changes for registry mainly due to the fact that DBAdaptor no longer inherits from DBConnection

modules/t/attributeAdaptor.t

@@ -50,7 +50,7 @@ $aa->store_on_MiscFeature($mf, [$attrib]);
 #
 # make sure the misc_attrib table was updated
 #
-my $count = $db->db_handle->selectall_arrayref
+my $count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM misc_attrib " .
    "WHERE misc_feature_id = 1")->[0]->[0];
 
@@ -59,7 +59,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code'")->[0]->[0];
 ok($count == 1);
@@ -87,7 +87,7 @@ $aa->remove_from_MiscFeature($mf);
 #
 # make sure the misc_attrib table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM misc_attrib " .
    "WHERE misc_feature_id = 1")->[0]->[0];
 
@@ -119,7 +119,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -128,7 +128,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code2'")->[0]->[0];
 ok($count == 1);
@@ -156,7 +156,7 @@ $aa->remove_from_Slice($slice);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
@@ -178,7 +178,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -187,7 +187,7 @@ ok($count == 1);
 #
 # make sure the attrib_type table was updated
 #
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM attrib_type " .
    "WHERE code = 'test_code2'")->[0]->[0];
 ok($count == 1);

modules/t/canonicalDBAdaptor.t

@@ -36,8 +36,8 @@ $test_adaptor = $db->get_ProteinFeatureAdaptor();
 ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor"));
 #$test_adaptor = $db->get_ProteinAdaptor();
 #ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProteinAdaptor"));
-$test_adaptor = $db->get_MapFragAdaptor();
-ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::MapFragAdaptor"));
+#$test_adaptor = $db->get_MapFragAdaptor();
+#ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::MapFragAdaptor"));
 #$test_adaptor = $db->get_CloneAdaptor();
 #ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::CloneAdaptor"));
 $test_adaptor = $db->get_PredictionTranscriptAdaptor();
@@ -74,8 +74,8 @@ $test_adaptor = $db->get_DBEntryAdaptor();
 ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::DBEntryAdaptor"));
 $test_adaptor = $db->get_KaryotypeBandAdaptor();
 ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor"));
-$test_adaptor = $db->get_ChromosomeAdaptor();
-ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ChromosomeAdaptor"));
+#$test_adaptor = $db->get_ChromosomeAdaptor();
+#ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ChromosomeAdaptor"));
 $test_adaptor = $db->get_SupportingFeatureAdaptor();
 ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor"));
 $test_adaptor = $db->get_MarkerFeatureAdaptor();
@@ -93,19 +93,20 @@ ok($test_adaptor->isa("Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor"));
 #ok($test_adaptor->isa("Bio::EnsEMBL::DBSQL::ProxySNPAdaptor"));
 
 # Should get an error if we ask for something non-existent
-eval { $db->get_adaptor("SomeNonExistentType") };
-ok($@);
+#eval { $db->get_adaptor("SomeNonExistentType") };
+#ok($@);
 
 # Check setting module with good values
 ok($db->set_adaptor("ArchiveStableId", "Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor" ));
 
-# Setting an unknown data type should give an error
-eval { $db->set_adaptor("SomeNonExistentType", "Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor") };
-ok($@);
+# Setting an unknown data type should NO LONGER give an error
+my $ret = $db->set_adaptor("SomeNonExistentType", "Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor");
+ok(defined($ret));
 
-# Setting to a non-subclass of the default should give an error
-eval { $db->set_adaptor("ArchiveStableId", "Bio::EnsEMBL::DBSQL::GeneAdaptor") };
-ok($@);
+
+# Setting to a non-subclass of the default should NOT give an error
+$ret =  $db->set_adaptor("ArchiveStableId", "Bio::EnsEMBL::DBSQL::GeneAdaptor");
+ok(defined($ret));
 
 # Generic adaptors
 

modules/t/compressedSequenceAdaptor.t

@@ -36,7 +36,7 @@ $multi_db->save('core', 'dnac', 'seq_region');
 #we can get weird padding at the end due to the last byte being not
 #fully packed but still labelled as non-gap 
 my $sth = 
-  $db->prepare('INSERT INTO seq_region (name, length, coord_system_id) ' .
+  $db->db->prepare('INSERT INTO seq_region (name, length, coord_system_id) ' .
                'VALUES (?,?,?)');
 $sth->execute('testfrag', $len,$contig_cs->dbID);
 

modules/t/coordSystemAdaptor.t

@@ -155,7 +155,7 @@ ok(!$cs->is_sequence_level);
 ok(!$cs->is_top_level);
 ok($cs->rank() == 10);
 
-my $sth = $db->prepare('SELECT attrib FROM coord_system ' .
+my $sth = $db->db->prepare('SELECT attrib FROM coord_system ' .
                        'WHERE  name = ? and version = ?');
 $sth->execute('newsystem', 'NCBI35');
 

modules/t/dbConnection.t

+use lib 't';
 use strict;
 use warnings;
 
 
 BEGIN { $| = 1;
 	use Test;
-	plan tests => 30;
+	plan tests => 24;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -29,12 +30,12 @@ my $db    = $multi->get_DBAdaptor('core');
 #
 my $dbc;
 {
-  my $db_name = $db->dbname;
-  my $port    = $db->port;
-  my $user    = $db->username;
-  my $pass    = $db->password;
-  my $host    = $db->host;
-  my $driver  = $db->driver;
+  my $db_name = $db->db->dbname;
+  my $port    = $db->db->port;
+  my $user    = $db->db->username;
+  my $pass    = $db->db->password;
+  my $host    = $db->db->host;
+  my $driver  = $db->db->driver;
 
   $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(-dbname => $db_name,
 						-user   => $user,
@@ -72,17 +73,17 @@ ok(test_getter_setter($dbc, 'username', 'ensembl_user'));
 ok(test_getter_setter($dbc, 'password', 'ensembl_password'));
 
 #
-# 8-9 _get_adaptor
+# 8-9 _get_adaptor NO LONGER ALLOWED MUST GO VIA DBAdaptor
 #
-my $adaptor_name = 'Bio::EnsEMBL::DBSQL::GeneAdaptor';
-my $adaptor = $dbc->_get_adaptor($adaptor_name);
-ok($adaptor->isa($adaptor_name));
-ok($adaptor == $dbc->_get_adaptor($adaptor_name)); #verify cache is used
+#my $adaptor_name = 'Bio::EnsEMBL::DBSQL::GeneAdaptor';
+#my $adaptor = $dbc->_get_adaptor($adaptor_name);
+#ok($adaptor->isa($adaptor_name));
+#ok($adaptor == $dbc->_get_adaptor($adaptor_name)); #verify cache is used
 
 #
 # 10 dbhandle
 #
-ok(test_getter_setter($dbc, 'db_handle', $db->db_handle));
+ok(test_getter_setter($dbc, 'db_handle', $dbc->db_handle));
 
 
 {
@@ -94,27 +95,29 @@ ok(test_getter_setter($dbc, 'db_handle', $db->db_handle));
   ok($sth->rows);
   $sth->finish;
 }
+
+# AGAIN NOW DONE VIA DBADAPTOR
 #
 # 12 add_db_adaptor
 #
-$dbc->add_db_adaptor('core', $db);
-
-my $db1 = $dbc->get_all_db_adaptors->{'core'};
-my $db2 = $db->_obj;
-debug("\n\ndb1=[$db1] db2=[$db2]\n\n"); 
-ok($db1 == $db2);
-
+#$dbc->add_db_adaptor('core', $db);
 #
-# 13 get_db_adaptor
-#
-ok($dbc->get_db_adaptor('core')->isa('Bio::EnsEMBL::DBSQL::DBConnection'));
-
+#my $db1 = $dbc->get_all_db_adaptors->{'core'};
+#my $db2 = $db->_obj;
+#debug("\n\ndb1=[$db1] db2=[$db2]\n\n"); 
+#ok($db1 == $db2);
 #
-# 14-15 remove_db_adaptor
+##
+## 13 get_db_adaptor
+##
+#ok($dbc->get_db_adaptor('core')->isa('Bio::EnsEMBL::DBSQL::DBConnection'));
 #
-$dbc->remove_db_adaptor('core');
-ok(!defined $dbc->get_db_adaptor('core'));
-ok(!defined $dbc->get_all_db_adaptors->{'core'});
+##
+## 14-15 remove_db_adaptor
+##
+#$dbc->remove_db_adaptor('core');
+#ok(!defined $dbc->get_db_adaptor('core'));
+#ok(!defined $dbc->get_all_db_adaptors->{'core'});
 
