Mercurial > repos > galaxyp > msconvert_nix

comparison msconvert_wrapper.py @ 1:b00023193f6e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
author galaxyp
date Tue, 14 Mar 2017 16:45:13 -0400
parents 5f8848c7d7b7
children
comparison
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0:5f8848c7d7b7 1:b00023193f6e
5 import tempfile 5 import tempfile
6 import shutil 6 import shutil
7 import subprocess 7 import subprocess
8 import re 8 import re
9 import logging 9 import logging
10 import shlex
10 11
11 assert sys.version_info[:2] >= (2, 6) 12 assert sys.version_info[:2] >= (2, 6)
12 13
13 log = logging.getLogger(__name__) 14 log = logging.getLogger(__name__)
14 working_directory = os.getcwd() 15 working_directory = os.getcwd()
38 39
39 def execute(command, stdin=None): 40 def execute(command, stdin=None):
40 try: 41 try:
41 with open(tmp_stderr_name, 'wb') as tmp_stderr: 42 with open(tmp_stderr_name, 'wb') as tmp_stderr:
42 with open(tmp_stdout_name, 'wb') as tmp_stdout: 43 with open(tmp_stdout_name, 'wb') as tmp_stdout:
43 proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) 44 args = shlex.split(command) # handle proper splitting of quoted args
45 proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
44 returncode = proc.wait() 46 returncode = proc.wait()
45 if returncode != 0: 47 if returncode != 0:
46 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) 48 raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
47 finally: 49 finally:
48 print(( open(tmp_stderr_name, "r").read() )) 50 print(( open(tmp_stderr_name, "r").read() ))