Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/singularity.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Support for executing Docker containers using the Singularity 2.x engine."""
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2 from __future__ import absolute_import
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3
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4 import os
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5 import os.path
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6 import re
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7 import shutil
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8 import tempfile
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9 import sys
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10 from distutils import spawn
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11 from io import open # pylint: disable=redefined-builtin
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12 from typing import Dict, List, MutableMapping, Optional, Tuple
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13
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14 from schema_salad.sourceline import SourceLine
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15 from typing_extensions import Text # pylint: disable=unused-import
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16 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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17
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18 from .context import RuntimeContext # pylint: disable=unused-import
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19 from .errors import WorkflowException
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20 from .job import ContainerCommandLineJob
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21 from .loghandler import _logger
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22 from .pathmapper import PathMapper, MapperEnt # pylint: disable=unused-import
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23 from .pathmapper import ensure_writable, ensure_non_writable
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24 from .process import UnsupportedRequirement
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25 from .utils import docker_windows_path_adjust
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26
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27 if os.name == 'posix':
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28 if sys.version_info < (3, 5):
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29 from subprocess32 import ( # nosec # pylint: disable=import-error,no-name-in-module
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30 check_call, check_output, CalledProcessError, DEVNULL, PIPE, Popen,
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31 TimeoutExpired)
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32 else:
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33 from subprocess import ( # nosec # pylint: disable=import-error,no-name-in-module
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34 check_call, check_output, CalledProcessError, DEVNULL, PIPE, Popen,
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35 TimeoutExpired)
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36
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37 else: # we're not on Unix, so none of this matters
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38 pass
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39
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40 _USERNS = None
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41 _SINGULARITY_VERSION = ""
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42
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43 def _singularity_supports_userns(): # type: ()->bool
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44 global _USERNS # pylint: disable=global-statement
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45 if _USERNS is None:
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46 try:
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47 hello_image = os.path.join(os.path.dirname(__file__), 'hello.simg')
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48 result = Popen( # nosec
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49 [u"singularity", u"exec", u"--userns", hello_image, u"true"],
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50 stderr=PIPE, stdout=DEVNULL,
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51 universal_newlines=True).communicate(timeout=60)[1]
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52 _USERNS = "No valid /bin/sh" in result
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53 except TimeoutExpired:
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54 _USERNS = False
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55 return _USERNS
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56
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57
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58 def get_version(): # type: ()->Text
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59 global _SINGULARITY_VERSION # pylint: disable=global-statement
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60 if not _SINGULARITY_VERSION:
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61 _SINGULARITY_VERSION = check_output(["singularity", "--version"], universal_newlines=True)
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62 if _SINGULARITY_VERSION.startswith("singularity version "):
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63 _SINGULARITY_VERSION = _SINGULARITY_VERSION[20:]
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64 return _SINGULARITY_VERSION
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65
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66 def is_version_2_6(): # type: ()->bool
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67 return get_version().startswith("2.6")
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68
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69 def is_version_3_or_newer(): # type: ()->bool
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70 return int(get_version()[0]) >= 3
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71
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72 def is_version_3_1_or_newer(): # type: ()->bool
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73 version = get_version().split('.')
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74 return int(version[0]) >= 4 or (int(version[0]) == 3 and int(version[1]) >= 1)
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75
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76 def _normalize_image_id(string): # type: (Text)->Text
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77 return string.replace('/', '_') + '.img'
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78
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79 def _normalize_sif_id(string): # type: (Text)->Text
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80 return string.replace('/', '_') + '.sif'
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81
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82 class SingularityCommandLineJob(ContainerCommandLineJob):
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83
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84 @staticmethod
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85 def get_image(dockerRequirement, # type: Dict[Text, Text]
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86 pull_image, # type: bool
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87 force_pull=False # type: bool
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88 ):
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89 # type: (...) -> bool
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90 """
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91 Acquire the software container image in the specified dockerRequirement.
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92
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93 Uses Singularity and returns the success as a bool. Updates the
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94 provided dockerRequirement with the specific dockerImageId to the full
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95 path of the local image, if found. Likewise the
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96 dockerRequirement['dockerPull'] is updated to a docker:// URI if needed.
