List of usage examples for org.apache.commons.exec CommandLine CommandLine
public CommandLine(final CommandLine other)
From source file:com.netflix.genie.web.tasks.job.JobCompletionService.java
/** * Delete the application dependencies off disk to save space. * * @param jobId The ID of the job to delete dependencies for * @param jobDir The job working directory *//* w w w. j a v a 2s . co m*/ private void deleteApplicationDependencies(final String jobId, final File jobDir) { log.debug("Deleting dependencies as its enabled."); if (jobDir.exists()) { try { final List<String> appIds = this.jobSearchService.getJobApplications(jobId).stream() .map(Application::getId).filter(Optional::isPresent).map(Optional::get) .collect(Collectors.toList()); for (final String appId : appIds) { final File appDependencyDir = new File(jobDir, JobConstants.GENIE_PATH_VAR + JobConstants.FILE_PATH_DELIMITER + JobConstants.APPLICATION_PATH_VAR + JobConstants.FILE_PATH_DELIMITER + appId + JobConstants.FILE_PATH_DELIMITER + JobConstants.DEPENDENCY_FILE_PATH_PREFIX); if (appDependencyDir.exists()) { if (this.runAsUserEnabled) { final CommandLine deleteCommand = new CommandLine("sudo"); deleteCommand.addArgument("rm"); deleteCommand.addArgument("-rf"); deleteCommand.addArgument(appDependencyDir.getCanonicalPath()); log.debug("Delete command is {}", deleteCommand.toString()); this.executor.execute(deleteCommand); } else { FileUtils.deleteDirectory(appDependencyDir); } } } } catch (Exception e) { log.error("Could not delete job dependencies after completion for job: {} due to error {}", jobId, e); this.deleteDependenciesFailure.increment(); } } }
From source file:com.tupilabs.pbs.PBS.java
/** * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit, and resource overrides * <p>//from www . ja v a 2s.c o m * Equivalent to qsub -t 1,2,3 -l [resource_name=value,resource_name=value] [param] * * @param input job input file * @param pbsArrayIDs of specified PBS indices * @param resourceOverrides list of resource overrides * @return job id of array job */ public static String qsubArrayJob(String input, List<Integer> pbsArrayIDs, String... resourceOverrides) { final CommandLine cmdLine = new CommandLine(COMMAND_QSUB); cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS); String listArgument = StringUtils.join(pbsArrayIDs, ","); cmdLine.addArgument(listArgument); cmdLine.addArgument(PARAMETER_RESOURCE_OVERRIDE_STATUS); String resourceOverrideArgument = StringUtils.join(resourceOverrides, ","); cmdLine.addArgument(resourceOverrideArgument); cmdLine.addArgument(input); final OutputStream out = new ByteArrayOutputStream(); final OutputStream err = new ByteArrayOutputStream(); DefaultExecuteResultHandler resultHandler; try { resultHandler = execute(cmdLine, out, err); resultHandler.waitFor(DEFAULT_TIMEOUT); } catch (ExecuteException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (IOException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (InterruptedException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } final int exitValue = resultHandler.getExitValue(); LOGGER.info("qsub exit value: " + exitValue); LOGGER.fine("qsub output: " + out.toString()); if (exitValue != 0) throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString()); String jobId = out.toString(); return jobId.trim(); }
From source file:com.boundlessgeo.wps.grass.GrassProcesses.java
/** * Define a GISBASE/LOCATION_NAME for the provided dem. * * @param operation Name used for the location on disk * @param dem File used to establish CRS and Bounds for the location * @return// ww w . jav a 2s . co m * @throws Exception */ static File location(CoordinateReferenceSystem crs) throws Exception { String code = CRS.toSRS(crs, true); File geodb = new File(System.getProperty("user.home"), "grassdata"); File location = Files.createTempDirectory(geodb.toPath(), code).toFile(); KVP kvp = new KVP("geodb", geodb, "location", location); // grass70 + ' -c epsg:' + myepsg + ' -e ' + location_path CommandLine cmd = new CommandLine(EXEC); cmd.addArgument("-c"); cmd.addArgument("epsg:" + code); cmd.addArgument("-e"); cmd.addArgument("${location}"); cmd.setSubstitutionMap(kvp); DefaultExecutor executor = new DefaultExecutor(); executor.setExitValue(0); executor.setWatchdog(new ExecuteWatchdog(60000)); executor.setStreamHandler(new PumpStreamHandler(System.out)); int exitValue = executor.execute(cmd); return location; }
From source file:com.tibco.tgdb.test.lib.TGAdmin.java
/** * Invoke TG admin synchronously. //from www .j ava2 s . c o m * Admin operation blocks until it is completed. * * @param tgHome TG admin home * @param url Url to connect to TG server * @param user System User name * @param pwd System User password * @param logFile TG admin log file location - Generated by admin * @param logLevel Specify the log level: info/user1/user2/user3/debug/debugmemory/debugwire * @param cmd TG admin command file or command string * @param memSize Specify the maximum memory usage (MB). -1 for default (8 MB) * @param timeout Number of milliseconds allowed to complete admin operation * * @return Output console of admin operation * @throws TGAdminException Admin execution fails or timeout occurs */ public static String invoke(String tgHome, String url, String user, String pwd, String logFile, String logLevel, String cmd, int memSize, long timeout) throws TGAdminException { if (tgHome == null) throw new TGAdminException("TGAdmin - TGDB home is not defined"); File ftgHome = new File(tgHome); if (!ftgHome.exists()) throw new TGAdminException("TGAdmin - TGDB home '" + tgHome + "' does not exist"); ByteArrayOutputStream output = new ByteArrayOutputStream(); PumpStreamHandler psh = new PumpStreamHandler(output); Executor tgExec = new DefaultExecutor(); tgExec.setStreamHandler(psh); tgExec.setWorkingDirectory(new File(tgHome + "/bin")); CommandLine tgCL = new CommandLine((new File(tgHome + "/bin/" + process)).getAbsolutePath()); // Define arguments List<String> args = new ArrayList<String>(); if (url != null) { args.add("--url"); args.add(url); } if (user != null) { args.add("--uid"); args.add(user); } if (pwd != null) { args.add("--pwd"); args.add(pwd); } if (logFile != null) { args.add("--log"); args.add(logFile); } if (logLevel != null) { args.add("--log-level"); args.add(logLevel); } if (memSize >= 0) { args.add("--max-memory"); args.add(Integer.toString(memSize)); } File cmdFile = null; if (cmd == null) throw new TGAdminException("TGAdmin - Command is required."); if (cmd.matches( "(?s)^(kill|show|describe|create|stop|info|checkpoint|dump|set|connect|disconnect|export|import|exit).*$")) { try { cmdFile = new File(tgHome + "/invokeAdminScript.txt"); Files.write(Paths.get(cmdFile.toURI()), cmd.getBytes(StandardCharsets.UTF_8)); } catch (IOException ioe) { throw new TGAdminException("TGAdmin - " + ioe.getMessage()); } } else { cmdFile = new File(cmd); } if (!cmdFile.exists()) { throw new TGAdminException("TGAdmin - Command file '" + cmdFile + "' does not exist"); } args.add("--file"); args.add(cmdFile.getAbsolutePath()); tgCL.addArguments((String[]) args.toArray(new String[args.size()])); ExecuteWatchdog tgWatch = new ExecuteWatchdog(timeout); tgExec.setWatchdog(tgWatch); System.out.println("TGAdmin - Invoking " + StringUtils.toString(tgCL.toStrings(), " ")); long endProcTime = 0; long totalProcTime = 0; try { TGAdmin.startProcTime = System.currentTimeMillis(); tgExec.execute(tgCL); endProcTime = System.currentTimeMillis(); } catch (IOException ee) { if (tgWatch.killedProcess()) throw new TGAdminException("TGAdmin - Operation did not complete within " + timeout + " ms", output.toString()); else { try { Thread.sleep(1000); // make sure output has time to fill up } catch (InterruptedException ie) { ; } throw new TGAdminException("TGAdmin - Execution failed: " + ee.getMessage(), output.toString()); } } if (url != null && !output.toString().contains("Successfully connected to server")) throw new TGAdminException("TGAdmin - Admin could not connect to server " + url + " with user " + user, output.toString()); if (endProcTime != 0) totalProcTime = endProcTime - TGAdmin.startProcTime; if (TGAdmin.showOperationBanner) System.out.println( "TGAdmin - Operation completed" + (totalProcTime > 0 ? " in " + totalProcTime + " msec" : "")); return output.toString(); }
From source file:com.googlecode.mycontainer.maven.plugin.ExecMojo.java
CommandLine getExecutablePath(Map enviro, File dir) {
File execFile = new File(executable);
String exec = null;/*from ww w . j a v a 2 s . c om*/
if (execFile.exists()) {
getLog().debug("Toolchains are ignored, 'executable' parameter is set to " + executable);
exec = execFile.getAbsolutePath();
} else {
Toolchain tc = getToolchain();
// if the file doesn't exist & toolchain is null, the exec is
// probably in the PATH...
// we should probably also test for isFile and canExecute, but the
// second one is only
// available in SDK 6.
if (tc != null) {
getLog().info("Toolchain in exec-maven-plugin: " + tc);
exec = tc.findTool(executable);
} else {
if (OS.isFamilyWindows()) {
String ex = executable.indexOf(".") < 0 ? executable + ".bat" : executable;
File f = new File(dir, ex);
if (f.exists()) {
exec = ex;
} else {
// now try to figure the path from PATH, PATHEXT env
// vars
// if bat file, wrap in cmd /c
String path = (String) enviro.get("PATH");
if (path != null) {
String[] elems = StringUtils.split(path, File.pathSeparator);
for (int i = 0; i < elems.length; i++) {
f = new File(new File(elems[i]), ex);
if (f.exists()) {
exec = ex;
break;
}
}
}
}
}
}
}
if (exec == null) {
exec = executable;
}
CommandLine toRet;
if (OS.isFamilyWindows() && exec.toLowerCase(Locale.getDefault()).endsWith(".bat")) {
toRet = new CommandLine("cmd");
toRet.addArgument("/c");
toRet.addArgument(exec);
} else {
toRet = new CommandLine(exec);
}
return toRet;
}
From source file:edu.isi.misd.scanner.network.registry.data.service.RegistryServiceImpl.java
@Override public String convertDataProcessingSpecification(String workingDir, String execName, String args, String input, Integer dataSetId) throws Exception { Executor exec = new DefaultExecutor(); exec.setWorkingDirectory(new File(workingDir)); CommandLine cl = new CommandLine(execName); cl.addArgument(args);//ww w . j a v a 2 s. c o m ByteArrayInputStream in = new ByteArrayInputStream(input.getBytes("UTF-8")); ByteArrayOutputStream out = new ByteArrayOutputStream(); ByteArrayOutputStream err = new ByteArrayOutputStream(); PumpStreamHandler streamHandler = new PumpStreamHandler(out, err, in); exec.setStreamHandler(streamHandler); try { exec.execute(cl); } catch (Exception e) { throw new Exception(e.toString() + "\n\n" + err.toString("UTF-8")); } String output = out.toString("UTF-8"); if (dataSetId != null) { DataSetDefinition dataSet = dataSetDefinitionRepository.findOne(dataSetId); if (dataSet == null) { throw new ResourceNotFoundException(dataSetId); } dataSet.setDataProcessingSpecification(input); dataSet.setDataProcessingProgram(output); dataSetDefinitionRepository.save(dataSet); } return output; }
From source file:com.netflix.genie.web.tasks.job.JobCompletionService.java
/** * Uploads the job directory to the archive location. * * @param job The job./*ww w . j a v a 2 s. c o m*/ * @throws GenieException if there is any problem */ private boolean processJobDir(final Job job) throws GenieException, IOException { log.debug("Got a job finished event. Will process job directory."); boolean result = false; final Optional<String> oJobId = job.getId(); // The deletion of dependencies and archiving only happens for job requests which are not Invalid. if (oJobId.isPresent() && !(this.jobSearchService.getJobStatus(job.getId().get()).equals(JobStatus.INVALID))) { final String jobId = oJobId.get(); final File jobDir = new File(this.baseWorkingDir, jobId); if (jobDir.exists()) { if (this.deleteDependencies) { this.deleteApplicationDependencies(jobId, jobDir); } final Optional<String> archiveLocation = job.getArchiveLocation(); if (archiveLocation.isPresent() && !Strings.isNullOrEmpty(archiveLocation.get())) { log.debug("Archiving job directory"); // Create the tar file final File localArchiveFile = new File(jobDir, "genie/logs/" + jobId + ".tar.gz"); final CommandLine commandLine; if (this.runAsUserEnabled) { commandLine = new CommandLine("sudo"); commandLine.addArgument("tar"); } else { commandLine = new CommandLine("tar"); } commandLine.addArgument("-c"); commandLine.addArgument("-z"); commandLine.addArgument("-f"); commandLine.addArgument(localArchiveFile.getCanonicalPath()); commandLine.addArgument("./"); this.executor.setWorkingDirectory(jobDir); log.debug("Archive command : {}", commandLine.toString()); this.executor.execute(commandLine); // Upload the tar file to remote location this.genieFileTransferService.putFile(localArchiveFile.getCanonicalPath(), archiveLocation.get()); // At this point the archive file is successfully uploaded to archive location specified in the job. // Now we can delete it from local disk to save space if enabled. if (this.deleteArchiveFile) { log.debug("Deleting archive file"); try { if (this.runAsUserEnabled) { final CommandLine deleteCommand = new CommandLine("sudo"); deleteCommand.addArgument("rm"); deleteCommand.addArgument("-f"); deleteCommand.addArgument(localArchiveFile.getCanonicalPath()); this.executor.setWorkingDirectory(jobDir); log.debug("Delete command: {}", deleteCommand.toString()); this.executor.execute(deleteCommand); } else if (!localArchiveFile.delete()) { log.error("Failed to delete archive file for job: {}", jobId); this.archiveFileDeletionFailure.increment(); } } catch (final Exception e) { log.error("Failed to delete archive file for job: {}", jobId, e); this.archiveFileDeletionFailure.increment(); } } result = true; } } } return result; }
