Mercurial > repos > shellac > guppy_basecaller
comparison env/lib/python3.7/site-packages/rdflib/plugins/parsers/ntriples.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
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| date | Sat, 02 May 2020 07:14:21 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:26e78fe6e8c4 |
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| 1 #!/usr/bin/env python | |
| 2 __doc__ = """ | |
| 3 N-Triples Parser | |
| 4 License: GPL 2, W3C, BSD, or MIT | |
| 5 Author: Sean B. Palmer, inamidst.com | |
| 6 """ | |
| 7 | |
| 8 import re | |
| 9 import codecs | |
| 10 | |
| 11 from rdflib.term import URIRef as URI | |
| 12 from rdflib.term import BNode as bNode | |
| 13 from rdflib.term import Literal | |
| 14 | |
| 15 from rdflib.py3compat import cast_bytes, decodeUnicodeEscape | |
| 16 | |
| 17 __all__ = ['unquote', 'uriquote', 'Sink', 'NTriplesParser'] | |
| 18 | |
| 19 uriref = r'<([^:]+:[^\s"<>]+)>' | |
| 20 literal = r'"([^"\\]*(?:\\.[^"\\]*)*)"' | |
| 21 litinfo = r'(?:@([a-z]+(?:-[a-zA-Z0-9]+)*)|\^\^' + uriref + r')?' | |
| 22 | |
| 23 r_line = re.compile(r'([^\r\n]*)(?:\r\n|\r|\n)') | |
| 24 r_wspace = re.compile(r'[ \t]*') | |
| 25 r_wspaces = re.compile(r'[ \t]+') | |
| 26 r_tail = re.compile(r'[ \t]*\.[ \t]*(#.*)?') | |
| 27 r_uriref = re.compile(uriref) | |
| 28 r_nodeid = re.compile(r'_:([A-Za-z0-9]*)') | |
| 29 r_literal = re.compile(literal + litinfo) | |
| 30 | |
| 31 bufsiz = 2048 | |
| 32 validate = False | |
| 33 | |
| 34 | |
| 35 class Node(str): | |
| 36 pass | |
| 37 | |
| 38 | |
| 39 class ParseError(Exception): | |
| 40 pass | |
| 41 | |
| 42 | |
| 43 class Sink(object): | |
| 44 def __init__(self): | |
| 45 self.length = 0 | |
| 46 | |
| 47 def triple(self, s, p, o): | |
| 48 self.length += 1 | |
| 49 print((s, p, o)) | |
| 50 | |
| 51 quot = {'t': '\t', 'n': '\n', 'r': '\r', '"': '"', '\\': | |
| 52 '\\'} | |
| 53 r_safe = re.compile(r'([\x20\x21\x23-\x5B\x5D-\x7E]+)') | |
| 54 r_quot = re.compile(r'\\(t|n|r|"|\\)') | |
| 55 r_uniquot = re.compile(r'\\u([0-9A-F]{4})|\\U([0-9A-F]{8})') | |
| 56 | |
| 57 | |
| 58 def unquote(s): | |
| 59 """Unquote an N-Triples string.""" | |
| 60 if not validate: | |
| 61 | |
| 62 if isinstance(s, str): # nquads | |
| 63 s = decodeUnicodeEscape(s) | |
| 64 else: | |
| 65 s = s.decode('unicode-escape') | |
| 66 | |
| 67 return s | |
| 68 else: | |
| 69 result = [] | |
| 70 while s: | |
| 71 m = r_safe.match(s) | |
| 72 if m: | |
| 73 s = s[m.end():] | |
| 74 result.append(m.group(1)) | |
| 75 continue | |
| 76 | |
| 77 m = r_quot.match(s) | |
| 78 if m: | |
| 79 s = s[2:] | |
| 80 result.append(quot[m.group(1)]) | |
| 81 continue | |
| 82 | |
| 83 m = r_uniquot.match(s) | |
| 84 if m: | |
| 85 s = s[m.end():] | |
| 86 u, U = m.groups() | |
| 87 codepoint = int(u or U, 16) | |
| 88 if codepoint > 0x10FFFF: | |
| 89 raise ParseError("Disallowed codepoint: %08X" % codepoint) | |
| 90 result.append(chr(codepoint)) | |
| 91 elif s.startswith('\\'): | |
