elasticsearch - No query registered for [query]]

The exception basically means "There is no known query type called query". I'm guessing that your client library is automatically inserting the top-level query property, so your generated query actually looks like this:

{
    "query" : {
        "query" : { 
          "match_all" : {} 
        }
    }
}

If your client can dump the JSON representation of the query, that can help a lot in debugging.

Try removing the query portion from your text file so that it is just the match_all query, see if that works for you.