view env/lib/python3.9/site-packages/planemo/ @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
line wrap: on
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"""The module describes a CLI framework extending ``click``."""
import functools
import os
import sys

import click

from planemo import __version__
from planemo.context import configure_standard_planemo_logging, PlanemoContext
from planemo.exit_codes import ExitCodeException
from planemo.galaxy import profiles
from .config import OptionSource
from .io import error

CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
    "l": "lint",
    "o": "open",
    "t": "test",
    "s": "serve",

class PlanemoCliContext(PlanemoContext):
    """Describe context of Planemo CLI computation.

    Extend PlanemoContext with operations for CLI concerns (exit code) and
    for interacting with the click library.

    def _log_message(self, message):
        click.echo(message, file=sys.stderr)

    def exit(self, exit_code):
        """Exit planemo with the supplied exit code."""
        self.vlog("Exiting planemo with exit code [%d]" % exit_code)
        raise ExitCodeException(exit_code)

pass_context = click.make_pass_decorator(PlanemoCliContext, ensure=True)
cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),

def list_cmds():
    """List planemo commands from commands folder."""
    rv = []
    for filename in os.listdir(cmd_folder):
        if filename.endswith('.py') and \
    return rv

def name_to_command(name):
    """Convert a subcommand name to the cli function for that command.

    Command <X> is defined by the method 'planemo.commands.cmd_<x>:cli',
    this method uses `__import__` to load and return that method.
        if sys.version_info[0] == 2:
            name = name.encode('ascii', 'replace')
        mod_name = 'planemo.commands.cmd_' + name
        mod = __import__(mod_name, None, None, ['cli'])
    except ImportError as e:
        error("Problem loading command %s, exception %s" % (name, e))
    return mod.cli

class PlanemoCLI(click.MultiCommand):

    def list_commands(self, ctx):
        return list_cmds()

    def get_command(self, ctx, name):
        if name in COMMAND_ALIASES:
            name = COMMAND_ALIASES[name]
        return name_to_command(name)

def command_function(f):
    """Extension point for processing kwds after click callbacks."""
    def handle_blended_options(*args, **kwds):
        profile = kwds.get("profile", None)
        if profile:
            ctx = args[0]
            profile_defaults = profiles.ensure_profile(
                ctx, profile, **kwds
            _setup_profile_options(ctx, profile_defaults, kwds)

            return f(*args, **kwds)
        except ExitCodeException as e:

    return pass_context(handle_blended_options)

def _setup_profile_options(ctx, profile_defaults, kwds):
    for key, value in profile_defaults.items():
        option_present = key in kwds
        option_cli_specified = option_present and (ctx.get_option_source(key) == OptionSource.cli)
        use_profile_option = not option_present or not option_cli_specified
        if use_profile_option:
            kwds[key] = value
                key, OptionSource.profile, force=True

@click.command(cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
@click.option('-v', '--verbose', is_flag=True,
              help='Enables verbose mode.')
              help="Planemo configuration YAML file.")
              help="Workspace for planemo.")
def planemo(ctx, config, directory, verbose, configure_logging=True):
    """A command-line toolkit for building tools and workflows for Galaxy.

    Check out the full documentation for Planemo online or open with ``planemo docs``.

    All the individual planemo commands support the ``--help`` option, for
    example use ``planemo lint --help`` for more details on checking tools.
    ctx.verbose = verbose
    if configure_logging:
    ctx.planemo_config = os.path.expanduser(config)
    ctx.planemo_directory = os.path.expanduser(directory)

__all__ = (