nus-yam/ex-repair huggingface dataset:
Program: 38058
Project: 38058
Buggy source:
@Override public boolean update(CalibratedAxis other){
  if (other instanceof ExponentialRecoveryAxis) {
    ExponentialRecoveryAxis axis=(ExponentialRecoveryAxis)other;
    setType(axis.type());
    setUnit(axis.unit());
    setA(axis.a());
    setB(axis.b());
    setC(axis.c());
    setD(axis.d());
  }
  return false;
}

Fixed version (ground truth):
@Override public boolean update(CalibratedAxis other){
  if (other instanceof ExponentialRecoveryAxis) {
    ExponentialRecoveryAxis axis=(ExponentialRecoveryAxis)other;
    setType(axis.type());
    setUnit(axis.unit());
    setA(axis.a());
    setB(axis.b());
    setC(axis.c());
    setD(axis.d());
    return true;
  }
  return false;
}
Program: 38059
Project: 38059
Buggy source:
@Test public void test2(){
  RealInterval interval=new FinalRealInterval(new double[]{7,13});
  double[] extents=IntervalUtils.getExtents(interval);
  assertEquals(6,extents[0],0);
  assertEquals(12,extents[1],0);
}

Fixed version (ground truth):
@Test public void test2(){
  final RealInterval interval=new FinalRealInterval(new double[]{0,0},new double[]{7,13});
  final double[] extents=IntervalUtils.getExtents(interval);
  assertEquals(7,extents[0],0);
  assertEquals(13,extents[1],0);
}
Program: 38060
Project: 38060
Buggy source:
@Test public void test3(){
  DefaultCalibratedRealInterval interval=new DefaultCalibratedRealInterval(new double[]{10,20});
  DefaultCalibratedAxis axis0=new DefaultCalibratedAxis(Axes.X,null,7);
  DefaultCalibratedAxis axis1=new DefaultCalibratedAxis(Axes.Y,null,9);
  interval.setAxis(axis0,0);
  interval.setAxis(axis1,1);
  double[] extents=IntervalUtils.getCalibratedExtents(interval);
  assertEquals(9 * axis0.calibration(),extents[0],0);
  assertEquals(19 * axis1.calibration(),extents[1],0);
}

Fixed version (ground truth):
@Test public void test3(){
  final DefaultCalibratedRealInterval interval=new DefaultCalibratedRealInterval(new double[]{10,20});
  final DefaultCalibratedAxis axis0=new DefaultCalibratedAxis(Axes.X,null,7);
  final DefaultCalibratedAxis axis1=new DefaultCalibratedAxis(Axes.Y,null,9);
  interval.setAxis(axis0,0);
  interval.setAxis(axis1,1);
  final double[] extents=IntervalUtils.getCalibratedExtents(interval);
  assertEquals(9 * axis0.calibration(),extents[0],0);
  assertEquals(19 * axis1.calibration(),extents[1],0);
}
Program: 38061
Project: 38061
Buggy source:
@Test public void test1(){
  Interval interval=new FinalInterval(new long[]{10,20});
  long[] dims=IntervalUtils.getDims(interval);
  assertEquals(10,dims[0]);
  assertEquals(20,dims[1]);
}

Fixed version (ground truth):
@Test public void test1(){
  final Interval interval=new FinalInterval(new long[]{10,20});
  final long[] dims=IntervalUtils.getDims(interval);
  assertEquals(10,dims[0]);
  assertEquals(20,dims[1]);
}
Program: 38062
Project: 38062
Buggy source:
@Override public View onCreateView(LayoutInflater inflater,ViewGroup parent,Bundle savedInstanceState){
  View v=inflater.inflate(R.layout.location_fragment,parent,false);
  LinearLayout firstPage=(LinearLayout)v.findViewById(R.id.onePage);
  LinearLayout.LayoutParams params=(LinearLayout.LayoutParams)firstPage.getLayoutParams();
  params.height=mForecastApplication.getHeight();
  firstPage.setLayoutParams(params);
  TextView textView=(TextView)v.findViewById(R.id.location);
  textView.setText(mLocation.getName());
  Weather weather=mLocation.getWeather();
  textView=(TextView)v.findViewById(R.id.temp);
  textView.setText("String_Node_Str" + Math.round(weather.getTemperature()));
  textView=(TextView)v.findViewById(R.id.summary);
  textView.setText("String_Node_Str" + weather.getSummary());
  GraphView.GraphViewData[] points;
  int length=24;
  points=new GraphView.GraphViewData[length];
  for (int x=0; x < length; x++) {
    int time=weather.getHourly().get(x).getTime();
    double temp=weather.getHourly().get(x).getTemperature();
    points[x]=new GraphView.GraphViewData(time,temp);
  }
  GraphView graphView=new LineGraphView(mContext,"String_Node_Str");
  graphView.getGraphViewStyle().setNumHorizontalLabels(1);
  graphView.getGraphViewStyle().setGridColor(Color.TRANSPARENT);
  graphView.getGraphViewStyle().setNumVerticalLabels(5);
  graphView.addSeries(new GraphViewSeries(points));
  LinearLayout layout=(LinearLayout)v.findViewById(R.id.graph);
  layout.addView(graphView);
  return v;
}

