Skip to content
Snippets Groups Projects
Commit 98a33c67 authored by Leo Gordon's avatar Leo Gordon
Browse files

turn Utils::Graph into Configurable and use the same interface to config as Meadow and Valley

parent b67dbcc3
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
+ 22
− 38
View file @ 98a33c67
......@@ -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'),
);
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment