Source code for datalad.cmdline.main

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#   See COPYING file distributed along with the datalad package for the
#   copyright and license terms.
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from datalad.ui.utils import get_console_width

__docformat__ = 'restructuredtext'

import logging
lgr = logging.getLogger('datalad.cmdline')

lgr.log(5, "Importing cmdline.main")

import argparse
from collections import defaultdict
import sys
import textwrap
import os

import datalad

from datalad.cmdline import helpers
from import InsufficientArgumentsError
from import IncompleteResultsError
from import CommandError
from .helpers import strip_arg_from_argv
from ..utils import (
from ..dochelpers import exc_str
from ..version import __full_version__

def _license_info():
    return """\
Copyright (c) 2013-2019 DataLad developers

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.


[docs]class ArgumentParserDisableAbbrev(argparse.ArgumentParser): # Don't accept abbreviations for long options. This kludge was originally # added at a time when our minimum required Python version was below 3.5, # preventing us from using allow_abbrev=False. Now our minimum Python # version is high enough, but we still can't use allow_abbrev=False because # it suffers from the problem described in 6b3f2fffe (BF: cmdline: Restore # handling of short options, 2018-07-23). # # Modified from the solution posted at # def _get_option_tuples(self, option_string): chars = self.prefix_chars if option_string[0] in chars and option_string[1] in chars: # option_string is a long flag. Disable abbreviation. return [] return super(ArgumentParserDisableAbbrev, self)._get_option_tuples( option_string)
# TODO: OPT look into making setup_parser smarter to become faster # Now it seems to take up to 200ms to do all the parser setup # even though it might not be necessary to know about all the commands etc. # I wondered if it could somehow decide on what commands to worry about etc # by going through sys.args first
[docs]def setup_parser( cmdlineargs, formatter_class=argparse.RawDescriptionHelpFormatter, return_subparsers=False, # Was this triggered by argparse? completing=False, # prevent loading of extension entrypoints when --help is requested # this is enabled when building docs to avoid pollution of generated # manpages with extensions commands (that should appear in their own # docs, but not in the core datalad package docs) help_ignore_extensions=False): lgr.log(5, "Starting to setup_parser") # delay since it can be a heavy import from ..interface.base import dedent_docstring, get_interface_groups, \ get_cmdline_command_name, alter_interface_docs_for_cmdline, \ load_interface, get_cmd_doc, get_cmd_ex # setup cmdline args parser parts = {} # main parser parser = ArgumentParserDisableAbbrev( fromfile_prefix_chars=None, # usage="%(prog)s ...", description=dedent_docstring("""\ Comprehensive data management solution DataLad provides a unified data distribution system built on the Git and Git-annex. DataLad command line tools allow to manipulate (obtain, create, update, publish, etc.) datasets and provide a comprehensive toolbox for joint management of data and code. Compared to Git/annex it primarly extends their functionality to transparently and simultaneously work with multiple inter-related repositories."""), epilog='"Be happy!"', formatter_class=formatter_class, add_help=False) # common options helpers.parser_add_common_opt(parser, 'log_level') helpers.parser_add_common_opt(parser, 'pbs_runner') helpers.parser_add_common_opt(parser, 'change_path') helpers.parser_add_common_opt( parser, 'version', version='datalad %s\n' % datalad.__version__) if __debug__: parser.add_argument( '--dbg', action='store_true', dest='common_debug', help="enter Python debugger when uncaught exception happens") parser.add_argument( '--idbg', action='store_true', dest='common_idebug', help="enter IPython debugger when uncaught exception happens") parser.add_argument( '-c', action='append', dest='cfg_overrides', metavar='KEY=VALUE', help="""configuration variable setting. Overrides any configuration read from a file, but is potentially overridden itself by configuration variables in the process environment.""") parser.add_argument( '-f', '--output-format', dest='common_output_format', default='default', type=assure_unicode, metavar="{default,json,json_pp,tailored,'<template>'}", help="""select format for returned command results. 'default' give one line per result reporting action, status, path and an optional message; 'json' renders a JSON object with all properties for each result (one per line); 'json_pp' pretty-prints JSON spanning multiple lines; 'tailored' enables a command-specific rendering style that is typically tailored to human consumption (no result output otherwise), '<template>' reports any value(s) of any result properties in any format indicated by the template (e.g. '{path}'; compare with JSON output for all key-value choices). The template syntax follows the Python "format() language". It is possible to report individual dictionary values, e.g. '{metadata[name]}'. If a 2nd-level key contains a colon, e.g. 'music:Genre', ':' must be substituted by '#' in the template, like so: '{metadata[music#Genre]}'.""") parser.add_argument( '--report-status', dest='common_report_status', choices=['success', 'failure', 'ok', 'notneeded', 'impossible', 'error'], help="""constrain command result report to records matching the given status. 'success' is a synonym for 'ok' OR 'notneeded', 'failure' stands for 'impossible' OR 'error'.""") parser.add_argument( '--report-type', dest='common_report_type', choices=['dataset', 'file'], action='append', help="""constrain command result report to records matching the given type. Can be given more than once to match multiple types.""") parser.add_argument( '--on-failure', dest='common_on_failure', choices=['ignore', 'continue', 'stop'], # no default: better be configure per-command help="""when an operation fails: 'ignore' and continue with remaining operations, the error is logged but does not lead to a non-zero exit code of the command; 'continue' works like 'ignore', but an error causes a non-zero exit code; 'stop' halts on first failure and yields non-zero exit code. A failure is any result with status 'impossible' or 'error'.""") parser.add_argument( '--cmd', dest='_', action='store_true', help="""syntactical helper that can be used to end the list of global command line options before the subcommand label. Options taking an arbitrary number of arguments may require to be followed by a single --cmd in order to enable identification of the subcommand.""") # yoh: atm we only dump to console. Might adopt the same separation later on # and for consistency will call it --verbose-level as well for now # log-level is set via common_opts ATM # parser.add_argument('--log-level', # choices=('critical', 'error', 'warning', 'info', 'debug'), # dest='common_log_level', # help="""level of verbosity in log files. By default # everything, including debug messages is logged.""") #parser.add_argument('-l', '--verbose-level', # choices=('critical', 'error', 'warning', 'info', 'debug'), # dest='common_verbose_level', # help="""level of verbosity of console output. By default # only warnings and errors are printed.""") # Before doing anything additional and possibly expensive see may be that # we have got the command already need_single_subparser = False if return_subparsers else None fail_handler = (lambda *a, **kw: True) \ if return_subparsers else fail_with_short_help try: parsed_args, unparsed_args = parser._parse_known_args( cmdlineargs[1:], argparse.Namespace()) if not (completing or unparsed_args): fail_handler(parser, msg="too few arguments", exit_code=2) lgr.debug("Command line args 1st pass for DataLad %s. Parsed: %s Unparsed: %s", __full_version__, parsed_args, unparsed_args) except Exception as exc: lgr.debug("Early parsing failed with %s", exc_str(exc)) need_single_subparser = False unparsed_args = cmdlineargs[1:] # referenced before assignment otherwise interface_groups = get_interface_groups(include_plugins=True) # First unparsed could be either unknown option to top level "datalad" # or a command. Among unknown could be --help/--help-np which would # need to be dealt with unparsed_arg = unparsed_args[0] if unparsed_args else None if need_single_subparser is not None \ or unparsed_arg in ('--help', '--help-np', '-h'): need_single_subparser = False if not help_ignore_extensions: add_entrypoints_to_interface_groups(interface_groups) elif not completing and unparsed_arg.startswith('-'): # unknown option fail_with_short_help(parser, msg="unrecognized argument %s" % unparsed_arg, exit_code=2) # if we could get a list of options known to parser, # we could suggest them # known=get_all_options(parser), provided=unparsed_arg) else: # the command to handle known_commands = get_commands_from_groups(interface_groups) if unparsed_arg not in known_commands: # need to load all the extensions and try again add_entrypoints_to_interface_groups(interface_groups) known_commands = get_commands_from_groups(interface_groups) if unparsed_arg not in known_commands: # check if might be coming from known extensions from ..interface import ( _known_extension_commands, _deprecated_commands, ) extension_commands = { c: e for e, commands in _known_extension_commands.items() for c in commands } hint = None if unparsed_arg in extension_commands: hint = "Command %s is provided by (not installed) extension %s." \ % (unparsed_arg, extension_commands[unparsed_arg]) elif unparsed_arg in _deprecated_commands: hint_cmd = _deprecated_commands[unparsed_arg] hint = "Command %r was deprecated" % unparsed_arg hint += (" in favor of %r command." % hint_cmd) if hint_cmd else '.' if not completing: fail_with_short_help( parser, hint=hint, provided=unparsed_arg, known=list(known_commands.keys()) + list(extension_commands.keys()) ) if need_single_subparser is None: need_single_subparser = unparsed_arg # --help specification was delayed since it causes immediate printout of # --help output before we setup --help for each command helpers.parser_add_common_opt(parser, 'help') grp_short_descriptions = defaultdict(list) # create subparser, use module suffix as cmd name subparsers = parser.add_subparsers() for group_name, _, _interfaces \ in sorted(interface_groups, key=lambda x: x[1]): for _intfspec in _interfaces: cmd_name = get_cmdline_command_name(_intfspec) if need_single_subparser and cmd_name != need_single_subparser: continue _intf = load_interface(_intfspec) if _intf is None: # TODO(yoh): add doc why we could skip this one... makes this # loop harder to extract into a dedicated function continue # deal with optional parser args if hasattr(_intf, 'parser_args'): parser_args = _intf.parser_args else: parser_args = dict(formatter_class=formatter_class) # use class description, if no explicit description is available intf_doc = get_cmd_doc(_intf) parser_args['description'] = alter_interface_docs_for_cmdline( intf_doc) if hasattr(_intf, '_examples_'): intf_ex = alter_interface_docs_for_cmdline(get_cmd_ex(_intf)) parser_args['description'] += intf_ex subparser = subparsers.add_parser(cmd_name, add_help=False, **parser_args) # our own custom help for all commands helpers.parser_add_common_opt(subparser, 'help') # let module configure the parser _intf.setup_parser(subparser) # logger for command # configure 'run' function for this command plumbing_args = dict( func=_intf.call_from_parser, logger=logging.getLogger(_intf.__module__), subparser=subparser) if hasattr(_intf, 'result_renderer_cmdline'): plumbing_args['result_renderer'] = _intf.result_renderer_cmdline subparser.set_defaults(**plumbing_args) parts[cmd_name] = subparser # store short description for later sdescr = getattr(_intf, 'short_description', parser_args['description'].split('\n')[0]) grp_short_descriptions[group_name].append((cmd_name, sdescr)) # create command summary if '--help' in cmdlineargs or '--help-np' in cmdlineargs: parser.description = get_description_with_cmd_summary( grp_short_descriptions, interface_groups, parser.description) parts['datalad'] = parser lgr.log(5, "Finished setup_parser") if return_subparsers: return parts else: return parser
[docs]def fail_with_short_help(parser=None, msg=None, known=None, provided=None, hint=None, exit_code=1, what="command", out=None): """Generic helper to fail with short help possibly hinting on what was intended if `known` were provided """ out = out or sys.stderr if msg: out.write("error: %s\n" % msg) if not known: if parser: # just to appear in print_usage also consistent with --help output parser.add_argument("command [command-opts]") parser.print_usage(file=out) else: out.write( "datalad: Unknown %s %r. See 'datalad --help'.\n\n" % (what, provided,)) if provided not in known: out.write(get_suggestions_msg(provided, known)) # Too noisy # sys.stderr.write(" All known %ss: %s\n" # % (what, ", ".join(sorted(known)))) if hint: out.write("Hint: %s\n" % hint) raise SystemExit(exit_code)
[docs]def get_description_with_cmd_summary(grp_short_descriptions, interface_groups, parser_description): from ..interface.base import dedent_docstring from ..interface.base import get_cmd_summaries lgr.debug("Generating detailed description for the parser") console_width = get_console_width() cmd_summary = get_cmd_summaries(grp_short_descriptions, interface_groups, width=console_width) # we need one last formal section to not have the trailed be # confused with the last command group cmd_summary.append('\n*General information*\n') detailed_description = '%s\n%s\n\n%s' \ % (parser_description, '\n'.join(cmd_summary), textwrap.fill(dedent_docstring("""\ Detailed usage information for individual commands is available via command-specific --help, i.e.: datalad <command> --help"""), console_width - 5, initial_indent='', subsequent_indent='')) return detailed_description
[docs]def get_commands_from_groups(groups): """Get a dictionary of command: interface_spec""" from ..interface.base import get_cmdline_command_name return { get_cmdline_command_name(_intfspec): _intfspec for _, _, _interfaces in groups for _intfspec in _interfaces }
[docs]def add_entrypoints_to_interface_groups(interface_groups): lgr.debug("Loading entrypoints") from pkg_resources import iter_entry_points # delay expensive import for ep in iter_entry_points('datalad.extensions'): lgr.debug( 'Loading entrypoint %s from datalad.extensions for docs building', try: spec = ep.load() if len(spec) < 2 or not spec[1]: lgr.debug( 'Extension does not provide a command suite: %s', continue interface_groups.append((, spec[0], spec[1])) lgr.debug('Loaded entrypoint %s', except Exception as e: lgr.warning('Failed to load entrypoint %s: %s',, exc_str(e)) continue
