Annotation of loncom/homework/lonr.pm, revision 1.9
1.1 www 1: # The LearningOnline Network with CAPA
2: # Interface routines to R CAS
3: #
1.9 ! www 4: # $Id: lonr.pm,v 1.8 2009/08/12 20:09:02 www Exp $
1.1 www 5: #
6: # Copyright Michigan State University Board of Trustees
7: #
8: # This file is part of the LearningOnline Network with CAPA (LON-CAPA).
9: #
10: # LON-CAPA is free software; you can redistribute it and/or modify
11: # it under the terms of the GNU General Public License as published by
12: # the Free Software Foundation; either version 2 of the License, or
13: # (at your option) any later version.
14: #
15: # LON-CAPA is distributed in the hope that it will be useful,
16: # but WITHOUT ANY WARRANTY; without even the implied warranty of
17: # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18: # GNU General Public License for more details.
19: #
20: # You should have received a copy of the GNU General Public License
21: # along with LON-CAPA; if not, write to the Free Software
22: # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
23: #
24: # /home/httpd/html/adm/gpl.txt
25: #
26: # http://www.lon-capa.org/
27: #
28:
29: package Apache::lonr;
30:
31: use strict;
32: use IO::Socket;
33: use Apache::lonnet;
34: use Apache::response();
35: use LONCAPA;
1.6 www 36:
37: ### You need to install the libraries below for this to work!
38:
39: ###use Tie::IxHash::Easy; # autoties all subhashes to keep index order
40: ###use Data::Dumper; # used to output hash contents
1.5 www 41:
42: my $errormsg='';
43:
44: #
45: # Rcroak: for use with R-error messages
46: #
47: sub Rcroak {
48: $errormsg=$_[0];
49: }
50:
51: #
52: #
53: # Rpeel takes a string containing serialized values from R,
54: # peels off the first syntactically complete unit (number, string or array),
55: # and returns a list (first unit, remainder).
56: #
57: sub Rpeel {
58: my $x = $_[0]; # the string containing the serialized R object(s)
59: if ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
60: return ($1, $+); # x starts with a number
1.9 ! www 61: } elsif ($x =~ /^s:(\d+):/) {
1.5 www 62: my $n = $1; # x starts with a string of length n
63: if ($x =~ /^(s:\d+:\"(.{$n})\";)(.*)$/) {
64: return ($1, $+); # x starts with a valid string
65: } else {
66: &Rcroak('invalid string detected');
67: }
1.9 ! www 68: } elsif ($x =~ /^a:/) {
1.5 www 69: # x starts with an array -- need to find the closing brace
70: my $i = index $x, '{', 0; # position of first opening brace
71: if ($i < 0) {
72: &Rcroak('array with no opening brace');
73: }
74: my $open = 1; # counts open braces
75: my $j = index $x, '}', $i; # position of first closing brace
76: $i = index $x, '{', $i + 1; # position of next opening brace (if any)
77: my $pos = -1; # position of final closing brace
78: do {
79: if (($i < $j) && ($i > 0)) {
80: # encounter another opening brace before next closing brace
81: $open++;
82: $i = index $x, '{', $i + 1; # find the next opening brace
83: } elsif ($j > 0) {
84: # next brace encountered is a closing brace
85: $open--;
86: $pos = $j;
87: $j = index $x, '}', $j + 1;
88: } else {
89: &Rcroak('unmatched left brace');
90: }
91: } until ($open eq 0);
92: # array runs from start to $pos
93: my $a = substr $x, 0, $pos + 1; # array
94: my $b = substr $x, $pos + 1; # remainder
95: return ($a, $b);
96: } else {
97: &Rcroak('unrecognized R value');
98: }
99: }
100: # --- end Rpeel ---
101:
102: #
103: # Rreturn accepts a string containing a serialized R object
104: # and returns either the object's value (if it is scalar) or a reference
105: # to a hash containing the contents of the object. Any null keys in the hash
1.6 www 106: # are replaced by 'resultNNN' where NNN is the index of the entry in the original
1.5 www 107: # R array.
108: #
109: sub Rreturn {
1.6 www 110: my $x = $_[0]; # the string containing the serialized R object(s)
111: $x=~s/^\"//;
112: $x=~s/\"$//;
113: $x=~s/\\\"/\"/g;
114: $errormsg='';
115: if ($x =~ /^(?:i|d):(.+?);$/) {
116: return $1; # return the value of the number
117: } elsif ($x =~ /^s:(\d+):\"(.*)\";$/) {
118: # string -- verify the length
119: if (length($2) eq $1) {
120: return $2; # return the string
121: } else {
122: return 'mismatch in string length';
123: }
124: } elsif ($x =~ /^a:(\d+):\{(.*)\}$/) {
125: # array
126: my $dim = $1; # array size
127: $x = $2; # array contents
128: tie(my %h,'Tie::IxHash::Easy'); # start a hash
129: keys(%h) = $dim; # allocate space for the hash
130: my $key;
131: my $y;
132: for (my $i = 0; $i < $dim; $i++) {
133: ($y, $x) = &Rpeel($x); # strip off the entry for the key
134: if ($y eq '') {
135: &Rcroak('ran out of keys');
136: }
137: $key = &Rreturn($y);
138: if ($key eq '') {
139: $key = "result$i"; # correct null key
140: }
141: ($y, $x) = &Rpeel($x); # strip off the value
142: if ($y eq '') {
143: &Rcroak('ran out of values');
144: }
145: if ($y =~ /^a:/) {
146: $h{$key} = \&Rreturn($y); # array value: store as reference
147: } else {
148: $h{$key} = &Rreturn($y); # scalar value: store the entry in the hash
149: }
1.5 www 150: }
1.6 www 151: if ($errormsg) { return $errormsg; }
152: return \%h; # return a reference to the hash
153: } else {
154: return 'Unrecognized output';
155: }
1.5 www 156: }
157: # --- end Rreturn ---
158:
159: sub Rentry {
1.6 www 160: my $hash = shift; # pointer to tied hash
161: my $i;
162: if (ref($hash) ne 'HASH') {
163: return 'Argument to cas_hashref_entry is not a hash!';
164: }
165: while ($i = shift) {
166: if (exists($hash->{$i})) {
167: $hash = $hash->{$i};
168: } else {
169: return undef;
170: }
171: if (ref($hash) eq 'REF') {
172: $hash = $$hash; # dereference one layer
173: } elsif (ref($hash) ne 'HASH') {
174: return $hash; # drilled down to a scalar
175: }
176: }
1.5 www 177: }
178:
1.6 www 179: sub Rarray {
180: my $hash = shift; # pointer to tied hash
181: my $i;
182: if (ref($hash) ne 'HASH') {
183: return 'Argument to cas_hashref_array is not a hash!';
184: }
185: while ($i = shift) {
186: if (exists($hash->{$i})) {
187: $hash = $hash->{$i};
188: } else {
189: return undef;
190: }
191: if (ref($hash) eq 'REF') {
192: $hash = $$hash; # dereference one layer
193: }
194: }
195: my @returnarray=();
196: foreach my $key (keys(%{$hash})) {
197: $returnarray[$key-1]=$$hash{$key};
198: }
199: return @returnarray;
200: }
1.1 www 201:
202: sub connect {
203: return IO::Socket::UNIX->new(Peer => $Apache::lonnet::perlvar{'lonSockDir'}.'/rsock',
204: Type => SOCK_STREAM,
205: Timeout => 10);
206: }
207:
208: sub disconnect {
209: my ($socket)=@_;
210: if ($socket) { close($socket); }
211: }
212:
213: sub rreply {
214: my ($socket,$cmd)=@_;
215: if ($socket) {
216: print $socket &escape($cmd)."\n";
217: my $reply=<$socket>;
218: chomp($reply);
219: if ($reply=~/^Incorrect/) { $reply='Error: '.$reply; }
220: return &unescape($reply);
221: } else {
222: return 'Error: no connection.';
223: }
224: }
225:
226: sub blacklisted {
227: my ($cmd)=@_;
228: foreach my $forbidden (
1.3 www 229: 'read','write','scan','save','socket','connections',
230: 'open','close',
231: 'plot','X11','windows','quartz',
1.2 www 232: 'postscript','pdf','png','jpeg',
233: 'dev\.list','dev\.next','dev\.prev','dev\.set',
1.3 www 234: 'dev\.off','dev\.copy','dev\.print','graphics',
235: 'library','package','source','sink','objects',
1.4 www 236: 'Sys\.','unlink','file\.','on\.exit','error',
237: 'q\(\)'
1.1 www 238: ) {
239: if ($cmd=~/$forbidden/s) { return 1; }
240: }
241: return 0;
242: }
243:
244: sub r_allowed_libraries {
1.8 www 245: return ('alr3','boot','car','class','cluster','datasets','Hmisc','KernSmooth','leaps','lmtest',
246: 'MASS','methods','mgcv','nlme','nnet','qAnalyst','quadprog','rpart','SuppDists','spatial',
247: 'splines','stats','stats4','survival','tseries','zoo');
1.1 www 248: }
249:
250: sub r_is_allowed_library {
251: my ($library)=@_;
252: foreach my $allowed_library (&r_allowed_libraries()) {
253: if ($library eq $allowed_library) { return 1; }
254: }
255: return 0;
256: }
257:
258: sub runscript {
