janwielemaker/rserve_client

SWI-Prolog/SWISH client for Rserve

Rserve client for SWI-Prolog/SWISH

Rserve R-package:

• https://rforge.net/Rserve/doc.html
• https://github.com/s-u/Rserve
• Installation of Rserve:
  • Default version (1.7.3):
    • install.packages("Rserve")
  • Latest (1.8.5, has lots of enhancements)
    • install.packages("Rserve",,"http://rforge.net/",type="source")

Compiling this package

This library is configured as a SWI-Prolog pack. It can be installed using the command below. The installation requires git, autoconf and the common C++ build tools.

?- pack_install('rserve_client').

This is tested on Ubuntu (14.04 and 16.04). It performs these steps:

• Clone my fork of Rserve (some extensions to the C++ client)
• Configure and build the C++ client library
• Build the SWI-Prolog interface rserve.so

Using this package

This package is primarily intended for accessing R in server environments such as SWISH. We created a Docker container that runs Rserve in a sandbox. The container exposes Rserve using a Unix-domain socket at the following address:

/home/rserve/socket

With SWISH and is interface installed in adjacent directories, i.e., below the same parent, R may be linked to SWISH doing

:- use_module(lib/r_swish).

Now, R is not safe. You should either run Rserve in a tight OS container and load library(r/r_sandbox) or run SWISH in authenticated mode by loading lib/authenticate.pl.

Libraries provided

User libraries

• library(r/r_call) Defines basic user API to R
• library(r/r_data) Utilities to create and fetch R data frames

Implementation libraries

• library(r/r_expand_dot) Allow for dots in atoms and functors without quotes.
• library(r/r_grammar) R Parser utilities (lexer) that support R quasi quotations
• library(r/r_term) DCG non-terminal to translate a term into an R command string
• library(r/r_sandbox) Declare the R API sandbox-safe
• library(r/r_serve) Low-level level communication library

Status

This is just a proof of context. Obviously missing functionality:

• Cover more Prolog term --> R translations, following Real.
• Support OOB (Out Of Band) communication introduced in recent versions of Rserve to deal with R I/O.

Related projects

This interface is inspired by Real by Nicos Angelopoulos. Main differences:

• Real is embedded in SWI-Prolog. This is more productive for local deployment as the communication is faster and R has access to its default environment. Thus, R can open graphical windows and can read and write files. Real is also much more mature, notably in the supporting a much larger part of the R syntax from Prolog.

• Rserve runs typically using a different user in a different environment. The R environment cannot easily communicate with your local development environment. When used in a (web) server environment this comes with several advantages. We can seriously sandbox the R executable, each query in SWISH gets its own R instance and information can thus nog leak between queries and users.

rserve_client's Issues

Support for(i in 1:10)

Library options

When running swish with the latest swipl version I get

Mar 14 11:45:02 cpr run.sh[1277]: ERROR: /home/rzf/swish/pack/rserve_client/prolog/r/r_call.pl:61:
Mar 14 11:45:02 cpr run.sh[1277]: ERROR:    source_sink `library(options)' does not exist
Mar 14 11:45:02 cpr run.sh[1277]: Warning: /home/rzf/swish/pack/rserve_client/prolog/r/r_call.pl:61:
Mar 14 11:45:02 cpr run.sh[1277]: Warning:    Goal (directive) failed: r_call:use_module(library(options))

Support array[,1:14]

Support for HTML output (e.g., heatmaply)

loading twice foreign library gives error

Makes swish not working with R (error while loadin lib r/r_serve)

rzf@cpr:~/swish$ swipl
Welcome to SWI-Prolog (threaded, 64 bits, version 7.7.20-63-g9d33c3f81)
SWI-Prolog comes with ABSOLUTELY NO WARRANTY. This is free software.
Please run ?- license. for legal details.

For online help and background, visit http://www.swi-prolog.org
For built-in help, use ?- help(Topic). or ?- apropos(Word).

?- use_foreign_library(foreign(rserve)).
true.

?- use_foreign_library(foreign(rserve)).
ERROR: Initialization goal shlib:load_foreign_library(user:foreign(rserve)) rais ed exception:
ERROR: No install function in '/home/rzf/lib/swipl/pack/rserve_client/lib/x86_64 -linux/rserve.so'
ERROR: Tried: [install_rserve,install]
true.

Adopt width of console

Console width can be set with options(width=150). Default width should be computed from the interface.