def _fix_datalad_ri(s): """Fixup argument if it was a DataLadRI and had leading / removed See gh-2643 """ if s.startswith('//') and (len(s) == 2 or (len(s) > 2 and s[2] != '/')): "Changing %s back to /%s as it was probably changed by MINGW/MSYS, " "see", s, s) return "/" + s return s
[docs]def main(args=None): lgr.log(5, "Starting main(%r)", args) args = args or sys.argv if on_msys_tainted_paths: # Possibly present DataLadRIs were stripped of a leading / args = [_fix_datalad_ri(s) for s in args] # PYTHON_ARGCOMPLETE_OK parser = setup_parser(args, completing="_ARGCOMPLETE" in os.environ) try: import argcomplete argcomplete.autocomplete(parser) except ImportError: pass # parse cmd args lgr.debug("Parsing known args among %s", repr(args)) cmdlineargs, unparsed_args = parser.parse_known_args(args[1:]) has_func = hasattr(cmdlineargs, 'func') and cmdlineargs.func is not None if unparsed_args: if has_func and cmdlineargs.func.__self__.__name__ != 'Export': lgr.error('unknown argument{}: {}'.format( 's' if len(unparsed_args) > 1 else '', unparsed_args if len(unparsed_args) > 1 else unparsed_args[0])) cmdlineargs.subparser.print_usage() sys.exit(1) else: # store all unparsed arguments cmdlineargs.datalad_unparsed_args = unparsed_args # to possibly be passed into PBS scheduled call args_ = args or sys.argv if cmdlineargs.cfg_overrides is not None: import re # this expression is deliberately loose as gitconfig offers # quite some flexibility -- this is just meant to catch stupid # errors: we need a section, a variable, and a value at minimum # otherwise we break our own config parsing helpers # noassign_expr = re.compile(r'[^\s]+\.[^\s]+=[\S]+') noassign = [ o for o in cmdlineargs.cfg_overrides if not noassign_expr.match(o) ] if noassign: lgr.error( "Configuration override without section/variable " "or value assignment (must be 'section.variable=value'): %s", noassign) sys.exit(3) overrides = dict([ (o.split('=')[0], '='.join(o.split('=')[1:])) for o in cmdlineargs.cfg_overrides]) datalad.cfg.overrides.update(overrides) # enable overrides datalad.cfg.reload(force=True) if cmdlineargs.change_path is not None: from .common_args import change_path as change_path_opt for path in cmdlineargs.change_path: chpwd(path) args_ = strip_arg_from_argv(args_, path, change_path_opt[1]) ret = None if cmdlineargs.pbs_runner: from .helpers import run_via_pbs from .common_args import pbs_runner as pbs_runner_opt args_ = strip_arg_from_argv(args_, cmdlineargs.pbs_runner, pbs_runner_opt[1]) # run the function associated with the selected command run_via_pbs(args_, cmdlineargs.pbs_runner) elif has_func: if cmdlineargs.common_debug or cmdlineargs.common_idebug: # so we could see/stop clearly at the point of failure setup_exceptionhook(ipython=cmdlineargs.common_idebug) from datalad.interface.base import Interface Interface._interrupted_exit_code = None ret = cmdlineargs.func(cmdlineargs) else: # otherwise - guard and only log the summary. Postmortem is not # as convenient if being caught in this ultimate except try: ret = cmdlineargs.func(cmdlineargs) except InsufficientArgumentsError as exc: # if the func reports inappropriate usage, give help output lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__)) cmdlineargs.subparser.print_usage(sys.stderr) sys.exit(2) except IncompleteResultsError as exc: # rendering for almost all commands now happens 'online' # hence we are no longer attempting to render the actual # results in an IncompleteResultsError, ubt rather trust that # this happened before # in general we do not want to see the error again, but # present in debug output lgr.debug('could not perform all requested actions: %s', exc_str(exc)) sys.exit(1) except CommandError as exc: # behave as if the command ran directly, importantly pass # exit code as is # to not duplicate any captured output in the exception # rendering, will come next exc_msg = exc.to_str(include_output=False) if exc_msg: msg = exc_msg.encode() if isinstance(exc_msg, str) else exc_msg os.write(2, msg + b"\n") if exc.stdout: os.write(1, exc.stdout.encode() if isinstance(exc.stdout, str) else exc.stdout) if exc.stderr: os.write(2, exc.stderr.encode() if isinstance(exc.stderr, str) else exc.stderr) # We must not exit with 0 code if any exception got here but # had no code defined sys.exit(exc.code if exc.code is not None else 1) except Exception as exc: lgr.error('%s (%s)' % (exc_str(exc), exc.__class__.__name__)) sys.exit(1) else: # just let argparser spit out its error, since there is smth wrong parser.parse_args(args) # if that one didn't puke -- we should parser.print_usage() lgr.error("Please specify the command") sys.exit(2) try: if hasattr(cmdlineargs, 'result_renderer'): cmdlineargs.result_renderer(ret, cmdlineargs) except Exception as exc: lgr.error("Failed to render results due to %s", exc_str(exc)) sys.exit(1)
lgr.log(5, "Done importing cmdline.main")