Raw content of Bio::EnsEMBL::Hive::AnalysisJob
<![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::AnalysisJob
=head1 DESCRIPTION
An AnalysisJob is the link between the input_id control data, the analysis and
the rule system. It also tracks the state of the job as it is processed
=head1 CONTACT
Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=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::AnalysisJob;
use strict;
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::Worker;
sub new {
my ($class,@args) = @_;
my $self = bless {}, $class;
return $self;
}
sub adaptor {
my $self = shift;
$self->{'_adaptor'} = shift if(@_);
return $self->{'_adaptor'};
}
sub dbID {
my $self = shift;
$self->{'_dbID'} = shift if(@_);
return $self->{'_dbID'};
}
sub input_id {
my $self = shift;
$self->{'_input_id'} = shift if(@_);
return $self->{'_input_id'};
}
sub hive_id {
my $self = shift;
$self->{'_hive_id'} = shift if(@_);
return $self->{'_hive_id'};
}
sub analysis_id {
my $self = shift;
$self->{'_analysis_id'} = shift if(@_);
return $self->{'_analysis_id'};
}
sub job_claim {
my $self = shift;
$self->{'_job_claim'} = shift if(@_);
return $self->{'_job_claim'};
}
sub status {
my $self = shift;
$self->{'_status'} = shift if(@_);
return $self->{'_status'};
}
sub update_status {
my ($self, $status ) = @_;
return unless($self->adaptor);
$self->status($status);
$self->adaptor->update_status($self);
}
sub retry_count {
my $self = shift;
$self->{'_retry_count'} = shift if(@_);
$self->{'_retry_count'} = 0 unless(defined($self->{'_retry_count'}));
return $self->{'_retry_count'};
}
sub completed {
my $self = shift;
$self->{'_completed'} = shift if(@_);
return $self->{'_completed'};
}
sub runtime_msec {
my $self = shift;
$self->{'_runtime_msec'} = shift if(@_);
$self->{'_runtime_msec'} = 0 unless(defined($self->{'_runtime_msec'}));
return $self->{'_runtime_msec'};
}
sub query_count {
my $self = shift;
$self->{'_query_count'} = shift if(@_);
$self->{'_query_count'} = 0 unless(defined($self->{'_query_count'}));
return $self->{'_query_count'};
}
sub branch_code {
my $self = shift;
$self->{'_branch_code'} = shift if(@_);
$self->{'_branch_code'} = 1 unless(defined($self->{'_branch_code'}));
return $self->{'_branch_code'};
}
sub stdout_file {
my $self = shift;
$self->{'_stdout_file'} = shift if(@_);
return $self->{'_stdout_file'};
}
sub stderr_file {
my $self = shift;
$self->{'_stderr_file'} = shift if(@_);
return $self->{'_stderr_file'};
}
sub print_job {
my $self = shift;
my $logic_name ='';
$logic_name = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->analysis_id)->logic_name if($self->adaptor);
printf("job_id=%d %s(%d) retry=%d input_id='%s'\n",
$self->dbID,
$logic_name,
$self->analysis_id,
$self->retry_count,
$self->input_id);
}
1;
]]>