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Commit 2f308e8f authored by Leo Gordon's avatar Leo Gordon
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a big switch from using cluster labels in _allocate_to_subgraph() to setting... 

a big switch from using cluster labels in _allocate_to_subgraph() to setting {'_funnel_dfr'} of each graph's node and edge
parent ba4be746
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Showing with 65 additions and 80 deletions
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
View file @ 2f308e8f
......@@ -180,18 +180,17 @@ sub build {
if( my $funnel_dataflow_rule_id = $df_rule->funnel_dataflow_rule_id ) {
my $funnel_dataflow_rule = $all_dataflow_rules_coll->find_one_by('dbID', $funnel_dataflow_rule_id );
$funnel_dataflow_rule->{'_is_a_funnel'}++;
$df_rule->funnel_dataflow_rule( $funnel_dataflow_rule );
}
}
my %subgraph_allocation = (); # maps node names to midpoint names of the funnel dataflow rule (or null if toplevel)
# NB: this is a very approximate algorithm with rough edges!
# It will not find all start nodes in cyclic components!
foreach my $source_analysis ( $all_analyses_coll->list ) {
unless( $source_analysis->{'_inflow_count'} ) { # if there is no dataflow into this analysis
# run the recursion in each component that has a non-cyclic start:
$self->_allocate_to_subgraph( $source_analysis, \%subgraph_allocation );
$self->_propagate_allocation( $source_analysis );
}
}
......@@ -201,12 +200,14 @@ sub build {
}
foreach my $analysis ( $all_analyses_coll->list ) {
$self->_control_rules( $analysis->control_rules_collection );
$self->_dataflow_rules( $analysis->dataflow_rules_collection, \%subgraph_allocation );
$self->_dataflow_rules( $analysis->dataflow_rules_collection );
}
if($self->config_get('DisplayStretched') ) {
while( my($from, $to) = each %subgraph_allocation) {
if($to && $from=~/^analysis/) {
if($self->config_get('DisplayStretched') ) { # put each analysis before its' funnel midpoint
foreach my $analysis ( $all_analyses_coll->list ) {
if($analysis->{'_funnel_dfr'}) { # this should only affect analyses that have a funnel
my $from = _analysis_node_name( $analysis );
my $to = _midpoint_name( $analysis->{'_funnel_dfr'} );
$self->graph->add_edge( $from => $to,
color => 'black',
style => 'invis', # toggle visibility by changing 'invis' to 'dashed'
......@@ -216,7 +217,26 @@ sub build {
}
if($self->config_get('DisplaySemaphoreBoxes') ) {
$self->graph->subgraphs( \%subgraph_allocation );
my %cluster_2_nodes = ( # initialize with top clusters
'' => [ map { _midpoint_name( $_ ) } grep { $_->{'_is_a_funnel'} and ! $_->{'_funnel_dfr'} } $all_dataflow_rules_coll->list ]
);
foreach ($all_analyses_coll->list) {
if(my $funnel = $_->{'_funnel_dfr'}) {
push @{$cluster_2_nodes{ _midpoint_name( $funnel ) } }, _analysis_node_name( $_ );
}
}
foreach ( grep { UNIVERSAL::isa($_->to_analysis,'Bio::EnsEMBL::Hive::NakedTable') } $all_dataflow_rules_coll->list ) {
if(my $funnel = $_->to_analysis->{'_funnel_dfr'}) {
push @{$cluster_2_nodes{ _midpoint_name( $funnel ) } }, $self->_table_node_name( $_ );
}
}
foreach ( $all_dataflow_rules_coll->list ) {
if(my $funnel = $_->{'_funnel_dfr'}) {
push @{$cluster_2_nodes{ _midpoint_name( $funnel ) } }, _midpoint_name( $_ );
}
}
$self->graph->cluster_2_nodes( \%cluster_2_nodes );
$self->graph->colour_scheme( $self->config_get('Box', 'ColourScheme') );
$self->graph->colour_offset( $self->config_get('Box', 'ColourOffset') );
}
......@@ -225,10 +245,8 @@ sub build {
}
sub _allocate_to_subgraph {
my ($self, $source_analysis, $subgraph_allocation ) = @_;
my $source_analysis_allocation = $subgraph_allocation->{ _analysis_node_name( $source_analysis ) }; # for some analyses it will be undef
sub _propagate_allocation {
my ($self, $source_analysis ) = @_;
foreach my $df_rule ( @{ $source_analysis->dataflow_rules_collection } ) { # this will only work if the analyses objects are ALL cached before loading DFRs
my $target_object = $df_rule->to_analysis();
......@@ -245,43 +263,40 @@ sub _allocate_to_subgraph {
next;
}
my $proposed_allocation; # will depend on whether we start a new semaphore
my $proposed_funnel_dfr; # will depend on whether we start a new semaphore
my $funnel_dataflow_rule = $df_rule->funnel_dataflow_rule();
if( $funnel_dataflow_rule ) {
$proposed_allocation =
_midpoint_name( $funnel_dataflow_rule ); # if we do start a new semaphore, report to the new funnel (based on common funnel rule's midpoint)
if( $funnel_dataflow_rule ) { # if there is a new semaphore, the dfrs involved (their midpoints) will also have to be allocated
$proposed_funnel_dfr = $funnel_dataflow_rule; # if we do start a new semaphore, report to the new funnel (based on common funnel rule's midpoint)
my $fan_midpoint_name = _midpoint_name( $df_rule );
$subgraph_allocation->{ $fan_midpoint_name } = $proposed_allocation;
$df_rule->{'_funnel_dfr'} = $proposed_funnel_dfr;
my $funnel_midpoint_name = _midpoint_name( $funnel_dataflow_rule );
$subgraph_allocation->{ $funnel_midpoint_name } = $source_analysis_allocation; # draw the funnel's midpoint outside of the box
$funnel_dataflow_rule->{'_funnel_dfr'} = $source_analysis->{'_funnel_dfr'}; # draw the funnel's midpoint outside of the box
} else {
$proposed_allocation = $source_analysis_allocation; # if we don't start a new semaphore, inherit the allocation of the source
$proposed_funnel_dfr = $source_analysis->{'_funnel_dfr'} || ''; # if we don't start a new semaphore, inherit the allocation of the source
}
# we allocate on first-come basis at the moment:
if( exists $subgraph_allocation->{ $target_node_name } ) { # already allocated?
my $known_allocation = $subgraph_allocation->{ $target_node_name } || '';
$proposed_allocation ||= '';
if( exists $target_object->{'_funnel_dfr'} ) { # node is already allocated?
if( $known_allocation eq $proposed_allocation) {
# warn "analysis '$target_node_name' has already been allocated to the same '$known_allocation' by another branch";
my $known_funnel_dfr = $target_object->{'_funnel_dfr'};
if( $known_funnel_dfr eq $proposed_funnel_dfr) {
# warn "analysis '$target_node_name' has already been allocated to the same '$known_funnel_dfr' by another branch";
} else {
# warn "analysis '$target_node_name' has already been allocated to '$known_allocation' however this branch would allocate it to '$proposed_allocation'";
# warn "analysis '$target_node_name' has already been allocated to '$known_funnel_dfr' however this branch would allocate it to '$proposed_funnel_dfr'";
}
if($funnel_dataflow_rule) { # correction for multiple entries into the same box (probably needs re-thinking)
my $fan_midpoint_name = _midpoint_name( $df_rule );
$subgraph_allocation->{ $fan_midpoint_name } = $subgraph_allocation->{ $target_node_name };
$df_rule->{'_funnel_dfr'} = $target_object->{'_funnel_dfr'};
}
} else {
# warn "allocating analysis '$target_node_name' to '$proposed_allocation'";
$subgraph_allocation->{ $target_node_name } = $proposed_allocation;
# warn "allocating analysis '$target_node_name' to '$proposed_funnel_dfr'";
$target_object->{'_funnel_dfr'} = $proposed_funnel_dfr;
if(UNIVERSAL::isa($target_object, 'Bio::EnsEMBL::Hive::Analysis')) {
$self->_allocate_to_subgraph( $target_object, $subgraph_allocation );
$self->_propagate_allocation( $target_object );
}
}
}
......@@ -401,7 +416,7 @@ sub _control_rules {
sub _dataflow_rules {
my ($self, $dataflow_rules, $subgraph_allocation) = @_;
my ($self, $dataflow_rules) = @_;
my $graph = $self->graph();
my $dataflow_colour = $self->config_get('Edge', 'Data', 'Colour');
......@@ -409,14 +424,6 @@ sub _dataflow_rules {
