Source code for datalad.cmd

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#   See COPYING file distributed along with the datalad package for the
#   copyright and license terms.
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Wrapper for command and function calls, allowing for dry runs and output handling


import time
import subprocess
import sys
import logging
import os
import atexit
import functools
import tempfile
from locale import getpreferredencoding
import asyncio
from collections import (

from .consts import GIT_SSH_COMMAND
from .dochelpers import (
from .support import path as op
from .support.exceptions import CommandError
from .support.protocol import (
from .utils import (

lgr = logging.getLogger('datalad.cmd')

# In python3 to split byte stream on newline, it must be bytes
linesep_bytes = os.linesep.encode()

_TEMP_std = sys.stdout, sys.stderr
# To be used in the temp file name to distinguish the ones we create
# in Runner so we take care about their removal, in contrast to those
# which might be created outside and passed into Runner
_MAGICAL_OUTPUT_MARKER = "_runneroutput_"

from io import IOBase as file_class

def _decide_to_log(v):
    """Hacky workaround for now so we could specify per each which to
    log online and which to the log"""
    if isinstance(v, bool) or callable(v):
        return v
    elif v in {'online'}:
        return True
    elif v in {'offline'}:
        return False
        raise ValueError("can be bool, callable, 'online' or 'offline'")

def _get_output_stream(log_std, false_value):
    """Helper to prepare output stream for Popen and use file for 'offline'

    Necessary to avoid lockdowns when both stdout and stderr are pipes
    if log_std:
        if log_std == 'offline':
            # we will open a temporary file

            tf = tempfile.mktemp(
                **get_tempfile_kwargs({}, prefix=_MAGICAL_OUTPUT_MARKER)
            return open(tf, 'w')  # XXX PY3 should be 'b' may be?
            return subprocess.PIPE
        return false_value

def _cleanup_output(stream, std):
    if isinstance(stream, file_class) and \
        _MAGICAL_OUTPUT_MARKER in getattr(stream, 'name', ''):
        if not stream.closed:
        if op.exists(
    elif stream == subprocess.PIPE:

[docs]def run_gitcommand_on_file_list_chunks(func, cmd, files, *args, **kwargs): """Run a git command multiple times if `files` is too long Parameters ---------- func : callable Typically a variant. Assumed to return a 2-tuple with stdout and stderr as strings. cmd : list Base Git command argument list, to be amended with '--', followed by a file list chunk. files : list List of files. args, kwargs : Passed to `func` Returns ------- str, str Concatenated stdout and stderr. """ assert isinstance(cmd, list) if not files: file_chunks = [[]] else: file_chunks = generate_file_chunks(files, cmd) results = [] for i, file_chunk in enumerate(file_chunks): if file_chunk: lgr.debug('Process file list chunk %i (length %i)', i, len(file_chunk)) results.append(func(cmd + ['--'] + file_chunk, *args, **kwargs)) else: results.append(func(cmd, *args, **kwargs)) # if it was a -- we would get dicts. # If old Runner -- stdout, stderr strings if results: if isinstance(results[0], dict): result = defaultdict(str) for r in results: for k, v in r.items(): if k in ('stdout', 'stderr'): result[k] += v elif k == 'status': if k: # this wrapper expects commands to succeed or exception # being thrown raise RuntimeError( "Running %s with WitlessRunner resulted in " "exit %d but there were no exception" % (cmd, k)) elif v: raise RuntimeError( "Have no clue what to do about %s=%r" % (k, v)) return result['stdout'], result['stderr'] else: return ''.join(r[0] for r in results), \ ''.join(r[1] for r in results)
[docs]async def run_async_cmd(loop, cmd, protocol, stdin, protocol_kwargs=None, **kwargs): """Run a command in a subprocess managed by asyncio This implementation has been inspired by Parameters ---------- loop : asyncio.AbstractEventLoop asyncio event loop instance. Must support subprocesses on the target platform. cmd : list Command to be executed, passed to `subprocess_exec`. protocol : WitlessProtocol Protocol class to be instantiated for managing communication with the subprocess. stdin : file-like or None Passed to the subprocess as its standard input. protocol_kwargs : dict, optional Passed to the Protocol class constructor. kwargs : Pass to `subprocess_exec`, will typically be parameters supported by `subprocess.Popen`. Returns ------- undefined The nature of the return value is determined by the given protocol class. """ lgr.debug('Async run %s', cmd) if protocol_kwargs is None: protocol_kwargs = {} cmd_done = asyncio.Future(loop=loop) factory = functools.partial(protocol, cmd_done, **protocol_kwargs) proc = loop.subprocess_exec( factory, *cmd, stdin=stdin, # ask the protocol which streams to capture stdout=asyncio.subprocess.PIPE if protocol.proc_out else None, stderr=asyncio.subprocess.PIPE if protocol.proc_err else None, **kwargs ) transport = None result = None try: lgr.debug('Launching process %s', cmd) transport, protocol = await proc lgr.debug('Waiting for process %i to complete', transport.get_pid()) # The next wait is a workaround that avoids losing the output of # quickly exiting commands ( await asyncio.ensure_future(transport._wait()) await cmd_done result = protocol._prepare_result() finally: # protect against a crash whe launching the process if transport: transport.close() return result
[docs]class WitlessProtocol(asyncio.SubprocessProtocol): """Subprocess communication protocol base class for `run_async_cmd` This class implements basic subprocess output handling. Derived classes like `StdOutCapture` should be used for subprocess communication that need to capture and return output. In particular, the `pipe_data_received()` method can be overwritten to implement "online" processing of process output. This class defines a default return value setup that causes `run_async_cmd()` to return a 2-tuple with the subprocess's exit code and a list with bytestrings of all captured output streams. """ FD_NAMES = ['stdin', 'stdout', 'stderr'] proc_out = None proc_err = None def __init__(self, done_future): # future promise to be fulfilled when process exits self.done = done_future # capture output in bytearrays while the process is running Streams = namedtuple('Streams', ['out', 'err']) self.buffer = Streams( out=bytearray() if self.proc_out else None, err=bytearray() if self.proc_err else None, ) = None super().__init__() self.encoding = getpreferredencoding(do_setlocale=False) self._log_outputs = False if lgr.isEnabledFor(5): try: from . import cfg self._log_outputs = cfg.getbool('datalad.log', 'outputs', default=False) except ImportError: pass self._log = self._log_summary else: self._log = self._log_nolog def _log_nolog(self, *args): pass def _log_summary(self, fd, data): fd_name = self.FD_NAMES[fd] lgr.log(5, 'Read %i bytes from %i[%s]%s', len(data),, fd_name, ':' if self._log_outputs else '') if self._log_outputs: log_data = assure_unicode(data) # The way we log is to stay consistent with Runner. # TODO: later we might just log in a single entry, without # fd_name prefix lgr.log(5, "%s| %s " % (fd_name, log_data))
[docs] def connection_made(self, transport): self.transport = transport = transport.get_pid() lgr.debug('Process %i started',
[docs] def pipe_data_received(self, fd, data): self._log(fd, data) # store received output if stream was to be captured if self.buffer[fd - 1] is not None: self.buffer[fd - 1].extend(data)
def _prepare_result(self): """Prepares the final result to be returned to the runner Note for derived classes overwriting this method: The result must be a dict with keys that do not unintentionally conflict with the API of CommandError, as the result dict is passed to this exception class as kwargs on error. The Runner will overwrite 'cmd' and 'cwd' on error, if they are present in the result. """ return_code = self.transport.get_returncode() lgr.debug( 'Process %i exited with return code %i',, return_code) # give captured process output back to the runner as string(s) results = { name: bytes(byt).decode(self.encoding) if byt else '' for name, byt in zip(self.FD_NAMES[1:], self.buffer) } results['code'] = return_code return results
[docs] def process_exited(self): # actually fulfill the future promise and let the execution finish self.done.set_result(True)
[docs]class NoCapture(WitlessProtocol): """WitlessProtocol that captures no subprocess output As this is identical with the behavior of the WitlessProtocol base class, this class is merely a more readable convenience alias. """ pass
[docs]class StdOutCapture(WitlessProtocol): """WitlessProtocol that only captures and returns stdout of a subprocess""" proc_out = True
[docs]class StdErrCapture(WitlessProtocol): """WitlessProtocol that only captures and returns stderr of a subprocess""" proc_err = True
[docs]class StdOutErrCapture(WitlessProtocol): """WitlessProtocol that captures and returns stdout/stderr of a subprocess """ proc_out = True proc_err = True
[docs]class KillOutput(WitlessProtocol): """WitlessProtocol that swallows stdout/stderr of a subprocess """ proc_out = True proc_err = True
[docs] def pipe_data_received(self, fd, data): if lgr.isEnabledFor(5): lgr.log( 5, 'Discarded %i bytes from %i[%s]', len(data),, self.FD_NAMES[fd])
