Source code for galaxy.jobs.runners.util.cli.shell.local

import os
from logging import getLogger
from subprocess import (
    PIPE,
    Popen
)
from tempfile import TemporaryFile
from time import sleep

import six

from galaxy.util.bunch import Bunch
from . import BaseShellExec
from ....util.process_groups import (
    check_pg,
    kill_pg
)

log = getLogger(__name__)

TIMEOUT_ERROR_MESSAGE = u'Execution timed out'
TIMEOUT_RETURN_CODE = -1
DEFAULT_TIMEOUT = 60
DEFAULT_TIMEOUT_CHECK_INTERVAL = 3


[docs]class LocalShell(BaseShellExec): """ >>> shell = LocalShell() >>> def exec_python(script, **kwds): return shell.execute(['python', '-c', script], **kwds) >>> exec_result = exec_python("from __future__ import print_function; print('Hello World')") >>> exec_result.stderr == u'' True >>> exec_result.stdout.strip() == u'Hello World' True >>> exec_result.returncode 0 >>> exec_result = exec_python("import time; time.sleep(10)", timeout=1, timeout_check_interval=.1) >>> exec_result.stdout == u'' True >>> exec_result.stderr == 'Execution timed out' True >>> exec_result.returncode == TIMEOUT_RETURN_CODE True >>> shell.execute('echo hi').stdout == "hi\\n" True """
[docs] def __init__(self, **kwds): pass
[docs] def execute(self, cmd, persist=False, timeout=DEFAULT_TIMEOUT, timeout_check_interval=DEFAULT_TIMEOUT_CHECK_INTERVAL, **kwds): is_cmd_string = isinstance(cmd, six.string_types) outf = TemporaryFile() p = Popen(cmd, stdin=None, stdout=outf, stderr=PIPE, shell=is_cmd_string, preexec_fn=os.setpgrp) # check process group until timeout for i in range(int(timeout / timeout_check_interval)): sleep(0.1) # For fast returning commands if not check_pg(p.pid): break sleep(timeout_check_interval) else: kill_pg(p.pid) return Bunch(stdout=u'', stderr=TIMEOUT_ERROR_MESSAGE, returncode=TIMEOUT_RETURN_CODE) outf.seek(0) # Need to poll once to establish return code p.poll() return Bunch(stdout=_read_str(outf), stderr=_read_str(p.stderr), returncode=p.returncode)
def _read_str(stream): contents = stream.read() return contents.decode('UTF-8') if isinstance(contents, bytes) else contents __all__ = ('LocalShell',)