Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/containers/__init__.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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1 """
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2 Interfaces to containerization software
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3 """
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4 from __future__ import absolute_import
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5
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6 import errno
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7 import inspect
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8 import logging
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9 import shlex
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10 import subprocess
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11 import sys
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12 import uuid
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13 from abc import (
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14 ABCMeta,
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15 abstractmethod,
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16 abstractproperty
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17 )
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18 from collections import namedtuple
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19
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20 import yaml
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21 from six import string_types, with_metaclass
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22 from six.moves import shlex_quote
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23
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24 from galaxy.exceptions import ContainerCLIError
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25 from galaxy.util.submodules import import_submodules
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26
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27
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28 DEFAULT_CONTAINER_TYPE = 'docker'
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29 DEFAULT_CONF = {'_default_': {'type': DEFAULT_CONTAINER_TYPE}}
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30
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31 log = logging.getLogger(__name__)
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32
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33
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34 class ContainerPort(namedtuple('ContainerPort', ('port', 'protocol', 'hostaddr', 'hostport'))):
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35 """Named tuple representing ports published by a container, with attributes:
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36
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37 :ivar port: Port number (inside the container)
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38 :vartype port: int
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39 :ivar protocol: Port protocol, either ``tcp`` or ``udp``
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40 :vartype protocol: str
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41 :ivar hostaddr: Address or hostname where the published port can be accessed
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42 :vartype hostaddr: str
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43 :ivar hostport: Published port number on which the container can be accessed
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44 :vartype hostport: int
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45 """
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46
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47
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48 class ContainerVolume(with_metaclass(ABCMeta, object)):
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49
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50 valid_modes = frozenset({"ro", "rw"})
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51
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52 def __init__(self, path, host_path=None, mode=None):
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53 self.path = path
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54 self.host_path = host_path
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55 self.mode = mode
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56 if mode and not self.mode_is_valid:
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57 raise ValueError("Invalid container volume mode: %s" % mode)
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58
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59 @abstractmethod
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60 def from_str(cls, as_str):
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61 """Classmethod to convert from this container type's string representation.
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62
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63 :param as_str: string representation of volume
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64 :type as_str: str
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65 """
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66
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67 @abstractmethod
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68 def __str__(self):
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69 """Return this container type's string representation of the volume.
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70 """
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71
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72 @abstractmethod
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73 def to_native(self):
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74 """Return this container type's native representation of the volume.
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75 """
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76
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77 @property
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78 def mode_is_valid(self):
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79 return self.mode in self.valid_modes
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80
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81
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82 class Container(with_metaclass(ABCMeta, object)):
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83
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84 def __init__(self, interface, id, name=None, **kwargs):
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85 """:param interface: Container interface for the given container type
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86 :type interface: :class:`ContainerInterface` subclass instance
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87 :param id: Container identifier
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88 :type id: str
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89 :param name: Container name
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90 :type name: str
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91 """
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92 self._interface = interface
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93 self._id = id
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94 self._name = name
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95
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96 @property
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97 def id(self):
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98 """The container's id"""
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99 return self._id
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100
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101 @property
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102 def name(self):
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103 """The container's name"""
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104 return self._name
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105
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106 @abstractmethod
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107 def from_id(cls, interface, id):
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108 """Classmethod to create an instance of Container from the container system's id for the given container type.
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109
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110 :param interface: Container insterface for the given id
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111 :type interface: :class:`ContainerInterface` subclass instance
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112 :param id: Container identifier
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113 :type id: str
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114 :returns: Container object
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115 :rtype: :class:`Container` subclass instance
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116 """
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117
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118 @abstractproperty
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119 def ports(self):
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120 """Attribute for accessing details of ports published by the container.
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121
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122 :returns: Port details
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123 :rtype: list of :class:`ContainerPort`s
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124 """
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125
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126 @abstractproperty
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127 def address(self):
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128 """Attribute for accessing the address or hostname where published ports can be accessed.
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129
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130 :returns: Hostname or IP address
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131 :rtype: str
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132 """
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133
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134 @abstractmethod
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135 def is_ready(self):
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136 """Indicate whether or not the container is "ready" (up, available, running).
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137
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138 :returns: True if ready, else False
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139 :rtpe: bool
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140 """
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141
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142 def map_port(self, port):
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143 """Map a given container port to a host address/port.
