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Source code for galaxy.tools.deps.commands
"""Generic I/O and shell processing code used by Galaxy tool dependencies."""
import logging
import os
import subprocess
import sys as _sys
import six
from six.moves import shlex_quote
from galaxy.util import (
unicodify,
which
)
log = logging.getLogger(__name__)
STDOUT_INDICATOR = "-"
[docs]def redirecting_io(sys=_sys):
"""Predicate to determine if we are redicting stdout in process."""
assert sys is not None
try:
# Need to explicitly call fileno() because sys.stdout could be a
# io.StringIO object, which has a fileno() method but only raises an
# io.UnsupportedOperation exception
sys.stdout.fileno()
except Exception:
return True
else:
return False
[docs]def redirect_aware_commmunicate(p, sys=_sys):
"""Variant of process.communicate that works with in process I/O redirection."""
assert sys is not None
out, err = p.communicate()
if redirecting_io(sys=sys):
if out:
# We don't unicodify in Python2 because sys.stdout may be a
# cStringIO.StringIO object, which does not accept Unicode strings
if not six.PY2:
out = unicodify(out)
sys.stdout.write(out)
out = None
if err:
if not six.PY2:
err = unicodify(err)
sys.stderr.write(err)
err = None
return out, err
[docs]def shell(cmds, env=None, **kwds):
"""Run shell commands with `shell_process` and wait."""
sys = kwds.get("sys", _sys)
assert sys is not None
p = shell_process(cmds, env, **kwds)
if redirecting_io(sys=sys):
redirect_aware_commmunicate(p, sys=sys)
exit = p.returncode
return exit
else:
return p.wait()
[docs]def shell_process(cmds, env=None, **kwds):
"""A high-level method wrapping subprocess.Popen.
Handles details such as environment extension and in process I/O
redirection.
"""
sys = kwds.get("sys", _sys)
popen_kwds = dict()
if isinstance(cmds, six.string_types):
log.warning("Passing program arguments as a string may be a security hazard if combined with untrusted input")
popen_kwds['shell'] = True
if kwds.get("stdout", None) is None and redirecting_io(sys=sys):
popen_kwds["stdout"] = subprocess.PIPE
if kwds.get("stderr", None) is None and redirecting_io(sys=sys):
popen_kwds["stderr"] = subprocess.PIPE
popen_kwds.update(**kwds)
if env:
new_env = os.environ.copy()
new_env.update(env)
popen_kwds["env"] = new_env
p = subprocess.Popen(cmds, **popen_kwds)
return p
[docs]def execute(cmds):
"""Execute commands and throw an exception on a non-zero exit.
Return the standard output if the commands are successful
"""
return _wait(cmds, shell=False, stdin=subprocess.PIPE, stdout=subprocess.PIPE)
[docs]def argv_to_str(command_argv, quote=True):
"""Convert an argv command list to a string for shell subprocess.
If None appears in the command list it is simply excluded.
Arguments are quoted with shlex_quote. That said, this method is not meant to be
used in security critical paths of code and should not be used to sanitize
code.
"""
map_func = shlex_quote if quote else lambda x: x
return " ".join([map_func(c) for c in command_argv if c is not None])
def _wait(cmds, **popen_kwds):
p = subprocess.Popen(cmds, **popen_kwds)
stdout, stderr = p.communicate()
if p.returncode != 0:
raise CommandLineException(argv_to_str(cmds), stdout, stderr, p.returncode)
return stdout
[docs]def download_command(url, to=STDOUT_INDICATOR, quote_url=False):
"""Build a command line to download a URL.
By default the URL will be downloaded to standard output but a specific
file can be specified with the `to` argument.
"""
if quote_url:
url = "'%s'" % url
if to != STDOUT_INDICATOR:
to = "'%s'" % to
if which("wget"):
download_cmd = ["wget", "-q"]
if to == STDOUT_INDICATOR:
download_cmd.extend(["-O", STDOUT_INDICATOR, url])
else:
download_cmd.extend(["--recursive", "-O", to, url])
else:
download_cmd = ["curl", "-L", url]
if to != STDOUT_INDICATOR:
download_cmd.extend(["-o", to])
return download_cmd
[docs]class CommandLineException(Exception):
"""An exception indicating a non-zero command-line exit."""
[docs] def __init__(self, command, stdout, stderr, returncode):
"""Construct a CommandLineException from command and standard I/O."""
self.command = command
self.stdout = stdout
self.stderr = stderr
self.returncode = returncode
self.message = ("Failed to execute command-line %s, stderr was:\n"
"-------->>begin stderr<<--------\n"
"%s\n"
"-------->>end stderr<<--------\n"
"-------->>begin stdout<<--------\n"
"%s\n"
"-------->>end stdout<<--------\n"
) % (command, stderr, stdout)
def __str__(self):
"""Return a verbose error message indicating the command problem."""
return self.message
__all__ = (
'argv_to_str',
'CommandLineException',
'download_command',
'execute',
'redirect_aware_commmunicate',
'redirecting_io',
'shell',
'shell_process',
'which',
)