org.renci.common.exec.Executor.execute()方法的使用及代码示例

x33g5p2x  于2022-01-19 转载在 其他  
字(16.5k)|赞(0)|评价(0)|浏览(240)

本文整理了Java中org.renci.common.exec.Executor.execute()方法的一些代码示例，展示了Executor.execute()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Executor.execute()方法的具体详情如下：
包路径：org.renci.common.exec.Executor
类名称：Executor
方法名：execute

Executor.execute介绍

[英]run the command
[中]运行命令

代码示例

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   Properties readLengthProperties = new Properties();
  5.   FileInputStream fis = new FileInputStream(this.readLength);
  6.   readLengthProperties.loadFromXML(fis);
  7.   fis.close();
  8.   StringBuilder command = new StringBuilder(getExecutable());
  9.   command.append(" ").append(junction.getAbsolutePath());
  10.   command.append(" ").append(readLengthProperties.getProperty("maxLength"));
  11.   command.append(" ").append(minimumAnchor.toString());
  12.   command.append(" ").append(referenceSequenceDirectory.getAbsolutePath());
  13.   command.append(" ").append(sam.getAbsolutePath());
  14.   CommandInput commandInput = new CommandInput();
  15.   logger.info("command.toString(): {}", command.toString());
  16.   commandInput.setCommand(command.toString());
  17.   CommandOutput commandOutput;
  18.   try {
  19.     Executor executor = BashExecutor.getInstance();
  20.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  21.   } catch (ExecutorException e) {
  22.     throw new ModuleException(e);
  23.   }
  24.   return new ShellModuleOutput(commandOutput);
  25. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   StringBuilder command = new StringBuilder(getExecutable());
  5.   command.append(" ").append(input.getAbsolutePath());
  6.   command.append(" ").append(outputDirectory.getAbsolutePath());
  7.   if (this.outputDirectory.isDirectory() && !this.outputDirectory.getAbsolutePath().endsWith("/")) {
  8.     command.append("/");
  9.   }
  10.   CommandInput commandInput = new CommandInput();
  11.   logger.info("command.toString(): {}", command.toString());
  12.   commandInput.setCommand(command.toString());
  13.   CommandOutput commandOutput;
  14.   try {
  15.     Executor executor = BashExecutor.getInstance();
  16.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  17.   } catch (ExecutorException e) {
  18.     throw new ModuleException(e);
  19.   }
  20.   return new ShellModuleOutput(commandOutput);
  21. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   StringBuilder command = new StringBuilder();
  5.   command.append(getModuleClass().getAnnotation(Executable.class).value());
  6.   command.append(" ").append(inFile.getAbsolutePath());
  7.   command.append(" ").append(outFile.getAbsolutePath());
  8.   command.append(" ").append(transcriptDB.getAbsolutePath());
  9.   command.append(" ").append(sqHeader.getAbsolutePath());
  10.   commandInput.setCommand(command.toString());
  11.   CommandOutput commandOutput;
  12.   try {
  13.     Executor executor = BashExecutor.getInstance();
  14.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  15.   } catch (ExecutorException e) {
  16.     throw new ModuleException(e);
  17.   }
  18.   return new ShellModuleOutput(commandOutput);
  19. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   StringBuilder command = new StringBuilder(getExecutable());
  5.   command.append(" ").append(this.minimumAnchorWidth.toString());
  6.   command.append(" ").append(this.maximumAnchor.toString());
  7.   command.append(" ").append(this.maximumThresholdEach.toString());
  8.   command.append(" ").append(this.maximumThresholdTotal.toString());
  9.   command.append(" ").append(this.junction.getAbsolutePath());
  10.   command.append(" 1");
  11.   command.append(" ").append(this.fusionJunction.getAbsolutePath());
  12.   command.append(" 1");
  13.   command.append(" ").append(this.referenceSequenceDirectory.getAbsolutePath());
  14.   if (this.referenceSequenceDirectory.isDirectory()
  15.       && !this.referenceSequenceDirectory.getAbsolutePath().endsWith("/")) {
  16.     command.append("/");
  17.   }
  18.   command.append(" ").append(this.output.getAbsolutePath());
  19.   CommandInput commandInput = new CommandInput();
  20.   logger.info("command.toString(): {}", command.toString());
  21.   commandInput.setCommand(command.toString());
  22.   CommandOutput commandOutput;
  23.   try {
  24.     Executor executor = BashExecutor.getInstance();
  25.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  26.   } catch (ExecutorException e) {
  27.     throw new ModuleException(e);
  28.   }
  29.   return new ShellModuleOutput(commandOutput);
  30. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   StringBuilder command = new StringBuilder(getExecutable());
  5.   command.append(" ").append(this.minimumAnchor.toString());
  6.   command.append(" ").append(this.maximumAnchor.toString());
  7.   command.append(" ").append(this.maximumSequenceThreshold.toString());
  8.   command.append(" ").append(this.junction.getAbsolutePath());
  9.   command.append(" ").append(this.referenceSequenceDirectory.getAbsolutePath());
  10.   if (this.referenceSequenceDirectory.isDirectory()
  11.       && !this.referenceSequenceDirectory.getAbsolutePath().endsWith("/")) {
  12.     command.append("/");
  13.   }
  14.   command.append(" ").append(this.output.getAbsolutePath());
  15.   CommandInput commandInput = new CommandInput();
  16.   logger.info("command.toString(): {}", command.toString());
  17.   commandInput.setCommand(command.toString());
  18.   CommandOutput commandOutput;
  19.   try {
  20.     Executor executor = BashExecutor.getInstance();
  21.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  22.   } catch (ExecutorException e) {
  23.     throw new ModuleException(e);
  24.   }
  25.   return new ShellModuleOutput(commandOutput);
  26. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   CommandInput commandInput = new CommandInput();
  4.   StringBuilder command = new StringBuilder();
  5.   command.append(getModuleClass().getAnnotation(Executable.class).value());
  6.   command.append(" -c ").append(column.toString());
  7.   command.append(" -q ").append(quantile.toString());
  8.   command.append(" -t ").append(target.toString());
  9.   command.append(" -o ").append(output.getAbsolutePath());
  10.   command.append(" ").append(input.getAbsolutePath());
  11.   commandInput.setCommand(command.toString());
  12.   CommandOutput commandOutput;
  13.   try {
  14.     Executor executor = BashExecutor.getInstance();
  15.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  16.   } catch (ExecutorException e) {
  17.     throw new ModuleException(e);
  18.   }
  19.   return new ShellModuleOutput(commandOutput);
  20. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   StringBuilder command = new StringBuilder(getExecutable());
  5.   command.append(" ").append(clusterDirectory.getAbsolutePath()).append("/");
  6.   CommandInput commandInput = new CommandInput();
  7.   logger.info("command.toString(): {}", command.toString());
  8.   commandInput.setCommand(command.toString());
  9.   CommandOutput commandOutput;
  10.   try {
  11.     Executor executor = BashExecutor.getInstance();
  12.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  13.   } catch (ExecutorException e) {
  14.     throw new ModuleException(e);
  15.   }
  16.   return new ShellModuleOutput(commandOutput);
  17. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   CommandInput commandInput = new CommandInput();
  4.   StringBuilder commandSB = new StringBuilder();
  5.   commandSB.append(this.executable);
  6.   if (argument != null) {
  7.     for (String arg : argument) {
  8.       commandSB.append(String.format(" %s", arg));
  9.     }
  10.   }
  11.   commandInput.setCommand(commandSB.toString());
  12.   CommandOutput commandOutput;
  13.   try {
  14.     Executor executor = BashExecutor.getInstance();
  15.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  16.   } catch (ExecutorException e) {
  17.     throw new ModuleException(e);
  18.   }
  19.   return new ShellModuleOutput(commandOutput);
  20. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   logger.debug("ENTERING call()");
  4.   StringBuilder command = new StringBuilder(getExecutable());
  5.   command.append(" ").append(output.getAbsolutePath());
  6.   if (fastq) {
  7.     command.append(" 1");
  8.   }
  9.   command.append(" ").append(input.getAbsolutePath());
  10.   CommandInput commandInput = new CommandInput();
  11.   logger.info("command.toString(): {}", command.toString());
  12.   commandInput.setCommand(command.toString());
  13.   CommandOutput commandOutput;
  14.   try {
  15.     Executor executor = BashExecutor.getInstance();
  16.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  17.   } catch (ExecutorException e) {
  18.     throw new ModuleException(e);
  19.   }
  20.   return new ShellModuleOutput(commandOutput);
  21. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   File userHome = new File(System.getProperty("user.home"));
  4.   CommandInput commandInput = new CommandInput();
  5.   StringBuilder command = new StringBuilder();
  6.   command.append(String.format(getModuleClass().getAnnotation(Executable.class).value()));
  7.   commandInput.setCommand(command.toString());
  8.   CommandOutput commandOutput;
  9.   try {
  10.     Executor executor = BashExecutor.getInstance();
  11.     commandOutput = executor.execute(commandInput, new File(userHome, ".mapseqrc"));
  12.   } catch (ExecutorException e) {
  13.     throw new ModuleException(e);
  14.   }
  15.   return new ShellModuleOutput(commandOutput);
  16. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandOutput commandOutput = null;
  4.   try {
  5.     StringBuilder command = new StringBuilder();
  6.     command.append("/bin/ln -s ").append(fastaDB).append(" ").append(symlinkFile.getAbsolutePath()).append(";");
  7.     command.append(String.format("$%s_%s", getWorkflowName().toUpperCase(),
  8.         getModuleClass().getAnnotation(Executable.class).value()));
  9.     command.append(" ")
  10.         .append(getModuleClass().getDeclaredField("algorithm").getAnnotation(InputArgument.class).flag())
  11.         .append(" ").append(algorithm.getValue());
  12.     command.append(" ").append(symlinkFile.getAbsolutePath());
  13.     CommandInput commandInput = new CommandInput();
  14.     File mapseqTmpDir = new File(System.getenv("MAPSEQ_HOME"), "tmp");
  15.     commandInput.setWorkDir(mapseqTmpDir);
  16.     commandInput.setCommand(command.toString());
  17.     Executor executor = BashExecutor.getInstance();
  18.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  19.   } catch (Exception e) {
  20.     throw new ModuleException(e);
  21.   }
  22.   return new ShellModuleOutput(commandOutput);
  23. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
  5.       getWorkflowName().toUpperCase(), input.getAbsolutePath(), output.getAbsolutePath()));
  6.   CommandOutput commandOutput;
  7.   try {
  8.     Executor executor = BashExecutor.getInstance();
  9.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  10.   } catch (ExecutorException e) {
  11.     throw new ModuleException(e);
  12.   }
  13.   return new ShellModuleOutput(commandOutput);
  14. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   CommandInput commandInput = new CommandInput();
  4.   commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
  5.       geneResults.getAbsolutePath(), origGeneResults.getAbsolutePath()));
  6.   CommandOutput commandOutput;
  7.   try {
  8.     Executor executor = BashExecutor.getInstance();
  9.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  10.   } catch (ExecutorException e) {
  11.     throw new ModuleException(e);
  12.   }
  13.   return new ShellModuleOutput(commandOutput);
  14. }

代码示例来源：origin: edu.unc.mapseq.mapseq-modules/mapseq-module-samtools

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
  5.       getWorkflowName().toUpperCase(), input.getAbsolutePath(), output.getAbsolutePath()));
  6.   CommandOutput commandOutput;
  7.   try {
  8.     Executor executor = BashExecutor.getInstance();
  9.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  10.   } catch (ExecutorException e) {
  11.     throw new ModuleException(e);
  12.   }
  13.   return new ShellModuleOutput(commandOutput);
  14. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   StringBuilder command = new StringBuilder();
  5.   command.append(getModuleClass().getAnnotation(Executable.class).value());
  6.   try {
  7.     command.append(output.getAbsolutePath());
  8.     for (File f : entry) {
  9.       command.append(" ").append(f.getAbsolutePath());
  10.     }
  11.   } catch (Exception e) {
  12.     throw new ModuleException(e);
  13.   }
  14.   commandInput.setCommand(command.toString());
  15.   CommandOutput commandOutput;
  16.   try {
  17.     Executor executor = BashExecutor.getInstance();
  18.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  19.   } catch (ExecutorException e) {
  20.     throw new ModuleException(e);
  21.   }
  22.   return new ShellModuleOutput(commandOutput);
  23. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws Exception {
  3.   CommandInput commandInput = new CommandInput();
  4.   StringBuilder command = new StringBuilder();
  5.   command.append(getModuleClass().getAnnotation(Executable.class).value());
  6.   command.append(" ").append(input.getAbsolutePath()).append(" ").append(output.getAbsolutePath());
  7.   commandInput.setCommand(command.toString());
  8.   CommandOutput commandOutput;
  9.   try {
  10.     Executor executor = BashExecutor.getInstance();
  11.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  12.   } catch (ExecutorException e) {
  13.     throw new ModuleException(e);
  14.   }
  15.   FileData fileData = new FileData();
  16.   fileData.setMimeType(MimeType.APPLICATION_PDF);
  17.   fileData.setName(output.getName());
  18.   addFileData(fileData);
  19.   return new ShellModuleOutput(commandOutput);
  20. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
  5.       flagstatInput.getAbsolutePath(), output.getAbsolutePath()));
  6.   CommandOutput commandOutput;
  7.   try {
  8.     Executor executor = BashExecutor.getInstance();
  9.     commandOutput = executor.execute(commandInput);
  10.   } catch (ExecutorException e) {
  11.     throw new ModuleException(e);
  12.   }
  13.   return new ShellModuleOutput(commandOutput);
  14. }

