Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/compression_utils.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import gzip |
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2 import io |
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3 import logging |
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4 import os |
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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 galaxy.util.path import safe_relpath |
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9 from .checkers import ( |
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10 bz2, |
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11 is_bz2, |
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12 is_gzip |
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13 ) |
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14 |
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15 log = logging.getLogger(__name__) |
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16 |
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17 |
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18 def get_fileobj(filename, mode="r", compressed_formats=None): |
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19 """ |
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20 Returns a fileobj. If the file is compressed, return an appropriate file |
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21 reader. In text mode, always use 'utf-8' encoding. |
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22 |
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23 :param filename: path to file that should be opened |
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24 :param mode: mode to pass to opener |
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25 :param compressed_formats: list of allowed compressed file formats among |
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26 'bz2', 'gzip' and 'zip'. If left to None, all 3 formats are allowed |
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27 """ |
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28 return get_fileobj_raw(filename, mode, compressed_formats)[1] |
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29 |
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30 |
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31 def get_fileobj_raw(filename, mode="r", compressed_formats=None): |
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32 if compressed_formats is None: |
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33 compressed_formats = ['bz2', 'gzip', 'zip'] |
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34 # Remove 't' from mode, which may cause an error for compressed files |
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35 mode = mode.replace('t', '') |
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36 # 'U' mode is deprecated, we open in 'r'. |
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37 if mode == 'U': |
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38 mode = 'r' |
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39 compressed_format = None |
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40 if 'gzip' in compressed_formats and is_gzip(filename): |
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41 fh = gzip.GzipFile(filename, mode) |
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42 compressed_format = 'gzip' |
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43 elif 'bz2' in compressed_formats and is_bz2(filename): |
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44 fh = bz2.BZ2File(filename, mode) |
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45 compressed_format = 'bz2' |
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46 elif 'zip' in compressed_formats and zipfile.is_zipfile(filename): |
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47 # Return fileobj for the first file in a zip file. |
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48 # 'b' is not allowed in the ZipFile mode argument |
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49 # since it always opens files in binary mode. |
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50 # For emulating text mode, we will be returning the binary fh in a |
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51 # TextIOWrapper. |
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52 zf_mode = mode.replace('b', '') |
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53 with zipfile.ZipFile(filename, zf_mode) as zh: |
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54 fh = zh.open(zh.namelist()[0], zf_mode) |
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55 compressed_format = 'zip' |
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56 elif 'b' in mode: |
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57 return compressed_format, open(filename, mode) |
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58 else: |
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59 return compressed_format, open(filename, mode, encoding='utf-8') |
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60 if 'b' not in mode: |
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61 return compressed_format, io.TextIOWrapper(fh, encoding='utf-8') |
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62 else: |
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63 return compressed_format, fh |
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64 |
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65 |
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66 def file_iter(fname, sep=None): |
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67 """ |
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68 This generator iterates over a file and yields its lines |
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69 splitted via the C{sep} parameter. Skips empty lines and lines starting with |
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70 the C{#} character. |
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71 |
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72 >>> lines = [ line for line in file_iter(__file__) ] |
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73 >>> len(lines) != 0 |
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74 True |
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75 """ |
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76 with get_fileobj(fname) as fh: |
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77 for line in fh: |
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78 if line and line[0] != '#': |
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79 yield line.split(sep) |
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80 |
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81 |
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82 class CompressedFile: |
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83 |
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84 @staticmethod |
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85 def can_decompress(file_path): |
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86 return tarfile.is_tarfile(file_path) or zipfile.is_zipfile(file_path) |
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87 |
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88 def __init__(self, file_path, mode='r'): |
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89 if tarfile.is_tarfile(file_path): |
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90 self.file_type = 'tar' |
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91 elif zipfile.is_zipfile(file_path) and not file_path.endswith('.jar'): |
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92 self.file_type = 'zip' |
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93 self.file_name = os.path.splitext(os.path.basename(file_path))[0] |
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94 if self.file_name.endswith('.tar'): |
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95 self.file_name = os.path.splitext(self.file_name)[0] |
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96 self.type = self.file_type |
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97 method = 'open_%s' % self.file_type |
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98 if hasattr(self, method): |
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99 self.archive = getattr(self, method)(file_path, mode) |
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100 else: |
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101 raise NameError('File type %s specified, no open method found.' % self.file_type) |
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102 |
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103 @property |
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104 def common_prefix_dir(self): |
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105 """ |
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106 Get the common prefix directory for all the files in the archive, if any. |
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107 |
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108 Returns '' if the archive contains multiple files and/or directories at |
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109 the root of the archive. |
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110 """ |
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111 contents = self.getmembers() |
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112 common_prefix = '' |
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113 if len(contents) > 1: |
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114 common_prefix = os.path.commonprefix([self.getname(item) for item in contents]) |
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115 # If the common_prefix does not end with a slash, check that is a |
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116 # directory and all other files are contained in it |
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117 if len(common_prefix) >= 1 and not common_prefix.endswith(os.sep) and self.isdir(self.getmember(common_prefix)) \ |
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118 and all(self.getname(item).startswith(common_prefix + os.sep) for item in contents if self.isfile(item)): |
