe漏洞
    SAXBuilder saxBuilder = new SAXBuilder();

    //todo 修复方式1
//    SAXBuilder saxBuilder = new SAXBuilder(true);

    //todo 修复方式2
//    SAXBuilder saxBuilder = new SAXBuilder();
//    saxBuilder.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
//    saxBuilder.setFeature("http://xml.org/sax/features/external-general-entities", false);
//    saxBuilder.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
//    saxBuilder.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

    ByteArrayInputStream byteArrayInputStream = new ByteArrayInputStream(Payloads.FEEDBACK.getBytes());
    Document document = saxBuilder.build(byteArrayInputStream);
    Element element = document.getRootElement();
    List<Content> contents = element.getContent();
    for (Content content : contents) {
      System.out.println(content.getValue());
    }
  }
 

@NotNull
@Override
public Module createModule(@NotNull ModifiableModuleModel moduleModel)
    throws InvalidDataException, IOException, ModuleWithNameAlreadyExists, JDOMException,
    ConfigurationException {
  Module module = super.createModule(moduleModel);
  getApplication().invokeLater(() -> {
    ProgressManager.getInstance().runProcessWithProgressSynchronously(() -> {
      try {
        InitializerDownloader downloader = new InitializerDownloader(this);
        downloader.execute(ProgressManager.getInstance().getProgressIndicator());
      } catch (IOException var2) {
        getApplication()
            .invokeLater(() -> showErrorDialog("Error: " + var2.getMessage(), "Creation Failed"));
      }
    }, "Downloading Required Files...", true, null);
    ModuleBuilderPostProcessor[] postProcessors =
        ModuleBuilderPostProcessor.EXTENSION_POINT_NAME.getExtensions();
    for (ModuleBuilderPostProcessor postProcessor : postProcessors) {
      if (!postProcessor.postProcess(module)) {
        return;
      }
    }
  }, current());
  return module;
}
 

@Nullable
public Element findDefaultStoreElement(@Nonnull Class<?> clazz, @Nonnull String path) {
  Object result = myUrlCache.computeIfAbsent(Pair.create(clazz.getClassLoader(), path), pair -> {
    URL resource = pair.getFirst().getResource(pair.getSecond());

    if(resource != null) {
      try {
        Document document = JDOMUtil.loadDocument(resource);
        Element rootElement = document.getRootElement();
        rootElement.detach();
        return rootElement;
      }
      catch (JDOMException | IOException e) {
        throw new RuntimeException(e);
      }
    }

    return ObjectUtil.NULL;
  });

  return result == ObjectUtil.NULL ? null : (Element)result;
}
 

public static Element parseDocument(final InputStream is) {
  try {
    final SAXBuilder builder = new SAXBuilder();
    builder.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

    final Document doc = builder.build(is);
    if (doc == null) {
      return null;
    }

    final Element root = doc.getRootElement();
    return root;
  } catch (final IOException ioe) {
    LOGGER.warn("parse error", ioe);
    return null;
  } catch (final JDOMException jdome) {
    LOGGER.warn("parse error", jdome);
    return null;
  }
}
 

@SuppressWarnings("unchecked")
public void createIndex() throws JDOMException, IOException, MappingException, ClassNotFoundException {
	buildAnalyzerMap();
	SAXBuilder builder = new SAXBuilder();
	Document doc = builder.build(config);
	Element root = doc.getRootElement();
	SessionFactory sf = createSessionFactory(root.getAttributeValue("url"),
			root.getAttributeValue("login"),
			root.getAttributeValue("passwd"),
			root.getAttributeValue("dialect"),
			root.getAttributeValue("driverClass"),
			root.getAttributeValue("mappedClasses"));
	Directory indexDir = FSDirectory.open(new File(output));

	Version lucene47 = Version.LUCENE_47;
	IndexWriter writer = new IndexWriter(indexDir,new IndexWriterConfig(lucene47,new StandardAnalyzer(lucene47)));
	for (Element classToIndex:(Collection<Element>)root.getChildren("index-class")) {
		processClass(classToIndex,writer,sf);
	}
	log.info("Closing index");
	writer.close();
	log.info("All done!");
}
 

public BeastImporter(Reader reader) throws IOException, JDOMException, Importer.ImportException {
        SAXBuilder builder = new SAXBuilder();

