Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/singularity.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 """Support for executing Docker containers using the Singularity 2.x engine.""" |
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2 |
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3 import os |
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4 import os.path |
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5 import re |
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6 import shutil |
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7 import sys |
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8 from distutils import spawn |
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9 from subprocess import ( # nosec |
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10 DEVNULL, |
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11 PIPE, |
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12 Popen, |
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13 TimeoutExpired, |
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14 check_call, |
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15 check_output, |
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16 ) |
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17 from typing import Callable, Dict, List, MutableMapping, Optional, Tuple, cast |
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18 |
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19 from schema_salad.sourceline import SourceLine |
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20 |
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21 from .builder import Builder |
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22 from .context import RuntimeContext |
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23 from .errors import UnsupportedRequirement, WorkflowException |
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24 from .job import ContainerCommandLineJob |
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25 from .loghandler import _logger |
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26 from .pathmapper import MapperEnt, PathMapper |
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27 from .utils import ( |
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28 CWLObjectType, |
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29 create_tmp_dir, |
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30 docker_windows_path_adjust, |
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31 ensure_non_writable, |
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32 ensure_writable, |
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33 ) |
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34 |
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35 _USERNS = None # type: Optional[bool] |
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36 _SINGULARITY_VERSION = "" |
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37 |
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38 |
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39 def _singularity_supports_userns() -> bool: |
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40 global _USERNS # pylint: disable=global-statement |
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41 if _USERNS is None: |
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42 try: |
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43 hello_image = os.path.join(os.path.dirname(__file__), "hello.simg") |
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44 result = Popen( # nosec |
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45 ["singularity", "exec", "--userns", hello_image, "true"], |
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46 stderr=PIPE, |
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47 stdout=DEVNULL, |
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48 universal_newlines=True, |
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49 ).communicate(timeout=60)[1] |
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50 _USERNS = ( |
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51 "No valid /bin/sh" in result |
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52 or "/bin/sh doesn't exist in container" in result |
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53 or "executable file not found in" in result |
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54 ) |
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55 except TimeoutExpired: |
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56 _USERNS = False |
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57 return _USERNS |
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58 |
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59 |
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60 def get_version() -> str: |
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61 global _SINGULARITY_VERSION # pylint: disable=global-statement |
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62 if not _SINGULARITY_VERSION: |
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63 _SINGULARITY_VERSION = check_output( # nosec |
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64 ["singularity", "--version"], universal_newlines=True |
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65 ) |
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66 if _SINGULARITY_VERSION.startswith("singularity version "): |
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67 _SINGULARITY_VERSION = _SINGULARITY_VERSION[20:] |
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68 return _SINGULARITY_VERSION |
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69 |
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70 |
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71 def is_version_2_6() -> bool: |
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72 return get_version().startswith("2.6") |
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73 |
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74 |
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75 def is_version_3_or_newer() -> bool: |
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76 return int(get_version()[0]) >= 3 |
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77 |
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78 |
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79 def is_version_3_1_or_newer() -> bool: |
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80 version = get_version().split(".") |
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81 return int(version[0]) >= 4 or (int(version[0]) == 3 and int(version[1]) >= 1) |
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82 |
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83 |
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84 def _normalize_image_id(string: str) -> str: |
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85 return string.replace("/", "_") + ".img" |
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86 |
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87 |
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88 def _normalize_sif_id(string: str) -> str: |
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89 return string.replace("/", "_") + ".sif" |
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90 |
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91 |
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92 class SingularityCommandLineJob(ContainerCommandLineJob): |
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93 def __init__( |
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94 self, |
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95 builder: Builder, |
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96 joborder: CWLObjectType, |
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97 make_path_mapper: Callable[..., PathMapper], |
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98 requirements: List[CWLObjectType], |
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99 hints: List[CWLObjectType], |
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100 name: str, |
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101 ) -> None: |
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102 """Builder for invoking the Singularty software container engine.""" |
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103 super().__init__(builder, joborder, make_path_mapper, requirements, hints, name) |
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104 |
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105 @staticmethod |
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106 def get_image( |
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107 dockerRequirement: Dict[str, str], |
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108 pull_image: bool, |
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109 force_pull: bool = False, |
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110 ) -> bool: |
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111 """ |
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112 Acquire the software container image in the specified dockerRequirement. |
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113 |
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114 Uses Singularity and returns the success as a bool. Updates the |
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115 provided dockerRequirement with the specific dockerImageId to the full |
