Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/utils.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 """Shared functions and other definitions."""
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2 from __future__ import absolute_import
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3
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4 import collections
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5 import os
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6 import platform
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7 import random
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8 import shutil
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9 import string
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10 import sys
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11 import tempfile
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12 from functools import partial # pylint: disable=unused-import
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13 from typing import (IO, Any, AnyStr, Callable, # pylint: disable=unused-import
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14 Dict, Iterable, List, MutableMapping, MutableSequence,
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15 Optional, Union)
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16
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17 import pkg_resources
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18 from mypy_extensions import TypedDict
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19 from schema_salad.utils import json_dump, json_dumps # pylint: disable=unused-import
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20 from six.moves import urllib, zip_longest
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21 from typing_extensions import Deque, Text # pylint: disable=unused-import
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22 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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23
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24 from pathlib2 import Path
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25
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26 # no imports from cwltool allowed
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27 if os.name == 'posix':
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28 if sys.version_info < (3, 5):
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29 import subprocess32 as subprocess # nosec # pylint: disable=unused-import
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30 else:
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31 import subprocess # nosec # pylint: disable=unused-import
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32 else:
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33 import subprocess # type: ignore # nosec
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34
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35 windows_default_container_id = "frolvlad/alpine-bash"
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36
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37 Directory = TypedDict('Directory',
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38 {'class': Text, 'listing': List[Dict[Text, Text]],
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39 'basename': Text})
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40
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41 DEFAULT_TMP_PREFIX = tempfile.gettempdir() + os.path.sep
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42
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43 processes_to_kill = collections.deque() # type: Deque[subprocess.Popen]
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44
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45 def versionstring():
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46 # type: () -> Text
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47 """Version of CWLtool used to execute the workflow."""
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48 pkg = pkg_resources.require("cwltool")
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49 if pkg:
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50 return u"%s %s" % (sys.argv[0], pkg[0].version)
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51 return u"%s %s" % (sys.argv[0], "unknown version")
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52
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53 def aslist(l): # type: (Any) -> MutableSequence[Any]
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54 """Wrap any non-MutableSequence/list in a list."""
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55 if isinstance(l, MutableSequence):
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56 return l
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57 return [l]
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58
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59 def copytree_with_merge(src, dst): # type: (Text, Text) -> None
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60 if not os.path.exists(dst):
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61 os.makedirs(dst)
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62 shutil.copystat(src, dst)
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63 lst = os.listdir(src)
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64 for item in lst:
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65 spath = os.path.join(src, item)
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66 dpath = os.path.join(dst, item)
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67 if os.path.isdir(spath):
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68 copytree_with_merge(spath, dpath)
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69 else:
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70 shutil.copy2(spath, dpath)
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71
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72 def docker_windows_path_adjust(path):
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73 # type: (Text) -> Text
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74 r"""
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75 Adjust only windows paths for Docker.
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76
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77 The docker run command treats them as unix paths.
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78
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79 Example: 'C:\Users\foo to /C/Users/foo (Docker for Windows) or /c/Users/foo
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80 (Docker toolbox).
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81 """
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82 if onWindows():
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83 split = path.split(':')
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84 if len(split) == 2:
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85 if platform.win32_ver()[0] in ('7', '8'): # type: ignore
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86 split[0] = split[0].lower() # Docker toolbox uses lowecase windows Drive letters
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87 else:
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88 split[0] = split[0].capitalize()
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89 # Docker for Windows uses uppercase windows Drive letters
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90 path = ':'.join(split)
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91 path = path.replace(':', '').replace('\\', '/')
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92 return path if path[0] == '/' else '/' + path
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93 return path
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94
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95
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96 def docker_windows_reverse_path_adjust(path):
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97 # type: (Text) -> (Text)
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98 r"""
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99 Change docker path (only on windows os) appropriately back to Windows path.
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100
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101 Example: /C/Users/foo to C:\Users\foo
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102 """
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103 if path is not None and onWindows():
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104 if path[0] == '/':
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105 path = path[1:]
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106 else:
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107 raise ValueError("not a docker path")
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108 splitpath = path.split('/')
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109 splitpath[0] = splitpath[0]+':'
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110 return '\\'.join(splitpath)
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111 return path
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112
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113
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114 def docker_windows_reverse_fileuri_adjust(fileuri):
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115 # type: (Text) -> (Text)
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116 r"""
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117 Convert fileuri to be MS Windows comptabile, if needed.
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118
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119 On docker in windows fileuri do not contain : in path
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120 To convert this file uri to windows compatible add : after drive letter,
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121 so file:///E/var becomes file:///E:/var
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122 """
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123 if fileuri is not None and onWindows():
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124 if urllib.parse.urlsplit(fileuri).scheme == "file":
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125 filesplit = fileuri.split("/")
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126 if filesplit[3][-1] != ':':
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127 filesplit[3] = filesplit[3]+':'
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128 return '/'.join(filesplit)
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129 return fileuri
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130 raise ValueError("not a file URI")
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131 return fileuri
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132
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133
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134 def onWindows():
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135 # type: () -> (bool)
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136 """Check if we are on Windows OS."""
