Merge pull request #900 from Ensembl/feature/genome_factory_integrati…

…on_homology_pipeline

genome factory integration for homology pipeline

modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblHomologyAnnotation_conf.pm

@@ -0,0 +1,102 @@
+=head1 LICENSE
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2024] 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.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::Compara::PipeConfig::HomologyAnnotation_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl Bio::EnsEMBL::Production::Pipeline::PipeConfig::EnsemblHomologyAnnotation_conf -host mysql-ens-compara-prod-X -port XXXX \
+         -dataset_type  -dataset_status Submitted -metadata_db_uri mysql://localhost:3366/ensembl_genome_metadata
+
+=head1 DESCRIPTION
+
+The PipeConfig file for the pipeline that annotates gene members by homology
+
+=cut
+
+
+package Bio::EnsEMBL::Production::Pipeline::PipeConfig::EnsemblHomologyAnnotation_conf;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
+use Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf;
+use base ('Bio::EnsEMBL::Compara::PipeConfig::HomologyAnnotation_conf');
+
+
+sub default_options {
+    my ($self) = @_;
+
+    return {
+        %{$self->SUPER::default_options},   # Inherit the generic ones
+        #genome factory params
+        'metadata_db_uri'       => $self->o('metadata_db_uri'),
+        'genome_uuid'           => [],
+        'dataset_uuid'          => [],
+        'dataset_status'        => 'Submitted',
+        'organism_group_type'   => 'DIVISION',
+        'dataset_type'          => 'homology_compute',
+        'antispecies'           => [],
+        'batch_size'            => 50,
+        'meta_filters'          => {},
+        'update_dataset_status' => 'Processing', #updates dataset status in new metadata db
+        #param to connect to old pipeline analysis name
+    };
+}
+sub core_pipeline_analyses {
+    my ($self) = @_;
+    my %dc_parameters = (
+        'datacheck_groups' => $self->o('dc_pipeline_grp'),
+        'db_type'          => $self->o('db_type'),
+        'old_server_uri'   => $self->o('old_server_uri'),
+        'registry_file'    => undef,
+    );
+
+    my @core_compara_analyses = ();
+    foreach my $hash (@{Bio::EnsEMBL::Compara::PipeConfig::HomologyAnnotation_conf::core_pipeline_analyses($self)}) {
+        if ($hash->{'-logic_name'} eq 'core_species_factory') {
+            $hash->{'-parameters'} = $hash->{'-input_ids'}->[0];
+            delete $hash->{'-input_ids'};
+        }
+        push @core_compara_analyses, $hash;
+    }
+
+    my @production_factories = ();
+    foreach my $hash (@{Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf::factory_analyses($self)}) {
+        if ($hash->{'-logic_name'} eq 'GenomeFactory') {
+            $hash->{'-parameters'}->{'division'} = []; # let it to empty array as it conflicts with the division defined in base class  Bio::EnsEMBL::Compara::PipeConfig::HomologyAnnotation_conf -> 'division' => 'homology_annotation',
+            $hash->{'-parameters'}->{'dataset_uuid'} = $self->o('dataset_uuid');
+            $hash->{'-rc_name'} = '2Gb_job';
+            $hash->{'-flow_into'} = {
+                      '3->A'    => { 'core_species_factory'  => INPUT_PLUS()  }, # logic name core_species_factory is from base class  Bio::EnsEMBL::Compara::PipeConfig::HomologyAnnotation_conf
+                      'A->3'    => [{'UpdateDatasetStatus'=> INPUT_PLUS()}]
+            },
+        }
+        push @production_factories, $hash;
+    }
+    return [
+        @production_factories,
+        @core_compara_analyses,
+    ];
+}
+
+
+1;