Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boltons/ioutils.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 # -*- coding: utf-8 -*-
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2
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3 # Coding decl above needed for rendering the emdash properly in the
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4 # documentation.
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5
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6 """
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7 Module ``ioutils`` implements a number of helper classes and functions which
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8 are useful when dealing with input, output, and bytestreams in a variety of
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9 ways.
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10 """
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11 import os
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12 from io import BytesIO
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13 from abc import (
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14 ABCMeta,
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15 abstractmethod,
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16 abstractproperty,
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17 )
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18 from errno import EINVAL
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19 from codecs import EncodedFile
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20 from tempfile import TemporaryFile
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21
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22 try:
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23 text_type = unicode # Python 2
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24 binary_type = str
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25 except NameError:
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26 text_type = str # Python 3
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27 binary_type = bytes
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28
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29 READ_CHUNK_SIZE = 21333
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30 """
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31 Number of bytes to read at a time. The value is ~ 1/3rd of 64k which means that
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32 the value will easily fit in the L2 cache of most processors even if every
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33 codepoint in a string is three bytes long which makes it a nice fast default
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34 value.
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35 """
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36
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37
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38 class SpooledIOBase(object):
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39 """
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40 The SpooledTempoaryFile class doesn't support a number of attributes and
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41 methods that a StringIO instance does. This brings the api as close to
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42 compatible as possible with StringIO so that it may be used as a near
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43 drop-in replacement to save memory.
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44
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45 Another issue with SpooledTemporaryFile is that the spooled file is always
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46 a cStringIO rather than a StringIO which causes issues with some of our
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47 tools.
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48 """
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49 __metaclass__ = ABCMeta
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50
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51 def __init__(self, max_size=5000000, dir=None):
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52 self._max_size = max_size
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53 self._dir = dir
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54
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55 @abstractmethod
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56 def read(self, n=-1):
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57 """Read n characters from the buffer"""
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58
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59 @abstractmethod
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60 def write(self, s):
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61 """Write into the buffer"""
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62
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63 @abstractmethod
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64 def seek(self, pos, mode=0):
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65 """Seek to a specific point in a file"""
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66
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67 @abstractmethod
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68 def readline(self, length=None):
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69 """Returns the next available line"""
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70
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71 @abstractmethod
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72 def readlines(self, sizehint=0):
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73 """Returns a list of all lines from the current position forward"""
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74
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75 @abstractmethod
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76 def rollover(self):
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77 """Roll file-like-object over into a real temporary file"""
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78
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79 @abstractmethod
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80 def tell(self):
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81 """Return the current position"""
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82
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83 @abstractproperty
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84 def buffer(self):
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85 """Should return a flo instance"""
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86
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87 @abstractproperty
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88 def _rolled(self):
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89 """Returns whether the file has been rolled to a real file or not"""
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90
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91 @abstractproperty
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92 def len(self):
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93 """Returns the length of the data"""
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94
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95 def _get_softspace(self):
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96 return self.buffer.softspace
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97
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98 def _set_softspace(self, val):
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99 self.buffer.softspace = val
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100
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101 softspace = property(_get_softspace, _set_softspace)
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102
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103 @property
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104 def _file(self):
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105 return self.buffer
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106
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107 def close(self):
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108 return self.buffer.close()
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109
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110 def flush(self):
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111 return self.buffer.flush()
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112
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113 def isatty(self):
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114 return self.buffer.isatty()
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115
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116 def next(self):
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117 line = self.readline()
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118 if not line:
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119 pos = self.buffer.tell()
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120 self.buffer.seek(0, os.SEEK_END)
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121 if pos == self.buffer.tell():
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122 raise StopIteration
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123 else:
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124 self.buffer.seek(pos)
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125 return line
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126
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127 @property
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128 def closed(self):
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129 return self.buffer.closed
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130
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131 @property
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132 def pos(self):
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133 return self.tell()
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134
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135 @property
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136 def buf(self):
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137 return self.getvalue()
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138
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139 def fileno(self):
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140 self.rollover()
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141 return self.buffer.fileno()
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142
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143 def truncate(self, size=None):
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144 """
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145 Custom version of truncate that takes either no arguments (like the
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146 real SpooledTemporaryFile) or a single argument that truncates the
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147 value to a certain index location.