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116 path of the local image, if found. Likewise the |
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117 dockerRequirement['dockerPull'] is updated to a docker:// URI if needed. |
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118 """ |
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119 found = False |
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120 |
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121 candidates = [] |
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122 |
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123 cache_folder = None |
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124 if "CWL_SINGULARITY_CACHE" in os.environ: |
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125 cache_folder = os.environ["CWL_SINGULARITY_CACHE"] |
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126 elif is_version_2_6() and "SINGULARITY_PULLFOLDER" in os.environ: |
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127 cache_folder = os.environ["SINGULARITY_PULLFOLDER"] |
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128 |
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129 if ( |
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130 "dockerImageId" not in dockerRequirement |
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131 and "dockerPull" in dockerRequirement |
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132 ): |
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133 match = re.search( |
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134 pattern=r"([a-z]*://)", string=dockerRequirement["dockerPull"] |
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135 ) |
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136 img_name = _normalize_image_id(dockerRequirement["dockerPull"]) |
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137 candidates.append(img_name) |
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138 if is_version_3_or_newer(): |
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139 sif_name = _normalize_sif_id(dockerRequirement["dockerPull"]) |
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140 candidates.append(sif_name) |
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141 dockerRequirement["dockerImageId"] = sif_name |
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142 else: |
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143 dockerRequirement["dockerImageId"] = img_name |
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144 if not match: |
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145 dockerRequirement["dockerPull"] = ( |
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146 "docker://" + dockerRequirement["dockerPull"] |
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147 ) |
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148 elif "dockerImageId" in dockerRequirement: |
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149 if os.path.isfile(dockerRequirement["dockerImageId"]): |
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150 found = True |
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151 candidates.append(dockerRequirement["dockerImageId"]) |
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152 candidates.append(_normalize_image_id(dockerRequirement["dockerImageId"])) |
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153 if is_version_3_or_newer(): |
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154 candidates.append(_normalize_sif_id(dockerRequirement["dockerPull"])) |
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155 |
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156 targets = [os.getcwd()] |
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157 if "CWL_SINGULARITY_CACHE" in os.environ: |
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158 targets.append(os.environ["CWL_SINGULARITY_CACHE"]) |
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159 if is_version_2_6() and "SINGULARITY_PULLFOLDER" in os.environ: |
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160 targets.append(os.environ["SINGULARITY_PULLFOLDER"]) |
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161 for target in targets: |
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162 for dirpath, _subdirs, files in os.walk(target): |
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163 for entry in files: |
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164 if entry in candidates: |
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165 path = os.path.join(dirpath, entry) |
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166 if os.path.isfile(path): |
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167 _logger.info( |
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168 "Using local copy of Singularity image found in %s", |
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169 dirpath, |
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170 ) |
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171 dockerRequirement["dockerImageId"] = path |
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172 found = True |
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173 if (force_pull or not found) and pull_image: |
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174 cmd = [] # type: List[str] |
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175 if "dockerPull" in dockerRequirement: |
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176 if cache_folder: |
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177 env = os.environ.copy() |
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178 if is_version_2_6(): |
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179 env["SINGULARITY_PULLFOLDER"] = cache_folder |
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180 cmd = [ |
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181 "singularity", |
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182 "pull", |
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183 "--force", |
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184 "--name", |
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185 dockerRequirement["dockerImageId"], |
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186 str(dockerRequirement["dockerPull"]), |
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187 ] |
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188 else: |
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189 cmd = [ |
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190 "singularity", |
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191 "pull", |
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192 "--force", |
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193 "--name", |
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194 "{}/{}".format( |
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195 cache_folder, dockerRequirement["dockerImageId"] |
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196 ), |
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197 str(dockerRequirement["dockerPull"]), |
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198 ] |
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199 |
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200 _logger.info(str(cmd)) |
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201 check_call(cmd, env=env, stdout=sys.stderr) # nosec |
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202 dockerRequirement["dockerImageId"] = "{}/{}".format( |
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203 cache_folder, dockerRequirement["dockerImageId"] |
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204 ) |
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205 found = True |
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206 else: |
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207 cmd = [ |
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208 "singularity", |
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209 "pull", |
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210 "--force", |
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211 "--name", |
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212 str(dockerRequirement["dockerImageId"]), |
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213 str(dockerRequirement["dockerPull"]), |
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214 ] |
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215 _logger.info(str(cmd)) |
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216 check_call(cmd, stdout=sys.stderr) # nosec |
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217 found = True |
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218 |
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219 elif "dockerFile" in dockerRequirement: |
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220 raise WorkflowException( |
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221 SourceLine(dockerRequirement, "dockerFile").makeError( |
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222 "dockerFile is not currently supported when using the " |
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223 "Singularity runtime for Docker containers." |
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224 ) |
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225 ) |
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226 elif "dockerLoad" in dockerRequirement: |
