--- loncom/homework/grades.pm	2007/01/04 14:59:57	1.386
+++ loncom/homework/grades.pm	2007/08/10 20:09:30	1.426
@@ -1,7 +1,7 @@
 # The LearningOnline Network with CAPA
 # The LON-CAPA Grading handler
 #
-# $Id: grades.pm,v 1.386 2007/01/04 14:59:57 raeburn Exp $
+# $Id: grades.pm,v 1.426 2007/08/10 20:09:30 albertel Exp $
 #
 # Copyright Michigan State University Board of Trustees
 #
@@ -41,12 +41,10 @@ use Apache::Constants qw(:common);
 use Apache::lonlocal;
 use Apache::lonenc;
 use String::Similarity;
-use lib '/home/httpd/lib/perl';
 use LONCAPA;
 
 use POSIX qw(floor);
 
-my %oldessays=();
 my %perm=();
 
 # ----- These first few routines are general use routines.----
@@ -94,6 +92,7 @@ sub get_symb {
 	    return ();
 	}
     }
+    &Apache::lonenc::check_decrypt(\$symb);
     return ($symb);
 }
 
@@ -102,10 +101,10 @@ sub get_symb {
 sub nameUserString {
     my ($type,$fullname,$uname,$udom) = @_;
     if ($type eq 'header') {
-	return '<b>&nbsp;Fullname&nbsp;</b><font color="#999999">(Username)</font>';
+	return '<b>&nbsp;Fullname&nbsp;</b><span class="LC_internal_info">(Username)</span>';
     } else {
-	return '&nbsp;'.$fullname.'<font color="#999999">&nbsp;('.$uname.
-	    ($env{'user.domain'} eq $udom ? '' : ' ('.$udom.')').')</font>';
+	return '&nbsp;'.$fullname.'<span class="LC_internal_info">&nbsp;('.$uname.
+	    ($env{'user.domain'} eq $udom ? '' : ' ('.$udom.')').')</span>';
     }
 }
 
@@ -117,8 +116,12 @@ sub response_type {
     my $navmap = Apache::lonnavmaps::navmap->new();
     my $res = $navmap->getBySymb($symb);
     my $partlist = $res->parts();
+    my %vPart = 
+	map { $_ => 1 } (&Apache::loncommon::get_env_multiple('form.vPart'));
     my (%response_types,%handgrade);
     foreach my $part (@{ $partlist }) {
+	next if (%vPart && !exists($vPart{$part}));
+
 	my @types = $res->responseType($part);
 	my @ids = $res->responseIds($part);
 	for (my $i=0; $i < scalar(@ids); $i++) {
@@ -147,7 +150,7 @@ sub get_display_part {
     my ($partID,$symb)=@_;
     my $display=&Apache::lonnet::EXT('resource.'.$partID.'.display',$symb);
     if (defined($display) and $display ne '') {
-	$display.= " (<font color=\"#999900\">id $partID</font>)";
+	$display.= " (<span class=\"LC_internal_info\">id $partID</span>)";
     } else {
 	$display=$partID;
     }
@@ -160,9 +163,8 @@ sub showResourceInfo {
     my ($symb,$probTitle,$checkboxes) = @_;
     my $col=3;
     if ($checkboxes) { $col=4; }
-    my $result ='<table border="0">'.
-	'<tr><td colspan="'.$col.'"><font size="+1"><b>'.&mt('Current Resource').': </b>'.
-	$probTitle.'</font></td></tr>'."\n";
+    my $result = '<h3>'.&mt('Current Resource').': '.$probTitle.'</h3>'."\n";
+    $result .='<table border="0">';
     my ($partlist,$handgrade,$responseType) = &response_type($symb);
     my %resptype = ();
     my $hdgrade='no';
@@ -177,13 +179,13 @@ sub showResourceInfo {
 		if (exists($partsseen{$partID})) {
 		    $result.="<td>&nbsp;</td>";
 		} else {
-		    $result.="<td><input type='checkbox' name='vPart' value='$partID' checked='on' /></td>";
+		    $result.="<td><input type='checkbox' name='vPart' value='$partID' checked='checked' /></td>";
 		}
 		$partsseen{$partID}=1;
 	    }
 	    my $display_part=&get_display_part($partID,$symb);
-	    $result.='<td><b>Part: </b>'.$display_part.' <font color="#999999">'.
-		$resID.'</font></td>'.
+	    $result.='<td><b>Part: </b>'.$display_part.' <span class="LC_internal_info">'.
+		$resID.'</span></td>'.
 		'<td><b>Type: </b>'.$responsetype.'</td></tr>';
 #	    '<td><b>Handgrade: </b>'.$handgrade.'</td></tr>';
 	}
@@ -214,7 +216,7 @@ sub get_order {
 sub cleanRecord {
     my ($answer,$response,$symb,$partid,$respid,$record,$order,$version,
 	$uname,$udom) = @_;
-    my $grayFont = '<font color="#999999">';
+    my $grayFont = '<span class="LC_internal_info">';
     if ($response =~ /^(option|rank)$/) {
 	my %answer=&Apache::lonnet::str2hash($answer);
 	my %grading=&Apache::lonnet::str2hash($record->{$version."resource.$partid.$respid.submissiongrading"});
@@ -225,11 +227,11 @@ sub cleanRecord {
 	    } else {
 		$toprow.='<td><i>'.$answer{$foil}.'&nbsp;</i></td>';
 	    }
-	    $bottomrow.='<td>'.$grayFont.$foil.'</font>&nbsp;</td>';
+	    $bottomrow.='<td>'.$grayFont.$foil.'</span>&nbsp;</td>';
 	}
 	return '<blockquote><table border="1">'.
 	    '<tr valign="top"><td>Answer</td>'.$toprow.'</tr>'.
-	    '<tr valign="top"><td>'.$grayFont.'Option ID</font></td>'.
+	    '<tr valign="top"><td>'.$grayFont.'Option ID</span></td>'.
 	    $grayFont.$bottomrow.'</tr>'.'</table></blockquote>';
     } elsif ($response eq 'match') {
 	my %answer=&Apache::lonnet::str2hash($answer);
@@ -240,18 +242,18 @@ sub cleanRecord {
 	    my $item=shift(@items);
 	    if ($grading{$foil} == 1) {
 		$toprow.='<td><b>'.$item.'&nbsp;</b></td>';
-		$middlerow.='<td><b>'.$grayFont.$answer{$foil}.'&nbsp;</font></b></td>';
+		$middlerow.='<td><b>'.$grayFont.$answer{$foil}.'&nbsp;</span></b></td>';
 	    } else {
 		$toprow.='<td><i>'.$item.'&nbsp;</i></td>';
-		$middlerow.='<td><i>'.$grayFont.$answer{$foil}.'&nbsp;</font></i></td>';
+		$middlerow.='<td><i>'.$grayFont.$answer{$foil}.'&nbsp;</span></i></td>';
 	    }
-	    $bottomrow.='<td>'.$grayFont.$foil.'</font>&nbsp;</td>';
+	    $bottomrow.='<td>'.$grayFont.$foil.'</span>&nbsp;</td>';
 	}
 	return '<blockquote><table border="1">'.
 	    '<tr valign="top"><td>Answer</td>'.$toprow.'</tr>'.
-	    '<tr valign="top"><td>'.$grayFont.'Item ID</font></td>'.
+	    '<tr valign="top"><td>'.$grayFont.'Item ID</span></td>'.
 	    $middlerow.'</tr>'.
-	    '<tr valign="top"><td>'.$grayFont.'Option ID</font></td>'.
+	    '<tr valign="top"><td>'.$grayFont.'Option ID</span></td>'.
 	    $bottomrow.'</tr>'.'</table></blockquote>';
     } elsif ($response eq 'radiobutton') {
 	my %answer=&Apache::lonnet::str2hash($answer);
@@ -268,11 +270,11 @@ sub cleanRecord {
 	    } else {
 		$toprow.='<td>false</td>';
 	    }
-	    $bottomrow.='<td>'.$grayFont.$foil.'</font>&nbsp;</td>';
+	    $bottomrow.='<td>'.$grayFont.$foil.'</span>&nbsp;</td>';
 	}
 	return '<blockquote><table border="1">'.
 	    '<tr valign="top"><td>Answer</td>'.$toprow.'</tr>'.
-	    '<tr valign="top"><td>'.$grayFont.'Option ID</font></td>'.
+	    '<tr valign="top"><td>'.$grayFont.'Option ID</span></td>'.
 	    $grayFont.$bottomrow.'</tr>'.'</table></blockquote>';
     } elsif ($response eq 'essay') {
 	if (! exists ($env{'form.'.$symb})) {
@@ -490,7 +492,7 @@ sub jscriptNform {
 	'    }'."\n".
 	'</script>'."\n";
     $jscript.= '<form action="/adm/grades" method="post" name="onestudent">'."\n".
-	'<input type="hidden" name="symb"    value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb"    value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="saveState" value="'.$env{'form.saveState'}.'" />'."\n".
 	'<input type="hidden" name="probTitle" value="'.$env{'form.probTitle'}.'" />'."\n".
 	'<input type="hidden" name="Status"  value="'.$env{'form.Status'}.'" />'."\n".
@@ -535,7 +537,7 @@ sub compute_points {
 #
 
 sub most_similar {
-    my ($uname,$udom,$uessay)=@_;
+    my ($uname,$udom,$uessay,$old_essays)=@_;
 
 # ignore spaces and punctuation
 
@@ -552,23 +554,22 @@ sub most_similar {
     my $scrsid='';
     my $sessay='';
 # go through all essays ...
-    foreach my $tkey (keys %oldessays) {
-	my ($tname,$tdom,$tcrsid)=split(/\./,$tkey);
+    foreach my $tkey (keys(%$old_essays)) {
+	my ($tname,$tdom,$tcrsid)=map {&unescape($_)} (split(/\./,$tkey));
 # ... except the same student
-        if (($tname ne $uname) || ($tdom ne $udom)) {
-	    my $tessay=$oldessays{$tkey};
-            $tessay=~s/\W+/ /gs;
+        next if (($tname eq $uname) && ($tdom eq $udom));
+	my $tessay=$old_essays->{$tkey};
+	$tessay=~s/\W+/ /gs;
 # String similarity gives up if not even limit
-            my $tsimilar=&String::Similarity::similarity($uessay,$tessay,$limit);
+	my $tsimilar=&String::Similarity::similarity($uessay,$tessay,$limit);
 # Found one
-            if ($tsimilar>$limit) {
-		$limit=$tsimilar;
-                $sname=$tname;
-                $sdom=$tdom;
-                $scrsid=$tcrsid;
-                $sessay=$oldessays{$tkey};
-            }
-        } 
+	if ($tsimilar>$limit) {
+	    $limit=$tsimilar;
+	    $sname=$tname;
+	    $sdom=$tdom;
+	    $scrsid=$tcrsid;
+	    $sessay=$old_essays->{$tkey};
+	}
     }
     if ($limit>0.6) {
        return ($sname,$sdom,$scrsid,$sessay,$limit);
@@ -591,15 +592,16 @@ sub verifyreceipt {
     $receipt     =~ s/[^\-\d]//g;
     my ($symb)   = &get_symb($request);
 
-    my $title.='<h3><font color="#339933">Verifying Submission Receipt '.
-	$receipt.'</h3></font>'."\n".
-	'<font size=+1><b>Resource: </b>'.$env{'form.probTitle'}.'</font><br /><br />'."\n";
+    my $title.='<h3><span class="LC_info">Verifying Submission Receipt '.
+	$receipt.'</h3></span>'."\n".
+	'<h4><b>Resource: </b>'.$env{'form.probTitle'}.'</h4><br /><br />'."\n";
 
     my ($string,$contents,$matches) = ('','',0);
     my (undef,undef,$fullname) = &getclasslist('all','0');
     
     my $receiptparts=0;
-    if ($env{"course.$courseid.receiptalg"} eq 'receipt2') { $receiptparts=1; }
+    if ($env{"course.$courseid.receiptalg"} eq 'receipt2' ||
+	$env{"course.$courseid.receiptalg"} eq 'receipt3') { $receiptparts=1; }
     my $parts=['0'];
     if ($receiptparts) { ($parts)=&response_type($symb); }
     foreach (sort 
@@ -614,7 +616,7 @@ sub verifyreceipt {
 	    if ($receipt eq &Apache::lonnet::ireceipt($uname,$udom,$courseid,$symb,$part)) {
 		$contents.='<tr bgcolor="#ffffe6"><td>&nbsp;'."\n".
 		    '<a href="javascript:viewOneStudent(\''.$uname.'\',\''.$udom.
-		    '\')"; TARGET=_self>'.$$fullname{$_}.'</a>&nbsp;</td>'."\n".
+		    '\');" target="_self">'.$$fullname{$_}.'</a>&nbsp;</td>'."\n".
 		    '<td>&nbsp;'.$uname.'&nbsp;</td>'.
 		    '<td>&nbsp;'.$udom.'&nbsp;</td>';
 		if ($receiptparts) {
@@ -663,8 +665,8 @@ sub listStudents {
     $env{'form.probTitle'} = $env{'form.probTitle'} eq '' ? 
 	&Apache::lonnet::gettitle($symb) : $env{'form.probTitle'};
 
-    my $result='<h3><font color="#339933">&nbsp;'.$viewgrade.
-	' Submissions for a Student or a Group of Students</font></h3>';
+    my $result='<h3><span class="LC_info">&nbsp;'.$viewgrade.
+	' Submissions for a Student or a Group of Students</span></h3>';
 
     my ($table,undef,$hdgrade,$partlist,$handgrade) = &showResourceInfo($symb,$env{'form.probTitle'},($env{'form.showgrading'} eq 'yes'));
 
@@ -704,16 +706,16 @@ LISTJAVASCRIPT
     &commonJSfunctions($request);
     $request->print($result);
 
-    my $checkhdgrade = ($env{'form.handgrade'} eq 'yes' && scalar(@$partlist) > 1 ) ? 'checked' : '';
-    my $checklastsub = $checkhdgrade eq '' ? 'checked' : '';
+    my $checkhdgrade = ($env{'form.handgrade'} eq 'yes' && scalar(@$partlist) > 1 ) ? 'checked="checked"' : '';
+    my $checklastsub = $checkhdgrade eq '' ? 'checked="checked"' : '';
     my $gradeTable='<form action="/adm/grades" method="post" name="gradesub">'.
 	"\n".$table.
-	'&nbsp;<b>View Problem Text: </b><label><input type="radio" name="vProb" value="no" checked="on" /> no </label>'."\n".
+	'&nbsp;<b>View Problem Text: </b><label><input type="radio" name="vProb" value="no" checked="checked" /> no </label>'."\n".
 	'<label><input type="radio" name="vProb" value="yes" /> one student </label>'."\n".
 	'<label><input type="radio" name="vProb" value="all" /> all students </label><br />'."\n".
 	'&nbsp;<b>View Answer: </b><label><input type="radio" name="vAns" value="no"  /> no </label>'."\n".
 	'<label><input type="radio" name="vAns" value="yes" /> one student </label>'."\n".
-	'<label><input type="radio" name="vAns" value="all" checked="on" /> all students </label><br />'."\n".
+	'<label><input type="radio" name="vAns" value="all" checked="checked" /> all students </label><br />'."\n".
 	'&nbsp;<b>Submissions: </b>'."\n";
     if ($env{'form.handgrade'} eq 'yes' && scalar(@$partlist) > 1) {
 	$gradeTable.='<label><input type="radio" name="lastSub" value="hdgrade" '.$checkhdgrade.' /> essay part only </label>'."\n";
@@ -739,7 +741,7 @@ LISTJAVASCRIPT
 	'<input type="hidden" name="showgrading" value="'.$env{'form.showgrading'}.'" /><br />'."\n".
 	'<input type="hidden" name="saveState"   value="'.$env{'form.saveState'}.'" />'."\n".
 	'<input type="hidden" name="probTitle"   value="'.$env{'form.probTitle'}.'" />'."\n".
-	'<input type="hidden" name="symb" value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb" value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="saveStatusOld" value="'.$saveStatus.'" />'."\n";
 
     if (exists($env{'form.gradingMenu'}) && exists($env{'form.Status'})) {
@@ -759,7 +761,7 @@ LISTJAVASCRIPT
 	'onClick="javascript:checkSelect(this.form.stuinfo);" '."\n".
 	'value="Next->" /> <br />'."\n";
     $gradeTable.=&check_buttons();
-    $gradeTable.='<label><input type="checkbox" name="checkPlag" checked="on" />Check For Plagiarism</label>';
+    $gradeTable.='<label><input type="checkbox" name="checkPlag" checked="checked" />Check For Plagiarism</label>';
     my ($classlist, undef, $fullname) = &getclasslist($getsec,'1');
     $gradeTable.='<table border="0"><tr><td bgcolor="#777777">'.
 	'<table border="0"><tr bgcolor="#e6ffff">';
@@ -876,15 +878,15 @@ LISTJAVASCRIPT
     if ($ctr == 0) {
 	my $num_students=(scalar(keys(%$fullname)));
 	if ($num_students eq 0) {
-	    $gradeTable='<br />&nbsp;<font color="red">There are no students currently enrolled.</font>';
+	    $gradeTable='<br />&nbsp;<span class="LC_warning">There are no students currently enrolled.</span>';
 	} else {
 	    my $submissions='submissions';
 	    if ($submitonly eq 'incorrect') { $submissions = 'incorrect submissions'; }
 	    if ($submitonly eq 'graded'   ) { $submissions = 'ungraded submissions'; }
 	    if ($submitonly eq 'queued'   ) { $submissions = 'queued submissions'; }
-	    $gradeTable='<br />&nbsp;<font color="red">'.
+	    $gradeTable='<br />&nbsp;<span class="LC_warning">'.
 		'No '.$submissions.' found for this resource for any students. ('.$num_students.
-		' students checked for '.$submissions.')</font><br />';
+		' students checked for '.$submissions.')</span><br />';
 	}
     } elsif ($ctr == 1) {
 	$gradeTable =~ s/type=checkbox/type=checkbox checked/;
@@ -948,8 +950,8 @@ sub processGroup {
     my @stuchecked = &Apache::loncommon::get_env_multiple('form.stuinfo');
     my $total      = scalar(@stuchecked)-1;
 
