Program: 122261
Project: 122261
Buggy source:
@Override public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
  monitor.setCanceled(false);
  int size=(results.size() * 2 + 1) * UpdatesConstants.SCALE;
  monitor.beginTask(Messages.getString("String_Node_Str"),size);
  ProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
  Map<String,Set<String>> jobIdToVersion=new HashMap<String,Set<String>>();
  Map<String,Boolean> jobIdClosed=new HashMap<String,Boolean>();
  for (  UpdateResult result : results) {
    String id=result.getObjectId();
    String version=result.getObjectVersion();
    if (id == null) {
      if (result.getJob() != null && result.getJob() instanceof IProcess) {
        IProcess process=(IProcess)result.getJob();
        if (process instanceof IProcess2 && ERepositoryStatus.LOCK_BY_OTHER.equals(factory.getStatus(((IProcess2)process).getProperty().getItem()))) {
          continue;
        }
        id=process.getId();
        version=process.getVersion();
        result.setObjectId(id);
        result.setObjectVersion(version);
      }
 else {
        continue;
      }
    }
    Set<String> versionList;
    if (!jobIdToVersion.containsKey(id)) {
      versionList=new HashSet<String>();
      jobIdToVersion.put(id,versionList);
    }
 else {
      versionList=jobIdToVersion.get(id);
    }
    versionList.add(version);
    jobIdClosed.put(id + "String_Node_Str" + version,result.isFromItem());
  }
  for (  String currentId : jobIdToVersion.keySet()) {
    for (    String version : jobIdToVersion.get(currentId)) {
      IRepositoryViewObject currentObj=null;
      boolean closedItem=jobIdClosed.get(currentId + "String_Node_Str" + version);
      IProcess process=null;
      Item item=null;
      if (closedItem) {
        boolean checkOnlyLastVersion=Boolean.parseBoolean(DesignerPlugin.getDefault().getPreferenceStore().getString("String_Node_Str"));
        try {
          if (checkOnlyLastVersion || version == null) {
            currentObj=factory.getLastVersion(currentId);
          }
 else {
            List<IRepositoryViewObject> allVersion=factory.getAllVersion(currentId);
            for (            IRepositoryViewObject obj : allVersion) {
              if (obj.getVersion().equals(version)) {
                currentObj=obj;
              }
            }
          }
        }
 catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
        if (currentObj == null) {
          continue;
        }
        item=currentObj.getProperty().getItem();
        IDesignerCoreService designerCoreService=CorePlugin.getDefault().getDesignerCoreService();
        if (item instanceof ProcessItem) {
          process=designerCoreService.getProcessFromProcessItem((ProcessItem)item);
        }
 else         if (item instanceof JobletProcessItem) {
          process=designerCoreService.getProcessFromJobletProcessItem((JobletProcessItem)item);
        }
      }
      for (      UpdateResult result : results) {
        if (!StringUtils.equals(currentId,result.getObjectId())) {
          continue;
        }
        if (closedItem) {
          result.setJob(process);
        }
        executeUpdate(result,monitor,updateAllJobs);
        if (closedItem) {
          result.setJob(null);
        }
      }
      if (closedItem && process instanceof IProcess2) {
        IProcess2 process2=(IProcess2)process;
        ProcessType processType;
        try {
          processType=process2.saveXmlFile(false);
          if (item instanceof JobletProcessItem) {
            ((JobletProcessItem)item).setJobletProcess((JobletProcess)processType);
          }
 else {
            ((ProcessItem)item).setProcess(processType);
          }
          factory.save(item);
        }
 catch (        IOException e) {
          ExceptionHandler.process(e);
        }
catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
      }
      if (closedItem && !ERepositoryStatus.LOCK_BY_USER.equals(factory.getStatus(item))) {
        try {
          factory.unloadResources(item.getProperty());
        }
 catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
      }
    }
  }
  upadateJobletReferenceInfor();
  refreshRelatedViewers(results);
  checkandRefreshProcess(results);
  monitor.worked(1 * UpdatesConstants.SCALE);
  monitor.done();
}

