Annotation of loncom/homework/lonr.pm, revision 1.12
1.1 www 1: # The LearningOnline Network with CAPA
2: # Interface routines to R CAS
3: #
1.12 ! raeburn 4: # $Id: lonr.pm,v 1.11 2014/11/19 21:14:47 raeburn 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 = $_[0]; # the string containing the serialized R object(s)
1.11 raeburn 56: if ($x =~ /^N\;(.*)$/) {
57: return ('',$1);
58: } elsif ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
1.5 www 59: return ($1, $+); # x starts with a number
1.9 www 60: } elsif ($x =~ /^s:(\d+):/) {
1.5 www 61: my $n = $1; # x starts with a string of length n
62: if ($x =~ /^(s:\d+:\"(.{$n})\";)(.*)$/) {
63: return ($1, $+); # x starts with a valid string
64: } else {
65: &Rcroak('invalid string detected');
66: }
1.9 www 67: } elsif ($x =~ /^a:/) {
1.5 www 68: # x starts with an array -- need to find the closing brace
69: my $i = index $x, '{', 0; # position of first opening brace
70: if ($i < 0) {
71: &Rcroak('array with no opening brace');
72: }
73: my $open = 1; # counts open braces
74: my $j = index $x, '}', $i; # position of first closing brace
75: $i = index $x, '{', $i + 1; # position of next opening brace (if any)
76: my $pos = -1; # position of final closing brace
77: do {
78: if (($i < $j) && ($i > 0)) {
79: # encounter another opening brace before next closing brace
80: $open++;
81: $i = index $x, '{', $i + 1; # find the next opening brace
82: } elsif ($j > 0) {
83: # next brace encountered is a closing brace
84: $open--;
85: $pos = $j;
86: $j = index $x, '}', $j + 1;
87: } else {
88: &Rcroak('unmatched left brace');
89: }
90: } until ($open eq 0);
91: # array runs from start to $pos
92: my $a = substr $x, 0, $pos + 1; # array
93: my $b = substr $x, $pos + 1; # remainder
94: return ($a, $b);
95: } else {
96: &Rcroak('unrecognized R value');
97: }
98: }
99: # --- end Rpeel ---
100:
101: #
102: # Rreturn accepts a string containing a serialized R object
103: # and returns either the object's value (if it is scalar) or a reference
104: # to a hash containing the contents of the object. Any null keys in the hash
1.6 www 105: # are replaced by 'resultNNN' where NNN is the index of the entry in the original
1.5 www 106: # R array.
107: #
108: sub Rreturn {
1.6 www 109: my $x = $_[0]; # the string containing the serialized R object(s)
110: $x=~s/^\"//;
111: $x=~s/\"$//;
112: $x=~s/\\\"/\"/g;
113: $errormsg='';
114: if ($x =~ /^(?:i|d):(.+?);$/) {
115: return $1; # return the value of the number
116: } elsif ($x =~ /^s:(\d+):\"(.*)\";$/) {
117: # string -- verify the length
118: if (length($2) eq $1) {
119: return $2; # return the string
120: } else {
121: return 'mismatch in string length';
122: }
123: } elsif ($x =~ /^a:(\d+):\{(.*)\}$/) {
124: # array
125: my $dim = $1; # array size
126: $x = $2; # array contents
127: tie(my %h,'Tie::IxHash::Easy'); # start a hash
128: keys(%h) = $dim; # allocate space for the hash
129: my $key;
130: my $y;
131: for (my $i = 0; $i < $dim; $i++) {
132: ($y, $x) = &Rpeel($x); # strip off the entry for the key
133: if ($y eq '') {
134: &Rcroak('ran out of keys');
135: }
136: $key = &Rreturn($y);
137: if ($key eq '') {
138: $key = "result$i"; # correct null key
139: }
140: ($y, $x) = &Rpeel($x); # strip off the value
141: if ($y eq '') {
142: &Rcroak('ran out of values');
143: }
144: if ($y =~ /^a:/) {
145: $h{$key} = \&Rreturn($y); # array value: store as reference
146: } else {
147: $h{$key} = &Rreturn($y); # scalar value: store the entry in the hash
148: }
1.5 www 149: }
1.6 www 150: if ($errormsg) { return $errormsg; }
151: return \%h; # return a reference to the hash
