Bio::EnsEMBL::Hive::RunnableDB SystemCmd
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Summary
Bio::EnsEMBL::Hive::RunnableDB::SystemCmd
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor
Bio::EnsEMBL::Hive::Process
Inherit
Bio::EnsEMBL::Hive::Process
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
Description
This object is a very simple module. It takes the input_id
and runs it as a system command.
Methods
fetch_input
No description
Code
run
No description
Code
write_output
No description
Code
Methods description
None available.
Methods code
fetch_inputdescriptionprevnextTop
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;
}
rundescriptionprevnextTop
sub run {
  my $self = shift;
  system($self->{'cmd'}) == 0 or die "system ".$self->{'cmd'}." failed: $?";
  return 1;
}
write_outputdescriptionprevnextTop
sub write_output {
  my $self = shift;
  return 1;
}

1;
}
General documentation
CONTACTTop
jessica@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _