Raw content of Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
my $runDB = Bio::EnsEMBL::Hive::RunnableDB::SystemCmd->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$runDB->fetch_input(); #reads from DB
$runDB->run();
$runDB->output();
$runDB->write_output(); #writes to DB
=cut
=head1 DESCRIPTION
This object is a very simple module. It takes the input_id
and runs it as a system command.
=cut
=head1 CONTACT
jessica@ebi.ac.uk
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
use strict;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Hive::Process;
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
##############################################################
#
# override inherited fetch_input, run, write_output methods
# so that nothing is done
#
##############################################################
sub fetch_input {
my $self = shift;
print("input_id\n ", $self->input_id,"\n");
$self->{'cmd'} = $self->input_id;
if($self->input_id =~ /^{/) {
my $input_hash = eval($self->input_id);
if($input_hash) {
$self->{'cmd'} = $input_hash->{'cmd'} if($input_hash->{'cmd'});
if($input_hash->{'did'}) {
$self->{'cmd'} = $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($input_hash->{'did'});
}
}
}
print("cmd\n ", $self->{'cmd'},"\n");
return 1;
}
sub run
{
my $self = shift;
system($self->{'cmd'}) == 0 or die "system ".$self->{'cmd'}." failed: $?";
return 1;
}
sub write_output {
my $self = shift;
return 1;
}
1;
]]>