[Bio] / FigWebServices / check_ann_errs.cgi Repository:
ViewVC logotype

View of /FigWebServices/check_ann_errs.cgi

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.3 - (download) (annotate)
Mon Sep 22 16:42:31 2008 UTC (11 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, myrast_rel40, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, 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_0923, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, HEAD
Changes since 1.2: +1 -1 lines
add target to links in check_ann_err.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;
use DBKernel;

my $fig = new FIG;
use HTML;
use strict;
use URI::Escape;

use CGI;
my $cgi = new CGI;

if (0)
{
    my $VAR1;
    eval(join("",`cat /tmp/check_err_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_err_parms"))
	{
	    print TMP &Dumper($cgi);
	    close(TMP);
	}
    }
    exit;
}

my $html = [];
unshift @$html, "<TITLE>Check Errors in Subsystem PEGs</TITLE>\n";

my $user       = $cgi->param('user');
my @remove     = $cgi->param('remove');

if (! $user)
{
    push(@$html,$cgi->h1('you need to specify a user'));
}
elsif ($cgi->param('process removals from list') && (@remove > 0))
{
    &remove($fig,\@remove);
    my $n = @remove;
    push(@$html,$cgi->h1("removed $n pegs"));
    &show_stuff($fig,$cgi,$html,$user);
}
else
{
    &show_stuff($fig,$cgi,$html,$user);
}
&HTML::show_page($cgi,$html, 1, undef, undef, undef, undef, { no_fig_search => 1 });

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

    my $errs = &load_pegs($fig,$cgi,$user);
    my $sample = &extract_sample($errs);

    push(@$html,$cgi->start_form(-action => "check_ann_errs.cgi"));
    my $col_hdrs = ["it's OK","PEG","Subsystems","function"];
    my $tab = [];
    my $peg;
    foreach $peg (@$errs)
    {
	my @sub = $fig->peg_to_subsystems($peg,1);
	my $sub_to_show = join("<br>",@sub);
	my $link = "<a href=seedviewer.cgi?page=Annotation;feature=$peg target=_blank>$peg</a>";
	my $func = $fig->function_of($peg);
	my $checked = $cgi->checkbox(-name => 'remove', -value => $peg, -checked => 0, -label => "");
	push(@$tab,[$checked,$link,$sub_to_show,$func]);
    }
    push(@$html,&HTML::make_table($col_hdrs,$tab,"PEGs To Check"));
    push(@$html,$cgi->br,$cgi->hidden(-name => 'user', -value => $user),
	        $cgi->submit('process removals from list'), $cgi->end_form,$cgi->br);

}

sub remove {
    my($fig,$pegs) = @_;

    my %to_remove = map { $_ => 1 } @$pegs;

    if (-s "$FIG_Config::global/PEGs.to.check~") { unlink("$FIG_Config::global/PEGs.to.check~") }
    if (rename("$FIG_Config::global/PEGs.to.check","$FIG_Config::global/PEGs.to.check~") &&
	open(IN,"<$FIG_Config::global/PEGs.to.check~") &&
	open(OUT,">$FIG_Config::global/PEGs.to.check"))
    {
	my $x;
	while (defined($x = <IN>))
	{
	    if (($x =~ /^(\S+)\t(\S.*\S)/) && (! $to_remove{$1}) && ($2 eq $fig->function_of($1)))
	    {
		print OUT $x;
	    }
	}
	close(IN);
	close(OUT);
    }
}

sub extract_sample {
    my($xL) = @_;

    if (@$xL < 200) { return $xL }
    my %seen;
    my $i;
    my $sample = [];
    for ($i=0; ($i < 50); $i++)
    {
	my $n = int(rand() * @$xL);
	if (($n >= 0) && ($n < @$xL) && (! $seen{$n}))
	{
	    $seen{$n} = 1;
	    push(@$sample,$xL->[$n]);
	}
    }
    return $sample;
}

sub load_pegs {
    my($fig,$cgi,$user) = @_;
    my(%user_subs,$sub);

    foreach $sub ($fig->all_subsystems)
    {
	if ($fig->subsystem_curator($sub) eq $user)
	{
	    $user_subs{$sub} = 1;
	}
    }

    my @pegs;
    if (open(PEGS,"<$FIG_Config::global/PEGs.to.check"))
    {
	while (defined($_ = <PEGS>))
	{
	    if ($_ =~ /^(fig\|\d+\.\d+\.peg\.\d+)\t(\S.*\S)/)
	    {
		my $peg = $1;
		my $func = $2;
		if ($func eq $fig->function_of($peg))
		{
                    my @subs = $fig->subsystems_for_peg_complete($peg);
                    my $i;
                    for ($i=0; ($i < @subs) && ((! $user_subs{$subs[$i]->[0]}) ||
                                                ($subs[$i]->[2] =~ /^(0|-1)$/) ||
                                                $subs[$i]->[3]);
                         $i++) {}
                    if ($i < @subs)
                    {
                        push(@pegs,$peg);
                    }
		}
	    }
	}
	close(PEGS);
	return \@pegs;
    }
    else
    {
	print STDERR "no PEGs.to.check file\n";
	return [];
    }
}


MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3