Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/config.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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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
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5 import aenum
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6 import click
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7 import yaml
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8
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9 PLANEMO_CONFIG_ENV_PROP = "PLANEMO_GLOBAL_CONFIG_PATH"
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10 DEFAULT_CONFIG = {
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11 }
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12
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13 VALUE_UNSET = object()
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14
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15
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16 OptionSource = aenum.Enum(
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17 "OptionSource", 'cli profile global_config default'
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18 )
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19
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20
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21 def _default_callback(
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22 default, use_global_config=False, resolve_path=False, extra_global_config_vars=[],
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23 ):
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24
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25 def callback(ctx, param, value):
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26 planemo_ctx = ctx.obj
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27 param_name = param.name
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28 if value is not None:
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29 result = value
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30 option_source = OptionSource.cli
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31 else:
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32 result, option_source = _find_default(
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33 planemo_ctx,
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34 param,
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35 use_global_config=use_global_config,
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36 extra_global_config_vars=extra_global_config_vars,
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37 )
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38
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39 if result is VALUE_UNSET:
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40 result = default
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41 option_source = OptionSource.default
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42
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43 assert option_source is not None
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44 assert result is not VALUE_UNSET
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45
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46 if resolve_path and result is not None:
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47 result = os.path.abspath(result)
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48
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49 planemo_ctx.set_option_source(param_name, option_source)
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50 return result
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51
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52 return callback
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53
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54
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55 def _find_default(ctx, param, use_global_config, extra_global_config_vars):
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56 if use_global_config:
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57 global_config = ctx.global_config
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58 global_config_keys = ["default_%s" % param.name] + extra_global_config_vars
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59 for global_config_key in global_config_keys:
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60 if global_config_key in global_config:
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61 default_value = global_config[global_config_key]
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62 return default_value, OptionSource.global_config
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63
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64 return VALUE_UNSET, None
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65
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66
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67 def planemo_option(*args, **kwargs):
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68 """Extend ``click.option`` with planemo-config aware configuration.
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69
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70 This extends click.option to use a callback when assigning default
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71 values, add ``use_global_config`` keyword argument to allow reading
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72 defaults from ~/.planemo.yml, and tracks how parameters are specified
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73 using the Planemo Context object.
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74 """
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75 option_type = kwargs.get("type", None)
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76 use_global_config = kwargs.pop("use_global_config", False)
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77 use_env_var = kwargs.pop("use_env_var", False)
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78 extra_global_config_vars = kwargs.pop("extra_global_config_vars", [])
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79
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80 default_specified = "default" in kwargs
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81 default = None
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82 if default_specified:
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83 default = kwargs.pop("default")
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84
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85 if default_specified or use_global_config or use_env_var:
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86 outer_callback = kwargs.pop("callback", None)
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87
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88 def callback(ctx, param, value):
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89 resolve_path = option_type and getattr(option_type, "resolve_path", False)
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90 result = _default_callback(
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91 default,
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92 use_global_config=use_global_config,
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93 extra_global_config_vars=extra_global_config_vars,
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94 resolve_path=resolve_path,
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95 )(ctx, param, value)
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96
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97 if outer_callback is not None:
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98 result = outer_callback(ctx, param, result)
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99
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100 return result
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101
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102 kwargs["callback"] = callback
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103
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104 if default_specified:
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105 kwargs["default"] = None
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106
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107 if use_env_var:
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108 name = None
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109 for arg in args:
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110 if arg.startswith("--"):
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111 name = arg[len("--"):]
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112 assert name
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113 kwargs["envvar"] = "PLANEMO_%s" % name.upper()
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114
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115 option = click.option(*args, **kwargs)
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116 return option
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117
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118
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119 def global_config_path(config_path=None):
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120 if not config_path:
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121 config_path = os.environ.get(
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122 PLANEMO_CONFIG_ENV_PROP,
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123 "~/.planemo.yml"
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124 )
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125 config_path = os.path.expanduser(config_path)
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126 return config_path
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127
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128
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129 def read_global_config(config_path):
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130 config_path = global_config_path(config_path)
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131 if not os.path.exists(config_path):
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132 return DEFAULT_CONFIG
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133
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134 with open(config_path) as f:
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135 return yaml.safe_load(f)
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136
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137
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138 __all__ = (
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139 "global_config_path",
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140 "read_global_config",
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141 "planemo_option",
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142 )