Mercurial > repos > shellac > sam_consensus_v3

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

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 from __future__ import absolute_import, division, print_function, unicode_literals
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5
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6 import argparse
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7 import codecs
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8 import gettext
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9 import hashlib
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10 import logging
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11 import multiprocessing
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12 import os
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13 import re
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14 import signal
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15 import sys
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16 import tempfile
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17 import unicodedata
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18 import warnings
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19 from collections import defaultdict
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20 from datetime import date
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21 from functools import partial
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22 from os.path import abspath, isdir, isfile, join
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23
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24 from pkg_resources import DistributionNotFound, get_distribution
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25
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26 try:
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27 from urllib.parse import urlparse
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28 except ImportError:
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29 from urlparse import urlparse
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30
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31
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32 def find_locale_dir():
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33 for prefix in (os.path.dirname(__file__), sys.prefix):
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34 locale_dir = os.path.join(prefix, "locale")
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35 if os.path.isdir(locale_dir):
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36 return locale_dir
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37
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38
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39 TRANSLATION_CATALOG = gettext.translation(
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40 "bagit-python", localedir=find_locale_dir(), fallback=True
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41 )
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42 if sys.version_info < (3,):
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43 _ = TRANSLATION_CATALOG.ugettext
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44 else:
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45 _ = TRANSLATION_CATALOG.gettext
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46
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47 MODULE_NAME = "bagit" if __name__ == "__main__" else __name__
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48
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49 LOGGER = logging.getLogger(MODULE_NAME)
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50
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51 try:
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52 VERSION = get_distribution(MODULE_NAME).version
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53 except DistributionNotFound:
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54 VERSION = "0.0.dev0"
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55
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56 PROJECT_URL = "https://github.com/LibraryOfCongress/bagit-python"
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57
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58 __doc__ = (
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59 _(
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60 """
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61 BagIt is a directory, filename convention for bundling an arbitrary set of
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62 files with a manifest, checksums, and additional metadata. More about BagIt
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63 can be found at:
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64
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65 http://purl.org/net/bagit
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66
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67 bagit.py is a pure python drop in library and command line tool for creating,
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68 and working with BagIt directories.
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69
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70
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71 Command-Line Usage:
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72
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73 Basic usage is to give bagit.py a directory to bag up:
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74
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75 $ bagit.py my_directory
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76
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77 This does a bag-in-place operation where the current contents will be moved
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78 into the appropriate BagIt structure and the metadata files will be created.
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79
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80 You can bag multiple directories if you wish:
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81
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82 $ bagit.py directory1 directory2
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83
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84 Optionally you can provide metadata which will be stored in bag-info.txt:
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85
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86 $ bagit.py --source-organization "Library of Congress" directory
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87
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88 You can also select which manifest algorithms will be used:
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89
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90 $ bagit.py --sha1 --md5 --sha256 --sha512 directory
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91
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92
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93 Using BagIt from your Python code:
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94
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95 import bagit
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96 bag = bagit.make_bag('example-directory', {'Contact-Name': 'Ed Summers'})
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97 print(bag.entries)
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98
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99 For more information or to contribute to bagit-python's development, please
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100 visit %(PROJECT_URL)s
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101 """
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102 )
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103 % globals()
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104 )
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105
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106 # standard bag-info.txt metadata
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107 STANDARD_BAG_INFO_HEADERS = [
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108 "Source-Organization",
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109 "Organization-Address",
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110 "Contact-Name",
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111 "Contact-Phone",
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112 "Contact-Email",
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113 "External-Description",
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114 "External-Identifier",
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115 "Bag-Size",
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116 "Bag-Group-Identifier",
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117 "Bag-Count",
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118 "Internal-Sender-Identifier",
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119 "Internal-Sender-Description",
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120 "BagIt-Profile-Identifier",
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121 # Bagging-Date is autogenerated
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122 # Payload-Oxum is autogenerated
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123 ]
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124
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125 try:
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126 CHECKSUM_ALGOS = hashlib.algorithms_guaranteed
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127 except AttributeError:
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128 # FIXME: remove when we drop Python 2 (https://github.com/LibraryOfCongress/bagit-python/issues/102)
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129 # Python 2.7.0-2.7.8
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130 CHECKSUM_ALGOS = set(hashlib.algorithms)
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131 DEFAULT_CHECKSUMS = ["sha256", "sha512"]
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132
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133 #: Block size used when reading files for hashing:
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134 HASH_BLOCK_SIZE = 512 * 1024
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135
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136 #: Convenience function used everywhere we want to open a file to read text
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137 #: rather than undecoded bytes:
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138 open_text_file = partial(codecs.open, encoding="utf-8", errors="strict")
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139
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140 # This is the same as decoding the byte values in codecs.BOM:
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141 UNICODE_BYTE_ORDER_MARK = "\uFEFF"
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142
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143
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144 def make_bag(
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145 bag_dir, bag_info=None, processes=1, checksums=None, checksum=None, encoding="utf-8"
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146 ):
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147 """
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148 Convert a given directory into a bag. You can pass in arbitrary
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149 key/value pairs to put into the bag-info.txt metadata file as
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150 the bag_info dictionary.
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151 """
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152
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153 if checksum is not None:
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154 warnings.warn(
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155 _(
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156 "The `checksum` argument for `make_bag` should be replaced with `checksums`"
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157 ),
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158 DeprecationWarning,
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159 )
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160 checksums = checksum
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161
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162 if checksums is None:
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163 checksums = DEFAULT_CHECKSUMS
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164
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165 bag_dir = os.path.abspath(bag_dir)
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166 cwd = os.path.abspath(os.path.curdir)
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167
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168 if cwd.startswith(bag_dir) and cwd != bag_dir:
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169 raise RuntimeError(
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170 _("Bagging a parent of the current directory is not supported")
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171 )
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172
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173 LOGGER.info(_("Creating bag for directory %s"), bag_dir)
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174
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175 if not os.path.isdir(bag_dir):
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176 LOGGER.error(_("Bag directory %s does not exist"), bag_dir)
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177 raise RuntimeError(_("Bag directory %s does not exist") % bag_dir)
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178
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179 # FIXME: we should do the permissions checks before changing directories
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180 old_dir = os.path.abspath(os.path.curdir)
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181
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182 try:
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183 # TODO: These two checks are currently redundant since an unreadable directory will also
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184 # often be unwritable, and this code will require review when we add the option to
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185 # bag to a destination other than the source. It would be nice if we could avoid
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186 # walking the directory tree more than once even if most filesystems will cache it
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187
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188 unbaggable = _can_bag(bag_dir)
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189
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190 if unbaggable:
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191 LOGGER.error(
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192 _("Unable to write to the following directories and files:\n%s"),
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193 unbaggable,
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194 )
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195 raise BagError(_("Missing permissions to move all files and directories"))
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196
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197 unreadable_dirs, unreadable_files = _can_read(bag_dir)
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198
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199 if unreadable_dirs or unreadable_files:
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200 if unreadable_dirs:
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201 LOGGER.error(
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202 _("The following directories do not have read permissions:\n%s"),
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203 unreadable_dirs,
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204 )
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205 if unreadable_files:
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206 LOGGER.error(
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207 _("The following files do not have read permissions:\n%s"),
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208 unreadable_files,
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209 )
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210 raise BagError(
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211 _("Read permissions are required to calculate file fixities")
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212 )
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213 else:
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214 LOGGER.info(_("Creating data directory"))
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215
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216 # FIXME: if we calculate full paths we won't need to deal with changing directories
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217 os.chdir(bag_dir)
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218 cwd = os.getcwd()
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219 temp_data = tempfile.mkdtemp(dir=cwd)
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220
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221 for f in os.listdir("."):
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222 if os.path.abspath(f) == temp_data:
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223 continue
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224 new_f = os.path.join(temp_data, f)
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225 LOGGER.info(
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226 _("Moving %(source)s to %(destination)s"),
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227 {"source": f, "destination": new_f},
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228 )
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229 os.rename(f, new_f)
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230
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231 LOGGER.info(
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232 _("Moving %(source)s to %(destination)s"),
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233 {"source": temp_data, "destination": "data"},
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234 )
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235 os.rename(temp_data, "data")
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236
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237 # permissions for the payload directory should match those of the
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238 # original directory
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239 os.chmod("data", os.stat(cwd).st_mode)
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240
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241 total_bytes, total_files = make_manifests(
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242 "data", processes, algorithms=checksums, encoding=encoding
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243 )
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244
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245 LOGGER.info(_("Creating bagit.txt"))
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246 txt = """BagIt-Version: 0.97\nTag-File-Character-Encoding: UTF-8\n"""
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247 with open_text_file("bagit.txt", "w") as bagit_file:
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248 bagit_file.write(txt)
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249
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250 LOGGER.info(_("Creating bag-info.txt"))
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251 if bag_info is None:
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252 bag_info = {}
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253
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254 # allow 'Bagging-Date' and 'Bag-Software-Agent' to be overidden
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255 if "Bagging-Date" not in bag_info:
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parents:
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256 bag_info["Bagging-Date"] = date.strftime(date.today(), "%Y-%m-%d")
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parents:
diff changeset
257 if "Bag-Software-Agent" not in bag_info:
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parents:
diff changeset
258 bag_info["Bag-Software-Agent"] = "bagit.py v%s <%s>" % (
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parents:
diff changeset
259 VERSION,
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parents:
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260 PROJECT_URL,
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shellac
parents:
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261 )
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262
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parents:
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263 bag_info["Payload-Oxum"] = "%s.%s" % (total_bytes, total_files)
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parents:
diff changeset
264 _make_tag_file("bag-info.txt", bag_info)
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265
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parents:
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266 for c in checksums:
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267 _make_tagmanifest_file(c, bag_dir, encoding="utf-8")
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268 except Exception:
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269 LOGGER.exception(_("An error occurred creating a bag in %s"), bag_dir)
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270 raise
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parents:
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271 finally:
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272 os.chdir(old_dir)
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273
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274 return Bag(bag_dir)
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275
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276
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277 class Bag(object):
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278 """A representation of a bag."""
