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annotate planemo/lib/python3.7/site-packages/galaxy/containers/docker_swarm.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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0
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1 """
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2 Docker Swarm mode interface
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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.path
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8 import subprocess
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9 from functools import partial
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10
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11 try:
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12 import docker.types
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13 except ImportError:
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14 from galaxy.util.bunch import Bunch
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15 docker = Bunch(types=Bunch(
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16 ContainerSpec=None,
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17 RestartPolicy=None,
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18 Resources=None,
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19 Placement=None,
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20 ))
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21
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22 from galaxy.containers.docker import (
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23 DockerAPIInterface,
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24 DockerCLIInterface,
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25 DockerInterface
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26 )
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27 from galaxy.containers.docker_decorators import docker_columns, docker_json
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28 from galaxy.containers.docker_model import (
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29 CPUS_CONSTRAINT,
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30 DockerNode,
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31 DockerService,
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32 DockerTask,
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33 IMAGE_CONSTRAINT
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34 )
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35 from galaxy.exceptions import ContainerRunError
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36 from galaxy.util import unicodify
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37 from galaxy.util.json import safe_dumps_formatted
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38
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39 log = logging.getLogger(__name__)
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40
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41 SWARM_MANAGER_PATH = os.path.abspath(
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42 os.path.join(
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43 os.path.dirname(__file__),
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44 os.path.pardir,
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45 os.path.pardir,
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46 os.path.pardir,
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47 'scripts',
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48 'docker_swarm_manager.py'))
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49
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50
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51 class DockerSwarmInterface(DockerInterface):
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52
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53 container_class = DockerService
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54 conf_defaults = {
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55 'ignore_volumes': False,
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56 'node_prefix': None,
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57 'service_create_image_constraint': False,
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58 'service_create_cpus_constraint': False,
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59 'resolve_image_digest': False,
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60 'managed': True,
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61 'manager_autostart': True,
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62 }
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63 publish_port_list_required = True
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64 supports_volumes = False
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65
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66 def validate_config(self):
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67 super(DockerSwarmInterface, self).validate_config()
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68 self._node_prefix = self._conf.node_prefix
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69
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70 def run_in_container(self, command, image=None, **kwopts):
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71 """Run a service like a detached container
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72 """
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73 kwopts['replicas'] = 1
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74 kwopts['restart_condition'] = 'none'
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75 if kwopts.get('publish_all_ports', False):
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76 # not supported for services
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77 # TODO: inspect image (or query registry if possible) for port list
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78 if kwopts.get('publish_port_random', False) or kwopts.get('ports', False):
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79 # assume this covers for publish_all_ports
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80 del kwopts['publish_all_ports']
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81 else:
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82 raise ContainerRunError(
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83 "Publishing all ports is not supported in Docker swarm"
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84 " mode, use `publish_port_random` or `ports`",
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85 image=image,
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86 command=command
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87 )
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88 if not kwopts.get('detach', True):
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89 raise ContainerRunError(
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90 "Running attached containers is not supported in Docker swarm mode",
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91 image=image,
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92 command=command
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93 )
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94 elif kwopts.get('detach', None):
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95 del kwopts['detach']
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96 if kwopts.get('volumes', None):
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97 if self._conf.ignore_volumes:
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98 log.warning(
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99 "'volumes' kwopt is set and not supported in Docker swarm "
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100 "mode, volumes will not be passed (set 'ignore_volumes: "
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101 "False' in containers config to fail instead): %s" % kwopts['volumes']
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102 )
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103 else:
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104 raise ContainerRunError(
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105 "'volumes' kwopt is set and not supported in Docker swarm "
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106 "mode (set 'ignore_volumes: True' in containers config to "
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107 "warn instead): %s" % kwopts['volumes'],
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108 image=image,
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109 command=command
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110 )
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111 # ensure the volumes key is removed from kwopts
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112 kwopts.pop('volumes', None)
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113 service = self.service_create(command, image=image, **kwopts)
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114 self._run_swarm_manager()
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115 return service
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116
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117 #
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118 # helpers
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119 #
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120
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121 def _run_swarm_manager(self):
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122 if self._conf.managed and self._conf.manager_autostart:
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123 try:
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124 # sys.exectuable would be preferable to using $PATH, but sys.executable is probably uwsgi
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125 subprocess.check_call(['python', SWARM_MANAGER_PATH, '--containers-config-file',
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126 self.containers_config_file, '--swarm', self.key])
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127 except subprocess.CalledProcessError as exc:
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128 log.error('Failed to launch swarm manager: %s', unicodify(exc))
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129
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130 def _get_image(self, image):
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131 """Get the image string, either from the argument, or from the
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132 configured interface default if ``image`` is ``None``. Optionally
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133 resolve the image to its digest if ``resolve_image_digest`` is set in
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134 the interface configuration.