[docs]class WitlessRunner(object): """Minimal Runner with support for online command output processing It aims to be as simple as possible, providing only essential functionality. """ __slots__ = ['cwd', 'env'] def __init__(self, cwd=None, env=None): """ Parameters ---------- cwd : path-like, optional If given, commands are executed with this path as PWD, the PWD of the parent process is used otherwise. env : dict, optional Environment to be used for command execution. If `cwd` was given, 'PWD' in the environment is set to its value. This must be a complete environment definition, no values from the current environment will be inherited. """ self.env = env # stringify to support Path instances on PY35 self.cwd = str(cwd) if cwd is not None else None def _get_adjusted_env(self, env=None, cwd=None, copy=True): """Return an adjusted copy of an execution environment Or return an unaltered copy of the environment, if no adjustments need to be made. """ if copy: env = env.copy() if env else None if cwd and env is not None: # if CWD was provided, we must not make it conflict with # a potential PWD setting env['PWD'] = cwd return env
[docs] def run(self, cmd, protocol=None, stdin=None, cwd=None, env=None, **kwargs): """Execute a command and communicate with it. Parameters ---------- cmd : list Sequence of program arguments. Passing a single string means that it is simply the name of the program, no complex shell commands are supported. protocol : WitlessProtocol, optional Protocol class handling interaction with the running process (e.g. output capture). A number of pre-crafted classes are provided (e.g `KillOutput`, `NoCapture`, `GitProgress`). stdin : byte stream, optional File descriptor like, used as stdin for the process. Passed verbatim to subprocess.Popen(). cwd : path-like, optional If given, commands are executed with this path as PWD, the PWD of the parent process is used otherwise. Overrides any `cwd` given to the constructor. env : dict, optional Environment to be used for command execution. If `cwd` was given, 'PWD' in the environment is set to its value. This must be a complete environment definition, no values from the current environment will be inherited. Overrides any `env` given to the constructor. kwargs : Passed to the Protocol class constructor. Returns ------- dict At minimum there will be keys 'stdout', 'stderr' with unicode strings of the cumulative standard output and error of the process as values. Raises ------ CommandError On execution failure (non-zero exit code) this exception is raised which provides the command (cmd), stdout, stderr, exit code (status), and a message identifying the failed command, as properties. FileNotFoundError When a given executable does not exist. """ if protocol is None: # by default let all subprocess stream pass through protocol = NoCapture cwd = cwd or self.cwd env = self._get_adjusted_env( env or self.env, cwd=cwd, ) # start a new event loop, which we will close again further down # if this is not done events like this will occur # BlockingIOError: [Errno 11] Resource temporarily unavailable # Exception ignored when trying to write to the signal wakeup fd: # It is unclear to me why it happens when reusing an event looped # that it stopped from time to time, but starting fresh and doing # a full termination seems to address the issue if sys.platform == "win32": # use special event loop that supports subprocesses on windows event_loop = asyncio.ProactorEventLoop() else: event_loop = asyncio.SelectorEventLoop() asyncio.set_event_loop(event_loop) try: # include the subprocess manager in the asyncio event loop results = event_loop.run_until_complete( run_async_cmd( event_loop, cmd, protocol, stdin, protocol_kwargs=kwargs, cwd=cwd, env=env, ) ) finally: # be kind to callers and leave asyncio as we found it asyncio.set_event_loop(None) # terminate the event loop, cannot be undone, hence we start a fresh # one each time (see BlockingIOError notes above) event_loop.close() # log before any exception is raised lgr.log(8, "Finished running %r with status %s", cmd, results['code']) # make it such that we always blow if a protocol did not report # a return code at all if results.get('code', True) not in [0, None]: # the runner has a better idea, doc string warns Protocol # implementations not to return these results.pop('cmd', None) results.pop('cwd', None) raise CommandError( # whatever the results were, we carry them forward cmd=cmd, cwd=self.cwd, **results, ) # denoise, must be zero at this point results.pop('code', None) return results
