Added an option to duplicate the tables and include them into their parent...

Added an option to duplicate the tables and include them into their parent boxes in the graphical output of the pipeline

hive_config.json

@@ -52,5 +52,6 @@
         "DisplayDetails"        : 1,
         "DisplayStretched"      : 0,
         "DisplaySemaphoreBoxes" : 1,
+	  "DuplicateTables"       : 0,
     }
 }

modules/Bio/EnsEMBL/Hive/Utils/Graph.pm

@@ -24,11 +24,11 @@ See inline
 
 =head1 AUTHOR
 
-$Author: lg4 $
+$Author: mm14 $
 
 =head1 VERSION
 
-$Revision: 1.18 $
+$Revision: 1.19 $
 
 =cut
 
@@ -173,7 +173,7 @@ sub build {
     foreach my $analysis_id ( map { $_->dbID } @$all_analyses ) {
         my $analysis_node_name =  _analysis_node_name( $analysis_id );
         unless($inflow_count{$analysis_node_name}) {
-            _allocate_to_subgraph(\%outflow_rules, \%dfr_flows_into, $analysis_node_name, \%subgraph_allocation ); # run the recursion in each component that has a non-cyclic start
+            _allocate_to_subgraph(\%outflow_rules, \%dfr_flows_into, $analysis_node_name, \%subgraph_allocation, $self->config ); # run the recursion in each component that has a non-cyclic start
         }
     }
 
@@ -206,15 +206,21 @@ sub build {
 
 
 sub _allocate_to_subgraph {
-    my ( $outflow_rules, $dfr_flows_into, $parent_analysis_node_name, $subgraph_allocation ) = @_;
+    my ( $outflow_rules, $dfr_flows_into, $parent_analysis_node_name, $subgraph_allocation, $config ) = @_;
 
     my $parent_allocation = $subgraph_allocation->{ $parent_analysis_node_name };  # for some analyses it will be undef
 
     foreach my $rule ( @{ $outflow_rules->{$parent_analysis_node_name} } ) {
         my $to_analysis                 = $rule->to_analysis();
-        next unless( $to_analysis->can('dbID'));    # skip dataflow-into-tables
+        next unless $to_analysis->can('dbID') or $config->get('Graph', 'DuplicateTables');
 
-        my $this_analysis_node_name     = _analysis_node_name( $rule->to_analysis->dbID() );
+        my $this_analysis_node_name;
+        if ($to_analysis->can('dbID')) {
+            $this_analysis_node_name = _analysis_node_name( $rule->to_analysis->dbID() );
+        } else {
+            $this_analysis_node_name = $to_analysis->table_name();
+            $this_analysis_node_name .= '_'.$rule->from_analysis_id() if $config->get('Graph', 'DuplicateTables');
+        }
         my $funnel_dataflow_rule_id     = $rule->funnel_dataflow_rule_id();
 
         my $proposed_allocation = $funnel_dataflow_rule_id  # depends on whether we start a new semaphore
@@ -243,7 +249,7 @@ sub _allocate_to_subgraph {
             # warn "allocating analysis '$this_analysis_node_name' to '$proposed_allocation'";
             $subgraph_allocation->{ $this_analysis_node_name } = $proposed_allocation;
 
-            _allocate_to_subgraph( $outflow_rules, $dfr_flows_into, $this_analysis_node_name, $subgraph_allocation );
+            _allocate_to_subgraph( $outflow_rules, $dfr_flows_into, $this_analysis_node_name, $subgraph_allocation, $config );
         }
     }
 }
@@ -338,6 +344,7 @@ sub _dataflow_rules {
             $to_node = _analysis_node_name($to_id);
         } elsif(check_ref($to, 'Bio::EnsEMBL::Hive::NakedTable')) {
             $to_node = $to->table_name();
+            $to_node .= '_'.$from_analysis_id if $self->config->get('Graph', 'DuplicateTables');
             $self->_add_table_node($to_node);
         } else {
             warn('Do not know how to handle the type '.ref($to));
@@ -391,8 +398,14 @@ sub _add_table_node {
 
   my $node_fontname    = $self->config->get('Graph', 'Node', 'Table', 'Font');
 
+  my $table_name = $table;
+  if ($self->config->get('Graph', 'DuplicateTables')) {
+    $table =~ /^(.*)_([^_]*)$/;
+    $table_name = $1;
+  }
+
   $self->graph()->add_node( $table, 
-    label => $table.'\n', 
+    label => $table_name.'\n', 
     shape => 'tab',
     fontname => $node_fontname,
     color => $self->config->get('Graph', 'Node', 'Table', 'Colour'),