Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/galaxy/util/checkers.py @ 0:4f3585e2f14b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
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diff changeset
1 import bz2
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2 import gzip
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3 import re
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4 import tarfile
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5 import zipfile
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6 from io import (
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7 BytesIO,
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8 StringIO
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9 )
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10
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11 from galaxy import util
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12 from galaxy.util.image_util import image_type
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13
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14 HTML_CHECK_LINES = 100
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15 CHUNK_SIZE = 2 ** 15 # 32Kb
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16 HTML_REGEXPS = (
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17 re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I),
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18 re.compile(r"<IFRAME[^>]*>", re.I),
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19 re.compile(r"<FRAMESET[^>]*>", re.I),
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20 re.compile(r"<META[\W][^>]*>", re.I),
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21 re.compile(r"<SCRIPT[^>]*>", re.I),
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22 )
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23
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24
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25 def check_html(name, file_path=True):
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26 """
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27 Returns True if the file/string contains HTML code.
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28 """
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29 # Handles files if file_path is True or text if file_path is False
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30 if file_path:
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31 temp = open(name, encoding='utf-8')
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32 else:
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33 temp = StringIO(util.unicodify(name))
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34 try:
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35 for _ in range(HTML_CHECK_LINES):
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36 line = temp.readline(CHUNK_SIZE)
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37 if not line:
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38 break
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39 if any(regexp.search(line) for regexp in HTML_REGEXPS):
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40 return True
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41 except UnicodeDecodeError:
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42 return False
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43 finally:
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44 temp.close()
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45 return False
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46
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47
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48 def check_binary(name, file_path=True):
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49 # Handles files if file_path is True or text if file_path is False
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50 if file_path:
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51 temp = open(name, "rb")
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52 else:
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53 temp = BytesIO(name)
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54 try:
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55 return util.is_binary(temp.read(1024))
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56 finally:
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57 temp.close()
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58
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59
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60 def check_gzip(file_path, check_content=True):
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61 # This method returns a tuple of booleans representing ( is_gzipped, is_valid )
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62 # Make sure we have a gzipped file
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63 try:
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64 with open(file_path, "rb") as temp:
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65 magic_check = temp.read(2)
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66 if magic_check != util.gzip_magic:
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67 return (False, False)
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68 except Exception:
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69 return (False, False)
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70 # We support some binary data types, so check if the compressed binary file is valid
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71 # If the file is Bam, it should already have been detected as such, so we'll just check
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72 # for sff format.
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73 try:
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74 with gzip.open(file_path, 'rb') as fh:
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75 header = fh.read(4)
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76 if header == b'.sff':
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77 return (True, True)
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78 except Exception:
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79 return(False, False)
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80
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81 if not check_content:
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82 return (True, True)
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83
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84 with gzip.open(file_path, mode='rb') as gzipped_file:
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85 chunk = gzipped_file.read(CHUNK_SIZE)
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86 # See if we have a compressed HTML file
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87 if check_html(chunk, file_path=False):
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88 return (True, False)
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89 return (True, True)
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90
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91
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92 def check_bz2(file_path, check_content=True):
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93 try:
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94 with open(file_path, "rb") as temp:
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95 magic_check = temp.read(3)
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96 if magic_check != util.bz2_magic:
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97 return (False, False)
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98 except Exception:
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99 return(False, False)
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100
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101 if not check_content:
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102 return (True, True)
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103
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104 with bz2.BZ2File(file_path, mode='rb') as bzipped_file:
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105 chunk = bzipped_file.read(CHUNK_SIZE)
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106 # See if we have a compressed HTML file
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107 if check_html(chunk, file_path=False):
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108 return (True, False)
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109 return (True, True)
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110
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111
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112 def check_zip(file_path, check_content=True, files=1):
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113 if not zipfile.is_zipfile(file_path):
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114 return (False, False)
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115
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116 if not check_content:
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117 return (True, True)
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118
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119 chunk = None
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120 for filect, member in enumerate(iter_zip(file_path)):
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121 handle, name = member
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122 chunk = handle.read(CHUNK_SIZE)
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123 if chunk and check_html(chunk, file_path=False):
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124 return (True, False)
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125 if filect >= files:
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126 break
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127 return (True, True)
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128
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129
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130 def is_bz2(file_path):
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131 is_bz2, is_valid = check_bz2(file_path, check_content=False)
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132 return is_bz2
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133
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134
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135 def is_gzip(file_path):
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136 is_gzipped, is_valid = check_gzip(file_path, check_content=False)
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137 return is_gzipped
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138
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139
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140 def is_zip(file_path):
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141 is_zipped, is_valid = check_zip(file_path, check_content=False)
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142 return is_zipped
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143
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144
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145 def is_single_file_zip(file_path):
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146 for i, _ in enumerate(iter_zip(file_path)):
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147 if i > 1:
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148 return False
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149 return True
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150
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151
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152 def is_tar(file_path):
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153 return tarfile.is_tarfile(file_path)
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154
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155
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156 def iter_zip(file_path):
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157 with zipfile.ZipFile(file_path) as z:
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158 for f in filter(lambda x: not x.endswith('/'), z.namelist()):
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159 yield (z.open(f), f)
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160
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161
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162 def check_image(file_path):
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163 """ Simple wrapper around image_type to yield a True/False verdict """
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164 if image_type(file_path):
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165 return True
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166 return False
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167
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168
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169 __all__ = (
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170 'check_binary',
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171 'check_bz2',
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172 'check_gzip',
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173 'check_html',
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174 'check_image',
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175 'check_zip',
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176 'is_gzip',
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177 'is_bz2',
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178 'is_zip',
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179 )