Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/containers/docker.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 Interface to Docker |
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3 """ |
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4 |
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5 import logging |
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6 import os |
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7 import shlex |
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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 from typing import Any, Dict, Optional, Type |
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12 |
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13 try: |
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14 import docker |
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15 except ImportError: |
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16 docker = None # type: ignore |
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17 |
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18 try: |
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19 from requests.exceptions import ConnectionError, ReadTimeout |
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20 except ImportError: |
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21 ConnectionError = None # type: ignore |
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22 ReadTimeout = None # type: ignore |
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23 |
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24 from galaxy.containers import Container, ContainerInterface |
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25 from galaxy.containers.docker_decorators import ( |
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26 docker_columns, |
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27 docker_json |
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28 ) |
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29 from galaxy.containers.docker_model import ( |
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30 DockerContainer, |
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31 DockerVolume |
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32 ) |
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33 from galaxy.exceptions import ( |
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34 ContainerCLIError, |
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35 ContainerImageNotFound, |
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36 ContainerNotFound |
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37 ) |
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38 from galaxy.util.json import safe_dumps_formatted |
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39 |
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40 log = logging.getLogger(__name__) |
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41 |
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42 |
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43 class DockerInterface(ContainerInterface): |
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44 |
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45 container_class: Type[Container] = DockerContainer |
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46 volume_class = DockerVolume |
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47 conf_defaults: Dict[str, Optional[Any]] = { |
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48 'host': None, |
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49 'tls': False, |
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50 'force_tlsverify': False, |
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51 'auto_remove': True, |
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52 'image': None, |
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53 'cpus': None, |
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54 'memory': None, |
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55 } |
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56 # These values are inserted into kwopts for run commands |
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57 conf_run_kwopts = ( |
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58 'cpus', |
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59 'memory', |
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60 ) |
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61 |
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62 def validate_config(self): |
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63 super().validate_config() |
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64 self.__host_iter = None |
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65 if self._conf.host is None or isinstance(self._conf.host, str): |
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66 self.__host_iter = repeat(self._conf.host) |
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67 else: |
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68 self.__host_iter = cycle(self._conf.host) |
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69 |
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70 @property |
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71 def _default_image(self): |
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72 assert self._conf.image is not None, "No default image for this docker interface" |
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73 return self._conf.image |
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74 |
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75 def run_in_container(self, command, image=None, **kwopts): |
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76 for opt in self.conf_run_kwopts: |
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77 if self._conf[opt]: |
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78 kwopts[opt] = self._conf[opt] |
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79 self.set_kwopts_name(kwopts) |
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80 return self.run(command, image=image, **kwopts) |
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81 |
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82 def image_repodigest(self, image): |
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83 """Get the digest image string for an image. |
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84 |
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85 :type image: str |
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86 :param image: image id or image name and optionally, tag |
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87 |
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88 :returns: digest string, having the format `<name>@<hash_alg>:<digest>`, e.g.: |
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89 `'bgruening/docker-jupyter-notebook@sha256:3ec0bc9abc9d511aa602ee4fff2534d80dd9b1564482de52cb5de36cce6debae'` |
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90 or, the original image name if the digest cannot be |
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91 determined (the image has not been pulled) |
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92 """ |
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93 try: |
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94 inspect = self.image_inspect(image) |
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95 return inspect['RepoDigests'][0] |
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96 except ContainerImageNotFound: |
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97 return image |
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98 |
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99 @property |
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100 def host(self): |
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101 return next(self.__host_iter) |
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102 |
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103 @property |
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104 def host_iter(self): |
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105 return self.__host_iter |
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106 |
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107 |
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108 class DockerCLIInterface(DockerInterface): |
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109 |
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110 container_type = 'docker_cli' |
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111 conf_defaults: Dict[str, Optional[Any]] = { |
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112 'command_template': '{executable} {global_kwopts} {subcommand} {args}', |
