Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/rdflib/plugins/parsers/rdfxml.py @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
---|---|
date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
children |
line wrap: on
line source
""" An RDF/XML parser for RDFLib """ from xml.sax import make_parser from xml.sax.handler import ErrorHandler from xml.sax.saxutils import handler, quoteattr, escape from urllib.parse import urljoin, urldefrag from rdflib.namespace import RDF, is_ncname from rdflib.term import URIRef from rdflib.term import BNode from rdflib.term import Literal from rdflib.exceptions import ParserError, Error from rdflib.parser import Parser __all__ = ['create_parser', 'BagID', 'ElementHandler', 'RDFXMLHandler', 'RDFXMLParser'] RDFNS = RDF # http://www.w3.org/TR/rdf-syntax-grammar/#eventterm-attribute-URI # A mapping from unqualified terms to their qualified version. UNQUALIFIED = {"about": RDF.about, "ID": RDF.ID, "type": RDF.type, "resource": RDF.resource, "parseType": RDF.parseType} # http://www.w3.org/TR/rdf-syntax-grammar/#coreSyntaxTerms CORE_SYNTAX_TERMS = [RDF.RDF, RDF.ID, RDF.about, RDF.parseType, RDF.resource, RDF.nodeID, RDF.datatype] # http://www.w3.org/TR/rdf-syntax-grammar/#syntaxTerms SYNTAX_TERMS = CORE_SYNTAX_TERMS + [RDF.Description, RDF.li] # http://www.w3.org/TR/rdf-syntax-grammar/#oldTerms OLD_TERMS = [ URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#aboutEach"), URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#aboutEachPrefix"), URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#bagID")] NODE_ELEMENT_EXCEPTIONS = CORE_SYNTAX_TERMS + [RDF.li, ] + OLD_TERMS NODE_ELEMENT_ATTRIBUTES = [RDF.ID, RDF.nodeID, RDF.about] PROPERTY_ELEMENT_EXCEPTIONS = \ CORE_SYNTAX_TERMS + [RDF.Description, ] + OLD_TERMS PROPERTY_ATTRIBUTE_EXCEPTIONS = \ CORE_SYNTAX_TERMS + [RDF.Description, RDF.li] + OLD_TERMS PROPERTY_ELEMENT_ATTRIBUTES = [RDF.ID, RDF.resource, RDF.nodeID] XMLNS = "http://www.w3.org/XML/1998/namespace" BASE = (XMLNS, "base") LANG = (XMLNS, "lang") class BagID(URIRef): __slots__ = ['li'] def __init__(self, val): super(URIRef, self).__init__(val) self.li = 0 def next_li(self): self.li += 1 return RDFNS[self.li] class ElementHandler(object): __slots__ = ['start', 'char', 'end', 'li', 'id', 'base', 'subject', 'predicate', 'object', 'list', 'language', 'datatype', 'declared', 'data'] def __init__(self): self.start = None self.char = None self.end = None self.li = 0 self.id = None self.base = None self.subject = None self.object = None self.list = None self.language = None self.datatype = None self.declared = None self.data = None def next_li(self): self.li += 1 return RDFNS[self.li] class RDFXMLHandler(handler.ContentHandler): def __init__(self, store): self.store = store self.preserve_bnode_ids = False self.reset() def reset(self): document_element = ElementHandler() document_element.start = self.document_element_start document_element.end = lambda name, qname: None self.stack = [None, document_element, ] self.ids = {} # remember IDs we have already seen self.bnode = {} self._ns_contexts = [{}] # contains uri -> prefix dicts self._current_context = self._ns_contexts[-1] # ContentHandler methods def setDocumentLocator(self, locator): self.locator = locator def startDocument(self): pass def startPrefixMapping(self, prefix, namespace): self._ns_contexts.append(self._current_context.copy()) self._current_context[namespace] = prefix self.store.bind(prefix, namespace or "", override=False) def endPrefixMapping(self, prefix): self._current_context = self._ns_contexts[-1] del self._ns_contexts[-1] def startElementNS(self, name, qname, attrs): stack = self.stack stack.append(ElementHandler()) current = self.current parent = self.parent base = attrs.get(BASE, None) if base is not None: base, frag = urldefrag(base) if parent and parent.base: base = urljoin(parent.base, base) else: systemId = self.locator.getPublicId() \ or self.locator.getSystemId() if systemId: base = urljoin(systemId, base) else: if parent: base = parent.base if base is None: systemId = self.locator.getPublicId() \ or self.locator.getSystemId() if systemId: base, frag = urldefrag(systemId) current.base = base language = attrs.get(LANG, None) if language is None: if parent: language = parent.language current.language = language current.start(name, qname, attrs) def endElementNS(self, name, qname): self.current.end(name, qname) self.stack.pop() def characters(self, content): char = self.current.char if char: char(content) def ignorableWhitespace(self, content): pass def processingInstruction(self, target, data): pass def add_reified(self, sid, xxx_todo_changeme): (s, p, o) = xxx_todo_changeme self.store.add((sid, RDF.type, RDF.Statement)) self.store.add((sid, RDF.subject, s)) self.store.add((sid, RDF.predicate, p)) self.store.add((sid, RDF.object, o)) def error(self, message): locator = self.locator info = "%s:%s:%s: " % (locator.getSystemId(), locator.getLineNumber(), locator.getColumnNumber()) raise ParserError(info + message) def get_current(self): return self.stack[-2] # Create a read only property called current so that self.current # give the current element handler. current = property(get_current) def get_next(self): return self.stack[-1] # Create a read only property that gives the element handler to be # used for the next element. next = property(get_next) def get_parent(self): return self.stack[-3] # Create a read only property that gives the current parent # element handler parent = property(get_parent) def absolutize(self, uri): result = urljoin(self.current.base, uri, allow_fragments=1) if uri and uri[-1] == "#" and result[-1] != "#": result = "%s#" % result return URIRef(result) def convert(self, name, qname, attrs): if name[0] is None: name = URIRef(name[1]) else: name = URIRef("".join(name)) atts = {} for (n, v) in list(attrs.items()): # attrs._attrs.iteritems(): # if n[0] is None: att = n[1] else: att = "".join(n) if att.startswith(XMLNS) or att[0:3].lower() == "xml": pass elif att in UNQUALIFIED: # if not RDFNS[att] in atts: atts[RDFNS[att]] = v else: atts[URIRef(att)] = v return name, atts def document_element_start(self, name, qname, attrs): if name[0] and URIRef("".join(name)) == RDF.RDF: # Cheap hack so 2to3 doesn't turn it into __next__ next = getattr(self, 'next') next.start = self.node_element_start next.end = self.node_element_end else: self.node_element_start(name, qname, attrs) # self.current.end = self.node_element_end # TODO... set end to something that sets start such that # another element will cause error def node_element_start(self, name, qname, attrs): name, atts = self.convert(name, qname, attrs) current = self.current absolutize = self.absolutize # Cheap hack so 2to3 doesn't turn it into __next__ next = getattr(self, 'next') next.start = self.property_element_start next.end = self.property_element_end if name in NODE_ELEMENT_EXCEPTIONS: self.error("Invalid node element URI: %s" % name) if RDF.ID in atts: if RDF.about in atts or RDF.nodeID in atts: self.error( "Can have at most one of rdf:ID, rdf:about, and rdf:nodeID" ) id = atts[RDF.ID] if not is_ncname(id): self.error("rdf:ID value is not a valid NCName: %s" % id) subject = absolutize("#%s" % id) if subject in self.ids: self.error( "two elements cannot use the same ID: '%s'" % subject) self.ids[subject] = 1 # IDs can only appear once within a document elif RDF.nodeID in atts: if RDF.ID in atts or RDF.about in atts: self.error( "Can have at most one of rdf:ID, rdf:about, and rdf:nodeID" ) nodeID = atts[RDF.nodeID] if not is_ncname(nodeID): self.error( "rdf:nodeID value is not a valid NCName: %s" % nodeID) if self.preserve_bnode_ids is False: if nodeID in self.bnode: subject = self.bnode[nodeID] else: subject = BNode() self.bnode[nodeID] = subject else: subject = BNode(nodeID) elif RDF.about in atts: if RDF.ID in atts or RDF.nodeID in atts: self.error( "Can have at most one of rdf:ID, rdf:about, and rdf:nodeID" ) subject = absolutize(atts[RDF.about]) else: subject = BNode() if name != RDF.Description: # S1 self.store.add((subject, RDF.type, absolutize(name))) language = current.language for att in atts: if not att.startswith(str(RDFNS)): predicate = absolutize(att) try: object = Literal(atts[att], language) except Error as e: self.error(e.msg) elif att == RDF.type: # S2 predicate = RDF.type object = absolutize(atts[RDF.type]) elif att in NODE_ELEMENT_ATTRIBUTES: continue elif att in PROPERTY_ATTRIBUTE_EXCEPTIONS: # S3 self.error("Invalid property attribute URI: %s" % att) continue # for when error does not throw an exception else: predicate = absolutize(att) try: object = Literal(atts[att], language) except Error as e: self.error(e.msg) self.store.add((subject, predicate, object)) current.subject = subject def node_element_end(self, name, qname): # repeat node-elements are only allowed # at at top-level if self.parent.object and self.current != self.stack[2]: self.error("Repeat node-elements inside property elements: %s"%"".join(name)) self.parent.object = self.current.subject def property_element_start(self, name, qname, attrs): name, atts = self.convert(name, qname, attrs) current = self.current absolutize = self.absolutize # Cheap hack so 2to3 doesn't turn it into __next__ next = getattr(self, 'next') object = None current.data = None current.list = None if not name.startswith(str(RDFNS)): current.predicate = absolutize(name) elif name == RDF.li: current.predicate = current.next_li() elif name in PROPERTY_ELEMENT_EXCEPTIONS: self.error("Invalid property element URI: %s" % name) else: current.predicate = absolutize(name) id = atts.get(RDF.ID, None) if id is not None: if not is_ncname(id): self.error("rdf:ID value is not a value NCName: %s" % id) current.id = absolutize("#%s" % id) else: current.id = None resource = atts.get(RDF.resource, None) nodeID = atts.get(RDF.nodeID, None) parse_type = atts.get(RDF.parseType, None) if resource is not None and nodeID is not None: self.error( "Property element cannot have both rdf:nodeID and rdf:resource" ) if resource is not None: object = absolutize(resource) next.start = self.node_element_start next.end = self.node_element_end elif nodeID is not None: if not is_ncname(nodeID): self.error( "rdf:nodeID value is not a valid NCName: %s" % nodeID) if self.preserve_bnode_ids is False: if nodeID in self.bnode: object = self.bnode[nodeID] else: subject = BNode() self.bnode[nodeID] = subject object = subject else: object = subject = BNode(nodeID) next.start = self.node_element_start next.end = self.node_element_end else: if parse_type is not None: for att in atts: if att != RDF.parseType and att != RDF.ID: self.error("Property attr '%s' now allowed here" % att) if parse_type == "Resource": current.subject = object = BNode() current.char = self.property_element_char next.start = self.property_element_start next.end = self.property_element_end elif parse_type == "Collection": current.char = None object = current.list = RDF.nil # BNode() # self.parent.subject next.start = self.node_element_start next.end = self.list_node_element_end else: # if parse_type=="Literal": # All other values are treated as Literal # See: http://www.w3.org/TR/rdf-syntax-grammar/ # parseTypeOtherPropertyElt object = Literal("", datatype=RDF.XMLLiteral) current.char = self.literal_element_char current.declared = {XMLNS: 'xml'} next.start = self.literal_element_start next.char = self.literal_element_char next.end = self.literal_element_end current.object = object return else: object = None current.char = self.property_element_char next.start = self.node_element_start next.end = self.node_element_end datatype = current.datatype = atts.get(RDF.datatype, None) language = current.language if datatype is not None: # TODO: check that there are no atts other than datatype and id datatype = absolutize(datatype) else: for att in atts: if not att.startswith(str(RDFNS)): predicate = absolutize(att) elif att in PROPERTY_ELEMENT_ATTRIBUTES: continue elif att in PROPERTY_ATTRIBUTE_EXCEPTIONS: self.error("""Invalid property attribute URI: %s""" % att) else: predicate = absolutize(att) if att == RDF.type: o = URIRef(atts[att]) else: if datatype is not None: language = None o = Literal(atts[att], language, datatype) if object is None: object = BNode() self.store.add((object, predicate, o)) if object is None: current.data = "" current.object = None else: current.data = None current.object = object def property_element_char(self, data): current = self.current if current.data is not None: current.data += data def property_element_end(self, name, qname): current = self.current if current.data is not None and current.object is None: literalLang = current.language if current.datatype is not None: literalLang = None current.object = Literal( current.data, literalLang, current.datatype) current.data = None if self.next.end == self.list_node_element_end: if current.object != RDF.nil: self.store.add((current.list, RDF.rest, RDF.nil)) if current.object is not None: self.store.add( (self.parent.subject, current.predicate, current.object)) if current.id is not None: self.add_reified(current.id, (self.parent.subject, current.predicate, current.object)) current.subject = None def list_node_element_end(self, name, qname): current = self.current if self.parent.list == RDF.nil: list = BNode() # Removed between 20030123 and 20030905 # self.store.add((list, RDF.type, LIST)) self.parent.list = list self.store.add((self.parent.list, RDF.first, current.subject)) self.parent.object = list self.parent.char = None else: list = BNode() # Removed between 20030123 and 20030905 # self.store.add((list, RDF.type, LIST)) self.store.add((self.parent.list, RDF.rest, list)) self.store.add((list, RDF.first, current.subject)) self.parent.list = list def literal_element_start(self, name, qname, attrs): current = self.current self.next.start = self.literal_element_start self.next.char = self.literal_element_char self.next.end = self.literal_element_end current.declared = self.parent.declared.copy() if name[0]: prefix = self._current_context[name[0]] if prefix: current.object = "<%s:%s" % (prefix, name[1]) else: current.object = "<%s" % name[1] if not name[0] in current.declared: current.declared[name[0]] = prefix if prefix: current.object += (' xmlns:%s="%s"' % (prefix, name[0])) else: current.object += (' xmlns="%s"' % name[0]) else: current.object = "<%s" % name[1] for (name, value) in list(attrs.items()): if name[0]: if not name[0] in current.declared: current.declared[name[0]] = self._current_context[name[0]] name = current.declared[name[0]] + ":" + name[1] else: name = name[1] current.object += (' %s=%s' % (name, quoteattr(value))) current.object += ">" def literal_element_char(self, data): self.current.object += escape(data) def literal_element_end(self, name, qname): if name[0]: prefix = self._current_context[name[0]] if prefix: end = "</%s:%s>" % (prefix, name[1]) else: end = "</%s>" % name[1] else: end = "</%s>" % name[1] self.parent.object += self.current.object + end def create_parser(target, store): parser = make_parser() try: # Workaround for bug in expatreader.py. Needed when # expatreader is trying to guess a prefix. parser.start_namespace_decl( "xml", "http://www.w3.org/XML/1998/namespace") except AttributeError: pass # Not present in Jython (at least) parser.setFeature(handler.feature_namespaces, 1) rdfxml = RDFXMLHandler(store) rdfxml.setDocumentLocator(target) # rdfxml.setDocumentLocator(_Locator(self.url, self.parser)) parser.setContentHandler(rdfxml) parser.setErrorHandler(ErrorHandler()) return parser class RDFXMLParser(Parser): def __init__(self): pass def parse(self, source, sink, **args): self._parser = create_parser(source, sink) content_handler = self._parser.getContentHandler() preserve_bnode_ids = args.get("preserve_bnode_ids", None) if preserve_bnode_ids is not None: content_handler.preserve_bnode_ids = preserve_bnode_ids # # We're only using it once now # content_handler.reset() # self._parser.reset() self._parser.parse(source)