-    foreach (@stuchecked) {
-	my ($uname,$udom,$fullname) = split(/:/);
+    foreach my $student (@stuchecked) {
+	my ($uname,$udom,$fullname) = split(/:/,$student);
 	$env{'form.student'}        = $uname;
 	$env{'form.userdom'}        = $udom;
 	$env{'form.fullname'}       = $fullname;
@@ -1339,7 +1341,7 @@ INNERJS
 
     pDoc.write("<form action=\\"inactive\\" name=\\"msgcenter\\">");
     pDoc.write("<input value=\\""+usrctr+"\\" name=\\"usrctr\\" type=\\"hidden\\">");
-    pDoc.write("<font color=\\"green\\" size=+1>&nbsp;Compose Message for \"+fullname+\"</font><br /><br />");
+    pDoc.write("<h3><span class=\\"LC_info\\">&nbsp;Compose Message for \"+fullname+\"</span></h3><br /><br />");
 
     pDoc.write("<table border=0 width=100%><tr><td bgcolor=\\"#777777\\">");
     pDoc.write("<table border=0 width=100%><tr bgcolor=\\"#ddffff\\">");
@@ -1424,7 +1426,7 @@ INNERJS
     hDoc.$docopen;
     hDoc.write('$start_page_highlight_central');
     hDoc.write("<form action=\\"inactive\\" name=\\"hlCenter\\">");
-    hDoc.write("<font color=\\"green\\" size=+1>&nbsp;Keyword Highlight Options</font><br /><br />");
+    hDoc.write("<h3><span class=\\"LC_info\\">&nbsp;Keyword Highlight Options</span></h3><br /><br />");
 
     hDoc.write("<table border=0 width=100%><tr><td bgcolor=\\"#777777\\">");
     hDoc.write("<table border=0 width=100%><tr bgcolor=\\"#ddffff\\">");
@@ -1475,7 +1477,7 @@ sub gradeBox {
 	'/check.gif" height="16" border="0" />';
     my $wgt    = &Apache::lonnet::EXT('resource.'.$partid.'.weight',$symb,$udom,$uname);
     my $wgtmsg = ($wgt > 0 ? '(problem weight)' : 
-		  '<font color="red">problem weight assigned by computer</font>');
+		  '<span class="LC_info">problem weight assigned by computer</span>');
     $wgt       = ($wgt > 0 ? $wgt : '1');
     my $score  = ($$record{'resource.'.$partid.'.awarded'} eq '' ?
 		  '' : &compute_points($$record{'resource.'.$partid.'.awarded'},$wgt));
@@ -1497,7 +1499,7 @@ sub gradeBox {
 	$result.= '<td><span style="white-space: nowrap;"><label><input type="radio" name="RADVAL'.$counter.'_'.$partid.'" '.
 	    'onclick="javascript:writeBox(this.form,\''.$counter.'_'.$partid.'\','.
 	    $thisweight.')" value="'.$thisweight.'" '.
-	    ($score eq $thisweight ? 'checked':'').' /> '.$thisweight."</label></span></td>\n";
+	    ($score eq $thisweight ? 'checked="checked"':'').' /> '.$thisweight."</label></span></td>\n";
 	$result.=(($ctr+1)%10 == 0 ? '</tr><tr>' : '');
         $thisweight += $increment;
 	$ctr++;
@@ -1515,9 +1517,9 @@ sub gradeBox {
 	'onChange="javascript:clearRadBox(this.form,\''.$counter.'_'.$partid.'\')" >'."\n";
     if ($$record{'resource.'.$partid.'.solved'} eq 'excused') {
 	$result.='<option></option>'.
-	    '<option selected="on">excused</option>';
+	    '<option selected="selected">excused</option>';
     } else {
-	$result.='<option selected="on"></option>'.
+	$result.='<option selected="selected"></option>'.
 	    '<option>excused</option>';
     }
     $result.='<option>reset status</option></select>'."\n";
@@ -1622,6 +1624,43 @@ sub show_problem {
     return $result;
 }
 
+sub files_exist {
+    my ($r, $symb) = @_;
+    my @students = &Apache::loncommon::get_env_multiple('form.stuinfo');
+
+    foreach my $student (@students) {
+        my ($uname,$udom,$fullname) = split(/:/,$student);
+        my %record = &Apache::lonnet::restore($symb,$env{'request.course.id'},
+					      $udom,$uname);
+        my ($string,$timestamp)= &get_last_submission(\%record);
+        foreach my $submission (@$string) {
+            my ($partid,$respid) =
+		($submission =~ /^resource\.([^\.]*)\.([^\.]*)\.submission/);
+            my $files=&get_submitted_files($udom,$uname,$partid,$respid,
+					   \%record);
+            return 1 if (@$files);
+        }
+    }
+    return 0;
+}
+
+sub download_all_link {
+    my ($r,$symb) = @_;
+    my $all_students = 
+	join("\n", &Apache::loncommon::get_env_multiple('form.stuinfo'));
+
+    my $parts =
+	join("\n",&Apache::loncommon::get_env_multiple('form.vPart'));
+
+    my $identifier = &Apache::loncommon::get_cgi_id();
+    &Apache::lonnet::appenv('cgi.'.$identifier.'.students' => $all_students,
+                            'cgi.'.$identifier.'.symb' => $symb,
+                            'cgi.'.$identifier.'.parts' => $parts,);
+    $r->print('<a href="/cgi-bin/multidownload.pl?'.$identifier.'">'.
+	      &mt('Download All Submitted Documents').'</a>');
+    return
+}
+
 # --------------------------- show submissions of a student, option to grade 
 sub submission {
     my ($request,$counter,$total) = @_;
@@ -1635,9 +1674,9 @@ sub submission {
     if ($symb eq '') { $request->print("Unable to handle ambiguous references:."); return ''; }
 
     if (!&canview($usec)) {
-	$request->print('<font color="red">Unable to view requested student.('.
-			$uname.'@'.$udom.' in section '.$usec.' in course id '.
-			$env{'request.course.id'}.')</font>');
+	$request->print('<span class="LC_warning">Unable to view requested student.('.
+			$uname.':'.$udom.' in section '.$usec.' in course id '.
+			$env{'request.course.id'}.')</span>');
 	$request->print(&show_grading_menu_form($symb));
 	return;
     }
@@ -1650,15 +1689,18 @@ sub submission {
 	'" src="'.$request->dir_config('lonIconsURL').
 	'/check.gif" height="16" border="0" />';
 
+    my %old_essays;
     # header info
     if ($counter == 0) {
 	&sub_page_js($request);
 	&sub_page_kw_js($request) if ($env{'form.handgrade'} eq 'yes');
 	$env{'form.probTitle'} = $env{'form.probTitle'} eq '' ? 
 	    &Apache::lonnet::gettitle($symb) : $env{'form.probTitle'};
-
-	$request->print('<h3>&nbsp;<font color="#339933">Submission Record</font></h3>'."\n".
-			'<font size=+1>&nbsp;<b>Resource: </b>'.$env{'form.probTitle'}.'</font>'."\n");
+	if ($env{'form.handgrade'} eq 'yes' && &files_exist($request, $symb)) {
+	    &download_all_link($request, $symb);
+	}
+	$request->print('<h3>&nbsp;<span class="LC_info">Submission Record</span></h3>'."\n".
+			'<h4>&nbsp;<b>Resource: </b>'.$env{'form.probTitle'}.'</h4>'."\n");
 
 	if ($env{'form.handgrade'} eq 'no') {
 	    my $checkMark='<br /><br />&nbsp;<b>Note:</b> Part(s) graded correct by the computer is marked with a '.
@@ -1709,7 +1751,7 @@ sub submission {
 			'<input type="hidden" name="refresh"    value="off" />'."\n".
 			'<input type="hidden" name="studentNo"  value="" />'."\n".
 			'<input type="hidden" name="gradeOpt"   value="" />'."\n".
-			'<input type="hidden" name="symb"       value="'.$symb.'" />'."\n".
+			'<input type="hidden" name="symb"       value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 			'<input type="hidden" name="showgrading" value="'.$env{'form.showgrading'}.'" />'."\n".
 			'<input type="hidden" name="vProb"      value="'.$env{'form.vProb'}.'" />'."\n".
 			'<input type="hidden" name="vAns"       value="'.$env{'form.vAns'}.'" />'."\n".
@@ -1750,10 +1792,10 @@ sub submission {
 #
 	    $request->print(<<KEYWORDS);
 &nbsp;<b>Keyword Options:</b>&nbsp;
-<a href="javascript:keywords(document.SCORE)"; TARGET=_self>List</a>&nbsp; &nbsp;
+<a href="javascript:keywords(document.SCORE);" target="_self">List</a>&nbsp; &nbsp;
 <a href="#" onMouseDown="javascript:getSel(); return false"
  CLASS="page">Paste Selection to List</a>&nbsp; &nbsp;
-<a href="javascript:kwhighlight()"; TARGET=_self>Highlight Attribute</a><br /><br />
+<a href="javascript:kwhighlight();" target="_self">Highlight Attribute</a><br /><br />
 KEYWORDS
 #
 # Load the other essays for similarity check
@@ -1762,7 +1804,7 @@ KEYWORDS
 	    my ($adom,$aname,$apath)=($essayurl=~/^($LONCAPA::domain_re)\/($LONCAPA::username_re)\/(.*)$/);
 	    $apath=&escape($apath);
 	    $apath=~s/\W/\_/gs;
-	    %oldessays=&Apache::lonnet::dump('nohist_essay_'.$apath,$adom,$aname);
+	    %old_essays=&Apache::lonnet::dump('nohist_essay_'.$apath,$adom,$aname);
         }
     }
 
@@ -1867,6 +1909,9 @@ KEYWORDS
 	    my %seenparts;
 	    my @part_response_id = &flatten_responseType($responseType);
 	    foreach my $part (@part_response_id) {
+		next if ($env{'form.lastSub'} eq 'hdgrade' 
+			 && $$handgrade{$$part[0].'_'.$$part[1]} ne 'yes');
+
 		my ($partid,$respid) = @{ $part };
 		my $display_part=&get_display_part($partid,$symb);
 		if ($env{"form.$uname:$udom:$partid:submitted_by"}) {
@@ -1876,7 +1921,7 @@ KEYWORDS
 			' <b>Collaborative submission by:</b> '.
 			'<a href="javascript:viewSubmitter(\''.
 			$env{"form.$uname:$udom:$partid:submitted_by"}.
-			'\')"; TARGET=_self>'.
+			'\');" target="_self">'.
 			$$fullname{$env{"form.$uname:$udom:$partid:submitted_by"}}.'</a><br />';
 		    $request->print($submitby);
 		    next;
@@ -1884,9 +1929,9 @@ KEYWORDS
 		my $responsetype = $responseType->{$partid}->{$respid};
 		if (!exists($record{"resource.$partid.$respid.submission"})) {
 		    $lastsubonly.='<tr><td bgcolor="#ffffe6"><b>Part:</b> '.
-			$display_part.' <font color="#999999">( ID '.$respid.
-			' )</font>&nbsp; &nbsp;'.
-			'<font color="red">Nothing submitted - no attempts</font><br /><br />';
+			$display_part.' <span class="LC_internal_info">( ID '.$respid.
+			' )</span>&nbsp; &nbsp;'.
+			'<span class="LC_warning">Nothing submitted - no attempts</span><br /><br />';
 		    next;
 		}
 		foreach (@$string) {
@@ -1897,13 +1942,20 @@ KEYWORDS
 		    my $similar='';
 		    if($env{'form.checkPlag'}){
 			my ($oname,$odom,$ocrsid,$oessay,$osim)=
-			    &most_similar($uname,$udom,$subval);
+			    &most_similar($uname,$udom,$subval,\%old_essays);
 			if ($osim) {
 			    $osim=int($osim*100.0);
-			    $similar="<hr /><h3><font color=\"#FF0000\">Essay".
-				" is $osim% similar to an essay by ".
-				&Apache::loncommon::plainname($oname,$odom).
-				'</font></h3><blockquote><i>'.
+			    my %old_course_desc = 
+				&Apache::lonnet::coursedescription($ocrsid,
+								   {'one_time' => 1});
+
+			    $similar="<hr /><h3><span class=\"LC_warning\">".
+				&mt('Essay is [_1]% similar to an essay by [_2] in course [_3]:[_4]',
+				    $osim,
+				    &Apache::loncommon::plainname($oname,$odom),
+				    $old_course_desc{'description'},
+				    $old_course_desc{'domain'}).
+				'</span></h3><blockquote><i>'.
 				&keywords_highlight($oessay).
 				'</i></blockquote><hr />';
 			}
@@ -1914,11 +1966,11 @@ KEYWORDS
 			 $$handgrade{$$part[0].'_'.$$part[1]} eq 'yes')) {
 			my $display_part=&get_display_part($partid,$symb);
 			$lastsubonly.='<tr><td bgcolor="#ffffe6"><b>Part:</b> '.
-			    $display_part.' <font color="#999999">( ID '.$respid.
-			    ' )</font>&nbsp; &nbsp;';
+			    $display_part.' <span class="LC_internal_info">( ID '.$respid.
+			    ' )</span>&nbsp; &nbsp;';
 			my $files=&get_submitted_files($udom,$uname,$partid,$respid,\%record);
 			if (@$files) {
-			    $lastsubonly.='<br /><font color="red" size="1">Like all files provided by users, this file may contain virusses</font><br />';
+			    $lastsubonly.='<br /><span class="LC_warning">Like all files provided by users, this file may contain virusses</span><br />';
 			    my $file_counter = 0;
 			    foreach my $file (@$files) {
 			        $file_counter ++;
@@ -1954,7 +2006,7 @@ KEYWORDS
     if ($env{'form.showgrading'} eq '' || (!&canmodify($usec))) {
 	my $toGrade.='<input type="button" value="Grade Student" '.
 	    'onClick="javascript:checksubmit(this.form,\'Grade Student\',\''
-	    .$counter.'\');" TARGET=_self> &nbsp;'."\n" if (&canmodify($usec));
+	    .$counter.'\');" target="_self" /> &nbsp;'."\n" if (&canmodify($usec));
 	$toGrade.='</td></tr></table></td></tr></table>'."\n";
 	if (($env{'form.command'} eq 'submission') || 
 	    ($env{'form.command'} eq 'processGroup' && $counter == $total)) {
@@ -1978,7 +2030,7 @@ KEYWORDS
 	$result='<input type="hidden" name="includemsg'.$counter.'" value="" />'."\n".
 	    '<input type="hidden" name="newmsg'.$counter.'" value="" />'."\n";
 	$result.='&nbsp;<a href="javascript:msgCenter(document.SCORE,'.$counter.
-	    ',\''.$msgfor.'\')"; TARGET=_self>'.
+	    ',\''.$msgfor.'\');" target="_self">'.
 	    &mt('Compose message to student').(scalar(@col_fullnames) >= 1 ? 's' : '').'</a><label> ('.
 	    &mt('incl. grades').' <input type="checkbox" name="withgrades'.$counter.'" /></label>)'.
 	    '<img src="'.$request->dir_config('lonIconsURL').
@@ -2007,7 +2059,8 @@ KEYWORDS
 	my $part_resp = join('_',@{ $part_response_id });
 	next if ($seen{$partid} > 0);
 	$seen{$partid}++;
-	next if ($$handgrade{$part_resp} =~ /:no$/ && $env{'form.lastSub'} =~ /^(hdgrade)$/);
+	next if ($$handgrade{$part_resp} ne 'yes' 
+		 && $env{'form.lastSub'} eq 'hdgrade');
 	push @partlist,$partid;
 	push @gradePartRespid,$partid.'.'.$respid;
 	$request->print(&gradeBox($request,$symb,$uname,$udom,$counter,$partid,\%record));
@@ -2029,18 +2082,18 @@ KEYWORDS
 	my $endform='<table border="0"><tr><td>'."\n";
 	$endform.='<input type="button" value="Save & Next" '.
 	    'onClick="javascript:checksubmit(this.form,\'Save & Next\','.
-	    $total.','.scalar(@partlist).');" TARGET=_self> &nbsp;'."\n";
+	    $total.','.scalar(@partlist).');" target="_self" /> &nbsp;'."\n";
 	my $ntstu ='<select name="NTSTU">'.
 	    '<option>1</option><option>2</option>'.
 	    '<option>3</option><option>5</option>'.
 	    '<option>7</option><option>10</option></select>'."\n";
 	my $nsel = ($env{'form.NTSTU'} ne '' ? $env{'form.NTSTU'} : '1');
-	$ntstu =~ s/<option>$nsel</<option selected="on">$nsel</;
+	$ntstu =~ s/<option>$nsel</<option selected="selected">$nsel</;
 	$endform.=$ntstu.'student(s) &nbsp;&nbsp;';
 	$endform.='<input type="button" value="Previous" '.
-	    'onClick="javascript:checksubmit(this.form,\'Previous\');" TARGET=_self> &nbsp;'."\n".
+	    'onClick="javascript:checksubmit(this.form,\'Previous\');" target="_self" /> &nbsp;'."\n".
 	    '<input type="button" value="Next" '.
-	    'onClick="javascript:checksubmit(this.form,\'Next\');" TARGET=_self> &nbsp;';
+	    'onClick="javascript:checksubmit(this.form,\'Next\');" target="_self" /> &nbsp;';
 	$endform.='(Next and Previous (student) do not save the scores.)'."\n" ;
         $endform.="<input type='hidden' value='".&get_increment().
             "' name='increment' />";
@@ -2059,22 +2112,27 @@ sub get_last_submission {
 	my %lasthash=();
 	my ($version);
 	for ($version=1;$version<=$$returnhash{'version'};$version++) {
-	    foreach (sort(split(/\:/,$$returnhash{$version.':keys'}))) {
-		$lasthash{$_}=$$returnhash{$version.':'.$_};
-		   $timestamp = scalar(localtime($$returnhash{$version.':timestamp'}));
+	    foreach my $key (sort(split(/\:/,
+					$$returnhash{$version.':keys'}))) {
+		$lasthash{$key}=$$returnhash{$version.':'.$key};
+		$timestamp = 
+		    scalar(localtime($$returnhash{$version.':timestamp'}));
 	    }
 	}
-	foreach ((keys %lasthash)) {
-	    if ($_ =~ /\.submission$/) {
-		my ($partid,$foo) = split(/submission$/,$_);
-		my $draft  = $lasthash{$partid.'awarddetail'} eq 'DRAFT' ?
-		    '<font color="red">Draft Copy</font> ' : '';
-		push @string, (join(':',$_,$draft.$lasthash{$_}));
-	    }
+	foreach my $key (keys(%lasthash)) {
+	    next if ($key !~ /\.submission$/);
+
+	    my ($partid,$foo) = split(/submission$/,$key);
+	    my $draft  = $lasthash{$partid.'awarddetail'} eq 'DRAFT' ?
+		'<span class="LC_warning">Draft Copy</span> ' : '';
+	    push(@string, join(':', $key, $draft.$lasthash{$key}));
 	}
     }
-    @string = $string[0] eq '' ? '<font color="red">Nothing submitted - no attempts.</font>' : @string;
-    return \@string,\$timestamp;
+    if (!@string) {
+	$string[0] =
+	    '<span class="LC_warning">Nothing submitted - no attempts.</span>';
+    }
+    return (\@string,\$timestamp);
 }
 