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113 'executable': 'docker', |
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114 } |
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115 option_map = { |
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116 # `run` options |
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117 'environment': {'flag': '--env', 'type': 'list_of_kvpairs'}, |
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118 'volumes': {'flag': '--volume', 'type': 'docker_volumes'}, |
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119 'name': {'flag': '--name', 'type': 'string'}, |
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120 'detach': {'flag': '--detach', 'type': 'boolean'}, |
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121 'publish_all_ports': {'flag': '--publish-all', 'type': 'boolean'}, |
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122 'publish_port_random': {'flag': '--publish', 'type': 'string'}, |
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123 'auto_remove': {'flag': '--rm', 'type': 'boolean'}, |
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124 'cpus': {'flag': '--cpus', 'type': 'string'}, |
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125 'memory': {'flag': '--memory', 'type': 'string'}, |
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126 } |
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127 |
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128 def validate_config(self): |
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129 log.warning('The `docker_cli` interface is deprecated and will be removed in Galaxy 18.09, please use `docker`') |
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130 super().validate_config() |
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131 global_kwopts = [] |
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132 if self._conf.host: |
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133 global_kwopts.append('--host') |
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134 global_kwopts.append(shlex.quote(self._conf.host)) |
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135 if self._conf.force_tlsverify: |
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136 global_kwopts.append('--tlsverify') |
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137 self._docker_command = self._conf['command_template'].format( |
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138 executable=self._conf['executable'], |
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139 global_kwopts=' '.join(global_kwopts), |
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140 subcommand='{subcommand}', |
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141 args='{args}' |
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142 ) |
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143 |
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144 def _filter_by_id_or_name(self, id, name): |
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145 if id: |
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146 return f'--filter id={id}' |
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147 elif name: |
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148 return f'--filter name={name}' |
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149 return None |
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150 |
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151 def _stringify_kwopt_docker_volumes(self, flag, val): |
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152 """The docker API will take a volumes argument in many formats, try to |
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153 deal with that for the command line |
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154 """ |
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155 l = [] |
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156 if isinstance(val, list): |
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157 # ['/host/vol'] |
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158 l = val |
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159 else: |
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160 for hostvol, guestopts in val.items(): |
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161 if isinstance(guestopts, str): |
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162 # {'/host/vol': '/container/vol'} |
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163 l.append(f'{hostvol}:{guestopts}') |
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164 else: |
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165 # {'/host/vol': {'bind': '/container/vol'}} |
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166 # {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}} |
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167 mode = guestopts.get('mode', '') |
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168 l.append('{vol}:{bind}{mode}'.format( |
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169 vol=hostvol, |
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170 bind=guestopts['bind'], |
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171 mode=':' + mode if mode else '' |
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172 )) |
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173 return self._stringify_kwopt_list(flag, l) |
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174 |
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175 def _run_docker(self, subcommand, args=None, verbose=False): |
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176 command = self._docker_command.format(subcommand=subcommand, args=args or '') |
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177 return self._run_command(command, verbose=verbose) |
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178 |
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179 # |
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180 # docker subcommands |
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181 # |
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182 |
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183 @docker_columns |
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184 def ps(self, id=None, name=None): |
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185 return self._run_docker(subcommand='ps', args=self._filter_by_id_or_name(id, name)) |
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186 |
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187 def run(self, command, image=None, **kwopts): |
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188 args = '{kwopts} {image} {command}'.format( |
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189 kwopts=self._stringify_kwopts(kwopts), |
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190 image=image or self._default_image, |
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191 command=command if command else '' |
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192 ).strip() |
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193 container_id = self._run_docker(subcommand='run', args=args, verbose=True) |
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194 return DockerContainer.from_id(self, container_id) |
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195 |
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196 @docker_json |
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197 def inspect(self, container_id): |
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198 try: |
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199 return self._run_docker(subcommand='inspect', args=container_id)[0] |
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200 except (IndexError, ContainerCLIError) as exc: |
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201 msg = "Invalid container id: %s" % container_id |
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202 if exc.stdout == '[]' and exc.stderr == f'Error: no such object: {container_id}': |
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203 log.warning(msg) |
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204 return [] |
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205 else: |
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206 raise ContainerNotFound(msg, container_id=container_id) |
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207 |
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208 @docker_json |
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209 def image_inspect(self, image): |
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210 try: |
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211 return self._run_docker(subcommand='image inspect', args=image)[0] |
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212 except (IndexError, ContainerCLIError) as exc: |
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213 msg = "%s not pulled, cannot get digest" % image |
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214 if exc.stdout == '[]' and exc.stderr == f'Error: no such image: {image}': |
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215 log.warning(msg, image) |
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216 return [] |
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217 else: |
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218 raise ContainerImageNotFound(msg, image=image) |
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219 |
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220 |
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221 class DockerAPIClient: |
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222 """Wraps a ``docker.APIClient`` to catch exceptions. |
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223 """ |
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224 |
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225 _exception_retry_time = 5 |
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226 _default_max_tries = 10 |
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227 _host_iter = None |
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228 _client = None |
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229 _client_args = () |
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230 _client_kwargs: Dict[str, Optional[Any]] = {} |
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231 |
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232 @staticmethod |
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233 def _qualname(f): |
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234 if isinstance(f, partial): |
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235 f = f.func |
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236 try: |
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237 return getattr(f, '__qualname__', f.im_class.__name__ + '.' + f.__name__) |
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238 except AttributeError: |
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239 return f.__name__ |
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240 |
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241 @staticmethod |
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242 def _should_retry_request(response_code): |
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243 return response_code >= 500 or response_code in (404, 408, 409, 429) |
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244 |
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245 @staticmethod |
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246 def _nonfatal_error(response_code): |
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247 return response_code in (404,) |
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248 |
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249 @staticmethod |
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250 def _unwrapped_attr(attr): |
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251 return getattr(DockerAPIClient._client, attr) |
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252 |
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253 @staticmethod |
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254 def _init_client(): |
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255 kwargs = DockerAPIClient._client_kwargs.copy() |
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256 if DockerAPIClient._host_iter is not None and 'base_url' not in kwargs: |
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257 kwargs['base_url'] = next(DockerAPIClient._host_iter) |
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258 DockerAPIClient._client = docker.APIClient(*DockerAPIClient._client_args, **kwargs) |
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259 log.info('Initialized Docker API client for server: %s', kwargs.get('base_url', 'localhost')) |
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260 |
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261 @staticmethod |
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262 def _default_client_handler(fname, *args, **kwargs): |
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263 success_test = kwargs.pop('success_test', None) |
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264 max_tries = kwargs.pop('max_tries', DockerAPIClient._default_max_tries) |
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265 for tries in range(1, max_tries + 1): |
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266 retry_time = DockerAPIClient._exception_retry_time |
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267 reinit = False |
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268 exc = None |
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269 # re-get the APIClient method every time as a different caller (such as the success test function) may have |
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270 # already reinitialized the client, and we always want to use the current client |
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271 f = DockerAPIClient._unwrapped_attr(fname) |
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272 qualname = DockerAPIClient._qualname(f) |
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273 try: |
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274 r = f(*args, **kwargs) |
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275 if tries > 1: |
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276 log.info('%s() succeeded on attempt %s', qualname, tries) |
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277 return r |
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278 except ConnectionError: |
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279 reinit = True |
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280 except docker.errors.APIError as exc: |
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281 if not DockerAPIClient._should_retry_request(exc.response.status_code): |
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282 raise |
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283 except ReadTimeout: |
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284 reinit = True |
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285 retry_time = 0 |
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286 finally: |
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287 # 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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288 # the exception is raised) |
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289 if exc is not None: |
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290 log.warning("Caught exception on %s(): %s: %s", |
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291 DockerAPIClient._qualname(f), exc.__class__.__name__, exc) |
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292 if reinit: |
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293 log.warning("Reinitializing Docker API client due to connection-oriented failure") |
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294 DockerAPIClient._init_client() |
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295 f = DockerAPIClient._unwrapped_attr(fname) |
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296 qualname = DockerAPIClient._qualname(f) |
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297 r = None |
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298 if success_test is not None: |
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299 log.info("Testing if %s() succeeded despite the exception", qualname) |
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300 r = success_test() |
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301 if r: |
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302 log.warning("The request appears to have succeeded, will not retry. Response is: %s", str(r)) |
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303 return r |
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304 elif tries >= max_tries: |
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305 log.error("Maximum number of attempts (%s) exceeded", max_tries) |
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306 if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code): |
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307 return None |
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308 else: |
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309 raise |
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310 else: |
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311 log.error("Retrying %s() in %s seconds (attempt: %s of %s)", qualname, retry_time, tries, |
