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Commit d73d1781 authored by Leo Gordon's avatar Leo Gordon
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Graph.pm uses cache collections (no change in interface) ;... 

Graph.pm uses cache collections (no change in interface) ; A.control_rules_collection and A.dataflow_rules_collection lazy-load from collections
parent c245f10b
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Showing with 29 additions and 41 deletions
modules/Bio/EnsEMBL/Hive/Analysis.pm
View file @ d73d1781
......@@ -37,6 +37,7 @@ package Bio::EnsEMBL::Hive::Analysis;
use strict;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use base ( 'Bio::EnsEMBL::Hive::Storable' );
......@@ -212,8 +213,7 @@ sub control_rules_collection {
$self->{'_control_rules_collection'} = shift if(@_);
return $self->{'_control_rules_collection'} ||= [];
# $self->adaptor->db->get_AnalysisCtrlRuleAdaptor->fetch_all_by_ctrled_analysis_id( $self->dbID );
return $self->{'_control_rules_collection'} || Bio::EnsEMBL::Hive->collection('AnalysisCtrlRule')->find_all_by('ctrled_analysis', $self);
}
......@@ -222,7 +222,8 @@ sub dataflow_rules_collection {
$self->{'_dataflow_rules_collection'} = shift if(@_);
return $self->{'_dataflow_rules_collection'} ||= [];
return $self->{'_dataflow_rules_collection'} || Bio::EnsEMBL::Hive->collection('DataflowRule')->find_all_by('from_analysis', $self);
# return $self->{'_dataflow_rules_collection'} ||= [];
}
......
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
View file @ d73d1781
......@@ -6,8 +6,8 @@
=head1 SYNOPSIS
my $dba = get_hive_dba();
my $g = Bio::EnsEMBL::Hive::Utils::Graph->new(-DBA => $dba);
my $hive_dba = get_hive_dba();
my $g = Bio::EnsEMBL::Hive::Utils::Graph->new(-DBA => $hive_dba);
my $graphviz = $g->build();
$graphviz->as_png('location.png');
......@@ -48,6 +48,7 @@ package Bio::EnsEMBL::Hive::Utils::Graph;
use strict;
use warnings;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Hive::Utils::GraphViz;
use Bio::EnsEMBL::Hive::Utils::Collection;
use Bio::EnsEMBL::Hive::Utils::Config;
......@@ -57,7 +58,7 @@ use base ('Bio::EnsEMBL::Hive::Configurable');
=head2 new()
Arg [1] : Bio::EnsEMBL::Hive::DBSQL::DBAdaptor $dba;
Arg [1] : Bio::EnsEMBL::Hive::DBSQL::DBAdaptor $hive_dba;
The adaptor to get information from
Arg [2] : (optional) string $config_file_name;
A JSON file name to initialize the Config object with.
......@@ -70,11 +71,11 @@ use base ('Bio::EnsEMBL::Hive::Configurable');
=cut
sub new {
my ($class, $dba, $config_file_name) = @_;
my ($class, $hive_dba, $config_file_name) = @_;
my $self = bless({}, ref($class) || $class);
$self->dba($dba);
$self->dba($hive_dba);
my $config = Bio::EnsEMBL::Hive::Utils::Config->new( $config_file_name ? $config_file_name : () );
$self->config($config);
$self->context( [ 'Graph' ] );
......@@ -161,69 +162,54 @@ sub _midpoint_name {
sub build {
my ($self) = @_;
my $dba = $self->dba();
my $hive_dba = $self->dba;
my $all_analyses_coll = Bio::EnsEMBL::Hive::Utils::Collection->new( $dba->get_AnalysisAdaptor()->fetch_all );
my $all_control_rules_coll = Bio::EnsEMBL::Hive::Utils::Collection->new( $dba->get_AnalysisCtrlRuleAdaptor()->fetch_all );
my $all_dataflow_rules_coll = Bio::EnsEMBL::Hive::Utils::Collection->new( $dba->get_DataflowRuleAdaptor()->fetch_all );
Bio::EnsEMBL::Hive->load_collections_from_dba( $hive_dba );
if( my $job_limit = $self->config_get('DisplayJobs') ) {
my $job_adaptor = $dba->get_AnalysisJobAdaptor();
foreach my $analysis ( $all_analyses_coll->list ) {
if( my $job_limit = $self->config_get('DisplayJobs') and my $job_adaptor = $hive_dba && $hive_dba->get_AnalysisJobAdaptor ) {
foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
my @jobs = sort {$a->dbID <=> $b->dbID} @{ $job_adaptor->fetch_some_by_analysis_id_limit( $analysis->dbID, $job_limit+1 )};
$analysis->jobs_collection( \@jobs );
