another example: potential for a double fan using JobFactory

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

+
+=pod 
+
+=head1 NAME
+
+  Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf
+
+=head1 SYNOPSIS
+
+    init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf -password <your_password>
+
+    init_pipeline.pl Bio::EnsEMBL::Hive::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 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+package Bio::EnsEMBL::Hive::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 {
+        'ensembl_cvs_root_dir' => $ENV{'HOME'}.'/work',     # some Compara developers might prefer $ENV{'HOME'}.'/ensembl_main'
+
+        'pipeline_name' => 'apply_to_databases',            # 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)
+        },
+
+        'source_server1' => {
+            -host   => 'ens-staging',
+            -port   => 3306,
+            -user   => 'ensro',
+            -pass   => '',
+        },
+
+        'source_server2' => {
+            -host   => 'ens-staging2',
+            -port   => 3306,
+            -user   => 'ensro',
+            -pass   => '',
+        },
+        
+        '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{"},
+            },
+            -hive_capacity => 5,       # allow several workers to perform identical tasks in parallel
+            -input_ids => [
+                { 'db_conn' => $self->o('source_server1'), 'input_id' => { 'db_conn' => {'-host' => $self->o('source_server1', '-host'), '-port' => $self->o('source_server1', '-port'), '-user' => $self->o('source_server1', '-user'), '-pass' => $self->o('source_server1', '-pass'), '-dbname' => '#_range_start#'}, }, },
+                { 'db_conn' => $self->o('source_server2'), 'input_id' => { 'db_conn' => {'-host' => $self->o('source_server2', '-host'), '-port' => $self->o('source_server2', '-port'), '-user' => $self->o('source_server2', '-user'), '-pass' => $self->o('source_server2', '-pass'), '-dbname' => '#_range_start#'}, }, },
+            ],
+            -flow_into => {
+                2 => [ 'dummy' ],   # will create a fan of jobs
+            },
+        },
+
+        {   -logic_name    => 'dummy',
+            -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    => {
+            },
+            -hive_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;
+