import codecs
import functools
import io
import logging
import os
import select
import shutil
import subprocess
import sys
import time
import timeit
import warnings
from multiprocessing import Pipe
from threading import Thread
#
# run() - A function to synchronously run an external process, supporting
# the following features:
#
# - runs an external process and waits for it to finish
# - does not deadlock, no matter the process stdout/stderr output behaviour
# - returns the exit code, stdout, stderr (separately) as a
# subprocess.CompletedProcess object
# - process can run in a custom environment, either as a modification of
# the current environment or in a new environment from scratch
# - stdin can be fed to the process
# - stdout and stderr is printed by default, can be disabled
# - stdout and stderr can be passed to any arbitrary function for
# live processing
# - optionally enforces a time limit on the process
#
#
# Usage example:
#
# import procrunner
# result = procrunner.run(['/bin/ls', '/some/path/containing spaces'])
#
# Returns:
#
# ReturnObject(
# args=('/bin/ls', '/some/path/containing spaces'),
# returncode=2,
# stdout=b'',
# stderr=b'/bin/ls: cannot access /some/path/containing spaces: No such file or directory\n'
# )
#
# which also offers (albeit deprecated)
#
# result.runtime == 0.12990689277648926
# result.time_end == '2017-11-12 19:54:49 GMT'
# result.time_start == '2017-11-12 19:54:49 GMT'
# result.timeout == False
__author__ = """Markus Gerstel"""
__email__ = "scientificsoftware@diamond.ac.uk"
__version__ = "2.3.1"
logger = logging.getLogger("procrunner")
logger.addHandler(logging.NullHandler())
class _LineAggregator:
"""
Buffer that can be filled with stream data and will aggregate complete
lines. Lines can be printed or passed to an arbitrary callback function.
The lines passed to the callback function are UTF-8 decoded and do not
contain a trailing newline character.
"""
def __init__(self, print_line=False, callback=None):
"""Create aggregator object."""
self._buffer = ""
self._print = print_line
self._callback = callback
self._decoder = codecs.getincrementaldecoder("utf-8")("replace")
def add(self, data):
"""
Add a single character to buffer. If one or more full lines are found,
print them (if desired) and pass to callback function.
"""
data = self._decoder.decode(data)
if not data:
return
self._buffer += data
if "\n" in data:
to_print, remainder = self._buffer.rsplit("\n")
if self._print:
try:
print(to_print)
except UnicodeEncodeError:
print(to_print.encode(sys.getdefaultencoding(), errors="replace"))
if not hasattr(self, "_warned"):
logger.warning("output encoding error, characters replaced")
setattr(self, "_warned", True)
if self._callback:
self._callback(to_print)
self._buffer = remainder
def flush(self):
"""Print/send any remaining data to callback function."""
self._buffer += self._decoder.decode(b"", final=True)
if self._buffer:
if self._print:
print(self._buffer)
if self._callback:
self._callback(self._buffer)
self._buffer = ""
class _NonBlockingStreamReader:
"""Reads a stream in a thread to avoid blocking/deadlocks"""
def __init__(self, stream, output=True, debug=False, notify=None, callback=None):
"""Creates and starts a thread which reads from a stream."""
self._buffer = io.BytesIO()
self._closed = False
self._closing = False
self._debug = debug
self._stream = stream
self._terminated = False
def _thread_write_stream_to_buffer():
la = _LineAggregator(print_line=output, callback=callback)
char = True
while char:
if select.select([self._stream], [], [], 0.1)[0]:
char = self._stream.read(1)
if char:
self._buffer.write(char)
la.add(char)
else:
if self._closing:
break
self._stream.close()
self._terminated = True
la.flush()
if self._debug:
logger.debug("Stream reader terminated")
if notify:
notify()
def _thread_write_stream_to_buffer_windows():
line = True
while line:
line = self._stream.readline()
if line:
self._buffer.write(line)
if output or callback:
linedecode = line.decode("utf-8", "replace")
if output:
print(linedecode)
if callback:
callback(linedecode)
self._stream.close()
self._terminated = True
if self._debug:
logger.debug("Stream reader terminated")
if notify:
notify()
if os.name == "nt":
self._thread = Thread(target=_thread_write_stream_to_buffer_windows)
else:
self._thread = Thread(target=_thread_write_stream_to_buffer)
self._thread.daemon = True
self._thread.start()
def has_finished(self):
"""
Returns whether the thread reading from the stream is still alive.
"""
return self._terminated
def get_output(self):
"""
Retrieve the stored data in full.
This call may block if the reading thread has not yet terminated.
"""
self._closing = True
if not self.has_finished():
if self._debug:
# Main thread overtook stream reading thread.
underrun_debug_timer = timeit.default_timer()
logger.warning("NBSR underrun")
self._thread.join()
if not self.has_finished():
if self._debug:
logger.debug(
"NBSR join after %f seconds, underrun not resolved",
timeit.default_timer() - underrun_debug_timer,
)
raise Exception("thread did not terminate")
if self._debug:
logger.debug(
"NBSR underrun resolved after %f seconds",
timeit.default_timer() - underrun_debug_timer,
)
if self._closed:
raise Exception("streamreader double-closed")
self._closed = True
data = self._buffer.getvalue()
self._buffer.close()
return data
class _NonBlockingStreamWriter:
"""Writes to a stream in a thread to avoid blocking/deadlocks"""
def __init__(self, stream, data, debug=False, notify=None):
"""Creates and starts a thread which writes data to stream."""
self._buffer = data
self._buffer_len = len(data)
self._buffer_pos = 0
self._max_block_len = 4096
self._stream = stream
self._terminated = False
def _thread_write_buffer_to_stream():
while self._buffer_pos < self._buffer_len:
if (self._buffer_len - self._buffer_pos) > self._max_block_len:
block = self._buffer[
self._buffer_pos : (self._buffer_pos + self._max_block_len)
]
else:
block = self._buffer[self._buffer_pos :]
try:
self._stream.write(block)
except OSError as e:
if (
e.errno == 32
): # broken pipe, ie. process terminated without reading entire stdin
self._stream.close()
self._terminated = True
if notify:
notify()
return
raise
self._buffer_pos += len(block)
if debug:
logger.debug("wrote %d bytes to stream", len(block))
self._stream.close()
self._terminated = True
if notify:
notify()
self._thread = Thread(target=_thread_write_buffer_to_stream)
self._thread.daemon = True
self._thread.start()
def has_finished(self):
"""Returns whether the thread writing to the stream is still alive."""
return self._terminated
def bytes_sent(self):
"""Return the number of bytes written so far."""
return self._buffer_pos
def bytes_remaining(self):
"""Return the number of bytes still to be written."""
return self._buffer_len - self._buffer_pos
def _path_resolve(obj):
"""
Resolve file system path (PEP-519) objects to strings.
:param obj: A file system path object or something else.
:return: A string representation of a file system path object or, for
anything that was not a file system path object, the original
object.
"""
if obj and hasattr(obj, "__fspath__"):
return obj.__fspath__()
return obj
def _windows_resolve(command, path=None):
"""
Try and find the full path and file extension of the executable to run.
This is so that e.g. calls to 'somescript' will point at 'somescript.cmd'
without the need to set shell=True in the subprocess.
:param command: The command array to be run, with the first element being
the command with or w/o path, with or w/o extension.
:return: Returns the command array with the executable resolved with the
correct extension. If the executable cannot be resolved for any
reason the original command array is returned.
"""
if not command or not isinstance(command[0], str):
return command
found_executable = shutil.which(command[0], path=path)
if found_executable:
logger.debug("Resolved %s as %s", command[0], found_executable)
return (found_executable, *command[1:])
if "\\" in command[0]:
# Special case. shutil.which may not detect file extensions if a full
# path is given, so try to resolve the executable explicitly
for extension in os.getenv("PATHEXT").split(os.pathsep):
found_executable = shutil.which(command[0] + extension, path=path)
if found_executable:
return (found_executable, *command[1:])
logger.warning("Error trying to resolve the executable: %s", command[0])
return command
[docs]class ReturnObject(subprocess.CompletedProcess):
"""
A subprocess.CompletedProcess-like object containing the executed
command, stdout and stderr (both as bytestrings), and the exitcode.
The check_returncode() function raises an exception if the process
exited with a non-zero exit code.