From source file:com.tupilabs.pbs.PBS.java
/** * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit * <p>//w w w. ja v a 2s .c om * Equivalent to qsub -t 5-20 [param] * * @param input job input file * @param beginIndex beginning of index range * @param endIndex end of index range * @return job id of array job */ public static String qsubArrayJob(String input, int beginIndex, int endIndex) { final CommandLine cmdLine = new CommandLine(COMMAND_QSUB); cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS); String rangeArgument = beginIndex + "-" + endIndex; cmdLine.addArgument(rangeArgument); cmdLine.addArgument(input); final OutputStream out = new ByteArrayOutputStream(); final OutputStream err = new ByteArrayOutputStream(); DefaultExecuteResultHandler resultHandler; try { resultHandler = execute(cmdLine, out, err); resultHandler.waitFor(DEFAULT_TIMEOUT); } catch (ExecuteException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (IOException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (InterruptedException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } final int exitValue = resultHandler.getExitValue(); LOGGER.info("qsub exit value: " + exitValue); LOGGER.fine("qsub output: " + out.toString()); if (exitValue != 0) throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString()); String jobId = out.toString(); return jobId.trim(); }
From source file:com.tupilabs.pbs.PBS.java
/** * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit AND a range to submit * <p>//from w w w .ja v a 2 s . c o m * Equivalent to qsub -t 1,2,3,5-20 [param] * * @param input job input file * @param pbsArrayIDs list of specified indices * @param beginIndex beginning of index range * @param endIndex end of index range * @return job id of array job */ public static String qsubArrayJob(String input, List<Integer> pbsArrayIDs, int beginIndex, int endIndex) { final CommandLine cmdLine = new CommandLine(COMMAND_QSUB); cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS); String rangeArgument = beginIndex + "-" + endIndex; String listArgument = StringUtils.join(pbsArrayIDs, ","); String combinedArgument = listArgument + "," + rangeArgument; cmdLine.addArgument(combinedArgument); cmdLine.addArgument(input); final OutputStream out = new ByteArrayOutputStream(); final OutputStream err = new ByteArrayOutputStream(); DefaultExecuteResultHandler resultHandler; try { resultHandler = execute(cmdLine, out, err); resultHandler.waitFor(DEFAULT_TIMEOUT); } catch (ExecuteException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (IOException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } catch (InterruptedException e) { throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e); } final int exitValue = resultHandler.getExitValue(); LOGGER.info("qsub exit value: " + exitValue); LOGGER.fine("qsub output: " + out.toString()); if (exitValue != 0) throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString()); String jobId = out.toString(); return jobId.trim(); }
From source file:it.drwolf.ridire.index.cwb.CWBPatternSearcher.java
private void executeCQPQuery(File queryFile) throws ExecuteException, IOException { Executor executor = new DefaultExecutor(); File tempSh = File.createTempFile("ridireSH", ".sh"); StringBuffer stringBuffer = new StringBuffer(); stringBuffer.append("export LC_ALL=C\n"); stringBuffer.append(this.cqpExecutable + " -f " + queryFile.getAbsolutePath() + " -D " + this.cqpCorpusName + " -r " + this.cqpRegistry + "\n"); FileUtils.writeStringToFile(tempSh, stringBuffer.toString()); tempSh.setExecutable(true);/*w ww . j av a 2s . c o m*/ CommandLine commandLine = new CommandLine(tempSh.getAbsolutePath()); executor.execute(commandLine); FileUtils.deleteQuietly(tempSh); }