erserve - An Erlang/Rserve communication application

Introduction

Rserve

Rserve is a TCP/IP server running in R, allowing interfacing to R from many languages without explicitly initialising R or linking with it.

erserve

erserve is an Erlang application that implements the communication with Rserve, making it possible to make calls to R from Erlang, and to receive data back.

The interface is very simple, and the functionality implemented is at this point limited, but includes the most common and useful data types.

Quickstart

Download and install R.
Install Rserve, which can be easily done using R's package system:

install.packages('Rserve')

Start the Rserve server in R:

library(Rserve)
Rserve()

Open a terminal and clone the erserve git library:

git clone https://github.com/del/erserve.git

Compile erserve:

cd erserve
./rebar compile

Start an erlang node with erserve in its path:

erl -pa ebin/

Start the erserve application and connect to your Rserve

application:start(erserve).
Conn = erserve:open("localhost", 6311).

Send a message to R to verify the connection works:

{ok, Rdata} = erserve:eval(Conn, "c(1, 2, 3)"),
erserve:type(Rdata),  % xt_array_double
erserve:parse(Rdata). % [1.0,2.0,3.0]

Connections

An erserve connection is opened using one of functions open/0, open/1 or open/2, where the arguments, if given, are hostname and port:

Conn1 = erserve:open(),                 %% erserve:open("localhost", 6311)
Conn2 = erserve:open("somehost"),       %% erserve:open("somehost",  6311)
Conn3 = erserve:open("somehost", 1163).

To close a connection, simply send it to close/1:

ok = erserve:close(Conn).

If you are in need of connection pooling, take a look at erserve_pool.

Issuing R commands

erserve supports two ways of running R commands: eval_void/2 and eval/2. The difference is that eval_void/2 only receives an ok or {error, ErrorCode, Reason} as reply, whereas eval/2 returns {ok, Rdata} or {error, ErrorCode, Reason}.

eval_void(Conn, Expr) is used when you're issuing a command for the reason of side effects:

ok = erserve:eval_void(Conn, "some.var <- 42").

whereas eval(Conn, Expr) is used when you wish to receive a reply from R. The return is in an internal format which should not be matched on, since it is subject to change. To use the returned data, make use of the type/1 and parse/1 functions:

{ok, Rdata} = erserve:eval(Conn, "some.var"),
[42.0]      = case erserve:type(Rdata) of
                xt_array_double -> erserve:parse(Rdata);
                _OtherType      -> error
              end.

Sending/receiving data

It's possible to upload a variable to R directly in binary format, to avoid having to create expression strings for everything. To do this, use set_variable/4, which has the signature set_variable(Conn, Name, Type, Value).

ok                     = erserve:set_variable(Conn, "some.var", xt_array_str, ["bla", "bla"]),
{ok, Rdata}            = erserve:eval(Conn, "some.var"),
xt_array_str           = erserve:type(Rdata),
[<<"bla">>, <<"bla">>] = erserve:parse(Rdata).

Note that erserve outputs all strings in binary format.

Note that R allows NA values in all forms of arrays. These become the atom null in the data returned by erserve:parse/1. E.g. the R list c(1.0, NA, 2.0) becomes [1.0, null, 2.0]. Conversely, you can upload an NA by inserting the atom null into the data you send.

Uploading NAs is supported in int and double arrays, as well as booleans, but for the latter, there is an issue: if such a boolean array is stored using R's save() function, and then read up in a regular R instance using load(), the NA values will be interpreted as TRUE. It's not clear exactly what the issue is, but it might have to do with Rserve itself.

At the moment, uploading of variables supports the simple R types xt_str, xt_array_double, xt_array_int and xt_array_str. On top of this, it also supports the more advanced formats xt_vector and dataframe.

An xt_vector consists of a list of tuples {Type, Value} where Type is one of the just mentioned types.

A dataframe is a list of tuples {Name, Type, Value}. Each such tuple generates a column in the resulting dataframe, where Name is a string that becomes the column's name, and Type and Value are as described before.

Some examples of variable uploading:

ok = erserve:set_variable(Conn, "some.var", xt_str,          "hello world"),
ok = erserve:set_variable(Conn, "some.var", xt_array_double, [1.1, 2.2, 3.3]),
ok = erserve:set_variable(Conn, "some.var", xt_array_int,    [1, 2, 3]),
ok = erserve:set_variable(Conn, "some.var", xt_array_str,    ["hello", "world"]),
ok = erserve:set_variable(Conn, "some.var", xt_vector,       [ {xt_array_str, ["a", "b"]}
                                                             , {xt_array_int, [1, 3, 5]} ]),
ok = erserve:set_variable(Conn, "some.var", dataframe,       [ {"Letters", xt_array_str, ["a", "b"]}
                                                             , {"Numbers", xt_array_int, [1, 3]} ]).

Implementation details of interest

The communication with Rserve is done using gen_tcp, and messages are read from Rserve into memory. This means that some caution is needed to avoid calling R code that will return very large data sets.

String arrays are returned as arrays of binary strings. However, there is conversion over lists internally, so the individual strings do not reference the original binary containing the whole string array.

Acknowledgements

Thanks to my employer, Klarna for allowing me to contribute to open source as part of my work.

DavidAlphaFox / erserve