List of usage examples for org.apache.commons.cli BasicParser BasicParser
BasicParser
From source file:com.genentech.retrival.tabExport.TABExporter.java
public static void main(String[] args) throws ParseException, JDOMException, IOException { long start = System.currentTimeMillis(); int nStruct = 0; // create command line Options object Options options = new Options(); Option opt = new Option("sqlFile", true, "sql-xml file"); opt.setRequired(true);//www. j a va2s.com options.addOption(opt); opt = new Option("sqlName", true, "name of SQL element in xml file"); opt.setRequired(true); options.addOption(opt); opt = new Option("o", true, "output file"); opt.setRequired(false); options.addOption(opt); opt = new Option("newLineReplacement", true, "If given newlines in fields will be replaced by this string."); options.addOption(opt); opt = new Option("noHeader", false, "Do not output header line"); options.addOption(opt); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); String outFile = cmd.getOptionValue("o"); String sqlFile = cmd.getOptionValue("sqlFile"); String sqlName = cmd.getOptionValue("sqlName"); String newLineReplacement = cmd.getOptionValue("newLineReplacement"); args = cmd.getArgs(); try { PrintStream out = System.out; if (outFile != null) out = new PrintStream(outFile); SQLStatement stmt = SQLStatement.createFromFile(new File(sqlFile), sqlName); Object[] sqlArgs = args; if (stmt.getParamTypes().length != args.length) { System.err.printf( "\nWarining sql statement needs %d parameters but got only %d. Filling up with NULLs.\n", stmt.getParamTypes().length, args.length); sqlArgs = new Object[stmt.getParamTypes().length]; System.arraycopy(args, 0, sqlArgs, 0, args.length); } Selecter sel = Selecter.factory(stmt); if (!sel.select(sqlArgs)) { System.err.println("No rows returned!"); System.exit(0); } String[] fieldNames = sel.getFieldNames(); if (fieldNames.length == 0) { System.err.println("Query did not return any columns"); exitWithHelp(options); } if (!cmd.hasOption("noHeader")) { StringBuilder sb = new StringBuilder(200); for (String f : fieldNames) sb.append(f).append('\t'); if (sb.length() > 1) sb.setLength(sb.length() - 1); // chop last \t String header = sb.toString(); out.println(header); } StringBuilder sb = new StringBuilder(200); while (sel.hasNext()) { Record sqlRec = sel.next(); sb.setLength(0); for (int i = 0; i < fieldNames.length; i++) { String fld = sqlRec.getStrg(i); if (newLineReplacement != null) fld = NEWLinePattern.matcher(fld).replaceAll(newLineReplacement); sb.append(fld).append('\t'); } if (sb.length() > 1) sb.setLength(sb.length() - 1); // chop last \t String row = sb.toString(); out.println(row); nStruct++; } } catch (Exception e) { throw new Error(e); } finally { System.err.printf("TABExporter: Exported %d records in %dsec\n", nStruct, (System.currentTimeMillis() - start) / 1000); } }
From source file:io.github.azige.whitespace.Cli.java
public static void main(String[] args) { Options options = new Options().addOption("h", "help", false, "??") .addOptionGroup(new OptionGroup() .addOption(new Option("p", "????????")) .addOption(new Option("c", "?????"))) .addOption(null, "szm", false, "????") .addOption("e", "encoding", true, "??" + DEFAULT_ENCODING); try {/* w w w .j a va2 s. c o m*/ CommandLineParser parser = new BasicParser(); CommandLine cl = parser.parse(options, args); if (cl.hasOption('h')) { printHelp(System.out, options); return; } if (cl.hasOption('e')) { encoding = Charset.forName(cl.getOptionValue('e')); } else { encoding = Charset.forName(DEFAULT_ENCODING); } if (cl.hasOption("szm")) { useSzm = true; } String[] fileArgs = cl.getArgs(); if (fileArgs.length != 1) { printHelp(System.err, options); return; } try (InputStream input = Files.newInputStream(Paths.get(fileArgs[0]))) { if (cl.hasOption('p')) { printPseudoCode(input); } else if (cl.hasOption('c')) { compile(input, fileArgs[0]); } else { execute(input, fileArgs[0]); } } } catch (ParseException ex) { ex.printStackTrace(); printHelp(System.err, options); } catch (Exception ex) { ex.printStackTrace(); } }
From source file:FULRequestor.java
