annotate env/lib/python3.9/site-packages/cwltool/utils.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Shared functions and other definitions."""
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2
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3 import collections
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4 import os
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5 import platform
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6 import random
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7 import shutil
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8 import stat
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9 import string
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10 import subprocess # nosec
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11 import sys
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12 import tempfile
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13 import urllib
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14 import uuid
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15 from functools import partial
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16 from itertools import zip_longest
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17 from pathlib import Path, PurePosixPath
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18 from tempfile import NamedTemporaryFile
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19 from types import ModuleType
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20 from typing import (
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21 IO,
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22 Any,
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23 Callable,
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24 Dict,
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25 Generator,
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26 Iterable,
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27 List,
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28 MutableMapping,
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29 MutableSequence,
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30 NamedTuple,
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31 Optional,
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32 Set,
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33 Union,
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34 cast,
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35 )
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36
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37 import pkg_resources
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38 import requests
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39 from cachecontrol import CacheControl
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40 from cachecontrol.caches import FileCache
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41 from mypy_extensions import TypedDict
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42 from schema_salad.exceptions import ValidationException
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43 from schema_salad.ref_resolver import Loader
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44 from typing_extensions import TYPE_CHECKING, Deque
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45
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46 if TYPE_CHECKING:
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47 from .command_line_tool import CallbackJob, ExpressionJob
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48 from .job import CommandLineJob, JobBase
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49 from .stdfsaccess import StdFsAccess
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50 from .workflow_job import WorkflowJob
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51
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52 __random_outdir = None # type: Optional[str]
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53
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54 CONTENT_LIMIT = 64 * 1024
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55
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56 windows_default_container_id = "frolvlad/alpine-bash"
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57
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58 DEFAULT_TMP_PREFIX = tempfile.gettempdir() + os.path.sep
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59
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60 processes_to_kill = collections.deque() # type: Deque[subprocess.Popen[str]]
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61
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62 CWLOutputAtomType = Union[
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63 None,
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64 bool,
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65 str,
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66 int,
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67 float,
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68 MutableSequence[
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69 Union[
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70 None, bool, str, int, float, MutableSequence[Any], MutableMapping[str, Any]
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71 ]
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72 ],
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73 MutableMapping[
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74 str,
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75 Union[
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76 None, bool, str, int, float, MutableSequence[Any], MutableMapping[str, Any]
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77 ],
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78 ],
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79 ]
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80 CWLOutputType = Union[
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81 bool,
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82 str,
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83 int,
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84 float,
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85 MutableSequence[CWLOutputAtomType],
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86 MutableMapping[str, CWLOutputAtomType],
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87 ]
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88 CWLObjectType = MutableMapping[str, Optional[CWLOutputType]]
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89 JobsType = Union[
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90 "CommandLineJob", "JobBase", "WorkflowJob", "ExpressionJob", "CallbackJob"
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91 ]
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92 JobsGeneratorType = Generator[Optional[JobsType], None, None]
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93 OutputCallbackType = Callable[[Optional[CWLObjectType], str], None]
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94 ResolverType = Callable[["Loader", str], Optional[str]]
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95 DestinationsType = MutableMapping[str, Optional[CWLOutputType]]
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96 ScatterDestinationsType = MutableMapping[str, List[Optional[CWLOutputType]]]
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97 ScatterOutputCallbackType = Callable[[Optional[ScatterDestinationsType], str], None]
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98 SinkType = Union[CWLOutputType, CWLObjectType]
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99 DirectoryType = TypedDict(
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100 "DirectoryType", {"class": str, "listing": List[CWLObjectType], "basename": str}
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101 )
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102 JSONAtomType = Union[Dict[str, Any], List[Any], str, int, float, bool, None]
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103 JSONType = Union[
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104 Dict[str, JSONAtomType], List[JSONAtomType], str, int, float, bool, None
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105 ]
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106 WorkflowStateItem = NamedTuple(
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107 "WorkflowStateItem",
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108 [
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109 ("parameter", CWLObjectType),
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110 ("value", Optional[CWLOutputType]),
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111 ("success", str),
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112 ],
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113 )
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114
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115 ParametersType = List[CWLObjectType]
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116 StepType = CWLObjectType # WorkflowStep
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117
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118
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119 def versionstring() -> str:
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120 """Version of CWLtool used to execute the workflow."""
