AnalysisJob.pm 3.09 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1 2 3 4 5 6 7 8 9
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME

Jessica Severin's avatar
Jessica Severin committed
10
  Bio::EnsEMBL::Hive::AnalysisJob
Jessica Severin's avatar
Jessica Severin committed
11 12

=head1 DESCRIPTION
Jessica Severin's avatar
Jessica Severin committed
13

14
  An AnalysisJob is the link between the input_id control data, the analysis and
Jessica Severin's avatar
Jessica Severin committed
15
  the rule system.  It also tracks the state of the job as it is processed
Jessica Severin's avatar
Jessica Severin committed
16 17

=head1 CONTACT
Jessica Severin's avatar
Jessica Severin committed
18

19 20
  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
21 22

=head1 APPENDIX
Jessica Severin's avatar
Jessica Severin committed
23

24 25
  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
26

Jessica Severin's avatar
Jessica Severin committed
27 28 29 30 31 32 33 34 35 36
=cut

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

use strict;

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

37 38 39 40 41
sub new {
  my ($class,@args) = @_;
  my $self = bless {}, $class;
  return $self;
}
Jessica Severin's avatar
Jessica Severin committed
42 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

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 ) = @_;
81
  $self->{'_status'} = $value if($value);
Jessica Severin's avatar
Jessica Severin committed
82 83 84
  return $self->{'_status'};
}

85 86 87 88 89 90 91
sub update_status {
  my ($self, $status ) = @_;
  return unless($self->adaptor);
  $self->status($status);
  $self->adaptor->update_status($self);
}

Jessica Severin's avatar
Jessica Severin committed
92 93 94 95 96 97 98 99 100 101 102 103
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'};
}

104 105 106 107 108 109 110 111 112 113 114 115 116 117
sub runtime_msec {
  my( $self, $value ) = @_;
  $self->{'_runtime_msec'} = $value if($value);
  $self->{'_runtime_msec'} = 0 unless(defined($self->{'_runtime_msec'}));
  return $self->{'_runtime_msec'};
}

sub query_count {
  my( $self, $value ) = @_;
  $self->{'_query_count'} = $value if($value);
  $self->{'_query_count'} = 0 unless(defined($self->{'_query_count'}));
  return $self->{'_query_count'};
}

Jessica Severin's avatar
Jessica Severin committed
118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145
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;