List of usage examples for org.apache.commons.exec PumpStreamHandler PumpStreamHandler
public PumpStreamHandler(final OutputStream outAndErr)
PumpStreamHandler. From source file:com.cws.esolutions.agent.processors.impl.ApplicationManagerProcessorImpl.java
/** * @see com.cws.esolutions.agent.processors.interfaces.IApplicationManagerProcessor#installApplication(com.cws.esolutions.agent.processors.dto.ApplicationManagerRequest) */// w ww. j a v a 2 s . c om public ApplicationManagerResponse installApplication(final ApplicationManagerRequest request) throws ApplicationManagerException { final String methodName = IApplicationManagerProcessor.CNAME + "#installApplication(final ApplicationManagerRequest request) throws ApplicationManagerException"; if (DEBUG) { DEBUGGER.debug(methodName); DEBUGGER.debug("ApplicationManagerRequest: {}", request); } BufferedWriter writer = null; ApplicationManagerResponse response = new ApplicationManagerResponse(); final double version = request.getVersion(); final DefaultExecutor executor = new DefaultExecutor(); final String installerOptions = request.getInstallerOptions(); final File installPath = FileUtils.getFile(request.getInstallPath()); final ExecuteWatchdog watchdog = new ExecuteWatchdog(CONNECT_TIMEOUT * 1000); final DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler(); final File packageInstaller = FileUtils.getFile(request.getPackageInstaller()); if (DEBUG) { DEBUGGER.debug("double: {}", version); DEBUGGER.debug("DefaultExecutor: {}", executor); DEBUGGER.debug("String: {}", installerOptions); DEBUGGER.debug("File: {}", installPath); DEBUGGER.debug("ExecuteWatchdog: {}", watchdog); DEBUGGER.debug("DefaultExecuteResultHandler: {}", resultHandler); DEBUGGER.debug("File:{}", packageInstaller); } try { if (!(packageInstaller.canExecute())) { throw new ApplicationManagerException("Unable to execute package installer. Cannot continue."); } if (!(installPath.canWrite()) && (!(installPath.mkdirs()))) { throw new ApplicationManagerException("Unable to create installation target. Cannot continue."); } CommandLine command = CommandLine.parse(packageInstaller.getAbsolutePath()); command.addArgument(installerOptions, false); command.addArgument(request.getPackageLocation(), false); if (DEBUG) { DEBUGGER.debug("CommandLine: {}", command); } ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); ExecuteStreamHandler streamHandler = new PumpStreamHandler(outputStream); streamHandler.start(); executor.setWatchdog(watchdog); executor.setStreamHandler(streamHandler); if (DEBUG) { DEBUGGER.debug("ExecuteStreamHandler: {}", streamHandler); DEBUGGER.debug("ExecuteWatchdog: {}", watchdog); DEBUGGER.debug("DefaultExecuteResultHandler: {}", resultHandler); DEBUGGER.debug("DefaultExecutor: {}", executor); } executor.execute(command, resultHandler); resultHandler.waitFor(); int exitCode = resultHandler.getExitValue(); writer = new BufferedWriter(new FileWriter(LOGS_DIRECTORY + "/" + request.getPackageName() + ".log")); writer.write(outputStream.toString()); writer.flush(); if (DEBUG) { DEBUGGER.debug("exitCode: {}", exitCode); } if (executor.isFailure(exitCode)) { throw new ApplicationManagerException("Application installation failed: Result Code: " + exitCode); } response.setResponse(outputStream.toString()); response.setRequestStatus(AgentStatus.SUCCESS); } catch (ExecuteException eex) { ERROR_RECORDER.error(eex.getMessage(), eex); throw new ApplicationManagerException(eex.getMessage(), eex); } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); throw new ApplicationManagerException(iox.getMessage(), iox); } catch (InterruptedException ix) { ERROR_RECORDER.error(ix.getMessage(), ix); throw new ApplicationManagerException(ix.getMessage(), ix); } finally { try { writer.close(); } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); } } return response; }
