bugfix: updated examples of how to use JobFactory without and with input_id_template

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

@@ -40,21 +40,10 @@ sub default_options {
 
         'pipeline_name' => 'apply_to_databases',            # name used by the beekeeper to prefix job names on the farm
 
-        'source_server1' => {
-            -host   => 'ens-staging',
-            -port   => 3306,
-            -user   => 'ensro',
-            -pass   => '',
-        },
+        'source_server1' => 'mysql://ensadmin:'.$self->o('password').'@127.0.0.1:3306/',
+        'source_server2' => 'mysql://ensadmin:'.$self->o('password').'@127.0.0.1:2914/',
 
-        'source_server2' => {
-            -host   => 'ens-staging2',
-            -port   => 3306,
-            -user   => 'ensro',
-            -pass   => '',
-        },
-        
-        'only_databases'   => '%\_core\_%',                           # use '%' to get a list of all available databases
+        'only_databases'   => '%\_core\_%',                 # use '%' to get a list of all available databases
     };
 }
 
@@ -68,15 +57,16 @@ sub pipeline_analyses {
                 'column_names' => [ 'dbname' ],
             },
             -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' => '#dbname#'}, }, },
-                { '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' => '#dbname#'}, }, },
+                { 'db_conn' => $self->o('source_server1') },
+                { 'db_conn' => $self->o('source_server2') },
             ],
             -flow_into => {
-                2 => [ 'dummy' ],   # will create a fan of jobs
+                2 => { 'run_sql' => { 'db_conn' => '#db_conn##dbname#' },
+                }
             },
         },
 
-        {   -logic_name    => 'dummy',
+        {   -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    => {
             },

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

@@ -83,23 +83,20 @@ sub pipeline_analyses {
                 'column_names' => [ 'value' ],
             },
             -input_ids => [
-                {
-                    'job_count'    => $self->o('job_count'),            # turn this option into a passable parameter
-                    'input_id' => {
-                        'value'         => '#value#',
-                        'divisor'       => $self->o('failure_rate'),
-                        'state'         => $self->o('state'),
-                        'lethal_after'  => $self->o('lethal_after'),
-                    },
-                },
+                { 'job_count'    => $self->o('job_count') },
             ],
             -flow_into => {
-                2 => [ 'failure_test' ],   # will create a fan of jobs
+                2 => [ 'failure_test' ],
             },
         },
 
         {   -logic_name    => 'failure_test',
             -module        => 'Bio::EnsEMBL::Hive::RunnableDB::FailureTest',
+            -parameters    => {
+                'divisor'       => $self->o('failure_rate'),
+                'state'         => $self->o('state'),
+                'lethal_after'  => $self->o('lethal_after'),
+            }
         },
     ];
 }