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279
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280 valid_files = ["bagit.txt", "fetch.txt"]
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281 valid_directories = ["data"]
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282
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283 def __init__(self, path=None):
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284 super(Bag, self).__init__()
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285 self.tags = {}
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286 self.info = {}
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287 #: Dictionary of manifest entries and the checksum values for each
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288 #: algorithm:
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289 self.entries = {}
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parents:
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290
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parents:
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291 # To reliably handle Unicode normalization differences, we maintain
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parents:
diff changeset
292 # lookup dictionaries in both directions for the filenames read from
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293 # the filesystem and the manifests so we can handle cases where the
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parents:
diff changeset
294 # normalization form changed between the bag being created and read.
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diff changeset
295 # See https://github.com/LibraryOfCongress/bagit-python/issues/51.
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296
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parents:
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297 #: maps Unicode-normalized values to the raw value from the filesystem
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parents:
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298 self.normalized_filesystem_names = {}
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299
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diff changeset
300 #: maps Unicode-normalized values to the raw value in the manifest
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parents:
diff changeset
301 self.normalized_manifest_names = {}
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302
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parents:
diff changeset
303 self.algorithms = []
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parents:
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304 self.tag_file_name = None
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parents:
diff changeset
305 self.path = abspath(path)
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shellac
parents:
diff changeset
306 if path:
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parents:
diff changeset
307 # if path ends in a path separator, strip it off
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shellac
parents:
diff changeset
308 if path[-1] == os.sep:
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parents:
diff changeset
309 self.path = path[:-1]
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parents:
diff changeset
310 self._open()
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parents:
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311
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parents:
diff changeset
312 def __str__(self):
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313 # FIXME: develop a more informative string representation for a Bag
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parents:
diff changeset
314 return self.path
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parents:
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315
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parents:
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316 @property
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parents:
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317 def algs(self):
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318 warnings.warn(_("Use Bag.algorithms instead of Bag.algs"), DeprecationWarning)
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parents:
diff changeset
319 return self.algorithms
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shellac
parents:
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320
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parents:
diff changeset
321 @property
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parents:
diff changeset
322 def version(self):
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parents:
diff changeset
323 warnings.warn(
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parents:
diff changeset
324 _("Use the Bag.version_info tuple instead of Bag.version"),
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parents:
diff changeset
325 DeprecationWarning,
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shellac
parents:
diff changeset
326 )
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shellac
parents:
diff changeset
327 return self._version
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shellac
parents:
diff changeset
328
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parents:
diff changeset
329 def _open(self):
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parents:
diff changeset
330 # Open the bagit.txt file, and load any tags from it, including
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shellac
parents:
diff changeset
331 # the required version and encoding.
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parents:
diff changeset
332 bagit_file_path = os.path.join(self.path, "bagit.txt")
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shellac
parents:
diff changeset
333
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shellac
parents:
diff changeset
334 if not isfile(bagit_file_path):
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shellac
parents:
diff changeset
335 raise BagError(_("Expected bagit.txt does not exist: %s") % bagit_file_path)
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shellac
parents:
diff changeset
336
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shellac
parents:
diff changeset
337 self.tags = tags = _load_tag_file(bagit_file_path)
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shellac
parents:
diff changeset
338
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shellac
parents:
diff changeset
339 required_tags = ("BagIt-Version", "Tag-File-Character-Encoding")
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shellac
parents:
diff changeset
340 missing_tags = [i for i in required_tags if i not in tags]
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shellac
parents:
diff changeset
341 if missing_tags:
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shellac
parents:
diff changeset
342 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
343 _("Missing required tag in bagit.txt: %s") % ", ".join(missing_tags)
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shellac
parents:
diff changeset
344 )
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shellac
parents:
diff changeset
345
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shellac
parents:
diff changeset
346 # To avoid breaking existing code we'll leave self.version as the string
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shellac
parents:
diff changeset
347 # and parse it into a numeric version_info tuple. In version 2.0 we can
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shellac
parents:
diff changeset
348 # break that.
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shellac
parents:
diff changeset
349
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parents:
diff changeset
350 self._version = tags["BagIt-Version"]
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shellac
parents:
diff changeset
351
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shellac
parents:
diff changeset
352 try:
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parents:
diff changeset
353 self.version_info = tuple(int(i) for i in self._version.split(".", 1))
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shellac
parents:
diff changeset
354 except ValueError:
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shellac
parents:
diff changeset
355 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
356 _("Bag version numbers must be MAJOR.MINOR numbers, not %s")
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shellac
parents:
diff changeset
357 % self._version
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shellac
parents:
diff changeset
358 )
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shellac
parents:
diff changeset
359
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shellac
parents:
diff changeset
360 if (0, 93) <= self.version_info <= (0, 95):
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shellac
parents:
diff changeset
361 self.tag_file_name = "package-info.txt"
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shellac
parents:
diff changeset
362 elif (0, 96) <= self.version_info < (2,):
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shellac
parents:
diff changeset
363 self.tag_file_name = "bag-info.txt"
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shellac
parents:
diff changeset
364 else:
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parents:
diff changeset
365 raise BagError(_("Unsupported bag version: %s") % self._version)
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shellac
parents:
diff changeset
366
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shellac
parents:
diff changeset
367 self.encoding = tags["Tag-File-Character-Encoding"]
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shellac
parents:
diff changeset
368
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shellac
parents:
diff changeset
369 try:
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parents:
diff changeset
370 codecs.lookup(self.encoding)
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shellac
parents:
diff changeset
371 except LookupError:
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shellac
parents:
diff changeset
372 raise BagValidationError(_("Unsupported encoding: %s") % self.encoding)
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shellac
parents:
diff changeset
373
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shellac
parents:
diff changeset
374 info_file_path = os.path.join(self.path, self.tag_file_name)
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shellac
parents:
diff changeset
375 if os.path.exists(info_file_path):
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shellac
parents:
diff changeset
376 self.info = _load_tag_file(info_file_path, encoding=self.encoding)
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shellac
parents:
diff changeset
377
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shellac
parents:
diff changeset
378 self._load_manifests()
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shellac
parents:
diff changeset
379
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shellac
parents:
diff changeset
380 def manifest_files(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
381 for filename in ["manifest-%s.txt" % a for a in CHECKSUM_ALGOS]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
382 f = os.path.join(self.path, filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
383 if isfile(f):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
384 yield f
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
385
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
386 def tagmanifest_files(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
387 for filename in ["tagmanifest-%s.txt" % a for a in CHECKSUM_ALGOS]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
388 f = os.path.join(self.path, filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
389 if isfile(f):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
390 yield f
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
391
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
392 def compare_manifests_with_fs(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
393 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
394 Compare the filenames in the manifests to the filenames present on the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
395 local filesystem and returns two lists of the files which are only
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
396 present in the manifests and the files which are only present on the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
397 local filesystem, respectively.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
398 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
399
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
400 # We compare the filenames after Unicode normalization so we can
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
401 # reliably detect normalization changes after bag creation:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
402 files_on_fs = set(normalize_unicode(i) for i in self.payload_files())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
403 files_in_manifest = set(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
404 normalize_unicode(i) for i in self.payload_entries().keys()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
405 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
406
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
407 if self.version_info >= (0, 97):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
408 files_in_manifest.update(self.missing_optional_tagfiles())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
409
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
410 only_on_fs = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
411 only_in_manifest = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
412
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
413 for i in files_on_fs.difference(files_in_manifest):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
414 only_on_fs.append(self.normalized_filesystem_names[i])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
415
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
416 for i in files_in_manifest.difference(files_on_fs):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
417 only_in_manifest.append(self.normalized_manifest_names[i])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
418
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
419 return only_in_manifest, only_on_fs
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
420
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
421 def compare_fetch_with_fs(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
422 """Compares the fetch entries with the files actually
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
423 in the payload, and returns a list of all the files
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
424 that still need to be fetched.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
426
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 files_on_fs = set(self.payload_files())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428 files_in_fetch = set(self.files_to_be_fetched())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
429
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 return list(files_in_fetch - files_on_fs)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
431
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
432 def payload_files(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
433 """Returns a list of filenames which are present on the local filesystem"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
434 payload_dir = os.path.join(self.path, "data")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436 for dirpath, _, filenames in os.walk(payload_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 for f in filenames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 # Jump through some hoops here to make the payload files are
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
439 # returned with the directory structure relative to the base
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
440 # directory rather than the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
441 normalized_f = os.path.normpath(f)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
442 rel_path = os.path.relpath(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
443 os.path.join(dirpath, normalized_f), start=self.path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
444 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
445
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
446 self.normalized_filesystem_names[normalize_unicode(rel_path)] = rel_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
447 yield rel_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
449 def payload_entries(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 """Return a dictionary of items """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
451 # Don't use dict comprehension (compatibility with Python < 2.7)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
452 return dict(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 (key, value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
454 for (key, value) in self.entries.items()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
455 if key.startswith("data" + os.sep)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 def save(self, processes=1, manifests=False):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 save will persist any changes that have been made to the bag
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461 metadata (self.info).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
462
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 If you have modified the payload of the bag (added, modified,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 removed files in the data directory) and want to regenerate manifests
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 set the manifests parameter to True. The default is False since you
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466 wouldn't want a save to accidentally create a new manifest for
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467 a corrupted bag.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 If you want to control the number of processes that are used when
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 recalculating checksums use the processes parameter.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 # Error checking
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 if not self.path:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 raise BagError(_("Bag.save() called before setting the path!"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 if not os.access(self.path, os.R_OK | os.W_OK | os.X_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 _("Cannot save bag to non-existent or inaccessible directory %s")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 % self.path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 unbaggable = _can_bag(self.path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483 if unbaggable:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 LOGGER.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 "Missing write permissions for the following directories and files:\n%s"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 unbaggable,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
489 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490 raise BagError(_("Missing permissions to move all files and directories"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
492 unreadable_dirs, unreadable_files = _can_read(self.path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
493 if unreadable_dirs or unreadable_files:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
494 if unreadable_dirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
495 LOGGER.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
496 _("The following directories do not have read permissions:\n%s"),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497 unreadable_dirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
498 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499 if unreadable_files:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500 LOGGER.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
501 _("The following files do not have read permissions:\n%s"),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
502 unreadable_files,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505 _("Read permissions are required to calculate file fixities")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
506 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
507
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
508 # Change working directory to bag directory so helper functions work
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parents:
diff changeset
509 old_dir = os.path.abspath(os.path.curdir)
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parents:
diff changeset
510 os.chdir(self.path)
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parents:
diff changeset
511
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parents:
diff changeset
512 # Generate new manifest files
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parents:
diff changeset
513 if manifests:
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parents:
diff changeset
514 total_bytes, total_files = make_manifests(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
515 "data", processes, algorithms=self.algorithms, encoding=self.encoding
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parents:
diff changeset
516 )
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parents:
diff changeset
517
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parents:
diff changeset
518 # Update Payload-Oxum
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parents:
diff changeset
519 LOGGER.info(_("Updating Payload-Oxum in %s"), self.tag_file_name)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
520 self.info["Payload-Oxum"] = "%s.%s" % (total_bytes, total_files)
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parents:
diff changeset
521
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parents:
diff changeset
522 _make_tag_file(self.tag_file_name, self.info)
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parents:
diff changeset
523
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parents:
diff changeset
524 # Update tag-manifest for changes to manifest & bag-info files
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parents:
diff changeset
525 for alg in self.algorithms:
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parents:
diff changeset
526 _make_tagmanifest_file(alg, self.path, encoding=self.encoding)
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parents:
diff changeset
527
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parents:
diff changeset
528 # Reload the manifests
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diff changeset
529 self._load_manifests()
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diff changeset
530
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diff changeset
531 os.chdir(old_dir)
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diff changeset
532
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diff changeset
533 def tagfile_entries(self):
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534 return dict(
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parents:
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535 (key, value)
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536 for (key, value) in self.entries.items()
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diff changeset
537 if not key.startswith("data" + os.sep)
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parents:
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538 )
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parents:
diff changeset
539
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parents:
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540 def missing_optional_tagfiles(self):
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parents:
diff changeset
541 """
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parents:
diff changeset
542 From v0.97 we need to validate any tagfiles listed
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diff changeset
543 in the optional tagmanifest(s). As there is no mandatory
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parents:
diff changeset
544 directory structure for additional tagfiles we can
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parents:
diff changeset
545 only check for entries with missing files (not missing
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546 entries for existing files).
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547 """
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parents:
diff changeset
548 for tagfilepath in self.tagfile_entries().keys():
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parents:
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549 if not os.path.isfile(os.path.join(self.path, tagfilepath)):
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parents:
diff changeset
550 yield tagfilepath
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parents:
diff changeset
551
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parents:
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552 def fetch_entries(self):
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diff changeset
553 """Load fetch.txt if present and iterate over its contents
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diff changeset
554
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diff changeset
555 yields (url, size, filename) tuples
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parents:
diff changeset
556
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diff changeset
557 raises BagError for errors such as an unsafe filename referencing
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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558 data outside of the bag directory
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diff changeset
559 """
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diff changeset
560
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561 fetch_file_path = os.path.join(self.path, "fetch.txt")
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562
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563 if isfile(fetch_file_path):
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diff changeset
564 with open_text_file(
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parents:
diff changeset
565 fetch_file_path, "r", encoding=self.encoding
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parents:
diff changeset
566 ) as fetch_file:
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diff changeset
567 for line in fetch_file:
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diff changeset
568 url, file_size, filename = line.strip().split(None, 2)
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diff changeset
569
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570 if self._path_is_dangerous(filename):
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diff changeset
571 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
572 _('Path "%(payload_file)s" in "%(source_file)s" is unsafe')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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573 % {
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parents:
diff changeset
574 "payload_file": filename,
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parents:
diff changeset
575 "source_file": os.path.join(self.path, "fetch.txt"),
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diff changeset
576 }
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parents:
diff changeset
577 )
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parents:
diff changeset
578
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diff changeset
579 yield url, file_size, filename
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parents:
diff changeset
580
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parents:
diff changeset
581 def files_to_be_fetched(self):
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parents:
diff changeset
582 """
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shellac
parents:
diff changeset
583 Convenience wrapper for fetch_entries which returns only the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 local filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 """
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shellac
parents:
diff changeset
586
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parents:
diff changeset
587 for url, file_size, filename in self.fetch_entries():
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parents:
diff changeset
588 yield filename
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parents:
diff changeset
589
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parents:
diff changeset
590 def has_oxum(self):
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parents:
diff changeset
591 return "Payload-Oxum" in self.info
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diff changeset
592
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parents:
diff changeset
593 def validate(self, processes=1, fast=False, completeness_only=False):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
594 """Checks the structure and contents are valid.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595
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shellac
parents:
diff changeset
596 If you supply the parameter fast=True the Payload-Oxum (if present) will
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
597 be used to check that the payload files are present and accounted for,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 instead of re-calculating fixities and comparing them against the
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shellac
parents:
diff changeset
599 manifest. By default validate() will re-calculate fixities (fast=False).