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119 common_prefix += os.sep |
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120 if not common_prefix.endswith(os.sep): |
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121 common_prefix = '' |
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122 return common_prefix |
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123 |
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124 def extract(self, path): |
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125 '''Determine the path to which the archive should be extracted.''' |
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126 contents = self.getmembers() |
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127 extraction_path = path |
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128 common_prefix_dir = self.common_prefix_dir |
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129 if len(contents) == 1: |
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130 # The archive contains a single file, return the extraction path. |
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131 if self.isfile(contents[0]): |
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132 extraction_path = os.path.join(path, self.file_name) |
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133 if not os.path.exists(extraction_path): |
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134 os.makedirs(extraction_path) |
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135 self.archive.extractall(extraction_path, members=self.safemembers()) |
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136 else: |
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137 if not common_prefix_dir: |
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138 extraction_path = os.path.join(path, self.file_name) |
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139 if not os.path.exists(extraction_path): |
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140 os.makedirs(extraction_path) |
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141 self.archive.extractall(extraction_path, members=self.safemembers()) |
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142 # Since .zip files store unix permissions separately, we need to iterate through the zip file |
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143 # and set permissions on extracted members. |
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144 if self.file_type == 'zip': |
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145 for zipped_file in contents: |
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146 filename = self.getname(zipped_file) |
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147 absolute_filepath = os.path.join(extraction_path, filename) |
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148 external_attributes = self.archive.getinfo(filename).external_attr |
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149 # The 2 least significant bytes are irrelevant, the next two contain unix permissions. |
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150 unix_permissions = external_attributes >> 16 |
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151 if unix_permissions != 0: |
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152 if os.path.exists(absolute_filepath): |
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153 os.chmod(absolute_filepath, unix_permissions) |
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154 else: |
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155 log.warning("Unable to change permission on extracted file '%s' as it does not exist" % absolute_filepath) |
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156 return os.path.abspath(os.path.join(extraction_path, common_prefix_dir)) |
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157 |
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158 def safemembers(self): |
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159 members = self.archive |
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160 common_prefix_dir = self.common_prefix_dir |
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161 if self.file_type == "tar": |
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162 for finfo in members: |
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163 if not safe_relpath(finfo.name): |
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164 raise Exception("Path '%s' is blocked (illegal path)." % finfo.name) |
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165 if finfo.issym() or finfo.islnk(): |
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166 link_target = os.path.join(os.path.dirname(finfo.name), finfo.linkname) |
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167 if not safe_relpath(link_target) or not os.path.normpath(link_target).startswith(common_prefix_dir): |
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168 raise Exception(f"Link '{finfo.name}' to '{finfo.linkname}' is blocked.") |
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169 yield finfo |
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170 elif self.file_type == "zip": |
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171 for name in members.namelist(): |
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172 if not safe_relpath(name): |
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173 raise Exception(name + " is blocked (illegal path).") |
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174 yield name |
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175 |
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176 def getmembers_tar(self): |
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177 return self.archive.getmembers() |
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178 |
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179 def getmembers_zip(self): |
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180 return self.archive.infolist() |
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181 |
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182 def getname_tar(self, item): |
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183 return item.name |
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184 |
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185 def getname_zip(self, item): |
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186 return item.filename |
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187 |
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188 def getmember(self, name): |
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189 for member in self.getmembers(): |
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190 if self.getname(member) == name: |
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191 return member |
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192 |
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193 def getmembers(self): |
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194 return getattr(self, 'getmembers_%s' % self.type)() |
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195 |
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196 def getname(self, member): |
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197 return getattr(self, 'getname_%s' % self.type)(member) |
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198 |
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199 def isdir(self, member): |
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200 return getattr(self, 'isdir_%s' % self.type)(member) |
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201 |
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202 def isdir_tar(self, member): |
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203 return member.isdir() |
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204 |
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205 def isdir_zip(self, member): |
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206 if member.filename.endswith(os.sep): |
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207 return True |
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208 return False |
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209 |
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210 def isfile(self, member): |
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211 if not self.isdir(member): |
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212 return True |
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213 return False |
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214 |
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215 def open_tar(self, filepath, mode): |
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216 return tarfile.open(filepath, mode, errorlevel=0) |
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217 |
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218 def open_zip(self, filepath, mode): |
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219 return zipfile.ZipFile(filepath, mode) |
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220 |
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221 def zipfile_ok(self, path_to_archive): |
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222 """ |
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223 This function is a bit pedantic and not functionally necessary. It checks whether there is |
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224 no file pointing outside of the extraction, because ZipFile.extractall() has some potential |
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225 security holes. See python zipfile documentation for more details. |
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226 """ |
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227 basename = os.path.realpath(os.path.dirname(path_to_archive)) |
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228 zip_archive = zipfile.ZipFile(path_to_archive) |
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229 for member in zip_archive.namelist(): |
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230 member_path = os.path.realpath(os.path.join(basename, member)) |
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231 if not member_path.startswith(basename): |
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232 return False |
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233 return True |