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annotate planemo/lib/python3.7/site-packages/galaxy/containers/docker.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 Interface to Docker
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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 logging
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7 import os
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8 from functools import partial
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9 from itertools import cycle, repeat
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10 from time import sleep
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11
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12 try:
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13 import docker
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14 except ImportError:
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15 docker = None
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16
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17 try:
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18 from requests.exceptions import ConnectionError, ReadTimeout
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19 except ImportError:
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20 ConnectionError = None
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21 ReadTimeout = None
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22 from six import string_types
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23 from six.moves import shlex_quote
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24
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25 from galaxy.containers import ContainerInterface
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26 from galaxy.containers.docker_decorators import (
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27 docker_columns,
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28 docker_json
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29 )
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30 from galaxy.containers.docker_model import (
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31 DockerContainer,
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32 DockerVolume
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33 )
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34 from galaxy.exceptions import (
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35 ContainerCLIError,
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36 ContainerImageNotFound,
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37 ContainerNotFound
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38 )
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39 from galaxy.util.json import safe_dumps_formatted
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40
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41 log = logging.getLogger(__name__)
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42
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43
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44 class DockerInterface(ContainerInterface):
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45
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46 container_class = DockerContainer
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47 volume_class = DockerVolume
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48 conf_defaults = {
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49 'host': None,
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50 'tls': False,
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51 'force_tlsverify': False,
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52 'auto_remove': True,
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53 'image': None,
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54 'cpus': None,
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55 'memory': None,
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56 }
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57 # These values are inserted into kwopts for run commands
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58 conf_run_kwopts = (
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59 'cpus',
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60 'memory',
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61 )
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62
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63 def validate_config(self):
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64 super(DockerInterface, self).validate_config()
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65 self.__host_iter = None
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66 if self._conf.host is None or isinstance(self._conf.host, string_types):
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67 self.__host_iter = repeat(self._conf.host)
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68 else:
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69 self.__host_iter = cycle(self._conf.host)
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70
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71 @property
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72 def _default_image(self):
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73 assert self._conf.image is not None, "No default image for this docker interface"
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74 return self._conf.image
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75
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76 def run_in_container(self, command, image=None, **kwopts):
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77 for opt in self.conf_run_kwopts:
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78 if self._conf[opt]:
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79 kwopts[opt] = self._conf[opt]
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80 self.set_kwopts_name(kwopts)
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81 return self.run(command, image=image, **kwopts)
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82
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83 def image_repodigest(self, image):
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84 """Get the digest image string for an image.
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85
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86 :type image: str
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87 :param image: image id or image name and optionally, tag
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88
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89 :returns: digest string, having the format `<name>@<hash_alg>:<digest>`, e.g.:
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90 `'bgruening/docker-jupyter-notebook@sha256:3ec0bc9abc9d511aa602ee4fff2534d80dd9b1564482de52cb5de36cce6debae'`
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91 or, the original image name if the digest cannot be
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92 determined (the image has not been pulled)
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93 """
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94 try:
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95 inspect = self.image_inspect(image)
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96 return inspect['RepoDigests'][0]
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97 except ContainerImageNotFound:
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98 return image
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99
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100 @property
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101 def host(self):
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102 return next(self.__host_iter)
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103
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104 @property
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105 def host_iter(self):
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106 return self.__host_iter
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107
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108
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109 class DockerCLIInterface(DockerInterface):
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110
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111 container_type = 'docker_cli'
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112 conf_defaults = {
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113 'command_template': '{executable} {global_kwopts} {subcommand} {args}',
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114 'executable': 'docker',
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115 }
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116 option_map = {
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117 # `run` options
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118 'environment': {'flag': '--env', 'type': 'list_of_kvpairs'},
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119 'volumes': {'flag': '--volume', 'type': 'docker_volumes'},
