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annotate env/lib/python3.9/site-packages/planemo/cli.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """The module describes a CLI framework extending ``click``."""
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2 import functools
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3 import os
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4 import sys
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5
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6 import click
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7
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8 from planemo import __version__
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9 from planemo.context import configure_standard_planemo_logging, PlanemoContext
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10 from planemo.exit_codes import ExitCodeException
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11 from planemo.galaxy import profiles
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12 from .config import OptionSource
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13 from .io import error
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14
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15
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16 CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
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17 COMMAND_ALIASES = {
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18 "l": "lint",
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19 "o": "open",
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20 "t": "test",
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21 "s": "serve",
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22 }
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23
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24
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25 class PlanemoCliContext(PlanemoContext):
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26 """Describe context of Planemo CLI computation.
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27
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28 Extend PlanemoContext with operations for CLI concerns (exit code) and
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29 for interacting with the click library.
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30 """
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31
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32 def _log_message(self, message):
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33 click.echo(message, file=sys.stderr)
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34
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35 def exit(self, exit_code):
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36 """Exit planemo with the supplied exit code."""
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37 self.vlog("Exiting planemo with exit code [%d]" % exit_code)
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38 raise ExitCodeException(exit_code)
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39
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40
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41 pass_context = click.make_pass_decorator(PlanemoCliContext, ensure=True)
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42 cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),
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43 'commands'))
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44
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45
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46 def list_cmds():
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47 """List planemo commands from commands folder."""
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48 rv = []
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49 for filename in os.listdir(cmd_folder):
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50 if filename.endswith('.py') and \
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51 filename.startswith('cmd_'):
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52 rv.append(filename[len("cmd_"):-len(".py")])
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53 rv.sort()
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54 return rv
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55
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56
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57 def name_to_command(name):
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58 """Convert a subcommand name to the cli function for that command.
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59
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60 Command <X> is defined by the method 'planemo.commands.cmd_<x>:cli',
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61 this method uses `__import__` to load and return that method.
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62 """
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63 try:
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64 if sys.version_info[0] == 2:
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65 name = name.encode('ascii', 'replace')
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66 mod_name = 'planemo.commands.cmd_' + name
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67 mod = __import__(mod_name, None, None, ['cli'])
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68 except ImportError as e:
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69 error("Problem loading command %s, exception %s" % (name, e))
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70 return
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71 return mod.cli
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72
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73
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74 class PlanemoCLI(click.MultiCommand):
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75
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76 def list_commands(self, ctx):
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77 return list_cmds()
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78
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79 def get_command(self, ctx, name):
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80 if name in COMMAND_ALIASES:
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81 name = COMMAND_ALIASES[name]
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82 return name_to_command(name)
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83
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84
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85 def command_function(f):
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86 """Extension point for processing kwds after click callbacks."""
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87 @functools.wraps(f)
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88 def handle_blended_options(*args, **kwds):
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89 profile = kwds.get("profile", None)
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90 if profile:
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91 ctx = args[0]
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92 profile_defaults = profiles.ensure_profile(
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93 ctx, profile, **kwds
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94 )
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95 _setup_profile_options(ctx, profile_defaults, kwds)
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96
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97 try:
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98 return f(*args, **kwds)
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99 except ExitCodeException as e:
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100 sys.exit(e.exit_code)
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101
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102 return pass_context(handle_blended_options)
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103
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104
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105 def _setup_profile_options(ctx, profile_defaults, kwds):
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106 for key, value in profile_defaults.items():
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107 option_present = key in kwds
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108 option_cli_specified = option_present and (ctx.get_option_source(key) == OptionSource.cli)
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109 use_profile_option = not option_present or not option_cli_specified
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110 if use_profile_option:
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111 kwds[key] = value
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112 ctx.set_option_source(
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113 key, OptionSource.profile, force=True
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114 )
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115
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116
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117 @click.command(cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
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118 @click.version_option(__version__)
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119 @click.option('-v', '--verbose', is_flag=True,
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120 help='Enables verbose mode.')
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121 @click.option('--config',
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122 default="~/.planemo.yml",
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123 envvar="PLANEMO_GLOBAL_CONFIG_PATH",
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124 help="Planemo configuration YAML file.")
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125 @click.option('--directory',
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126 default="~/.planemo",
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127 envvar="PLANEMO_GLOBAL_WORKSPACE",
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128 help="Workspace for planemo.")
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129 @pass_context
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130 def planemo(ctx, config, directory, verbose, configure_logging=True):
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131 """A command-line toolkit for building tools and workflows for Galaxy.
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132
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133 Check out the full documentation for Planemo online
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134 http://planemo.readthedocs.org or open with ``planemo docs``.
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135
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136 All the individual planemo commands support the ``--help`` option, for
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137 example use ``planemo lint --help`` for more details on checking tools.
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138 """
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139 ctx.verbose = verbose
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140 if configure_logging:
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141 configure_standard_planemo_logging(verbose)
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142 ctx.planemo_config = os.path.expanduser(config)
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143 ctx.planemo_directory = os.path.expanduser(directory)
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144
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145
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146 __all__ = (
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147 "command_function",
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148 "list_cmds",
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149 "name_to_command",
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150 "planemo",
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151 "PlanemoCliContext",
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152 )