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121 pkg = pkg_resources.require("cwltool")
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122 if pkg:
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123 return "{} {}".format(sys.argv[0], pkg[0].version)
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124 return "{} {}".format(sys.argv[0], "unknown version")
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125
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126
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127 def aslist(thing: Any) -> MutableSequence[Any]:
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128 """Wrap any non-MutableSequence/list in a list."""
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129 if isinstance(thing, MutableSequence):
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130 return thing
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131 return [thing]
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132
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133
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134 def copytree_with_merge(src: str, dst: str) -> None:
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135 if not os.path.exists(dst):
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136 os.makedirs(dst)
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137 shutil.copystat(src, dst)
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138 lst = os.listdir(src)
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139 for item in lst:
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140 spath = os.path.join(src, item)
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141 dpath = os.path.join(dst, item)
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142 if os.path.isdir(spath):
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143 copytree_with_merge(spath, dpath)
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144 else:
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145 shutil.copy2(spath, dpath)
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146
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147
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148 def docker_windows_path_adjust(path: str) -> str:
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149 r"""
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150 Adjust only windows paths for Docker.
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151
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152 The docker run command treats them as unix paths.
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153
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154 Example: 'C:\Users\foo to /C/Users/foo (Docker for Windows) or /c/Users/foo
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155 (Docker toolbox).
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156 """
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157 if onWindows():
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158 split = path.split(":")
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159 if len(split) == 2:
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160 if platform.win32_ver()[0] in ("7", "8"):
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161 # Docker toolbox uses lowecase windows Drive letters
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162 split[0] = split[0].lower()
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163 else:
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164 split[0] = split[0].capitalize()
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165 # Docker for Windows uses uppercase windows Drive letters
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166 path = ":".join(split)
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167 path = path.replace(":", "").replace("\\", "/")
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168 return path if path[0] == "/" else "/" + path
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169 return path
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170
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171
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172 def docker_windows_reverse_path_adjust(path: str) -> str:
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173 r"""
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174 Change docker path (only on windows os) appropriately back to Windows path.
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175
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176 Example: /C/Users/foo to C:\Users\foo
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177 """
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178 if path is not None and onWindows():
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179 if path[0] == "/":
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180 path = path[1:]
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181 else:
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182 raise ValueError("not a docker path")
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183 splitpath = path.split("/")
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184 splitpath[0] = splitpath[0] + ":"
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185 return "\\".join(splitpath)
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186 return path
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187
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188
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189 def docker_windows_reverse_fileuri_adjust(fileuri: str) -> str:
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190 r"""
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191 Convert fileuri to be MS Windows comptabile, if needed.
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192
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193 On docker in windows fileuri do not contain : in path
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194 To convert this file uri to windows compatible add : after drive letter,
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195 so file:///E/var becomes file:///E:/var
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196 """
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197 if fileuri is not None and onWindows():
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198 if urllib.parse.urlsplit(fileuri).scheme == "file":
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199 filesplit = fileuri.split("/")
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200 if filesplit[3][-1] != ":":
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201 filesplit[3] = filesplit[3] + ":"
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202 return "/".join(filesplit)
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203 return fileuri
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204 raise ValueError("not a file URI")
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205 return fileuri
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206
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207
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208 def onWindows() -> bool:
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209 """Check if we are on Windows OS."""
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210 return os.name == "nt"
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211
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212
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213 def convert_pathsep_to_unix(path: str) -> str:
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214 """
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215 Convert path seperators to unix style.
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216
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217 On windows os.path.join would use backslash to join path, since we would
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218 use these paths in Docker we would convert it to use forward slashes: /
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219 """
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220 if path is not None and onWindows():
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221 return path.replace("\\", "/")
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222 return path
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223
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224
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225 def cmp_like_py2(dict1: Dict[str, Any], dict2: Dict[str, Any]) -> int:
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226 """
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227 Compare in the same manner as Python2.
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228
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229 Comparision function to be used in sorting as python3 doesn't allow sorting
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230 of different types like str() and int().
