--- loncom/homework/grades.pm	2003/09/25 08:30:57	1.130.2.1.2.3
+++ loncom/homework/grades.pm	2003/10/14 00:05:16	1.130.2.1.2.9
@@ -1,7 +1,7 @@
 # The LearningOnline Network with CAPA
 # The LON-CAPA Grading handler
 #
-# $Id: grades.pm,v 1.130.2.1.2.3 2003/09/25 08:30:57 albertel Exp $
+# $Id: grades.pm,v 1.130.2.1.2.9 2003/10/14 00:05:16 albertel Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -3146,17 +3146,18 @@ sub getSequenceDropDown {
 }
 
 sub scantron_uploads {
-    #FIXME need to support scantron files put in another location,
-    # maybe the course directory? a scantron dir in the course directory?
     if (!-e $Apache::lonnet::perlvar{'lonScansDir'}) { return ''};
     my $result=	'<select name="scantron_selectfile">';
-    opendir(DIR,$Apache::lonnet::perlvar{'lonScansDir'});
-    my @files=sort(readdir(DIR));
+    my $cdom=$ENV{'course.'.$ENV{'request.course.id'}.'.domain'};
+    my $cname=$ENV{'course.'.$ENV{'request.course.id'}.'.num'};
+    my @files=&Apache::lonnet::dirlist('userfiles',$cdom,$cname,
+			      &Apache::loncreatecourse::propath($cdom,$cname));
     foreach my $filename (@files) {
-	if ($filename eq '.' or $filename eq '..') { next; }
+	($filename)=split(/&/,$filename);
+	if ($filename!~/^scantron_orig_/) { next ; }
+	$filename=~s/^scantron_orig_//;
 	$result.="<option>$filename</option>\n";
     }
-    closedir(DIR);
     $result.="</select>";
     return $result;
 }
@@ -3214,6 +3215,13 @@ sub scantron_selectphase {
               Format of data file: $format_selector
 	    </td>
           </tr>
+          <tr bgcolor="#ffffe6">
+            <td>
+<!-- FIXME this is lazy, a single parse of the set should let me know what this is -->
+              Last line to expect an answer on: 
+                <input type="text" name="scantron_maxbubble" />
+	    </td>
+          </tr>
         </table>
       </td>
     </tr>
@@ -3269,23 +3277,52 @@ sub username_to_idmap {
 }
 
 sub scantron_fixup_scanline {
-    my ($scantron_config,$line,$field,$newvalue) = @_;
+    my ($scantron_config,$scan_data,$line,$whichline,$field,$args)=@_;
     if ($field eq 'ID') {
-	if ($newvalue > $$scantron_config{'IDlength'}) {
+	if (length($args->{'newid'}) > $$scantron_config{'IDlength'}) {
 	    return ($line,1,'New value to large');
 	}
-	if ($newvalue < $$scantron_config{'IDlength'}) {
-	    $newvalue=sprintf('%-'.$$scantron_config{'IDlength'}.'s',
-			      $newvalue);
+	if (length($args->{'newid'}) < $$scantron_config{'IDlength'}) {
+	    $args->{'newid'}=sprintf('%-'.$$scantron_config{'IDlength'}.'s',
+				     $args->{'newid'});
 	}
 	substr($line,$$scantron_config{'IDstart'}-1,
-	       $$scantron_config{'IDlength'})=$newvalue;
+	       $$scantron_config{'IDlength'})=$args->{'newid'};
+	if ($args->{'newid'}=~/^\s*$/) {
+	    &scan_data($scan_data,"$whichline.user",
+		       $args->{'username'}.':'.$args->{'domain'});
+	}
+    } elsif ($field eq 'answer') {
+	my $length=$scantron_config->{'Qlength'};
+	my $off=$scantron_config->{'Qoff'};
+	my $on=$scantron_config->{'Qon'};
+	my $answer=${off}x$length;
+	if ($args->{'response'} eq 'none') {
+	    &scan_data($scan_data,
+		       "$whichline.no_bubble.".$args->{'question'},'1');
+	} else {
+	    substr($answer,$args->{'response'},1)=$on;
+	    &scan_data($scan_data,
+		       "$whichline.no_bubble.".$args->{'question'},undef,'1');
+	}
+	my $where=$length*($args->{'question'}-1)+$scantron_config->{'Qstart'};
+	substr($line,$where-1,$length)=$answer;
     }
     return $line;
 }
 