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parents:
diff changeset
600 """
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parents:
diff changeset
601
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parents:
diff changeset
602 self._validate_structure()
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parents:
diff changeset
603 self._validate_bagittxt()
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parents:
diff changeset
604
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parents:
diff changeset
605 self.validate_fetch()
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parents:
diff changeset
606
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parents:
diff changeset
607 self._validate_contents(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
608 processes=processes, fast=fast, completeness_only=completeness_only
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
609 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
611 return True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
612
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parents:
diff changeset
613 def is_valid(self, fast=False, completeness_only=False):
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shellac
parents:
diff changeset
614 """Returns validation success or failure as boolean.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
615 Optional fast parameter passed directly to validate().
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parents:
diff changeset
616 """
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shellac
parents:
diff changeset
617
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
618 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
619 self.validate(fast=fast, completeness_only=completeness_only)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
620 except BagError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
621 return False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
622
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parents:
diff changeset
623 return True
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parents:
diff changeset
624
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parents:
diff changeset
625 def _load_manifests(self):
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parents:
diff changeset
626 self.entries = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
627 manifests = list(self.manifest_files())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
628
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parents:
diff changeset
629 if self.version_info >= (0, 97):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
630 # v0.97+ requires that optional tagfiles are verified.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
631 manifests += list(self.tagmanifest_files())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
632
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parents:
diff changeset
633 for manifest_filename in manifests:
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parents:
diff changeset
634 if manifest_filename.find("tagmanifest-") != -1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
635 search = "tagmanifest-"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
636 else:
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parents:
diff changeset
637 search = "manifest-"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 alg = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 os.path.basename(manifest_filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 .replace(search, "")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
641 .replace(".txt", "")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
643 if alg not in self.algorithms:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
644 self.algorithms.append(alg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
645
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
646 with open_text_file(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
647 manifest_filename, "r", encoding=self.encoding
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
648 ) as manifest_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
649 if manifest_file.encoding.startswith("UTF"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
650 # We'll check the first character to see if it's a BOM:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
651 if manifest_file.read(1) == UNICODE_BYTE_ORDER_MARK:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
652 # We'll skip it either way by letting line decoding
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
653 # happen at the new offset but we will issue a warning
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
654 # for UTF-8 since the presence of a BOM is contrary to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
655 # the BagIt specification:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
656 if manifest_file.encoding == "UTF-8":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
657 LOGGER.warning(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
658 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
659 "%s is encoded using UTF-8 but contains an unnecessary"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
660 " byte-order mark, which is not in compliance with the"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
661 " BagIt RFC"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
662 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
663 manifest_file.name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
664 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
665 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
666 manifest_file.seek(0) # Pretend the first read never happened
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
667
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
668 for line in manifest_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
669 line = line.strip()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
670
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
671 # Ignore blank lines and comments.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
672 if line == "" or line.startswith("#"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
673 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
674
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
675 entry = line.split(None, 1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
677 # Format is FILENAME *CHECKSUM
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678 if len(entry) != 2:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
679 LOGGER.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
680 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
681 "%(bag)s: Invalid %(algorithm)s manifest entry: %(line)s"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
682 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 {"bag": self, "algorithm": alg, "line": line},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
684 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
686
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
687 entry_hash = entry[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
688 entry_path = os.path.normpath(entry[1].lstrip("*"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
689 entry_path = _decode_filename(entry_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
690
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
691 if self._path_is_dangerous(entry_path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
692 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
693 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
694 'Path "%(payload_file)s" in manifest "%(manifest_file)s" is unsafe'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
696 % {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697 "payload_file": entry_path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
698 "manifest_file": manifest_file.name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702 entry_hashes = self.entries.setdefault(entry_path, {})
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704 if alg in entry_hashes:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705 warning_ctx = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 "bag": self,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 "algorithm": alg,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
708 "filename": entry_path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
709 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710 if entry_hashes[alg] == entry_hash:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711 msg = _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 "%(bag)s: %(algorithm)s manifest lists %(filename)s"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 " multiple times with the same value"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 if self.version_info >= (1,):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716 raise BagError(msg % warning_ctx)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718 LOGGER.warning(msg, warning_ctx)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 raise BagError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 "%(bag)s: %(algorithm)s manifest lists %(filename)s"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 " multiple times with conflicting values"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 % warning_ctx
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 entry_hashes[alg] = entry_hash
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 self.normalized_manifest_names.update(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 (normalize_unicode(i), i) for i in self.entries.keys()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 def _validate_structure(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 Checks the structure of the bag to determine whether it conforms to the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 BagIt spec. Returns true on success, otherwise it will raise a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 BagValidationError exception.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 self._validate_structure_payload_directory()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 self._validate_structure_tag_files()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 def _validate_structure_payload_directory(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745 data_dir_path = os.path.join(self.path, "data")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 if not isdir(data_dir_path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749 _("Expected data directory %s does not exist") % data_dir_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 def _validate_structure_tag_files(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753 # Note: we deviate somewhat from v0.96 of the spec in that it allows
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 # other files and directories to be present in the base directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 if not list(self.manifest_files()):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 raise BagValidationError(_("No manifest files found"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 if "bagit.txt" not in os.listdir(self.path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 _('Expected %s to contain "bagit.txt"') % self.path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 def validate_fetch(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 """Validate the fetch.txt file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766 Raises `BagError` for errors and otherwise returns no value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769 for url, file_size, filename in self.fetch_entries():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
770 # fetch_entries will raise a BagError for unsafe filenames
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
771 # so at this point we will check only that the URL is minimally
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
772 # well formed:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
773 parsed_url = urlparse(url)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
774
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
775 if not all((parsed_url.scheme, parsed_url.netloc)):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
776 raise BagError(_("Malformed URL in fetch.txt: %s") % url)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
778 def _validate_contents(self, processes=1, fast=False, completeness_only=False):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
779 if fast and not self.has_oxum():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
780 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
781 _("Fast validation requires bag-info.txt to include Payload-Oxum")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
782 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
783
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 # Perform the fast file count + size check so we can fail early:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 self._validate_oxum()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
786
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
787 if fast:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
790 self._validate_completeness()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
791
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
792 if completeness_only:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
793 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
794
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
795 self._validate_entries(processes)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
796
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
797 def _validate_oxum(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
798 oxum = self.info.get("Payload-Oxum")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
799
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
800 if oxum is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
801 return
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
802
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
803 # If multiple Payload-Oxum tags (bad idea)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
804 # use the first listed in bag-info.txt
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
805 if isinstance(oxum, list):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
806 LOGGER.warning(_("bag-info.txt defines multiple Payload-Oxum values!"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
807 oxum = oxum[0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
808
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
809 oxum_byte_count, oxum_file_count = oxum.split(".", 1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
810
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
811 if not oxum_byte_count.isdigit() or not oxum_file_count.isdigit():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
812 raise BagError(_("Malformed Payload-Oxum value: %s") % oxum)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
813
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
814 oxum_byte_count = int(oxum_byte_count)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
815 oxum_file_count = int(oxum_file_count)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
816 total_bytes = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
817 total_files = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
818
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
819 for payload_file in self.payload_files():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
820 payload_file = os.path.join(self.path, payload_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
821 total_bytes += os.stat(payload_file).st_size
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
822 total_files += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
824 if oxum_file_count != total_files or oxum_byte_count != total_bytes:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
825 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
826 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
827 "Payload-Oxum validation failed."
