Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/rdflib/plugins/serializers/rdfxml.py @ 4:79f47841a781 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:47:39 -0400 |
parents | 26e78fe6e8c4 |
children |
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from rdflib.plugins.serializers.xmlwriter import XMLWriter from rdflib.namespace import Namespace, RDF, RDFS # , split_uri from rdflib.term import URIRef, Literal, BNode from rdflib.util import first, more_than from rdflib.collection import Collection from rdflib.serializer import Serializer # from rdflib.exceptions import Error from rdflib.py3compat import b from xml.sax.saxutils import quoteattr, escape import xml.dom.minidom from .xmlwriter import ESCAPE_ENTITIES __all__ = ['fix', 'XMLSerializer', 'PrettyXMLSerializer'] class XMLSerializer(Serializer): def __init__(self, store): super(XMLSerializer, self).__init__(store) def __bindings(self): store = self.store nm = store.namespace_manager bindings = {} for predicate in set(store.predicates()): prefix, namespace, name = nm.compute_qname(predicate) bindings[prefix] = URIRef(namespace) RDFNS = URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#") if "rdf" in bindings: assert bindings["rdf"] == RDFNS else: bindings["rdf"] = RDFNS for prefix, namespace in bindings.items(): yield prefix, namespace def serialize(self, stream, base=None, encoding=None, **args): self.base = base self.__stream = stream self.__serialized = {} encoding = self.encoding self.write = write = lambda uni: stream.write( uni.encode(encoding, 'replace')) # startDocument write('<?xml version="1.0" encoding="%s"?>\n' % self.encoding) # startRDF write('<rdf:RDF\n') # If provided, write xml:base attribute for the RDF if "xml_base" in args: write(' xml:base="%s"\n' % args['xml_base']) # TODO: # assert( # namespaces["http://www.w3.org/1999/02/22-rdf-syntax-ns#"]=='rdf') bindings = list(self.__bindings()) bindings.sort() for prefix, namespace in bindings: if prefix: write(' xmlns:%s="%s"\n' % (prefix, namespace)) else: write(' xmlns="%s"\n' % namespace) write('>\n') # write out triples by subject for subject in self.store.subjects(): self.subject(subject, 1) # endRDF write("</rdf:RDF>\n") # Set to None so that the memory can get garbage collected. # self.__serialized = None del self.__serialized def subject(self, subject, depth=1): if not subject in self.__serialized: self.__serialized[subject] = 1 if isinstance(subject, (BNode, URIRef)): write = self.write indent = " " * depth element_name = "rdf:Description" if isinstance(subject, BNode): write('%s<%s rdf:nodeID="%s"' % ( indent, element_name, subject)) else: uri = quoteattr(self.relativize(subject)) write("%s<%s rdf:about=%s" % (indent, element_name, uri)) if (subject, None, None) in self.store: write(">\n") for predicate, object in self.store.predicate_objects( subject): self.predicate(predicate, object, depth + 1) write("%s</%s>\n" % (indent, element_name)) else: write("/>\n") def predicate(self, predicate, object, depth=1): write = self.write indent = " " * depth qname = self.store.namespace_manager.qname(predicate) if isinstance(object, Literal): attributes = "" if object.language: attributes += ' xml:lang="%s"' % object.language if object.datatype: attributes += ' rdf:datatype="%s"' % object.datatype write("%s<%s%s>%s</%s>\n" % (indent, qname, attributes, escape(object, ESCAPE_ENTITIES), qname)) else: if isinstance(object, BNode): write('%s<%s rdf:nodeID="%s"/>\n' % (indent, qname, object)) else: write("%s<%s rdf:resource=%s/>\n" % (indent, qname, quoteattr(self.relativize(object)))) XMLLANG = "http://www.w3.org/XML/1998/namespacelang" XMLBASE = "http://www.w3.org/XML/1998/namespacebase" OWL_NS = Namespace('http://www.w3.org/2002/07/owl#') # TODO: def fix(val): "strip off _: from nodeIDs... as they are not valid NCNames" if val.startswith("_:"): return val[2:] else: return val class PrettyXMLSerializer(Serializer): def __init__(self, store, max_depth=3): super(PrettyXMLSerializer, self).__init__(store) self.forceRDFAbout = set() def serialize(self, stream, base=None, encoding=None, **args): self.