 #--- High light keywords, with style choosen by user.
@@ -2084,8 +2142,8 @@ sub keywords_highlight {
     my $styleon   = $env{'form.kwstyle'} eq ''  ? '' : $env{'form.kwstyle'};
     (my $styleoff = $styleon) =~ s/\</\<\//;
     my @keylist   = split(/[,\s+]/,$env{'form.keywords'});
-    foreach (@keylist) {
-	$string =~ s/\b\Q$_\E(\b|\.)/<font color\=$env{'form.kwclr'} $size\>$styleon$_$styleoff<\/font>/gi;
+    foreach my $keyword (@keylist) {
+	$string =~ s/\b\Q$keyword\E(\b|\.)/<font color\=$env{'form.kwclr'} $size\>$styleon$keyword$styleoff<\/font>/gi;
     }
     return $string;
 }
@@ -2111,21 +2169,16 @@ sub processHandGrade {
 		next;
 	    }
 	    if ($errorflag eq 'not_allowed') {
-		$request->print("<font color=\"red\">Not allowed to modify grades for $uname:$udom</font>");
+		$request->print("<span class=\"LC_warning\">Not allowed to modify grades for $uname:$udom</span>");
 		$ctr++;
 		next;
 	    }
 	    my $includemsg = $env{'form.includemsg'.$ctr};
 	    my ($subject,$message,$msgstatus) = ('','','');
-            my $restitle = &Apache::lonnet::gettitle($symb);
-            my $encrypturl=&Apache::lonnet::EXT('resource.0.encrypturl',
-                                                $symb,$udom,$uname);
-            my ($feedurl,$baseurl,$showsymb,$messagetail);
-            $feedurl = &Apache::lonnet::clutter($url);
-            if ($encrypturl =~ /^yes$/i) {
-                $baseurl = &Apache::lonenc::encrypted($feedurl,1);
-                $showsymb = &Apache::lonenc::encrypted($symb,1);
-            }
+	    my $restitle = &Apache::lonnet::gettitle($symb);
+            my ($feedurl,$showsymb) =
+		&get_feedurl_and_symb($symb,$uname,$udom);
+	    my $messagetail;
 	    if ($includemsg =~ /savemsg|newmsg\Q$ctr\E/) {
 		$subject = $env{'form.msgsub'} if ($includemsg =~ /msgsub/);
 		unless ($subject=~/\w/) { $subject=&mt('Grading Feedback'); }
@@ -2138,12 +2191,12 @@ sub processHandGrade {
 		if ($env{'form.withgrades'.$ctr}) {
 		    $message.="\n\nPoint".($pts > 1 ? 's':'').' awarded = '.$pts.' out of '.$wgt;
 		    $messagetail = " for <a href=\"".
-		                   $baseurl."?symb=$showsymb\">$env{'form.probTitle'}</a>";
+		                   $feedurl."?symb=$showsymb\">$env{'form.probTitle'}</a>";
 		}
 		$msgstatus = 
                     &Apache::lonmsg::user_normal_msg($uname,$udom,$subject,
 						     $message.$messagetail,
-                                                     undef,$baseurl,undef,
+                                                     undef,$feedurl,undef,
                                                      undef,undef,$showsymb,
                                                      $restitle);
 		$request->print('<br />'.&mt('Sending message to [_1]:[_2]',$uname,$udom).': '.
@@ -2160,26 +2213,16 @@ sub processHandGrade {
 			if ($errorflag eq 'not_allowed') {
 			    $request->print("<span class=\"LC_error\">".&mt('Not allowed to modify grades for [_1]',"$collaborator:$udom")."</span>");
 			    next;
-			} else {
-			    if ($message ne '') {
-                                $encrypturl=
-                                  &Apache::lonnet::EXT('resource.0.encrypturl',
-                                                       $symb,$udom,$collaborator);
-                                if ($encrypturl =~ /^yes$/i) {
-                                    $baseurl = &Apache::lonenc::encrypted($feedurl,1);
-                                    $showsymb = &Apache::lonenc::encrypted($symb,1);
-                                } else {
-                                    $baseurl = $feedurl;
-                                    $showsymb = $symb;
-                                }
-                                if ($env{'form.withgrades'.$ctr}) {
-                                    $messagetail = " for <a href=\"".
+			} elsif ($message ne '') {
+			    my ($baseurl,$showsymb) = 
+				&get_feedurl_and_symb($symb,$collaborator,
+						      $udom);
+			    if ($env{'form.withgrades'.$ctr}) {
+				$messagetail = " for <a href=\"".
                                     $baseurl."?symb=$showsymb\">$env{'form.probTitle'}</a>";
-
-                                }
-				$msgstatus = 
-                                    &Apache::lonmsg::user_normal_msg($collaborator,$udom,$subject,$message.$messagetail,undef,$baseurl,undef,undef,undef,$showsymb,$restitle);
 			    }
+			    $msgstatus = 
+				&Apache::lonmsg::user_normal_msg($collaborator,$udom,$subject,$message.$messagetail,undef,$baseurl,undef,undef,undef,$showsymb,$restitle);
 			}
 		    }
 		}
@@ -2337,7 +2380,7 @@ sub processHandGrade {
 	$ctr++;
     }
     if ($total < 0) {
-	my $the_end = '<h3><font color="red">LON-CAPA User Message</font></h3><br />'."\n";
+	my $the_end = '<h3><span class="LC_info">LON-CAPA User Message</span></h3><br />'."\n";
 	$the_end.='<b>Message: </b> No more students for this section or class.<br /><br />'."\n";
 	$the_end.='Click on the button below to return to the grading menu.<br /><br />'."\n";
 	$the_end.=&show_grading_menu_form($symb);
@@ -2510,8 +2553,8 @@ sub handback_files {
             	                                $newflg.'_'.$part_resp.'_returndoc'.$file_counter,
             	                                $save_file_name);
                     if ($result !~ m|^/uploaded/|) {
-                        $request->print('<font color="red"> An errror occured ('.$result.
-                        ') while trying to upload '.$newflg.'_'.$part_resp.'_returndoc'.$file_counter.'</font><br />');
+                        $request->print('<span class="LC_error">An error occurred ('.$result.
+                        ') while trying to upload '.$newflg.'_'.$part_resp.'_returndoc'.$file_counter.'</span><br />');
                     } else {
                         # mark the file as read only
                         my @files = ($save_file_name);
@@ -2533,28 +2576,31 @@ sub handback_files {
 		$message .= "<strong>".&Apache::lonnet::gettitle($symb)."</strong><br />";
 		$message .= ' The returned file(s) are named: '. $file_msg;
 		$message .= " and can be found in your portfolio space.";
-		my $url = (&Apache::lonnet::decode_symb($symb))[2];
-		my $feedurl = &Apache::lonnet::declutter($url);
-                my $encrypturl=&Apache::lonnet::EXT('resource.0.encrypturl',
-                                                    $symb,$domain,$stuname);
-                my ($baseurl,$showsymb);
-                if ($encrypturl =~ /^yes$/i) {
-                    $baseurl = &Apache::lonenc::encrypted($feedurl,1);
-                    $showsymb = &Apache::lonenc::encrypted($symb,1);
-                } else {
-                    $baseurl = $feedurl;
-                    $showsymb = $symb;
-                }
+		my ($feedurl,$showsymb) = 
+		    &get_feedurl_and_symb($symb,$domain,$stuname);
                 my $restitle = &Apache::lonnet::gettitle($symb);
 		my $msgstatus = 
                    &Apache::lonmsg::user_normal_msg($stuname,$domain,$subject.
 			 ' (File Returned) ['.$restitle.']',$message,undef,
-                         $baseurl,undef,undef,undef,$showsymb,$restitle);
+                         $feedurl,undef,undef,undef,$showsymb,$restitle);
             }
         }
     return;
 }
 
+sub get_feedurl_and_symb {
+    my ($symb,$uname,$udom) = @_;
+    my (undef,undef,$url) = &Apache::lonnet::decode_symb($symb);
+    $url = &Apache::lonnet::clutter($url);
+    my $encrypturl=&Apache::lonnet::EXT('resource.0.encrypturl',
+					$symb,$udom,$uname);
+    if ($encrypturl =~ /^yes$/i) {
+	&Apache::lonenc::encrypted(\$url,1);
+	&Apache::lonenc::encrypted(\$symb,1);
+    }
+    return ($url,$symb);
+}
+
 sub get_submitted_files {
     my ($udom,$uname,$partid,$respid,$record) = @_;
     my @files;
@@ -2907,15 +2953,15 @@ sub viewgrades {
                  $env{'course.'.$env{'request.course.id'}.'.domain'});
     &Apache::lonnet::clear_EXT_cache_status();
 
-    my $result='<h3><font color="#339933">'.&mt('Manual Grading').'</font></h3>';
-    $result.='<font size=+1><b>Current Resource: </b>'.$env{'form.probTitle'}.'</font>'."\n";
+    my $result='<h3><span class="LC_info">'.&mt('Manual Grading').'</span></h3>';
+    $result.='<h4><b>Current Resource: </b>'.$env{'form.probTitle'}.'</h4>'."\n";
 
     #view individual student submission form - called using Javascript viewOneStudent
     $result.=&jscriptNform($symb);
 
     #beginning of class grading form
     $result.= '<form action="/adm/grades" method="post" name="classgrade">'."\n".
-	'<input type="hidden" name="symb"    value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb"    value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="command" value="editgrades" />'."\n".
 	'<input type="hidden" name="section" value="'.$env{'form.section'}.'" />'."\n".
 	'<input type="hidden" name="saveState" value="'.$env{'form.saveState'}.'" />'."\n".
@@ -2973,7 +3019,7 @@ sub viewgrades {
 	$result.= '</td><td><select name="SELVAL_'.$partid.'"'.
 	    'onChange="javascript:writeRadText(\''.$partid.'\','.
 		$weight{$partid}.')"> '.
-	    '<option selected="on"> </option>'.
+	    '<option selected="selected"> </option>'.
 	    '<option>excused</option>'.
 	    '<option>reset status</option></select></td>'.
             '<td><label><input type="checkbox" name="FORCE_'.$partid.'" /> Override "Correct"</label></td></tr>'."\n";
@@ -2981,8 +3027,8 @@ sub viewgrades {
     }
     $result.='</table>'.'</td></tr></table>'.'</td></tr></table>'."\n".
 	'<input type="hidden" name="totalparts" value="'.$ctsparts.'" />';
-    $result.='<input type="button" value="Reset" '.
-	'onClick="javascript:resetEntry('.$ctsparts.');" TARGET=_self>';
+    $result.='<input type="button" value="Revert to Default" '.
+	'onClick="javascript:resetEntry('.$ctsparts.');" target="_self" />';
 
     #table listing all the students in a section/class
     #header of table
@@ -3033,11 +3079,11 @@ sub viewgrades {
     $result.='</table></td></tr></table>';
     $result.='<input type="hidden" name="total" value="'.$ctr.'" />'."\n";
     $result.='<input type="button" value="Save" '.
-	'onClick="javascript:submit();" TARGET=_self /></form>'."\n";
+	'onClick="javascript:submit();" target="_self" /></form>'."\n";
     if (scalar(%$fullname) eq 0) {
 	my $colspan=3+scalar(@parts);
-	$result='<font color="red">There are no students in section "'.$env{'form.section'}.
-	    '" with enrollment status "'.$env{'form.Status'}.'" to modify or grade.</font>';
+	$result='<span class="LC_warning">There are no students in section "'.$env{'form.section'}.
+	    '" with enrollment status "'.$env{'form.Status'}.'" to modify or grade.</span>';
     }
     $result.=&show_grading_menu_form($symb);
     return $result;
@@ -3053,8 +3099,8 @@ sub viewstudentgrade {
 	'<input type="hidden" name="ctr'.($ctr-1).'" value="'.$student.'" />'.
 	"\n".$ctr.'&nbsp;</td><td>&nbsp;'.
 	'<a href="javascript:viewOneStudent(\''.$uname.'\',\''.$udom.
-	'\')"; TARGET=_self>'.$fullname.'</a> '.
-	'<font color="#999999">('.$uname.($env{'user.domain'} eq $udom ? '' : ':'.$udom).')</font></td>'."\n";
+	'\');" target="_self">'.$fullname.'</a> '.
+	'<span class="LC_internal_info">('.$uname.($env{'user.domain'} eq $udom ? '' : ':'.$udom).')</span></td>'."\n";
     $student=~s/:/_/; # colon doen't work in javascript for names
     foreach my $apart (@$parts) {
 	my ($part,$type) = &split_part_type($apart);
@@ -3091,8 +3137,8 @@ sub viewstudentgrade {
 	    $result.='&nbsp;<select name="'.
 		'GD_'.$student.'_'.$part.'_solved" '.
 		'onChange="javascript:changeOneScore(\''.$part.'\',\''.$student.'\')" >'."\n";
-	    $result.= (($status eq 'excused') ? '<option> </option><option selected="on">excused</option>' 
-		: '<option selected="on"> </option><option>excused</option>')."\n";
+	    $result.= (($status eq 'excused') ? '<option> </option><option selected="selected">excused</option>' 
+		: '<option selected="selected"> </option><option>excused</option>')."\n";
 	    $result.='<option>reset status</option>';
 	    $result.="</select>&nbsp;</td>\n";
 	} else {
@@ -3114,9 +3160,9 @@ sub editgrades {
     my ($request) = @_;
 
     my $symb=&get_symb($request);
-    my $title='<h3><font color="#339933">Current Grade Status</font></h3>';
-    $title.='<font size=+1><b>Current Resource: </b>'.$env{'form.probTitle'}.'</font><br />'."\n";
-    $title.='<font size=+1><b>Section: </b>'.$env{'form.section'}.'</font>'."\n";
+    my $title='<h3><span class="LC_info">Current Grade Status</span></h3>';
+    $title.='<h4><b>Current Resource: </b>'.$env{'form.probTitle'}.'</h4><br />'."\n";
+    $title.='<h4><b>Section: </b>'.$env{'form.section'}.'</h4>'."\n";
 
     my $result= '<table border="0"><tr><td bgcolor="#777777">'."\n";
     $result.= '<table border="0"><tr bgcolor="#deffff">'.
@@ -3184,7 +3230,7 @@ sub editgrades {
 	my $usec=$classlist->{"$uname:$udom"}[5];
 	if (!&canmodify($usec)) {
 	    my $numcols=scalar(@partid)*4+2;
-	    $noupdate.=$line."<td colspan=\"$numcols\"><font color=\"red\">Not allowed to modify student</font></td></tr>";
+	    $noupdate.=$line."<td colspan=\"$numcols\"><span class=\"LC_warning\">Not allowed to modify student</span></td></tr>";
 	    next;
 	}
         my %aggregate = ();
@@ -3417,9 +3463,10 @@ sub csvuploadmap_header {
     my ($result) = &showResourceInfo($symb,$env{'form.probTitle'});
     my $checked=(($env{'form.noFirstLine'})?' checked="checked"':'');
     my $ignore=&mt('Ignore First Line');
+    $symb = &Apache::lonenc::check_encrypt($symb);
     $request->print(<<ENDPICK);
 <form method="post" enctype="multipart/form-data" action="/adm/grades" name="gradesupload">
-<h3><font color="#339933">Uploading Class Grades</font></h3>
+<h3><span class="LC_info">Uploading Class Grades</span></h3>
 $result
 <hr />
 <h3>Identify fields</h3>
@@ -3511,6 +3558,7 @@ sub upcsvScores_form {
     my $upload=&mt("Upload Scores");
     my $upfile_select=&Apache::loncommon::upfile_select_html();
     my $ignore=&mt('Ignore First Line');
+    $symb = &Apache::lonenc::check_encrypt($symb);
     $result.=<<ENDUPFORM;
 <form method="post" enctype="multipart/form-data" action="/adm/grades" name="gradesupload">
 <input type="hidden" name="symb" value="$symb" />
@@ -3582,7 +3630,7 @@ sub csvuploadoptions {
     my $ignore=&mt('Ignore First Line');
     $request->print(<<ENDPICK);
 <form method="post" enctype="multipart/form-data" action="/adm/grades" name="gradesupload">
-<h3><font color="#339933">Uploading Class Grade Options</font></h3>
+<h3><span class="LC_info">Uploading Class Grade Options</span></h3>
 <input type="hidden" name="command"    value="csvuploadassign" />
 <!--
 <p>
@@ -3716,7 +3764,7 @@ sub csvuploadassign {
 		$grades{$store_key}=$entries{$fields{$dest}};
 	    }
 	}
-	if (! %grades) { push(@skipped,"$username:$domain no data to store"); }
+	if (! %grades) { push(@skipped,"$username:$domain no data to save"); }
 	$grades{"resource.regrader"}="$env{'user.name'}:$env{'user.domain'}";
 #	&Apache::lonnet::logthis(" storing ".(join('-',%grades)));
 	my $result=&Apache::lonnet::cstore(\%grades,$symb,
@@ -3726,22 +3774,22 @@ sub csvuploadassign {
 	    $request->print('.');
 	} else {
 	    $request->print("<p>
-                              <font color='red'>
-                                 Failed to store student $username\@$domain.
-                                 Message when trying to store was ($result)
-                              </font>
+                              <span class=\"LC_error\">
+                                 Failed to save student $username:$domain.
+                                 Message when trying to save was ($result)
+                              </span>
                              </p>" );
 	}
 	$request->rflush();
 	$countdone++;
     }
-    $request->print("<br />Stored $countdone students\n");
+    $request->print("<br />Saved $countdone students\n");
     if (@skipped) {
-	$request->print('<p><font size="+1"><b>Skipped Students</b></font></p>');
+	$request->print('<p><h4><b>Skipped Students</b></h4></p>');
 	foreach my $student (@skipped) { $request->print("$student<br />\n"); }
     }
     if (@notallowed) {
-	$request->print('<p><font size="+1" color="red"><b>Students Not Allowed to Modify</b></font></p>');
+	$request->print('<p><span class="LC_error">Students Not Allowed to Modify</span></p>');
 	foreach my $student (@notallowed) { $request->print("$student<br />\n"); }
     }
     $request->print("<br />\n");
@@ -3780,12 +3828,12 @@ LISTJAVASCRIPT
     my $cnum      = $env{"course.$env{'request.course.id'}.num"};
     my $getsec    = $env{'form.section'} eq '' ? 'all' : $env{'form.section'};
 
-    my $result='<h3><font color="#339933">&nbsp;'.
-	'Manual Grading by Page or Sequence</font></h3>';
+    my $result='<h3><span class="LC_info">&nbsp;'.
+	'Manual Grading by Page or Sequence</span></h3>';
 
     $result.='<form action="/adm/grades" method="post" name="displayPage">'."\n";
     $result.='&nbsp;<b>Problems from:</b> <select name="selectpage">'."\n";
-    my ($titles,$symbx) = &getSymbMap($request);
+    my ($titles,$symbx) = &getSymbMap();
     my ($curpage) =&Apache::lonnet::decode_symb($symb); 
 #    my ($curpage,$mapId) =&Apache::lonnet::decode_symb($symb); 
 #    my $type=($curpage =~ /\.(page|sequence)/);
@@ -3793,7 +3841,7 @@ LISTJAVASCRIPT
     foreach (@$titles) {
 	my ($minder,$showtitle) = ($_ =~ /(\d+)\.(.*)/);
 	$result.='<option value="'.$ctr.'" '.
-	    ($$symbx{$_} =~ /$curpage$/ ? 'selected="on"' : '').
+	    ($$symbx{$_} =~ /$curpage$/ ? 'selected="selected"' : '').
 	    '>'.$showtitle.'</option>'."\n";
 	$ctr++;
     }
@@ -3808,18 +3856,18 @@ LISTJAVASCRIPT
     $result.='<input type="hidden" name="page" />'."\n".
 	'<input type="hidden" name="title" />'."\n";
 
-    $result.='&nbsp;<b>View Problems Text: </b><label><input type="radio" name="vProb" value="no" checked="on" /> no </label>'."\n".
+    $result.='&nbsp;<b>View Problems Text: </b><label><input type="radio" name="vProb" value="no" checked="checked" /> no </label>'."\n".
 	'<label><input type="radio" name="vProb" value="yes" /> yes </label>'."<br />\n";
 
     $result.='&nbsp;<b>Submission Details: </b>'.
 	'<label><input type="radio" name="lastSub" value="none" /> none</label>'."\n".
-	'<label><input type="radio" name="lastSub" value="datesub" checked /> by dates and submissions</label>'."\n".
+	'<label><input type="radio" name="lastSub" value="datesub" checked="checked" /> by dates and submissions</label>'."\n".
 	'<label><input type="radio" name="lastSub" value="all" /> all details</label>'."\n";
 
     $result.='<input type="hidden" name="section"     value="'.$getsec.'" />'."\n".
 	'<input type="hidden" name="Status"  value="'.$env{'form.Status'}.'" />'."\n".
 	'<input type="hidden" name="command" value="displayPage" />'."\n".
-	'<input type="hidden" name="symb"    value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb"    value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="saveState" value="'.$env{'form.saveState'}.'" />'."<br />\n";
 
     $result.='&nbsp;<b>'.&mt('Use CODE:').' </b>'.
@@ -3867,7 +3915,6 @@ LISTJAVASCRIPT
 }
 
 sub getSymbMap {
-    my ($request) = @_;
     my $navmap = Apache::lonnavmaps::navmap->new();
 
     my %symbx = ();
@@ -3911,11 +3958,11 @@ sub displayPage {
     &Apache::lonnet::clear_EXT_cache_status();
 
     if (!&canview($usec)) {
-	$request->print('<font color="red">Unable to view requested student.('.$env{'form.student'}.')</font>');
+	$request->print('<span class="LC_warning">Unable to view requested student.('.$env{'form.student'}.')</span>');
 	$request->print(&show_grading_menu_form($symb));
 	return;
     }
-    my $result='<h3><font color="#339933">&nbsp;'.$env{'form.title'}.'</font></h3>';
+    my $result='<h3><span class="LC_info">&nbsp;'.$env{'form.title'}.'</span></h3>';
     $result.='<h3>&nbsp;Student: '.&nameUserString(undef,$$fullname{$env{'form.student'}},$uname,$udom).
 	'</h3>'."\n";
     if (&Apache::lonnet::validCODE($env{'form.CODE'})) {
@@ -3930,7 +3977,7 @@ sub displayPage {
     my ($mapUrl, $id, $resUrl)=&Apache::lonnet::decode_symb($env{'form.page'});
     my $map = $navmap->getResourceByUrl($resUrl); # add to navmaps
     if (!$map) {
-	$request->print('<font color="red">Unable to view requested sequence. ('.$resUrl.')</font>');
+	$request->print('<span class="LC_warning">Unable to view requested sequence. ('.$resUrl.')</span>');
 	$request->print(&show_grading_menu_form($symb));
 	return; 
     }
@@ -3943,7 +3990,7 @@ sub displayPage {
 	'<input type="hidden" name="student" value="'.$env{'form.student'}.'" />'."\n".
 	'<input type="hidden" name="page"    value="'.$pageTitle.'" />'."\n".
 	'<input type="hidden" name="title"   value="'.$env{'form.title'}.'" />'."\n".
-	'<input type="hidden" name="symb"    value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb"    value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="overRideScore" value="no" />'."\n".
 	'<input type="hidden" name="saveState" value="'.$env{'form.saveState'}.'" />'."\n";
 
@@ -3997,7 +4044,7 @@ sub displayPage {
 
 	    if ($env{'form.lastSub'} eq 'datesub') {
 		if ($record{'version'} eq '') {
-		    $studentTable.='<br />&nbsp;<font color="red">No recorded submission for this problem</font><br />';
+		    $studentTable.='<br />&nbsp;<span class="LC_warning">No recorded submission for this problem</span><br />';
 		} else {
 		    my %responseType = ();
 		    foreach my $partid (@{$parts}) {
@@ -4059,7 +4106,7 @@ sub displaySubByDates {
     my %orders;
     $mark{'correct_by_student'} = $checkIcon;
     if (!exists($$record{'1:timestamp'})) {
-	return '<br />&nbsp;<font color="red">Nothing submitted - no attempts</font><br />';
+	return '<br />&nbsp;<span class="LC_warning">Nothing submitted - no attempts</span><br />';
     }
 
     my $interaction;
@@ -4093,8 +4140,8 @@ sub displaySubByDates {
 				               : ($matchKey=~ /^resource\.\Q$partid\E\.(.*?)\.submission$/));
 		    #&Apache::lonnet::logthis("match $matchKey $responseId (".$$record{$version.':'.$matchKey});
 		    $displaySub[0].='<b>Part:</b>&nbsp;'.$display_part.'&nbsp;';
-		    $displaySub[0].='<font color="#999999">(ID&nbsp;'.
-			$responseId.')</font>&nbsp;<b>';
+		    $displaySub[0].='<span class="LC_internal_info">(ID&nbsp;'.
+			$responseId.')</span>&nbsp;<b>';
 		    if ($$record{"$where.$partid.tries"} eq '') {
 			$displaySub[0].='Trial&nbsp;not&nbsp;counted';
 		    } else {
@@ -4159,11 +4206,11 @@ sub updateGradeByPage {
     my ($uname,$udom) = split(/:/,$env{'form.student'});
     my $usec=$classlist->{$env{'form.student'}}[5];
     if (!&canmodify($usec)) {
-	$request->print('<font color="red">Unable to modify requested student.('.$env{'form.student'}.'</font>');
+	$request->print('<span class="LC_warning">Unable to modify requested student.('.$env{'form.student'}.'</span>');
 	$request->print(&show_grading_menu_form($env{'form.symb'}));
 	return;
     }
-    my $result='<h3><font color="#339933">&nbsp;'.$env{'form.title'}.'</font></h3>';
+    my $result='<h3><span class="LC_info">&nbsp;'.$env{'form.title'}.'</span></h3>';
     $result.='<h3>&nbsp;Student: '.&nameUserString(undef,$env{'form.fullname'},$uname,$udom).
 	'</h3>'."\n";
 
@@ -4173,7 +4220,7 @@ sub updateGradeByPage {
     my ($mapUrl, $id, $resUrl) = &Apache::lonnet::decode_symb( $env{'form.page'});
     my $map = $navmap->getResourceByUrl($resUrl); # add to navmaps
     if (!$map) {
-	$request->print('<font color="red">Unable to grade requested sequence. ('.$resUrl.')</font>');
+	$request->print('<span class="LC_warning">Unable to grade requested sequence. ('.$resUrl.')</span>');
 	my ($symb)=&get_symb($request);
 	$request->print(&show_grading_menu_form($symb));
 	return; 
@@ -4312,24 +4359,97 @@ sub updateGradeByPage {
 #
 #------ start of section for handling grading by page/sequence ---------
 
+=pod
+
+=head1 Bubble sheet grading routines
+
+  For this documentation:
+
+   'scanline' refers to the full line of characters
+   from the file that we are parsing that represents one entire sheet
+
+   'bubble line' refers to the data
+   representing the line of bubbles that are on the physical bubble sheet
+
+
+The overall process is that a scanned in bubble sheet data is uploaded
+into a course. When a user wants to grade, they select a
+sequence/folder of resources, a file of bubble sheet info, and pick
+one of the predefined configurations for what each scanline looks
+like.
+
+Next each scanline is checked for any errors of either 'missing
+bubbles' (it's an error because it may have been missed scanned
+because too light bubbling), 'double bubble' (each bubble line should
+have no more that one letter picked), invalid or duplicated CODE,
+invalid student ID
+
+If the CODE option is used that determines the randomization of the
+homework problems, either way the student ID is looked up into a
+username:domain.
+
+During the validation phase the instructor can choose to skip scanlines. 
+
+After the validation phase, there is now 3 bubble sheet files
+
+  scantron_original_filename (unmodified original file)
+  scantron_corrected_filename (file where the corrected information has replaced the original information)
+  scantron_skipped_filename (contains the exact text of scanlines that where skipped)
+
+Also there is a separate hash nohist_scantrondata that contains extra
+correction information that isn't representable in the bubble sheet
+file (see &scantron_getfile() for more information)
+
+After all scanlines are either valid, marked as valid or skipped, then
+foreach line foreach problem in the picked sequence, an ssi request is
+made that simulates a user submitting their selected letter(s) against
+the homework problem.
+
+=over 4
+
+=cut
+
+
+=pod 
+
+=item defaultFormData
+
+  Returns html hidden inputs used to hold context/default values.
+
+ Arguments:
+  $symb - $symb of the current resource 
+
+=cut
+
 sub defaultFormData {
     my ($symb)=@_;
     return '
-      <input type="hidden" name="symb"    value="'.$symb.'" />'."\n".
+      <input type="hidden" name="symb"    value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
      '<input type="hidden" name="saveState" value="'.$env{'form.saveState'}.'" />'."\n".
      '<input type="hidden" name="probTitle" value="'.$env{'form.probTitle'}.'" />'."\n";
 }
 
+=pod 
+
+=item getSequenceDropDown
+
+   Return html dropdown of possible sequences to grade
+ 
+ Arguments:
+   $symb - $symb of the current resource 
+
+=cut
+
 sub getSequenceDropDown {
-    my ($request,$symb)=@_;
+    my ($symb)=@_;
     my $result='<select name="selectpage">'."\n";
-    my ($titles,$symbx) = &getSymbMap($request);
+    my ($titles,$symbx) = &getSymbMap();
     my ($curpage)=&Apache::lonnet::decode_symb($symb); 
     my $ctr=0;
     foreach (@$titles) {
 	my ($minder,$showtitle) = ($_ =~ /(\d+)\.(.*)/);
 	$result.='<option value="'.$$symbx{$_}.'" '.
-	    ($$symbx{$_} =~ /$curpage$/ ? 'selected="on"' : '').
+	    ($$symbx{$_} =~ /$curpage$/ ? 'selected="selected"' : '').
 	    '>'.$showtitle.'</option>'."\n";
 	$ctr++;
     }
@@ -4337,6 +4457,15 @@ sub getSequenceDropDown {
     return $result;
 }
 
+
+=pod 
+
+=item scantron_filenames
+
+   Returns a list of the scantron files in the current course 
+
+=cut
+
 sub scantron_filenames {
     my $cdom=$env{'course.'.$env{'request.course.id'}.'.domain'};
     my $cname=$env{'course.'.$env{'request.course.id'}.'.num'};
@@ -4352,17 +4481,37 @@ sub scantron_filenames {
     return @possiblenames;
 }
 
+=pod 
+
+=item scantron_uploads
+
+   Returns  html drop-down list of scantron files in current course.
+
+ Arguments:
+   $file2grade - filename to set as selected in the dropdown
+
+=cut
+
 sub scantron_uploads {
     my ($file2grade) = @_;
     my $result=	'<select name="scantron_selectfile">';
     $result.="<option></option>";
     foreach my $filename (sort(&scantron_filenames())) {
-	$result.="<option".($filename eq $file2grade ? ' selected="on"':'').">$filename</option>\n";
+	$result.="<option".($filename eq $file2grade ? ' selected="selected"':'').">$filename</option>\n";
     }
     $result.="</select>";
     return $result;
 }
 
+=pod 
+
+=item scantron_scantab
+
+  Returns html drop down of the scantron formats in the scantronformat.tab
+  file.
+
+=cut
+
 sub scantron_scantab {
     my $fh=Apache::File->new($Apache::lonnet::perlvar{'lonTabDir'}.'/scantronformat.tab');
     my $result='<select name="scantron_format">'."\n";
@@ -4377,6 +4526,15 @@ sub scantron_scantab {
     return $result;
 }
 
+=pod 
+
+=item scantron_CODElist
+
+  Returns html drop down of the saved CODE lists from current course,
+  generated from earlier printings.
+
+=cut
+
 sub scantron_CODElist {
     my $cdom = $env{'course.'.$env{'request.course.id'}.'.domain'};
     my $cnum = $env{'course.'.$env{'request.course.id'}.'.num'};
@@ -4391,23 +4549,48 @@ sub scantron_CODElist {
     return $namechoice;
 }
 
+=pod 
+
+=item scantron_CODEunique
+
+  Returns the html for "Each CODE to be used once" radio.
+
+=cut
+
 sub scantron_CODEunique {
     my $result='<span style="white-space: nowrap;">
                  <label><input type="radio" name="scantron_CODEunique"
-                        value="yes" checked="checked" /> Yes </label>
+                        value="yes" checked="checked" />'.&mt('Yes').' </label>
                 </span>
                 <span style="white-space: nowrap;">
                  <label><input type="radio" name="scantron_CODEunique"
-                        value="no" /> No </label>
+                        value="no" />'.&mt('No').' </label>
                 </span>';
     return $result;
 }
 
+=pod 
+
+=item scantron_selectphase
+
+  Generates the initial screen to start the bubble sheet process.
+  Allows for - starting a grading run.
+             - downloading existing scan data (original, corrected
+                                                or skipped info)
+
+             - uploading new scan data
+
+ Arguments:
+  $r          - The Apache request object
+  $file2grade - name of the file that contain the scanned data to score
+
+=cut
+
 sub scantron_selectphase {
     my ($r,$file2grade) = @_;
     my ($symb)=&get_symb($r);
     if (!$symb) {return '';}
-    my $sequence_selector=&getSequenceDropDown($r,$symb);
+    my $sequence_selector=&getSequenceDropDown($symb);
     my $default_form_data=&defaultFormData($symb);
     my $grading_menu_button=&show_grading_menu_form($symb);
     my $file_selector=&scantron_uploads($file2grade);
@@ -4415,8 +4598,9 @@ sub scantron_selectphase {
     my $CODE_selector=&scantron_CODElist();
     my $CODE_unique=&scantron_CODEunique();
     my $result;
-    #FIXME allow instructor to be able to download the scantron file
-    # and to upload it,
+
+    # Chunk of form to prompt for a file to grade and how:
+
     $result.= <<SCANTRONFORM;
     <table width="100%" border="0">
     <tr>
@@ -4449,7 +4633,7 @@ sub scantron_selectphase {
 	    <td> Options: </td>
             <td>
 	       <label><input type="checkbox" name="scantron_options_redo" value="redo_skipped"/> Do only previously skipped records</label> <br />
-               <label><input type="checkbox" name="scantron_options_ignore" value="ignore_corrections"/> Remove all exisiting corrections</label> <br />
+               <label><input type="checkbox" name="scantron_options_ignore" value="ignore_corrections"/> Remove all existing corrections</label> <br />
                <label><input type="checkbox" name="scantron_options_hidden" value="ignore_hidden"/> Skip hidden resources when grading</label>
 	    </td>
           </tr>
@@ -4469,6 +4653,8 @@ SCANTRONFORM
     if (&Apache::lonnet::allowed('usc',$env{'request.role.domain'}) ||
         &Apache::lonnet::allowed('usc',$env{'request.course.id'})) {
 