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
828 " Expected %(oxum_file_count)d files and %(oxum_byte_count)d bytes"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
829 " but found %(found_file_count)d files and %(found_byte_count)d bytes"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
830 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
831 % {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
832 "found_file_count": total_files,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
833 "found_byte_count": total_bytes,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
834 "oxum_file_count": oxum_file_count,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
835 "oxum_byte_count": oxum_byte_count,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
836 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
837 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
838
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
839 def _validate_completeness(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
840 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841 Verify that the actual file manifests match the files in the data directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
843 errors = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
844
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
845 # First we'll make sure there's no mismatch between the filesystem
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
846 # and the list of files in the manifest(s)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
847 only_in_manifests, only_on_fs = self.compare_manifests_with_fs()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 for path in only_in_manifests:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 e = FileMissing(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850 LOGGER.warning(force_unicode(e))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 errors.append(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852 for path in only_on_fs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 e = UnexpectedFile(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 LOGGER.warning(force_unicode(e))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855 errors.append(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857 if errors:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 raise BagValidationError(_("Bag validation failed"), errors)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 def _validate_entries(self, processes):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862 Verify that the actual file contents match the recorded hashes stored in the manifest files
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864 errors = list()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
866 if os.name == "posix":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 worker_init = posix_multiprocessing_worker_initializer
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869 worker_init = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
871 args = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 self.path,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
874 self.normalized_filesystem_names.get(rel_path, rel_path),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875 hashes,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 self.algorithms,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
877 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 for rel_path, hashes in self.entries.items()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
879 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882 if processes == 1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883 hash_results = [_calc_hashes(i) for i in args]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886 pool = multiprocessing.Pool(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 processes if processes else None, initializer=worker_init
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889 hash_results = pool.map(_calc_hashes, args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 finally:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 pool.terminate()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 # Any unhandled exceptions are probably fatal
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894 except:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895 LOGGER.exception(_("Unable to calculate file hashes for %s"), self)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 raise
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 for rel_path, f_hashes, hashes in hash_results:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 for alg, computed_hash in f_hashes.items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 stored_hash = hashes[alg]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 if stored_hash.lower() != computed_hash:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 e = ChecksumMismatch(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903 rel_path, alg, stored_hash.lower(), computed_hash
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 LOGGER.warning(force_unicode(e))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 errors.append(e)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
907
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
908 if errors:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
909 raise BagValidationError(_("Bag validation failed"), errors)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
910
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
911 def _validate_bagittxt(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
912 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 Verify that bagit.txt conforms to specification
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
914 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
915 bagit_file_path = os.path.join(self.path, "bagit.txt")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
916
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
917 # Note that we are intentionally opening this file in binary mode so we can confirm
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
918 # that it does not start with the UTF-8 byte-order-mark
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
919 with open(bagit_file_path, "rb") as bagit_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
920 first_line = bagit_file.read(4)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
921 if first_line.startswith(codecs.BOM_UTF8):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
922 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
923 _("bagit.txt must not contain a byte-order mark")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
924 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
925
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
926 def _path_is_dangerous(self, path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
927 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
928 Return true if path looks dangerous, i.e. potentially operates
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
929 outside the bagging directory structure, e.g. ~/.bashrc, ../../../secrets.json,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
930 \\?\c:\, D:\sys32\cmd.exe
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932 if os.path.isabs(path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
933 return True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 if os.path.expanduser(path) != path:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 return True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
936 if os.path.expandvars(path) != path:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
937 return True
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938 real_path = os.path.realpath(os.path.join(self.path, path))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939 real_path = os.path.normpath(real_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
940 bag_path = os.path.realpath(self.path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941 bag_path = os.path.normpath(bag_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 common = os.path.commonprefix((bag_path, real_path))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
943 return not (common == bag_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
945
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
946 class BagError(Exception):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
947 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
948
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
950 class BagValidationError(BagError):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
951 def __init__(self, message, details=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
952 super(BagValidationError, self).__init__()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
953
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
954 if details is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
955 details = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
956
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
957 self.message = message
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
958 self.details = details
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
959
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
960 def __str__(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
961 if len(self.details) > 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
962 details = "; ".join([force_unicode(e) for e in self.details])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
963 return "%s: %s" % (self.message, details)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
964 return self.message
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
965
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
966
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
967 class ManifestErrorDetail(BagError):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
968 def __init__(self, path):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
969 super(ManifestErrorDetail, self).__init__()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
970
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
971 self.path = path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
973
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
974 class ChecksumMismatch(ManifestErrorDetail):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
975 def __init__(self, path, algorithm=None, expected=None, found=None):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
976 super(ChecksumMismatch, self).__init__(path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
977
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
978 self.path = path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
979 self.algorithm = algorithm
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
980 self.expected = expected
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
981 self.found = found
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
982
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
983 def __str__(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
984 return _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
985 '%(path)s %(algorithm)s validation failed: expected="%(expected)s" found="%(found)s"'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
986 ) % {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
987 "path": force_unicode(self.path),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
988 "algorithm": self.algorithm,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
989 "expected": self.expected,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
990 "found": self.found,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
991 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
992
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
993
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
994 class FileMissing(ManifestErrorDetail):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
995 def __str__(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
996 return _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
997 "%s exists in manifest but was not found on filesystem"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
998 ) % force_unicode(self.path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
999
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1000
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1001 class UnexpectedFile(ManifestErrorDetail):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1002 def __str__(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1003 return _("%s exists on filesystem but is not in the manifest") % self.path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1004
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1005
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1006 class FileNormalizationConflict(BagError):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1007 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1008 Exception raised when two files differ only in normalization and thus
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1009 are not safely portable
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1010 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1011
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1012 def __init__(self, file_a, file_b):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1013 super(FileNormalizationConflict, self).__init__()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1014
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1015 self.file_a = file_a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1016 self.file_b = file_b
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1017
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1018 def __str__(self):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1019 return _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1020 'Unicode normalization conflict for file "%(file_a)s" and "%(file_b)s"'
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1021 ) % {"file_a": self.file_a, "file_b": self.file_b}
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shellac
parents:
diff changeset
1022
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shellac
parents:
diff changeset
1023
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shellac
parents:
diff changeset
1024 def posix_multiprocessing_worker_initializer():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1025 """Ignore SIGINT in multiprocessing workers on POSIX systems"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1026 signal.signal(signal.SIGINT, signal.SIG_IGN)
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shellac
parents:
diff changeset
1027
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shellac
parents:
diff changeset
1028
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1029 # The Unicode normalization form used here doesn't matter – all we care about
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1030 # is consistency since the input value will be preserved:
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shellac
parents:
diff changeset
1031
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shellac
parents:
diff changeset
1032
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shellac
parents:
diff changeset
1033 def normalize_unicode_py3(s):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1034 return unicodedata.normalize("NFC", s)
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shellac
parents:
diff changeset
1035
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shellac
parents:
diff changeset
1036
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1037 def normalize_unicode_py2(s):
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shellac
parents:
diff changeset
1038 if isinstance(s, str):
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shellac
parents:
diff changeset
1039 s = s.decode("utf-8")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1040 return unicodedata.normalize("NFC", s)
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shellac
parents:
diff changeset
1041
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shellac
parents:
diff changeset
1042
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shellac
parents:
diff changeset
1043 if sys.version_info > (3, 0):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1044 normalize_unicode = normalize_unicode_py3
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shellac
parents:
diff changeset
1045 else:
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shellac
parents:
diff changeset
1046 normalize_unicode = normalize_unicode_py2
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shellac
parents:
diff changeset
1047
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shellac
parents:
diff changeset
1048
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1049 def build_unicode_normalized_lookup_dict(filenames):
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shellac
parents:
diff changeset
1050 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1051 Return a dictionary mapping unicode-normalized filenames to as-encoded
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1052 values to efficiently detect conflicts between the filesystem and manifests.
