Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/rdflib/plugins/parsers/ntriples.py @ 4:79f47841a781 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 16:47:39 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2 __doc__ = """
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3 N-Triples Parser
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4 License: GPL 2, W3C, BSD, or MIT
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5 Author: Sean B. Palmer, inamidst.com
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6 """
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7
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8 import re
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9 import codecs
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10
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11 from rdflib.term import URIRef as URI
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12 from rdflib.term import BNode as bNode
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13 from rdflib.term import Literal
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14
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15 from rdflib.py3compat import cast_bytes, decodeUnicodeEscape
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16
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17 __all__ = ['unquote', 'uriquote', 'Sink', 'NTriplesParser']
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18
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19 uriref = r'<([^:]+:[^\s"<>]+)>'
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20 literal = r'"([^"\\]*(?:\\.[^"\\]*)*)"'
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21 litinfo = r'(?:@([a-z]+(?:-[a-zA-Z0-9]+)*)|\^\^' + uriref + r')?'
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22
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23 r_line = re.compile(r'([^\r\n]*)(?:\r\n|\r|\n)')
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24 r_wspace = re.compile(r'[ \t]*')
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25 r_wspaces = re.compile(r'[ \t]+')
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26 r_tail = re.compile(r'[ \t]*\.[ \t]*(#.*)?')
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27 r_uriref = re.compile(uriref)
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28 r_nodeid = re.compile(r'_:([A-Za-z0-9]*)')
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29 r_literal = re.compile(literal + litinfo)
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30
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31 bufsiz = 2048
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32 validate = False
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33
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34
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35 class Node(str):
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36 pass
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37
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38
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39 class ParseError(Exception):
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40 pass
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41
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42
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43 class Sink(object):
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44 def __init__(self):
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45 self.length = 0
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46
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47 def triple(self, s, p, o):
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48 self.length += 1
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49 print((s, p, o))
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50
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51 quot = {'t': '\t', 'n': '\n', 'r': '\r', '"': '"', '\\':
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52 '\\'}
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53 r_safe = re.compile(r'([\x20\x21\x23-\x5B\x5D-\x7E]+)')
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54 r_quot = re.compile(r'\\(t|n|r|"|\\)')
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55 r_uniquot = re.compile(r'\\u([0-9A-F]{4})|\\U([0-9A-F]{8})')
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56
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57
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58 def unquote(s):
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59 """Unquote an N-Triples string."""
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60 if not validate:
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61
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62 if isinstance(s, str): # nquads
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63 s = decodeUnicodeEscape(s)
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64 else:
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65 s = s.decode('unicode-escape')
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66
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67 return s
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68 else:
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69 result = []
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70 while s:
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71 m = r_safe.match(s)
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72 if m:
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73 s = s[m.end():]
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74 result.append(m.group(1))
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75 continue
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76
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77 m = r_quot.match(s)
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78 if m:
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79 s = s[2:]
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80 result.append(quot[m.group(1)])
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81 continue
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82
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83 m = r_uniquot.match(s)
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84 if m:
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85 s = s[m.end():]
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86 u, U = m.groups()
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87 codepoint = int(u or U, 16)
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88 if codepoint > 0x10FFFF:
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89 raise ParseError("Disallowed codepoint: %08X" % codepoint)
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90 result.append(chr(codepoint))
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91 elif s.startswith('\\'):
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92 raise ParseError("Illegal escape at: %s..." % s[:10])
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93 else:
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94 raise ParseError("Illegal literal character: %r" % s[0])
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95 return ''.join(result)
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96
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97 r_hibyte = re.compile(r'([\x80-\xFF])')
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98
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99
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100 def uriquote(uri):
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101 if not validate:
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102 return uri
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103 else:
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104 return r_hibyte.sub(
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105 lambda m: '%%%02X' % ord(m.group(1)), uri)
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106
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107
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108 class NTriplesParser(object):
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109 """An N-Triples Parser.
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110
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111 Usage::
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112
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113 p = NTriplesParser(sink=MySink())
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114 sink = p.parse(f) # file; use parsestring for a string
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115 """
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116
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117 _bnode_ids = {}
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118
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119 def __init__(self, sink=None):
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120 if sink is not None:
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121 self.sink = sink
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122 else:
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123 self.sink = Sink()
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124
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125 def parse(self, f):
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126 """Parse f as an N-Triples file."""
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127 if not hasattr(f, 'read'):
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128 raise ParseError("Item to parse must be a file-like object.")
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129
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130 # since N-Triples 1.1 files can and should be utf-8 encoded
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131 f = codecs.getreader('utf-8')(f)
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132
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133 self.file = f
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134 self.buffer = ''
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diff changeset
135 while True:
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diff changeset
136 self.line = self.readline()
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137 if self.line is None:
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138 break
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139 try:
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140 self.parseline()
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141 except ParseError:
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142 raise ParseError("Invalid line: %r" % self.line)
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143 return self.sink
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144
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145 def parsestring(self, s):
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146 """Parse s as an N-Triples string."""
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147 if not isinstance(s, str):
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148 raise ParseError("Item to parse must be a string instance.")
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149 try:
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150 from io import BytesIO
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151 assert BytesIO
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152 except ImportError:
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153 from io import StringIO as BytesIO
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154 assert BytesIO
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155 f = BytesIO()
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156 f.write(cast_bytes(s))
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157 f.seek(0)
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158 self.parse(f)
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159
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160 def readline(self):
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161 """Read an N-Triples line from buffered input."""
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162 # N-Triples lines end in either CRLF, CR, or LF
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163 # Therefore, we can't just use f.readline()
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164 if not self.buffer:
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165 buffer = self.file.read(bufsiz)
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166 if not buffer:
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167 return None
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168 self.buffer = buffer
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169
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170 while True:
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171 m = r_line.match(self.buffer)
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172 if m: # the more likely prospect
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173 self.buffer = self.buffer[m.end():]
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174 return m.group(1)
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175 else:
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176 buffer = self.file.read(bufsiz)
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177 if not buffer and not self.buffer.isspace():
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178 # Last line does not need to be terminated with a newline
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179 buffer += "\n"
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180 elif not buffer:
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181 return None
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182 self.buffer += buffer
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183
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184 def parseline(self):
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185 self.eat(r_wspace)
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186 if (not self.line) or self.line.startswith('#'):
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187 return # The line is empty or a comment
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188
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189 subject = self.subject()
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190 self.eat(r_wspaces)
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191
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192 predicate = self.predicate()
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193 self.eat(r_wspaces)
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194
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195 object = self.object()
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196 self.eat(r_tail)
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197
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198 if self.line:
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199 raise ParseError("Trailing garbage")
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200 self.sink.triple(subject, predicate, object)
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201
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202 def peek(self, token):
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203 return self.line.startswith(token)
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204
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205 def eat(self, pattern):
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206 m = pattern.match(self.line)
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207 if not m: # @@ Why can't we get the original pattern?
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208 # print(dir(pattern))
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diff changeset
209 # print repr(self.line), type(self.line)
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diff changeset
210 raise ParseError("Failed to eat %s at %s" % (pattern.pattern, self.line))
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211 self.line = self.line[m.end():]
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diff changeset
212 return m
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diff changeset
213
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214 def subject(self):
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diff changeset
215 # @@ Consider using dictionary cases
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diff changeset
216 subj = self.uriref() or self.nodeid()
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217 if not subj:
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diff changeset
218 raise ParseError("Subject must be uriref or nodeID")
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219 return subj
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220
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221 def predicate(self):
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222 pred = self.uriref()
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diff changeset
223 if not pred:
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diff changeset
224 raise ParseError("Predicate must be uriref")
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diff changeset
225 return pred
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226
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diff changeset
227 def object(self):
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228 objt = self.uriref() or self.nodeid() or self.literal()
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diff changeset
229 if objt is False:
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diff changeset
230 raise ParseError("Unrecognised object type")
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diff changeset
231 return objt
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diff changeset
232
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diff changeset
233 def uriref(self):
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diff changeset
234 if self.peek('<'):
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parents:
diff changeset
235 uri = self.eat(r_uriref).group(1)
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parents:
diff changeset
236 uri = unquote(uri)
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diff changeset
237 uri = uriquote(uri)
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parents:
diff changeset
238 return URI(uri)
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diff changeset
239 return False
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diff changeset
240
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parents:
diff changeset
241 def nodeid(self):
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parents:
diff changeset
242 if self.peek('_'):
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parents:
diff changeset
243 # Fix for https://github.com/RDFLib/rdflib/issues/204
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shellac
parents:
diff changeset
244 bnode_id = self.eat(r_nodeid).group(1)
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parents:
diff changeset
245 new_id = self._bnode_ids.get(bnode_id, None)
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parents:
diff changeset
246 if new_id is not None:
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parents:
diff changeset
247 # Re-map to id specfic to this doc
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parents:
diff changeset
248 return bNode(new_id)
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parents:
diff changeset
249 else:
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parents:
diff changeset
250 # Replace with freshly-generated document-specific BNode id
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parents:
diff changeset
251 bnode = bNode()
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parents:
diff changeset
252 # Store the mapping
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diff changeset
253 self._bnode_ids[bnode_id] = bnode
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parents:
diff changeset
254 return bnode
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parents:
diff changeset
255 return False
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parents:
diff changeset
256
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diff changeset
257 def literal(self):
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diff changeset
258 if self.peek('"'):
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parents:
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259 lit, lang, dtype = self.eat(r_literal).groups()
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260 if lang:
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261 lang = lang
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262 else:
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263 lang = None
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264 if dtype:
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265 dtype = dtype
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266 else:
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267 dtype = None
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268 if lang and dtype:
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269 raise ParseError("Can't have both a language and a datatype")
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270 lit = unquote(lit)
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271 return Literal(lit, lang, dtype)
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272 return False
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273
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274 # # Obsolete, unused
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275 # def parseURI(uri):
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276 # import urllib
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277 # parser = NTriplesParser()
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278 # u = urllib.urlopen(uri)
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279 # sink = parser.parse(u)
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280 # u.close()
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281 # # for triple in sink:
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282 # # print triple
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283 # print 'Length of input:', sink.length