Program: 90055
Project: 90055
Buggy source:
/** 
 * {@inheritDoc}
 */
@Override public void executeTask(@NotNull final Map<String,Object> context) throws GenieException, IOException {
  log.debug("String_Node_Str");
  super.executeTask(context);
  final String jobSetupFile=jobExecEnv.getJobRequest().getSetupFile();
  if (jobSetupFile != null && StringUtils.isNotBlank(jobSetupFile)) {
    final String localPath=this.jobWorkingDirectory + JobConstants.FILE_PATH_DELIMITER + jobSetupFile.substring(jobSetupFile.lastIndexOf(JobConstants.FILE_PATH_DELIMITER) + 1);
    this.fts.getFile(jobSetupFile,localPath);
    writer.write("String_Node_Str" + System.lineSeparator());
    writer.write(JobConstants.SOURCE + localPath.replace(this.jobWorkingDirectory,"String_Node_Str" + JobConstants.GENIE_JOB_DIR_ENV_VAR + "String_Node_Str") + System.lineSeparator());
    writer.write(System.lineSeparator());
  }
  for (  final String dependencyFile : jobExecEnv.getJobRequest().getDependencies()) {
    final String localPath=this.jobWorkingDirectory + JobConstants.FILE_PATH_DELIMITER + dependencyFile.substring(dependencyFile.lastIndexOf(JobConstants.FILE_PATH_DELIMITER) + 1);
    this.fts.getFile(dependencyFile,localPath);
  }
  this.attachmentService.copy(jobExecEnv.getJobRequest().getId(),jobExecEnv.getJobWorkingDir());
  writer.write(System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(jobExecEnv.getCommand().getExecutable() + JobConstants.WHITE_SPACE + jobExecEnv.getJobRequest().getCommandArgs()+ JobConstants.STDOUT_REDIRECT+ JobConstants.STDOUT_LOG_FILE_NAME+ JobConstants.STDERR_REDIRECT+ JobConstants.STDERR_LOG_FILE_NAME+ "String_Node_Str"+ System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(JobConstants.GENIE_DONE_FILE_CONTENT_PREFIX + JobConstants.GENIE_DONE_FILE_NAME + System.lineSeparator());
}

Fixed version (ground truth):
/** 
 * {@inheritDoc}
 */
@Override public void executeTask(@NotNull final Map<String,Object> context) throws GenieException, IOException {
  log.debug("String_Node_Str");
  super.executeTask(context);
  final String jobSetupFile=jobExecEnv.getJobRequest().getSetupFile();
  if (jobSetupFile != null && StringUtils.isNotBlank(jobSetupFile)) {
    final String localPath=this.jobWorkingDirectory + JobConstants.FILE_PATH_DELIMITER + jobSetupFile.substring(jobSetupFile.lastIndexOf(JobConstants.FILE_PATH_DELIMITER) + 1);
    this.fts.getFile(jobSetupFile,localPath);
    writer.write("String_Node_Str" + System.lineSeparator());
    writer.write(JobConstants.SOURCE + localPath.replace(this.jobWorkingDirectory,"String_Node_Str" + JobConstants.GENIE_JOB_DIR_ENV_VAR + "String_Node_Str") + System.lineSeparator());
    writer.write(System.lineSeparator());
  }
  for (  final String dependencyFile : jobExecEnv.getJobRequest().getDependencies()) {
    final String localPath=this.jobWorkingDirectory + JobConstants.FILE_PATH_DELIMITER + dependencyFile.substring(dependencyFile.lastIndexOf(JobConstants.FILE_PATH_DELIMITER) + 1);
    this.fts.getFile(dependencyFile,localPath);
  }
  this.attachmentService.copy(jobExecEnv.getJobRequest().getId(),jobExecEnv.getJobWorkingDir());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write("String_Node_Str" + "String_Node_Str" + JobConstants.GENIE_JOB_DIR_ENV_VAR + "String_Node_Str"+ JobConstants.GENIE_ENV_PATH+ System.lineSeparator());
  writer.write(System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(jobExecEnv.getCommand().getExecutable() + JobConstants.WHITE_SPACE + jobExecEnv.getJobRequest().getCommandArgs()+ JobConstants.STDOUT_REDIRECT+ JobConstants.STDOUT_LOG_FILE_NAME+ JobConstants.STDERR_REDIRECT+ JobConstants.STDERR_LOG_FILE_NAME+ "String_Node_Str"+ System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(System.lineSeparator());
  writer.write("String_Node_Str" + System.lineSeparator());
  writer.write(JobConstants.GENIE_DONE_FILE_CONTENT_PREFIX + JobConstants.GENIE_DONE_FILE_NAME + System.lineSeparator());
}