@Override public ModuleOutput call() throws ModuleException { CommandInput commandInput = new CommandInput(); StringBuilder command = new StringBuilder(); command.append(getModuleClass().getAnnotation(Executable.class).value()); command.append(" ").append(inFile.getAbsolutePath()); command.append(" ").append(outFile.getAbsolutePath()); command.append(" ").append(transcriptDB.getAbsolutePath()); command.append(" ").append(sqHeader.getAbsolutePath()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { CommandOutput commandOutput = null; try { StringBuilder command = new StringBuilder(); command.append("/bin/ln -s ").append(fastaDB).append(" ").append(symlinkFile.getAbsolutePath()).append(";"); command.append(String.format("$%s_%s", getWorkflowName().toUpperCase(), getModuleClass().getAnnotation(Executable.class).value())); command.append(" ") .append(getModuleClass().getDeclaredField("algorithm").getAnnotation(InputArgument.class).flag()) .append(" ").append(algorithm.getValue()); command.append(" ").append(symlinkFile.getAbsolutePath()); CommandInput commandInput = new CommandInput(); File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp"); commandInput.setWorkDir(mapseqTmpDir); commandInput.setCommand(command.toString()); Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (Exception e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
CommandInput commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imkdir -p %s", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s Project NCGENES", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, participantId)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setExitImmediately(Boolean.FALSE); registerCommandSB.append(String.format("if [ $? != 0 ]; then %s; %s; fi%n", deRegistrationCommand, registrationCommand)); commandInput.setCommand(registerCommandSB.toString()); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -d %s/%s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, bean.getFile().getName(), participantId));
: sourceFileSB.toString(), input.getWorkDir().getAbsolutePath(), input.getCommand()); try { wrapperFile = File.createTempFile("shellwrapper-", ".sh", input.getWorkDir()); logger.info("wrapperContents: {}", wrapperContents); FileUtils.writeStringToFile(wrapperFile, wrapperContents, "UTF-8"); if (input.getEnvironment() != null) { env = environmentToArray(input.getEnvironment()); logger.info("running command: {}", input.getCommand()); process = runtime.exec(wrapperFile.getAbsolutePath(), env, input.getWorkDir()); if (input.getStdin() != null) { stdinStream = new BufferedOutputStream(process.getOutputStream()); stdinStream.write(input.getStdin().toString().getBytes()); if (input.getMaxRunTime() > 0) { boolean stillRunning = true; while (stillRunning) { if (currentRunTime > input.getMaxRunTime()) { process.destroy(); delayedError = "Process timed out";
CommandInput commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imkdir -p %s", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s Project NCGENES", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, participantId)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setExitImmediately(Boolean.FALSE); registerCommandSB.append(String.format("if [ $? != 0 ]; then %s; %s; fi%n", deRegistrationCommand, registrationCommand)); commandInput.setCommand(registerCommandSB.toString()); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -d %s/%s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, bean.getFile().getName(), participantId));
@Override public ModuleOutput call() throws Exception { CommandInput commandInput = new CommandInput(); StringBuilder commandSB = new StringBuilder(); commandSB.append(this.executable); if (argument != null) { for (String arg : argument) { commandSB.append(String.format(" %s", arg)); } } commandInput.setCommand(commandSB.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { CommandOutput commandOutput = null; try { StringBuilder command = new StringBuilder(); command.append("/bin/ln -s ").append(fastaDB).append(" ").append(symlinkFile.getAbsolutePath()).append(";"); command.append(String.format("$%s_%s", getWorkflowName().toUpperCase(), getModuleClass().getAnnotation(Executable.class).value())); command.append(" ") .append(getModuleClass().getDeclaredField("algorithm").getAnnotation(InputArgument.class).flag()) .append(" ").append(algorithm.getValue()); command.append(" ").append(symlinkFile.getAbsolutePath()); CommandInput commandInput = new CommandInput(); File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp"); commandInput.setWorkDir(mapseqTmpDir); commandInput.setCommand(command.toString()); Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (Exception e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
CommandInput commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imkdir -p %s", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s Project NCGENES", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, participantId)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setExitImmediately(Boolean.FALSE); registerCommandSB.append(String.format("if [ $? != 0 ]; then %s; %s; fi%n", deRegistrationCommand, registrationCommand)); commandInput.setCommand(registerCommandSB.toString()); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -d %s/%s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, bean.getFile().getName(), participantId));
@Override public ModuleOutput call() throws Exception { logger.debug("ENTERING call()"); StringBuilder command = new StringBuilder(getExecutable()); command.append(" ").append(input.getAbsolutePath()); command.append(" ").append(outputDirectory.getAbsolutePath()); if (this.outputDirectory.isDirectory() && !this.outputDirectory.getAbsolutePath().endsWith("/")) { command.append("/"); } CommandInput commandInput = new CommandInput(); logger.info("command.toString(): {}", command.toString()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { logger.debug("ENTERING call()"); CommandOutput commandOutput; try { StringBuilder command = new StringBuilder(); command.append(getModuleClass().getAnnotation(Executable.class).value()); command.append(" ").append(regularExpression); command.append(" > ").append(outputFile.getAbsolutePath()); CommandInput commandInput = new CommandInput(); commandInput.setWorkDir(directory); commandInput.setCommand(command.toString()); Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (mimeType != null) { FileData fileData = new FileData(); fileData.setName(outputFile.getName()); fileData.setMimeType(mimeType); addFileData(fileData); } } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