 
 #

modules/t/dbEntries.t

@@ -37,7 +37,7 @@ ok( $db );
 my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
 
 
-my $sth = $db->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
+my $sth = $db->db->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
 $sth->execute();
 
 my ( $xref_count )  = $sth->fetchrow_array();

modules/t/gene.t

@@ -30,7 +30,7 @@ ok( $db );
 
 my $gene;
 my $ga = $db->get_GeneAdaptor();
-
+print STDERR $ga."\n";
 debug ("Gene->list_dbIDs");
 my $ids = $ga->list_dbIDs();
 ok (@{$ids});
@@ -41,6 +41,8 @@ ok (@{$stable_ids});
 
 $gene = $ga->fetch_by_stable_id( "ENSG00000171456" );
 
+print STDERR $gene."\n";
+
 debug( "Gene->fetch_by_stable_id()" );
 ok( $gene );
 
@@ -602,7 +604,7 @@ debug( "Storing gene" );
 $gene_ad->store($gene);
 
 
-my $dbe_id = $db->db_handle->selectall_arrayref("SELECT display_xref_id FROM gene")->[0]->[0];
+my $dbe_id = $db->db->db_handle->selectall_arrayref("SELECT display_xref_id FROM gene")->[0]->[0];
 
 ok($dbe_id && $dbe_id == $dbe->dbID());
 

modules/t/markerFeatureAdaptor.t

@@ -109,7 +109,7 @@ ok($marker_feature->dbID &&
    $marker_feature->adaptor == $mfa);
 
 
-my $sth = $db->prepare('SELECT count(*) from marker_feature');
+my $sth = $db->db->prepare('SELECT count(*) from marker_feature');
 $sth->execute;
 my ($count) = $sth->fetchrow_array;
 $sth->finish();

modules/t/miscSetAdaptor.t

@@ -8,7 +8,6 @@ BEGIN { $| = 1;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::MiscSet;
 use Bio::EnsEMBL::Test::TestUtils;
-
 our $verbose = 0; #set to 1 to turn on debug printouts
 
 
@@ -74,7 +73,7 @@ $msa->store($misc_set);
 ok($misc_set->dbID());
 ok($misc_set->adaptor() == $msa);
 
-my $count = $db->db_handle->selectall_arrayref
+my $count = $db->db->db_handle->selectall_arrayref
   ("SELECT COUNT(*) FROM misc_set WHERE code = 'code'")->[0]->[0];
 
 ok($count == 1);
@@ -100,7 +99,7 @@ $msa->store($misc_set);
 
 ok($misc_set->dbID && $misc_set->adaptor);
 
-$count = $db->db_handle->selectall_arrayref
+$count = $db->db->db_handle->selectall_arrayref
   ("SELECT COUNT(*) FROM misc_set WHERE code = 'code'")->[0]->[0];
 ok($count == 1);
 

modules/t/sliceAdaptor.t

@@ -28,7 +28,7 @@ my $db    = $multi->get_DBAdaptor('core');
 #
 # SliceAdaptor::new
 #
-my $slice_adaptor = Bio::EnsEMBL::DBSQL::SliceAdaptor->new($db->_obj);
+my $slice_adaptor = Bio::EnsEMBL::DBSQL::SliceAdaptor->new($db);
 ok($slice_adaptor->isa('Bio::EnsEMBL::DBSQL::SliceAdaptor'));
 ok($slice_adaptor->db);
 
@@ -406,7 +406,7 @@ ok($slice->seq_region_name =~ /$clone_name\.\d+/);
 # highest (lowest-numbered) ranked comes out first
 $multi->hide('core', 'seq_region');
 
-my $sth = $db->prepare(qq{INSERT INTO seq_region (coord_system_id, name,
+my $sth = $db->db->prepare(qq{INSERT INTO seq_region (coord_system_id, name,
                                                   length)
                 SELECT cs.coord_system_id, 'TESTREGION', 1000000
                 FROM coord_system cs