[docs]class Runner(object): """Provides a wrapper for calling functions and commands. An object of this class provides a methods that calls shell commands or python functions, allowing for protocolling the calls and output handling. Outputs (stdout and stderr) can be either logged or streamed to system's stdout/stderr during execution. This can be enabled or disabled for both of them independently. Additionally, a protocol object can be a used with the Runner. Such a protocol has to implement, is able to record calls and allows for dry runs. """ __slots__ = ['commands', 'dry', 'cwd', 'env', 'protocol', '_log_opts'] def __init__(self, cwd=None, env=None, protocol=None, log_outputs=None): """ Parameters ---------- cwd: string, optional Base current working directory for commands. Could be overridden per run call via cwd option env: dict, optional Custom environment to use for calls. Could be overridden per run call via env option protocol: ProtocolInterface Protocol object to write to. log_outputs : bool, optional Switch to instruct whether outputs should be logged or not. If not set (default), config 'datalad.log.outputs' would be consulted """ self.cwd = cwd self.env = env if protocol is None: # TODO: config cmd.protocol = null protocol_str = os.environ.get('DATALAD_CMD_PROTOCOL', 'null') protocol = { 'externals-time': ExecutionTimeExternalsProtocol, 'time': ExecutionTimeProtocol, 'null': NullProtocol }[protocol_str]() if protocol_str != 'null': # we need to dump it into a file at the end # TODO: config cmd.protocol_prefix = protocol filename = '%s-%s.log' % ( os.environ.get('DATALAD_CMD_PROTOCOL_PREFIX', 'protocol'), id(self) ) atexit.register(functools.partial(protocol.write_to_file, filename)) self.protocol = protocol # Various options for logging self._log_opts = {} # we don't know yet whether we need to log every output or not if log_outputs is not None: self._log_opts['outputs'] = log_outputs def __call__(self, cmd, *args, **kwargs): """Convenience method This will call run() or call() depending on the kind of `cmd`. If `cmd` is a string it is interpreted as the to be executed command. Otherwise it is expected to be a callable. Any other argument is passed to the respective method. Parameters ---------- cmd: str or callable command string to be executed via shell or callable to be called. `*args`: `**kwargs`: see and for available arguments. Raises ------ TypeError if cmd is neither a string nor a callable. """ if isinstance(cmd, str) or isinstance(cmd, list): return, *args, **kwargs) elif callable(cmd): return, *args, **kwargs) else: raise TypeError("Argument 'command' is neither a string, " "nor a list nor a callable.") def _opt_env_adapter(v): """If value is a string, split by ,""" if v: if v.isdigit(): log_env = bool(int(v)) else: log_env = v.split(',') return log_env else: return False _LOG_OPTS_ADAPTERS = OrderedDict([ ('outputs', None), ('cwd', None), ('env', _opt_env_adapter), ('stdin', None), ]) def _get_log_setting(self, opt, default=False): try: return self._log_opts[opt] except KeyError: try: from . import cfg except ImportError: return default adapter = self._LOG_OPTS_ADAPTERS.get(opt, None) self._log_opts[opt] = \ (cfg.getbool if not adapter else cfg.get_value)( 'datalad.log', opt, default=default) if adapter: self._log_opts[opt] = adapter(self._log_opts[opt]) return self._log_opts[opt] @property def log_outputs(self): return self._get_log_setting('outputs') @property def log_cwd(self): return self._get_log_setting('cwd') @property def log_stdin(self): return self._get_log_setting('stdin') @property def log_env(self): return self._get_log_setting('env') # Two helpers to encapsulate formatting/output def _log_out(self, line): if line and self.log_outputs: self.log("stdout| " + line.rstrip('\n')) def _log_err(self, line, expected=False): if line and self.log_outputs: self.log("stderr| " + line.rstrip('\n'), level={True: 5, False: 11}[expected]) def _get_output_online(self, proc, log_stdout, log_stderr, outputstream, errstream, expect_stderr=False, expect_fail=False): """ If log_stdout or log_stderr are callables, they will be given a read line to be processed, and return processed result. So if they need to 'swallow' the line from being logged, should just return None Parameters ---------- proc log_stdout: bool or callable or 'online' or 'offline' log_stderr: : bool or callable or 'online' or 'offline' If any of those 'offline', we would call proc.communicate at the end to grab possibly outstanding output from it expect_stderr expect_fail Returns ------- """ stdout, stderr = bytes(), bytes() log_stdout_ = _decide_to_log(log_stdout) log_stderr_ = _decide_to_log(log_stderr) log_stdout_is_callable = callable(log_stdout_) log_stderr_is_callable = callable(log_stderr_) # arguments to be passed into _process_one_line stdout_args = ( 'stdout', proc, log_stdout_, log_stdout_is_callable ) stderr_args = ( 'stderr', proc, log_stderr_, log_stderr_is_callable, expect_stderr or expect_fail ) while proc.poll() is None: # see for a possibly useful approach to processing output # in another thread # current problem is that if there is no output on stderr # it stalls # Monitor if anything was output and if nothing, sleep a bit stdout_, stderr_ = None, None if log_stdout_: stdout_ = self._process_one_line(*stdout_args) stdout += stdout_ if log_stderr_: stderr_ = self._process_one_line(*stderr_args) stderr += stderr_ if stdout_ is None and stderr_ is None: # no output was really produced, so sleep a tiny bit time.sleep(0.001) # Handle possible remaining output if log_stdout_ and log_stderr_: # If Popen was called with more than two pipes, calling # communicate() after we partially read the stream will return # empty output. stdout += self._process_remaining_output( outputstream,, *stdout_args) stderr += self._process_remaining_output( errstream,, *stderr_args) stdout_, stderr_ = proc.communicate() # ??? should we condition it on log_stdout in {'offline'} ??? stdout += self._process_remaining_output(outputstream, stdout_, *stdout_args) stderr += self._process_remaining_output(errstream, stderr_, *stderr_args) return stdout, stderr def _process_remaining_output(self, stream, out_, *pargs): """Helper to process output which might have been obtained from popen or should be loaded from file""" out = bytes() if isinstance(stream, file_class) and \ _MAGICAL_OUTPUT_MARKER in getattr(stream, 'name', ''): assert out_ is None, "should have gone into a file" if not stream.closed: stream.close() with open(, 'rb') as f: for line in f: out += self._process_one_line(*pargs, line=line) else: if out_: # resolving a once in a while failing test #2185 if isinstance(out_, str): out_ = out_.encode('utf-8') for line in out_.split(linesep_bytes): out += self._process_one_line( *pargs, line=line, suf=linesep_bytes) return out def _process_one_line(self, out_type, proc, log_, log_is_callable, expected=False, line=None, suf=None): if line is None: lgr.log(3, "Reading line from %s", out_type) line = {'stdout': proc.stdout, 'stderr': proc.stderr}[out_type].readline() else: lgr.log(3, "Processing provided line") if line and log_is_callable: # Let it be processed line = log_(assure_unicode(line)) if line is not None: # we are working with binary type here line = assure_bytes(line) if line: if out_type == 'stdout': self._log_out(assure_unicode(line)) elif out_type == 'stderr': self._log_err(line.decode('utf-8'), expected) else: # pragma: no cover raise RuntimeError("must not get here") return (line + suf) if suf else line # it was output already directly but for code to work, return "" return bytes()
[docs] def run(self, cmd, log_stdout=True, log_stderr=True, log_online=False, expect_stderr=False, expect_fail=False, cwd=None, env=None, shell=None, stdin=None): """Runs the command `cmd` using shell. In case of dry-mode `cmd` is just added to `commands` and it is actually executed otherwise. Allows for separately logging stdout and stderr or streaming it to system's stdout or stderr respectively. Note: Using a string as `cmd` and shell=True allows for piping, multiple commands, etc., but that implies split_cmdline() is not used. This is considered to be a security hazard. So be careful with input. Parameters ---------- cmd : str, list String (or list) defining the command call. No shell is used if cmd is specified as a list log_stdout: bool, optional If True, stdout is logged. Goes to sys.stdout otherwise. log_stderr: bool, optional If True, stderr is logged. Goes to sys.stderr otherwise. log_online: bool, optional Whether to log as output comes in. Setting to True is preferable for running user-invoked actions to provide timely output expect_stderr: bool, optional Normally, having stderr output is a signal of a problem and thus it gets logged at level 11. But some utilities, e.g. wget, use stderr for their progress output. Whenever such output is expected, set it to True and output will be logged at level 5 unless exit status is non-0 (in non-online mode only, in online -- would log at 5) expect_fail: bool, optional Normally, if command exits with non-0 status, it is considered an error and logged at level 11 (above DEBUG). But if the call intended for checking routine, such messages are usually not needed, thus it will be logged at level 5. cwd : string, optional Directory under which run the command (passed to Popen) env : string, optional Custom environment to pass shell: bool, optional Run command in a shell. If not specified, then it runs in a shell only if command is specified as a string (not a list) stdin: file descriptor input stream to connect to stdin of the process. Returns ------- (stdout, stderr) - bytes! Raises ------ CommandError if command's exitcode