Document вот так: Document doc = update.getMessage().getDocument();, а из него получить file_id но как его загрузить на сервер? 
getFile
Use this method to get basic info about a file and prepare it for downloading. For the moment, bots can download files of up to 20MB in size. On success, a File object is returned. The file can then be downloaded via the link https://api.telegram.org/file/bot%token%/%file_path%, where %file_path% is taken from the response. It is guaranteed that the link will be valid for at least 1 hour. When the link expires, a new one can be requested by calling getFile again.
Простой
Простой
Средний
Простой
Средний
