#!/usr/bin/perl

# CGI script to facilitate advanced retrieval search for the Textpresso system.
# 
# copyright (c) Hans-Michael Muller & Juancarlos Chan, Pasadena, California, 2002-2004
#

use strict;
use CGI;
use POSIX;

### INITIALIZE GLOBALS ###
### globals
#

# handle to this CGI and own address
my $query = new CGI;
my $absmyself = $query->url(absolute=>1);

# directories of importance
my $databaseroot = "/var/www/html/text/tdb/";
my $indexattspec = $databaseroot . "ind/attspec";
my $indexkey = $databaseroot . "ind/key/";

# cookies
my %generalsettings = $query->cookie('generalsettings');	# general settings

my %displayoptions; 						# display options
if ($query->cookie('displayoptions')) {				# if options in cookie
    %displayoptions = $query->cookie('displayoptions');
} else {							# else use default
    $displayoptions{'Source Type'} = 1;
    $displayoptions{Title} = 1;
    $displayoptions{Abstract} = 1;
    $displayoptions{Author} = 1;
    $displayoptions{Journal} = 1;
    $displayoptions{Year} = 1;
    $displayoptions{Citation} = 1;
    $displayoptions{'Number of matches'} = 1;
    $displayoptions{Select} = 1;  
} # else # if ($query->cookie('displayoptions'))

my %displayvalues;						# display values
if ($query->cookie('displayvalues')) {				# if values in cookie
    %displayvalues = $query->cookie('displayvalues');
} else {							# else use default
    $displayvalues{ResultsPerPage} = 10;
    $displayvalues{SentencesPerMatch} = 10;
} # else # if ($query->cookie('displayvalues'))

my %advretoptions;						# query options
if ($query->cookie('advretoptions')) {				# if values in cookie
    %advretoptions = $query->cookie('advretoptions');
} else {							# else use default
    $advretoptions{NumberOfCategories} = 3;
    $advretoptions{NumberOfKeywords} = 3;
} # else # if ($query->cookie('advretoptions'))

my %lastadvancedquery = $query->cookie('lastadvancedquery'); 	# last query

  # other globals of interest
my %targetdirectories = (Title => 'tit/', Abstract => 'abs/', Paper => 'art/');
my %searchtargets = (Title => 0, Abstract => 0, Paper => 0);	# This hash defines the search targets
my %labels = ReadElements("/var/www/html/text/textpresso.dtd");	# read in elements that can be searched for.
my @elementkeys = sort keys % labels; 				# list of elements, abbreviated. 

my @attributes = ReadAttributes("/var/www/html/text/textpresso.dtd");
my %attnmecde = ();
for (my $j = 0; $j <@attributes; $j++) {			# separate code from label
    (my $cde, my $value) = split(/-/,$attributes[$j]);
    my $label = "";
    if ($value =~ /(\w+)\s+\((.+)\)/) { $label = $2 . ": " . $1; }
    $attnmecde { $label } = $cde;
    $attributes[$j] = $label;
} # for (my $j = 0; $j <@attributes; $j++) 

  # format of result: $searchresult{ searchtarget }{ file }{ sentence } = no. of occ.;
my %searchresults = ();
my $lastsearchfilename = $query->param('lsfilename'); 
my $displaypage = 1;
my @displayedkeys = $query->param('dispkeys');
my @expandedabs = $query->param('expandedabs');
my $totalpages = $query->param('totalpages');
my $execcommand = "";

my $catrows;
if (defined($query->param('catrows'))) { $catrows = $query->param('catrows'); } 
  else { $catrows = $advretoptions{NumberOfCategories}; }

my $keyrows;
if (defined($query->param('keyrows'))) { $keyrows = $query->param('keyrows'); } 
  else { $keyrows = $advretoptions{NumberOfKeywords}; }

my $firstpage = 1;			# default is firstpage unless already displayed via &display();

my $clearquery = 0;						# flag to $query->delete_all();

my @specchoices = ( 'named', 'unnamed', 'all' );		# possible specialization choices

#
### end globals;
### INITIALIZE GLOBALS ###




### PROCESS ###
### process form
#

my $abstractkeyhit = 0;
foreach my $key (@displayedkeys) {
    if ($query->param("expanded$key")) {
	push @expandedabs, $key;
	$abstractkeyhit = 1;
    }
    if ($query->param("collapse$key")) {
	for (my $i = 0; $i < @expandedabs; $i++) { delete $expandedabs[$i] if ($expandedabs[$i] eq $key) }
	$abstractkeyhit = 1;
    }
} # foreach my $key (@displayedkeys)


if ($query->param('querytable')) {
  $catrows = $query->param('catrows'); $keyrows = $query->param('keyrows');
  &display();
} # if ($query->param('querytable'))
    
if ($query->param('lastquery')) {
  &processLastquery();
  my $lsqcookie = &setlsqCookie();
  &PrintHeader($query, $lsqcookie);
  &displayMainForm();
  &overrideCatAttCookies();		# get cookie values to override catatt selections
  &displayOutput();
  &passHidden();
  &closeForm();
  $firstpage = 0;
} # if ($query->param('lastquery'))

if ($query->param('clearquery')) {
  $query->delete_all(); $clearquery = 1;
  &display();
}

if ($query->param('search')) {
  my $lsqcookie = &setlsqCookie();
  &PrintHeader($query, $lsqcookie);
  &displayMainForm();
  &processSearch();
#   &overrideCatAttCookies();		# get cookie values to override catatt selections
#   foreach my $key (sort keys %lastadvancedquery) { print STDERR "SEARCH $key\t$lastadvancedquery{$key}\n"; }
  print "<SCRIPT LANGUAGE=\"JavaScript1.2\">load_catcat_and_catatt();</SCRIPT>\n";
  &displayOutput();
  &passHidden();
  &closeForm();
  $firstpage = 0;
} # if ($query->param('search'))


if (($query->param('lastsearch')) || ($query->param('emailresults'))
    || ($query->param('previouspage')) || ($query->param('nextpage'))
    || $abstractkeyhit) {
  &processVarious();
  &display();
} 

if ($firstpage) { &display(); }		# if firstpage, display it

if ($query->param('emailresults')) {	# deal with emailing stuff
    if ($query->param('recipient') ne "") {
	my $subject = "Your request from Texpresso -  Advanced Query ";
	my $recipient = $query->param('recipient');
	my $matchsentences = -1; # negative number indicates no sentences incl.
	if ($query->param('emailmatches')) {
	    $matchsentences = $displayvalues{SentencesPerMatch};
	}
	my $options = "";
	foreach my $key (keys % displayoptions) {
	    $options .= "\"" . $key . "\" " if ($displayoptions{$key});
	}
	my $comment = "Y O U R   Q U E R Y \n";
	$comment .=   "------------------- \n";
	$comment .= "CATEGORIES:\n" if ($catrows > 0);	
	for (my $i = 0; $i < $catrows; $i++) {
	    my $catvarname = "catcat" . $i;
	    my $category = $query->param($catvarname);
	    my $boolvarname = "catbool" . $i;
	    my $bool = $query->param($boolvarname);
	    my $attvarname = "catatt" . $i;
	    my @att = $query->param($attvarname);
	    my $specvarname = "catspec" . $i;
	    my $specification = $query->param($specvarname);
	    my $compvarname = "catcomp" . $i;
	    my $comparison = $query->param($compvarname);
	    my $numvarname = "catnum" . $i;
	    my $number = $query->param($numvarname);
	    if ($category ne "") {
		$comment .= $labels{$category} . "( - ";
		$comment .= "Boolean operation: " . $bool . " - " if (defined($bool));
		if (@att) {
		    $comment .= "Attributes: ";
		    my $attstring = "";
		    foreach my $attribute (@att) {
			$attribute =~ s/\,/ /g;
			$attstring .= $attribute . " & ";
		    }
		    chop ($attstring); chop ($attstring); chop ($attstring);
		    $comment .= $attstring . " - ";
		}
		$comment .= "Specification: " . $specification . " - " if (defined($specification));
		$comment .= "Comparison: " . $comparison . " - " if (defined($comparison));
		$comment .= "Number of matches: " . $number . " - " if (defined($number));
		$comment .= ")\n";
	    }
	}
	$comment .= "KEYWORDS:\n" if ($keyrows > 0);
	for (my $i = 0; $i < $keyrows; $i++) {
	    my $keyvarname = "keykey" . $i;
	    my $keyword = $query->param($keyvarname);
	    my $exactvarname = "keyexact" . $i;
	    my $boolvarname = "keybool" . $i;
	    my $bool = $query->param($boolvarname);
	    my $compvarname = "keycomp" . $i;
	    my $comparison = $query->param($compvarname);
	    my $numvarname = "keynum" . $i;
	    my $number = $query->param($numvarname);
	    if (($keyword ne "") && (!$query->param($exactvarname))) {
		$keyword .= "*";
	    }
	    if ($keyword ne "") {
		$comment .= $keyword ."( - ";
		$comment .= "Boolean operation: " . $bool . " - " if (defined($bool));
		$comment .= "Comparison: " . $comparison . " - " if (defined($comparison));
		$comment .= "Number of matches: ".  $number . " - " if (defined($number));
		$comment .=")\n";
	    }
	}
	$execcommand = "echo \'nice $databaseroot/scr/mailresults.pl $recipient \"$subject\" \"$comment\" $lastsearchfilename $matchsentences $options\' \| at now";	
    }
} # if ($query->param('emailresults'))

### exec system command 'offline'
#

system($execcommand);			# mail results if so chosen

#
###



### SUBROUTINES ###

sub processLastquery {
    $catrows = $lastadvancedquery{catrows};
    $keyrows = $lastadvancedquery{keyrows};
    for (my $i = 0; $i < $catrows; $i++) {
	my $varname = "catbool" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "catcat" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "catspec" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "catcomp" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "catnum" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
    }
    for (my $i = 0; $i < $keyrows; $i++) {
	my $varname = "keybool" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "keykey" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "keyexact" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "keycomp" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
	$varname = "keynum" . $i;
	$query->param(-name => $varname, -value => $lastadvancedquery{$varname});
    }
} # sub processLastquery

sub processSearch {
    print $query->hr;
    print $query->b($query->font({-face => 'verdana, helvetica', -size => '2', -color => 'green'}, 'Searching..'));
    %searchresults = ();
    my $mode = $query->param('searchmode');
    if ($query->param('searchtargets')) {
        foreach my $key (keys % searchtargets) { $searchtargets{$key} =  0}
        foreach my $key ($query->param('searchtargets')) {
	    $searchtargets{$key} = 1;
        }
    } # if ($query->param('searchtargets'))
    if ($searchtargets{Paper} || $searchtargets{Abstract} || $searchtargets{Title}) {
	for (my $i = 0; $i < $catrows; $i++) {
	    my $catvarname = "catcat" . $i;
	    my $category = $query->param($catvarname);
	    if ($category ne "") {
		my $attvarname = "catatt" . $i;
		my @attributes = $query->param($attvarname);
		my $specvarname = "catspec" . $i;
		my $specification = $query->param($specvarname);
		my $numcompvarname = "catcomp" . $i;
		my $comparison = $query->param($numcompvarname);
		my $nummatchvarname = "catnum" . $i;
		my $numberofmatches = $query->param($nummatchvarname);
		if ($i > 0) {
		    my %auxlist = GetListFromCategories($indexattspec, $databaseroot, 
							\%targetdirectories, $category,
							\%searchtargets, \%attnmecde, \@attributes,
							$specification, $comparison, $numberofmatches);
		    my $boolvarname = "catbool" . $i;
		    my $bool = $query->param($boolvarname);
		    if ($bool eq "and") {
			%searchresults = AndLists(\%searchresults, \%auxlist, $mode);
		    } elsif ($bool eq "or") {
			%searchresults = OrLists(\%searchresults, \%auxlist);
		    } elsif ($bool eq "not") {
			%searchresults = ListAAndNotListB(\%searchresults, \%auxlist, $mode);
		    }
		} else {
		    %searchresults = GetListFromCategories($indexattspec, $databaseroot, 
							   \%targetdirectories, $category,
							   \%searchtargets, \%attnmecde, \@attributes,
							   $specification, $comparison, $numberofmatches);
		}
	    }
	}
    }
    for (my $i = 0; $i < $keyrows; $i++) {
	my $keyvarname = "keykey" . $i;
	my $keyword = $query->param($keyvarname);
	if ($keyword ne "") {
	    my $exactvarname = "keyexact" . $i;
	    my $numcompvarname = "keycomp" . $i;
	    my $comparison = $query->param($numcompvarname);
	    my $nummatchvarname = "keynum" . $i;
	    my $numberofmatches = $query->param($nummatchvarname);
	    if (($keyword ne "") && (!$query->param($exactvarname))) { 
		$keyword .= "*"; 
	    }
	    unless(($catrows < 1) && ($i < 1)) {
		my %auxlist = GetListFromKeyword($indexkey, \%targetdirectories,
						 $keyword, \%searchtargets,
						 $comparison, $numberofmatches);
		my $boolvarname = "keybool" . $i;
		my $bool = $query->param($boolvarname);
		if ($bool eq "and") {
		    %searchresults = AndLists(\%searchresults, \%auxlist, $mode);
		} elsif ($bool eq "or") {
		    %searchresults = OrLists(\%searchresults, \%auxlist);
		} elsif ($bool eq "not") {
		    %searchresults = ListAAndNotListB(\%searchresults, \%auxlist, $mode);
		}
	    } else {
		%searchresults = GetListFromKeyword($indexkey, \%targetdirectories,
						    $keyword, \%searchtargets,
						    $comparison, $numberofmatches);
	    }
	}
    }
    my $tmp1filename;
    do { $tmp1filename = tmpnam() } until (!-e "$databaseroot/$tmp1filename");
    open (OUT1,">$databaseroot/$tmp1filename");
    for (my $i = 0; $i < $catrows; $i++) {
	my $catvarname = "catcat" . $i;
	my $category = $query->param($catvarname);
	my $boolvarname = "catbool" . $i;
	my $bool = $query->param($boolvarname);
	my $attvarname = "catatt" . $i;
	my @att = $query->param($attvarname);
	my $specvarname = "catspec" . $i;
	my $specification = $query->param($specvarname);
	my $compvarname = "catcomp" . $i;
	my $comparison = $query->param($compvarname);
	my $numvarname = "catnum" . $i;
	my $number = $query->param($numvarname);
	if ($category ne "") {
	    print OUT1 $category;
	    print OUT1 "# - "; # when category is specified, comment is always required
	    print OUT1 "Boolean operation: ", $bool, " - " if (defined($bool));
	    if (@att) {
		print OUT1 "Attributes: ";
		my $attstring = "";
		foreach my $attribute (@att) {
		    $attribute =~ s/\,/ /g;
		    $attstring .= $attribute . " & ";
		}
		chop ($attstring); chop ($attstring); chop ($attstring);
		print OUT1 $attstring, " - ";
	    }
	    print OUT1 "Specification: ", $specification, " - " if (defined($specification));
	    print OUT1 "Comparison: ", $comparison, " - " if (defined($comparison));
	    print OUT1 "Number of matches: ", $number, " - " if (defined($number));
	    print OUT1 ",";
	}
    }
    print OUT1 "\n";
    for (my $i = 0; $i < $keyrows; $i++) {
	my $keyvarname = "keykey" . $i;
	my $keyword = $query->param($keyvarname);
	my $exactvarname = "keyexact" . $i;
	my $boolvarname = "keybool" . $i;
	my $bool = $query->param($boolvarname);
	my $compvarname = "keycomp" . $i;
	my $comparison = $query->param($compvarname);
	my $numvarname = "keynum" . $i;
	my $number = $query->param($numvarname);
	if (($keyword ne "") && (!$query->param($exactvarname))) {
	    $keyword .= "*";
	}
	if ($keyword ne "") {
	    print OUT1 $keyword;
	    print OUT1 "# - "; # when keyword is specified, comment is always required
	    print OUT1 "Boolean operation: ", $bool, " - " if (defined($bool));
	    print OUT1 "Comparison: ", $comparison, " - " if (defined($comparison));
	    print OUT1 "Number of matches: ", $number, " - " if (defined($number));
	    print OUT1 ",";
	}
    }
    print OUT1 "\n";
    foreach my $target (keys % searchresults) {
	foreach my $key (keys %{ $searchresults{$target} }) {
	    print OUT1 $target . "," . $key . ",";
	    foreach my $sentence (keys % { $searchresults{$target}{$key} }) {
		print OUT1 $sentence . ",";
	    }
	    print OUT1 "\n";
	}
    }
    close (OUT1);

    $lastsearchfilename = $tmp1filename;
    $query->param(-name => 'lsfilename', -value => $lastsearchfilename);
    $query->param(-name => 'page', -value => 1);
    print $query->b($query->font({-face => 'verdana, helvetica', -size => '2', -color => 'green'}, '..done.'));
} # sub processSearch

sub processVarious {
    %searchresults = ();
    if ($lastsearchfilename) {
	open (IN, "$databaseroot/$lastsearchfilename");
	my $junk = <IN>;
	$junk = <IN>; # first two lines (query) are of no interest here.
	while (my $line = <IN>) {
	    chomp ($line);
	    my @items = split (/\,/, $line);
	    my $target = shift(@items);
	    my $key = shift(@items);
	    while (my $sentence = shift(@items)) {
		$searchresults{$target}{$key}{$sentence} = 1;
	    }
	}
	close (IN);
    }

    if ($query->param('previouspage')) {
	if ($query->param('page') == 1) {
	    $displaypage = 1;
	    $query->param(-name => 'page', -value => 1);
	} else {
	    $displaypage = $query->param('page') - 1;
	    $query->param(-name => 'page', -value => $displaypage);
	}
    } elsif ($query->param('nextpage')) {
	$displaypage = $query->param('page') + 1;
	$displaypage = ($displaypage > $totalpages) ? $totalpages : $displaypage;
	$query->param(-name => 'page', -value => $displaypage);
    } else {
	$displaypage = $query->param('page');
    }
} # sub processVarious
    

#
### PROCESS ###




### DISPLAY ###

sub display {
  my $lsqcookie = &setlsqCookie();
  &PrintHeader($query, $lsqcookie);
  &displayMainForm();
  &displayOutput();
  &passHidden();
  &closeForm();
  $firstpage = 0;
} # sub display


