Program: 133454
Project: 133454
Buggy source:
/** 
 * This method generates the YAML and Action syntax files in the local projectSpace/MOOSE directory from a remotely hosted MOOSE-based application.
 * @param monitor
 */
public FormStatus execute(Dictionary<String,String> map){
  IRemoteProcessService processService=null;
  IRemoteProcess yamlRemoteJob=null, syntaxRemoteJob=null;
  try {
    connection.open(null);
  }
 catch (  RemoteConnectionException e) {
    logger.error(getClass().getName() + "String_Node_Str",e);
    String errorMessage="String_Node_Str";
    return FormStatus.InfoError;
  }
  if (connection.isOpen()) {
    logger.info("String_Node_Str" + "String_Node_Str");
    processService=connection.getService(IRemoteProcessService.class);
    IRemoteProcessBuilder yamlProcessBuilder=processService.getProcessBuilder("String_Node_Str","String_Node_Str",appPath + "String_Node_Str");
    IRemoteProcessBuilder syntaxProcessBuilder=processService.getProcessBuilder("String_Node_Str","String_Node_Str",appPath + "String_Node_Str");
    yamlProcessBuilder.redirectErrorStream(false);
    syntaxProcessBuilder.redirectErrorStream(false);
    try {
      logger.info("String_Node_Str" + "String_Node_Str");
      logger.info("String_Node_Str" + yamlProcessBuilder.command().toString());
      yamlRemoteJob=yamlProcessBuilder.start(IRemoteProcessBuilder.FORWARD_X11);
      syntaxRemoteJob=syntaxProcessBuilder.start(IRemoteProcessBuilder.FORWARD_X11);
    }
 catch (    IOException e) {
      logger.error(getClass().getName() + "String_Node_Str",e);
      String errorMessage="String_Node_Str";
      return FormStatus.InfoError;
    }
    while (!yamlRemoteJob.isCompleted() && !syntaxRemoteJob.isCompleted()) {
      try {
        Thread.currentThread();
        Thread.sleep(1000);
      }
 catch (      InterruptedException e) {
        logger.error(getClass().getName() + "String_Node_Str",e);
      }
    }
    InputStream yamlStream=yamlRemoteJob.getInputStream();
    InputStream syntaxStream=syntaxRemoteJob.getInputStream();
    try {
      String yamlString=IOUtils.toString(yamlStream);
      String syntaxString=IOUtils.toString(syntaxStream);
      String animal=Paths.get(appPath).getFileName().toString();
      Path yamlPath=Paths.get(mooseFolder.getLocation().toOSString() + "String_Node_Str" + animal+ "String_Node_Str");
      Path syntaxPath=Paths.get(mooseFolder.getLocation().toOSString() + "String_Node_Str" + animal+ "String_Node_Str");
      if (Files.exists(yamlPath)) {
        Files.delete(yamlPath);
      }
      if (Files.exists(syntaxPath)) {
        Files.delete(syntaxPath);
      }
      Files.write(yamlPath,yamlString.getBytes());
      Files.write(syntaxPath,syntaxString.getBytes());
    }
 catch (    IOException e) {
      logger.error(getClass().getName() + "String_Node_Str",e);
      String errorMessage="String_Node_Str";
      return FormStatus.InfoError;
    }
  }
  return FormStatus.Processed;
}

Fixed version (ground truth):
/** 
 * This method generates the YAML and Action syntax files in the local projectSpace/MOOSE directory from a remotely hosted MOOSE-based application.
 * @param monitor
 */
public FormStatus execute(Dictionary<String,String> map){
  File appFile=new File(appPath);
  IRemoteProcessService processService=null;
  try {
    connection.open(null);
  }
 catch (  RemoteConnectionException e) {
    logger.error(getClass().getName() + "String_Node_Str",e);
    return FormStatus.InfoError;
  }
  if (connection.isOpen()) {
    logger.info("String_Node_Str" + "String_Node_Str");
    try {
      String remoteSeparator=connection.getProperty(IRemoteConnection.FILE_SEPARATOR_PROPERTY);
      String script=remoteSeparator + "String_Node_Str" + remoteSeparator+ "String_Node_Str";
      String fileLoc=remoteSeparator + "String_Node_Str" + remoteSeparator+ appFile.getName();
      IRemoteFileService fileManager=connection.getService(IRemoteFileService.class);
      IFileStore tmp=fileManager.getResource(script);
      PrintStream p=new PrintStream(tmp.openOutputStream(EFS.NONE,null));
      p.println("String_Node_Str");
      p.println(appPath + "String_Node_Str" + fileLoc+ "String_Node_Str");
      p.println(appPath + "String_Node_Str" + fileLoc+ "String_Node_Str");
      p.close();
      IFileInfo info=tmp.fetchInfo();
      info.setAttribute(EFS.ATTRIBUTE_EXECUTABLE,true);
      tmp.putInfo(info,EFS.SET_ATTRIBUTES,null);
      processService=connection.getService(IRemoteProcessService.class);
      IRemoteProcessBuilder pb=processService.getProcessBuilder(script);
      IRemoteProcess process=pb.start(IRemoteProcessBuilder.FORWARD_X11);
      while (!process.isCompleted()) {
        try {
          Thread.currentThread();
          Thread.sleep(1000);
        }
 catch (        InterruptedException e) {
          logger.error(getClass().getName() + "String_Node_Str",e);
        }
      }
      IFileStore localMooseFolder=EFS.getLocalFileSystem().fromLocalFile(mooseFolder.getLocation().toFile());
      IFileStore yamlStore=localMooseFolder.getChild(appFile.getName() + "String_Node_Str");
      IFileStore actionStore=localMooseFolder.getChild(appFile.getName() + "String_Node_Str");
      IFileStore remoteYaml=fileManager.getResource(fileLoc + "String_Node_Str");
      IFileStore remoteAction=fileManager.getResource(fileLoc + "String_Node_Str");
      remoteYaml.copy(yamlStore,EFS.OVERWRITE,null);
      remoteAction.copy(actionStore,EFS.OVERWRITE,null);
      tmp.delete(EFS.NONE,null);
      remoteYaml.delete(EFS.NONE,null);
      remoteAction.delete(EFS.NONE,null);
    }
 catch (    Exception e) {
      logger.error("String_Node_Str",e);
      return FormStatus.InfoError;
    }
  }
  return FormStatus.Processed;
}