Annotation of loncom/homework/lonr.pm, revision 1.8
1.1 www 1: # The LearningOnline Network with CAPA
2: # Interface routines to R CAS
3: #
1.8 ! www 4: # $Id: lonr.pm,v 1.7 2009/08/12 15:30:16 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, $+); # x starts with a number
61: }
62: elsif ($x =~ /^s:(\d+):/) {
63: my $n = $1; # x starts with a string of length n
64: if ($x =~ /^(s:\d+:\"(.{$n})\";)(.*)$/) {
65: return ($1, $+); # x starts with a valid string
66: } else {
67: &Rcroak('invalid string detected');
68: }
69: }
70: elsif ($x =~ /^a:/) {
71: # x starts with an array -- need to find the closing brace
72: my $i = index $x, '{', 0; # position of first opening brace
73: if ($i < 0) {
74: &Rcroak('array with no opening brace');
75: }
76: my $open = 1; # counts open braces
77: my $j = index $x, '}', $i; # position of first closing brace
78: $i = index $x, '{', $i + 1; # position of next opening brace (if any)
79: my $pos = -1; # position of final closing brace
80: do {
81: if (($i < $j) && ($i > 0)) {
82: # encounter another opening brace before next closing brace
83: $open++;
84: $i = index $x, '{', $i + 1; # find the next opening brace
85: } elsif ($j > 0) {
86: # next brace encountered is a closing brace
87: $open--;
88: $pos = $j;
89: $j = index $x, '}', $j + 1;
90: } else {
91: &Rcroak('unmatched left brace');
92: }
93: } until ($open eq 0);
94: # array runs from start to $pos
95: my $a = substr $x, 0, $pos + 1; # array
96: my $b = substr $x, $pos + 1; # remainder
97: return ($a, $b);
98: } else {
99: &Rcroak('unrecognized R value');
100: }
101: }
102: # --- end Rpeel ---
103:
104: #
105: # Rreturn accepts a string containing a serialized R object
106: # and returns either the object's value (if it is scalar) or a reference
107: # to a hash containing the contents of the object. Any null keys in the hash
1.6 www 108: # are replaced by 'resultNNN' where NNN is the index of the entry in the original
1.5 www 109: # R array.
110: #
111: sub Rreturn {
1.6 www 112: my $x = $_[0]; # the string containing the serialized R object(s)
113: $x=~s/^\"//;
114: $x=~s/\"$//;
115: $x=~s/\\\"/\"/g;
116: $errormsg='';
117: if ($x =~ /^(?:i|d):(.+?);$/) {
118: return $1; # return the value of the number
119: } elsif ($x =~ /^s:(\d+):\"(.*)\";$/) {
120: # string -- verify the length
121: if (length($2) eq $1) {
122: return $2; # return the string
123: } else {
124: return 'mismatch in string length';
125: }
126: } elsif ($x =~ /^a:(\d+):\{(.*)\}$/) {
127: # array
128: my $dim = $1; # array size
129: $x = $2; # array contents
130: tie(my %h,'Tie::IxHash::Easy'); # start a hash
131: keys(%h) = $dim; # allocate space for the hash
132: my $key;
133: my $y;
134: for (my $i = 0; $i < $dim; $i++) {
135: ($y, $x) = &Rpeel($x); # strip off the entry for the key
136: if ($y eq '') {
137: &Rcroak('ran out of keys');
138: }
139: $key = &Rreturn($y);
140: if ($key eq '') {
141: $key = "result$i"; # correct null key
142: }
143: ($y, $x) = &Rpeel($x); # strip off the value
144: if ($y eq '') {
145: &Rcroak('ran out of values');
146: }
147: if ($y =~ /^a:/) {
148: $h{$key} = \&Rreturn($y); # array value: store as reference
149: } else {
150: $h{$key} = &Rreturn($y); # scalar value: store the entry in the hash
151: }
1.5 www 152: }
1.6 www 153: if ($errormsg) { return $errormsg; }
154: return \%h; # return a reference to the hash
155: } else {
156: return 'Unrecognized output';
157: }
1.5 www 158: }
159: # --- end Rreturn ---
160:
161: sub Rentry {
1.6 www 162: my $hash = shift; # pointer to tied hash
163: my $i;
164: if (ref($hash) ne 'HASH') {
165: return 'Argument to cas_hashref_entry is not a hash!';
166: }
167: while ($i = shift) {
168: if (exists($hash->{$i})) {
169: $hash = $hash->{$i};
170: } else {
171: return undef;
172: }
173: if (ref($hash) eq 'REF') {
174: $hash = $$hash; # dereference one layer
175: } elsif (ref($hash) ne 'HASH') {
176: return $hash; # drilled down to a scalar
177: }
178: }
1.5 www 179: }
180:
1.6 www 181: sub Rarray {
182: my $hash = shift; # pointer to tied hash
183: my $i;
184: if (ref($hash) ne 'HASH') {
185: return 'Argument to cas_hashref_array is not a hash!';
186: }
187: while ($i = shift) {
188: if (exists($hash->{$i})) {
189: $hash = $hash->{$i};
190: } else {
191: return undef;
192: }
193: if (ref($hash) eq 'REF') {
194: $hash = $$hash; # dereference one layer
195: }
196: }
197: my @returnarray=();
198: foreach my $key (keys(%{$hash})) {
199: $returnarray[$key-1]=$$hash{$key};
200: }
201: return @returnarray;
202: }
1.1 www 203:
204: sub connect {
205: return IO::Socket::UNIX->new(Peer => $Apache::lonnet::perlvar{'lonSockDir'}.'/rsock',
206: Type => SOCK_STREAM,
207: Timeout => 10);
208: }
209:
210: sub disconnect {
211: my ($socket)=@_;
212: if ($socket) { close($socket); }
213: }
214:
215: sub rreply {
216: my ($socket,$cmd)=@_;
217: if ($socket) {
218: print $socket &escape($cmd)."\n";
219: my $reply=<$socket>;
220: chomp($reply);
221: if ($reply=~/^Incorrect/) { $reply='Error: '.$reply; }
222: return &unescape($reply);
223: } else {
224: return 'Error: no connection.';
225: }
226: }
227:
228: sub blacklisted {
229: my ($cmd)=@_;
230: foreach my $forbidden (
1.3 www 231: 'read','write','scan','save','socket','connections',
232: 'open','close',
233: 'plot','X11','windows','quartz',
1.2 www 234: 'postscript','pdf','png','jpeg',
235: 'dev\.list','dev\.next','dev\.prev','dev\.set',
1.3 www 236: 'dev\.off','dev\.copy','dev\.print','graphics',
237: 'library','package','source','sink','objects',
1.4 www 238: 'Sys\.','unlink','file\.','on\.exit','error',
239: 'q\(\)'
1.1 www 240: ) {
241: if ($cmd=~/$forbidden/s) { return 1; }
242: }
243: return 0;
244: }
245:
246: sub r_allowed_libraries {
1.8 ! www 247: return ('alr3','boot','car','class','cluster','datasets','Hmisc','KernSmooth','leaps','lmtest',
! 248: 'MASS','methods','mgcv','nlme','nnet','qAnalyst','quadprog','rpart','SuppDists','spatial',
! 249: 'splines','stats','stats4','survival','tseries','zoo');
1.1 www 250: }
251:
252: sub r_is_allowed_library {
253: my ($library)=@_;
254: foreach my $allowed_library (&r_allowed_libraries()) {
255: if ($library eq $allowed_library) { return 1; }
256: }
257: return 0;
258: }
259:
260: sub runscript {
261: my ($socket,$fullscript,$libraries)=@_;
262: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
263: my $reply;
264: $fullscript=~s/[\n\r\l]//gs;
265: if ($libraries) {
266: foreach my $library (split(/\s*\,\s*/,$libraries)) {
267: unless ($library=~/\w/) { next; }
268: if (&r_is_allowed_library($library)) {
269: $reply=&rreply($socket,'library('.$library.');'."\n");
270: if ($reply=~/^Error\:/) { return $reply; }
271: } else {
272: return 'Error: blacklisted';
273: }
274: }
275: }
1.7 www 276: foreach my $line (split(/[\n\r]+/s,$fullscript)) {
1.1 www 277: if ($line=~/\w/) { $reply=&rreply($socket,$line.";\n"); }