+	# Chunk of form to prompt for a scantron file upload.
+
         $r->print(<<SCANTRONFORM);
     <tr>
       <td bgcolor="#777777">
@@ -4514,6 +4700,10 @@ UPLOAD
     </tr>
 SCANTRONFORM
     }
+
+    # Chunk of the form that prompts to view a scoring office file,
+    # corrected file, skipped records in a file.
+
     $r->print(<<SCANTRONFORM);
     <tr>
       <form action='/adm/grades' name='scantron_download'>
@@ -4548,6 +4738,63 @@ SCANTRONFORM
     return
 }
 
+=pod
+
+=item get_scantron_config
+
+   Parse and return the scantron configuration line selected as a
+   hash of configuration file fields.
+
+ Arguments:
+    which - the name of the configuration to parse from the file.
+
+
+ Returns:
+            If the named configuration is not in the file, an empty
+            hash is returned.
+    a hash with the fields
+      name         - internal name for the this configuration setup
+      description  - text to display to operator that describes this config
+      CODElocation - if 0 or the string 'none'
+                          - no CODE exists for this config
+                     if -1 || the string 'letter'
+                          - a CODE exists for this config and is
+                            a string of letters
+                     Unsupported value (but planned for future support)
+                          if a positive integer
+                               - The CODE exists as the first n items from
+                                 the question section of the form
+                          if the string 'number'
+                               - The CODE exists for this config and is
+                                 a string of numbers
+      CODEstart   - (only matter if a CODE exists) column in the line where
+                     the CODE starts
+      CODElength  - length of the CODE
+      IDstart     - column where the student ID number starts
+      IDlength    - length of the student ID info
+      Qstart      - column where the information from the bubbled
+                    'questions' start
+      Qlength     - number of columns comprising a single bubble line from
+                    the sheet. (usually either 1 or 10)
+      Qon         - either a single character representing the character used
+                    to signal a bubble was chosen in the positional setup, or
+                    the string 'letter' if the letter of the chosen bubble is
+                    in the final, or 'number' if a number representing the
+                    chosen bubble is in the file (1->A 0->J)
+      Qoff        - the character used to represent that a bubble was
+                    left blank
+      PaperID     - if the scanning process generates a unique number for each
+                    sheet scanned the column that this ID number starts in
+      PaperIDlength - number of columns that comprise the unique ID number
+                      for the sheet of paper
+      FirstName   - column that the first name starts in
+      FirstNameLength - number of columns that the first name spans
+ 
+      LastName    - column that the last name starts in
+      LastNameLength - number of columns that the last name spans
+
+=cut
+
 sub get_scantron_config {
     my ($which) = @_;
     my $fh=Apache::File->new($Apache::lonnet::perlvar{'lonTabDir'}.'/scantronformat.tab');
@@ -4580,6 +4827,25 @@ sub get_scantron_config {
     return %config;
 }
 
+=pod 
+
+=item username_to_idmap
+
+    creates a hash keyed by student id with values of the corresponding
+    student username:domain.
+
+  Arguments:
+
+    $classlist - reference to the class list hash. This is a hash
+                 keyed by student name:domain  whose elements are references
+                 to arrays containing various chunks of information
+                 about the student. (See loncoursedata for more info).
+
+  Returns
+    %idmap - the constructed hash
+
+=cut
+
 sub username_to_idmap {
     my ($classlist)= @_;
     my %idmap;
@@ -4590,8 +4856,50 @@ sub username_to_idmap {
     return %idmap;
 }
 
+=pod
+
+=item scantron_fixup_scanline
+
+   Process a requested correction to a scanline.
+
+  Arguments:
+    $scantron_config   - hash from &get_scantron_config()
+    $scan_data         - hash of correction information 
+                          (see &scantron_getfile())
+    $line              - existing scanline
+    $whichline         - line number of the passed in scanline
+    $field             - type of change to process 
+                         (either 
+                          'ID'     -> correct the student ID number
+                          'CODE'   -> correct the CODE
+                          'answer' -> fixup the submitted answers)
+    
+   $args               - hash of additional info,
+                          - 'ID' 
+                               'newid' -> studentID to use in replacement
+                                          of existing one
+                          - 'CODE' 
+                               'CODE_ignore_dup' - set to true if duplicates
+                                                   should be ignored.
+	                       'CODE' - is new code or 'use_unfound'
+                                        if the existing unfound code should
+                                        be used as is
+                          - 'answer'
+                               'response' - new answer or 'none' if blank
+                               'question' - the bubble line to change
+
+  Returns:
+    $line - the modified scanline
+
+  Side effects: 
+    $scan_data - may be updated
+
+=cut
+
+
 sub scantron_fixup_scanline {
     my ($scantron_config,$scan_data,$line,$whichline,$field,$args)=@_;
+
     if ($field eq 'ID') {
 	if (length($args->{'newid'}) > $$scantron_config{'IDlength'}) {
 	    return ($line,1,'New value too large');
@@ -4635,6 +4943,7 @@ sub scantron_fixup_scanline {
 		$answer=$alphabet[$args->{'response'}];
 	    } elsif ($on eq 'number') {
 		$answer=$args->{'response'}+1;
+		if ($answer == 10) { $answer = '0'; }
 	    } else {
 		substr($answer,$args->{'response'},1)=$on;
 	    }
@@ -4647,6 +4956,25 @@ sub scantron_fixup_scanline {
     return $line;
 }
 
+=pod
+
+=item scan_data
+
+    Edit or look up  an item in the scan_data hash.
+
+  Arguments:
+    $scan_data  - The hash (see scantron_getfile)
+    $key        - shorthand of the key to edit (actual key is
+                  scantronfilename_key).
+    $data        - New value of the hash entry.
+    $delete      - If true, the entry is removed from the hash.
+
+  Returns:
+    The new value of the hash table field (undefined if deleted).
+
+=cut
+
+
 sub scan_data {
     my ($scan_data,$key,$value,$delete)=@_;
     my $filename=$env{'form.scantron_selectfile'};
@@ -4657,11 +4985,63 @@ sub scan_data {
     return $scan_data->{$filename.'_'.$key};
 }
 
+=pod 
+
+=item scantron_parse_scanline
+
+  Decodes a scanline from the selected scantron file
+
+ Arguments:
+    line             - The text of the scantron file line to process
+    whichline        - Line number
+    scantron_config  - Hash describing the format of the scantron lines.
+    scan_data        - Hash of extra information about the scanline
+                       (see scantron_getfile for more information)
+    just_header      - True if should not process question answers but only
+                       the stuff to the left of the answers.
+ Returns:
+   Hash containing the result of parsing the scanline
+
+   Keys are all proceeded by the string 'scantron.'
+
+       CODE    - the CODE in use for this scanline
+       useCODE - 1 if the CODE is invalid but it usage has been forced
+                 by the operator
+       CODE_ignore_dup - 1 if the CODE is a duplicated use when unique
+                            CODEs were selected, but the usage has been
+                            forced by the operator
+       ID  - student ID
+       PaperID - if used, the ID number printed on the sheet when the 
+                 paper was scanned
+       FirstName - first name from the sheet
+       LastName  - last name from the sheet
+
+     if just_header was not true these key may also exist
+
+       missingerror - a list of bubbled line numbers that had a blank bubble
+                      that is considered an error (if the operator had already
+                      okayed a blank bubble line as really being blank then
+                      that bubble line number won't appear here.
+       doubleerror  - a list of bubbled line numbers that had more than one
+                      bubble filled in and has not been corrected by the
+                      operator
+       maxquest     - the number of the last bubble line that was parsed
+
+       (<number> starts at 1)
+       <number>.answer - zero or more letters representing the selected
+                         letters from the scanline for the bubble line 
+                         <number>.
+                         if blank there was either no bubble or there where
+                         multiple bubbles, (consult the keys missingerror and
+                         doubleerror if this is an error condition)
+
+=cut
+
 sub scantron_parse_scanline {
-    my ($line,$whichline,$scantron_config,$scan_data,$justHeader)=@_;
+    my ($line,$whichline,$scantron_config,$scan_data,$just_header)=@_;
     my %record;
-    my $questions=substr($line,$$scantron_config{'Qstart'}-1);
-    my $data=substr($line,0,$$scantron_config{'Qstart'}-1);
+    my $questions=substr($line,$$scantron_config{'Qstart'}-1);  # Answers
+    my $data=substr($line,0,$$scantron_config{'Qstart'}-1);     # earlier stuff
     if (!($$scantron_config{'CODElocation'} eq 0 ||
 	  $$scantron_config{'CODElocation'} eq 'none')) {
 	if ($$scantron_config{'CODElocation'} < 0 ||
@@ -4691,7 +5071,7 @@ sub scantron_parse_scanline {
     $record{'scantron.LastName'}=
 	substr($data,$$scantron_config{'LastName'}-1,
 	       $$scantron_config{'LastNamelength'});
-    if ($justHeader) { return \%record; }
+    if ($just_header) { return \%record; }
 
     my @alphabet=('A'..'Z');
     my $questnum=0;
@@ -4705,7 +5085,7 @@ sub scantron_parse_scanline {
 		|| $currentquest eq '*') {
 		push(@{$record{'scantron.doubleerror'}},$questnum);
 		$record{"scantron.$questnum.answer"}='';
-	    } elsif (!$currentquest 
+	    } elsif (!defined($currentquest)
 		     || $currentquest eq $$scantron_config{'Qoff'}
 		     || $currentquest !~ /^[A-Z]$/) {
 		$record{"scantron.$questnum.answer"}='';
@@ -4720,9 +5100,9 @@ sub scantron_parse_scanline {
 		|| $currentquest eq '*') {
 		push(@{$record{'scantron.doubleerror'}},$questnum);
 		$record{"scantron.$questnum.answer"}='';
-		} elsif (!$currentquest 
-			 || $currentquest eq $$scantron_config{'Qoff'} 
-			 || $currentquest !~ /^\d$/) {
+	    } elsif (!defined($currentquest)
+		     || $currentquest eq $$scantron_config{'Qoff'} 
+		     || $currentquest !~ /^\d$/) {
 		$record{"scantron.$questnum.answer"}='';
 		if (!&scan_data($scan_data,"$whichline.no_bubble.$questnum")) {
 		    push(@{$record{"scantron.missingerror"}},$questnum);
@@ -4764,6 +5144,24 @@ sub scantron_parse_scanline {
     return \%record;
 }
 
+=pod
+
+=item scantron_add_delay
+
+   Adds an error message that occurred during the grading phase to a
+   queue of messages to be shown after grading pass is complete
+
+ Arguments:
+   $delayqueue  - arrary ref of hash ref of error messages
+   $scanline    - the scanline that caused the error
+   $errormesage - the error message
+   $errorcode   - a numeric code for the error
+
+ Side Effects:
+   updates the $delayqueue to have a new hash ref of the error
+
+=cut
+
 sub scantron_add_delay {
     my ($delayqueue,$scanline,$errormessage,$errorcode)=@_;
     push(@$delayqueue,
@@ -4772,6 +5170,24 @@ sub scantron_add_delay {
 	 );
 }
 
+=pod
+
+=item scantron_find_student
+
+   Finds the username for the current scanline
+
+  Arguments:
+   $scantron_record - hash result from scantron_parse_scanline
+   $scan_data       - hash of correction information 
+                      (see &scantron_getfile() form more information)
+   $idmap           - hash from &username_to_idmap()
+   $line            - number of current scanline
+ 
+  Returns:
+   Either 'username:domain' or undef if unknown
+
+=cut
+
 sub scantron_find_student {
     my ($scantron_record,$scan_data,$idmap,$line)=@_;
     my $scanID=$$scantron_record{'scantron.ID'};
@@ -4786,6 +5202,15 @@ sub scantron_find_student {
     return undef;
 }
 
+=pod
+
+=item scantron_filter
+
+   Filter sub for lonnavmaps, filters out hidden resources if ignore
+   hidden resources was selected
+
+=cut
+
 sub scantron_filter {
     my ($curres)=@_;
 
@@ -4802,6 +5227,15 @@ sub scantron_filter {
     return 0;
 }
 
+=pod
+
+=item scantron_process_corrections
+
+   Gets correction information out of submitted form data and corrects
+   the scanline
+
+=cut
+
 sub scantron_process_corrections {
     my ($r) = @_;
     my %scantron_config=&get_scantron_config($env{'form.scantron_format'});
@@ -4852,19 +5286,37 @@ sub scantron_process_corrections {
 	}
     }
     if ($err) {
-	$r->print("<font color='red'>Unable to accept last correction, an error occurred :$errmsg:</font>");
+	$r->print("<span class=\"LC_warning\">Unable to accept last correction, an error occurred :$errmsg:</span>");
     } else {
 	&scantron_put_line($scanlines,$scan_data,$which,$line,$skip);
 	&scantron_putfile($scanlines,$scan_data);
     }
 }
 
+=pod
+
+=item reset_skipping_status
+
+   Forgets the current set of remember skipped scanlines (and thus
+   reverts back to considering all lines in the
+   scantron_skipped_<filename> file)
+
+=cut
+
 sub reset_skipping_status {
     my ($scanlines,$scan_data)=&scantron_getfile();
     &scan_data($scan_data,'remember_skipping',undef,1);
     &scantron_putfile(undef,$scan_data);
 }
 
+=pod
+
+=item start_skipping
+
+   Marks a scanline to be skipped. 
+
+=cut
+
 sub start_skipping {
     my ($scan_data,$i)=@_;
     my %remembered=split(':',&scan_data($scan_data,'remember_skipping'));
@@ -4876,6 +5328,14 @@ sub start_skipping {
     &scan_data($scan_data,'remember_skipping',join(':',%remembered));
 }
 
+=pod
+
+=item should_be_skipped
+
+   Checks whether a scanline should be skipped.
+
+=cut
+
 sub should_be_skipped {
     my ($scanlines,$scan_data,$i)=@_;
     if ($env{'form.scantron_options_redo'} !~ /^redo_/) {
@@ -4891,6 +5351,15 @@ sub should_be_skipped {
     return 1;
 }
 
+=pod
+
+=item remember_current_skipped
+
+   Discovers what scanlines are in the scantron_skipped_<filename>
+   file and remembers them into scan_data for later use.
+
+=cut
+
 sub remember_current_skipped {
     my ($scanlines,$scan_data)=&scantron_getfile();
     my %to_remember;
@@ -4904,13 +5373,32 @@ sub remember_current_skipped {
     &scantron_putfile(undef,$scan_data);
 }
 
+=pod
+
+=item check_for_error
+
+    Checks if there was an error when attempting to remove a specific
+    scantron_.. bubble sheet data file. Prints out an error if
+    something went wrong.
+
+=cut
+
 sub check_for_error {
     my ($r,$result)=@_;
     if ($result ne 'ok' && $result ne 'not_found' ) {
-	$r->print("An error occured ($result) when trying to Remove the existing corrections.");
+	$r->print("An error occurred ($result) when trying to Remove the existing corrections.");
     }
 }
 
+=pod
+
+=item scantron_warning_screen
+
+   Interstitial screen to make sure the operator has selected the
+   correct options before we start the validation phase.
+
+=cut
+
 sub scantron_warning_screen {
     my ($button_text)=@_;
     my $title=&Apache::lonnet::gettitle($env{'form.selectpage'});
@@ -4920,22 +5408,21 @@ sub scantron_warning_screen {
 	$scantron_config{'CODEstart'} &&
 	$scantron_config{'CODElength'}) {
 	$CODElist=$env{'form.scantron_CODElist'};
-	if ($env{'form.scantron_CODElist'} eq '') { $CODElist='<font color="red">None</font>'; }
+	if ($env{'form.scantron_CODElist'} eq '') { $CODElist='<span class="LC_warning">None</span>'; }
 	$CODElist=
 	    '<tr><td><b>List of CODES to validate against:</b></td><td><tt>'.
 	    $env{'form.scantron_CODElist'}.'</tt></td></tr>';
     }
     return (<<STUFF);
 <p>
-<font color="red">Please double check the information
-                 below before clicking on '$button_text'</font>
+<span class="LC_warning">Please double check the information
+                 below before clicking on '$button_text'</span>
 </p>
 <table>
 <tr><td><b>Sequence to be Graded:</b></td><td>$title</td></tr>
 <tr><td><b>Data File that will be used:</b></td><td><tt>$env{'form.scantron_selectfile'}</tt></td></tr>
 $CODElist
 </table>
-</font>
 <br />
 <p> If this information is correct, please click on '$button_text'.</p>
 <p> If something is incorrect, please click the 'Grading Menu' button to start over.</p>
@@ -4944,6 +5431,15 @@ $CODElist
 STUFF
 }
 
+=pod
+
+=item scantron_do_warning
+
+   Check if the operator has picked something for all required
+   fields. Error out if something is missing.
+
+=cut
+
 sub scantron_do_warning {
     my ($r)=@_;
     my ($symb)=&get_symb($r);
@@ -4955,13 +5451,13 @@ sub scantron_do_warning {
 	 $env{'form.scantron_format'} eq '' ) {
 	$r->print("<p>You have forgetten to specify some information. Please go Back and try again.</p>");
 	if ( $env{'form.selectpage'} eq '') {
-	    $r->print('<p><font color="red">You have not selected a Sequence to grade</font></p>');
+	    $r->print('<p><span class="LC_error">You have not selected a Sequence to grade</span></p>');
 	} 
 	if ( $env{'form.scantron_selectfile'} eq '') {
-	    $r->print('<p><font color="red">You have not selected a file that contains the student\'s response data.</font></p>');
+	    $r->print('<p><span class="LC_error">You have not selected a file that contains the student\'s response data.</span></p>');
 	} 
 	if ( $env{'form.scantron_format'} eq '') {
-	    $r->print('<p><font color="red">You have not selected a the format of the student\'s response data.</font></p>');
+	    $r->print('<p><span class="LC_error">You have not selected a the format of the student\'s response data.</span></p>');
 	} 
     } else {
 	my $warning=&scantron_warning_screen('Grading: Validate Records');
@@ -4975,6 +5471,14 @@ STUFF
     return '';
 }
 
