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Revision 1.2 - (download) (as text) (annotate)
Thu Mar 23 03:47:11 2006 UTC (13 years, 7 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
Changes since 1.1: +22 -20 lines
RAE: New delete attribute files to remove all files. maybe this will work

# 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.
#

#__perl__

use FIG;
use Tracer;
use strict;

my $fig = new FIG;

=pod

=head1 delete_all_attribute_files

Look through the sources for all the atttributes file and remove the files. This should be done when you are ready to reload all attributes.

This script takes one optional parameter, and that is the name of the file (-name=filename).

If the name is provided, only that file will be deleted. If the name is not provided, all files will be deleted. 

Note that the old files are moved to "$FIG_Config::temp/Attributes/deleted_attributes/" and not actually deleted!

=cut 

my ($options, @genomes) = StandardSetup([],
        { 
        name => ['', "Name of a single attribute that you want to remove. For example, -name=evidence_code will remove all the evidence code files everywhere"],
        }, "",
        @ARGV);

my $delete = "$FIG_Config::temp/Attributes/deleted_attributes/"; # this is the place that we are actually going to move things to

foreach my $genome ($fig->genomes)
{
    my $dir = "$FIG_Config::organisms/$genome/Attributes";
    if (-e $dir)
    {
        `mkdir -p $delete/$genome/Attributes/`;
        opendir(ATTR,$dir) || die "Can't open directory $dir??";
        foreach my $f (grep { $_ !~ /^\./ } readdir(ATTR)) 
        {
            next if ($options->{name} && ($f ne $options->{name}));
            `mv $FIG_Config::organisms/$genome/Attributes/$f $delete/$genome/Attributes/`
        } 
    }

    my $fattdir="$FIG_Config::organisms/$genome/Features";
    if (-e $fattdir)
    {
        opendir(FEATURES, $fattdir) || die "Can't open dir $fattdir";
        foreach my $dir (grep { $_ !~ /^\./ && $_ !~ /^\#/ } readdir(FEATURES))
        {
            if (-e "$fattdir/$dir/Attributes") 
            {
                `mkdir -p $delete/$genome/Features/$dir/Attributes`;
                opendir(ATTR,"$fattdir/$dir/Attributes") || die "Can't open $fattdir/$dir/Attributes even though it exists";
                foreach my $f (grep { $_ !~ /^\./ } readdir(ATTR))
                {
                    next if ($options->{name} && ($f ne $options->{name}));
                    `mv $fattdir/$dir/Attributes/$f $delete/$genome/Features/$dir/Attributes/$f`;
                }
            }
        }
    }
}
    

# now we need to load the global attributes files
`mkdir -p $delete/Global/Attributes/`;
if (opendir(DIR, "$FIG_Config::global/Attributes/")) 
{
    foreach my $f (grep {$_ !~ /^\./ } readdir(DIR))
    {
        next if ($options->{name} && ($f ne $options->{name}));
        `mv $FIG_Config::global/Attributes/$f $delete/Global/Attributes/`;
    }
}

if ($options->{name}) 
{
    print STDERR "Attributes called ", $options->{name}, " have been moved to $delete\n";
}
else
{
    print STDERR "All attribute files have been moved to $delete\n";
}

print STDERR "You can still dump all the existing attributes using dump_attributes or fig get_all_attributes as they have not been deleted from the database\n";


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