Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/context.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 """Define the context around Planemo computation.
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2
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3 Abstractions for cross cutting concerns (logging, workspace management,
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4 etc.).
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5 """
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6 import abc
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7 import logging.config
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8 import os
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9 import shutil
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10 import sys
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11 import traceback
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12 from urllib.request import urlopen
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13
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14 from planemo.config import read_global_config
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15
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16
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17 class PlanemoContextInterface(metaclass=abc.ABCMeta):
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18 """Interface Planemo operations use to access workspace context."""
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19
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20 @abc.abstractmethod
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21 def set_option_source(self, param_name, option_source, force=False):
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22 """Specify how an option was set."""
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23
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24 @abc.abstractmethod
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25 def get_option_source(self, param_name):
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26 """Return OptionSource value indicating how the option was set."""
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27
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28 @abc.abstractproperty
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29 def global_config(self):
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30 """Read Planemo's global configuration."""
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31
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32 @abc.abstractmethod
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33 def log(self, msg, *args):
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34 """Log a message."""
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35
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36 @abc.abstractmethod
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37 def vlog(self, msg, *args, **kwds):
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38 """Log a message only if verbose is enabled."""
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39
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40 @abc.abstractproperty
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41 def workspace(self):
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42 """Create and return Planemo's workspace."""
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43
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44 @abc.abstractproperty
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45 def galaxy_profiles_directory(self):
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46 """Create a return a directory for storing Galaxy profiles."""
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47
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48 @abc.abstractmethod
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49 def cache_download(self, url, destination):
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50 """Use workspace to cache download of ``url``."""
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51
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52
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53 class PlanemoContext(PlanemoContextInterface):
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54 """Implementation of ``PlanemoContextInterface``"""
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55
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56 def __init__(self):
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57 """Construct a Context object using execution environment."""
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58 self.home = os.getcwd()
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59 self._global_config = None
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60 # Will be set by planemo CLI driver
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61 self.verbose = False
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62 self.planemo_config = None
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63 self.planemo_directory = None
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64 self.option_source = {}
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65
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66 def set_option_source(self, param_name, option_source, force=False):
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67 """Specify how an option was set."""
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68 if not force:
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69 assert param_name not in self.option_source, "No option source for [%s]" % param_name
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70 self.option_source[param_name] = option_source
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71
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72 def get_option_source(self, param_name):
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73 """Return OptionSource value indicating how the option was set."""
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74 assert param_name in self.option_source, "No option source for [%s]" % param_name
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75 return self.option_source[param_name]
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76
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77 @property
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78 def global_config(self):
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79 """Read Planemo's global configuration.
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80
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81 As defined most simply by ~/.planemo.yml.
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82 """
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83 if self._global_config is None:
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84 self._global_config = read_global_config(self.planemo_config)
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85 return self._global_config or {}
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86
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87 def log(self, msg, *args):
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88 """Log a message."""
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89 if args:
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90 msg %= args
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91 self._log_message(msg)
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92
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93 def vlog(self, msg, *args, **kwds):
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94 """Log a message only if verbose is enabled."""
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95 if self.verbose:
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96 self.log(msg, *args)
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97 if kwds.get("exception", False):
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98 traceback.print_exc(file=sys.stderr)
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99
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100 @property
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101 def workspace(self):
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102 """Create and return Planemo's workspace.
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103
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104 By default this will be ``~/.planemo``.
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105 """
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106 if not self.planemo_directory:
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107 raise Exception("No planemo workspace defined.")
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108 workspace = self.planemo_directory
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109 return self._ensure_directory(workspace, "workspace")
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110
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111 @property
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112 def galaxy_profiles_directory(self):
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113 """Create a return a directory for storing Galaxy profiles."""
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114 path = os.path.join(self.workspace, "profiles")
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115 return self._ensure_directory(path, "Galaxy profiles")
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116
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117 def cache_download(self, url, destination):
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118 """Use workspace to cache download of ``url``."""
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119 cache = os.path.join(self.workspace, "cache")
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120 if not os.path.exists(cache):
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121 os.makedirs(cache)
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122 filename = os.path.basename(url)
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123 cache_destination = os.path.join(cache, filename)
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124 if not os.path.exists(cache_destination):
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125 with urlopen(url) as fh:
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126 content = fh.read()
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127 if len(content) == 0:
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128 raise Exception("Failed to download [%s]." % url)
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129 with open(cache_destination, "wb") as f:
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130 f.write(content)
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131
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132 shutil.copy(cache_destination, destination)
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133
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134 def _ensure_directory(self, path, name):
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135 if not os.path.exists(path):
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136 os.makedirs(path)
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137 if not os.path.isdir(path):
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138 template = "Planemo %s directory [%s] unavailable."
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139 message = template % (name, path)
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140 raise Exception(message)
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141 return path
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142
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143 def _log_message(self, message):
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144 """Extension point for overriding I/O."""
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145 print(message)
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146
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147
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148 def configure_standard_planemo_logging(verbose):
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149 """Configure Planemo's default logging rules."""
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150 logging_config = {
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151 'version': 1,
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152 'disable_existing_loggers': False,
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153 'formatters': {
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154 'verbose': {
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155 'format': '%(name)s %(levelname)s %(asctime)s: %(message)s'
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156 },
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157 'simple': {
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158 'format': '%(name)s %(levelname)s: %(message)s'
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159 },
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160 },
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161 'handlers': {
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162 'console': {
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163 'level': 'DEBUG',
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164 'class': 'logging.StreamHandler',
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165 'formatter': 'simple' if not verbose else 'verbose'
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166 },
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167 },
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168 'loggers': {
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169 # Suppress CWL is beta warning, for Planemo purposes - it is absolutely not.
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170 'galaxy.tools.parser.factory': {
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171 'handlers': ['console'],
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172 'propagate': False,
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173 'level': 'ERROR' if not verbose else "DEBUG",
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174 },
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175 'galaxy.tools.deps.commands': {
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176 'handlers': ['console'],
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177 'propagate': False,
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178 'level': 'ERROR' if not verbose else "DEBUG",
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179 },
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180 'galaxy': {
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181 'handlers': ['console'],
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182 'propagate': False,
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183 'level': 'INFO' if not verbose else "DEBUG",
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184 },
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185 # @jmchilton
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186 # I'm fixing up Planemo's lint functionality for CWL and I keep seeing this for the
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187 # schema metadata stuff (e.g. in the workflows repo). "rdflib.term WARNING:
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188 # http://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to
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189 # serialize this will break.". I'm going to suppress this warning I think, or are the
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190 # examples wrong and should declare their namespaces differently in some way?
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191 # @mr-c
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192 # That particular warning is worth suppressing. A PR to silence it permanently would be very welcome!
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193 # https://github.com/RDFLib/rdflib/blob/master/rdflib/term.py#L225
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194 'rdflib.term': {
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195 'handlers': ['console'],
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196 'propagate': False,
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197 'level': 'ERROR' if not verbose else "DEBUG",
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198 }
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199 },
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200 'root': {
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201 'handlers': ['console'],
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202 'propagate': False,
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203 'level': 'WARNING' if not verbose else "DEBUG",
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204 }
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205 }
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206 logging.config.dictConfig(logging_config)
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207
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208
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209 __all__ = (
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210 'configure_standard_planemo_logging',
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211 'PlanemoContextInterface',
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212 'PlanemoContext',
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213 )