Program: 133485
Project: 133485
Buggy source:
@Override public FormStatus execute(Dictionary<String,String> dictionary){
  IRemoteProcessService processService=null;
  IRemoteProcess checkInputRemoteJob=null;
  MOOSEFileHandler writer=new MOOSEFileHandler();
  Form tempForm=new Form();
  String checkInputString="String_Node_Str", line;
  status=FormStatus.ReadyToProcess;
  IFile inputFile=project.getFile(appComponent.retrieveEntry("String_Node_Str").getValue());
  URI appUri=URI.create(appComponent.retrieveEntry("String_Node_Str").getValue());
  if (!validateFileEntries()) {
    status=FormStatus.InfoError;
    return status;
  }
  tempForm.addComponent(mooseTree);
  writer.write(tempForm,inputFile);
  if (connection != null) {
    ArrayList<IFile> files=new ArrayList<IFile>();
    files.add(inputFile);
    for (    Entry fileE : getFileEntries()) {
      files.add(project.getFile(fileE.getValue()));
    }
    try {
      connection.open(null);
    }
 catch (    RemoteConnectionException e) {
      logger.error(getClass().getName() + "String_Node_Str",e);
      String errorMessage="String_Node_Str";
      throwErrorMessage("String_Node_Str","String_Node_Str",errorMessage,errorMessage);
      status=FormStatus.InfoError;
      return status;
    }
    if (connection.isOpen()) {
      RemoteFileUploadAction uploadAction=new RemoteFileUploadAction(files,connection);
      uploadAction.execute(null);
      processService=connection.getService(IRemoteProcessService.class);
      processService.setWorkingDirectory(uploadAction.getRemoteUploadDirectoryPath());
      IRemoteProcessBuilder checkInputProcessBuilder=processService.getProcessBuilder("String_Node_Str","String_Node_Str",appUri.getRawPath() + "String_Node_Str" + uploadAction.getRemoteUploadDirectoryPath()+ System.getProperty("String_Node_Str")+ inputFile.getName());
      checkInputProcessBuilder.redirectErrorStream(true);
      try {
        checkInputRemoteJob=checkInputProcessBuilder.start(IRemoteProcessBuilder.FORWARD_X11);
      }
 catch (      IOException e) {
        logger.error(getClass().getName() + "String_Node_Str",e);
        String errorMessage="String_Node_Str";
        throwErrorMessage("String_Node_Str","String_Node_Str",errorMessage,errorMessage);
        status=FormStatus.InfoError;
        return status;
      }
      while (!checkInputRemoteJob.isCompleted()) {
        try {
          Thread.currentThread();
          Thread.sleep(1000);
        }
 catch (        InterruptedException e) {
          logger.error(getClass().getName() + "String_Node_Str",e);
        }
      }
      try {
        BufferedReader input=new BufferedReader(new InputStreamReader(checkInputRemoteJob.getInputStream()));
        while ((line=input.readLine()) != null) {
          System.out.println(line);
          checkInputString+=line + "String_Node_Str";
        }
        input.close();
        if (checkInputString.contains("String_Node_Str")) {
          String errorString=checkInputString.substring(checkInputString.indexOf("String_Node_Str"),checkInputString.indexOf("String_Node_Str"));
          errorString="String_Node_Str" + errorString.trim() + "String_Node_Str";
          throwErrorMessage("String_Node_Str","String_Node_Str",errorString,"String_Node_Str" + checkInputString.trim());
          status=FormStatus.InfoError;
          return status;
        }
      }
 catch (      IOException e) {
        logger.error(getClass().getName() + "String_Node_Str",e);
        status=FormStatus.InfoError;
        return status;
      }
    }
  }
 else {
    File execFile=new File(appUri);
    String[] checkInputCmd={"String_Node_Str","String_Node_Str",execFile.getAbsolutePath() + "String_Node_Str" + project.getLocation().toOSString()+ System.getProperty("String_Node_Str")+ inputFile.getName()+ "String_Node_Str"};
    try {
      ProcessBuilder builder=new ProcessBuilder(checkInputCmd).directory(new File(project.getLocation().toOSString()));
      builder.redirectErrorStream(true);
      Process checkInputProcess=builder.start();
      BufferedReader input=new BufferedReader(new InputStreamReader(checkInputProcess.getInputStream()));
      while ((line=input.readLine()) != null) {
        checkInputString+=line + "String_Node_Str";
      }
      input.close();
    }
 catch (    IOException e) {
      e.printStackTrace();
      logger.error(getClass().getName() + "String_Node_Str",e);
      status=FormStatus.InfoError;
      return status;
    }
    if (checkInputString.contains("String_Node_Str")) {
      String errorString=checkInputString.substring(checkInputString.indexOf("String_Node_Str"),checkInputString.indexOf("String_Node_Str"));