From source file:eu.creatingfuture.propeller.blocklyprop.propeller.OpenSpin.java
protected boolean compileForRam(String executable, File sourceFile, File destinationFile) { try {//w w w . ja v a2 s. c om File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-lib"); Map map = new HashMap(); map.put("sourceFile", sourceFile); map.put("destinationFile", destinationFile); map.put("libDirectory", libDirectory); CommandLine cmdLine = new CommandLine(executable); cmdLine.addArgument("-b"); cmdLine.addArgument("-o").addArgument("${destinationFile}"); cmdLine.addArgument("-L").addArgument("${libDirectory}"); cmdLine.addArgument("${sourceFile}"); cmdLine.setSubstitutionMap(map); DefaultExecutor executor = new DefaultExecutor(); // executor.setExitValues(new int[]{402, 101}); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(outputStream); executor.setStreamHandler(streamHandler); try { exitValue = executor.execute(cmdLine); } catch (ExecuteException ee) { exitValue = ee.getExitValue(); logger.log(Level.SEVERE, "Unexpected exit value: {0}", exitValue); success = false; return false; } finally { output = outputStream.toString(); } // System.out.println("output: " + output); /* Scanner scanner = new Scanner(output); Pattern chipFoundPattern = Pattern.compile(".*?(EVT:505).*?"); Pattern pattern = Pattern.compile(".*?found on (?<comport>[a-zA-Z0-9]*).$"); while (scanner.hasNextLine()) { String portLine = scanner.nextLine(); if (chipFoundPattern.matcher(portLine).matches()) { Matcher portMatch = pattern.matcher(portLine); if (portMatch.find()) { // String port = portMatch.group("comport"); } } } */ // System.out.println("output: " + output); // System.out.println("exitValue: " + exitValue); success = true; return true; } catch (IOException ioe) { logger.log(Level.SEVERE, null, ioe); success = false; return false; } }
From source file:modules.GeneralNativeCommandModule.java
protected KeyValueResult extractNative(String command, String options, Path path) throws NativeExecutionException { if (command == null || command.equals("")) { System.err.println("command null at GeneralNativeCommandModule.extractNative()"); return null; }/*from ww w .j a va 2 s .c o m*/ CommandLine commandLine = new CommandLine(command); if (options != null && !options.equals("")) { String[] args = options.split(" "); commandLine.addArguments(args); } if (path != null) { commandLine.addArgument(path.toAbsolutePath().toString(), false); } DefaultExecutor executor = new DefaultExecutor(); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(outputStream); executor.setStreamHandler(streamHandler); GeneralExecutableModuleConfig generalExecutableModuleConfig = getConfig(); executor.setWatchdog(new ExecuteWatchdog(generalExecutableModuleConfig.timeout)); if (getConfig().workingDirectory != null && getConfig().workingDirectory.exists()) { executor.setWorkingDirectory(getConfig().workingDirectory); } try { // System.out.println(commandLine); executor.execute(commandLine); } catch (ExecuteException xs) { NativeExecutionException n = new NativeExecutionException(); n.initCause(xs); if (path != null) { n.path = path.toAbsolutePath().toString(); } n.executionResult = outputStream.toString(); n.exitCode = xs.getExitValue(); throw n; } catch (IOException xs) { // System.out.println(commandLine); NativeExecutionException n = new NativeExecutionException(); n.initCause(xs); if (path != null) { n.path = path.toAbsolutePath().toString(); } n.executionResult = outputStream.toString(); throw n; } KeyValueResult t = new KeyValueResult("GeneralNativeCommandResults"); t.add("fullOutput", outputStream.toString().trim()); return t; }
From source file:com.thinkbiganalytics.spark.shell.MultiUserProcessManager.java
/** * Calls kinit to request a new Kerberos ticket if the previous one is about to expire. */// w ww . j av a2 s.c om private void refreshKerberosTicket() { // Determine if a new ticket is needed if (kerberos == null || kerberos.getInitInterval() <= 0 || kerberosNextInit > DateTimeUtils.currentTimeMillis()) { return; } // Build executor final Executor executor = new DefaultExecutor(); final ShutdownHookProcessDestroyer processDestroyer = new ShutdownHookProcessDestroyer(); executor.setProcessDestroyer(processDestroyer); final Logger outputLogger = LoggerFactory.getLogger(getClass().getName() + ".kinit"); final LoggerOutputStream outputStream = new LoggerOutputStream(outputLogger); final PumpStreamHandler streamHandler = new PumpStreamHandler(outputStream); executor.setStreamHandler(streamHandler); final ExecuteWatchdog watchdog = new ExecuteWatchdog(TimeUnit.SECONDS.toMillis(kerberos.getInitTimeout())); executor.setWatchdog(watchdog); // Run kinit to acquire a new ticket final CommandLine command = new CommandLine("kinit").addArgument("-kt") .addArgument(kerberos.getKeytabLocation()).addArgument(kerberos.getKerberosPrincipal()); log.debug("Acquiring a new Kerberos ticket with command: {}", command); int exitCode; try { exitCode = executor.execute(command); } catch (final IOException e) { log.error("Failed to execute kinit", e); exitCode = -1; } // Record next time to acquire ticket if (!executor.isFailure(exitCode)) { kerberosNextInit = DateTimeUtils.currentTimeMillis() + TimeUnit.SECONDS.toMillis(kerberos.getInitInterval()); } else { if (watchdog.killedProcess()) { log.error("Failed to acquire a Kerberos ticket within the allotted time: {}", kerberos.getInitTimeout()); } else { log.error("Kinit exited with non-zero status: {}", exitCode); } kerberosNextInit = DateTimeUtils.currentTimeMillis() + TimeUnit.SECONDS.toMillis(kerberos.getRetryInterval()); throw new IllegalStateException("Failed to acquire a Kerberos ticket"); } }
From source file:com.boundlessgeo.wps.grass.GrassProcesses.java
@DescribeProcess(title = "GRASS Version", description = "Retreive the version of GRASS used for computation") @DescribeResult(description = "Version") public static String version() { if (EXEC == null) { return "unavailable"; }/*ww w.jav a 2s . co m*/ CommandLine cmd = new CommandLine(EXEC); cmd.addArgument("-v"); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); ExecuteWatchdog watchdog = new ExecuteWatchdog(60000); executor.setWatchdog(watchdog); try { ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); executor.setStreamHandler(new PumpStreamHandler(outputStream)); LOGGER.info("exec: " + cmd.toString()); int exitValue = executor.execute(cmd); return outputStream.toString(); } catch (ExecuteException huh) { return "exit code: " + huh.getExitValue() + " (" + huh.getMessage() + ")"; } catch (IOException e) { return "unavailable: " + e.getClass().getSimpleName() + ":" + e.getMessage(); } }
From source file:net.robyf.dbpatcher.util.MySqlUtil.java
private static InputStream executeAndGetOutput(final CommandLine commandLine) { try {/*from w ww . j a va 2 s. co m*/ ByteArrayOutputStream outStream = new ByteArrayOutputStream(); PumpStreamHandler handler = new PumpStreamHandler(outStream); DefaultExecutor executor = new DefaultExecutor(); executor.setWatchdog(new ExecuteWatchdog(300000L)); executor.setStreamHandler(handler); int returnCode = executor.execute(commandLine); if (returnCode != 0) { throw new UtilException("Error executing: " + commandLine //NOSONAR + ", return code = " + returnCode); //NOSONAR } return new ByteArrayInputStream(outStream.toByteArray()); } catch (IOException ioe) { throw new UtilException("Error executing: " + commandLine, ioe); //NOSONAR } }
From source file:io.takari.maven.testing.executor.ForkedLauncher.java
public int run(String[] cliArgs, Map<String, String> envVars, File multiModuleProjectDirectory, File workingDirectory, File logFile) throws IOException, LauncherException { String javaHome;/*from w w w . j a v a 2 s .c om*/ if (envVars == null || envVars.get("JAVA_HOME") == null) { javaHome = System.getProperty("java.home"); } else { javaHome = envVars.get("JAVA_HOME"); } File executable = new File(javaHome, Os.isFamily(Os.FAMILY_WINDOWS) ? "bin/javaw.exe" : "bin/java"); CommandLine cli = new CommandLine(executable); cli.addArgument("-classpath").addArgument(classworldsJar.getAbsolutePath()); cli.addArgument("-Dclassworlds.conf=" + new File(mavenHome, "bin/m2.conf").getAbsolutePath()); cli.addArgument("-Dmaven.home=" + mavenHome.getAbsolutePath()); cli.addArgument("-Dmaven.multiModuleProjectDirectory=" + multiModuleProjectDirectory.getAbsolutePath()); cli.addArgument("org.codehaus.plexus.classworlds.launcher.Launcher"); cli.addArguments(args.toArray(new String[args.size()])); if (extensions != null && !extensions.isEmpty()) { cli.addArgument("-Dmaven.ext.class.path=" + toPath(extensions)); } cli.addArguments(cliArgs); Map<String, String> env = new HashMap<>(); if (mavenHome != null) { env.put("M2_HOME", mavenHome.getAbsolutePath()); } if (envVars != null) { env.putAll(envVars); } if (envVars == null || envVars.get("JAVA_HOME") == null) { env.put("JAVA_HOME", System.getProperty("java.home")); } DefaultExecutor executor = new DefaultExecutor(); executor.setProcessDestroyer(new ShutdownHookProcessDestroyer()); executor.setWorkingDirectory(workingDirectory.getAbsoluteFile()); try (OutputStream log = new FileOutputStream(logFile)) { PrintStream out = new PrintStream(log); out.format("Maven Executor implementation: %s\n", getClass().getName()); out.format("Maven home: %s\n", mavenHome); out.format("Build work directory: %s\n", workingDirectory); out.format("Environment: %s\n", env); out.format("Command line: %s\n\n", cli.toString()); out.flush(); PumpStreamHandler streamHandler = new PumpStreamHandler(log); executor.setStreamHandler(streamHandler); return executor.execute(cli, env); // this throws ExecuteException if process return code != 0 } catch (ExecuteException e) { throw new LauncherException("Failed to run Maven: " + e.getMessage() + "\n" + cli, e); } }
From source file:eu.crisis_economics.abm.dashboard.cluster.script.BashScheduler.java
/** {@inheritDoc} * @throws SchedulerException // w ww .j a v a 2s . c om */ @Override public String runParameterSweep(final Model paramSweepConfig, final String timeLimit, final File workDir) throws SchedulerException { File file = null; try { // file = File.createTempFile("paramsweep-", ".xml"); file = new File(workDir, "paramsweep-config.xml"); Marshaller marshaller = JAXBContext.newInstance(Model.class).createMarshaller(); marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); marshaller.marshal(paramSweepConfig, file); // } catch (IOException e) { // throw new SchedulerException("Could not create temporary parameter-sweep configuration xml.", e); } catch (JAXBException e) { throw new SchedulerException( "Could not write temporary parameter-sweep configuration xml: " + file.toString(), e); } CommandLine cmd = new CommandLine(cmdFile); Map<String, Object> substitutions = new HashMap<String, Object>(); substitutions.put(CMD_SUBSTITUTION_NAME_FILE, file); cmd.setSubstitutionMap(substitutions); if (timeLimit != null && !timeLimit.isEmpty()) { cmd.addArgument("-t", false); cmd.addArgument(timeLimit, false); } // add server port argument cmd.addArgument("-p", false); cmd.addArgument(String.valueOf(serverPort), false); cmd.addArgument("${" + CMD_SUBSTITUTION_NAME_FILE + "}", false); DefaultExecutor executor = new DefaultExecutor(); executor.setWorkingDirectory(workDir); ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(byteArrayOutputStream); executor.setStreamHandler(streamHandler); try { executor.execute(cmd); } catch (ExecuteException e) { throw new SchedulerException( paramSweepCmd + " exited with " + e.getExitValue() + ". Output:\n" + byteArrayOutputStream, e); } catch (IOException e) { throw new SchedulerException( "Execution of " + paramSweepCmd + " failed. Output:\n" + byteArrayOutputStream, e); } // the standard output of the script is the job id final String jobId = byteArrayOutputStream.toString(); return jobId; }
From source file:edu.cornell.med.icb.goby.modes.RunParallelMode.java
public void execute() throws IOException { final Slice slices[] = new Slice[numParts]; File file = new File(input); if (!(file.isFile() && file.exists() && file.canRead())) { System.err.println("Input file cannot be read: " + input); System.exit(1);//from www . j av a 2 s .c o m } int i = 0; for (final Slice slice : slices) { slices[i++] = new Slice(); } final long fileLength = file.length(); final long sliceLength = fileLength / numParts; long currentOffset = 0; for (final Slice slice : slices) { slice.startOffset = currentOffset; slice.endOffset = currentOffset + sliceLength; currentOffset = slice.endOffset; } final ObjectOpenHashSet<String> allOutputs = new ObjectOpenHashSet<String>(); final ObjectOpenHashSet<String> allFastq = new ObjectOpenHashSet<String>(); final DoInParallel loop = new DoInParallel(numParts) { IsDone done = new IsDone(); @Override public void action(final DoInParallel forDataAccess, final String inputBasename, final int loopIndex) { try { CompactToFastaMode ctfm = new CompactToFastaMode(); ctfm.setInputFilename(input); ctfm.setOutputFormat(CompactToFastaMode.OutputFormat.FASTQ); ctfm.setStartPosition(slices[loopIndex].startOffset); ctfm.setEndPosition(slices[loopIndex].endOffset); String s = FilenameUtils.getBaseName(FilenameUtils.removeExtension(input)) + "-" + Integer.toString(loopIndex); String fastqFilename = s + "-input.fq"; allFastq.add(fastqFilename); File tmp1 = new File(s + "-tmp"); tmp1.deleteOnExit(); File output = new File(s + "-out"); output.deleteOnExit(); ctfm.setOutputFilename(fastqFilename); LOG.info(String.format("Extracting FASTQ for slice [%d-%d] loopIndex=%d %n", slices[loopIndex].startOffset, slices[loopIndex].endOffset, loopIndex)); ctfm.execute(); if (loopIndex > 0) { while (!done.isDone()) { // wait a bit to give the first thread the time to load the database and establish shared memory pool // System.out.println("sleep 5 thread "+loopIndex); sleep(5); } System.out.println("Thread " + loopIndex + " can now start."); } final Map<String, String> replacements = new HashMap<String, String>(); final String outputFilename = output.getName(); replacements.put("%read.fastq%", fastqFilename); replacements.put("%tmp1%", tmp1.getName()); replacements.put("%output%", outputFilename); final String transformedCommand = transform(processPartCommand, replacements); final DefaultExecutor executor = new DefaultExecutor(); OutputStream logStream = null; try { logStream = new LoggingOutputStream(getClass(), Level.INFO, ""); executor.setStreamHandler( new PumpStreamHandler(new StreamSignal(done, "scanning", logStream))); final CommandLine parse = CommandLine.parse(transformedCommand, replacements); LOG.info("About to execute: " + parse); final int exitValue = executor.execute(parse); LOG.info("Exit value = " + exitValue); if (new File(outputFilename + ".header").exists()) { // found output alignment: System.out.println("found output file: " + outputFilename); allOutputs.add(outputFilename + ".header"); } else { System.out.println("Warning: did not find output alignment: " + outputFilename); } } finally { IOUtils.closeQuietly(logStream); // remove the fastq file new File(fastqFilename).delete(); } } catch (IOException e) { LOG.error("Error processing index " + loopIndex + ", " + inputBasename, e); } } }; String[] parts = new String[numParts]; for (int j = 0; j < numParts; j++) { parts[j] = Integer.toString(j); } try { loop.execute(true, parts); } catch (Exception e) { System.err.println("An error occurred executing a parallel command: "); e.printStackTrace(); } System.out.printf("Preparing to concatenate %d outputs..%n", allOutputs.size()); final ConcatenateAlignmentMode concat = new ConcatenateAlignmentMode(); concat.setInputFileNames(allOutputs.toArray(new String[allOutputs.size()])); concat.setOutputFilename(output); concat.setAdjustQueryIndices(false); concat.setAdjustSampleIndices(false); concat.execute(); }
