List of usage examples for org.apache.commons.exec DefaultExecutor setExitValue
public void setExitValue(final int value)
From source file:io.manasobi.utils.CmdUtils.java
/** * (commandLine) ? ?? ? ? ?/*from ww w. jav a 2 s. co m*/ * * @param commandLine * @param argument ? * @param timeout * * @return int ? */ public static int execute(CommandLine commandLine, String argument, long timeout) { ByteArrayOutputStream baos = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(baos); DefaultExecutor executor = new DefaultExecutor(); executor.setStreamHandler(streamHandler); // ? if (StringUtils.isNotEmpty(argument)) { commandLine.addArguments(argument); } // if (timeout > 0) { ExecuteWatchdog watchdog = new ExecuteWatchdog(timeout); executor.setWatchdog(watchdog); } // ?? ? executor.setExitValue(SUCCESS_RETURN_CODE); try { DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler(); executor.execute(commandLine, resultHandler); resultHandler.waitFor(); return resultHandler.getExitValue(); } catch (Exception e) { throw new CmdUtilsException(e.getMessage()); } }
From source file:com.tupilabs.pbs.PBS.java
/** * Executes a PBS command./* w w w . j a va2 s.co m*/ * * @param cmdLine command * @param environment env vars * @param out output stream * @param err err stream * @return execute handler * @throws ExecuteException if there is an error executing a command * @throws IOException in case of an IO problem */ static DefaultExecuteResultHandler execute(CommandLine cmdLine, Map<String, String> environment, OutputStream out, OutputStream err) throws ExecuteException, IOException { DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler(); ExecuteStreamHandler streamHandler = new PumpStreamHandler(out, err); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); executor.setStreamHandler(streamHandler); if (environment != null) { executor.execute(cmdLine, environment, resultHandler); } else { executor.execute(cmdLine, resultHandler); } return resultHandler; }
From source file:io.github.binout.wordpress2html.writer.Html2AsciidocConverter.java
private void execute(CommandLine cmdLine) throws IOException { DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); ExecuteWatchdog watchdog = new ExecuteWatchdog(60000); executor.setWatchdog(watchdog);/* w w w .j a v a2s. co m*/ int exitValue = executor.execute(cmdLine); if (exitValue != 0) { throw new RuntimeException("Pandoc is not installed !"); } }
From source file:edu.buffalo.fusim.ReadSimulator.java
public void run(String artBinPath, File fusionFile, String outputPrefix, int readLength, int meanFragSize, int readCoverage, boolean pairedEnd) { // Example art call: // art_illumina -i fusion.txt -o testsim -l 75 -f 10 -p -m 400 -s 10 CommandLine cmdLine = new CommandLine(artBinPath); // the filename of input DNA reference cmdLine.addArgument("-i"); cmdLine.addArgument("${file}"); // the prefix of output files cmdLine.addArgument("-o"); cmdLine.addArgument("${outputPrefix}"); // the length of reads to be simulated cmdLine.addArgument("-l"); cmdLine.addArgument("" + readLength); // the fold of read coverage to be simulated cmdLine.addArgument("-f"); cmdLine.addArgument("" + readCoverage); if (pairedEnd) { // indicate a paired-end read simulation cmdLine.addArgument("-p"); // the mean size of DNA fragments for paired-end simulations cmdLine.addArgument("-m"); cmdLine.addArgument("" + meanFragSize); // the standard deviation of DNA fragment size for paired-end simulations. cmdLine.addArgument("-s"); cmdLine.addArgument("10"); }/*from ww w. j ava2 s . com*/ // quite - turn off end of run summary cmdLine.addArgument("-q"); Map map = new HashMap(); map.put("file", fusionFile); map.put("outputPrefix", outputPrefix); cmdLine.setSubstitutionMap(map); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); // Timeout after 5 minutes ExecuteWatchdog watchdog = new ExecuteWatchdog(300000); executor.setWatchdog(watchdog); try { int exitValue = executor.execute(cmdLine); } catch (Exception e) { logger.fatal("Failed to execute ART for simulating Illumina reads: " + e.getMessage()); } }
From source file:com.meltmedia.cadmium.blackbox.test.CliCommitCloneTest.java
/** * <p>Runs the Cadmium CLI command commit from Apache Commons Exec library. Then uses {@link CadmiumAssertions#assertContentDeployed(String, java.io.File, String)} to assert that the content deployed properly.</p> * <p>To override the site url, pass <code>-Dcom.meltmedia.cadmium.test.site.url=[URL]</code> to the jvm that this test case will be running in. The site url defaults to <code>http://localhost</code> if not set.</p> * @throws IOException See {@link DefaultExecutor#execute(CommandLine)} for more information. * @throws ExecuteException See {@link DefaultExecutor#execute(CommandLine)} for more information. * @throws InterruptedException //from w ww.jav a 2 s.c om * * @see <a href="http://commons.apache.org/exec">Apache Commons Exec</a> */ @Test public void testCommit() throws ExecuteException, IOException { String deployUrl = System.getProperty("com.meltmedia.cadmium.test.site.url", DEPLOY_URL); CommandLine commitCmd = CommandLine .parse("cadmium commit -m \"Testing commit command\" " + TEST_CONTENT_LOCATION + " " + deployUrl); DefaultExecutor exec = new DefaultExecutor(); exec.setExitValue(0); ExecuteWatchdog watchDog = new ExecuteWatchdog(60000); exec.setWatchdog(watchDog); int exitValue = exec.execute(commitCmd); assertEquals("Commit command returned with an error status.", exitValue, 0); assertContentDeployed("Failed to commit content to remote site.", new File(TEST_CONTENT_LOCATION), DEPLOY_URL); }