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120 'name': {'flag': '--name', 'type': 'string'},
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121 'detach': {'flag': '--detach', 'type': 'boolean'},
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122 'publish_all_ports': {'flag': '--publish-all', 'type': 'boolean'},
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123 'publish_port_random': {'flag': '--publish', 'type': 'string'},
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124 'auto_remove': {'flag': '--rm', 'type': 'boolean'},
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125 'cpus': {'flag': '--cpus', 'type': 'string'},
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126 'memory': {'flag': '--memory', 'type': 'string'},
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127 }
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128
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129 def validate_config(self):
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130 log.warning('The `docker_cli` interface is deprecated and will be removed in Galaxy 18.09, please use `docker`')
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131 super(DockerCLIInterface, self).validate_config()
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132 global_kwopts = []
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133 if self._conf.host:
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134 global_kwopts.append('--host')
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135 global_kwopts.append(shlex_quote(self._conf.host))
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136 if self._conf.force_tlsverify:
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137 global_kwopts.append('--tlsverify')
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138 self._docker_command = self._conf['command_template'].format(
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139 executable=self._conf['executable'],
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140 global_kwopts=' '.join(global_kwopts),
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141 subcommand='{subcommand}',
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142 args='{args}'
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143 )
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144
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145 def _filter_by_id_or_name(self, id, name):
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146 if id:
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147 return '--filter id={}'.format(id)
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148 elif name:
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149 return '--filter name={}'.format(name)
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150 return None
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151
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152 def _stringify_kwopt_docker_volumes(self, flag, val):
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153 """The docker API will take a volumes argument in many formats, try to
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154 deal with that for the command line
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155 """
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156 l = []
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157 if isinstance(val, list):
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158 # ['/host/vol']
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159 l = val
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160 else:
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161 for hostvol, guestopts in val.items():
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162 if isinstance(guestopts, string_types):
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163 # {'/host/vol': '/container/vol'}
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164 l.append('{}:{}'.format(hostvol, guestopts))
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165 else:
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166 # {'/host/vol': {'bind': '/container/vol'}}
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167 # {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}}
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168 mode = guestopts.get('mode', '')
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169 l.append('{vol}:{bind}{mode}'.format(
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170 vol=hostvol,
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171 bind=guestopts['bind'],
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172 mode=':' + mode if mode else ''
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173 ))
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174 return self._stringify_kwopt_list(flag, l)
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175
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176 def _run_docker(self, subcommand, args=None, verbose=False):
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177 command = self._docker_command.format(subcommand=subcommand, args=args or '')
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178 return self._run_command(command, verbose=verbose)
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179
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180 #
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181 # docker subcommands
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182 #
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183
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184 @docker_columns
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185 def ps(self, id=None, name=None):
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186 return self._run_docker(subcommand='ps', args=self._filter_by_id_or_name(id, name))
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187
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188 def run(self, command, image=None, **kwopts):
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189 args = '{kwopts} {image} {command}'.format(
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190 kwopts=self._stringify_kwopts(kwopts),
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191 image=image or self._default_image,
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192 command=command if command else ''
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193 ).strip()
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194 container_id = self._run_docker(subcommand='run', args=args, verbose=True)
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195 return DockerContainer.from_id(self, container_id)
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196
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197 @docker_json
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198 def inspect(self, container_id):
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199 try:
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200 return self._run_docker(subcommand='inspect', args=container_id)[0]
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201 except (IndexError, ContainerCLIError) as exc:
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202 msg = "Invalid container id: %s" % container_id
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203 if exc.stdout == '[]' and exc.stderr == 'Error: no such object: {container_id}'.format(container_id=container_id):
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204 log.warning(msg)
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205 return []
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206 else:
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207 raise ContainerNotFound(msg, container_id=container_id)
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208
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209 @docker_json
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210 def image_inspect(self, image):
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211 try:
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212 return self._run_docker(subcommand='image inspect', args=image)[0]
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213 except (IndexError, ContainerCLIError) as exc:
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214 msg = "%s not pulled, cannot get digest" % image
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215 if exc.stdout == '[]' and exc.stderr == 'Error: no such image: {image}'.format(image=image):
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216 log.warning(msg, image)
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217 return []
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218 else:
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219 raise ContainerImageNotFound(msg, image=image)
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220
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221
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222 class DockerAPIClient(object):
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223 """Wraps a ``docker.APIClient`` to catch exceptions.
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224 """
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225
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226 _exception_retry_time = 5
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227 _default_max_tries = 10
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228 _host_iter = None
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229 _client = None
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230 _client_args = ()
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231 _client_kwargs = {}
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232
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233 @staticmethod
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234 def _qualname(f):
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235 if isinstance(f, partial):
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236 f = f.func
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237 try:
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238 return getattr(f, '__qualname__', f.im_class.__name__ + '.' + f.__name__)
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239 except AttributeError:
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240 return f.__name__
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241
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242 @staticmethod
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243 def _should_retry_request(response_code):
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244 return response_code >= 500 or response_code in (404, 408, 409, 429)
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245
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246 @staticmethod
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247 def _nonfatal_error(response_code):
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248 return response_code in (404,)
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249
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250 @staticmethod
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251 def _unwrapped_attr(attr):
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252 return getattr(DockerAPIClient._client, attr)
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253
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254 @staticmethod
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255 def _init_client():
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256 kwargs = DockerAPIClient._client_kwargs.copy()
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257 if DockerAPIClient._host_iter is not None and 'base_url' not in kwargs:
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258 kwargs['base_url'] = next(DockerAPIClient._host_iter)
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259 DockerAPIClient._client = docker.APIClient(*DockerAPIClient._client_args, **kwargs)
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260 log.info('Initialized Docker API client for server: %s', kwargs.get('base_url', 'localhost'))
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261
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262 @staticmethod
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263 def _default_client_handler(fname, *args, **kwargs):
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264 success_test = kwargs.pop('success_test', None)
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265 max_tries = kwargs.pop('max_tries', DockerAPIClient._default_max_tries)
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266 for tries in range(1, max_tries + 1):
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267 retry_time = DockerAPIClient._exception_retry_time
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268 reinit = False
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269 exc = None
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270 # re-get the APIClient method every time as a different caller (such as the success test function) may have
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271 # already reinitialized the client, and we always want to use the current client
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272 f = DockerAPIClient._unwrapped_attr(fname)
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273 qualname = DockerAPIClient._qualname(f)
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274 try:
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275 r = f(*args, **kwargs)
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276 if tries > 1:
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277 log.info('%s() succeeded on attempt %s', qualname, tries)
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278 return r
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279 except ConnectionError:
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280 reinit = True
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281 except docker.errors.APIError as exc:
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282 if not DockerAPIClient._should_retry_request(exc.response.status_code):
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283 raise
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284 except ReadTimeout:
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285 reinit = True
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286 retry_time = 0
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287 finally:
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288 # this is inside the finally context so we can do a bare raise when we give up (so the real stack for
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289 # the exception is raised)
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290 if exc is not None:
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291 log.warning("Caught exception on %s(): %s: %s",
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292 DockerAPIClient._qualname(f), exc.__class__.__name__, exc)
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293 if reinit:
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294 log.warning("Reinitializing Docker API client due to connection-oriented failure")
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295 DockerAPIClient._init_client()
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296 f = DockerAPIClient._unwrapped_attr(fname)
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297 qualname = DockerAPIClient._qualname(f)
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298 r = None
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299 if success_test is not None:
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300 log.info("Testing if %s() succeeded despite the exception", qualname)
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301 r = success_test()
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302 if r:
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303 log.warning("The request appears to have succeeded, will not retry. Response is: %s", str(r))
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304 return r
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305 elif tries >= max_tries:
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306 log.error("Maximum number of attempts (%s) exceeded", max_tries)
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307 if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
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308 return None
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309 else:
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310 raise
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311 else:
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312 log.error("Retrying %s() in %s seconds (attempt: %s of %s)", qualname, retry_time, tries,
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313 max_tries)
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314 sleep(retry_time)
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315
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316 def __init__(self, *args, **kwargs):
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317 # Only initialize the host iterator once
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318 host_iter = kwargs.pop('host_iter', None)
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319 DockerAPIClient._host_iter = DockerAPIClient._host_iter or host_iter
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320 DockerAPIClient._client_args = args
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321 DockerAPIClient._client_kwargs = kwargs
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322 DockerAPIClient._init_client()
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323
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324 def __getattr__(self, attr):
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325 """Allow the calling of methods on this class as if it were a docker.APIClient instance.
