Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/util/checkers.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 import gzip
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2 import io
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3 import re
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4 import sys
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5 import tarfile
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6 import zipfile
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7
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8 from six import (
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9 BytesIO,
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10 StringIO
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11 )
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12 from six.moves import filter
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13
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14 from galaxy import util
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15 from galaxy.util.image_util import image_type
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16
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17 if sys.version_info < (3, 3):
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18 gzip.GzipFile.read1 = gzip.GzipFile.read # workaround for https://bugs.python.org/issue12591
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19 try:
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20 import bz2file as bz2
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21 except ImportError:
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22 # If bz2file is unavailable, just fallback to not having pbzip2 support.
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23 import bz2
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24 else:
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25 import bz2
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26
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27 HTML_CHECK_LINES = 100
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28 CHUNK_SIZE = 2 ** 15 # 32Kb
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29 HTML_REGEXPS = (
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30 re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I),
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31 re.compile(r"<IFRAME[^>]*>", re.I),
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32 re.compile(r"<FRAMESET[^>]*>", re.I),
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33 re.compile(r"<META[\W][^>]*>", re.I),
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34 re.compile(r"<SCRIPT[^>]*>", re.I),
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35 )
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36
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37
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38 def check_html(name, file_path=True):
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39 """
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40 Returns True if the file/string contains HTML code.
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41 """
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42 # Handles files if file_path is True or text if file_path is False
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43 if file_path:
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44 temp = io.open(name, "r", encoding='utf-8')
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45 else:
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46 temp = StringIO(util.unicodify(name))
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47 try:
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48 for _ in range(HTML_CHECK_LINES):
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49 line = temp.readline(CHUNK_SIZE)
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50 if not line:
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51 break
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52 if any(regexp.search(line) for regexp in HTML_REGEXPS):
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53 return True
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54 except UnicodeDecodeError:
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55 return False
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56 finally:
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57 temp.close()
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58 return False
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59
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60
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61 def check_binary(name, file_path=True):
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62 # Handles files if file_path is True or text if file_path is False
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63 if file_path:
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64 temp = open(name, "rb")
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65 else:
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66 temp = BytesIO(name)
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67 try:
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68 return util.is_binary(temp.read(1024))
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69 finally:
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70 temp.close()
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71
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72
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73 def check_gzip(file_path, check_content=True):
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74 # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
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75 # Make sure we have a gzipped file
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76 try:
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77 with open(file_path, "rb") as temp:
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78 magic_check = temp.read(2)
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79 if magic_check != util.gzip_magic:
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80 return (False, False)
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81 except Exception:
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82 return (False, False)
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83 # We support some binary data types, so check if the compressed binary file is valid
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84 # If the file is Bam, it should already have been detected as such, so we'll just check
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85 # for sff format.
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86 try:
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87 with gzip.open(file_path, 'rb') as fh:
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88 header = fh.read(4)
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89 if header == b'.sff':
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90 return (True, True)
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91 except Exception:
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92 return(False, False)
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93
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94 if not check_content:
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95 return (True, True)
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96
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97 with gzip.open(file_path, mode='rb') as gzipped_file:
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98 chunk = gzipped_file.read(CHUNK_SIZE)
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99 # See if we have a compressed HTML file
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100 if check_html(chunk, file_path=False):
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101 return (True, False)
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102 return (True, True)
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103
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104
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105 def check_bz2(file_path, check_content=True):
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106 try:
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107 with open(file_path, "rb") as temp:
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108 magic_check = temp.read(3)
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109 if magic_check != util.bz2_magic:
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110 return (False, False)
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111 except Exception:
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112 return(False, False)
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113
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114 if not check_content:
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115 return (True, True)
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116
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117 with bz2.BZ2File(file_path, mode='rb') as bzipped_file:
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118 chunk = bzipped_file.read(CHUNK_SIZE)
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119 # See if we have a compressed HTML file
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120 if check_html(chunk, file_path=False):
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121 return (True, False)
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122 return (True, True)
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123
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124
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125 def check_zip(file_path, check_content=True, files=1):
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126 if not zipfile.is_zipfile(file_path):
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127 return (False, False)
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128
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129 if not check_content:
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130 return (True, True)
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131
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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(chunk, file_path=False):
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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 )