        Document doc = builder.build(reader);
        root = doc.getRootElement();
        if (!root.getName().equalsIgnoreCase("beast")) {
            throw new Importer.ImportException("Unrecognized root element in XML file");
        }

        dateFormat = DateFormat.getDateInstance(java.text.DateFormat.SHORT, Locale.UK);
        dateFormat.setLenient(true);

        Calendar cal = Calendar.getInstance(Locale.getDefault());

        // set uses a zero based month (Jan = 0):
        cal.set(0000, 00, 01);
//        origin = cal.getTime();

        cal.setTimeInMillis(0);
        origin = cal.getTime();
    }
 

/**
 * Parses the provider looking for PRELINK XML.
 * 
 * @param provider The provider to parse.
 * @param monitor A monitor.
 * @return A list of discovered {@link PrelinkMap}s.  An empty list indicates that the provider
 *   did not represent valid Mach-O PRELINK binary.
 * @throws IOException if there was an IO-related issue.
 * @throws JDOMException if there was a issue parsing the PRELINK XML.
 */
public static List<PrelinkMap> parsePrelinkXml(ByteProvider provider, TaskMonitor monitor)
		throws IOException, JDOMException {

	try {
		MachHeader mainHeader =
			MachHeader.createMachHeader(RethrowContinuesFactory.INSTANCE, provider);
		mainHeader.parse(); // make sure first Mach-O header is valid....

		monitor.setMessage("Parsing PRELINK XML...");
		return new PrelinkParser(mainHeader, provider).parse(monitor);
	}
	catch (NoPreLinkSectionException | MachException e) {
		return Collections.emptyList();
	}
}
 

@SuppressWarnings("unchecked")
public void createIndex() throws JDOMException, IOException, MappingException, ClassNotFoundException {
	buildAnalyzerMap();
	SAXBuilder builder = new SAXBuilder();
	Document doc = builder.build(config);
	Element root = doc.getRootElement();
	SessionFactory sf = createSessionFactory(root.getAttributeValue("url"),
			root.getAttributeValue("login"),
			root.getAttributeValue("passwd"),
			root.getAttributeValue("dialect"),
			root.getAttributeValue("driverClass"),
			root.getAttributeValue("mappedClasses"));
	Directory indexDir = FSDirectory.open(new File(output));

	Version lucene47 = Version.LUCENE_47;
	IndexWriter writer = new IndexWriter(indexDir,new IndexWriterConfig(lucene47,new StandardAnalyzer(lucene47)));
	for (Element classToIndex:(Collection<Element>)root.getChildren("index-class")) {
		processClass(classToIndex,writer,sf);
	}
	log.info("Closing index");
	writer.close();
	log.info("All done!");
}
 

@Nullable
@Override
public Project doOpenProject(
    VirtualFile file, @Nullable Project projectToClose, boolean forceOpenInNewFrame) {
  ProjectManager pm = ProjectManager.getInstance();
  if (projectToClose != null) {
    pm.closeProject(projectToClose);
  }
  try {
    VirtualFile ideaSubdirectory = getIdeaSubdirectory(file);
    if (ideaSubdirectory == null) {
      return null;
    }
    VirtualFile projectSubdirectory = ideaSubdirectory.getParent();
    return pm.loadAndOpenProject(projectSubdirectory.getPath());
  } catch (IOException | JDOMException e) {
    return null;
  }
}
 