### Set cookie (last advanced query) to current query, if current query is not empty
sub setlsqCookie {			# if search and data, save query in cookie
  my $realquery = 0;
  for (my $i = 0; $i < $catrows; $i++) {
      my $varname = "catcat" . $i;
      if ($query->param($varname) ne "") { $realquery = 1 };
  }
  for (my $i = 0; $i < $keyrows; $i++) {
      my $varname = "keykey" . $i;
      if ($query->param($varname)) { $realquery = 1 };
  }
  
  my $lsqcookie;			# initialize the cookie
  if ($realquery) {
    %lastadvancedquery = ();
      $lastadvancedquery{catrows} = $catrows;
      $lastadvancedquery{keyrows} = $keyrows;
      for (my $i = 0; $i < $catrows; $i++) {
	  my $varname = "catbool" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "catcat" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "catatt" . $i;
          my @catatt = $query->param($varname);			# get the catatt values
          my $catattlen = $varname . 'len';			# set length variable
          $lastadvancedquery{$catattlen} = scalar(@catatt);	# pass length to hash
          for (my $j = 0; $j < scalar(@catatt); $j++) {		# for each value
            my $attattarrval = $varname . 'val' . $j;		# set variable name
            $lastadvancedquery{$attattarrval} = $catatt[$j];	# pass value to hash
          }
	  $varname = "catspec" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "catcomp" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "catnum" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
      }
      for (my $i = 0; $i < $keyrows; $i++) {
	  my $varname = "keybool" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "keykey" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "keyexact" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "keycomp" . $i;
	  $lastadvancedquery{$varname} = $query->param($varname);
	  $varname = "keynum" . $i;
      }
      if ($query->param('search')) {	# if search, set cookie
        $lsqcookie = $query->cookie(-name => 'lastadvancedquery', 
			             -value => \%lastadvancedquery,
			             -path => '/cgi-bin/',
			             -expires => '+730d');
      } # if ($query->param('search') 
  } # if ($realquery)
  return $lsqcookie;
} # setlsqCookie






### FORM ###
### start form
#

sub displayMainForm {

  print $query->start_form(-method => 'POST', -name => 'form1', -action => $absmyself);
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		   'In the advanced retrieval, searches of categories or keywords ');
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		   'at any level of sophistication can be undertaken. ');
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		   'Specify boolean operators, attributes, number of occurrences, etc.. In a keyword row, specify only one keyword per row. ');
  print $query->start_b;
  print $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'darkred'},
		   'This interface requires javascript. It does not work well with Netscape 4.79 or earlier versions.');
  print $query->end_b;
  print $query->p;

  my @tablecontent = ();
  my @columns = ();
  push @columns, "boolean<br>operation";
  push @columns, "category<br>or keyword";
  push @columns, "category or<br>match attributes";
  push @columns, "specification" if ($catrows > 0);
  push @columns, "numerical<br>comparison<br>of matches";
  push @columns, "number<br>of matches";

  push @tablecontent , $query->th([@columns]);

  for (my $i = 0; $i < $catrows; $i++) {
    @columns = ();
    my $varname = "catbool" . $i;
    if ($i > 0) {
	push @columns, $query->popup_menu(-name => $varname,
				      -values =>["and", "or", "not"]);
    } else {
	push @columns, $query->font({-color => 'darkred'}, 'required<br>field');
    }
    $varname = "catcat" . $i;
    push @columns, $query->popup_menu(-name => $varname, 
				      -values => [@elementkeys], 
				      -onChange => 'javascript:checkifselected()',
				      -labels => \%labels); 
    $varname = "catatt" . $i;
    push @columns, $query->scrolling_list(-name => $varname, 
					  -values => [ 'Please select a category or keyword.' ],
					  -size => 5, -multiple=> 'true');
    $varname = "catspec". $i;
    push @columns, $query->popup_menu(-name => $varname, 
				      -values => [ 'n/a' ],
				      -size => 3);
    $varname = "catcomp" . $i;
    push @columns, $query->popup_menu(-name => $varname,
				      -values => ['less than', 'greater than',
						  'equal to'],
				      -default => 'greater than');
    $varname = "catnum" . $i;
    push @columns, $query->popup_menu(-name => $varname,
				      -values => [0,1,2,3,4,5,6,7,8,9,10],
				      -default => 0);

    push @tablecontent, $query->td([@columns]);
  } # for (my $i = 0; $i < $catrows; $i++)
  for (my $i = 0; $i < $keyrows; $i++ ) {
    @columns = ();
    my $varname = "keybool" . $i;
    unless(($catrows < 1) && ($i < 1)) {
	push @columns, $query->popup_menu(-name => $varname,
					  -values =>["and", "or", "not"]);
    } else {
	push @columns, $query->font({-color => 'darkred'}, 'required<br>field');
    }
    $varname = "keykey" . $i;
    push @columns, $query->textfield(-name => $varname,
				     -size => 20,
				     -maxlength => 255);
    $varname = "keyexact" . $i;
    push @columns, $query->checkbox(-name => $varname,
				    -label => 'Exact match'); 
    push @columns, "" if ($catrows > 0); # specification doesn't make sense for keywords
    $varname = "keycomp" . $i;
    push @columns, $query->popup_menu(-name => $varname,
				      -values => ['less than', 'greater than',
						  'equal to'],
				      -default => 'greater than');
    $varname = "keynum" . $i;
    push @columns, $query->popup_menu(-name => $varname,
				      -values => [0,1,2,3,4,5,6,7,8,9,10],
				      -default => 0);

    push @tablecontent, $query->td([@columns]);
  } # for (my $i = 0; $i < $keyrows; $i++ )

  print $query->table({-border => '1', -cellpadding => '4',
		       -cellspacing => '1'},
		      $query->caption($query->b("Q U E R Y")),
		      $query->Tr([@tablecontent]));

  print $query->p;
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		   'These criteria should be met in a ');
  my %locallabel;
  $locallabel{sentence} = " sentence";
  $locallabel{publication} = " publication";
  print $query->radio_group(-name => 'searchmode',
			    -linebreak => 0,
			    -value => ['sentence', 'publication'],
			    -default => 'sentence',
			    -labels => \%locallabel);
  print $query->br;
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		     ' and searched in ');
  my @defaults = ("Abstract", "Paper");
  foreach my $key (sort keys % searchtargets) {
    if ($searchtargets{$key}) { push @defaults, $key}
  }
  my %locallabel2;
  foreach my $key (keys % searchtargets) {
      if ($key eq "Paper") {
	  $locallabel2{$key} = " Full Text";
      } else {
	  $locallabel2{$key} = " " . $key;
      }
  }
  print $query->checkbox_group(-name=>'searchtargets',
			       -value => [sort keys % searchtargets],
			       -defaults => [sort @defaults],
			       -linebreak => 'false',
			       -rows => 1,
			       -labels => \%locallabel2);
  print $query->p;
  print $query->submit(-name => 'search', -value => 'Search!');
  print $query->font("&nbsp;");
  print $query->submit(-name => 'lastquery', -value => 'Load last query!');
  print $query->font("&nbsp;");
  print $query->submit(-name => 'clearquery', -value => 'Clear last query!');
  print $query->font("&nbsp;");
  print $query->button(-value => 'Undo current changes!', -onClick => 'javascript:load_catcat_and_catatt()');

  print $query->p;
  print $query->submit(-name => 'querytable', -value => 'Reproduce query table');
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		     ' with ');
  print $query->popup_menu(-name => 'catrows',
			   -values => [0,1,2,3,4,5,6,7,8,9,10],
			   -default => $catrows);
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		   ' category row(s) and ');
  print $query->popup_menu(-name => 'keyrows',
			   -values => [0,1,2,3,4,5,6,7,8,9,10],
			   -default => $keyrows);
  print $query->font({-face => 'verdana, helvetica', -size => '2'},
		     ' keyword row(s).');


  my ($menu, %menuhash) = &readDtd();		# read dtd into menu variable to pass to javascript
						# and menu hash to deal with searched values


  my $menu_catrow_forjavascript = 'var catrowmenu = new Array();'. "\n";
  my $menu_catatt_forjavascript = 'var catattmenu = new Array();'. "\n";
  my $menu_catspec_forjavascript = 'var catspecmenu = new Array();'. "\n";
  if ($catrows > 0) {
    for (my $i = 0; $i < $catrows; $i++) {		# for each of the catrows
      my $catname = 'none';				# init name of catcat
      my $catindex = 0;					# init index of catcat
      my @catatt = ();					# init array of attributes
      my @catspec = ();					# init array of specifications
      my @selected_att_index = ();			# array or selected catatt indices
      my @selected_spec_index = ();			# array or selected catspec indices

      my @catrow = ();

      my ($oop, $catcat) = &getHtmlVar($query, "catcat$i");
      if ($catcat) { 					# if there was a value
        @catatt = $query->param("catatt$i");		# get the catatt values
        if ($menuhash{$catcat}{name}) { 		# if catcat has a name
          $catname = $menuhash{$catcat}{name};		# pass the name
        }
        if ($menuhash{$catcat}{index}) { 		# if catcat has an index
          $catindex = $menuhash{$catcat}{index};	# pass the index
        }
        foreach my $catatt (@catatt) {			# for each of the catatt values from form
          for (my $j = 0; $j < scalar(@{ $menuhash{$catcat}{vals} }); $j++) {
							# for each possible value from menuhash
            if ($catatt eq $menuhash{$catcat}{vals}[$j]) { 	# if they match
              push @selected_att_index, $j;		# add index to array for javascript
            }
          } # for (my $j = 0; $j < scalar(@{ $menuhash{$catcat}{vals} }); $j++)
        } # foreach my $catatt (@catatt) 
        @catspec = $query->param("catspec$i");		# get the catspec values
        foreach my $catspec (@catspec) {		# for each of the catspec values from form
          for (my $j = 0; $j < scalar(@specchoices); $j++) {
							# for each possible value from menuhash
            if ($catspec eq $specchoices[$j]) { 		# if they match
              push @selected_spec_index, $j;		# add index to array for javascript
            }
          } # for (my $j = 0; $j < scalar(@specchoices); $j++)
        } # foreach my $catspec (@catspec) 
      } # if ($catcat)
      push @catrow, $catindex;
      push @catrow, $catname;
      push @catrow, $catcat;
  
      my $catrow = join"', '", @catrow;
      $menu_catrow_forjavascript .= 'var menu' . $i . ' = new Array(\'' .  $catrow . '\');' . "\n";
      $menu_catrow_forjavascript .= 'catrowmenu[' . $i . '] = menu' . $i . ";\n";
  
