Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/cli.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 """The module describes a CLI framework extending ``click``."""
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2 import functools
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3 import logging.config
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4 import os
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5 import shutil
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6 import sys
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7 import traceback
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8
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9 import click
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10 from six.moves.urllib.request import urlopen
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11
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12 from planemo import __version__
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13 from planemo.exit_codes import ExitCodeException
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14 from planemo.galaxy import profiles
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15 from .config import (
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16 OptionSource,
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17 read_global_config,
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18 )
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19 from .io import error
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20
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21
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22 CONTEXT_SETTINGS = dict(auto_envvar_prefix='PLANEMO')
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23 COMMAND_ALIASES = {
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24 "l": "lint",
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25 "o": "open",
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26 "t": "test",
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27 "s": "serve",
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28 }
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29
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30
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31 class Context(object):
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32 """Describe context of Planemo computation.
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33
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34 Handles cross cutting concerns for Planemo such as verbose log
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35 tracking, the definition of the Planemo workspace (``~/.planemo``),
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36 and the global configuraton defined in ``~/.planemo.yml``.
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37 """
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38
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39 def __init__(self):
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40 """Construct a Context object using execution environment."""
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41 self.home = os.getcwd()
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42 self._global_config = None
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43 # Will be set by planemo CLI driver
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44 self.verbose = False
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45 self.planemo_config = None
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46 self.planemo_directory = None
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47 self.option_source = {}
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48
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49 def set_option_source(self, param_name, option_source, force=False):
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50 """Specify how an option was set."""
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51 if not force:
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52 assert param_name not in self.option_source, "No option source for [%s]" % param_name
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53 self.option_source[param_name] = option_source
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54
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55 def get_option_source(self, param_name):
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56 """Return OptionSource value indicating how the option was set."""
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57 assert param_name in self.option_source, "No option source for [%s]" % param_name
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58 return self.option_source[param_name]
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59
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60 @property
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61 def global_config(self):
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62 """Read Planemo's global configuration.
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63
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64 As defined most simply by ~/.planemo.yml.
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65 """
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66 if self._global_config is None:
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67 self._global_config = read_global_config(self.planemo_config)
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68 return self._global_config or {}
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69
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70 def log(self, msg, *args):
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71 """Log a message to stderr."""
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72 if args:
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73 msg %= args
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74 click.echo(msg, file=sys.stderr)
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75
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76 def vlog(self, msg, *args, **kwds):
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77 """Log a message to stderr only if verbose is enabled."""
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78 if self.verbose:
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79 self.log(msg, *args)
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80 if kwds.get("exception", False):
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81 traceback.print_exc(file=sys.stderr)
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82
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83 @property
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84 def workspace(self):
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85 """Create and return Planemo's workspace.
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86
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87 By default this will be ``~/.planemo``.
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88 """
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89 if not self.planemo_directory:
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90 raise Exception("No planemo workspace defined.")
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91 workspace = self.planemo_directory
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92 return self._ensure_directory(workspace, "workspace")
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93
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94 @property
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95 def galaxy_profiles_directory(self):
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96 """Create a return a directory for storing Galaxy profiles."""
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97 path = os.path.join(self.workspace, "profiles")
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98 return self._ensure_directory(path, "Galaxy profiles")
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99
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100 def _ensure_directory(self, path, name):
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101 if not os.path.exists(path):
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102 os.makedirs(path)
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103 if not os.path.isdir(path):
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104 template = "Planemo %s directory [%s] unavailable."
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105 message = template % (name, path)
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106 raise Exception(message)
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107 return path
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108
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109 def exit(self, exit_code):
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110 """Exit planemo with the supplied exit code."""
