ApplyToDatabases_conf.pm

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=pod 
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::ApplyToDatabases_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::ApplyToDatabases_conf -password <your_password>
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::Factories::PipeConfig::ApplyToDatabases_conf -password <your_password> -only_databases '%'
 
=head1 DESCRIPTION  
 
    This is an example framework to run queries against databases whose names have been fetched from server:
 
    Analysis_1: JobFactory.pm is used to turn the list of databases on a particular mysql instance into jobs
 
    these jobs are sent down the branch #2 into the second analysis
 
    Analysis_2: Use SqlCmd.pm to run queries directly or another JobFactory.pm if you need a further fan on tables.
 
=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::Factories::PipeConfig::ApplyToDatabases_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 default_options {
    my ($self) = @_;
    return {
        %{ $self->SUPER::default_options() },               # inherit other stuff from the base class
 
        'pipeline_name' => 'apply_to_databases',            # name used by the beekeeper to prefix job names on the farm
 
        'source_server1' => 'mysql://ensadmin:'.$self->o('password').'@127.0.0.1:3306/',
        'source_server2' => 'mysql://ensadmin:'.$self->o('password').'@127.0.0.1:2914/',
 
        'only_databases'   => '%\_core\_%',                 # use '%' to get a list of all available databases
    };
}
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'get_databases',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -parameters => {
                'inputquery'   => q{SHOW DATABASES LIKE "}.$self->o('only_databases').q{"},
                'column_names' => [ 'dbname' ],
            },
            -input_ids => [
                { 'db_conn' => $self->o('source_server1') },
                { 'db_conn' => $self->o('source_server2') },
            ],
            -flow_into => {
                2 => { 'run_sql' => { 'db_conn' => '#db_conn##dbname#' },
                }
            },
        },
 
        {   -logic_name    => 'run_sql',
            -module        => 'Bio::EnsEMBL::Hive::RunnableDB::Dummy',  # use SqlCmd.pm to run your query or another JobFactory.pm to make another fan on table names
            -parameters    => {
            },
            -analysis_capacity => 10,       # allow several workers to perform identical tasks in parallel
            -input_ids     => [
                # (jobs for this analysis will be flown_into via branch-2 from 'get_databases' jobs above)
            ],
        },
    ];
}
 
1;