From 2755272e8073fada9d695bc8a45e8ffffa03eaf2 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Wed, 8 Jun 2005 12:30:14 +0000
Subject: [PATCH] made all registry calls case INsensetive as it was very
annoying having to have species, group and type all in the correct case. Also
added load_registry_from_db which will load the latest ensembl databases
given a database host (and optionally port, user, pass) to search. At prsent
only core,variation,estgene,compara and go adaptors are loaded via this
method.
---
modules/Bio/EnsEMBL/Registry.pm | 294 ++++++++++++++++++++++++--------
1 file changed, 219 insertions(+), 75 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 2575cdc23b..61d8a9fe7e 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -99,8 +99,10 @@ package Bio::EnsEMBL::Registry;
use strict;
use Bio::EnsEMBL::DBSQL::MergedAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use DBI;
use vars qw(%registry_register);
@@ -189,8 +191,8 @@ sub add_db{
my ($class, $db, $name, $adap) = @_;
- if($db->species() ne $adap->species){
- $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = $adap;
+ if(lc($db->species()) ne lc($adap->species)){
+ $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
}
}
@@ -207,8 +209,8 @@ sub add_db{
sub remove_db{
my ($class, $db, $name) = @_;
- my $ret = $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
- $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = undef;
+ my $ret = $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
+ $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = undef;
return $ret;
}
@@ -226,12 +228,12 @@ sub remove_db{
sub get_db{
my ($class, $db, $name) = @_;
- my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor($db->species,$name);
+ my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
if(defined($ret)){
return $ret;
}
- return $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
+ return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
}
=head2 get_all_db_adaptors
@@ -251,13 +253,13 @@ sub get_all_db_adaptors{
# as add_db_adaptor does not add if it is from the same species.
foreach my $dba (@{$registry_register{'_DBA'}}){
- if($dba->species() eq $db->species()){
+ if(lc($dba->species()) eq lc($db->species())){
$ret{$dba->group()} = $dba;
}
}
foreach my $key (keys %{$registry_register{$class->get_alias($db->species())}{$db->group()}{'_special'}}){
- $ret{$key} = $registry_register{$class->get_alias($db->species())}{$db->group()}{'_special'}{$key};
+ $ret{$key} = $registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}{$key};
}
return \%ret;
@@ -289,7 +291,7 @@ sub add_DBAdaptor{
$species = $class->get_alias($species);
- $registry_register{$species}{$group}{'_DB'} = $adap;
+ $registry_register{$species}{lc($group)}{'_DB'} = $adap;
if(!defined($registry_register{'_DBA'})){
my @list =();
@@ -320,7 +322,7 @@ sub get_DBAdaptor{
$species = $class->get_alias($species);
if(defined($group)){ # group defined so return standard DB Adaptor
- return $registry_register{$species}{$group}{'_DB'};
+ return $registry_register{$species}{lc($group)}{'_DB'};
}
else{ #return a merged db adaptor
return new_merged Bio::EnsEMBL::DBSQL::DBAdaptor($species);
@@ -365,8 +367,8 @@ sub add_DNAAdaptor{
deprecated("");
}
else{
- $registry_register{$species}{$group}{'_DNA'} = $dnadb_group;
- $registry_register{$species}{$group}{'_DNA2'} = $dnadb_species;
+ $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
+ $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
}
}
@@ -384,8 +386,8 @@ sub get_DNAAdaptor{
my ($class, $species, $group) = @_;
$species = $class->get_alias($species);
- my $new_group = $registry_register{$species}{$group}{'_DNA'};
- my $new_species = $registry_register{$species}{$group}{'_DNA2'};
+ my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
+ my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
if( defined $new_group ) {
return $class->get_DBAdaptor($new_species,$new_group);
} else {
@@ -425,15 +427,15 @@ sub add_adaptor{
#
if(defined($reset)){ # JUST REST THE HASH VLAUE NO MORE PROCESSING NEEDED
- $registry_register{$species}{$group}{$type} = $adap;
+ $registry_register{$species}{lc($group)}{lc($type)} = $adap;
return;
}
- if(defined($registry_register{$species}{$group}{$type})){
+ if(defined($registry_register{$species}{lc($group)}{lc($type)})){
print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
- $registry_register{$species}{$group}{$type} = $adap;
+ $registry_register{$species}{lc($group)}{lc($type)} = $adap;
return;
}
- $registry_register{$species}{$group}{$type} = $adap;
+ $registry_register{$species}{lc($group)}{lc($type)} = $adap;
if(!defined ($registry_register{$species}{'list'})){
@@ -447,40 +449,18 @@ sub add_adaptor{
# print STDERR "REGADD $species \t $group \t $type\t to the registry\n";
- if(!defined ($registry_register{$type}{$species})){
+ if(!defined ($registry_register{lc($type)}{$species})){
my @list =();
push(@list,$adap);
- $registry_register{$type}{$species}= \@list;
+ $registry_register{lc($type)}{$species}= \@list;
}
else{
- push(@{$registry_register{$type}{$species}},$adap);
+ push(@{$registry_register{lc($type)}{$species}},$adap);
}
}
-=head2 set_get_via_dnadb_if_set
-
- set the flag so that for this type of adaptor the data is obtained
- from the dna source and not centrally i.e. estgenes where the sequence
- data is held in the core.
