Example usage for org.dom4j Document getRootElement

List of usage examples for org.dom4j Document getRootElement

Introduction

In this page you can find the example usage for org.dom4j Document getRootElement.

Prototype

Element getRootElement();

Source Link

Document

Returns the root Element for this document.

Usage

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

SequenceFromDasUcsc() {//get build names and DAS urls
    try {//from  w  w  w  .  j  a  v a  2s.  com
        SAXReader reader = new SAXReader();
        URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");//usa    
        //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");    
        Document dasXml;
        dasXml = reader.read(url);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element source = dsn.element("SOURCE");
            Attribute build = source.attribute("id");
            Element mapmaster = dsn.element("MAPMASTER");
            buildToMapMaster.put(build.getValue(), mapmaster.getText());
        }
    } catch (DocumentException | MalformedURLException ex) {
        //TO DO - handle (throw) this error properly
        ex.printStackTrace();
    }
}

From source file:com.github.autoprimer3.SequenceFromDasUcsc.java

License:Open Source License

public String retrieveSequence(String build, String chrom, Integer start, Integer end)
        throws DocumentException, MalformedURLException {
    if (!buildToMapMaster.containsKey(build)) {
        return null;
    } else {/*from w  ww .j  a va  2s.c o  m*/
        String chromNumber = chrom.replaceFirst("chr", "");
        int length = 0;
        URL entryPointUrl = new URL(buildToMapMaster.get(build) + "/entry_points");
        Document dasXml;
        SAXReader reader = new SAXReader();
        dasXml = reader.read(entryPointUrl);
        Element root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("ENTRY_POINTS"); i.hasNext();) {
            Element dsn = (Element) i.next();
            for (Iterator j = dsn.elementIterator("SEGMENT"); j.hasNext();) {
                Element seg = (Element) j.next();
                String id = seg.attributeValue("id");
                if (id != null && id.equals(chromNumber)) {
                    String stop = seg.attributeValue("stop");
                    length = Integer.valueOf(stop);
                    break;
                }
            }
        }
        if (length > 0) {
            end = end <= length ? end : length;
        }
        StringBuilder dna = new StringBuilder();
        URL genomeUrl = new URL(
                buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
        dasXml = reader.read(genomeUrl);
        root = dasXml.getRootElement();
        for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element seq = dsn.element("DNA");
            String text = seq.getText().replaceAll("\n", "");
            dna.append(text);
            //dna.append(seq.getText());
        }
        return dna.toString();

    }

}

From source file:com.github.ipaas.ifw.util.XmlUtil.java

License:Apache License

/**
 * xml??map/*  w  w w.  j  ava2  s . c  o  m*/
 * 
 * @param in
 *            -- xml?
 * @return -- map
 */
public static Map toMap(InputStream in) {

    try {
        SAXReader reader = new SAXReader();
        Document doc = reader.read(in);
        return toMap(doc.getRootElement());
    } catch (Exception ex) {
        throw new RuntimeException("?xml?map", ex);
    }
}

From source file:com.github.megatronking.svg.applet.graphics.VdTree.java

License:Apache License

void parse(Document doc) {
    Element rootNode = doc.getRootElement();
    if (SHAPE_VECTOR.equals(rootNode.getName())) {
        parseRootNode(rootNode);/*ww w  .  j a  v a  2  s. c o  m*/
        parseTree(rootNode, mRootGroup);
    } else {
        throw new RuntimeException("The root node is not vector!");
    }
}

