From 36da09d079c2c693b2c8f27f6e47c021227d7d73 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 5 Aug 2004 14:38:55 +0000
Subject: [PATCH] get_all_db fix
---
modules/Bio/EnsEMBL/Registry.pm | 56 +++++++++++++++++++--------------
1 file changed, 33 insertions(+), 23 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index f177688042..8449aa789b 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -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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