      errorString="String_Node_Str" + errorString.trim() + "String_Node_Str";
      throwErrorMessage("String_Node_Str","String_Node_Str",errorString,"String_Node_Str" + checkInputString.trim());
      status=FormStatus.InfoError;
      return status;
    }
  }
  return status;
}

Fixed version (ground truth):
@Override public FormStatus execute(Dictionary<String,String> dictionary){
  IRemoteProcessService processService=null;
  IRemoteProcess checkInputRemoteJob=null;
  MOOSEFileHandler writer=new MOOSEFileHandler();
  Form tempForm=new Form();
  InputStream inputStream=null;
  String checkInputString="String_Node_Str", line;
  status=FormStatus.ReadyToProcess;
  IFile inputFile=project.getFile(appComponent.retrieveEntry("String_Node_Str").getValue());
  URI appUri=URI.create(appComponent.retrieveEntry("String_Node_Str").getValue());
  if (!validateFileEntries()) {
    status=FormStatus.InfoError;
    return status;
  }
  tempForm.addComponent(mooseTree);
  writer.write(tempForm,inputFile);
  if (connection != null) {
    ArrayList<IFile> files=new ArrayList<IFile>();
    files.add(inputFile);
    for (    Entry fileE : getFileEntries()) {
      files.add(project.getFile(fileE.getValue()));
    }
    try {
      connection.open(null);
    }
 catch (    RemoteConnectionException e) {
      logger.error(getClass().getName() + "String_Node_Str",e);
      String errorMessage="String_Node_Str";
      throwErrorMessage("String_Node_Str","String_Node_Str",errorMessage,errorMessage);
      status=FormStatus.InfoError;
      return status;
    }
    if (connection.isOpen()) {
      RemoteFileUploadAction uploadAction=new RemoteFileUploadAction(files,connection);
      uploadAction.execute(null);
      processService=connection.getService(IRemoteProcessService.class);
      processService.setWorkingDirectory(uploadAction.getRemoteUploadDirectoryPath());
      IRemoteProcessBuilder checkInputProcessBuilder=processService.getProcessBuilder("String_Node_Str","String_Node_Str",appUri.getRawPath() + "String_Node_Str" + uploadAction.getRemoteUploadDirectoryPath()+ System.getProperty("String_Node_Str")+ inputFile.getName());
      checkInputProcessBuilder.redirectErrorStream(true);
      try {
        checkInputRemoteJob=checkInputProcessBuilder.start(IRemoteProcessBuilder.FORWARD_X11);
      }
 catch (      IOException e) {
        logger.error(getClass().getName() + "String_Node_Str",e);
        String errorMessage="String_Node_Str";
        throwErrorMessage("String_Node_Str","String_Node_Str",errorMessage,errorMessage);
        status=FormStatus.InfoError;
        return status;
      }
      while (!checkInputRemoteJob.isCompleted()) {
        try {
          Thread.currentThread();
          Thread.sleep(1000);
        }
 catch (        InterruptedException e) {
          logger.error(getClass().getName() + "String_Node_Str",e);
        }
      }
      inputStream=checkInputRemoteJob.getInputStream();
    }
  }
 else {
    File execFile=new File(appUri);
    String[] checkInputCmd={"String_Node_Str","String_Node_Str",execFile.getAbsolutePath() + "String_Node_Str" + project.getLocation().toOSString()+ System.getProperty("String_Node_Str")+ inputFile.getName()+ "String_Node_Str"};
    try {
      ProcessBuilder builder=new ProcessBuilder(checkInputCmd).directory(new File(project.getLocation().toOSString()));
      builder.redirectErrorStream(true);
      Process checkInputProcess=builder.start();
      inputStream=checkInputProcess.getInputStream();
    }
 catch (    IOException e) {
      e.printStackTrace();
      logger.error(getClass().getName() + "String_Node_Str",e);
      status=FormStatus.InfoError;
      return status;
    }
  }
  try {
    BufferedReader input=new BufferedReader(new InputStreamReader(inputStream));
    while ((line=input.readLine()) != null) {
      checkInputString+=line + "String_Node_Str";
    }
    input.close();
    if (checkInputString.contains("String_Node_Str")) {
      String errorString=checkInputString.substring(checkInputString.indexOf("String_Node_Str"),checkInputString.indexOf("String_Node_Str"));
      errorString="String_Node_Str" + errorString.trim() + "String_Node_Str";
      throwErrorMessage("String_Node_Str","String_Node_Str",errorString,"String_Node_Str" + checkInputString.trim());
      status=FormStatus.InfoError;
      return status;
    }
  }
 catch (  IOException e) {
    logger.error(getClass().getName() + "String_Node_Str",e);
    status=FormStatus.InfoError;
    return status;
  }
  return status;
}