annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/docker_util.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Utilities for building up Docker commands...
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2
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3 ...using common defaults and configuration mechanisms.
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4 """
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5 import os
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6 import shlex
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7
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8 from galaxy.util.commands import argv_to_str
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9
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10 DEFAULT_DOCKER_COMMAND = "docker"
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11 DEFAULT_SUDO = False
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12 DEFAULT_SUDO_COMMAND = "sudo"
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13 DEFAULT_HOST = None
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14 DEFAULT_VOLUME_MOUNT_TYPE = "rw"
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15 DEFAULT_WORKING_DIRECTORY = None
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16 DEFAULT_NET = None
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17 DEFAULT_MEMORY = None
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18 DEFAULT_VOLUMES_FROM = None
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19 DEFAULT_AUTO_REMOVE = True
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20 DEFAULT_SET_USER = "$UID"
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21 DEFAULT_RUN_EXTRA_ARGUMENTS = None
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22
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23
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24 def kill_command(
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25 container,
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26 signal=None,
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27 **kwds
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28 ):
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29 args = (["-s", signal] if signal else []) + [container]
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30 return command_list("kill", args, **kwds)
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31
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32
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33 def logs_command(
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34 container,
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35 **kwds
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36 ):
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37 return command_list("logs", [container], **kwds)
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38
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39
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40 def build_command(
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41 image,
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42 docker_build_path,
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43 **kwds
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44 ):
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45 if os.path.isfile(docker_build_path):
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46 docker_build_path = os.path.dirname(os.path.abspath(docker_build_path))
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47 return command_list("build", ["-t", image, docker_build_path], **kwds)
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48
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49
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50 def build_save_image_command(
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51 image,
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52 destination,
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53 **kwds
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54 ):
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55 return command_list("save", ["-o", destination, image], **kwds)
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56
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57
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58 def build_pull_command(
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59 tag,
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60 **kwds
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61 ):
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62 return command_list("pull", [tag], **kwds)
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63
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64
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65 def build_docker_cache_command(
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66 image,
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67 **kwds
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68 ):
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69 inspect_image_command = command_shell("inspect", [image], **kwds)
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70 pull_image_command = command_shell("pull", [image], **kwds)
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71 cache_command = f"{inspect_image_command} > /dev/null 2>&1\n[ $? -ne 0 ] && {pull_image_command} > /dev/null 2>&1\n"
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72 return cache_command
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73
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74
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75 def build_docker_images_command(truncate=True, **kwds):
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76 args = ["--no-trunc"] if not truncate else[]
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77 return command_shell("images", args, **kwds)
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78
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79
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80 def build_docker_load_command(**kwds):
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81 return command_shell("load", [])
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82
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83
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84 def build_docker_simple_command(
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85 command,
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86 docker_cmd=DEFAULT_DOCKER_COMMAND,
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87 sudo=DEFAULT_SUDO,
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88 sudo_cmd=DEFAULT_SUDO_COMMAND,
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89 container_name=None,
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90 **kwd
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91 ):
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92 command_parts = _docker_prefix(
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93 docker_cmd=docker_cmd,
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94 sudo=sudo,
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95 sudo_cmd=sudo_cmd,
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96 )
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97 command_parts.append(command)
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98 command_parts.append(container_name or '{CONTAINER_NAME}')
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99 return " ".join(command_parts)
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100
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101
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102 def build_docker_run_command(
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103 container_command,
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104 image,
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105 interactive=False,
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106 terminal=False,
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107 tag=None,
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108 volumes=None,
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109 volumes_from=DEFAULT_VOLUMES_FROM,
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110 memory=DEFAULT_MEMORY,
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111 env_directives=None,
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112 working_directory=DEFAULT_WORKING_DIRECTORY,
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113 name=None,
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114 net=DEFAULT_NET,
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115 run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS,
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116 docker_cmd=DEFAULT_DOCKER_COMMAND,
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117 sudo=DEFAULT_SUDO,
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118 sudo_cmd=DEFAULT_SUDO_COMMAND,
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119 auto_rm=DEFAULT_AUTO_REMOVE,
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120 set_user=DEFAULT_SET_USER,
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121 host=DEFAULT_HOST,
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122 guest_ports=False,
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123 container_name=None
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124 ):
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125 env_directives = env_directives or []
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126 volumes = volumes or []
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127 command_parts = _docker_prefix(
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128 docker_cmd=docker_cmd,
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129 sudo=sudo,
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130 sudo_cmd=sudo_cmd,
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131 host=host
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132 )
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133 command_parts.append("run")
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134 if interactive:
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135 command_parts.append("-i")
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136 if terminal:
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137 command_parts.append("-t")
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138 for env_directive in env_directives:
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139 # e.g. -e "GALAXY_SLOTS=$GALAXY_SLOTS"
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140 # These are environment variable expansions so we don't quote these.
