List of usage examples for java.io PrintStream PrintStream
public PrintStream(File file) throws FileNotFoundException
From source file:com.denimgroup.threadfix.importer.cli.CommandLineMigration.java
public static void main(String[] args) { if (!check(args)) return;/*from ww w .j a v a 2s.c o m*/ try { String inputScript = args[0]; String inputMySqlConfig = args[1]; String outputScript = "import.sql"; String outputMySqlConfigTemp = "jdbc_temp.properties"; String errorLogFile = "error.log"; String fixedSqlFile = "error_sql.sql"; String errorLogAttemp1 = "error1.log"; String infoLogFile = "info.log"; String rollbackScript = "rollback.sql"; deleteFile(outputScript); deleteFile(errorLogFile); deleteFile(errorLogFile); deleteFile(fixedSqlFile); deleteFile(errorLogAttemp1); deleteFile(infoLogFile); deleteFile(rollbackScript); PrintStream infoPrintStream = new PrintStream(new FileOutputStream(new File(infoLogFile))); System.setOut(infoPrintStream); long startTime = System.currentTimeMillis(); copyFile(inputMySqlConfig, outputMySqlConfigTemp); LOGGER.info("Creating threadfix table in mySql database ..."); ScriptRunner scriptRunner = SpringConfiguration.getContext().getBean(ScriptRunner.class); startTime = printTimeConsumed(startTime); convert(inputScript, outputScript); startTime = printTimeConsumed(startTime); PrintStream errPrintStream = new PrintStream(new FileOutputStream(new File(errorLogFile))); System.setErr(errPrintStream); LOGGER.info("Sending sql script to MySQL server ..."); scriptRunner.run(outputScript, outputMySqlConfigTemp); long errorCount = scriptRunner.checkRunningAndFixStatements(errorLogFile, fixedSqlFile); long lastCount = errorCount + 1; int times = 1; int sameFixedSet = 0; // Repeat while (errorCount > 0) { //Flush error log screen to other file errPrintStream = new PrintStream(new FileOutputStream(new File(errorLogAttemp1))); System.setErr(errPrintStream); times += 1; if (errorCount == lastCount) { sameFixedSet++; } else { sameFixedSet = 0; } LOGGER.info("Found " + errorCount + " error statements. Sending fixed sql script to MySQL server " + times + " times ..."); scriptRunner.run(fixedSqlFile, outputMySqlConfigTemp); lastCount = errorCount; errorCount = scriptRunner.checkRunningAndFixStatements(errorLogAttemp1, fixedSqlFile); if (errorCount > lastCount || sameFixedSet > SAME_SET_TRY_LIMIT) break; } if (errorCount > 0) { LOGGER.error("After " + times + " of trying, still found errors in sql script. " + "Please check error_sql.sql and error1.log for more details."); LOGGER.info("Do you want to keep data in MySQL, and then import manually error statements (y/n)? "); try (java.util.Scanner in = new java.util.Scanner(System.in)) { String answer = in.nextLine(); if (!answer.equalsIgnoreCase("y")) { rollbackData(scriptRunner, outputMySqlConfigTemp, rollbackScript); } else { LOGGER.info( "Data imported to MySQL, but still have some errors. Please check error_sql.sql and error1.log to import manually."); } } } else { printTimeConsumed(startTime); LOGGER.info("Migration successfully finished"); } deleteFile(outputMySqlConfigTemp); } catch (Exception e) { LOGGER.error("Error: ", e); } }
From source file:com.xylocore.copybook.runtime.internal.AbstractCopybookGenerator.java
public static void main(String[] args) { try {// www . jav a 2s. co m PrintStream myOutputStream = System.out; myOutputStream = new PrintStream(new FileOutputStream( "src/main/java/com/xylocore/commons/data/copybook/runtime/AbstractCopybook.java.new")); AbstractCopybookGenerator myGenerator = new AbstractCopybookGenerator(); myGenerator.generate(myOutputStream); myOutputStream.close(); } catch (Exception myException) { myException.printStackTrace(); } }
From source file:hadoopInstaller.Main.java