        # compose array of catatt selected indices to pass to javascript from search results
      my $selected_att_index = join"', '", @selected_att_index;
      $menu_catatt_forjavascript .= 'var attmenu' . $i . ' = new Array(\'' .  $selected_att_index . '\');' . "\n";
      $menu_catatt_forjavascript .= 'catattmenu[' . $i . '] = attmenu' . $i . ";\n";

      my $selected_spec_index = join"', '", @selected_spec_index;
      $menu_catspec_forjavascript .= 'var specmenu' . $i . ' = new Array(\'' .  $selected_spec_index . '\');' . "\n";
      $menu_catspec_forjavascript .= 'catspecmenu[' . $i . '] = specmenu' . $i . ";\n";
  
    } # for (my $i = 0; $i < $catrows; $i++) 

    print <<"EndOfText";
  <script language="JavaScript1.1">
    function load_catcat_and_catatt() {				// reset form and load catcat and catatt values
      document.form1.reset();					// reset form before doing stuff

      $menu_catrow_forjavascript				// get menu catrow from perl
      catrows = $catrows;
      $menu_catatt_forjavascript				// get menu catatt from perl
      $menu_catspec_forjavascript				// get menu catspec from perl
      $menu							// get menu from perl

      for (row = 0; row < catrows; row++) {
        // reset catrow form values according to values read by perl
        catindex = catrowmenu[row][0];
        if (catindex) { 
          catname = catrowmenu[row][1];
          catcat = catrowmenu[row][2];
          len = eval("document.form1.catcat"+row+".options.length");	// get length of catcat
          eval("document.form1.catcat"+row+".options[len] = new Option(catname, catcat);" );
              // create last option of groupN1 to be like the selected option
          eval("document.form1.catcat"+row+".options[len].selected = true;");
  
          if (catindex > 0) {				// if a catcat was chosen.  if it wasn't, then menu will break
							// because the catindex doesn't have a value
            if (menu[catindex][0] == '') { 				// if the catatt menu is empty (first value is blank)
              for (z = eval("document.form1.catatt"+row+".options.length"); z>=1; z--) {
                eval("document.form1.catatt"+row+".options[z] = null;");	// set catatt to empty
              }
              eval("document.form1.catatt"+row+".options[0] = new Option('This category has no attributes', '');" );	
              eval("document.form1.catatt"+row+".disabled=true");// reset row's catatt as enabled	
            } else {
              eval("document.form1.catatt"+row+".disabled=false");	// reset row's catatt as enabled	
              for (indC2=0; indC2<menu[catindex].length; indC2++) {	// reset all options in group N2
      							      // indC2 is the index of Column 2
                eval("document.form1.catatt"+row+".options[indC2] = new Option(menu[catindex][indC2], menu[catindex][indC2]);" );
              }
              if ( catattmenu[row][0] != '' ) {		// if any indices were selected (first value is not blank)
                for (indSel = 0; indSel < catattmenu[row].length; indSel++) {
                  eval("document.form1.catatt"+row+".options[catattmenu[row][indSel]].selected = true;");
                }
              } // if ( catattmenu[row][0] != '' )
            } // else if (menu[catindex][0] == '') 
            if (menuspec[catindex][0] == '') { 				// if the catspec menuspec is empty (first value is blank)
              for (z = eval("document.form1.catspec"+row+".options.length"); z>=1; z--) {
                eval("document.form1.catspec"+row+".options[z] = null;");	// set catspec to empty
              }
              eval("document.form1.catspec"+row+".options[0] = new Option('n/a', '');" );	
              eval("document.form1.catspec"+row+".disabled=true");	// reset row's catspec as enabled	
            } else {
              eval("document.form1.catspec"+row+".disabled=false");	// reset row's catspec as enabled	
              for (indC2=0; indC2<menuspec[catindex].length; indC2++) {	// reset all options in group N2
      							      // indC2 is the index of Column 2
                eval("document.form1.catspec"+row+".options[indC2] = new Option(menuspec[catindex][indC2], menuspec[catindex][indC2]);" );
              }
              for (indSel = 0; indSel < catspecmenu[row].length; indSel++) {
                eval("document.form1.catspec"+row+".options[catspecmenu[row][indSel]].selected = true;");
              }
            }
          } else { // if (catindex > 0)			// if there was no catcat chosen, reset catatt to original
          						// if a catcat was chosen.  if it wasn't, then menu will break
            for (z = eval("document.form1.catatt"+row+".options.length"); z>=1; z--) {
              eval("document.form1.catatt"+row+".options[z] = null;"); 			// set catatt to empty
            }
            eval("document.form1.catatt"+row+".options[0] = new Option('Please select a category or keyword', '');" );	
            eval("document.form1.catatt"+row+".disabled=true");	// reset row's catatt as enabled	
            for (z = eval("document.form1.catspec"+row+".options.length"); z>=1; z--) {
              eval("document.form1.catspec"+row+".options[z] = null;"); 			// set catspec to empty
            }
            eval("document.form1.catspec"+row+".options[0] = new Option('n/a', '');" );	
            eval("document.form1.catspec"+row+".disabled=true");	// reset row's catspec as enabled	
          } // else // if (catindex > 0)
        } // if (catindex)
      } // for (row = 0; row < catrows; row++)
    } // function load_catcat_and_catatt()
  </script>
EndOfText

  } # if ($catrows > 0)
  
  print <<"EndOfText";
    <SCRIPT LANGUAGE="JavaScript1.2">

    $menu					// pass dtd menu to javascript

    function checkifselected() {
//      eval("document.form1.keykey1.value += 'Q';"); // test

      for (row = 0; row<$catrows; row++) {			// for each of the rows
        flagcatcat = 0;						// has anything been selected in row's catcat ?
        for (k=0; k<eval("document.form1.catcat"+row+".options.length"); k++) {		// check values in group N1, k is index
          if ( eval("document.form1.catcat"+row+".options[k].selected") == true ) {	// if something is chosen
            flagcatcat += k;					// flag something selected in row's catcat
          } // if (document.form1.group01.options[k].selected == true) 
        } // for (k=0; k<eval("document.form1.group"+row+"1.options.length"); k++)
        if (flagcatcat == 0) {					// if nothing selected in catcat
          eval("document.form1.catatt"+row+".disabled=true");	// initialize row's catatt as disabled	
          eval("document.form1.catspec"+row+".disabled=true");	// initialize row's catspec as disabled	
        }
    
        for (indC1=1; indC1<menu.length; indC1++) {		// for each of the action options in group N1
								// indC1 is the index of Column 1
          var flag_selected = 'no';
          if ( eval("document.form1.catcat"+row+".options[indC1].selected") == true ) {	// if selected, do stuff
            flag_selected = 'yes';
            for (z = eval("document.form1.catatt"+row+".options.length"); z>=1; z--) {
              eval("document.form1.catatt"+row+".options[z] = null;"); 			// set catatt to empty
            }
            eval("document.form1.catatt"+row+".disabled=false");	// if catcat selected, enable catatt
            for (z = eval("document.form1.catspec"+row+".options.length"); z>=1; z--) {
              eval("document.form1.catspec"+row+".options[z] = null;");			// set catspec to empty
            }
            eval("document.form1.catspec"+row+".disabled=false");	// if catcat selected, enable catspec
    
            if (menu[indC1][0] == '') { 				// if the catatt menu is empty (first value is blank)
              eval("document.form1.catatt"+row+".options[0] = new Option('This category has no attributes', '');" );	
									// set option to say so
              eval("document.form1.catatt"+row+".disabled=true");	// set row's catatt as disabled	
            } else {
              for (indC2=0; indC2<menu[indC1].length; indC2++) {	// reset all options in group N2
				      // indC2 is the index of Column 2
                eval("document.form1.catatt"+row+".options[indC2] = new Option(menu[indC1][indC2], menu[indC1][indC2]);" );
                  // set options of groupN2 from the menu array, move index of options up by one
              }
            }
            if (menuspec[indC1][0] == '') { 				// if the catspec menu is empty (first value is blank)
              eval("document.form1.catspec"+row+".options[0] = new Option('n/a', '');" );	// set option to say so
              eval("document.form1.catspec"+row+".disabled=true");	// set row's catspec as disabled	
            } else {
              for (indC2=0; indC2<menuspec[indC1].length; indC2++) {	// reset all options for catspec
                eval("document.form1.catspec"+row+".options[indC2] = new Option(menuspec[indC1][indC2], menuspec[indC1][indC2]);" ); }
              eval("document.form1.catspec"+row+".options[2].selected = true;");
            } 
            eval("document.form1.catcat"+row+".options[0] = new Option('none', 'none');" );
    
            for (z = eval("document.form1.catcat"+row+".options.length"); z>=1; z--) {
              eval("document.form1.catcat"+row+".options[z] = null;");	// set catcat to empty
            }
            for (org=0; org<orig_menu_name.length; org++) {		// reset menu options for group N1
              eval("document.form1.catcat"+row+".options[org] = new Option(orig_menu_name[org], orig_menu_val[org]);" );
            } // for (org=0; org<orig_menu_name.length; org++)
    
            len = eval("document.form1.catcat"+row+".options.length");	// get length of catcat
            eval("document.form1.catcat"+row+".options[len] = new Option(orig_menu_name[indC1], orig_menu_val[indC1]);" );
              // create last option of groupN1 to be like the selected option
            eval("document.form1.catcat"+row+".options[len].selected = true;");
              // set group N1 to have the last option selected 
	      // (can't be the selected or it will loop, can't be 0 because it will grey out)
    
