Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boltons/jsonutils.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # -*- coding: utf-8 -*-
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2 """``jsonutils`` aims to provide various helpers for working with
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3 JSON. Currently it focuses on providing a reliable and intuitive means
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4 of working with `JSON Lines`_-formatted files.
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5
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6 .. _JSON Lines: http://jsonlines.org/
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7
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8 """
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9
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10 from __future__ import print_function
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11
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12 import os
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13 import json
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14
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15
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16 DEFAULT_BLOCKSIZE = 4096
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17
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18 # reverse iter lines algorithm:
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19 #
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20 # - if it ends in a newline, add an empty string to the line list
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21 # - if there's one item, then prepend it to the buffer, continue
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22 # - if there's more than one item, pop the last item and prepend it
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23 # to the buffer, yielding it
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24 # - yield all remaining items in reverse, except for the first
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25 # - first item becomes the new buffer
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26 #
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27 # - when the outer loop completes, yield the buffer
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28
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29
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30 __all__ = ['JSONLIterator', 'reverse_iter_lines']
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31
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32
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33 def reverse_iter_lines(file_obj, blocksize=DEFAULT_BLOCKSIZE, preseek=True):
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34 """Returns an iterator over the lines from a file object, in
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35 reverse order, i.e., last line first, first line last. Uses the
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36 :meth:`file.seek` method of file objects, and is tested compatible with
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37 :class:`file` objects, as well as :class:`StringIO.StringIO`.
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38
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39 Args:
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40 file_obj (file): An open file object. Note that ``reverse_iter_lines``
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41 mutably reads from the file and other functions should not mutably
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42 interact with the file object.
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43 blocksize (int): The block size to pass to :meth:`file.read()`
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44 preseek (bool): Tells the function whether or not to automatically
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45 seek to the end of the file. Defaults to ``True``.
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46 ``preseek=False`` is useful in cases when the
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47 file cursor is already in position, either at the end of
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48 the file or in the middle for relative reverse line
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49 generation.
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50 """
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51 if preseek:
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52 file_obj.seek(0, os.SEEK_END)
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53 cur_pos = file_obj.tell()
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54 buff = ''
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55 while 0 < cur_pos:
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56 read_size = min(blocksize, cur_pos)
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57 cur_pos -= read_size
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58 file_obj.seek(cur_pos, os.SEEK_SET)
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59 cur = file_obj.read(read_size)
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60 lines = cur.splitlines()
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61 if cur[-1] == '\n':
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62 lines.append('')
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63 if len(lines) == 1:
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64 buff = lines[0] + buff
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65 continue
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66 last = lines.pop()
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67 yield last + buff
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68 for line in lines[:0:-1]:
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69 yield line
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70 buff = lines[0]
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71 if buff:
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72 # TODO: test this, does an empty buffer always mean don't yield?
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73 yield buff
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74
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75
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76 """
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77 TODO: allow passthroughs for:
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78
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79 json.load(fp[, encoding[, cls[, object_hook[, parse_float[, parse_int[, parse_constant[, object_pairs_hook[, **kw]]]]]]]])
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80 """
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81
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82
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83 class JSONLIterator(object):
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84 """The ``JSONLIterator`` is used to iterate over JSON-encoded objects
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85 stored in the `JSON Lines format`_ (one object per line).
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86
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87 Most notably it has the ability to efficiently read from the
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88 bottom of files, making it very effective for reading in simple
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89 append-only JSONL use cases. It also has the ability to start from
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90 anywhere in the file and ignore corrupted lines.
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91
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92 Args:
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93 file_obj (file): An open file object.
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94 ignore_errors (bool): Whether to skip over lines that raise an error on
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95 deserialization (:func:`json.loads`).
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96 reverse (bool): Controls the direction of the iteration.
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97 Defaults to ``False``. If set to ``True`` and *rel_seek*
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98 is unset, seeks to the end of the file before iteration
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99 begins.
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100 rel_seek (float): Used to preseek the start position of
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101 iteration. Set to 0.0 for the start of the file, 1.0 for the
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102 end, and anything in between.