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148 """
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149 if size is None:
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150 return self.buffer.truncate()
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151
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152 if size < 0:
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153 raise IOError(EINVAL, "Negative size not allowed")
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154
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155 # Emulate truncation to a particular location
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156 pos = self.tell()
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157 self.seek(size)
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158 self.buffer.truncate()
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159 if pos < size:
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160 self.seek(pos)
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161
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162 def getvalue(self):
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163 """Return the entire files contents"""
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164 pos = self.tell()
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165 self.seek(0)
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166 val = self.read()
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167 self.seek(pos)
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168 return val
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169
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170 def seekable(self):
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171 return True
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172
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173 def readable(self):
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174 return True
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175
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176 def writable(self):
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177 return True
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178
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179 __next__ = next
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180
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181 def __len__(self):
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182 return self.len
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183
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184 def __iter__(self):
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185 return self
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186
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187 def __enter__(self):
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188 return self
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189
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190 def __exit__(self, *args):
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191 self._file.close()
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192
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193 def __eq__(self, other):
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194 if isinstance(other, self.__class__):
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195 return self.getvalue() == other.getvalue()
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196 return False
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197
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198 def __ne__(self, other):
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199 return not self.__eq__(other)
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200
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201 def __bool__(self):
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202 return True
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203
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204 __nonzero__ = __bool__
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205
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206
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207 class SpooledBytesIO(SpooledIOBase):
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208 """
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209 SpooledBytesIO is a spooled file-like-object that only accepts bytes. On
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210 Python 2.x this means the 'str' type; on Python 3.x this means the 'bytes'
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211 type. Bytes are written in and retrieved exactly as given, but it will
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212 raise TypeErrors if something other than bytes are written.
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213
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214 Example::
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215
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216 >>> from boltons import ioutils
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217 >>> with ioutils.SpooledBytesIO() as f:
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218 ... f.write(b"Happy IO")
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219 ... _ = f.seek(0)
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220 ... isinstance(f.getvalue(), ioutils.binary_type)
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221 True
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222 """
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223
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224 def read(self, n=-1):
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225 return self.buffer.read(n)
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226
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227 def write(self, s):
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228 if not isinstance(s, binary_type):
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229 raise TypeError("{0} expected, got {1}".format(
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230 binary_type.__name__,
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231 type(s).__name__
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232 ))
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233
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234 if self.tell() + len(s) >= self._max_size:
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235 self.rollover()
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236 self.buffer.write(s)
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237
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238 def seek(self, pos, mode=0):
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239 return self.buffer.seek(pos, mode)
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240
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241 def readline(self, length=None):
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242 if length:
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243 return self.buffer.readline(length)
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244 else:
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245 return self.buffer.readline()
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246
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247 def readlines(self, sizehint=0):
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248 return self.buffer.readlines(sizehint)
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249
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250 def rollover(self):
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251 """Roll the StringIO over to a TempFile"""
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252 if not self._rolled:
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253 tmp = TemporaryFile(dir=self._dir)
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254 pos = self.buffer.tell()
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255 tmp.write(self.buffer.getvalue())
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256 tmp.seek(pos)
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257 self.buffer.close()
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258 self._buffer = tmp
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259
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260 @property
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261 def _rolled(self):
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262 return not isinstance(self.buffer, BytesIO)
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263
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264 @property
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265 def buffer(self):
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266 try:
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267 return self._buffer
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268 except AttributeError:
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269 self._buffer = BytesIO()
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270 return self._buffer
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271
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272 @property
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273 def len(self):
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274 """Determine the length of the file"""
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275 pos = self.tell()
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276 if self._rolled:
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277 self.seek(0)
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278 val = os.fstat(self.fileno()).st_size
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279 else:
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280 self.seek(0, os.SEEK_END)
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281 val = self.tell()
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282 self.seek(pos)
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283 return val
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284
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285 def tell(self):
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286 return self.buffer.tell()
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287
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288
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289 class SpooledStringIO(SpooledIOBase):
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290 """
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291 SpooledStringIO is a spooled file-like-object that only accepts unicode
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292 values. On Python 2.x this means the 'unicode' type and on Python 3.x this
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293 means the 'str' type. Values are accepted as unicode and then coerced into
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294 utf-8 encoded bytes for storage. On retrieval, the values are returned as
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295 unicode.