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135
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136 If the image has not been pulled, the repo digest cannot be determined
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137 and the image name will be returned.
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138
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139 :type image: str or None
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140 :param image: image id or name
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141
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142 :returns: image name or image repo digest
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143 """
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144 if not image:
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145 image = self._conf.image
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146 assert image is not None, "No image supplied as parameter and no image set as default in config, cannot create service"
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147 if self._conf.resolve_image_digest:
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148 image = self.image_repodigest(image)
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149 return image
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150
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151 def _objects_by_attribute(self, generator, attribute_name):
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152 rval = {}
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153 for obj in generator:
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154 attr = getattr(obj, attribute_name)
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155 if attr not in rval:
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156 rval[attr] = []
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157 rval[attr].append(obj)
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158 return rval
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159
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160 #
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161 # docker object generators
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162 #
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163
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164 def services(self, id=None, name=None):
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165 for service_dict in self.service_ls(id=id, name=name):
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166 service_id = service_dict['ID']
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167 service = DockerService(self, service_id, inspect=service_dict)
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168 if service.name.startswith(self._name_prefix):
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169 yield service
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170
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171 def service(self, id=None, name=None):
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172 try:
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173 return next(self.services(id=id, name=name))
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174 except StopIteration:
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175 return None
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176
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177 def services_in_state(self, desired, current, tasks='any'):
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178 for service in self.services():
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179 if service.in_state(desired, current, tasks=tasks):
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180 yield service
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181
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182 def service_tasks(self, service):
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183 for task_dict in self.service_ps(service.id):
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184 yield DockerTask.from_api(self, task_dict, service=service)
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185
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186 def nodes(self, id=None, name=None):
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187 for node_dict in self.node_ls(id=id, name=name):
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188 node_id = node_dict['ID']
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189 node = DockerNode(self, node_id, inspect=node_dict)
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190 if self._node_prefix and not node.name.startswith(self._node_prefix):
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191 continue
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192 yield node
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193
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194 def node(self, id=None, name=None):
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195 try:
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196 return next(self.nodes(id=id, name=name))
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197 except StopIteration:
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198 return None
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199
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200 def nodes_in_state(self, status, availability):
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201 for node in self.nodes():
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202 if node.in_state(status, availability):
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203 yield node
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204
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205 def node_tasks(self, node):
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206 for task_dict in self.node_ps(node.id):
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207 yield DockerTask.from_api(self, task_dict, node=node)
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208
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209 #
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210 # higher level queries
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211 #
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212
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213 def services_waiting(self):
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214 return self.services_in_state('Running', 'Pending')
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215
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216 def services_waiting_by_constraints(self):
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217 return self._objects_by_attribute(self.services_waiting(), 'constraints')
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218
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219 def services_completed(self):
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220 return self.services_in_state('Shutdown', 'Complete', tasks='all')
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221
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222 def services_terminal(self):
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223 return [s for s in self.services() if s.terminal]
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224
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225 def nodes_active(self):
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226 return self.nodes_in_state('Ready', 'Active')
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227
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228 def nodes_active_by_constraints(self):
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229 return self._objects_by_attribute(self.nodes_active(), 'labels_as_constraints')
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230
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231 #
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232 # operations
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233 #
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234
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235 def services_clean(self):
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236 cleaned_service_ids = []
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237 completed_services = list(self.services_completed()) # returns a generator, should probably fix this
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238 if completed_services:
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239 cleaned_service_ids.extend(self.service_rm([x.id for x in completed_services]))
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240 terminal_services = list(self.services_terminal())
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241 for service in terminal_services:
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242 log.warning('cleaned service in abnormal terminal state: %s (%s). state: %s', service.name, service.id, service.state)
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243 if terminal_services:
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244 cleaned_service_ids.extend(self.service_rm([x.id for x in terminal_services]))
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245 return filter(lambda x: x.id in cleaned_service_ids, completed_services + terminal_services)
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246
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247
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248 class DockerSwarmCLIInterface(DockerSwarmInterface, DockerCLIInterface):
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249
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250 container_type = 'docker_swarm_cli'
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251 option_map = {
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252 # `service create` options
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253 'constraint': {'flag': '--constraint', 'type': 'list_of_kovtrips'},
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254 'replicas': {'flag': '--replicas', 'type': 'string'},
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255 'restart_condition': {'flag': '--restart-condition', 'type': 'string'},
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256 'environment': {'flag': '--env', 'type': 'list_of_kvpairs'},
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257 'name': {'flag': '--name', 'type': 'string'},
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258 'publish_port_random': {'flag': '--publish', 'type': 'string'},
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259 'cpu_limit': {'flag': '--limit-cpu', 'type': 'string'},
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260 'mem_limit': {'flag': '--limit-memory', 'type': 'string'},
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261 'cpu_reservation': {'flag': '--reserve-cpu', 'type': 'string'},
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262 'mem_reservation': {'flag': '--reserve-memory', 'type': 'string'},
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263 # `service update` options
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264 'label_add': {'flag': '--label-add', 'type': 'list_of_kvpairs'},
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265 'label_rm': {'flag': '--label-rm', 'type': 'list_of_kvpairs'},
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266 'availability': {'flag': '--availability', 'type': 'string'},
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267 }
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268
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269 #
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270 # docker object generators
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271 #
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272
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273 def services(self, id=None, name=None):
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274 for service_dict in self.service_ls(id=id, name=name):
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275 service_id = service_dict['ID']
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276 service_name = service_dict['NAME']
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277 if not service_name.startswith(self._name_prefix):
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278 continue
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279 task_list = self.service_ps(service_id)
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280 yield DockerService.from_cli(self, service_dict, task_list)
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281
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282 def service_tasks(self, service):
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283 for task_dict in self.service_ps(service.id):
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284 if task_dict['NAME'].strip().startswith(r'\_'):
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285 continue # historical task
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286 yield DockerTask.from_cli(self, task_dict, service=service)
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287
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288 def nodes(self, id=None, name=None):
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289 for node_dict in self.node_ls(id=id, name=name):
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290 node_id = node_dict['ID'].strip(' *')
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291 node_name = node_dict['HOSTNAME']
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292 if self._node_prefix and not node_name.startswith(self._node_prefix):
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293 continue
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294 task_list = filter(lambda x: x['NAME'].startswith(self._name_prefix), self.node_ps(node_id))
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295 yield DockerNode.from_cli(self, node_dict, task_list)
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296
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297 #
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298 # docker subcommands
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299 #
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300
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301 def service_create(self, command, image=None, **kwopts):
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302 if ('service_create_image_constraint' in self._conf or 'service_create_cpus_constraint' in self._conf) and 'constraint' not in kwopts:
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303 kwopts['constraint'] = []
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304 image = self._get_image(image)
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305 if self._conf.service_create_image_constraint:
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306 kwopts['constraint'].append((IMAGE_CONSTRAINT, '==', image))
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307 if self._conf.service_create_cpus_constraint:
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308 cpus = kwopts.get('reserve_cpus', kwopts.get('limit_cpus', '1'))
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309 kwopts['constraint'].append((CPUS_CONSTRAINT, '==', cpus))
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310 if self._conf.cpus:
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311 kwopts['cpu_limit'] = self._conf.cpus
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312 kwopts['cpu_reservation'] = self._conf.cpus
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313 if self._conf.memory:
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314 kwopts['mem_limit'] = self._conf.memory
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315 kwopts['mem_reservation'] = self._conf.memory
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316 self.set_kwopts_name(kwopts)
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317 args = '{kwopts} {image} {command}'.format(