259: my ($socket,$fullscript,$libraries)=@_;
260: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
1.9 ! www 261: my $reply='';
1.1 www 262: $fullscript=~s/[\n\r\l]//gs;
263: if ($libraries) {
264: foreach my $library (split(/\s*\,\s*/,$libraries)) {
265: unless ($library=~/\w/) { next; }
266: if (&r_is_allowed_library($library)) {
1.9 ! www 267: $reply=&rreply($socket,'library('.$library.');');
1.1 www 268: if ($reply=~/^Error\:/) { return $reply; }
269: } else {
270: return 'Error: blacklisted';
271: }
272: }
273: }
1.9 ! www 274: $fullscript=~s/\;+\s*$//s;
! 275: if ($fullscript=~/\w/) { $reply=&rreply($socket,$fullscript.';'); }
! 276: if ($reply=~/^Error\:/) { return $reply; }
1.1 www 277: $reply=~s/^\s*//gs;
278: $reply=~s/\s*$//gs;
279: &Apache::lonxml::debug("r $fullscript \n reply $reply");
280: return $reply;
281: }
282:
1.6 www 283: sub runserializedscript {
284: my ($socket,$fullscript,$libraries)=@_;
285: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
286: my $reply;
287: $fullscript=~s/[\n\r\l]//gs;
288: if ($libraries) {
289: foreach my $library (split(/\s*\,\s*/,$libraries)) {
290: unless ($library=~/\w/) { next; }
291: if (&r_is_allowed_library($library)) {
1.9 ! www 292: $reply=&rreply($socket,'library('.$library.');');
1.6 www 293: if ($reply=~/^Error\:/) { return($reply,$reply); }
294: } else {
295: return 'Error: blacklisted';
296: }
297: }
298: }
1.9 ! www 299: $fullscript=~s/\;+\s*$//s;
! 300: my $lastline='';
! 301: my $firstpart='';
! 302: if ($fullscript=~/\;/) {
! 303: ($firstpart,$lastline)=($fullscript=~/^(.*\;)([^\;]+)$/);
! 304: } else {
! 305: $lastline=$fullscript;
1.6 www 306: }
1.9 ! www 307: if ($firstpart) {
! 308: $firstpart=~s/\;+\s*$//s;
! 309: $reply=&rreply($socket,$firstpart.';');
1.6 www 310: if ($reply=~/^Error\:/) { return($reply,$reply); }
311: }
312: # The last line needs to be serialized
1.9 ! www 313: $reply=&Rreturn(&rreply($socket,"phpSerialize($lastline);"));
1.6 www 314: return($reply,&Dumper($reply));
315: }
316:
1.1 www 317: sub r_cas_formula_fix {
318: my ($expression)=@_;
319: return &Apache::response::implicit_multiplication($expression);
320: }
321:
322: sub r_run {
323: my ($script,$submission,$argument,$libraries) = @_;
324: my $socket=&connect();
325: my @submissionarray=split(/\s*\,\s*/,$submission);
326: for (my $i=0;$i<=$#submissionarray;$i++) {
327: my $n=$i+1;
328: my $fixedsubmission=&r_cas_formula_fix($submissionarray[$i]);
329: $script=~s/RESPONSE\[$n\]/$fixedsubmission/gs;
330: }
331: my @argumentarray=@{$argument};
332: for (my $i=0;$i<=$#argumentarray;$i++) {
333: my $n=$i+1;
334: my $fixedargument=&r_cas_formula_fix($argumentarray[$i]);
335: $script=~s/LONCAPALIST\[$n\]/$fixedargument/gs;
336: }
337: my $reply=&runscript($socket,$script,$libraries);
338: &disconnect($socket);
339: if ($reply=~/^\s*true\s*$/i) { return 'EXACT_ANS'; }
340: if ($reply=~/^\s*false\s*$/i) { return 'INCORRECT'; }
341: return 'BAD_FORMULA';
342: }
343:
344: sub r_eval {
1.6 www 345: my ($script,$libraries,$hashflag) = @_;
1.1 www 346: my $socket=&connect();
1.6 www 347: my $reply;
348: my $dump='';
349: if ($hashflag) {
350: ($reply,$dump)=&runserializedscript($socket,$script,$libraries);
351: } else {
352: $reply=&runscript($socket,$script,$libraries);
353: }
1.1 www 354: &disconnect($socket);
1.6 www 355: return ($reply,$dump);
1.1 www 356: }
357:
358:
359: sub compareterms {
360: my ($socket,$terma,$termb)=@_;
361: my $difference=$terma.'-('.$termb.')';
362: if (&blacklisted($difference)) { return 'Error: blacklisted'; }
363: my $reply=&rreply($socket,$difference.';');
364: if ($reply=~/^\s*0\s*$/) { return 'true'; }
365: if ($reply=~/^Error\:/) { return $reply; }
366: return 'false';
367: }
368:
369: sub r_check {
370: my ($response,$answer,$reterror) = @_;
371: my $socket=&connect();
372: my $reply=&compareterms($socket,$response,$answer);
373: &disconnect($socket);
374: # integer to string mappings come from capaParser.h
375: # 1 maps to 'EXACT_ANS'
376: if ($reply eq 'true') { return 1; }
377: # 11 maps to 'BAD_FORMULA'
378: if ($reply=~/^Error\:/) { return 11; }
379: # 7 maps to 'INCORRECT'
380: return 7;
381: }
382:
383: 1;
384: __END__;
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