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296
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297 Example::
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298
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299 >>> from boltons import ioutils
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300 >>> with ioutils.SpooledStringIO() as f:
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301 ... f.write(u"\u2014 Hey, an emdash!")
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302 ... _ = f.seek(0)
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303 ... isinstance(f.read(), ioutils.text_type)
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304 True
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305
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306 """
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307 def __init__(self, *args, **kwargs):
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308 self._tell = 0
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309 super(SpooledStringIO, self).__init__(*args, **kwargs)
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310
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311 def read(self, n=-1):
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312 ret = self.buffer.reader.read(n, n)
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313 self._tell = self.tell() + len(ret)
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314 return ret
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315
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316 def write(self, s):
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317 if not isinstance(s, text_type):
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318 raise TypeError("{0} expected, got {1}".format(
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319 text_type.__name__,
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320 type(s).__name__
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321 ))
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322 current_pos = self.tell()
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323 if self.buffer.tell() + len(s.encode('utf-8')) >= self._max_size:
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324 self.rollover()
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325 self.buffer.write(s.encode('utf-8'))
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326 self._tell = current_pos + len(s)
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327
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328 def _traverse_codepoints(self, current_position, n):
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329 """Traverse from current position to the right n codepoints"""
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330 dest = current_position + n
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331 while True:
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332 if current_position == dest:
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333 # By chance we've landed on the right position, break
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334 break
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335
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336 # If the read would take us past the intended position then
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337 # seek only enough to cover the offset
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338 if current_position + READ_CHUNK_SIZE > dest:
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339 self.read(dest - current_position)
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340 break
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341 else:
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342 ret = self.read(READ_CHUNK_SIZE)
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343
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344 # Increment our current position
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345 current_position += READ_CHUNK_SIZE
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346
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347 # If we kept reading but there was nothing here, break
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348 # as we are at the end of the file
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349 if not ret:
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350 break
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351
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352 return dest
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353
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354 def seek(self, pos, mode=0):
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355 """Traverse from offset to the specified codepoint"""
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356 # Seek to position from the start of the file
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357 if mode == os.SEEK_SET:
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358 self.buffer.seek(0)
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359 self._traverse_codepoints(0, pos)
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360 self._tell = pos
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361 # Seek to new position relative to current position
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362 elif mode == os.SEEK_CUR:
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363 start_pos = self.tell()
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364 self._traverse_codepoints(self.tell(), pos)
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365 self._tell = start_pos + pos
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366 elif mode == os.SEEK_END:
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367 self.buffer.seek(0)
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368 dest_position = self.len - pos
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369 self._traverse_codepoints(0, dest_position)
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370 self._tell = dest_position
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371 else:
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372 raise ValueError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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373 "Invalid whence ({0}, should be 0, 1, or 2)".format(mode)
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374 )
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375 return self.tell()
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376
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377 def readline(self, length=None):
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378 ret = self.buffer.readline(length).decode('utf-8')
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379 self._tell = self.tell() + len(ret)
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380 return ret
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381
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382 def readlines(self, sizehint=0):
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383 ret = [x.decode('utf-8') for x in self.buffer.readlines(sizehint)]
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384 self._tell = self.tell() + sum((len(x) for x in ret))
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385 return ret
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386
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387 @property
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388 def buffer(self):
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389 try:
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390 return self._buffer
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diff changeset
391 except AttributeError:
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392 self._buffer = EncodedFile(BytesIO(), data_encoding='utf-8')
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393 return self._buffer
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394
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395 @property
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396 def _rolled(self):
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diff changeset
397 return not isinstance(self.buffer.stream, BytesIO)
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shellac
parents:
diff changeset
398
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parents:
diff changeset
399 def rollover(self):
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diff changeset
400 """Roll the StringIO over to a TempFile"""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
401 if not self._rolled:
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402 tmp = EncodedFile(TemporaryFile(dir=self._dir),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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403 data_encoding='utf-8')
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parents:
diff changeset
404 pos = self.buffer.tell()
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parents:
diff changeset
405 tmp.write(self.buffer.getvalue())