From source file:com.glaf.activiti.extension.xml.ExtensionReader.java

License:Apache License

public List<ExtensionEntity> readTasks(java.io.InputStream inputStream) {
    List<ExtensionEntity> extensions = new java.util.ArrayList<ExtensionEntity>();
    SAXReader xmlReader = new SAXReader();
    try {//from w w  w  .j a  v a  2s.  c om
        Document doc = xmlReader.read(inputStream);
        Element root = doc.getRootElement();
        String x_type = root.attributeValue("type");
        List<?> rows = root.elements("taskmgr");
        Iterator<?> iterator = rows.iterator();
        while (iterator.hasNext()) {
            Element element = (Element) iterator.next();
            ExtensionEntity extension = new ExtensionEntity();
            extension.setProcessName(element.attributeValue("processName"));
            extension.setTaskName(element.attributeValue("taskName"));
            extension.setType(x_type);
            if (element.elementTextTrim("taskMgmtType") != null) {
                ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                extensionField.setName("taskMgmtType");
                extensionField.setValue(element.elementTextTrim("taskMgmtType"));
                extension.addField(extensionField);
            }
            Element propertiesE = element.element("properties");
            if (propertiesE != null) {
                List<?> properties = propertiesE.elements("property");
                Iterator<?> iter = properties.iterator();
                while (iter.hasNext()) {
                    Element elem = (Element) iter.next();
                    String propertyName = elem.attributeValue("key");
                    String propertyValue = null;
                    if (elem.attribute("value") != null) {
                        propertyValue = elem.attributeValue("value");
                    } else {
                        propertyValue = elem.getTextTrim();
                    }
                    if (StringUtils.isNotEmpty(propertyName) && StringUtils.isNotEmpty(propertyValue)) {
                        ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                        extensionField.setName(propertyName.trim());
                        extensionField.setValue(propertyValue.trim());
                        extension.addField(extensionField);
                    }
                }
            }
            if (element.elementText("handlers") != null) {
                ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                extensionField.setName("handlers");
                extensionField.setValue(element.elementTextTrim("handlers"));
                extension.addField(extensionField);
            }
            extensions.add(extension);
        }

    } catch (Exception ex) {
        throw new RuntimeException(ex);
    }
    return extensions;
}

From source file:com.glaf.activiti.extension.xml.ExtensionReader.java

License:Apache License

public List<ExtensionEntity> readActions(java.io.InputStream inputStream) {
    List<ExtensionEntity> extensions = new java.util.ArrayList<ExtensionEntity>();
    SAXReader xmlReader = new SAXReader();
    try {/*from   w  w  w  . jav  a2s. c  o  m*/
        Document doc = xmlReader.read(inputStream);
        Element root = doc.getRootElement();
        String x_type = root.attributeValue("type");
        List<?> actions = root.elements("action");
        Iterator<?> iter = actions.iterator();
        while (iter.hasNext()) {
            Element element = (Element) iter.next();
            ExtensionEntity extension = new ExtensionEntity();
            extension.setProcessName(element.attributeValue("processName"));
            extension.setTaskName(element.attributeValue("taskName"));
            extension.setName(element.attributeValue("name"));
            extension.setType(x_type);
            extension.setDescription(element.elementTextTrim("description"));
            Iterator<?> it99 = element.elementIterator();
            while (it99.hasNext()) {
                Element elem = (Element) it99.next();
                String propertyName = elem.getName();
                String propertyValue = elem.getTextTrim();
                if (StringUtils.isNotEmpty(propertyValue)) {
                    ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                    extensionField.setName(propertyName.trim());
                    extensionField.setValue(propertyValue.trim());
                    extension.addField(extensionField);
                }
            }
            if (element.elementText("sql") != null) {
                ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                extensionField.setName("sql");
                extensionField.setValue(element.elementTextTrim("sql"));
                extension.addField(extensionField);

            }
            if (element.elementText("handlers") != null) {
                ExtensionFieldEntity extensionField = new ExtensionFieldEntity();
                extensionField.setName("handlers");
                extensionField.setValue(element.elementTextTrim("handlers"));
                extension.addField(extensionField);
            }

