Bio::EnsEMBL::Hive AnalysisJob
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Summary
  Bio::EnsEMBL::Hive::AnalysisJob
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis
Bio::EnsEMBL::DBSQL::DBAdaptor
Bio::EnsEMBL::Hive::Worker
Synopsis
No synopsis!
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
Methods
adaptor
No description
Code
analysis_id
No description
Code
branch_code
No description
Code
completed
No description
Code
dbID
No description
Code
hive_id
No description
Code
input_id
No description
Code
job_claim
No description
Code
new
No description
Code
print_job
No description
Code
query_count
No description
Code
retry_count
No description
Code
runtime_msec
No description
Code
status
No description
Code
stderr_file
No description
Code
stdout_file
No description
Code
update_status
No description
Code
Methods description
None available.
Methods code
adaptordescriptionprevnextTop
sub adaptor {
  my $self = shift;
  $self->{'_adaptor'} = shift if(@_);
  return $self->{'_adaptor'};
}
analysis_iddescriptionprevnextTop
sub analysis_id {
  my $self = shift;
  $self->{'_analysis_id'} = shift if(@_);
  return $self->{'_analysis_id'};
}
branch_codedescriptionprevnextTop
sub branch_code {
  my $self = shift;
  $self->{'_branch_code'} = shift if(@_);
  $self->{'_branch_code'} = 1 unless(defined($self->{'_branch_code'}));
  return $self->{'_branch_code'};
}
completeddescriptionprevnextTop
sub completed {
  my $self = shift;
  $self->{'_completed'} = shift if(@_);
  return $self->{'_completed'};
}
dbIDdescriptionprevnextTop
sub dbID {
  my $self = shift;
  $self->{'_dbID'} = shift if(@_);
  return $self->{'_dbID'};
}
hive_iddescriptionprevnextTop
sub hive_id {
  my $self = shift;
  $self->{'_hive_id'} = shift if(@_);
  return $self->{'_hive_id'};
}
input_iddescriptionprevnextTop
sub input_id {
  my $self = shift;
  $self->{'_input_id'} = shift if(@_);
  return $self->{'_input_id'};
}
job_claimdescriptionprevnextTop
sub job_claim {
  my $self = shift;
  $self->{'_job_claim'} = shift if(@_);
  return $self->{'_job_claim'};
}
newdescriptionprevnextTop
sub new {
  my ($class,@args) = @_;
  my $self = bless {}, $class;
  return $self;
}
print_jobdescriptionprevnextTop
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;
}
query_countdescriptionprevnextTop
sub query_count {
  my $self = shift;
  $self->{'_query_count'} = shift if(@_);
  $self->{'_query_count'} = 0 unless(defined($self->{'_query_count'}));
  return $self->{'_query_count'};
}
retry_countdescriptionprevnextTop
sub retry_count {
  my $self = shift;
  $self->{'_retry_count'} = shift if(@_);
  $self->{'_retry_count'} = 0 unless(defined($self->{'_retry_count'}));
  return $self->{'_retry_count'};
}
runtime_msecdescriptionprevnextTop
sub runtime_msec {
  my $self = shift;
  $self->{'_runtime_msec'} = shift if(@_);
  $self->{'_runtime_msec'} = 0 unless(defined($self->{'_runtime_msec'}));
  return $self->{'_runtime_msec'};
}
statusdescriptionprevnextTop
sub status {
  my $self = shift;
  $self->{'_status'} = shift if(@_);
  return $self->{'_status'};
}
stderr_filedescriptionprevnextTop
sub stderr_file {
  my $self = shift;
  $self->{'_stderr_file'} = shift if(@_);
  return $self->{'_stderr_file'};
}
stdout_filedescriptionprevnextTop
sub stdout_file {
  my $self = shift;
  $self->{'_stdout_file'} = shift if(@_);
  return $self->{'_stdout_file'};
}
update_statusdescriptionprevnextTop
sub update_status {
  my ($self, $status ) = @_;
  return unless($self->adaptor);
  $self->status($status);
  $self->adaptor->update_status($self);
}
General documentation
CONTACTTop
  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
APPENDIXTop
  The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _