bugfix: make sure -wait_for is working properly again (do not auto-initialize Cacheable)

modules/Bio/EnsEMBL/Hive/Analysis.pm

@@ -200,8 +200,11 @@ sub display_name {
 sub stats {
     my $self = shift @_;
 
-    return Bio::EnsEMBL::Hive::AnalysisStats->collection()->find_one_by('analysis', $self)
-        || $self->adaptor->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id( $self->dbID );
+    my $collection = Bio::EnsEMBL::Hive::AnalysisStats->collection();
+
+    return $collection
+        ? $collection->find_one_by('analysis', $self)
+        : $self->adaptor->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id( $self->dbID );
 }
 
 
@@ -217,17 +220,18 @@ sub jobs_collection {
 sub control_rules_collection {
     my $self = shift @_;
 
-    return Bio::EnsEMBL::Hive::AnalysisCtrlRule->collection()->find_all_by('ctrled_analysis', $self)
-        || $self->adaptor->db->get_AnalysisCtrlRuleAdaptor->fetch_all_by_ctrled_analysis_id( $self->dbID );
+    my $collection = Bio::EnsEMBL::Hive::AnalysisCtrlRule->collection();
+
+    return $collection
+        ? $collection->find_all_by('ctrled_analysis', $self)
+        : $self->adaptor->db->get_AnalysisCtrlRuleAdaptor->fetch_all_by_ctrled_analysis_id( $self->dbID );
 }
 
 
 sub dataflow_rules_collection {
     my $self = shift @_;
 
-    $self->{'_dataflow_rules_collection'} = shift if(@_);
-
-    return $self->{'_dataflow_rules_collection'} || Bio::EnsEMBL::Hive::DataflowRule->collection()->find_all_by('from_analysis', $self);
+    return Bio::EnsEMBL::Hive::DataflowRule->collection()->find_all_by('from_analysis', $self);
 }
 
 

modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm

@@ -118,7 +118,9 @@ sub condition_analysis {
         # lazy load the analysis object if I can
     if( !$self->{'_condition_analysis'} and my $condition_analysis_url = $self->condition_analysis_url ) {
 
-        if( $self->{'_condition_analysis'} = Bio::EnsEMBL::Hive::Analysis->collection()->find_one_by('logic_name', $condition_analysis_url) ) {
+        my $collection = Bio::EnsEMBL::Hive::Analysis->collection();
+
+        if( $collection and $self->{'_condition_analysis'} = $collection->find_one_by('logic_name', $condition_analysis_url) ) {
 #            warn "Lazy-loading object from 'Analysis' collection\n";
         } elsif(my $adaptor = $self->adaptor) {
 #            warn "Lazy-loading object from AnalysisAdaptor\n";

modules/Bio/EnsEMBL/Hive/Cacheable.pm

@@ -13,7 +13,7 @@ sub collection {
         $cache_by_class{$class} = shift @_;
     }
 
-    return $cache_by_class{$class} ||= Bio::EnsEMBL::Hive::Utils::Collection->new();
+    return $cache_by_class{$class};
 }
 
 

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -41,6 +41,10 @@ use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
 use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('throw');
 use Bio::EnsEMBL::Hive::Utils::Collection;
+use Bio::EnsEMBL::Hive::ResourceClass;
+use Bio::EnsEMBL::Hive::ResourceDescription;
+use Bio::EnsEMBL::Hive::Analysis;
+use Bio::EnsEMBL::Hive::AnalysisStats;
 
 
 sub new {
@@ -256,6 +260,19 @@ sub AUTOLOAD {
 }
 
 
+sub init_collections {  # should not really belong to DBAdaptor, temporarily squatting here...
+
+    foreach my $AdaptorType ('Meta', 'PipelineWideParameters') {
+        Bio::EnsEMBL::Hive->collection( $AdaptorType, {} );
+    }
+
+    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+        my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
+        $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new() );
+    }
+}
+
+
 sub load_collections {
     my $self = shift @_;
 

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -160,8 +160,9 @@ sub to_analysis {
 
         # lazy load the analysis object if I can
     if( !$self->{'_to_analysis'} and my $to_analysis_url = $self->to_analysis_url ) {
+        my $collection = Bio::EnsEMBL::Hive::Analysis->collection();
 
-        if( $self->{'_to_analysis'} = Bio::EnsEMBL::Hive::Analysis->collection()->find_one_by('logic_name', $to_analysis_url) ) {
+        if( $collection and $self->{'_to_analysis'} = $collection->find_one_by('logic_name', $to_analysis_url) ) {
 #            warn "Lazy-loading object from 'Analysis' collection\n";
         } elsif(my $adaptor = $self->adaptor) {
 #            warn "Lazy-loading object from AnalysisAdaptor\n";

modules/Bio/EnsEMBL/Hive/Storable.pm

@@ -156,7 +156,8 @@ sub AUTOLOAD {
                 # attempt to lazy-load:
             } elsif( !$self->{$foo_obj_method_name} and my $foo_object_id = $self->{$foo_id_method_name}) {
                 my $foo_class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
-                if( $self->{$foo_obj_method_name} = $foo_class->collection()->find_one_by('dbID', $foo_object_id) ) { # careful: $AdaptorType may not be unique (aliases)
+                my $collection = $foo_class->collection();
+                if( $collection and $self->{$foo_obj_method_name} = $collection->find_one_by('dbID', $foo_object_id) ) { # careful: $AdaptorType may not be unique (aliases)
 #                    warn "Lazy-loading object from $AdaptorType collection\n";
                 } elsif(my $adaptor = $self->adaptor) {
 #                    warn "Lazy-loading object from $AdaptorType adaptor\n";

scripts/generate_graph.pl

@@ -72,6 +72,9 @@ sub main {
         );
 
         $self->{'dba'}->load_collections();
+    } else {
+
+        Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->init_collections();
     }
 
     if($self->{'pipeconfig'}) {