1.11 raeburn 152: } elsif ($x eq '') {
153: return '';
1.6 www 154: } else {
155: return 'Unrecognized output';
156: }
1.5 www 157: }
158: # --- end Rreturn ---
159:
160: sub Rentry {
1.6 www 161: my $hash = shift; # pointer to tied hash
162: my $i;
163: if (ref($hash) ne 'HASH') {
164: return 'Argument to cas_hashref_entry is not a hash!';
165: }
166: while ($i = shift) {
167: if (exists($hash->{$i})) {
168: $hash = $hash->{$i};
169: } else {
170: return undef;
171: }
172: if (ref($hash) eq 'REF') {
173: $hash = $$hash; # dereference one layer
174: } elsif (ref($hash) ne 'HASH') {
175: return $hash; # drilled down to a scalar
176: }
177: }
1.5 www 178: }
179:
1.6 www 180: sub Rarray {
181: my $hash = shift; # pointer to tied hash
182: my $i;
183: if (ref($hash) ne 'HASH') {
184: return 'Argument to cas_hashref_array is not a hash!';
185: }
186: while ($i = shift) {
187: if (exists($hash->{$i})) {
188: $hash = $hash->{$i};
189: } else {
190: return undef;
191: }
192: if (ref($hash) eq 'REF') {
193: $hash = $$hash; # dereference one layer
194: }
195: }
196: my @returnarray=();
197: foreach my $key (keys(%{$hash})) {
198: $returnarray[$key-1]=$$hash{$key};
199: }
200: return @returnarray;
201: }
1.1 www 202:
203: sub connect {
204: return IO::Socket::UNIX->new(Peer => $Apache::lonnet::perlvar{'lonSockDir'}.'/rsock',
205: Type => SOCK_STREAM,
206: Timeout => 10);
207: }
208:
209: sub disconnect {
210: my ($socket)=@_;
211: if ($socket) { close($socket); }
212: }
213:
214: sub rreply {
215: my ($socket,$cmd)=@_;
216: if ($socket) {
217: print $socket &escape($cmd)."\n";
218: my $reply=<$socket>;
219: chomp($reply);
220: if ($reply=~/^Incorrect/) { $reply='Error: '.$reply; }
221: return &unescape($reply);
222: } else {
223: return 'Error: no connection.';
224: }
225: }
226:
227: sub blacklisted {
228: my ($cmd)=@_;
229: foreach my $forbidden (
1.3 www 230: 'read','write','scan','save','socket','connections',
231: 'open','close',
232: 'plot','X11','windows','quartz',
1.2 www 233: 'postscript','pdf','png','jpeg',
234: 'dev\.list','dev\.next','dev\.prev','dev\.set',
1.3 www 235: 'dev\.off','dev\.copy','dev\.print','graphics',
236: 'library','package','source','sink','objects',
1.4 www 237: 'Sys\.','unlink','file\.','on\.exit','error',
238: 'q\(\)'
1.1 www 239: ) {
240: if ($cmd=~/$forbidden/s) { return 1; }
241: }
242: return 0;
243: }
244:
245: sub r_allowed_libraries {
1.12 ! raeburn 246: return ('alr3','boot','car','class','cluster','datasets','FactoMineR','Hmisc','KernSmooth','leaps',
! 247: 'lmtest','MASS','mdatools','methods','mgcv','nlme','nnet','qAnalyst','quadprog','rpart',
! 248: 'SuppDists','spatial','splines','stats','stats4','survival','tseries','zoo');
1.1 www 249: }
250:
251: sub r_is_allowed_library {
252: my ($library)=@_;
253: foreach my $allowed_library (&r_allowed_libraries()) {
254: if ($library eq $allowed_library) { return 1; }
255: }
256: return 0;
257: }
258:
259: sub runscript {
260: my ($socket,$fullscript,$libraries)=@_;
261: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
1.9 www 262: my $reply='';
1.1 www 263: $fullscript=~s/[\n\r\l]//gs;
264: if ($libraries) {
265: foreach my $library (split(/\s*\,\s*/,$libraries)) {
266: unless ($library=~/\w/) { next; }
267: if (&r_is_allowed_library($library)) {
1.9 www 268: $reply=&rreply($socket,'library('.$library.');');
1.1 www 269: if ($reply=~/^Error\:/) { return $reply; }
270: } else {
271: return 'Error: blacklisted';
272: }
273: }
274: }
1.9 www 275: $fullscript=~s/\;+\s*$//s;
276: if ($fullscript=~/\w/) { $reply=&rreply($socket,$fullscript.';'); }
