From 858dc42c101444d3b1d5e9333535e34e61089dad Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 19 Oct 2011 11:08:21 +0000
Subject: [PATCH] Bit of error checking/throwing put in to stop bad file system
paths from being produced when we lack a CS version
---
modules/Bio/EnsEMBL/DataFile.pm | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DataFile.pm b/modules/Bio/EnsEMBL/DataFile.pm
index ef1a40b014..de1ef20b58 100644
--- a/modules/Bio/EnsEMBL/DataFile.pm
+++ b/modules/Bio/EnsEMBL/DataFile.pm
@@ -77,7 +77,8 @@ sub new_fast {
path to the file or a URL but it is up to the using code to
know how to interprate the different returned forms
Returntype : Scalar the absolute path/url to the given resource
- Exceptions : None
+ Exceptions : Thrown if the linked Coordinate System lacks a version and the
+ current database also lacks a default version
Caller : public
=cut
@@ -92,15 +93,20 @@ sub path {
if(! $base) {
throw 'No base given';
}
-
+
+ my $production_name = $self->adaptor()->db()->get_MetaContainer()->get_production_name();
my $cs_version = $self->coord_system()->version();
if(! $cs_version) {
my ($highest_cs) = @{$self->adaptor()->db()->get_CoordSystemAdaptor()->fetch_all()};
$cs_version = $highest_cs->version();
}
+ if(!$cs_version) {
+ my $name = $self->name();
+ throw "The file '${name}' in species '${$production_name} is attached to a CoordinateSystem lacking a version and has no default assembly. Please fix";
+ }
my @portions;
- push(@portions, $self->adaptor()->db()->get_MetaContainer()->get_production_name());
+ push(@portions, $production_name);
push(@portions, $self->coord_system()->version());
push(@portions, software_version()) if $self->version_lock();
push(@portions, $self->adaptor()->db()->group());
--
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