Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/docker_util.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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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 |