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231 This function re-creates sorting nature in py2 of heterogeneous list of
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232 `int` and `str`
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233 """
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234 # extract lists from both dicts
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235 first, second = dict1["position"], dict2["position"]
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236 # iterate through both list till max of their size
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237 for i, j in zip_longest(first, second):
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238 if i == j:
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239 continue
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240 # in case 1st list is smaller
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241 # should come first in sorting
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242 if i is None:
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243 return -1
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244 # if 1st list is longer,
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245 # it should come later in sort
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246 elif j is None:
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247 return 1
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248
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249 # if either of the list contains str element
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250 # at any index, both should be str before comparing
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251 if isinstance(i, str) or isinstance(j, str):
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252 return 1 if str(i) > str(j) else -1
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253 # int comparison otherwise
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254 return 1 if i > j else -1
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255 # if both lists are equal
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256 return 0
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257
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258
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259 def bytes2str_in_dicts(
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260 inp: Union[MutableMapping[str, Any], MutableSequence[Any], Any],
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261 ):
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262 # type: (...) -> Union[str, MutableSequence[Any], MutableMapping[str, Any]]
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263 """
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264 Convert any present byte string to unicode string, inplace.
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265
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266 input is a dict of nested dicts and lists
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267 """
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268 # if input is dict, recursively call for each value
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269 if isinstance(inp, MutableMapping):
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270 for k in inp:
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271 inp[k] = bytes2str_in_dicts(inp[k])
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272 return inp
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273
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274 # if list, iterate through list and fn call
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275 # for all its elements
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276 if isinstance(inp, MutableSequence):
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277 for idx, value in enumerate(inp):
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278 inp[idx] = bytes2str_in_dicts(value)
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279 return inp
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280
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281 # if value is bytes, return decoded string,
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282 elif isinstance(inp, bytes):
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283 return inp.decode("utf-8")
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284
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285 # simply return elements itself
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286 return inp
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287
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288
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289 def visit_class(rec: Any, cls: Iterable[Any], op: Callable[..., Any]) -> None:
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290 """Apply a function to with "class" in cls."""
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291 if isinstance(rec, MutableMapping):
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292 if "class" in rec and rec.get("class") in cls:
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293 op(rec)
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294 for d in rec:
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295 visit_class(rec[d], cls, op)
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296 if isinstance(rec, MutableSequence):
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297 for d in rec:
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298 visit_class(d, cls, op)
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299
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300
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301 def visit_field(rec: Any, field: str, op: Callable[..., Any]) -> None:
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302 """Apply a function to mapping with 'field'."""
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303 if isinstance(rec, MutableMapping):
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304 if field in rec:
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305 rec[field] = op(rec[field])
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306 for d in rec:
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307 visit_field(rec[d], field, op)
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308 if isinstance(rec, MutableSequence):
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309 for d in rec:
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310 visit_field(d, field, op)
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311
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312
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313 def random_outdir() -> str:
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314 """Return the random directory name chosen to use for tool / workflow output."""
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315 global __random_outdir
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316 if not __random_outdir:
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317 __random_outdir = "/" + "".join(
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318 [random.choice(string.ascii_letters) for _ in range(6)] # nosec
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319 )
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320 return __random_outdir
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321 return __random_outdir
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322
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323
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324 #
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325 # Simple multi-platform (fcntl/msvrt) file locking wrapper
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326 #
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327 fcntl = None # type: Optional[ModuleType]
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328 msvcrt = None # type: Optional[ModuleType]
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329 try:
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330 import fcntl # type: ignore
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331 except ImportError:
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332 import msvcrt # type: ignore
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333
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334
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335 def shared_file_lock(fd: IO[Any]) -> None:
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336 if fcntl:
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337 fcntl.flock(fd.fileno(), fcntl.LOCK_SH) # type: ignore
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338 elif msvcrt:
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339 msvcrt.locking(fd.fileno(), msvcrt.LK_LOCK, 1024) # type: ignore
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340
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341
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342 def upgrade_lock(fd: IO[Any]) -> None:
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343 if fcntl:
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344 fcntl.flock(fd.fileno(), fcntl.LOCK_EX) # type: ignore
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345 elif msvcrt:
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346 pass
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347
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348
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349 def adjustFileObjs(
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350 rec, op
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351 ): # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
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352 """Apply an update function to each File object in the object `rec`."""
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353 visit_class(rec, ("File",), op)
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354
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355
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356 def adjustDirObjs(rec, op):
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357 # type: (Any, Union[Callable[..., Any], partial[Any]]) -> None
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358 """Apply an update function to each Directory object in the object `rec`."""