From source file:edu.buffalo.fusim.BowtieAlignment.java
public void run(String bowtiePath, String index, File read1, File read2, File outFile, int threads) { // Example bowtie call: // bowtie -t -v 2 -p 12 -m 10 -S CommandLine cmdLine = new CommandLine(bowtiePath); // print wall-clock time taken by search phases cmdLine.addArgument("-t"); // eport end-to-end hits w/ <=v mismatches; ignore qualities cmdLine.addArgument("-v"); cmdLine.addArgument("2"); // number of alignment threads to launch cmdLine.addArgument("-p"); cmdLine.addArgument("" + threads); // suppress all alignments if > <int> exist cmdLine.addArgument("-m"); cmdLine.addArgument("10"); // write hits in SAM format cmdLine.addArgument("-S"); // bowtie index cmdLine.addArgument("${index}"); if (read2 != null) { // fastq1 cmdLine.addArgument("-1"); cmdLine.addArgument("${read1}"); // fastq2 cmdLine.addArgument("-2"); cmdLine.addArgument("${read2}"); } else {// ww w .j a va2 s . com cmdLine.addArgument("${read1}"); } // output SAM file cmdLine.addArgument("${outFile}"); Map map = new HashMap(); map.put("index", index); map.put("read1", read1); if (read2 != null) { map.put("read2", read2); } map.put("outFile", outFile); cmdLine.setSubstitutionMap(map); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); // Never timeout ExecuteWatchdog watchdog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT); executor.setWatchdog(watchdog); try { int exitValue = executor.execute(cmdLine); } catch (Exception e) { logger.fatal( "Failed to execute bowtie for aligning simulated Illumina reads from ART: " + e.getMessage()); } }
From source file:com.alibaba.jstorm.yarn.utils.JStormUtils.java
/** * If it is backend, please set resultHandler, such as DefaultExecuteResultHandler If it is frontend, ByteArrayOutputStream.toString get the result * <p/>// w w w . j a v a2s . c om * This function don't care whether the command is successfully or not * * @param command * @param environment * @param workDir * @param resultHandler * @return * @throws IOException */ @Deprecated public static ByteArrayOutputStream launchProcess(String command, final Map environment, final String workDir, ExecuteResultHandler resultHandler) throws IOException { String[] cmdlist = command.split(" "); CommandLine cmd = new CommandLine(cmdlist[0]); for (String cmdItem : cmdlist) { if (StringUtils.isBlank(cmdItem) == false) { cmd.addArgument(cmdItem); } } DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); if (StringUtils.isBlank(workDir) == false) { executor.setWorkingDirectory(new File(workDir)); } ByteArrayOutputStream out = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(out, out); if (streamHandler != null) { executor.setStreamHandler(streamHandler); } try { if (resultHandler == null) { executor.execute(cmd, environment); } else { executor.execute(cmd, environment, resultHandler); } } catch (ExecuteException e) { // @@@@ // failed to run command } return out; }
From source file:com.nts.alphamale.shell.AdbShellExecutor.java
/** * @param cmd adb // www . j a va 2 s.c o m * @param synch ? ? true: synchronous, false: asynchronous * @param (ms) * @return Executor Standard Output? Map */ public int execute(CommandLine cmd, int exitValue) { int rtnValue = -1; DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(exitValue); try { rtnValue = executor.execute(cmd); } catch (Exception e) { log.error(e.getCause() + ":" + e.getMessage() + "[" + cmd + "]"); } return rtnValue; }
From source file:com.blackducksoftware.tools.scmconnector.core.CommandLineExecutor.java
@Override public CommandResults executeCommandForOutput(Logger log, CommandLine command, File targetDir) throws Exception { DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); PumpStreamHandler psh = new PumpStreamHandler(outputStream); executor.setStreamHandler(psh);//from ww w . j a va 2 s. co m int exitStatus = 1; executor.setWorkingDirectory(targetDir); exitStatus = executor.execute(command); String outputString = outputStream.toString(); // This log msg would reveal password // log.info("Command: " + command.toString() + " executed in: " // + targetDir.toString() + "; output: " + outputString); return new CommandResults(exitStatus, outputString); }
From source file:com.blackducksoftware.tools.scmconnector.core.CommandLineExecutor.java
@Override public int executeCommand(Logger log, CommandLine command, File targetDir, String promptResponse) throws Exception { DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); PumpStreamHandler psh = new PumpStreamHandler(new ExecLogHangler(log, Level.INFO)); executor.setStreamHandler(psh);//from w w w . jav a 2 s .c om providePromptResponse(psh, promptResponse); executor.setWorkingDirectory(targetDir); // This log msg would reveal password // log.info("Command: " + command.toString() + " executed in: " // + targetDir.toString()); int exitStatus = 1; try { exitStatus = executor.execute(command, EnvironmentUtils.getProcEnvironment()); } catch (Exception e) { log.error("Failure executing Command: " + e.getMessage()); } return exitStatus; }