__serialized = {} store = self.store self.base = base self.max_depth = args.get("max_depth", 3) assert self.max_depth > 0, "max_depth must be greater than 0" self.nm = nm = store.namespace_manager self.writer = writer = XMLWriter(stream, nm, encoding) namespaces = {} possible = set(store.predicates()).union( store.objects(None, RDF.type)) for predicate in possible: prefix, namespace, local = nm.compute_qname(predicate) namespaces[prefix] = namespace namespaces["rdf"] = "http://www.w3.org/1999/02/22-rdf-syntax-ns#" writer.push(RDF.RDF) if "xml_base" in args: writer.attribute(XMLBASE, args["xml_base"]) writer.namespaces(iter(namespaces.items())) # Write out subjects that can not be inline for subject in store.subjects(): if (None, None, subject) in store: if (subject, None, subject) in store: self.subject(subject, 1) else: self.subject(subject, 1) # write out anything that has not yet been reached # write out BNodes last (to ensure they can be inlined where possible) bnodes = set() for subject in store.subjects(): if isinstance(subject, BNode): bnodes.add(subject) continue self.subject(subject, 1) # now serialize only those BNodes that have not been serialized yet for bnode in bnodes: if bnode not in self.__serialized: self.subject(subject, 1) writer.pop(RDF.RDF) stream.write(b("\n")) # Set to None so that the memory can get garbage collected. self.__serialized = None def subject(self, subject, depth=1): store = self.store writer = self.writer if subject in self.forceRDFAbout: writer.push(RDF.Description) writer.attribute(RDF.about, self.relativize(subject)) writer.pop(RDF.Description) self.forceRDFAbout.remove(subject) elif not subject in self.__serialized: self.__serialized[subject] = 1 type = first(store.objects(subject, RDF.type)) try: self.nm.qname(type) except: type = None element = type or RDF.Description writer.push(element) if isinstance(subject, BNode): def subj_as_obj_more_than(ceil): return True # more_than(store.triples((None, None, subject)), ceil) # here we only include BNode labels if they are referenced # more than once (this reduces the use of redundant BNode # identifiers) if subj_as_obj_more_than(1): writer.attribute(RDF.nodeID, fix(subject)) else: writer.attribute(RDF.about, self.relativize(subject)) if (subject, None, None) in store: for predicate, object in store.predicate_objects(subject): if not (predicate == RDF.type and object == type): self.predicate(predicate, object, depth + 1) writer.pop(element) elif subject in self.forceRDFAbout: writer.push(RDF.Description) writer.attribute(RDF.about, self.relativize(subject)) writer.pop(RDF.Description) self.forceRDFAbout.remove(subject) def predicate(self, predicate, object, depth=1): writer = self.writer store = self.store writer.push(predicate) if isinstance(object, Literal): if object.language: writer.attribute(XMLLANG, object.language) if (object.datatype == RDF.XMLLiteral and isinstance(object.value, xml.dom.minidom.Document)): writer.attribute(RDF.parseType, "Literal") writer.text("") writer.stream.write(object) else: if object.datatype: writer.attribute(RDF.datatype, object.datatype) writer.text(object) elif object in self.__serialized or not (object, None, None) in store: if isinstance(object, BNode): if more_than(store.triples((None, None, object)), 0): writer.attribute(RDF.nodeID, fix(object)) else: writer.attribute(RDF.resource, self.relativize(object)) else: if first(store.objects(object, RDF.first)): # may not have type # RDF.List self.__serialized[object] = 1 # Warn that any assertions on object other than # RDF.first and RDF.rest are ignored... including RDF.List import warnings warnings.warn( "Assertions on %s other than RDF.first " % repr(object) + "and RDF.rest are ignored ... including RDF.List", UserWarning, stacklevel=2) writer.attribute(RDF.parseType, "Collection") col = Collection(store, object) for item in col: if isinstance(item, URIRef): self.forceRDFAbout.add(item) self.subject(item) if not isinstance(item, URIRef): self.__serialized[item] = 1 else: if first(store.triples_choices( (object, RDF.type, [OWL_NS.Class, RDFS.Class]))) \ and isinstance(object, URIRef): writer.attribute(RDF.resource, self.relativize(object)) elif depth <= self.max_depth: self.subject(object, depth + 1) elif isinstance(object, BNode): if not object in self.__serialized \ and (object, None, None) in store \ and len(list(store.subjects(object=object))) == 1: # inline blank nodes if they haven't been serialized yet # and are only referenced once (regardless of depth) self.subject(object, depth + 1) else: writer.attribute(RDF.nodeID, fix(object)) else: writer.attribute(RDF.resource, self.relativize(object)) writer.pop(predicate)