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shellac
parents:
diff changeset
1053
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shellac
parents:
diff changeset
1054 This is necessary because some filesystems and utilities may automatically
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1055 apply a different Unicode normalization form to filenames than was applied
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1056 when the bag was originally created.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1057
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shellac
parents:
diff changeset
1058 The best known example of this is when a bag is created using a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1059 normalization form other than NFD and then transferred to a Mac where the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1060 HFS+ filesystem will transparently normalize filenames to a variant of NFD
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1061 for every call:
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shellac
parents:
diff changeset
1062
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shellac
parents:
diff changeset
1063 https://developer.apple.com/legacy/library/technotes/tn/tn1150.html#UnicodeSubtleties
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shellac
parents:
diff changeset
1064
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shellac
parents:
diff changeset
1065 Windows is documented as storing filenames exactly as provided:
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shellac
parents:
diff changeset
1066
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1067 https://msdn.microsoft.com/en-us/library/windows/desktop/aa365247%28v=vs.85%29.aspx
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shellac
parents:
diff changeset
1068
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shellac
parents:
diff changeset
1069 Linux performs no normalization in the kernel but it is technically
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1070 valid for a filesystem to perform normalization, such as when an HFS+
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1071 volume is mounted.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1072
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1073 See http://www.unicode.org/reports/tr15/ for a full discussion of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1074 equivalence and normalization in Unicode.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1075 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1076
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shellac
parents:
diff changeset
1077 output = dict()
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shellac
parents:
diff changeset
1078
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shellac
parents:
diff changeset
1079 for filename in filenames:
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shellac
parents:
diff changeset
1080 normalized_filename = normalize_unicode(filename)
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shellac
parents:
diff changeset
1081 if normalized_filename in output:
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shellac
parents:
diff changeset
1082 raise FileNormalizationConflict(filename, output[normalized_filename])
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shellac
parents:
diff changeset
1083 else:
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shellac
parents:
diff changeset
1084 output[normalized_filename] = filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1085
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shellac
parents:
diff changeset
1086 return output
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1087
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shellac
parents:
diff changeset
1088
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shellac
parents:
diff changeset
1089 def get_hashers(algorithms):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1090 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1091 Given a list of algorithm names, return a dictionary of hasher instances
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1092
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1093 This avoids redundant code between the creation and validation code where in
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1094 both cases we want to avoid reading the same file more than once. The
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1095 intended use is a simple for loop:
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shellac
parents:
diff changeset
1096
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1097 for block in file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1098 for hasher in hashers.values():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1099 hasher.update(block)
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shellac
parents:
diff changeset
1100 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1101
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shellac
parents:
diff changeset
1102 hashers = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1103
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1104 for alg in algorithms:
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shellac
parents:
diff changeset
1105 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1106 hasher = hashlib.new(alg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1107 except ValueError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1108 LOGGER.warning(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1109 _("Disabling requested hash algorithm %s: hashlib does not support it"),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1110 alg,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1111 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1112 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1113
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1114 hashers[alg] = hasher
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1115
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shellac
parents:
diff changeset
1116 if not hashers:
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shellac
parents:
diff changeset
1117 raise ValueError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1118 _(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1119 "Unable to continue: hashlib does not support any of the requested algorithms!"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1120 )
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shellac
parents:
diff changeset
1121 )
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shellac
parents:
diff changeset
1122
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1123 return hashers
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1124
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1125
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1126 def _calc_hashes(args):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1127 # auto unpacking of sequences illegal in Python3
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1128 (base_path, rel_path, hashes, algorithms) = args
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1129 full_path = os.path.join(base_path, rel_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1130
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1131 # Create a clone of the default empty hash objects:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1132 f_hashers = dict((alg, hashlib.new(alg)) for alg in hashes if alg in algorithms)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1133
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shellac
parents:
diff changeset
1134 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1135 f_hashes = _calculate_file_hashes(full_path, f_hashers)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1136 except BagValidationError as e:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1137 f_hashes = dict((alg, force_unicode(e)) for alg in f_hashers.keys())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1138
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shellac
parents:
diff changeset
1139 return rel_path, f_hashes, hashes
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1140
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1141
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1142 def _calculate_file_hashes(full_path, f_hashers):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1143 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1144 Returns a dictionary of (algorithm, hexdigest) values for the provided
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1145 filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1146 """
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shellac
parents:
diff changeset
1147 LOGGER.info(_("Verifying checksum for file %s"), full_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1148
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1149 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1150 with open(full_path, "rb") as f:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1151 while True:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1152 block = f.read(HASH_BLOCK_SIZE)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1153 if not block:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1154 break
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1155 for i in f_hashers.values():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1156 i.update(block)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1157 except (OSError, IOError) as e:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1158 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1159 _("Could not read %(filename)s: %(error)s")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1160 % {"filename": full_path, "error": force_unicode(e)}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1161 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1162
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1163 return dict((alg, h.hexdigest()) for alg, h in f_hashers.items())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1164
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1165
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1166 def _load_tag_file(tag_file_name, encoding="utf-8-sig"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1167 with open_text_file(tag_file_name, "r", encoding=encoding) as tag_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1168 # Store duplicate tags as list of vals
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1169 # in order of parsing under the same key.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1170 tags = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1171 for name, value in _parse_tags(tag_file):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1172 if name not in tags:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1173 tags[name] = value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1174 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1175
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1176 if not isinstance(tags[name], list):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1177 tags[name] = [tags[name], value]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1178 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1179 tags[name].append(value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1180
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1181 return tags
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1182
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1183
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1184 def _parse_tags(tag_file):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1185 """Parses a tag file, according to RFC 2822. This
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1186 includes line folding, permitting extra-long
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1187 field values.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1188
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1189 See http://www.faqs.org/rfcs/rfc2822.html for
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1190 more information.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1191 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1192
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1193 tag_name = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1194 tag_value = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1195
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1196 # Line folding is handled by yielding values only after we encounter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1197 # the start of a new tag, or if we pass the EOF.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1198 for num, line in enumerate(tag_file):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1199 # Skip over any empty or blank lines.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1200 if len(line) == 0 or line.isspace():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1201 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1202 elif line[0].isspace() and tag_value is not None: # folded line
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1203 tag_value += line
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1204 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1205 # Starting a new tag; yield the last one.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1206 if tag_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1207 yield (tag_name, tag_value.strip())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1208
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1209 if ":" not in line:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1210 raise BagValidationError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1211 _("%(filename)s contains invalid tag: %(line)s")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1212 % {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1213 "line": line.strip(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1214 "filename": os.path.basename(tag_file.name),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1215 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1216 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1217
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1218 parts = line.strip().split(":", 1)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1219 tag_name = parts[0].strip()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1220 tag_value = parts[1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1221
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1222 # Passed the EOF. All done after this.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1223 if tag_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1224 yield (tag_name, tag_value.strip())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1225
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1226
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1227 def _make_tag_file(bag_info_path, bag_info):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1228 headers = sorted(bag_info.keys())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1229 with open_text_file(bag_info_path, "w") as f:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1230 for h in headers:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1231 values = bag_info[h]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1232 if not isinstance(values, list):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1233 values = [values]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1234 for txt in values:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1235 # strip CR, LF and CRLF so they don't mess up the tag file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1236 txt = re.sub(r"\n|\r|(\r\n)", "", force_unicode(txt))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1237 f.write("%s: %s\n" % (h, txt))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1238
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1239
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1240 def make_manifests(data_dir, processes, algorithms=DEFAULT_CHECKSUMS, encoding="utf-8"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1241 LOGGER.info(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1242 _("Using %(process_count)d processes to generate manifests: %(algorithms)s"),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1243 {"process_count": processes, "algorithms": ", ".join(algorithms)},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1244 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1245
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1246 manifest_line_generator = partial(generate_manifest_lines, algorithms=algorithms)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1247
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1248 if processes > 1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1249 pool = multiprocessing.Pool(processes=processes)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1250 checksums = pool.map(manifest_line_generator, _walk(data_dir))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1251 pool.close()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1252 pool.join()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1253 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1254 checksums = [manifest_line_generator(i) for i in _walk(data_dir)]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1255
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1256 # At this point we have a list of tuples which start with the algorithm name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1257 manifest_data = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1258 for batch in checksums:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1259 for entry in batch:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1260 manifest_data.setdefault(entry[0], []).append(entry[1:])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1261
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1262 # These will be keyed on the algorithm name so we can perform sanity checks
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1263 # below to catch failures in the hashing process:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1264 num_files = defaultdict(lambda: 0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1265 total_bytes = defaultdict(lambda: 0)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1266
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1267 for algorithm, values in manifest_data.items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1268 manifest_filename = "manifest-%s.txt" % algorithm
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1269
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1270 with open_text_file(manifest_filename, "w", encoding=encoding) as manifest:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1271 for digest, filename, byte_count in values:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1272 manifest.write("%s %s\n" % (digest, _encode_filename(filename)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1273 num_files[algorithm] += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1274 total_bytes[algorithm] += byte_count
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1275
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1276 # We'll use sets of the values for the error checks and eventually return the payload oxum values:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1277 byte_value_set = set(total_bytes.values())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1278 file_count_set = set(num_files.values())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1279
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1280 # allow a bag with an empty payload
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1281 if not byte_value_set and not file_count_set:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1282 return 0, 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1283