          } // if ( eval("document.form1.catcat"+row+".options[indC1].selected") == true )
        } // for (indC1=1; indC1<menu.length; indC1++)
      } // for (row = 0; row<$catrows; row++)
    } // function checkifselected 
    
    checkifselected();					// initialize

    function shake_xy(n) {
      if (self.moveBy) {
        for (i = 10; i > 0; i--) {
          for (j = n; j > 0; j--) {
            self.moveBy(0,i);
            self.moveBy(i,0);
            self.moveBy(0,-i);
            self.moveBy(-i,0);
          }
        }
      }
    }
    </SCRIPT>
EndOfText

} # sub displayMainForm

#
### FORM ###


### OUTPUT ###
### output goes here
#

sub displayOutput {
  if (%searchresults) {
    my $total = 0;
    my $occurrence = 0;
    my %keychecker = ();
    foreach my $target (keys % searchresults) {
	foreach my $key (keys %{ $searchresults{$target} }) {
	    if ((%{$searchresults{$target}{$key}}) && (!$keychecker{$key})) {$total++}
	    $keychecker{$key} = 1;
	    foreach my $sentence (keys % { $searchresults{$target}{$key} }) {
		$occurrence ++;
	    }
	}
    }
    print $query->hr;
    print $query->start_b;
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       $occurrence, ' matches ', ' in ', $total, ' publication(s) found.');
    print $query->end_b;

    print $query->p;
    print $query->submit(-name => 'lastsearch', -value => 'Display');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ' page ');
    my @choices;
    $totalpages = int($total/($displayvalues{ResultsPerPage} || 10) + 1);
    $query->param(-name => 'totalpages', -value => $totalpages);
    for (my $j = 0; $j < $totalpages; $j++) {
	push @choices, $j + 1;
    }
    print $query->popup_menu(-name =>'page',
			     -default => $displaypage,
			     -values => \@choices);
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ', or ');
    print $query->submit(-name =>'previouspage', -value => 'previous');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ' or ');
    print $query->submit(-name =>'nextpage', -value => 'next');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ' page.');
    print $query->p;
    print $query->submit(-name => 'emailresults', -value => 'E-mail');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ' results to ');
    print $query->textfield(-name => 'recipient', 
			    -size => 35, 
			    -maxlength => 255,
			    -default => $generalsettings{'Email'});
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
		       ', ');
    print $query->checkbox(-name => 'emailmatches',
			   -checked => 'checked',
			   -value => 'ON',
			   -label => 'including matches.');

    (my $selectid = $lastsearchfilename) =~ s/\/tmp\/file//g;

    my @giftable = ();
    push @giftable, $query->a({-href => "introducepdf.cgi?id=$selectid", 
			       -target => '_blank'},  
			      $query->img({-src => "/text/gif/resultsinpdf.gif", 
					   -border => 0, -alt => 'results in PDF'})) 
	            .
		    $query->a({-href => "exportendnote.cgi?mode=aen&id=$selectid"},
			      $query->img({-src => "/text/gif/allend.jpg", 
					   -border => 0, -alt => 'export endnote (all)'}))
		    .
		    $query->br
                    .
		    $query->a({-href => "showmatches.cgi?id=$selectid", 
			       -target => '_blank'}, 
			      $query->img({-src => "/text/gif/viewallmatches.gif", 
					   -border => 0, -alt => 'view all matches'}))
		    .
		    $query->a({-href => "exportendnote.cgi?mode=aea&id=$selectid"},
			      $query->img({-src => "/text/gif/alleab.jpg", 
					   -border => 0, -alt => 'export endnote (all) with abstract'}));
    my @minitable = ();
    push @minitable, $query->td({-align => 'center', -valign => 'center'},
				[
				 $query->img({-src => "/text/gif/vm.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "view matches for respective reference"),
				 $query->img({-src => "/text/gif/ot.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "journal's online text"),
				 $query->img({-src => "/text/gif/ra.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "related articles (PubMed)")
				 ]);
    push @minitable, $query->td({-align => 'center', -valign => 'center'},
				[
				 $query->img({-src => "/text/gif/en.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "export bibliography for Endnote"),
				 $query->img({-src => "/text/gif/ea.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "export bibliography including abstracts for Endnote"),
				 $query->img({-src => "/text/gif/pf.jpg", -width => "100%",
					      -border => 0, -align => 'center'}),
				 $query->font({-size => 1}, "download PDF of article ", $query->b("(Caltech only)"))
				 ]);
    push @giftable, $query->table({-border => '1', -cellpadding => '0',
				   -cellspacing => '0', -width => '80%'},
				  $query->caption("Abbreviation Index"),
				  $query->Tr([@minitable]));
    print $query->p;
    print $query->table({-border => '0', -cellpadding => '4',
			 -cellspacing => '1', -width => '100%'},
			$query->Tr([$query->td({-align => 'left', -valign => 'center'},[@giftable])]));

    @displayedkeys = DisplayAsHTML($query, $displaypage, \@expandedabs, 
				   \%searchresults, $databaseroot, $lastsearchfilename,  
				   \%displayoptions, \%displayvalues);
    $query->param(-name => 'dispkeys', -value => [@displayedkeys]);
    $query->param(-name => 'expandedabs', -value => [@expandedabs]);
    print $query->p;
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
                       'Go to ');
    print $query->submit(-name =>'previouspage', -value => 'previous');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
                       ' or ');
    print $query->submit(-name =>'nextpage', -value => 'next');
    print $query->font({-face => 'verdana, helvetica', -size => '2'},
                       ' page.');
    print $query->p;
  } elsif (($lastsearchfilename ne "") && (!$query->param('querytable')) && (!$clearquery) && (!$query->param('lastquery'))) {
    print $query->hr;
    print $query->start_b;
    print $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'red'},
		       'No matches found.');
    print $query->end_b;
  } # if (%searchresults)
} # sub displayOutput

#
### OUTPUT ###

### end form here
#

# pass last search result file name to next round

sub passHidden {
  print $query->hidden(-name => 'lsfilename', -default => $lastsearchfilename);
  print $query->hidden(-name => 'dispkeys', -default => [@displayedkeys]);
  print $query->hidden(-name => 'expandedabs', -default => [@expandedabs]);
  print $query->hidden(-name => 'totalpages', -default => $totalpages);
} # sub passHidden
  
sub closeForm {
  print $query->end_form;
  print $query->end_html;
} # sub closeForm

#
###
### DISPLAY ###


### AUXILIARY SUBS ###

sub overrideCatAttCookies {		# get cookie values to override catatt selections
  my %lastadvancedquery = $query->cookie('lastadvancedquery');	# get last query cookie values
#   foreach my $key (sort keys %lastadvancedquery) { print STDERR "$key\t$lastadvancedquery{$key}\n"; }
  my ($menu, %menuhash) = &readDtd();				# need menu hash to deal with searched values
  my $catrows = $lastadvancedquery{catrows};
  for (my $i = 0; $i < $catrows; $i++) {
    my $varname = "catcat" . $i;	# get catcat to compare versus menuhash
    my $catcat = $lastadvancedquery{$varname};
    if ($catcat) {			# if there's a value
      $varname = "catatt" . $i;
      my $catattlen = $varname . 'len';			# set length variable
      my $length = $lastadvancedquery{$catattlen};	# pass variable
      if ($length > 0) { 				# if there were values in cookie
        for (my $j = 0; $j < $length; $j++) {		# for each of those values
          my $attattarrval = $varname . 'val' . $j;	# set to get it
          my $catatt = $lastadvancedquery{$attattarrval};	# pass it to $catatt
          for (my $k = 0; $k < scalar(@{ $menuhash{$catcat}{vals} }); $k++) {
							  	# for each possible value from menuhash
            if ($catatt eq $menuhash{$catcat}{vals}[$k]) {	# if they match
              print "<SCRIPT LANGUAGE=\"JavaScript1.2\">eval(\"document.form1.catatt\"+$i+\".options[$k].selected = true;\");</SCRIPT>\n";
            }
          } # for (my $k = 0; $k < scalar(@{ $menuhash{$catcat}{vals} }); $k++)
        } # for (my $j = 0; $j < $length; $j++)
      } # if ($length > 0)
      $varname = 'catspec' . $i;					# get spec value
      for (my $k = 0; $k < scalar(@specchoices); $k++) {		# for each of the spec choices
        if ($lastadvancedquery{$varname} eq $specchoices[$k]) {		# if they match
          print "<SCRIPT LANGUAGE=\"JavaScript1.2\">eval(\"document.form1.catspec\"+$i+\".options[$k].selected = true;\");</SCRIPT>\n";
        }
      }
    } # if ($catcat)
  } # for (my $i = 0; $i < $catrows; $i++)
} # sub overrideCatAttCookies

sub PrintHeader { # begin PrintHeader
    
    my $query = shift;
    my @cookies = ();
    while (@_) { push @cookies, shift(@_)}
    
