comparison msconvert_wrapper.py @ 1:7016f1f10f42 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848

0:baa6c072fccc

import tempfile
import shutil
import subprocess
import re
import logging

assert sys.version_info[:2] >= (2, 6)

log = logging.getLogger(__name__)
working_directory = os.getcwd()

def execute(command, stdin=None):
    try:
        with open(tmp_stderr_name, 'wb') as tmp_stderr:
            with open(tmp_stdout_name, 'wb') as tmp_stdout:
                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print(( open(tmp_stderr_name, "r").read() ))

1:7016f1f10f42

import tempfile
import shutil
import subprocess
import re
import logging
import shlex

assert sys.version_info[:2] >= (2, 6)

log = logging.getLogger(__name__)
working_directory = os.getcwd()

def execute(command, stdin=None):
    try:
        with open(tmp_stderr_name, 'wb') as tmp_stderr:
            with open(tmp_stdout_name, 'wb') as tmp_stdout:
                args = shlex.split(command) # handle proper splitting of quoted args
                proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print(( open(tmp_stderr_name, "r").read() ))