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