Fixed version (ground truth):
@Override public View onCreateView(LayoutInflater inflater,ViewGroup parent,Bundle savedInstanceState){
  View v=inflater.inflate(R.layout.location_fragment,parent,false);
  LinearLayout firstPage=(LinearLayout)v.findViewById(R.id.onePage);
  LinearLayout.LayoutParams params=(LinearLayout.LayoutParams)firstPage.getLayoutParams();
  params.height=mForecastApplication.getHeight();
  firstPage.setLayoutParams(params);
  TextView textView=(TextView)v.findViewById(R.id.location);
  textView.setText(mLocation.getName());
  Weather weather=mLocation.getWeather();
  textView=(TextView)v.findViewById(R.id.temp);
  textView.setText(Integer.toString((int)Math.round(weather.getTemperature())) + (char)0x00B0);
  textView=(TextView)v.findViewById(R.id.summary);
  textView.setText(weather.getSummary());
  GraphView.GraphViewData[] points;
  int length=24;
  points=new GraphView.GraphViewData[length];
  for (int x=0; x < length; x++) {
    int time=weather.getHourly().get(x).getTime();
    double temp=weather.getHourly().get(x).getTemperature();
    points[x]=new GraphView.GraphViewData(time,temp);
  }
  GraphView graphView=new LineGraphView(mContext,"String_Node_Str");
  graphView.getGraphViewStyle().setNumHorizontalLabels(1);
  graphView.getGraphViewStyle().setGridColor(Color.TRANSPARENT);
  graphView.getGraphViewStyle().setNumVerticalLabels(5);
  graphView.addSeries(new GraphViewSeries(points));
  LinearLayout layout=(LinearLayout)v.findViewById(R.id.graph);
  layout.addView(graphView);
  return v;
}
Program: 38063
Project: 38063
Buggy source:
@Override public void onCreate(Bundle savedInstanceState){
  super.onCreate(savedInstanceState);
  setContentView(R.layout.locations);
  mContext=this;
  DatabaseHandler databaseHandler=new DatabaseHandler(this);
  List<Location> locations=databaseHandler.getAllLocations();
  List<String> locationsArry=new ArrayList<String>();
  for (int x=0; x < locations.size(); x++) {
    locationsArry.add(locations.get(0).getName());
    setListAdapter(new ArrayAdapter<String>(this,android.R.layout.simple_list_item_1,locationsArry));
  }
  addLocationEditText=(EditText)findViewById(R.id.add_location);
  setupListeners();
}

Fixed version (ground truth):
@Override public void onCreate(Bundle savedInstanceState){
  super.onCreate(savedInstanceState);
  setContentView(R.layout.locations);
  mContext=this;
  DatabaseHandler databaseHandler=new DatabaseHandler(this);
  List<Location> locations=databaseHandler.getAllLocations();
  List<String> locationsArry=new ArrayList<String>();
  for (int x=0; x < locations.size(); x++) {
    locationsArry.add(locations.get(x).getName());
    setListAdapter(new ArrayAdapter<String>(this,android.R.layout.simple_list_item_1,locationsArry));
  }
  addLocationEditText=(EditText)findViewById(R.id.add_location);
  setupListeners();
}
Program: 38065
Project: 38065
Buggy source:
/** 
 * The all() method is a "mixin" that allows for a list of objects to be returned. By passing in a class and path url, the list of objects is abstracted away along with the http requests.  A JSON object will be returned with 
 * @param path -- url path for the list resource
 * @param params -- url query parameters
 * @param clazz -- class of the resource object to be returned
 * @param apiKey -- optional parameter if you want to override apiKey
 * @return <Resource>Collection of type class that you pass in
 * @throws APIException
 * @throws AuthenticationException
 * @throws InvalidRequestException
 * @throws APIConnectionException
 */
protected static <T>T all(String path,Map<String,Object> params,Class<T> clazz,Map<String,String> keys) throws APIException, AuthenticationException, InvalidRequestException, APIConnectionException {
  System.out.println(path);
  KloudlessResponse response=request(RequestMethod.GET,path,params,keys);
  int rCode=response.responseCode;
  String rBody=response.responseBody;
  if (rCode < 200 || rCode >= 300) {
    handleAPIError(rBody,rCode);
  }
  return GSON.fromJson(rBody,clazz);
}

Fixed version (ground truth):
/** 
 * The all() method is a "mixin" that allows for a list of objects to be returned. By passing in a class and path url, the list of objects is abstracted away along with the http requests.  A JSON object will be returned with 
 * @param path -- url path for the list resource
 * @param params -- url query parameters
 * @param clazz -- class of the resource object to be returned
 * @param apiKey -- optional parameter if you want to override apiKey
 * @return <Resource>Collection of type class that you pass in
 * @throws APIException
 * @throws AuthenticationException
 * @throws InvalidRequestException
 * @throws APIConnectionException
 */
protected static <T>T all(String path,Map<String,Object> params,Class<T> clazz,Map<String,String> keys) throws APIException, AuthenticationException, InvalidRequestException, APIConnectionException {
  KloudlessResponse response=request(RequestMethod.GET,path,params,keys);
  int rCode=response.responseCode;
  String rBody=response.responseBody;
  if (rCode < 200 || rCode >= 300) {
    handleAPIError(rBody,rCode);
  }
  return GSON.fromJson(rBody,clazz);
}
Program: 38068
Project: 38068
Buggy source:
/** 
 * Erzeugt einen Text, der die Vertretung beschreibt (ohne die Art und die Stunde).
 */
public String toString(){
  String string="String_Node_Str";
  if (containsInformation(subject)) {
    string+=subject;
    if (containsInformation(teacher))     string+="String_Node_Str" + teacher + "String_Node_Str";
  }
 else   if (containsInformation(teacher))   string+=teacher;
  if (containsInformation(previousSubject) && !(previousSubject.equals(subject) && (previousTeacher != null && previousTeacher.equals(teacher) || (previousTeacher == null && teacher == null)))) {
    if (containsInformation(subject))     string+="String_Node_Str" + previousSubject;
 else     string+=previousSubject;
    if (containsInformation(previousTeacher))     string+="String_Node_Str" + previousTeacher + "String_Node_Str";
  }
 else   if (!containsInformation(previousSubject) && containsInformation(previousTeacher)) {
    if (containsInformation(subject) || containsInformation(teacher))     string+="String_Node_Str" + previousTeacher;
 else     string+=previousTeacher;
  }
  if (containsInformation(room))   string+="String_Node_Str" + room;
  if (containsInformation(previousRoom) && !previousRoom.equals(room)) {
    if (containsInformation(room))     string+="String_Node_Str" + previousRoom;
 else     string+="String_Node_Str" + previousRoom;
  }
  if (containsInformation(desc)) {
    if (!string.equals("String_Node_Str"))     string+="String_Node_Str";
    string+=desc;
  }
  return string;
}

Fixed version (ground truth):
/** 
 * Erzeugt einen Text, der die Vertretung beschreibt (ohne die Art und die Stunde).
 */
public String toString(){
  String string="String_Node_Str";
  if (containsInformation(subject)) {
    string+=subject;
    if (containsInformation(teacher))     string+="String_Node_Str" + teacher + "String_Node_Str";
  }
 else   if (containsInformation(teacher))   string+=teacher;
  if (containsInformation(previousSubject) && !(previousSubject.equals(subject) && (previousTeacher != null && previousTeacher.equals(teacher) || (previousTeacher == null && teacher == null)))) {
    if (containsInformation(subject) || containsInformation(teacher))     string+="String_Node_Str" + previousSubject;
 else     string+=previousSubject;
    if (containsInformation(previousTeacher))     string+="String_Node_Str" + previousTeacher + "String_Node_Str";
  }
 else   if (!containsInformation(previousSubject) && containsInformation(previousTeacher)) {
    if (containsInformation(subject) || containsInformation(teacher))     string+="String_Node_Str" + previousTeacher;
 else     string+=previousTeacher;
  }
  if (containsInformation(room))   string+="String_Node_Str" + room;
  if (containsInformation(previousRoom) && !previousRoom.equals(room)) {
    if (containsInformation(room))     string+="String_Node_Str" + previousRoom;
 else     string+="String_Node_Str" + previousRoom;
  }
  if (containsInformation(desc)) {
    if (!string.equals("String_Node_Str"))     string+="String_Node_Str";
    string+=desc;
  }
  return string;
}
Program: 38069
Project: 38069
Buggy source:
private void insertDeviceInfo(String deviceInfo,String klasse,String schoolId,String login,String password,String registration) throws IOException {
  String url=BASE_URL + "String_Node_Str" + registration+ "String_Node_Str"+ klasse+ "String_Node_Str"+ schoolId+ "String_Node_Str"+ deviceInfo+ "String_Node_Str"+ URLEncoder.encode(login,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(password,"String_Node_Str");
  Response response=new Request(url).getResource("String_Node_Str");
  if (response.getResponseCode() == 200) {
    Log.d("String_Node_Str","String_Node_Str");
  }
}

Fixed version (ground truth):
private void insertDeviceInfo(String deviceInfo,String klasse,String schoolId,String login,String password,String registration) throws IOException {
  String url=BASE_URL + "String_Node_Str" + URLEncoder.encode(registration,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(klasse,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(schoolId,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(deviceInfo,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(login,"String_Node_Str")+ "String_Node_Str"+ URLEncoder.encode(password,"String_Node_Str");
  Response response=new Request(url).getResource("String_Node_Str");
  if (response.getResponseCode() == 200) {
    Log.d("String_Node_Str","String_Node_Str");
  }
}
Program: 38071
Project: 38071
Buggy source:
public void refresh(){
  if (ready && v != null && getView() != null) {
    listadapter.clear();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      for (      String message : tag.getNachrichten()) {
        listadapter.addItem(Html.fromHtml(message));
      }
      if (tag.getNachrichten().size() == 0)       listadapter.addItem(getResources().getString(R.string.no_info));
    }
    for (    AdditionalInfo info : v.getAdditionalInfos()) {
      listadapter.addSeparatorItem(info.getTitle());
      listadapter.addItem(info.getText());
    }
    progress(false);
  }
}

Fixed version (ground truth):
public void refresh(){
  progress(false);
  if (ready && v != null && getView() != null) {
    listadapter.clear();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      for (      String message : tag.getNachrichten()) {
        listadapter.addItem(Html.fromHtml(message));
      }
      if (tag.getNachrichten().size() == 0)       listadapter.addItem(getResources().getString(R.string.no_info));
    }
    for (    AdditionalInfo info : v.getAdditionalInfos()) {
      listadapter.addSeparatorItem(info.getTitle());
      listadapter.addItem(info.getText());
    }
    progress(false);
  }
}
Program: 38072
Project: 38072
Buggy source:
@Override public void onViewCreated(View view,Bundle savedInstanceState){
  progress(showProgress);
  ready=true;
  refresh();
  super.onViewCreated(view,savedInstanceState);
}

Fixed version (ground truth):
@Override public void onViewCreated(View view,Bundle savedInstanceState){
  progress(showProgress);
  ready=true;
  if (mCallback.getVertretungsplan() != null)   setVertretungsplan(mCallback.getVertretungsplan());
  super.onViewCreated(view,savedInstanceState);
}
Program: 38073
Project: 38073
Buggy source:
public void refresh(){
  if (ready && v != null) {
    listadapter.clear();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      for (      String message : tag.getNachrichten()) {
        listadapter.addItem(Html.fromHtml(message));
      }
      if (tag.getNachrichten().size() == 0)       listadapter.addItem(getResources().getString(R.string.no_info));
    }
    for (    AdditionalInfo info : v.getAdditionalInfos()) {
      listadapter.addSeparatorItem(info.getTitle());
      listadapter.addItem(info.getText());
    }
    progress(false);
  }
}

Fixed version (ground truth):
public void refresh(){
  if (ready && v != null && getView() != null) {
    listadapter.clear();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      for (      String message : tag.getNachrichten()) {
        listadapter.addItem(Html.fromHtml(message));
      }
      if (tag.getNachrichten().size() == 0)       listadapter.addItem(getResources().getString(R.string.no_info));
    }
    for (    AdditionalInfo info : v.getAdditionalInfos()) {
      listadapter.addSeparatorItem(info.getTitle());
      listadapter.addItem(info.getText());
    }
    progress(false);
  }
}
Program: 38074
Project: 38074
Buggy source:
public void refresh(){
  if (ready && v != null) {
    txtStand.setText(v.getTage().get(0).getStand());
    listadapter.clear();
    klasse=(String)klassen.getSelectedItem();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      if (tag.getKlassen().get(klasse) != null) {
        if (tag.getKlassen().get(klasse).getVertretung().size() > 0) {
          for (          Vertretung item : tag.getKlassen().get(klasse).getVertretung()) {
            listadapter.addItem(item);
          }
        }
 else {
          listadapter.addTextItem(getResources().getString(R.string.no_info));
        }
      }
 else {
        listadapter.addTextItem(getResources().getString(R.string.no_info));
      }
    }
  }
}

