3 # Copyright (C) 2007-2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # Read records from a MySQL query.
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
30 use Maasha::Biopieces;
35 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 my ( $run_time_beg, $run_time_end, $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
40 $default_user = Maasha::UCSC::ucsc_get_user();
41 $default_password = Maasha::UCSC::ucsc_get_password();
43 $options = Maasha::Biopieces::parse_options(
45 { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
46 { long => 'query', short => 'q', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
47 { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => $default_user, allowed => undef, disallowed => undef },
48 { long => 'password', short => 'p', type => 'string', mandatory => 'no', default => $default_password, allowed => undef, disallowed => undef },
52 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
53 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
55 while ( $record = Maasha::Biopieces::get_record( $in ) ) {
56 Maasha::Biopieces::put_record( $record, $out );
59 $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
61 $results = Maasha::SQL::query_hashref_list( $dbh, $options->{ "query" } );
63 Maasha::SQL::disconnect( $dbh );
65 map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
68 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
73 $run_time_beg = Maasha::Biopieces::run_time();
75 Maasha::Biopieces::log_biopiece();
80 Maasha::Biopieces::close_stream( $in );
81 Maasha::Biopieces::close_stream( $out );
83 $run_time_end = Maasha::Biopieces::run_time();
85 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
89 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<