}
}
foreach my $c_rule ( $all_control_rules_coll->list ) {
my $ctrled_analysis = $all_analyses_coll->find_one_by('dbID', $c_rule->ctrled_analysis_id );
$c_rule->ctrled_analysis( $ctrled_analysis );
push @{$ctrled_analysis->control_rules_collection}, $c_rule;
}
foreach my $df_rule ( $all_dataflow_rules_coll->list ) {
my $from_analysis = $all_analyses_coll->find_one_by('dbID', $df_rule->from_analysis_id );
$df_rule->from_analysis( $from_analysis );
push @{$from_analysis->dataflow_rules_collection}, $df_rule;
foreach my $df_rule ( Bio::EnsEMBL::Hive->collection('DataflowRule')->list ) {
if(my $target_object = $all_analyses_coll->find_one_by('logic_name', $df_rule->to_analysis_url )) {
if(my $target_object = Bio::EnsEMBL::Hive->collection('Analysis')->find_one_by('logic_name', $df_rule->to_analysis_url )) {
$df_rule->to_analysis( $target_object );
if(UNIVERSAL::isa($target_object, 'Bio::EnsEMBL::Hive::Analysis')) {
$target_object->{'_inflow_count'}++;
}
} # otherwise it may be a link out (unsupported at the moment)
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 );
if( my $funnel_dataflow_rule = $df_rule->funnel_dataflow_rule ) {
$funnel_dataflow_rule->{'_is_a_funnel'}++;
$df_rule->funnel_dataflow_rule( $funnel_dataflow_rule );
}
}
# 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 ) {
foreach my $source_analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->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->_propagate_allocation( $source_analysis );
}
}
if( $self->config_get('DisplayDetails') ) {
my $dbc = $dba->dbc();
if( $self->config_get('DisplayDetails') and my $dbc = $hive_dba && $hive_dba->dbc ) {
my $pipeline_label = sprintf('%s@%s', $dbc->dbname, $dbc->host || '-');
$self->_add_pipeline_label( $pipeline_label );
}
foreach my $analysis ( $all_analyses_coll->list ) {
foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
$self->_add_analysis_node($analysis);
}
foreach my $analysis ( $all_analyses_coll->list ) {
foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
$self->_add_control_rules( $analysis->control_rules_collection );
$self->_add_dataflow_rules( $analysis->dataflow_rules_collection );
}
if($self->config_get('DisplayStretched') ) { # put each analysis before its' funnel midpoint
foreach my $analysis ( $all_analyses_coll->list ) {
foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
if($analysis->{'_funnel_dfr'}) { # this should only affect analyses that have a funnel
my $from = _analysis_node_name( $analysis );
my $to = _midpoint_name( $analysis->{'_funnel_dfr'} );
......@@ -238,7 +224,7 @@ sub build {
if($self->config_get('DisplaySemaphoreBoxes') ) {
my %cluster_2_nodes = ();
foreach my $analysis ($all_analyses_coll->list) {
foreach my $analysis (Bio::EnsEMBL::Hive->collection('Analysis')->list) {
if(my $funnel = $analysis->{'_funnel_dfr'}) {
push @{$cluster_2_nodes{ _midpoint_name( $funnel ) } }, _analysis_node_name( $analysis );
}
......@@ -531,13 +517,14 @@ sub _add_table_node {
my $node_fontname = $self->config_get('Node', 'Table', 'Font');
my (@column_names, $columns, $table_data, $data_limit, $hit_limit);
if( $data_limit = $self->config_get('DisplayData') ) {
my $adaptor = $self->dba->get_NakedTableAdaptor();
$adaptor->table_name( $table_name );
my $hive_dba = $self->dba;
if( $data_limit = $self->config_get('DisplayData') and my $naked_table_adaptor = $hive_dba && $hive_dba->get_NakedTableAdaptor ) {
$naked_table_adaptor->table_name( $table_name );
@column_names = sort keys %{$adaptor->column_set};
@column_names = sort keys %{$naked_table_adaptor->column_set};
$columns = scalar(@column_names);
$table_data = $adaptor->fetch_all( 'LIMIT '.($data_limit+1) );
$table_data = $naked_table_adaptor->fetch_all( 'LIMIT '.($data_limit+1) );
if(scalar(@$table_data)>$data_limit) {
pop @$table_data;
......
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