Fixed version (ground truth):
public void refresh(){
  if (ready && v != null && getView() != null) {
    txtStand.setText(v.getTage().get(0).getStand());
    listadapter.clear();
    klasse=(String)klassen.getSelectedItem();
    for (    VertretungsplanTag tag : v.getTage()) {
      listadapter.addSeparatorItem(tag.getDatum());
      if (tag.getKlassen().get(klasse) != null) {
        if (tag.getKlassen().get(klasse).getVertretung().size() > 0) {
          for (          Vertretung item : tag.getKlassen().get(klasse).getVertretung()) {
            listadapter.addItem(item);
          }
        }
 else {
          listadapter.addTextItem(getResources().getString(R.string.no_info));
        }
      }
 else {
        listadapter.addTextItem(getResources().getString(R.string.no_info));
      }
    }
  }
}
Program: 38075
Project: 38075
Buggy source:
@Override protected void onPostExecute(List<String> result){
  if (result != null)   settings.edit().putString("String_Node_Str",new Gson().toJson(result)).commit();
 else   result=new Gson().fromJson(settings.getString("String_Node_Str",null),new TypeToken<List<String>>(){
  }
.getType());
  klasse=settings.getString("String_Node_Str","String_Node_Str");
  klassen.setAdapter(new ArrayAdapter<String>(getActivity(),android.R.layout.simple_spinner_dropdown_item,result));
  for (int i=0; i < klassen.getAdapter().getCount(); i++) {
    if (klassen.getAdapter().getItem(i).toString().equals(klasse)) {
      klassen.setSelection(i);
      break;
    }
  }
}

Fixed version (ground truth):
@Override protected void onPostExecute(List<String> result){
  if (getActivity() == null)   return;
  if (result != null)   settings.edit().putString("String_Node_Str",new Gson().toJson(result)).commit();
 else   result=new Gson().fromJson(settings.getString("String_Node_Str",null),new TypeToken<List<String>>(){
  }
.getType());
  klasse=settings.getString("String_Node_Str","String_Node_Str");
  klassen.setAdapter(new ArrayAdapter<String>(getActivity(),android.R.layout.simple_spinner_dropdown_item,result));
  for (int i=0; i < klassen.getAdapter().getCount(); i++) {
    if (klassen.getAdapter().getItem(i).toString().equals(klasse)) {
      klassen.setSelection(i);
      break;
    }
  }
}
Program: 38076
Project: 38076
Buggy source:
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length == 1) {
    String username=event.getArgs()[0];
    if (!username.matches("String_Node_Str")) {
      event.respondWithPing(Colors.RED + "String_Node_Str");
      return true;
    }
    String uuid="String_Node_Str";
    boolean isValid;
    boolean hasPaid;
    try {
      UserProfile[] profiles=getProfiles(username);
      if (profiles.length > 0) {
        uuid=profiles[0].id;
      }
      isValid=getPageContents("String_Node_Str" + username).equalsIgnoreCase("String_Node_Str");
      hasPaid=getPageContents("String_Node_Str" + username).equalsIgnoreCase("String_Node_Str");
    }
 catch (    UnirestException e) {
      throw new GenericUrlConnectionException("String_Node_Str" + username + "String_Node_Str",e);
    }
    String valid=isValid ? Colors.RED + "String_Node_Str" + Colors.NORMAL+ "String_Node_Str" : Colors.GREEN + "String_Node_Str" + Colors.NORMAL+ "String_Node_Str";
    String paid=hasPaid ? "String_Node_Str" + Colors.GREEN + "String_Node_Str"+ Colors.NORMAL : Colors.RED + "String_Node_Str" + Colors.NORMAL;
    event.respond("String_Node_Str" + valid + "String_Node_Str"+ paid+ "String_Node_Str",username,uuid);
    return true;
  }
  return false;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length == 1) {
    String username=event.getArgs()[0];
    if (!username.matches("String_Node_Str")) {
      event.respondWithPing(Colors.RED + "String_Node_Str");
      return true;
    }
    if (username.length() > 16) {
      event.respondWithPing(Colors.RED + "String_Node_Str");
      return true;
    }
    if (username.length() < 2) {
      event.respondWithPing(Colors.RED + "String_Node_Str");
      return true;
    }
    try {
      UserProfile[] profiles=getProfiles(username);
      if (profiles.length > 0) {
        String uuid=profiles[0].id;
        boolean hasPaid=getPageContents("String_Node_Str" + username).equalsIgnoreCase("String_Node_Str");
        String paid=hasPaid ? "String_Node_Str" + Colors.GREEN + "String_Node_Str"+ Colors.NORMAL : Colors.RED + "String_Node_Str" + Colors.NORMAL;
        event.respond("String_Node_Str" + Colors.GREEN + "String_Node_Str"+ Colors.NORMAL+ "String_Node_Str"+ paid+ "String_Node_Str",username,uuid);
      }
 else {
        event.respond("String_Node_Str" + Colors.RED + "String_Node_Str",username);
      }
    }
 catch (    UnirestException e) {
      throw new GenericUrlConnectionException("String_Node_Str" + username + "String_Node_Str",e);
    }
    return true;
  }
  return false;
}
Program: 38078
Project: 38078
Buggy source:
@Override public void publish(LogRecord record){
  if (Nexus.getInstance() == null || this.channelName == null) {
    return;
  }
  if (Nexus.getInstance().getChannel(this.channelName) == null) {
    return;
  }
  if (!isLoggable(record)) {
    return;
  }
  String[] parts=record.getMessage().split("String_Node_Str");
  for (int i=0; i < parts.length; i++) {
    String part=parts[i];
    Iterator<User> iter=Nexus.getInstance().getChannel(this.channelName).getUsers().iterator();
    while (iter.hasNext()) {
      User u=iter.next();
      part=part.replace(u.getNick(),StringUtil.removePing(u.getNick())).replace(u.getNick().toLowerCase(),StringUtil.removePing(u.getNick().toLowerCase()));
    }
    parts[i]=part;
  }
  String message=StringUtil.join(parts,"String_Node_Str");
  for (  String exc : EXCLUSIONS) {
    if (message.toLowerCase().contains(exc.toLowerCase())) {
      return;
    }
  }
  Nexus.getInstance().send(this.channelName,message);
}

