Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/util.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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0
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1 """
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2 Some utility functions.
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3
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4 Miscellaneous utilities
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5
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6 * list2set
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7 * first
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8 * uniq
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9 * more_than
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10
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11 Term characterisation and generation
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12
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13 * to_term
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14 * from_n3
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15
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16 Date/time utilities
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17
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18 * date_time
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19 * parse_date_time
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20
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21 Statement and component type checkers
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22
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23 * check_context
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24 * check_subject
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25 * check_predicate
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26 * check_object
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27 * check_statement
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28 * check_pattern
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29
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30 """
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31
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32 from calendar import timegm
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33 from time import altzone
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34 # from time import daylight
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35 from time import gmtime
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36 from time import localtime
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37 from time import time
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38 from time import timezone
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39
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40 from os.path import splitext
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41 from io import StringIO
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42
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43 from rdflib.exceptions import ContextTypeError
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44 from rdflib.exceptions import ObjectTypeError
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45 from rdflib.exceptions import PredicateTypeError
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46 from rdflib.exceptions import SubjectTypeError
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47 from rdflib.graph import Graph
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48 from rdflib.graph import QuotedGraph
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49 from rdflib.namespace import Namespace
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50 from rdflib.namespace import NamespaceManager
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51 from rdflib.term import BNode
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52 from rdflib.term import Literal
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53 from rdflib.term import URIRef
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54 from rdflib.py3compat import sign
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55
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56 __all__ = [
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57 'list2set', 'first', 'uniq', 'more_than', 'to_term', 'from_n3',
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58 'date_time', 'parse_date_time', 'check_context', 'check_subject',
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59 'check_predicate', 'check_object', 'check_statement', 'check_pattern',
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60 'guess_format', 'find_roots', 'get_tree']
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61
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62
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63 def list2set(seq):
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64 """
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65 Return a new list without duplicates.
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66 Preserves the order, unlike set(seq)
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67 """
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68 seen = set()
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69 return [x for x in seq if x not in seen and not seen.add(x)]
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70
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71
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72 def first(seq):
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73 """
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74 return the first element in a python sequence
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75 for graphs, use graph.value instead
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76 """
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77 for result in seq:
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78 return result
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79 return None
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80
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81
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82 def uniq(sequence, strip=0):
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83 """removes duplicate strings from the sequence."""
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84 if strip:
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85 return set(s.strip() for s in sequence)
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86 else:
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87 return set(sequence)
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88
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89
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90 def more_than(sequence, number):
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91 "Returns 1 if sequence has more items than number and 0 if not."
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92 i = 0
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93 for item in sequence:
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94 i += 1
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95 if i > number:
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96 return 1
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97 return 0
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98
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99
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100 def to_term(s, default=None):
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101 """
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102 Creates and returns an Identifier of type corresponding
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103 to the pattern of the given positional argument string ``s``:
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104
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105 '' returns the ``default`` keyword argument value or ``None``
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106
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107 '<s>' returns ``URIRef(s)`` (i.e. without angle brackets)
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108
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109 '"s"' returns ``Literal(s)`` (i.e. without doublequotes)
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110
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111 '_s' returns ``BNode(s)`` (i.e. without leading underscore)
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112
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113 """
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114 if not s:
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115 return default
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116 elif s.startswith("<") and s.endswith(">"):
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117 return URIRef(s[1:-1])
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118 elif s.startswith('"') and s.endswith('"'):
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119 return Literal(s[1:-1])
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120 elif s.startswith("_"):
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121 return BNode(s)
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122 else:
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123 msg = "Unrecognised term syntax: '%s'" % s
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124 raise Exception(msg)
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125
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126
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127 def from_n3(s, default=None, backend=None, nsm=None):
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128 r'''
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129 Creates the Identifier corresponding to the given n3 string.
