Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/utils.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 """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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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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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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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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522 d["location"] = urllib.parse.urlunparse( |
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523 ( |
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524 parse.scheme, |
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525 parse.netloc, |
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526 path, |
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527 parse.params, |
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528 parse.query, |
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529 parse.fragment, |
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530 ) |
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531 ) |
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532 |
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533 if not d.get("basename"): |
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534 if path.startswith("_:"): |
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535 d["basename"] = str(path[2:]) |
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536 else: |
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537 d["basename"] = str(os.path.basename(urllib.request.url2pathname(path))) |
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538 |
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539 if d["class"] == "File": |
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540 nr, ne = os.path.splitext(d["basename"]) |
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541 if d.get("nameroot") != nr: |
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542 d["nameroot"] = str(nr) |
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543 if d.get("nameext") != ne: |
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544 d["nameext"] = str(ne) |
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545 |
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546 visit_class(job, ("File", "Directory"), addLocation) |
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547 |
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548 |
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549 def posix_path(local_path: str) -> str: |
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550 return str(PurePosixPath(Path(local_path))) |
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551 |
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552 |
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553 def local_path(posix_path: str) -> str: |
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554 return str(Path(posix_path)) |
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555 |
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556 |
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557 def create_tmp_dir(tmpdir_prefix: str) -> str: |
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558 """Create a temporary directory that respects the given tmpdir_prefix.""" |
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559 tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix) |
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560 return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir) |