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97 """
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98 found = False
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99
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100 candidates = []
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101
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102 cache_folder = None
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103 if "CWL_SINGULARITY_CACHE" in os.environ:
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104 cache_folder = os.environ["CWL_SINGULARITY_CACHE"]
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105 elif is_version_2_6() and "SINGULARITY_PULLFOLDER" in os.environ:
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106 cache_folder = os.environ["SINGULARITY_PULLFOLDER"]
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107
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108 if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
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109 match = re.search(pattern=r'([a-z]*://)', string=dockerRequirement["dockerPull"])
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110 img_name = _normalize_image_id(dockerRequirement['dockerPull'])
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111 candidates.append(img_name)
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112 if is_version_3_or_newer():
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113 sif_name = _normalize_sif_id(dockerRequirement['dockerPull'])
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114 candidates.append(sif_name)
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115 dockerRequirement["dockerImageId"] = sif_name
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116 else:
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117 dockerRequirement["dockerImageId"] = img_name
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118 if not match:
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119 dockerRequirement["dockerPull"] = "docker://" + dockerRequirement["dockerPull"]
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120 elif "dockerImageId" in dockerRequirement:
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121 if os.path.isfile(dockerRequirement['dockerImageId']):
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122 found = True
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123 candidates.append(dockerRequirement['dockerImageId'])
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124 candidates.append(_normalize_image_id(dockerRequirement['dockerImageId']))
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125 if is_version_3_or_newer():
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126 candidates.append(_normalize_sif_id(dockerRequirement['dockerPull']))
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127
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128 targets = [os.getcwd()]
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129 if "CWL_SINGULARITY_CACHE" in os.environ:
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130 targets.append(os.environ["CWL_SINGULARITY_CACHE"])
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131 if is_version_2_6() and "SINGULARITY_PULLFOLDER" in os.environ:
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132 targets.append(os.environ["SINGULARITY_PULLFOLDER"])
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133 for target in targets:
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134 for dirpath, subdirs, files in os.walk(target):
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135 for entry in files:
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136 if entry in candidates:
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137 path = os.path.join(dirpath, entry)
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138 if os.path.isfile(path):
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139 _logger.info(
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140 "Using local copy of Singularity image found in %s",
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141 dirpath)
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142 dockerRequirement["dockerImageId"] = path
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143 found = True
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144 if (force_pull or not found) and pull_image:
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145 cmd = [] # type: List[Text]
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146 if "dockerPull" in dockerRequirement:
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147 if cache_folder:
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148 env = os.environ.copy()
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149 if is_version_2_6():
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150 env['SINGULARITY_PULLFOLDER'] = cache_folder
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151 cmd = ["singularity", "pull", "--force", "--name",
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152 dockerRequirement["dockerImageId"],
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153 str(dockerRequirement["dockerPull"])]
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154 else:
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155 cmd = ["singularity", "pull", "--force", "--name",
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156 "{}/{}".format(
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157 cache_folder,
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158 dockerRequirement["dockerImageId"]),
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159 str(dockerRequirement["dockerPull"])]
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160
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161 _logger.info(Text(cmd))
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162 check_call(cmd, env=env, stdout=sys.stderr) # nosec
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163 dockerRequirement["dockerImageId"] = '{}/{}'.format(
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164 cache_folder, dockerRequirement["dockerImageId"])
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165 found = True
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166 else:
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167 cmd = ["singularity", "pull", "--force", "--name",
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168 str(dockerRequirement["dockerImageId"]),
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169 str(dockerRequirement["dockerPull"])]
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170 _logger.info(Text(cmd))
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171 check_call(cmd, stdout=sys.stderr) # nosec
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172 found = True
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173
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174 elif "dockerFile" in dockerRequirement:
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175 raise WorkflowException(SourceLine(
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176 dockerRequirement, 'dockerFile').makeError(
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177 "dockerFile is not currently supported when using the "
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178 "Singularity runtime for Docker containers."))
