--- loncom/homework/lonr.pm	2009/06/19 14:03:19	1.5
+++ loncom/homework/lonr.pm	2014/11/19 21:14:47	1.11
@@ -1,7 +1,7 @@
 # The LearningOnline Network with CAPA
 # Interface routines to R CAS
 #
-# $Id: lonr.pm,v 1.5 2009/06/19 14:03:19 www Exp $
+# $Id: lonr.pm,v 1.11 2014/11/19 21:14:47 raeburn Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -33,7 +33,8 @@ use IO::Socket;
 use Apache::lonnet;
 use Apache::response();
 use LONCAPA;
-### Commented out for now: use Tie::IxHash::Easy; # autoties all subhashes to keep index order
+use Tie::IxHash::Easy; # autoties all subhashes to keep index order
+use Data::Dumper;  # used to output hash contents
 
 my $errormsg='';
 
@@ -52,18 +53,18 @@ sub Rcroak {
 #
 sub Rpeel {
         my $x = $_[0];  # the string containing the serialized R object(s)
-        if ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
+        if ($x =~ /^N\;(.*)$/) {
+            return ('',$1);
+        } elsif ($x =~ /^((?:i|d):(.+?);)(.*)$/) {
                 return ($1, $+);  # x starts with a number
-        }
-        elsif ($x =~ /^s:(\d+):/) {
+        } 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:/) {
+        } 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) {
@@ -101,82 +102,103 @@ sub 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 'capaNNN' where NNN is the index of the entry in the original
+# 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)
-        $errormsg='';
-        if ($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 '') {
-                                $key = "capa$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
+    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 $errormsg; }
+        return \%h;  # return a reference to the hash
+    } elsif ($x eq '') {
+        return '';
+    } else {
+        return 'Unrecognized output';
+    }
 }
 # --- end Rreturn ---
 
-#
-# Rentry takes a list of indices and gets the entry in a hash generated by Rreturn.
-# Call: Rentry(Rvalue, index1, index2, ...) where Rvalue is a hash returned by Rreturn.
-# Rentry will return the first scalar value it encounters (ignoring excess indices).
-# If an invalid key is given, Rentry returns undef.
-#
 sub Rentry {
-        my $hash = shift;  # pointer to hash
-        my $x;
-        my $i;
-        if (ref($hash) ne 'HASH') {
-                &Rcroak('argument to Rentry is not a hash');
-        }
-        while ($i = shift) {
-                if (exists $hash->{$i}) {
-                   $hash = $hash->{$i};
-                } else {
-                   return undef;
-                }
-                if (ref($hash) eq 'REF') {
-                   $hash = $$hash;  # dereference one layer
-                } elsif (ref($hash) ne 'HASH') {
-                   return $hash;  # drilled down to a scalar
-                }
-        }
+    my $hash = shift;  # pointer to tied hash
+    my $i;
+    if (ref($hash) ne 'HASH') {
+       return 'Argument to cas_hashref_entry is not a hash!';
+    }
+    while ($i = shift) {
+       if (exists($hash->{$i})) {
+          $hash = $hash->{$i};
+       } else {
+          return undef;
+       }
+       if (ref($hash) eq 'REF') {
+          $hash = $$hash;  # dereference one layer
+       } elsif (ref($hash) ne 'HASH') {
+          return $hash;  # drilled down to a scalar
+       }
+    }
 }
-# --- end Rentry ---
 
+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',
@@ -221,9 +243,9 @@ sub blacklisted {
 }
 
 sub r_allowed_libraries {
-   return ('boot','class','cluster','datasets','KernSmooth','MASS',
-           'methods','mgcv','nlme','nnet','rpart','spatial',
-           'splines','stats','stats4','survival');
+   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 {
@@ -237,29 +259,62 @@ sub r_is_allowed_library {
 sub runscript {
     my ($socket,$fullscript,$libraries)=@_;
     if (&blacklisted($fullscript)) { return 'Error: blacklisted'; }
-    my $reply;
+    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.');'."\n");
+              $reply=&rreply($socket,'library('.$library.');');
               if ($reply=~/^Error\:/) { return $reply; }
           } else { 
              return 'Error: blacklisted'; 
           }
        }
     }
-    foreach my $line (split(/\;/s,$fullscript)) {
-	if ($line=~/\w/) { $reply=&rreply($socket,$line.";\n"); }
-	if ($reply=~/^Error\:/) { return $reply; }
-    }
+    $fullscript=~s/\;+\s*$//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);
@@ -288,11 +343,17 @@ sub r_run {
 }
 
 sub r_eval {
-    my ($script,$libraries) = @_;
+    my ($script,$libraries,$hashflag) = @_;
     my $socket=&connect();
-    my $reply=&runscript($socket,$script,$libraries);
+    my $reply;
+    my $dump='';
+    if ($hashflag) {
+       ($reply,$dump)=&runserializedscript($socket,$script,$libraries);
+    } else {
+       $reply=&runscript($socket,$script,$libraries);
+    }
     &disconnect($socket);
-    return $reply;
+    return ($reply,$dump);
 }