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312 max_tries) |
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313 sleep(retry_time) |
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314 |
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315 def __init__(self, *args, **kwargs): |
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316 # Only initialize the host iterator once |
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317 host_iter = kwargs.pop('host_iter', None) |
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318 DockerAPIClient._host_iter = DockerAPIClient._host_iter or host_iter |
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319 DockerAPIClient._client_args = args |
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320 DockerAPIClient._client_kwargs = kwargs |
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321 DockerAPIClient._init_client() |
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322 |
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323 def __getattr__(self, attr): |
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324 """Allow the calling of methods on this class as if it were a docker.APIClient instance. |
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325 """ |
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326 cattr = DockerAPIClient._unwrapped_attr(attr) |
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327 if callable(cattr): |
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328 return partial(DockerAPIClient._default_client_handler, attr) |
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329 else: |
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330 return cattr |
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331 |
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332 |
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333 class DockerAPIInterface(DockerInterface): |
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334 |
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335 container_type = 'docker' |
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336 |
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337 # 'publish_port_random' and 'volumes' are special cases handled in _create_host_config() |
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338 host_config_option_map = { |
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339 'auto_remove': {}, |
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340 'publish_all_ports': {}, |
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341 'cpus': {'param': 'nano_cpus', 'map': lambda x: int(x * 1000000000)}, |
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342 'memory': {'param': 'mem_limit'}, |
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343 'binds': {}, |
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344 'port_bindings': {}, |
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345 } |
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346 |
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347 def validate_config(self): |
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348 assert docker is not None, "Docker module could not be imported, DockerAPIInterface unavailable" |
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349 super().validate_config() |
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350 self.__client = None |
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351 |
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352 @property |
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353 def _client(self): |
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354 # TODO: add cert options to containers conf |
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355 cert_path = os.environ.get('DOCKER_CERT_PATH') or None |
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356 if not cert_path: |
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357 cert_path = os.path.join(os.path.expanduser('~'), '.docker') |
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358 if self._conf.force_tlsverify or self._conf.tls: |
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359 tls_config = docker.tls.TLSConfig( |
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360 client_cert=(os.path.join(cert_path, 'cert.pem'), |
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361 os.path.join(cert_path, 'key.pem')), |
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362 ca_cert=os.path.join(cert_path, 'ca.pem'), |
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363 verify=self._conf.force_tlsverify, |
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364 ) |
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365 else: |
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366 tls_config = False |
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367 if not self.__client: |
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368 self.__client = DockerAPIClient( |
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369 host_iter=self.host_iter, |
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370 tls=tls_config, |
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371 ) |
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372 return self.__client |
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373 |
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374 @staticmethod |
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375 def _first(f, *args, **kwargs): |
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376 try: |
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377 return f(*args, **kwargs)[0] |
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378 except IndexError: |
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379 return None |
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380 |
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381 @staticmethod |
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382 def _filter_by_id_or_name(id, name): |
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383 if id: |
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384 return {'id': id} |
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385 elif name: |
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386 return {'name': name} |
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387 return None |
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388 |
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389 @staticmethod |
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390 def _kwopt_to_param_names(map_spec, key): |
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391 """For a given containers lib method parameter name, return the matching docker-py parameter name(s). |
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392 |
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393 See :meth:`_create_docker_api_spec`. |
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394 """ |
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395 params = [] |
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396 if 'param' not in map_spec and 'params' not in map_spec: |
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397 params.append(key) |
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398 elif 'param' in map_spec: |
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399 params.append(map_spec['param']) |
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400 params.extend(map_spec.get('params', ())) |
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401 return params |
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402 |
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403 @staticmethod |
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404 def _kwopt_to_params(map_spec, key, value): |
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405 """For a given containers lib method parameter name and value, return the matching docker-py parameters with |
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406 values set (including transformation with an optional map function). |
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407 |
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408 See :meth:`_create_docker_api_spec`. |
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409 """ |
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410 params = {} |
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411 if 'map' in map_spec: |
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412 value = map_spec['map'](value) |
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413 for param in DockerAPIInterface._kwopt_to_param_names(map_spec, key): |
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414 params[param] = value |
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415 return params |
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416 |
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417 def _create_docker_api_spec(self, option_map_name, spec_class, kwopts): |
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418 """Create docker-py objects used as arguments to docker-py methods. |
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419 |
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420 This method modifies ``kwopts`` by removing options that match the spec. |
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421 |
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422 An option map is a class-level variable with name ``<map_name>_option_map`` and is a dict with format: |
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423 |
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424 .. code-block:: python |
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425 |
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426 sample_option_map = { |
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427 'containers_lib_option_name': { |
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428 'param': docker_lib_positional_argument_int or 'docker_lib_keyword_argument_name', |
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429 'params': like 'param' but an iterable containing multiple docker lib params to set, |
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430 'default': default value, |
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431 'map': function with with to transform the value, |
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432 'required': True if this param is required, else False (default), |
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433 }, |
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434 '_spec_param': { |
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435 'spec_class': class of param value, |
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436 } |
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437 } |
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438 |
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439 All members of the mapping value are optional. |
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440 |
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441 For example, a spec map for (some of) the possible values of the :class:`docker.types.TaskTemplate`, which is |
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442 used as the ``task_template`` argument to :meth:`docker.APIClient.create_service`, and the possible values of |
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443 the :class`:docker.types.ContainerSpec`, which is used as the ``container_spec`` argument to the |
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444 ``TaskTemplate`` would be: |
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445 |
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446 .. code-block:: python |
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447 |
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448 task_template_option_map = { |
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449 # TaskTemplate's 'container_spec' param is a ContainerSpec |
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450 '_container_spec': { |
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451 'spec_class': docker.types.ContainerSpec, |
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452 'required': True |
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453 } |
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454 } |
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455 container_spec_option_map = { |
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456 'image': {'param': 0}, # positional argument 0 to ContainerSpec() |
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457 'command': {}, # 'command' keyword argument to ContainerSpec() |
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458 'environment': { # 'env' keyword argument to ContainerSpec(), 'environment' keyword argument |
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459 'param': 'env' # to ContainerInterface.run_in_container() |
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460 }, |
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461 } |
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462 |
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463 Thus, calling ``DockerInterface.run_in_contaner('true', image='busybox', environment={'FOO': 'foo'}`` will |
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464 essentially do this (for example, if using Docker Swarm mode): |
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465 |
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466 .. code-block:: python |
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467 |
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468 container_spec = docker.types.ContainerSpec('busybox', command='true', env={'FOO': 'foo'}) |
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469 task_template = docker.types.TaskTemplate(container_spec=container_spec) |
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470 docker.APIClient().create_service(task_template) |
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471 |
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472 :param option_map_name: Name of option map class variable (``_option_map`` is automatically appended) |
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473 :type option_map_name: str |
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474 :param spec_class: docker-py specification class or callable returning an instance |
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475 :type spec_class: :class:`docker.types.Resources`, :class:`docker.types.ContainerSpec`, etc. or |
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476 callable |
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477 :param kwopts: Keyword options passed to calling method (e.g. |
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478 :meth:`DockerInterface.run_in_container`) |
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479 :type kwopts: dict |
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480 :returns: Instantiated ``spec_class`` object |
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481 :rtype: ``type(spec_class)`` |
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482 """ |
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483 def _kwopt_to_arg(map_spec, key, value, param=None): |
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484 # determines whether the given param is a positional or keyword argument in docker-py and adds it to the |
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485 # list of arguments |
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486 if isinstance(map_spec.get('param'), int): |
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487 spec_opts.append((map_spec.get('param'), value)) |
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488 elif param is not None: |
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489 spec_kwopts[param] = value |
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490 else: |
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491 spec_kwopts.update(DockerAPIInterface._kwopt_to_params(map_spec, key, value)) |
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492 # positional arguments |
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493 spec_opts = [] |
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494 # keyword arguments |
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495 spec_kwopts = {} |
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496 # retrieve the option map for the docker-py object we're creating |
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497 option_map = getattr(self, option_map_name + '_option_map') |
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498 # set defaults |
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499 for key in filter(lambda k: option_map[k].get('default'), option_map.keys()): |
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500 map_spec = option_map[key] |
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501 _kwopt_to_arg(map_spec, key, map_spec['default']) |
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502 # don't allow kwopts that start with _, those are reserved for "child" object params |
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503 for kwopt in filter(lambda k: not k.startswith('_') and k in option_map, list(kwopts.keys())): |
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504 map_spec = option_map[kwopt] |
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505 _v = kwopts.pop(kwopt) |
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506 _kwopt_to_arg(map_spec, kwopt, _v) |