Fixed version (ground truth):
@Override public void publish(LogRecord record){
  if (Nexus.getInstance() == null || this.channelName == null) {
    return;
  }
  if (Nexus.getInstance().getChannel(this.channelName) == null) {
    return;
  }
  if (!isLoggable(record)) {
    return;
  }
  String[] parts=record.getMessage().split("String_Node_Str");
  for (int i=0; i < parts.length; i++) {
    String part=parts[i];
    Iterator<User> iter=Nexus.getInstance().getChannel(this.channelName).getUsers().iterator();
    while (iter.hasNext()) {
      User u=iter.next();
      part=part.replace(u.getNick(),StringUtil.removePing(u.getNick())).replace(u.getNick().toLowerCase(),StringUtil.removePing(u.getNick().toLowerCase()));
    }
    parts[i]=part;
  }
  String message=StringUtil.join(parts,"String_Node_Str");
  for (  String exc : EXCLUSIONS) {
    if (message.toLowerCase().contains(exc.toLowerCase())) {
      return;
    }
  }
  Nexus.getInstance().sendIRC().message(this.channelName,message);
}
Program: 38079
Project: 38079
Buggy source:
@Override public void run(){
  while (running) {
    try {
      reader=new jline.console.ConsoleReader();
      reader.addCompleter(new FileNameCompleter());
      reader.setPrompt("String_Node_Str");
      String line;
      PrintWriter out=new PrintWriter(System.out);
      while ((line=reader.readLine("String_Node_Str")) != null) {
        if (Nexus.getInstance() != null) {
          if (line.equalsIgnoreCase("String_Node_Str") || line.equalsIgnoreCase("String_Node_Str") || line.equalsIgnoreCase("String_Node_Str")|| line.equalsIgnoreCase("String_Node_Str")) {
            Nexus.getInstance().endProcess();
          }
 else           if (line.toLowerCase().startsWith("String_Node_Str")) {
            if (line.contains("String_Node_Str")) {
              String[] parts=line.split("String_Node_Str");
              String channel=parts[1];
              Nexus.LOGGER.info("String_Node_Str" + channel);
              Nexus.getInstance().sendRaw().rawLineNow("String_Node_Str" + channel);
            }
 else {
              Nexus.LOGGER.info("String_Node_Str");
            }
          }
        }
        out.flush();
      }
    }
 catch (    IOException e) {
      e.printStackTrace();
    }
 finally {
      if (reader != null) {
        try {
          reader.getTerminal().restore();
        }
 catch (        Exception e) {
          e.printStackTrace();
        }
      }
    }
  }
}

Fixed version (ground truth):
@Override public void run(){
  while (running) {
    try {
      reader=new jline.console.ConsoleReader();
      reader.addCompleter(new FileNameCompleter());
      reader.setPrompt("String_Node_Str");
      String line;
      PrintWriter out=new PrintWriter(System.out);
      while ((line=reader.readLine("String_Node_Str")) != null) {
        if (Nexus.getInstance() != null) {
          if (line.equalsIgnoreCase("String_Node_Str") || line.equalsIgnoreCase("String_Node_Str") || line.equalsIgnoreCase("String_Node_Str")|| line.equalsIgnoreCase("String_Node_Str")) {
            Nexus.getInstance().endProcess();
          }
 else           if (line.toLowerCase().startsWith("String_Node_Str")) {
            if (line.contains("String_Node_Str")) {
              String[] parts=line.split("String_Node_Str");
              String channel=parts[1];
              Nexus.LOGGER.info("String_Node_Str" + channel);
              Nexus.getInstance().sendIRC().joinChannel(channel);
            }
 else {
              Nexus.LOGGER.info("String_Node_Str");
            }
          }
        }
        out.flush();
      }
    }
 catch (    IOException e) {
      e.printStackTrace();
    }
 finally {
      if (reader != null) {
        try {
          reader.getTerminal().restore();
        }
 catch (        Exception e) {
          e.printStackTrace();
        }
      }
    }
  }
}
Program: 38080
Project: 38080
Buggy source:
private void prepare(){
  Unirest.setTimeouts(10000,10000);
  Unirest.setDefaultHeader("String_Node_Str",getConfig().get("String_Node_Str","String_Node_Str"));
  this.registerLogger();
  LOGGER.info("String_Node_Str");
  commandManager=new CommandManager();
  commandManager.registerDefaults();
  LOGGER.info("String_Node_Str");
  responseManager=new ResponseManager();
  responseManager.load();
  if (!this.config.getJenkinsUrl().isEmpty()) {
    LOGGER.info("String_Node_Str");
    this.jenkins=new Jenkins();
  }
  LOGGER.info("String_Node_Str");
  this.github=new GitHub();
  RemindCommand remindCommand=this.getCommandManager().getModuleOfType(RemindCommand.class);
  if (remindCommand != null) {
    LOGGER.info("String_Node_Str");
    remindCommand.loadReminders();
  }
  LOGGER.info("String_Node_Str");
  LOGGER.info("String_Node_Str");
  this.prepareConsoleReader();
  LOGGER.info("String_Node_Str");
  LOGGER.info("String_Node_Str" + config.getServer() + "String_Node_Str"+ config.getChannels().size()+ "String_Node_Str");
  try {
    this.startBot();
  }
 catch (  IrcException|IOException ignored) {
  }
}

Fixed version (ground truth):
private void prepare(){
  Unirest.setTimeouts(10000,10000);
  Unirest.setDefaultHeader("String_Node_Str",getConfig().get("String_Node_Str","String_Node_Str"));
  this.registerLogger();
  LOGGER.info("String_Node_Str");
  commandManager=new CommandManager();
  commandManager.registerDefaults();
  LOGGER.info("String_Node_Str");
  responseManager=new ResponseManager();
  responseManager.load();
  if (!this.config.getJenkinsUrl().isEmpty()) {
    LOGGER.info("String_Node_Str");
    this.jenkins=new Jenkins();
  }
  LOGGER.info("String_Node_Str");
  this.github=new GitHub();
  RemindCommand remindCommand=this.getCommandManager().getModuleOfType(RemindCommand.class);
  if (remindCommand != null) {
    LOGGER.info("String_Node_Str");
    remindCommand.loadReminders();
  }
  LOGGER.info("String_Node_Str");
  LOGGER.info("String_Node_Str");
  this.prepareConsoleReader();
  ColorUtil.validColours();
  LOGGER.info("String_Node_Str");
  LOGGER.info("String_Node_Str" + config.getServer() + "String_Node_Str"+ config.getChannels().size()+ "String_Node_Str");
  try {
    this.startBot();
  }
 catch (  IrcException|IOException ignored) {
  }
}
Program: 38081
Project: 38081
Buggy source:
public static void endProcess(){
  if (INSTANCE != null) {
    try {
      LOGGER.info("String_Node_Str");
      INSTANCE.saveAll();
      try {
        if (Jenkins.getJenkins() != null && Jenkins.getJenkins().TASK != null) {
          Jenkins.getJenkins().TASK.cancel();
        }
        if (GitHub.getGitHub().TASK != null) {
          GitHub.getGitHub().TASK.cancel();
        }
      }
 catch (      Exception e) {
        e.printStackTrace();
      }
      try {
        Unirest.shutdown();
      }
 catch (      Exception e) {
        LOGGER.severe("String_Node_Str");
        e.printStackTrace();
      }
      LOGGER.info("String_Node_Str");
      TimeoutUtil.timeout(new Thread(){
        @Override public void run(){
          while (INSTANCE.sendRaw().getOutgoingQueueSize() > 0)           ;
        }
      }
,TimeUtil.convert(5,'s'));
      INSTANCE.shutdown(true);
      try {
        INSTANCE.consoleReader.reader.getTerminal().restore();
      }
 catch (      Exception e) {
        e.printStackTrace();
      }
      INSTANCE.consoleReader.setRunning(false);
      INSTANCE.channelLogHandler.close();
      INSTANCE=null;
      LOGGER.info("String_Node_Str");
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
 finally {
      System.exit(-1);
      LOGGER.info("String_Node_Str");
    }
  }
}