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parents:
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406 tmp.seek(pos)
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407 self.buffer.close()
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408 self._buffer = tmp
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409
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410 def tell(self):
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411 """Return the codepoint position"""
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412 return self._tell
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413
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414 @property
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415 def len(self):
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416 """Determine the number of codepoints in the file"""
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417 pos = self.buffer.tell()
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418 self.buffer.seek(0)
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419 total = 0
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420 while True:
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421 ret = self.read(READ_CHUNK_SIZE)
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422 if not ret:
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423 break
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parents:
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424 total += len(ret)
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parents:
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425 self.buffer.seek(pos)
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426 return total
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parents:
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427
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428
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429 def is_text_fileobj(fileobj):
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430 if getattr(fileobj, 'encoding', False):
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431 # codecs.open and io.TextIOBase
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432 return True
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433 if getattr(fileobj, 'getvalue', False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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434 # StringIO.StringIO / cStringIO.StringIO / io.StringIO
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435 try:
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436 if isinstance(fileobj.getvalue(), type(u'')):
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437 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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438 except Exception:
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439 pass
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440 return False
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441
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442
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443 class MultiFileReader(object):
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444 """Takes a list of open files or file-like objects and provides an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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445 interface to read from them all contiguously. Like
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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446 :func:`itertools.chain()`, but for reading files.
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447
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448 >>> mfr = MultiFileReader(BytesIO(b'ab'), BytesIO(b'cd'), BytesIO(b'e'))
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449 >>> mfr.read(3).decode('ascii')
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450 u'abc'
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451 >>> mfr.read(3).decode('ascii')
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diff changeset
452 u'de'
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453
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454 The constructor takes as many fileobjs as you hand it, and will
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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455 raise a TypeError on non-file-like objects. A ValueError is raised
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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456 when file-like objects are a mix of bytes- and text-handling
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457 objects (for instance, BytesIO and StringIO).
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458 """
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459
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460 def __init__(self, *fileobjs):
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461 if not all([callable(getattr(f, 'read', None)) and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
462 callable(getattr(f, 'seek', None)) for f in fileobjs]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
463 raise TypeError('MultiFileReader expected file-like objects'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
464 ' with .read() and .seek()')
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465 if all([is_text_fileobj(f) for f in fileobjs]):
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diff changeset
466 # codecs.open and io.TextIOBase
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467 self._joiner = u''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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468 elif any([is_text_fileobj(f) for f in fileobjs]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
469 raise ValueError('All arguments to MultiFileReader must handle'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
470 ' bytes OR text, not a mix')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
471 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
472 # open/file and io.BytesIO
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parents:
diff changeset
473 self._joiner = b''
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diff changeset
474 self._fileobjs = fileobjs
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parents:
diff changeset
475 self._index = 0
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diff changeset
476
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parents:
diff changeset
477 def read(self, amt=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
478 """Read up to the specified *amt*, seamlessly bridging across
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
479 files. Returns the appropriate type of string (bytes or text)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
480 for the input, and returns an empty string when the files are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
481 exhausted.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
482 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
483 if not amt:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
484 return self._joiner.join(f.read() for f in self._fileobjs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
485 parts = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
486 while amt > 0 and self._index < len(self._fileobjs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
487 parts.append(self._fileobjs[self._index].read(amt))
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parents:
diff changeset
488 got = len(parts[-1])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
489 if got < amt:
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parents:
diff changeset
490 self._index += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
491 amt -= got
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parents:
diff changeset
492 return self._joiner.join(parts)
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parents:
diff changeset
493
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parents:
diff changeset
494 def seek(self, offset, whence=os.SEEK_SET):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
495 """Enables setting position of the file cursor to a given
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
496 *offset*. Currently only supports ``offset=0``.
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diff changeset
497 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
498 if whence != os.SEEK_SET:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
499 raise NotImplementedError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
500 'MultiFileReader.seek() only supports os.SEEK_SET')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
501 if offset != 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
502 raise NotImplementedError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
503 'MultiFileReader only supports seeking to start at this time')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
504 for f in self._fileobjs:
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parents:
diff changeset
505 f.seek(0)