+=pod
+
+=item scantron_form_start
+
+    html hidden input for remembering all selected grading options
+
+=cut
+
 sub scantron_form_start {
     my ($max_bubble)=@_;
     my $result= <<SCANTRONFORM;
@@ -4992,6 +5496,18 @@ SCANTRONFORM
     return $result;
 }
 
+=pod
+
+=item scantron_validate_file
+
+    Dispatch routine for doing validation of a bubble sheet data file.
+
+    Also processes any necessary information resets that need to
+    occur before validation begins (ignore previous corrections,
+    restarting the skipped records processing)
+
+=cut
+
 sub scantron_validate_file {
     my ($r) = @_;
     my ($symb)=&get_symb($r);
@@ -4999,7 +5515,7 @@ sub scantron_validate_file {
     my $default_form_data=&defaultFormData($symb);
     
     # do the detection of only doing skipped records first befroe we delete
-    # them  when doing the corrections reset
+    # them when doing the corrections reset
     if ($env{'form.scantron_options_redo'} ne 'redo_skipped_ready') {
 	&reset_skipping_status();
     }
@@ -5018,7 +5534,7 @@ sub scantron_validate_file {
     if ($env{'form.scantron_corrections'}) {
 	&scantron_process_corrections($r);
     }
-    $r->print("<p>Gathering neccessary info.</p>");$r->rflush();
+    $r->print("<p>Gathering necessary info.</p>");$r->rflush();
     #get the student pick code ready
     $r->print(&Apache::loncommon::studentbrowser_javascript());
     my $max_bubble=&scantron_get_maxbubble();
@@ -5075,6 +5591,17 @@ STUFF
     return '';
 }
 
+
+=pod
+
+=item scantron_remove_file
+
+   Removes the requested bubble sheet data file, makes sure that
+   scantron_original_<filename> is never removed
+
+
+=cut
+
 sub scantron_remove_file {
     my ($which)=@_;
     my $cname=$env{'course.'.$env{'request.course.id'}.'.num'};
@@ -5089,6 +5616,18 @@ sub scantron_remove_file {
     return &Apache::lonnet::removeuserfile($cname,$cdom,$file);
 }
 
+
+=pod
+
+=item scantron_remove_scan_data
+
+   Removes all scan_data correction for the requested bubble sheet
+   data file.  (In the case that both the are doing skipped records we need
+   to remember the old skipped lines for the time being so that element
+   persists for a while.)
+
+=cut
+
 sub scantron_remove_scan_data {
     my $cname=$env{'course.'.$env{'request.course.id'}.'.num'};
     my $cdom=$env{'course.'.$env{'request.course.id'}.'.domain'};
@@ -5111,6 +5650,51 @@ sub scantron_remove_scan_data {
     return $result;
 }
 
+
+=pod
+
+=item scantron_getfile
+
+    Fetches the requested bubble sheet data file (all 3 versions), and
+    the scan_data hash
+  
+  Arguments:
+    None
+
+  Returns:
+    2 hash references
+
+     - first one has 
+         orig      -
+         corrected -
+         skipped   -  each of which points to an array ref of the specified
+                      file broken up into individual lines
+         count     - number of scanlines
+ 
+     - second is the scan_data hash possible keys are
+       ($number refers to scanline numbered $number and thus the key affects
+        only that scanline
+        $bubline refers to the specific bubble line element and the aspects
+        refers to that specific bubble line element)
+
+       $number.user - username:domain to use
+       $number.CODE_ignore_dup 
+                    - ignore the duplicate CODE error 
+       $number.useCODE
+                    - use the CODE in the scanline as is
+       $number.no_bubble.$bubline
+                    - it is valid that there is no bubbled in bubble
+                      at $number $bubline
+       remember_skipping
+                    - a frozen hash containing keys of $number and values
+                      of either 
+                        1 - we are on a 'do skipped records pass' and plan
+                            on processing this line
+                        2 - we are on a 'do skipped records pass' and this
+                            scanline has been marked to skip yet again
+
+=cut
+
 sub scantron_getfile {
     #FIXME really would prefer a scantron directory
     my $cname=$env{'course.'.$env{'request.course.id'}.'.num'};
@@ -5143,6 +5727,21 @@ sub scantron_getfile {
     return (\%scanlines,\%scan_data);
 }
 
+=pod
+
+=item lonnet_putfile
+
+   Wrapper routine to call &Apache::lonnet::finishuserfileupload
+
+ Arguments:
+   $contents - data to store
+   $filename - filename to store $contents into
+
+ Returns:
+   result value from &Apache::lonnet::finishuserfileupload
+
+=cut
+
 sub lonnet_putfile {
     my ($contents,$filename)=@_;
     my $docuname=$env{'course.'.$env{'request.course.id'}.'.num'};
@@ -5152,6 +5751,22 @@ sub lonnet_putfile {
 
 }
 
+=pod
+
+=item scantron_putfile
+
+    Stores the current version of the bubble sheet data files, and the
+    scan_data hash. (Does not modify the original version only the
+    corrected and skipped versions.
+
+ Arguments:
+    $scanlines - hash ref that looks like the first return value from
+                 &scantron_getfile()
+    $scan_data - hash ref that looks like the second return value from
+                 &scantron_getfile()
+
+=cut
+
 sub scantron_putfile {
     my ($scanlines,$scan_data) = @_;
     #FIXME really would prefer a scantron directory
@@ -5172,6 +5787,28 @@ sub scantron_putfile {
     &Apache::lonnet::put('nohist_scantrondata',$scan_data,$cdom,$cname);
 }
 
+=pod
+
+=item scantron_get_line
+
+   Returns the correct version of the scanline
+
+ Arguments:
+    $scanlines - hash ref that looks like the first return value from
+                 &scantron_getfile()
+    $scan_data - hash ref that looks like the second return value from
+                 &scantron_getfile()
+    $i         - number of the requested line (starts at 0)
+
+ Returns:
+   A scanline, (either the original or the corrected one if it
+   exists), or undef if the requested scanline should be
+   skipped. (Either because it's an skipped scanline, or it's an
+   unskipped scanline and we are not doing a 'do skipped scanlines'
+   pass.
+
+=cut
+
 sub scantron_get_line {
     my ($scanlines,$scan_data,$i)=@_;
     if (&should_be_skipped($scanlines,$scan_data,$i)) { return undef; }
@@ -5180,6 +5817,23 @@ sub scantron_get_line {
     return $scanlines->{'orig'}[$i]; 
 }
 
+=pod
+
+=item scantron_todo_count
+
+    Counts the number of scanlines that need processing.
+
+ Arguments:
+    $scanlines - hash ref that looks like the first return value from
+                 &scantron_getfile()
+    $scan_data - hash ref that looks like the second return value from
+                 &scantron_getfile()
+
+ Returns:
+    $count - number of scanlines to process
+
+=cut
+
 sub get_todo_count {
     my ($scanlines,$scan_data)=@_;
     my $count=0;
@@ -5191,6 +5845,25 @@ sub get_todo_count {
     return $count;
 }
 
+=pod
+
+=item scantron_put_line
+
+    Updates the 'corrected' or 'skipped' versions of the bubble sheet
+    data file.
+
+ Arguments:
+    $scanlines - hash ref that looks like the first return value from
+                 &scantron_getfile()
+    $scan_data - hash ref that looks like the second return value from
+                 &scantron_getfile()
+    $i         - line number to update
+    $newline   - contents of the updated scanline
+    $skip      - if true make the line for skipping and update the
+                 'skipped' file
+
+=cut
+
 sub scantron_put_line {
     my ($scanlines,$scan_data,$i,$newline,$skip)=@_;
     if ($skip) {
@@ -5201,6 +5874,21 @@ sub scantron_put_line {
     $scanlines->{'corrected'}[$i]=$newline;
 }
 
+=pod
+
+=item scantron_clear_skip
+
+   Remove a line from the 'skipped' file
+
+ Arguments:
+    $scanlines - hash ref that looks like the first return value from
+                 &scantron_getfile()
+    $scan_data - hash ref that looks like the second return value from
+                 &scantron_getfile()
+    $i         - line number to update
+
+=cut
+
 sub scantron_clear_skip {
     my ($scanlines,$scan_data,$i)=@_;
     if (exists($scanlines->{'skipped'}[$i])) {
@@ -5210,6 +5898,15 @@ sub scantron_clear_skip {
     return 0;
 }
 
+=pod
+
+=item scantron_filter_not_exam
+
+   Filter routine used by &Apache::lonnavmaps::retrieveResources(), to
+   filter out resources that are not marked as 'exam' mode
+
+=cut
+
 sub scantron_filter_not_exam {
     my ($curres)=@_;
     
@@ -5226,6 +5923,15 @@ sub scantron_filter_not_exam {
     return 0;
 }
 
+=pod
+
+=item scantron_validate_sequence
+
+    Validates the selected sequence, checking for resource that are
+    not set to exam mode.
+
+=cut
+
 sub scantron_validate_sequence {
     my ($r,$currentphase) = @_;
 
@@ -5249,6 +5955,15 @@ sub scantron_validate_sequence {
     return (0,$currentphase+1);
 }
 
+=pod
+
+=item scantron_validate_ID
+
+   Validates all scanlines in the selected file to not have any
+   invalid or underspecified student IDs
+
+=cut
+
 sub scantron_validate_ID {
     my ($r,$currentphase) = @_;
     
@@ -5311,6 +6026,36 @@ sub scantron_validate_ID {
     return (0,$currentphase+1);
 }
 
+=pod
+
+=item scantron_get_correction
+
+   Builds the interface screen to interact with the operator to fix a
+   specific error condition in a specific scanline
+
+ Arguments:
+    $r           - Apache request object
+    $i           - number of the current scanline
+    $scan_record - hash ref as returned from &scantron_parse_scanline()
+    $scan_config - hash ref as returned from &get_scantron_config()
+    $line        - full contents of the current scanline
+    $error       - error condition, valid values are
+                   'incorrectCODE', 'duplicateCODE',
+                   'doublebubble', 'missingbubble',
+                   'duplicateID', 'incorrectID'
+    $arg         - extra information needed
+       For errors:
+         - duplicateID   - paper number that this studentID was seen before on
+         - duplicateCODE - array ref of the paper numbers this CODE was
+                           seen on before
+         - incorrectCODE - current incorrect CODE 
+         - doublebubble  - array ref of the bubble lines that have double
+                           bubble errors
+         - missingbubble - array ref of the bubble lines that have missing
+                           bubble errors
+
+=cut
+
 sub scantron_get_correction {
     my ($r,$i,$scan_record,$scan_config,$line,$error,$arg)=@_;
 
@@ -5370,7 +6115,7 @@ sub scantron_get_correction {
 	    if ($closest > 0) {
 		foreach my $testcode (@{$closest}) {
 		    my $checked='';
-		    if (!$i) { $checked=' checked="on" '; }
+		    if (!$i) { $checked=' checked="checked" '; }
 		    $r->print("<label><input type='radio' name='scantron_CODE_resolution' value='use_closest_$i' $checked /> Use the similar CODE <b><tt>".$testcode."</tt></b> instead.</label><input type='hidden' name='scantron_CODE_closest_$i' value='$testcode' />");
 		    $r->print("\n<br />");
 		    $i++;
@@ -5378,7 +6123,7 @@ sub scantron_get_correction {
 	    }
 	}
 	if ($$scan_record{'scantron.CODE'}=~/\S/ ) {
-	    my $checked; if (!$i) { $checked=' checked="on" '; }
+	    my $checked; if (!$i) { $checked=' checked="checked" '; }
 	    $r->print("<label><input type='radio' name='scantron_CODE_resolution' value='use_unfound' $checked /> Use the CODE <b><tt>".$$scan_record{'scantron.CODE'}."</tt></b> that is was on the paper, ignoring the error.</label>");
 	    $r->print("\n<br />");
 	}
@@ -5414,7 +6159,8 @@ ENDSCRIPT
 	$r->print("<p>Please indicate which bubble should be used for grading</p>");
 	foreach my $question (@{$arg}) {
 	    my $selected=$$scan_record{"scantron.$question.answer"};
-	    &scantron_bubble_selector($r,$scan_config,$question,split('',$selected));
+	    &scantron_bubble_selector($r,$scan_config,$question,
+				      split('',$selected));
 	}
     } elsif ($error eq 'missingbubble') {
 	$r->print("<p>There have been <b>no</b> bubbles scanned for some question(s)</p>\n");
@@ -5434,32 +6180,99 @@ ENDSCRIPT
 
 }
 
+=pod
+
+=item scantron_bubble_selector
+  
+   Generates the html radiobuttons to correct a single bubble line
+   possibly showing the existing the selected bubbles if known
+
+ Arguments:
+    $r           - Apache request object
+    $scan_config - hash from &get_scantron_config()
+    $quest       - number of the bubble line to make a corrector for
+    $selected    - array of letters of previously selected bubbles
+    $lines       - if present, number of bubble lines to show
+
+=cut
+
 sub scantron_bubble_selector {
-    my ($r,$scan_config,$quest,@selected)=@_;
+    my ($r,$scan_config,$quest,@selected, $lines)=@_;
     my $max=$$scan_config{'Qlength'};
 
     my $scmode=$$scan_config{'Qon'};
     if ($scmode eq 'number' || $scmode eq 'letter') { $max=10; }	     
 
-    my @alphabet=('A'..'Z');
-    $r->print("<table border='1'><tr><td rowspan='2'>$quest</td>");
-    for (my $i=0;$i<$max+1;$i++) {
-	$r->print("\n".'<td align="center">');
-	if ($selected[0] eq $alphabet[$i]) { $r->print('X'); shift(@selected) }
-	else { $r->print('&nbsp;'); }
-	$r->print('</td>');
-    }
-    $r->print('</tr><tr>');
-    for (my $i=0;$i<$max;$i++) {
-	$r->print("\n".
-		  '<td><label><input type="radio" name="scantron_correct_Q_'.
-		  $quest.'" value="'.$i.'" />'.$alphabet[$i]."</label></td>");
+
+    if (!defined($lines)) {
+	$lines = 1;
     }
-    $r->print('<td><label><input type="radio" name="scantron_correct_Q_'.
+    my $total_lines = $lines*2;
+    my @alphabet=('A'..'Z');
+    $r->print("<table border='1'><tr><td rowspan='".$total_lines."'>$quest</td>");
+
+    for (my $l = 0; $l < $lines; $l++) {
+	if ($l != 0) {
+	    $r->print('<tr>');
+	}
+
+	# FIXME:  This loop probably has to be considerably more clever for
+	#  multiline bubbles: User can multibubble by having bubbles in
+	#  several lines.  User can skip lines legitimately etc. etc.
+
+	for (my $i=0;$i<$max;$i++) {
+	    $r->print("\n".'<td align="center">');
+	    if ($selected[0] eq $alphabet[$i]) { 
+		$r->print('X'); 
+		shift(@selected) ;
+	    } else { 
+		$r->print('&nbsp;'); 
+	    }
+	    $r->print('</td>');
+	    
+	}
+
+	if ($l == 0) {
+	    my $lspan = $total_lines * 2;   #  2 table rows per bubble line.
+
+	    $r->print('<td rowspan='.$lspan.'><label><input type="radio" name="scantron_correct_Q_'.
 	      $quest.'" value="none" /> No bubble </label></td>');
-    $r->print('</tr></table>');
+	
+	}
+
+	$r->print('</tr><tr>');
+
+	# FIXME: This may have to be a bit more clever for
+	#        multiline questions (different values e.g..).
+
+	for (my $i=0;$i<$max;$i++) {
+	    $r->print("\n".
+		      '<td><label><input type="radio" name="scantron_correct_Q_'.
+		      $quest.'" value="'.$i.'" />'.$alphabet[$i]."</label></td>");
+	}
+	$r->print('</tr>');
+
+	    
+    }
+    $r->print('</table>');
 }
 
+=pod
+
+=item num_matches
+
+   Counts the number of characters that are the same between the two arguments.
+
+ Arguments:
+   $orig - CODE from the scanline
+   $code - CODE to match against
+
+ Returns:
+   $count - integer count of the number of same characters between the
+            two arguments
+
+=cut
+
 sub num_matches {
     my ($orig,$code) = @_;
     my @code=split(//,$code);
@@ -5471,6 +6284,26 @@ sub num_matches {
     return $same;
 }
 
+=pod
+
+=item scantron_get_closely_matching_CODEs
+
+   Cycles through all CODEs and finds the set that has the greatest
+   number of same characters as the provided CODE
+
+ Arguments:
+   $allcodes - hash ref returned by &get_codes()
+   $CODE     - CODE from the current scanline
+
+ Returns:
+   2 element list
+    - first elements is number of how closely matching the best fit is 
+      (5 means best set has 5 matching characters)
+    - second element is an arrary ref containing the set of valid CODEs
+      that best fit the passed in CODE
+
+=cut
+
 sub scantron_get_closely_matching_CODEs {
     my ($allcodes,$CODE)=@_;
     my @CODEs;
@@ -5481,6 +6314,23 @@ sub scantron_get_closely_matching_CODEs
     return ($#CODEs,$CODEs[-1]);
 }
 
+=pod
+
+=item get_codes
+
+   Builds a hash which has keys of all of the valid CODEs from the selected
+   set of remembered CODEs.
+
+ Arguments:
+  $old_name - name of the set of remembered CODEs
+  $cdom     - domain of the course
+  $cnum     - internal course name
+
+ Returns:
+  %allcodes - keys are the valid CODEs, values are all 1
+
+=cut
+
 sub get_codes {
     my ($old_name, $cdom, $cnum) = @_;
     if (!$old_name) {
@@ -5503,6 +6353,16 @@ sub get_codes {
     return %allcodes;
 }
 
+=pod
+
+=item scantron_validate_CODE
+
+   Validates all scanlines in the selected file to not have any
+   invalid or underspecified CODEs and that none of the codes are
+   duplicated if this was requested.
+
+=cut
+
 sub scantron_validate_CODE {
     my ($r,$currentphase) = @_;
     my %scantron_config=&get_scantron_config($env{'form.scantron_format'});
@@ -5554,6 +6414,15 @@ sub scantron_validate_CODE {
     return (0,$currentphase+1);
 }
 
