Annotation of loncom/homework/lonr.pm, revision 1.10
1.1 www 1: # The LearningOnline Network with CAPA
2: # Interface routines to R CAS
3: #
1.10 ! www 4: # $Id: lonr.pm,v 1.9 2009/08/14 01:58:52 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;
1.10 ! www 36: use Tie::IxHash::Easy; # autoties all subhashes to keep index order
! 37: use Data::Dumper; # used to output hash contents
1.5 www 38:
39: my $errormsg='';
40:
41: #
42: # Rcroak: for use with R-error messages
43: #
44: sub Rcroak {
45: $errormsg=$_[0];
46: }
47:
48: #
49: #
50: # Rpeel takes a string containing serialized values from R,
51: # peels off the first syntactically complete unit (number, string or array),
52: # and returns a list (first unit, remainder).
53: #
54: sub Rpeel {
55: my $x = $_[0]; # the string containing the serialized R object(s)
56: if ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
57: return ($1, $+); # x starts with a number
1.9 www 58: } elsif ($x =~ /^s:(\d+):/) {
1.5 www 59: my $n = $1; # x starts with a string of length n
60: if ($x =~ /^(s:\d+:\"(.{$n})\";)(.*)$/) {
61: return ($1, $+); # x starts with a valid string
62: } else {
63: &Rcroak('invalid string detected');
64: }
1.9 www 65: } elsif ($x =~ /^a:/) {
1.5 www 66: # x starts with an array -- need to find the closing brace
67: my $i = index $x, '{', 0; # position of first opening brace
68: if ($i < 0) {
69: &Rcroak('array with no opening brace');
70: }
71: my $open = 1; # counts open braces
72: my $j = index $x, '}', $i; # position of first closing brace
73: $i = index $x, '{', $i + 1; # position of next opening brace (if any)
74: my $pos = -1; # position of final closing brace
75: do {
76: if (($i < $j) && ($i > 0)) {
77: # encounter another opening brace before next closing brace
78: $open++;
79: $i = index $x, '{', $i + 1; # find the next opening brace
80: } elsif ($j > 0) {
81: # next brace encountered is a closing brace
82: $open--;
83: $pos = $j;
84: $j = index $x, '}', $j + 1;
85: } else {
86: &Rcroak('unmatched left brace');
87: }
88: } until ($open eq 0);
89: # array runs from start to $pos
90: my $a = substr $x, 0, $pos + 1; # array
91: my $b = substr $x, $pos + 1; # remainder
92: return ($a, $b);
93: } else {
94: &Rcroak('unrecognized R value');
95: }
96: }
97: # --- end Rpeel ---
98:
99: #
100: # Rreturn accepts a string containing a serialized R object
101: # and returns either the object's value (if it is scalar) or a reference
102: # to a hash containing the contents of the object. Any null keys in the hash
1.6 www 103: # are replaced by 'resultNNN' where NNN is the index of the entry in the original
1.5 www 104: # R array.
105: #
106: sub Rreturn {
1.6 www 107: my $x = $_[0]; # the string containing the serialized R object(s)
108: $x=~s/^\"//;
109: $x=~s/\"$//;
110: $x=~s/\\\"/\"/g;
111: $errormsg='';
112: if ($x =~ /^(?:i|d):(.+?);$/) {
113: return $1; # return the value of the number
114: } elsif ($x =~ /^s:(\d+):\"(.*)\";$/) {
115: # string -- verify the length
116: if (length($2) eq $1) {
117: return $2; # return the string
118: } else {
119: return 'mismatch in string length';
120: }
121: } elsif ($x =~ /^a:(\d+):\{(.*)\}$/) {
122: # array
123: my $dim = $1; # array size
124: $x = $2; # array contents
125: tie(my %h,'Tie::IxHash::Easy'); # start a hash
126: keys(%h) = $dim; # allocate space for the hash
127: my $key;
128: my $y;
129: for (my $i = 0; $i < $dim; $i++) {
130: ($y, $x) = &Rpeel($x); # strip off the entry for the key
131: if ($y eq '') {
132: &Rcroak('ran out of keys');
133: }
134: $key = &Rreturn($y);
135: if ($key eq '') {
136: $key = "result$i"; # correct null key
137: }
138: ($y, $x) = &Rpeel($x); # strip off the value
139: if ($y eq '') {
140: &Rcroak('ran out of values');
141: }
142: if ($y =~ /^a:/) {
143: $h{$key} = \&Rreturn($y); # array value: store as reference
144: } else {
145: $h{$key} = &Rreturn($y); # scalar value: store the entry in the hash
146: }
1.5 www 147: }
1.6 www 148: if ($errormsg) { return $errormsg; }
149: return \%h; # return a reference to the hash
150: } else {
151: return 'Unrecognized output';
152: }
1.5 www 153: }
154: # --- end Rreturn ---
155:
156: sub Rentry {
1.6 www 157: my $hash = shift; # pointer to tied hash
158: my $i;
159: if (ref($hash) ne 'HASH') {
160: return 'Argument to cas_hashref_entry is not a hash!';
161: }
162: while ($i = shift) {
163: if (exists($hash->{$i})) {
164: $hash = $hash->{$i};
165: } else {
166: return undef;
167: }
168: if (ref($hash) eq 'REF') {
169: $hash = $$hash; # dereference one layer
170: } elsif (ref($hash) ne 'HASH') {
171: return $hash; # drilled down to a scalar
172: }
173: }
1.5 www 174: }
175:
1.6 www 176: sub Rarray {
177: my $hash = shift; # pointer to tied hash
178: my $i;
179: if (ref($hash) ne 'HASH') {
180: return 'Argument to cas_hashref_array is not a hash!';
181: }
182: while ($i = shift) {
183: if (exists($hash->{$i})) {
184: $hash = $hash->{$i};
185: } else {
186: return undef;
187: }
188: if (ref($hash) eq 'REF') {
189: $hash = $$hash; # dereference one layer
190: }
191: }
192: my @returnarray=();
193: foreach my $key (keys(%{$hash})) {
194: $returnarray[$key-1]=$$hash{$key};
195: }
196: return @returnarray;
197: }
1.1 www 198:
199: sub connect {
200: return IO::Socket::UNIX->new(Peer => $Apache::lonnet::perlvar{'lonSockDir'}.'/rsock',
201: Type => SOCK_STREAM,
202: Timeout => 10);
203: }
204:
205: sub disconnect {
206: my ($socket)=@_;
207: if ($socket) { close($socket); }
208: }
209:
210: sub rreply {
211: my ($socket,$cmd)=@_;
212: if ($socket) {
213: print $socket &escape($cmd)."\n";
214: my $reply=<$socket>;
215: chomp($reply);
216: if ($reply=~/^Incorrect/) { $reply='Error: '.$reply; }
217: return &unescape($reply);
218: } else {
219: return 'Error: no connection.';
220: }
221: }
222:
223: sub blacklisted {
224: my ($cmd)=@_;
225: foreach my $forbidden (
1.3 www 226: 'read','write','scan','save','socket','connections',
227: 'open','close',
228: 'plot','X11','windows','quartz',
1.2 www 229: 'postscript','pdf','png','jpeg',
230: 'dev\.list','dev\.next','dev\.prev','dev\.set',
1.3 www 231: 'dev\.off','dev\.copy','dev\.print','graphics',
232: 'library','package','source','sink','objects',
1.4 www 233: 'Sys\.','unlink','file\.','on\.exit','error',
234: 'q\(\)'
1.1 www 235: ) {
236: if ($cmd=~/$forbidden/s) { return 1; }
237: }
238: return 0;
239: }
240:
241: sub r_allowed_libraries {
1.8 www 242: return ('alr3','boot','car','class','cluster','datasets','Hmisc','KernSmooth','leaps','lmtest',
243: 'MASS','methods','mgcv','nlme','nnet','qAnalyst','quadprog','rpart','SuppDists','spatial',
244: 'splines','stats','stats4','survival','tseries','zoo');
1.1 www 245: }
246:
247: sub r_is_allowed_library {
248: my ($library)=@_;
249: foreach my $allowed_library (&r_allowed_libraries()) {
250: if ($library eq $allowed_library) { return 1; }
251: }
252: return 0;
253: }
254:
255: sub runscript {
256: my ($socket,$fullscript,$libraries)=@_;
257: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
1.9 www 258: my $reply='';
1.1 www 259: $fullscript=~s/[\n\r\l]//gs;
260: if ($libraries) {
261: foreach my $library (split(/\s*\,\s*/,$libraries)) {
262: unless ($library=~/\w/) { next; }
263: if (&r_is_allowed_library($library)) {
1.9 www 264: $reply=&rreply($socket,'library('.$library.');');
1.1 www 265: if ($reply=~/^Error\:/) { return $reply; }
266: } else {
267: return 'Error: blacklisted';
