Package: release.debian.org Severity: normal User: release.debian....@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 <ti...@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 <ti...@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