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144
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145 For legacy reasons, if port is ``None``, the first port (if any) will be returned
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146
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147 :param port: Container port to map
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148 :type port: int
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149 :returns: Mapping to host address/port for given container port
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150 :rtype: :class:`ContainerPort` instance
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151 """
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152 mapping = None
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153 ports = self.ports or []
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154 for mapping in ports:
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155 if port == mapping.port:
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156 return mapping
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157 if port is None:
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158 log.warning("Container %s (%s): Don't know how to map ports to containers with multiple exposed ports "
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159 "when a specific port is not requested. Arbitrarily choosing first: %s",
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160 self.name, self.id, mapping)
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161 return mapping
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162 else:
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163 if port is None:
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164 log.warning("Container %s (%s): No exposed ports found!", self.name, self.id)
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165 else:
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166 log.warning("Container %s (%s): No mapping found for port: %s", self.name, self.id, port)
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167 return None
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168
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169
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170 class ContainerInterface(with_metaclass(ABCMeta, object)):
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171
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172 container_type = None
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173 container_class = None
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174 volume_class = None
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175 conf_defaults = {
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176 'name_prefix': 'galaxy_',
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177 }
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178 option_map = {}
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179 publish_port_list_required = False
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180 supports_volumes = True
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181
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182 def __init__(self, conf, key, containers_config_file):
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183 self._key = key
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184 self._containers_config_file = containers_config_file
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185 mro = reversed(self.__class__.__mro__)
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186 next(mro)
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187 self._conf = ContainerInterfaceConfig()
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188 for c in mro:
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189 self._conf.update(c.conf_defaults)
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190 self._conf.update(conf)
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191 self.validate_config()
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192
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193 def _normalize_command(self, command):
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194 if isinstance(command, string_types):
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195 command = shlex.split(command)
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196 return command
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197
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198 def _guess_kwopt_type(self, val):
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199 opttype = 'string'
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200 if isinstance(val, bool):
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201 opttype = 'boolean'
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202 elif isinstance(val, list):
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203 opttype = 'list'
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204 try:
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205 if isinstance(val[0], tuple) and len(val[0]) == 3:
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206 opttype = 'list_of_kovtrips'
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207 except IndexError:
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208 pass
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209 elif isinstance(val, dict):
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210 opttype = 'list_of_kvpairs'
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211 return opttype
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212
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213 def _guess_kwopt_flag(self, opt):
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214 return '--%s' % opt.replace('_', '-')
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215
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216 def _stringify_kwopts(self, kwopts):
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217 opts = []
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218 for opt, val in kwopts.items():
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219 try:
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220 optdef = self.option_map[opt]
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221 except KeyError:
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222 optdef = {
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223 'flag': self._guess_kwopt_flag(opt),
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224 'type': self._guess_kwopt_type(val),
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225 }
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226 log.warning("option '%s' not in %s.option_map, guessing flag '%s' type '%s'",
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227 opt, self.__class__.__name__, optdef['flag'], optdef['type'])
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228 opts.append(getattr(self, '_stringify_kwopt_' + optdef['type'])(optdef['flag'], val))
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229 return ' '.join(opts)
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230
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231 def _stringify_kwopt_boolean(self, flag, val):
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232 """
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233 """
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234 return '{flag}={value}'.format(flag=flag, value=str(val).lower())
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235
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236 def _stringify_kwopt_string(self, flag, val):
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237 """
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238 """
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239 return '{flag} {value}'.format(flag=flag, value=shlex_quote(str(val)))
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240
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241 def _stringify_kwopt_list(self, flag, val):
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242 """
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243 """
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244 if isinstance(val, string_types):
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245 return self._stringify_kwopt_string(flag, val)
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246 return ' '.join('{flag} {value}'.format(flag=flag, value=shlex_quote(str(v))) for v in val)
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247
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248 def _stringify_kwopt_list_of_kvpairs(self, flag, val):
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249 """
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250 """
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251 l = []
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252 if isinstance(val, list):
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253 # ['foo=bar', 'baz=quux']
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254 l = val
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255 else:
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256 # {'foo': 'bar', 'baz': 'quux'}
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257 for k, v in dict(val).items():
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258 l.append('{k}={v}'.format(k=k, v=v))
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259 return self._stringify_kwopt_list(flag, l)
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260
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261 def _stringify_kwopt_list_of_kovtrips(self, flag, val):
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262 """
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263 """
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264 if isinstance(val, string_types):
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265 return self._stringify_kwopt_string(flag, val)
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266 l = []
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267 for k, o, v in val:
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268 l.append('{k}{o}{v}'.format(k=k, o=o, v=v))
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269 return self._stringify_kwopt_list(flag, l)
