From 98a33c67453873430f58a39b5857773e531c4f29 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 16 Nov 2012 23:27:58 +0000
Subject: [PATCH] turn Utils::Graph into Configurable and use the same
interface to config as Meadow and Valley
---
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm | 60 +++++++++----------------
1 file changed, 22 insertions(+), 38 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Utils/Graph.pm b/modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
index bd151769d..f3c14ba64 100644
--- a/modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
+++ b/modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
@@ -32,6 +32,8 @@ use Bio::EnsEMBL::Utils::Scalar qw(check_ref assert_ref);
use Bio::EnsEMBL::Hive::Utils::GraphViz;
use Bio::EnsEMBL::Hive::Utils::Config;
+use base ('Bio::EnsEMBL::Hive::Configurable');
+
=head2 new()
@@ -55,6 +57,7 @@ sub new {
$self->dba($dba);
my $config = Bio::EnsEMBL::Hive::Utils::Config->new( $config_file_name ? $config_file_name : () );
$self->config($config);
+ $self->context( [ 'Graph' ] );
return $self;
}
@@ -97,31 +100,13 @@ sub dba {
}
-=head2 config()
-
- Arg [1] : The graph configuration object
- Returntype : Bio::EnsEMBL::Hive::Utils::Config.
- Exceptions : If the object given is not of the required type
- Status : Beta
-
-=cut
-
-sub config {
- my ($self, $config) = @_;
- if(defined $config) {
- assert_ref($config, 'Bio::EnsEMBL::Hive::Utils::Config');
- $self->{config} = $config;
- }
- return $self->{config};
-}
-
-
sub _analysis_node_name {
my $analysis_id = shift @_;
return 'analysis_' . $analysis_id;
}
+
sub _midpoint_name {
my $rule_id = shift @_;
@@ -176,7 +161,7 @@ sub build {
$self->_control_rules( $all_ctrl_rules );
$self->_dataflow_rules( $all_dataflow_rules );
- if($self->config->get('Graph', 'DisplayStretched') ) {
+ if($self->config_get('DisplayStretched') ) {
# The invisible edges will be linked to the destination analysis instead of the midpoint
my $id_to_rule = {map { $_->dbID => $_ } @$all_dataflow_rules};
@@ -193,10 +178,10 @@ sub build {
}
}
- if($self->config->get('Graph', 'DisplaySemaphoreBoxes') ) {
+ if($self->config_get('DisplaySemaphoreBoxes') ) {
$self->graph->subgraphs( \%subgraph_allocation );
- $self->graph->colour_scheme( $self->config->get('Graph', 'Box', 'ColourScheme') );
- $self->graph->colour_offset( $self->config->get('Graph', 'Box', 'ColourOffset') );
+ $self->graph->colour_scheme( $self->config_get('Box', 'ColourScheme') );
+ $self->graph->colour_offset( $self->config_get('Box', 'ColourOffset') );
}
return $self->graph();
@@ -207,18 +192,17 @@ sub _allocate_to_subgraph {
my ($self, $outflow_rules, $dfr_flows_into, $parent_analysis_node_name, $subgraph_allocation ) = @_;
my $parent_allocation = $subgraph_allocation->{ $parent_analysis_node_name }; # for some analyses it will be undef
- my $config = $self->config();
foreach my $rule ( @{ $outflow_rules->{$parent_analysis_node_name} } ) {
my $to_analysis = $rule->to_analysis();
- next unless $to_analysis->can('dbID') or $config->get('Graph', 'DuplicateTables');
+ next unless $to_analysis->can('dbID') or $self->config_get('DuplicateTables');
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');
+ $this_analysis_node_name .= '_'.$rule->from_analysis_id() if $self->config_get('DuplicateTables');
}
my $funnel_dataflow_rule_id = $rule->funnel_dataflow_rule_id();
@@ -257,9 +241,9 @@ sub _allocate_to_subgraph {
sub _add_hive_details {
my ($self) = @_;
- my $node_fontname = $self->config->get('Graph', 'Node', 'Details', 'Font');
+ my $node_fontname = $self->config_get('Node', 'Details', 'Font');
- if($self->config->get('Graph', 'DisplayDetails') ) {
+ if( $self->config_get('DisplayDetails') ) {
my $dbc = $self->dba()->dbc();
my $label = sprintf('%s@%s', $dbc->dbname, $dbc->host || '-');
$self->graph()->add_node( 'Details',
@@ -280,8 +264,8 @@ sub _add_analysis_node {
my $analysis_label = $a->logic_name().' ('.$a->dbID().')\n'.$breakout_label;
my $shape = $a->can_be_empty() ? 'doubleoctagon' : 'ellipse' ;
- my $status_colour = $self->config->get('Graph', 'Node', $stats->status, 'Colour');
- my $node_fontname = $self->config->get('Graph', 'Node', $stats->status, 'Font');
+ my $status_colour = $self->config_get('Node', $stats->status, 'Colour');
+ my $node_fontname = $self->config_get('Node', $stats->status, 'Font');
$self->graph->add_node( _analysis_node_name( $a->dbID() ),
label => $analysis_label,
@@ -296,7 +280,7 @@ sub _add_analysis_node {
sub _control_rules {
my ($self, $all_ctrl_rules) = @_;
- my $control_colour = $self->config->get('Graph', 'Edge', 'Control', 'Colour');
+ my $control_colour = $self->config_get('Edge', 'Control', 'Colour');
my $graph = $self->graph();
#The control rules are always from and to an analysis so no need to search for odd cases here
@@ -314,9 +298,9 @@ sub _dataflow_rules {
my ($self, $all_dataflow_rules) = @_;
my $graph = $self->graph();
- my $dataflow_colour = $self->config->get('Graph', 'Edge', 'Data', 'Colour');
- my $semablock_colour = $self->config->get('Graph', 'Edge', 'Semablock', 'Colour');
- my $df_edge_fontname = $self->config->get('Graph', 'Edge', 'Data', 'Font');
+ my $dataflow_colour = $self->config_get('Edge', 'Data', 'Colour');
+ my $semablock_colour = $self->config_get('Edge', 'Semablock', 'Colour');
+ my $df_edge_fontname = $self->config_get('Edge', 'Data', 'Font');
my %needs_a_midpoint = ();
my %aid2aid_nonsem = (); # simply a directed graph between numerical analysis_ids, except for semaphored rules
@@ -344,7 +328,7 @@ 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');
+ $to_node .= '_'.$from_analysis_id if $self->config_get('DuplicateTables');
$self->_add_table_node($to_node);
} else {
warn('Do not know how to handle the type '.ref($to));
@@ -396,10 +380,10 @@ sub _dataflow_rules {
sub _add_table_node {
my ($self, $table) = @_;
- my $node_fontname = $self->config->get('Graph', 'Node', 'Table', 'Font');
+ my $node_fontname = $self->config_get('Node', 'Table', 'Font');
my $table_name = $table;
- if ($self->config->get('Graph', 'DuplicateTables')) {
+ if( $self->config_get('DuplicateTables') ) {
$table =~ /^(.*)_([^_]*)$/;
$table_name = $1;
}
@@ -408,7 +392,7 @@ sub _add_table_node {
label => $table_name.'\n',
shape => 'tab',
fontname => $node_fontname,
- color => $self->config->get('Graph', 'Node', 'Table', 'Colour'),
+ color => $self->config_get('Node', 'Table', 'Colour'),
);
}
--
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