bugfix: prevent PostgreSQL from padding the test numbers with spaces

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

@@ -83,7 +83,7 @@ sub pipeline_create_commands {
         @{$self->SUPER::pipeline_create_commands},  # inheriting database and hive tables' creation
 
             # additional tables needed for long multiplication pipeline's operation:
-        $self->db_cmd('CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'),
+        $self->db_cmd('CREATE TABLE final_result (a_multiplier varchar(255) NOT NULL, b_multiplier varchar(255) NOT NULL, result varchar(255) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'),
     ];
 }
 

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

+=pod 
+
+=head1 NAME
+
+    Bio::EnsEMBL::Hive::PipeConfig::LongMultWf_conf;
+
+=head1 SYNOPSIS
+
+       # initialize the database and build the graph in it (it will also print the value of EHIVE_URL) :
+    init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMultWf_conf -password <mypass>
+
+        # optionally also seed it with your specific values:
+    seed_pipeline.pl -url $EHIVE_URL -logic_name take_b_apart -input_id '{ "a_multiplier" => "12345678", "b_multiplier" => "3359559666" }'
+
+        # run the pipeline:
+    beekeeper.pl -url $EHIVE_URL -loop
+
+=head1 DESCRIPTION
+
+    This is the PipeConfig file for the long multiplication pipeline example.
+    The main point of this pipeline is to provide an example of how to write Hive Runnables and link them together into a pipeline.
+
+    Please refer to Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf module to understand the interface implemented here.
+
+    The setting. let's assume we are given two loooooong numbers to multiply. reeeeally long.
+    soooo long that they do not fit into registers of the cpu and should be multiplied digit-by-digit.
+    For the purposes of this example we also assume this task is very computationally intensive and has to be done in parallel.
+
+    The long multiplication pipeline consists of three "analyses" (types of tasks):
+        'take_b_apart', 'part_multiply' and 'add_together' that we use to examplify various features of the Hive.
+
+        * A 'take_b_apart' job takes in two string parameters, 'a_multiplier' and 'b_multiplier',
+          takes the second one apart into digits, finds what _different_ digits are there,
+          creates several jobs of the 'part_multiply' analysis and one job of 'add_together' analysis.
+
+        * A 'part_multiply' job takes in 'a_multiplier' and 'digit', multiplies them and accumulates the result in 'partial_product' accumulator.
+
+        * An 'add_together' job waits for the first two analyses to complete,
+          takes in 'a_multiplier', 'b_multiplier' and 'partial_product' hash and produces the final result in 'final_result' table.
+
+    Please see the implementation details in Runnable modules themselves.
+
+=head1 LICENSE
+
+    Copyright [1999-2015] Wellcome Trust Sanger Institute and the 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::PipeConfig::LongMultWf_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
+
+
+=head2 pipeline_create_commands
+
+    Description : Implements pipeline_create_commands() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that lists the commands that will create and set up the Hive database.
+                  In addition to the standard creation of the database and populating it with Hive tables and procedures it also creates two pipeline-specific tables used by Runnables to communicate.
+
+=cut
+
+sub pipeline_create_commands {
+    my ($self) = @_;
+    return [
+        @{$self->SUPER::pipeline_create_commands},  # inheriting database and hive tables' creation
+
+            # additional tables needed for long multiplication pipeline's operation:
+        $self->db_cmd('CREATE TABLE final_result (a_multiplier varchar(255) NOT NULL, b_multiplier varchar(255) NOT NULL, result varchar(255) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'),
+        $self->db_cmd('CREATE TABLE intermediate_result (a_multiplier varchar(255) NOT NULL, digit char(1) NOT NULL, partial_product varchar(255) NOT NULL, PRIMARY KEY (a_multiplier, digit))'),
+    ];
+}
+
+
+=head2 pipeline_wide_parameters
+
+    Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+                  The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
+                  Please see existing PipeConfig modules for examples.
+
+=cut
+
+sub pipeline_wide_parameters {
+    my ($self) = @_;
+    return {
+        %{$self->SUPER::pipeline_wide_parameters},          # here we inherit anything from the base class
+
+        'take_time'     => 1,
+    };
+}
+
+
+=head2 pipeline_analyses
+
+    Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc.
+                  Here it defines three analyses:
+                    * 'take_b_apart' that is auto-seeded with a pair of jobs (to check the commutativity of multiplication).
+                      Each job will dataflow (create more jobs) via branch #2 into 'part_multiply' and via branch #1 into 'add_together'.
+
+                    * 'part_multiply' with jobs fed from take_b_apart#2.
+                        It multiplies input parameters 'a_multiplier' and 'digit' and dataflows 'partial_product' parameter into branch #1.
+
+                    * 'add_together' with jobs fed from take_b_apart#1.
+                        It adds together results of partial multiplication computed by 'part_multiply'.
+                        These results are accumulated in 'partial_product' hash.
+                        Until the hash is complete the corresponding 'add_together' job is blocked by a semaphore.
+
+=cut
+
+sub pipeline_analyses {
+    my ($self) = @_;
+    return [
+        {   -logic_name => 'take_b_apart',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory',
+            -meadow_type=> 'LOCAL',     # do not bother the farm with such a simple task (and get it done faster)
+            -analysis_capacity  =>  2,  # use per-analysis limiter
+            -input_ids => [
+                { 'a_multiplier' => '9650156169', 'b_multiplier' => '327358788' },
+                { 'a_multiplier' => '327358788', 'b_multiplier' => '9650156169' },
+            ],
+            -flow_into => {
+                2 => { 'part_multiply' => { 'a_multiplier' => '#a_multiplier#', 'digit' => '#digit#', 'take_time' => '#take_time#' } },
+                1 => [ 'add_together'  ],
+            },
+        },
+
+        {   -logic_name => 'part_multiply',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply',
+            -analysis_capacity  =>  4,  # use per-analysis limiter
+            -flow_into => {
+                1 => [ ':////intermediate_result' ],
+            },
+            -can_be_empty       => 1,
+        },
+        
+        {   -logic_name => 'add_together',
+            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether',
+#           -analysis_capacity  =>  0,  # this is a way to temporarily block a given analysis
+            -parameters => {
+                'intermediate_table_name' => 'intermediate_result',
+            },
+            -wait_for => [ 'part_multiply' ],
+            -flow_into => {
+                1 => [ ':////final_result' ],
+            },
+        },
+    ];
+}
+
+1;
+

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

@@ -81,7 +81,7 @@ sub pipeline_create_commands {
         @{$self->SUPER::pipeline_create_commands},  # inheriting database and hive tables' creation
 
             # additional tables needed for long multiplication pipeline's operation:
-        $self->db_cmd('CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'),
+        $self->db_cmd('CREATE TABLE final_result (a_multiplier varchar(255) NOT NULL, b_multiplier varchar(255) NOT NULL, result varchar(255) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'),
     ];
 }