nus-yam/ex-repair huggingface dataset:
Program: 50947
Project: 50947
Buggy source:
private void deployToTomcatServer(String serverprotocol,String serverhost,String serverport,String serverusername,String serverpassword) throws MojoExecutionException {
  try {
    StringBuilder sb=new StringBuilder();
    sb.append(MVN_CMD);
    sb.append(STR_SPACE);
    sb.append(TOMCAT_GOAL);
    sb.append(STR_SPACE);
    sb.append(SERVER_HOST);
    sb.append(serverhost);
    sb.append(STR_SPACE);
    sb.append(SERVER_PORT);
    sb.append(serverport);
    sb.append(STR_SPACE);
    sb.append(SERVER_USERNAME);
    sb.append(serverusername);
    sb.append(STR_SPACE);
    sb.append(SERVER_PASSWORD);
    sb.append(serverpassword);
    sb.append(STR_SPACE);
    sb.append(SKIP_TESTS);
    Commandline cl=new Commandline(sb.toString());
    cl.setWorkingDirectory(baseDir);
    Process process=cl.execute();
    getLog().info("String_Node_Str" + serverprotocol + "String_Node_Str"+ serverhost+ "String_Node_Str"+ serverport+ "String_Node_Str"+ context);
  }
 catch (  CommandLineException e) {
    throw new MojoExecutionException(e.getMessage(),e);
  }
}

Fixed version (ground truth):
private void deployToTomcatServer(String serverprotocol,String serverhost,String serverport,String serverusername,String serverpassword) throws MojoExecutionException {
  BufferedReader in=null;
  boolean errorParam=false;
  try {
    StringBuilder sb=new StringBuilder();
    sb.append(MVN_CMD);
    sb.append(STR_SPACE);
    sb.append(TOMCAT_GOAL);
    sb.append(STR_SPACE);
    sb.append(SERVER_HOST);
    sb.append(serverhost);
    sb.append(STR_SPACE);
    sb.append(SERVER_PORT);
    sb.append(serverport);
    sb.append(STR_SPACE);
    sb.append(SERVER_USERNAME);
    sb.append(serverusername);
    sb.append(STR_SPACE);
    sb.append(SERVER_PASSWORD);
    sb.append(serverpassword);
    sb.append(STR_SPACE);
    sb.append(SKIP_TESTS);
    Commandline cl=new Commandline(sb.toString());
    Process process=cl.execute();
    cl.setWorkingDirectory(baseDir);
    in=new BufferedReader(new InputStreamReader(process.getInputStream()));
    String line=null;
    while ((line=in.readLine()) != null) {
      if (line.startsWith("String_Node_Str")) {
        System.out.println(line);
        errorParam=true;
      }
    }
    if (errorParam) {
      throw new MojoExecutionException("String_Node_Str");
    }
 else {
      getLog().info("String_Node_Str" + serverprotocol + "String_Node_Str"+ serverhost+ "String_Node_Str"+ serverport+ "String_Node_Str"+ context);
    }
  }
 catch (  CommandLineException e) {
    throw new MojoExecutionException(e.getMessage(),e);
  }
catch (  IOException e) {
    throw new MojoExecutionException(e.getMessage(),e);
  }
}
Program: 50951
Project: 50951
Buggy source:
public void setDefaultEnvironment(String environmentName,File sourceConfigXML) throws PhrescoException {
  try {
    DocumentBuilderFactory docFactory=DocumentBuilderFactory.newInstance();
    docFactory.setNamespaceAware(false);
    DocumentBuilder docBuilder=docFactory.newDocumentBuilder();
    Document doc=docBuilder.parse(sourceConfigXML);
    NodeList environmentList=doc.getElementsByTagName("String_Node_Str");
    for (int i=0; i < environmentList.getLength(); i++) {
      Element environment=(Element)environmentList.item(i);
      String envName=environment.getAttribute("String_Node_Str");
      String[] envs=environmentName.split("String_Node_Str");
      for (      String envsName : envs) {
        if (envsName.equals(envName)) {
          environment.setAttribute("String_Node_Str","String_Node_Str");
          TransformerFactory transformerFactory=TransformerFactory.newInstance();
          Transformer transformer=transformerFactory.newTransformer();
          DOMSource source=new DOMSource(doc);
          StreamResult result=new StreamResult(sourceConfigXML);
          transformer.transform(source,result);
        }
      }
    }
  }
 catch (  ParserConfigurationException e) {
    throw new PhrescoException(e);
  }
catch (  TransformerException e) {
    throw new PhrescoException(e);
  }
catch (  IOException e) {
    throw new PhrescoException(e);
  }
catch (  SAXException e) {
    throw new PhrescoException(e);
  }
}

Fixed version (ground truth):
public void setDefaultEnvironment(String environmentName,File sourceConfigXML) throws PhrescoException {
  try {
    DocumentBuilderFactory docFactory=DocumentBuilderFactory.newInstance();
    docFactory.setNamespaceAware(false);
    DocumentBuilder docBuilder=docFactory.newDocumentBuilder();
    Document doc=docBuilder.parse(sourceConfigXML);
    NodeList environmentList=doc.getElementsByTagName("String_Node_Str");
    for (int i=0; i < environmentList.getLength(); i++) {
      Element environment=(Element)environmentList.item(i);
      String envName=environment.getAttribute("String_Node_Str");
      String[] envs=environmentName.split("String_Node_Str");
      for (      String envsName : envs) {
        if (envsName.equals(envName)) {
          environment.setAttribute("String_Node_Str","String_Node_Str");
          TransformerFactory transformerFactory=TransformerFactory.newInstance();
          Transformer transformer=transformerFactory.newTransformer();
          DOMSource source=new DOMSource(doc);
          StreamResult result=new StreamResult(sourceConfigXML.toURI().getPath());
          transformer.transform(source,result);
        }
      }
    }
  }
 catch (  ParserConfigurationException e) {
    throw new PhrescoException(e);
  }
catch (  TransformerException e) {
    throw new PhrescoException(e);
  }
catch (  IOException e) {
    throw new PhrescoException(e);
  }
catch (  SAXException e) {
    throw new PhrescoException(e);
  }
}
Program: 50953
Project: 50953
Buggy source:
/** 
 * @param id
 * @return
 * @throws PhrescoPomException
 */
public AndroidProfile getProfileElement(String id) throws PhrescoPomException {
  Profile profile=getProfile(id);
  AndroidProfile androidProfile=new AndroidProfile();
  List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
  for (  Plugin plugin2 : plugin) {
    List<PluginExecution> execution=plugin2.getExecutions().getExecution();
    for (    PluginExecution pluginExecution : execution) {
      List<Element> any=pluginExecution.getConfiguration().getAny();
      processProfiles(androidProfile,any);
    }
  }
  return androidProfile;
}

