switch MetaParameters to the common cache (from a simple hash)

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

@@ -266,12 +266,12 @@ sub AUTOLOAD {
 
 sub init_collections {  # should not really belong to DBAdaptor, temporarily squatting here...
 
-    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters') {
+    foreach my $AdaptorType ('PipelineWideParameters') {
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         $class->collection( {} );
     }
 
-    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new() );
     }
@@ -281,13 +281,13 @@ sub init_collections {  # should not really belong to DBAdaptor, temporarily squ
 sub load_collections {
     my $self = shift @_;
 
-    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters') {
+    foreach my $AdaptorType ('PipelineWideParameters') {
         my $adaptor = $self->get_adaptor( $AdaptorType );
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         $class->collection( $adaptor->fetch_param_hash() );
     }
 
-    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
         my $adaptor = $self->get_adaptor( $AdaptorType );
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new( $adaptor->fetch_all ) );
@@ -298,7 +298,7 @@ sub load_collections {
 sub save_collections {
     my $self = shift @_;
 
-    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters') {
+    foreach my $AdaptorType ('PipelineWideParameters') {
         my $adaptor = $self->get_adaptor( $AdaptorType );
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         while( my ($hash_key,$hash_value) = each %{ $class->collection() } ) {
@@ -307,11 +307,11 @@ sub save_collections {
         }
     }
 
-    foreach my $AdaptorType ('ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
         my $adaptor = $self->get_adaptor( $AdaptorType );
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         foreach my $storable_object ( $class->collection()->list ) {
-            $adaptor->store_or_update_one( $storable_object );
+            $adaptor->store_or_update_one( $storable_object, $class->unikey() );
 #            warn "Stored/updated ".$storable_object->toString()."\n";
         }
     }

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

@@ -45,27 +45,12 @@ sub default_table_name {
 }
 
 
-sub replace_pair {
-    my ($self, $meta_key, $meta_value) = @_;
-
-    $self->remove_all_by_meta_key($meta_key);   # make sure the previous values are gone
-    return $self->store( { 'meta_key' => $meta_key, 'meta_value' => $meta_value } );
-}
-
-
-sub fetch_param_hash {
-    my $self = shift @_;
-
-    return $self->fetch_HASHED_FROM_meta_key_TO_meta_value();
-}
-
-
 sub get_value_by_key {
     my ($self, $meta_key) = @_;
 
     if( my $collection = Bio::EnsEMBL::Hive::MetaParameters->collection() ) {
 
-        return $collection->{ $meta_key };
+        return $collection->find_one_by( 'meta_key', $meta_key );
 
     } else {
 

modules/Bio/EnsEMBL/Hive/MetaParameters.pm

@@ -33,6 +33,11 @@ package Bio::EnsEMBL::Hive::MetaParameters;
 use strict;
 
 use base ( 'Bio::EnsEMBL::Hive::Cacheable' );
- 
+
+
+sub unikey {    # override the default from Cacheable parent
+    return [ 'meta_key' ];
+}
+
 1;
 

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -455,8 +455,13 @@ sub add_objects_from_config {
     my $self                = shift @_;
 
     warn "Adding hive_meta table entries ...\n";
-    my $hm_coll = Bio::EnsEMBL::Hive::MetaParameters->collection();
-    %$hm_coll = (%$hm_coll, %{$self->hive_meta_table()} );
+    my $new_meta_entries = $self->hive_meta_table();
+    while( my ($meta_key, $meta_value) = each %$new_meta_entries ) {
+        Bio::EnsEMBL::Hive::MetaParameters->add_new_or_update(
+            'meta_key'      => $meta_key,
+            'meta_value'    => $meta_value,
+        );
+    }
     warn "Done.\n\n";
 
     warn "Adding pipeline-wide parameters ...\n";