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

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

@@ -266,12 +266,7 @@ sub AUTOLOAD {
 
 sub init_collections {  # should not really belong to DBAdaptor, temporarily squatting here...
 
-    foreach my $AdaptorType ('PipelineWideParameters') {
-        my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
-        $class->collection( {} );
-    }
-
-    foreach my $AdaptorType ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
         my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
         $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new() );
     }
@@ -281,13 +276,7 @@ sub init_collections {  # should not really belong to DBAdaptor, temporarily squ
 sub load_collections {
     my $self = shift @_;
 
-    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 ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', '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 ) );
@@ -298,16 +287,7 @@ sub load_collections {
 sub save_collections {
     my $self = shift @_;
 
-    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() } ) {
-            $adaptor->replace_pair( $hash_key, $hash_value );
-#            warn "Stored/updated '$hash_key' => '$hash_value'\n";
-        }
-    }
-
-    foreach my $AdaptorType ('MetaParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
+    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', '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 ) {

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

@@ -52,7 +52,7 @@ sub get_value_by_key {
 
         return $collection->find_one_by( 'meta_key', $meta_key );
 
-    } else {
+    } else {    # TODO: to be removed when beekeeper.pl/runWorker.pl become collection-aware
 
         my $pair = $self->fetch_by_meta_key( $meta_key );
         return $pair && $pair->{'meta_value'};

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

@@ -45,27 +45,26 @@ sub default_table_name {
 }
 
 
-sub replace_pair {
-    my ($self, $param_name, $param_value) = @_;
-
-    $self->remove_all_by_param_name($param_name);   # make sure the previous values are gone
-    return $self->store( { 'param_name' => $param_name, 'param_value' => stringify( $param_value ) } );
-}
-
-
 =head2 fetch_param_hash
 
-    Description: returns the content of the 'meta' table as a hash
+    Description: returns the contents of the 'pipeline_wide_parameters' table as a hash
 
 =cut
 
 sub fetch_param_hash {
     my $self = shift @_;
 
-    my $original_value      = $self->fetch_HASHED_FROM_param_name_TO_param_value();
-    my %destringified_hash  = map { $_, destringify($original_value->{$_}) } keys %$original_value;
+    if( my $collection = Bio::EnsEMBL::Hive::PipelineWideParameters->collection() ) {
+
+        return { map { $_->{'param_name'} => destringify($->{'param_value'}) } $collection->list() };
+
+    } else {    # TODO: to be removed when beekeeper.pl/runWorker.pl become collection-aware
+
+        my $original_value      = $self->fetch_HASHED_FROM_param_name_TO_param_value();
+        my %destringified_hash  = map { $_, destringify($original_value->{$_}) } keys %$original_value;
 
-    return \%destringified_hash;
+        return \%destringified_hash;
+    }
 }
 
 1;

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

@@ -465,8 +465,13 @@ sub add_objects_from_config {
     warn "Done.\n\n";
 
     warn "Adding pipeline-wide parameters ...\n";
-    my $mc_coll = Bio::EnsEMBL::Hive::PipelineWideParameters->collection();
-    %$mc_coll = (%$mc_coll, %{$self->pipeline_wide_parameters()} );
+    my $new_pwp_entries = $self->pipeline_wide_parameters();
+    while( my ($param_name, $param_value) = each %$new_pwp_entries ) {
+        Bio::EnsEMBL::Hive::PipelineWideParameters->add_new_or_update(
+            'param_name'    => $param_name,
+            'param_value'   => $param_value,
+        );
+    }
     warn "Done.\n\n";
 
     warn "Adding Resources ...\n";

modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm

@@ -34,5 +34,10 @@ use strict;
 
 use base ( 'Bio::EnsEMBL::Hive::Cacheable' );
  
+
+sub unikey {    # override the default from Cacheable parent
+    return [ 'param_name' ];
+}
+
 1;