Fixed version (ground truth):
/** 
 * @param id
 * @return
 * @throws PhrescoPomException
 */
public AndroidProfile getProfileElement(String id) throws PhrescoPomException {
  Profile profile=getProfile(id);
  AndroidProfile androidProfile=new AndroidProfile();
  List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
  for (  Plugin plugin2 : plugin) {
    List<PluginExecution> execution=plugin2.getExecutions().getExecution();
    if (execution != null) {
      for (      PluginExecution pluginExecution : execution) {
        if (pluginExecution.getConfiguration() != null) {
          List<Element> any=pluginExecution.getConfiguration().getAny();
          processProfiles(androidProfile,any);
        }
      }
    }
  }
  return androidProfile;
}
Program: 50954
Project: 50954
Buggy source:
/** 
 * @return
 */
public String getSigningProfile(){
  if (model.getProfiles() != null && model.getProfiles().getProfile() != null) {
    for (    Profile profile : model.getProfiles().getProfile()) {
      List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
      for (      Plugin plugin2 : plugin) {
        List<PluginExecution> execution=plugin2.getExecutions().getExecution();
        return getSigningProfilePlugin(profile,execution);
      }
    }
  }
  return "String_Node_Str";
}

Fixed version (ground truth):
/** 
 * @return
 */
public String getSigningProfile(){
  if (model.getProfiles() != null && model.getProfiles().getProfile() != null) {
    for (    Profile profile : model.getProfiles().getProfile()) {
      List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
      for (      Plugin plugin2 : plugin) {
        List<PluginExecution> execution=plugin2.getExecutions().getExecution();
        if (getSigningProfilePlugin(profile,execution).equals(profile.getId())) {
          return getSigningProfilePlugin(profile,execution);
        }
      }
    }
  }
  return "String_Node_Str";
}
Program: 50955
Project: 50955
Buggy source:
/** 
 * @param androidProfile
 * @param any
 */
private void processProfiles(AndroidProfile androidProfile,List<Element> any){
  for (  Element element : any) {
    String tagName=element.getTagName();
    if (tagName.equals("String_Node_Str")) {
      androidProfile.setKeystore(element.getTextContent());
    }
 else     if (tagName.equals("String_Node_Str")) {
      androidProfile.setStorepass(element.getTextContent());
    }
 else     if (tagName.equals("String_Node_Str")) {
      androidProfile.setKeypass(element.getTextContent());
    }
 else     if (tagName.equals("String_Node_Str")) {
      androidProfile.setAlias(element.getTextContent());
    }
  }
}

Fixed version (ground truth):
/** 
 * @param androidProfile
 * @param any
 */
private void processProfiles(AndroidProfile androidProfile,List<Element> any){
  for (  Element element : any) {
    String tagName=element.getTagName();
    if (tagName.equals(PomConstants.KEYSTORE)) {
      androidProfile.setKeystore(element.getTextContent());
    }
 else     if (tagName.equals(PomConstants.STOREPASS)) {
      androidProfile.setStorepass(element.getTextContent());
    }
 else     if (tagName.equals(PomConstants.KEYPASS)) {
      androidProfile.setKeypass(element.getTextContent());
    }
 else     if (tagName.equals(PomConstants.ALIAS)) {
      androidProfile.setAlias(element.getTextContent());
    }
  }
}
Program: 50956
Project: 50956
Buggy source:
/** 
 * @return
 */
public String getSigningProfile(){
  if (model.getProfiles().getProfile() != null) {
    for (    Profile profile : model.getProfiles().getProfile()) {
      List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
      for (      Plugin plugin2 : plugin) {
        List<PluginExecution> execution=plugin2.getExecutions().getExecution();
        return getSigningProfilePlugin(profile,execution);
      }
    }
  }
  return "String_Node_Str";
}

Fixed version (ground truth):
/** 
 * @return
 */
public String getSigningProfile(){
  if (model.getProfiles() != null && model.getProfiles().getProfile() != null) {
    for (    Profile profile : model.getProfiles().getProfile()) {
      List<Plugin> plugin=profile.getBuild().getPlugins().getPlugin();
      for (      Plugin plugin2 : plugin) {
        List<PluginExecution> execution=plugin2.getExecutions().getExecution();
        return getSigningProfilePlugin(profile,execution);
      }
    }
  }
  return "String_Node_Str";
}
Program: 50957
Project: 50957
Buggy source:
private String getSigningProfilePlugin(Profile profile,List<PluginExecution> execution){
  for (  PluginExecution pluginExecution : execution) {
    List<Element> any=pluginExecution.getConfiguration().getAny();
    for (    Element element : any) {
      if (element.getTagName().equals("String_Node_Str")) {
        return profile.getId();
      }
    }
  }
  return "String_Node_Str";
}

Fixed version (ground truth):
/** 
 * @param profile
 * @param execution
 * @return
 */
private String getSigningProfilePlugin(Profile profile,List<PluginExecution> execution){
  if (model.getProfiles() != null && model.getProfiles().getProfile() != null) {
    for (    PluginExecution pluginExecution : execution) {
      if (pluginExecution.getConfiguration() != null) {
        List<Element> any=pluginExecution.getConfiguration().getAny();
        for (        Element element : any) {
          if (element.getTagName().equals(PomConstants.KEYSTORE)) {
            return profile.getId();
          }
        }
      }
    }
  }
  return "String_Node_Str";
}
Program: 50958
Project: 50958
Buggy source:
/** 
 * @param reports
 * @param file
 */
public void addReportPlugin(List<Reports> reports,List<ReportCategories> reportCategories,File file){
  for (  Reports iterateReport : reports) {
    addReportPlugin(iterateReport,reportCategories,file);
  }
}