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137 return os.name == 'nt'
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138
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139
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140 def convert_pathsep_to_unix(path): # type: (Text) -> (Text)
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141 """
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142 Convert path seperators to unix style.
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143
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144 On windows os.path.join would use backslash to join path, since we would
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145 use these paths in Docker we would convert it to use forward slashes: /
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146 """
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147 if path is not None and onWindows():
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148 return path.replace('\\', '/')
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149 return path
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150
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151 def cmp_like_py2(dict1, dict2): # type: (Dict[Text, Any], Dict[Text, Any]) -> int
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152 """
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153 Compare in the same manner as Python2.
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154
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155 Comparision function to be used in sorting as python3 doesn't allow sorting
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156 of different types like str() and int().
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157 This function re-creates sorting nature in py2 of heterogeneous list of
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158 `int` and `str`
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159 """
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160 # extract lists from both dicts
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161 first, second = dict1["position"], dict2["position"]
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162 # iterate through both list till max of their size
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163 for i, j in zip_longest(first, second):
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164 if i == j:
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165 continue
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166 # in case 1st list is smaller
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167 # should come first in sorting
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168 if i is None:
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169 return -1
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170 # if 1st list is longer,
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171 # it should come later in sort
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172 elif j is None:
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173 return 1
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174
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175 # if either of the list contains str element
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176 # at any index, both should be str before comparing
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177 if isinstance(i, str) or isinstance(j, str):
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178 return 1 if str(i) > str(j) else -1
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179 # int comparison otherwise
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180 return 1 if i > j else -1
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181 # if both lists are equal
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182 return 0
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183
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184
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185 def bytes2str_in_dicts(inp # type: Union[MutableMapping[Text, Any], MutableSequence[Any], Any]
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186 ):
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187 # type: (...) -> Union[Text, MutableSequence[Any], MutableMapping[Text, Any]]
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188 """
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189 Convert any present byte string to unicode string, inplace.
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190
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191 input is a dict of nested dicts and lists
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192 """
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193 # if input is dict, recursively call for each value
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194 if isinstance(inp, MutableMapping):
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195 for k in inp:
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196 inp[k] = bytes2str_in_dicts(inp[k])
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197 return inp
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198
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199 # if list, iterate through list and fn call
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200 # for all its elements
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201 if isinstance(inp, MutableSequence):
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202 for idx, value in enumerate(inp):
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203 inp[idx] = bytes2str_in_dicts(value)
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204 return inp
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205
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206 # if value is bytes, return decoded string,
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207 elif isinstance(inp, bytes):
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208 return inp.decode('utf-8')
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209
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210 # simply return elements itself
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211 return inp
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212
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213
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214 def visit_class(rec, cls, op):
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215 # type: (Any, Iterable[Any], Union[Callable[..., Any], partial[Any]]) -> None
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216 """Apply a function to with "class" in cls."""
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217 if isinstance(rec, MutableMapping):
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218 if "class" in rec and rec.get("class") in cls:
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219 op(rec)
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220 for d in rec:
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221 visit_class(rec[d], cls, op)
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222 if isinstance(rec, MutableSequence):
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223 for d in rec:
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224 visit_class(d, cls, op)
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225
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226 def visit_field(rec, field, op):
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227 # type: (Any, Text, Union[Callable[..., Any], partial[Any]]) -> None
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228 """Apply a function to mapping with 'field'."""
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229 if isinstance(rec, MutableMapping):
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230 if field in rec:
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231 rec[field] = op(rec[field])
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232 for d in rec:
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233 visit_field(rec[d], field, op)
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234 if isinstance(rec, MutableSequence):
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235 for d in rec:
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236 visit_field(d, field, op)
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237
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238
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239 def random_outdir(): # type: () -> Text
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240 """Return the random directory name chosen to use for tool / workflow output."""
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241 # compute this once and store it as a function attribute - each subsequent call will return the same value
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242 if not hasattr(random_outdir, 'outdir'):
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243 random_outdir.outdir = '/' + ''.join([random.choice(string.ascii_letters) for _ in range(6)]) # type: ignore # nosec
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244 return random_outdir.outdir # type: ignore
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245
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246 #
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247 # Simple multi-platform (fcntl/msvrt) file locking wrapper
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248 #
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249 try:
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250 import fcntl
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251
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252 def shared_file_lock(fd): # type: (IO[Any]) -> None
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253 fcntl.flock(fd.fileno(), fcntl.LOCK_SH)
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254
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255 def upgrade_lock(fd): # type: (IO[Any]) -> None
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256 fcntl.flock(fd.fileno(), fcntl.LOCK_EX)
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257
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258 except ImportError:
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259 import msvcrt
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260
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261 def shared_file_lock(fd): # type: (IO[Any]) -> None
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262 msvcrt.locking(fd.fileno(), msvcrt.LK_LOCK, 1024) # type: ignore
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263
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264 def upgrade_lock(fd): # type: (IO[Any]) -> None
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265 pass