Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/docker.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 """Enables Docker software containers via the {dx-,u,}docker runtimes."""
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2 from __future__ import absolute_import
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3
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4 from distutils import spawn
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5 import datetime
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6 import os
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7 import re
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8 import shutil
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9 import sys
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10 import tempfile
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11 import threading
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12 from io import open # pylint: disable=redefined-builtin
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13 from typing import Dict, List, MutableMapping, Optional, Set, Tuple
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14
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15 import requests
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16 from typing_extensions import Text # pylint: disable=unused-import
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17 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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18
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19 from .context import RuntimeContext # pylint: disable=unused-import
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20 from .docker_id import docker_vm_id
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21 from .errors import WorkflowException
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22 from .job import ContainerCommandLineJob
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23 from .loghandler import _logger
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24 from .pathmapper import PathMapper, MapperEnt # pylint: disable=unused-import
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25 from .pathmapper import ensure_writable, ensure_non_writable
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26 from .secrets import SecretStore # pylint: disable=unused-import
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27 from .utils import (DEFAULT_TMP_PREFIX, docker_windows_path_adjust, onWindows,
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28 subprocess)
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29
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30
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31 _IMAGES = set() # type: Set[Text]
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32 _IMAGES_LOCK = threading.Lock()
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33 __docker_machine_mounts = None # type: Optional[List[Text]]
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34 __docker_machine_mounts_lock = threading.Lock()
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35
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36 def _get_docker_machine_mounts(): # type: () -> List[Text]
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37 global __docker_machine_mounts
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38 if __docker_machine_mounts is None:
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39 with __docker_machine_mounts_lock:
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40 if 'DOCKER_MACHINE_NAME' not in os.environ:
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41 __docker_machine_mounts = []
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42 else:
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43 __docker_machine_mounts = [
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44 u'/' + line.split(None, 1)[0] for line in
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45 subprocess.check_output(
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46 ['docker-machine', 'ssh',
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47 os.environ['DOCKER_MACHINE_NAME'], 'mount', '-t',
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48 'vboxsf'],
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49 universal_newlines=True).splitlines()]
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50 return __docker_machine_mounts
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51
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52 def _check_docker_machine_path(path): # type: (Optional[Text]) -> None
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53 if path is None:
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54 return
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55 if onWindows():
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56 path = path.lower()
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57 mounts = _get_docker_machine_mounts()
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58
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59 found = False
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60 for mount in mounts:
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61 if onWindows():
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62 mount = mount.lower()
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63 if path.startswith(mount):
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64 found = True
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65 break
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66
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67 if not found and mounts:
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68 name = os.environ.get("DOCKER_MACHINE_NAME", '???')
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69 raise WorkflowException(
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70 "Input path {path} is not in the list of host paths mounted "
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71 "into the Docker virtual machine named {name}. Already mounted "
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72 "paths: {mounts}.\n"
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73 "See https://docs.docker.com/toolbox/toolbox_install_windows/"
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74 "#optional-add-shared-directories for instructions on how to "
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75 "add this path to your VM.".format(
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76 path=path, name=name,
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77 mounts=mounts))
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78
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79 class DockerCommandLineJob(ContainerCommandLineJob):
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80 """Runs a CommandLineJob in a sofware container using the Docker engine."""
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81
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82 @staticmethod
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83 def get_image(docker_requirement, # type: Dict[Text, Text]
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84 pull_image, # type: bool
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85 force_pull=False, # type: bool
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86 tmp_outdir_prefix=DEFAULT_TMP_PREFIX # type: Text
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87 ): # type: (...) -> bool
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88 """
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89 Retrieve the relevant Docker container image.
