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"""Centralize running of external commands, providing logging and tracking. Integrated from bcbio package with some changes.
"""
import collections
import os
import subprocess
import logging
try:
basestring
except NameError:
basestring = str
logger = logging.getLogger("run")
def run(cmd, data=None, checks=None, region=None, log_error=True,
log_stdout=False):
"""Run the provided command, logging details and checking for errors.
"""
try:
logger.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, basestring) else cmd)
_do_run(cmd, checks, log_stdout)
except:
if log_error:
logger.info("error at command")
raise
def find_bash():
for test_bash in [find_cmd("bash"), "/bin/bash", "/usr/bin/bash", "/usr/local/bin/bash"]:
if test_bash and os.path.exists(test_bash):
return test_bash
raise IOError("Could not find bash in any standard location. Needed for unix pipes")
def find_cmd(cmd):
try:
return subprocess.check_output(["which", cmd]).strip()
except subprocess.CalledProcessError:
return None
def _normalize_cmd_args(cmd):
"""Normalize subprocess arguments to handle list commands, string and pipes.
Piped commands set pipefail and require use of bash to help with debugging
intermediate errors.
"""
if isinstance(cmd, basestring):
# check for standard or anonymous named pipes
if cmd.find(" | ") > 0 or cmd.find(">(") or cmd.find("<("):
return "set -o pipefail; " + cmd, True, find_bash()
else:
return cmd, True, None
else:
return [str(x) for x in cmd], False, None
def _do_run(cmd, checks, log_stdout=False):
"""Perform running and check results, raising errors for issues.
"""
cmd, shell_arg, executable_arg = _normalize_cmd_args(cmd)
s = subprocess.Popen(cmd, shell=shell_arg, executable=executable_arg,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, close_fds=True)
debug_stdout = collections.deque(maxlen=100)
while 1:
line = s.stdout.readline()
if line:
debug_stdout.append(line)
if log_stdout:
logger.debug(line.rstrip())
else:
logger.debug(line.rstrip())
exitcode = s.poll()
if exitcode is not None:
for line in s.stdout:
debug_stdout.append(line)
if exitcode is not None and exitcode != 0:
error_msg = " ".join(cmd) if not isinstance(cmd, basestring) else cmd
error_msg += "\n"
error_msg += "".join(bytes_out.decode('utf-8') for bytes_out in debug_stdout)
s.communicate()
s.stdout.close()
raise subprocess.CalledProcessError(exitcode, error_msg)
else:
break
s.communicate()
s.stdout.close()
# Check for problems not identified by shell return codes
if checks:
for check in checks:
if not check():
raise IOError("External command failed")
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