a pipeline to test the FailureTest

modules/Bio/EnsEMBL/Hive/PipeConfig/FailureTest_conf.pm

+
+=pod
+
+=head1 NAME
+
+  Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf -password <your_password>
+
+    init_pipeline.pl FailureTest_conf.pm -pipeline_db -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 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+package Bio::EnsEMBL::Hive::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
+
+                  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 {
+        'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/work',     # some Compara developers might prefer $ENV{'HOME'}.'/ensembl_main'
+
+        'pipeline_name' => 'failure_test',                  # name used by the beekeeper to prefix job names on the farm
+
+        'pipeline_db' => {                                  # connection parameters
+            -host   => 'compara3',
+            -port   => 3306,
+            -user   => 'ensadmin',
+            -pass   => $self->o('password'),                        # a rule where a previously undefined parameter is used (which makes either of them obligatory)
+            -dbname => $ENV{USER}.'_'.$self->o('pipeline_name'),    # a rule where a previously defined parameter is used (which makes both of them optional)
+        },
+
+        'job_count'         => 50,                                  # controls the total number of FailureTest jobs
+        'failure_rate'      =>  2,                                  # controls the rate of jobs that are programmed to fail
+    };
+}
+
+=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 ($self) = @_;
+    return [
+        {   -logic_name => 'generate_jobs',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
+            -parameters => {
+                'inputlist'    => '#expr([1..$job_count])expr#',    # this expression will evaluate into a listref
+            },
+            -input_ids => [
+                {
+                    'job_count'    => $self->o('job_count'),            # turn this option into a passable parameter
+                    'failure_rate' => $self->o('failure_rate'),         # turn the other option into a passable parameter as well
+                    'input_id' => { 'value' => '#_range_start#', 'divisor' => '#failure_rate#' },
+                },
+            ],
+            -flow_into => {
+                2 => [ 'failure_test' ],   # will create a fan of jobs
+            },
+        },
+
+        {   -logic_name    => 'failure_test',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::FailureTest',
+        },
+    ];
+}
+
+1;
+