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270
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271 def _run_command(self, command, verbose=False):
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272 if verbose:
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273 log.debug('running command: [%s]', command)
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274 command_list = self._normalize_command(command)
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275 p = subprocess.Popen(command_list, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True)
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276 stdout, stderr = p.communicate()
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277 if p.returncode == 0:
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278 return stdout.strip()
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279 else:
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280 msg = "Command '{}' returned non-zero exit status {}".format(command, p.returncode)
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281 log.error(msg + ': ' + stderr.strip())
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282 raise ContainerCLIError(
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283 msg,
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284 stdout=stdout.strip(),
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285 stderr=stderr.strip(),
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286 returncode=p.returncode,
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287 command=command,
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288 subprocess_command=command_list)
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289
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290 @property
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291 def key(self):
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292 return self._key
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293
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294 @property
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295 def containers_config_file(self):
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296 return self._containers_config_file
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297
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298 def get_container(self, container_id):
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299 return self.container_class.from_id(self, container_id)
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300
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301 def set_kwopts_name(self, kwopts):
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302 if self._name_prefix is not None:
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303 name = '{prefix}{name}'.format(
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304 prefix=self._name_prefix,
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305 name=kwopts.get('name', uuid.uuid4().hex)
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306 )
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307 kwopts['name'] = name
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308
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309 def validate_config(self):
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310 """
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311 """
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312 self._name_prefix = self._conf.name_prefix
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313
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314 @abstractmethod
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315 def run_in_container(self, command, image=None, **kwopts):
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316 """
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317 """
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318
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319
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320 class ContainerInterfaceConfig(dict):
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321
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322 def __setattr__(self, name, value):
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323 self[name] = value
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324
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325 def __getattr__(self, name):
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326 try:
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327 return self[name]
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328 except KeyError:
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329 raise AttributeError("'%s' object has no attribute '%s'" % (self.__class__.__name__, name))
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330
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331 def get(self, name, default=None):
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332 try:
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333 return self[name]
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334 except KeyError:
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335 return default
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336
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337
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338 def build_container_interfaces(containers_config_file, containers_conf=None):
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339 """Build :class:`ContainerInterface`s. Pass ``containers_conf`` to avoid rereading the config file.
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340
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341 :param containers_config_file: Filename of containers_conf.yml
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342 :type containers_config_file: str
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343 :param containers_conf: Optional containers conf (as read from containers_conf.yml), will be used in place
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344 of containers_config_file
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345 :type containers_conf: dict
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346 :returns: Instantiated container interfaces with keys corresponding to ``containers`` keys
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347 :rtype: dict of :class:`ContainerInterface` subclass instances
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348 """
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349 if not containers_conf:
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350 containers_conf = parse_containers_config(containers_config_file)
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351 interface_classes = _get_interface_modules()
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352 interfaces = {}
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353 for k, conf in containers_conf.items():
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354 container_type = conf.get('type', DEFAULT_CONTAINER_TYPE)
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355 assert container_type in interface_classes, "unknown container interface type: %s" % container_type
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356 interfaces[k] = interface_classes[container_type](conf, k, containers_config_file)
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357 return interfaces
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358
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359
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360 def parse_containers_config(containers_config_file):
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361 """Parse a ``containers_conf.yml`` and return the contents of its ``containers`` dictionary.
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362
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363 :param containers_config_file: Filename of containers_conf.yml
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364 :type containers_config_file: str
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365 :returns: Contents of the dictionary under the ``containers`` key
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366 :rtype: dict
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367 """
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368 conf = DEFAULT_CONF.copy()
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369 try:
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370 with open(containers_config_file) as fh:
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371 c = yaml.safe_load(fh)
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372 conf.update(c.get('containers', {}))
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373 except (OSError, IOError) as exc:
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374 if exc.errno == errno.ENOENT:
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375 log.debug("config file '%s' does not exist, running with default config", containers_config_file)
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376 else:
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377 raise
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378 return conf
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379
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380
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381 def _get_interface_modules():
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382 interfaces = []
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383 modules = import_submodules(sys.modules[__name__])
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384 for module in modules:
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385 module_names = [getattr(module, _) for _ in dir(module)]
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386 classes = [_ for _ in module_names if inspect.isclass(_) and
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387 not _ == ContainerInterface and issubclass(_, ContainerInterface)]
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388 interfaces.extend(classes)
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389 return dict((x.container_type, x) for x in interfaces)