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103
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104 .. _JSON Lines format: http://jsonlines.org/
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105 """
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106 def __init__(self, file_obj,
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107 ignore_errors=False, reverse=False, rel_seek=None):
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108 self._reverse = bool(reverse)
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109 self._file_obj = file_obj
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110 self.ignore_errors = ignore_errors
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111
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112 if rel_seek is None:
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113 if reverse:
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114 rel_seek = 1.0
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115 elif not -1.0 < rel_seek < 1.0:
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116 raise ValueError("'rel_seek' expected a float between"
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117 " -1.0 and 1.0, not %r" % rel_seek)
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118 elif rel_seek < 0:
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119 rel_seek = 1.0 - rel_seek
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120 self._rel_seek = rel_seek
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121 self._blocksize = 4096
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122 if rel_seek is not None:
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123 self._init_rel_seek()
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124 if self._reverse:
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125 self._line_iter = reverse_iter_lines(self._file_obj,
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126 blocksize=self._blocksize,
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127 preseek=False)
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128 else:
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129 self._line_iter = iter(self._file_obj)
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130
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131 @property
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132 def cur_byte_pos(self):
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133 "A property representing where in the file the iterator is reading."
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134 return self._file_obj.tell()
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135
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136 def _align_to_newline(self):
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137 "Aligns the file object's position to the next newline."
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138 fo, bsize = self._file_obj, self._blocksize
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139 cur, total_read = '', 0
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140 cur_pos = fo.tell()
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141 while '\n' not in cur:
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142 cur = fo.read(bsize)
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143 total_read += bsize
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144 try:
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145 newline_offset = cur.index('\n') + total_read - bsize
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146 except ValueError:
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147 raise # TODO: seek to end?
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148 fo.seek(cur_pos + newline_offset)
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149
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150 def _init_rel_seek(self):
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151 "Sets the file object's position to the relative location set above."
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152 rs, fo = self._rel_seek, self._file_obj
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153 if rs == 0.0:
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154 fo.seek(0, os.SEEK_SET)
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155 else:
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156 fo.seek(0, os.SEEK_END)
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157 size = fo.tell()
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158 if rs == 1.0:
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159 self._cur_pos = size
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160 else:
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161 target = int(size * rs)
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162 fo.seek(target, os.SEEK_SET)
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163 self._align_to_newline()
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164 self._cur_pos = fo.tell()
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165
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166 def __iter__(self):
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167 return self
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168
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169 def next(self):
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170 """Yields one :class:`dict` loaded with :func:`json.loads`, advancing
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171 the file object by one line. Raises :exc:`StopIteration` upon reaching
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172 the end of the file (or beginning, if ``reverse`` was set to ``True``.
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173 """
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174 while 1:
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175 line = next(self._line_iter).lstrip()
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176 if not line:
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177 continue
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178 try:
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179 obj = json.loads(line)
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180 except Exception:
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181 if not self.ignore_errors:
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182 raise
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183 continue
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184 return obj
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185
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186 __next__ = next
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187
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188
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189 if __name__ == '__main__':
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190 def _main():
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191 import sys
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192 if '-h' in sys.argv or '--help' in sys.argv:
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193 print('loads one or more JSON Line files for basic validation.')
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194 return
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195 verbose = False
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196 if '-v' in sys.argv or '--verbose' in sys.argv:
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197 verbose = True
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198 file_count, obj_count = 0, 0
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199 filenames = sys.argv[1:]
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200 for filename in filenames:
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201 if filename in ('-h', '--help', '-v', '--verbose'):
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202 continue
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203 file_count += 1
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204 with open(filename, 'rb') as file_obj:
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205 iterator = JSONLIterator(file_obj)
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206 cur_obj_count = 0
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207 while 1:
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208 try:
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209 next(iterator)
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210 except ValueError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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211 print('error reading object #%s around byte %s in %s'
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diff changeset
212 % (cur_obj_count + 1, iterator.cur_byte_pos, filename))
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213 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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214 except StopIteration:
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215 break
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216 obj_count += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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217 cur_obj_count += 1
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218 if verbose and obj_count and obj_count % 100 == 0:
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219 sys.stdout.write('.')
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220 if obj_count % 10000:
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diff changeset
221 sys.stdout.write('%s\n' % obj_count)
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222 if verbose:
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diff changeset
223 print('files checked: %s' % file_count)
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224 print('objects loaded: %s' % obj_count)
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225 return
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226
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diff changeset
227 _main()