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141 command_parts.extend(["-e", env_directive])
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142 if guest_ports is True:
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143 # When is True, expose all ports
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144 command_parts.append("-P")
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145 elif guest_ports:
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146 if not isinstance(guest_ports, list):
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147 guest_ports = [guest_ports]
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148 for guest_port in guest_ports:
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149 command_parts.extend(["-p", guest_port])
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150 if container_name:
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151 command_parts.extend(["--name", container_name])
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152 for volume in volumes:
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153 command_parts.extend(["-v", str(volume)])
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154 if volumes_from:
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155 command_parts.extend(["--volumes-from", shlex.quote(str(volumes_from))])
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156 if memory:
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157 command_parts.extend(["-m", shlex.quote(memory)])
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158 command_parts.extend(["--cpus", '${GALAXY_SLOTS:-1}'])
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159 if name:
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160 command_parts.extend(["--name", shlex.quote(name)])
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161 if working_directory:
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162 command_parts.extend(["-w", shlex.quote(working_directory)])
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163 if net:
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164 command_parts.extend(["--net", shlex.quote(net)])
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165 if auto_rm:
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166 command_parts.append("--rm")
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167 if run_extra_arguments:
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168 command_parts.append(run_extra_arguments)
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169 if set_user:
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170 user = set_user
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171 if set_user == DEFAULT_SET_USER:
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172 # If future-us is ever in here and fixing this for docker-machine just
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173 # use cwltool.docker_id - it takes care of this default nicely.
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174 euid = os.geteuid()
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175 egid = os.getgid()
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176
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177 user = "%d:%d" % (euid, egid)
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178 command_parts.extend(["--user", user])
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179 full_image = image
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180 if tag:
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181 full_image = f"{full_image}:{tag}"
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182 command_parts.append(shlex.quote(full_image))
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183 command_parts.append(container_command)
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184 return " ".join(command_parts)
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185
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186
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187 def command_list(command, command_args=None, **kwds):
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188 """Return Docker command as an argv list."""
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189 command_args = command_args or []
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190 command_parts = _docker_prefix(**kwds)
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191 command_parts.append(command)
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192 command_parts.extend(command_args)
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193 return command_parts
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194
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195
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196 def command_shell(command, command_args=None, **kwds):
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197 """Return Docker command as a string for a shell or command-list."""
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198 command_args = command_args or []
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199 cmd = command_list(command, command_args, **kwds)
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200 to_str = kwds.get("to_str", True)
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201 if to_str:
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202 return argv_to_str(cmd)
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203 else:
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204 return cmd
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205
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206
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207 def _docker_prefix(
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208 docker_cmd=DEFAULT_DOCKER_COMMAND,
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209 sudo=DEFAULT_SUDO,
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210 sudo_cmd=DEFAULT_SUDO_COMMAND,
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211 host=DEFAULT_HOST,
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212 **kwds
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213 ):
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214 """Prefix to issue a docker command."""
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215 command_parts = []
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216 if sudo:
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217 command_parts.append(sudo_cmd)
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218 command_parts.append(docker_cmd)
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219 if host:
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220 command_parts.extend(["-H", host])
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221 return command_parts
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222
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223
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224 def parse_port_text(port_text):
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225 """
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226
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227 >>> slurm_ports = parse_port_text("8888/tcp -> 0.0.0.0:32769")
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228 >>> slurm_ports[8888]['host']
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229 '0.0.0.0'
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230 """
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231 ports = None
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232 if port_text is not None:
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233 ports = {}
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234 for line in port_text.strip().split('\n'):
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235 if " -> " not in line:
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236 raise Exception("Cannot parse host and port from line [%s]" % line)
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237 tool, host = line.split(" -> ", 1)
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238 hostname, port = host.split(':')
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239 port = int(port)
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240 tool_p, tool_prot = tool.split("/")
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241 tool_p = int(tool_p)
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242 ports[tool_p] = dict(tool_port=tool_p, host=hostname, port=port, protocol=tool_prot)
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243 return ports