+sub scan_data {
+    my ($scan_data,$key,$value,$delete)=@_;
+    my $filename=$ENV{'form.scantron_selectfile'};
+    if (defined($value)) {
+	$scan_data->{$filename.'_'.$key} = $value;
+    }
+    if ($delete) { delete($scan_data->{$filename.'_'.$key}); }
+    return $scan_data->{$filename.'_'.$key};
+}
+
 sub scantron_parse_scanline {
-    my ($line,$scantron_config)=@_;
+    my ($line,$whichline,$scantron_config,$scan_data)=@_;
     my %record;
     my $questions=substr($line,$$scantron_config{'Qstart'}-1);
     my $data=substr($line,0,$$scantron_config{'Qstart'}-1);
@@ -3299,7 +3336,7 @@ sub scantron_parse_scanline {
     }
     $record{'scantron.ID'}=substr($data,$$scantron_config{'IDstart'}-1,
 				  $$scantron_config{'IDlength'});
-    $record{'scantron.paperID'}=
+    $record{'scantron.PaperID'}=
 	substr($data,$$scantron_config{'PaperID'}-1,
 	       $$scantron_config{'PaperIDlength'});
     $record{'scantron.FirstName'}=
@@ -3315,18 +3352,26 @@ sub scantron_parse_scanline {
 	my $currentquest=substr($questions,0,$$scantron_config{'Qlength'});
 	substr($questions,0,$$scantron_config{'Qlength'})='';
 	if (length($currentquest) < $$scantron_config{'Qlength'}) { next; }
-	my (@array)=split(/$$scantron_config{'Qon'}/,$currentquest);
-	if (scalar(@array) gt 2) {
-	    #FIXME do something intelligent with double bubbles
-	    #actually not a concern right now, should be taking care of later
-	    Apache->request->print("<br ><b>Wha!!!</b> <pre>".scalar(@array).
-				   '-'.$currentquest.'-'.$questnum.'</pre><br />');
-	}
+	my @array=split($$scantron_config{'Qon'},$currentquest,-1);
 	if (length($array[0]) eq $$scantron_config{'Qlength'}) {
 	    $record{"scantron.$questnum.answer"}='';
+	    if (!&scan_data($scan_data,"$whichline.no_bubble.$questnum")) {
+		push(@{$record{"scantron.missingerror"}},$questnum);
+	    }
 	} else {
 	    $record{"scantron.$questnum.answer"}=$alphabet[length($array[0])];
 	}
+	if (scalar(@array) gt 2) {
+	    Apache->request->print("snippet is <pre>$currentquest</pre>");
+	    push(@{$record{'scantron.doubleerror'}},$questnum);
+	    my @ans=@array;
+	    my $i=length($ans[0]);shift(@ans);
+	    while ($#ans) {
+		$i+=length($ans[0])+1;
+		$record{"scantron.$questnum.answer"}.=$alphabet[$i];
+		shift(@ans);
+	    }
+	}
     }
     $record{'scantron.maxquest'}=$questnum;
     return \%record;
@@ -3342,8 +3387,11 @@ sub scantron_add_delay {
 }
 
 sub scantron_find_student {
-    my ($scantron_record,$idmap)=@_;
+    my ($scantron_record,$scan_data,$idmap,$line)=@_;
     my $scanID=$$scantron_record{'scantron.ID'};
+    if ($scanID =~ /^\s*$/) {
+	return &scan_data($scan_data,"$line.user");
+    }
     foreach my $id (keys(%$idmap)) {
 	#Apache->request->print('<pre>checking studnet -'.$id.'- againt -'.$scanID.'- </pre>');
 	if (lc($id) eq lc($scanID)) {
@@ -3362,36 +3410,44 @@ sub scantron_filter {
     return 0;
 }
 