Fixed version (ground truth):
public static void endProcess(){
  if (INSTANCE != null) {
    try {
      LOGGER.info("String_Node_Str");
      INSTANCE.channelLogHandler.close();
      INSTANCE.saveAll();
      try {
        if (Jenkins.getJenkins() != null && Jenkins.getJenkins().TASK != null) {
          Jenkins.getJenkins().TASK.cancel();
        }
        if (GitHub.getGitHub().TASK != null) {
          GitHub.getGitHub().TASK.cancel();
        }
      }
 catch (      Exception e) {
        e.printStackTrace();
      }
      try {
        Unirest.shutdown();
      }
 catch (      Exception e) {
        LOGGER.severe("String_Node_Str");
        e.printStackTrace();
      }
      try {
        INSTANCE.consoleReader.reader.getTerminal().restore();
      }
 catch (      Exception e) {
        e.printStackTrace();
      }
      INSTANCE.consoleReader.setRunning(false);
      INSTANCE.shutdown(true);
      INSTANCE=null;
      LOGGER.info("String_Node_Str");
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
 finally {
      System.exit(-1);
    }
  }
}
Program: 38082
Project: 38082
Buggy source:
@Override public void run(){
  while (INSTANCE.sendRaw().getOutgoingQueueSize() > 0)   ;
}

Fixed version (ground truth):
@Override public void run(){
  for (  String channel : getConfig().getChannels()) {
    if (getChannel(channel) == null) {
      sendIRC().joinChannel(channel);
    }
  }
}
Program: 38083
Project: 38083
Buggy source:
public void onConnect(){
  registerChannelLogger();
  for (  String channel : getConfig().getChannels()) {
    if (getChannel(channel) == null) {
      sendRaw().rawLineNow("String_Node_Str" + channel);
    }
  }
  if (!getConfig().getStartupMessage().isEmpty()) {
    send(getConfig().getAdminChannel(),getConfig().getStartupMessage());
  }
}

Fixed version (ground truth):
public void onConnect(){
  registerChannelLogger();
  new Thread(new Runnable(){
    @Override public void run(){
      for (      String channel : getConfig().getChannels()) {
        if (getChannel(channel) == null) {
          sendIRC().joinChannel(channel);
        }
      }
    }
  }
).start();
  if (!getConfig().getStartupMessage().isEmpty()) {
    sendIRC().message(getConfig().getAdminChannel(),getConfig().getStartupMessage());
  }
}
Program: 38085
Project: 38085
Buggy source:
protected boolean checkPerm(Channel channel,User sender){
  if (Nexus.getInstance().isAdmin(sender)) {
    return true;
  }
  if (adminOnly()) {
    Nexus.getInstance().send(sender.getNick(),Colors.RED + "String_Node_Str");
    return false;
  }
  return true;
}

Fixed version (ground truth):
protected boolean checkPerm(Channel channel,User sender){
  if (Nexus.getInstance().isAdmin(sender)) {
    return true;
  }
  if (adminOnly()) {
    Nexus.getInstance().sendIRC().message(sender.getNick(),Colors.RED + "String_Node_Str");
    return false;
  }
  return true;
}
Program: 38086
Project: 38086
Buggy source:
public CommandPerformEvent(Channel channel,User sender,String command,String... args){
  if (channel == null) {
    this.sender=sender;
    this.command=command;
    this.args=args;
    this.inPrivateMessage=true;
  }
 else {
    this.channel=channel;
    this.sender=sender;
    this.command=command;
    this.args=args;
  }
}

Fixed version (ground truth):
public CommandPerformEvent(Channel channel,User sender,String command,String... args){
  if (channel == null) {
    this.inPrivateMessage=true;
  }
 else {
    this.channel=channel;
  }
  this.sender=sender;
  this.command=command;
  this.args=args;
}
Program: 38087
Project: 38087
Buggy source:
public void respond(String message,boolean forcePrivateMessage){
  if (this.inPrivateMessage || forcePrivateMessage) {
    Nexus.getInstance().send(sender.getNick(),message);
  }
 else {
    Nexus.getInstance().send(channel.getName(),message);
  }
}

Fixed version (ground truth):
public void respond(String message,boolean forcePrivateMessage){
  if (this.inPrivateMessage || forcePrivateMessage) {
    Nexus.getInstance().sendIRC().message(sender.getNick(),message);
  }
 else {
    Nexus.getInstance().sendIRC().message(channel.getName(),message);
  }
}
Program: 38088
Project: 38088
Buggy source:
public String getActionText(String... args){
  Validate.notNull(args);
  if (args.length < 1) {
    throw new InvalidInputException("String_Node_Str");
  }
  String sentenceList=StringUtil.buildSentenceList(args[0].split("String_Node_Str"));
  String additional="String_Node_Str";
  if (args.length > 1) {
    additional+=StringUtil.join(Arrays.copyOfRange(args,1,args.length),"String_Node_Str");
  }
  return verb + (isOverriden() ? "String_Node_Str" : "String_Node_Str") + sentenceList+ additional;
}