Fixed version (ground truth):
/** 
 * @param file
 * @return
 * @deprecated
 */
public void addReportPlugin(List<Reports> reports,File file){
  addReportPlugin(reports,null,file);
}
Program: 50959
Project: 50959
Buggy source:
/** 
 * @param file
 * @return
 */
public List<Reports> getReports(File file){
  try {
    PomProcessor processor=new PomProcessor(file);
    List<ReportPlugin> reportPlugin=processor.getReportPlugin();
    if (reportPlugin != null) {
      List<Reports> reports=new ArrayList<Reports>();
      List<ReportCategories> categories=new ArrayList<ReportCategories>();
      for (      ReportPlugin reportPlugin2 : reportPlugin) {
        Reports reports1=new Reports();
        reports1.setGroupId(reportPlugin2.getGroupId());
        reports1.setArtifactId(reportPlugin2.getArtifactId());
        List<String> projectInfoReportCategories=processor.getProjectInfoReportCategories();
        if (projectInfoReportCategories != null && reportPlugin2.getArtifactId().equals(Reports.PROJECT_INFO.getArtifactId())) {
          for (          String name : projectInfoReportCategories) {
            ReportCategories reportCategories=new ReportCategories();
            reportCategories.setName(name);
            categories.add(reportCategories);
            reports1.setReportCategories(categories);
          }
        }
        reports.add(reports1);
      }
      return reports;
    }
  }
 catch (  JAXBException e) {
    LOGGER.debug(e);
  }
catch (  IOException e) {
    LOGGER.debug(e);
  }
  return null;
}

Fixed version (ground truth):
public List<Reports> getReports(File file){
  try {
    PomProcessor processor=new PomProcessor(file);
    List<ReportPlugin> reportPlugin=processor.getReportPlugin();
    if (reportPlugin != null) {
      List<Reports> reports=new ArrayList<Reports>();
      List<ReportCategories> categories=new ArrayList<ReportCategories>();
      for (      ReportPlugin reportPlugin2 : reportPlugin) {
        Reports reports1=new Reports();
        reports1.setGroupId(reportPlugin2.getGroupId());
        reports1.setArtifactId(reportPlugin2.getArtifactId());
        List<String> projectInfoReportCategories=processor.getProjectInfoReportCategories();
        if (projectInfoReportCategories != null && reportPlugin2.getArtifactId().equals(Reports.PROJECT_INFO.getArtifactId())) {
          for (          String name : projectInfoReportCategories) {
            ReportCategories reportCategories=new ReportCategories();
            reportCategories.setName(name);
            categories.add(reportCategories);
            reports1.setReportCategories(categories);
          }
        }
        reports.add(reports1);
      }
      return reports;
    }
  }
 catch (  JAXBException e) {
    LOGGER.debug(e);
  }
catch (  IOException e) {
    LOGGER.debug(e);
  }
  return null;
}
Program: 50961
Project: 50961
Buggy source:
public static void updatePomProject(ProjectInfo projectInfo) throws PhrescoException, JDOMException, IOException {
  File path=new File(Utility.getProjectHome() + File.separator + projectInfo.getCode()+ File.separator+ POM_FILE);
  try {
    SAXBuilder builder=new SAXBuilder();
    Document doc=(Document)builder.build(path);
    Element rootNode=doc.getRootElement();
    Element dependencies=rootNode.getChild("String_Node_Str",rootNode.getNamespace());
    Namespace ns=rootNode.getNamespace();
    List<ModuleGroup> modules=projectInfo.getTechnology().getModules();
    if (CollectionUtils.isEmpty(modules)) {
      return;
    }
    for (    ModuleGroup moduleGroup : modules) {
      Element dependency=new Element("String_Node_Str",ns);
      dependency.addContent(new Element("String_Node_Str",ns).setText(moduleGroup.getGroupId()));
      dependency.addContent(new Element("String_Node_Str",ns).setText(moduleGroup.getArtifactId()));
      List<Module> versions=moduleGroup.getVersions();
      for (      Module version : versions) {
        dependency.addContent(new Element("String_Node_Str",ns).setText(version.getVersion()));
      }
      dependencies.addContent(dependency);
    }
    XMLOutputter xmlOutput=new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(doc,new FileWriter(path));
  }
 catch (  Exception e) {
    throw new PhrescoException(e);
  }
}

Fixed version (ground truth):
public static void updatePomProject(ProjectInfo projectInfo) throws PhrescoException, PhrescoPomException {
  File path=new File(Utility.getProjectHome() + File.separator + projectInfo.getCode()+ File.separator+ POM_FILE);
  try {
    PomProcessor pomProcessor=new PomProcessor(path);
    List<ModuleGroup> modules=projectInfo.getTechnology().getModules();
    if (CollectionUtils.isEmpty(modules)) {
      return;
    }
    for (    ModuleGroup moduleGroup : modules) {
      pomProcessor.addDependency(moduleGroup.getGroupId(),moduleGroup.getArtifactId(),moduleGroup.getVersions().get(0).getVersion());
      pomProcessor.save();
    }
  }
 catch (  JAXBException e) {
    throw new PhrescoException(e);
  }
catch (  IOException e) {
    throw new PhrescoException(e);
  }
}
Program: 50963
Project: 50963
Buggy source:
@Override public void process(ProjectInfo info,File path) throws PhrescoException {
  if (isDebugEnabled) {
    S_LOGGER.debug("String_Node_Str");
    S_LOGGER.debug("String_Node_Str" + info.getCode());
    S_LOGGER.debug("String_Node_Str" + path.getPath());
  }
  Technology technology=info.getTechnology();
  if (StringUtils.isNotBlank(info.getPilotProjectName())) {
    List<ProjectInfo> pilotProjects=getRepositoryManager().getPilotProjects(technology.getId());
    if (CollectionUtils.isEmpty(pilotProjects)) {
      return;
    }
    for (    ProjectInfo projectInfo : pilotProjects) {
      String urls[]=projectInfo.getPilotProjectUrls();
      if (urls != null) {
        for (        String url : urls) {
          DependencyUtils.extractFiles(url,path);
        }
      }
    }
  }
  updateAndroidVersion(path,info);
  POMUpdater.updatePOM(path,technology);
  AndroidTestPOMUpdater.updatePOM(path);
  if (technology.getId().equals(TechnologyTypes.ANDROID_HYBRID)) {
    extractJsLibraries(path,info.getTechnology().getJsLibraries());
  }
}

Fixed version (ground truth):
@Override public void process(ProjectInfo info,File path) throws PhrescoException {
  if (isDebugEnabled) {
    S_LOGGER.debug("String_Node_Str");
    S_LOGGER.debug("String_Node_Str" + info.getCode());
    S_LOGGER.debug("String_Node_Str" + path.getPath());
  }
  Technology technology=info.getTechnology();
  if (StringUtils.isNotBlank(info.getPilotProjectName())) {
    List<ProjectInfo> pilotProjects=getRepositoryManager().getPilotProjects(technology.getId());
    if (CollectionUtils.isEmpty(pilotProjects)) {
      return;
    }
    for (    ProjectInfo projectInfo : pilotProjects) {
      String urls[]=projectInfo.getPilotProjectUrls();
      if (urls != null) {
        for (        String url : urls) {
          DependencyUtils.extractFiles(url,path);
        }
      }
    }
  }
  updateAndroidVersion(path,info);
  try {
    List<ModuleGroup> modules=technology.getModules();
    if ((CollectionUtils.isNotEmpty(modules)) && modules != null) {
      updatePOMModules(path,modules);
    }
  }
 catch (  JAXBException e) {
    e.printStackTrace();
  }
catch (  PhrescoPomException e) {
    e.printStackTrace();
  }
  AndroidTestPOMUpdater.updatePOM(path);
  if (technology.getId().equals(TechnologyTypes.ANDROID_HYBRID)) {
    extractJsLibraries(path,info.getTechnology().getJsLibraries());
  }
}
Program: 50964
Project: 50964
Buggy source:
@Override protected String getModulePathKey(){
  return null;
}

Fixed version (ground truth):
@Override protected String getModulePathKey(){
  return "String_Node_Str";
}
Program: 50965
Project: 50965
Buggy source:
@Test public void testGetModuleById(){
  String techId="String_Node_Str";
  List<ModuleGroup> modules=new ArrayList<ModuleGroup>();
  try {
    List<ModuleGroup> modulesList=mongoOperation.getCollection(MODULES_COLLECTION_NAME,ModuleGroup.class);
    for (    ModuleGroup moduleGroup : modulesList) {
      if (moduleGroup.getTechId().equals(techId)) {
        modules.add(moduleGroup);
      }
    }
    String json=new Gson().toJson(modules);
    System.out.println(json);
  }
 catch (  Exception e) {
  }
}

Fixed version (ground truth):
@Test public void testGetModuleById(){
  String techId="String_Node_Str";
  List<ModuleGroup> modules=new ArrayList<ModuleGroup>();
  try {
    List<ModuleGroup> modulesList=mongoOperation.getCollection(MODULES_COLLECTION_NAME,ModuleGroup.class);
    for (    ModuleGroup moduleGroup : modulesList) {
    }
    String json=new Gson().toJson(modules);
    System.out.println(json);
  }
 catch (  Exception e) {
  }
}
Program: 50966
Project: 50966
Buggy source:
/** 
 * Updates List of objects for the given type 
 * @param infos
 * @param type
 * @return
 * @throws PhrescoException
 */
@SuppressWarnings("String_Node_Str") public List<E> update(List<E> infos,GenericType<List<E>> gtype,String accept,String type) throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  ClientResponse clientResponse=builder.put(ClientResponse.class,infos);
  isErrorThrow(clientResponse);
  return clientResponse.getEntity(gtype);
}

Fixed version (ground truth):
/** 
 * Updates List of objects for the given type 
 * @param infos
 * @param type
 * @return
 * @throws PhrescoException
 */
public List<E> update(List<E> infos,GenericType<List<E>> gtype,String accept,String type) throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  ClientResponse clientResponse=builder.put(ClientResponse.class,infos);
  isErrorThrow(clientResponse);
  return clientResponse.getEntity(gtype);
}
Program: 50967
Project: 50967
Buggy source:
/** 
 * Update the given object by using the type given
 * @param obj
 * @param type
 * @return
 * @throws PhrescoException
 */
@SuppressWarnings("String_Node_Str") public ClientResponse updateById(E obj,Type gType,String accept,String type) throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  ClientResponse clientResponse=builder.put(ClientResponse.class,new Gson().toJson(obj));
  isErrorThrow(clientResponse);
  return clientResponse;
}

Fixed version (ground truth):
/** 
 * Update the given object by using the type given
 * @param obj
 * @param type
 * @return
 * @throws PhrescoException
 */
public E updateById(E obj,GenericType<E> genericType,String accept,String type) throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  ClientResponse clientResponse=builder.put(ClientResponse.class,obj);
  isErrorThrow(clientResponse);
  return clientResponse.getEntity(genericType);
}
Program: 50968
Project: 50968
Buggy source:
/** 
 * Get List of objects for the specified generic type object
 * @param genericType
 * @return
 */
@SuppressWarnings("String_Node_Str") public List<E> get(GenericType<List<E>> genericType,String accept,String type){
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  return builder.get(genericType);
}

