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shell.py
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# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2008, 2009, 2010, 2011, 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later version.
#
# Invenio is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Invenio; if not, write to the Free Software Foundation, Inc.,
# 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""
The shellutils module contains helper functions useful for interacting
with the operating system shell.
The main API functions are:
- run_shell_command()
"""
import os
import fcntl
import tempfile
import time
import signal
import six
import select
from itertools import chain
from six import StringIO
import subprocess
__all__ = ['run_shell_command',
'run_process_with_timeout',
'Timeout',
'split_cli_ids_arg']
"""
This module implements two functions:
- L{run_shell_command}
- L{run_process_with_timeout}
L{run_shell_command} will run a command through a shell, capturing its
standard output and standard error.
L{run_process_with_timeout} will run a process on its own allowing to
specify a input file, capturing the standard output and standard error and
killing the process after a given timeout.
"""
try:
from shutil import which
except ImportError:
# CPython <3.3
from distutils.spawn import find_executable as which
class Timeout(Exception):
"""Exception raised by with_timeout() when the operation takes too long.
"""
pass
def run_shell_command(cmd, args=None, filename_out=None, filename_err=None):
"""Run operating system command cmd with arguments from the args
tuple in a sub-shell and return tuple (exit status code, stdout
info, stderr info).
@param cmd: Command to execute in a shell; may contain %s
placeholders for arguments that will be expanded from the args
tuple. Example: cmd='echo %s', args = ('hello',).
@type cmd: string
@param args: Arguments to be escaped and substituted for %s
placeholders in cmd.
@type args: tuple of strings
@param filename_out: Desired filename for stdout output
(optional; see below).
@type filename_out: string
@param filename_err: Desired filename for stderr output
(optional; see below).
@type filename_err: string
@return: Tuple (exit code, string containing stdout output buffer,
string containing stderr output buffer).
However, if either filename_out or filename_err are defined,
then the output buffers are not passed back but rather written
into filename_out/filename_err pathnames. This is useful for
commands that produce big files, for which it is not practical
to pass results back to the callers in a Python text buffer.
Note that it is the client's responsibility to name these
files in the proper fashion (e.g. to be unique) and to close
these files after use.
@rtype: (number, string, string)
@raise TypeError: if the number of args does not correspond to the
number of placeholders in cmd.
@note: Uses temporary files to store out/err output, not pipes due
to potential pipe race condition on some systems. If either
filename_out or filename_err are defined, then do not create
temporary files, but store stdout or stderr output directly in
these files instead, and do not delete them after execution.
"""
# wash args value:
if args:
args = tuple(args)
else:
args = ()
# construct command with argument substitution:
try:
cmd = cmd % tuple([escape_shell_arg(x) for x in args])
except TypeError:
# there were problems with %s and args substitution, so raise an error:
raise
cmd_out = ''
cmd_err = ''
# create files:
if filename_out:
cmd_out_fd = os.open(filename_out, os.O_CREAT, 0o644)
file_cmd_out = filename_out
else:
cmd_out_fd, file_cmd_out = \
tempfile.mkstemp("invenio.utils.shell-cmd-out")
if filename_err:
cmd_err_fd = os.open(filename_err, os.O_CREAT, 0o644)
file_cmd_err = filename_err
else:
cmd_err_fd, file_cmd_err = \
tempfile.mkstemp("invenio.utils.shell-cmd-err")
# run command:
cmd_exit_code = os.system("%s > %s 2> %s" % (cmd,
file_cmd_out,
file_cmd_err))
# delete temporary files: (if applicable)
if not filename_out:
if os.path.exists(file_cmd_out):
cmd_out_fo = open(file_cmd_out)
cmd_out = cmd_out_fo.read()
cmd_out_fo.close()
os.remove(file_cmd_out)
if not filename_err:
if os.path.exists(file_cmd_err):
cmd_err_fo = open(file_cmd_err)
cmd_err = cmd_err_fo.read()
cmd_err_fo.close()
os.remove(file_cmd_err)
os.close(cmd_out_fd)
os.close(cmd_err_fd)
# return results:
return cmd_exit_code, cmd_out, cmd_err
def run_process_with_timeout(args, filename_in=None, filename_out=None, filename_err=None, cwd=None, timeout=None, sudo=None):
"""Execute the specified process but within a certain timeout.
@param args: the actuall process. This should be a list of string as in:
['/usr/bin/foo', '--bar', 'baz']
@type args: list of string
@param filename_in: the path to a file that should be provided as standard
input to the process. If None this will default to /dev/null
@type filename_in: string
@param filename_out: Desired filename for stdout output
(optional; see below).
@type filename_out: string
@param filename_err: Desired filename for stderr output
(optional; see below).
@type filename_err: string
@param cwd: the path from where to execute the process
@type cwd: string
@param timeout: the timeout in seconds after which to consider the
process execution as failed. a Timeout exception will be raised
@type timeout: int
@param sudo: the optional name of the user under which to execute the
process (by using sudo, without prompting for a password)
@type sudo: string
@return: Tuple (exit code, string containing stdout output buffer,
string containing stderr output buffer).
However, if either filename_out or filename_err are defined,
then the output buffers are not passed back but rather written
into filename_out/filename_err pathnames. This is useful for
commands that produce big files, for which it is not practical
to pass results back to the callers in a Python text buffer.
Note that it is the client's responsibility to name these
files in the proper fashion (e.g. to be unique) and to close
these files after use.