-
- Arg [1] : name of the species to set flag for.
- Arg [2] : name of the type to set flag for. (i.e. Sequence)
- Example : Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set("Human","Sequence");
- Returntype : none
- Exceptions : none
-
-
-
-=cut
-
-#sub set_get_via_dnadb_if_set{
-# my ($class,$species,$type) = @_;
-#
-# $registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
-#}
-
=head2 get_adaptor
Arg [1] : name of the species to add the adaptor to in the registry.
@@ -496,21 +476,21 @@ sub get_adaptor{
my ($class,$species,$group,$type)= @_;
$species = $class->get_alias($species);
- my %dnadb_adaptors = qw(Sequence 1 AssemblyMapper 1 KaryotypeBand 1 RepeatFeature 1 CoordSystem 1 AssemblyExceptionFeature 1 );
+ my %dnadb_adaptors = qw(sequence 1 assemblymapper 1 karyotypeband 1 repeatfeature 1 coordsystem 1 assemblyexceptionfeature 1 );
- my $dnadb_group = $registry_register{$species}{$group}{_DNA};
+ my $dnadb_group = $registry_register{$species}{lc($group)}{_DNA};
- if( defined($dnadb_group) && defined($dnadb_adaptors{$type}) ) {
- $species = $registry_register{$species}{$group}{'_DNA2'};
+ if( defined($dnadb_group) && defined($dnadb_adaptors{lc($type)}) ) {
+ $species = $registry_register{$species}{lc($group)}{'_DNA2'};
$group = $dnadb_group;
}
- my $ret = $registry_register{$species}{$group}{$type};
+ my $ret = $registry_register{$species}{lc($group)}{lc($type)};
if(!defined($ret)){
return undef;
}
if(!ref($ret)){ # not instantiated yet
- my $dba = $registry_register{$species}{$group}{'_DB'};
+ my $dba = $registry_register{$species}{lc($group)}{'_DB'};
my $module = $ret;
eval "require $module";
@@ -543,26 +523,6 @@ sub get_all_adaptors{
}
-=head2 get_MergedAdaptor
-
- Arg [1] : name of the species to get the adaptors for in the registry.
- Arg [2] : name of the type to get the adaptors for in the registry.
- Example : $merged = Bio::EnsEMBL::Registry->get_MergedAdaptor("Mouse","Gene");
- Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
- Exceptions : none
-
-=cut
-
-sub get_MergedAdaptor{
- my ($class,$species,$type)=@_;
-
- $species = $class->get_alias($species);
- my $ret = new Bio::EnsEMBL::DBSQL::MergedAdaptor();
- $ret->add_list(@{$registry_register{$type}{$species}});
-
- return $ret;
-}
-
=head2 add_alias
Arg [1] : name of the species to add alias for
@@ -577,7 +537,7 @@ sub get_MergedAdaptor{
sub add_alias{
my ($class, $species,$key) = @_;
- $registry_register{'_ALIAS'}{$key} = $species;
+ $registry_register{'_ALIAS'}{lc($key)} = lc($species);
}
=head2 get_alias
@@ -593,10 +553,10 @@ sub add_alias{
sub get_alias{
my ($class, $key) = @_;
- if(!defined($registry_register{'_ALIAS'}{$key})){
+ if(!defined($registry_register{'_ALIAS'}{lc($key)})){
return $key;
}
- return $registry_register{'_ALIAS'}{$key};
+ return $registry_register{'_ALIAS'}{lc($key)};
}
=head2 alias_exists
@@ -613,7 +573,7 @@ sub get_alias{
sub alias_exists{
my ($class, $key) = @_;
- if(defined($registry_register{'_ALIAS'}{$key})){
+ if(defined($registry_register{'_ALIAS'}{lc($key)})){
return 1;
}
return 0;
@@ -635,6 +595,7 @@ sub disconnect_all {
$dbc->disconnect_if_idle() if $dbc->connected();
}
}
+
=head2 change_access
Will change the username and password for a set of databases.
@@ -691,8 +652,188 @@ sub get_all_DBAdaptors_by_connection{
}
+=head2 load_registry_from_db
+
+ Arg [HOST] : The domain name of the database host to connect to.
+
+ Arg [USER] : string
+ The name of the database user to connect with
+ Arg [PASS] : (optional) string
+ The password to be used to connect to the database
+ Arg [PORT] : int
+ The port to use when connecting to the database
+ Arg [VERBOSE]: (optional) Wether to print database messages
+
+ Example : load_registry_from_db( -host => 'ensembldb.ensembl.org',
+ -user => 'anonymous',
+ -verbose => "1" );
+
+ Description: Will load the latest versions of the ensembl databases it
+ can find on a database instance into the registry.
+
+ Exceptions : None.