278: if ($reply=~/^Error\:/) { return $reply; }
279: }
280: $reply=~s/^\s*//gs;
281: $reply=~s/\s*$//gs;
282: &Apache::lonxml::debug("r $fullscript \n reply $reply");
283: return $reply;
284: }
285:
1.6 www 286: sub runserializedscript {
287: my ($socket,$fullscript,$libraries)=@_;
288: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
289: my $reply;
290: $fullscript=~s/[\n\r\l]//gs;
291: if ($libraries) {
292: foreach my $library (split(/\s*\,\s*/,$libraries)) {
293: unless ($library=~/\w/) { next; }
294: if (&r_is_allowed_library($library)) {
295: $reply=&rreply($socket,'library('.$library.');'."\n");
296: if ($reply=~/^Error\:/) { return($reply,$reply); }
297: } else {
298: return 'Error: blacklisted';
299: }
300: }
301: }
302: my @actuallines=();
303: foreach my $line (split(/\;/s,$fullscript)) {
304: if ($line=~/\w/) { push (@actuallines,$line); }
305: }
306: for (my $i=0; $i<$#actuallines; $i++) {
307: $reply=&rreply($socket,$actuallines[$i].";\n");
308: if ($reply=~/^Error\:/) { return($reply,$reply); }
309: }
310: # The last line needs to be serialized
311: $reply=&Rreturn(&rreply($socket,"phpSerialize($actuallines[-1]);\n"));
312: return($reply,&Dumper($reply));
313: }
314:
1.1 www 315: sub r_cas_formula_fix {
316: my ($expression)=@_;
317: return &Apache::response::implicit_multiplication($expression);
318: }
319:
320: sub r_run {
321: my ($script,$submission,$argument,$libraries) = @_;
322: my $socket=&connect();
323: my @submissionarray=split(/\s*\,\s*/,$submission);
324: for (my $i=0;$i<=$#submissionarray;$i++) {
325: my $n=$i+1;
326: my $fixedsubmission=&r_cas_formula_fix($submissionarray[$i]);
327: $script=~s/RESPONSE\[$n\]/$fixedsubmission/gs;
328: }
329: my @argumentarray=@{$argument};
330: for (my $i=0;$i<=$#argumentarray;$i++) {
331: my $n=$i+1;
332: my $fixedargument=&r_cas_formula_fix($argumentarray[$i]);
333: $script=~s/LONCAPALIST\[$n\]/$fixedargument/gs;
334: }
335: my $reply=&runscript($socket,$script,$libraries);
336: &disconnect($socket);
337: if ($reply=~/^\s*true\s*$/i) { return 'EXACT_ANS'; }
338: if ($reply=~/^\s*false\s*$/i) { return 'INCORRECT'; }
339: return 'BAD_FORMULA';
340: }
341:
342: sub r_eval {
1.6 www 343: my ($script,$libraries,$hashflag) = @_;
1.1 www 344: my $socket=&connect();
1.6 www 345: my $reply;
346: my $dump='';
347: if ($hashflag) {
348: ($reply,$dump)=&runserializedscript($socket,$script,$libraries);
349: } else {
350: $reply=&runscript($socket,$script,$libraries);
351: }
1.1 www 352: &disconnect($socket);
1.6 www 353: return ($reply,$dump);
1.1 www 354: }
355:
356:
357: sub compareterms {
358: my ($socket,$terma,$termb)=@_;
359: my $difference=$terma.'-('.$termb.')';
360: if (&blacklisted($difference)) { return 'Error: blacklisted'; }
361: my $reply=&rreply($socket,$difference.';');
362: if ($reply=~/^\s*0\s*$/) { return 'true'; }
363: if ($reply=~/^Error\:/) { return $reply; }
364: return 'false';
365: }
366:
367: sub r_check {
368: my ($response,$answer,$reterror) = @_;
369: my $socket=&connect();
370: my $reply=&compareterms($socket,$response,$answer);
371: &disconnect($socket);
372: # integer to string mappings come from capaParser.h
373: # 1 maps to 'EXACT_ANS'
374: if ($reply eq 'true') { return 1; }
375: # 11 maps to 'BAD_FORMULA'
376: if ($reply=~/^Error\:/) { return 11; }
377: # 7 maps to 'INCORRECT'
378: return 7;
379: }
380:
381: 1;
382: __END__;
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