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227 if is_version_3_1_or_newer(): |
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228 if "dockerImageId" in dockerRequirement: |
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229 name = "{}.sif".format(dockerRequirement["dockerImageId"]) |
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230 else: |
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231 name = "{}.sif".format(dockerRequirement["dockerLoad"]) |
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232 cmd = [ |
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233 "singularity", |
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234 "build", |
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235 name, |
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236 "docker-archive://{}".format(dockerRequirement["dockerLoad"]), |
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237 ] |
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238 _logger.info(str(cmd)) |
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239 check_call(cmd, stdout=sys.stderr) # nosec |
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240 found = True |
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241 dockerRequirement["dockerImageId"] = name |
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242 raise WorkflowException( |
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243 SourceLine(dockerRequirement, "dockerLoad").makeError( |
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244 "dockerLoad is not currently supported when using the " |
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245 "Singularity runtime (version less than 3.1) for Docker containers." |
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246 ) |
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247 ) |
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248 elif "dockerImport" in dockerRequirement: |
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249 raise WorkflowException( |
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250 SourceLine(dockerRequirement, "dockerImport").makeError( |
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251 "dockerImport is not currently supported when using the " |
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252 "Singularity runtime for Docker containers." |
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253 ) |
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254 ) |
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255 |
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256 return found |
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257 |
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258 def get_from_requirements( |
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259 self, |
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260 r: CWLObjectType, |
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261 pull_image: bool, |
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262 force_pull: bool, |
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263 tmp_outdir_prefix: str, |
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264 ) -> Optional[str]: |
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265 """ |
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266 Return the filename of the Singularity image. |
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267 |
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268 (e.g. hello-world-latest.{img,sif}). |
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269 """ |
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270 if not bool(spawn.find_executable("singularity")): |
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271 raise WorkflowException("singularity executable is not available") |
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272 |
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273 if not self.get_image(cast(Dict[str, str], r), pull_image, force_pull): |
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274 raise WorkflowException( |
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275 "Container image {} not found".format(r["dockerImageId"]) |
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276 ) |
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277 |
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278 return os.path.abspath(cast(str, r["dockerImageId"])) |
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279 |
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280 @staticmethod |
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281 def append_volume( |
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282 runtime: List[str], source: str, target: str, writable: bool = False |
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283 ) -> None: |
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284 runtime.append("--bind") |
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285 runtime.append( |
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286 "{}:{}:{}".format( |
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287 docker_windows_path_adjust(source), |
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288 docker_windows_path_adjust(target), |
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289 "rw" if writable else "ro", |
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290 ) |
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291 ) |
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292 |
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293 def add_file_or_directory_volume( |
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294 self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str] |
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295 ) -> None: |
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296 if host_outdir_tgt is not None: |
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297 # workaround for lack of overlapping mounts in Singularity |
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298 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052 |
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299 # once https://github.com/sylabs/singularity/issues/1607 |
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300 # is fixed |
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301 if volume.type == "File": |
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302 shutil.copy(volume.resolved, host_outdir_tgt) |
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303 else: |
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304 shutil.copytree(volume.resolved, host_outdir_tgt) |
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305 ensure_non_writable(host_outdir_tgt) |
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306 elif not volume.resolved.startswith("_:"): |
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307 self.append_volume(runtime, volume.resolved, volume.target) |
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308 |
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309 def add_writable_file_volume( |
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310 self, |
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311 runtime: List[str], |
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312 volume: MapperEnt, |
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313 host_outdir_tgt: Optional[str], |
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314 tmpdir_prefix: str, |
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315 ) -> None: |
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316 if host_outdir_tgt is not None: |
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317 # workaround for lack of overlapping mounts in Singularity |
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318 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052 |
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319 # once https://github.com/sylabs/singularity/issues/1607 |
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320 # is fixed |
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321 if self.inplace_update: |
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322 try: |
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323 os.link(os.path.realpath(volume.resolved), host_outdir_tgt) |
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324 except os.error: |
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325 shutil.copy(volume.resolved, host_outdir_tgt) |
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326 else: |
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327 shutil.copy(volume.resolved, host_outdir_tgt) |
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328 ensure_writable(host_outdir_tgt) |
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329 elif self.inplace_update: |
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330 self.append_volume(runtime, volume.resolved, volume.target, writable=True) |
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331 ensure_writable(volume.resolved) |
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332 else: |
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333 file_copy = os.path.join( |
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334 create_tmp_dir(tmpdir_prefix), |
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335 os.path.basename(volume.resolved), |
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336 ) |
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337 shutil.copy(volume.resolved, file_copy) |