| 92 raise ParseError("Illegal escape at: %s..." % s[:10]) | |
| 93 else: | |
| 94 raise ParseError("Illegal literal character: %r" % s[0]) | |
| 95 return ''.join(result) | |
| 96 | |
| 97 r_hibyte = re.compile(r'([\x80-\xFF])') | |
| 98 | |
| 99 | |
| 100 def uriquote(uri): | |
| 101 if not validate: | |
| 102 return uri | |
| 103 else: | |
| 104 return r_hibyte.sub( | |
| 105 lambda m: '%%%02X' % ord(m.group(1)), uri) | |
| 106 | |
| 107 | |
| 108 class NTriplesParser(object): | |
| 109 """An N-Triples Parser. | |
| 110 | |
| 111 Usage:: | |
| 112 | |
| 113 p = NTriplesParser(sink=MySink()) | |
| 114 sink = p.parse(f) # file; use parsestring for a string | |
| 115 """ | |
| 116 | |
| 117 _bnode_ids = {} | |
| 118 | |
| 119 def __init__(self, sink=None): | |
| 120 if sink is not None: | |
| 121 self.sink = sink | |
| 122 else: | |
| 123 self.sink = Sink() | |
| 124 | |
| 125 def parse(self, f): | |
| 126 """Parse f as an N-Triples file.""" | |
| 127 if not hasattr(f, 'read'): | |
| 128 raise ParseError("Item to parse must be a file-like object.") | |
| 129 | |
| 130 # since N-Triples 1.1 files can and should be utf-8 encoded | |
| 131 f = codecs.getreader('utf-8')(f) | |
| 132 | |
| 133 self.file = f | |
| 134 self.buffer = '' | |
| 135 while True: | |
| 136 self.line = self.readline() | |
| 137 if self.line is None: | |
| 138 break | |
| 139 try: | |
| 140 self.parseline() | |
| 141 except ParseError: | |
| 142 raise ParseError("Invalid line: %r" % self.line) | |
| 143 return self.sink | |
| 144 | |
| 145 def parsestring(self, s): | |
| 146 """Parse s as an N-Triples string.""" | |
| 147 if not isinstance(s, str): | |
| 148 raise ParseError("Item to parse must be a string instance.") | |
| 149 try: | |
| 150 from io import BytesIO | |
| 151 assert BytesIO | |
| 152 except ImportError: | |
| 153 from io import StringIO as BytesIO | |
| 154 assert BytesIO | |
| 155 f = BytesIO() | |
| 156 f.write(cast_bytes(s)) | |
| 157 f.seek(0) | |
| 158 self.parse(f) | |
| 159 | |
| 160 def readline(self): | |
| 161 """Read an N-Triples line from buffered input.""" | |
| 162 # N-Triples lines end in either CRLF, CR, or LF | |
| 163 # Therefore, we can't just use f.readline() | |
| 164 if not self.buffer: | |
| 165 buffer = self.file.read(bufsiz) | |
| 166 if not buffer: | |
| 167 return None | |
| 168 self.buffer = buffer | |
| 169 | |
| 170 while True: | |
| 171 m = r_line.match(self.buffer) | |
| 172 if m: # the more likely prospect | |
| 173 self.buffer = self.buffer[m.end():] | |
| 174 return m.group(1) | |
| 175 else: | |
| 176 buffer = self.file.read(bufsiz) | |
| 177 if not buffer and not self.buffer.isspace(): | |
| 178 # Last line does not need to be terminated with a newline | |
| 179 buffer += "\n" | |
| 180 elif not buffer: | |
| 181 return None | |
| 182 self.buffer += buffer | |
| 183 | |
| 184 def parseline(self): | |
| 185 self.eat(r_wspace) | |
| 186 if (not self.line) or self.line.startswith('#'): | |
| 187 return # The line is empty or a comment | |
| 188 | |
| 189 subject = self.subject() | |