From source file:com.github.zeroxff.executor.ExtendedExecutor.java
public ExecuteResult execute() throws ExtendedExecuteException { this.clearOut(); if (this.commandLine == null) { throw new ExtendedExecuteException("CommandLine cannot be null", Executor.INVALID_EXITVALUE); }//from w w w .j ava 2 s .c o m if (this.commandLine.length == 0) { throw new ExtendedExecuteException("CommandLine cannot be empty", Executor.INVALID_EXITVALUE); } if (this.maxExecutiontime != ExecuteWatchdog.INFINITE_TIMEOUT && this.maxExecutiontime < 1) { throw new ExtendedExecuteException("Max execution time must not be less than 1", Executor.INVALID_EXITVALUE); } try { // load the command line as an array of strings CommandLine cmdLine = new CommandLine(this.commandLine[0]); for (int counter = 1; counter < commandLine.length; counter++) { cmdLine.addArgument(this.commandLine[counter], quoteCommandlineArgs); } // load the substitution map, if defined if (this.substitutionMap != null) { cmdLine.setSubstitutionMap(this.substitutionMap); } // load the watchdog timer, it can be set to infinite time ExecuteWatchdog watchdog = new ExecuteWatchdog(this.maxExecutiontime); ExtendedResultHandler resultHandler = new ExtendedResultHandler(watchdog); // inizialize outputstream processors. OutStreamProcessor outLinee = null; OutStreamProcessor errLinee = null; PumpStreamHandler streamHandler = null; if (outputFilter != null && outputFilter.size() > 0) { outLinee = new OutStreamProcessor(outputFilter); } else { outLinee = new OutStreamProcessor(); } if (this.enableAllLinesOut) { outLinee.enableAllLines(); } if (mergeOutStreams) { // Using Std out for the output/error stream streamHandler = new PumpStreamHandler(outLinee); } else { if (errorFilter != null && errorFilter.size() > 0) { errLinee = new OutStreamProcessor(errorFilter); } else { errLinee = new OutStreamProcessor(); } if (enableAllLinesErr) { errLinee.enableAllLines(); } // Using Std out for the output/error stream streamHandler = new PumpStreamHandler(outLinee, errLinee); } DefaultExecutor executor = new DefaultExecutor(); // set the working directory... // if the working directory doesn't exists, it can crash the // executor. if (workingDirecory != null) { executor.setWorkingDirectory(workingDirecory); } // set the accepted exit values for the command line // default is '0'. if (okExitValues != null && okExitValues.length > 0) { executor.setExitValues(okExitValues); } executor.setWatchdog(watchdog); executor.setStreamHandler(streamHandler); try { executor.execute(cmdLine, resultHandler); resultHandler.waitFor(); returnCode = resultHandler.getExitValue(); exitMode = resultHandler.getExitMode(); switch (exitMode) { case ERROR_IN_EXECUTION: this.message = resultHandler.getException().getMessage(); break; default: break; } } catch (ExecuteException e) { exitMode = ExecuteResult.EXCEPTION; exception = e; this.message = e.getMessage(); } catch (IOException e) { exitMode = ExecuteResult.EXCEPTION; exception = e; this.message = e.getMessage(); } catch (InterruptedException e) { exitMode = ExecuteResult.EXCEPTION; exception = e; this.message = e.getMessage(); } // if (outLinee != null) { outputLines = outLinee.getLines(); allOutputLines = outLinee.getAllLines(); } if (errLinee != null) { errorLines = errLinee.getLines(); allErrorLines = errLinee.getAllLines(); } this.closeStreams(outLinee, errLinee); } catch (Exception e) { throw new ExtendedExecuteException(e.getMessage(), Executor.INVALID_EXITVALUE, e); } return exitMode; }