            Element parametersE = element.element("parameters");
            if (parametersE != null) {
                List<?> parameters = parametersE.elements("parameter");
                Iterator<?> it = parameters.iterator();
                while (it.hasNext()) {
                    Element elem = (Element) it.next();
                    String propertyName = elem.attributeValue("name");
                    String type = elem.attributeValue("type");
                    String propertyValue = null;
                    if (elem.attribute("value") != null) {
                        propertyValue = elem.attributeValue("value");
                    } else {
                        propertyValue = elem.getTextTrim();
                    }
                    if (StringUtils.isNotEmpty(propertyName) && StringUtils.isNotEmpty(propertyValue)) {
                        ExtensionParamEntity extensionParam = new ExtensionParamEntity();
                        extensionParam.setName(propertyName.trim());
                        extensionParam.setValue(propertyValue.trim());
                        extensionParam.setType(type);
                        extension.addParam(extensionParam);
                    }
                }
            }

            extensions.add(extension);
        }
    } catch (Exception ex) {
        throw new RuntimeException(ex);
    }
    return extensions;
}

From source file:com.glaf.activiti.spring.SpringProcessEngineConfigurationBean.java

License:Apache License

@Override
protected void initSqlSessionFactory() {
    logger.info("-------------------------------------------");
    logger.info("-------------initSqlSessionFactory()-------");
    logger.info("sqlSessionFactory:" + sqlSessionFactory);
    logger.info("transactionFactory:" + transactionFactory);
    if (sqlSessionFactory == null) {
        InputStream inputStream = null;
        try {//from   www  . j a v  a  2 s  .  c  om
            if (configLocation != null) {
                logger.info("mybatis config:" + this.configLocation.getFile().getAbsolutePath());
                inputStream = this.configLocation.getInputStream();
            } else {
                Resource resource = new ClassPathResource("com/glaf/activiti/activiti.mybatis.conf.xml");
                inputStream = resource.getInputStream();
            }

            if (!ObjectUtils.isEmpty(this.mapperLocations)) {
                SAXReader xmlReader = new SAXReader();
                EntityResolver entityResolver = new XMLMapperEntityResolver();
                xmlReader.setEntityResolver(entityResolver);
                Document doc = xmlReader.read(inputStream);
                Element root = doc.getRootElement();
                Element mappers = root.element("mappers");
                if (mappers != null) {
                    java.util.List<?> list = mappers.elements();
                    Collection<String> files = new HashSet<String>();

                    if (list != null && !list.isEmpty()) {
                        Iterator<?> iterator = list.iterator();
                        while (iterator.hasNext()) {
                            Element elem = (Element) iterator.next();
                            if (elem.attributeValue("resource") != null) {
                                String file = elem.attributeValue("resource");
                                files.add(file);
                            } else if (elem.attributeValue("url") != null) {
                                String file = elem.attributeValue("url");
                                files.add(file);
                            }
                        }
                    }

                    for (Resource mapperLocation : this.mapperLocations) {
                        if (mapperLocation == null) {
                            continue;
                        }
                        String url = mapperLocation.getURL().toString();
                        // logger.debug("find mapper:" + url);
                        if (!files.contains(url)) {
                            Element element = mappers.addElement("mapper");
                            element.addAttribute("url", url);
                        }
                    }
                }

                IOUtils.closeStream(inputStream);

                byte[] bytes = Dom4jUtils.getBytesFromPrettyDocument(doc);
                inputStream = new ByteArrayInputStream(bytes);

            }

            // update the jdbc parameters to the configured ones...
            Environment environment = new Environment("default", transactionFactory, dataSource);
            Reader reader = new InputStreamReader(inputStream);
            Properties properties = new Properties();
            properties.put("prefix", databaseTablePrefix);
            if (databaseType != null) {
                properties.put("limitBefore",
                        DbSqlSessionFactory.databaseSpecificLimitBeforeStatements.get(databaseType));
                properties.put("limitAfter",
                        DbSqlSessionFactory.databaseSpecificLimitAfterStatements.get(databaseType));
                properties.put("limitBetween",
                        DbSqlSessionFactory.databaseSpecificLimitBetweenStatements.get(databaseType));
                properties.put("orderBy",
                        DbSqlSessionFactory.databaseSpecificOrderByStatements.get(databaseType));
            }
            XMLConfigBuilder parser = new XMLConfigBuilder(reader, "", properties);
            Configuration configuration = parser.getConfiguration();
            configuration.setEnvironment(environment);
            configuration.getTypeHandlerRegistry().register(VariableType.class, JdbcType.VARCHAR,
                    new IbatisVariableTypeHandler());
            configuration = parser.parse();

            sqlSessionFactory = new DefaultSqlSessionFactory(configuration);

        } catch (Exception e) {
            throw new ActivitiException("Error while building ibatis SqlSessionFactory: " + e.getMessage(), e);
        } finally {
            IoUtil.closeSilently(inputStream);
        }
    }
}

From source file:com.glaf.activiti.xml.BpmnXmlReader.java

License:Apache License

public Element getRootElement(InputStream inputStream) {
    SAXReader xmlReader = new SAXReader();
    Document doc = null;
    try {//from  w  w w  .  j  a v a 2  s . c  om
        doc = xmlReader.read(inputStream);
    } catch (DocumentException ex) {
        throw new RuntimeException(ex);
    }
    Element root = doc.getRootElement();
    return root;
}

From source file:com.glaf.core.provider.ServiceProviderConfigReader.java

License:Apache License

void process(String prefix, Document doc) {
    checkName(doc.getRootElement(), "provider");
    for (final Object o : doc.getRootElement().elements()) {
        final Element elem = (Element) o;
        checkName(elem, "bean");
        // now check for three children:
        final String name = getValue(elem, "name", true);
        final String clzName = getValue(elem, "class", true);
        Class<?> clz = null;
        try {/* w  w  w .j  a  v  a2  s  .  c  om*/
            clz = BaseClassLoader.getInstance().loadClass(clzName);
        } catch (final ClassNotFoundException e) {
            // catch ClassNotFoundException
            log.warn("Class " + clzName + " can not be loaded. This can happen "
                    + "when rebuilding after installing new modules. "
                    + "The system needs to be restarted to find " + "new services");
            continue;
        }
        if (ServiceModulePrefixRequired.class.isAssignableFrom(clz) && prefix != null
                && prefix.trim().length() > 0) {
            ServiceProvider.getInstance().register(prefix + "." + name, clz, true);
        } else {

            ServiceProvider.getInstance().register(name, clz, true);
        }
    }
}

From source file:com.glaf.core.todo.util.TodoXmlReader.java

License:Apache License

public List<Todo> read(java.io.InputStream inputStream) {
    List<Todo> todos = new java.util.ArrayList<Todo>();
    SAXReader xmlReader = new SAXReader();
    int sortNo = 1;
    try {//from  w  ww.j  a v  a2s. co m
        Document doc = xmlReader.read(inputStream);
        Element root = doc.getRootElement();
        List<?> rows = root.elements();
        Iterator<?> iterator = rows.iterator();
        while (iterator.hasNext()) {
            Element element = (Element) iterator.next();
            String id = element.attributeValue("id");
            Map<String, Object> rowMap = new java.util.HashMap<String, Object>();
            rowMap.put("id", id);
            List<?> properties = element.elements("property");
            Iterator<?> iter = properties.iterator();
            while (iter.hasNext()) {
                Element elem = (Element) iter.next();
                String propertyName = elem.attributeValue("name");
                String propertyValue = null;
                if (elem.attribute("value") != null) {
                    propertyValue = elem.attributeValue("value");
                } else {
                    propertyValue = elem.getTextTrim();
                }
                if (StringUtils.isNotEmpty(propertyName) && StringUtils.isNotEmpty(propertyValue)) {
                    rowMap.put(propertyName, propertyValue);
                }
            }

            Todo model = new Todo();
            model.setSortNo(sortNo++);
            Tools.populate(model, rowMap);

            todos.add(model);
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        throw new RuntimeException(ex.getMessage());
    }
    return todos;
}