#!/usr/bin/perl

# CGI script provides one part of the homepage of the Textpresso system.
# 
# copyright (c) Hans-Michael Muller, Pasadena, California, 2002-2004
#

use strict;
use CGI;


### globals
#

my $query = new CGI;
my $absmyself = $query->url(absolute=>1);
my %generalsettings = $query->cookie('generalsettings');
my %displayoptions = $query->cookie('displayoptions');

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 %searchtargets = (Author => 0, Title => 0, 
		     Abstract => 0, Paper => 0,
		     Year => 0); 
#
### end globals;

PrintHeader($query);

print $query->p;


my $lefthead = $query->font({-face => 'verdana, arial, helvetica', -size => '3', -color => 'white'}, 'Simple Retrieval');
my $righthead = $query->font({-face => 'verdana, arial, helvetica', -size => '3', -color => 'white'}, 'News and Messages');




my $leftcont;
### start form
#

$leftcont .= $query->start_form(-method => 'POST', -action => 'simpleretrieval.cgi');

#
###

### present input fields
#
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'Query should be met in a ');

my %locallabel;
$locallabel{sentence} = " sentence";
$locallabel{publication} = " publication";
$leftcont .= $query->radio_group(-name => 'searchmode',
				 -linebreak => 0,
				 -value => ['sentence', 'publication'],
				 -default => 'sentence',
				 -labels => \%locallabel);
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  '.');
$leftcont .= $query->p;

$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'Type in keywords to be searched for, ');
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'separated by ');
$leftcont .= $query->start_b;
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'white spaces: ');
$leftcont .= $query->end_b;
$leftcont .= $query->p;
$leftcont .= $query->textfield(-name => 'simplesearchstring', -size => 40, -maxlength => 255);
$leftcont .= $query->checkbox(-name => 'exactmatch',
			      -value => 'OFF',
			      -label => ' Exact match');
$leftcont .= $query->p;

$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'Specify categories that should also be met (optional): ');
$leftcont .= $query->p;
$leftcont .= $query->popup_menu(-name => 'inc0', 
				-values => [@elementkeys], 
				-labels=>\%labels);
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  ', ');
$leftcont .= $query->popup_menu(-name => 'inc1', 
				-values => [@elementkeys], 
				-labels=>\%labels);
$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  '. ');
$leftcont .= $query->p;

$leftcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			  'Search 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;
    }
}

$leftcont .= $query->checkbox_group(-name => 'searchtargets',
				    -value => [sort keys % searchtargets],
				    -defaults => [sort @defaults],
				    -linebreak => 'false',
				    -rows => 1,
				    -labels => \%locallabel2);
$leftcont .= $query->p;
$leftcont .= $query->submit(-name => 'search', -value => 'Search!');
$leftcont .= $query->font(" ");

#
###

### end form
#

$leftcont .= $query->end_form;

#
### 

my $rightcont;

$rightcont .= $query->start_b;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'Welcome to ');
$rightcont .= $query->start_em;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'Textpresso ');
$rightcont .= $query->end_em;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   '! The '); 
$rightcont .= $query->start_em;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'Textpresso ');
$rightcont .= $query->end_em;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
                           'search engine for ');
$rightcont .= $query->start_i;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'biological ');
$rightcont .= $query->end_i;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'abstracts and fulltexts was developed at ');
$rightcont .= $query->a({-href=>'http://www.wormbase.org', -target => '_blank'}, "Wormbase");
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
                           ' to service the ');
$rightcont .= $query->start_i;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'biological ');
$rightcont .= $query->end_i;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
                           'community. ');
$rightcont .= $query->end_b;
$rightcont .= $query->p;

$rightcont .= $query->img({-src=>'/text/gif/ball_yellow.gif', 
			   -align=>'center'});
$rightcont .= $query->start_b;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'darkred'},
			   'November 17th, 2003: ');
$rightcont .= $query->end_b;

$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'darkred'},
			   'Textpresso has been featured in an article about text mining by Steven Dickman. ');
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'darkred'},
			   'You can find it in PLoS Biology by clicking ');
$rightcont .= $query->a({-href=>'http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0000048', -target => '_blank'}, "here");
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2', -color => 'darkred'},
			   '.');
$rightcont .= $query->p;

$rightcont .= $query->img({-src=>'/text/gif/ball_yellow.gif', 
			   -align=>'center'});
$rightcont .= $query->start_b;
$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'Month, Day, Year: ');
$rightcont .= $query->end_b;