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90
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91 Returns True upon success
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92 """
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93 found = False
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94
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95 if "dockerImageId" not in docker_requirement \
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96 and "dockerPull" in docker_requirement:
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97 docker_requirement["dockerImageId"] = docker_requirement["dockerPull"]
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98
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99 with _IMAGES_LOCK:
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100 if docker_requirement["dockerImageId"] in _IMAGES:
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101 return True
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102
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103 for line in subprocess.check_output(
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104 ["docker", "images", "--no-trunc", "--all"]).decode('utf-8').splitlines():
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105 try:
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106 match = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", line)
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107 split = docker_requirement["dockerImageId"].split(":")
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108 if len(split) == 1:
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109 split.append("latest")
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110 elif len(split) == 2:
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111 # if split[1] doesn't match valid tag names, it is a part of repository
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112 if not re.match(r'[\w][\w.-]{0,127}', split[1]):
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113 split[0] = split[0] + ":" + split[1]
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114 split[1] = "latest"
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115 elif len(split) == 3:
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116 if re.match(r'[\w][\w.-]{0,127}', split[2]):
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117 split[0] = split[0] + ":" + split[1]
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118 split[1] = split[2]
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119 del split[2]
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120
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121 # check for repository:tag match or image id match
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122 if (match
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123 and (
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124 (split[0] == match.group(1) and split[1] == match.group(2))
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125 or docker_requirement["dockerImageId"] == match.group(3))):
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126 found = True
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127 break
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128 except ValueError:
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129 pass
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130
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131 if (force_pull or not found) and pull_image:
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132 cmd = [] # type: List[Text]
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133 if "dockerPull" in docker_requirement:
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134 cmd = ["docker", "pull", str(docker_requirement["dockerPull"])]
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135 _logger.info(Text(cmd))
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136 subprocess.check_call(cmd, stdout=sys.stderr)
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137 found = True
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138 elif "dockerFile" in docker_requirement:
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139 dockerfile_dir = str(tempfile.mkdtemp(prefix=tmp_outdir_prefix))
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140 with open(os.path.join(
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141 dockerfile_dir, "Dockerfile"), "wb") as dfile:
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142 dfile.write(docker_requirement["dockerFile"].encode('utf-8'))
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143 cmd = ["docker", "build", "--tag=%s" %
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144 str(docker_requirement["dockerImageId"]), dockerfile_dir]
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145 _logger.info(Text(cmd))
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146 subprocess.check_call(cmd, stdout=sys.stderr)
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147 found = True
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148 elif "dockerLoad" in docker_requirement:
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149 cmd = ["docker", "load"]
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150 _logger.info(Text(cmd))
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151 if os.path.exists(docker_requirement["dockerLoad"]):
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152 _logger.info(u"Loading docker image from %s", docker_requirement["dockerLoad"])
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153 with open(docker_requirement["dockerLoad"], "rb") as dload:
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154 loadproc = subprocess.Popen(cmd, stdin=dload, stdout=sys.stderr)
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155 else:
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156 loadproc = subprocess.Popen(cmd, stdin=subprocess.PIPE,
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157 stdout=sys.stderr)
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158 assert loadproc.stdin is not None # nosec
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159 _logger.info(u"Sending GET request to %s", docker_requirement["dockerLoad"])
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160 req = requests.get(docker_requirement["dockerLoad"], stream=True)
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161 size = 0
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162 for chunk in req.iter_content(1024 * 1024):
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163 size += len(chunk)
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164 _logger.info("\r%i bytes", size)
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165 loadproc.stdin.write(chunk)
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166 loadproc.stdin.close()
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167 rcode = loadproc.wait()
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168 if rcode != 0:
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169 raise WorkflowException(
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170 "Docker load returned non-zero exit status %i" % (rcode))
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171 found = True
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172 elif "dockerImport" in docker_requirement:
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173 cmd = ["docker", "import", str(docker_requirement["dockerImport"]),
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174 str(docker_requirement["dockerImageId"])]
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175 _logger.info(Text(cmd))
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176 subprocess.check_call(cmd, stdout=sys.stderr)
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177 found = True
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178
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179 if found:
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180 with _IMAGES_LOCK:
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181 _IMAGES.add(docker_requirement["dockerImageId"])
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182
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183 return found
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184
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185 def get_from_requirements(self,
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186 r, # type: Dict[Text, Text]
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187 pull_image, # type: bool
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188 force_pull=False, # type: bool
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189 tmp_outdir_prefix=DEFAULT_TMP_PREFIX # type: Text
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190 ): # type: (...) -> Optional[Text]
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191 if not spawn.find_executable('docker'):
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192 raise WorkflowException("docker executable is not available")
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193
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194
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195 if self.get_image(r, pull_image, force_pull, tmp_outdir_prefix):
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196 return r["dockerImageId"]
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197 raise WorkflowException(u"Docker image %s not found" % r["dockerImageId"])
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198
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199 @staticmethod
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200 def append_volume(runtime, source, target, writable=False):
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201 # type: (List[Text], Text, Text, bool) -> None
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202 """Add binding arguments to the runtime list."""
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203 runtime.append(u"--volume={}:{}:{}".format(
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204 docker_windows_path_adjust(source), target,
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205 "rw" if writable else "ro"))
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206
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207 def add_file_or_directory_volume(self,
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208 runtime, # type: List[Text]
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209 volume, # type: MapperEnt
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210 host_outdir_tgt # type: Optional[Text]
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211 ): # type: (...) -> None
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212 """Append volume a file/dir mapping to the runtime option list."""
