#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Get an EMBL entry from the MySQL database and flatfiles.

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


use warnings;
use strict;
use Data::Dumper;
use Maasha::SQL;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::EMBL;


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


my ( $options, $user, $password, $database, $table, $dbh, $in, $out, $record, $entry, @ids, $id, $file, $offset, $len, $results, $result, $fh, %fh_hash );

$user     = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
$database = Maasha::Biopieces::biopiecesrc( "EMBL_DATABASE" );
$table    = Maasha::Biopieces::biopiecesrc( "EMBL_TABLE" );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'user',       short => 'u', type => 'string', mandatory => 'no', default => $user,     allowed => undef, disallowed => undef },
        { long => 'password',   short => 'p', type => 'string', mandatory => 'no', default => $password, allowed => undef, disallowed => undef },
        { long => 'database',   short => 'd', type => 'string', mandatory => 'no', default => $database, allowed => undef, disallowed => undef },
        { long => 'table',      short => 't', type => 'string', mandatory => 'no', default => $table,    allowed => undef, disallowed => undef },
        { long => 'ids',        short => 'i', 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 => 'features',   short => 'f', type => 'list',   mandatory => 'no', default => undef,     allowed => undef, disallowed => undef },
        { long => 'qualifiers', short => 'q', type => 'list',   mandatory => 'no', default => undef,     allowed => undef, disallowed => undef },
    ]   
);

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

if ( not Maasha::SQL::database_exists( $options->{ 'database' }, $options->{ 'user' }, $options->{ 'password' } ) ) {
    Maasha::Common::error( qq(Database "$options->{ 'database' }" don't exists) );
}

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

if ( not Maasha::SQL::table_exists( $dbh, $options->{ 'table' } ) ) {
    Maasha::Common::error( qq(Table "$options->{ 'table' }" don't exists) );
}

@ids = @{ $options->{ 'ids' } } if defined $options->{ 'ids' };

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    push @ids, $record->{ 'ID' } if exists $record->{ 'ID' };

    Maasha::Biopieces::put_record( $record, $out );
}

foreach $id ( @ids )
{
    $results = Maasha::SQL::query_array( $dbh, qq(SELECT FILE,OFFSET,LEN from $options->{ 'table' } WHERE ID="$id") );

    foreach $result ( @{ $results } )
    {
        ( $file, $offset, $len ) =  @{ $result };

        if ( not exists $fh_hash{ $file } )
        {
            $fh = Maasha::Filesys::file_read_open( $file );

            $fh_hash{ $file } = $fh;
        }

        $entry = Maasha::Filesys::file_read( $fh_hash{ $file }, $offset, $len );

        map { Maasha::Biopieces::put_record( $_, $out ) } Maasha::EMBL::embl2biopieces( $entry, $options );
    }
}

map { close $fh_hash{ $_ } } keys %fh_hash;

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


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


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


END
{
    Maasha::SQL::disconnect( $dbh ) if $dbh;
    Maasha::Biopieces::status_log();
}


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


__END__