List of usage examples for org.dom4j.io XMLWriter XMLWriter
public XMLWriter(OutputStream out, OutputFormat format) throws UnsupportedEncodingException
From source file:architecture.ee.component.core.lifecycle.RepositoryImpl.java
License:Apache License
public ApplicationProperties getSetupApplicationProperties() { if (setupProperties == null) { try {/*from w w w.j ava2 s.com*/ File file = getFile(ApplicationConstants.DEFAULT_STARTUP_FILENAME); if (!file.exists()) { boolean error = false; // create default file... log.debug("No startup file now create !!!"); Writer writer = null; try { writer = new OutputStreamWriter(new FileOutputStream(file), ApplicationConstants.DEFAULT_CHAR_ENCODING); XMLWriter xmlWriter = new XMLWriter(writer, OutputFormat.createPrettyPrint()); StringBuilder sb = new StringBuilder(); org.dom4j.Document document = org.dom4j.DocumentHelper.createDocument(); org.dom4j.Element root = document.addElement("startup-config"); // setup start // ------------------------------------------------------------ org.dom4j.Element setupNode = root.addElement("setup"); setupNode.addElement("complete").setText("false"); // setup end // -------------------------------------------------------------- // license start org.dom4j.Element licenseNode = root.addElement("license"); // license end // view start org.dom4j.Element viewNode = root.addElement("view"); org.dom4j.Element renderNode = viewNode.addElement("render"); org.dom4j.Element freemarkerNode = renderNode.addElement("freemarker"); freemarkerNode.addElement("enabled").setText("true"); freemarkerNode.addElement("source").addElement("location"); org.dom4j.Element velocityNode = renderNode.addElement("velocity"); velocityNode.addElement("enabled").setText("false"); // view end // security start org.dom4j.Element securityNode = root.addElement("security"); securityNode.addElement("authentication").addElement("encoding").addElement("algorithm") .setText("SHA-256"); // security end // scripting start org.dom4j.Element scriptingNode = root.addElement("scripting"); org.dom4j.Element groovyNode = scriptingNode.addElement("groovy"); groovyNode.addElement("debug").setText("false"); org.dom4j.Element sourceGroovyNode = groovyNode.addElement("source"); sourceGroovyNode.addElement("location"); sourceGroovyNode.addElement("encoding").setText(ApplicationConstants.DEFAULT_CHAR_ENCODING); sourceGroovyNode.addElement("recompile").setText("true"); // scripting end // database start org.dom4j.Element databaseNode = root.addElement("database"); // database end xmlWriter.write(document); } catch (Exception e) { log.error(L10NUtils.format("003007", file.getName(), e.getMessage())); error = true; } finally { try { writer.flush(); writer.close(); } catch (Exception e) { log.error(e); error = true; } } } this.setupProperties = new XmlApplicationProperties(file); } catch (Exception e) { log.warn("I warning you!"); log.debug(e.getMessage(), e); return EmptyApplicationProperties.getInstance(); } } return setupProperties; }
From source file:architecture.ee.component.RepositoryImpl.java
License:Apache License
public ApplicationProperties getSetupApplicationProperties() { if (setupProperties == null) { if (initailized.get()) { File file = getFile(ApplicationConstants.DEFAULT_STARTUP_FILENAME); if (!file.exists()) { boolean error = false; // create default file... log.debug(CommonLogLocalizer.format("003012", file.getAbsolutePath())); Writer writer = null; try { lock.lock();/*from w w w . jav a 2s. c o m*/ writer = new OutputStreamWriter(new FileOutputStream(file), StandardCharsets.UTF_8); XMLWriter xmlWriter = new XMLWriter(writer, OutputFormat.createPrettyPrint()); StringBuilder sb = new StringBuilder(); org.dom4j.Document document = org.dom4j.DocumentHelper.createDocument(); org.dom4j.Element root = document.addElement("startup-config"); // setup start // ------------------------------------------------------------ org.dom4j.Element setupNode = root.addElement("setup"); setupNode.addElement("complete").setText("false"); // setup end // license start root.addComment("LICENSE SETTING"); org.dom4j.Element licenseNode = root.addElement("license"); // license