"""
def __init__(self, exitcode=None, command=None, stdout=None, stderr=None, **kw):
super().__init__(
args=command, returncode=exitcode, stdout=stdout, stderr=stderr
)
self._extras = {
"timeout": kw.get("timeout"),
"runtime": kw.get("runtime"),
"time_start": kw.get("time_start"),
"time_end": kw.get("time_end"),
}
def __getitem__(self, key):
warnings.warn(
"dictionary access to a procrunner return object is deprecated",
DeprecationWarning,
stacklevel=2,
)
if key in self._extras:
return self._extras[key]
if not hasattr(self, key):
raise KeyError(f"Unknown attribute {key}")
return getattr(self, key)
def __eq__(self, other):
"""Override equality operator to account for added fields"""
if type(other) is type(self):
return self.__dict__ == other.__dict__
return False
def __hash__(self):
"""This object is not immutable, so mark it as unhashable"""
return None
@property
def cmd(self):
warnings.warn(
"procrunner return object .cmd is deprecated, use .args",
DeprecationWarning,
stacklevel=2,
)
return self.args
@property
def command(self):
warnings.warn(
"procrunner return object .command is deprecated, use .args",
DeprecationWarning,
stacklevel=2,
)
return self.args
@property
def exitcode(self):
warnings.warn(
"procrunner return object .exitcode is deprecated, use .returncode",
DeprecationWarning,
stacklevel=2,
)
return self.returncode
@property
def timeout(self):
warnings.warn(
"procrunner return object .timeout is deprecated",
DeprecationWarning,
stacklevel=2,
)
return self._extras["timeout"]
@property
def runtime(self):
warnings.warn(
"procrunner return object .runtime is deprecated",
DeprecationWarning,
stacklevel=2,
)
return self._extras["runtime"]
@property
def time_start(self):
warnings.warn(
"procrunner return object .time_start is deprecated",
DeprecationWarning,
stacklevel=2,
)
return self._extras["time_start"]
@property
def time_end(self):
warnings.warn(
"procrunner return object .time_end is deprecated",
DeprecationWarning,
stacklevel=2,
)
return self._extras["time_end"]
def update(self, dictionary):
self._extras.update(dictionary)
def _deprecate_argument_calling(f):
@functools.wraps(f)
def wrapper(*args, **kwargs):
if len(args) > 1:
warnings.warn(
"Calling procrunner.run() with unnamed arguments (apart from "
"the command) is deprecated. Use keyword arguments instead.",
DeprecationWarning,
stacklevel=2,
)
return f(*args, **kwargs)
return wrapper
[docs]@_deprecate_argument_calling
def run(
command,
timeout=None,
debug=None,
stdin=None,
print_stdout=True,
print_stderr=True,
callback_stdout=None,
callback_stderr=None,
environment=None,
environment_override=None,
win32resolve=True,
working_directory=None,
raise_timeout_exception=False,
):
"""
Run an external process.
File system path objects (PEP-519) are accepted in the command, environment,
and working directory arguments.
:param array command: Command line to be run, specified as array.
:param timeout: Terminate program execution after this many seconds.
:param boolean debug: Enable further debug messages. (deprecated)
:param stdin: Optional bytestring that is passed to command stdin.
:param boolean print_stdout: Pass stdout through to sys.stdout.
:param boolean print_stderr: Pass stderr through to sys.stderr.
:param callback_stdout: Optional function which is called for each
stdout line.
:param callback_stderr: Optional function which is called for each
stderr line.
:param dict environment: The full execution environment for the command.
:param dict environment_override: Change environment variables from the
current values for command execution.
:param boolean win32resolve: If on Windows, find the appropriate executable
first. This allows running of .bat, .cmd, etc.
files without explicitly specifying their
extension.
:param string working_directory: If specified, run the executable from
within this working directory.
:param boolean raise_timeout_exception: Forward compatibility flag. If set
then a subprocess.TimeoutExpired exception is raised
instead of returning an object that can be checked
for a timeout condition. Defaults to False, will be
changed to True in a future release.
:return: The exit code, stdout, stderr (separately, as byte strings)
as a subprocess.CompletedProcess object.
