Program: 141231
Project: 141231
Buggy source:
@Override public StepResult execute(final Design design,final StepContext context,final StepStatus status){
  final StringBuilder log=new StringBuilder();
  final WorkflowContext fullContext=(WorkflowContext)context;
  final Map<DataFile,DataFile> filesToCopy=newHashMap();
  File repackagedJarFile=null;
  try {
    for (    Sample sample : design.getSamples())     filesToCopy.putAll(findDataFilesInWorkflow(sample,context));
    removeNotExistingDataFile(filesToCopy);
    if (getDest().exists()) {
      throw new IOException("String_Node_Str" + getDest());
    }
    if (!context.getRuntime().isHadoopMode()) {
      repackagedJarFile=HadoopJarRepackager.repack();
      final DataFile jarDataFile=new DataFile(repackagedJarFile.getAbsolutePath());
      filesToCopy.put(jarDataFile,getUploadedDataFile(jarDataFile));
    }
    final Settings settings=context.getRuntime().getSettings();
    reWriteDesign(context,filesToCopy);
    if (settings.isObfuscateDesign()) {
      DesignUtils.obfuscate(design,settings.isObfuscateDesignRemoveReplicateInfo());
    }
    final File newDesignFile=writeTempDesignFile(context,design);
    final DataFile uploadedDesignDataFile=getUploadedDataFile(new DataFile(context.getDesignPathname()));
    filesToCopy.put(new DataFile(newDesignFile.getAbsolutePath()),uploadedDesignDataFile);
    final DataFile currentParamDataFile=new DataFile(context.getWorkflowPathname());
    final DataFile uploadedParamDataFile=getUploadedDataFile(currentParamDataFile);
    filesToCopy.put(currentParamDataFile,uploadedParamDataFile);
    for (    Map.Entry<DataFile,DataFile> e : filesToCopy.entrySet()) {
      log.append("String_Node_Str");
      log.append(e.getKey());
      log.append("String_Node_Str");
      log.append(e.getValue());
      log.append('\n');
    }
    copy(filesToCopy);
    if (!newDesignFile.delete()) {
      LOGGER.warning("String_Node_Str" + newDesignFile);
    }
    fullContext.setDesignPathname(uploadedDesignDataFile.getSource());
    fullContext.setWorkflowPathname(uploadedParamDataFile.getSource());
  }
 catch (  IOException e) {
    return status.createStepResult(e);
  }
catch (  EoulsanIOException e) {
    return status.createStepResult(e);
  }
  if (!context.getRuntime().isHadoopMode()) {
    fullContext.setJarPathname(getDest().toString() + "String_Node_Str" + repackagedJarFile.getName());
  }
  status.setStepMessage(log.toString());
  return status.createStepResult();
}

Fixed version (ground truth):
@Override public StepResult execute(final Design design,final StepContext context,final StepStatus status){
  final StringBuilder log=new StringBuilder();
  final WorkflowContext fullContext=((AbstractWorkflow)context.getWorkflow()).getWorkflowContext();
  final Map<DataFile,DataFile> filesToCopy=newHashMap();
  File repackagedJarFile=null;
  try {
    for (    Sample sample : design.getSamples())     filesToCopy.putAll(findDataFilesInWorkflow(sample,context));
    removeNotExistingDataFile(filesToCopy);
    if (getDest().exists()) {
      throw new IOException("String_Node_Str" + getDest());
    }
    if (!context.getRuntime().isHadoopMode()) {
      repackagedJarFile=HadoopJarRepackager.repack();
      final DataFile jarDataFile=new DataFile(repackagedJarFile.getAbsolutePath());
      filesToCopy.put(jarDataFile,getUploadedDataFile(jarDataFile));
    }
    final Settings settings=context.getRuntime().getSettings();
    reWriteDesign(context,filesToCopy);
    if (settings.isObfuscateDesign()) {
      DesignUtils.obfuscate(design,settings.isObfuscateDesignRemoveReplicateInfo());
    }
    final File newDesignFile=writeTempDesignFile(context,design);
    final DataFile uploadedDesignDataFile=getUploadedDataFile(new DataFile(context.getDesignPathname()));
    filesToCopy.put(new DataFile(newDesignFile.getAbsolutePath()),uploadedDesignDataFile);
    final DataFile currentParamDataFile=new DataFile(context.getWorkflowPathname());
    final DataFile uploadedParamDataFile=getUploadedDataFile(currentParamDataFile);
    filesToCopy.put(currentParamDataFile,uploadedParamDataFile);
    for (    Map.Entry<DataFile,DataFile> e : filesToCopy.entrySet()) {
      log.append("String_Node_Str");
      log.append(e.getKey());
      log.append("String_Node_Str");
      log.append(e.getValue());
      log.append('\n');
    }
    copy(filesToCopy);
    if (!newDesignFile.delete()) {
      LOGGER.warning("String_Node_Str" + newDesignFile);
    }
    fullContext.setDesignPathname(uploadedDesignDataFile.getSource());
    fullContext.setWorkflowPathname(uploadedParamDataFile.getSource());
  }
 catch (  IOException e) {
    return status.createStepResult(e);
  }
catch (  EoulsanIOException e) {
    return status.createStepResult(e);
  }
  if (!context.getRuntime().isHadoopMode()) {
    fullContext.setJarPathname(getDest().toString() + "String_Node_Str" + repackagedJarFile.getName());
  }
  status.setStepMessage(log.toString());
  return status.createStepResult();
}