    $|=1;
    print $query->header(-cookie=>[@cookies]);
    print $query->start_html(-title=>'Advanced Retrieval', -author=>'Hans-Michael Muller',
			     -bgcolor=>'#e6e6f6',
			     -text=>'#000000', -link=>'#662222', -vlink=>'#993333');
    print $query->br;
    print $query->font({-face => 'verdana, arial, helvetica', -size => '5'}, 'Advanced Retrieval');
    print $query->p;
    
} # end PrintHeader

sub ReadElements {

    my $dtdfile = shift;
    my %labels = ();
    $labels { "" } = "none"; # include empty tag for search
    open (DTDFILE, "$dtdfile") or die "Can't open DTD file $dtdfile.";   

    while (my $line = <DTDFILE>) {
	chomp ($line);
	if ($line =~ /<!ELEMENT\s+(\w+)\s\(\#PCDATA\)> <\!--\s((\w|\s)+)\s-->/) {
	    my $key = $1;
	    my $label = $2;
# print STDERR "ReadElements\t$key\t$label\n";

	    if (($key ne "sentence") && ($key ne "article")){  #because pattern above is more specific, this isn't really necessary
		 $labels { substr($key, 0, 2) } = $label;
	    }
	}
    }
    close (DTDFILE);
    return %labels;
}

sub ReadAttributes {

    my $dtdfile = shift;
    my @names_codes_and_attributes = ();
    open (DTDFILE, "$dtdfile") or die "Can't open DTD file $dtdfile.";   

    while (my $line = <DTDFILE>) {
	chomp ($line);
	if ($line =~ /<!ATTLIST\s+(\w+)\s+(\w+)\s+\(((\w|\s|\|)+)\)\s+\#IMPLIED> <!--\s+\(((-|\w|\s|\|)+)\)\s+((\w|\s|\,)+)\s-->/) {
	    my $official_attribute_name = $2;
	    my $label = $7;
	    my @values = split(/\s\|\s/, $5);
	    foreach my $value (@values) {
		my $key = $official_attribute_name . " " . $value . " (" . $label . ")";
		push @names_codes_and_attributes, $key;
	    }
	}
    }
    close (DTDFILE);
    return (@names_codes_and_attributes);
}

sub DisplayAsHTML {

    my $query = shift;
    my $page = shift;
    my $pExpandedabs = shift;
    my $pSearchresults = shift;
    my $databaseroot = shift;
    my $selectfilename = shift;
    my $pDisplayoptions = shift;
    my $pDisplayvalues = shift;

    my %sortscorelist = SortedList($pSearchresults);
    my @tablecontent = ();
    my @displayedkeys = ();
    
    # make  headline
    my @columns = DefineColumns($pDisplayoptions);
    push @tablecontent, $query->th([@columns]);
    
    # fill table
    my $counter = 0;
    foreach my $score (sort numerically keys % sortscorelist) {
	foreach my $key (sort keys %{$sortscorelist{$score}}) {
	    $counter++;
	    next unless ($counter > $displayvalues{ResultsPerPage}*($page-1));
	    next unless ($counter <= $displayvalues{ResultsPerPage}*$page);
	    my $expanded = 0;
	    foreach my $element (@$pExpandedabs) { next unless ($element eq $key); $expanded = 1;}
	    my @columns = FillColumns($query, $databaseroot, $selectfilename, $pDisplayoptions,
				      $pSearchresults, $key, $score, $expanded);
	    push @tablecontent, $query->td([@columns]);
	    push @displayedkeys, $key;
	}
    }
    
    print $query->table({-border => '1', -cellpadding => '4',
			 -cellspacing => '1', -width => '100%'},
			$query->caption($query->b("Search Results")),
			$query->Tr([@tablecontent]));
    
    return @displayedkeys;
} # sub DisplayAsHTML

sub SortedList {	# for DisplayAsHtml

    my $pSearchresults = shift;

    my %scorelist = ();
    foreach my $target (keys % {$pSearchresults}) {
	foreach my $key (keys % { $$pSearchresults{$target} }) {
	    foreach my $sentence (keys % { $$pSearchresults{$target}{$key} }) {
		$scorelist{$key} += $searchresults{$target}{$key}{$sentence};
	    }
	}
    }
    
    my %sortscorelist = ();
    foreach my $key (keys % scorelist) {
	$sortscorelist{$scorelist{$key}}{$key} = 1;
    }    

    return %sortscorelist;
} # sub SortedList

sub numerically { $b <=> $a }

sub DefineColumns {	# for DisplayAsHtml

    my $pDisplayoptions = shift;
    my @columns = ();
    if ($$pDisplayoptions{'Source Type'}) { push @columns, 'Publication type' }
    if ($$pDisplayoptions{Title}) { push @columns, 'Title' }
    if ($$pDisplayoptions{Abstract}) { push @columns, 'Abstract' }
    if ($$pDisplayoptions{Author}) { push @columns, 'Author' }
    if ($$pDisplayoptions{Journal}) { push @columns, 'Journal' }
    if ($$pDisplayoptions{Year}) { push @columns, 'Year' }
    if ($$pDisplayoptions{Citation}) { push @columns, 'Citation' }
    if ($$pDisplayoptions{'Number of matches'}) { push @columns, 'Number of matches' }
    if ($$pDisplayoptions{Select}) { push @columns, 'Select' }

    return @columns;
}

sub FillColumns {	# for DisplayAsHtml

    my $query = shift;
    my $databaseroot = shift;
    my $selectfilename = shift;
    my $pDisplayoptions = shift;
    my $pSearchresults = shift;
    my $key = shift;
    my $score = shift;
    my $expanded = shift;
    my @columns = ();


    if ($$pDisplayoptions{'Source Type'}) {
        my $content = join ("\n", GetContents("$databaseroot/typ/$key"));
        $content =~ s/\_/ /g;
        push @columns, "\L$content\E";
    }

    if ($$pDisplayoptions{Title}) {
        my @aux = GetContents("$databaseroot/tit/xml/$key");
        my $content = join ("\n", WormBaseLinks ("$databaseroot/ind/wbl/tit/$key",
                                                 "$databaseroot/wbl/", $query, @aux));
        push @columns, $content;
    }

    if ($$pDisplayoptions{Abstract}) {
        my @aux = GetContents("$databaseroot/abs/xml/$key");
        my @neat = WormBaseLinks ("$databaseroot/ind/wbl/abs/$key",
				  "$databaseroot/wbl/", $query, @aux);
        my $content;
        if ($expanded) {
            $content = join ("\n", @neat);
            if ($content) {
                $content .= $query->submit(-name => "collapse$key",
                                           -value => 'Collapse abstract');
            }
        } else {
            $content = $neat[3] . $neat[4];
            if ($content) {
                $content .= $query->submit(-name => "expanded$key",
                                           -value => 'Expand abstract');
            }
        }
        push @columns, $content;
    }

    if ($$pDisplayoptions{Author}) {
        my $content = join ("\n", GetContents("$databaseroot/aut/$key"));
        $content =~ s/\n/<br>/g;
        push @columns, $content;
    }

    if ($$pDisplayoptions{Journal}) {
        my $content = join ("\n", GetContents("$databaseroot/jou/$key"));
        push @columns, $content;
    }

    if ($$pDisplayoptions{Year}) {
        my $content = join ("\n", GetContents("$databaseroot/yea/$key"));
        push @columns, $content;
    }

    if ($$pDisplayoptions{Citation}) {
        my $content = join ("\n", GetContents("$databaseroot/cit/$key"));
        $content =~ s/P\:\s+(\d+)\s+(\d+)/Pages $1-$2/g;
        $content =~ s/V\:/<br>Vol\./g;
        push @columns, $content;
    }

    if ($$pDisplayoptions{'Number of matches'}) { 
	push @columns, $score;
    }

    if ($$pDisplayoptions{Select}) {
	my $content = $query->start_center;
	$content .= "$key";
	$content .= $query->end_center;
	if (!-e "$databaseroot/$selectfilename\.$key") {
	    open (IN, "$databaseroot/$selectfilename");
	    my $firstline = <IN>;
	    my $secondline = <IN>;
	    close (IN);
	    open (OUT, ">$databaseroot/$selectfilename\.$key");
	    print OUT $firstline;
	    print OUT $secondline; # make sure queries are saved.
	    foreach my $target (keys %{ $pSearchresults}) {
		print OUT $target . "," . $key . ",";
		foreach my  $sentence (keys % { $$pSearchresults{$target}{$key} }) {
		    print OUT $sentence . ",";
		}
		print OUT "\n";
	    }
	    close (OUT);
	}
	(my $selectid = "$selectfilename\.$key") =~ s/\/tmp\/file//g;
	$content .= $query->start_center;
	$content .= $query->a({-href => "showmatches.cgi?id=$selectid", -target => '_blank'}, 
			      $query->img({-src => "/text/gif/vm.jpg", 
					  -border => 0, -alt => 'view matches'}));
        if (-e "$databaseroot/pdf/$key.pdf") {
	    if ($query->remote_host() =~ /(131\.215\.|\.caltech\.edu)/) {
		$content .= $query->a({href => "/text/tdb/pdf/$key.pdf", target => "_blank"},
				      $query->img({-src => "/text/gif/pf.jpg", -border => 0, -alt => 'PDF'}));
	    }
        }
        if (-e "$databaseroot/url/$key") {
            open (URL, "$databaseroot/url/$key");
            my $url = <URL>;
            chomp ($url);
            $content .= $query->a({href => "$url", target => "_blank"},
                                  $query->img({-src => "/text/gif/ot.jpg", -border => 0, -alt => 'article text from journal'}));	    
            close(URL);
        }
        if (-e "$databaseroot/rel/$key") {
            open (URL, "$databaseroot/rel/$key");
            my $url = <URL>;
            chomp ($url);
            $content .= $query->a({href => "$url", target => "_blank"},
                                  $query->img({-src => "/text/gif/ra.jpg", -border => 0, -alt => 'related articles'}));
            close(URL);
        }
	if (-e "$databaseroot/end/$key") {
	    $content .= $query->a({href => "exportendnote.cgi?mode=sen&id=$key"},
				  $query->img({-src => "/text/gif/en.jpg", -border => 0, -alt => 'Endnote'}));
	}				  
	if (-e "$databaseroot/eab/$key") {
	    $content .= $query->a({href => "exportendnote.cgi?mode=sea&id=$key"},
				  $query->img({-src => "/text/gif/ea.jpg", -border => 0, -alt => 'Endnote (w/ abstract)'}));
	}				  
	$content .= $query->end_center;
        push @columns, $content;
    }

    return @columns;
}


sub GetContents { # for FillColumns	# for DisplayAsHtml

    my $filename = shift;
    my @return = ();
    open (IN,"$filename");
    while (my $line = <IN>) {
        chomp ($line);
        push @return, $line;
    }
    close (IN);
    return @return;

}


sub WormBaseLinks {

    my $indexfile = shift;
    my $linkdir = shift;
    my $query = shift;
    my @lines = ();
    while (@_) {push @lines, shift;}
    if (-e "$indexfile") {
        my %indexcontent = ();
        open (INDEX, $indexfile);
        while (my $line = <INDEX>) {
            chomp $line;
            my @words = split(/\t/, $line);
            my $id = shift(@words);
            while (@words) { push @{ $indexcontent{$id} }, shift(@words)};
        }
        close (INDEX);
        for (my $i = 0; $i < @lines; $i++) {
            if ($lines[$i] =~ /<sentence id=\'(s\d+)\'/) {
                my $id = $1;
                $lines[$i] =~ s/<.+?>//g; # remove xml brackets
                $lines[$i] =~ s/<\/.+?>//g;
                if ($indexcontent{$id}) {
                    while (@{$indexcontent{$id}}) {
                        my $term = shift (@{$indexcontent{$id}});
                        (my $lookup = $term) =~ s/\s//g;
                        my $lcflookup = lcfirst($lookup);
                        open (URL, "$linkdir/$lookup") or open(URL, "$linkdir/$lcflookup");
                        my $url = <URL>;
                        close (URL);
                        if ($url) {
                            chomp($url);
                            my $replacement = " " . $query->a({-href => $url, -target => '_blank'}, "$term") . " ";
                            $lines[$i] =~ s/(^|\s)$term($|\s)/$replacement/g;
                        }
                    }
                }
            } else {
                $lines[$i] =~ s/<.+?>//g; # remove xml brackets
                $lines[$i] =~ s/<\/.+?>//g;
            }
        }
    }
    return @lines;
}


sub GetListFromKeyword {	# %searchresult or %auxlist for   if ($query->param('search')) 
    
    my $indexkey = shift;
    my $pTargetdirectories = shift;
    my $keyword = shift;
    my $pSearchtargets = shift;
    my $numcomp = shift;
    my $numofmatches = shift;
    
    my %result = ();
    
    foreach my $target (keys % $pSearchtargets) {
	if ($$pSearchtargets{$target}) {
	    my $keydir = $indexkey . $$pTargetdirectories{$target};
	    my $lowered = "\L$keyword\E";
	    my @keywordfiles = <$keydir/$lowered>;
	    foreach my $file (@keywordfiles) {
		open (INKEY, "$file");
		print $query->b($query->font({-face => 'verdana, helvetica', -size => '2', color => 'green'}, '.'));
		while (my $line = <INKEY>) {
		    chomp ($line);
		    my @entry = split(/\,/, $line);
		    my $key = shift (@entry);
		    foreach my $sentence (@entry) {
			$result{$target}{$key}{$sentence}++;
		    }
		}
		close (INKEY);
		foreach my $key (keys %{$result{$target}}) {
		    if ($numcomp eq 'equal to') {
			foreach my $sentence (keys %{$result{$target}{$key}}) {
			    if ($result{$target}{$key}{$sentence} != $numofmatches) {
				delete $result{$target}{$key}{$sentence};
			    }
			}
		    } elsif ($numcomp eq 'greater than') {
			foreach my $sentence (keys %{$result{$target}{$key}}) {
			    if ($result{$target}{$key}{$sentence} <= $numofmatches) {
				delete $result{$target}{$key}{$sentence};
			    }
			}
		    } elsif ($numcomp eq 'less than') {
			foreach my $sentence (keys %{$result{$target}{$key}}) {
			    if ($result{$target}{$key}{$sentence} >= $numofmatches) {
				delete $result{$target}{$key}{$sentence};
			    }
			}
		    }
		}
	    }
	}
    }
    # delete all $result{$target}{$key} if empty
    foreach my $target (keys % result) {
	foreach my $key (keys %{$result{$target}}) {
	    my @aux = keys %{$result{$target}{$key}};
	    delete $result{$target}{$key} if (@aux < 1);
	}
    }
    return %result;
} # sub GetListFromKeyword

sub GetListFromCategories {	# %searchresult or %auxlist for   if ($query->param('search')) 

    my $indexattspec = shift;
    my $databaseroot = shift;
    my $pTargetdirectories = shift;
    my $category = shift;
    my $pSearchtargets = shift;
    my $pAttnmecde = shift;
    my $pAttributes = shift;
    my $specification = shift;
    my $numcomp = shift;
    my $numofmatches = shift;
    
    my %result = ();
    
    foreach my $target (keys % $pSearchtargets) {
	if ($$pSearchtargets{$target}) {
	    my %checklist = ();
	    my $total = 1;
	    my $filename = $indexattspec . "/" . $$pTargetdirectories{$target} . "/" . $category . "/" ."cat" . $category;
	    open (INCAT, "$filename");
	    print $query->b($query->font({-face => 'verdana, helvetica', -size => '2', -color => 'green'}, '.'));
	    while (my $line = <INCAT>) {
		chomp ($line);
		my @entry = split (/\,/, $line);
		my $key = shift (@entry);
		foreach my $id (@entry) {
		    (my $sentence, my $token) = split(/-/, $id);
		    $checklist{$key}{$sentence}{$token}++;
		}
	    }
	    close (INCAT);
	    
	    if (@$pAttributes > 0) {
		my @locallist = ();
		foreach my $key (@$pAttributes) { push @locallist, $$pAttnmecde{$key}}
		$total += @locallist;
		foreach my $entry (sort @locallist) {
		    (my $localname, my $localcde) = split(/ /, $entry);
		    my $filename = $indexattspec . "/" .$$pTargetdirectories{$target} . "/" . $category . "/" . $localcde;
		    open (ATT, "$filename");
		    while (my $line = <ATT>) {
			chomp ($line);
			my @entry = split (/\,/, $line);
			my $key = shift (@entry);
			foreach my $id (@entry) {
			    (my $sentence, my $token) = split(/-/, $id);
			    $checklist{$key}{$sentence}{$token}++;
			}
		    }
		    close (ATT);
		}
	    }
	    if (($specification eq 'named') || ($specification eq 'unnamed')) {
		$total += 1;
		my $spec = ($specification eq 'named') ? 'd' : 'i';
		my $filename = $indexattspec . "/" . $$pTargetdirectories{$target} . "/" . $category . "/" ."spec" . $spec;
		open (SPEC, "$filename");
		while (my $line = <SPEC>) {
		    chomp($line);
		    my @entry = split (/\,/, $line);
		    my $key = shift (@entry);
		    foreach my $id (@entry) {
			(my $sentence, my $token) = split(/-/, $id);
			$checklist{$key}{$sentence}{$token}++;
		    }
		}
		close (SPEC);
	    }
	    foreach my $key (keys % checklist) {
		foreach my $sentence (keys %{$checklist{$key}}) {
		    foreach my $token (keys %{$checklist{$key}{$sentence}}) {
			if ($checklist{$key}{$sentence}{$token} == $total) {
			    $result{$target}{$key}{$sentence}++;
			}
		    }
		}
	    }
	    