+
+=cut
+
+sub load_registry_from_db{
+ my($self, @args) = @_;
+ my ($host, $port, $user, $pass, $verbose) =
+ rearrange([qw(HOST PORT USER PASS VERBOSE)], @args);
+
+ my $go_version = 0;
+ my $compara_version =0;
+
+ $user ||= "ensro";
+ my $db = DBI->connect( "DBI:mysql:host=$host;port=$port" , $user, $pass );
+
+ my $res = $db->selectall_arrayref( "show databases" );
+ my @dbnames = map {$_->[0] } @$res;
+
+ my %temp;
+ for my $db (@dbnames){
+ if($db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\d+)_(\d+[a-z]*)/){
+ if(defined($temp{$1})){
+ my ($r1,$r2) = split($temp{$1},"_");
+ if($r1 < $2){
+ $temp{$1} = $2."_".$3;
+ }
+ }
+ else{
+ $temp{$1} = $2."_".$3;
+ }
+ }
+ elsif($db =~ /^ensembl_compara_(\d+)/){
+ if($compara_version < $1){
+ $compara_version = $1;
+ }
+ }
+ elsif($db =~ /^ensembl_go_(\d+)/){
+ if($go_version < $1){
+ $go_version = $1;
+ }
+ }
+ }
+
+ @dbnames =();
+
+ foreach my $key ( keys %temp){
+ push @dbnames, $key."_".$temp{$key};
+ }
+ # register core databases
+
+ my @core_dbs = grep { /^[a-z]+_[a-z]+_core_\d+_/ } @dbnames;
+
+ for my $coredb ( @core_dbs ) {
+ my ($species, $num ) = ( $coredb =~ /(^[a-z]+_[a-z]+)_core_(\d+)/ );
+ my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
+ ( -group => "core",
+ -species => $species,
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $coredb
+ );
+ (my $sp = $species ) =~ s/_/ /g;
+ $self->add_alias( $species, $sp );
+ print $coredb." loaded\n" if ($verbose);
+ }
+
+ my @estgene_dbs = grep { /^[a-z]+_[a-z]+_estgene_\d+_/ } @dbnames;
+
+ for my $estgene_db ( @estgene_dbs ) {
+ my ($species, $num) = ( $estgene_db =~ /(^[a-z]+_[a-z]+)_estgene_(\d+)/ );
+ my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
+ ( -group => "estgene",
+ -species => $species,
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $estgene_db
+ );
+ print $estgene_db." loaded\n" if ($verbose);
+ }
+
+
+ eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
+ if($@) {
+ #ignore variations as code required not there for this
+ print "Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found\n" if ($verbose);
+ }
+ else{
+ my @variation_dbs = grep { /^[a-z]+_[a-z]+_variation_\d+_/ } @dbnames;
+
+ for my $variation_db ( @variation_dbs ) {
+ my ($species, $num ) = ( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(\d+)/ );
+ my $dba = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new
+ ( -group => "variation",
+ -species => $species,
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $variation_db
+ );
+ print $variation_db." loaded\n" if ($verbose);
+ }
+ }
+
+ #Compara
+ if($compara_version){
+ eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
+ if($@) {
+ #ignore compara as code required not there for this
+ print "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so compara database ensembl_compara_$compara_version will be ignored\n" if ($verbose);
+ }
+ else{
+ my $compara_db = "ensembl_compara_".$compara_version;
+
+ my $dba = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new
+ ( -group => "compara",
+ -species => "multi",
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $compara_db
+ );
+ print $compara_db." loaded\n" if ($verbose);
+ }
+ }
+ else{
+ print "No Compara database found" if ($verbose);
+ }
+
+
+ #GO
+ if($go_version){
+ eval "use Bio::EnsEMBL::ExternalData::GO::GOAdaptor";
+ if($@) {
+ #ignore go as code required not there for this
+ print "Bio::EnsEMBL::ExternalData::GO::GOAdaptor::DBAdaptor not found so go database ensemb_go_$go_version will be ignored\n" if ($verbose);
+ }
+ else{
+ my $go_db = "ensembl_go_".$go_version;
+ my $dba = Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new
+ ( -group => "go",
+ -species => "multi",
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $go_db
+ );
+ print $go_db." loaded\n" if ($verbose);
+ }
+ }
+ else{
+ print "No go database found" if ($verbose);
+ }
+
+}
#
@@ -700,6 +841,7 @@ sub get_all_DBAdaptors_by_connection{
#
+
=head2 load_registry_with_web_adaptors
Will load the registry with all the Adaptors used in the Web server.
Providing Sitedefs and SpeciesDefs can be found on PERL5LIB path.
@@ -746,7 +888,8 @@ sub load_registry_with_web_adaptors{
sub set_default_track{
my ($class, $species, $group) = @_;
- $registry_register{'def_track'}{$species}{$group} = 1;
+ $species = get_alias($species);
+ $registry_register{'def_track'}{$species}{lc($group)} = 1;
}
=head2 default_track
@@ -763,7 +906,8 @@ sub set_default_track{
sub default_track{
my ($class, $species, $group) = @_;
- if(defined($registry_register{'def_track'}{$species}{$group})){
+ $species = get_alias($species);
+ if(defined($registry_register{'def_track'}{$species}{lc($group)})){
return 1;
}
--
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