end // view start /* org.dom4j.Element viewNode = root.addElement("view"); org.dom4j.Element renderNode = viewNode.addElement("render"); org.dom4j.Element freemarkerNode = renderNode.addElement("freemarker"); freemarkerNode.addElement("enabled").setText("true"); freemarkerNode.addElement("source").addElement("location"); org.dom4j.Element velocityNode = renderNode.addElement("velocity"); velocityNode.addElement("enabled").setText("false"); */ // view end // security start root.addComment("SECURITY SETTING"); org.dom4j.Element securityNode = root.addElement("security"); org.dom4j.Element encrpptNode = securityNode.addElement("encrypt"); encrpptNode.addElement("algorithm").setText("Blowfish"); encrpptNode.addElement("key").addElement("current"); org.dom4j.Element encrpptPropertyNode = encrpptNode.addElement("property"); encrpptPropertyNode.addElement("name").setText("username"); encrpptPropertyNode.addElement("name").setText("password"); securityNode.addElement("authentication").addElement("encoding").addElement("algorithm") .setText("SHA-256"); // security end // services start root.addComment("SERVICES SETTING"); org.dom4j.Element servicesNode = root.addElement("services"); servicesNode.addElement("sql").addElement("location").addText("sql"); // services end // database start root.addComment("DATABASE SETTING"); org.dom4j.Element databaseNode = root.addElement("database"); org.dom4j.Element databaseDefaultNode = databaseNode.addElement("default"); databaseDefaultNode.addComment(" 1. jndi datasource "); databaseDefaultNode.addComment((new StringBuilder()).append("\n").append(" ") .append("<jndiDataSourceProvider>").append("\n").append(" ") .append(" <jndiName></jndiName>").append("\n").append(" ") .append("</jndiDataSourceProvider>").append("\n").toString()); databaseDefaultNode.addComment(" 2. connection pool datasource using dbcp "); databaseDefaultNode.addComment((new StringBuilder()).append("\n").append(" ") .append("<pooledDataSourceProvider> ").append("\n").append(" ") .append(" <driverClassName></driverClassName> ").append("\n").append(" ") .append(" <url></url>").append("\n").append(" ") .append(" <username></username>").append("\n").append(" ") .append(" <password></password>").append("\n").append(" ") .append(" <connectionProperties>").append("\n").append(" ") .append(" <initialSize>1</initialSize>").append("\n").append(" ") .append(" <maxActive>8</maxActive>").append("\n").append(" ") .append(" <maxIdle>8</maxIdle>").append("\n").append(" ") .append(" <maxWait>-1</maxWait>").append("\n").append(" ") .append(" <minIdle>0</minIdle>").append("\n").append(" ") .append(" <testOnBorrow>true</testOnBorrow>").append("\n").append(" ") .append(" <testOnReturn>false</testOnReturn>").append("\n").append(" ") .append(" <testWhileIdle>false</testWhileIdle>").append("\n") .append(" ") .append(" <validationQuery>select 1 from dual</validationQuery>") .append("\n").append(" ").append(" </connectionProperties>").append("\n") .append(" ").append("</pooledDataSourceProvider>").toString()); // database end xmlWriter.write(document); } catch (Exception e) { log.error("fail to making {} - {}", file.getName(), e.getMessage()); error = true; } finally { try { writer.flush(); writer.close(); } catch (Exception e) { log.error("error", e); error = true; } lock.unlock(); } } else { try { log.debug(CommonLogLocalizer.format("003011", file.getPath())); this.setupProperties = new LocalApplicationProperties(file); } catch (IOException e) { log.error(CommonLogLocalizer.getMessage("003013"), e); } } } else { return LocalApplicationProperties.EMPTY_APPLICATION_PROPERTIES; } } return setupProperties; }
From source file:au.com.acegi.xmlformat.FormatUtil.java
License:Apache License
