Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/lxml/ElementInclude.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #
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2 # ElementTree
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3 # $Id: ElementInclude.py 1862 2004-06-18 07:31:02Z Fredrik $
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4 #
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5 # limited xinclude support for element trees
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6 #
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7 # history:
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8 # 2003-08-15 fl created
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9 # 2003-11-14 fl fixed default loader
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10 #
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11 # Copyright (c) 2003-2004 by Fredrik Lundh. All rights reserved.
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12 #
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13 # fredrik@pythonware.com
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14 # http://www.pythonware.com
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15 #
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16 # --------------------------------------------------------------------
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17 # The ElementTree toolkit is
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18 #
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19 # Copyright (c) 1999-2004 by Fredrik Lundh
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20 #
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21 # By obtaining, using, and/or copying this software and/or its
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22 # associated documentation, you agree that you have read, understood,
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23 # and will comply with the following terms and conditions:
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24 #
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25 # Permission to use, copy, modify, and distribute this software and
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26 # its associated documentation for any purpose and without fee is
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27 # hereby granted, provided that the above copyright notice appears in
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28 # all copies, and that both that copyright notice and this permission
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29 # notice appear in supporting documentation, and that the name of
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30 # Secret Labs AB or the author not be used in advertising or publicity
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31 # pertaining to distribution of the software without specific, written
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32 # prior permission.
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33 #
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34 # SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD
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35 # TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANT-
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36 # ABILITY AND FITNESS. IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR
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37 # BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY
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38 # DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
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39 # WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS
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40 # ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE
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41 # OF THIS SOFTWARE.
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42 # --------------------------------------------------------------------
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43
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44 """
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45 Limited XInclude support for the ElementTree package.
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46
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47 While lxml.etree has full support for XInclude (see
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48 `etree.ElementTree.xinclude()`), this module provides a simpler, pure
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49 Python, ElementTree compatible implementation that supports a simple
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50 form of custom URL resolvers.
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51 """
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52
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53 from lxml import etree
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54 try:
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55 from urlparse import urljoin
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56 from urllib2 import urlopen
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57 except ImportError:
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58 # Python 3
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59 from urllib.parse import urljoin
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60 from urllib.request import urlopen
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61
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62 XINCLUDE = "{http://www.w3.org/2001/XInclude}"
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63
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64 XINCLUDE_INCLUDE = XINCLUDE + "include"
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65 XINCLUDE_FALLBACK = XINCLUDE + "fallback"
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66 XINCLUDE_ITER_TAG = XINCLUDE + "*"
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67
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68 # For security reasons, the inclusion depth is limited to this read-only value by default.
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69 DEFAULT_MAX_INCLUSION_DEPTH = 6
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70
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71
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72 ##
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73 # Fatal include error.
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74
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75 class FatalIncludeError(etree.LxmlSyntaxError):
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76 pass
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77
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78
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79 class LimitedRecursiveIncludeError(FatalIncludeError):
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80 pass
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81
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82
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83 ##
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84 # ET compatible default loader.
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85 # This loader reads an included resource from disk.
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86 #
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87 # @param href Resource reference.
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88 # @param parse Parse mode. Either "xml" or "text".
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89 # @param encoding Optional text encoding.
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90 # @return The expanded resource. If the parse mode is "xml", this
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91 # is an ElementTree instance. If the parse mode is "text", this
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92 # is a Unicode string. If the loader fails, it can return None
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93 # or raise an IOError exception.
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94 # @throws IOError If the loader fails to load the resource.
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95
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96 def default_loader(href, parse, encoding=None):
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97 file = open(href, 'rb')
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98 if parse == "xml":
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99 data = etree.parse(file).getroot()
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100 else:
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101 data = file.read()
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102 if not encoding:
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103 encoding = 'utf-8'
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104 data = data.decode(encoding)
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105 file.close()
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106 return data
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107
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108
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109 ##
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110 # Default loader used by lxml.etree - handles custom resolvers properly
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111 #
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112
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113 def _lxml_default_loader(href, parse, encoding=None, parser=None):
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114 if parse == "xml":
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115 data = etree.parse(href, parser).getroot()
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116 else:
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117 if "://" in href:
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118 f = urlopen(href)
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119 else:
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120 f = open(href, 'rb')
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121 data = f.read()
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122 f.close()
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123 if not encoding:
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124 encoding = 'utf-8'
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125 data = data.decode(encoding)
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126 return data
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127
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128
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129 ##
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130 # Wrapper for ET compatibility - drops the parser
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131
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132 def _wrap_et_loader(loader):
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133 def load(href, parse, encoding=None, parser=None):
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134 return loader(href, parse, encoding)
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135 return load
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136
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137
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138 ##
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139 # Expand XInclude directives.