	    # compare to numofmatches here
	    foreach my $key (keys %{$result{$target}}) {
		if ($numcomp eq 'equal to') {
		    foreach my $sentence (keys %{$result{$target}{$key}}) {
			if ($result{$target}{$key}{$sentence} != $numofmatches) {
			    delete $result{$target}{$key}{$sentence};
			}
		    }
		} elsif ($numcomp eq 'greater than') {
		    foreach my $sentence (keys %{$result{$target}{$key}}) {
			if ($result{$target}{$key}{$sentence} <= $numofmatches) {
			    delete $result{$target}{$key}{$sentence};
			}
		    }
		} elsif ($numcomp eq 'less than') {
		    foreach my $sentence (keys %{$result{$target}{$key}}) {
			if ($result{$target}{$key}{$sentence} >= $numofmatches) {
			    delete $result{$target}{$key}{$sentence};
			}
		    }
		}
	    }		
	}
    }
    # delete all $result{$target}{$key} if empty
    foreach my $target (keys % result) {
	foreach my $key (keys %{$result{$target}}) {
	    my @aux = keys %{$result{$target}{$key}};
	    delete $result{$target}{$key} if (@aux < 1);
	}
    }
    return %result;
} # sub GetListFromCategories 


sub OrLists {			# %searchresult for   if ($query->param('search')) 

    my $pListA = shift;
    my $pListB = shift;

    my %result = ();
    foreach my $target (keys % $pListA) {
	foreach my $key (keys %{$$pListA{$target}}) {
	    foreach my $sentence (keys %{$$pListA{$target}{$key}}) {
		$result{$target}{$key}{$sentence} = 1;
	    }
	}
    }
    foreach my $target (keys % $pListB) {
	foreach my $key (keys %{$$pListB{$target}}) {
	    foreach my $sentence (keys %{$$pListB{$target}{$key}}) {
		$result{$target}{$key}{$sentence} = 1;
	    }
	}
    }
    return %result;
}

sub AndLists {			# %searchresult for   if ($query->param('search')) 

    my $pListA = shift;
    my $pListB = shift;
    my $mode = shift;

    my %result = ();
    foreach my $target (keys % $pListA) {
	foreach my $key (keys %{$$pListA{$target}}) {
	    foreach my $sentenceA (keys %{$$pListA{$target}{$key}}) {
		if ($mode eq 'sentence') {
		    if ($$pListB{$target}{$key}{$sentenceA}) {
			$result{$target}{$key}{$sentenceA} = 1;
		    }
		} elsif ($mode eq 'publication') {
		    foreach my $sentenceB (keys %{$$pListB{$target}{$key}}) {
			$result{$target}{$key}{$sentenceA} = 1;
			$result{$target}{$key}{$sentenceB} = 1;
		    }
		}
	    }
	}
    }
    return %result;
}

sub ListAAndNotListB {		# %searchresult for   if ($query->param('search')) 
    
    my $pListA = shift;
    my $pListB = shift;
    my $mode = shift;
    
    my %result = ();
    foreach my $target (keys % $pListA) {
	foreach my $key (keys %{$$pListA{$target}}) {
	    foreach my $sentenceA (keys %{$$pListA{$target}{$key}}) {
		if ($mode eq 'sentence') {
		    if (!$$pListB{$target}{$key}{$sentenceA}) {
			$result{$target}{$key}{$sentenceA} = 1;
		    }
		} elsif ($mode eq 'publication') {
		    $result{$target}{$key}{$sentenceA} = 1 if (keys %{$$pListB{$target}{$key}} < 1);
		} 
	    }
	}
    }
    return %result;
}

sub readDtd {
  my $dtdfile = '/var/www/html/text/textpresso.dtd';
  $/ = '';                              # set <> to paragraph mode
  open (DTD, "$dtdfile") or die "Can't open DTD file $dtdfile.";
  my %menuhash;                         # hash of menu stuff  key is catcatvalue
                                        # name is catcatname vals are catattvalues
  my $menu1 = '';			# parts of array
  my %readElementsCompatibility;	# sub ReadElements outputs a hash that is sorted
					# this hash is just to sort these values
  my %readElementsSpecCompatibility;	# like above
  my $menu2 = 'var menu = new Array();' . "\n";		# full array of arrays
  my $menuspec1 = '';			# parts of array for specification
  my $menuspec2 = 'var menuspec = new Array();' . "\n";	# full array of arrays for specification
  my @orig_menu_name = ('none');	# want original value to be empty so don't pass values where not selected
  my @orig_menu_val = (' ');		# init menu
  my %orig_menu_name;			# hash to filter (sort) values by key value
  my $count1 = 1;                       # count of first submenu
  while (my $entry = <DTD>) {           # while there are paragraphs in dtd
    next unless ($entry =~ m/ELEMENT.*!--/);    # skip non-data lines
    my @lines = split /\n/, $entry;     # break paragraphs into lines
    my ($main_val, $main_name) = $lines[0] =~ m/ELEMENT\s+(\w\w)\w*? .*!-- (.*?) --/;
    $orig_menu_name{$main_val} = $main_name;
    $menuhash{$main_val}{name} = $main_name;
    $menuhash{$main_val}{index} = $count1;
    my @groupN2_vals = qw();		# array of values for menu$count1
    my @groupSpec_vals = qw();		# array of values for menuspec$count1
    foreach my $line (@lines) {         # check each line for implied attributes for second column
      if ($line =~ /<!ATTLIST\s+(\w+)\s+(\w+)\s+\(((\w|\s|\|)+)\)\s+\#IMPLIED> <!--\s+\(((-|\w|\s|\|)+)\)\s+((\w|\s|\,)+)\s-->/) {
        my $label = $7;
        my @values = split(/\s\|\s/, $5);
        foreach my $value (@values) {
          $value =~ s/^\w+\-//g;        # take out the first 2 letters and hyphen
          $value = $label . ": " . $value;
          push @groupN2_vals, $value;
          push @{ $menuhash{$main_val}{vals} }, $value;
        } # foreach my $value (@values)
      } # if ..
      if ($line =~ m/<!ATTLIST\s+(\w+)\s+reference/) {
        my $word = $1;
        if ($line =~ m/\bdirect\b/) { push @groupSpec_vals, 'named'; }
        if ($line =~ m/\bindirect\b/) { push @groupSpec_vals, 'unnamed'; }
        if ( scalar(@groupSpec_vals) > 0 ) { push @groupSpec_vals, 'all'; }
      } # if ($line =~ m/<!ATTLIST\s+\w+\w+reference/)
    } # foreach my $line (@lines)
    my $groupN2_vals = join"', '", @groupN2_vals;
    my $menu1 = ' = new Array(\'' . $groupN2_vals .  '\');' . "\n";
    my $groupSpec_vals = join"', '", @groupSpec_vals;
    my $menuspec1 = ' = new Array(\'' . $groupSpec_vals .  '\');' . "\n";
    $readElementsCompatibility{$main_val} = $menu1;
    $readElementsSpecCompatibility{$main_val} = $menuspec1;
    $count1++;                          # add to counter
  } # while (my $line = <DTD>)
  close (DTD);
  $/ = "\n";                            # reset <> to line at a time
  my $count2 = 1;                       # count of first submenu
  foreach (sort keys %readElementsCompatibility) { 
    $menu1 .= 'var menu' . $count2 . $readElementsCompatibility{$_};
    $menu2 .= 'menu[' . $count2 . '] = menu' . $count2 . ";\n";
    $menuspec1 .= 'var menuspec' . $count2 . $readElementsSpecCompatibility{$_};
    $menuspec2 .= 'menuspec[' . $count2 . '] = menuspec' . $count2 . ";\n";
    $count2++;
  } # foreach (sort keys %readElementsCompatibility)
  foreach (sort keys %orig_menu_name) { push @orig_menu_val, $_; push @orig_menu_name, $orig_menu_name{$_}; }
    # get the hash values sorted into the arrays
  my $orig_menu_name = join"', '", @orig_menu_name;
  my $orig_menu_val = join"', '", @orig_menu_val;
  my $menu3 = 'var orig_menu_name = new Array(\'' . $orig_menu_name .  '\');' . "\n";
  my $menu4 = 'var orig_menu_val = new Array(\'' . $orig_menu_val .  '\');' . "\n";
  my $menu = $menu1 . $menu2 . $menuspec1 . $menuspec2 . $menu3 . $menu4;
  return ($menu, %menuhash);
} # sub readDtd


sub getHtmlVar {                # get variables from html form and untaint them
  no strict 'refs';             # need to disable refs to get the values
                                # possibly a better way than this
  my ($query, $var, $err) = @_; # get the CGI query val,
                                # get the name of the variable to query->param,
                                # get whether to display and error if no such
                                # variable found
  unless ($query->param("$var")) {              # if no such variable found
    if ($err) {                 # if we want error displayed, display error
      print "<FONT COLOR=blue>ERROR : No such variable : $var</FONT><BR>\n";
    } # if ($err)
  } else { # unless ($query->param("$var"))     # if we got a value
    my $oop = $query->param("$var");            # get the value
    $$var = &untaint($oop);                     # untaint and put value under ref
    return ($var, $$var);                       # return the variable and value
  } # else # unless ($query->param("$var"))
} # sub getHtmlVar

sub untaint {
  my $tainted = shift;
  my $untainted;
  if ($tainted eq "") {
    $untainted = "";
  } else { # if ($tainted eq "")
    $tainted =~ s/[^\w\-.,;:?\/\\@#\$\%\^&*(){}[\]+=!~|' \t\n\r\f]//g;
    if ($tainted =~ m/^([\w\-.,;:?\/\\@#\$\%&\^*(){}[\]+=!~|' \t\n\r\f]+)$/) {
      $untainted = $1;
    } else {
      die "Bad data in $tainted";
    }
  } # else # if ($tainted eq "")
  return $untainted;
} # sub untaint

### AUXILIARY SUBS ###