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Source code for galaxy.tool_util.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 (

log = logging.getLogger(__name__)


[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', )