Commit 36da09d0 authored by Ian Longden's avatar Ian Longden
Browse files

get_all_db fix

parent a56d25b8
......@@ -21,12 +21,13 @@ $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Homo Sapiens","core","Gene"
All Adaptors are stored/registered using this module. This module should then
be used to get the adaptors needed.
The registry can be loaded from a configuration file. If the enviroment
variable ENSEMBL_REGISTRY is set then the file pointed to by it is executed.
If not set then if the file ~/.ensembl_init exists then this will be executed.
An example of such configuration file can be found in
ensembl/modules/Bio/EnsEMBL/Utils/ensembl_init.example
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.
The registry can be loaded from a configuration file using the method load_all.
If a file is passed to load_all then this is used.
Else if the enviroment variable ENSEMBL_REGISTRY is set then this is used
Else if the file .ensembl_init in your home directory exist it is used.
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm, which will
pass this on to load_all.
The four types of registrys are for db adaptors, dba adaptors, dna adaptors
and the standard type.
......@@ -158,23 +159,23 @@ sub load_all{
# }
}
=head2 check_if_already_there
Arg [DBNAME] : string
The name of the database to check for.
Arg [HOST] : (optional) string
The domain name of the database host to check for
Arg [PORT] : int
The port to check for when connecting to the database
Arg [DRIVER] : (optional) string
The type of database driver to check for
Description: Check to see if the database is already stored.
Returntype : 0 if not found else the species and group.
Exceptions : none
=cut
#=head2 check_if_already_there
#
# Arg [DBNAME] : string
# The name of the database to check for.
# Arg [HOST] : (optional) string
# The domain name of the database host to check for
# Arg [PORT] : int
# The port to check for when connecting to the database
# Arg [DRIVER] : (optional) string
# The type of database driver to check for
#
# Description: Check to see if the database is already stored.
# Returntype : 0 if not found else the species and group.
# Exceptions : none
#
#
#=cut
#sub check_if_already_there{
......@@ -276,6 +277,15 @@ sub get_all_db_adaptors{
my ($class,$db) = @_;
my %ret=();
# we now also want to add all the DBAdaptors for the same species.
# 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()){
$ret{$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};
}
......
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