/**
 * Sends the SPR order to the bank. After that you have to start over with sending INI and HIA.
 *
 * @throws IOException Communication exception
 * @throws AxelorException
 * @throws JDOMException
 * @throws EbicsException Error message generated by the bank.
 */
public void lockAccess() throws IOException, AxelorException, JDOMException {
  HttpRequestSender sender;
  SPRRequestElement request;
  SPRResponseElement response;
  int httpCode;

  sender = new HttpRequestSender(session);
  request = new SPRRequestElement(session);
  request.build();
  request.validate();
  httpCode = sender.send(new ByteArrayContentFactory(request.prettyPrint()));
  EbicsUtils.checkHttpCode(httpCode);
  response = new SPRResponseElement(sender.getResponseBody(), session.getUser());
  response.build();
  response.report(new EbicsRootElement[] {request, response});
}
 

/**
 * Constructor from URL
 * @param configFileURL URL of feature config XML file
 */
public FeatureSpecification(URL configFileURL) {
  url = configFileURL;

  SAXBuilder saxBuilder = new SAXBuilder(false);
  try {
    try {
      jdomDocConf = saxBuilder.build(configFileURL);
      parseConfigXml();
    } catch (JDOMException jde) {
      throw new GateRuntimeException(jde);
    }
  } catch (java.io.IOException ex) {
    throw new GateRuntimeException("Error parsing config file URL " + url, ex);
  }
}
 

@Test
public void testL5a1a() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
	List<RankedResult> result =  phylotree.search(TestSample.parse("1	1-16569	73G	152C	182T	189G	195C	247A	263G	315.1C	455.1T	455.2T	455.3C	522del	523del	709A	750G	769A	825A	851G	930A	1018A	1438G	1822C	2706G	3423C	3594T	4104G	4496T	4769G	5004C	5111T	5147A	5656G	6182A	6297C	7028T	256T	7424G	7521A	7873T	7972G	8155A	8188G	8582T	8655T	8701G	8754T	8860G	9305A	9329A	9540C	9899C	10398G	10688A	10810C	10873C	11015G	11025C	11719A	11881T	12236A	12432T	12705T	12950G	13105G	13506T	13650T	13722G	14212C	14239T	14581C	14766T	14905A	14971C	15217A	15326G	15884A	16129A	16148T	16166G	16187T	16189C	16223T	16278T	16311C	16355T	16362C"),new HammingRanking());
	
	Assert.assertEquals("L5a1a", result.get(0).getHaplogroup().toString());
}
 

@Test
public void testL3e1c() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
	List<RankedResult> result =  phylotree.search(TestSample.parse("549	1-16569	L3e1c	73G	150T	189G	200G	263G	309.1C	315.1C	750G	1438G	2352C	2706G	3106N	3675G	4769G	5460A	6221C	6587T	7028T	8289.1C	8289.2C	8289.3C	8289.4C	8289.5C	8289.6T	8289.7C	8289.8T	8289.9A	8289.10C	8289.11C	8289.12C	8289.13C	8289.14C	8289.15T	8289.16C	8289.17T	8289.18A	8860G	9540C	10398G	10819G	10873C	11719A	12705T	14152G	14212C	14323A	14766T	15301A	15326G	15670C	15942C	16327T "),new HammingRanking());
	
	Assert.assertEquals("L3e1c", result.get(0).getHaplogroup().toString());
}
 

@Test
public void testHV() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
	List<RankedResult> result =  phylotree.search(TestSample.parse("1	1-16569	 	263G 8860G 15326G 750G 4769G 1438G 2706G 7028T"),new HammingRanking());
	
	Assert.assertEquals("HV", result.get(0).getHaplogroup().toString());
}
 

@Override
@Nullable
public Project loadProject(@Nonnull String filePath) throws IOException, JDOMException, InvalidDataException {
  try {
    ProjectImpl project = createProject(null, filePath, false, false);
    initProject(project, null);
    return project;
  }
  catch (Throwable t) {
    LOG.info(t);
    throw new IOException(t);
  }
}
 

@Test
public void testH() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{

	List<RankedResult> result =  phylotree.search(TestSample.parse("1	1-16569	 	263G 8860G 15326G 750G 4769G 1438G"),new HammingRanking());
	
