Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boto/pyami/config.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 # Copyright (c) 2006,2007 Mitch Garnaat http://garnaat.org/
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2 # Copyright (c) 2011 Chris Moyer http://coredumped.org/
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3 #
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4 # Permission is hereby granted, free of charge, to any person obtaining a
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5 # copy of this software and associated documentation files (the
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6 # "Software"), to deal in the Software without restriction, including
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7 # without limitation the rights to use, copy, modify, merge, publish, dis-
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8 # tribute, sublicense, and/or sell copies of the Software, and to permit
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9 # persons to whom the Software is furnished to do so, subject to the fol-
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10 # lowing conditions:
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11 #
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12 # The above copyright notice and this permission notice shall be included
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13 # in all copies or substantial portions of the Software.
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14 #
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15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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21 # IN THE SOFTWARE.
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22 #
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23 import os
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24 import re
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25 import warnings
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26
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27 import boto
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28
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29 from boto.compat import expanduser, ConfigParser, NoOptionError, NoSectionError, StringIO
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30
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31
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32 # By default we use two locations for the boto configurations,
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33 # /etc/boto.cfg and ~/.boto (which works on Windows and Unix).
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34 BotoConfigPath = '/etc/boto.cfg'
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35 BotoConfigLocations = [BotoConfigPath]
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36 UserConfigPath = os.path.join(expanduser('~'), '.boto')
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37 BotoConfigLocations.append(UserConfigPath)
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38
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39 # If there's a BOTO_CONFIG variable set, we load ONLY
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40 # that variable
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41 if 'BOTO_CONFIG' in os.environ:
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42 BotoConfigLocations = [expanduser(os.environ['BOTO_CONFIG'])]
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43
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44 # If there's a BOTO_PATH variable set, we use anything there
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45 # as the current configuration locations, split with os.pathsep.
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46 elif 'BOTO_PATH' in os.environ:
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47 BotoConfigLocations = []
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48 for path in os.environ['BOTO_PATH'].split(os.pathsep):
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49 BotoConfigLocations.append(expanduser(path))
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50
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51
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52 class Config(object):
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53
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54 def __init__(self, path=None, fp=None, do_load=True):
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55 self._parser = ConfigParser({'working_dir': '/mnt/pyami',
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56 'debug': '0'})
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57 if do_load:
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58 if path:
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59 self.load_from_path(path)
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60 elif fp:
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61 self.readfp(fp)
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62 else:
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63 self.read(BotoConfigLocations)
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64 if "AWS_CREDENTIAL_FILE" in os.environ:
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65 full_path = expanduser(os.environ['AWS_CREDENTIAL_FILE'])
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66 try:
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67 self.load_credential_file(full_path)
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68 except IOError:
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69 warnings.warn('Unable to load AWS_CREDENTIAL_FILE (%s)' % full_path)
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70
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71 def __setstate__(self, state):
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72 # There's test that verify that (transitively) a Config
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73 # object can be pickled. Now that we're storing a _parser
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74 # attribute and relying on __getattr__ to proxy requests,
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75 # we need to implement setstate to ensure we don't get
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76 # into recursive loops when looking up _parser when
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77 # this object is unpickled.
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78 self._parser = state['_parser']
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79
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80 def __getattr__(self, name):
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81 return getattr(self._parser, name)
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82
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83 def has_option(self, *args, **kwargs):
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84 return self._parser.has_option(*args, **kwargs)
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85
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86 def load_credential_file(self, path):
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87 """Load a credential file as is setup like the Java utilities"""
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88 c_data = StringIO()
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89 c_data.write("[Credentials]\n")
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90 for line in open(path, "r").readlines():
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91 c_data.write(line.replace("AWSAccessKeyId", "aws_access_key_id").replace("AWSSecretKey", "aws_secret_access_key"))
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92 c_data.seek(0)
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93 self.readfp(c_data)
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94
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95 def load_from_path(self, path):
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96 file = open(path)
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97 for line in file.readlines():
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98 match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
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99 if match:
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100 extended_file = match.group(1)
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101 (dir, file) = os.path.split(path)
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102 self.load_from_path(os.path.join(dir, extended_file))
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103 self.read(path)
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104
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105 def save_option(self, path, section, option, value):
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106 """
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107 Write the specified Section.Option to the config file specified by path.
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108 Replace any previous value. If the path doesn't exist, create it.
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109 Also add the option the the in-memory config.