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130
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131 >>> from_n3('<http://ex.com/foo>') == URIRef('http://ex.com/foo')
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132 True
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133 >>> from_n3('"foo"@de') == Literal('foo', lang='de')
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134 True
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135 >>> from_n3('"""multi\nline\nstring"""@en') == Literal(
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136 ... 'multi\nline\nstring', lang='en')
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137 True
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138 >>> from_n3('42') == Literal(42)
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139 True
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140 >>> from_n3(Literal(42).n3()) == Literal(42)
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141 True
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142 >>> from_n3('"42"^^xsd:integer') == Literal(42)
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143 True
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144 >>> from rdflib import RDFS
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145 >>> from_n3('rdfs:label') == RDFS['label']
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146 True
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147 >>> nsm = NamespaceManager(Graph())
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148 >>> nsm.bind('dbpedia', 'http://dbpedia.org/resource/')
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149 >>> berlin = URIRef('http://dbpedia.org/resource/Berlin')
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150 >>> from_n3('dbpedia:Berlin', nsm=nsm) == berlin
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151 True
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152
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153 '''
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154 if not s:
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155 return default
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156 if s.startswith('<'):
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157 return URIRef(s[1:-1])
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158 elif s.startswith('"'):
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159 if s.startswith('"""'):
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160 quotes = '"""'
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161 else:
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162 quotes = '"'
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163 value, rest = s.rsplit(quotes, 1)
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164 value = value[len(quotes):] # strip leading quotes
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165 datatype = None
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166 language = None
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167
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168 # as a given datatype overrules lang-tag check for it first
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169 dtoffset = rest.rfind('^^')
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170 if dtoffset >= 0:
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171 # found a datatype
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172 # datatype has to come after lang-tag so ignore everything before
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173 # see: http://www.w3.org/TR/2011/WD-turtle-20110809/
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174 # #prod-turtle2-RDFLiteral
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175 datatype = from_n3(rest[dtoffset + 2:], default, backend, nsm)
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176 else:
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177 if rest.startswith("@"):
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178 language = rest[1:] # strip leading at sign
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179
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180 value = value.replace(r'\"', '"')
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181 # Hack: this should correctly handle strings with either native unicode
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182 # characters, or \u1234 unicode escapes.
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183 value = value.encode("raw-unicode-escape").decode("unicode-escape")
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184 return Literal(value, language, datatype)
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185 elif s == 'true' or s == 'false':
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186 return Literal(s == 'true')
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187 elif s.isdigit():
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188 return Literal(int(s))
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189 elif s.startswith('{'):
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190 identifier = from_n3(s[1:-1])
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191 return QuotedGraph(backend, identifier)
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192 elif s.startswith('['):
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193 identifier = from_n3(s[1:-1])
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194 return Graph(backend, identifier)
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195 elif s.startswith("_:"):
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196 return BNode(s[2:])
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197 elif ':' in s:
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198 if nsm is None:
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199 # instantiate default NamespaceManager and rely on its defaults
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200 nsm = NamespaceManager(Graph())
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201 prefix, last_part = s.split(':', 1)
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202 ns = dict(nsm.namespaces())[prefix]
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203 return Namespace(ns)[last_part]
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204 else:
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205 return BNode(s)
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206
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207
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208 def check_context(c):
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209 if not (isinstance(c, URIRef) or
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210 isinstance(c, BNode)):
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211 raise ContextTypeError("%s:%s" % (c, type(c)))
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212
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213
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214 def check_subject(s):
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215 """ Test that s is a valid subject identifier."""
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216 if not (isinstance(s, URIRef) or isinstance(s, BNode)):
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217 raise SubjectTypeError(s)
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218
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219
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220 def check_predicate(p):
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221 """ Test that p is a valid predicate identifier."""
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222 if not isinstance(p, URIRef):
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223 raise PredicateTypeError(p)
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224
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225
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226 def check_object(o):
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227 """ Test that o is a valid object identifier."""
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228 if not (isinstance(o, URIRef) or
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229 isinstance(o, Literal) or
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230 isinstance(o, BNode)):
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231 raise ObjectTypeError(o)
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232
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233
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234 def check_statement(triple):
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235 (s, p, o) = triple
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236 if not (isinstance(s, URIRef) or isinstance(s, BNode)):
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237 raise SubjectTypeError(s)
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238
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239 if not isinstance(p, URIRef):
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240 raise PredicateTypeError(p)
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241
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242 if not (isinstance(o, URIRef) or
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243 isinstance(o, Literal) or
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parents:
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244 isinstance(o, BNode)):
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245 raise ObjectTypeError(o)
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246
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247
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248 def check_pattern(triple):
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249 (s, p, o) = triple
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250 if s and not (isinstance(s, URIRef) or isinstance(s, BNode)):
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251 raise SubjectTypeError(s)
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252
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253 if p and not isinstance(p, URIRef):
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254 raise PredicateTypeError(p)
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255
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256 if o and not (isinstance(o, URIRef) or
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257 isinstance(o, Literal) or
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258 isinstance(o, BNode)):
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259 raise ObjectTypeError(o)
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260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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261
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262 def date_time(t=None, local_time_zone=False):
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263 """http://www.w3.org/TR/NOTE-datetime ex: 1997-07-16T19:20:30Z
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264
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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265 >>> date_time(1126482850)
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266 '2005-09-11T23:54:10Z'
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267
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268 @@ this will change depending on where it is run
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269 #>>> date_time(1126482850, local_time_zone=True)
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270 #'2005-09-11T19:54:10-04:00'
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271
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272 >>> date_time(1)
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273 '1970-01-01T00:00:01Z'
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274
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275 >>> date_time(0)
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276 '1970-01-01T00:00:00Z'
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277 """
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278 if t is None:
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279 t = time()
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280
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281 if local_time_zone:
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282 time_tuple = localtime(t)
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283 if time_tuple[8]:
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284 tz_mins = altzone // 60
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285 else:
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286 tz_mins = timezone // 60
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287 tzd = "-%02d:%02d" % (tz_mins // 60, tz_mins % 60)
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288 else:
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289 time_tuple = gmtime(t)
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290 tzd = "Z"
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291
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292 year, month, day, hh, mm, ss, wd, y, z = time_tuple
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293 s = "%0004d-%02d-%02dT%02d:%02d:%02d%s" % (
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294 year, month, day, hh, mm, ss, tzd)
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295 return s
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296
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297
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298 def parse_date_time(val):
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299 """always returns seconds in UTC
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300
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301 # tests are written like this to make any errors easier to understand
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302 >>> parse_date_time('2005-09-11T23:54:10Z') - 1126482850.0
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303 0.0
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304
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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305 >>> parse_date_time('2005-09-11T16:54:10-07:00') - 1126482850.0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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306 0.0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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307
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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308 >>> parse_date_time('1970-01-01T00:00:01Z') - 1.0
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309 0.0
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310
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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311 >>> parse_date_time('1970-01-01T00:00:00Z') - 0.0
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312 0.0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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313 >>> parse_date_time("2005-09-05T10:42:00") - 1125916920.0
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314 0.0
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315 """
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316
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317 if "T" not in val:
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318 val += "T00:00:00Z"
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319
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320 ymd, time = val.split("T")
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321 hms, tz_str = time[0:8], time[8:]
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322
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323 if not tz_str or tz_str == "Z":
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324 time = time[:-1]
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325 tz_offset = 0
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326 else:
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327 signed_hrs = int(tz_str[:3])
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328 mins = int(tz_str[4:6])
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329 secs = (sign(signed_hrs) * mins + signed_hrs * 60) * 60
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330 tz_offset = -secs
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331
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332 year, month, day = ymd.split("-")
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333 hour, minute, second = hms.split(":")
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334
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335 t = timegm((int(year), int(month), int(day), int(hour),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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336 int(minute), int(second), 0, 0, 0))
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337 t = t + tz_offset
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338 return t
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339
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340
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341
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342
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343
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344 SUFFIX_FORMAT_MAP = {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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345 'rdf': 'xml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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346 'rdfs': 'xml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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347 'owl': 'xml',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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348 'n3': 'n3',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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349 'ttl': 'turtle',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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350 'nt': 'nt',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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351 'trix': 'trix',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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352 'xhtml': 'rdfa',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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353 'html': 'rdfa',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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354 'svg': 'rdfa',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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355 'nq': 'nquads',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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356 'trig': 'trig'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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357 }
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358
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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359
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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360 def guess_format(fpath, fmap=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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361 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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362 Guess RDF serialization based on file suffix. Uses
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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363 ``SUFFIX_FORMAT_MAP`` unless ``fmap`` is provided. Examples:
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364
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
365 >>> guess_format('path/to/file.rdf')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
366 'xml'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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367 >>> guess_format('path/to/file.owl')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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368 'xml'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
369 >>> guess_format('path/to/file.ttl')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
370 'turtle'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
371 >>> guess_format('path/to/file.xhtml')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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372 'rdfa'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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373 >>> guess_format('path/to/file.svg')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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374 'rdfa'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
375 >>> guess_format('path/to/file.xhtml', {'xhtml': 'grddl'})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
376 'grddl'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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377
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
378 This also works with just the suffixes, with or without leading dot, and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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379 regardless of letter case::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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380
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
381 >>> guess_format('.rdf')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
382 'xml'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
383 >>> guess_format('rdf')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
384 'xml'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
385 >>> guess_format('RDF')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
386 'xml'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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387 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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388 fmap = fmap or SUFFIX_FORMAT_MAP
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389 return fmap.get(_get_ext(fpath)) or fmap.get(fpath.lower())
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390
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391
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392 def _get_ext(fpath, lower=True):
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393 """
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394 Gets the file extension from a file(path); stripped of leading '.' and in
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395 lower case. Examples:
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396
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397 >>> _get_ext("path/to/file.txt")
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398 'txt'
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399 >>> _get_ext("OTHER.PDF")
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400 'pdf'
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401 >>> _get_ext("noext")
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402 ''
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403 >>> _get_ext(".rdf")
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404 'rdf'
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405 """
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406 ext = splitext(fpath)[-1]
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407 if ext == '' and fpath.startswith("."):
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408 ext = fpath
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409 if lower:
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410 ext = ext.lower()
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411 if ext.startswith('.'):
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412 ext = ext[1:]
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413 return ext
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414
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415
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416 def find_roots(graph, prop, roots=None):
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417 """
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418 Find the roots in some sort of transitive hierarchy.
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419
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420 find_roots(graph, rdflib.RDFS.subClassOf)
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421 will return a set of all roots of the sub-class hierarchy
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422
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423 Assumes triple of the form (child, prop, parent), i.e. the direction of
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424 RDFS.subClassOf or SKOS.broader
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425
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426 """
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427
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428 non_roots = set()
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429 if roots is None:
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430 roots = set()
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431 for x, y in graph.subject_objects(prop):
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432 non_roots.add(x)
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433 if x in roots:
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434 roots.remove(x)
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435 if y not in non_roots:
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436 roots.add(y)
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437 return roots
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438
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439
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440 def get_tree(graph,
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441 root,
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442 prop,
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443 mapper=lambda x: x,
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444 sortkey=None,
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445 done=None,
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446 dir='down'):
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447 """
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448 Return a nested list/tuple structure representing the tree
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449 built by the transitive property given, starting from the root given
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450
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451 i.e.
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452
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453 get_tree(graph,
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454 rdflib.URIRef("http://xmlns.com/foaf/0.1/Person"),
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455 rdflib.RDFS.subClassOf)
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456
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457 will return the structure for the subClassTree below person.
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458
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459 dir='down' assumes triple of the form (child, prop, parent),
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460 i.e. the direction of RDFS.subClassOf or SKOS.broader
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461 Any other dir traverses in the other direction
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462
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463 """
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464
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465 if done is None:
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466 done = set()
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467 if root in done:
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468 return
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469 done.add(root)
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470 tree = []
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471
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472 if dir == 'down':
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473 branches = graph.subjects(prop, root)
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474 else:
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475 branches = graph.objects(root, prop)
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476
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477 for branch in branches:
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478 t = get_tree(graph, branch, prop, mapper, sortkey, done, dir)
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479 if t:
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480 tree.append(t)
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481
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482 return (mapper(root), sorted(tree, key=sortkey))
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483
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484
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485
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486
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487 def test():
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488 import doctest
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489 doctest.testmod()
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490
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491 if __name__ == "__main__":
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492 # try to make the tests work outside of the time zone they were written in
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493 # import os, time
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494 # os.environ['TZ'] = 'US/Pacific'
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495 # try:
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496 # time.tzset()
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497 # except AttributeError, e:
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498 # print e
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499 # pass
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500 # tzset missing! see
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501 # http://mail.python.org/pipermail/python-dev/2003-April/034480.html
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502 test() # pragma: no cover