wasn't 0 or None. exitcode is passed to CommandError's `code`-field. Command's stdout and stderr are stored in CommandError's `stdout` and `stderr` fields respectively. """ outputstream = _get_output_stream(log_stdout, sys.stdout) errstream = _get_output_stream(log_stderr, sys.stderr) popen_env = env or self.env popen_cwd = cwd or self.cwd if popen_cwd and popen_env and 'PWD' in popen_env: # we must have inherited PWD, but cwd was provided, so we must # adjust it popen_env = popen_env.copy() # to avoid side-effects popen_env['PWD'] = popen_cwd # TODO: if outputstream is sys.stdout and that one is set to StringIO # we have to "shim" it with something providing fileno(). # This happens when we do not swallow outputs, while allowing nosetest's # StringIO to be provided as stdout, crashing the Popen requiring # fileno(). In out swallow_outputs, we just use temporary files # to overcome this problem. # For now necessary test code should be wrapped into swallow_outputs cm # to avoid the problem log_msgs = ["Running: %s"] log_args = [cmd] if self.log_cwd: log_msgs += ['cwd=%r'] log_args += [popen_cwd] if self.log_stdin: log_msgs += ['stdin=%r'] log_args += [stdin] log_env = self.log_env if log_env and popen_env: log_msgs += ["env=%r"] log_args.append( popen_env if log_env is True else {k: popen_env[k] for k in log_env if k in popen_env} ) log_msg = '\n'.join(log_msgs) self.log(log_msg, *log_args) if self.protocol.do_execute_ext_commands: if shell is None: shell = isinstance(cmd, str) if self.protocol.records_ext_commands: prot_exc = None prot_id = self.protocol.start_section( split_cmdline(cmd) if isinstance(cmd, str) else cmd) try: proc = subprocess.Popen(cmd, stdout=outputstream, stderr=errstream, shell=shell, cwd=popen_cwd, env=popen_env, stdin=stdin) except Exception as e: prot_exc = e lgr.log(11, "Failed to start %r%r: %s" % (cmd, " under %r" % cwd if cwd else '', exc_str(e))) raise finally: if self.protocol.records_ext_commands: self.protocol.end_section(prot_id, prot_exc) try: if log_online: out = self._get_output_online(proc, log_stdout, log_stderr, outputstream, errstream, expect_stderr=expect_stderr, expect_fail=expect_fail) else: out = proc.communicate() # Decoding was delayed to this point def decode_if_not_None(x): return "" if x is None else bytes.decode(x) out = tuple(map(decode_if_not_None, out)) status = proc.poll() # needs to be done after we know status if not log_online: self._log_out(out[0]) if status not in [0, None]: self._log_err(out[1], expected=expect_fail) else: # as directed self._log_err(out[1], expected=expect_stderr) if status not in [0, None]: exc = CommandError( cmd=cmd, code=status, stdout=out[0], stderr=out[1], cwd=popen_cwd, ) lgr.log(5 if expect_fail else 11, str(exc)) raise exc else: self.log("Finished running %r with status %s" % (cmd, status), level=8) except CommandError: # do not bother with reacting to "regular" CommandError # exceptions. Somehow if we also terminate here for them # some processes elsewhere might stall: # see raise except BaseException as exc: exc_info = sys.exc_info() # KeyboardInterrupt is subclass of BaseException lgr.debug("Terminating process for %s upon exception: %s", cmd, exc_str(exc)) try: # there are still possible (although unlikely) cases when # we fail to interrupt but we # should not crash if we fail to terminate the process proc.terminate() except BaseException as exc2: lgr.warning("Failed to terminate process for %s: %s", cmd, exc_str(exc2)) raise exc_info[1] finally: # Those streams are for us to close if we asked for a PIPE # TODO -- assure closing the files _cleanup_output(outputstream, proc.stdout) _cleanup_output(errstream, proc.stderr) else: if self.protocol.records_ext_commands: self.protocol.add_section(split_cmdline(cmd) if isinstance(cmd, str) else cmd, None) out = ("DRY", "DRY") return out
[docs] def call(self, f, *args, **kwargs): """Helper to unify collection of logging all "dry" actions. Calls `f` if `Runner`-object is not in dry-mode. Adds `f` along with its arguments to `commands` otherwise. Parameters ---------- f: callable """ if self.protocol.do_execute_callables: if self.protocol.records_callables: prot_exc = None prot_id = self.protocol.start_section( [str(f), "args=%s" % str(args), "kwargs=%s" % str(kwargs)]) try: return f(*args, **kwargs) except Exception as e: prot_exc = e raise finally: if self.protocol.records_callables: self.protocol.end_section(prot_id, prot_exc) else: if self.protocol.records_callables: self.protocol.add_section( [str(f), "args=%s" % str(args), "kwargs=%s" % str(kwargs)], None)
[docs] def log(self, msg, *args, **kwargs): """log helper Logs at level 5 by default and adds "Protocol:"-prefix in order to log the used protocol. """ level = kwargs.pop('level', 5) if isinstance(self.protocol, NullProtocol): lgr.log(level, msg, *args, **kwargs) else: if args: msg = msg % args lgr.log(level, "{%s} %s" % ( self.protocol.__class__.__name__, msg) )
[docs]class GitRunnerBase(object): """ Mix-in class for Runners to be used to run git and git annex commands Overloads the runner class to check & update GIT_DIR and GIT_WORK_TREE environment variables set to the absolute path if is defined and is relative path """ _GIT_PATH = None @staticmethod def _check_git_path(): """If using bundled git-annex, we would like to use bundled with it git Thus we will store _GIT_PATH a path to git in the same directory as annex if found. If it is empty (but not None), we do nothing """ if GitRunnerBase._GIT_PATH is None: from distutils.spawn import find_executable # with all the nesting of config and this runner, cannot use our # cfg here, so will resort to dark magic of environment options if (os.environ.get('DATALAD_USE_DEFAULT_GIT', '0').lower() in ('1', 'on', 'true', 'yes')): git_fpath = find_executable("git") if git_fpath: GitRunnerBase._GIT_PATH = '' lgr.log(9, "Will use default git %s", git_fpath) return # we are done - there is a default git avail. # if not -- we will look for a bundled one GitRunnerBase._GIT_PATH = GitRunnerBase._get_bundled_path() lgr.log(9, "Will use git under %r (no adjustments to PATH if empty " "string)", GitRunnerBase._GIT_PATH) assert(GitRunnerBase._GIT_PATH is not None) # we made the decision! @staticmethod def _get_bundled_path(): from distutils.spawn import find_executable annex_fpath = find_executable("git-annex") if not annex_fpath: # not sure how to live further anyways! ;) alongside = False else: annex_path = op.dirname(op.realpath(annex_fpath)) bundled_git_path = op.join(annex_path, 'git') # we only need to consider bundled git if it's actually different # from default. (see issue #5030) alongside = op.lexists(bundled_git_path) and \ bundled_git_path != op.realpath(find_executable('git')) return annex_path if alongside else ''
[docs] @staticmethod def get_git_environ_adjusted(env=None): """ Replaces GIT_DIR and GIT_WORK_TREE with absolute paths if relative path and defined """ # if env set copy else get os environment git_env = env.copy() if env else os.environ.copy() if GitRunnerBase._GIT_PATH: git_env['PATH'] = op.pathsep.join([GitRunnerBase._GIT_PATH, git_env['PATH']]) \ if 'PATH' in git_env \ else GitRunnerBase._GIT_PATH for varstring in ['GIT_DIR', 'GIT_WORK_TREE']: var = git_env.get(varstring) if var: # if env variable set if not op.isabs(var): # and it's a relative path git_env[varstring] = op.abspath(var) # to absolute path lgr.log(9, "Updated %s to %s", varstring, git_env[varstring]) if 'GIT_SSH_COMMAND' not in git_env: git_env['GIT_SSH_COMMAND'] = GIT_SSH_COMMAND git_env['GIT_SSH_VARIANT'] = 'ssh' # We are parsing error messages and hints. For those to work more # reliably we are doomed to sacrifice i18n effort of git, and enforce # consistent language of the messages git_env['LC_MESSAGES'] = 'C' # But since LC_ALL takes precedence, over LC_MESSAGES, we cannot # "leak" that one inside, and are doomed to pop it git_env.pop('LC_ALL', None) return git_env
[docs]class GitRunner(Runner, GitRunnerBase): """A Runner for git and git-annex commands. See GitRunnerBase it mixes in for more details """ @borrowdoc(Runner) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._check_git_path()
[docs] def run(self, cmd, env=None, *args, **kwargs): out, err = super().run( cmd, env=self.get_git_environ_adjusted(env), *args, **kwargs) # All communication here will be returned as unicode # TODO: do that instead within the super's run! return assure_unicode(out), assure_unicode(err)
[docs]class GitWitlessRunner(WitlessRunner, GitRunnerBase): """A WitlessRunner for git and git-annex commands. See GitRunnerBase it mixes in for more details """ @borrowdoc(WitlessRunner) def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._check_git_path() def _get_adjusted_env(self, env=None, cwd=None, copy=True): env = GitRunnerBase.get_git_environ_adjusted(env=env) return super()._get_adjusted_env( env=env, cwd=cwd, # git env above is already a copy, so we have no choice, # but we can prevent duplication copy=False, )
[docs]def readline_rstripped(stdout): #return iter(stdout.readline, b'').next().rstrip() return stdout.readline().rstrip()
[docs]class SafeDelCloseMixin(object): """A helper class to use where __del__ would call .close() which might fail if "too late in GC game" """ def __del__(self): try: self.close() except TypeError: if os.fdopen is None or lgr.debug is None: # if we are late in the game and things already gc'ed in py3, # it is Ok return raise
[docs]@auto_repr class BatchedCommand(SafeDelCloseMixin): """Container for a process which would allow for persistent communication """ def __init__(self, cmd, path=None, output_proc=None): if not isinstance(cmd, list): cmd = [cmd] self.cmd = cmd self.path = path self.output_proc = output_proc if output_proc else readline_rstripped self._process = None self._stderr_out = None self._stderr_out_fname = None def _initialize(self): lgr.debug("Initiating a new process for %s" % repr(self)) lgr.log(5, "Command: %s" % self.cmd) # according to the internet wisdom there is no easy way with subprocess # while avoid deadlocks etc. We would need to start a thread/subprocess # to timeout etc # kwargs = dict(bufsize=1, universal_newlines=True) if PY3 else {} self._stderr_out, self._stderr_out_fname = tempfile.mkstemp() self._process = subprocess.Popen( self.cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=self._stderr_out, env=GitRunnerBase.get_git_environ_adjusted(), cwd=self.path, bufsize=1, universal_newlines=True # **kwargs ) def _check_process(self, restart=False): """Check if the process was terminated and restart if restart Returns ------- bool True if process was alive. str stderr if any recorded if was terminated """ process = self._process ret = True ret_stderr = None if process and process.poll(): lgr.warning("Process %s was terminated with returncode %s" % (process, process.returncode)) ret_stderr = self.close(return_stderr=True) ret = False if self._process is None and restart: lgr.warning("Restarting the process due to previous failure") self._initialize() return ret, ret_stderr def __call__(self, cmds): """ Parameters ---------- cmds : str or tuple or list of (str or tuple) Returns ------- str or list Output received from process. list in case if cmds was a list """ input_multiple = isinstance(cmds, list) if not input_multiple: cmds = [cmds] output = [o for o in self.yield_(cmds)] return output if input_multiple else output[0]
[docs] def yield_(self, cmds): """Same as __call__, but requires `cmds` to be an iterable and yields results for each item.""" for entry in cmds: if not isinstance(entry, str): entry = ' '.join(entry) yield self.proc1(entry)
[docs] def proc1(self, arg): """Same as __call__, but only takes a single command argument and returns a single result. """ # TODO: add checks -- may be process died off and needs to be reinitiated if not self._process: self._initialize() entry = arg + '\n' lgr.log(5, "Sending %r to batched command %s" % (entry, self)) # apparently communicate is just a one time show # stdout, stderr = self._process.communicate(entry) # according to the internet wisdom there is no easy way with subprocess self._check_process(restart=True) process = self._process # _check_process might have restarted it process.stdin.write(entry) process.stdin.flush() lgr.log(5, "Done sending.") still_alive, stderr = self._check_process(restart=False) # TODO: we might want to handle still_alive, e.g. to allow for # a number of restarts/resends, but it should be per command # since for some we cannot just resend the same query. But if # it is just a "get"er - we could resend it few times # The default output_proc expects a single line output. # TODO: timeouts etc stdout = assure_unicode(self.output_proc(process.stdout)) \ if not process.stdout.closed else None if stderr: lgr.warning("Received output in stderr: %r", stderr) lgr.log(5, "Received output: %r" % stdout) return stdout
[docs] def close(self, return_stderr=False): """Close communication and wait for process to terminate Returns ------- str stderr output if return_stderr and stderr file was there. None otherwise """ ret = None process = self._process if self._stderr_out: # close possibly still open fd lgr.debug( "Closing stderr of %s", process) os.fdopen(self._stderr_out).close() self._stderr_out = None if process: lgr.debug( "Closing stdin of %s and waiting process to finish", process) process.stdin.close() process.stdout.close() process.wait() self._process = None lgr.debug("Process %s has finished", process) # It is hard to debug when something is going wrong. Hopefully logging stderr # if generally asked might be of help if lgr.isEnabledFor(5): from . import cfg log_stderr = cfg.getbool('datalad.log', 'outputs', default=False) else: log_stderr = False if self._stderr_out_fname and os.path.exists(self._stderr_out_fname): if return_stderr or log_stderr: with open(self._stderr_out_fname, 'r') as f: stderr = if return_stderr: ret = stderr if log_stderr: stderr = ensure_unicode(stderr) stderr = stderr.splitlines() lgr.log(5, "stderr of %s had %d lines:",, len(stderr)) for l in stderr: lgr.log(5, "| " + l) # remove the file where we kept dumping stderr unlink(self._stderr_out_fname) self._stderr_out_fname = None return ret