Fixed version (ground truth):
@Override public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
  monitor.setCanceled(false);
  int size=(results.size() * 2 + 1) * UpdatesConstants.SCALE;
  monitor.beginTask(Messages.getString("String_Node_Str"),size);
  ProxyRepositoryFactory factory=ProxyRepositoryFactory.getInstance();
  Map<String,Set<String>> jobIdToVersion=new HashMap<String,Set<String>>();
  Map<String,Boolean> jobIdClosed=new HashMap<String,Boolean>();
  for (  UpdateResult result : results) {
    String id=result.getObjectId();
    String version=result.getObjectVersion();
    if (id == null) {
      if (result.getJob() != null && result.getJob() instanceof IProcess) {
        IProcess process=(IProcess)result.getJob();
        if (process instanceof IProcess2 && ERepositoryStatus.LOCK_BY_OTHER.equals(factory.getStatus(((IProcess2)process).getProperty().getItem()))) {
          continue;
        }
        id=process.getId();
        version=process.getVersion();
        result.setObjectId(id);
        result.setObjectVersion(version);
      }
 else {
        continue;
      }
    }
    Set<String> versionList;
    if (!jobIdToVersion.containsKey(id)) {
      versionList=new HashSet<String>();
      jobIdToVersion.put(id,versionList);
    }
 else {
      versionList=jobIdToVersion.get(id);
    }
    versionList.add(version);
    jobIdClosed.put(id + "String_Node_Str" + version,result.isFromItem());
  }
  for (  String currentId : jobIdToVersion.keySet()) {
    for (    String version : jobIdToVersion.get(currentId)) {
      IRepositoryViewObject currentObj=null;
      boolean closedItem=jobIdClosed.get(currentId + "String_Node_Str" + version);
      IProcess process=null;
      Item item=null;
      if (closedItem) {
        boolean checkOnlyLastVersion=Boolean.parseBoolean(DesignerPlugin.getDefault().getPreferenceStore().getString("String_Node_Str"));
        try {
          if (checkOnlyLastVersion || version == null) {
            currentObj=factory.getLastVersion(currentId);
          }
 else {
            List<IRepositoryViewObject> allVersion=factory.getAllVersion(currentId);
            for (            IRepositoryViewObject obj : allVersion) {
              if (obj.getVersion().equals(version)) {
                currentObj=obj;
              }
            }
          }
        }
 catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
        if (currentObj == null) {
          continue;
        }
        item=currentObj.getProperty().getItem();
        IDesignerCoreService designerCoreService=CorePlugin.getDefault().getDesignerCoreService();
        if (item instanceof ProcessItem) {
          process=designerCoreService.getProcessFromProcessItem((ProcessItem)item);
        }
 else         if (item instanceof JobletProcessItem) {
          process=designerCoreService.getProcessFromJobletProcessItem((JobletProcessItem)item);
        }
      }
      for (      UpdateResult result : results) {
        if (!StringUtils.equals(currentId,result.getObjectId())) {
          continue;
        }
        if (closedItem) {
          result.setJob(process);
        }
        executeUpdate(result,monitor);
        if (closedItem) {
          result.setJob(null);
        }
      }
      if (closedItem && process instanceof IProcess2) {
        IProcess2 process2=(IProcess2)process;
        ProcessType processType;
        try {
          processType=process2.saveXmlFile();
          if (item instanceof JobletProcessItem) {
            ((JobletProcessItem)item).setJobletProcess((JobletProcess)processType);
          }
 else {
            ((ProcessItem)item).setProcess(processType);
          }
          factory.save(item);
        }
 catch (        IOException e) {
          ExceptionHandler.process(e);
        }
catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
      }
      if (closedItem && !ERepositoryStatus.LOCK_BY_USER.equals(factory.getStatus(item))) {
        try {
          factory.unloadResources(item.getProperty());
        }
 catch (        PersistenceException e) {
          ExceptionHandler.process(e);
        }
      }
    }
  }
  upadateJobletReferenceInfor();
  refreshRelatedViewers(results);
  checkandRefreshProcess(results);
  monitor.worked(1 * UpdatesConstants.SCALE);
  monitor.done();
}