代码示例来源：origin: edu.unc.mapseq.mapseq-modules/mapseq-module-samtools

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   CommandInput commandInput = new CommandInput();
  4.   commandInput.setCommand(String.format(getModuleClass().getAnnotation(Executable.class).value(),
  5.       flagstatInput.getAbsolutePath(), output.getAbsolutePath()));
  6.   CommandOutput commandOutput;
  7.   try {
  8.     Executor executor = BashExecutor.getInstance();
  9.     commandOutput = executor.execute(commandInput);
  10.   } catch (ExecutorException e) {
  11.     throw new ModuleException(e);
  12.   }
  13.   return new ShellModuleOutput(commandOutput);
  14. }

代码示例来源：origin: edu.unc.mapseq/modules

  1. @Override
  2. public ModuleOutput call() throws ModuleException {
  3.   logger.debug("ENTERING call()");
  4.   CommandOutput commandOutput;
  5.   try {
  6.     StringBuilder command = new StringBuilder();
  7.     command.append(getModuleClass().getAnnotation(Executable.class).value());
  8.     command.append(" ").append(regularExpression);
  9.     command.append(" > ").append(outputFile.getAbsolutePath());
  10.     CommandInput commandInput = new CommandInput();
  11.     commandInput.setWorkDir(directory);
  12.     commandInput.setCommand(command.toString());
  13.     Executor executor = BashExecutor.getInstance();
  14.     commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc"));
  15.     if (mimeType != null) {
  16.       FileData fileData = new FileData();
  17.       fileData.setName(outputFile.getName());
  18.       fileData.setMimeType(mimeType);
  19.       addFileData(fileData);
  20.     }
  21.   } catch (ExecutorException e) {
  22.     throw new ModuleException(e);
  23.   }
  24.   return new ShellModuleOutput(commandOutput);
  25. }

代码示例来源：origin: org.renci.launchers/launcher-core

  1. public void run() {
  2.   for (LaunchDescriptorBean ldb : getLaunchDescriptorBeans()) {
  3.     String command = ldb.getCommands().get(0);
  4.     logger.debug("command = " + command);
  5.     Executor sh = new Executor(command);
  6.     sh.setEnvironment(new HashMap<String, String>());
  7.     sh.setWorkDir(getWorkDirectory());
  8.     try {
  9.       sh.execute();
  10.     } catch (ExecutorException e) {
  11.       logger.error("Execution error: " + e.getMessage());
  12.     }
  13.     setStdOut(sh.getStdout());
  14.     setStdErr(sh.getStderr());
  15.     setExitCode(sh.getExitCode());
  16.   }
  17. }

内容来源于网络，如有侵权，请联系作者删除！

Executor

相关文章

    查看更多

    热门标签

    更多
    JavaquerypythonNode开发语言requestUtil数据库Table后端算法LoggerMessageElementParser

    最新文章

    更多
    • 蜀ICP备13028337号-1 大数据知识库 https://www.saoniuhuo.com © All rights reserved
    • 本站内容来源互联网,如果侵犯您的权益请联系我们删除, 联系方式：448109455@qq.com