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Commit 1a7d316d authored by Ian Longden's avatar Ian Longden
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dnadb now holds name core and not the adaptor so that forking and order are not important

parent aa3c78a2
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Showing with 67 additions and 51 deletions
modules/Bio/EnsEMBL/Registry.pm
View file @ 1a7d316d
......@@ -382,12 +382,17 @@ sub get_all_DBAdaptors{
=cut
sub add_DNAAdaptor{
my ($class, $species, $group, $adap) = @_;
my ($class, $species, $group, $dnadb_group) = @_;
$species = $class->get_alias($species);
$registry_register{$species}{$group}{'_DNA'} = $adap;
if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
# print STDERR "AHHH ".caller()."\n";
$registry_register{$species}{$group}{'_DNA'} = $dnadb_group->group();
}
else{
# print STDERR "AHHH MEN ".caller()."\n";
$registry_register{$species}{$group}{'_DNA'} = $dnadb_group;
}
}
=head2 get_DNAAdaptor
......@@ -404,7 +409,12 @@ sub get_DNAAdaptor{
my ($class, $species, $group) = @_;
$species = $class->get_alias($species);
return $registry_register{$species}{$group}{'_DNA'};
my $new_group = $registry_register{$species}{$group}{'_DNA'};
if( defined $new_group ) {
return $class->get_DBAdaptor($species,$new_group);
} else {
return undef;
}
}
#
......@@ -489,11 +499,11 @@ sub add_adaptor{
=cut
sub set_get_via_dnadb_if_set{
my ($class,$species,$type) = @_;
$registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
}
#sub set_get_via_dnadb_if_set{
# my ($class,$species,$type) = @_;
#
# $registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
#}
=head2 get_adaptor
......@@ -508,15 +518,27 @@ sub set_get_via_dnadb_if_set{
sub get_adaptor{
my ($class,$species,$group,$type)= @_;
$species = $class->get_alias($species);
#throw in a check to see if we should get the dnadb one and not the normal
if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
my $dna = $class->get_DNAAdaptor($species,$group);
$species = $dna->species();
$group = $dna->group();
$species = $class->get_alias($species);
my %dnadb_adaptors = qw(Sequence 1 AssemblyMapper 1 KaryotypeBand 1 RepeatFeature 1 CoordSystem 1 AssemblyExceptionFeature 1 );
my $dnadb_group = $registry_register{$species}{$group}{_DNA};
if( defined($dnadb_group) && defined($dnadb_adaptors{$type}) ) {
# print STDERR "new### $group $dnadb_group \n";
$group = $dnadb_group;
}
# else{
# if (defined($dnadb_adaptors{$type}) ) {
# print STDERR "old### $species $group $type no dnadb \n";
# }
# }
#throw in a check to see if we should get the dnadb one and not the normal
# if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
# my $dna = $class->get_DNAAdaptor($species,$group);
# $species = $dna->species();
# $group = $dna->group();
# }
my $ret = $registry_register{$species}{$group}{$type};
if(!defined($ret)){
......
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
View file @ 1a7d316d
......@@ -110,16 +110,19 @@ sub gen_load{
}
elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
#vega uses the core DBAdaptor so test if vega is in the dbname
if($dba->dbc->dbname() =~ /vega/){
if(!defined($dba->group())){
$dba->group('vega');
}
if(!defined($dba->group())){
$dba->group('core');
}
if($dba->group eq "estgene"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
}
elsif($dba->group eq "est"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_est;
}
elsif($dba->group eq "vega"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
}
else{
if(!defined($dba->group())){
$dba->group('core');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
}
}
......@@ -195,10 +198,6 @@ sub load_core{
}
foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
}
}
......@@ -221,7 +220,6 @@ sub load_SNP{
sub attach_database{
my ($class, $species, $core, $name1) = @_;
print STDERR "attach_databse called ".caller(). "\n";
my $first = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$name1);
my $coredb = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$core);
......@@ -232,7 +230,6 @@ sub attach_database{
sub attach_dna{
my ($class, $species, $main, $attach) = @_;
print STDERR "attach_dna called ".caller(). "\n";
my $no_seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$main);
my $seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$attach);
......@@ -282,16 +279,14 @@ sub load_estgene{
Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key});
}
#if dnadb has been set then for the follwing use it.
foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
}
## if the core exists then set this for the dna getting
my $core = $reg->get_DBAdaptor($dba->species,"core");
if(defined($core)){
$reg->add_DNAAdaptor($dba->species,$dba->group,$core);
}
# #if dnadb has been set then for the follwing use it.
# foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
# Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
# }
$reg->add_DNAAdaptor($dba->species,$dba->group,"core");
}
......@@ -305,13 +300,13 @@ sub load_est{
}
#if dnadb has been set then for the follwing use it.
foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
}
my $core = $reg->get_DBAdaptor($dba->species,"core");
if(defined($core)){
$reg->add_DNAAdaptor($dba->species,$dba->group,$core);
}
# foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
# Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
# }
# my $core = $reg->get_DBAdaptor($dba->species,"core");
# if(defined($core)){
$reg->add_DNAAdaptor($dba->species,$dba->group,"core");
# }
}
......@@ -323,10 +318,10 @@ sub load_vega{
foreach my $key (keys %pairs){
Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key});
}
my $core = $reg->get_DBAdaptor($dba->species,"core");
if(defined($core)){
$reg->add_DNAAdaptor($dba->species,$dba->group,$core);
}
# my $core = $reg->get_DBAdaptor($dba->species,"core");
# if(defined($core)){
$reg->add_DNAAdaptor($dba->species,$dba->group,"core");
# }
}
......@@ -397,7 +392,6 @@ sub load_pipeline{
sub dnadb_add{
my $class = shift;
my ($dnaspecies, $dnagroup, $species, $group) = @_;
print STDERR "dnadb_add called ".caller(). "\n";
my $dnadb = Bio::EnsEMBL::Registry->get_DBAdaptor($dnaspecies, $dnagroup);
my $featdb = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
......
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