-#FIXME I think I am doing this in the wrong order, I think it would be
-#better to make a several passes analyzing all of the lines in the
-#file for common errors wrong/invalid PID/username duplicated
-#PID/username, missing bubbles, double bubbles, missing/invalid CODE
-#and then get the instructor to fix all of these errors, then grade
-#the corrected one, I'll still need to catch error conditions, but
-#maybe most will taken care even before we start
-
 sub scantron_process_corrections {
     my ($r) = @_;
-    if ($ENV{'form.scantron_corrections'} =~ /^(duplicate|incorrect)ID$/) {
-	my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
-	my $scanlines=&scantron_getfile();
-	my $classlist=&Apache::loncoursedata::get_classlist();
-	my $which=$ENV{'form.scantron_line'};
-	my $line=&scantron_get_line($scanlines,$which);
+    my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
+    my ($scanlines,$scan_data)=&scantron_getfile();
+    my $classlist=&Apache::loncoursedata::get_classlist();
+    my $which=$ENV{'form.scantron_line'};
+    my $line=&scantron_get_line($scanlines,$which);
+    my ($skip,$err,$errmsg);
+    if ($ENV{'form.scantron_skip_record'}) {
+	$skip=1;
+    } elsif ($ENV{'form.scantron_corrections'} =~ /^(duplicate|incorrect)ID$/) {
 	my $newstudent=$ENV{'form.scantron_username'}.':'.
 	    $ENV{'form.scantron_domain'};
 	my $newid=$classlist->{$newstudent}->[&Apache::loncoursedata::CL_ID];
-	($line,my $err,my $errmsg)=
-	    &scantron_fixup_scanline(\%scantron_config,$line,'ID',$newid);
-	if ($err) {
-	    $r->print("Unable to accept last correction, an error occurred :$errmsg:");
-	} else {
-	    &scantron_put_line($scanlines,$which,$line);
-	    &scantron_putfile($scanlines);
+	($line,$err,$errmsg)=
+	    &scantron_fixup_scanline(\%scantron_config,$scan_data,$line,$which,
+				     'ID',{'newid'=>$newid,
+				    'username'=>$ENV{'form.scantron_username'},
+				    'domain'=>$ENV{'form.scantron_domain'}});
+    } elsif ($ENV{'form.scantron_corrections'} =~ /^(missing|double)bubble$/) {
+	foreach my $question (split(',',$ENV{'form.scantron_questions'})) {
+	    ($line,$err,$errmsg)=
+		&scantron_fixup_scanline(\%scantron_config,$scan_data,$line,
+					 $which,'answer',
+					 { 'question'=>$question,
+		       'response'=>$ENV{"form.scantron_correct_Q_$question"}});
+	    if ($err) { last; }
 	}
     }
+    if ($err) {
+	$r->print("Unable to accept last correction, an error occurred :$errmsg:");
+    } else {
+	&scantron_put_line($scanlines,$which,$line,$skip);
+	&scantron_putfile($scanlines,$scan_data);
+    }
 }
 
+
 sub scantron_validate_file {
     my ($r) = @_;
     my ($symb,$url)=&get_symb_and_url($r);
@@ -3405,10 +3461,10 @@ sub scantron_validate_file {
     $r->print(&Apache::loncommon::studentbrowser_javascript());
     my $result= <<SCANTRONFORM;
 <form method="post" enctype="multipart/form-data" action="/adm/grades" name="scantronupload">
-  <input type="hidden" name="command" value="scantron_validate" />
   <input type="hidden" name="selectpage" value="$ENV{'form.selectpage'}" />
   <input type="hidden" name="scantron_format" value="$ENV{'form.scantron_format'}" />
   <input type="hidden" name="scantron_selectfile" value="$ENV{'form.scantron_selectfile'}" />
+  <input type="hidden" name="scantron_maxbubble" value="$ENV{'form.scantron_maxbubble'}" />
   $default_form_data
 SCANTRONFORM
     $r->print($result);
@@ -3428,52 +3484,60 @@ SCANTRONFORM
     }
     my $stop=0;
     while (!$stop && $currentphase < scalar(@validate_phases)) {
+	$r->print("<p> Validating ".$validate_phases[$currentphase]."</p>");
+	$r->rflush();
 	my $which="scantron_validate_".$validate_phases[$currentphase];
 	{
 	    no strict 'refs';
 	    ($stop,$currentphase)=&$which($r,$currentphase);
 	}
     }
-    $r->print("<input type='hidden' name='validatepass' value='".$currentphase."' />");
+    if (!$stop) {
+	$r->print("Validation process complete, click 'Submit' to start proccssing");
+	$r->print('<input type="hidden" name="command" value="scantron_process" />');
+    } else {
+	$r->print('<input type="hidden" name="command" value="scantron_validate" />');
+	$r->print("<input type='hidden' name='validatepass' value='".$currentphase."' />");
+    }
+    $r->print('<input type="submit" name="submit" /></form></body></html>');
     return '';
 }
 
