From c2be78dee78142b712331b99c35085ab1e707778 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 23 May 2012 15:02:58 +0000
Subject: [PATCH] Adding a registry version to CliHelper
---
modules/Bio/EnsEMBL/Utils/CliHelper.pm | 32 ++++++++++++++++++++++++++
1 file changed, 32 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Utils/CliHelper.pm b/modules/Bio/EnsEMBL/Utils/CliHelper.pm
index c71085e160..7317a254c8 100644
--- a/modules/Bio/EnsEMBL/Utils/CliHelper.pm
+++ b/modules/Bio/EnsEMBL/Utils/CliHelper.pm
@@ -82,6 +82,7 @@ use Carp;
use Data::Dumper;
use Getopt::Long qw(:config auto_version no_ignore_case);
+use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
@@ -251,4 +252,35 @@ sub get_dbas_for_opts {
}
return $dbas;
}
+
+=head2 load_registry_for_opts
+
+ Arg [1] : Hash of options (e.g. parsed from command line options by process_args())
+ Arg [2] : Optional prefix to use when parsing e.g. dna or master
+ Description : Loads a Registry from the given options hash. If a C<registry>
+ option is given then the code will call C<load_all>. Otherwise
+ we use the database parameters given to call
+ C<load_registry_from_db()>.
+ Returntype : Integer of the number of DBAdaptors loaded
+ Status : Under development
+
+=cut
+
+sub load_registry_for_opts {
+ my ($self, $opts, $prefix) = @_;
+ $prefix ||= q{};
+ if($opts->{registry}) {
+ my $location = $opts->{registry};
+ return Bio::EnsEMBL::Registry->load_all($location);
+ }
+ my ( $host, $port, $user, $pass ) = map { $prefix . $_ } qw(host port user pass);
+ my %args = (
+ -HOST => $opts->{$host},
+ -PORT => $opts->{$port},
+ -USER => $opts->{$user},
+ );
+ $args{-PASS} = $opts->{$pass};
+ return Bio::EnsEMBL::Registry->load_registry_from_db(%args);
+}
+
1;
--
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