Fixed version (ground truth):
/** 
 * Get List of objects for the specified generic type object
 * @param genericType
 * @return
 */
public List<E> get(GenericType<List<E>> genericType,String accept,String type){
  S_LOGGER.debug("String_Node_Str");
  builder=resource.accept(accept).type(type);
  return builder.get(genericType);
}
Program: 50969
Project: 50969
Buggy source:
@Test public void testGetTechnologies(){
  try {
    serviceManager=ServiceClientFactory.getServiceManager(context);
    RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
    techClient.setPath("String_Node_Str");
    GenericType<List<Technology>> genericType=new GenericType<List<Technology>>(){
    }
;
    List<Technology> list=techClient.get(genericType);
    for (    Technology tech : list) {
      System.out.println("String_Node_Str" + tech.getName() + "String_Node_Str"+ tech.getId());
    }
  }
 catch (  PhrescoException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
@Test public void testGetTechnologies(){
  try {
    serviceManager=ServiceClientFactory.getServiceManager(context);
    RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
    techClient.setPath("String_Node_Str");
    GenericType<List<Technology>> genericType=new GenericType<List<Technology>>(){
    }
;
    List<Technology> list=techClient.get(genericType);
    id=list.get(0).getId();
    id2=list.get(1).getId();
    id3=list.get(2).getId();
    for (    Technology tech : list) {
      System.out.println("String_Node_Str" + tech.getName() + "String_Node_Str"+ tech.getId());
      System.out.println("String_Node_Str" + tech);
    }
  }
 catch (  PhrescoException e) {
    e.printStackTrace();
  }
}
Program: 50970
Project: 50970
Buggy source:
@Test public void testCreateServer() throws PhrescoException {
  List<Technology> techs=new ArrayList<Technology>();
  Technology tech=new Technology();
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  techs.add(tech);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  ClientResponse create=techClient.create(techs);
}

Fixed version (ground truth):
@Test public void testCreateServer() throws PhrescoException {
  List<Technology> techs=new ArrayList<Technology>();
  Technology tech=new Technology();
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  techs.add(tech);
  Technology tech2=new Technology();
  tech2.setName("String_Node_Str");
  List<String> versions2=new ArrayList<String>();
  versions2.add("String_Node_Str");
  versions2.add("String_Node_Str");
  tech2.setVersions(versions2);
  techs.add(tech2);
  Technology tech3=new Technology();
  tech2.setName("String_Node_Str");
  List<String> versions3=new ArrayList<String>();
  versions3.add("String_Node_Str");
  versions3.add("String_Node_Str");
  tech3.setVersions(versions3);
  techs.add(tech3);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  ClientResponse response=techClient.create(techs);
  System.out.println("String_Node_Str" + response.getStatus());
}
Program: 50971
Project: 50971
Buggy source:
@Ignore public void testDeleteServerById() throws PhrescoException {
  String id="String_Node_Str";
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str" + id);
  ClientResponse response=techClient.deleteById();
}

Fixed version (ground truth):
@Test public void testDeleteServerById() throws PhrescoException {
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  techClient.setPath(id3);
  ClientResponse response=techClient.deleteById();
  System.out.println(response.getStatus());
}
Program: 50972
Project: 50972
Buggy source:
@Ignore public void testPutServer() throws PhrescoException {
  List<Technology> techs=new ArrayList<Technology>();
  Technology tech=new Technology();
  tech.setId("String_Node_Str");
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  techs.add(tech);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  GenericType<List<Technology>> type=new GenericType<List<Technology>>(){
  }
;
  List<Technology> entity=techClient.update(techs,type);
  for (  Technology technology : entity) {
    System.out.println("String_Node_Str" + technology);
  }
}

Fixed version (ground truth):
@Test public void testPutServer() throws PhrescoException {
  List<Technology> techs=new ArrayList<Technology>();
  Technology tech=new Technology();
  System.out.println("String_Node_Str" + id);
  tech.setId(id);
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  techs.add(tech);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  GenericType<List<Technology>> type=new GenericType<List<Technology>>(){
  }
;
  List<Technology> entity=techClient.update(techs,type);
  for (  Technology technology : entity) {
    System.out.println("String_Node_Str" + technology);
  }
}
Program: 50973
Project: 50973
Buggy source:
@Ignore public void testGetServerById() throws PhrescoException {
  try {
    String id="String_Node_Str";
    serviceManager=ServiceClientFactory.getServiceManager(context);
    RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str" + id);
    GenericType<Technology> genericType=new GenericType<Technology>(){
    }
;
    Technology tech=techClient.getById(genericType);
    System.out.println("String_Node_Str" + tech);
  }
 catch (  PhrescoException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
@Test public void testGetServerById() throws PhrescoException {
  try {
    serviceManager=ServiceClientFactory.getServiceManager(context);
    RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
    techClient.setPath(id2);
    GenericType<Technology> genericType=new GenericType<Technology>(){
    }
;
    Technology tech=techClient.getById(genericType);
    System.out.println("String_Node_Str" + tech);
  }
 catch (  PhrescoException e) {
    e.printStackTrace();
  }
}
Program: 50974
Project: 50974
Buggy source:
@Ignore public void testPutServerById() throws PhrescoException {
  String id="String_Node_Str";
  Technology tech=new Technology();
  tech.setId("String_Node_Str");
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str" + id);
  Type type=new TypeToken<Technology>(){
  }
.getType();
  ClientResponse clientResponse=techClient.updateById(tech,type);
}

Fixed version (ground truth):
@Test public void testPutServerById() throws PhrescoException {
  Technology tech=new Technology();
  tech.setId(id2);
  tech.setName("String_Node_Str");
  List<String> versions=new ArrayList<String>();
  versions.add("String_Node_Str");
  versions.add("String_Node_Str");
  tech.setVersions(versions);
  serviceManager=ServiceClientFactory.getServiceManager(context);
  RestClient<Technology> techClient=serviceManager.getRestClient("String_Node_Str");
  techClient.setPath(id2);
  GenericType<Technology> genericType=new GenericType<Technology>(){
  }
;
  Technology technology=techClient.updateById(tech,genericType);
  System.out.println(technology);
}
Program: 50975
Project: 50975
Buggy source:
public String update() throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  try {
    if (validateForm()) {
      setErrorFound(true);
      return SUCCESS;
    }
    SimpleDateFormat dateFormat=new SimpleDateFormat("String_Node_Str");
    Customer customer=new Customer(customerId,name,description);
    if (StringUtils.isNotEmpty(validFrom)) {
      customer.setValidFrom(dateFormat.parse(validFrom));
    }
    if (StringUtils.isNotEmpty(validUpTo)) {
      customer.setValidUpto(dateFormat.parse(validUpTo));
    }
    customer.setRepoURL(repoURL);
    RestClient<Customer> editCustomer=getServiceManager().getRestClient("String_Node_Str" + REST_API_CUSTOMERS + "String_Node_Str"+ customerId);
    Type type=new TypeToken<Customer>(){
    }
.getType();
    ClientResponse clientResponse=editCustomer.updateById(customer,type);
    if (clientResponse.getStatus() != 200) {
      addActionError(getText(CUSTOMER_NOT_UPDATED,Collections.singletonList(oldName)));
    }
 else {
      addActionMessage(getText(CUSTOMER_UPDATED,Collections.singletonList(oldName)));
    }
  }
 catch (  Exception e) {
    throw new PhrescoException(e);
  }
  return list();
}

