added an example PipeConfig and corresponding .t to check the funnel-…

…leaching capability

modules/Bio/EnsEMBL/Hive/Examples/Factories/PipeConfig/LeachingTest_conf.pm

@@ -0,0 +1,97 @@
+=pod
+
+=head1 NAME
+
+    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::LeachingTest_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::LeachingTest_conf -password <your_password>
+
+=head1 DESCRIPTION
+
+    When we attempt to create a new semaphored group of jobs and the creation of the funnel job fails
+    because there is already a job with the same primary key, we reuse this funnel job and simply top up
+    the semaphore group with extra fan jobs. This is what we call "leaching".
+
+    This is a small pipeline to test leaching via using templates.
+
+    Note 1: this is not the recommended way to create a single backbone from multiple independent streams!
+
+    Note 2: the 'start' analysis is only needed because of the recently adopted rule of automatically param-stacking
+            the very first job that does not have a local parent (used mainly for maintaining cross-database return capability,
+            but could prove itself useful in other contexts as well). If/when we decide against this feature,
+            we can also drop the 'start' analysis, leaving two independent seeding jobs in 'factory' analysis
+            and changing the leeching.t test accordingly (removing one execution of runWorker).
+
+=head1 LICENSE
+
+    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+    Copyright [2016] EMBL-European Bioinformatics Institute
+
+    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::Factories::PipeConfig::LeachingTest_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
+
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+        {   -logic_name => 'start',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+            -input_ids => [
+                {},
+            ],
+            -flow_into => {
+                1 => { 'factory' => [ {'inputlist' => [ 11, 33, 55, 77 ]}, {'inputlist' => [22, 44, 66 ]} ] },
+            },
+        },
+
+        {   -logic_name => 'factory',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
+            -parameters => {
+                'column_names' => [ 'alpha' ],
+            },
+            -flow_into => {                                         # There are two input jobs...
+                '2->A'  => 'fan',
+                'A->1'  => { 'funnel' => { 'funnel_id' => 7 }},     # ...however we want all of the children to report to one common funnel
+            },
+        },
+
+        {   -logic_name    => 'fan',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',
+            -flow_into => {
+                1 => '?accu_name=alphas&accu_input_variable=alpha&accu_address=[]',
+            },
+        },
+
+        {   -logic_name    => 'funnel',
+            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -parameters => {
+                'alpha_csv' => '#expr( join(",", @{#alphas#}) )expr#',
+                'cmd'       => 'echo "#alpha_csv#"',
+            },
+        },
+    ];
+}
+
+1;

t/10.pipeconfig/leeching.t

@@ -0,0 +1,64 @@
+#!/usr/bin/env perl
+
+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016] EMBL-European Bioinformatics Institute
+#
+# 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.
+
+
+use strict;
+use warnings;
+
+use Test::More;
+
+use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline runWorker get_test_url_or_die);
+
+
+# eHive needs this to initialize the pipeline (and run db_cmd.pl)
+$ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ) );
+
+my $pipeline_url = get_test_url_or_die();
+
+my $url = init_pipeline(
+    'Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::LeachingTest_conf',
+    [-pipeline_url => $pipeline_url, -hive_force_init => 1],
+);
+
+my $pipeline = Bio::EnsEMBL::Hive::HivePipeline->new(
+    -url                        => $url,
+    -disconnect_when_inactive   => 1,
+);
+
+runWorker($pipeline);   # 'start' analysis
+runWorker($pipeline);   # 'factory' analysis
+
+my $analyses_coll   = $pipeline->collection_of('Analysis');
+my $fan_analysis    = $analyses_coll->find_one_by( 'logic_name' => 'fan' );
+my $funnel_analysis = $analyses_coll->find_one_by( 'logic_name' => 'funnel' );
+
+my $hive_dba        = $pipeline->hive_dba;
+my $job_adaptor     = $hive_dba->get_AnalysisJobAdaptor;
+my @funnel_jobs     = @{ $job_adaptor->fetch_all_by_analysis_id( $funnel_analysis->dbID ) };
+
+is(scalar(@funnel_jobs), 1, 'There has to be only one funnel job');
+
+my $funnel_job      = shift @funnel_jobs;
+my $fan_job_count   = $job_adaptor->count_all_by_analysis_id( $fan_analysis->dbID );
+
+is($funnel_job->semaphore_count, $fan_job_count, 'All the fan jobs ('.$fan_job_count.') share the same funnel');
+
+$hive_dba->dbc->disconnect_if_idle();
+system( @{ $hive_dba->dbc->to_cmd(undef, undef, undef, 'DROP DATABASE') } );
+
+done_testing();
+