+=pod
+
+=item scantron_validate_doublebubble
+
+   Validates all scanlines in the selected file to not have any
+   bubble lines with multiple bubbles marked.
+
+=cut
+
 sub scantron_validate_doublebubble {
     my ($r,$currentphase) = @_;
     #get student info
@@ -5577,6 +6446,19 @@ sub scantron_validate_doublebubble {
     return (0,$currentphase+1);
 }
 
+=pod
+
+=item scantron_get_maxbubble
+
+   Returns the maximum number of bubble lines that are expected to
+   occur. Does this by walking the selected sequence rendering the
+   resource and then checking &Apache::lonxml::get_problem_counter()
+   for what the current value of the problem counter is.
+
+   Caches the result to $env{'form.scantron_maxbubble'}
+
+=cut
+
 sub scantron_get_maxbubble {    
     if (defined($env{'form.scantron_maxbubble'}) &&
 	$env{'form.scantron_maxbubble'}) {
@@ -5603,6 +6485,15 @@ sub scantron_get_maxbubble {
     return $env{'form.scantron_maxbubble'};
 }
 
+=pod
+
+=item scantron_validate_missingbubbles
+
+   Validates all scanlines in the selected file to not have any
+   bubble lines with missing bubbles that haven't been verified as missing.
+
+=cut
+
 sub scantron_validate_missingbubbles {
     my ($r,$currentphase) = @_;
     #get student info
@@ -5635,6 +6526,30 @@ sub scantron_validate_missingbubbles {
     return (0,$currentphase+1);
 }
 
+=pod
+
+=item scantron_process_students
+
+   Routine that does the actual grading of the bubble sheet information.
+
+   The parsed scanline hash is added to %env 
+
+   Then foreach unskipped scanline it does an &Apache::lonnet::ssi()
+   foreach resource , with the form data of
+
+	'submitted'     =>'scantron' 
+	'grade_target'  =>'grade',
+	'grade_username'=> username of student
+	'grade_domain'  => domain of student
+	'grade_courseid'=> of course
+	'grade_symb'    => symb of resource to grade
+
+    This triggers a grading pass. The problem grading code takes care
+    of converting the bubbled letter information (now in %env) into a
+    valid submission.
+
+=cut
+
 sub scantron_process_students {
     my ($r) = @_;
     my (undef,undef,$sequence)=&Apache::lonnet::decode_symb($env{'form.selectpage'});
@@ -5739,6 +6654,14 @@ SCANTRONFORM
     return '';
 }
 
+=pod
+
+=item scantron_upload_scantron_data
+
+    Creates the screen for adding a new bubble sheet data file to a course.
+
+=cut
+
 sub scantron_upload_scantron_data {
     my ($r)=@_;
     $r->print(&Apache::loncommon::coursebrowser_javascript($env{'request.role.domain'}));
@@ -5775,6 +6698,15 @@ UPLOAD
     return '';
 }
 
+=pod
+
+=item scantron_upload_scantron_data_save
+
+   Adds a provided bubble information data file to the course if user
+   has the correct privileges to do so.  
+
+=cut
+
 sub scantron_upload_scantron_data_save {
     my($r)=@_;
     my ($symb)=&get_symb($r,1);
@@ -5813,13 +6745,13 @@ sub scantron_upload_scantron_data_save {
     my $uploadedfile=$fname;
     $fname='scantron_orig_'.$fname;
     if (length($env{'form.upfile'}) < 2) {
-	$r->print("<font color='red'>Error:</font> The file you attempted to upload, <tt>".&HTML::Entities::encode($env{'form.upfile.filename'},'<>&"')."</tt>, contained no information. Please check that you entered the correct filename.");
+	$r->print("<span class=\"LC_error\">Error:</span> The file you attempted to upload, <tt>".&HTML::Entities::encode($env{'form.upfile.filename'},'<>&"')."</tt>, contained no information. Please check that you entered the correct filename.");
     } else {
 	my $result=&Apache::lonnet::finishuserfileupload($env{'form.courseid'},$env{'form.domainid'},'upfile',$fname);
 	if ($result =~ m|^/uploaded/|) {
-	    $r->print("<font color='green'>Success:</font> Successfully uploaded ".(length($env{'form.upfile'})-1)." bytes of data into location <tt>".$result."</tt>");
+	    $r->print("<span class=\"LC_success\">Success:</span> Successfully uploaded ".(length($env{'form.upfile'})-1)." bytes of data into location <tt>".$result."</tt>");
 	} else {
-	    $r->print("<font color='red'>Error:</font> An error (".$result.") occurred when attempting to upload the file, <tt>".&HTML::Entities::encode($env{'form.upfile.filename'},'<>&"')."</tt>");
+	    $r->print("<span class=\"LC_error\">Error:</span> An error (".$result.") occurred when attempting to upload the file, <tt>".&HTML::Entities::encode($env{'form.upfile.filename'},'<>&"')."</tt>");
 	}
     }
     if ($symb) {
@@ -5830,6 +6762,14 @@ sub scantron_upload_scantron_data_save {
     return '';
 }
 
+=pod
+
+=item valid_file
+
+   Validates that the requested bubble data file exists in the course.
+
+=cut
+
 sub valid_file {
     my ($requested_file)=@_;
     foreach my $filename (sort(&scantron_filenames())) {
@@ -5838,6 +6778,16 @@ sub valid_file {
     return 0;
 }
 
+=pod
+
+=item scantron_download_scantron_data
+
+   Shows a list of the three internal files (original, corrected,
+   skipped) for a specific bubble sheet data file that exists in the
+   course.
+
+=cut
+
 sub scantron_download_scantron_data {
     my ($r)=@_;
     my $default_form_data=&defaultFormData(&get_symb($r,1));
@@ -5874,6 +6824,12 @@ DOWNLOAD
     return '';
 }
 
+=pod
+
+=back
+
+=cut
+
 #-------- end of section for handling grading scantron forms -------
 #
 #-------------------------------------------------------------------
@@ -5884,7 +6840,7 @@ DOWNLOAD
 sub show_grading_menu_form {
     my ($symb)=@_;
     my $result.='<br /><form action="/adm/grades" method="post">'."\n".
-	'<input type="hidden" name="symb" value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb" value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="saveState"  value="'.$env{'form.saveState'}.'" />'."\n".
 	'<input type="hidden" name="command" value="gradingmenu" />'."\n".
 	'<input type="submit" name="submit" value="Grading Menu" />'."\n".
@@ -5948,7 +6904,7 @@ sub gradingmenu {
 </script>
 GRADINGMENUJS
     &commonJSfunctions($request);
-    my $result='<h3>&nbsp;<font color="#339933">Manual Grading/View Submission</font></h3>';
+    my $result='<h3>&nbsp;<span class="LC_info">Manual Grading/View Submission</span></h3>';
     my ($table,undef,$hdgrade) = &showResourceInfo($symb,$probTitle);
     $result.=$table;
     my (undef,$sections) = &getclasslist('all','0');
@@ -5959,7 +6915,7 @@ GRADINGMENUJS
     my $saveStatus = ($$savedState{'saveStatus'} eq '' ? 'Active' : $$savedState{'saveStatus'});
 
     $result.='<form action="/adm/grades" method="post" name="gradingMenu">'."\n".
-	'<input type="hidden" name="symb"        value="'.$symb.'" />'."\n".
+	'<input type="hidden" name="symb"        value="'.&Apache::lonenc::check_encrypt($symb).'" />'."\n".
 	'<input type="hidden" name="handgrade"   value="'.$hdgrade.'" />'."\n".
 	'<input type="hidden" name="probTitle"   value="'.$probTitle.'" />'."\n".
 	'<input type="hidden" name="command"     value="" />'."\n".
@@ -5978,38 +6934,38 @@ GRADINGMENUJS
     if (ref($sections)) {
 	foreach (sort (@$sections)) {
 	    $result.='<option value="'.$_.'" '.
-		($saveSec eq $_ ? 'selected="on"':'').'>'.$_.'</option>'."\n";
+		($saveSec eq $_ ? 'selected="selected"':'').'>'.$_.'</option>'."\n";
 	}
     }
-    $result.= '<option value="all" '.($saveSec eq 'all' ? 'selected="on"' : ''). '>all</option></select> &nbsp; ';
+    $result.= '<option value="all" '.($saveSec eq 'all' ? 'selected="selected"' : ''). '>all</option></select> &nbsp; ';
 
-    $result.=&mt('Student Status').':</b>'.&Apache::lonhtmlcommon::StatusOptions($saveStatus,undef,1,undef);
+    $result.=&mt('Student Status').':'.&Apache::lonhtmlcommon::StatusOptions($saveStatus,undef,1,undef);
 
     $result.='</td></tr>';
 
     $result.='<tr bgcolor="#ffffe6"valign="top"><td><label>'.
 	'<input type="radio" name="radioChoice" value="submission" '.
-	($saveCmd eq 'submission' ? 'checked' : '').' /> '.'<b>'.&mt('Current Resource').':</b> '.&mt('For one or more students').
+	($saveCmd eq 'submission' ? 'checked="checked"' : '').' /> '.'<b>'.&mt('Current Resource').':</b> '.&mt('For one or more students').
 	'</label> <select name="submitonly">'.
 	'<option value="yes" '.
-	($saveSub eq 'yes' ? 'selected="on"' : '').' />'.&mt('with submissions').'</option>'.
+	($saveSub eq 'yes' ? 'selected="selected"' : '').'>'.&mt('with submissions').'</option>'.
 	'<option value="queued" '.
-	($saveSub eq 'queued' ? 'selected="on"' : '').' />'.&mt('in grading queue').'</option>'.
+	($saveSub eq 'queued' ? 'selected="selected"' : '').'>'.&mt('in grading queue').'</option>'.
 	'<option value="graded" '.
-	($saveSub eq 'graded' ? 'selected="on"' : '').' />'.&mt('with ungraded submissions').'</option>'.
+	($saveSub eq 'graded' ? 'selected="selected"' : '').'>'.&mt('with ungraded submissions').'</option>'.
 	'<option value="incorrect" '.
-	($saveSub eq 'incorrect' ? 'selected="on"' : '').' />'.&mt('with incorrect submissions').'</option>'.
+	($saveSub eq 'incorrect' ? 'selected="selected"' : '').'>'.&mt('with incorrect submissions').'</option>'.
 	'<option value="all" '.
-	($saveSub eq 'all' ? 'selected="on"' : '').' />'.&mt('with any status').'</option></select></td></tr>'."\n";
+	($saveSub eq 'all' ? 'selected="selected"' : '').'>'.&mt('with any status').'</option></select></td></tr>'."\n";
 
     $result.='<tr bgcolor="#ffffe6"valign="top"><td>'.
 	'<label><input type="radio" name="radioChoice" value="viewgrades" '.
-	($saveCmd eq 'viewgrades' ? 'checked' : '').' /> '.
+	($saveCmd eq 'viewgrades' ? 'checked="checked"' : '').' /> '.
 	'<b>Current Resource:</b> For all students in selected section or course</label></td></tr>'."\n";
 
     $result.='<tr bgcolor="#ffffe6" valign="top"><td>'.
 	'<label><input type="radio" name="radioChoice" value="pickStudentPage" '.
-	($saveCmd eq 'pickStudentPage' ? 'checked' : '').' /> '.
+	($saveCmd eq 'pickStudentPage' ? 'checked="checked"' : '').' /> '.
 	'The <b>complete</b> set/page/sequence: For one student</label></td></tr>'."\n";
 
     $result.='<tr bgcolor="#ffffe6"><td><br />'.
@@ -6023,6 +6979,10 @@ GRADINGMENUJS
 	'<input type="button" onClick="javascript:checkChoice(this.form,\'3\',\'csvform\');" value="'.&mt('Upload').'" />'.
 	' '.&mt('scores from file').' </td></tr>'."\n";
 
+    $result.='<tr bgcolor="#ffffe6"><td>'.
+        '<input type="button" onClick="javascript:checkChoice(this.form,\'6\',\'processclicker\');" value="'.&mt('Process').'" />'.
+        ' '.&mt('clicker file').' </td></tr>'."\n";
+
     $result.='<tr bgcolor="#ffffe6"valign="top"><td colspan="2">'.
 	'<input type="button" onClick="javascript:checkChoice(this.form,\'4\',\'scantron_selectphase\');'.
 	'" value="'.&mt('Grade').'" /> scantron forms</td></tr>'."\n";
@@ -6042,9 +7002,9 @@ GRADINGMENUJS
 	'<input type="button" onClick="javascript:this.form.command.value=\'codelist\';this.form.action=\'/adm/pickcode\';this.form.submit();'.
 	'" value="'.&mt('View').'" /> saved CODEs.</td></tr>'."\n";
 
-    $result.='</form></td></tr></table>'."\n".
+    $result.='</table>'."\n".
 	'</td></tr></table>'."\n".
-	'</td></tr></table>'."\n";
+	'</td></tr></table></form>'."\n";
     return $result;
 }
 