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326 """
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327 cattr = DockerAPIClient._unwrapped_attr(attr)
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328 if callable(cattr):
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329 return partial(DockerAPIClient._default_client_handler, attr)
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330 else:
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331 return cattr
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332
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333
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334 class DockerAPIInterface(DockerInterface):
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335
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336 container_type = 'docker'
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337
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338 # 'publish_port_random' and 'volumes' are special cases handled in _create_host_config()
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339 host_config_option_map = {
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340 'auto_remove': {},
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341 'publish_all_ports': {},
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342 'cpus': {'param': 'nano_cpus', 'map': lambda x: int(x * 1000000000)},
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343 'memory': {'param': 'mem_limit'},
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344 'binds': {},
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345 'port_bindings': {},
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346 }
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347
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348 def validate_config(self):
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349 assert docker is not None, "Docker module could not be imported, DockerAPIInterface unavailable"
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350 super(DockerAPIInterface, self).validate_config()
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351 self.__client = None
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352
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353 @property
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354 def _client(self):
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355 # TODO: add cert options to containers conf
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356 cert_path = os.environ.get('DOCKER_CERT_PATH') or None
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357 if not cert_path:
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358 cert_path = os.path.join(os.path.expanduser('~'), '.docker')
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359 if self._conf.force_tlsverify or self._conf.tls:
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360 tls_config = docker.tls.TLSConfig(
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361 client_cert=(os.path.join(cert_path, 'cert.pem'),
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362 os.path.join(cert_path, 'key.pem')),
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363 ca_cert=os.path.join(cert_path, 'ca.pem'),
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364 verify=self._conf.force_tlsverify,
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365 )
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366 else:
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367 tls_config = False
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368 if not self.__client:
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369 self.__client = DockerAPIClient(
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370 host_iter=self.host_iter,
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371 tls=tls_config,
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372 )
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373 return self.__client
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374
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375 @staticmethod
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376 def _first(f, *args, **kwargs):
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377 try:
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378 return f(*args, **kwargs)[0]
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379 except IndexError:
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380 return None
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381
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382 @staticmethod
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383 def _filter_by_id_or_name(id, name):
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384 if id:
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385 return {'id': id}
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386 elif name:
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387 return {'name': name}
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388 return None
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389
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390 @staticmethod
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391 def _kwopt_to_param_names(map_spec, key):
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392 """For a given containers lib method parameter name, return the matching docker-py parameter name(s).
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393
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394 See :meth:`_create_docker_api_spec`.
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395 """
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396 params = []
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397 if 'param' not in map_spec and 'params' not in map_spec:
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398 params.append(key)
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399 elif 'param' in map_spec:
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400 params.append(map_spec['param'])
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401 params.extend(map_spec.get('params', ()))
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402 return params
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403
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404 @staticmethod
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405 def _kwopt_to_params(map_spec, key, value):
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406 """For a given containers lib method parameter name and value, return the matching docker-py parameters with
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407 values set (including transformation with an optional map function).
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408
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409 See :meth:`_create_docker_api_spec`.
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410 """
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411 params = {}
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412 if 'map' in map_spec:
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413 value = map_spec['map'](value)
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414 for param in DockerAPIInterface._kwopt_to_param_names(map_spec, key):
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415 params[param] = value
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416 return params
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417
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418 def _create_docker_api_spec(self, option_map_name, spec_class, kwopts):
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419 """Create docker-py objects used as arguments to docker-py methods.
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420
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421 This method modifies ``kwopts`` by removing options that match the spec.