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507 # find any child objects that need to be created and recurse to create them |
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508 for _sub_k in filter(lambda k: k.startswith('_') and 'spec_class' in option_map[k], option_map.keys()): |
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509 map_spec = option_map[_sub_k] |
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510 param = _sub_k.lstrip('_') |
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511 _sub_v = self._create_docker_api_spec(param, map_spec['spec_class'], kwopts) |
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512 if _sub_v is not None or map_spec.get('required') or isinstance(map_spec.get('param'), int): |
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513 _kwopt_to_arg(map_spec, None, _sub_v, param=param) |
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514 # sort positional args and make into a flat tuple |
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515 if spec_opts: |
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516 spec_opts = sorted(spec_opts, key=lambda x: x[0]) |
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517 spec_opts = [i[1] for i in spec_opts] |
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518 # create spec object |
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519 if spec_opts or spec_kwopts: |
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520 return spec_class(*spec_opts, **spec_kwopts) |
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521 else: |
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522 return None |
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523 |
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524 def _volumes_to_native(self, volumes): |
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525 """Convert a list of volume definitions to the docker-py container creation method parameters. |
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526 |
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527 :param volumes: List of volumes to translate |
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528 :type volumes: list of :class:`galaxy.containers.docker_model.DockerVolume`s |
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529 """ |
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530 paths = [] |
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531 binds = {} |
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532 for v in volumes: |
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533 path, bind = v.to_native() |
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534 paths.append(path) |
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535 binds.update(bind) |
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536 return (paths, binds) |
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537 |
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538 def _create_host_config(self, kwopts): |
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539 """Build the host configuration parameter for docker-py container creation. |
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540 |
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541 This method modifies ``kwopts`` by removing host config options and potentially setting the ``ports`` and |
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542 ``volumes`` keys. |
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543 |
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544 :param kwopts: Keyword options passed to calling method (e.g. :method:`DockerInterface.run()`) |
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545 :type kwopts: dict |
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546 :returns: The return value of `docker.APIClient.create_host_config()` |
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547 :rtype: dict |
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548 """ |
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549 if 'publish_port_random' in kwopts: |
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550 port = int(kwopts.pop('publish_port_random')) |
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551 kwopts['port_bindings'] = {port: None} |
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552 kwopts['ports'] = [port] |
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553 if 'volumes' in kwopts: |
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554 paths, binds = self._volumes_to_native(kwopts.pop('volumes')) |
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555 kwopts['binds'] = binds |
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556 kwopts['volumes'] = paths |
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557 return self._create_docker_api_spec('host_config', self._client.create_host_config, kwopts) |
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558 |
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559 # |
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560 # docker subcommands |
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561 # |
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562 |
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563 def ps(self, id=None, name=None, running=True): |
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564 return self._client.containers(all=not running, filters=self._filter_by_id_or_name(id, name)) |
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565 |
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566 def run(self, command, image=None, **kwopts): |
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567 image = image or self._default_image |
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568 command = command or None |
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569 log.debug("Creating docker container with image '%s' for command: %s", image, command) |
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570 host_config = self._create_host_config(kwopts) |
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571 log.debug("Docker container host configuration:\n%s", safe_dumps_formatted(host_config)) |
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572 log.debug("Docker container creation parameters:\n%s", safe_dumps_formatted(kwopts)) |
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573 success_test = partial(self._first, self.ps, name=kwopts['name'], running=False) |
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574 # this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class |
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575 container = self._client.create_container( |
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576 image, |
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577 command=command if command else None, |
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578 host_config=host_config, |
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579 success_test=success_test, |
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580 max_tries=5, |
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581 **kwopts |
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582 ) |
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583 container_id = container.get('Id') |
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584 log.debug("Starting container: %s (%s)", kwopts['name'], str(container_id)) |
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585 # start can safely be run more than once |
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586 self._client.start(container=container_id) |
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587 return DockerContainer.from_id(self, container_id) |
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588 |
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589 def inspect(self, container_id): |
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590 try: |
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591 return self._client.inspect_container(container_id) |
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592 except docker.errors.NotFound: |
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593 raise ContainerNotFound("Invalid container id: %s" % container_id, container_id=container_id) |
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594 |
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595 def image_inspect(self, image): |
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596 try: |
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597 return self._client.inspect_image(image) |
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598 except docker.errors.NotFound: |
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599 raise ContainerImageNotFound("%s not pulled, cannot get digest" % image, image=image) |