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359 visit_class(rec, ("Directory",), op)
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360
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361
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362 def dedup(listing: List[CWLObjectType]) -> List[CWLObjectType]:
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363 marksub = set()
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364
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365 def mark(d: Dict[str, str]) -> None:
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366 marksub.add(d["location"])
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367
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368 for entry in listing:
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369 if entry["class"] == "Directory":
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370 for e in cast(List[CWLObjectType], entry.get("listing", [])):
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371 adjustFileObjs(e, mark)
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372 adjustDirObjs(e, mark)
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373
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374 dd = []
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375 markdup = set() # type: Set[str]
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376 for r in listing:
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377 if r["location"] not in marksub and r["location"] not in markdup:
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378 dd.append(r)
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379 markdup.add(cast(str, r["location"]))
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380
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381 return dd
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382
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383
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384 def get_listing(
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385 fs_access: "StdFsAccess", rec: CWLObjectType, recursive: bool = True
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386 ) -> None:
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387 if rec.get("class") != "Directory":
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388 finddirs = [] # type: List[CWLObjectType]
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389 visit_class(rec, ("Directory",), finddirs.append)
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390 for f in finddirs:
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391 get_listing(fs_access, f, recursive=recursive)
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392 return
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393 if "listing" in rec:
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394 return
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395 listing = [] # type: List[CWLOutputAtomType]
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396 loc = cast(str, rec["location"])
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397 for ld in fs_access.listdir(loc):
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398 parse = urllib.parse.urlparse(ld)
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399 bn = os.path.basename(urllib.request.url2pathname(parse.path))
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400 if fs_access.isdir(ld):
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401 ent = {
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402 "class": "Directory",
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403 "location": ld,
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404 "basename": bn,
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405 } # type: MutableMapping[str, Any]
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406 if recursive:
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407 get_listing(fs_access, ent, recursive)
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408 listing.append(ent)
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409 else:
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410 listing.append({"class": "File", "location": ld, "basename": bn})
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411 rec["listing"] = listing
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412
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413
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414 def trim_listing(obj): # type: (Dict[str, Any]) -> None
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415 """
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416 Remove 'listing' field from Directory objects that are file references.
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417
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418 It redundant and potentially expensive to pass fully enumerated Directory
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419 objects around if not explicitly needed, so delete the 'listing' field when
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420 it is safe to do so.
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421 """
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422 if obj.get("location", "").startswith("file://") and "listing" in obj:
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423 del obj["listing"]
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424
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425
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426 def downloadHttpFile(httpurl):
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427 # type: (str) -> str
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428 cache_session = None
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429 if "XDG_CACHE_HOME" in os.environ:
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430 directory = os.environ["XDG_CACHE_HOME"]
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431 elif "HOME" in os.environ:
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432 directory = os.environ["HOME"]
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433 else:
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434 directory = os.path.expanduser("~")
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435
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436 cache_session = CacheControl(
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437 requests.Session(),
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438 cache=FileCache(os.path.join(directory, ".cache", "cwltool")),
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439 )
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440
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441 r = cache_session.get(httpurl, stream=True)
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442 with NamedTemporaryFile(mode="wb", delete=False) as f:
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443 for chunk in r.iter_content(chunk_size=16384):
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444 if chunk: # filter out keep-alive new chunks
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445 f.write(chunk)
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446 r.close()
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447 return str(f.name)
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448
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449
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450 def ensure_writable(path): # type: (str) -> None
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451 if os.path.isdir(path):
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452 for root, dirs, files in os.walk(path):
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453 for name in files:
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454 j = os.path.join(root, name)
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455 st = os.stat(j)
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456 mode = stat.S_IMODE(st.st_mode)
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457 os.chmod(j, mode | stat.S_IWUSR)
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458 for name in dirs:
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459 j = os.path.join(root, name)
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460 st = os.stat(j)
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461 mode = stat.S_IMODE(st.st_mode)
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462 os.chmod(j, mode | stat.S_IWUSR)
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463 else:
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464 st = os.stat(path)
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465 mode = stat.S_IMODE(st.st_mode)
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466 os.chmod(path, mode | stat.S_IWUSR)
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467
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468
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469 def ensure_non_writable(path): # type: (str) -> None
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470 if os.path.isdir(path):
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471 for root, dirs, files in os.walk(path):
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472 for name in files:
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473 j = os.path.join(root, name)
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474 st = os.stat(j)
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475 mode = stat.S_IMODE(st.st_mode)
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476 os.chmod(j, mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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477 for name in dirs:
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478 j = os.path.join(root, name)
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479 st = os.stat(j)
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480 mode = stat.S_IMODE(st.st_mode)
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diff changeset
481 os.chmod(j, mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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482 else:
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483 st = os.stat(path)
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484 mode = stat.S_IMODE(st.st_mode)
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diff changeset
485 os.chmod(path, mode & ~stat.S_IWUSR & ~stat.S_IWGRP & ~stat.S_IWOTH)
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486
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487
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488 def normalizeFilesDirs(
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489 job: Optional[
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490 Union[
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491 MutableSequence[MutableMapping[str, Any]],
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492 MutableMapping[str, Any],
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493 DirectoryType,
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494 ]
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495 ]
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496 ) -> None:
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497 def addLocation(d): # type: (Dict[str, Any]) -> None
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498 if "location" not in d:
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499 if d["class"] == "File" and ("contents" not in d):
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500 raise ValidationException(
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501 "Anonymous file object must have 'contents' and 'basename' fields."
