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 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:4f3585e2f14b |
---|---|
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 ) |