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1284 if len(file_count_set) != 1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1285 raise RuntimeError(_("Expected the same number of files for each checksum"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1286
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1287 if len(byte_value_set) != 1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1288 raise RuntimeError(_("Expected the same number of bytes for each checksums"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1289
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1290 return byte_value_set.pop(), file_count_set.pop()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1291
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1292
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1293 def _make_tagmanifest_file(alg, bag_dir, encoding="utf-8"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1294 tagmanifest_file = join(bag_dir, "tagmanifest-%s.txt" % alg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1295 LOGGER.info(_("Creating %s"), tagmanifest_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1296
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1297 checksums = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1298 for f in _find_tag_files(bag_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1299 if re.match(r"^tagmanifest-.+\.txt$", f):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1300 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1301 with open(join(bag_dir, f), "rb") as fh:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1302 m = hashlib.new(alg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1303 while True:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1304 block = fh.read(HASH_BLOCK_SIZE)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1305 if not block:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1306 break
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1307 m.update(block)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1308 checksums.append((m.hexdigest(), f))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1309
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1310 with open_text_file(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1311 join(bag_dir, tagmanifest_file), mode="w", encoding=encoding
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1312 ) as tagmanifest:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1313 for digest, filename in checksums:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1314 tagmanifest.write("%s %s\n" % (digest, filename))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1315
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1316
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1317 def _find_tag_files(bag_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1318 for dir in os.listdir(bag_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1319 if dir != "data":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1320 if os.path.isfile(dir) and not dir.startswith("tagmanifest-"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1321 yield dir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1322 for dir_name, _, filenames in os.walk(dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1323 for filename in filenames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1324 if filename.startswith("tagmanifest-"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1325 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1326 # remove everything up to the bag_dir directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1327 p = join(dir_name, filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1328 yield os.path.relpath(p, bag_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1329
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1330
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1331 def _walk(data_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1332 for dirpath, dirnames, filenames in os.walk(data_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1333 # if we don't sort here the order of entries is non-deterministic
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1334 # which makes it hard to test the fixity of tagmanifest-md5.txt
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1335 filenames.sort()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1336 dirnames.sort()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1337 for fn in filenames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1338 path = os.path.join(dirpath, fn)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1339 # BagIt spec requires manifest to always use '/' as path separator
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1340 if os.path.sep != "/":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1341 parts = path.split(os.path.sep)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1342 path = "/".join(parts)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1343 yield path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1344
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1345
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1346 def _can_bag(test_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1347 """Scan the provided directory for files which cannot be bagged due to insufficient permissions"""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1348 unbaggable = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1349
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1350 if not os.access(test_dir, os.R_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1351 # We cannot continue without permission to read the source directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1352 unbaggable.append(test_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1353 return unbaggable
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1354
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1355 if not os.access(test_dir, os.W_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1356 unbaggable.append(test_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1357
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1358 for dirpath, dirnames, filenames in os.walk(test_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1359 for directory in dirnames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1360 full_path = os.path.join(dirpath, directory)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1361 if not os.access(full_path, os.W_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1362 unbaggable.append(full_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1363
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1364 return unbaggable
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1365
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1366
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1367 def _can_read(test_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1368 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1369 returns ((unreadable_dirs), (unreadable_files))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1370 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1371 unreadable_dirs = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1372 unreadable_files = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1373
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1374 if not os.access(test_dir, os.R_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1375 unreadable_dirs.append(test_dir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1376 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1377 for dirpath, dirnames, filenames in os.walk(test_dir):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1378 for dn in dirnames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1379 full_path = os.path.join(dirpath, dn)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1380 if not os.access(full_path, os.R_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1381 unreadable_dirs.append(full_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1382 for fn in filenames:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1383 full_path = os.path.join(dirpath, fn)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1384 if not os.access(full_path, os.R_OK):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1385 unreadable_files.append(full_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1386 return (tuple(unreadable_dirs), tuple(unreadable_files))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1387
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1388
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1389 def generate_manifest_lines(filename, algorithms=DEFAULT_CHECKSUMS):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1390 LOGGER.info(_("Generating manifest lines for file %s"), filename)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1391
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1392 # For performance we'll read the file only once and pass it block
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1393 # by block to every requested hash algorithm:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1394 hashers = get_hashers(algorithms)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1395
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1396 total_bytes = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1397
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1398 with open(filename, "rb") as f:
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shellac
parents:
diff changeset
1399 while True:
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shellac
parents:
diff changeset
1400 block = f.read(HASH_BLOCK_SIZE)
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shellac
parents:
diff changeset
1401
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shellac
parents:
diff changeset
1402 if not block:
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shellac
parents:
diff changeset
1403 break
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shellac
parents:
diff changeset
1404
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shellac
parents:
diff changeset
1405 total_bytes += len(block)
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shellac
parents:
diff changeset
1406 for hasher in hashers.values():
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shellac
parents:
diff changeset
1407 hasher.update(block)
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parents:
diff changeset
1408
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shellac
parents:
diff changeset
1409 decoded_filename = _decode_filename(filename)
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shellac
parents:
diff changeset
1410
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shellac
parents:
diff changeset
1411 # We'll generate a list of results in roughly manifest format but prefixed with the algorithm:
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shellac
parents:
diff changeset
1412 results = [
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shellac
parents:
diff changeset
1413 (alg, hasher.hexdigest(), decoded_filename, total_bytes)
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shellac
parents:
diff changeset
1414 for alg, hasher in hashers.items()
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shellac
parents:
diff changeset
1415 ]
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shellac
parents:
diff changeset
1416
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shellac
parents:
diff changeset
1417 return results
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shellac
parents:
diff changeset
1418
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parents:
diff changeset
1419
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parents:
diff changeset
1420 def _encode_filename(s):
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shellac
parents:
diff changeset
1421 s = s.replace("\r", "%0D")
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shellac
parents:
diff changeset
1422 s = s.replace("\n", "%0A")
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shellac
parents:
diff changeset
1423 return s
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shellac
parents:
diff changeset
1424
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shellac
parents:
diff changeset
1425
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shellac
parents:
diff changeset
1426 def _decode_filename(s):
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shellac
parents:
diff changeset
1427 s = re.sub(r"%0D", "\r", s, re.IGNORECASE)
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shellac
parents:
diff changeset
1428 s = re.sub(r"%0A", "\n", s, re.IGNORECASE)
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shellac
parents:
diff changeset
1429 return s
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shellac
parents:
diff changeset
1430
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shellac
parents:
diff changeset
1431
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shellac
parents:
diff changeset
1432 def force_unicode_py2(s):
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shellac
parents:
diff changeset
1433 """Reliably return a Unicode string given a possible unicode or byte string"""
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shellac
parents:
diff changeset
1434 if isinstance(s, str):
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shellac
parents:
diff changeset
1435 return s.decode("utf-8")
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parents:
diff changeset
1436 else:
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shellac
parents:
diff changeset
1437 return unicode(s)
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shellac
parents:
diff changeset
1438
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shellac
parents:
diff changeset
1439
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shellac
parents:
diff changeset
1440 if sys.version_info > (3, 0):
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shellac
parents:
diff changeset
1441 force_unicode = str
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parents:
diff changeset
1442 else:
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shellac
parents:
diff changeset
1443 force_unicode = force_unicode_py2
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shellac
parents:
diff changeset
1444
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shellac
parents:
diff changeset
1445 # following code is used for command line program
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shellac
parents:
diff changeset
1446
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shellac
parents:
diff changeset
1447
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shellac
parents:
diff changeset
1448 class BagArgumentParser(argparse.ArgumentParser):
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shellac
parents:
diff changeset
1449 def __init__(self, *args, **kwargs):
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shellac
parents:
diff changeset
1450 argparse.ArgumentParser.__init__(self, *args, **kwargs)
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shellac
parents:
diff changeset
1451 self.set_defaults(bag_info={})
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shellac
parents:
diff changeset
1452
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parents:
diff changeset
1453
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shellac
parents:
diff changeset
1454 class BagHeaderAction(argparse.Action):
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shellac
parents:
diff changeset
1455 def __call__(self, parser, namespace, values, option_string=None):
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shellac
parents:
diff changeset
1456 opt = option_string.lstrip("--")
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shellac
parents:
diff changeset
1457 opt_caps = "-".join([o.capitalize() for o in opt.split("-")])
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shellac
parents:
diff changeset
1458 namespace.bag_info[opt_caps] = values
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shellac
parents:
diff changeset
1459
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shellac
parents:
diff changeset
1460
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shellac
parents:
diff changeset
1461 def _make_parser():
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shellac
parents:
diff changeset
1462 parser = BagArgumentParser(
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shellac
parents:
diff changeset
1463 formatter_class=argparse.RawDescriptionHelpFormatter,
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shellac
parents:
diff changeset
1464 description="bagit-python version %s\n\n%s\n" % (VERSION, __doc__.strip()),
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parents:
diff changeset
1465 )
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shellac
parents:
diff changeset
1466 parser.add_argument(
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shellac
parents:
diff changeset
1467 "--processes",
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shellac
parents:
diff changeset
1468 type=int,
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shellac
parents:
diff changeset
1469 dest="processes",
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shellac
parents:
diff changeset
1470 default=1,
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shellac
parents:
diff changeset
1471 help=_(
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shellac
parents:
diff changeset
1472 "Use multiple processes to calculate checksums faster (default: %(default)s)"
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shellac
parents:
diff changeset
1473 ),
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parents:
diff changeset
1474 )
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shellac
parents:
diff changeset
1475 parser.add_argument("--log", help=_("The name of the log file (default: stdout)"))
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shellac
parents:
diff changeset
1476 parser.add_argument(
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shellac
parents:
diff changeset
1477 "--quiet",
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shellac
parents:
diff changeset
1478 action="store_true",
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shellac
parents:
diff changeset
1479 help=_("Suppress all progress information other than errors"),
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shellac
parents:
diff changeset
1480 )
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shellac
parents:
diff changeset
1481 parser.add_argument(
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shellac
parents:
diff changeset
1482 "--validate",
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shellac
parents:
diff changeset
1483 action="store_true",
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shellac
parents:
diff changeset
1484 help=_(
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shellac
parents:
diff changeset
1485 "Validate existing bags in the provided directories instead of"
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shellac
parents:
diff changeset
1486 " creating new ones"
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shellac
parents:
diff changeset
1487 ),
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shellac
parents:
diff changeset
1488 )
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shellac
parents:
diff changeset
1489 parser.add_argument(
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shellac
parents:
diff changeset
1490 "--fast",
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shellac
parents:
diff changeset
1491 action="store_true",
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shellac
parents:
diff changeset
1492 help=_(
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shellac
parents:
diff changeset
1493 "Modify --validate behaviour to only test whether the bag directory"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1494 " has the number of files and total size specified in Payload-Oxum"
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shellac
parents:
diff changeset
1495 " without performing checksum validation to detect corruption."