| 190 self.eat(r_wspaces) | |
| 191 | |
| 192 predicate = self.predicate() | |
| 193 self.eat(r_wspaces) | |
| 194 | |
| 195 object = self.object() | |
| 196 self.eat(r_tail) | |
| 197 | |
| 198 if self.line: | |
| 199 raise ParseError("Trailing garbage") | |
| 200 self.sink.triple(subject, predicate, object) | |
| 201 | |
| 202 def peek(self, token): | |
| 203 return self.line.startswith(token) | |
| 204 | |
| 205 def eat(self, pattern): | |
| 206 m = pattern.match(self.line) | |
| 207 if not m: # @@ Why can't we get the original pattern? | |
| 208 # print(dir(pattern)) | |
| 209 # print repr(self.line), type(self.line) | |
| 210 raise ParseError("Failed to eat %s at %s" % (pattern.pattern, self.line)) | |
| 211 self.line = self.line[m.end():] | |
| 212 return m | |
| 213 | |
| 214 def subject(self): | |
| 215 # @@ Consider using dictionary cases | |
| 216 subj = self.uriref() or self.nodeid() | |
| 217 if not subj: | |
| 218 raise ParseError("Subject must be uriref or nodeID") | |
| 219 return subj | |
| 220 | |
| 221 def predicate(self): | |
| 222 pred = self.uriref() | |
| 223 if not pred: | |
| 224 raise ParseError("Predicate must be uriref") | |
| 225 return pred | |
| 226 | |
| 227 def object(self): | |
| 228 objt = self.uriref() or self.nodeid() or self.literal() | |
| 229 if objt is False: | |
| 230 raise ParseError("Unrecognised object type") | |
| 231 return objt | |
| 232 | |
| 233 def uriref(self): | |
| 234 if self.peek('<'): | |
| 235 uri = self.eat(r_uriref).group(1) | |
| 236 uri = unquote(uri) | |
| 237 uri = uriquote(uri) | |
| 238 return URI(uri) | |
| 239 return False | |
| 240 | |
| 241 def nodeid(self): | |
| 242 if self.peek('_'): | |
| 243 # Fix for https://github.com/RDFLib/rdflib/issues/204 | |
| 244 bnode_id = self.eat(r_nodeid).group(1) | |
| 245 new_id = self._bnode_ids.get(bnode_id, None) | |
| 246 if new_id is not None: | |
| 247 # Re-map to id specfic to this doc | |
| 248 return bNode(new_id) | |
| 249 else: | |
| 250 # Replace with freshly-generated document-specific BNode id | |
| 251 bnode = bNode() | |
| 252 # Store the mapping | |
| 253 self._bnode_ids[bnode_id] = bnode | |
| 254 return bnode | |
| 255 return False | |
| 256 | |
| 257 def literal(self): | |
| 258 if self.peek('"'): | |
| 259 lit, lang, dtype = self.eat(r_literal).groups() | |
| 260 if lang: | |
| 261 lang = lang | |
| 262 else: | |
| 263 lang = None | |
| 264 if dtype: | |
| 265 dtype = dtype | |
| 266 else: | |
| 267 dtype = None | |
| 268 if lang and dtype: | |
| 269 raise ParseError("Can't have both a language and a datatype") | |
| 270 lit = unquote(lit) | |
| 271 return Literal(lit, lang, dtype) | |
| 272 return False | |
| 273 | |
| 274 # # Obsolete, unused | |
| 275 # def parseURI(uri): | |
| 276 # import urllib | |
| 277 # parser = NTriplesParser() | |
| 278 # u = urllib.urlopen(uri) | |
| 279 # sink = parser.parse(u) | |
| 280 # u.close() | |
| 281 # # for triple in sink: | |
| 282 # # print triple | |
| 283 # print 'Length of input:', sink.length |