277: if ($reply=~/^Error\:/) { return $reply; }
1.1 www 278: $reply=~s/^\s*//gs;
279: $reply=~s/\s*$//gs;
280: &Apache::lonxml::debug("r $fullscript \n reply $reply");
281: return $reply;
282: }
283:
1.6 www 284: sub runserializedscript {
285: my ($socket,$fullscript,$libraries)=@_;
286: if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
287: my $reply;
288: $fullscript=~s/[\n\r\l]//gs;
289: if ($libraries) {
290: foreach my $library (split(/\s*\,\s*/,$libraries)) {
291: unless ($library=~/\w/) { next; }
292: if (&r_is_allowed_library($library)) {
1.9 www 293: $reply=&rreply($socket,'library('.$library.');');
1.6 www 294: if ($reply=~/^Error\:/) { return($reply,$reply); }
295: } else {
296: return 'Error: blacklisted';
297: }
298: }
299: }
1.9 www 300: $fullscript=~s/\;+\s*$//s;
301: my $lastline='';
302: my $firstpart='';
303: if ($fullscript=~/\;/) {
304: ($firstpart,$lastline)=($fullscript=~/^(.*\;)([^\;]+)$/);
305: } else {
306: $lastline=$fullscript;
1.6 www 307: }
1.9 www 308: if ($firstpart) {
309: $firstpart=~s/\;+\s*$//s;
310: $reply=&rreply($socket,$firstpart.';');
1.6 www 311: if ($reply=~/^Error\:/) { return($reply,$reply); }
312: }
313: # The last line needs to be serialized
1.9 www 314: $reply=&Rreturn(&rreply($socket,"phpSerialize($lastline);"));
1.6 www 315: return($reply,&Dumper($reply));
316: }
317:
1.1 www 318: sub r_cas_formula_fix {
319: my ($expression)=@_;
320: return &Apache::response::implicit_multiplication($expression);
321: }
322:
323: sub r_run {
324: my ($script,$submission,$argument,$libraries) = @_;
325: my $socket=&connect();
326: my @submissionarray=split(/\s*\,\s*/,$submission);
327: for (my $i=0;$i<=$#submissionarray;$i++) {
328: my $n=$i+1;
329: my $fixedsubmission=&r_cas_formula_fix($submissionarray[$i]);
330: $script=~s/RESPONSE\[$n\]/$fixedsubmission/gs;
331: }
332: my @argumentarray=@{$argument};
333: for (my $i=0;$i<=$#argumentarray;$i++) {
334: my $n=$i+1;
335: my $fixedargument=&r_cas_formula_fix($argumentarray[$i]);
336: $script=~s/LONCAPALIST\[$n\]/$fixedargument/gs;
337: }
338: my $reply=&runscript($socket,$script,$libraries);
339: &disconnect($socket);
340: if ($reply=~/^\s*true\s*$/i) { return 'EXACT_ANS'; }
341: if ($reply=~/^\s*false\s*$/i) { return 'INCORRECT'; }
342: return 'BAD_FORMULA';
343: }
344:
345: sub r_eval {
1.6 www 346: my ($script,$libraries,$hashflag) = @_;
1.1 www 347: my $socket=&connect();
1.6 www 348: my $reply;
349: my $dump='';
350: if ($hashflag) {
351: ($reply,$dump)=&runserializedscript($socket,$script,$libraries);
352: } else {
353: $reply=&runscript($socket,$script,$libraries);
354: }
1.1 www 355: &disconnect($socket);
1.6 www 356: return ($reply,$dump);
1.1 www 357: }
358:
359:
360: sub compareterms {
361: my ($socket,$terma,$termb)=@_;
362: my $difference=$terma.'-('.$termb.')';
363: if (&blacklisted($difference)) { return 'Error: blacklisted'; }
364: my $reply=&rreply($socket,$difference.';');
365: if ($reply=~/^\s*0\s*$/) { return 'true'; }
366: if ($reply=~/^Error\:/) { return $reply; }
367: return 'false';
368: }
369:
370: sub r_check {
371: my ($response,$answer,$reterror) = @_;
372: my $socket=&connect();
373: my $reply=&compareterms($socket,$response,$answer);
374: &disconnect($socket);
375: # integer to string mappings come from capaParser.h
376: # 1 maps to 'EXACT_ANS'
377: if ($reply eq 'true') { return 1; }
378: # 11 maps to 'BAD_FORMULA'
379: if ($reply=~/^Error\:/) { return 11; }
380: # 7 maps to 'INCORRECT'
381: return 7;
382: }
383:
384: 1;
385: __END__;
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