"""
time_start = time.strftime("%Y-%m-%d %H:%M:%S GMT", time.gmtime())
logger.debug("Starting external process: %s", command)
if stdin is None:
stdin_pipe = None
else:
assert sys.platform != "win32", "stdin argument not supported on Windows"
stdin_pipe = subprocess.PIPE
if debug is not None:
warnings.warn(
"Use of the debug parameter is deprecated", DeprecationWarning, stacklevel=3
)
start_time = timeit.default_timer()
if timeout is not None:
max_time = start_time + timeout
if not raise_timeout_exception:
warnings.warn(
"Using procrunner with timeout and without raise_timeout_exception set is deprecated",
DeprecationWarning,
stacklevel=3,
)
if environment is not None:
env = {key: _path_resolve(environment[key]) for key in environment}
else:
env = {key: value for key, value in os.environ.items()}
if environment_override:
env.update(
{
key: str(_path_resolve(environment_override[key]))
for key in environment_override
}
)
command = tuple(_path_resolve(part) for part in command)
if win32resolve and sys.platform == "win32":
command = _windows_resolve(command)
if working_directory and sys.version_info < (3, 7):
working_directory = os.fspath(working_directory)
p = subprocess.Popen(
command,
shell=False,
cwd=working_directory,
env=env,
stdin=stdin_pipe,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
thread_pipe_pool = []
notifyee, notifier = Pipe(False)
thread_pipe_pool.append(notifyee)
stdout = _NonBlockingStreamReader(
p.stdout,
output=print_stdout,
debug=debug,
notify=notifier.close,
callback=callback_stdout,
)
notifyee, notifier = Pipe(False)
thread_pipe_pool.append(notifyee)
stderr = _NonBlockingStreamReader(
p.stderr,
output=print_stderr,
debug=debug,
notify=notifier.close,
callback=callback_stderr,
)
if stdin is not None:
notifyee, notifier = Pipe(False)
thread_pipe_pool.append(notifyee)
stdin = _NonBlockingStreamWriter(
p.stdin, data=stdin, debug=debug, notify=notifier.close
)
timeout_encountered = False
while (p.returncode is None) and (
(timeout is None) or (timeit.default_timer() < max_time)
):
if debug and timeout is not None:
logger.debug("still running (T%.2fs)", timeit.default_timer() - max_time)
# wait for some time or until a stream is closed
try:
if thread_pipe_pool:
# Wait for up to 0.5 seconds or for a signal on a remaining stream,
# which could indicate that the process has terminated.
try:
event = thread_pipe_pool[0].poll(0.5)
except BrokenPipeError as e:
# on Windows this raises "BrokenPipeError: [Errno 109] The pipe has been ended"
# which is for all intents and purposes equivalent to a True return value.
if e.winerror != 109:
raise
event = True
if event:
# One-shot, so remove stream and watch remaining streams
thread_pipe_pool.pop(0)
if debug:
logger.debug("Event received from stream thread")
else:
time.sleep(0.5)
except KeyboardInterrupt:
p.kill() # if user pressed Ctrl+C we won't be able to produce a proper report anyway
# but at least make sure the child process dies with us
raise
# check if process is still running
p.poll()
if p.returncode is None:
# timeout condition
timeout_encountered = True
if debug:
logger.debug("timeout (T%.2fs)", timeit.default_timer() - max_time)
# send terminate signal and wait some time for buffers to be read
p.terminate()
if thread_pipe_pool:
try:
thread_pipe_pool[0].poll(0.5)
except BrokenPipeError as e:
# on Windows this raises "BrokenPipeError: [Errno 109] The pipe has been ended"
# which is for all intents and purposes equivalent to a True return value.
if e.winerror != 109:
raise
thread_pipe_pool.pop(0)
if not stdout.has_finished() or not stderr.has_finished():
time.sleep(2)
p.poll()
if p.returncode is None:
# thread still alive
# send kill signal and wait some more time for buffers to be read
p.kill()
if thread_pipe_pool:
try:
thread_pipe_pool[0].poll(0.5)
except BrokenPipeError as e:
# on Windows this raises "BrokenPipeError: [Errno 109] The pipe has been ended"
# which is for all intents and purposes equivalent to a True return value.
if e.winerror != 109:
raise
thread_pipe_pool.pop(0)
if not stdout.has_finished() or not stderr.has_finished():
time.sleep(5)
p.poll()
if p.returncode is None:
raise RuntimeError("Process won't terminate")
runtime = timeit.default_timer() - start_time
if timeout is not None:
logger.debug(
"Process ended after %.1f seconds with exit code %d (T%.2fs)",
runtime,
p.returncode,
timeit.default_timer() - max_time,
)
else:
logger.debug(
"Process ended after %.1f seconds with exit code %d", runtime, p.returncode
)
stdout = stdout.get_output()
stderr = stderr.get_output()
if timeout_encountered and raise_timeout_exception:
raise subprocess.TimeoutExpired(
cmd=command, timeout=timeout, output=stdout, stderr=stderr
)
time_end = time.strftime("%Y-%m-%d %H:%M:%S GMT", time.gmtime())
result = ReturnObject(
exitcode=p.returncode,
command=command,
stdout=stdout,
stderr=stderr,
timeout=timeout_encountered,
runtime=runtime,
time_start=time_start,
time_end=time_end,
)
if stdin is not None:
result.update(
{
"stdin_bytes_sent": stdin.bytes_sent(),
"stdin_bytes_remain": stdin.bytes_remaining(),
}
)
return result