-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::SQL;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
+my ( $user, $password, $options, $in, $out, $record, $dbh, $results );
-$default_user = Maasha::UCSC::ucsc_get_user();
-$default_password = Maasha::UCSC::ucsc_get_password();
+$user = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
+$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
$options = Maasha::Biopieces::parse_options(
[
- { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'query', short => 'q', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => $default_user, allowed => undef, disallowed => undef },
- { long => 'password', short => 'p', type => 'string', mandatory => 'no', default => $default_password, allowed => undef, disallowed => undef },
+ { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'query', short => 'q', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { 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 },
]
);
map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
BEGIN
{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
+ Maasha::Biopieces::status_set();
}
+
END
{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
-
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+ Maasha::Biopieces::status_log();
}