	Assert.assertEquals("H", result.get(0).getHaplogroup().toString());
}
 

/**
 * Constructs an XmlStringBuffer whose initial value is Document
 *
 * @param jdomDoc
 *
 * @deprecated using XmlStringBuffer(org.w3c.dom.Document document) instead.
 */
public XmlStringBuffer(org.jdom.Document jdomDoc)
{
  try
  {
    this.document = new DOMOutputter().output(jdomDoc);
  }
  catch(JDOMException e)
  {
    log.error(e.getMessage(), e);
  }
}
 

@Test
public void testR0() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
	List<RankedResult> result =  phylotree.search(TestSample.parse("1	1-16569	 	263G 8860G 15326G 750G 4769G 1438G 2706G 7028T 14766T"),new HammingRanking());
	
	Assert.assertEquals("R0", result.get(0).getHaplogroup().toString());
}
 

/**
 * Sends encryption and authentication keys to the bank. This order is only allowed for a new user
 * at the bank side that has been created by copying the A005 key. The keys will be activated
 * immediately after successful completion of the transfer.
 *
 * @param orderId the order ID. Let it null to generate a random one.
 * @throws IOException communication error
 * @throws GeneralSecurityException data decryption error
 * @throws AxelorException
 * @throws JDOMException
 * @throws EbicsException server generated error message
 */
public X509Certificate[] sendHPB()
    throws IOException, GeneralSecurityException, AxelorException, JDOMException {

  HPBRequestElement request;
  KeyManagementResponseElement response;
  HttpRequestSender sender;
  HPBResponseOrderDataElement orderData;
  ContentFactory factory;
  int httpCode;

  sender = new HttpRequestSender(session);
  request = new HPBRequestElement(session);
  request.build();
  request.validate();
  httpCode = sender.send(new ByteArrayContentFactory(request.prettyPrint()));
  EbicsUtils.checkHttpCode(httpCode);
  response =
      new KeyManagementResponseElement(
          sender.getResponseBody(), "HBPResponse", session.getUser());
  response.build();
  response.report(new EbicsRootElement[] {request, response});
  EbicsUserService userService = Beans.get(EbicsUserService.class);
  factory =
      new ByteArrayContentFactory(
          EbicsUtils.unzip(
              userService.decrypt(
                  session.getUser(), response.getOrderData(), response.getTransactionKey())));
  orderData = new HPBResponseOrderDataElement(factory, session.getUser());
  orderData.build();

  return createCertificates(orderData);
}
 

@Test
public void testH2a2b() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{
	List<RankedResult> result =  phylotree.search(TestSample.parse("549	1-16569	H2a2b	263G	309.1C	309.2T	4080C	8860G	15326G	16291T"),new HammingRanking());
	
	Assert.assertEquals("H2a2b3", result.get(0).getHaplogroup().toString());
}
 

@Test //GH #11
public void testW1_119() throws NumberFormatException, JDOMException, IOException, InvalidPolymorphismException, HsdFileException, InvalidColumnCountException
{

	List<RankedResult> result =  phylotree.search(TestSample.parse("ID	1-16569	W1+119	73G 94A 103A 118C 119C 189G 195C 198T 204C 207A 263G 709A 750G 1243C 1438G 2706G 3505G 4769G 5046A 5460A 7028T 7864T 8251A 8860G 8994A 11674T 11719A 11947G 12414C 12705T 14766T 15326G 15884C 16223T 16278T 16292T 16295T 16519C"),new HammingRanking());
		
	Assert.assertEquals("W1+119", result.get(0).getHaplogroup().toString());
}
 

@Nonnull
public static Profile load(@Nonnull File file,
                           @Nonnull InspectionToolRegistrar registrar,
                           @Nonnull ProfileManager profileManager) throws JDOMException, IOException, InvalidDataException {
  Element element = JDOMUtil.loadDocument(file).getRootElement();
  InspectionProfileImpl profile = new InspectionProfileImpl(getProfileName(file, element), registrar, profileManager);
  final Element profileElement = element.getChild(PROFILE_TAG);
  if (profileElement != null) {
    element = profileElement;
  }
  profile.readExternal(element);
  return profile;
}