$rightcont .= $query->font({-face => 'verdana, helvetica', -size => '2'},
			   'Add your own news items here. ');

$rightcont .= $query->p;

my $lefthead2 = $query->font({-face => 'verdana, arial, helvetica', -size => '3', -color => 'white'}, 'Textpresso Database');
my $righthead2 = "";

my $leftcont2;
$leftcont2 .= $query->start_b;
$leftcont2 .= $query->font({-face => 'verdana, helvetica', -size => '2'}, 'Add description about your own database here.');
$leftcont2 .= $query->end_b;
$leftcont2 .= $query->br;
$leftcont2 .= $query->font({-face => 'verdana, helvetica', -size => '2'}, 'Currently, the database contains:');
$leftcont2 .= $query->start_ul;
$leftcont2 .= $query->li($query->font({-face => 'verdana, helvetica', -size => '2'}, 'XX,XXX fulltext papers '));
$leftcont2 .= $query->li($query->font({-face => 'verdana, helvetica', -size => '2'}, 'XX,XXX  paper abstracts, XX,XXX meeting abstracts and XX,XXX PMID abstracts'));
$leftcont2 .= $query->li($query->font({-face => 'verdana, helvetica', -size => '2'}, 'Citation information for a total XX,XXX publications'));
$leftcont2 .= $query->end_ul;
$leftcont2 .= $query->a({-href=>'/text/doc/abouttextpresso/paperdetails.html', -target => 'middle'}, 
			'More details');
$leftcont2 .= $query->br;
$leftcont2 .= $query->br;
$leftcont2 .= $query->a({-href=>'/text/textpresso/chart.html', -target => '_blank'}, 
			'Compare Textpresso to other search engines!');
my $rightcont2 = "";

print $query->start_table;
print $query->start_Tr;
print $query->start_td;
PrintTable ($query, $lefthead, $righthead, $leftcont, $rightcont);
print $query->end_td;
print $query->end_Tr;
print $query->start_Tr;
print $query->start_td;
Print1ColumnTable ($query, $lefthead2, $leftcont2);
print $query->end_td;
print $query->end_Tr;
print $query->end_table;


#
###

### end page
#

print $query->end_html;

#
###

sub PrintTable {

    my $query = shift;
    my $lefttablehead = shift;
    my $righttablehead = shift;
    my $leftcontent = shift;
    my $rightcontent = shift;

    print $query->table({-border => '0', -width =>'100%', -align => 'left', valign => 'top',
			 -cellpadding => '5', -cellspacing => '4'},
			$query->Tr({-align => 'left', valign => 'top' },
				   [ $query->th({-bgcolor => '#888d8d', -width => '50%'},[$lefttablehead, $righttablehead]),
				     $query->td({-bgcolor => '#e6e6f6'},[$leftcontent, $rightcontent])
				     ]));
}

sub Print1ColumnTable {

    my $query = shift;
    my $tablehead = shift;
    my $tablecontent = shift;

    print $query->table({-border => '0', -width =>'100%', -align => 'left', valign => 'top',
			 -cellpadding => '5', -cellspacing => '4'},
			$query->Tr({-align => 'left', valign => 'top' },
				   [ $query->th({-bgcolor => '#888d8d', -width => '50%'}, $tablehead),
				     $query->td({-bgcolor => '#e6e6f6'}, $tablecontent)
				     ]));
}

sub PrintHeader { # begin PrintHeader

    my $query = shift;

    print $query->header;
    print $query->start_html(-title=>'Textpresso Homepage', -author=>'Hans-Michael Muller',
			     -bgcolor => '#e6e6f6',
			     -text =>'#282d2d', -link=>'#484d4d');
    print $query->br;
    print $query->img({-src=>'/text/gif/textpressobanner48.jpg',
		   -alt => 'Textpresso'});
    print $query->br;
    print $query->start_em;
    print $query->font({-face => 'adobe-courier', -size => '4'},
		       '  An information retrieval and extraction system for ');
    print $query->font({-face => 'adobe-courier', -size => '4'},
		       'C. elegans ');
    print $query->font({-face => 'adobe-courier', -size => '4'},
		       'literature');
    print $query->end_em;

} # end PrintHeader

sub PrintBottom { # begin PrintBottom
    my $query = shift;
}   # end PrintBottom

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 = $2;
	    if (($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;
}