From b2ede769ab25cfe0590a07b093462fbba91aa18e Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 6 Jan 2012 17:14:55 +0000
Subject: [PATCH] Adding trinomial support for database names
---
modules/Bio/EnsEMBL/Registry.pm | 78 +++++++++++++++++++++++++++++----
1 file changed, 69 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index d2c749dab8..40064dc0b5 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -127,6 +127,7 @@ use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::ApiVersion;
+use Bio::EnsEMBL::Utils::URI qw/parse_uri/;
use DBI qw(:sql_types);
@@ -1352,6 +1353,15 @@ sub change_access{
Example : load_registry_from_url(
'mysql://anonymous@ensembldb.ensembl.org:3306');
+
+ load_registry_from_url(
+ 'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core&species=homo_sapiens'
+ );
+
+ load_registry_from_url(
+ 'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core'
+ );
+
Description: Will load the correct versions of the ensembl
databases for the software release it can find on
@@ -1363,6 +1373,11 @@ sub change_access{
script may crash as the API version won't match the
DB version.
+ You can also specify a database name which will cause the
+ loading of a single DBAdaptor instance. Parameters are
+ mapped from a normal URL parameter set to their DBAdaptor
+ equivalent. Group must be defined.
+
Returntype : Int count of the DBAdaptor instances which can be found in the
registry
@@ -1376,7 +1391,7 @@ sub change_access{
sub load_registry_from_url {
my ( $self, $url, $verbose, $no_cache ) = @_;
- if ( $url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?/x ) {
+ if ( $url =~ /^mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?$/x ) {
my $user_pass = $1;
my $host = $2;
my $port = $3;
@@ -1398,6 +1413,23 @@ sub load_registry_from_url {
-no_cache => $no_cache
);
}
+ my $uri = parse_uri($url);
+ if($uri) {
+ if($uri->scheme() eq 'mysql') {
+ my %params = $uri->generate_dbsql_params();
+ if($params{-DBNAME}) {
+ $params{-SPECIES} = $params{-DBNAME} unless $params{-SPECIES};
+ $params{-NO_CACHE} = 1 if $no_cache;
+ my $group = $params{-GROUP};
+ my $class = $self->_group_to_adaptor_class($group);
+ if($verbose) {
+ printf("Loading database '%s' from group '%s' with DBAdaptor class '%s' from url %s\n", $params{-DBNAME}, $group, $class, $url);
+ }
+ $class->new(%params);
+ return 1;
+ }
+ }
+ }
throw("Only MySQL URLs are accepted. Given URL was '${url}'");
} ## end sub load_registry_from_url
@@ -1578,14 +1610,14 @@ sub load_registry_from_db {
$ontology_version = $1;
}
} elsif (
- $db =~ /^([a-z]+_[a-z0-9]+ # species name e.g. homo_sapiens
+ $db =~ /^([a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name e.g. homo_sapiens or canis_lupus_familiaris
_
[a-z]+ # db type
(?:_\d+)?) # optional end bit for ensembl genomes databases
_
(\d+) # database release
_
- (\w+) # assembly number can have letters too e.g 37c
+ (\w+)$ # assembly number can have letters too e.g 37c
/x
)
{
@@ -1614,7 +1646,7 @@ sub load_registry_from_db {
# Register Core like databases
foreach my $type (qw(core cdna vega otherfeatures rnaseq)) {
- my @dbs = grep { /^[a-z]+_[a-z0-9]+ # species name
+ my @dbs = grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name
_
$type # the database type
_
@@ -1631,7 +1663,7 @@ sub load_registry_from_db {
my ( $species, $num ) =
- ( $database =~ /(^[a-z]+_[a-z0-9]+) # species name
+ ( $database =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?) # species name
_
$type # type
_
@@ -1779,7 +1811,7 @@ sub load_registry_from_db {
}
else {
my @variation_dbs =
- grep { /^[a-z]+_[a-z0-9]+_variation_(?:\d+_)?\d+_/ } @dbnames;
+ grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_variation_(?:\d+_)?\d+_/ } @dbnames;
for my $variation_db (@variation_dbs) {
@@ -1789,7 +1821,7 @@ sub load_registry_from_db {
}
my ( $species, $num ) =
- ( $variation_db =~ /(^[a-z]+_[a-z0-9]+)_variation_(?:\d+_)?(\d+)_/ );
+ ( $variation_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_variation_(?:\d+_)?(\d+)_/ );
my $dba =
Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(
-group => "variation",
@@ -1856,7 +1888,7 @@ sub load_registry_from_db {
}
} else {
my @funcgen_dbs =
- grep { /^[a-z]+_[a-z0-9]+_funcgen_(?:\d+_)?\d+_/ } @dbnames;
+ grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_funcgen_(?:\d+_)?\d+_/ } @dbnames;
for my $funcgen_db (@funcgen_dbs) {
if ( index( $funcgen_db, 'collection' ) != -1 ) {
@@ -1865,7 +1897,7 @@ sub load_registry_from_db {
}
my ( $species, $num ) =
- ( $funcgen_db =~ /(^[a-z]+_[a-z0-9]+)_funcgen_(?:\d+_)?(\d+)_/ );
+ ( $funcgen_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_funcgen_(?:\d+_)?(\d+)_/ );
my $dba = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
-group => "funcgen",
-species => $species.$species_suffix,
@@ -2053,6 +2085,34 @@ sub load_registry_from_db {
} ## end sub load_registry_from_db
+=head2 _group_to_adaptor_class
+
+ Arg [1] : The group you wish to decode to an adaptor class
+ Example : Bio::EnsEMBL::Registry->_group_to_adaptor_class('core');
+ Description : Has an internal lookup of groups to their adaptor classes
+ Returntype : String
+ Exceptions : Thrown if the group is unknown
+ Status : Stable
+
+=cut
+
+sub _group_to_adaptor_class {
+ my ($self, $group) = @_;
+ my $class = {
+ core => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ cdna => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ otherfeatures => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ rnaseq => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ vega => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ variation => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
+ funcgen => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
+ compara => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
+ }->{$group};
+ throw "Group '${group}' is unknown";
+ return $class;
+}
+
+
=head2 find_and_add_aliases
Arg [ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor
--
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