Example usage for org.dom4j.io SAXReader SAXReader

List of usage examples for org.dom4j.io SAXReader SAXReader

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Introduction

In this page you can find the example usage for org.dom4j.io SAXReader SAXReader.

Prototype

public SAXReader()

Source Link

Usage

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

License:Open Source License

SequenceFromDasUcsc() {//get build names and DAS urls
    try {//from  w ww.j  av a 2 s  . co  m
        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 w  w.j  ava 2  s  .  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.cutstock.utils.ResourceUtil.java

License:Apache License

private ResourceUtil() {
    SAXReader reader = new SAXReader();
    InputStream is = CutStockPlugin.class.getClassLoader().getResourceAsStream(DEF_RESOURCE);

    try {//from  w w  w  .  j  a v a2  s.c o  m
        if (is != null) {
            document = reader.read(is);
        } else {
            throw new Exception("resource not found");
        }
    } catch (DocumentException e) {
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:com.github.gekoh.yagen.ddl.DDLGenerator.java

License:Apache License

private static Document getPersistenceDocument(String persistenceXml) {
    if (StringUtils.isEmpty(persistenceXml)) {
        LOG.warn("empty persistence.xml or orm file specified");
        return null;
    }/* w  w  w  .j a  va  2 s  .  co  m*/
    try {
        InputStream resource = DDLGenerator.class.getResourceAsStream("/" + persistenceXml);
        if (resource == null) {
            resource = new FileInputStream(persistenceXml);
        }
        return new SAXReader().read(resource);
    } catch (Exception e) {
        throw new IllegalArgumentException(
                "unable to find resource " + persistenceXml + " in classpath or filesystem", e);
    }
}

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

License:Apache License

/**
 * xml??map// w  ww . j av  a 2  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.VdParser.java

License:Apache License

VdTree parse(InputStream is, StringBuilder vdErrorLog) {
    final VdTree tree = new VdTree();
    try {/*from  ww  w .  ja va2 s. c  o  m*/
        SAXReader reader = new SAXReader();
        reader.setEntityResolver(new IgnoreDTDEntityResolver());
        tree.parse(reader.read(is));
    } catch (Exception e) {
        vdErrorLog.append(e.getMessage());
    }
    return tree;
}

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 {/* ww  w. j  a v a 2s  . c o m*/
        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 www  .  j  av a 2s .  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  .ja va 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;/*  w w w. j  ava2 s. c  om*/
    try {
        doc = xmlReader.read(inputStream);
    } catch (DocumentException ex) {
        throw new RuntimeException(ex);
    }
    Element root = doc.getRootElement();
    return root;
}