Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/object_wrapper.py @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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0
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1 """
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2 Classes for wrapping Objects and Sanitizing string output.
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3 """
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4 from __future__ import absolute_import
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5
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6 import collections
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7 import inspect
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8 import logging
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9 import string
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10 import sys
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11 from numbers import Number
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12 from types import (
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13 BuiltinFunctionType,
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14 BuiltinMethodType,
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15 CodeType,
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16 FrameType,
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17 FunctionType,
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18 GeneratorType,
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19 GetSetDescriptorType,
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20 MemberDescriptorType,
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21 MethodType,
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22 ModuleType,
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23 TracebackType,
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24 )
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25
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26 try:
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27 from types import NoneType
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28 except ImportError:
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29 NoneType = type(None)
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30 try:
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31 from types import NotImplementedType
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32 except ImportError:
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33 NotImplementedType = type(NotImplemented)
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34
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35 try:
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36 from types import EllipsisType
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37 except ImportError:
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38 EllipsisType = type(Ellipsis)
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39
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40 try:
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41 from types import XRangeType
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42 except ImportError:
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43 XRangeType = range
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44
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45 try:
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46 from types import SliceType
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47 except ImportError:
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48 SliceType = slice
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49
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50 try:
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51 from types import (
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52 BufferType,
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53 DictProxyType
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54 )
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55 except ImportError:
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56 # Py3 doesn't have these concepts, just treat them like SliceType that
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57 # so they are __WRAP_NO_SUBCLASS__.
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58 BufferType = SliceType
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59 DictProxyType = SliceType
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60
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61 from six.moves import (
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62 copyreg as copy_reg,
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63 UserDict
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64 )
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65
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66 from galaxy.util import sanitize_lists_to_string as _sanitize_lists_to_string
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67
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68 log = logging.getLogger(__name__)
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69
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70 # Define different behaviors for different types, see also: https://docs.python.org/2/library/types.html
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71
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72 # Known Callable types
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73 __CALLABLE_TYPES__ = (FunctionType, MethodType, GeneratorType, CodeType, BuiltinFunctionType, BuiltinMethodType, )
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74
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75 # Always wrap these types without attempting to subclass
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76 __WRAP_NO_SUBCLASS__ = (ModuleType, XRangeType, SliceType, BufferType, TracebackType, FrameType, DictProxyType,
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77 GetSetDescriptorType, MemberDescriptorType) + __CALLABLE_TYPES__
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78
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79 # Don't wrap or sanitize.
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80 __DONT_SANITIZE_TYPES__ = (Number, bool, NoneType, NotImplementedType, EllipsisType, bytearray, )
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81
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82 # Don't wrap, but do sanitize.
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83 __DONT_WRAP_TYPES__ = tuple() # ( basestring, ) so that we can get the unsanitized string, we will now wrap basestring instances
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84
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85 # Wrap contents, but not the container
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86 __WRAP_SEQUENCES__ = (tuple, list, )
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87 __WRAP_SETS__ = (set, frozenset, )
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88 __WRAP_MAPPINGS__ = (dict, UserDict, )
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89
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90
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91 # Define the set of characters that are not sanitized, and define a set of mappings for those that are.
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92 # characters that are valid
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93 VALID_CHARACTERS = set(string.ascii_letters + string.digits + " -=_.()/+*^,:?!@")
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94
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95 # characters that are allowed but need to be escaped
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96 CHARACTER_MAP = {'>': '__gt__',
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97 '<': '__lt__',
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98 "'": '__sq__',
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99 '"': '__dq__',
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100 '[': '__ob__',
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101 ']': '__cb__',
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102 '{': '__oc__',
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103 '}': '__cc__',
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104 '\n': '__cn__',
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105 '\r': '__cr__',
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106 '\t': '__tc__',
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107 '#': '__pd__'}
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108
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109 INVALID_CHARACTER = "X"
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110
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111 if sys.version_info > (3, 0):
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112 # __coerce__ doesn't do anything under Python anyway.
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113 def coerce(x, y):
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114 return x
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115
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116
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117 def cmp(x, y):
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118 # Builtin in Python 2, but not Python 3.
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119 return (x > y) - (x < y)
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120
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121
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122 def sanitize_lists_to_string(values, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP, invalid_character=INVALID_CHARACTER):
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123 return _sanitize_lists_to_string(values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
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124
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125
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126 def wrap_with_safe_string(value, no_wrap_classes=None):
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127 """
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128 Recursively wrap values that should be wrapped.
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129 """
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130
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131 def __do_wrap(value):
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132 if isinstance(value, SafeStringWrapper):
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133 # Only ever wrap one-layer
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134 return value
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135 if isinstance(value, collections.Callable):
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136 safe_class = CallableSafeStringWrapper
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137 else:
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138 safe_class = SafeStringWrapper
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139 if isinstance(value, no_wrap_classes):
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140 return value
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141 if isinstance(value, __DONT_WRAP_TYPES__):
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142 return sanitize_lists_to_string(value, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)
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143 if isinstance(value, __WRAP_NO_SUBCLASS__):
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144 return safe_class(value, safe_string_wrapper_function=__do_wrap)
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145 for this_type in __WRAP_SEQUENCES__ + __WRAP_SETS__:
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146 if isinstance(value, this_type):
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147 return this_type(map(__do_wrap, value))
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148 for this_type in __WRAP_MAPPINGS__:
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149 if isinstance(value, this_type):
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150 # Wrap both key and value
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151 return this_type((__do_wrap(x[0]), __do_wrap(x[1])) for x in value.items())
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152 # Create a dynamic class that joins SafeStringWrapper with the object being wrapped.
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153 # This allows e.g. isinstance to continue to work.
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154 try:
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155 wrapped_class_name = value.__name__
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156 wrapped_class = value
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157 except Exception:
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158 wrapped_class_name = value.__class__.__name__
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159 wrapped_class = value.__class__
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160 value_mod = inspect.getmodule(value)
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161 if value_mod:
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162 wrapped_class_name = "%s.%s" % (value_mod.__name__, wrapped_class_name)
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163 wrapped_class_name = "SafeStringWrapper(%s:%s)" % (wrapped_class_name, ",".join(sorted(map(str, no_wrap_classes))))
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164 do_wrap_func_name = "__do_wrap_%s" % (wrapped_class_name)
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165 do_wrap_func = __do_wrap
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166 global_dict = globals()
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167 if wrapped_class_name in global_dict:
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168 # Check to see if we have created a wrapper for this class yet, if so, reuse
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169 wrapped_class = global_dict.get(wrapped_class_name)
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170 do_wrap_func = global_dict.get(do_wrap_func_name, __do_wrap)
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171 else:
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172 try:
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173 wrapped_class = type(wrapped_class_name, (safe_class, wrapped_class, ), {})
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174 except TypeError as e:
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175 # Fail-safe for when a class cannot be dynamically subclassed.
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176 log.warning("Unable to create dynamic subclass for %s, %s: %s", type(value), value, e)
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177 wrapped_class = type(wrapped_class_name, (safe_class, ), {})
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178 if wrapped_class not in (SafeStringWrapper, CallableSafeStringWrapper):
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179 # Save this wrapper for reuse and pickling/copying
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180 global_dict[wrapped_class_name] = wrapped_class
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181 do_wrap_func.__name__ = do_wrap_func_name
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182 global_dict[do_wrap_func_name] = do_wrap_func
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183
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184 def pickle_safe_object(safe_object):
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185 return (wrapped_class, (safe_object.unsanitized, do_wrap_func, ))
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186 # Set pickle and copy properties
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187 copy_reg.pickle(wrapped_class, pickle_safe_object, do_wrap_func)
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188 return wrapped_class(value, safe_string_wrapper_function=do_wrap_func)
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189
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190 # Determine classes not to wrap
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191 if no_wrap_classes:
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192 if not isinstance(no_wrap_classes, (tuple, list)):
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193 no_wrap_classes = [no_wrap_classes]
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194 no_wrap_classes = list(no_wrap_classes) + list(__DONT_SANITIZE_TYPES__) + [SafeStringWrapper]
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195 else:
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196 no_wrap_classes = list(__DONT_SANITIZE_TYPES__) + [SafeStringWrapper]
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197 no_wrap_classes = tuple(set(sorted(no_wrap_classes, key=str)))
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198 return __do_wrap(value)
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199
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200
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201 # N.B. refer to e.g. https://docs.python.org/2/reference/datamodel.html for information on Python's Data Model.
