AnalysisJob.pm 2.65 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1 2 3 4 5 6 7 8
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME
9
  Bio::EnsEMBL::Hive::AnalysisJob
Jessica Severin's avatar
Jessica Severin committed
10 11 12 13 14 15
=cut

=head1 SYNOPSIS
=cut

=head1 DESCRIPTION
16 17
  An AnalysisJob is the link between the input_id control data, the analysis and
  the rule system.  It also tracks the state the state of the job as it's processed
Jessica Severin's avatar
Jessica Severin committed
18 19 20
=cut

=head1 CONTACT
21 22
  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Jessica Severin's avatar
Jessica Severin committed
23 24 25
=cut

=head1 APPENDIX
26 27
  The rest of the documentation details each of the object methods.
  Internal methods are usually preceded with a _
Jessica Severin's avatar
Jessica Severin committed
28 29 30 31 32 33 34 35 36 37
=cut

package Bio::EnsEMBL::Hive::AnalysisJob;

use strict;

use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::Worker;

38 39 40 41 42
sub new {
  my ($class,@args) = @_;
  my $self = bless {}, $class;
  return $self;
}
Jessica Severin's avatar
Jessica Severin committed
43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129

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, $value ) = @_;
  $self->{'_input_id'} = $value if($value);
  return $self->{'_input_id'};
}

sub hive_id {
  my $self = shift;
  $self->{'_hive_id'} = shift if(@_);
  return $self->{'_hive_id'};
}

sub analysis_id {
  my( $self, $value ) = @_;
  $self->{'_analysis_id'} = $value if($value);
  return $self->{'_analysis_id'};
}

sub job_claim {
  my( $self, $value ) = @_;
  $self->{'_job_claim'} = $value if($value);
  return $self->{'_job_claim'};
}

sub status {
  my( $self, $value ) = @_;

  if($value) {
    $self->{'_status'} = $value;
    $self->adaptor->update_status($self) if($self->adaptor);
  }
  return $self->{'_status'};
}

sub retry_count {
  my( $self, $value ) = @_;
  $self->{'_retry_count'} = $value if($value);
  return $self->{'_retry_count'};
}

sub completed {
  my( $self, $value ) = @_;
  $self->{'_completed'} = $value if($value);
  return $self->{'_completed'};
}

sub branch_code {
  my( $self, $value ) = @_;
  $self->{'_branch_code'} = $value if(defined($value));
  $self->{'_branch_code'} = 1 unless(defined($self->{'_branch_code'}));
  return $self->{'_branch_code'};
}

sub stdout_file {
  my( $self, $value ) = @_;
  $self->{'_stdout_file'} = $value if(defined($value));
  return $self->{'_stdout_file'};
}

sub stderr_file {
  my( $self, $value ) = @_;
  $self->{'_stderr_file'} = $value if(defined($value));
  return $self->{'_stderr_file'};
}

sub print_job {
  my $self = shift;
  print("WORKER: hive_id=",$self->hive_id,
     " host=",$self->host,
     " ppid=",$self->process_id,
     "\n");  
}

1;