Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/xml_macros.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 import os
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2 from copy import deepcopy
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3 from xml.etree import ElementInclude, ElementTree
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4
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5
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6 REQUIRED_PARAMETER = object()
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7
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8
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9 def load_with_references(path):
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10 """Load XML documentation from file system and preprocesses XML macros.
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11
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12 Return the XML representation of the expanded tree and paths to
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13 referenced files that were imported (macros).
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14 """
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15 tree = raw_xml_tree(path)
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16 root = tree.getroot()
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17
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18 macro_paths = _import_macros(root, path)
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19
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20 # Collect tokens
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21 tokens = _macros_of_type(root, 'token', lambda el: el.text or '')
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22 tokens = expand_nested_tokens(tokens)
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23
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24 # Expand xml macros
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25 macro_dict = _macros_of_type(root, 'xml', lambda el: XmlMacroDef(el))
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26 _expand_macros([root], macro_dict, tokens)
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27
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28 return tree, macro_paths
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30
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31 def load(path):
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32 tree, _ = load_with_references(path)
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33 return tree
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34
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35
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36 def template_macro_params(root):
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37 """
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38 Look for template macros and populate param_dict (for cheetah)
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39 with these.
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40 """
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41 param_dict = {}
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42 macro_dict = _macros_of_type(root, 'template', lambda el: el.text)
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43 for key, value in macro_dict.items():
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44 param_dict[key] = value
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45 return param_dict
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46
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47
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48 def raw_xml_tree(path):
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49 """ Load raw (no macro expansion) tree representation of XML represented
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50 at the specified path.
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51 """
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52 tree = _parse_xml(path)
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53 return tree
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54
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55
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56 def imported_macro_paths(root):
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57 macros_el = _macros_el(root)
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58 return _imported_macro_paths_from_el(macros_el)
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59
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60
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61 def _import_macros(root, path):
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62 xml_base_dir = os.path.dirname(path)
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63 macros_el = _macros_el(root)
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64 if macros_el is not None:
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65 macro_els, macro_paths = _load_macros(macros_el, xml_base_dir)
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66 _xml_set_children(macros_el, macro_els)
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67 return macro_paths
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68
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69
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70 def _macros_el(root):
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71 return root.find('macros')
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72
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73
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74 def _macros_of_type(root, type, el_func):
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75 macros_el = root.find('macros')
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76 macro_dict = {}
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77 if macros_el is not None:
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78 macro_els = macros_el.findall('macro')
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79 filtered_els = [(macro_el.get("name"), el_func(macro_el))
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80 for macro_el in macro_els
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81 if macro_el.get('type') == type]
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82 macro_dict = dict(filtered_els)
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83 return macro_dict
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84
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85
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86 def expand_nested_tokens(tokens):
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87 for token_name in tokens.keys():
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88 for current_token_name, current_token_value in tokens.items():
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89 if token_name in current_token_value:
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90 if token_name == current_token_name:
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91 raise Exception("Token '%s' cannot contain itself" % token_name)
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92 tokens[current_token_name] = current_token_value.replace(token_name, tokens[token_name])
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93 return tokens
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94
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95
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96 def _expand_tokens(elements, tokens):
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97 if not tokens or elements is None:
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98 return
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99
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100 for element in elements:
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101 _expand_tokens_for_el(element, tokens)
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102
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103
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104 def _expand_tokens_for_el(element, tokens):
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105 value = element.text
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106 if value:
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107 new_value = _expand_tokens_str(element.text, tokens)
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108 if not (new_value is value):
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109 element.text = new_value
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110 for key, value in element.attrib.items():
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111 new_value = _expand_tokens_str(value, tokens)
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112 if not (new_value is value):
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113 element.attrib[key] = new_value
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114 _expand_tokens(list(element), tokens)
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115
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116
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117 def _expand_tokens_str(s, tokens):
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118 for key, value in tokens.items():
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119 if key in s:
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120 s = s.replace(key, value)
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121 return s
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122
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123
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124 def _expand_macros(elements, macros, tokens):
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125 if not macros and not tokens:
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126 return
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127
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128 for element in elements:
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129 while True:
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130 expand_el = element.find('.//expand')
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131 if expand_el is None:
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132 break
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133 _expand_macro(element, expand_el, macros, tokens)
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134
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135 _expand_tokens_for_el(element, tokens)
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136
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137
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138 def _expand_macro(element, expand_el, macros, tokens):
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139 macro_name = expand_el.get('macro')
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140 macro_def = macros[macro_name]
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141 expanded_elements = deepcopy(macro_def.elements)
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142
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143 _expand_yield_statements(expanded_elements, expand_el)
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144
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145 # Recursively expand contained macros.
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146 _expand_macros(expanded_elements, macros, tokens)
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147 macro_tokens = macro_def.macro_tokens(expand_el)
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148 if macro_tokens:
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149 _expand_tokens(expanded_elements, macro_tokens)
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150
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151 # HACK for elementtree, newer implementations (etree/lxml) won't
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152 # require this parent_map data structure but elementtree does not
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153 # track parents or recognize .find('..').
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154 # TODO fix this now that we're not using elementtree
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155 parent_map = dict((c, p) for p in element.iter() for c in p)
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156 _xml_replace(expand_el, expanded_elements, parent_map)
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157
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158
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159 def _expand_yield_statements(macro_def, expand_el):
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160 yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
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161
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162 expand_el_children = list(expand_el)
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163 macro_def_parent_map = \
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164 dict((c, p) for macro_def_el in macro_def for p in macro_def_el.iter() for c in p)
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165
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166 for yield_el in yield_els:
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167 _xml_replace(yield_el, expand_el_children, macro_def_parent_map)
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168
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169 # Replace yields at the top level of a macro, seems hacky approach
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170 replace_yield = True
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171 while replace_yield:
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172 for i, macro_def_el in enumerate(macro_def):
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173 if macro_def_el.tag == "yield":
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174 for target in expand_el_children:
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175 i += 1
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176 macro_def.insert(i, target)
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177 macro_def.remove(macro_def_el)
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178 continue
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179
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180 replace_yield = False
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181
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182
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183 def _load_macros(macros_el, xml_base_dir):
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184 macros = []
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185 # Import macros from external files.
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186 imported_macros, macro_paths = _load_imported_macros(macros_el, xml_base_dir)
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187 macros.extend(imported_macros)
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188 # Load all directly defined macros.
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189 macros.extend(_load_embedded_macros(macros_el, xml_base_dir))
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190 return macros, macro_paths
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191
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192
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193 def _load_embedded_macros(macros_el, xml_base_dir):
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194 macros = []
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195
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196 macro_els = []
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197 # attribute typed macro
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198 if macros_el is not None:
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199 macro_els = macros_el.findall("macro")
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200 for macro in macro_els:
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201 if 'type' not in macro.attrib:
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202 macro.attrib['type'] = 'xml'
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203 macros.append(macro)
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204
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205 # type shortcuts (<xml> is a shortcut for <macro type="xml",
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206 # likewise for <template>.
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207 typed_tag = ['template', 'xml', 'token']
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208 for tag in typed_tag:
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209 macro_els = []
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210 if macros_el is not None:
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211 macro_els = macros_el.findall(tag)
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212 for macro_el in macro_els:
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213 macro_el.attrib['type'] = tag
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214 macro_el.tag = 'macro'
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215 macros.append(macro_el)
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216
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217 return macros
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218
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219
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220 def _load_imported_macros(macros_el, xml_base_dir):
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221 macros = []
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222 macro_paths = []
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223
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224 for tool_relative_import_path in _imported_macro_paths_from_el(macros_el):
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225 import_path = \
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226 os.path.join(xml_base_dir, tool_relative_import_path)
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227 macro_paths.append(import_path)
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228 file_macros, current_macro_paths = _load_macro_file(import_path, xml_base_dir)
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229 macros.extend(file_macros)
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230 macro_paths.extend(current_macro_paths)
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231
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232 return macros, macro_paths
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233
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234
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235 def _imported_macro_paths_from_el(macros_el):
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236 imported_macro_paths = []
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237 macro_import_els = []
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238 if macros_el is not None:
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239 macro_import_els = macros_el.findall("import")
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240 for macro_import_el in macro_import_els:
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241 raw_import_path = macro_import_el.text
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242 imported_macro_paths.append(raw_import_path)
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243 return imported_macro_paths
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244
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245
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246 def _load_macro_file(path, xml_base_dir):
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247 tree = _parse_xml(path)
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248 root = tree.getroot()
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249 return _load_macros(root, xml_base_dir)
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250
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251
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252 def _xml_set_children(element, new_children):
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253 for old_child in element:
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254 element.remove(old_child)
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255 for i, new_child in enumerate(new_children):
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256 element.insert(i, new_child)
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257
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258
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259 def _xml_replace(query, targets, parent_map):
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260 # parent_el = query.find('..') ## Something like this would be better with newer xml library
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261 parent_el = parent_map[query]
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262 matching_index = -1
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263 # for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation
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264 for index, el in enumerate(list(parent_el)):
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265 if el == query:
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266 matching_index = index
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267 break
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268 assert matching_index >= 0
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269 current_index = matching_index
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270 for target in targets:
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271 current_index += 1
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272 parent_el.insert(current_index, deepcopy(target))
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273 parent_el.remove(query)
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274
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275
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276 class XmlMacroDef(object):
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277
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278 def __init__(self, el):
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279 self.elements = list(el)
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280 parameters = {}
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281 tokens = []
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282 token_quote = "@"
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283 for key, value in el.attrib.items():
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284 if key == "token_quote":
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285 token_quote = value
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286 if key == "tokens":
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287 for token in value.split(","):
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288 tokens.append((token, REQUIRED_PARAMETER))
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289 elif key.startswith("token_"):
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290 token = key[len("token_"):]
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291 tokens.append((token, value))
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292 for name, default in tokens:
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293 parameters[name] = (token_quote, default)
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294 self.parameters = parameters
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295
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296 def macro_tokens(self, expand_el):
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297 tokens = {}
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298 for key, (wrap_char, default_val) in self.parameters.items():
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299 token_value = expand_el.attrib.get(key, default_val)
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300 if token_value is REQUIRED_PARAMETER:
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301 message = "Failed to expand macro - missing required parameter [%s]."
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302 raise ValueError(message % key)
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303 token_name = "%s%s%s" % (wrap_char, key.upper(), wrap_char)
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304 tokens[token_name] = token_value
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305 return tokens
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306
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307
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308 def _parse_xml(fname):
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309 tree = ElementTree.parse(fname)
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310 root = tree.getroot()
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311 ElementInclude.include(root)
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312 return tree
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313
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314
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315 __all__ = (
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316 "imported_macro_paths",
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317 "load",
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318 "load_with_references",
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319 "raw_xml_tree",
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320 "template_macro_params",
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321 )