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111 self.vlog("Exiting planemo with exit code [%d]" % exit_code)
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112 raise ExitCodeException(exit_code)
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113
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114 def cache_download(self, url, destination):
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115 cache = os.path.join(self.workspace, "cache")
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116 if not os.path.exists(cache):
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117 os.makedirs(cache)
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118 filename = os.path.basename(url)
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119 cache_destination = os.path.join(cache, filename)
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120 if not os.path.exists(cache_destination):
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121 with urlopen(url) as fh:
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122 content = fh.read()
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123 if len(content) == 0:
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124 raise Exception("Failed to download [%s]." % url)
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125 with open(cache_destination, "wb") as f:
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126 f.write(content)
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127
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128 shutil.copy(cache_destination, destination)
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129
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130
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131 pass_context = click.make_pass_decorator(Context, ensure=True)
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132 cmd_folder = os.path.abspath(os.path.join(os.path.dirname(__file__),
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133 'commands'))
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134
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135
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136 def list_cmds():
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137 """List planemo commands from commands folder."""
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138 rv = []
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139 for filename in os.listdir(cmd_folder):
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140 if filename.endswith('.py') and \
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141 filename.startswith('cmd_'):
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142 rv.append(filename[len("cmd_"):-len(".py")])
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143 rv.sort()
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144 return rv
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145
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146
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147 def name_to_command(name):
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148 """Convert a subcommand name to the cli function for that command.
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149
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150 Command <X> is defined by the method 'planemo.commands.cmd_<x>:cli',
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151 this method uses `__import__` to load and return that method.
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152 """
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153 try:
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154 if sys.version_info[0] == 2:
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155 name = name.encode('ascii', 'replace')
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156 mod_name = 'planemo.commands.cmd_' + name
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157 mod = __import__(mod_name, None, None, ['cli'])
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158 except ImportError as e:
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159 error("Problem loading command %s, exception %s" % (name, e))
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160 return
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161 return mod.cli
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162
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163
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164 class PlanemoCLI(click.MultiCommand):
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165
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166 def list_commands(self, ctx):
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167 return list_cmds()
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168
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169 def get_command(self, ctx, name):
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170 if name in COMMAND_ALIASES:
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171 name = COMMAND_ALIASES[name]
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172 return name_to_command(name)
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173
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174
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175 def command_function(f):
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176 """Extension point for processing kwds after click callbacks."""
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177 @functools.wraps(f)
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178 def handle_blended_options(*args, **kwds):
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179 profile = kwds.get("profile", None)
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180 if profile:
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181 ctx = args[0]
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182 profile_defaults = profiles.ensure_profile(
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183 ctx, profile, **kwds
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184 )
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185 _setup_profile_options(ctx, profile_defaults, kwds)
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186
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187 _setup_galaxy_source_options(args[0], kwds)
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188
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189 try:
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190 return f(*args, **kwds)
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191 except ExitCodeException as e:
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192 sys.exit(e.exit_code)
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193
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194 return pass_context(handle_blended_options)
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195
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196
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197 EXCLUSIVE_OPTIONS_LIST = [
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198 ]
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199
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200
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201 def _setup_galaxy_source_options(ctx, kwds):
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202 for exclusive_options in EXCLUSIVE_OPTIONS_LIST:
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203 option_source = {}
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204 for option in exclusive_options:
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205 if option in kwds:
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206 option_source[option] = ctx.get_option_source(option)
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207 else:
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208 option_source[option] = None
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209
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210 most_authoratative_source = None
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211 most_authoratative_source_options = []
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212 for key, value in option_source.items():
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213 if value is None:
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214 continue
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215 if most_authoratative_source is None or value.value < most_authoratative_source.value:
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216 most_authoratative_source = value
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217 most_authoratative_source_options = [key]
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218 elif value == most_authoratative_source:
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219 most_authoratative_source_options.append(key)
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220
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221 if most_authoratative_source != OptionSource.default and len(most_authoratative_source_options) > 1:
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222 raise click.UsageError("Cannot specify multiple of %s" % most_authoratative_source_options)
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223
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224 for option in exclusive_options:
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225 if option in kwds and option not in most_authoratative_source_options:
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226 del kwds[option]
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227
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228
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229 def _setup_profile_options(ctx, profile_defaults, kwds):
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230 for key, value in profile_defaults.items():
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231 option_present = key in kwds
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232 option_cli_specified = option_present and (ctx.get_option_source(key) == OptionSource.cli)
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233 use_profile_option = not option_present or not option_cli_specified
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234 if use_profile_option:
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235 kwds[key] = value
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236 ctx.set_option_source(
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237 key, OptionSource.profile, force=True
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238 )
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239
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240
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241 @click.command(cls=PlanemoCLI, context_settings=CONTEXT_SETTINGS)
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242 @click.version_option(__version__)
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243 @click.option('-v', '--verbose', is_flag=True,
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244 help='Enables verbose mode.')
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245 @click.option('--config',
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246 default="~/.planemo.yml",
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247 envvar="PLANEMO_GLOBAL_CONFIG_PATH",
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248 help="Planemo configuration YAML file.")
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249 @click.option('--directory',
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250 default="~/.planemo",
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251 envvar="PLANEMO_GLOBAL_WORKSPACE",
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252 help="Workspace for planemo.")
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253 @pass_context
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254 def planemo(ctx, config, directory, verbose, configure_logging=True):
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255 """A command-line toolkit for building tools and workflows for Galaxy.
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256
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257 Check out the full documentation for Planemo online
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258 http://planemo.readthedocs.org or open with ``planemo docs``.
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259
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260 All the individual planemo commands support the ``--help`` option, for
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261 example use ``planemo lint --help`` for more details on checking tools.
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262 """
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263 ctx.verbose = verbose
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264 if configure_logging:
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265 logging_config = {
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266 'version': 1,
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267 'disable_existing_loggers': False,
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268 'formatters': {
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269 'verbose': {
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270 'format': '%(name)s %(levelname)s %(asctime)s: %(message)s'
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271 },
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272 'simple': {
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273 'format': '%(name)s %(levelname)s: %(message)s'
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274 },
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275 },
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276 'handlers': {
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277 'console': {
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278 'level': 'DEBUG',
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279 'class': 'logging.StreamHandler',
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280 'formatter': 'simple' if not verbose else 'verbose'
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281 },
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282 },
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283 'loggers': {
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284 # Suppress CWL is beta warning, for Planemo purposes - it is absolutely not.
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285 'galaxy.tools.parser.factory': {
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286 'handlers': ['console'],
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287 'propagate': False,
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288 'level': 'ERROR' if not verbose else "DEBUG",
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289 },
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290 'galaxy.tools.deps.commands': {
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291 'handlers': ['console'],
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292 'propagate': False,
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293 'level': 'ERROR' if not verbose else "DEBUG",
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294 },
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295 'galaxy': {
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296 'handlers': ['console'],
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297 'propagate': False,
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298 'level': 'INFO' if not verbose else "DEBUG",
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299 },
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300 # @jmchilton
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301 # I'm fixing up Planemo's lint functionality for CWL and I keep seeing this for the
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302 # schema metadata stuff (e.g. in the workflows repo). "rdflib.term WARNING:
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303 # http://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to
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304 # serialize this will break.". I'm going to suppress this warning I think, or are the
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305 # examples wrong and should declare their namespaces differently in some way?
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306 # @mr-c
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307 # That particular warning is worth suppressing. A PR to silence it permanently would be very welcome!
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308 # https://github.com/RDFLib/rdflib/blob/master/rdflib/term.py#L225
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309 'rdflib.term': {
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310 'handlers': ['console'],
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311 'propagate': False,
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312 'level': 'ERROR' if not verbose else "DEBUG",
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313 }
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314 },
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315 'root': {
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316 'handlers': ['console'],
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317 'propagate': False,
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318 'level': 'WARNING' if not verbose else "DEBUG",
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319 }
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320 }
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321 logging.config.dictConfig(logging_config)
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322 ctx.planemo_config = os.path.expanduser(config)
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323 ctx.planemo_directory = os.path.expanduser(directory)
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324
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325
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326 __all__ = (
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327 "command_function",
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328 "Context",
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329 "list_cmds",
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330 "name_to_command",
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331 "planemo",
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332 )