public static void main(String[] args) throws Exception { String hostId = ""; String partnerId = ""; String userId = ""; CommandLineParser parser = new BasicParser(); Options options = new Options(); options.addOption("h", "host", true, "EBICS Host ID"); options.addOption("p", "partner", true, "Registred Partner ID for you user"); options.addOption("u", "user", true, "User ID to initiate"); // Parse the program arguments CommandLine commandLine = parser.parse(options, args); if (!commandLine.hasOption('h')) { System.out.println("Host-ID is mandatory"); System.exit(0);//from w ww . j av a2 s. com } else { hostId = commandLine.getOptionValue('h'); System.out.println("host: " + hostId); } if (!commandLine.hasOption('p')) { System.out.println("Partner-ID is mandatory"); System.exit(0); } else { partnerId = commandLine.getOptionValue('p'); System.out.println("partnerId: " + partnerId); } if (!commandLine.hasOption('u')) { System.out.println("User-ID is mandatory"); System.exit(0); } else { userId = commandLine.getOptionValue('u'); System.out.println("userId: " + userId); } FULRequestor hbbRequestor; PasswordCallback pwdHandler; Product product; String filePath; hbbRequestor = new FULRequestor(); product = new Product("kopiLeft Dev 1.0", Locale.FRANCE, null); pwdHandler = new UserPasswordHandler(userId, "2012"); // Load alredy created user hbbRequestor.loadUser(hostId, partnerId, userId, pwdHandler); filePath = System.getProperty("user.home") + File.separator + "test.txt"; // Send FUL Requets hbbRequestor.sendFile(filePath, userId, product); }
From source file:diffhunter.DiffHunter.java
/** * @param args the command line arguments * @throws org.apache.commons.cli.ParseException * @throws java.io.IOException//w ww .j av a2 s . c om */ public static void main(String[] args) throws ParseException, IOException { //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString(); // TODO code application logic here /*args = new String[] { "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData" };*/ /*args = new String[] { "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData" };*/ Options options = new Options(); // add t option options.addOption("i", "index", false, "Indexing BED files."); options.addOption("b", "bed", true, "bed file to be indexed"); options.addOption("o", "output", true, "Folder that the index/comparison file will be created."); options.addOption("r", "reference", true, "Reference annotation file to be used for indexing"); options.addOption("c", "compare", false, "Finding differences between two conditions"); options.addOption("1", "first", true, "First sample index location"); options.addOption("2", "second", true, "Second sample index location"); options.addOption("w", "window", true, "Length of window for identifying differences"); options.addOption("s", "sliding", true, "Length of sliding"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); boolean indexing = false; boolean comparing = false; //Indexing! if (cmd.hasOption("i")) { //if(cmd.hasOption("1")) //System.err.println("sasan"); //System.out.println("sasa"); indexing = true; } else if (cmd.hasOption("c")) { //System.err.println(""); comparing = true; } else { //System.err.println("Option is not deteced."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } //Indexing is selected // if (indexing == true) { //Since indexing is true. //User have to provide file for indexing. if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String bedfile_ = cmd.getOptionValue("b"); String reference_file = cmd.getOptionValue("r"); String folder_loc = cmd.getOptionValue("o"); String sample_name = FilenameUtils.getBaseName(bedfile_); try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB( Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) { Indexer indexing_ = new Indexer(reference_file); indexing_.Make_Index(B2, bedfile_, Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString()); B2.close(); } } else if (comparing == true) { if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1") || cmd.hasOption("2"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String folder_loc = cmd.getOptionValue("o"); int window_ = Integer.parseInt(cmd.getOptionValue("w")); //int window_=600; int slide_ = Integer.parseInt(cmd.getOptionValue("s")); String first = cmd.getOptionValue("1").replace("_BDB", ""); String second = cmd.getOptionValue("2").replace("_BDB", ""); String reference_file = cmd.getOptionValue("r"); //String folder_loc=cmd.getOptionValue("o"); String sample_name_first = FilenameUtils.getBaseName(first); String sample_name_second = FilenameUtils.getBaseName(second); Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first); Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second); List<String> first_condition_genes = Files .