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502 )
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503 if d["class"] == "Directory" and (
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504 "listing" not in d or "basename" not in d
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505 ):
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506 raise ValidationException(
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507 "Anonymous directory object must have 'listing' and 'basename' fields."
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508 )
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509 d["location"] = "_:" + str(uuid.uuid4())
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510 if "basename" not in d:
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511 d["basename"] = d["location"][2:]
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parents:
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512
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513 parse = urllib.parse.urlparse(d["location"])
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514 path = parse.path
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515 # strip trailing slash
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516 if path.endswith("/"):
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517 if d["class"] != "Directory":
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518 raise ValidationException(
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519 "location '%s' ends with '/' but is not a Directory" % d["location"]
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520 )
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521 path = path.rstrip("/")
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parents:
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522 d["location"] = urllib.parse.urlunparse(
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shellac
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523 (
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shellac
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524 parse.scheme,
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shellac
parents:
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525 parse.netloc,
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shellac
parents:
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526 path,
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shellac
parents:
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527 parse.params,
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shellac
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528 parse.query,
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shellac
parents:
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529 parse.fragment,
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shellac
parents:
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530 )
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shellac
parents:
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531 )
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shellac
parents:
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532
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shellac
parents:
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533 if not d.get("basename"):
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shellac
parents:
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534 if path.startswith("_:"):
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shellac
parents:
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535 d["basename"] = str(path[2:])
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shellac
parents:
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536 else:
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shellac
parents:
diff changeset
537 d["basename"] = str(os.path.basename(urllib.request.url2pathname(path)))
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shellac
parents:
diff changeset
538
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shellac
parents:
diff changeset
539 if d["class"] == "File":
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shellac
parents:
diff changeset
540 nr, ne = os.path.splitext(d["basename"])
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shellac
parents:
diff changeset
541 if d.get("nameroot") != nr:
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shellac
parents:
diff changeset
542 d["nameroot"] = str(nr)
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shellac
parents:
diff changeset
543 if d.get("nameext") != ne:
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shellac
parents:
diff changeset
544 d["nameext"] = str(ne)
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shellac
parents:
diff changeset
545
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shellac
parents:
diff changeset
546 visit_class(job, ("File", "Directory"), addLocation)
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shellac
parents:
diff changeset
547
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shellac
parents:
diff changeset
548
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shellac
parents:
diff changeset
549 def posix_path(local_path: str) -> str:
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shellac
parents:
diff changeset
550 return str(PurePosixPath(Path(local_path)))
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shellac
parents:
diff changeset
551
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shellac
parents:
diff changeset
552
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shellac
parents:
diff changeset
553 def local_path(posix_path: str) -> str:
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shellac
parents:
diff changeset
554 return str(Path(posix_path))
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shellac
parents:
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555
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shellac
parents:
diff changeset
556
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shellac
parents:
diff changeset
557 def create_tmp_dir(tmpdir_prefix: str) -> str:
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shellac
parents:
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558 """Create a temporary directory that respects the given tmpdir_prefix."""
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shellac
parents:
diff changeset
559 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
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shellac
parents:
diff changeset
560 return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)