moved loading/saving of the collections into DBAdaptor module

modules/Bio/EnsEMBL/Hive.pm

@@ -67,55 +67,14 @@ use Bio::EnsEMBL::Hive::Utils::Collection;
 our %hash_of_collections;
 
 sub collection {
-    my $key = pop @_;
+    my $class = shift @_;
+    my $key   = shift @_;
 
-    return $hash_of_collections{$key} ||= Bio::EnsEMBL::Hive::Utils::Collection->new();
-}
-
-
-sub load_collections_from_dba {
-    my $hive_dba = pop @_;
-
-    foreach my $AdaptorType ('Meta', 'MetaContainer') {
-        my $adaptor = $hive_dba->get_adaptor( $AdaptorType );
-        $hash_of_collections{$AdaptorType} = $adaptor->get_param_hash();
-    }
-
-    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
-        my $adaptor = $hive_dba->get_adaptor( $AdaptorType );
-        $hash_of_collections{$AdaptorType} = Bio::EnsEMBL::Hive::Utils::Collection->new( $adaptor->fetch_all );
-    }
-}
-
-
-sub save_collections_to_dba {
-    my $hive_dba = pop @_;
-
-    foreach my $AdaptorType ('Meta', 'MetaContainer') {
-        my $adaptor = $hive_dba->get_adaptor( $AdaptorType );
-        while(my ($meta_key, $meta_value) = each %{ $hash_of_collections{$AdaptorType} } ) {
-            $adaptor->remove_all_by_meta_key($meta_key);        # make sure the previous values are gone
-            $adaptor->store_pair( $meta_key, $meta_value );
-        }
+    if(@_) {
+        $hash_of_collections{$key} = shift @_;
     }
 
-    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
-        my $adaptor = $hive_dba->get_adaptor( $AdaptorType );
-        foreach my $storable_object ( Bio::EnsEMBL::Hive->collection( $AdaptorType )->list ) {
-            $adaptor->store_or_update_one( $storable_object );
-#            warn "Stored/updated ".$storable_object->toString()."\n";
-        }
-    }
-
-    my $job_adaptor = $hive_dba->get_AnalysisJobAdaptor;
-    foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
-        if(my $our_jobs = $analysis->jobs_collection ) {
-            $job_adaptor->store( $our_jobs );
-            foreach my $job (@$our_jobs) {
-#                warn "Stored ".$job->toString()."\n";
-            }
-        }
-    }
+    return $hash_of_collections{$key} ||= Bio::EnsEMBL::Hive::Utils::Collection->new();
 }
 
 1;

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

@@ -36,9 +36,11 @@ package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 
 use strict;
 
-use Bio::EnsEMBL::Hive::Utils ('throw');
+use Bio::EnsEMBL::Hive;
 use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
 use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
+use Bio::EnsEMBL::Hive::Utils ('throw');
+use Bio::EnsEMBL::Hive::Utils::Collection;
 
 
 sub new {
@@ -253,5 +255,51 @@ sub AUTOLOAD {
     return $self->get_adaptor($type, @_);
 }
 
+
+sub load_collections {
+    my $self = shift @_;
+
+    foreach my $AdaptorType ('Meta', 'MetaContainer') {
+        my $adaptor = $self->get_adaptor( $AdaptorType );
+        Bio::EnsEMBL::Hive->collection( $AdaptorType, $adaptor->get_param_hash() );
+    }
+
+    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+        my $adaptor = $self->get_adaptor( $AdaptorType );
+        Bio::EnsEMBL::Hive->collection( $AdaptorType, Bio::EnsEMBL::Hive::Utils::Collection->new( $adaptor->fetch_all ) );
+    }
+}
+
+
+sub save_collections {
+    my $self = shift @_;
+
+    foreach my $AdaptorType ('Meta', 'MetaContainer') {
+        my $adaptor = $self->get_adaptor( $AdaptorType );
+        while(my ($meta_key, $meta_value) = each %{ Bio::EnsEMBL::Hive->collection( $AdaptorType ) } ) {
+            $adaptor->remove_all_by_meta_key($meta_key);        # make sure the previous values are gone
+            $adaptor->store_pair( $meta_key, $meta_value );
+        }
+    }
+
+    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+        my $adaptor = $self->get_adaptor( $AdaptorType );
+        foreach my $storable_object ( Bio::EnsEMBL::Hive->collection( $AdaptorType )->list ) {
+            $adaptor->store_or_update_one( $storable_object );
+#            warn "Stored/updated ".$storable_object->toString()."\n";
+        }
+    }
+
+    my $job_adaptor = $self->get_AnalysisJobAdaptor;
+    foreach my $analysis ( Bio::EnsEMBL::Hive->collection('Analysis')->list ) {
+        if(my $our_jobs = $analysis->jobs_collection ) {
+            $job_adaptor->store( $our_jobs );
+            foreach my $job (@$our_jobs) {
+#                warn "Stored ".$job->toString()."\n";
+            }
+        }
+    }
+}
+
 1;
 

scripts/generate_graph.pl

@@ -15,7 +15,6 @@ BEGIN {
 use Getopt::Long qw(:config pass_through no_auto_abbrev);
 use Pod::Usage;
 
-use Bio::EnsEMBL::Hive;
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module');
 use Bio::EnsEMBL::Hive::Utils::Graph;
@@ -72,7 +71,7 @@ sub main {
             -no_sql_schema_version_check    => $self->{'nosqlvc'},
         );
 
-        Bio::EnsEMBL::Hive->load_collections_from_dba( $self->{'dba'} );
+        $self->{'dba'}->load_collections();
     }
 
     if($self->{'pipeconfig'}) {

scripts/init_pipeline.pl

@@ -42,11 +42,11 @@ sub main {
 
     my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeconfig_object->pipeline_url(), -no_sql_schema_version_check => 1 );
 
-    Bio::EnsEMBL::Hive->load_collections_from_dba( $hive_dba );
+    $hive_dba->load_collections();
 
     $pipeconfig_object->add_objects_from_config();
 
-    Bio::EnsEMBL::Hive->save_collections_to_dba( $hive_dba );
+    $hive_dba->save_collections();
 
     $pipeconfig_object->show_useful_commands();
 }