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110 """
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111 config = ConfigParser()
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112 config.read(path)
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113 if not config.has_section(section):
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114 config.add_section(section)
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115 config.set(section, option, value)
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116 fp = open(path, 'w')
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117 config.write(fp)
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118 fp.close()
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119 if not self.has_section(section):
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120 self.add_section(section)
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121 self.set(section, option, value)
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122
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123 def save_user_option(self, section, option, value):
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124 self.save_option(UserConfigPath, section, option, value)
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125
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126 def save_system_option(self, section, option, value):
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127 self.save_option(BotoConfigPath, section, option, value)
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128
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129 def get_instance(self, name, default=None):
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130 try:
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131 val = self.get('Instance', name)
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132 except (NoOptionError, NoSectionError):
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133 val = default
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134 return val
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135
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136 def get_user(self, name, default=None):
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137 try:
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138 val = self.get('User', name)
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139 except (NoOptionError, NoSectionError):
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140 val = default
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141 return val
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142
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143 def getint_user(self, name, default=0):
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144 try:
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145 val = self.getint('User', name)
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146 except (NoOptionError, NoSectionError):
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147 val = default
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148 return val
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149
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150 def get_value(self, section, name, default=None):
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151 return self.get(section, name, default)
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152
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153 def get(self, section, name, default=None):
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154 try:
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155 return self._parser.get(section, name)
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156 except (NoOptionError, NoSectionError):
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157 return default
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158
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159 def getint(self, section, name, default=0):
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parents:
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160 try:
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161 return self._parser.getint(section, name)
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parents:
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162 except (NoOptionError, NoSectionError):
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parents:
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163 return int(default)
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164
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165 def getfloat(self, section, name, default=0.0):
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166 try:
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parents:
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167 return self._parser.getfloat(section, name)
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parents:
diff changeset
168 except (NoOptionError, NoSectionError):
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parents:
diff changeset
169 return float(default)
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170
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parents:
diff changeset
171 def getbool(self, section, name, default=False):
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parents:
diff changeset
172 if self.has_option(section, name):
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173 val = self.get(section, name)
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parents:
diff changeset
174 if val.lower() == 'true':
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175 val = True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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176 else:
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177 val = False
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178 else:
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179 val = default
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180 return val
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181
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182 def setbool(self, section, name, value):
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parents:
diff changeset
183 if value:
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184 self.set(section, name, 'true')
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diff changeset
185 else:
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diff changeset
186 self.set(section, name, 'false')
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187
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parents:
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188 def dump(self):
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parents:
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189 s = StringIO()
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parents:
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190 self.write(s)
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parents:
diff changeset
191 print(s.getvalue())
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192
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parents:
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193 def dump_safe(self, fp=None):
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parents:
diff changeset
194 if not fp:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
195 fp = StringIO()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
196 for section in self.sections():
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parents:
diff changeset
197 fp.write('[%s]\n' % section)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
198 for option in self.options(section):
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parents:
diff changeset
199 if option == 'aws_secret_access_key':
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parents:
diff changeset
200 fp.write('%s = xxxxxxxxxxxxxxxxxx\n' % option)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
201 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
202 fp.write('%s = %s\n' % (option, self.get(section, option)))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
203
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parents:
diff changeset
204 def dump_to_sdb(self, domain_name, item_name):
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parents:
diff changeset
205 from boto.compat import json
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parents:
diff changeset
206 sdb = boto.connect_sdb()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
207 domain = sdb.lookup(domain_name)
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parents:
diff changeset
208 if not domain:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
209 domain = sdb.create_domain(domain_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
210 item = domain.new_item(item_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
211 item.active = False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
212 for section in self.sections():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
213 d = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
214 for option in self.options(section):
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parents:
diff changeset
215 d[option] = self.get(section, option)
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parents:
diff changeset
216 item[section] = json.dumps(d)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
217 item.save()
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parents:
diff changeset
218
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parents:
diff changeset
219 def load_from_sdb(self, domain_name, item_name):
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parents:
diff changeset
220 from boto.compat import json
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parents:
diff changeset
221 sdb = boto.connect_sdb()
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parents:
diff changeset
222 domain = sdb.lookup(domain_name)
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parents:
diff changeset
223 item = domain.get_item(item_name)
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shellac
parents:
diff changeset
224 for section in item.keys():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
225 if not self.has_section(section):
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parents:
diff changeset
226 self.add_section(section)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
227 d = json.loads(item[section])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
228 for attr_name in d.keys():
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parents:
diff changeset
229 attr_value = d[attr_name]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
230 if attr_value is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
231 attr_value = 'None'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
232 if isinstance(attr_value, bool):
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parents:
diff changeset
233 self.setbool(section, attr_name, attr_value)
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shellac
parents:
diff changeset
234 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
235 self.set(section, attr_name, attr_value)