Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/planemo/config.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
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"""Module defines abstractions for configuring Planemo.""" import os import aenum import click import yaml PLANEMO_CONFIG_ENV_PROP = "PLANEMO_GLOBAL_CONFIG_PATH" DEFAULT_CONFIG = { } VALUE_UNSET = object() OptionSource = aenum.Enum( "OptionSource", 'cli profile global_config default' ) def _default_callback( default, use_global_config=False, resolve_path=False, extra_global_config_vars=[], ): def callback(ctx, param, value): planemo_ctx = ctx.obj param_name = param.name if value is not None: result = value option_source = OptionSource.cli else: result, option_source = _find_default( planemo_ctx, param, use_global_config=use_global_config, extra_global_config_vars=extra_global_config_vars, ) 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" % param.name] + 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 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 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 def read_global_config(config_path): 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", )