/** * Ingest an input stream, writing formatted XML to the output stream. The * caller is responsible for closing the input and output streams. Any errors * in the input stream will cause an exception and the output stream should * not be relied upon.//from w w w . j a v a 2s. co m * * @param in input XML stream * @param out output XML stream * @param fmt format configuration to apply * @throws DocumentException if input XML could not be parsed * @throws IOException if output XML stream could not be written */ static void format(final InputStream in, final OutputStream out, final OutputFormat fmt) throws DocumentException, IOException { final SAXReader reader = new SAXReader(); reader.setEntityResolver(new EntityResolver() { @Override public InputSource resolveEntity(final String publicId, final String systemId) throws SAXException, IOException { return new InputSource(new StringReader("")); } }); final Document xmlDoc = reader.read(in); final XMLWriter xmlWriter = new XMLWriter(out, fmt); xmlWriter.write(xmlDoc); xmlWriter.flush(); }
From source file:be.hikage.maven.plugin.xmlmerge.MergeXmlMojo.java
License:Apache License
private void writeMergedXml(File baseFile, Document base, StringBuilder prologHeader) throws IOException { FileOutputStream fos = new FileOutputStream(baseFile); if (processProlog && prologHeader != null && StringUtils.isNotEmpty(prologHeader.toString())) { fos.write(prologHeader.toString().getBytes()); }/*from w w w . j a v a 2s . co m*/ OutputFormat format = OutputFormat.createPrettyPrint(); format.setSuppressDeclaration(true); format.setNewLineAfterDeclaration(false); XMLWriter writer = new XMLWriter(fos, format); writer.write(base); writer.flush(); writer.close(); }
From source file:bio.pih.genoogle.interfaces.Console.java
public void execute(InputStreamReader isr, boolean echo) { BufferedReader lineReader = new BufferedReader(isr); boolean executePrev = false; String prev = null;//from w w w . j ava2s . co m String line = null; Map<Parameter, Object> consoleParameters = SearchParams.getSearchParamsMap(); System.out.print("genoogle console> "); try { while (running && (executePrev || (line = lineReader.readLine()) != null)) { long begin = System.currentTimeMillis(); long end = -1; if (echo) { System.out.println(line); } try { line = line.trim(); if (line.length() == 0) { continue; } if (executePrev) { if (prev == null) { System.out.println("no previous commands."); executePrev = false; continue; } line = prev; System.out.println(line); executePrev = false; } String[] commands = line.split("[ \t]+"); if (commands[0].equals(SEARCH)) { if (commands.length >= 3) { String db = commands[1]; String queryFile = commands[2]; Map<Parameter, Object> searchParameters = Maps.newHashMap(); searchParameters.putAll(consoleParameters); for (int i = 4; i < commands.length; i++) { String command = commands[i]; String[] split = command.split("="); if (split.length != 2) { System.out.println(command + " is an invalid parameter."); } String paramName = split[0]; String paramValue = split[1]; Parameter p = Parameter.getParameterByName(paramName); if (p == null) { System.out.println(paramName + " is an invalid parameter name"); continue; } Object value = p.convertValue(paramValue); searchParameters.put(p, value); } if (new File(queryFile).exists()) { BufferedReader in = new BufferedReader(new FileReader(queryFile)); profileLogger.info("<" + line + ">"); List<SearchResults> results = genoogle.doBatchSyncSearch(in, db, searchParameters); end = System.currentTimeMillis(); long total = end - begin; profileLogger.info("</" + line + ":" + total + ">"); Document document = Output.genoogleOutputToXML(results); OutputFormat outformat = OutputFormat.createPrettyPrint(); outformat.setTrimText(false); outformat.setEncoding("UTF-8"); OutputStream os; if (commands.length >= 4) { String outputFile = commands[3]; os = new FileOutputStream(new File(outputFile + ".xml")); } else { os = System.out; } XMLWriter writer = new XMLWriter(os, outformat); writer.write(document); writer.flush(); } else { System.err.println("query file: " + queryFile + " does not exist."); } } else { System.out.println("SEARCH DB QUERY_FILE OUTPUT_FILE"); } } else if (commands[0].equals(GC)) { System.gc(); } else if (commands[0].equals(LIST)) { for (AbstractSequenceDataBank db : genoogle.getDatabanks()) { System.out.println(db.getName() + " - " + db.getAlphabet().getName() + "(" + db.getClass().getName() + ")"); } } else if (commands[0].equals(DEFAULT)) { System.out.println(genoogle.getDefaultDatabank()); } else if (commands[0].equals(PARAMETERS)) { for (Entry<Parameter, Object> entry : consoleParameters.entrySet()) { System.out.println(entry.getKey().getName() + "=" + entry.getValue()); } } else if (commands[0].equals(SET)) { String[] split = commands[1].split("="); if (split.length != 2) { System.out.println(commands[1] + " is invalid set parameters option."); } String paramName = split[0]; String paramValue = split[1]; Parameter p = Parameter.getParameterByName(paramName); if (p == null) { System.out.println(paramName + " is an invalid parameter name"); continue; } Object value = p.convertValue(paramValue); consoleParameters.put(p, value); System.out.println(paramName + " is " + paramValue); } else if (commands[0].equals(SEQ)) { if (commands.length != 3) { System.out.println("SEQ database id"); continue; } String db = commands[1]; int id = Integer.parseInt(commands[2]); String seq = genoogle.getSequence(db, id); System.out.println(seq); } else if (commands[0].equals(PREV) || commands[0].equals("p")) { executePrev = true; continue; } else if (commands[0].endsWith(BATCH)) { if (commands.length != 2) { System.out.println("BATCH <batchfile>"); continue; } File f = new File(commands[1]); execute(new InputStreamReader(new FileInputStream(f)), true); end = System.currentTimeMillis(); } else if (commands[0].equals(EXIT)) { genoogle.finish(); } else if (commands[0].equals(HELP)) { System.out.println("Commands:"); System.out.println( "search <data bank> <input file> <output file> <parameters>: does the search"); System.out.println("list : lists the data banks."); System.out.println("parameters : shows the search parameters and their values."); System.out.println("set <parameter>=<value> : set the parameters value."); System.out.println("gc : executes the java garbage collection."); System.out.println("prev or l: executes the last command."); System.out.println("batch <batch file> : runs the commands listed in this batch file."); System.out.println("help: this help."); System.out.println("exit : finish Genoogle execution."); System.out.println(); System.out.println("Search Parameters:"); System.out.println( "MaxSubSequenceDistance : maximum index entries distance to be considered in the same HSPs."); System.out.println("SequencesExtendDropoff : drop off for sequence extension."); System.out.println("MaxHitsResults : maximum quantity of returned results."); System.out.println("QuerySplitQuantity : how many slices the input query will be divided."); System.out.println("MinQuerySliceLength : minimum size of each input query slice."); System.out.println( "MaxThreadsIndexSearch : quantity of threads which will be used to index search."); System.out.println( "MaxThreadsExtendAlign : quantity of threads which will be used to extend and align the HSPs."); System.out.println("MatchScore : score when has a match at the alignment."); System.out.println("MismatchScore : score when has a mismatch at the alignment."); } else { System.err.println("Unknow command: " + commands[0]); continue; } prev = line; System.out.print("genoogle console> "); } catch (IndexOutOfBoundsException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (UnsupportedEncodingException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (FileNotFoundException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (ParseException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (IOException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (NoSuchElementException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (UnknowDataBankException e) { logger.error(e.getStackTrace(), e); continue; } catch (InterruptedException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (ExecutionException e) { logger.fatal(e.getStackTrace(), e); continue; } catch (IllegalSymbolException e) { logger.fatal(e.getStackTrace(), e); continue; } } } catch (IOException e) { logger.fatal(e.getStackTrace(), e); return; } }
From source file:bio.pih.genoogle.interfaces.WebServices.java
private String xmlToString(Document doc) { ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); OutputFormat outformat = OutputFormat.createPrettyPrint(); outformat.setTrimText(false);//from w w w . j a va 2s .c om XMLWriter writer = null; try { writer = new XMLWriter(outputStream, outformat); } catch (UnsupportedEncodingException e) { logger.fatal(e); return e.getLocalizedMessage(); } try { writer.write(doc); } catch (IOException e) { logger.fatal(e); return e.getLocalizedMessage(); } try { return outputStream.toString("UTF-8"); } catch (UnsupportedEncodingException e) { logger.fatal(e); return e.getLocalizedMessage(); } }
From source file:BlastResultXMLsplit.BlastXMLsplit.java
public BlastXMLsplit(String filepath, int seqnumber) throws FileNotFoundException, IOException, ParserConfigurationException { SAXReader reader = new SAXReader(); reader.setValidation(false);//from w w w . jav a2 s.c o m try { System.out.println("Xlmfile reading"); Document document = reader.read(new FileInputStream(filepath));//XMLdocument? System.out.println("Xlmfile read done!"); org.dom4j.DocumentFactory DocumentFactory = new org.dom4j.DocumentFactory(); ArrayList str = new ArrayList();//??? String fileoutpath; org.dom4j.Element rootElm = document.getRootElement();// File f = new File(filepath); int count = 1; List<org.dom4j.Element> blastOutput_iterations = rootElm.element("BlastOutput_iterations").elements();//? org.dom4j.Element BlastOutput_program = rootElm.element("BlastOutput_program"); org.dom4j.Element BlastOutput_version = rootElm.element("BlastOutput_version"); org.dom4j.Element BlastOutput_reference = rootElm.element("BlastOutput_reference"); org.dom4j.Element BlastOutput_db = rootElm.element("BlastOutput_db"); //? BlastOutput_program.getParent().remove(BlastOutput_program); BlastOutput_version.getParent().remove(BlastOutput_version); BlastOutput_reference.getParent().remove(BlastOutput_reference); BlastOutput_db.getParent().remove(BlastOutput_db); // org.dom4j.Element BlastOutput_query_def=rootElm.element("BlastOutput_query-def"); //org.dom4j.Element BBlastOutput_query_len=rootElm.element("BlastOutput_query-len"); org.dom4j.Element BlastOutput_param = rootElm.element("BlastOutput_param"); rootElm.remove(BlastOutput_param); String Iteration_queryIDstr, Iteration_queryDefstr, Iteration_query_len; List<org.dom4j.Element> Iterationlist = null; int size = blastOutput_iterations.size(); System.out.println("Your query seqcount is " + size + "\r\n Start dividing your file"); for (int i = 0; i < size; i = i + seqnumber) { //?? fileoutpath = f.getParent() + System.getProperty("file.separator") + count + ".xml"; count++; System.out.println("The " + count + " is located in " + fileoutpath); FileOutputStream fos = new FileOutputStream(fileoutpath); OutputFormat format = OutputFormat.createPrettyPrint(); XMLWriter writer = new XMLWriter(fos, format); // XMLWriter writer = new XMLWriter(new FileOutputStream(fileoutpath)); //w?? org.dom4j.Element firstelement = blastOutput_iterations.get(i); Iteration_queryIDstr = firstelement.element("Iteration_query-ID").getText(); Iteration_queryDefstr = firstelement.element("Iteration_query-def").getText(); Iteration_query_len = firstelement.element("Iteration_query-len").getText(); //org.dom4j.DocumentFactory DocumentFactory = new org.dom4j.DocumentFactory(); Document document2 = DocumentHelper.createDocument(); ; org.dom4j.Element BlastOutputElement = document2.addElement("BlastOutput"); //doc.setRootElement(BlastOutputElement); //; BlastOutputElement.add(BlastOutput_program); BlastOutputElement.add(BlastOutput_version); BlastOutputElement.add(BlastOutput_reference); BlastOutputElement.add(BlastOutput_db); BlastOutputElement.addElement("BlastOutput_query-ID"); BlastOutputElement.element("BlastOutput_query-ID").setText(Iteration_queryIDstr); BlastOutputElement.addElement("BlastOutput_query-def"); BlastOutputElement.element("BlastOutput_query-def").setText(Iteration_queryDefstr); BlastOutputElement.addElement("BlastOutput_query-len"); BlastOutputElement.element("BlastOutput_query-len").setText(Iteration_query_len); // Element BlastOutput_param_new=DocumentFactory.createElement("BlastOutput_param"); // for (Iterator it = BlastOutput_param.elementIterator(); it.hasNext();) { // Element