CommandInput commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imkdir -p %s", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s Project NCGENES", irodsHome, ncgenesIRODSDirectory)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -C %s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, participantId)); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setExitImmediately(Boolean.FALSE); registerCommandSB.append(String.format("if [ $? != 0 ]; then %s; %s; fi%n", deRegistrationCommand, registrationCommand)); commandInput.setCommand(registerCommandSB.toString()); commandInput.setWorkDir(tmpDir); commandInputList.add(commandInput); commandInput = new CommandInput(); commandInput.setCommand(String.format("%s/bin/imeta add -d %s/%s ParticipantID %s NCGENES", irodsHome, ncgenesIRODSDirectory, bean.getFile().getName(), participantId));
@Override public ModuleOutput call() throws Exception { logger.debug("ENTERING call()"); Properties readLengthProperties = new Properties(); FileInputStream fis = new FileInputStream(this.readLength); readLengthProperties.loadFromXML(fis); fis.close(); StringBuilder command = new StringBuilder(getExecutable()); command.append(" ").append(junction.getAbsolutePath()); command.append(" ").append(readLengthProperties.getProperty("maxLength")); command.append(" ").append(minimumAnchor.toString()); command.append(" ").append(referenceSequenceDirectory.getAbsolutePath()); command.append(" ").append(sam.getAbsolutePath()); CommandInput commandInput = new CommandInput(); logger.info("command.toString(): {}", command.toString()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { CommandInput commandInput = new CommandInput(); StringBuilder command = new StringBuilder(); command.append(getModuleClass().getAnnotation(Executable.class).value()); if (threads != null) { try { command.append(" "); command.append(getModuleClass().getDeclaredField("threads").getAnnotation(InputArgument.class).flag()); command.append(" "); command.append(threads); } catch (Exception e) { throw new ModuleException(e); } } if (StringUtils.isNotEmpty(target)) { command.append(" ").append(target); } commandInput.setCommand(command.toString()); commandInput.setWorkDir(this.workDir); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { File userHome = new File(System.getProperty("user.home")); CommandInput commandInput = new CommandInput(); StringBuilder command = new StringBuilder(); command.append(String.format(getModuleClass().getAnnotation(Executable.class).value())); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(userHome, ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws Exception { CommandInput commandInput = new CommandInput(); File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp"); commandInput.setWorkDir(mapseqTmpDir); StringBuilder command = new StringBuilder(); command.append(String.format(getModuleClass().getAnnotation(Executable.class).value(), commandInput.setCommand(command.toString()); CommandOutput commandOutput; try {
@Override public ModuleOutput call() throws Exception { logger.debug("ENTERING call()"); StringBuilder command = new StringBuilder(getExecutable()); command.append(" ").append(this.minimumAnchor.toString()); command.append(" ").append(this.maximumAnchor.toString()); command.append(" ").append(this.maximumSequenceThreshold.toString()); command.append(" ").append(this.junction.getAbsolutePath()); command.append(" ").append(this.referenceSequenceDirectory.getAbsolutePath()); if (this.referenceSequenceDirectory.isDirectory() && !this.referenceSequenceDirectory.getAbsolutePath().endsWith("/")) { command.append("/"); } command.append(" ").append(this.output.getAbsolutePath()); CommandInput commandInput = new CommandInput(); logger.info("command.toString(): {}", command.toString()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws ModuleException { CommandInput commandInput = new CommandInput(); File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp"); commandInput.setWorkDir(mapseqTmpDir); StringBuilder command = new StringBuilder(); command.append(String.format(getModuleClass().getAnnotation(Executable.class).value(), commandInput.setCommand(command.toString()); CommandOutput commandOutput; try {
@Override public ModuleOutput call() throws Exception { logger.debug("ENTERING call()"); StringBuilder command = new StringBuilder(getExecutable()); command.append(" ").append(clusterDirectory.getAbsolutePath()).append("/"); CommandInput commandInput = new CommandInput(); logger.info("command.toString(): {}", command.toString()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }
@Override public ModuleOutput call() throws Exception { CommandInput commandInput = new CommandInput(); File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp"); commandInput.setWorkDir(mapseqTmpDir); StringBuilder command = new StringBuilder(); command.append(String.format(getModuleClass().getAnnotation(Executable.class).value(), commandInput.setCommand(command.toString()); CommandOutput commandOutput; try {
@Override public ModuleOutput call() throws Exception { logger.debug("ENTERING call()"); StringBuilder command = new StringBuilder(getExecutable()); command.append(" ").append(this.minimumAnchorWidth.toString()); command.append(" ").append(this.maximumAnchor.toString()); command.append(" ").append(this.maximumThresholdEach.toString()); command.append(" ").append(this.maximumThresholdTotal.toString()); command.append(" ").append(this.junction.getAbsolutePath()); command.append(" 1"); command.append(" ").append(this.fusionJunction.getAbsolutePath()); command.append(" 1"); command.append(" ").append(this.referenceSequenceDirectory.getAbsolutePath()); if (this.referenceSequenceDirectory.isDirectory() && !this.referenceSequenceDirectory.getAbsolutePath().endsWith("/")) { command.append("/"); } command.append(" ").append(this.output.getAbsolutePath()); CommandInput commandInput = new CommandInput(); logger.info("command.toString(): {}", command.toString()); commandInput.setCommand(command.toString()); CommandOutput commandOutput; try { Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); } catch (ExecutorException e) { throw new ModuleException(e); } return new ShellModuleOutput(commandOutput); }