File:
[LON-CAPA] /
loncom /
homework /
lonr.pm
Revision
1.5:
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Fri Jun 19 14:03:19 2009 UTC (15 years, 2 months ago) by
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Paul Rubin's code to unserialize R objects
- use tie::ixhash::easy commented out for now. Not sure if we actually want
that => code will be defunct
- needs better error handling, original code had 'die'
# The LearningOnline Network with CAPA
# Interface routines to R CAS
#
# $Id: lonr.pm,v 1.5 2009/06/19 14:03:19 www Exp $
#
# Copyright Michigan State University Board of Trustees
#
# This file is part of the LearningOnline Network with CAPA (LON-CAPA).
#
# LON-CAPA is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# LON-CAPA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with LON-CAPA; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# /home/httpd/html/adm/gpl.txt
#
# http://www.lon-capa.org/
#
package Apache::lonr;
use strict;
use IO::Socket;
use Apache::lonnet;
use Apache::response();
use LONCAPA;
### Commented out for now: use Tie::IxHash::Easy; # autoties all subhashes to keep index order
my $errormsg='';
#
# Rcroak: for use with R-error messages
#
sub Rcroak {
$errormsg=$_[0];
}
#
#
# Rpeel takes a string containing serialized values from R,
# peels off the first syntactically complete unit (number, string or array),
# and returns a list (first unit, remainder).
#
sub Rpeel {
my $x = $_[0]; # the string containing the serialized R object(s)
if ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
return ($1, $+); # x starts with a number
}
elsif ($x =~ /^s:(\d+):/) {
my $n = $1; # x starts with a string of length n
if ($x =~ /^(s:\d+:\"(.{$n})\";)(.*)$/) {
return ($1, $+); # x starts with a valid string
} else {
&Rcroak('invalid string detected');
}
}
elsif ($x =~ /^a:/) {
# x starts with an array -- need to find the closing brace
my $i = index $x, '{', 0; # position of first opening brace
if ($i < 0) {
&Rcroak('array with no opening brace');
}
my $open = 1; # counts open braces
my $j = index $x, '}', $i; # position of first closing brace
$i = index $x, '{', $i + 1; # position of next opening brace (if any)
my $pos = -1; # position of final closing brace
do {
if (($i < $j) && ($i > 0)) {
# encounter another opening brace before next closing brace
$open++;
$i = index $x, '{', $i + 1; # find the next opening brace
} elsif ($j > 0) {
# next brace encountered is a closing brace
$open--;
$pos = $j;
$j = index $x, '}', $j + 1;
} else {
&Rcroak('unmatched left brace');
}
} until ($open eq 0);
# array runs from start to $pos
my $a = substr $x, 0, $pos + 1; # array
my $b = substr $x, $pos + 1; # remainder
return ($a, $b);
} else {
&Rcroak('unrecognized R value');
}
}
# --- end Rpeel ---
#
# Rreturn accepts a string containing a serialized R object
# and returns either the object's value (if it is scalar) or a reference
# to a hash containing the contents of the object. Any null keys in the hash
# are replaced by 'capaNNN' where NNN is the index of the entry in the original
# R array.
#
sub Rreturn {
my $x = $_[0]; # the string containing the serialized R object(s)
$errormsg='';
if ($x =~ /^(?:i|d):(.+?);$/) {
return $1; # return the value of the number
} elsif ($x =~ /^s:(\d+):\"(.*)\";$/) {
# string -- verify the length
if (length($2) eq $1) {
return $2; # return the string
} else {
return 'mismatch in string length';
}
} elsif ($x =~ /^a:(\d+):\{(.*)\}$/) {
# array
my $dim = $1; # array size
$x = $2; # array contents
tie(my %h,'Tie::IxHash::Easy'); # start a hash
keys(%h) = $dim; # allocate space for the hash
my $key;
my $y;
for (my $i = 0; $i < $dim; $i++) {
($y, $x) = &Rpeel($x); # strip off the entry for the key
if ($y eq '') {
&Rcroak('ran out of keys');
}
$key = &Rreturn($y);
if ($key eq '') {
$key = "capa$i"; # correct null key
}
($y, $x) = &Rpeel($x); # strip off the value
if ($y eq '') {
&Rcroak('ran out of values');