 sub scantron_getfile {
-    #my $scanlines=Apache::File->new($Apache::lonnet::perlvar{'lonScansDir'}."/$ENV{'form.scantron_selectfile'}");
     #FIXME really would prefer a scantron directory but tokenwrapper
     # doesn't allow access to subdirs of userfiles
+    my $cname=$ENV{'course.'.$ENV{'request.course.id'}.'.num'};
+    my $cdom=$ENV{'course.'.$ENV{'request.course.id'}.'.domain'};
     my $lines;
-    $lines=&Apache::lonnet::getfile('/uploaded/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.domain'}.'/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.num'}.'/'.
+    $lines=&Apache::lonnet::getfile('/uploaded/'.$cdom.'/'.$cname.'/'.
 		       'scantron_orig_'.$ENV{'form.scantron_selectfile'});
     if ($lines eq '-1') {
-       #FIXME need to actually replicate file to course space
+	#FIXME need to actually replicate file to course space
+	#FIXME when replicating strip CRLF to LF or CR to LF
     }
     my %scanlines;
-    $scanlines{'orig'}=[split("\n",$lines)];
+    $scanlines{'orig'}=[(split("\n",$lines,-1))];
     my $temp=$scanlines{'orig'};
     $scanlines{'count'}=$#$temp;
 
-    $lines=&Apache::lonnet::getfile('/uploaded/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.domain'}.'/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.num'}.'/'.
+    $lines=&Apache::lonnet::getfile('/uploaded/'.$cdom.'/'.$cname.'/'.
 		       'scantron_corrected_'.$ENV{'form.scantron_selectfile'});
     if ($lines eq '-1') {
 	$scanlines{'corrected'}=[];
     } else {
-	$scanlines{'corrected'}=[split("\n",$lines)];
+	$scanlines{'corrected'}=[(split("\n",$lines,-1))];
     }
-    $lines=&Apache::lonnet::getfile('/uploaded/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.domain'}.'/'.
-		   $ENV{'course.'.$ENV{'request.course.id'}.'.num'}.'/'.
+    $lines=&Apache::lonnet::getfile('/uploaded/'.$cdom.'/'.$cname.'/'.
 		       'scantron_skipped_'.$ENV{'form.scantron_selectfile'});
     if ($lines eq '-1') {
 	$scanlines{'skipped'}=[];
     } else {
-	$scanlines{'skipped'}=[split("\n",$lines)];
+	$scanlines{'skipped'}=[(split("\n",$lines,-1))];
     }
-    return \%scanlines;
+    my @tmp=&Apache::lonnet::dump('scantrondata',$cdom,$cname);
+    if ($tmp[0] =~ /^(error:|no_such_host)/) { @tmp=(); }
+    my %scan_data = @tmp;
+    return (\%scanlines,\%scan_data);
 }
 
 sub lonnet_putfile {
@@ -3487,13 +3551,11 @@ sub lonnet_putfile {
 }
 
 sub scantron_putfile {
-    my ($scanlines) = @_;
+    my ($scanlines,$scan_data) = @_;
     #FIXME really would prefer a scantron directory but tokenwrapper
     # doesn't allow access to subdirs of userfiles
-    my $prefix='/uploaded/'.
-	$ENV{'course.'.$ENV{'request.course.id'}.'.domain'}.'/'.
-	$ENV{'course.'.$ENV{'request.course.id'}.'.num'}.'/'.
-	'scantron_';
+    my $cname=$ENV{'course.'.$ENV{'request.course.id'}.'.num'};
+    my $cdom=$ENV{'course.'.$ENV{'request.course.id'}.'.domain'};
     my $prefix='scantron_';
 # no need to update orig, shouldn't change
 #   &lonnet_putfile(join("\n",@{$scanlines->{'orig'}}),$prefix.'orig_'.
@@ -3504,6 +3566,7 @@ sub scantron_putfile {
     &lonnet_putfile(join("\n",@{$scanlines->{'skipped'}}),
 		    $prefix.'skipped_'.
 		    $ENV{'form.scantron_selectfile'});
+    &Apache::lonnet::put('scantrondata',$scan_data,$cdom,$cname);
 }
 
 sub scantron_get_line {
@@ -3515,7 +3578,10 @@ sub scantron_get_line {
 
 sub scantron_put_line {
     my ($scanlines,$i,$newline,$skip)=@_;
-    if ($skip) { $scanlines->{'skipped'}[$i]=$newline;return; }
+    if ($skip) {
+	$scanlines->{'skipped'}[$i]=$newline;
+	return;
+    }
     $scanlines->{'corrected'}[$i]=$newline;
 }
 
@@ -3528,70 +3594,205 @@ sub scantron_validate_ID {
 
     #get scantron line setup
     my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
-    my $scanlines=&scantron_getfile();
+    my ($scanlines,$scan_data)=&scantron_getfile();
 
     my %found=('ids'=>{},'usernames'=>{});
     for (my $i=0;$i<=$scanlines->{'count'};$i++) {
 	my $line=&scantron_get_line($scanlines,$i);
 	if (!$line) { next; }
-	my $scan_record=&scantron_parse_scanline($line,\%scantron_config);
+	my $scan_record=&scantron_parse_scanline($line,$i,\%scantron_config,
+						 $scan_data);
 	my $id=$$scan_record{'scantron.ID'};
-	$r->print("<p>Checking ID ".$$scan_record{'scantron.ID'}."</p>\n");
+#	$r->print("<p>Checking ID ".$$scan_record{'scantron.ID'}.
+#		  " on paper ID ".$$scan_record{'scantron.PaperID'}."</p>\n");
 	my $found;
 	foreach my $checkid (keys(%idmap)) {
 	    if (lc($checkid) eq lc($id)) {
 		if ($checkid ne $id) {
-		    $r->print("<p>Using $checkid for bubbled $id</p>\n");
+		    #$r->print("<p>Using $checkid for encoded $id</p>\n");
 		}
 		$found=$checkid;last;
 	    }
 	}
 	if ($found) {
+	    my $username=$idmap{$found};
 	    if ($found{'ids'}{$found}) {
-		#FIXME store away line we prviously saw the ID on
-		&scantron_get_ID_correction($r,$i,$scan_record,
-					    'duplicateID',$found);
+		&scantron_get_correction($r,$i,$scan_record,\%scantron_config,
+					 $line,'duplicateID',$found);
+		return(1);
+	    } elsif ($found{'usernames'}{$username}) {
+		&scantron_get_correction($r,$i,$scan_record,\%scantron_config,
+					 $line,'duplicateID',$username);
 		return(1);
-	    } else {
-		$found{'ids'}{$found}++;
 	    }
+	    #FIXME store away line we prviously saw the ID on to use above
+	    $found{'ids'}{$found}++;
+	    $found{'usernames'}{$username}++;
 	} else {
-	    &scantron_get_ID_correction($r,$i,$scan_record,'incorrectID');
-	    return(1);
+	    if ($id =~ /^\s*$/) {
+		my $username=&scan_data($scan_data,"$i.user");
+		if (defined($username) && $found{'usernames'}{$username}) {
+		    &scantron_get_correction($r,$i,$scan_record,
+					     \%scantron_config,
+					     $line,'duplicateID',$username);
+		    return(1);
+		} elsif (!defined($username)) {
+		    &scantron_get_correction($r,$i,$scan_record,
+					     \%scantron_config,
+					     $line,'incorrectID');
+		    return(1);
+		}
+		$found{'usernames'}{$username}++;
+	    } else {
+		&scantron_get_correction($r,$i,$scan_record,\%scantron_config,
+					 $line,'incorrectID');
+		return(1);
+	    }
 	}
     }
 
     return (0,$currentphase+1);
 }
 
-sub scantron_get_ID_correction {
-    my ($r,$i,$scan_record,$error,$arg)=@_;
-#FIXME allow th poosibility of skipping a line, or in the case of a duplicated ID the previous line, probaly need to show both the current line and the previous one.
-    $r->print("<p>need to correct ID</p>\n");
+sub scantron_get_correction {
+    my ($r,$i,$scan_record,$scan_config,$line,$error,$arg)=@_;
+
+#FIXME in the case of a duplicated ID the previous line, probaly need
+#to show both the current line and the previous one and allow skipping
+#the previous one or the current one
+
+    $r->print("<p>This scantron record has an error ($error). ");
+    if ( defined($$scan_record{'scantron.PaperID'}) ) {
+	$r->print("The current PaperID is <tt>".
+		  $$scan_record{'scantron.PaperID'}."</tt> \n");
+    } else {
+	$r->print("The current scanline is <pre>".
+		  $line."</pre> \n");
+    }
     $r->print('<input type="hidden" name="scantron_corrections" value="'.$error.'" />'."\n");
     $r->print('<input type="hidden" name="scantron_line" value="'.$i.'" />'."\n");
-    if ($error eq 'unknownID') {
-	$r->print("<p> Unknown ID </p>\n");
-    } elsif ($error eq 'duplicateID') {
-	$r->print("<p> Duplicated ID </p>\n");
-    }
-    $r->print("<p>Original ID is ".$$scan_record{'scantron.ID'}."</p>\n");
-    $r->print("<p>Name on paper is ".$$scan_record{'scantron.LastName'}.",".
-	      $$scan_record{'scantron.FirstName'}."</p>");
-    $r->print("Corrected User -- ");
-    $r->print("\nusername:<input type='text' name='scantron_username' value='' />");
-    $r->print("\ndomain:".
-	      &Apache::loncommon::select_dom_form(undef,'scantron_domain'));
-    #FIXME it would be nice if this sent back the user ID and
-    #could do partial userID matches
-    $r->print(&Apache::loncommon::selectstudent_link('scantronupload',
-				       'scantron_username','scantron_domain'));
-    &scantron_end_validate_form($r);
+    if ($error =~ /ID$/) {
+	if ($error eq 'unknownID') {
+	    $r->print("The encoded ID is not in the classlist</p>\n");
+	} elsif ($error eq 'duplicateID') {
+	    $r->print("The encoded ID has also been used by a previous paper $arg</p>\n");
+	}
+	$r->print("<p>Original ID is <tt>".$$scan_record{'scantron.ID'}.
+		  "</tt><br />\n");
+	$r->print("Name on paper is ".$$scan_record{'scantron.LastName'}.",".
+		  $$scan_record{'scantron.FirstName'}."</p>");
+	$r->print("<p>Please correct <br /> \n");
+	$r->print("\n<ul><li> Pick a specific user -- username:<input type='text' name='scantron_username' value='' />");
+	$r->print("\ndomain:".
+		 &Apache::loncommon::select_dom_form(undef,'scantron_domain'));
+	#FIXME it would be nice if this sent back the user ID and
+	#could do partial userID matches
+	$r->print(&Apache::loncommon::selectstudent_link('scantronupload',
+				      'scantron_username','scantron_domain'));
+	$r->print('</li>');
+    } elsif ($error eq 'doublebubble') {
+	$r->print("<pre>$line</pre>");
+	$Apache::lonxml::debug=1;
+	&Apache::lonhomework::showhashsubset($scan_record,'.');
+	$Apache::lonxml::debug=0;
+	$r->print("There have been multiple bubbles scanned for a single question\n");
+	$r->print('<input type="hidden" name="scantron_questions" value="'.
+		  join(',',@{$arg}).'" />');
+	foreach my $question (@{$arg}) {
+	    my $selected=$$scan_record{"scantron.$question.answer"};
+	    $r->print("<p> For question $question, selected bubbles were ".
+		      join(" ",split('',$selected,-1)).
+              " <br />Please pick which one should be used for grading<br />");
+	    &scantron_bubble_selector($r,$scan_config,$question);
+	}
+    } elsif ($error eq 'missingbubble') {
+	$r->print("Some questions have no scanned bubbles\n");
+	$r->print('<input type="hidden" name="scantron_questions" value="'.
+		  join(',',@{$arg}).'" />');
+	foreach my $question (@{$arg}) {
+	    my $selected=$$scan_record{"scantron.$question.answer"};
+	    $r->print("<p>Question $question, Please select a bubble to use ");
+	    &scantron_bubble_selector($r,$scan_config,$question);
+	}
+    } else {
+	$r->print("\n<ul>");
+    }
+    $r->print("<li>Skip this scanline saving it for later  ");
+    $r->print("\n<input type='checkbox' name='scantron_skip_record' /> </li></ul>");
 }
 