Fixed version (ground truth):
public String update() throws PhrescoException {
  S_LOGGER.debug("String_Node_Str");
  try {
    if (validateForm()) {
      setErrorFound(true);
      return SUCCESS;
    }
    SimpleDateFormat dateFormat=new SimpleDateFormat("String_Node_Str");
    Customer customer=new Customer(customerId,name,description);
    if (StringUtils.isNotEmpty(validFrom)) {
      customer.setValidFrom(dateFormat.parse(validFrom));
    }
    if (StringUtils.isNotEmpty(validUpTo)) {
      customer.setValidUpto(dateFormat.parse(validUpTo));
    }
    customer.setRepoURL(repoURL);
    RestClient<Customer> editCustomer=getServiceManager().getRestClient("String_Node_Str" + REST_API_CUSTOMERS + "String_Node_Str"+ customerId);
    GenericType<Customer> genericType=new GenericType<Customer>(){
    }
;
    Customer updatedCustomer=editCustomer.updateById(customer,genericType);
    if (updatedCustomer == null) {
      addActionError(getText(CUSTOMER_NOT_UPDATED,Collections.singletonList(oldName)));
    }
 else {
      addActionMessage(getText(CUSTOMER_UPDATED,Collections.singletonList(oldName)));
    }
  }
 catch (  Exception e) {
    throw new PhrescoException(e);
  }
  return list();
}
Program: 50976
Project: 50976
Buggy source:
public String browse(){
  S_LOGGER.debug("String_Node_Str");
  try {
    String projectLocation=Utility.getProjectHome() + projectCode;
    getHttpRequest().setAttribute(REQ_PROJECT_LOCATION,projectLocation);
    getHttpRequest().setAttribute(REQ_PROJECT_CODE,projectCode);
  }
 catch (  Exception e) {
    S_LOGGER.error("String_Node_Str" + FrameworkUtil.getStackTraceAsString(e));
    new LogErrorReport(e,"String_Node_Str");
  }
  return SUCCESS;
}

Fixed version (ground truth):
public String browse(){
  S_LOGGER.debug("String_Node_Str");
  try {
    String projectLocation=Utility.getProjectHome() + projectCode;
    getHttpRequest().setAttribute(REQ_PROJECT_LOCATION,projectLocation.replace(File.separator,FORWARD_SLASH));
    getHttpRequest().setAttribute(REQ_PROJECT_LOCATION,projectLocation);
    getHttpRequest().setAttribute(REQ_PROJECT_CODE,projectCode);
  }
 catch (  Exception e) {
    S_LOGGER.error("String_Node_Str" + FrameworkUtil.getStackTraceAsString(e));
    new LogErrorReport(e,"String_Node_Str");
  }
  return SUCCESS;
}
Program: 50979
Project: 50979
Buggy source:
public static void main(String[] args){
  List<UGraph<String>> graphs=new ArrayList<UGraph<String>>();
  List<Double> labels=new ArrayList<Double>();
  createDataSet(MUTAG_DIR,graphs,labels);
  experiment(graphs,labels);
  graphs=new ArrayList<UGraph<String>>();
  labels=new ArrayList<Double>();
  createDataSet(ENZYMES_DIR,graphs,labels);
  experiment(graphs,labels);
}

Fixed version (ground truth):
public static void main(String[] args){
  List<UGraph<String>> graphs=new ArrayList<UGraph<String>>();
  List<Double> labels=new ArrayList<Double>();
  graphs=new ArrayList<UGraph<String>>();
  labels=new ArrayList<Double>();
  createDataSet(ENZYMES_DIR,graphs,labels);
  experiment(graphs,labels);
}
Program: 50981
Project: 50981
Buggy source:
@Override public void run(){
  long tic, toc;
  List<Double> tempLabels=new ArrayList<Double>();
  tempLabels.addAll(labels);
  Map<String,double[][]> matrices=new HashMap<String,double[][]>();
  tic=System.currentTimeMillis();
  System.out.println("String_Node_Str");
  for (  RDFDTGraphIntersectionSubTreeKernel kernel : kernels) {
    double[][] matrix=kernel.compute(graph,iNodes);
    matrices.put(kernel.getLabel(),matrix);
  }
  toc=System.currentTimeMillis();
  compR.setLabel("String_Node_Str");
  System.out.println("String_Node_Str");
  for (int j=0; j < seeds.length; j++) {
    for (    String k : matrices.keySet()) {
      matrices.put(k,KernelUtils.shuffle(matrices.get(k),seeds[j]));
    }
    Collections.shuffle(tempLabels,new Random(seeds[j]));
    double[] target=new double[tempLabels.size()];
    for (int i=0; i < target.length; i++) {
      target[i]=tempLabels.get(i);
    }
    Prediction[] pred=LibSVM.crossValidateWithMultipleKernels(matrices,target,svmParms,svmParms.getNumFolds());
    for (    EvaluationFunction ef : evalFunctions) {
      resultMap.get(ef)[j]=ef.computeScore(target,pred);
    }
  }
  double[] comp={toc - tic};
  compR.setScores(comp);
}

