Source code for planemo.config

"""Module defines abstractions for configuring Planemo."""

import os
from enum import Enum
from typing import (

import click
import yaml

DEFAULT_CONFIG = {}  # type: Dict[str, Any]

VALUE_UNSET = object()

OptionSource = Enum("OptionSource", "cli profile global_config default")

def _default_callback(
    def callback(ctx, param, value):
        planemo_ctx = ctx.obj
        param_name =
        if value is not None:
            result = value
            option_source = OptionSource.cli
            result, option_source = _find_default(

        if result is VALUE_UNSET:
            result = default
            option_source = OptionSource.default

        assert option_source is not None
        assert result is not VALUE_UNSET

        if resolve_path and result is not None:
            result = os.path.abspath(result)

        planemo_ctx.set_option_source(param_name, option_source)
        return result

    return callback

def _find_default(ctx, param, use_global_config, extra_global_config_vars):
    if use_global_config:
        global_config = ctx.global_config
        global_config_keys = ["default_%s" %] + extra_global_config_vars
        for global_config_key in global_config_keys:
            if global_config_key in global_config:
                default_value = global_config[global_config_key]
                return default_value, OptionSource.global_config

    return VALUE_UNSET, None

[docs]def planemo_option(*args, **kwargs): """Extend ``click.option`` with planemo-config aware configuration. This extends click.option to use a callback when assigning default values, add ``use_global_config`` keyword argument to allow reading defaults from ~/.planemo.yml, and tracks how parameters are specified using the Planemo Context object. """ option_type = kwargs.get("type", None) use_global_config = kwargs.pop("use_global_config", False) use_env_var = kwargs.pop("use_env_var", False) extra_global_config_vars = kwargs.pop("extra_global_config_vars", []) default_specified = "default" in kwargs default = None if default_specified: default = kwargs.pop("default") if default_specified or use_global_config or use_env_var: outer_callback = kwargs.pop("callback", None) def callback(ctx, param, value): resolve_path = option_type and getattr(option_type, "resolve_path", False) result = _default_callback( default, use_global_config=use_global_config, extra_global_config_vars=extra_global_config_vars, resolve_path=resolve_path, )(ctx, param, value) if outer_callback is not None: result = outer_callback(ctx, param, result) return result kwargs["callback"] = callback if default_specified: kwargs["default"] = None if use_env_var: name = None for arg in args: if arg.startswith("--"): name = arg[len("--") :] assert name kwargs["envvar"] = "PLANEMO_%s" % name.upper() option = click.option(*args, **kwargs) return option
[docs]def global_config_path(config_path=None): if not config_path: config_path = os.environ.get(PLANEMO_CONFIG_ENV_PROP, "~/.planemo.yml") config_path = os.path.expanduser(config_path) return config_path
[docs]def read_global_config(config_path: str): config_path = global_config_path(config_path) if not os.path.exists(config_path): return DEFAULT_CONFIG with open(config_path) as f: return yaml.safe_load(f)
__all__ = ( "global_config_path", "read_global_config", "planemo_option", )