From b51546435eeee26a59025cffdfbe204c0dd19215 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 19 Oct 2011 11:34:36 +0000
Subject: [PATCH] Test case added for unversioned CS and subsequent bugfix
---
modules/Bio/EnsEMBL/DataFile.pm | 2 +-
modules/t/dataFile.t | 21 ++++++++++++++++-----
2 files changed, 17 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DataFile.pm b/modules/Bio/EnsEMBL/DataFile.pm
index de1ef20b58..48820b7b8d 100644
--- a/modules/Bio/EnsEMBL/DataFile.pm
+++ b/modules/Bio/EnsEMBL/DataFile.pm
@@ -107,7 +107,7 @@ sub path {
my @portions;
push(@portions, $production_name);
- push(@portions, $self->coord_system()->version());
+ push(@portions, $cs_version);
push(@portions, software_version()) if $self->version_lock();
push(@portions, $self->adaptor()->db()->group());
diff --git a/modules/t/dataFile.t b/modules/t/dataFile.t
index eb15fe5b37..4bdc5d85b8 100644
--- a/modules/t/dataFile.t
+++ b/modules/t/dataFile.t
@@ -36,7 +36,7 @@ my %base_args = (
my $df = new_ok('Bio::EnsEMBL::DataFile' => [
%base_args
], 'data file');
- is($df->path($base), $expected_base.'/core/wibble.bam', 'Checking path non-absolute path');
+ is($df->path($base), $expected_base.'/core/wibble.bam', 'Checking non-absolute path');
}
{
@@ -45,16 +45,27 @@ my %base_args = (
-VERSION_LOCK => 1,
], 'data file');
- is($df->path($base), $expected_base.'/'.software_version().'/core/wibble.bam', 'Checking path non-absolute path');
+ is($df->path($base), $expected_base.'/'.software_version().'/core/wibble.bam', 'Checking non-absolute version locked path');
}
{
+ my $url = 'http://www.google.co.uk/wibble.bam';
my $df = new_ok('Bio::EnsEMBL::DataFile' => [
%base_args,
- -VERSION_LOCK => 1,
+ -ABSOLUTE => 1,
+ -URL => $url
], 'data file');
- is($df->path($base), $expected_base.'/'.software_version().'/core/wibble.bam', 'Checking path non-absolute path');
+ is($df->path(), $url, 'Checking absolute path');
+}
+
+{
+ my $supercontig_cs = $csa->fetch_by_dbID(2);
+ my $df = new_ok('Bio::EnsEMBL::DataFile' => [
+ %base_args,
+ -COORD_SYSTEM => $supercontig_cs
+ ], 'data file');
+ is($df->path($base), $expected_base.'/core/wibble.bam', 'Checking non-absolute unversioned cs path');
}
{
@@ -80,7 +91,7 @@ my %base_args = (
is_deeply($dfa->fetch_all_by_Analysis($a), [$df], 'Checking retrieved data is the same as what we currently hold');
is_deeply($dfa->fetch_all_by_CoordSystem($cs), [$df], 'Checking retrieved data is the same as what we currently hold');
is_deeply($dfa->fetch_by_name_and_type('wibble', 'BAM'), $df, 'Checking retrieved data is the same as what we currently hold');
-
+
$multi->restore(qw/core data_file/);
}
--
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