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202
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203
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204 class SafeStringWrapper(object):
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205 """
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206 Class that wraps and sanitizes any provided value's attributes
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207 that will attempt to be cast into a string.
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208
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209 Attempts to mimic behavior of original class, including operands.
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210
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211 To ensure proper handling of e.g. subclass checks, the *wrap_with_safe_string()*
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212 method should be used.
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213
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214 This wrapping occurs in a recursive/parasitic fashion, as all called attributes of
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215 the originally wrapped object will also be wrapped and sanitized, unless the attribute
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216 is of a type found in __DONT_SANITIZE_TYPES__ + __DONT_WRAP_TYPES__, where e.g. ~(strings
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217 will still be sanitized, but not wrapped), and e.g. integers will have neither.
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218 """
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219 __UNSANITIZED_ATTRIBUTE_NAME__ = 'unsanitized'
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220 __NO_WRAP_NAMES__ = ['__safe_string_wrapper_function__', '__class__', __UNSANITIZED_ATTRIBUTE_NAME__]
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221
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222 def __new__(cls, *arg, **kwd):
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223 # We need to define a __new__ since, we are subclassing from e.g. immutable str, which internally sets data
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224 # that will be used when other + this (this + other is handled by __add__)
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225 try:
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226 sanitized_value = sanitize_lists_to_string(arg[0], valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)
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227 return super(SafeStringWrapper, cls).__new__(cls, sanitized_value)
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228 except TypeError:
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229 # Class to be wrapped takes no parameters.
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230 # This is pefectly normal for mutable types.
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231 return super(SafeStringWrapper, cls).__new__(cls)
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232
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233 def __init__(self, value, safe_string_wrapper_function=wrap_with_safe_string):
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234 self.unsanitized = value
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235 self.__safe_string_wrapper_function__ = safe_string_wrapper_function
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236
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237 def __str__(self):
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238 return sanitize_lists_to_string(self.unsanitized, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP)
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239
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240 def __repr__(self):
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241 return "%s object at %x on: %s" % (sanitize_lists_to_string(self.__class__.__name__, valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP), id(self), sanitize_lists_to_string(repr(self.unsanitized), valid_characters=VALID_CHARACTERS, character_map=CHARACTER_MAP))
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242
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243 def __lt__(self, other):
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244 while isinstance(other, SafeStringWrapper):
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245 other = other.unsanitized
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246 return self.unsanitized < other
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247
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248 def __le__(self, other):
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249 while isinstance(other, SafeStringWrapper):
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250 other = other.unsanitized
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251 return self.unsanitized <= other
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252
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253 def __eq__(self, other):
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254 while isinstance(other, SafeStringWrapper):
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255 other = other.unsanitized
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256 return self.unsanitized == other
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257
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258 def __ne__(self, other):
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259 while isinstance(other, SafeStringWrapper):
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260 other = other.unsanitized
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261 return self.unsanitized != other
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262
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263 def __gt__(self, other):
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264 while isinstance(other, SafeStringWrapper):
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265 other = other.unsanitized
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266 return self.unsanitized > other
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267
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268 def __ge__(self, other):
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269 while isinstance(other, SafeStringWrapper):
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270 other = other.unsanitized
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271 return self.unsanitized >= other
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272
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273 def __cmp__(self, other):
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274 while isinstance(other, SafeStringWrapper):
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275 other = other.unsanitized
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276 return cmp(self.unsanitized, other)
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277
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278 # Do not implement __rcmp__, python 2.2 < 2.6
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279
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280 def __hash__(self):
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281 return hash(self.unsanitized)
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282
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283 def __bool__(self):
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284 return bool(self.unsanitized)
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285 __nonzero__ = __bool__
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286
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287 # Do not implement __unicode__, we will rely on __str__
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288
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289 def __getattr__(self, name):
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290 if name in SafeStringWrapper.__NO_WRAP_NAMES__:
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291 # FIXME: is this ever reached?