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179 elif "dockerLoad" in dockerRequirement:
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180 if is_version_3_1_or_newer():
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181 if 'dockerImageId' in dockerRequirement:
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182 name = "{}.sif".format(dockerRequirement["dockerImageId"])
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183 else:
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184 name = "{}.sif".format(dockerRequirement["dockerLoad"])
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185 cmd = ["singularity", "build", name,
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186 "docker-archive://{}".format(dockerRequirement["dockerLoad"])]
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187 _logger.info(Text(cmd))
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188 check_call(cmd, stdout=sys.stderr) # nosec
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189 found = True
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190 dockerRequirement['dockerImageId'] = name
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191 raise WorkflowException(SourceLine(
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192 dockerRequirement, 'dockerLoad').makeError(
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193 "dockerLoad is not currently supported when using the "
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194 "Singularity runtime (version less than 3.1) for Docker containers."))
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195 elif "dockerImport" in dockerRequirement:
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196 raise WorkflowException(SourceLine(
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197 dockerRequirement, 'dockerImport').makeError(
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198 "dockerImport is not currently supported when using the "
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199 "Singularity runtime for Docker containers."))
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200
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201 return found
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202
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203 def get_from_requirements(self,
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204 r, # type: Dict[Text, Text]
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205 pull_image, # type: bool
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206 force_pull=False, # type: bool
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207 tmp_outdir_prefix=None # type: Optional[Text]
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208 ):
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209 # type: (...) -> Optional[Text]
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210 """
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211 Return the filename of the Singularity image.
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212
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213 (e.g. hello-world-latest.{img,sif}).
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214 """
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215 if not bool(spawn.find_executable('singularity')):
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216 raise WorkflowException('singularity executable is not available')
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217
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218 if not self.get_image(r, pull_image, force_pull):
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219 raise WorkflowException(u"Container image {} not "
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220 "found".format(r["dockerImageId"]))
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221
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222 return os.path.abspath(r["dockerImageId"])
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223
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224 @staticmethod
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225 def append_volume(runtime, source, target, writable=False):
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226 # type: (List[Text], Text, Text, bool) -> None
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227 runtime.append(u"--bind")
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228 runtime.append("{}:{}:{}".format(
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229 docker_windows_path_adjust(source),
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230 docker_windows_path_adjust(target), "rw" if writable else "ro"))
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231
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232 def add_file_or_directory_volume(self,
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233 runtime, # type: List[Text]
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234 volume, # type: MapperEnt
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235 host_outdir_tgt # type: Optional[Text]
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236 ): # type: (...) -> None
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237 if host_outdir_tgt is not None:
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238 # workaround for lack of overlapping mounts in Singularity
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239 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052
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240 # once https://github.com/sylabs/singularity/issues/1607
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241 # is fixed
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242 if volume.type == "File":
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243 shutil.copy(volume.resolved, host_outdir_tgt)
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244 else:
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245 shutil.copytree(volume.resolved, host_outdir_tgt)
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246 ensure_non_writable(host_outdir_tgt)
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247 elif not volume.resolved.startswith("_:"):
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248 self.append_volume(runtime, volume.resolved, volume.target)
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249
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250 def add_writable_file_volume(self,
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251 runtime, # type: List[Text]
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252 volume, # type: MapperEnt
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253 host_outdir_tgt, # type: Optional[Text]
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254 tmpdir_prefix # type: Text
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255 ): # type: (...) -> None
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256 if host_outdir_tgt is not None:
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257 # workaround for lack of overlapping mounts in Singularity
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258 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052
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259 # once https://github.com/sylabs/singularity/issues/1607
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260 # is fixed
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261 if self.inplace_update:
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262 try:
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263 os.link(os.path.realpath(volume.resolved),
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264 host_outdir_tgt)
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265 except os.error:
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266 shutil.copy(volume.resolved, host_outdir_tgt)
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267 else:
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268 shutil.copy(volume.resolved, host_outdir_tgt)
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269 ensure_writable(host_outdir_tgt)
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270 elif self.inplace_update:
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271 self.append_volume(
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272 runtime, volume.resolved, volume.target, writable=True)
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273 ensure_writable(volume.resolved)
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274 else:
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275 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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276 file_copy = os.path.join(
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277 tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
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278 os.path.basename(volume.resolved))
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279 shutil.copy(volume.resolved, file_copy)
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280 #volume.resolved = file_copy
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281 self.append_volume(
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282 runtime, file_copy, volume.target, writable=True)
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283 ensure_writable(file_copy)
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284
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285 def add_writable_directory_volume(self,
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286 runtime, # type: List[Text]
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287 volume, # type: MapperEnt
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288 host_outdir_tgt, # type: Optional[Text]
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289 tmpdir_prefix # type: Text
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290 ): # type: (...) -> None
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291 if volume.resolved.startswith("_:"):
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292 if host_outdir_tgt is not None:
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293 new_dir = host_outdir_tgt
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294 else:
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295 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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296 new_dir = os.path.join(
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297 tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
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298 os.path.basename(volume.resolved))
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299 os.makedirs(new_dir)
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300 else:
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301 if host_outdir_tgt is not None:
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302 # workaround for lack of overlapping mounts in Singularity
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303 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052
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304 # once https://github.com/sylabs/singularity/issues/1607
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305 # is fixed
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306 shutil.copytree(volume.resolved, host_outdir_tgt)
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307 ensure_writable(host_outdir_tgt)
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308 else:
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diff changeset
309 if not self.inplace_update:
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diff changeset
310 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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311 dir_copy = os.path.join(
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diff changeset
312 tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
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diff changeset
313 os.path.basename(volume.resolved))
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314 shutil.copytree(volume.resolved, dir_copy)
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315 source = dir_copy
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316 #volume.resolved = dir_copy
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317 else:
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318 source = volume.resolved
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319 self.append_volume(
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320 runtime, source, volume.target, writable=True)
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321 ensure_writable(source)
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322
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323
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324 def create_runtime(self,
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325 env, # type: MutableMapping[Text, Text]
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326 runtime_context # type: RuntimeContext
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327 ): # type: (...) -> Tuple[List[Text], Optional[Text]]
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328 """Return the Singularity runtime list of commands and options."""
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329 any_path_okay = self.builder.get_requirement("DockerRequirement")[1] \
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330 or False
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331 runtime = [u"singularity", u"--quiet", u"exec", u"--contain", u"--pid",
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332 u"--ipc"]
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333 if _singularity_supports_userns():
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334 runtime.append(u"--userns")
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diff changeset
335 if is_version_3_1_or_newer():
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336 runtime.append(u"--home")
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337 runtime.append(u"{}:{}".format(
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338 docker_windows_path_adjust(os.path.realpath(self.outdir)),
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diff changeset
339 self.builder.outdir))
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diff changeset
340 else:
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341 runtime.append(u"--bind")
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342 runtime.append(u"{}:{}:rw".format(
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343 docker_windows_path_adjust(os.path.realpath(self.outdir)),
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diff changeset
344 self.builder.outdir))
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345 runtime.append(u"--bind")
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346 tmpdir = "/tmp" # nosec
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diff changeset
347 runtime.append(u"{}:{}:rw".format(
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diff changeset
348 docker_windows_path_adjust(os.path.realpath(self.tmpdir)), tmpdir))
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349
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350 self.add_volumes(self.pathmapper, runtime, any_path_okay=True,
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351 secret_store=runtime_context.secret_store,
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diff changeset
352 tmpdir_prefix=runtime_context.tmpdir_prefix)
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diff changeset
353 if self.generatemapper is not None:
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diff changeset
354 self.add_volumes(
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diff changeset
355 self.generatemapper, runtime, any_path_okay=any_path_okay,
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diff changeset
356 secret_store=runtime_context.secret_store,
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diff changeset
357 tmpdir_prefix=runtime_context.tmpdir_prefix)
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diff changeset
358
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diff changeset
359 runtime.append(u"--pwd")
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diff changeset
360 runtime.append(u"%s" % (docker_windows_path_adjust(self.builder.outdir)))
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parents:
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361
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362
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diff changeset
363 if runtime_context.custom_net:
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diff changeset
364 raise UnsupportedRequirement(
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diff changeset
365 "Singularity implementation does not support custom networking")
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diff changeset
366 elif runtime_context.disable_net:
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diff changeset
367 runtime.append(u"--net")
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diff changeset
368
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diff changeset
369 env["SINGULARITYENV_TMPDIR"] = tmpdir
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diff changeset
370 env["SINGULARITYENV_HOME"] = self.builder.outdir
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371
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diff changeset
372 for name, value in self.environment.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
373 env["SINGULARITYENV_{}".format(name)] = str(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
374 return (runtime, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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375