diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/Test.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/Test.pm
index 417c80ec6623cfef153fd838a044ce857d8da7b8..c3618f9cd8b310699b472b3d47e67f065cc390a9 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/Test.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/Test.pm
@@ -1,7 +1,3 @@
-#
-# You may distribute this module under the same terms as perl itself
-#
-# POD documentation - main docs before the code
=pod
@@ -11,255 +7,106 @@ Bio::EnsEMBL::Hive::RunnableDB::Test
=head1 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
+This is a RunnableDB module that implements Bio::EnsEMBL::Hive::Process interface
+and is ran by Workers during the execution of eHive pipelines.
+It is not generally supposed to be instantiated and used outside of this framework.
+
+Please refer to Bio::EnsEMBL::Hive::Process documentation to understand the basics of the RunnableDB interface.
+
+Please refer to Bio::EnsEMBL::Hive::PipeConfig::* pipeline configuration files to understand how to configure pipelines.
=head1 DESCRIPTION
-This object is used to test failure of jobs in the hive system.
+This RunnableDB module is used to test failure of jobs in the hive system.
-It is intended for development purposes only!!
+It is intended for development/training 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.
+Available parameters:
-=head1 CONTACT
+ param('value'): is essentially your job's number.
+ If you are intending to create 100 jobs, let the param('value') take consecutive values from 1 to 100.
- Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+ param('divisor'): defines the failure rate for this particular analysis. If the modulo (value % divisor) is 0, the job will fail.
+ For example, if param('divisor')==5, jobs with 5, 10, 15, 20, 25,... param('value') will fail.
-=head1 APPENDIX
+ param('time_fetching'): is time in seconds that the job will spend sleeping in FETCH_INPUT state.
-The rest of the documentation details each of the object methods.
-Internal methods are usually preceded with a _
+ param('time_running'): is time in seconds that the job will spend sleeping in RUN state.
-=cut
+ param('time_writing'): is time in seconds that the job will spend sleeping in WRITE_OUTPUT state.
+=head1 CONTACT
+
+ Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
package Bio::EnsEMBL::Hive::RunnableDB::Test;
use strict;
-use Bio::EnsEMBL::Hive::Process;
-our @ISA = qw(Bio::EnsEMBL::Hive::Process);
-
+use base ('Bio::EnsEMBL::Hive::ProcessWithParams');
=head2 fetch_input
- Implementation of the Bio::EnsEMBL::Hive::Process interface
+ Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
+ Here it only sets default values of parameters and sleeps for param('time_fetching').
=cut
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);
+ my $self = shift @_;
- # Read parameters and input
- $self->get_params($self->parameters);
- $self->get_params($self->input_id);
+ $self->param_init(
+ 'value' => 1, # normally you generate a batch of jobs with different values of param('value')
+ 'divisor' => 2, # but the same param('divisor') and see how every param('divisor')'s job will crash
- # Sleep as required
- sleep($self->time_fetching);
+ 'time_fetching' => 0, # how much time fetch_input() will spend in sleeping state
+ 'time_running' => 0, # how much time run() will spend in sleeping state
+ 'time_writing' => 0, # how much time write_output() will spend in sleeping state
+ );
- return 1;
+ # Sleep as required:
+ sleep($self->param('time_fetching'));
}
-
=head2 run
- Implementation of the Bio::EnsEMBL::Hive::Process interface
+ Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process that is used to perform the main bulk of the job (minus input and output).
+ Here it sleeps for param('time_running') and then decides whether to fail or succeed depending on param('value') and param('divisor').
=cut
-sub run
-{
- my $self = shift;
+sub run {
+ my $self = shift @_;
- # Sleep as required
- sleep($self->time_running);
+ my $value = $self->param('value');
+ my $divisor = $self->param('divisor');
- # 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 % $divisor is 0 => die!\n";
- }
+ # Sleep as required:
+ sleep($self->param('time_running'));
- return 1;
+ if(!$divisor or !$value) {
+ die "Wrong parameters: divisor = $divisor and value = $value\n";
+ } elsif ($value % $divisor == 0) {
+ die "$value % $divisor is 0 => die!\n";
+ }
}
-
=head2 write_output
- Implementation of the Bio::EnsEMBL::Hive::Process interface
+ Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
+ Here it only sleeps for param('time_writing').
=cut
sub write_output {
- my $self = shift;
-
- # Sleep as required
- sleep($self->time_writting);
-
- return 1;
-}
-
-
-=head2 divisor
-
- 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
-
-=cut
-
-sub divisor {
- my $self = shift;
- if (@_) {
- $self->{_divisor} = shift;
- }
- return $self->{_divisor};
-}
-
-
-=head2 value
-
- 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
-
-=cut
+ my $self = shift @_;
-sub value {
- my $self = shift;
- if (@_) {
- $self->{_value} = shift;
- }
- return $self->{_value};
-}
-
-
-=head2 time_fetching
-
- 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
-
-=cut
-
-sub time_fetching {
- my $self = shift;
- if (@_) {
- $self->{_time_fetching} = shift;
- }
- return $self->{_time_fetching};
-}
-
-
-=head2 time_running
-
- 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
-
-=cut
-
-sub time_running {
- my $self = shift;
- if (@_) {
- $self->{_time_running} = shift;
- }
- return $self->{_time_running};
-}
-
-
-=head2 time_writting
-
- 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
-
-=cut
-
-sub time_writting {
- my $self = shift;
- if (@_) {
- $self->{_time_writting} = shift;
- }
- return $self->{_time_writting};
-}
-
-
-=head2 get_params
-
-=cut
-
-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'});
- }
+ # Sleep as required:
+ sleep($self->param('time_writing'));
}
1;
+