[med-svn] r22717 - trunk/packages/srst2/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2016-08-25 09:23:48 +0000 (Thu, 25 Aug 2016)
New Revision: 22717

Added:
   trunk/packages/srst2/trunk/debian/patches/fix_test.patch
Removed:
   trunk/packages/srst2/trunk/debian/patches/debug_test.patch
Modified:
   trunk/packages/srst2/trunk/debian/patches/series
Log:
Upstream has fixed test


Deleted: trunk/packages/srst2/trunk/debian/patches/debug_test.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/debug_test.patch	2016-08-24 19:15:23 UTC (rev 22716)
+++ trunk/packages/srst2/trunk/debian/patches/debug_test.patch	2016-08-25 09:23:48 UTC (rev 22717)
@@ -1,22 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 09 Aug 2016 23:27:52 +0200
-Description: bowtie2 definitely stumbles upon -foo argument  - but what else might be wrong?
-
---- a/tests/test_srst2.py
-+++ b/tests/test_srst2.py
-@@ -169,12 +169,14 @@ class TestRunBowtie(unittest.TestCase):
- 			'/usr/bin/bowtie2',
- 			'-U', 'fastq',
- 			'-S', 'mapping_file.sam',
--			'-foo',
- 			'--very-sensitive-local',
- 			'--no-unal',
- 			'-a',
- 			'-x', 'db_path'
- 		]
-+		fp=open('srst2_debug_test','w')
-+		print >>fp, expected_bowtie2_command
-+		fp.close()
- 		run_mock.assert_called_once_with(expected_bowtie2_command)
- 
- 	@patch('srst2.logging')

Added: trunk/packages/srst2/trunk/debian/patches/fix_test.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/fix_test.patch	                        (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/fix_test.patch	2016-08-25 09:23:48 UTC (rev 22717)
@@ -0,0 +1,45 @@
+Author: Ryan Wick <rrwick at gmail.com>
+Last-Update: Mon Aug 22 16:25:02 2016 +1000
+Origin: Upstream commit cd93cde1f2e4639db426e8b57b6ec5d278c0d02f
+Description: Update test for recent version
+
+--- a/tests/test_srst2.py
++++ b/tests/test_srst2.py
+@@ -158,6 +158,8 @@ class TestRunBowtie(unittest.TestCase):
+ 		arg_mock.read_type = 'foo'
+ 		arg_mock.stop_after = False
+ 		arg_mock.other = False
++		arg_mock.threads = 4
++		arg_mock.use_existing_bowtie2_sam = False
+ 		actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'], arg_mock,
+ 									  'db_name', 'db_path')
+ 		self.assertEqual(actual_sam, 'mapping_file.sam')
+@@ -173,7 +175,8 @@ class TestRunBowtie(unittest.TestCase):
+ 			'--very-sensitive-local',
+ 			'--no-unal',
+ 			'-a',
+-			'-x', 'db_path'
++			'-x', 'db_path',
++			'--threads', '4'
+ 		]
+ 		run_mock.assert_called_once_with(expected_bowtie2_command)
+ 
+@@ -191,6 +194,8 @@ class TestRunBowtie(unittest.TestCase):
+ 		arg_mock.read_type = 'foo'
+ 		arg_mock.stop_after = False
+ 		arg_mock.other = False
++		arg_mock.threads = 4
++		arg_mock.use_existing_bowtie2_sam = False
+ 		actual_sam = srst2.run_bowtie('mapping_file', 'sample', ['fastq'], arg_mock,
+ 									  'db_name', 'db_path')
+ 		self.assertEqual(actual_sam, 'mapping_file.sam')
+@@ -206,7 +211,8 @@ class TestRunBowtie(unittest.TestCase):
+ 			'--very-sensitive-local',
+ 			'--no-unal',
+ 			'-a',
+-			'-x', 'db_path'
++			'-x', 'db_path',
++			'--threads', '4'
+ 		]
+ 		run_mock.assert_called_once_with(expected_bowtie2_command)
+ 

Modified: trunk/packages/srst2/trunk/debian/patches/series
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/series	2016-08-24 19:15:23 UTC (rev 22716)
+++ trunk/packages/srst2/trunk/debian/patches/series	2016-08-25 09:23:48 UTC (rev 22717)
@@ -1,3 +1,3 @@
 check_command_line_arguments.patch
 add_usr_bin_python_to_scripts.patch
-debug_test.patch
+fix_test.patch