AnalysisDataAdaptor now inherits from NakedTableAdaptor

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

@@ -42,62 +42,20 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
 
 use strict;
 
-use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
+use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
 
 
-sub fetch_by_dbID {
-  my ($self, $data_id) = @_;
-
-  my $sql = "SELECT data FROM analysis_data WHERE analysis_data_id = ?";
-  my $sth = $self->prepare($sql);
-  $sth->execute($data_id);
-
-  my ($data) = $sth->fetchrow_array();
-  $sth->finish();
-  return $data;
-}
-
-#
-# STORE METHODS
-#
-################
-
-sub store {
-  my ($self, $data) = @_;
-  
-  return 0 unless($data);
-  
-  my $sth = $self->prepare("INSERT INTO analysis_data (data) VALUES (?)");
-  $sth->execute($data);
-  my $data_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'analysis_data', 'analysis_data_id');
-  $sth->finish;
-
-  return $data_id;
+sub default_table_name {
+    return 'analysis_data';
 }
 
 
 sub store_if_needed {
-  my ($self, $data) = @_;
-  my $data_id;
-
-  return 0 unless($data);
-
-  my $sth = $self->prepare("SELECT analysis_data_id FROM analysis_data WHERE data = ?");
-  $sth->execute($data);
-  ($data_id) = $sth->fetchrow_array();
-  $sth->finish;
+    my ($self, $data) = @_;
 
-  if($data_id) {
-    # print("data already stored as id $data_id\n");
-    return $data_id;
-  }
+    my ($stored_hash) = $self->store({'data'=> $data}, 1);
 
-  return $self->store($data);
+    return $stored_hash->{'analysis_data_id'};
 }
 
 1;
-
-
-
-
-

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

@@ -355,15 +355,15 @@ sub _objs_from_sth {
   while ($sth->fetch()) {
 
     my $input_id = ($column{'input_id'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
-            ? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($1)
+            ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
             : $column{'input_id'};
 
     my $param_id_stack = ($column{'param_id_stack'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
-            ? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($1)
+            ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
             : $column{'param_id_stack'};
 
     my $accu_id_stack = ($column{'accu_id_stack'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
-            ? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($1)
+            ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
             : $column{'accu_id_stack'};
 
 
@@ -815,7 +815,7 @@ sub fetch_input_ids_for_job_ids {
 
         while(my ($job_id, $input_id) = $sth->fetchrow_array() ) {
             if($input_id =~ /^_ext(?:\w+)_data_id (\d+)$/) {
-                $input_id = $self->db->get_AnalysisDataAdaptor->fetch_by_dbID($1);
+                $input_id = $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1);
             }
             $input_ids{$job_id * $id_scale + $id_offset} = $input_id;
         }