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Bug#856481: marked as done (unblock: srst2/0.2.0-4)

Your message dated Wed, 01 Mar 2017 17:10:24 +0000
with message-id <E1cj7lg-0005VV-Ab@respighi.debian.org>
and subject line unblock srst2
has caused the Debian Bug report #856481,
regarding unblock: srst2/0.2.0-4
to be marked as done.

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If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
856481: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=856481
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock

Please unblock package srst2

Fixes RC bug #856479

unblock srst2/0.2.0-4

-- System Information:
Debian Release: 8.7
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

diff -Nru srst2-0.2.0/debian/changelog srst2-0.2.0/debian/changelog
--- srst2-0.2.0/debian/changelog	2017-02-24 11:19:43.000000000 +0100
+++ srst2-0.2.0/debian/changelog	2017-03-01 14:23:12.000000000 +0100
@@ -1,3 +1,10 @@
+srst2 (0.2.0-4) unstable; urgency=medium
+
+  * Do not fail if search string contains special shell characters
+    Closes: #856479
+
+ -- Andreas Tille <tille@debian.org>  Wed, 01 Mar 2017 14:23:12 +0100
+
 srst2 (0.2.0-3) unstable; urgency=medium
 
   * Make sure Python scripts are executable if they are called via symlink
diff -Nru srst2-0.2.0/debian/patches/fix_grep_call.patch srst2-0.2.0/debian/patches/fix_grep_call.patch
--- srst2-0.2.0/debian/patches/fix_grep_call.patch	1970-01-01 01:00:00.000000000 +0100
+++ srst2-0.2.0/debian/patches/fix_grep_call.patch	2017-03-01 14:23:12.000000000 +0100
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille@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
diff -Nru srst2-0.2.0/debian/patches/series srst2-0.2.0/debian/patches/series
--- srst2-0.2.0/debian/patches/series	2016-08-09 16:57:15.000000000 +0200
+++ srst2-0.2.0/debian/patches/series	2017-03-01 11:15:13.000000000 +0100
@@ -1,3 +1,4 @@
 check_command_line_arguments.patch
 add_usr_bin_python_to_scripts.patch
 fix_test.patch
+fix_grep_call.patch

--- End Message ---
--- Begin Message --- 
Unblocked.

--- End Message ---
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