Fixed version (ground truth):
@Override public void run(){
  long tic, toc;
  List<Double> tempLabels=new ArrayList<Double>();
  tempLabels.addAll(labels);
  Map<String,double[][]> matrices=new HashMap<String,double[][]>();
  tic=System.currentTimeMillis();
  System.out.println("String_Node_Str");
  for (  RDFDTGraphIntersectionSubTreeKernel kernel : kernels) {
    double[][] matrix=kernel.compute(graph,iNodes);
    matrices.put(kernel.getLabel(),matrix);
  }
  toc=System.currentTimeMillis();
  System.out.println("String_Node_Str" + (toc - tic) + "String_Node_Str");
  compR.setLabel("String_Node_Str");
  System.out.println("String_Node_Str");
  for (int j=0; j < seeds.length; j++) {
    for (    String k : matrices.keySet()) {
      matrices.put(k,KernelUtils.shuffle(matrices.get(k),seeds[j]));
    }
    Collections.shuffle(tempLabels,new Random(seeds[j]));
    double[] target=new double[tempLabels.size()];
    for (int i=0; i < target.length; i++) {
      target[i]=tempLabels.get(i);
    }
    Prediction[] pred=LibSVM.crossValidateWithMultipleKernels(matrices,target,svmParms,svmParms.getNumFolds());
    for (    EvaluationFunction ef : evalFunctions) {
      resultMap.get(ef)[j]=ef.computeScore(target,pred);
    }
  }
  double[] comp={toc - tic};
  compR.setScores(comp);
}
Program: 50984
Project: 50984
Buggy source:
public double computeScore(double[] target,Prediction[] prediction){
  Map<Double,Double> counts=new HashMap<Double,Double>();
  for (int i=0; i < target.length; i++) {
    if (!counts.containsKey(target[i])) {
      counts.put(target[i],1.0);
    }
 else {
      counts.put(target[i],counts.get(target[i]) + 1);
    }
  }
  double f1=0, temp1=0, temp2=0;
  for (  double label : counts.keySet()) {
    for (int i=0; i < prediction.length; i++) {
      if ((prediction[i].getLabel() == label && target[i] == label)) {
        temp1+=1;
      }
      if ((prediction[i].getLabel() == label || target[i] == label)) {
        temp2+=1;
      }
    }
    f1+=temp1 / temp2;
    temp1=0;
    temp2=0;
  }
  return f1 / ((double)counts.size());
}

Fixed version (ground truth):
public double computeScore(double[] target,Prediction[] prediction){
  Map<Double,Double> counts=new HashMap<Double,Double>();
  for (int i=0; i < target.length; i++) {
    if (!counts.containsKey(target[i])) {
      counts.put(target[i],1.0);
    }
 else {
      counts.put(target[i],counts.get(target[i]) + 1);
    }
  }
  double f1=0, temp1=0, temp2=0;
  for (  double label : counts.keySet()) {
    for (int i=0; i < prediction.length; i++) {
      if ((prediction[i].getLabel() == label && target[i] == label)) {
        temp1+=1;
      }
 else       if ((prediction[i].getLabel() == label || target[i] == label)) {
        temp2+=1;
      }
    }
    f1+=(2 * temp1) / ((2 * temp1) + temp2);
    temp1=0;
    temp2=0;
  }
  return f1 / ((double)counts.size());
}
Program: 50985
Project: 50985
Buggy source:
/** 
 * Compute the F1 score for a prediction.  It computes the F1 per class and returns the average of these F1's, this is called the macro F1
 * @param target
 * @param prediction
 * @return use {@link org.data2semantics.proppred.learners.evaluation.F1}
 */
public static double computeF1(double[] target,double[] prediction){
  Map<Double,Double> targetCounts=computeClassCounts(target);
  double f1=0, temp1=0, temp2=0;
  for (  double label : targetCounts.keySet()) {
    for (int i=0; i < prediction.length; i++) {
      if ((prediction[i] == label && target[i] == label)) {
        temp1+=1;
      }
      if ((prediction[i] == label || target[i] == label)) {
        temp2+=1;
      }
    }
    f1+=temp1 / temp2;
    temp1=0;
    temp2=0;
  }
  return f1 / ((double)targetCounts.size());
}

Fixed version (ground truth):
/** 
 * Compute the F1 score for a prediction.  It computes the F1 per class and returns the average of these F1's, this is called the macro F1
 * @param target
 * @param prediction
 * @return use {@link org.data2semantics.proppred.learners.evaluation.F1}
 */
public static double computeF1(double[] target,double[] prediction){
  Map<Double,Double> targetCounts=computeClassCounts(target);
  double f1=0, temp1=0, temp2=0;
  for (  double label : targetCounts.keySet()) {
    for (int i=0; i < prediction.length; i++) {
      if ((prediction[i] == label && target[i] == label)) {
        temp1+=1;
      }
 else       if ((prediction[i] == label || target[i] == label)) {
        temp2+=1;
      }
    }
    f1+=(2 * temp1) / ((2 * temp1) + temp2);
    temp1=0;
    temp2=0;
  }
  return f1 / ((double)targetCounts.size());
}
Program: 50987
Project: 50987
Buggy source:
public static void main(String[] args) throws IOException {
  Run run=new Run();
  CmdLineParser parser=new CmdLineParser(run);
  try {
    parser.parseArgument(args);
  }
 catch (  CmdLineException e) {
    usageExit(e.getMessage(),parser);
  }
  if (run.arguments.size() > 1)   usageExit("String_Node_Str" + run.arguments,parser);
  File file;
  if (run.arguments.isEmpty())   file=new File("String_Node_Str");
 else   file=new File(run.arguments.get(0));
  if (!file.exists())   usageExit("String_Node_Str" + run.arguments.get(0) + "String_Node_Str",parser);
  Workflow workflow=WorkflowParser.parseYAML(file);
  ExecutionProfile executionProfile;
switch (execProfile) {
case LOCAL:
    executionProfile=new LocalExecutionProfile();
  break;
case THREADED:
executionProfile=new ThreadedLocalExecutionProfile();
break;
default :
executionProfile=new LocalExecutionProfile();
}
ResourceSpace rp=new ResourceSpace();
List<Reporter> reporters=Arrays.asList(new HTMLReporter(workflow,new File(output,"String_Node_Str")),new CSVReporter(workflow,new File(output,"String_Node_Str")),new PROVReporter(workflow,new File(output,"String_Node_Str")));
Orchestrator orchestrator=new Orchestrator(workflow,executionProfile,rp,reporters);
orchestrator.orchestrate();
for (Reporter reporter : reporters) reporter.report();
Global.log().info("String_Node_Str");
}