@@ -6070,6 +7030,468 @@ sub init_perm {
     }
 }
 
+sub gather_clicker_ids {
+    my %clicker_ids;
+
+    my $classlist = &Apache::loncoursedata::get_classlist();
+
+    # Set up a couple variables.
+    my $username_idx = &Apache::loncoursedata::CL_SNAME();
+    my $domain_idx   = &Apache::loncoursedata::CL_SDOM();
+
+    foreach my $student (keys(%$classlist)) {
+
+        my $username = $classlist->{$student}->[$username_idx];
+        my $domain   = $classlist->{$student}->[$domain_idx];
+        my $clickers =
+	    (&Apache::lonnet::userenvironment($domain,$username,'clickers'))[1];
+        foreach my $id (split(/\,/,$clickers)) {
+            $id=~s/^[\#0]+//;
+            $id=~s/[\-\:]//g;
+            if (exists($clicker_ids{$id})) {
+		$clicker_ids{$id}.=','.$username.':'.$domain;
+            } else {
+		$clicker_ids{$id}=$username.':'.$domain;
+            }
+        }
+    }
+    return %clicker_ids;
+}
+
+sub gather_adv_clicker_ids {
+    my %clicker_ids;
+    my $cnum=$env{'course.'.$env{'request.course.id'}.'.num'};
+    my $cdom=$env{'course.'.$env{'request.course.id'}.'.domain'};
+    my %coursepersonnel=&Apache::lonnet::get_course_adv_roles($cdom.'/'.$cnum);
+    foreach my $element (sort(keys(%coursepersonnel))) {
+        foreach my $person (split(/\,/,$coursepersonnel{$element})) {
+            my ($puname,$pudom)=split(/\:/,$person);
+            my $clickers =
+		(&Apache::lonnet::userenvironment($pudom,$puname,'clickers'))[1];
+            foreach my $id (split(/\,/,$clickers)) {
+		$id=~s/^[\#0]+//;
+                $id=~s/[\-\:]//g;
+		if (exists($clicker_ids{$id})) {
+		    $clicker_ids{$id}.=','.$puname.':'.$pudom;
+		} else {
+		    $clicker_ids{$id}=$puname.':'.$pudom;
+		}
+            }
+        }
+    }
+    return %clicker_ids;
+}
+
+sub clicker_grading_parameters {
+    return ('gradingmechanism' => 'scalar',
+            'upfiletype' => 'scalar',
+            'specificid' => 'scalar',
+            'pcorrect' => 'scalar',
+            'pincorrect' => 'scalar');
+}
+
+sub process_clicker {
+    my ($r)=@_;
+    my ($symb)=&get_symb($r);
+    if (!$symb) {return '';}
+    my $result=&checkforfile_js();
+    $env{'form.probTitle'} = &Apache::lonnet::gettitle($symb);
+    my ($table) = &showResourceInfo($symb,$env{'form.probTitle'});
+    $result.=$table;
+    $result.='<br /><table width="100%" border="0"><tr><td bgcolor="#777777">'."\n";
+    $result.='<table width="100%" border="0"><tr bgcolor="#e6ffff"><td>'."\n";
+    $result.='&nbsp;<b>'.&mt('Specify a file containing the clicker information for this resource').
+        '.</b></td></tr>'."\n";
+    $result.='<tr bgcolor=#ffffe6><td>'."\n";
+# Attempt to restore parameters from last session, set defaults if not present
+    my %Saveable_Parameters=&clicker_grading_parameters();
+    &Apache::loncommon::restore_course_settings('grades_clicker',
+                                                 \%Saveable_Parameters);
+    if (!$env{'form.pcorrect'}) { $env{'form.pcorrect'}=100; }
+    if (!$env{'form.pincorrect'}) { $env{'form.pincorrect'}=100; }
+    if (!$env{'form.gradingmechanism'}) { $env{'form.gradingmechanism'}='attendance'; }
+    if (!$env{'form.upfiletype'}) { $env{'form.upfiletype'}='iclicker'; }
+
+    my %checked;
+    foreach my $gradingmechanism ('attendance','personnel','specific') {
+       if ($env{'form.gradingmechanism'} eq $gradingmechanism) {
+          $checked{$gradingmechanism}="checked='checked'";
+       }
+    }
+
+    my $upload=&mt("Upload File");
+    my $type=&mt("Type");
+    my $attendance=&mt("Award points just for participation");
+    my $personnel=&mt("Correctness determined from response by course personnel");
+    my $specific=&mt("Correctness determined from response with clicker ID(s)"); 
+    my $pcorrect=&mt("Percentage points for correct solution");
+    my $pincorrect=&mt("Percentage points for incorrect solution");
+    my $selectform=&Apache::loncommon::select_form($env{'form.upfiletype'},'upfiletype',
+						   ('iclicker' => 'i>clicker',
+                                                    'interwrite' => 'interwrite PRS'));
+    $symb = &Apache::lonenc::check_encrypt($symb);
+    $result.=<<ENDUPFORM;
+<script type="text/javascript">
+function sanitycheck() {
+// Accept only integer percentages
+   document.forms.gradesupload.pcorrect.value=Math.round(document.forms.gradesupload.pcorrect.value);
+   document.forms.gradesupload.pincorrect.value=Math.round(document.forms.gradesupload.pincorrect.value);
+// Find out grading choice
+   for (i=0; i<document.forms.gradesupload.gradingmechanism.length; i++) {
+      if (document.forms.gradesupload.gradingmechanism[i].checked) {
+         gradingchoice=document.forms.gradesupload.gradingmechanism[i].value;
+      }
+   }
+// By default, new choice equals user selection
+   newgradingchoice=gradingchoice;
+// Not good to give more points for false answers than correct ones
+   if (Math.round(document.forms.gradesupload.pcorrect.value)<Math.round(document.forms.gradesupload.pincorrect.value)) {
+      document.forms.gradesupload.pcorrect.value=document.forms.gradesupload.pincorrect.value;
+   }
+// If new choice is attendance only, and old choice was correctness-based, restore defaults
+   if ((gradingchoice=='attendance') && (document.forms.gradesupload.waschecked.value!='attendance')) {
+      document.forms.gradesupload.pcorrect.value=100;
+      document.forms.gradesupload.pincorrect.value=100;
+   }
+// If the values are different, cannot be attendance only
+   if ((Math.round(document.forms.gradesupload.pcorrect.value)!=Math.round(document.forms.gradesupload.pincorrect.value)) &&
+       (gradingchoice=='attendance')) {
+       newgradingchoice='personnel';
+   }
+// Change grading choice to new one
+   for (i=0; i<document.forms.gradesupload.gradingmechanism.length; i++) {
+      if (document.forms.gradesupload.gradingmechanism[i].value==newgradingchoice) {
+         document.forms.gradesupload.gradingmechanism[i].checked=true;
+      } else {
+         document.forms.gradesupload.gradingmechanism[i].checked=false;
+      }
+   }
+// Remember the old state
+   document.forms.gradesupload.waschecked.value=newgradingchoice;
+}
+</script>
+<form method="post" enctype="multipart/form-data" action="/adm/grades" name="gradesupload">
+<input type="hidden" name="symb" value="$symb" />
+<input type="hidden" name="command" value="processclickerfile" />
+<input type="hidden" name="probTitle" value="$env{'form.probTitle'}" />
+<input type="hidden" name="saveState"  value="$env{'form.saveState'}" />
+<input type="file" name="upfile" size="50" />
+<br /><label>$type: $selectform</label>
+<br /><label>$attendance: <input type="radio" name="gradingmechanism" value="attendance" $checked{'attendance'} onClick="sanitycheck()" /></label>
+<br /><label>$personnel: <input type="radio" name="gradingmechanism" value="personnel" $checked{'personnel'} onClick="sanitycheck()" /></label>
+<br /><label>$specific: <input type="radio" name="gradingmechanism" value="specific" $checked{'specific'} onClick="sanitycheck()" /></label>
+<input type="text" name="specificid" value="$env{'form.specificid'}" size="20" />
+<input type="hidden" name="waschecked" value="$env{'form.gradingmechanism'}" />
+<br /><label>$pcorrect: <input type="text" name="pcorrect" size="4" value="$env{'form.pcorrect'}" onChange="sanitycheck()" /></label>
+<br /><label>$pincorrect: <input type="text" name="pincorrect" size="4" value="$env{'form.pincorrect'}" onChange="sanitycheck()" /></label>
+<br /><input type="button" onClick="javascript:checkUpload(this.form);" value="$upload" />
+</form>
+ENDUPFORM
+    $result.='</td></tr></table>'."\n".
+             '</td></tr></table><br /><br />'."\n";
+    $result.=&show_grading_menu_form($symb);
+    return $result;
+}
+
+sub process_clicker_file {
+    my ($r)=@_;
+    my ($symb)=&get_symb($r);
+    if (!$symb) {return '';}
+
+    my %Saveable_Parameters=&clicker_grading_parameters();
+    &Apache::loncommon::store_course_settings('grades_clicker',
+                                              \%Saveable_Parameters);
+
+    my ($result) = &showResourceInfo($symb,$env{'form.probTitle'});
+    if (($env{'form.gradingmechanism'} eq 'specific') && ($env{'form.specificid'}!~/\w/)) {
+	$result.='<span class="LC_error">'.&mt('You need to specify a clicker ID for the correct answer').'</span>';
+	return $result.&show_grading_menu_form($symb);
+    }
+    my %clicker_ids=&gather_clicker_ids();
+    my %correct_ids;
+    if ($env{'form.gradingmechanism'} eq 'personnel') {
+	%correct_ids=&gather_adv_clicker_ids();
+    }
+    if ($env{'form.gradingmechanism'} eq 'specific') {
+	foreach my $correct_id (split(/[\s\,]/,$env{'form.specificid'})) {;
+	   $correct_id=~tr/a-z/A-Z/;
+	   $correct_id=~s/\s//gs;
+	   $correct_id=~s/^[\#0]+//;
+           $correct_id=~s/[\-\:]//g;
+           if ($correct_id) {
+	      $correct_ids{$correct_id}='specified';
+           }
+        }
+    }
+    if ($env{'form.gradingmechanism'} eq 'attendance') {
+	$result.=&mt('Score based on attendance only');
+    } else {
+	my $number=0;
+	$result.='<p><b>'.&mt('Correctness determined by the following IDs').'</b>';
+	foreach my $id (sort(keys(%correct_ids))) {
+	    $result.='<br /><tt>'.$id.'</tt> - ';
+	    if ($correct_ids{$id} eq 'specified') {
+		$result.=&mt('specified');
+	    } else {
+		my ($uname,$udom)=split(/\:/,$correct_ids{$id});
+		$result.=&Apache::loncommon::plainname($uname,$udom);
+	    }
+	    $number++;
+	}
+        $result.="</p>\n";
+	if ($number==0) {
+	    $result.='<span class="LC_error">'.&mt('No IDs found to determine correct answer').'</span>';
+	    return $result.&show_grading_menu_form($symb);
+	}
+    }
+    if (length($env{'form.upfile'}) < 2) {
+        $result.=&mt('[_1] Error: [_2] The file you attempted to upload, [_3] contained no information. Please check that you entered the correct filename.',
+		     '<span class="LC_error">',
+		     '</span>',
+		     '<span class="LC_filename">'.&HTML::Entities::encode($env{'form.upfile.filename'},'<>&"').'</span>');
+        return $result.&show_grading_menu_form($symb);
+    }
+
+# Were able to get all the info needed, now analyze the file
+
+    $result.=&Apache::loncommon::studentbrowser_javascript();
+    $symb = &Apache::lonenc::check_encrypt($symb);
+    my $heading=&mt('Scanning clicker file');
+    $result.=(<<ENDHEADER);
+<br /><table width="100%" border="0"><tr><td bgcolor="#777777">
+<table width="100%" border="0"><tr bgcolor="#e6ffff"><td>
+<b>$heading</b></td></tr><tr bgcolor=#ffffe6><td>
+<form method="post" action="/adm/grades" name="clickeranalysis">
+<input type="hidden" name="symb" value="$symb" />
+<input type="hidden" name="command" value="assignclickergrades" />
+<input type="hidden" name="probTitle" value="$env{'form.probTitle'}" />
+<input type="hidden" name="saveState"  value="$env{'form.saveState'}" />
+<input type="hidden" name="gradingmechanism" value="$env{'form.gradingmechanism'}" />
+<input type="hidden" name="pcorrect" value="$env{'form.pcorrect'}" />
+<input type="hidden" name="pincorrect" value="$env{'form.pincorrect'}" />
+ENDHEADER
+    my %responses;
+    my @questiontitles;
+    my $errormsg='';
+    my $number=0;
+    if ($env{'form.upfiletype'} eq 'iclicker') {
+	($errormsg,$number)=&iclicker_eval(\@questiontitles,\%responses);
+    }
+    if ($env{'form.upfiletype'} eq 'interwrite') {
+        ($errormsg,$number)=&interwrite_eval(\@questiontitles,\%responses);
+    }
+    $result.='<br />'.&mt('Found [_1] question(s)',$number).'<br />'.
+             '<input type="hidden" name="number" value="'.$number.'" />'.
+             &mt('Awarding [_1] percent for correct and [_2] percent for incorrect responses',
+                 $env{'form.pcorrect'},$env{'form.pincorrect'}).
+             '<br />';
+# Remember Question Titles
+# FIXME: Possibly need delimiter other than ":"
+    for (my $i=0;$i<$number;$i++) {
+        $result.='<input type="hidden" name="question:'.$i.'" value="'.
+                 &HTML::Entities::encode($questiontitles[$i],'"&<>').'" />';
+    }
+    my $correct_count=0;
+    my $student_count=0;
+    my $unknown_count=0;
+# Match answers with usernames
+# FIXME: Possibly need delimiter other than ":"
+    foreach my $id (keys(%responses)) {
+       if ($correct_ids{$id}) {
+          $result.="\n".'<input type="hidden" name="correct:'.$correct_count.':'.$correct_ids{$id}.'" value="'.$responses{$id}.'" />';
+          $correct_count++;
+       } elsif ($clicker_ids{$id}) {
+          $result.="\n".'<input type="hidden" name="student:'.$clicker_ids{$id}.'" value="'.$responses{$id}.'" />';
+          $student_count++;
+       } else {
+          $result.="\n<hr />".&mt('Unregistered Clicker')." <tt>".$id."</tt><br />";
+          $result.="\n".'<input type="hidden" name="unknown:'.$id.'" value="'.$responses{$id}.'" />'.
+                   "\n".&mt("Username").": <input type='text' name='uname".$id."' />&nbsp;".
+                   "\n".&mt("Domain").": ".
+                   &Apache::loncommon::select_dom_form($env{'course.'.$env{'request.course.id'}.'.domain'},'udom'.$id).'&nbsp;'.
+                   &Apache::loncommon::selectstudent_link('clickeranalysis','uname'.$id,'udom'.$id);
+          $unknown_count++;
+       }
+    }
+    $result.='<hr />'.
+             &mt('Found [_1] registered and [_2] unregistered clickers.',$student_count,$unknown_count);
+    if ($env{'form.gradingmechanism'} ne 'attendance') {
+       if ($correct_count==0) {
+          $errormsg.="Found no correct answers answers for grading!";
+       } elsif ($correct_count>1) {
+          $result.='<br /><span class="LC_warning">'.&mt("Found [_1] entries for grading!",$correct_count).'</span>';
+       }
+    }
+    if ($errormsg) {
+       $result.='<br /><span class="LC_error">'.&mt($errormsg).'</span>';
+    } else {
+       $result.='<br /><input type="submit" name="finalize" value="'.&mt('Finalize Grading').'" />';
+    }
+    $result.='</form></td></tr></table>'."\n".
+             '</td></tr></table><br /><br />'."\n";
+    return $result.&show_grading_menu_form($symb);
+}
+
+sub iclicker_eval {
+    my ($questiontitles,$responses)=@_;
+    my $number=0;
+    my $errormsg='';
+    foreach my $line (split(/[\n\r]/,$env{'form.upfile'})) {
+        my %components=&Apache::loncommon::record_sep($line);
+        my @entries=map {$components{$_}} (sort(keys(%components)));
+	if ($entries[0] eq 'Question') {
+	    for (my $i=3;$i<$#entries;$i+=6) {
+		$$questiontitles[$number]=$entries[$i];
+		$number++;
+	    }
+	}
+	if ($entries[0]=~/^\#/) {
+	    my $id=$entries[0];
+	    my @idresponses;
+	    $id=~s/^[\#0]+//;
+	    for (my $i=0;$i<$number;$i++) {
+		my $idx=3+$i*6;
+		push(@idresponses,$entries[$idx]);
+	    }
+	    $$responses{$id}=join(',',@idresponses);
+	}
+    }
+    return ($errormsg,$number);
+}
+
+sub interwrite_eval {
+    my ($questiontitles,$responses)=@_;
+    my $number=0;
+    my $errormsg='';
+    my $skipline=1;
+    my $questionnumber=0;
+    my %idresponses=();
+    foreach my $line (split(/[\n\r]/,$env{'form.upfile'})) {
+        my %components=&Apache::loncommon::record_sep($line);
+        my @entries=map {$components{$_}} (sort(keys(%components)));
+        if ($entries[1] eq 'Time') { $skipline=0; next; }
+        if ($entries[1] eq 'Response') { $skipline=1; }
+        next if $skipline;
+        if ($entries[0]!=$questionnumber) {
+           $questionnumber=$entries[0];
+           $$questiontitles[$number]=&mt('Question [_1]',$questionnumber);
+           $number++;
+        }
+        my $id=$entries[4];
+        $id=~s/^[\#0]+//;
+        $id=~s/^v\d*\://i;
+        $id=~s/[\-\:]//g;
+        $idresponses{$id}[$number]=$entries[6];
+    }
+    foreach my $id (keys %idresponses) {
+       $$responses{$id}=join(',',@{$idresponses{$id}});
+       $$responses{$id}=~s/^\s*\,//;
+    }
+    return ($errormsg,$number);
+}
+
+sub assign_clicker_grades {
+    my ($r)=@_;
+    my ($symb)=&get_symb($r);
+    if (!$symb) {return '';}
+# See which part we are saving to
+    my ($partlist,$handgrade,$responseType) = &response_type($symb);
+# FIXME: This should probably look for the first handgradeable part
+    my $part=$$partlist[0];
+# Start screen output
+    my ($result) = &showResourceInfo($symb,$env{'form.probTitle'});
+
+    my $heading=&mt('Assigning grades based on clicker file');
+    $result.=(<<ENDHEADER);
+<br /><table width="100%" border="0"><tr><td bgcolor="#777777">
+<table width="100%" border="0"><tr bgcolor="#e6ffff"><td>
+<b>$heading</b></td></tr><tr bgcolor=#ffffe6><td>
+ENDHEADER
+# Get correct result
+# FIXME: Possibly need delimiter other than ":"
+    my @correct=();
+    my $gradingmechanism=$env{'form.gradingmechanism'};
+    my $number=$env{'form.number'};
+    if ($gradingmechanism ne 'attendance') {
+       foreach my $key (keys(%env)) {
+          if ($key=~/^form\.correct\:/) {
+             my @input=split(/\,/,$env{$key});
+             for (my $i=0;$i<=$#input;$i++) {
+                 if (($correct[$i]) && ($input[$i]) &&
+                     ($correct[$i] ne $input[$i])) {
+                    $result.='<br /><span class="LC_warning">'.
+                             &mt('More than one correct result given for question "[_1]": [_2] versus [_3].',
+                                 $env{'form.question:'.$i},$correct[$i],$input[$i]).'</span>';
+                 } elsif ($input[$i]) {
+                    $correct[$i]=$input[$i];
+                 }
+             }
+          }
+       }
+       for (my $i=0;$i<$number;$i++) {
+          if (!$correct[$i]) {
+             $result.='<br /><span class="LC_error">'.
+                      &mt('No correct result given for question "[_1]"!',
+                          $env{'form.question:'.$i}).'</span>';
+          }
+       }
+       $result.='<br />'.&mt("Correct answer: [_1]",join(', ',map { ($_?$_:'-') } @correct));
+    }
+# Start grading
+    my $pcorrect=$env{'form.pcorrect'};
+    my $pincorrect=$env{'form.pincorrect'};
+    my $storecount=0;
+    foreach my $key (keys(%env)) {
+       my $user='';
+       if ($key=~/^form\.student\:(.*)$/) {
+          $user=$1;
+       }
+       if ($key=~/^form\.unknown\:(.*)$/) {
+          my $id=$1;
+          if (($env{'form.uname'.$id}) && ($env{'form.udom'.$id})) {
+             $user=$env{'form.uname'.$id}.':'.$env{'form.udom'.$id};
+          }
+       }
+       if ($user) { 
+          my @answer=split(/\,/,$env{$key});
+          my $sum=0;
+          for (my $i=0;$i<$number;$i++) {
+             if ($answer[$i]) {
+                if ($gradingmechanism eq 'attendance') {
+                   $sum+=$pcorrect;
+                } else {
+                   if ($answer[$i] eq $correct[$i]) {
+                      $sum+=$pcorrect;
+                   } else {
+                      $sum+=$pincorrect;
+                   }
+                }
+             }
+          }
+          my $ave=$sum/(100*$number);
+# Store
+          my ($username,$domain)=split(/\:/,$user);
+          my %grades=();
+          $grades{"resource.$part.solved"}='correct_by_override';
+          $grades{"resource.$part.awarded"}=$ave;
+          $grades{"resource.regrader"}="$env{'user.name'}:$env{'user.domain'}";
+          my $returncode=&Apache::lonnet::cstore(\%grades,$symb,
+                                                 $env{'request.course.id'},
+                                                 $domain,$username);
+          if ($returncode ne 'ok') {
+             $result.="<br /><span class=\"LC_error\">Failed to save student $username:$domain. Message when trying to save was ($returncode)</span>";
+          } else {
+             $storecount++;
+          }
+       }
+    }
+# We are done
+    $result.='<br />'.&mt('Successfully stored grades for [_1] student(s).',$storecount).
+             '</td></tr></table>'."\n".
+             '</td></tr></table><br /><br />'."\n";
+    return $result.&show_grading_menu_form($symb);
+}
+
 sub handler {
     my $request=$_[0];
 
@@ -6137,6 +7559,12 @@ sub handler {
 	    $request->print(&editgrades($request));
 	} elsif ($command eq 'verify' && $perm{'vgr'}) {
 	    $request->print(&verifyreceipt($request));
+        } elsif ($command eq 'processclicker' && $perm{'mgr'}) {
+            $request->print(&process_clicker($request));
+        } elsif ($command eq 'processclickerfile' && $perm{'mgr'}) {
+            $request->print(&process_clicker_file($request));
+        } elsif ($command eq 'assignclickergrades' && $perm{'mgr'}) {
+            $request->print(&assign_clicker_grades($request));
 	} elsif ($command eq 'csvform' && $perm{'mgr'}) {
 	    $request->print(&upcsvScores_form($request));
 	} elsif ($command eq 'csvupload' && $perm{'mgr'}) {