[med-svn] r23697 - in trunk/packages/srst2/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2017-03-01 13:32:05 +0000 (Wed, 01 Mar 2017)
New Revision: 23697

Added:
   trunk/packages/srst2/trunk/debian/patches/fix_grep_call.patch
Modified:
   trunk/packages/srst2/trunk/debian/changelog
Log:
Commit patch, upload to unstable


Modified: trunk/packages/srst2/trunk/debian/changelog
===================================================================
--- trunk/packages/srst2/trunk/debian/changelog	2017-03-01 11:38:53 UTC (rev 23696)
+++ trunk/packages/srst2/trunk/debian/changelog	2017-03-01 13:32:05 UTC (rev 23697)
@@ -1,8 +1,9 @@
-srst2 (0.2.0-4) UNRELEASED; urgency=medium
+srst2 (0.2.0-4) unstable; urgency=medium
 
   * Do not fail if search string contains special shell characters
+    Closes: #856479
 
- -- Andreas Tille <tille at debian.org>  Wed, 01 Mar 2017 09:15:07 +0100
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Mar 2017 14:23:12 +0100
 
 srst2 (0.2.0-3) unstable; urgency=medium
 

Added: trunk/packages/srst2/trunk/debian/patches/fix_grep_call.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/fix_grep_call.patch	                        (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/fix_grep_call.patch	2017-03-01 13:32:05 UTC (rev 23697)
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 01 Mar 2017 09:15:07 +0100
+Bug-Debian: https://bugs.debian.org/856479
+Description: Do not fail if search string contains special shell characters
+
+--- a/scripts/srst2.py
++++ b/scripts/srst2.py
+@@ -23,6 +23,7 @@ from argparse import (ArgumentParser, Fi
+ import logging
+ from subprocess import call, check_output, CalledProcessError, STDOUT
+ import os, sys, re, collections, operator
++import subprocess
+ from scipy.stats import binom, linregress
+ from math import log
+ from itertools import groupby
+@@ -1499,7 +1500,7 @@ def map_fileSet_to_db(args, sample_name,
+ 			if args.no_gene_details:
+ 
+ 				# get annotation info
+-				header_string = os.popen(" ".join(["grep",allele,fasta]))
++				header_string = subprocess.check_output(["grep",allele,fasta])
+ 				try:
+ 					header = header_string.read().rstrip().split()
+ 					header.pop(0) # remove allele name