FailureTest_conf.pm

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=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::FailureTest_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::FailureTest_conf -password <your_password>
 
    init_pipeline.pl FailureTest_conf.pm -host=localhost -password <your_password> -job_count 100 -failure_rate 3
 
=head1 DESCRIPTION
 
    This is an example pipeline built around FailureTest.pm RunnableDB. It consists of two analyses:
 
    Analysis_1: JobFactory.pm is used to create an array of jobs -
 
        these jobs are sent down the branch #2 into the second analysis
 
    Analysis_2: FailureTest.pm either succeeds or dies, depending on the parameters.
 
=head1 LICENSE
 
    See the NOTICE file distributed with this work for additional information
    regarding copyright ownership.
 
    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
 
=head1 CONTACT
 
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
 
=cut
 
 
package Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::FailureTest_conf;
 
use strict;
use warnings;
 
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
 
=head2 default_options
 
    Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
                  In addition to the standard things it defines three options:
                    o('job_count')          controls the total number of FailureTest jobs
                    o('failure_rate')       controls the rate of jobs that are programmed to fail
                    o('state')              controls the state in which the jobs will be failing
                    o('lethal_after')       when job_number is above this (nonzero) threshold, job's death becomes lethal to the Worker
 
                  There is a rule dependent on one option that does not have a default (this makes it mandatory):
                    o('password')           your read-write password for creation and maintenance of the hive database
 
=cut
 
sub default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },               # inherit other stuff from the base class
 
        'job_count'         => 10,                          # controls the total number of FailureTest jobs
        'failure_rate'      =>  3,                          # controls the rate of jobs that are programmed to fail
        'state'             => 'RUN',                       # controls in which state the jobs are programmed to fail
        'lethal_after'      => 0,
    };
}
 
=head2 pipeline_analyses
 
    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
                  Here it defines two analyses:
 
                    * 'generate_jobs'       generates a list of jobs
 
                    * 'failure_test'        either succeeds or fails, depending on parameters
 
=cut
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'generate_jobs',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -parameters => {
                'inputlist'    => '#expr([0..#job_count#-1])expr#',    # this expression will evaluate into a listref
                'column_names' => [ 'value' ],
            },
            -input_ids => [
                { 'job_count'    => $self->o('job_count') },
            ],
            -flow_into => {
                '2->A' => [ 'failure_test' ],
                'A->1' => [ 'funnel' ],
            },
        },
 
        {   -logic_name    => 'failure_test',
            -module        => 'Bio::EnsEMBL::Hive::Examples::FailureTest::RunnableDB::FailureTest',
            -parameters    => {
                'divisor'       => $self->o('failure_rate'),
                'state'         => $self->o('state'),
                'lethal_after'  => $self->o('lethal_after'),
            }
        },
 
        {   -logic_name    => 'funnel',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
        },
    ];
}
 
1;