Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/rdflib/plugins/parsers/rdfxml.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
| author | shellac |
|---|---|
| date | Mon, 01 Jun 2020 08:59:25 -0400 |
| parents | 79f47841a781 |
| children |
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/rdflib/plugins/parsers/rdfxml.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,578 +0,0 @@ -""" -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)