From 5784cc0f4dcda3a6fd06785eac54bc1b457089c4 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 17 May 2013 16:42:45 +0000
Subject: [PATCH] [ENSCORESW-473]. Adding a fetch all CoordSystems by version
for regulation.
---
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 22 +++++++++++++++++++
modules/t/coordSystemAdaptor.t | 22 +++++++++++++++++++
2 files changed, 44 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index 685d8aea0a..49455208a4 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -516,9 +516,31 @@ sub fetch_all_by_name {
return $self->{'_name_cache'}->{$name} || [];
}
+=head2 fetch_all_by_version
+ Arg [1] : string $version
+ The version of the coordinate systems to retrieve.
+ Example : foreach my $cs (@{$csa->fetch_all_by_version('GRCh37')}){
+ print $cs->name(), ' ', $cs->version();
+ }
+ Description: Retrieves all coordinate systems of a particular version
+ Returntype : ArrayRef of Bio::EnsEMBL::CoordSystem objects
+ Exceptions : throw if no name argument provided
+ Caller : general
+ Status : Stable
+=cut
+sub fetch_all_by_version {
+ my ($self, $version) = @_;
+ throw "Version argument is required" if ! $version;
+ my $coord_systems = [
+ grep { $_->version() eq $version }
+ map { $self->{_rank_cache}->{$_} }
+ sort keys %{$self->{_rank_cache}}
+ ];
+ return $coord_systems;
+}
=head2 fetch_by_dbID
diff --git a/modules/t/coordSystemAdaptor.t b/modules/t/coordSystemAdaptor.t
index 91e6080bcb..507055435d 100644
--- a/modules/t/coordSystemAdaptor.t
+++ b/modules/t/coordSystemAdaptor.t
@@ -3,6 +3,7 @@ use strict;
use Test::More;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
+use Test::Exception;
our $verbose = 1; #set to 1 to turn on debug printouts
@@ -176,6 +177,27 @@ ok( @{$new_path} == 2 &&
my $new_paths2 = $csa->store_mapping_path( $cs, $cln_cs );
ok( @{$new_paths2} == 0 ); # Should not update second time round
+#
+# Do some inserting of mock coord systems and
+# do version retrieval
+#
+my $newcs_two = Bio::EnsEMBL::CoordSystem->new(
+ -NAME => 'newsystem_number_two',
+ -VERSION => 'NCBI35',
+ -DEFAULT => 0,
+ -SEQUENCE_LEVEL => 0,
+ -RANK => 11
+);
+$csa->store($newcs_two);
+
+dies_ok { $csa->fetch_all_by_version() } 'fetch_all_by_version should die if not given a version to check';
+is_deeply($csa->fetch_all_by_version('NCBI35'), [ $cs, $newcs_two ], 'Checking version rank retrieval works');
+is_deeply(
+ $csa->fetch_all_by_version('NCBI33'),
+ [$csa->fetch_by_name('chromosome')],
+ 'Retrieval by name should return the same as version for NCBI33');
+is_deeply($csa->fetch_all_by_version('thisdoesnotexist'), [], 'Bogus coordinate system results in no results');
+
$multi->restore('core', 'coord_system');
$multi->restore('core', 'meta');
--
GitLab