Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/planemo/config.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
| author | shellac |
|---|---|
| date | Mon, 22 Mar 2021 18:12:50 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:4f3585e2f14b |
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| 1 """Module defines abstractions for configuring Planemo.""" | |
| 2 | |
| 3 import os | |
| 4 from enum import Enum | |
| 5 from typing import Any, Dict | |
| 6 | |
| 7 import click | |
| 8 import yaml | |
| 9 | |
| 10 PLANEMO_CONFIG_ENV_PROP = "PLANEMO_GLOBAL_CONFIG_PATH" | |
| 11 DEFAULT_CONFIG = { | |
| 12 } # type: Dict[str, Any] | |
| 13 | |
| 14 VALUE_UNSET = object() | |
| 15 | |
| 16 | |
| 17 OptionSource = Enum( | |
| 18 "OptionSource", 'cli profile global_config default' | |
| 19 ) | |
| 20 | |
| 21 | |
| 22 def _default_callback( | |
| 23 default, use_global_config=False, resolve_path=False, extra_global_config_vars=[], | |
| 24 ): | |
| 25 | |
| 26 def callback(ctx, param, value): | |
| 27 planemo_ctx = ctx.obj | |
| 28 param_name = param.name | |
| 29 if value is not None: | |
| 30 result = value | |
| 31 option_source = OptionSource.cli | |
| 32 else: | |
| 33 result, option_source = _find_default( | |
| 34 planemo_ctx, | |
| 35 param, | |
| 36 use_global_config=use_global_config, | |
| 37 extra_global_config_vars=extra_global_config_vars, | |
| 38 ) | |
| 39 | |
| 40 if result is VALUE_UNSET: | |
| 41 result = default | |
| 42 option_source = OptionSource.default | |
| 43 | |
| 44 assert option_source is not None | |
| 45 assert result is not VALUE_UNSET | |
| 46 | |
| 47 if resolve_path and result is not None: | |
| 48 result = os.path.abspath(result) | |
| 49 | |
| 50 planemo_ctx.set_option_source(param_name, option_source) | |
| 51 return result | |
| 52 | |
| 53 return callback | |
| 54 | |
| 55 | |
| 56 def _find_default(ctx, param, use_global_config, extra_global_config_vars): | |
| 57 if use_global_config: | |
| 58 global_config = ctx.global_config | |
| 59 global_config_keys = ["default_%s" % param.name] + extra_global_config_vars | |
| 60 for global_config_key in global_config_keys: | |
| 61 if global_config_key in global_config: | |
| 62 default_value = global_config[global_config_key] | |
| 63 return default_value, OptionSource.global_config | |
| 64 | |
| 65 return VALUE_UNSET, None | |
| 66 | |
| 67 | |
| 68 def planemo_option(*args, **kwargs): | |
| 69 """Extend ``click.option`` with planemo-config aware configuration. | |
| 70 | |
| 71 This extends click.option to use a callback when assigning default | |
| 72 values, add ``use_global_config`` keyword argument to allow reading | |
| 73 defaults from ~/.planemo.yml, and tracks how parameters are specified | |
| 74 using the Planemo Context object. | |
| 75 """ | |
| 76 option_type = kwargs.get("type", None) | |
| 77 use_global_config = kwargs.pop("use_global_config", False) | |
| 78 use_env_var = kwargs.pop("use_env_var", False) | |
| 79 extra_global_config_vars = kwargs.pop("extra_global_config_vars", []) | |
| 80 | |
| 81 default_specified = "default" in kwargs | |
| 82 default = None | |
| 83 if default_specified: | |
| 84 default = kwargs.pop("default") | |
| 85 | |
| 86 if default_specified or use_global_config or use_env_var: | |
| 87 outer_callback = kwargs.pop("callback", None) | |
| 88 | |
| 89 def callback(ctx, param, value): | |
| 90 resolve_path = option_type and getattr(option_type, "resolve_path", False) | |
| 91 result = _default_callback( | |
| 92 default, | |
| 93 use_global_config=use_global_config, | |
| 94 extra_global_config_vars=extra_global_config_vars, | |
| 95 resolve_path=resolve_path, | |
| 96 )(ctx, param, value) | |
| 97 | |
| 98 if outer_callback is not None: | |
| 99 result = outer_callback(ctx, param, result) | |
| 100 | |
| 101 return result | |
| 102 | |
| 103 kwargs["callback"] = callback | |
| 104 | |
| 105 if default_specified: | |
| 106 kwargs["default"] = None | |
| 107 | |
| 108 if use_env_var: | |
| 109 name = None | |
| 110 for arg in args: | |
| 111 if arg.startswith("--"): | |
| 112 name = arg[len("--"):] | |
| 113 assert name | |
| 114 kwargs["envvar"] = "PLANEMO_%s" % name.upper() | |
| 115 | |
| 116 option = click.option(*args, **kwargs) | |
| 117 return option | |
| 118 | |
| 119 | |
| 120 def global_config_path(config_path=None): | |
| 121 if not config_path: | |
| 122 config_path = os.environ.get( | |
| 123 PLANEMO_CONFIG_ENV_PROP, | |
| 124 "~/.planemo.yml" | |
| 125 ) | |
| 126 config_path = os.path.expanduser(config_path) | |
| 127 return config_path | |
| 128 | |
| 129 | |
| 130 def read_global_config(config_path: str): | |
| 131 config_path = global_config_path(config_path) | |
| 132 if not os.path.exists(config_path): | |
| 133 return DEFAULT_CONFIG | |
| 134 | |
| 135 with open(config_path) as f: | |
| 136 return yaml.safe_load(f) | |
| 137 | |
| 138 | |
| 139 __all__ = ( | |
| 140 "global_config_path", | |
| 141 "read_global_config", | |
| 142 "planemo_option", | |
| 143 ) |