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292 return object.__getattribute__(self, name)
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293 return self.__safe_string_wrapper_function__(getattr(self.unsanitized, name))
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294
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295 def __setattr__(self, name, value):
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296 if name in SafeStringWrapper.__NO_WRAP_NAMES__:
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297 return object.__setattr__(self, name, value)
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298 return setattr(self.unsanitized, name, value)
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299
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300 def __delattr__(self, name):
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301 if name in SafeStringWrapper.__NO_WRAP_NAMES__:
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302 return object.__delattr__(self, name)
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303 return delattr(self.unsanitized, name)
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304
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305 def __getattribute__(self, name):
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306 if name in SafeStringWrapper.__NO_WRAP_NAMES__:
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307 return object.__getattribute__(self, name)
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308 return self.__safe_string_wrapper_function__(getattr(object.__getattribute__(self, 'unsanitized'), name))
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309
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310 # Skip Descriptors
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311
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312 # Skip __slots__
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313
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314 # Don't need to define a metaclass, we'll use the helper function to handle with subclassing for e.g. isinstance()
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315
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316 # Revisit:
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317 # __instancecheck__
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318 # __subclasscheck__
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319 # We are using a helper class to create dynamic subclasses to handle class checks
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320
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321 # We address __call__ as needed based upon unsanitized, through the use of a CallableSafeStringWrapper class
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322
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323 def __len__(self):
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324 original_value = self.unsanitized
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325 while isinstance(original_value, SafeStringWrapper):
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326 original_value = self.unsanitized
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327 return len(self.unsanitized)
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328
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329 def __getitem__(self, key):
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330 return self.__safe_string_wrapper_function__(self.unsanitized[key])
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331
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332 def __setitem__(self, key, value):
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333 while isinstance(value, SafeStringWrapper):
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334 value = value.unsanitized
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335 self.unsanitized[key] = value
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336
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337 def __delitem__(self, key):
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338 del self.unsanitized[key]
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339
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340 def __iter__(self):
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341 return iter(map(self.__safe_string_wrapper_function__, iter(self.unsanitized)))
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342
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343 # Do not implement __reversed__
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344
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345 def __contains__(self, item):
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346 # FIXME: Do we need to consider if item is/isn't or does/doesn't contain SafeStringWrapper?
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347 # When considering e.g. nested lists/dicts/etc, this gets complicated
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348 while isinstance(item, SafeStringWrapper):
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349 item = item.unsanitized
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350 return item in self.unsanitized
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351
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352 # Not sure that we need these slice methods, but will provide anyway
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353 def __getslice__(self, i, j):
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354 return self.__safe_string_wrapper_function__(self.unsanitized[i:j])
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355
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356 def __setslice__(self, i, j, value):
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357 self.unsanitized[i:j] = value
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358
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359 def __delslice__(self, i, j):
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360 del self.unsanitized[i:j]
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361
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362 def __add__(self, other):
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363 while isinstance(other, SafeStringWrapper):
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364 other = other.unsanitized
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365 return self.__safe_string_wrapper_function__(self.unsanitized + other)
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366
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367 def __sub__(self, other):
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368 while isinstance(other, SafeStringWrapper):
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369 other = other.unsanitized
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370 return self.__safe_string_wrapper_function__(self.unsanitized - other)
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371
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372 def __mul__(self, other):
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373 while isinstance(other, SafeStringWrapper):
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374 other = other.unsanitized
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375 return self.__safe_string_wrapper_function__(self.unsanitized * other)
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376
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377 def __floordiv__(self, other):
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378 while isinstance(other, SafeStringWrapper):
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379 other = other.unsanitized
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380 return self.__safe_string_wrapper_function__(self.unsanitized // other)
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381
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382 def __mod__(self, other):
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383 while isinstance(other, SafeStringWrapper):
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384 other = other.unsanitized
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385 return self.__safe_string_wrapper_function__(self.unsanitized % other)
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386
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387 def __divmod__(self, other):
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388 while isinstance(other, SafeStringWrapper):
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389 other = other.unsanitized
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390 return self.__safe_string_wrapper_function__(divmod(self.unsanitized, other))
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391
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392 def __pow__(self, *other):
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393 while isinstance(other, SafeStringWrapper):