-sub scantron_end_validate_form {
-    my ($r) = @_;
-    $r->print('<input type="submit" name="submit" /></form></body></html>');
+sub scantron_bubble_selector {
+    my ($r,$scan_config,$quest)=@_;
+    my $max=$$scan_config{'Qlength'};
+    my @alphabet=('A'..'Z');
+    for (my $i=0;$i<$max;$i++) {
+	$r->print('<input type="radio" name="scantron_correct_Q_'.$quest.
+		  '" value="'.$i.'" />'.$alphabet[$i]);
+    }
+    $r->print('<input type="radio" name="scantron_correct_Q_'.$quest.
+	      '" value="none" /> Nothing');
+    $r->print('<br />');
+}
+
+sub scantron_validate_CODE {
+    my ($r,$currentphase) = @_;
+    #FIXME doesn't do anything yet
+    return (0,$currentphase+1);
+}
+
+sub scantron_validate_doublebubble {
+    my ($r,$currentphase) = @_;
+    #get student info
+    my $classlist=&Apache::loncoursedata::get_classlist();
+    my %idmap=&username_to_idmap($classlist);
+
+    #get scantron line setup
+    my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
+    my ($scanlines,$scan_data)=&scantron_getfile();
+    for (my $i=0;$i<=$scanlines->{'count'};$i++) {
+	my $line=&scantron_get_line($scanlines,$i);
+	if (!$line) { next; }
+	my $scan_record=&scantron_parse_scanline($line,$i,\%scantron_config,
+						 $scan_data);
+	if (!defined($$scan_record{'scantron.doubleerror'})) { next; }
+	&scantron_get_correction($r,$i,$scan_record,\%scantron_config,$line,
+				 'doublebubble',
+				 $$scan_record{'scantron.doubleerror'});
+    	return (1,$currentphase);
+    }
+    return (0,$currentphase+1);
+}
+
+sub scantron_validate_missingbubbles {
+    my ($r,$currentphase) = @_;
+    #get student info
+    my $classlist=&Apache::loncoursedata::get_classlist();
+    my %idmap=&username_to_idmap($classlist);
+
+    #get scantron line setup
+    my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
+    my ($scanlines,$scan_data)=&scantron_getfile();
+    my $max_bubble=$ENV{'form.scantron_maxbubble'};
+    if (!$max_bubble) { $max_bubble=2**31; }
+    for (my $i=0;$i<=$scanlines->{'count'};$i++) {
+	my $line=&scantron_get_line($scanlines,$i);
+	if (!$line) { next; }
+	my $scan_record=&scantron_parse_scanline($line,$i,\%scantron_config,
+						 $scan_data);
+	if (!defined($$scan_record{'scantron.missingerror'})) { next; }
+	my @to_correct;
+	foreach my $missing (@{$$scan_record{'scantron.missingerror'}}) {
+	    if ($missing > $max_bubble) { next; }
+	    push(@to_correct,$missing);
+	}
+	if (@to_correct) {
+	    &scantron_get_correction($r,$i,$scan_record,\%scantron_config,
+				     $line,'missingbubble',\@to_correct);
+	    return (1,$currentphase);
+	}
+
+    }
+    return (0,$currentphase+1);
 }
 
 sub scantron_process_students {
@@ -3602,8 +3803,7 @@ sub scantron_process_students {
     my $default_form_data=&defaultFormData($symb,$url);
 
     my %scantron_config=&get_scantron_config($ENV{'form.scantron_format'});
-    my $scanlines=Apache::File->new($Apache::lonnet::perlvar{'lonScansDir'}."/$ENV{'form.scantron_selectfile'}");
-    my @scanlines=<$scanlines>;
+    my ($scanlines,$scan_data)=&scantron_getfile();
     my $classlist=&Apache::loncoursedata::get_classlist();
     my %idmap=&username_to_idmap($classlist);
     my $navmap=Apache::lonnavmaps::navmap->new($ENV{'request.course.fn'}.'.db',$ENV{'request.course.fn'}.'_parms.db',1, 1);
@@ -3620,18 +3820,25 @@ SCANTRONFORM
     my @delayqueue;
     my %completedstudents;
     
-    my %prog_state=&Apache::lonhtmlcommon::Create_PrgWin($r,
-	           'Scantron Status','Scantron Progress',scalar(@scanlines));
+    my %prog_state=&Apache::lonhtmlcommon::Create_PrgWin($r,'Scantron Status',
+				    'Scantron Progress',$scanlines->{'count'});
     &Apache::lonhtmlcommon::Update_PrgWin($r,\%prog_state,
 					  'Processing first student');
     my $start=&Time::HiRes::time();
-    foreach my $line (@scanlines) {
+    my $i=-1;
+    while ($i<$scanlines->{'count'}) {
+	$i++;
+	my $line=&scantron_get_line($scanlines,$i);
 	$r->print('<pre>line is'.$line.'</pre>');
-
-	chomp($line);
-	my $scan_record=&scantron_parse_scanline($line,\%scantron_config);
+	if (!defined($line)) { 
+	    $r->print('skipping');
+	    next;
+	}
+	my $scan_record=&scantron_parse_scanline($line,$i,\%scantron_config,
+						 $scan_data);
 	my ($uname,$udom);
-	unless ($uname=&scantron_find_student($scan_record,\%idmap)) {
+	unless ($uname=&scantron_find_student($scan_record,$scan_data,
+					      \%idmap,$i)) {
 	    &scantron_add_delay(\@delayqueue,$line,
 				'Unable to find a student that matches',1);
 	    next;
@@ -3711,6 +3918,51 @@ SCANTRONFORM
     
