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Summary

Bio::EnsEMBL::Hive::RunnableDB::Test

Package variables

Included modules

Inherit

Bio::EnsEMBL::Hive::Process

Synopsis

my $db = Bio::EnsEMBL::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Hive::RunnableDB::Dummy->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$repmask->fetch_input(); #reads from DB
$repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB

Description

This object is used to test failure of jobs in the hive system.
It is intended for development purposes only!!
It parses the analysis.parameters and analysis_job.input_id as
(string representing) hasrefs and extracts the divisor and the value.
If the modulo (value % divisor) is 0, the job will fail.

Methods

Methods description

  Arg [1]     : (optional) $divisor
  Example     : $object->divisor($divisor);
  Example     : $divisor = $object->divisor();
  Description : Getter/setter for the divisor attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable

  Implementation of the Bio::EnsEMBL::Hive::Process interface

  Implementation of the Bio::EnsEMBL::Hive::Process interface

  Arg [1]     : (optional) $time_fetching
  Example     : $object->time_fetching($time_fetching);
  Example     : $time_fetching = $object->time_fetching();
  Description : Getter/setter for the time_fetching attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable

  Arg [1]     : (optional) $time_running
  Example     : $object->time_running($time_running);
  Example     : $time_running = $object->time_running();
  Description : Getter/setter for the time_running attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable

  Arg [1]     : (optional) $time_writting
  Example     : $object->time_writting($time_writting);
  Example     : $time_writting = $object->time_writting();
  Description : Getter/setter for the time_writting attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable

  Arg [1]     : (optional) $value
  Example     : $object->value($value);
  Example     : $value = $object->value();
  Description : Getter/setter for the value attribute
  Returntype  : 
  Exceptions  : none
  Caller      : general
  Status      : Stable

  Implementation of the Bio::EnsEMBL::Hive::Process interface

Methods code

sub divisor {

  my $self = shift;
  if (@_) {
    $self->{_divisor} = shift;
  }
  return $self->{_divisor};

}

sub fetch_input {

  my $self = shift;

  # Initialise values
  $self->divisor(2);
  $self->value(1);
  $self->time_fetching(0);
  $self->time_running(0);
  $self->time_writting(0);

  # Read parameters and input
  $self->get_params($self->parameters);
  $self->get_params($self->input_id);

  # Sleep as required
  sleep($self->time_fetching);

  return 1;

}

sub get_params {

  my $self         = shift;
  my $param_string = shift;

  return unless($param_string);
#   print("parsing parameter string : ",$param_string,"\n");

  my $params = eval($param_string);
  return unless($params);

  if(defined($params->{'divisor'})) {
    $self->divisor($params->{'divisor'});
  }
  if(defined($params->{'value'})) {
    $self->value($params->{'value'});
  }
  if(defined($params->{'time_fetching'})) {
    $self->time_fetching($params->{'time_fetching'});
  }
  if(defined($params->{'time_running'})) {
    $self->time_running($params->{'time_running'});
  }
  if(defined($params->{'time_writting'})) {
    $self->time_writting($params->{'time_writting'});
  }
}

1;

}

sub run {

  my $self = shift;

  # Sleep as required
  sleep($self->time_running);

  # Fail if modulus of $value and $divisor is 0
  my $divisor = $self->divisor();
  my $value = $self->value();
  if (!$divisor or !defined($value)) {
    die "Wrong parameters: divisor = $divisor and value = $value\n";
  } elsif ($value % $divisor == 0) {
    die "$value % $divisor is 0 => die!\n";
  }

  return 1;

}

sub time_fetching {

  my $self = shift;
  if (@_) {
    $self->{_time_fetching} = shift;
  }
  return $self->{_time_fetching};

}

sub time_running {

  my $self = shift;
  if (@_) {
    $self->{_time_running} = shift;
  }
  return $self->{_time_running};

}

sub time_writting {

  my $self = shift;
  if (@_) {
    $self->{_time_writting} = shift;
  }
  return $self->{_time_writting};

}

sub value {

  my $self = shift;
  if (@_) {
    $self->{_value} = shift;
  }
  return $self->{_value};

}

sub write_output {

  my $self = shift;

  # Sleep as required
  sleep($self->time_writting);

  return 1;

}

General documentation

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _