Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/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 """Enables Docker software containers via the {u,}docker runtimes.""" |
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2 |
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3 import csv |
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4 import datetime |
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5 import os |
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6 import re |
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7 import shutil |
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8 import subprocess # nosec |
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9 import sys |
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10 import threading |
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11 from distutils import spawn |
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12 from io import StringIO # pylint: disable=redefined-builtin |
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13 from typing import Callable, Dict, List, MutableMapping, Optional, Set, Tuple, cast |
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14 |
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15 import requests |
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16 |
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17 from .builder import Builder |
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18 from .context import RuntimeContext |
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19 from .docker_id import docker_vm_id |
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20 from .errors import WorkflowException |
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21 from .job import ContainerCommandLineJob |
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22 from .loghandler import _logger |
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23 from .pathmapper import MapperEnt, PathMapper |
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24 from .utils import ( |
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25 CWLObjectType, |
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26 create_tmp_dir, |
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27 docker_windows_path_adjust, |
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28 ensure_writable, |
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29 onWindows, |
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30 ) |
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31 |
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32 _IMAGES = set() # type: Set[str] |
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33 _IMAGES_LOCK = threading.Lock() |
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34 __docker_machine_mounts = None # type: Optional[List[str]] |
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35 __docker_machine_mounts_lock = threading.Lock() |
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36 |
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37 |
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38 def _get_docker_machine_mounts() -> List[str]: |
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39 global __docker_machine_mounts |
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40 if __docker_machine_mounts is None: |
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41 with __docker_machine_mounts_lock: |
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42 if "DOCKER_MACHINE_NAME" not in os.environ: |
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43 __docker_machine_mounts = [] |
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44 else: |
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45 __docker_machine_mounts = [ |
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46 "/" + line.split(None, 1)[0] |
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47 for line in subprocess.check_output( # nosec |
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48 [ |
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49 "docker-machine", |
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50 "ssh", |
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51 os.environ["DOCKER_MACHINE_NAME"], |
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52 "mount", |
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53 "-t", |
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54 "vboxsf", |
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55 ], |
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56 universal_newlines=True, |
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57 ).splitlines() |
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58 ] |
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59 return __docker_machine_mounts |
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60 |
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61 |
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62 def _check_docker_machine_path(path: Optional[str]) -> None: |
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63 if path is None: |
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64 return |
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65 if onWindows(): |
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66 path = path.lower() |
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67 mounts = _get_docker_machine_mounts() |
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68 |
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69 found = False |
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70 for mount in mounts: |
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71 if onWindows(): |
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72 mount = mount.lower() |
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73 if path.startswith(mount): |
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74 found = True |
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75 break |
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76 |
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77 if not found and mounts: |
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78 name = os.environ.get("DOCKER_MACHINE_NAME", "???") |
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79 raise WorkflowException( |
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80 "Input path {path} is not in the list of host paths mounted " |
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81 "into the Docker virtual machine named {name}. Already mounted " |
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82 "paths: {mounts}.\n" |
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83 "See https://docs.docker.com/toolbox/toolbox_install_windows/" |
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84 "#optional-add-shared-directories for instructions on how to " |
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85 "add this path to your VM.".format(path=path, name=name, mounts=mounts) |
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86 ) |
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87 |
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88 |
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89 class DockerCommandLineJob(ContainerCommandLineJob): |
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90 """Runs a CommandLineJob in a sofware container using the Docker engine.""" |
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91 |
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92 def __init__( |
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93 self, |
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94 builder: Builder, |
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95 joborder: CWLObjectType, |
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96 make_path_mapper: Callable[..., PathMapper], |
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97 requirements: List[CWLObjectType], |
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98 hints: List[CWLObjectType], |
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99 name: str, |
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100 ) -> None: |
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101 """Initialize a command line builder using the Docker software container engine.""" |
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102 super().__init__(builder, joborder, make_path_mapper, requirements, hints, name) |
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103 |
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104 @staticmethod |
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105 def get_image( |
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106 docker_requirement: Dict[str, str], |
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107 pull_image: bool, |
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108 force_pull: bool, |
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109 tmp_outdir_prefix: str, |
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110 ) -> bool: |
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111 """ |
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112 Retrieve the relevant Docker container image. |
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113 |
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114 Returns True upon success |
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115 """ |
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116 found = False |
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117 |
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118 if ( |
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119 "dockerImageId" not in docker_requirement |
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120 and "dockerPull" in docker_requirement |
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121 ): |
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122 docker_requirement["dockerImageId"] = docker_requirement["dockerPull"] |
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123 |
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124 with _IMAGES_LOCK: |
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125 if docker_requirement["dockerImageId"] in _IMAGES: |
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126 return True |
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127 |
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128 for line in ( |
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129 subprocess.check_output( # nosec |
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130 ["docker", "images", "--no-trunc", "--all"] |
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131 ) |
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132 .decode("utf-8") |
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133 .splitlines() |
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134 ): |
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135 try: |
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136 match = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", line) |
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137 split = docker_requirement["dockerImageId"].split(":") |
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138 if len(split) == 1: |
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139 split.append("latest") |
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140 elif len(split) == 2: |
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141 # if split[1] doesn't match valid tag names, it is a part of repository |
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142 if not re.match(r"[\w][\w.-]{0,127}", split[1]): |
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143 split[0] = split[0] + ":" + split[1] |
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144 split[1] = "latest" |
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145 elif len(split) == 3: |
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146 if re.match(r"[\w][\w.-]{0,127}", split[2]): |
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147 split[0] = split[0] + ":" + split[1] |
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148 split[1] = split[2] |
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149 del split[2] |
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150 |
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151 # check for repository:tag match or image id match |
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152 if match and ( |
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153 (split[0] == match.group(1) and split[1] == match.group(2)) |
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154 or docker_requirement["dockerImageId"] == match.group(3) |
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155 ): |
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156 found = True |
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157 break |
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158 except ValueError: |
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159 pass |
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160 |
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161 if (force_pull or not found) and pull_image: |
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162 cmd = [] # type: List[str] |
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163 if "dockerPull" in docker_requirement: |
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164 cmd = ["docker", "pull", str(docker_requirement["dockerPull"])] |
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165 _logger.info(str(cmd)) |
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166 subprocess.check_call(cmd, stdout=sys.stderr) # nosec |
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167 found = True |
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168 elif "dockerFile" in docker_requirement: |
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169 dockerfile_dir = create_tmp_dir(tmp_outdir_prefix) |
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170 with open(os.path.join(dockerfile_dir, "Dockerfile"), "wb") as dfile: |
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171 dfile.write(docker_requirement["dockerFile"].encode("utf-8")) |
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172 cmd = [ |
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173 "docker", |
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174 "build", |
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175 "--tag=%s" % str(docker_requirement["dockerImageId"]), |
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176 dockerfile_dir, |
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177 ] |
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178 _logger.info(str(cmd)) |
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179 subprocess.check_call(cmd, stdout=sys.stderr) # nosec |
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180 found = True |
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181 elif "dockerLoad" in docker_requirement: |
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182 cmd = ["docker", "load"] |
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183 _logger.info(str(cmd)) |
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184 if os.path.exists(docker_requirement["dockerLoad"]): |
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185 _logger.info( |
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186 "Loading docker image from %s", |
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187 docker_requirement["dockerLoad"], |
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188 ) |
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189 with open(docker_requirement["dockerLoad"], "rb") as dload: |
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190 loadproc = subprocess.Popen( # nosec |
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191 cmd, stdin=dload, stdout=sys.stderr |
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192 ) |
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193 else: |
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194 loadproc = subprocess.Popen( # nosec |
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195 cmd, stdin=subprocess.PIPE, stdout=sys.stderr |
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196 ) |
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197 assert loadproc.stdin is not None # nosec |
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198 _logger.info( |
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199 "Sending GET request to %s", docker_requirement["dockerLoad"] |
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200 ) |
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201 req = requests.get(docker_requirement["dockerLoad"], stream=True) |
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202 size = 0 |
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203 for chunk in req.iter_content(1024 * 1024): |
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204 size += len(chunk) |
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205 _logger.info("\r%i bytes", size) |
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206 loadproc.stdin.write(chunk) |
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207 loadproc.stdin.close() |
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208 rcode = loadproc.wait() |
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209 if rcode != 0: |
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210 raise WorkflowException( |
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211 "Docker load returned non-zero exit status %i" % (rcode) |
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212 ) |
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213 found = True |
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214 elif "dockerImport" in docker_requirement: |
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215 cmd = [ |
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216 "docker", |
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217 "import", |
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218 str(docker_requirement["dockerImport"]), |
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219 str(docker_requirement["dockerImageId"]), |
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220 ] |
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221 _logger.info(str(cmd)) |
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222 subprocess.check_call(cmd, stdout=sys.stderr) # nosec |
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223 found = True |
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224 |
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225 if found: |
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226 with _IMAGES_LOCK: |
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227 _IMAGES.add(docker_requirement["dockerImageId"]) |
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228 |
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229 return found |
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230 |
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231 def get_from_requirements( |
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232 self, |
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233 r: CWLObjectType, |
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234 pull_image: bool, |
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235 force_pull: bool, |
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236 tmp_outdir_prefix: str, |
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237 ) -> Optional[str]: |
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238 if not spawn.find_executable("docker"): |
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239 raise WorkflowException("docker executable is not available") |
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240 |
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241 if self.get_image( |
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242 cast(Dict[str, str], r), pull_image, force_pull, tmp_outdir_prefix |
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243 ): |
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244 return cast(Optional[str], r["dockerImageId"]) |
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245 raise WorkflowException("Docker image %s not found" % r["dockerImageId"]) |
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246 |
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247 @staticmethod |
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248 def append_volume( |
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249 runtime: List[str], source: str, target: str, writable: bool = False |
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250 ) -> None: |
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251 """Add binding arguments to the runtime list.""" |
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252 options = [ |
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253 "type=bind", |
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254 "source=" + source, |
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255 "target=" + target, |
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256 ] |
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257 if not writable: |
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258 options.append("readonly") |
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259 output = StringIO() |
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260 csv.writer(output).writerow(options) |
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261 mount_arg = output.getvalue().strip() |
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262 runtime.append(f"--mount={mount_arg}") |
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263 # Unlike "--volume", "--mount" will fail if the volume doesn't already exist. |
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264 if not os.path.exists(source): |
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265 os.makedirs(source) |
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266 |
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267 def add_file_or_directory_volume( |
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268 self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str] |
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269 ) -> None: |
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270 """Append volume a file/dir mapping to the runtime option list.""" |
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271 if not volume.resolved.startswith("_:"): |
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272 _check_docker_machine_path(docker_windows_path_adjust(volume.resolved)) |
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273 self.append_volume(runtime, volume.resolved, volume.target) |
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274 |
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275 def add_writable_file_volume( |
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276 self, |
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277 runtime: List[str], |
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278 volume: MapperEnt, |
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279 host_outdir_tgt: Optional[str], |
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280 tmpdir_prefix: str, |
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281 ) -> None: |
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282 """Append a writable file mapping to the runtime option list.""" |
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283 if self.inplace_update: |
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284 self.append_volume(runtime, volume.resolved, volume.target, writable=True) |
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285 else: |
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286 if host_outdir_tgt: |
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287 # shortcut, just copy to the output directory |
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288 # which is already going to be mounted |
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289 if not os.path.exists(os.path.dirname(host_outdir_tgt)): |
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290 os.makedirs(os.path.dirname(host_outdir_tgt)) |
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291 shutil.copy(volume.resolved, host_outdir_tgt) |
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292 else: |
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293 tmpdir = create_tmp_dir(tmpdir_prefix) |
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294 file_copy = os.path.join(tmpdir, os.path.basename(volume.resolved)) |
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295 shutil.copy(volume.resolved, file_copy) |
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296 self.append_volume(runtime, file_copy, volume.target, writable=True) |
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297 ensure_writable(host_outdir_tgt or file_copy) |
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298 |
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299 def add_writable_directory_volume( |
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300 self, |
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301 runtime: List[str], |
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302 volume: MapperEnt, |
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303 host_outdir_tgt: Optional[str], |
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304 tmpdir_prefix: str, |
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305 ) -> None: |
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306 """Append a writable directory mapping to the runtime option list.""" |
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307 if volume.resolved.startswith("_:"): |
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308 # Synthetic directory that needs creating first |
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309 if not host_outdir_tgt: |
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310 new_dir = os.path.join( |
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311 create_tmp_dir(tmpdir_prefix), |
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312 os.path.basename(volume.target), |
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313 ) |
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314 self.append_volume(runtime, new_dir, volume.target, writable=True) |
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315 elif not os.path.exists(host_outdir_tgt): |
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316 os.makedirs(host_outdir_tgt) |
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317 else: |
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318 if self.inplace_update: |
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319 self.append_volume( |
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320 runtime, volume.resolved, volume.target, writable=True |
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321 ) |
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322 else: |
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323 if not host_outdir_tgt: |
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324 tmpdir = create_tmp_dir(tmpdir_prefix) |
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325 new_dir = os.path.join(tmpdir, os.path.basename(volume.resolved)) |
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326 shutil.copytree(volume.resolved, new_dir) |
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327 self.append_volume(runtime, new_dir, volume.target, writable=True) |
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328 else: |
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329 shutil.copytree(volume.resolved, host_outdir_tgt) |
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330 ensure_writable(host_outdir_tgt or new_dir) |
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331 |
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332 def create_runtime( |
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333 self, env: MutableMapping[str, str], runtimeContext: RuntimeContext |
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334 ) -> Tuple[List[str], Optional[str]]: |
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335 any_path_okay = self.builder.get_requirement("DockerRequirement")[1] or False |
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336 user_space_docker_cmd = runtimeContext.user_space_docker_cmd |
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337 if user_space_docker_cmd: |
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338 if "udocker" in user_space_docker_cmd and not runtimeContext.debug: |
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339 runtime = [user_space_docker_cmd, "--quiet", "run"] |
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340 # udocker 1.1.1 will output diagnostic messages to stdout |
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341 # without this |
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342 else: |
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343 runtime = [user_space_docker_cmd, "run"] |
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344 else: |
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345 runtime = ["docker", "run", "-i"] |
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346 self.append_volume( |
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347 runtime, os.path.realpath(self.outdir), self.builder.outdir, writable=True |
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348 ) |
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349 tmpdir = "/tmp" # nosec |
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350 self.append_volume( |
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351 runtime, os.path.realpath(self.tmpdir), tmpdir, writable=True |
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352 ) |
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353 self.add_volumes( |
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354 self.pathmapper, |
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355 runtime, |
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356 any_path_okay=True, |
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357 secret_store=runtimeContext.secret_store, |
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358 tmpdir_prefix=runtimeContext.tmpdir_prefix, |
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359 ) |
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360 if self.generatemapper is not None: |
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361 self.add_volumes( |
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362 self.generatemapper, |
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363 runtime, |
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364 any_path_okay=any_path_okay, |
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365 secret_store=runtimeContext.secret_store, |
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366 tmpdir_prefix=runtimeContext.tmpdir_prefix, |
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367 ) |
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368 |
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369 if user_space_docker_cmd: |
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370 runtime = [x.replace(":ro", "") for x in runtime] |
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371 runtime = [x.replace(":rw", "") for x in runtime] |
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372 |
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373 runtime.append( |
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374 "--workdir=%s" % (docker_windows_path_adjust(self.builder.outdir)) |
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375 ) |
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376 if not user_space_docker_cmd: |
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377 |
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378 if not runtimeContext.no_read_only: |
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379 runtime.append("--read-only=true") |
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380 |
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381 if self.networkaccess: |
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382 if runtimeContext.custom_net: |
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383 runtime.append(f"--net={runtimeContext.custom_net}") |
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384 else: |
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385 runtime.append("--net=none") |
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386 |
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387 if self.stdout is not None: |
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388 runtime.append("--log-driver=none") |
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389 |
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390 euid, egid = docker_vm_id() |
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391 if not onWindows(): |
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392 # MS Windows does not have getuid() or geteuid() functions |
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393 euid, egid = euid or os.geteuid(), egid or os.getgid() |
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394 |
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395 if runtimeContext.no_match_user is False and ( |
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396 euid is not None and egid is not None |
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397 ): |
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398 runtime.append("--user=%d:%d" % (euid, egid)) |
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399 |
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400 if runtimeContext.rm_container: |
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401 runtime.append("--rm") |
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402 |
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403 runtime.append("--env=TMPDIR=/tmp") |
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404 |
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405 # spec currently says "HOME must be set to the designated output |
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406 # directory." but spec might change to designated temp directory. |
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407 # runtime.append("--env=HOME=/tmp") |
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408 runtime.append("--env=HOME=%s" % self.builder.outdir) |
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409 |
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410 cidfile_path = None # type: Optional[str] |
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411 # add parameters to docker to write a container ID file |
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412 if runtimeContext.user_space_docker_cmd is None: |
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413 if runtimeContext.cidfile_dir: |
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414 cidfile_dir = runtimeContext.cidfile_dir |
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415 if not os.path.exists(str(cidfile_dir)): |
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416 _logger.error( |
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417 "--cidfile-dir %s error:\n%s", |
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418 cidfile_dir, |
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419 "directory doesn't exist, please create it first", |
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420 ) |
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421 exit(2) |
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422 if not os.path.isdir(cidfile_dir): |
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423 _logger.error( |
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424 "--cidfile-dir %s error:\n%s", |
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425 cidfile_dir, |
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426 cidfile_dir + " is not a directory, please check it first", |
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427 ) |
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428 exit(2) |
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429 else: |
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430 cidfile_dir = runtimeContext.create_tmpdir() |
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431 |
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432 cidfile_name = datetime.datetime.now().strftime("%Y%m%d%H%M%S-%f") + ".cid" |
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433 if runtimeContext.cidfile_prefix is not None: |
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434 cidfile_name = str(runtimeContext.cidfile_prefix + "-" + cidfile_name) |
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435 cidfile_path = os.path.join(cidfile_dir, cidfile_name) |
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436 runtime.append("--cidfile=%s" % cidfile_path) |
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437 for key, value in self.environment.items(): |
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438 runtime.append(f"--env={key}={value}") |
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439 |
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440 if runtimeContext.strict_memory_limit and not user_space_docker_cmd: |
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441 ram = self.builder.resources["ram"] |
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442 if not isinstance(ram, str): |
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443 runtime.append("--memory=%dm" % ram) |
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444 elif not user_space_docker_cmd: |
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445 res_req, _ = self.builder.get_requirement("ResourceRequirement") |
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446 if res_req and ("ramMin" in res_req or "ramMax" in res_req): |
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447 _logger.warning( |
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448 "[job %s] Skipping Docker software container '--memory' limit " |
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449 "despite presence of ResourceRequirement with ramMin " |
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450 "and/or ramMax setting. Consider running with " |
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451 "--strict-memory-limit for increased portability " |
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452 "assurance.", |
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453 self.name, |
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454 ) |
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455 |
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456 return runtime, cidfile_path |