Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/properties.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """ Module used to blend ini, environment, and explicit dictionary properties
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2 to determine application configuration. Some hard coded defaults for Galaxy but
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3 this should be reusable by tool shed and pulsar as well.
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4 """
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5 import os
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6 import os.path
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7 import sys
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8 from functools import partial
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9 from itertools import product, starmap
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10
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11 import yaml
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12 from six import iteritems, string_types
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13 from six.moves.configparser import ConfigParser
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14
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15 from galaxy.exceptions import InvalidFileFormatError
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16 from galaxy.util.path import extensions, has_ext, joinext
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17
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18
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19 def find_config_file(names, exts=None, dirs=None, include_samples=False):
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20 """Locate a config file in multiple directories, with multiple extensions.
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21
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22 >>> from shutil import rmtree
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23 >>> from tempfile import mkdtemp
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24 >>> def touch(d, f):
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25 ... open(os.path.join(d, f), 'w').close()
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26 >>> def _find_config_file(*args, **kwargs):
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27 ... return find_config_file(*args, **kwargs).replace(d, '')
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28 >>> d = mkdtemp()
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29 >>> d1 = os.path.join(d, 'd1')
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30 >>> d2 = os.path.join(d, 'd2')
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31 >>> os.makedirs(d1)
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32 >>> os.makedirs(d2)
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33 >>> touch(d1, 'foo.ini')
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34 >>> touch(d1, 'foo.bar')
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35 >>> touch(d1, 'baz.ini.sample')
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36 >>> touch(d2, 'foo.yaml')
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37 >>> touch(d2, 'baz.yml')
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38 >>> _find_config_file('foo', dirs=(d1, d2))
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39 '/d1/foo.ini'
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40 >>> _find_config_file('baz', dirs=(d1, d2))
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41 '/d2/baz.yml'
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42 >>> _find_config_file('baz', dirs=(d1, d2), include_samples=True)
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43 '/d2/baz.yml'
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44 >>> _find_config_file('baz', dirs=(d1,), include_samples=True)
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45 '/d1/baz.ini.sample'
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46 >>> _find_config_file('foo', dirs=(d2, d1))
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47 '/d2/foo.yaml'
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48 >>> find_config_file('quux', dirs=(d,))
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49 >>> _find_config_file('foo', exts=('bar', 'ini'), dirs=(d1,))
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50 '/d1/foo.bar'
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51 >>> rmtree(d)
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52 """
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53 found = __find_config_files(
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54 names,
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55 exts=exts or extensions['yaml'] + extensions['ini'],
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56 dirs=dirs or [os.getcwd(), os.path.join(os.getcwd(), 'config')],
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57 include_samples=include_samples,
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58 )
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59 if not found:
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60 return None
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61 # doesn't really make sense to log here but we should probably generate a warning of some kind if more than one
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62 # config is found.
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63 return found[0]
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64
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65
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66 def load_app_properties(
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67 kwds=None,
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68 ini_file=None,
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69 ini_section=None,
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70 config_file=None,
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71 config_section=None,
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72 config_prefix="GALAXY_CONFIG_"
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73 ):
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74 if config_file is None:
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75 config_file = ini_file
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76 config_section = ini_section
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77
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78 # read from file or init w/no file
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79 if config_file:
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80 properties = read_properties_from_file(config_file, config_section)
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81 else:
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82 properties = {'__file__': None}
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83
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84 # update from kwds
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85 if kwds:
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86 properties.update(kwds)
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87
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88 # update from env
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89 override_prefix = "%sOVERRIDE_" % config_prefix
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90 for key in os.environ:
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91 if key.startswith(override_prefix):
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92 config_key = key[len(override_prefix):].lower()
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93 properties[config_key] = os.environ[key]
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94 elif key.startswith(config_prefix):
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95 config_key = key[len(config_prefix):].lower()
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96 if config_key not in properties:
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97 properties[config_key] = os.environ[key]
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98
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99 return properties
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100
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101
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102 def read_properties_from_file(config_file, config_section=None):
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103 properties = {}
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104 if has_ext(config_file, 'yaml', aliases=True, ignore='sample'):
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105 if config_section is None:
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106 config_section = "galaxy"
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107 properties.update(__default_properties(config_file))
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108 raw_properties = _read_from_yaml_file(config_file)
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109 if raw_properties:
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110 properties.update(raw_properties.get(config_section) or {})
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111 elif has_ext(config_file, 'ini', aliases=True, ignore='sample'):
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112 if config_section is None:
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113 config_section = "app:main"
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114 parser = nice_config_parser(config_file) # default properties loaded w/parser
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115 if parser.has_section(config_section):
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116 properties.update(dict(parser.items(config_section)))
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117 else:
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118 properties.update(parser.defaults())
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119 else:
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120 raise InvalidFileFormatError()
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121 return properties
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122
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123
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124 def _read_from_yaml_file(path):
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125 with open(path, "r") as f:
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126 return yaml.safe_load(f)
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127
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128
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129 def nice_config_parser(path):
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130 parser = NicerConfigParser(path, defaults=__default_properties(path))
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131 parser.optionxform = str # Don't lower-case keys
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132 with open(path) as f:
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133 parser.read_file(f)
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134 return parser
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135
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136
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137 class NicerConfigParser(ConfigParser):
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138
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139 def __init__(self, filename, *args, **kw):
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140 ConfigParser.__init__(self, *args, **kw)
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141 self.filename = filename
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142 if hasattr(self, '_interpolation'):
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143 self._interpolation = self.InterpolateWrapper(self._interpolation)
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144
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145 read_file = getattr(ConfigParser, 'read_file', ConfigParser.readfp)
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146
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147 def defaults(self):
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148 """Return the defaults, with their values interpolated (with the
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149 defaults dict itself)
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150
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151 Mainly to support defaults using values such as %(here)s
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152 """
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153 defaults = ConfigParser.defaults(self).copy()
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154 for key, val in iteritems(defaults):
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155 defaults[key] = self.get('DEFAULT', key) or val
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156 return defaults
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157
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158 def _interpolate(self, section, option, rawval, vars):
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159 # Python < 3.2
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160 try:
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161 return ConfigParser._interpolate(
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162 self, section, option, rawval, vars)
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163 except Exception:
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164 e = sys.exc_info()[1]
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165 args = list(e.args)
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166 args[0] = 'Error in file %s: %s' % (self.filename, e)
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167 e.args = tuple(args)
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168 e.message = args[0]
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169 raise
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170
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171 class InterpolateWrapper(object):
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172 # Python >= 3.2
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173 def __init__(self, original):
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174 self._original = original
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175
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176 def __getattr__(self, name):
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177 return getattr(self._original, name)
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178
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179 def before_get(self, parser, section, option, value, defaults):
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180 try:
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181 return self._original.before_get(parser, section, option,
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182 value, defaults)
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183 except Exception:
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184 e = sys.exc_info()[1]
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185 args = list(e.args)
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186 args[0] = 'Error in file %s: %s' % (parser.filename, e)
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187 e.args = tuple(args)
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188 e.message = args[0]
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189 raise
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190
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191
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192 def _running_from_source():
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193 paths = ['run.sh', 'lib/galaxy/__init__.py', 'scripts/common_startup.sh']
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194 return all(map(os.path.exists, paths))
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195
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196
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197 running_from_source = _running_from_source()
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198
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199
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200 def get_data_dir(properties):
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201 data_dir = properties.get('data_dir', None)
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202 if data_dir is None:
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203 if running_from_source:
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204 data_dir = './database'
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205 else:
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206 config_dir = properties.get('config_dir', os.path.dirname(properties['__file__']))
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207 data_dir = os.path.join(config_dir, 'data')
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208 return data_dir
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209
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210
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211 def __get_all_configs(dirs, names):
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212 return list(filter(os.path.exists, starmap(os.path.join, product(dirs, names))))
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213
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214
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215 def __find_config_files(names, exts=None, dirs=None, include_samples=False):
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216 sample_names = []
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217 if isinstance(names, string_types):
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218 names = [names]
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219 if not dirs:
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220 dirs = [os.getcwd()]
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221 if exts:
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222 # add exts to names, converts back into a list because it's going to be small and we might consume names twice
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223 names = list(starmap(joinext, product(names, exts)))
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224 if include_samples:
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225 sample_names = map(partial(joinext, ext='sample'), names)
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226 # check for all names in each dir before moving to the next dir. could do it the other way around but that makes
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227 # less sense to me.
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228 return __get_all_configs(dirs, names) or __get_all_configs(dirs, sample_names)
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229
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230
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231 def __default_properties(path):
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232 return {
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233 'here': os.path.dirname(os.path.abspath(path)),
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234 '__file__': os.path.abspath(path)
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235 }
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236
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237
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238 __all__ = ('find_config_file', 'get_data_dir', 'load_app_properties', 'NicerConfigParser', 'running_from_source')