Fixed version (ground truth):
public static void main(String[] args) throws IOException {
  Run run=new Run();
  CmdLineParser parser=new CmdLineParser(run);
  try {
    parser.parseArgument(args);
  }
 catch (  CmdLineException e) {
    usageExit(e.getMessage(),parser);
  }
  if (run.arguments.size() > 1)   usageExit("String_Node_Str" + run.arguments,parser);
  File file;
  if (run.arguments.isEmpty())   file=new File("String_Node_Str");
 else   file=new File(run.arguments.get(0));
  if (!file.exists())   usageExit("String_Node_Str" + file + "String_Node_Str",parser);
  Workflow workflow=WorkflowParser.parseYAML(file);
  ExecutionProfile executionProfile;
switch (execProfile) {
case LOCAL:
    executionProfile=new LocalExecutionProfile();
  break;
case THREADED:
executionProfile=new ThreadedLocalExecutionProfile();
break;
default :
executionProfile=new LocalExecutionProfile();
}
ResourceSpace rp=new ResourceSpace();
List<Reporter> reporters=Arrays.asList(new HTMLReporter(workflow,new File(output,"String_Node_Str")),new CSVReporter(workflow,new File(output,"String_Node_Str")),new PROVReporter(workflow,new File(output,"String_Node_Str")));
Orchestrator orchestrator=new Orchestrator(workflow,executionProfile,rp,reporters);
orchestrator.orchestrate();
for (Reporter reporter : reporters) reporter.report();
Global.log().info("String_Node_Str");
}
Program: 50990
Project: 50990
Buggy source:
/** 
 * Add a multivalue input to the workflow
 * @param module
 * @param name
 * @param value
 * @return
 */
public WorkflowBuilder multiInput(String moduleName,String description,String name,List<Object> value,DataType type){
  check();
  if (!workflow.modules.containsKey(moduleName))   throw new IllegalArgumentException("String_Node_Str" + name + "String_Node_Str");
  ModuleImpl module=workflow.modules.get(moduleName);
  module.addMultiInput(name,description,value,type);
  return this;
}

Fixed version (ground truth):
/** 
 * Add a multivalue input to the workflow
 * @param module
 * @param name
 * @param value
 * @return
 */
public WorkflowBuilder multiInput(String moduleName,String description,String name,List<Object> value,DataType type){
  check();
  if (!workflow.modules.containsKey(moduleName))   throw new IllegalArgumentException("String_Node_Str" + moduleName + "String_Node_Str");
  ModuleImpl module=workflow.modules.get(moduleName);
  module.addMultiInput(name,description,value,type);
  return this;
}
Program: 50992
Project: 50992
Buggy source:
@MainMethod public RDFFileDataSet processRDFData(@InputParameter(name="String_Node_Str") Double fraction,@InputParameter(name="String_Node_Str") String dataDirectory,@InputParameter(name="String_Node_Str") String objectFilter1,@InputParameter(name="String_Node_Str") String predicateFilter1,@InputParameter(name="String_Node_Str") String predicateFilter2){
  LOG.info("String_Node_Str");
  dataset=new RDFFileDataSet(dataDirectory,RDFFormat.NTRIPLES);
  createGeoDataSet(2,fraction,123,predicateFilter2);
  LOG.info("String_Node_Str");
  return dataset;
}

Fixed version (ground truth):
@MainMethod public RDFFileDataSet processRDFData(@InputParameter(name="String_Node_Str") Double fraction,@InputParameter(name="String_Node_Str") String dataDirectory,@InputParameter(name="String_Node_Str") String objectFilter1,@InputParameter(name="String_Node_Str") String predicateFilter1,@InputParameter(name="String_Node_Str") String predicateFilter2){
  LOG.info("String_Node_Str");
  dataset=new RDFFileDataSet(dataDirectory,RDFFormat.NTRIPLES);
  createGeoDataSet(10,fraction,123,predicateFilter2);
  LOG.info("String_Node_Str");
  return dataset;
}
Program: 50999
Project: 50999
Buggy source:
public SparseVector[] computeFeatureVectors(RDFDataSet dataset,List<Resource> instances,List<Statement> blackList){
  SparseVector[] featureVectors=new SparseVector[instances.size()];
  for (int i=0; i < featureVectors.length; i++) {
    featureVectors[i]=new SparseVector();
  }
  DirectedGraph<Vertex<Map<Integer,StringBuilder>>,Edge<Map<Integer,StringBuilder>>> graph=createGraphFromRDF(dataset,instances,blackList);
  createInstanceIndexMaps(graph,instances);
  if (blankLabels) {
    setBlankLabels(graph);
  }
  computeFVs(graph,instances,Math.sqrt(1.0 / ((double)(iterations + 1))),featureVectors);
  int startLabel=1;
  for (int i=0; i < iterations; i++) {
    relabelGraph2MultisetLabels(graph,startLabel);
    startLabel=labelCounter;
    compressGraphLabels(graph);
    computeFVs(graph,instances,Math.sqrt((2.0 + i) / ((double)(iterations + 1))),featureVectors);
  }
  if (this.normalize) {
    featureVectors=KernelUtils.normalize(featureVectors);
  }
  return featureVectors;
}

Fixed version (ground truth):
public SparseVector[] computeFeatureVectors(RDFDataSet dataset,List<Resource> instances,List<Statement> blackList){
  SparseVector[] featureVectors=new SparseVector[instances.size()];
  for (int i=0; i < featureVectors.length; i++) {
    featureVectors[i]=new SparseVector();
  }
  DirectedGraph<Vertex<Map<Integer,StringBuilder>>,Edge<Map<Integer,StringBuilder>>> graph=createGraphFromRDF(dataset,instances,blackList);
  createInstanceIndexMaps(graph,instances);
  if (blankLabels) {
    setBlankLabels(graph);
  }
  computeFVs(graph,instances,Math.sqrt(1.0 / ((double)(iterations + 1))),featureVectors);
  for (int i=0; i < iterations; i++) {
    relabelGraph2MultisetLabels(graph);
    startLabel=labelCounter;
    compressGraphLabels(graph);
    computeFVs(graph,instances,Math.sqrt((2.0 + i) / ((double)(iterations + 1))),featureVectors);
  }
  if (this.normalize) {
    featureVectors=KernelUtils.normalize(featureVectors);
  }
  return featureVectors;
}