}
if ($y =~ /^a:/) {
$h{$key} = \&Rreturn($y); # array value: store as reference
} else {
$h{$key} = &Rreturn($y); # scalar value: store the entry in the hash
}
}
if ($errormsg) { return $errormsg; }
return \%h; # return a reference to the hash
}
}
# --- end Rreturn ---
#
# Rentry takes a list of indices and gets the entry in a hash generated by Rreturn.
# Call: Rentry(Rvalue, index1, index2, ...) where Rvalue is a hash returned by Rreturn.
# Rentry will return the first scalar value it encounters (ignoring excess indices).
# If an invalid key is given, Rentry returns undef.
#
sub Rentry {
my $hash = shift; # pointer to hash
my $x;
my $i;
if (ref($hash) ne 'HASH') {
&Rcroak('argument to Rentry is not a hash');
}
while ($i = shift) {
if (exists $hash->{$i}) {
$hash = $hash->{$i};
} else {
return undef;
}
if (ref($hash) eq 'REF') {
$hash = $$hash; # dereference one layer
} elsif (ref($hash) ne 'HASH') {
return $hash; # drilled down to a scalar
}
}
}
# --- end Rentry ---
sub connect {
return IO::Socket::UNIX->new(Peer => $Apache::lonnet::perlvar{'lonSockDir'}.'/rsock',
Type => SOCK_STREAM,
Timeout => 10);
}
sub disconnect {
my ($socket)=@_;
if ($socket) { close($socket); }
}
sub rreply {
my ($socket,$cmd)=@_;
if ($socket) {
print $socket &escape($cmd)."\n";
my $reply=<$socket>;
chomp($reply);
if ($reply=~/^Incorrect/) { $reply='Error: '.$reply; }
return &unescape($reply);
} else {
return 'Error: no connection.';
}
}
sub blacklisted {
my ($cmd)=@_;
foreach my $forbidden (
'read','write','scan','save','socket','connections',
'open','close',
'plot','X11','windows','quartz',
'postscript','pdf','png','jpeg',
'dev\.list','dev\.next','dev\.prev','dev\.set',
'dev\.off','dev\.copy','dev\.print','graphics',
'library','package','source','sink','objects',
'Sys\.','unlink','file\.','on\.exit','error',
'q\(\)'
) {
if ($cmd=~/$forbidden/s) { return 1; }
}
return 0;
}
sub r_allowed_libraries {
return ('boot','class','cluster','datasets','KernSmooth','MASS',
'methods','mgcv','nlme','nnet','rpart','spatial',
'splines','stats','stats4','survival');
}
sub r_is_allowed_library {
my ($library)=@_;
foreach my $allowed_library (&r_allowed_libraries()) {
if ($library eq $allowed_library) { return 1; }
}
return 0;
}
sub runscript {
my ($socket,$fullscript,$libraries)=@_;
if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
my $reply;
$fullscript=~s/[\n\r\l]//gs;
if ($libraries) {
foreach my $library (split(/\s*\,\s*/,$libraries)) {
unless ($library=~/\w/) { next; }
if (&r_is_allowed_library($library)) {
$reply=&rreply($socket,'library('.$library.');'."\n");
if ($reply=~/^Error\:/) { return $reply; }
} else {
return 'Error: blacklisted';
}
}
}
foreach my $line (split(/\;/s,$fullscript)) {
if ($line=~/\w/) { $reply=&rreply($socket,$line.";\n"); }
if ($reply=~/^Error\:/) { return $reply; }
}
$reply=~s/^\s*//gs;
$reply=~s/\s*$//gs;
&Apache::lonxml::debug("r $fullscript \n reply $reply");
return $reply;
}
sub r_cas_formula_fix {
my ($expression)=@_;
return &Apache::response::implicit_multiplication($expression);
}
sub r_run {
my ($script,$submission,$argument,$libraries) = @_;
my $socket=&connect();
my @submissionarray=split(/\s*\,\s*/,$submission);
for (my $i=0;$i<=$#submissionarray;$i++) {
my $n=$i+1;
my $fixedsubmission=&r_cas_formula_fix($submissionarray[$i]);
$script=~s/RESPONSE\[$n\]/$fixedsubmission/gs;
}
my @argumentarray=@{$argument};
for (my $i=0;$i<=$#argumentarray;$i++) {
my $n=$i+1;
my $fixedargument=&r_cas_formula_fix($argumentarray[$i]);
$script=~s/LONCAPALIST\[$n\]/$fixedargument/gs;
}
my $reply=&runscript($socket,$script,$libraries);
&disconnect($socket);
if ($reply=~/^\s*true\s*$/i) { return 'EXACT_ANS'; }
if ($reply=~/^\s*false\s*$/i) { return 'INCORRECT'; }
return 'BAD_FORMULA';
}
sub r_eval {
my ($script,$libraries) = @_;
my $socket=&connect();
my $reply=&runscript($socket,$script,$libraries);
&disconnect($socket);
return $reply;
}
sub compareterms {
my ($socket,$terma,$termb)=@_;
my $difference=$terma.'-('.$termb.')';
if (&blacklisted($difference)) { return 'Error: blacklisted'; }
my $reply=&rreply($socket,$difference.';');
if ($reply=~/^\s*0\s*$/) { return 'true'; }
if ($reply=~/^Error\:/) { return $reply; }
return 'false';
}
sub r_check {
my ($response,$answer,$reterror) = @_;
my $socket=&connect();
my $reply=&compareterms($socket,$response,$answer);
&disconnect($socket);
# integer to string mappings come from capaParser.h
# 1 maps to 'EXACT_ANS'
if ($reply eq 'true') { return 1; }
# 11 maps to 'BAD_FORMULA'
if ($reply=~/^Error\:/) { return 11; }
# 7 maps to 'INCORRECT'
return 7;
}
1;
__END__;
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