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422
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423 An option map is a class-level variable with name ``<map_name>_option_map`` and is a dict with format:
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424
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425 .. code-block:: python
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426
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427 sample_option_map = {
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428 'containers_lib_option_name': {
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429 'param': docker_lib_positional_argument_int or 'docker_lib_keyword_argument_name',
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430 'params': like 'param' but an iterable containing multiple docker lib params to set,
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431 'default': default value,
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432 'map': function with with to transform the value,
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433 'required': True if this param is required, else False (default),
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434 },
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435 '_spec_param': {
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436 'spec_class': class of param value,
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437 }
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438 }
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439
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440 All members of the mapping value are optional.
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441
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442 For example, a spec map for (some of) the possible values of the :class:`docker.types.TaskTemplate`, which is
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443 used as the ``task_template`` argument to :meth:`docker.APIClient.create_service`, and the possible values of
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444 the :class`:docker.types.ContainerSpec`, which is used as the ``container_spec`` argument to the
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445 ``TaskTemplate`` would be:
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446
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447 .. code-block:: python
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448
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449 task_template_option_map = {
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450 # TaskTemplate's 'container_spec' param is a ContainerSpec
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451 '_container_spec': {
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452 'spec_class': docker.types.ContainerSpec,
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453 'required': True
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454 }
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455 }
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456 container_spec_option_map = {
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457 'image': {'param': 0}, # positional argument 0 to ContainerSpec()
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458 'command': {}, # 'command' keyword argument to ContainerSpec()
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459 'environment': { # 'env' keyword argument to ContainerSpec(), 'environment' keyword argument
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460 'param': 'env' # to ContainerInterface.run_in_container()
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461 },
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462 }
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463
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464 Thus, calling ``DockerInterface.run_in_contaner('true', image='busybox', environment={'FOO': 'foo'}`` will
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465 essentially do this (for example, if using Docker Swarm mode):
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466
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467 .. code-block:: python
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468
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469 container_spec = docker.types.ContainerSpec('busybox', command='true', env={'FOO': 'foo'})
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470 task_template = docker.types.TaskTemplate(container_spec=container_spec)
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471 docker.APIClient().create_service(task_template)
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472
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473 :param option_map_name: Name of option map class variable (``_option_map`` is automatically appended)
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474 :type option_map_name: str
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475 :param spec_class: docker-py specification class or callable returning an instance
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476 :type spec_class: :class:`docker.types.Resources`, :class:`docker.types.ContainerSpec`, etc. or
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477 callable
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478 :param kwopts: Keyword options passed to calling method (e.g.
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479 :meth:`DockerInterface.run_in_container`)
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480 :type kwopts: dict
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481 :returns: Instantiated ``spec_class`` object
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482 :rtype: ``type(spec_class)``
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483 """
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484 def _kwopt_to_arg(map_spec, key, value, param=None):
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485 # determines whether the given param is a positional or keyword argument in docker-py and adds it to the
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486 # list of arguments
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487 if isinstance(map_spec.get('param'), int):
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488 spec_opts.append((map_spec.get('param'), value))
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489 elif param is not None:
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490 spec_kwopts[param] = value
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491 else:
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492 spec_kwopts.update(DockerAPIInterface._kwopt_to_params(map_spec, key, value))
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493 # positional arguments
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494 spec_opts = []
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495 # keyword arguments
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496 spec_kwopts = {}
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497 # retrieve the option map for the docker-py object we're creating
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498 option_map = getattr(self, option_map_name + '_option_map')
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499 # set defaults
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500 for key in filter(lambda k: option_map[k].get('default'), option_map.keys()):
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501 map_spec = option_map[key]
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502 _kwopt_to_arg(map_spec, key, map_spec['default'])
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503 # don't allow kwopts that start with _, those are reserved for "child" object params
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504 for kwopt in filter(lambda k: not k.startswith('_') and k in option_map, list(kwopts.keys())):
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505 map_spec = option_map[kwopt]
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506 _v = kwopts.pop(kwopt)
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507 _kwopt_to_arg(map_spec, kwopt, _v)
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508 # find any child objects that need to be created and recurse to create them
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509 for _sub_k in filter(lambda k: k.startswith('_') and 'spec_class' in option_map[k], option_map.keys()):
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510 map_spec = option_map[_sub_k]
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511 param = _sub_k.lstrip('_')
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512 _sub_v = self._create_docker_api_spec(param, map_spec['spec_class'], kwopts)
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513 if _sub_v is not None or map_spec.get('required') or isinstance(map_spec.get('param'), int):
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514 _kwopt_to_arg(map_spec, None, _sub_v, param=param)
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515 # sort positional args and make into a flat tuple
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516 if spec_opts:
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517 spec_opts = sorted(spec_opts, key=lambda x: x[0])
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518 spec_opts = [i[1] for i in spec_opts]
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519 # create spec object
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520 if spec_opts or spec_kwopts:
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521 return spec_class(*spec_opts, **spec_kwopts)
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522 else:
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523 return None
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524
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525 def _volumes_to_native(self, volumes):
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526 """Convert a list of volume definitions to the docker-py container creation method parameters.
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527
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528 :param volumes: List of volumes to translate
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529 :type volumes: list of :class:`galaxy.containers.docker_model.DockerVolume`s
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530 """
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531 paths = []
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532 binds = {}
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533 for v in volumes:
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534 path, bind = v.to_native()
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535 paths.append(path)
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536 binds.update(bind)
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537 return (paths, binds)
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538
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539 def _create_host_config(self, kwopts):
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540 """Build the host configuration parameter for docker-py container creation.
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541
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542 This method modifies ``kwopts`` by removing host config options and potentially setting the ``ports`` and
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543 ``volumes`` keys.
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544
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545 :param kwopts: Keyword options passed to calling method (e.g. :method:`DockerInterface.run()`)
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546 :type kwopts: dict
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547 :returns: The return value of `docker.APIClient.create_host_config()`
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548 :rtype: dict
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549 """
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550 if 'publish_port_random' in kwopts:
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551 port = int(kwopts.pop('publish_port_random'))
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552 kwopts['port_bindings'] = {port: None}
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553 kwopts['ports'] = [port]
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554 if 'volumes' in kwopts:
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555 paths, binds = self._volumes_to_native(kwopts.pop('volumes'))
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556 kwopts['binds'] = binds
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557 kwopts['volumes'] = paths
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558 return self._create_docker_api_spec('host_config', self._client.create_host_config, kwopts)
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559
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560 #
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561 # docker subcommands
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562 #
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563
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564 def ps(self, id=None, name=None, running=True):
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565 return self._client.containers(all=not running, filters=self._filter_by_id_or_name(id, name))
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566
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567 def run(self, command, image=None, **kwopts):
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568 image = image or self._default_image
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569 command = command or None
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570 log.debug("Creating docker container with image '%s' for command: %s", image, command)
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571 host_config = self._create_host_config(kwopts)
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572 log.debug("Docker container host configuration:\n%s", safe_dumps_formatted(host_config))
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573 log.debug("Docker container creation parameters:\n%s", safe_dumps_formatted(kwopts))
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574 success_test = partial(self._first, self.ps, name=kwopts['name'], running=False)
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575 # this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class
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576 container = self._client.create_container(
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577 image,
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578 command=command if command else None,
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579 host_config=host_config,
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580 success_test=success_test,
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581 max_tries=5,
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582 **kwopts
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583 )
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584 container_id = container.get('Id')
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585 log.debug("Starting container: %s (%s)", kwopts['name'], str(container_id))
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586 # start can safely be run more than once
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587 self._client.start(container=container_id)
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588 return DockerContainer.from_id(self, container_id)
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589
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590 def inspect(self, container_id):
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591 try:
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592 return self._client.inspect_container(container_id)
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593 except docker.errors.NotFound:
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594 raise ContainerNotFound("Invalid container id: %s" % container_id, container_id=container_id)
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595
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596 def image_inspect(self, image):
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597 try:
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598 return self._client.inspect_image(image)
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599 except docker.errors.NotFound:
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600 raise ContainerImageNotFound("%s not pulled, cannot get digest" % image, image=image)