ontology

#!/usr/bin/perl

# CGI script provides ontology page of Textpresso system
#
# Copyright (c) Hans-Michael Muller 2007.

use strict;
# The following line needs adjustments for each implementation
use lib "/usr/local/lib/textpresso/displaying/ecoli/";
# end line that needs adjustments
use CGI;
use TextpressoDisplayTasks;
use TextpressoDisplayGlobals;
use TextpressoGeneralGlobals;

my $query = new CGI;
my $myself = $query->url(-absolute => 1);
my $location = PrintTop($query, $myself, 1);

# Put form here, and interlace output

print $query->start_form(-method => 'POST', -action => $myself);

my $main = new TextpressoTable;
$main->init;
$main->addtablerow("Ontology Browser");
$main->addtablerow('This browser tests a keyword against all regular expressions in the lexicon. ');
$main->addtablerow('Type in one phrase, which can consist of several words: ');
$main->addtablerow($query->textfield(-name => 'simplestring', -size => 50, -maxlength => 255));
$main->addtablerow($query->submit(-name => 'search', -value => 'Test!'));

my $ael = (GE_DELIMITERS)->{annotation_entry_left};
my $aer = (GE_DELIMITERS)->{annotation_entry_right};
my $del = (GE_DELIMITERS)->{lexicon}; 

if (($query->param('search')) || $query->param("simplestring")) {
    use TextpressoGeneralTasks;
    use TextpressoDatabaseGlobals;
    use File::Basename;
    
    my %output = ();
    my $search_string = $query->param("simplestring");
    my @searchstringset = split (/($ael)|($aer)/, $search_string);
    push @searchstringset, $search_string;
    my %output = ();
    foreach my $lit (keys % { (DB_LITERATURE) }) {
	my $lexdir = DB_ROOT . (DB_LITERATURE)->{$lit} . (DB_SUPPLEMENTAL)->{lexicon};
	
	my $dirin = $lexdir;
	my @lexfiles = <$dirin/*>;
	
	foreach my $file (@lexfiles) {
	    (my $fname, my $fdir, my $fsuf) = fileparse($file, qr{\.\d+-gram});
	    $fsuf =~ s/^\.(\d+)-gram/$1/;
	    open (IN, "<$file");
	    my $inline = '';
	    my %possible_keys = ();
	    while (my $line = <IN>) {
		$inline .= $line;
		$possible_keys{$line} = 1;
	    }
	    my $actionflag = 0;
	    foreach my $searchitem (@searchstringset) {
		if ($possible_keys{"$searchitem\n"}) {
		    $actionflag = 1;
		}
	    }
	    if ($actionflag) {
		my @entries = split (/$del\n/, $inline);
		foreach my $searchitem (@searchstringset) {
		    foreach my $entry (@entries) {
			my @items = split (/\n/, $entry);
			my $key = shift(@items);
			if ($searchitem =~ m/($ael)($key)($aer)/i) {
			    $output{$lit}{$key}{$fname}{join(" ", @items)} = 1;
			}
		    }
		}
	    }
	    close (IN);
	}
    }
    
    if (%output) {
	my $rslt = new TextpressoTable;
	$rslt->init;
	$rslt->addtablerow("Literature", "Category", "Term", "Attributes");
	foreach my $l (sort keys % output) {
	    foreach my $k (sort keys % { $output{$l} }) {
		foreach my $c (sort keys % { $output{$l}{$k} }) {
		    my @nice = ();
		    use TextpressoDatabaseCategories;
		    foreach my $cc (keys %{(DB_CATEGORIES)}) {
			push @nice, $cc if ((DB_CATEGORIES)->{$cc} eq $c);
		    }
		    foreach my $o (sort keys % { $output{$l}{$k}{$c} }) {
			$rslt->addtablerow($l, join(" ", @nice) || $c, $k, $o);
		    }
		}
	    }
	}
	$main->addtablerow($rslt->maketable($query, width => "100%",
					    DSP_HDRCOLOR => 'black', DSP_HDRSIZE => 2));
    } else {
	my $warncolor = (DSP_HIGHLIGHT_COLOR)->{offcolor};
	$main->addtablerow($query->span({-style => "font-weight:bold;color:$warncolor;"}, "No matches found."));
    }
    
}

print $main->maketable($query, 
		       tablestyle => 'borderless-headerbackground', 
		       DSP_HDR_SIZE => 3,
		       width => "100%");

my $main2 = new TextpressoTable;
$main2->init;
$main2->addtablerow("Category Lists");
$main2->addtablerow('Choose category from popup menu whose lexicon you want to have displayed: ');
use TextpressoDatabaseCategories;
my @categories = sort (keys %{(DB_CATEGORIES)});
$main2->addtablerow($query->popup_menu(-name => 'category',
				       -values => [sort @categories]));
$main2->addtablerow($query->submit(-name => 'display', -value => 'Display!'));
if (($query->param('display'))) {
    use TextpressoGeneralTasks;
    use TextpressoGeneralGlobals;
    use TextpressoDatabaseGlobals;
    
    my $rslt = new TextpressoTable;
    $rslt->init;
    $rslt->addtablerow("Literature(s)", "Term", "Attributes");
    
    my $cat = $query->param('category');
    my $category = DB_CATEGORIES->{$cat};
    
    foreach my $lit (keys % { (DB_LITERATURE) }) {
	my $lex_dir = DB_ROOT . (DB_LITERATURE)->{$lit} . (DB_SUPPLEMENTAL)->{lexicon};
	my $files = $lex_dir . $category;
	my @lex_files = <$files*>;
	
	foreach my $file (@lex_files) {
	    (my $fname, my $fdir, my $fsuf) = fileparse($file, qr{\.\d+-gram});
	    $fsuf =~ s/^\.(\d+)-gram/$1/;
	    open (IN, "<$file");
	    my $inline = '';
	    while (my $line = <IN>) {
		$inline .= $line;
	    }
	    my @entries = split (/$del\n/, $inline);
	    foreach my $entry (@entries) {
		my @items = split (/\n/, $entry);
		my $key = shift(@items);
		$rslt->addtablerow($lit, $key, join(", ", @items));
	    }
	    close (IN);
	}
    }
    $main2->addtablerow($rslt->maketable($query, width => "100%",
					 DSP_HDRCOLOR => 'black', DSP_HDRSIZE => 2));
    
}
print $main2->maketable($query, 
			tablestyle => 'borderless-headerbackground', 
			DSP_HDR_SIZE => 3,
			width => "100%");

print $query->end_form;
# End of form                

PrintBottom($query);