my $accu_colour = $self->config_get('Edge', 'Accu', 'Colour');
my $df_edge_fontname = $self->config_get('Edge', 'Data', 'Font');
my %needs_a_midpoint = ();
foreach my $df_rule ( @$dataflow_rules ) {
if( my $funnel_dataflow_rule = $df_rule->funnel_dataflow_rule ) {
$df_rule->{'_needs_a_midpoint'}++;
$funnel_dataflow_rule->{'_needs_a_midpoint'}++;
}
}
foreach my $df_rule ( @$dataflow_rules ) {
my ($from_analysis, $branch_code, $funnel_dataflow_rule, $target_object) =
......@@ -426,21 +433,25 @@ sub _dataflow_rules {
# Different treatment for analyses and tables:
if(UNIVERSAL::isa($target_object, 'Bio::EnsEMBL::Hive::Analysis')) {
$target_node_name = _analysis_node_name( $target_object );
} elsif(UNIVERSAL::isa($target_object, 'Bio::EnsEMBL::Hive::NakedTable')) {
$target_node_name = $self->_table_node_name( $df_rule );
$self->_add_table_node($target_node_name, $target_object->table_name);
} elsif(UNIVERSAL::isa($target_object, 'Bio::EnsEMBL::Hive::Accumulator')) {
$target_node_name = $subgraph_allocation->{$from_node_name};
$target_node_name = _midpoint_name( $from_analysis->{'_funnel_dfr'} );
} else {
warn('Do not know how to handle the type '.ref($target_object));
next;
}
if( $df_rule->{'_needs_a_midpoint'} ) {
# a rule needs a midpoint either if it HAS a funnel or if it IS a funnel
if( $funnel_dataflow_rule or $df_rule->{'_is_a_funnel'} ) {
my $midpoint_name = _midpoint_name( $df_rule );
$graph->add_node( $midpoint_name, # midpoint itself
......@@ -489,7 +500,7 @@ sub _dataflow_rules {
fontcolor => $dataflow_colour,
label => '#'.$branch_code,
);
} # /if($needs_a_midpoint{$rule_id})
} # /if( "$df_rule needs a midpoint" )
} # /foreach my $df_rule (@$dataflow_rules)
}
......
modules/Bio/EnsEMBL/Hive/Utils/GraphViz.pm
View file @ 2f308e8f
......@@ -39,12 +39,12 @@ use warnings;
use base ('GraphViz');
sub subgraphs {
sub cluster_2_nodes {
my $self = shift @_;
if(@_) {
$self->{_subgraphs} = shift @_;
$self->{_cluster_2_nodes} = shift @_;
}
return $self->{_subgraphs};
return $self->{_cluster_2_nodes};
}
......@@ -66,35 +66,6 @@ sub colour_offset {
}
sub get_top_clusters {
my $self = shift @_;
my $subgraphs = $self->subgraphs();
my %set = ();
foreach my $potential_top_cluster (values %$subgraphs) {
if( $potential_top_cluster and !$subgraphs->{ $potential_top_cluster } ) { # if it's a valid node not mentioned in the keys, it is a top cluster
$set{$potential_top_cluster}++;
}
}
return [ keys %set ];
}
sub get_nodes_that_point_at {
my ($self, $node) = @_;
my $subgraphs = $self->subgraphs();
my %set = ();
while( my ($key,$value) = each %$subgraphs) {
if($value and ($value eq $node)) {
$set{$key}++;
}
}
return [ keys %set ];
}
sub display_subgraph {
my ($self, $cluster_name, $depth) = @_;
......@@ -106,15 +77,18 @@ sub display_subgraph {
my $text = '';
$text .= $prefix . "subgraph cluster_${cluster_name} {\n";
# uncomment the following line to see the cluster names:
# $text .= $prefix . "\tlabel=\"$cluster_name\";\n";
$text .= $prefix . "\tcolorscheme=$colour_scheme;\n";
$text .= $prefix . "\tstyle=filled;\n";
$text .= $prefix . "\tcolor=".($depth+$colour_offset).";\n";
foreach my $node_name ( @{ $self->get_nodes_that_point_at( $cluster_name ) } ) {
foreach my $node_name ( @{ $self->cluster_2_nodes->{ $cluster_name } || [] } ) {
$text .= $prefix . "\t${node_name};\n";
if( @{ $self->get_nodes_that_point_at( $node_name ) } ) {
if( @{ $self->cluster_2_nodes->{ $node_name } || [] } ) {
$text .= $self->display_subgraph( $node_name, $depth+1 );
}
}
......@@ -131,7 +105,7 @@ sub _as_debug {
$text=~s/^}$//m;
foreach my $node_name ( @{ $self->get_top_clusters() } ) {
foreach my $node_name ( sort @{ $self->cluster_2_nodes->{''} } ) {
$text .= $self->display_subgraph( $node_name, 1);
}
$text .= "}\n";
......
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