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath()) .collect(Collectors.toList()); List<String> second_condition_genes = Files .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath()) .collect(Collectors.toList()); System.out.println("First and second condition are loaded!!! "); List<String> intersection_ = new ArrayList<>(first_condition_genes); intersection_.retainAll(second_condition_genes); BufferedWriter output = new BufferedWriter( new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt") .toAbsolutePath().toString(), false)); List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>()); Worker_New worker_class = new Worker_New(); worker_class.Read_Reference(reference_file); while (!intersection_.isEmpty()) { List<String> selected_genes = new ArrayList<>(); //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));} //else selected_genes.addAll(intersection_.subList(0, 10000)); if (intersection_.size() <= intersection_.size()) { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } else { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } intersection_.removeAll(selected_genes); //System.out.println("Intersection count is:"+intersection_.size()); //final List<Result_Window> resultssss_=new ArrayList<>(); IntStream.range(0, selected_genes.size()).parallel().forEach(i -> { System.out.println(selected_genes.get(i) + "\tprocessing......"); String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2"; int start = worker_class.dic_genes.get(gene_of_interest).start_loc; int end = worker_class.dic_genes.get(gene_of_interest).end_loc; Map<Integer, Integer> first_ = Collections.EMPTY_MAP; try { first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } Map<Integer, Integer> second_ = Collections.EMPTY_MAP; try { second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_); List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_); //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i)); // System.out.println("top_window_first_Count\t"+top_windows_first.size()); // System.out.println("top_window_second_Count\t"+top_windows_second.size()); if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) { return; } List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, sample_name_first, sample_name_second, 0.01); if (!res_temp.isEmpty()) { final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01)); } //System.out.println(selected_genes.get(i)+"\tprocessed."); }); /*selected_genes.parallelStream().forEach(i -> { });*/ List<Double> pvals = new ArrayList<>(); for (int i = 0; i < final_results.size(); i++) { pvals.add(final_results.get(i).p_value); } List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals); System.out.println("Writing to file..."); output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR"); output.newLine(); for (int i = 0; i < final_results.size(); i++) { Result_Window item = final_results.get(i); output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } /* for (Result_Window item : final_results) { output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } */ final_results.clear(); } output.close(); } System.out.println("Done."); }
From source file:edu.cuhk.hccl.cmd.AppSearchEngine.java