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shellac
parents:
diff changeset
1496 ),
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shellac
parents:
diff changeset
1497 )
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shellac
parents:
diff changeset
1498 parser.add_argument(
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shellac
parents:
diff changeset
1499 "--completeness-only",
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shellac
parents:
diff changeset
1500 action="store_true",
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shellac
parents:
diff changeset
1501 help=_(
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shellac
parents:
diff changeset
1502 "Modify --validate behaviour to test whether the bag directory"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1503 " has the expected payload specified in the checksum manifests"
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shellac
parents:
diff changeset
1504 " without performing checksum validation to detect corruption."
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shellac
parents:
diff changeset
1505 ),
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shellac
parents:
diff changeset
1506 )
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shellac
parents:
diff changeset
1507
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shellac
parents:
diff changeset
1508 checksum_args = parser.add_argument_group(
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shellac
parents:
diff changeset
1509 _("Checksum Algorithms"),
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shellac
parents:
diff changeset
1510 _(
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shellac
parents:
diff changeset
1511 "Select the manifest algorithms to be used when creating bags"
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shellac
parents:
diff changeset
1512 " (default=%s)"
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shellac
parents:
diff changeset
1513 )
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shellac
parents:
diff changeset
1514 % ", ".join(DEFAULT_CHECKSUMS),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1515 )
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shellac
parents:
diff changeset
1516
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shellac
parents:
diff changeset
1517 for i in CHECKSUM_ALGOS:
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shellac
parents:
diff changeset
1518 alg_name = re.sub(r"^([A-Z]+)(\d+)$", r"\1-\2", i.upper())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1519 checksum_args.add_argument(
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shellac
parents:
diff changeset
1520 "--%s" % i,
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shellac
parents:
diff changeset
1521 action="append_const",
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shellac
parents:
diff changeset
1522 dest="checksums",
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shellac
parents:
diff changeset
1523 const=i,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1524 help=_("Generate %s manifest when creating a bag") % alg_name,
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shellac
parents:
diff changeset
1525 )
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shellac
parents:
diff changeset
1526
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shellac
parents:
diff changeset
1527 metadata_args = parser.add_argument_group(_("Optional Bag Metadata"))
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shellac
parents:
diff changeset
1528 for header in STANDARD_BAG_INFO_HEADERS:
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shellac
parents:
diff changeset
1529 metadata_args.add_argument(
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shellac
parents:
diff changeset
1530 "--%s" % header.lower(), type=str, action=BagHeaderAction, default=argparse.SUPPRESS
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parents:
diff changeset
1531 )
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parents:
diff changeset
1532
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parents:
diff changeset
1533 parser.add_argument(
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shellac
parents:
diff changeset
1534 "directory",
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parents:
diff changeset
1535 nargs="+",
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parents:
diff changeset
1536 help=_(
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parents:
diff changeset
1537 "Directory which will be converted into a bag in place"
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shellac
parents:
diff changeset
1538 " by moving any existing files into the BagIt structure"
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shellac
parents:
diff changeset
1539 " and creating the manifests and other metadata."
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parents:
diff changeset
1540 ),
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parents:
diff changeset
1541 )
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parents:
diff changeset
1542
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parents:
diff changeset
1543 return parser
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shellac
parents:
diff changeset
1544
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parents:
diff changeset
1545
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parents:
diff changeset
1546 def _configure_logging(opts):
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parents:
diff changeset
1547 log_format = "%(asctime)s - %(levelname)s - %(message)s"
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diff changeset
1548 if opts.quiet:
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parents:
diff changeset
1549 level = logging.ERROR
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parents:
diff changeset
1550 else:
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shellac
parents:
diff changeset
1551 level = logging.INFO
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shellac
parents:
diff changeset
1552 if opts.log:
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shellac
parents:
diff changeset
1553 logging.basicConfig(filename=opts.log, level=level, format=log_format)
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parents:
diff changeset
1554 else:
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shellac
parents:
diff changeset
1555 logging.basicConfig(level=level, format=log_format)
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shellac
parents:
diff changeset
1556
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diff changeset
1557
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parents:
diff changeset
1558 def main():
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parents:
diff changeset
1559 if "--version" in sys.argv:
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shellac
parents:
diff changeset
1560 print(_("bagit-python version %s") % VERSION)
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shellac
parents:
diff changeset
1561 sys.exit(0)
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shellac
parents:
diff changeset
1562
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diff changeset
1563 parser = _make_parser()
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shellac
parents:
diff changeset
1564 args = parser.parse_args()
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parents:
diff changeset
1565
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parents:
diff changeset
1566 if args.processes < 0:
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shellac
parents:
diff changeset
1567 parser.error(_("The number of processes must be 0 or greater"))
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parents:
diff changeset
1568
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parents:
diff changeset
1569 if args.fast and not args.validate:
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shellac
parents:
diff changeset
1570 parser.error(_("--fast is only allowed as an option for --validate!"))
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diff changeset
1571
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parents:
diff changeset
1572 _configure_logging(args)
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parents:
diff changeset
1573
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parents:
diff changeset
1574 rc = 0
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parents:
diff changeset
1575 for bag_dir in args.directory:
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shellac
parents:
diff changeset
1576 # validate the bag
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shellac
parents:
diff changeset
1577 if args.validate:
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shellac
parents:
diff changeset
1578 try:
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parents:
diff changeset
1579 bag = Bag(bag_dir)
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shellac
parents:
diff changeset
1580 # validate throws a BagError or BagValidationError
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shellac
parents:
diff changeset
1581 bag.validate(
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parents:
diff changeset
1582 processes=args.processes,
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parents:
diff changeset
1583 fast=args.fast,
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parents:
diff changeset
1584 completeness_only=args.completeness_only,
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parents:
diff changeset
1585 )
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parents:
diff changeset
1586 if args.fast:
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shellac
parents:
diff changeset
1587 LOGGER.info(_("%s valid according to Payload-Oxum"), bag_dir)
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parents:
diff changeset
1588 else:
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parents:
diff changeset
1589 LOGGER.info(_("%s is valid"), bag_dir)
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parents:
diff changeset
1590 except BagError as e:
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parents:
diff changeset
1591 LOGGER.error(
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parents:
diff changeset
1592 _("%(bag)s is invalid: %(error)s"), {"bag": bag_dir, "error": e}
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parents:
diff changeset
1593 )
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shellac
parents:
diff changeset
1594 rc = 1
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shellac
parents:
diff changeset
1595
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shellac
parents:
diff changeset
1596 # make the bag
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shellac
parents:
diff changeset
1597 else:
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shellac
parents:
diff changeset
1598 try:
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shellac
parents:
diff changeset
1599 make_bag(
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shellac
parents:
diff changeset
1600 bag_dir,
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shellac
parents:
diff changeset
1601 bag_info=args.bag_info,
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shellac
parents:
diff changeset
1602 processes=args.processes,
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shellac
parents:
diff changeset
1603 checksums=args.checksums,
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parents:
diff changeset
1604 )
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parents:
diff changeset
1605 except Exception as exc:
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shellac
parents:
diff changeset
1606 LOGGER.error(
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parents:
diff changeset
1607 _("Failed to create bag in %(bag_directory)s: %(error)s"),
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shellac
parents:
diff changeset
1608 {"bag_directory": bag_dir, "error": exc},
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shellac
parents:
diff changeset
1609 exc_info=True,
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shellac
parents:
diff changeset
1610 )
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shellac
parents:
diff changeset
1611 rc = 1
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shellac
parents:
diff changeset
1612
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shellac
parents:
diff changeset
1613 sys.exit(rc)
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shellac
parents:
diff changeset
1614
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shellac
parents:
diff changeset
1615
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shellac
parents:
diff changeset
1616 if __name__ == "__main__":
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shellac
parents:
diff changeset
1617 main()