     $navmap->untieHashes();
 }
+
+sub scantron_upload_scantron_data {
+    my ($r)=@_;
+    $r->print(&Apache::loncommon::coursebrowser_javascript($ENV{'request.role.domain'}));
+    my $select_link=&Apache::loncommon::selectcourse_link('rules','courseid',
+							  'domainid');
+    my $domsel=&Apache::loncommon::select_dom_form($ENV{'request.role.domain'},
+						   'domainid');
+    $r->print(<<UPLOAD);
+<script type="text/javascript" language="javascript">
+    function checkUpload(formname) {
+	if (formname.upfile.value == "") {
+	    alert("Please use the browse button to select a file from your local directory.");
+	    return false;
+	}
+	formname.submit();
+    }
+</script>
+
+<form enctype='multipart/form-data' action='/adm/grades' name='rules' method='post'>
+Course: <input name='courseid' type='text' />
+Domain: $domsel $select_link
+<br />
+<input name='command' value='scantronupload_save' type='hidden' />
+File to upload:<input type="file" name="upfile" size="50" />
+<br />
+<input type="button" onClick="javascript:checkUpload(this.form);" value="Upload Scantron Data" />
+</form>
+UPLOAD
+    return '';
+}
+
+sub scantron_upload_scantron_data_save {
+    my($r)=@_;
+    $r->print("Doing upload to ".$ENV{'form.courseid'});
+    my $home=&Apache::lonnet::homeserver($ENV{'form.courseid'},
+					 $ENV{'form.domainid'});
+    my $fname='scantron_orig_'.$ENV{'form.upfile.filename'};
+    $r->print(&Apache::lonnet::finishuserfileupload($ENV{'form.courseid'},
+						    $ENV{'form.domainid'},
+						    $home,'upfile',$fname));
+    return '';
+}
+
+
 #-------- end of section for handling grading scantron forms -------
 #
 #-------------------------------------------------------------------
@@ -3897,7 +4149,7 @@ sub handler {
 	$url = $ENV{'form.url'};
     }
     &send_header($request);
-    if ($url eq '' && $symb eq '') {
+    if ($url eq '' && $symb eq '' && $command eq '') {
 	if ($ENV{'user.adv'}) {
 	    if (($ENV{'form.codeone'}) && ($ENV{'form.codetwo'}) &&
 		($ENV{'form.codethree'})) {
@@ -3938,7 +4190,6 @@ sub handler {
 		delete($perm{'mgr'});
 	    }
 	}
-
 	if ($command eq 'submission' && $perm{'vgr'}) {
 	    ($ENV{'form.student'} eq '' ? &listStudents($request) : &submission($request,0,0));
 	} elsif ($command eq 'pickStudentPage' && $perm{'vgr'}) {
@@ -3982,6 +4233,13 @@ sub handler {
 	    $request->print(&scantron_validate_file($request));
 	} elsif ($command eq 'scantron_process' && $perm{'mgr'}) {
 	    $request->print(&scantron_process_students($request));
+	} elsif ($command eq 'scantronupload' && 
+		 &Apache::lonnet::allowed('usc',$ENV{'request.role.domain'})) {
+	    $request->print(&scantron_upload_scantron_data($request));
+
+	} elsif ($command eq 'scantronupload_save' &&
+		 &Apache::lonnet::allowed('usc',$ENV{'request.role.domain'})) {
+	    $request->print(&scantron_upload_scantron_data_save($request));
 	} elsif ($command) {
 	    $request->print("Access Denied");
 	}
@@ -3999,6 +4257,7 @@ sub send_header {
 #remotewindow.close();
 #</script>"); 
     $request->print(&Apache::loncommon::bodytag('Grading'));
+    $request->rflush();
 }
 
 sub send_footer {