public static void main(String[] args) throws IOException { // Get parameters CommandLineParser parser = new BasicParser(); Options options = createOptions();/*w ww . j ava 2 s. c om*/ File dataFolder = null; String queryStr = null; int topK = 0; File resultFile = null; String queryType = null; File similarityFile = null; try { CommandLine line = parser.parse(options, args); dataFolder = new File(line.getOptionValue('d')); queryStr = line.getOptionValue('q'); queryType = line.getOptionValue('t'); topK = Integer.parseInt(line.getOptionValue('k')); resultFile = new File(line.getOptionValue('f')); similarityFile = new File(line.getOptionValue('s')); if (line.hasOption('m')) { String modelPath = line.getOptionValue('m'); if (queryType.equalsIgnoreCase("WordVector")) { expander = new WordVectorExpander(modelPath); } else if (queryType.equalsIgnoreCase("WordNet")) { expander = new WordNetExpander(modelPath); } else { System.out.println("Please choose a correct expander: WordNet or WordVector!"); System.exit(-1); } } } catch (ParseException exp) { System.out.println("Error in parameters: \n" + exp.getMessage()); System.exit(-1); } // Create Index StandardAnalyzer analyzer = new StandardAnalyzer(); Directory index = createIndex(dataFolder, analyzer); // Build query Query query = buildQuery(analyzer, queryStr, queryType); // Search index for topK hits IndexReader reader = DirectoryReader.open(index); IndexSearcher searcher = new IndexSearcher(reader); TopScoreDocCollector collector = TopScoreDocCollector.create(topK, true); searcher.search(query, collector); ScoreDoc[] hits = collector.topDocs().scoreDocs; // Show search results System.out.println("\n[INFO] " + hits.length + " hits were returned:"); List<String> hitLines = new ArrayList<String>(); for (int i = 0; i < hits.length; i++) { int docId = hits[i].doc; Document d = searcher.doc(docId); String line = (i + 1) + "\t" + d.get(PATH_FIELD) + "\t" + hits[i].score; System.out.println(line); hitLines.add(line); } // Compute cosine similarity between documents List<String> simLines = new ArrayList<String>(); for (int m = 0; m < hits.length; m++) { int doc1 = hits[m].doc; Terms terms1 = reader.getTermVector(doc1, CONTENT_FIELD); for (int n = m + 1; n < hits.length; n++) { int doc2 = hits[n].doc; Terms terms2 = reader.getTermVector(doc2, CONTENT_FIELD); CosineDocumentSimilarity cosine = new CosineDocumentSimilarity(terms1, terms2); double similarity = cosine.getCosineSimilarity(); String line = searcher.doc(doc1).get(PATH_FIELD) + "\t" + searcher.doc(doc2).get(PATH_FIELD) + "\t" + similarity; simLines.add(line); } } // Release resources reader.close(); if (expander != null) { expander.close(); } // Save search results System.out.println("\n[INFO] Search results are saved in file: " + resultFile.getPath()); FileUtils.writeLines(resultFile, hitLines, false); System.out.println("\n[INFO] Cosine similarities are saved in file: " + similarityFile.getPath()); FileUtils.writeLines(similarityFile, simLines, false); }
From source file:com.ibm.soatf.SOATestingFramework.java
/** * SOA Testing Framework main static method. * * @param args Main input parameters./*from ww w. j a v a 2 s . c o m*/ */ public static void main(String[] args) { Options options = new Options(); options.addOption(new Option("gui", "Display a GUI")); options.addOption(OptionBuilder.withArgName("environment").hasArg() .withDescription("Environment to run the tests on").create("env")); // has a value options.addOption(OptionBuilder.withArgName("project").hasArg() .withDescription("Project to run the tests on").create("p")); // has a value options.addOption(OptionBuilder.withArgName("interface").hasArg() .withDescription("Interface to run the tests on").create("i")); // has a value CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); validate(cmd); if (cmd.hasOption("gui")) { /* Set the Nimbus look and feel */ //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) "> /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel. * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html */ try { if (false) { //disabled the OS Look'n'Feel UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } else { for (UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) { if ("Nimbus".equals(info.getName())) { javax.swing.UIManager.setLookAndFeel(info.getClassName()); break; } } UIManager.getLookAndFeelDefaults().put("nimbusOrange", (new Color(0, 128, 255))); } } catch (ClassNotFoundException | InstantiationException | IllegalAccessException | javax.swing.UnsupportedLookAndFeelException ex) { logger.error("Cannot set look and feel", ex); } //</editor-fold> final SOATestingFrameworkGUI soatfgui = new SOATestingFrameworkGUI(); java.awt.EventQueue.invokeLater(new Runnable() { @Override public void run() { soatfgui.setVisible(true); } }); } else { //<editor-fold defaultstate="collapsed" desc="Command line mode"> try { // Initialization of configuration manager. ConfigurationManager.getInstance().init(); String env = cmd.getOptionValue("env", null); String ifaceName; boolean inboundOnly = false; if (cmd.hasOption("p")) { String projectName = cmd.getOptionValue("p"); MasterConfiguration masterConfig = ConfigurationManager.getInstance().getMasterConfig(); List<SOATestingFrameworkMasterConfiguration.Interfaces.Interface> interfaces = masterConfig .getInterfaces(); all: for (Interface iface : interfaces) { List<Project> projects = iface.getProjects().getProject(); for (Project project : projects) { if (project.getName().equals(projectName)) { inboundOnly = "INBOUND".equalsIgnoreCase(project.getDirection()); ifaceName = iface.getName(); break all; } } } throw new FrameworkExecutionException( "No such project found in master configuration: " + projectName); } else { ifaceName = cmd.getOptionValue("i"); inboundOnly = false; } DirectoryStructureManager.checkFrameworkDirectoryStructure(ifaceName); FlowExecutor flowExecutor = new FlowExecutor(inboundOnly, env, ifaceName); flowExecutor.execute(); } catch (FrameworkConfigurationException ex) { logger.fatal("Configuration corrupted. See the exception stack trace for details.", ex); } catch (FrameworkException ex) { logger.fatal(ex); } //</editor-fold> } } catch (ParseException ex) { logger.fatal("Could not parse the command line arguments. Reason: " + ex); printUsage(); } catch (Throwable ex) { logger.fatal("Unexpected error occured: ", ex); printUsage(); System.exit(-1); } }
From source file:com.example.geomesa.kafka08.KafkaListener.java
public static void main(String[] args) throws Exception { // read command line args for a connection to Kafka CommandLineParser parser = new BasicParser(); Options options = getCommonRequiredOptions(); CommandLine cmd = parser.parse(options, args); // create the consumer KafkaDataStore object Map<String, String> dsConf = getKafkaDataStoreConf(cmd); dsConf.put("isProducer", "false"); DataStore consumerDS = DataStoreFinder.getDataStore(dsConf); // verify that we got back our KafkaDataStore object properly if (consumerDS == null) { throw new Exception("Null consumer KafkaDataStore"); }/* ww w.j a v a2 s. c om*/ // create the schema which creates a topic in Kafka // (only needs to be done once) // TODO: This should be rolled into the Command line options to make this more general. registerListeners(consumerDS); while (true) { // Wait for user to terminate with ctrl-C. } }
From source file:com.versusoft.packages.jodl.gui.CommandLineGUI.java
public static void main(String args[]) throws SAXException, IOException { Handler fh = new FileHandler(LOG_FILENAME_PATTERN); fh.setFormatter(new SimpleFormatter()); //removeAllLoggersHandlers(Logger.getLogger("")); Logger.getLogger("").addHandler(fh); Logger.getLogger("").setLevel(Level.FINEST); Options options = new Options(); Option option1 = new Option("in", "ODT file (required)"); option1.setRequired(true);//from w w w . j av a 2 s. c o m option1.setArgs(1); Option option2 = new Option("out", "Output file (required)"); option2.setRequired(false); option2.setArgs(1); Option option3 = new Option("pic", "extract pics"); option3.setRequired(false); option3.setArgs(1); Option option4 = new Option("page", "enable pagination processing"); option4.setRequired(false); option4.setArgs(0); options.addOption(option1); options.addOption(option2); options.addOption(option3); options.addOption(option4); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { printHelp(); return; } if (cmd.hasOption("help")) { printHelp(); return; } File outFile = new File(cmd.getOptionValue("out")); OdtUtils utils = new OdtUtils(); utils.open(cmd.getOptionValue("in")); //utils.correctionStep(); utils.saveXML(outFile.getAbsolutePath()); try { if (cmd.hasOption("page")) { OdtUtils.paginationProcessing(outFile.getAbsolutePath()); } OdtUtils.correctionProcessing(outFile.getAbsolutePath()); } catch (ParserConfigurationException ex) { logger.log(Level.SEVERE, null, ex); } catch (SAXException ex) { logger.log(Level.SEVERE, null, ex); } catch (IOException ex) { logger.log(Level.SEVERE, null, ex); } catch (TransformerConfigurationException ex) { logger.log(Level.SEVERE, null, ex); } catch (TransformerException ex) { logger.log(Level.SEVERE, null, ex); } if (cmd.hasOption("pic")) { String imageDir = cmd.getOptionValue("pic"); if (!imageDir.endsWith("/")) { imageDir += "/"; } try { String basedir = new File(cmd.getOptionValue("out")).getParent().toString() + System.getProperty("file.separator"); OdtUtils.extractAndNormalizeEmbedPictures(cmd.getOptionValue("out"), cmd.getOptionValue("in"), basedir, imageDir); } catch (SAXException ex) { logger.log(Level.SEVERE, null, ex); } catch (ParserConfigurationException ex) { logger.log(Level.SEVERE, null, ex); } catch (TransformerConfigurationException ex) { logger.log(Level.SEVERE, null, ex); } catch (TransformerException ex) { logger.log(Level.SEVERE, null, ex); } } }
From source file:com.hortonworks.registries.storage.tool.TablesInitializer.java
public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(Option.builder("s").numberOfArgs(1).longOpt(OPTION_SCRIPT_ROOT_PATH) .desc("Root directory of script path").build()); options.addOption(Option.builder("c").numberOfArgs(1).longOpt(OPTION_CONFIG_FILE_PATH) .desc("Config file path").build()); options.addOption(Option.builder("m").numberOfArgs(1).longOpt(OPTION_MYSQL_JAR_URL_PATH) .desc("Mysql client jar url to download").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CREATE_TABLE) .desc("Execute 'create table' script").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_DROP_TABLE) .desc("Execute 'drop table' script").build()); options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CHECK_CONNECTION) .desc("Check the connection for configured data source").build()); CommandLineParser parser = new BasicParser(); CommandLine commandLine = parser.parse(options, args); if (!commandLine.hasOption(OPTION_CONFIG_FILE_PATH) || !commandLine.hasOption(OPTION_SCRIPT_ROOT_PATH)) { usage(options);/* ww w .j a va2 s . c o m*/ System.exit(1); } // either create or drop should be specified, not both boolean executeCreate = commandLine.hasOption(OPTION_EXECUTE_CREATE_TABLE); boolean executeDrop = commandLine.hasOption(OPTION_EXECUTE_DROP_TABLE); boolean checkConnection = commandLine.hasOption(OPTION_EXECUTE_CHECK_CONNECTION); boolean moreThanOneOperationIsSpecified = executeCreate == executeDrop ? executeCreate : checkConnection; boolean noOperationSpecified = !(executeCreate || executeDrop || checkConnection); if (moreThanOneOperationIsSpecified) { System.out.println( "Only one operation can be execute at once, please select 'create' or 'drop', or 'check-connection'."); System.exit(1); } else if (noOperationSpecified) { System.out.println( "One of 'create', 'drop', 'check-connection' operation should be specified to execute."); System.exit(1); } String confFilePath = commandLine.getOptionValue(OPTION_CONFIG_FILE_PATH); String scriptRootPath = commandLine.getOptionValue(OPTION_SCRIPT_ROOT_PATH); String mysqlJarUrl = commandLine.getOptionValue(OPTION_MYSQL_JAR_URL_PATH); StorageProviderConfiguration storageProperties; try { Map<String, Object> conf = Utils.readConfig(confFilePath); StorageProviderConfigurationReader confReader = new StorageProviderConfigurationReader(); storageProperties = confReader.readStorageConfig(conf); } catch (IOException e) { System.err.println("Error occurred while reading config file: " + confFilePath); System.exit(1); throw new IllegalStateException("Shouldn't reach here"); } String bootstrapDirPath = null; try { bootstrapDirPath = System.getProperty("bootstrap.dir"); MySqlDriverHelper.downloadMySQLJarIfNeeded(storageProperties, bootstrapDirPath, mysqlJarUrl); } catch (Exception e) { System.err.println("Error occurred while downloading MySQL jar. bootstrap dir: " + bootstrapDirPath); System.exit(1); throw new IllegalStateException("Shouldn't reach here"); } try { SQLScriptRunner sqlScriptRunner = new SQLScriptRunner(storageProperties); try { sqlScriptRunner.initializeDriver(); } catch (ClassNotFoundException e) { System.err.println( "Driver class is not found in classpath. Please ensure that driver is in classpath."); System.exit(1); } if (checkConnection) { if (!sqlScriptRunner.checkConnection()) { System.exit(1); } } else if (executeDrop) { doExecuteDrop(sqlScriptRunner, storageProperties, scriptRootPath); } else { // executeCreate doExecuteCreate(sqlScriptRunner, storageProperties, scriptRootPath); } } catch (IOException e) { System.err.println("Error occurred while reading script file. Script root path: " + scriptRootPath); System.exit(1); } }