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394 other = other.unsanitized
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395 return self.__safe_string_wrapper_function__(pow(self.unsanitized, *other))
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396
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397 def __lshift__(self, other):
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398 while isinstance(other, SafeStringWrapper):
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399 other = other.unsanitized
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400 return self.__safe_string_wrapper_function__(self.unsanitized << other)
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401
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402 def __rshift__(self, other):
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403 while isinstance(other, SafeStringWrapper):
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404 other = other.unsanitized
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405 return self.__safe_string_wrapper_function__(self.unsanitized >> other)
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406
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407 def __and__(self, other):
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408 while isinstance(other, SafeStringWrapper):
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409 other = other.unsanitized
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410 return self.__safe_string_wrapper_function__(self.unsanitized & other)
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411
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412 def __xor__(self, other):
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413 while isinstance(other, SafeStringWrapper):
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414 other = other.unsanitized
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415 return self.__safe_string_wrapper_function__(self.unsanitized ^ other)
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416
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417 def __or__(self, other):
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418 while isinstance(other, SafeStringWrapper):
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419 other = other.unsanitized
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420 return self.__safe_string_wrapper_function__(self.unsanitized | other)
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421
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422 def __div__(self, other):
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423 while isinstance(other, SafeStringWrapper):
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424 other = other.unsanitized
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425 return self.__safe_string_wrapper_function__(self.unsanitized / other)
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426
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427 def __truediv__(self, other):
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428 while isinstance(other, SafeStringWrapper):
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429 other = other.unsanitized
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430 return self.__safe_string_wrapper_function__(self.unsanitized / other)
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431
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432 # The only reflected operand that we will define is __rpow__, due to coercion rules complications as per docs
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433 def __rpow__(self, other):
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434 while isinstance(other, SafeStringWrapper):
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435 other = other.unsanitized
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436 return self.__safe_string_wrapper_function__(pow(other, self.unsanitized))
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437
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438 # Do not implement in-place operands
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439
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440 def __neg__(self):
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441 return self.__safe_string_wrapper_function__(-self.unsanitized)
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442
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443 def __pos__(self):
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444 return self.__safe_string_wrapper_function__(+self.unsanitized)
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445
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446 def __abs__(self):
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447 return self.__safe_string_wrapper_function__(abs(self.unsanitized))
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448
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449 def __invert__(self):
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450 return self.__safe_string_wrapper_function__(~self.unsanitized)
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451
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452 def __complex__(self):
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453 return self.__safe_string_wrapper_function__(complex(self.unsanitized))
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454
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455 def __int__(self):
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456 return int(self.unsanitized)
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457
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458 def __float__(self):
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459 return float(self.unsanitized)
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460
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461 def __oct__(self):
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462 return oct(self.unsanitized)
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463
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464 def __hex__(self):
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465 return hex(self.unsanitized)
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466
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467 def __index__(self):
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468 return self.unsanitized.index()
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469
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470 def __coerce__(self, other):
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471 while isinstance(other, SafeStringWrapper):
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472 other = other.unsanitized
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473 return coerce(self.unsanitized, other)
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474
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475 def __enter__(self):
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476 return self.unsanitized.__enter__()
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477
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478 def __exit__(self, *args):
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479 return self.unsanitized.__exit__(*args)
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480
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481
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482 class CallableSafeStringWrapper(SafeStringWrapper):
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483
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484 def __call__(self, *args, **kwds):
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485 return self.__safe_string_wrapper_function__(self.unsanitized(*args, **kwds))
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486
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487
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488 # Enable pickling/deepcopy
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489 def pickle_SafeStringWrapper(safe_object):
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490 args = (safe_object.unsanitized, )
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491 cls = SafeStringWrapper
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492 if isinstance(safe_object, CallableSafeStringWrapper):
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493 cls = CallableSafeStringWrapper
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494 return (cls, args)
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495
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496
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497 copy_reg.pickle(SafeStringWrapper, pickle_SafeStringWrapper, wrap_with_safe_string)
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498 copy_reg.pickle(CallableSafeStringWrapper, pickle_SafeStringWrapper, wrap_with_safe_string)