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213 if not volume.resolved.startswith("_:"):
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214 _check_docker_machine_path(docker_windows_path_adjust(
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215 volume.resolved))
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216 self.append_volume(runtime, volume.resolved, volume.target)
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217
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218 def add_writable_file_volume(self,
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219 runtime, # type: List[Text]
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220 volume, # type: MapperEnt
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221 host_outdir_tgt, # type: Optional[Text]
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222 tmpdir_prefix # type: Text
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223 ): # type: (...) -> None
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224 """Append a writable file mapping to the runtime option list."""
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225 if self.inplace_update:
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226 self.append_volume(runtime, volume.resolved, volume.target,
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227 writable=True)
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228 else:
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229 if host_outdir_tgt:
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230 # shortcut, just copy to the output directory
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231 # which is already going to be mounted
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diff changeset
232 if not os.path.exists(os.path.dirname(host_outdir_tgt)):
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233 os.makedirs(os.path.dirname(host_outdir_tgt))
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234 shutil.copy(volume.resolved, host_outdir_tgt)
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235 else:
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236 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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237 tmpdir = tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
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238 file_copy = os.path.join(
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239 tmpdir, os.path.basename(volume.resolved))
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diff changeset
240 shutil.copy(volume.resolved, file_copy)
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241 self.append_volume(runtime, file_copy, volume.target,
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242 writable=True)
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243 ensure_writable(host_outdir_tgt or file_copy)
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244
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245 def add_writable_directory_volume(self,
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246 runtime, # type: List[Text]
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247 volume, # type: MapperEnt
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248 host_outdir_tgt, # type: Optional[Text]
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249 tmpdir_prefix # type: Text
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250 ): # type: (...) -> None
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251 """Append a writable directory mapping to the runtime option list."""
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252 if volume.resolved.startswith("_:"):
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253 # Synthetic directory that needs creating first
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254 if not host_outdir_tgt:
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255 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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256 new_dir = os.path.join(
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257 tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
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258 os.path.basename(volume.target))
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259 self.append_volume(runtime, new_dir, volume.target,
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260 writable=True)
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261 elif not os.path.exists(host_outdir_tgt):
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262 os.makedirs(host_outdir_tgt)
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263 else:
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264 if self.inplace_update:
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265 self.append_volume(runtime, volume.resolved, volume.target,
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266 writable=True)
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267 else:
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268 if not host_outdir_tgt:
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269 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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270 tmpdir = tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
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271 new_dir = os.path.join(
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272 tmpdir, os.path.basename(volume.resolved))
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273 shutil.copytree(volume.resolved, new_dir)
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274 self.append_volume(
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275 runtime, new_dir, volume.target,
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276 writable=True)
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277 else:
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278 shutil.copytree(volume.resolved, host_outdir_tgt)
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279 ensure_writable(host_outdir_tgt or new_dir)
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280
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281 def create_runtime(self,
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282 env, # type: MutableMapping[Text, Text]
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283 runtimeContext # type: RuntimeContext
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284 ): # type: (...) -> Tuple[List[Text], Optional[Text]]
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285 any_path_okay = self.builder.get_requirement("DockerRequirement")[1] \
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286 or False
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287 user_space_docker_cmd = runtimeContext.user_space_docker_cmd
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288 if user_space_docker_cmd:
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289 if 'udocker' in user_space_docker_cmd and not runtimeContext.debug:
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290 runtime = [user_space_docker_cmd, u"--quiet", u"run"]
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291 # udocker 1.1.1 will output diagnostic messages to stdout
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292 # without this
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293 else:
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294 runtime = [user_space_docker_cmd, u"run"]
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295 else:
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296 runtime = [u"docker", u"run", u"-i"]
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297 self.append_volume(runtime, os.path.realpath(self.outdir),
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298 self.builder.outdir, writable=True)
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299 tmpdir = "/tmp" # nosec
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300 self.append_volume(runtime, os.path.realpath(self.tmpdir), tmpdir,
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301 writable=True)
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302 self.add_volumes(self.pathmapper, runtime, any_path_okay=True,
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303 secret_store=runtimeContext.secret_store,
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304 tmpdir_prefix=runtimeContext.tmpdir_prefix)
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305 if self.generatemapper is not None:
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306 self.add_volumes(
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307 self.generatemapper, runtime, any_path_okay=any_path_okay,
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308 secret_store=runtimeContext.secret_store,
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309 tmpdir_prefix=runtimeContext.tmpdir_prefix)
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310
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diff changeset
311 if user_space_docker_cmd:
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diff changeset
312 runtime = [x.replace(":ro", "") for x in runtime]
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313 runtime = [x.replace(":rw", "") for x in runtime]
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314
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315 runtime.append(u"--workdir=%s" % (
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316 docker_windows_path_adjust(self.builder.outdir)))
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317 if not user_space_docker_cmd:
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318
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diff changeset
319 if not runtimeContext.no_read_only:
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diff changeset
320 runtime.append(u"--read-only=true")
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321
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diff changeset
322 if self.networkaccess:
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diff changeset
323 if runtimeContext.custom_net:
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diff changeset
324 runtime.append(u"--net={0}".format(runtimeContext.custom_net))
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diff changeset
325 else:
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diff changeset
326 runtime.append(u"--net=none")
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diff changeset
327
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328 if self.stdout is not None:
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diff changeset
329 runtime.append("--log-driver=none")
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diff changeset
330
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diff changeset
331 euid, egid = docker_vm_id()
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parents:
diff changeset
332 if not onWindows():
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parents:
diff changeset
333 # MS Windows does not have getuid() or geteuid() functions
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parents:
diff changeset
334 euid, egid = euid or os.geteuid(), egid or os.getgid()
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diff changeset
335
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parents:
diff changeset
336 if runtimeContext.no_match_user is False \
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parents:
diff changeset
337 and (euid is not None and egid is not None):
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parents:
diff changeset
338 runtime.append(u"--user=%d:%d" % (euid, egid))
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339
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diff changeset
340 if runtimeContext.rm_container:
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diff changeset
341 runtime.append(u"--rm")
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parents:
diff changeset
342
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343 runtime.append(u"--env=TMPDIR=/tmp")
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344
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345 # spec currently says "HOME must be set to the designated output
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diff changeset
346 # directory." but spec might change to designated temp directory.
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347 # runtime.append("--env=HOME=/tmp")
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348 runtime.append(u"--env=HOME=%s" % self.builder.outdir)
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349
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diff changeset
350 # add parameters to docker to write a container ID file
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parents:
diff changeset
351 if runtimeContext.user_space_docker_cmd is None:
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parents:
diff changeset
352 if runtimeContext.cidfile_dir:
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parents:
diff changeset
353 cidfile_dir = runtimeContext.cidfile_dir
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parents:
diff changeset
354 if not os.path.exists(str(cidfile_dir)):
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parents:
diff changeset
355 _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
356 "directory doesn't exist, please create it first")
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parents:
diff changeset
357 exit(2)
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parents:
diff changeset
358 if not os.path.isdir(cidfile_dir):
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parents:
diff changeset
359 _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
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parents:
diff changeset
360 cidfile_dir + " is not a directory, "
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parents:
diff changeset
361 "please check it first")
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parents:
diff changeset
362 exit(2)
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parents:
diff changeset
363 else:
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parents:
diff changeset
364 tmp_dir, tmp_prefix = os.path.split(runtimeContext.tmpdir_prefix)
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parents:
diff changeset
365 cidfile_dir = tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
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parents:
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366
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diff changeset
367 cidfile_name = datetime.datetime.now().strftime("%Y%m%d%H%M%S-%f") + ".cid"
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parents:
diff changeset
368 if runtimeContext.cidfile_prefix is not None:
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parents:
diff changeset
369 cidfile_name = str(runtimeContext.cidfile_prefix + "-" + cidfile_name)
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parents:
diff changeset
370 cidfile_path = os.path.join(cidfile_dir, cidfile_name)
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parents:
diff changeset
371 runtime.append(u"--cidfile=%s" % cidfile_path)
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372 else:
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373 cidfile_path = None
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374 for key, value in self.environment.items():
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375 runtime.append(u"--env=%s=%s" % (key, value))
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376
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377 if runtimeContext.strict_memory_limit and not user_space_docker_cmd:
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378 runtime.append("--memory=%dm" % self.builder.resources["ram"])
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379 elif not user_space_docker_cmd:
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380 res_req, _ = self.builder.get_requirement("ResourceRequirement")
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381 if res_req is not None and ("ramMin" in res_req or "ramMax" is res_req):
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382 _logger.warning(
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383 u"[job %s] Skipping Docker software container '--memory' limit "
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384 "despite presence of ResourceRequirement with ramMin "
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385 "and/or ramMax setting. Consider running with "
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386 "--strict-memory-limit for increased portability "
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387 "assurance.", self.name)
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388
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389 return runtime, cidfile_path