Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/checkers.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 import gzip
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2 import re
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3 import sys
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4 import tarfile
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5 import zipfile
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6
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7 from six import BytesIO
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8 from six.moves import filter
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9
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10 from galaxy import util
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11 from galaxy.util.image_util import image_type
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12
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13 if sys.version_info < (3, 3):
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14 gzip.GzipFile.read1 = gzip.GzipFile.read # workaround for https://bugs.python.org/issue12591
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15 try:
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16 import bz2file as bz2
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17 except ImportError:
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18 # If bz2file is unavailable, just fallback to not having pbzip2 support.
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19 import bz2
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20 else:
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21 import bz2
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22
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23 HTML_CHECK_LINES = 100
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24
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25
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26 def check_html(file_path, chunk=None):
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27 if chunk is None:
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28 temp = open(file_path, mode='rb')
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29 elif hasattr(chunk, "splitlines"):
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30 temp = chunk.splitlines()
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31 else:
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32 temp = chunk
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33 regexp1 = re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I)
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34 regexp2 = re.compile(r"<IFRAME[^>]*>", re.I)
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35 regexp3 = re.compile(r"<FRAMESET[^>]*>", re.I)
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36 regexp4 = re.compile(r"<META[\W][^>]*>", re.I)
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37 regexp5 = re.compile(r"<SCRIPT[^>]*>", re.I)
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38 lineno = 0
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39 # TODO: Potentially reading huge lines into string here, this should be
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40 # reworked.
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41 for line in temp:
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42 line = util.unicodify(line)
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43 lineno += 1
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44 matches = regexp1.search(line) or regexp2.search(line) or regexp3.search(line) or regexp4.search(line) or regexp5.search(line)
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45 if matches:
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46 if chunk is None:
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47 temp.close()
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48 return True
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49 if HTML_CHECK_LINES and (lineno > HTML_CHECK_LINES):
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50 break
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51 if chunk is None:
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52 temp.close()
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53 return False
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54
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55
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56 def check_binary(name, file_path=True):
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57 # Handles files if file_path is True or text if file_path is False
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58 if file_path:
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59 temp = open(name, "rb")
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60 else:
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61 temp = BytesIO(name)
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62 try:
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63 return util.is_binary(temp.read(1024))
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64 finally:
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65 temp.close()
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66
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67
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68 def check_gzip(file_path, check_content=True):
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69 # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
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70 # Make sure we have a gzipped file
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71 try:
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72 with open(file_path, "rb") as temp:
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73 magic_check = temp.read(2)
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74 if magic_check != util.gzip_magic:
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75 return (False, False)
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76 except Exception:
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77 return (False, False)
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78 # We support some binary data types, so check if the compressed binary file is valid
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79 # If the file is Bam, it should already have been detected as such, so we'll just check
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80 # for sff format.
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81 try:
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82 with gzip.open(file_path, 'rb') as fh:
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83 header = fh.read(4)
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84 if header == b'.sff':
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85 return (True, True)
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86 except Exception:
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87 return(False, False)
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88
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89 if not check_content:
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90 return (True, True)
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91
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92 CHUNK_SIZE = 2 ** 15 # 32Kb
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93 gzipped_file = gzip.GzipFile(file_path, mode='rb')
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94 chunk = gzipped_file.read(CHUNK_SIZE)
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95 gzipped_file.close()
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96 # See if we have a compressed HTML file
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97 if check_html(file_path, chunk=chunk):
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98 return (True, False)
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99 return (True, True)
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100
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101
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102 def check_bz2(file_path, check_content=True):
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103 try:
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104 with open(file_path, "rb") as temp:
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105 magic_check = temp.read(3)
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106 if magic_check != util.bz2_magic:
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107 return (False, False)
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108 except Exception:
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109 return(False, False)
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110
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111 if not check_content:
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112 return (True, True)
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113
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114 CHUNK_SIZE = 2 ** 15 # reKb
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115 bzipped_file = bz2.BZ2File(file_path, mode='rb')
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116 chunk = bzipped_file.read(CHUNK_SIZE)
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117 bzipped_file.close()
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118 # See if we have a compressed HTML file
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119 if check_html(file_path, chunk=chunk):
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120 return (True, False)
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121 return (True, True)
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122
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123
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124 def check_zip(file_path, check_content=True, files=1):
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125 if not zipfile.is_zipfile(file_path):
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126 return (False, False)
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127
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128 if not check_content:
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129 return (True, True)
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130
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131 CHUNK_SIZE = 2 ** 15 # 32Kb
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132 chunk = None
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133 for filect, member in enumerate(iter_zip(file_path)):
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134 handle, name = member
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135 chunk = handle.read(CHUNK_SIZE)
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136 if chunk and check_html(file_path, chunk):
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137 return (True, False)
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138 if filect >= files:
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139 break
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140 return (True, True)
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141
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142
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143 def is_bz2(file_path):
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144 is_bz2, is_valid = check_bz2(file_path, check_content=False)
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145 return is_bz2
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146
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147
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148 def is_gzip(file_path):
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149 is_gzipped, is_valid = check_gzip(file_path, check_content=False)
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150 return is_gzipped
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151
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152
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153 def is_zip(file_path):
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154 is_zipped, is_valid = check_zip(file_path, check_content=False)
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155 return is_zipped
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156
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157
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158 def is_single_file_zip(file_path):
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159 for i, member in enumerate(iter_zip(file_path)):
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160 if i > 1:
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161 return False
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162 return True
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163
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164
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165 def is_tar(file_path):
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166 return tarfile.is_tarfile(file_path)
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167
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168
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169 def iter_zip(file_path):
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170 with zipfile.ZipFile(file_path) as z:
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171 for f in filter(lambda x: not x.endswith('/'), z.namelist()):
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172 yield (z.open(f), f)
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173
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174
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175 def check_image(file_path):
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176 """ Simple wrapper around image_type to yield a True/False verdict """
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177 if image_type(file_path):
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178 return True
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179 return False
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180
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181
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182 __all__ = (
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183 'check_binary',
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184 'check_bz2',
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185 'check_gzip',
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186 'check_html',
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187 'check_image',
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188 'check_zip',
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189 'is_gzip',
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190 'is_bz2',
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191 'is_zip',
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192 )