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318 kwopts=self._stringify_kwopts(kwopts),
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319 image=image if image else '',
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320 command=command if command else '',
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321 ).strip()
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322 service_id = self._run_docker(subcommand='service create', args=args, verbose=True)
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323 return DockerService.from_id(self, service_id)
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324
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325 @docker_json
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326 def service_inspect(self, service_id):
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327 return self._run_docker(subcommand='service inspect', args=service_id)[0]
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328
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329 @docker_columns
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330 def service_ls(self, id=None, name=None):
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331 return self._run_docker(subcommand='service ls', args=self._filter_by_id_or_name(id, name))
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332
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333 @docker_columns
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334 def service_ps(self, service_id):
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335 return self._run_docker(subcommand='service ps', args='--no-trunc {}'.format(service_id))
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336
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337 def service_rm(self, service_ids):
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338 service_ids = ' '.join(service_ids)
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339 return self._run_docker(subcommand='service rm', args=service_ids).splitlines()
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340
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341 @docker_json
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342 def node_inspect(self, node_id):
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343 return self._run_docker(subcommand='node inspect', args=node_id)[0]
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344
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345 @docker_columns
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346 def node_ls(self, id=None, name=None):
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347 return self._run_docker(subcommand='node ls', args=self._filter_by_id_or_name(id, name))
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348
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349 @docker_columns
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350 def node_ps(self, node_id):
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351 return self._run_docker(subcommand='node ps', args='--no-trunc {}'.format(node_id))
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352
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353 def node_update(self, node_id, **kwopts):
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354 return self._run_docker(subcommand='node update', args='{kwopts} {node_id}'.format(
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355 kwopts=self._stringify_kwopts(kwopts),
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356 node_id=node_id
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357 ))
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358
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359 @docker_json
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360 def task_inspect(self, task_id):
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361 return self._run_docker(subcommand="inspect", args=task_id)
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362
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363
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364 class DockerSwarmAPIInterface(DockerSwarmInterface, DockerAPIInterface):
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365
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366 container_type = 'docker_swarm'
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367 placement_option_map = {
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368 'constraint': {'param': 'constraints'},
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369 }
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370 service_mode_option_map = {
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371 'service_mode': {'param': 0, 'default': 'replicated'},
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372 'replicas': {'default': 1},
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373 }
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374 endpoint_spec_option_map = {
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375 'ports': {},
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376 }
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377 resources_option_map = {
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378 'cpus': {'params': ('cpu_limit', 'cpu_reservation'), 'map': lambda x: int(x * 1000000000)},
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379 'memory': {'params': ('mem_limit', 'mem_reservation')},
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380 }
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381 container_spec_option_map = {
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382 'image': {'param': 0},
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383 'command': {},
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384 'environment': {'param': 'env'},
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385 'labels': {},
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386 }
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387 restart_policy_option_map = {
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388 'restart_condition': {'param': 'condition', 'default': 'none'},
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389 'restart_delay': {'param': 'delay'},
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390 'restart_max_attempts': {'param': 'max_attemps'},
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391 }
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392 task_template_option_map = {
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393 '_container_spec': {'spec_class': docker.types.ContainerSpec, 'required': True},
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394 '_resources': {'spec_class': docker.types.Resources},
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395 '_restart_policy': {'spec_class': docker.types.RestartPolicy},
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396 '_placement': {'spec_class': docker.types.Placement},
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397 }
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398 node_spec_option_map = {
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399 'availability': {'param': 'Availability'},
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400 'name': {'param': 'Name'},
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401 'role': {'param': 'Role'},
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402 'labels': {'param': 'Labels'},
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403 }
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404
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405 @staticmethod
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406 def create_random_port_spec(port):
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407 return {
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408 'Protocol': 'tcp',
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409 'PublishedPort': None,
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410 'TargetPort': port,
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411 }
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412
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413 #
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414 # docker subcommands
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415 #
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416
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417 def service_create(self, command, image=None, **kwopts):
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418 # TODO: some of this should probably move to run_in_container when the CLI interface is removed
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419 log.debug("Creating docker service with image '%s' for command: %s", image, command)
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420 # insert run kwopts from config
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421 for opt in self.conf_run_kwopts:
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422 if self._conf[opt]:
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423 kwopts[opt] = self._conf[opt]
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424 # image is part of the container spec
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425 kwopts['image'] = self._get_image(image)
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426 # service constraints
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427 kwopts['constraint'] = kwopts.get('constraint', [])
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428 if self._conf.service_create_image_constraint:
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429 kwopts['constraint'].append((IMAGE_CONSTRAINT + '==' + image))
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430 if self._conf.service_create_cpus_constraint:
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431 cpus = kwopts.get('reserve_cpus', kwopts.get('limit_cpus', '1'))
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432 kwopts['constraint'].append((CPUS_CONSTRAINT + '==' + cpus))
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433 # ports
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434 if 'publish_port_random' in kwopts:
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435 kwopts['ports'] = [DockerSwarmAPIInterface.create_random_port_spec(kwopts.pop('publish_port_random'))]
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436 # create specs
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437 service_mode = self._create_docker_api_spec('service_mode', docker.types.ServiceMode, kwopts)
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438 endpoint_spec = self._create_docker_api_spec('endpoint_spec', docker.types.EndpointSpec, kwopts)
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439 task_template = self._create_docker_api_spec('task_template', docker.types.TaskTemplate, kwopts)
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440 self.set_kwopts_name(kwopts)
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441 log.debug("Docker service task template:\n%s", safe_dumps_formatted(task_template))
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442 log.debug("Docker service endpoint specification:\n%s", safe_dumps_formatted(endpoint_spec))
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443 log.debug("Docker service mode:\n%s", safe_dumps_formatted(service_mode))
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444 log.debug("Docker service creation parameters:\n%s", safe_dumps_formatted(kwopts))
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445 success_test = partial(self._first, self.service_ls, name=kwopts['name'])
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446 # this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class
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447 service = self._client.create_service(
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448 task_template,
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449 mode=service_mode,
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450 endpoint_spec=endpoint_spec,
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451 success_test=success_test,
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452 max_tries=5,
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453 **kwopts)
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454 service_id = service.get('ID')
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455 log.debug('Created service: %s (%s)', kwopts['name'], service_id)
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456 return DockerService.from_id(self, service_id)
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457
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458 def service_inspect(self, service_id):
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459 return self._client.inspect_service(service_id)
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460
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461 def service_ls(self, id=None, name=None):
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462 return self._client.services(filters=self._filter_by_id_or_name(id, name))
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463
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464 # roughly `docker service ps`
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465 def service_ps(self, service_id):
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466 return self.task_ls(filters={'service': service_id})
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467
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468 def service_rm(self, service_ids):
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469 r = []
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470 for service_id in service_ids:
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471 self._client.remove_service(service_id)
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472 r.append(service_id)
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473 return r
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474
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475 def node_inspect(self, node_id):
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476 return self._client.inspect_node(node_id)
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477
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478 def node_ls(self, id=None, name=None):
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479 return self._client.nodes(filters=self._filter_by_id_or_name(id, name))
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480
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481 # roughly `docker node ps`
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482 def node_ps(self, node_id):
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483 return self.task_ls(filters={'node': node_id})
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484
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485 def node_update(self, node_id, **kwopts):
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486 node = DockerNode.from_id(self, node_id)
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487 spec = node.inspect['Spec']
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488 if 'label_add' in kwopts:
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489 kwopts['labels'] = spec.get('Labels', {})
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490 kwopts['labels'].update(kwopts.pop('label_add'))
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491 spec.update(self._create_docker_api_spec('node_spec', dict, kwopts))
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492 return self._client.update_node(node.id, node.version, node_spec=spec)
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493
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494 def task_inspect(self, task_id):
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495 return self._client.inspect_task(task_id)
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496
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497 def task_ls(self, filters=None):
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498 return self._client.tasks(filters=filters)