#!/usr/bin/env perl

# Copyright (C) 2007-2009 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Remove MySQL database tables.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Common;
use Maasha::SQL;
use Maasha::UCSC;


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


my ( $options, $in, $out, $record, $conf_file, %track_hash, $fh_in, $fh_out, $track, @tracks, $dbh, @new_tracks );

$conf_file = $ENV{ 'HOME' } . "/ucsc/my_tracks.ra";

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'database',    short => 'd', type => 'string', mandatory => 'yes', default => undef,      allowed => undef, disallowed => undef },
        { long => 'tables',      short => 't', type => 'list',   mandatory => 'no',  default => undef,      allowed => undef, disallowed => undef },
        { long => 'keys',        short => 'k', type => 'list',   mandatory => 'no',  default => undef,      allowed => undef, disallowed => undef },
        { long => 'config_file', short => 'c', type => 'file!',  mandatory => 'no',  default => $conf_file, allowed => undef, disallowed => undef },
        { long => 'user',        short => 'u', type => 'string', mandatory => 'no',  default => undef,      allowed => undef, disallowed => undef },
        { long => 'password',    short => 'p', type => 'string', mandatory => 'no',  default => undef,      allowed => undef, disallowed => undef },
    ]   
);

$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );

Maasha::Common::error( qq(both --tables and --keys specified) ) if     $options->{ "tables" } and     $options->{ "keys" };
Maasha::Common::error( qq(no --tables or --keys specified) )    if not $options->{ "tables" } and not $options->{ "keys" };

$options->{ "user" }     ||= Maasha::UCSC::ucsc_get_user();
$options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();

map { $track_hash{ $_ } = 1 } @{ $options->{ 'tracks' } };

while ( $record = Maasha::Biopieces::get_record( $in ) )
{
    map { $track_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };

    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
}

$fh_in = Maasha::Filesys::file_read_open( $options->{ 'config_file' } );

while ( $track = Maasha::UCSC::ucsc_config_entry_get( $fh_in ) ) {
    push @tracks, $track;
}

close $fh_in;

foreach $track ( @tracks )
{
    if ( $track->{ 'database' } eq $options->{ 'database' } and exists $track_hash{ $track->{ 'track' } } ) {
        print STDERR qq(Removing track "$track->{ 'track' }" from config file.\n) if $options->{ 'verbose' };
    } else {
        push @new_tracks, $track;
    }
}

rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";

$fh_out = Maasha::Filesys::file_write_open( $options->{ 'config_file' } );

map { Maasha::UCSC::ucsc_config_entry_put( $_, $fh_out ) } @new_tracks;

close $fh_out;

# ---- locate track in database ----

$dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );

foreach $track ( sort keys %track_hash )
{
    if ( Maasha::SQL::table_exists( $dbh, $track ) )
    {
        print STDERR qq(Removing table "$track" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
        Maasha::SQL::delete_table( $dbh, $track );
        print STDERR "done.\n" if $options->{ 'verbose' };
    }
    else
    {
        print STDERR qq(WARNING: table "$track" not found in database "$options->{ 'database' }\n");
    }
}

Maasha::SQL::disconnect( $dbh );

Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );

Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


BEGIN
{
    Maasha::Biopieces::status_set();
}


END
{
    Maasha::Biopieces::status_log();
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__