tempele=(Element) it.next(); // tempele.getParent().remove(tempele); // BlastOutput_param_new.add(tempele); // } BlastOutputElement.add(BlastOutput_param); //BlastOutputElement.add(BlastOutput_param); if (i + seqnumber < blastOutput_iterations.size()) { Iterationlist = blastOutput_iterations.subList(i, i + seqnumber); } else { Iterationlist = blastOutput_iterations.subList(i, blastOutput_iterations.size() - 1); } //System.out.println(Iterationlist.size()); //?query resetIterationlist(Iterationlist); //?BlastOutput_iterations Element BlastOutput_iterations = DocumentFactory.createElement("BlastOutput_iterations"); //BlastOutputElement.addAttribute("BlastOutput_iterations"); //org.dom4j.Element BlastOutput_iterations = new org.dom4j.Element("BlastOutput_iterations"); for (int j = 0; j < Iterationlist.size(); j++) { Iterationlist.get(j).getParent().remove(Iterationlist.get(j)); //System.out.println(j); BlastOutput_iterations.add(Iterationlist.get(j)); } BlastOutputElement.add(BlastOutput_iterations); // writer.write(document2); writer.close(); BlastOutput_program.getParent().remove(BlastOutput_program); BlastOutput_version.getParent().remove(BlastOutput_version); BlastOutput_reference.getParent().remove(BlastOutput_reference); BlastOutput_db.getParent().remove(BlastOutput_db); BlastOutput_param.getParent().remove(BlastOutput_param); } } catch (DocumentException ex) { Logger.getLogger(BlastXMLsplit.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:bookmarks.BookmarkXML.java
License:Open Source License
/** * // www . ja v a 2 s .co m * @return */ public String xml_out() { // return stripNonValidXMLCharacters(xmlDoc.asXML()); OutputFormat outFormat = new OutputFormat(); outFormat.setEncoding(Utilities.REQUEST_ENCODING); StringWriter writer = new StringWriter(); XMLWriter out = new XMLWriter(writer, outFormat); try { out.write(xmlDoc); } catch (Exception e) { } String s = writer.toString(); return s; }
From source file:ca.coder2000.recipes.RecipeFile.java
License:Mozilla Public License
/** * Returns formatted HTML from the xml file. * @param stylesheet The stylesheet to transform against. * @return The HTML to be used.// w w w . j a v a 2 s. co m */ public Document getHTML(File stylesheet) { Transformer transformer; TransformerFactory factory = TransformerFactory.newInstance(); DocumentSource source = new DocumentSource(doc); DocumentResult result = new DocumentResult(); try { transformer = factory.newTransformer(new StreamSource(stylesheet)); transformer.transform(source, result); // Hard coded path MUST remove OutputFormat format = OutputFormat.createPrettyPrint(); XMLWriter writer = new XMLWriter(new FileWriter("k:/recipe/recipe.tmp"), format); writer.write(result.getDocument()); } catch (TransformerException te) { } catch (IOException ioe) { } return result.getDocument(); }
From source file:cc.warlock.build.FeatureVersionReplacer.java
License:Open Source License
protected void replaceVersions() throws BuildException { SAXReader reader = new SAXReader(); try {//from w ww . j a v a 2 s . com File featureFile = new File(new File(new File(buildDirectory, "features"), feature), "feature.xml"); Document featureDoc = reader.read(featureFile); Element featureEl = featureDoc.getRootElement(); featureEl.attribute("version").setValue(version); // Properties versions = new Properties(); // File versionsFile = new File(buildDirectory, "finalPluginsVersions.properties"); // FileInputStream stream = new FileInputStream(versionsFile); // versions.load(stream); // stream.close(); // // for (Element pluginEl : (List<Element>) featureEl.elements("plugin")) // { // if (pluginEl.attributeValue("version").equals("0.0.0")) // { // if (versions.containsKey(pluginEl.attributeValue("id"))) // pluginEl.attribute("version").setValue(versions.getProperty(pluginEl.attributeValue("id"))); // } // } OutputFormat format = OutputFormat.createPrettyPrint(); FileOutputStream outStream = new FileOutputStream(featureFile); XMLWriter writer = new XMLWriter(outStream, format); writer.write(featureDoc); outStream.close(); } catch (FileNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (DocumentException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } }