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

# Upload data to local UCSC Genome Browser Database.

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


use warnings;
use strict;
use Maasha::Common;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::UCSC;
use Maasha::UCSC::Wiggle;
use Maasha::UCSC::PSL;
use Maasha::UCSC::BED;


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


my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'database',    short => 'd', type => 'string', mandatory => 'yes', default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'table',       short => 't', type => 'string', mandatory => 'yes', default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'no_stream',   short => 'x', type => 'flag',   mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'short_label', short => 's', type => 'string', mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'long_label',  short => 'l', type => 'string', mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'group',       short => 'g', type => 'string', mandatory => 'no',  default => $ENV{ 'LOGNAME' }, allowed => undef,                         disallowed => undef },
        { long => 'priority',    short => 'p', type => 'float',  mandatory => 'no',  default => 1,                 allowed => undef,                         disallowed => undef },
        { long => 'use_score',   short => 'u', type => 'flag',   mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'visibility',  short => 'V', type => 'string', mandatory => 'no',  default => 'pack',            allowed => 'hide,dense,squish,pack,full', disallowed => undef },
        { long => 'color',       short => 'c', type => 'string', mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
        { long => 'check',       short => 'C', type => 'flag',   mandatory => 'no',  default => undef,             allowed => undef,                         disallowed => undef },
    ]   
);

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

$tmp_dir = Maasha::Biopieces::get_tmpdir();

$options->{ "short_label" } ||= $options->{ 'table' };
$options->{ "long_label" }  ||= $options->{ 'table' };
$options->{ "color" }       ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
$options->{ "chunk_size" }  ||= 10_000_000_000;    # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.

$file   = "$tmp_dir/ucsc_upload.tmp";
$append = 0;
$first  = 1;
$i      = 0;

$fh_out = Maasha::Filesys::file_write_open( $file );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };

    if ( $record->{ "REC_TYPE" } eq "fixed_step" )
    {
        $format = "WIGGLE";

        if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
            Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
        }
    }
    elsif ( $record->{ "REC_TYPE" } eq "PSL" )
    {
        $format = "PSL";

        Maasha::UCSC::PSL::psl_put_header( $fh_out ) if $first;
        Maasha::UCSC::PSL::psl_put_entry( $record, $fh_out );
        
        $first = 0;
    }
    elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
    {
        # chrom chromStart  chromEnd    name    score   strand  size    secStr  conf 

        $format  = "BED_SS";

        print $fh_out join ( "\t",
            $record->{ "CHR" },
            $record->{ "CHR_BEG" },
            $record->{ "CHR_END" } + 1,
            $record->{ "Q_ID" },
            $record->{ "SCORE" },
            $record->{ "STRAND" },
            $record->{ "SIZE" },
            $record->{ "SEC_STRUCT" },
            $record->{ "CONF" },
        ), "\n";
    }
    elsif ( $record->{ "REC_TYPE" } eq "BED" )
    {
        $format  = "BED";
        $columns = $record->{ "BED_COLS" };

        if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
            Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
        }
    }
    elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
    {
        $format  = "BED";
        $columns = 6;

        if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
            Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
        }
    }
    elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
    {
        $format  = "BED";
        $columns = 6;

        $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;

        if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
            Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
        }
    }
    elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
    {
        $format  = "BED";
        $columns = 6;

        if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
            Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
        }
    }

    if ( $i == $options->{ "chunk_size" } )
    {
        close $fh_out;

        if ( $format eq "BED" ) {
            Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
        } elsif ( $format eq "PSL" ) {
            Maasha::UCSC::BED::psl_upload_to_ucsc( $file, $options, $append ); 
        }

        unlink $file;

        $first = 1;

        $append = 1;

        $fh_out = Maasha::Filesys::file_write_open( $file );
    }

    $i++;
}

close $fh_out;

if ( $format eq "BED" )
{
    $type = "bed $columns";

    Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
}
elsif ( $format eq "BED_SS" )
{
    $type = "type bed 6 +";

    Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
}
elsif ( $format eq "PSL" )
{
    $type = "psl";

    Maasha::UCSC::PSL::psl_upload_to_ucsc( $file, $options, $append ); 
}
elsif ( $format eq "WIGGLE" )
{
    $options->{ "visibility" } = "full";

    $wig_file = "$options->{ 'table' }.wig";
    $wib_file = "$options->{ 'table' }.wib";

    $wib_dir  = "$ENV{ 'HOME' }/ucsc/wib";

    Maasha::Filesys::dir_create_if_not_exists( $wib_dir );

    if ( $options->{ 'verbose' } ) {
        `cd $tmp_dir && wigEncode $file $wig_file $wib_file`;
    } else {
        `cd $tmp_dir && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
    }

    Maasha::Common::run( "mv", "$tmp_dir/$wib_file $wib_dir" );

    unlink $file;

    $file = $wig_file;

    $type = "wig 0";

    Maasha::UCSC::Wiggle::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
}

unlink $file;

Maasha::UCSC::ucsc_update_config( $options, $type );

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


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


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


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


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


__END__