From source file:com.github.zk1931.pulsefs.Main.java
public static void main(String[] args) throws Exception { // Options for command arguments. Options options = new Options(); Option port = OptionBuilder.withArgName("port").hasArg(true).isRequired(true).withDescription("port number") .create("port"); Option addr = OptionBuilder.withArgName("addr").hasArg(true).withDescription("addr (ip:port) for Zab.") .create("addr"); Option join = OptionBuilder.withArgName("join").hasArg(true).withDescription("the addr of server to join.") .create("join"); Option dir = OptionBuilder.withArgName("dir").hasArg(true).withDescription("the directory for logs.") .create("dir"); Option help = OptionBuilder.withArgName("h").hasArg(false).withLongOpt("help") .withDescription("print out usages.").create("h"); Option timeout = OptionBuilder.withArgName("timeout").hasArg(true) .withDescription("session timeout(seconds)").create("timeout"); options.addOption(port).addOption(addr).addOption(join).addOption(dir).addOption(timeout).addOption(help); CommandLineParser parser = new BasicParser(); CommandLine cmd;/*from w w w. j a v a 2 s . c o m*/ String usage = "./bin/pulsefs -port port [Options]"; try { cmd = parser.parse(options, args); if (cmd.hasOption("h")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(usage, options); return; } } catch (ParseException exp) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(usage, options); return; } PulseFSConfig config = new PulseFSConfig(); if (cmd.hasOption("addr")) { config.setServerId(cmd.getOptionValue("addr")); } if (cmd.hasOption("join")) { config.setJoinPeer(cmd.getOptionValue("join")); } if (cmd.hasOption("dir")) { config.setLogDir(cmd.getOptionValue("dir")); } if (cmd.hasOption("timeout")) { String sessionTimeout = cmd.getOptionValue("timeout"); config.setSessionTimeout(Integer.parseInt(sessionTimeout)); } if (cmd.hasOption("port")) { config.setPort(Integer.parseInt(cmd.getOptionValue("port"))); } Server server = new Server(config.getPort()); // Suppress "Server" header in HTTP response. for (Connector y : server.getConnectors()) { for (ConnectionFactory x : y.getConnectionFactories()) { if (x instanceof HttpConnectionFactory) { ((HttpConnectionFactory) x).getHttpConfiguration().setSendServerVersion(false); } } } PulseFS fs = new PulseFS(config); SessionFilter sessionFilter = new SessionFilter(fs); FilterHolder filters = new FilterHolder(sessionFilter); ServletContextHandler pulsefs = new ServletContextHandler(ServletContextHandler.SESSIONS); pulsefs.setContextPath(PulseFSConfig.PULSEFS_ROOT); pulsefs.setAllowNullPathInfo(true); pulsefs.addServlet(new ServletHolder(new PulseFSHandler(fs)), "/*"); pulsefs.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler servers = new ServletContextHandler(ServletContextHandler.SESSIONS); servers.setContextPath(PulseFSConfig.PULSEFS_SERVERS_PATH); // Redirects /pulsefs/servers to /pulsefs/servers/ servers.setAllowNullPathInfo(true); servers.addServlet(new ServletHolder(new PulseFSServersHandler(fs)), "/*"); servers.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler tree = new ServletContextHandler(ServletContextHandler.SESSIONS); tree.setContextPath("/"); tree.addServlet(new ServletHolder(new TreeHandler(fs)), "/*"); tree.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ServletContextHandler sessions = new ServletContextHandler(ServletContextHandler.SESSIONS); sessions.setContextPath(PulseFSConfig.PULSEFS_SESSIONS_PATH); // Redirects /pulsefs/sessions to /pulsefs/sessions/ sessions.setAllowNullPathInfo(true); sessions.addServlet(new ServletHolder(new PulseFSSessionsHandler(fs)), "/*"); sessions.addFilter(filters, "/*", EnumSet.of(DispatcherType.REQUEST)); ContextHandlerCollection contexts = new ContextHandlerCollection(); contexts.setHandlers(new Handler[] { sessions, servers, pulsefs, tree }); server.setHandler(contexts); server.start(); server.join(); }