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Revision 1.1 - (download) (annotate)
Thu Jul 6 17:19:42 2006 UTC (13 years, 4 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
add check_bad.cgi

# -*- perl -*-
#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#


use FIG;
my $fig = new FIG;

use HTML;
use strict;

use CGI;
my $cgi = new CGI;

if (0)
{
    my $VAR1;
    eval(join("",`cat /tmp/check_bad_parms`));
    $cgi = $VAR1;
#   print STDERR &Dumper($cgi);
}

if (0)
{
    print $cgi->header;
    my @params = $cgi->param;
    print "<pre>\n";
    foreach $_ (@params)
    {
	print "$_\t:",join(",",$cgi->param($_)),":\n";
    }

    if (0)
    {
	if (open(TMP,">/tmp/check_bad_parms"))
	{
	    print TMP &Dumper($cgi);
	    close(TMP);
	}
    }
    exit;
}
my($genome);


my $html = [];
unshift @$html, "<TITLE>Check Bad Conflicts</TITLE>\n";

if (open(BAD,"<$FIG_Config::global/bad.figfams"))
{
    my $user = $cgi->param('user'); 
    $user =~ s/^master://;
    if (! $user)
    {
	push(@$html, $cgi->start_form(-action => "check_bad.cgi",
				      -method => 'post'),
	             $cgi->textfield(-name => 'user', -size => 15, -override => 1),
	     $cgi->submit('set user'));
    }
    else
    {
	my $line = <BAD>;
	while ($line && ($line =~ /^(\S+)/))
	{
	    my $curr = $1;
	    my @set = ();
	    while ($line && ($line =~ /^(\S+)\t(\S+)/) && ($1 eq $curr))
	    {
		push(@set,$2);
		$line = <BAD>;
	    }
	    &process_set($fig,$cgi,$html,$user,\@set);
	}
    }
}
else
{
    push(@$html,$cgi->h1('Nothing bad to check'));
}
&HTML::show_page($cgi,$html);

sub process_set {
    my($fig,$cgi,$html,$user,$set) = @_;

    my $keep = 0;
    my @in_sub = ();
    foreach my $peg (@$set)
    {
        my @subs = grep { $fig->usable_subsystem($_) } $fig->peg_to_subsystems($peg);
        if (@subs > 0)
        {
	    if (! $keep)
	    {
		foreach my $sub (@subs)
		{
		    my $curator = $fig->subsystem_curator($sub);
		    $curator =~ s/^master://;
		    if ($curator eq $user)
		    {
			$keep = 1;
		    }
		}
	    }
            push(@in_sub,$peg);
        }
    }

    my $ok = 1;
    if ((@in_sub > 1) && $keep)
    {
        my $func = $fig->function_of($in_sub[0]);
        my $i;
        for ($i=1; ($i < @in_sub) && ($fig->function_of($in_sub[$i]) eq $func); $i++) {}
        $ok = ($i == @in_sub);
    }
    
    if (! $ok)
    {
	my $col_hdrs = ["PEG","Function"];
	my $tab = [];
	foreach my $peg (@in_sub)
	{
	    my $peg_link = &HTML::fid_link($cgi,$peg);
	    push(@$tab,[$peg_link,scalar $fig->function_of($peg)]);
	}
	push(@$html,&HTML::make_table($col_hdrs,$tab,""));
    }
}

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