@rtype: (number, string, string)
@raise Timeout: if the process does not terminate within the timeout
"""
if timeout is None:
from invenio.config import CFG_MISCUTIL_DEFAULT_PROCESS_TIMEOUT
timeout = CFG_MISCUTIL_DEFAULT_PROCESS_TIMEOUT
stdout = stderr = None
if filename_in is not None:
stdin = open(filename_in)
else:
## FIXME: should use NUL on Windows
stdin = open('/dev/null', 'r')
if filename_out:
stdout = open(filename_out, 'w')
if filename_err:
stderr = open(filename_err, 'w')
tmp_stdout = StringIO()
tmp_stderr = StringIO()
if sudo is not None:
args = ['sudo', '-u', sudo, '-S'] + list(args)
## See: <http://stackoverflow.com/questions/3876886/timeout-a-subprocess>
process = subprocess.Popen(args, stdin=stdin, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True, cwd=cwd, preexec_fn=os.setpgrp)
## See: <http://stackoverflow.com/questions/375427/non-blocking-read-on-a-stream-in-python>
fd = process.stdout.fileno()
fl = fcntl.fcntl(fd, fcntl.F_GETFL)
fcntl.fcntl(fd, fcntl.F_SETFL, fl | os.O_NONBLOCK)
fd = process.stderr.fileno()
fl = fcntl.fcntl(fd, fcntl.F_GETFL)
fcntl.fcntl(fd, fcntl.F_SETFL, fl | os.O_NONBLOCK)
fd_to_poll = [process.stdout, process.stderr]
select_timeout = 0.5
t1 = time.time()
try:
while process.poll() is None:
if time.time() - t1 >= timeout:
if process.stdin is not None:
process.stdin.close()
time.sleep(1)
if process.poll() is None:
## See: <http://stackoverflow.com/questions/3876886/timeout-a-subprocess>
os.killpg(process.pid, signal.SIGTERM)
time.sleep(1)
if process.poll() is None:
os.killpg(process.pid, signal.SIGKILL)
try:
os.waitpid(process.pid, 0)
except OSError:
pass
raise Timeout()
for fd in select.select(fd_to_poll, [], [], select_timeout)[0]:
if fd == process.stdout:
buf = process.stdout.read(65536)
if stdout is None:
tmp_stdout.write(buf)
else:
stdout.write(buf)
elif fd == process.stderr:
buf = process.stderr.read(65536)
if stderr is None:
tmp_stderr.write(buf)
else:
stderr.write(buf)
else:
raise OSError("fd %s is not a valid file descriptor" % fd)
finally:
while True:
## Let's just read what is remaining to read.
for fd in select.select(fd_to_poll, [], [], select_timeout)[0]:
if fd == process.stdout:
buf = process.stdout.read(65536)
tmp_stdout.write(buf)
if stdout is not None:
stdout.write(buf)
elif fd == process.stderr:
buf = process.stderr.read(65536)
tmp_stderr.write(buf)
if stderr is not None:
stderr.write(buf)
else:
raise OSError("fd %s is not a valid file descriptor" % fd)
else:
break
return process.poll(), tmp_stdout.getvalue(), tmp_stderr.getvalue()
def escape_shell_arg(shell_arg):
"""Escape shell argument shell_arg by placing it within
single-quotes. Any single quotes found within the shell argument
string will be escaped.
@param shell_arg: The shell argument to be escaped.
@type shell_arg: string
@return: The single-quote-escaped value of the shell argument.
@rtype: string
@raise TypeError: if shell_arg is not a string.
@see: U{http://mail.python.org/pipermail/python-list/2005-October/346957.html}
"""
if type(shell_arg) is six.text_type:
msg = "ERROR: escape_shell_arg() expected string argument but " \
"got '%s' of type '%s'." % (repr(shell_arg), type(shell_arg))
raise TypeError(msg)
return "'%s'" % shell_arg.replace("'", r"'\''")
def retry_mkstemp(suffix='', prefix='tmp', directory=None, max_retries=3):
"""
Make mkstemp more robust against AFS glitches.
"""
if directory is None:
from invenio.config import CFG_TMPSHAREDDIR
directory = CFG_TMPSHAREDDIR
for retry_count in range(1, max_retries + 1):
try:
tmp_file_fd, tmp_file_name = tempfile.mkstemp(suffix=suffix,
prefix=prefix,
dir=directory)
except OSError, e:
if e.errno == 19 and retry_count <= max_retries:
# AFS Glitch?
time.sleep(10)
else:
raise
else:
break
return tmp_file_fd, tmp_file_name
def mymkdir(newdir, mode=0o777):
"""works the way a good mkdir should :)
- already exists, silently complete
- regular file in the way, raise an exception
- parent directory(ies) does not exist, make them as well
"""
if os.path.isdir(newdir):
pass
elif os.path.isfile(newdir):
raise OSError("a file with the same name as the desired " \
"dir, '%s', already exists." % newdir)
else:
head, tail = os.path.split(newdir)
if head and not os.path.isdir(head):
mymkdir(head, mode)
if tail:
os.umask(0o022)
os.mkdir(newdir, mode)
def s(t):
## De-comment this to have lots of debugging information
#print time.time(), t
pass
def split_cli_ids_arg(value):
"""
Split ids given in the command line
Possible formats are:
* 1
* 1,2,3,4
* 1-5,20,30,40
Returns respectively
* set([1])
* set([1,2,3,4])
* set([1,2,3,4,5,20,30,40])
"""
def parse(el):
el = el.strip()
if not el:
ret = []
elif '-' in el:
start, end = el.split('-', 1)
ret = xrange(int(start), int(end) + 1)
else:
ret = [int(el)]
return ret
return set(chain(*(parse(c) for c in value.split(',') if c.strip())))

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