# The LearningOnline Network with CAPA # Interface routines to R CAS # # $Id: lonr.pm,v 1.9 2009/08/14 01:58:52 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; ### You need to install the libraries below for this to work! ###use Tie::IxHash::Easy; # autoties all subhashes to keep index order ###use Data::Dumper; # used to output hash contents 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 'resultNNN' 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) $x=~s/^\"//; $x=~s/\"$//; $x=~s/\\\"/\"/g; $errormsg=''; if ($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 '') { $key = "result$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 } else { return 'Unrecognized output'; } } # --- end Rreturn --- sub Rentry { my $hash = shift; # pointer to tied hash my $i; if (ref($hash) ne 'HASH') { return 'Argument to cas_hashref_entry is not a hash!'; } while ($i = shift) { if (exists($hash->{$i})) { $hash = $hash->{$i}; } else { return undef; } if (ref($hash) eq 'REF') { $hash = $$hash; # dereference one layer } elsif (ref($hash) ne 'HASH') { return $hash; # drilled down to a scalar } } } sub Rarray { my $hash = shift; # pointer to tied hash my $i; if (ref($hash) ne 'HASH') { return 'Argument to cas_hashref_array is not a hash!'; } while ($i = shift) { if (exists($hash->{$i})) { $hash = $hash->{$i}; } else { return undef; } if (ref($hash) eq 'REF') { $hash = $$hash; # dereference one layer } } my @returnarray=(); foreach my $key (keys(%{$hash})) { $returnarray[$key-1]=$$hash{$key}; } return @returnarray; } 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 ('alr3','boot','car','class','cluster','datasets','Hmisc','KernSmooth','leaps','lmtest', 'MASS','methods','mgcv','nlme','nnet','qAnalyst','quadprog','rpart','SuppDists','spatial', 'splines','stats','stats4','survival','tseries','zoo'); } 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('.$library.');'); if ($reply=~/^Error\:/) { return $reply; } } else { return 'Error: blacklisted'; } } } $fullscript=~s/\;+\s*$//s; if ($fullscript=~/\w/) { $reply=&rreply($socket,$fullscript.';'); } if ($reply=~/^Error\:/) { return $reply; } $reply=~s/^\s*//gs; $reply=~s/\s*$//gs; &Apache::lonxml::debug("r $fullscript \n reply $reply"); return $reply; } sub runserializedscript { my ($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('.$library.');'); if ($reply=~/^Error\:/) { return($reply,$reply); } } else { return 'Error: blacklisted'; } } } $fullscript=~s/\;+\s*$//s; my $lastline=''; my $firstpart=''; if ($fullscript=~/\;/) { ($firstpart,$lastline)=($fullscript=~/^(.*\;)([^\;]+)$/); } else { $lastline=$fullscript; } if ($firstpart) { $firstpart=~s/\;+\s*$//s; $reply=&rreply($socket,$firstpart.';'); if ($reply=~/^Error\:/) { return($reply,$reply); } } # The last line needs to be serialized $reply=&Rreturn(&rreply($socket,"phpSerialize($lastline);")); return($reply,&Dumper($reply)); } sub r_cas_formula_fix { my ($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,$libraries,$hashflag) = @_; my $socket=&connect(); my $reply; my $dump=''; if ($hashflag) { ($reply,$dump)=&runserializedscript($socket,$script,$libraries); } else { $reply=&runscript($socket,$script,$libraries); } &disconnect($socket); return ($reply,$dump); } sub compareterms { my ($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__;