Fixed version (ground truth):
public String getActionText(String... args){
  Validate.notNull(args);
  if (args.length < 1) {
    throw new InvalidInputException("String_Node_Str");
  }
  String sentenceList=StringUtil.buildSentenceList(args[0].split("String_Node_Str"));
  String additional="String_Node_Str";
  if (args.length > 1) {
    additional+=StringUtil.join(Arrays.copyOfRange(args,1,args.length),"String_Node_Str");
  }
  return verb + (isOverriden() ? "String_Node_Str" : "String_Node_Str") + sentenceList+ prefix+ additional;
}
Program: 38089
Project: 38089
Buggy source:
public WhipCommand(){
  this.setVerb("String_Node_Str");
}

Fixed version (ground truth):
public WhipCommand(){
  this.setVerb("String_Node_Str");
  this.setPrefix("String_Node_Str");
}
Program: 38090
Project: 38090
Buggy source:
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length != 1) {
    return false;
  }
  String channelName=event.getArgs()[0];
  if (!channelName.startsWith("String_Node_Str")) {
    channelName="String_Node_Str" + channelName;
  }
  event.respondWithPing("String_Node_Str" + channelName);
  Nexus.getInstance().sendRaw().rawLineNow("String_Node_Str" + channelName);
  return true;
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length != 1) {
    return false;
  }
  String channelName=event.getArgs()[0];
  if (!channelName.startsWith("String_Node_Str")) {
    channelName="String_Node_Str" + channelName;
  }
  event.respondWithPing("String_Node_Str" + channelName);
  Nexus.getInstance().sendIRC().joinChannel(channelName);
  return true;
}
Program: 38091
Project: 38091
Buggy source:
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length < 2) {
    return false;
  }
 else {
    String message=StringUtil.combineSplit(1,event.getArgs(),"String_Node_Str");
    Nexus.getInstance().send(event.getArgs()[0],message);
    return true;
  }
}

Fixed version (ground truth):
@Override public boolean onCommand(CommandPerformEvent event){
  if (event.getArgs().length < 2) {
    return false;
  }
 else {
    String message=StringUtil.combineSplit(1,event.getArgs(),"String_Node_Str");
    Nexus.getInstance().sendIRC().message(event.getArgs()[0],message);
    return true;
  }
}
Program: 38092
Project: 38092
Buggy source:
public String appendReplacements(CommandPerformEvent event){
  String response=ResponseFormatter.appendReplacements(this.response,event.getSender(),event.getChannel());
  Matcher matcher=Pattern.compile("String_Node_Str").matcher(response);
  while (matcher.find()) {
    int index=StringUtil.toInteger(matcher.group(1));
    response=response.replace(matcher.group(),(index >= event.getArgs().length ? matcher.group(2) : event.getArgs()[index]));
  }
  return event.getManager().format(null,response);
}

Fixed version (ground truth):
public String appendReplacements(CommandPerformEvent event){
  String response=ResponseFormatter.appendReplacements(this.response,event.getSender(),event.getChannel());
  StringBuffer buffer=new StringBuffer();
  Matcher matcher=Pattern.compile("String_Node_Str").matcher(response);
  while (matcher.find()) {
    int index=StringUtil.toInteger(matcher.group(1));
    matcher.appendReplacement(buffer,(index >= event.getArgs().length ? matcher.group(2) : event.getArgs()[index]));
  }
  matcher.appendTail(buffer);
  return event.getManager().format(null,buffer.toString());
}
Program: 38093
Project: 38093
Buggy source:
public void save(){
  PrintWriter writer=null;
  try {
    File commandsFolder=new File("String_Node_Str");
    if (!commandsFolder.exists()) {
      commandsFolder.mkdirs();
    }
    File saveFile=new File(commandsFolder,command + "String_Node_Str");
    if (saveFile.exists()) {
      saveFile.delete();
    }
    saveFile.createNewFile();
    HashMap<String,Object> valueMap=new HashMap<>();
    valueMap.put("String_Node_Str",command);
    valueMap.put("String_Node_Str",response);
    valueMap.put("String_Node_Str",needsChannel);
    valueMap.put("String_Node_Str",help);
    valueMap.put("String_Node_Str",extendedHelp);
    valueMap.put("String_Node_Str",aliases);
    valueMap.put("String_Node_Str",action);
    valueMap.put("String_Node_Str",commandResponse);
    writer=new PrintWriter(saveFile);
    Yaml yaml=new Yaml();
    writer.write(yaml.dump(valueMap));
  }
 catch (  IOException e) {
    Nexus.LOGGER.severe("String_Node_Str" + command + "String_Node_Str");
    e.printStackTrace();
  }
 finally {
    if (writer != null) {
      writer.close();
    }
  }
}

Fixed version (ground truth):
public void save(){
  PrintWriter writer=null;
  try {
    File commandsFolder=new File("String_Node_Str");
    if (!commandsFolder.exists()) {
      commandsFolder.mkdirs();
    }
    File saveFile=new File(commandsFolder,command + "String_Node_Str");
    if (saveFile.exists()) {
      saveFile.delete();
    }
    saveFile.createNewFile();
    HashMap<String,Object> valueMap=new HashMap<>();
    valueMap.put("String_Node_Str",ColorUtil.serialise(command));
    valueMap.put("String_Node_Str",ColorUtil.serialise(response));
    valueMap.put("String_Node_Str",needsChannel);
    valueMap.put("String_Node_Str",ColorUtil.serialise(help));
    valueMap.put("String_Node_Str",ColorUtil.serialise(extendedHelp));
    valueMap.put("String_Node_Str",aliases.length <= 0 ? new String[0] : ColorUtil.serialise(aliases)[0]);
    valueMap.put("String_Node_Str",action);
    valueMap.put("String_Node_Str",commandResponse);
    writer=new PrintWriter(saveFile);
    Yaml yaml=new Yaml();
    writer.write(yaml.dump(valueMap));
  }
 catch (  IOException e) {
    Nexus.LOGGER.severe("String_Node_Str" + command + "String_Node_Str");
    e.printStackTrace();
  }
 finally {
    if (writer != null) {
      writer.close();
    }
  }
}
Program: 38095
Project: 38095
Buggy source:
@Override public void run(){
  Nexus.getInstance().send(channelName.isEmpty() ? userToRemind : channelName,"String_Node_Str" + userToRemind + "String_Node_Str"+ Colors.BOLD+ reminder+ Colors.NORMAL+ "String_Node_Str"+ (from.equals(userToRemind) ? "String_Node_Str" : "String_Node_Str" + StringUtil.removePing(from) + "String_Node_Str"));
  this.cancel(true);
}