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338 # volume.resolved = file_copy |
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339 self.append_volume(runtime, file_copy, volume.target, writable=True) |
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340 ensure_writable(file_copy) |
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341 |
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342 def add_writable_directory_volume( |
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343 self, |
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344 runtime: List[str], |
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345 volume: MapperEnt, |
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346 host_outdir_tgt: Optional[str], |
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347 tmpdir_prefix: str, |
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348 ) -> None: |
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349 if volume.resolved.startswith("_:"): |
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350 if host_outdir_tgt is not None: |
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351 new_dir = host_outdir_tgt |
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352 else: |
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353 new_dir = os.path.join( |
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354 create_tmp_dir(tmpdir_prefix), |
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355 os.path.basename(volume.resolved), |
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356 ) |
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357 os.makedirs(new_dir) |
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358 else: |
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359 if host_outdir_tgt is not None: |
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360 # workaround for lack of overlapping mounts in Singularity |
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361 # revert to daa923d5b0be3819b6ed0e6440e7193e65141052 |
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362 # once https://github.com/sylabs/singularity/issues/1607 |
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363 # is fixed |
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364 shutil.copytree(volume.resolved, host_outdir_tgt) |
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365 ensure_writable(host_outdir_tgt) |
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366 else: |
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367 if not self.inplace_update: |
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368 dir_copy = os.path.join( |
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369 create_tmp_dir(tmpdir_prefix), |
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370 os.path.basename(volume.resolved), |
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371 ) |
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372 shutil.copytree(volume.resolved, dir_copy) |
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373 source = dir_copy |
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374 # volume.resolved = dir_copy |
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375 else: |
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376 source = volume.resolved |
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377 self.append_volume(runtime, source, volume.target, writable=True) |
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378 ensure_writable(source) |
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379 |
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380 def create_runtime( |
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381 self, env: MutableMapping[str, str], runtime_context: RuntimeContext |
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382 ) -> Tuple[List[str], Optional[str]]: |
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383 """Return the Singularity runtime list of commands and options.""" |
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384 any_path_okay = self.builder.get_requirement("DockerRequirement")[1] or False |
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385 runtime = [ |
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386 "singularity", |
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387 "--quiet", |
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388 "exec", |
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389 "--contain", |
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390 "--ipc", |
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391 ] |
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392 if _singularity_supports_userns(): |
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393 runtime.append("--userns") |
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394 else: |
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395 runtime.append("--pid") |
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396 if is_version_3_1_or_newer(): |
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397 runtime.append("--home") |
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398 runtime.append( |
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399 "{}:{}".format( |
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400 docker_windows_path_adjust(os.path.realpath(self.outdir)), |
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401 self.builder.outdir, |
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402 ) |
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403 ) |
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404 else: |
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405 runtime.append("--bind") |
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406 runtime.append( |
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407 "{}:{}:rw".format( |
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408 docker_windows_path_adjust(os.path.realpath(self.outdir)), |
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409 self.builder.outdir, |
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410 ) |
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411 ) |
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412 runtime.append("--bind") |
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413 tmpdir = "/tmp" # nosec |
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414 runtime.append( |
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415 "{}:{}:rw".format( |
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416 docker_windows_path_adjust(os.path.realpath(self.tmpdir)), tmpdir |
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417 ) |
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418 ) |
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419 |
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420 self.add_volumes( |
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421 self.pathmapper, |
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422 runtime, |
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423 any_path_okay=True, |
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424 secret_store=runtime_context.secret_store, |
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425 tmpdir_prefix=runtime_context.tmpdir_prefix, |
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426 ) |
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427 if self.generatemapper is not None: |
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428 self.add_volumes( |
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429 self.generatemapper, |
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430 runtime, |
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431 any_path_okay=any_path_okay, |
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432 secret_store=runtime_context.secret_store, |
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433 tmpdir_prefix=runtime_context.tmpdir_prefix, |
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434 ) |
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435 |
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436 runtime.append("--pwd") |
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437 runtime.append("%s" % (docker_windows_path_adjust(self.builder.outdir))) |
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438 |
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439 if runtime_context.custom_net: |
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440 raise UnsupportedRequirement( |
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441 "Singularity implementation does not support custom networking" |
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442 ) |
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443 elif runtime_context.disable_net: |
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444 runtime.append("--net") |
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445 |
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446 env["SINGULARITYENV_TMPDIR"] = tmpdir |
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447 env["SINGULARITYENV_HOME"] = self.builder.outdir |
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448 |
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449 for name, value in self.environment.items(): |
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450 env[f"SINGULARITYENV_{name}"] = str(value) |
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451 return (runtime, None) |