268: }
269: }
270: }
1.9 www 271: $fullscript=~s/\;+\s*$//s;
272: if ($fullscript=~/\w/) { $reply=&rreply($socket,$fullscript.';'); }
273: if ($reply=~/^Error\:/) { return $reply; }
1.1 www 274: $reply=~s/^\s*//gs;
275: $reply=~s/\s*$//gs;
276: &Apache::lonxml::debug("r $fullscript \n reply $reply");
277: return $reply;
278: }
279:
1.6 www 280: sub runserializedscript {
281: my ($socket,$fullscript,$libraries)=@_;
282: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
283: my $reply;
284: $fullscript=~s/[\n\r\l]//gs;
285: if ($libraries) {
286: foreach my $library (split(/\s*\,\s*/,$libraries)) {
287: unless ($library=~/\w/) { next; }
288: if (&r_is_allowed_library($library)) {
1.9 www 289: $reply=&rreply($socket,'library('.$library.');');
1.6 www 290: if ($reply=~/^Error\:/) { return($reply,$reply); }
291: } else {
292: return 'Error: blacklisted';
293: }
294: }
295: }
1.9 www 296: $fullscript=~s/\;+\s*$//s;
297: my $lastline='';
298: my $firstpart='';
299: if ($fullscript=~/\;/) {
300: ($firstpart,$lastline)=($fullscript=~/^(.*\;)([^\;]+)$/);
301: } else {
302: $lastline=$fullscript;
1.6 www 303: }
1.9 www 304: if ($firstpart) {
305: $firstpart=~s/\;+\s*$//s;
306: $reply=&rreply($socket,$firstpart.';');
1.6 www 307: if ($reply=~/^Error\:/) { return($reply,$reply); }
308: }
309: # The last line needs to be serialized
1.9 www 310: $reply=&Rreturn(&rreply($socket,"phpSerialize($lastline);"));
1.6 www 311: return($reply,&Dumper($reply));
312: }
313:
1.1 www 314: sub r_cas_formula_fix {
315: my ($expression)=@_;
316: return &Apache::response::implicit_multiplication($expression);
317: }
318:
319: sub r_run {
320: my ($script,$submission,$argument,$libraries) = @_;
321: my $socket=&connect();
322: my @submissionarray=split(/\s*\,\s*/,$submission);
323: for (my $i=0;$i<=$#submissionarray;$i++) {
324: my $n=$i+1;
325: my $fixedsubmission=&r_cas_formula_fix($submissionarray[$i]);
326: $script=~s/RESPONSE\[$n\]/$fixedsubmission/gs;
327: }
328: my @argumentarray=@{$argument};
329: for (my $i=0;$i<=$#argumentarray;$i++) {
330: my $n=$i+1;
331: my $fixedargument=&r_cas_formula_fix($argumentarray[$i]);
332: $script=~s/LONCAPALIST\[$n\]/$fixedargument/gs;
333: }
334: my $reply=&runscript($socket,$script,$libraries);
335: &disconnect($socket);
336: if ($reply=~/^\s*true\s*$/i) { return 'EXACT_ANS'; }
337: if ($reply=~/^\s*false\s*$/i) { return 'INCORRECT'; }
338: return 'BAD_FORMULA';
339: }
340:
341: sub r_eval {
1.6 www 342: my ($script,$libraries,$hashflag) = @_;
1.1 www 343: my $socket=&connect();
1.6 www 344: my $reply;
345: my $dump='';
346: if ($hashflag) {
347: ($reply,$dump)=&runserializedscript($socket,$script,$libraries);
348: } else {
349: $reply=&runscript($socket,$script,$libraries);
350: }
1.1 www 351: &disconnect($socket);
1.6 www 352: return ($reply,$dump);
1.1 www 353: }
354:
355:
356: sub compareterms {
357: my ($socket,$terma,$termb)=@_;
358: my $difference=$terma.'-('.$termb.')';
359: if (&blacklisted($difference)) { return 'Error: blacklisted'; }
360: my $reply=&rreply($socket,$difference.';');
361: if ($reply=~/^\s*0\s*$/) { return 'true'; }
362: if ($reply=~/^Error\:/) { return $reply; }
363: return 'false';
364: }
365:
366: sub r_check {
367: my ($response,$answer,$reterror) = @_;
368: my $socket=&connect();
369: my $reply=&compareterms($socket,$response,$answer);
370: &disconnect($socket);
371: # integer to string mappings come from capaParser.h
372: # 1 maps to 'EXACT_ANS'
373: if ($reply eq 'true') { return 1; }
374: # 11 maps to 'BAD_FORMULA'
375: if ($reply=~/^Error\:/) { return 11; }
376: # 7 maps to 'INCORRECT'
377: return 7;
378: }
379:
380: 1;
381: __END__;
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