Program: 62433
Project: 62433
Buggy source:
@Override protected boolean verifyUserInput(){
  if (shouldValidate()) {
    File file=newOperatorDescriptor.getMainToolFileLocation();
    if (file == null) {
      Object value=bindingContext.getBinding(ToolAdapterConstants.MAIN_TOOL_FILE_LOCATION).getPropertyValue();
      if (value != null) {
        file=value instanceof File ? (File)value : new File(value.toString());
      }
    }
    if (file == null) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_Tool_Path_Text());
      return false;
    }
    Path toolLocation=newOperatorDescriptor.resolveVariables(newOperatorDescriptor.getMainToolFileLocation()).toPath();
    if (!(Files.exists(toolLocation) && Files.isExecutable(toolLocation))) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_Tool_Path_Text());
      return false;
    }
    File workingDir=newOperatorDescriptor.resolveVariables(newOperatorDescriptor.getWorkingDir());
    if (!(workingDir != null && workingDir.exists() && workingDir.isDirectory())) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_WorkDir_Text());
      return false;
    }
  }
  java.util.List<SystemVariable> variables=newOperatorDescriptor.getVariables();
  if (variables != null) {
    for (    SystemVariable variable : variables) {
      String value=variable.getValue();
      if (value == null || value.isEmpty()) {
        Dialogs.showWarning(String.format(Bundle.MSG_Empty_Variable_Text(),variable.getKey()));
        return false;
      }
    }
  }
  if (shouldValidate()) {
    ParameterDescriptor[] parameterDescriptors=newOperatorDescriptor.getParameterDescriptors();
    if (parameterDescriptors != null && parameterDescriptors.length > 0) {
      for (      ParameterDescriptor parameterDescriptor : parameterDescriptors) {
        Class<?> dataType=parameterDescriptor.getDataType();
        String defaultValue=parameterDescriptor.getDefaultValue();
        if (File.class.isAssignableFrom(dataType) && (parameterDescriptor.isNotNull() || parameterDescriptor.isNotEmpty()) && (defaultValue == null || defaultValue.isEmpty() || !Files.exists(Paths.get(defaultValue)))) {
          Dialogs.showWarning(String.format(Bundle.MSG_Inexistem_Parameter_Value_Text(),parameterDescriptor.getName(),parameterDescriptor.isNotNull() ? ToolAdapterConstants.NOT_NULL : ToolAdapterConstants.NOT_EMPTY));
          return false;
        }
      }
    }
  }
  return true;
}

Fixed version (ground truth):
@Override protected boolean verifyUserInput(){
  varTable.stopVariablesTableEditing();
  paramsTable.stopVariablesTableEditing();
  if (shouldValidate()) {
    File file=newOperatorDescriptor.getMainToolFileLocation();
    if (file == null) {
      Object value=bindingContext.getBinding(ToolAdapterConstants.MAIN_TOOL_FILE_LOCATION).getPropertyValue();
      if (value != null) {
        file=value instanceof File ? (File)value : new File(value.toString());
      }
    }
    if (file == null) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_Tool_Path_Text());
      return false;
    }
    Path toolLocation=newOperatorDescriptor.resolveVariables(newOperatorDescriptor.getMainToolFileLocation()).toPath();
    if (!(Files.exists(toolLocation) && Files.isExecutable(toolLocation))) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_Tool_Path_Text());
      return false;
    }
    File workingDir=newOperatorDescriptor.resolveVariables(newOperatorDescriptor.getWorkingDir());
    if (!(workingDir != null && workingDir.exists() && workingDir.isDirectory())) {
      Dialogs.showWarning(Bundle.MSG_Inexistent_WorkDir_Text());
      return false;
    }
  }
  java.util.List<SystemVariable> variables=newOperatorDescriptor.getVariables();
  if (variables != null) {
    for (    SystemVariable variable : variables) {
      String key=variable.getKey();
      if (key == null || key.isEmpty()) {
        Dialogs.showWarning(String.format(Bundle.MSG_Empty_Variable_Key_Text()));
        return false;
      }
      String value=variable.getValue();
      if (value == null || value.isEmpty()) {
        Dialogs.showWarning(String.format(Bundle.MSG_Empty_Variable_Text(),key));
        return false;
      }
    }
  }
  if (shouldValidate()) {
    ParameterDescriptor[] parameterDescriptors=newOperatorDescriptor.getParameterDescriptors();
    if (parameterDescriptors != null && parameterDescriptors.length > 0) {
      for (      ParameterDescriptor parameterDescriptor : parameterDescriptors) {
        Class<?> dataType=parameterDescriptor.getDataType();
        String defaultValue=parameterDescriptor.getDefaultValue();
        if (File.class.isAssignableFrom(dataType) && (parameterDescriptor.isNotNull() || parameterDescriptor.isNotEmpty()) && (defaultValue == null || defaultValue.isEmpty() || !Files.exists(Paths.get(defaultValue)))) {
          Dialogs.showWarning(String.format(Bundle.MSG_Inexistem_Parameter_Value_Text(),parameterDescriptor.getName(),parameterDescriptor.isNotNull() ? ToolAdapterConstants.NOT_NULL : ToolAdapterConstants.NOT_EMPTY));
          return false;
        }
      }
    }
  }
  return true;
}