public static void main(String[] args) { // Disable VFS logging to console by default System.setProperty("org.apache.commons.logging.Log", //$NON-NLS-1$ "org.apache.commons.logging.impl.NoOpLog"); //$NON-NLS-1$ // Configure SimpleLog to show date and omit log name System.setProperty("org.apache.commons.logging.simplelog.showdatetime", "true"); //$NON-NLS-1$//$NON-NLS-2$ System.setProperty("org.apache.commons.logging.simplelog.showlogname", "false"); //$NON-NLS-1$//$NON-NLS-2$ System.setProperty("org.apache.commons.logging.simplelog.showShortLogname", "false"); //$NON-NLS-1$//$NON-NLS-2$ try (PrintStream filePrintStream = new PrintStream(VFS.getManager() .resolveFile(MessageFormat.format("file://{0}/{1}", //$NON-NLS-1$ System.getProperty("user.dir"), Main.FILE_LOG_NAME)) //$NON-NLS-1$ .getContent().getOutputStream(true))) { CompositeLog log = new CompositeLog(); Integer logLevel = detectLogLevel(args); PrintStreamLog consoleLog = new PrintStreamLog(Installer.INSTALLER_NAME, System.out); consoleLog.setLevel(logLevel);//from w ww . j av a 2 s . c o m log.addLog(consoleLog); PrintStreamLog fileLog = new PrintStreamLog(Installer.INSTALLER_NAME, filePrintStream); fileLog.setLevel(logLevel); log.addLog(fileLog); boolean deploy = Arrays.asList(args).contains("-deploy"); //$NON-NLS-1$ try { new Installer(log, deploy).run(); } catch (InstallationFatalError e) { log.fatal(e.getLocalizedMessage()); log.fatal(e.getCause().getLocalizedMessage()); log.trace(e.getLocalizedMessage(), e); } } catch (FileSystemException e) { new PrintStreamLog(Installer.INSTALLER_NAME, System.err).fatal(e.getLocalizedMessage(), e); System.exit(1); } /* * TODO-- ssh-ask * * Consider using a configuration that doesn't require password-less * authentication, but set's it up for the final cluster. */ }
From source file:it.cnr.isti.labse.glimpse.MainMonitoring.java
/** * Read the properties and init the connections to the enterprise service bus * //from w w w. jav a2 s .co m * @param is the systemSettings file */ public static void main(String[] args) { try { FileOutputStream fos = new FileOutputStream("glimpseLog.log"); PrintStream ps = new PrintStream(fos); System.setErr(ps); if (MainMonitoring.initProps(args[0]) && MainMonitoring.init()) { SplashScreen.Show(); System.out.println("Please wait until setup is done..."); //the buffer where the events are stored to be analyzed EventsBuffer<GlimpseBaseEvent<?>> buffer = new EventsBufferImpl<GlimpseBaseEvent<?>>(); //The complex event engine that will be used (in this case drools) ComplexEventProcessor engine = new ComplexEventProcessorImpl(Manager.Read(MANAGERPARAMETERFILE), buffer, connFact, initConn); engine.start(); try { Thread.sleep(3000); } catch (InterruptedException e) { e.printStackTrace(); } //the manager of all the architecture GlimpseManager manager = new GlimpseManager(Manager.Read(MANAGERPARAMETERFILE), connFact, initConn, engine.getRuleManager()); manager.start(); } } catch (Exception e) { System.out.println("USAGE: java -jar MainMonitoring.jar \"systemSettings\""); } }
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);/*from w w w. j a v a 2s. c o m*/ 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:ca.uqac.dim.mapreduce.ltl.ParaLTLValidation.java
/** * Program entry point.//from w w w . ja va2s . c o m * @param args Command-line arguments */ @SuppressWarnings("static-access") public static void main(String[] args) { // Define and process command line arguments Options options = new Options(); HelpFormatter help_formatter = new HelpFormatter(); Option opt; options.addOption("h", "help", false, "Show help"); opt = OptionBuilder.withArgName("property").hasArg() .withDescription("Property to verify, enclosed in double quotes").create("p"); options.addOption(opt); opt = OptionBuilder.withArgName("filename").hasArg().withDescription("Input filename").create("i"); options.addOption(opt); opt = OptionBuilder.withArgName("x").hasArg() .withDescription("Set verbosity level to x (default: 0 = quiet)").create("v"); options.addOption(opt); opt = OptionBuilder.withArgName("ParserType").hasArg().withDescription("Parser type (Dom or Sax)") .create("t"); options.addOption(opt); opt = OptionBuilder.withLongOpt("redirection").withArgName("x").hasArg() .withDescription("Set the redirection file for the System.out").create("r"); options.addOption(opt); opt = OptionBuilder.withLongOpt("mapper").withArgName("x").hasArg() .withDescription("Set the number of mapper").create("m"); options.addOption(opt); opt = OptionBuilder.withLongOpt("reducer").withArgName("x").hasArg() .withDescription("Set the number of reducer").create("n"); options.addOption(opt); CommandLine c_line = parseCommandLine(options, args); String redirectionFile = ""; //Contains a redirection file for the output if (c_line.hasOption("redirection")) { try { redirectionFile = c_line.getOptionValue("redirection"); PrintStream ps; ps = new PrintStream(redirectionFile); System.setOut(ps); } catch (FileNotFoundException e) { System.out.println("Redirection error !!!"); e.printStackTrace(); } } if (!c_line.hasOption("p") || !c_line.hasOption("i") | c_line.hasOption("h")) { help_formatter.printHelp(app_name, options); System.exit(1); } assert c_line.hasOption("p"); assert c_line.hasOption("i"); String trace_filename = c_line.getOptionValue("i"); String trace_format = getExtension(trace_filename); String property_str = c_line.getOptionValue("p"); String ParserType = ""; int MapperNum = 0; int ReducerNum = 0; //Contains a parser type if (c_line.hasOption("t")) { ParserType = c_line.getOptionValue("t"); } else { System.err.println("No Parser Type in Arguments"); System.exit(ERR_ARGUMENTS); } //Contains a mapper number if (c_line.hasOption("m")) { MapperNum = Integer.parseInt(c_line.getOptionValue("m")); } else { System.err.println("No Mapper Number in Arguments"); System.exit(ERR_ARGUMENTS); } //Contains a reducer number if (c_line.hasOption("n")) { ReducerNum = Integer.parseInt(c_line.getOptionValue("n")); } else { System.err.println("No Reducer Number in Arguments"); System.exit(ERR_ARGUMENTS); } if (c_line.hasOption("v")) m_verbosity = Integer.parseInt(c_line.getOptionValue("v")); // Obtain the property to verify and break into subformulas Operator property = null; try { int preset = Integer.parseInt(property_str); property = new Edoc2012Presets().property(preset); } catch (NumberFormatException e) { try { property = Operator.parseFromString(property_str); } catch (Operator.ParseException pe) { System.err.println("ERROR: parsing"); System.exit(1); } } Set<Operator> subformulas = property.getSubformulas(); // Initialize first collector depending on input file format int max_loops = property.getDepth(); int max_tuples_total = 0, total_tuples_total = 0; long time_begin = System.nanoTime(); TraceCollector initial_collector = null; { File in_file = new File(trace_filename); if (trace_format.compareToIgnoreCase(".txt") == 0) { initial_collector = new CharacterTraceCollector(in_file, subformulas); } else if (trace_format.compareToIgnoreCase(".xml") == 0) { if (ParserType.equals("Dom")) { initial_collector = new XmlDomTraceCollector(in_file, subformulas); } else if (ParserType.equals("Sax")) { initial_collector = new XmlSaxTraceCollector(in_file, subformulas); } else { initial_collector = new XmlSaxTraceCollector(in_file, subformulas); } } } if (initial_collector == null) { System.err.println("ERROR: unrecognized input format"); System.exit(1); } // Start workflow int trace_len = initial_collector.getTraceLength(); InCollector<Operator, LTLTupleValue> loop_collector = initial_collector; print(System.out, property.toString(), 2); print(System.out, loop_collector.toString(), 3); for (int i = 0; i < max_loops; i++) { print(System.out, "Loop " + i, 2); LTLParallelWorkflow w = new LTLParallelWorkflow(new LTLMapper(subformulas), new LTLReducer(subformulas, trace_len), loop_collector, new ResourceManager<Operator, LTLTupleValue>(MapperNum), new ResourceManager<Operator, LTLTupleValue>(ReducerNum)); loop_collector = w.run(); max_tuples_total += w.getMaxTuples(); total_tuples_total += w.getTotalTuples(); if (m_verbosity >= 3) { print(System.out, loop_collector.toString(), 3); } } boolean result = getVerdict(loop_collector, property); long time_end = System.nanoTime(); if (result) print(System.out, "Formula is true", 1); else print(System.out, "Formula is false", 1); long time_total = (time_end - time_begin) / 1000000; System.out.println(trace_len + "," + max_tuples_total + "," + total_tuples_total + "," + time_total); }
From source file:co.cask.cdap.data2.util.hbase.HBaseVersion.java
/** * Prints out the HBase {@link Version} enum value for the current version of HBase on the classpath. *///from ww w. jav a 2s. c o m public static void main(String[] args) { // Suppress any output to stdout PrintStream stdout = System.out; System.setOut(new PrintStream(new NullOutputStream())); Version version = HBaseVersion.get(); // Restore stdout System.setOut(stdout); System.out.println(version.getMajorVersion()); if (args.length == 1 && "-v".equals(args[0])) { // Print versionString if verbose System.out.println("versionString=" + getVersionString()); } }
From source file:at.tuwien.ifs.somtoolbox.doc.RunnablesReferenceCreator.java
public static void main(String[] args) { ArrayList<Class<? extends SOMToolboxApp>> runnables = SubClassFinder.findSubclassesOf(SOMToolboxApp.class, true);/* w ww . j a va2 s .c o m*/ Collections.sort(runnables, SOMToolboxApp.TYPE_GROUPED_COMPARATOR); StringBuilder sbIndex = new StringBuilder(runnables.size() * 50); StringBuilder sbDetails = new StringBuilder(runnables.size() * 200); sbIndex.append("\n<table border=\"0\">\n"); Type lastType = null; for (Class<? extends SOMToolboxApp> c : runnables) { try { // Ignore abstract classes and interfaces if (Modifier.isAbstract(c.getModifiers()) || Modifier.isInterface(c.getModifiers())) { continue; } Type type = Type.getType(c); if (type != lastType) { sbIndex.append(" <tr> <td colspan=\"2\"> <h5> " + type + " Applications </h5> </td> </tr>\n"); sbDetails.append("<h2> " + type + " Applications </h2>\n"); lastType = type; } String descr = "N/A"; try { descr = (String) c.getDeclaredField("DESCRIPTION").get(null); } catch (Exception e) { } String longDescr = "descr"; try { longDescr = (String) c.getDeclaredField("LONG_DESCRIPTION").get(null); } catch (Exception e) { } sbIndex.append(" <tr>\n"); sbIndex.append(" <td> <a href=\"#").append(c.getSimpleName()).append("\">") .append(c.getSimpleName()).append("</a> </td>\n"); sbIndex.append(" <td> ").append(descr).append(" </td>\n"); sbIndex.append(" </tr>\n"); sbDetails.append("<h3 id=\"").append(c.getSimpleName()).append("\">").append(c.getSimpleName()) .append("</h3>\n"); sbDetails.append("<p>").append(longDescr).append("</p>\n"); try { Parameter[] options = (Parameter[]) c.getField("OPTIONS").get(null); JSAP jsap = AbstractOptionFactory.registerOptions(options); final ByteArrayOutputStream os = new ByteArrayOutputStream(); PrintStream ps = new PrintStream(os); AbstractOptionFactory.printHelp(jsap, c.getName(), ps); sbDetails.append("<pre>").append(StringEscapeUtils.escapeHtml(os.toString())).append("</pre>"); } catch (Exception e1) { // we didn't find the options => let the class be invoked ... } } catch (SecurityException e) { // Should not happen - no Security } catch (IllegalArgumentException e) { e.printStackTrace(); } } sbIndex.append("</table>\n\n"); System.out.println(sbIndex); System.out.println(sbDetails); }
From source file:edu.msu.cme.rdp.taxatree.TreeBuilder.java
public static void main(String[] args) throws IOException { if (args.length != 3) { System.err.println("USAGE: TreeBuilder <idmapping> <merges.bin> <newick_out>"); return;/*from w w w . j a v a2 s.co m*/ } IdMapping<Integer> idMapping = IdMapping.fromFile(new File(args[0])); DataInputStream mergeStream = new DataInputStream(new BufferedInputStream(new FileInputStream(args[1]))); TaxonHolder lastMerged = null; int taxid = 0; final Map<Integer, Double> distMap = new HashMap(); Map<Integer, TaxonHolder> taxonMap = new HashMap(); try { while (true) { if (mergeStream.readBoolean()) { // Singleton int cid = mergeStream.readInt(); int intId = mergeStream.readInt(); TaxonHolder<Taxon> holder; List<String> seqids = idMapping.getIds(intId); if (seqids.size() == 1) { holder = new TaxonHolder(new Taxon(taxid++, seqids.get(0), "")); } else { holder = new TaxonHolder(new Taxon(taxid++, "", "")); for (String seqid : seqids) { int id = taxid++; distMap.put(id, 0.0); TaxonHolder th = new TaxonHolder(new Taxon(id, seqid, "")); th.setParent(holder); holder.addChild(th); } } lastMerged = holder; taxonMap.put(cid, holder); } else { int ci = mergeStream.readInt(); int cj = mergeStream.readInt(); int ck = mergeStream.readInt(); double dist = (double) mergeStream.readInt() / DistanceCalculator.MULTIPLIER; TaxonHolder holder = new TaxonHolder(new Taxon(taxid++, "", "")); taxonMap.put(ck, holder); holder.addChild(taxonMap.get(ci)); taxonMap.get(ci).setParent(holder); distMap.put(ci, dist); holder.addChild(taxonMap.get(cj)); taxonMap.get(cj).setParent(holder); distMap.put(cj, dist); lastMerged = holder; } } } catch (EOFException e) { } if (lastMerged == null) { throw new IOException("No merges in file"); } PrintStream newickTreeOut = new PrintStream(new File(args[2])); NewickPrintVisitor visitor = new NewickPrintVisitor(newickTreeOut, false, new NewickDistanceFactory() { public float getDistance(int i) { return distMap.get(i).floatValue(); } }); lastMerged.biDirectionDepthFirst(visitor); newickTreeOut.close(); }
From source file:edu.msu.cme.rdp.seqmatch.cli.SeqMatchMain.java
public static void main(String[] args) throws Exception { if (args.length == 0) { System.err.println("USAGE: SeqMatchMain [train|seqmatch] <args>"); return;/*from ww w. j av a2 s . c o m*/ } String cmd = args[0]; args = Arrays.copyOfRange(args, 1, args.length); if (cmd.equals("train")) { if (args.length != 2) { System.err.println("USAGE: train <reference sequences> <trainee_out_file_prefix>" + "\nMultiple trainee output files might be created, each containing maximum " + Trainee.MAX_NUM_SEQ + " sequences"); return; } File refSeqs = new File(args[0]); File traineeFileOut = new File(args[1]); //maybe more than 1 trainee files need to be created, depending on the number of seqs CreateMultiMatchFromFile.getMultiTrainee(refSeqs, traineeFileOut); } else if (cmd.equals("seqmatch")) { File refFile = null; File queryFile = null; HashMap<String, String> descMap = new HashMap<String, String>(); PrintStream out = new PrintStream(System.out); int knn = 20; float minSab = .5f; try { CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("knn")) { knn = Integer.parseInt(line.getOptionValue("knn")); } if (line.hasOption("sab")) { minSab = Float.parseFloat(line.getOptionValue("sab")); } if (line.hasOption("desc")) { descMap = readDesc(new File(line.getOptionValue("desc"))); } if (line.hasOption("outFile")) { out = new PrintStream(new File(line.getOptionValue("outFile"))); } args = line.getArgs(); if (args.length != 2) { throw new Exception("Unexpected number of command line arguments"); } refFile = new File(args[0]); queryFile = new File(args[1]); } catch (Exception e) { new HelpFormatter().printHelp("seqmatch <refseqs | trainee_file_or_dir> <query_file>\n" + " trainee_file_or_dir is a single trainee file or a directory containing multiple trainee files", options); System.err.println("Error: " + e.getMessage()); return; } SeqMatch seqmatch = null; if (refFile.isDirectory()) { // a directory of trainee files List<SeqMatch> engineList = new ArrayList<SeqMatch>(); for (File f : refFile.listFiles()) { if (!f.isHidden()) { TwowaySeqMatch match = new TwowaySeqMatch(new SeqMatchEngine(new StorageTrainee(f))); engineList.add(match); } } seqmatch = new MultiTraineeSeqMatch(engineList); } else { // a single fasta file or trainee file if (SeqUtils.guessFileFormat(refFile) == SequenceFormat.UNKNOWN) { seqmatch = CLISeqMatchFactory.trainTwowaySeqMatch(new StorageTrainee(refFile)); } else { seqmatch = CreateMultiMatchFromFile.getMultiMatch(refFile); } } out.println("query name\tmatch seq\torientation\tS_ab score\tunique oligomers\tdescription"); SeqReader reader = new SequenceReader(queryFile); Sequence seq; while ((seq = reader.readNextSequence()) != null) { SeqMatchResultSet resultSet = seqmatch.match(seq, knn); for (SeqMatchResult result : resultSet) { char r = '+'; if (result.isReverse()) { r = '-'; } if (result.getScore() > minSab) { out.println(seq.getSeqName() + "\t" + result.getSeqName() + "\t" + r + "\t" + result.getScore() + "\t" + resultSet.getQueryWordCount() + "\t" + descMap.get(result.getSeqName())); } } } out.close(); } else { throw new IllegalArgumentException("USAGE: SeqMatchMain [train|seqmatch] <args>"); } }