Fixed version (ground truth):
@Override public void run(){
  Nexus.getInstance().sendIRC().message(channelName.isEmpty() ? userToRemind : channelName,"String_Node_Str" + userToRemind + "String_Node_Str"+ Colors.BOLD+ reminder+ Colors.NORMAL+ "String_Node_Str"+ (from.equals(userToRemind) ? "String_Node_Str" : "String_Node_Str" + StringUtil.removePing(from) + "String_Node_Str"));
  this.cancel(true);
}
Program: 38096
Project: 38096
Buggy source:
protected GitHubUser getReporterOf(GitHubIssue issue,String userLogin){
  try {
    HttpResponse<JsonNode> response=makeRequest(getIssuesUrl(issue.getRepo().getFullName(),issue.getNumber()),userLogin);
    return getUser(response.getBody().getObject().getJSONObject("String_Node_Str").getString("String_Node_Str"),userLogin);
  }
 catch (  UnirestException e) {
    if (e.getCause() instanceof FileNotFoundException) {
      throw new GitHubNotFoundException("String_Node_Str" + issue.getRepo().getFullName(),e);
    }
    throw new GitHubException("String_Node_Str",e);
  }
}

Fixed version (ground truth):
protected GitHubUser getReporterOf(GitHubIssue issue,String userLogin){
  try {
    String issueUrl=issue instanceof GitHubPullRequest ? getPullsUrl(issue.getRepo().getFullName(),issue.getNumber()) : getIssuesUrl(issue.getRepo().getFullName(),issue.getNumber());
    HttpResponse<JsonNode> response=makeRequest(issueUrl,userLogin);
    return getUser(response.getBody().getObject().getJSONObject("String_Node_Str").getString("String_Node_Str"),userLogin);
  }
 catch (  UnirestException e) {
    if (e.getCause() instanceof FileNotFoundException) {
      throw new GitHubNotFoundException("String_Node_Str" + issue.getRepo().getFullName(),e);
    }
    throw new GitHubException("String_Node_Str",e);
  }
}
Program: 38097
Project: 38097
Buggy source:
protected String getNestedUsage(String[] args,int level,Method method,User user) throws CommandException {
  StringBuilder command=new StringBuilder();
  command.append(Nexus.getInstance().getConfig().getCommandPrefix());
  for (int i=0; i <= level; ++i) {
    command.append(args[i] + "String_Node_Str");
  }
  Map<String,Method> map=commands.get(method);
  boolean found=false;
  command.append("String_Node_Str");
  Set<String> allowedCommands=new HashSet<String>();
  for (  Map.Entry<String,Method> entry : map.entrySet()) {
    Method childMethod=entry.getValue();
    found=true;
    if (hasPermission(user,childMethod)) {
      Command childCmd=childMethod.getAnnotation(Command.class);
      allowedCommands.add(childCmd.aliases()[0]);
    }
  }
  if (allowedCommands.size() > 0) {
    command.append(StringUtils.join(allowedCommands,"String_Node_Str"));
  }
 else {
    if (!found) {
      command.append("String_Node_Str");
    }
 else {
      throw new CommandPermissionsException();
    }
  }
  command.append("String_Node_Str");
  return command.toString();
}

Fixed version (ground truth):
protected String getNestedUsage(String[] args,int level,Method method,User user) throws CommandException {
  StringBuilder command=new StringBuilder();
  command.append(Nexus.getInstance().getConfig().getCommandPrefix());
  for (int i=0; i <= level; ++i) {
    command.append(args[i] + "String_Node_Str");
  }
  Map<String,Method> map=commands.get(method);
  boolean found=false;
  command.append("String_Node_Str");
  Set<String> allowedCommands=new HashSet<String>();
  for (  Map.Entry<String,Method> entry : map.entrySet()) {
    Method childMethod=entry.getValue();
    found=true;
    if (hasPermission(user,childMethod)) {
      Command childCmd=childMethod.getAnnotation(Command.class);
      allowedCommands.add(childCmd.aliases()[0]);
    }
  }
  if (allowedCommands.size() > 0) {
    command.append(StringUtil.join(allowedCommands,"String_Node_Str"));
  }
 else {
    if (!found) {
      command.append("String_Node_Str");
    }
 else {
      throw new CommandPermissionsException();
    }
  }
  command.append("String_Node_Str");
  return command.toString();
}
Program: 38098
Project: 38098
Buggy source:
@Test public void convertShouldSucceed() throws ValidateException, InterruptedException, IOException {
  String res=Pyicos.runConvert(inSamFile.getCanonicalPath(),outWigFile.getCanonicalPath());
  assertTrue(outWigFile.exists());
  assertTrue(new File(res).exists());
}

Fixed version (ground truth):
@Test public void convertShouldSucceed() throws ValidateException, InterruptedException, IOException {
  String res=Pyicos.runConvert(inSamFile.getCanonicalPath(),outWigFile.getCanonicalPath(),true);
  assertTrue(outWigFile.exists());
  assertTrue(new File(res).exists());
}
Program: 38099
Project: 38099
Buggy source:
@Test public void shouldRunStaticCall() throws ProcessException, IOException, InterruptedException {
  String inFile="String_Node_Str";
  String outFile="String_Node_Str";
  RawToProfileConverter.procedureRaw(bowtieParams,inFile,outFile,true,true,"String_Node_Str",genomeBowtie2,"String_Node_Str","String_Node_Str");
}

Fixed version (ground truth):
@Test public void shouldRunStaticCall() throws ProcessException, IOException, InterruptedException {
  String inFile="String_Node_Str";
  String outFile="String_Node_Str";
  RawToProfileConverter.procedureRaw(bowtieParams,inFile,outFile,true,true,true,"String_Node_Str",genomeBowtie2,"String_Node_Str","String_Node_Str");
}