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140 #
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141 # @param elem Root element.
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142 # @param loader Optional resource loader. If omitted, it defaults
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143 # to {@link default_loader}. If given, it should be a callable
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144 # that implements the same interface as <b>default_loader</b>.
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145 # @param base_url The base URL of the original file, to resolve
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146 # relative include file references.
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147 # @param max_depth The maximum number of recursive inclusions.
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148 # Limited to reduce the risk of malicious content explosion.
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149 # Pass None to disable the limitation.
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150 # @throws LimitedRecursiveIncludeError If the {@link max_depth} was exceeded.
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151 # @throws FatalIncludeError If the function fails to include a given
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152 # resource, or if the tree contains malformed XInclude elements.
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153 # @throws IOError If the function fails to load a given resource.
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154 # @returns the node or its replacement if it was an XInclude node
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155
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156 def include(elem, loader=None, base_url=None,
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157 max_depth=DEFAULT_MAX_INCLUSION_DEPTH):
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158 if max_depth is None:
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159 max_depth = -1
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160 elif max_depth < 0:
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161 raise ValueError("expected non-negative depth or None for 'max_depth', got %r" % max_depth)
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162
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163 if base_url is None:
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164 if hasattr(elem, 'getroot'):
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165 tree = elem
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166 elem = elem.getroot()
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167 else:
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168 tree = elem.getroottree()
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169 if hasattr(tree, 'docinfo'):
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170 base_url = tree.docinfo.URL
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171 elif hasattr(elem, 'getroot'):
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172 elem = elem.getroot()
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173 _include(elem, loader, base_url, max_depth)
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174
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175
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176 def _include(elem, loader=None, base_url=None,
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177 max_depth=DEFAULT_MAX_INCLUSION_DEPTH, _parent_hrefs=None):
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178 if loader is not None:
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179 load_include = _wrap_et_loader(loader)
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180 else:
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181 load_include = _lxml_default_loader
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182
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183 if _parent_hrefs is None:
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184 _parent_hrefs = set()
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185
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186 parser = elem.getroottree().parser
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187
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188 include_elements = list(
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189 elem.iter(XINCLUDE_ITER_TAG))
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190
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191 for e in include_elements:
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192 if e.tag == XINCLUDE_INCLUDE:
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193 # process xinclude directive
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194 href = urljoin(base_url, e.get("href"))
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195 parse = e.get("parse", "xml")
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196 parent = e.getparent()
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197 if parse == "xml":
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198 if href in _parent_hrefs:
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199 raise FatalIncludeError(
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200 "recursive include of %r detected" % href
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201 )
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202 if max_depth == 0:
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203 raise LimitedRecursiveIncludeError(
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204 "maximum xinclude depth reached when including file %s" % href)
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205 node = load_include(href, parse, parser=parser)
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206 if node is None:
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207 raise FatalIncludeError(
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208 "cannot load %r as %r" % (href, parse)
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209 )
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210 node = _include(node, loader, href, max_depth - 1, {href} | _parent_hrefs)
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211 if e.tail:
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212 node.tail = (node.tail or "") + e.tail
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213 if parent is None:
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214 return node # replaced the root node!
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215 parent.replace(e, node)
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216 elif parse == "text":
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217 text = load_include(href, parse, encoding=e.get("encoding"))
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218 if text is None:
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219 raise FatalIncludeError(
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220 "cannot load %r as %r" % (href, parse)
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221 )
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222 predecessor = e.getprevious()
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223 if predecessor is not None:
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224 predecessor.tail = (predecessor.tail or "") + text
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225 elif parent is None:
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226 return text # replaced the root node!
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227 else:
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228 parent.text = (parent.text or "") + text + (e.tail or "")
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229 parent.remove(e)
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230 else:
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231 raise FatalIncludeError(
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232 "unknown parse type in xi:include tag (%r)" % parse
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233 )
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234 elif e.tag == XINCLUDE_FALLBACK:
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235 parent = e.getparent()
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236 if parent is not None and parent.tag != XINCLUDE_INCLUDE:
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237 raise FatalIncludeError(
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238 "xi:fallback tag must be child of xi:include (%r)" % e.tag
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239 )
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240 else:
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241 raise FatalIncludeError(
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242 "Invalid element found in XInclude namespace (%r)" % e.tag
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243 )
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244 return elem