core-independent version of DBAdaptor. new() clean from URLFactory and...

core-independent version of DBAdaptor. new() clean from URLFactory and self-reference, but still plays nice with optional Registry

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

@@ -6,12 +6,7 @@
 
 =head1 SYNOPSIS
 
-    $db = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new(
-        -user   => 'root',
-        -dbname => 'pog',
-        -host   => 'caldy',
-        -driver => 'mysql',
-    );
+    my $db = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => 'mysql://my_username:my_password@my_hostname:3306/my_hive_database' );
 
 =head1 DESCRIPTION
 
@@ -41,31 +36,32 @@ package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 
 use strict;
 
-use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Utils::Argument ('rearrange');
+use Bio::EnsEMBL::Utils::Exception ('throw');
 
-use Bio::EnsEMBL::Hive::URLFactory;
 use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
 use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
 
-use base ('Bio::EnsEMBL::DBSQL::DBAdaptor');
-
 
 sub new {
     my ($class, @args) = @_;
 
-    my ($url, $reg_conf, $reg_type, $reg_alias, $no_sql_schema_version_check)
-        = rearrange(['URL', 'REG_CONF', 'REG_TYPE', 'REG_ALIAS', 'NO_SQL_SCHEMA_VERSION_CHECK'], @args);
+    my ($dbconn, $url, $reg_conf, $reg_type, $reg_alias, $species, $no_sql_schema_version_check)
+        = rearrange(['DBCONN', 'URL', 'REG_CONF', 'REG_TYPE', 'REG_ALIAS', 'SPECIES', 'NO_SQL_SCHEMA_VERSION_CHECK'], @args);
 
     $url .= ';nosqlvc=1' if($url && $no_sql_schema_version_check);
 
     my $self;
 
     if($url) {
-        $self = Bio::EnsEMBL::Hive::URLFactory->fetch($url)
-            or die "Unable to connect to DBA using url='$url'\n";
+
+        $dbconn = Bio::EnsEMBL::Hive::DBSQL::DBConnection->new(-url => $url)
+            or die "Unable to create a DBC using url='$url'";
+
     } elsif($reg_alias) {
-        Bio::EnsEMBL::Registry->load_all($reg_conf) if($reg_conf);
+
+        require Bio::EnsEMBL::Registry;
+        Bio::EnsEMBL::Registry->load_all($reg_conf);    # if undefined, default reg_conf will be used
 
         $reg_type ||= 'hive';
 
@@ -73,11 +69,14 @@ sub new {
             or die "Unable to connect to DBA using reg_conf='$reg_conf', reg_type='$reg_type', reg_alias='$reg_alias'\n";
 
         if($reg_type ne 'hive') {   # ensure we are getting a Hive adaptor even from a non-Hive Registry entry:
-            $self = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -dbconn => $self->dbc(), -no_sql_schema_version_check => $no_sql_schema_version_check );
+            $dbconn = $self->dbc;
+            $self = undef;
         }
-    } else {
-        $self = $class->SUPER::new(@args)
-            or die "Unable to connect to DBA using parameters (".join(', ', @args).")\n"
+    }
+
+    if($dbconn && !$self) {
+        $self = bless {}, $class;
+        $self->dbc( $dbconn );
     }
 
     unless($no_sql_schema_version_check) {
@@ -105,7 +104,6 @@ sub new {
 
         } elsif($db_sql_schema_version < $code_sql_schema_version) {
 
-
             my $new_patches = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_sql_schema_patches( $db_sql_schema_version, $dbc->driver )
                 || die "DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
                       ."Unfortunately we cannot patch the database; you may have to create a new database or agree to run older code\n";
@@ -122,17 +120,21 @@ sub new {
         }
     }
 
+    if($species) {      # [compatibility with core code] store the DBAdaptor in Registry:
+        require Bio::EnsEMBL::Registry;
+        Bio::EnsEMBL::Registry->add_DBAdaptor( $species, 'hive', $self );
+    }
+
     return $self;
 }
 
 
 sub dbc {
-    my $self = shift @_;
+    my $self = shift;
 
-    my $dbc = $self->SUPER::dbc( @_ );
-    bless $dbc, 'Bio::EnsEMBL::Hive::DBSQL::DBConnection' if( $dbc );
+    $self->{'_dbc'} = bless shift, 'Bio::EnsEMBL::Hive::DBSQL::DBConnection' if(@_);
 
-    return $dbc;
+    return $self->{'_dbc'};
 }
 
 
@@ -161,27 +163,63 @@ sub hive_use_param_stack {  # getter only, not setter
 sub get_available_adaptors {
  
     my %pairs =  (
-            # Core adaptors extended with Hive stuff:
-        'MetaContainer'         => 'Bio::EnsEMBL::Hive::DBSQL::MetaContainer',
-
-            # "new" Hive adaptors (sharing the same fetching/storing code inherited from the BaseAdaptor class) :
+        'Accumulator'           => 'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor',
+        'Analysis'              => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
         'AnalysisCtrlRule'      => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor',
+        'AnalysisData'          => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
+        'AnalysisJob'           => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
+        'AnalysisStats'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor',
         'DataflowRule'          => 'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor',
-        'ResourceDescription'   => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
-        'ResourceClass'         => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
         'LogMessage'            => 'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor',
+        'Meta'                  => 'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor',
+        'MetaContainer'         => 'Bio::EnsEMBL::Hive::DBSQL::MetaContainer',
         'NakedTable'            => 'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor',
-        'Analysis'              => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
+        'ResourceClass'         => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
+        'ResourceDescription'   => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
         'Queen'                 => 'Bio::EnsEMBL::Hive::Queen',
-        'AnalysisData'          => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
-        'Accumulator'           => 'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor',
-        'Meta'                  => 'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor',
-
-            # "old" Hive adaptors (having their own fetching/storing code) :
-        'AnalysisJob'           => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
-        'AnalysisStats'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor',
     );
     return \%pairs;
 }
 
+
+sub get_adaptor {
+    my $self = shift;
+    my $type = shift;
+
+    my $signature = join(':', $type, @_);
+
+    unless( $self->{'_cached_adaptor'}{$signature} ) {
+        my $adaptor_package_name = $self->get_available_adaptors()->{$type}
+        or throw("Could not find a module corresponding to '$type'");
+
+        eval "require $adaptor_package_name"
+        or throw("Could not load or compile module '$adaptor_package_name'");
+
+        $self->{'_cached_adaptor'}{$signature} = $adaptor_package_name->new( $self, @_ );
+    }
+
+    return $self->{'_cached_adaptor'}{$signature};
+}
+
+
+sub DESTROY { }   # to simplify AUTOLOAD
+
+sub AUTOLOAD {
+    our $AUTOLOAD;
+
+    my $type;
+    if ( $AUTOLOAD =~ /^.*::get_(\w+)Adaptor$/ ) {
+        $type = $1;
+    } elsif ( $AUTOLOAD =~ /^.*::get_(\w+)$/ ) {
+        $type = $1;
+    } else {
+        die "DBAdaptor::AUTOLOAD: Could not interpret the method: $AUTOLOAD";
+    }
+
+    my $self = shift;
+
+    return $self->get_adaptor($type, @_);
+}
+
 1;
+