diff --git a/.gitignore b/.gitignore index 539527e..eeae3c2 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,4 @@ owlrl*.tar.gz # Mac .DS_Store +/.venv/ \ No newline at end of file diff --git a/README.rst b/README.rst index 68d187d..7c9831e 100644 --- a/README.rst +++ b/README.rst @@ -27,7 +27,7 @@ This package is a Python library that also contains a couple of scripts: Installation ------------ -This package requires RDFLib 7.1.3 as its only dependency and it can be installed from the Python Package index in the usual way: +This package requires RDFLib 7.5.0 or newer. It can be installed from the Python Package index in the usual way: :: @@ -40,6 +40,10 @@ or poetry add owlrl +Optional: run the closure against an `Oxigraph `_ in-memory store by installing the extra:: + + pip install owlrl[oxigraph] + Use --- @@ -54,6 +58,14 @@ For details on RDFS, see the `RDF Semantics Specification`_; for OWL 2 RL, see t View the **OWL-RL documentation** online: http://owl-rl.readthedocs.io/ +Oxigraph store (optional) +~~~~~~~~~~~~~~~~~~~~~~~~~ + +After installing the ``oxigraph`` extra (see **Installation** above), you may pass a `PyOxigraph `_ ``Store`` into ``owlrl.DeductiveClosure(...).expand(...)`` and related closure entry points wherever you would normally pass an RDFLib ``Graph`` or ``Dataset``. Inferred triples can still be written to a separate named graph on that store via the ``destination`` argument, as with RDFLib. + +This integration is provided for **compatibility** (for example, keeping the rest of an application on Oxigraph) rather than for speed. Converting terms to and from RDFLib objects removes most of the performance benefit of Oxigraph, and this project still uses RDFLib types and logic internally for all inference steps. + + License ------- This software is released under the W3C© SOFTWARE NOTICE AND LICENSE. See `LICENSE.txt `_. diff --git a/owlrl/AxiomaticTriples.py b/owlrl/AxiomaticTriples.py index 5eeec22..2114151 100755 --- a/owlrl/AxiomaticTriples.py +++ b/owlrl/AxiomaticTriples.py @@ -3,7 +3,7 @@ """ Axiomatic triples to be (possibly) added to the final graph. -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/Closure.py b/owlrl/Closure.py index 414b75c..c65a0b6 100755 --- a/owlrl/Closure.py +++ b/owlrl/Closure.py @@ -3,7 +3,7 @@ """ The generic superclasses for various rule based semantics and the possible extensions. -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib @@ -25,11 +25,13 @@ __contact__ = "Ivan Herman, ivan@w3.org" __license__ = "W3C® SOFTWARE NOTICE AND LICENSE, http://www.w3.org/Consortium/Legal/2002/copyright-software-20021231" -from typing import Union +from typing import Union, Any import rdflib from rdflib.namespace import RDF from rdflib import BNode, Literal, Graph, Dataset + +from owlrl.graph_abstraction import DataGraph from .Namespaces import ERRNS try: @@ -91,59 +93,73 @@ class Core: """ # noinspection PyUnusedLocal - def __init__(self, graph: Graph, axioms, daxioms, rdfs: bool = False, destination: Union[None, Graph] = None): + def __init__(self, graph: Union[DataGraph,Graph,Any], axioms, daxioms, rdfs: bool = False, destination: Union[DataGraph,Graph,Any] = None): """ The parameter descriptions here are from the old documentation. @param graph: the RDF graph to be extended - @type graph: Graph + @type graph: DataGraph @param axioms: whether axioms should be added or not @type axioms: boolean @param daxioms: whether datatype axioms should be added or not @type daxioms: boolean @param rdfs: whether RDFS inference is also done (used in subclassed only) @type rdfs: boolean - @param destination: the destination graph to which the results are written. If None, use the source graph. - @type destination: Graph + @param destination: the destination graph to which the results are written. If None, use the source datagraph. + @type destination: DataGraph """ self._debug = debugGlobal - # Calculate the maximum 'n' value for the '_i' type predicates (see Horst's paper) - n = 1 - maxnum = 0 - cont = True - while cont: - cont = False - predicate = RDF[("_%d" % n)] - for (s, p, o) in graph.triples((None, predicate, None)): - # there is at least one if we got here - maxnum = n - n += 1 - cont = True - self.IMaxNum = maxnum + if isinstance(graph, (Dataset, ConjunctiveGraph)): + graph.default_union = True + + if isinstance(graph, DataGraph): + graph.default_union = True + elif not isinstance(graph, Graph): + # Wrap a RDFlib Graph and Oxigraph Store in a DataGraph abstraction layer + graph = DataGraph(graph) + graph.default_union = True self.graph = graph - if isinstance(self.graph, (Dataset, ConjunctiveGraph)): - self.graph.default_union = True if destination is None: if isinstance(graph, (Dataset, ConjunctiveGraph)): self.destination = graph.default_context else: self.destination = graph + elif isinstance(destination, DataGraph): + self.destination = destination else: if isinstance(destination, (str, rdflib.URIRef)): - if isinstance(graph, (Dataset, ConjunctiveGraph)): + if isinstance(graph, (Dataset, ConjunctiveGraph, DataGraph)): self.destination = graph.get_context(destination) else: - raise ValueError("URIRef destinations are only supported for Datasets and ConjunctiveGraphs") + raise ValueError( + "URIRef or string destinations are only supported for Dataset, " + "ConjunctiveGraph, or Oxigraph/DataGraph instances" + ) else: + # destination is a rdflib Graph source_store = self.graph.store dest_store = destination.store if source_store is not dest_store: - raise ValueError("The source and destination graphs share the same backing store") + raise ValueError("The source and destination graphs must share the same backing store") self.destination = destination + # Calculate the maximum 'n' value for the '_i' type predicates (see Horst's paper) + n = 1 + maxnum = 0 + cont = True + while cont: + cont = False + predicate = RDF[("_%d" % n)] + for (s, p, o) in graph.triples((None, predicate, None)): + # there is at least one if we got here + maxnum = n + n += 1 + cont = True + self.IMaxNum = maxnum + self.axioms = axioms self.daxioms = daxioms diff --git a/owlrl/CombinedClosure.py b/owlrl/CombinedClosure.py index 9ea95c9..6b66102 100755 --- a/owlrl/CombinedClosure.py +++ b/owlrl/CombinedClosure.py @@ -7,7 +7,7 @@ triples concerning the container membership properties). Using this closure class the OWL 2 RL implementation becomes a full extension of RDFS. -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/DatatypeHandling.py b/owlrl/DatatypeHandling.py index 765396c..72898e2 100755 --- a/owlrl/DatatypeHandling.py +++ b/owlrl/DatatypeHandling.py @@ -11,7 +11,7 @@ python datatype (or return the original string if this is not possible) which will be used, e.g., for comparisons (equalities). If the lexical value constraints are not met, exceptions are raised. -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/OWLRL.py b/owlrl/OWLRL.py index 33f1b63..5bdaa65 100755 --- a/owlrl/OWLRL.py +++ b/owlrl/OWLRL.py @@ -9,7 +9,7 @@ removed from the graph before serialization to produce 'standard' RDF (which is o.k. for RL, too, because the consequent triples are all right, generalized triples might have had a role in the deduction steps only). -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/OWLRLExtras.py b/owlrl/OWLRLExtras.py index ebb2b7e..6bc3580 100755 --- a/owlrl/OWLRLExtras.py +++ b/owlrl/OWLRLExtras.py @@ -17,7 +17,7 @@ 1. self restriction 1: :code:`?z owl:hasSelf ?x. ?x owl:onProperty ?p. ?y rdf:type ?z. => ?y ?p ?y.` 2. self restriction 2: :code:`?z owl:hasSelf ?x. ?x owl:onProperty ?p. ?y ?p ?y. => ?y rdf:type ?z.` -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/RDFSClosure.py b/owlrl/RDFSClosure.py index c3020b8..e275be7 100755 --- a/owlrl/RDFSClosure.py +++ b/owlrl/RDFSClosure.py @@ -5,7 +5,7 @@ introductory text). -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/RestrictedDatatype.py b/owlrl/RestrictedDatatype.py index 9b921df..84cd280 100644 --- a/owlrl/RestrictedDatatype.py +++ b/owlrl/RestrictedDatatype.py @@ -33,7 +33,7 @@ - checking whether a facet is of a datatype that is allowed for that facet - handling of non-literals in the facets (ie, if the resource is defined to be of type literal, but whose value is defined via a separate :code:`owl:sameAs` somewhere else) -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/XsdDatatypes.py b/owlrl/XsdDatatypes.py index adb4a9a..36e36c7 100755 --- a/owlrl/XsdDatatypes.py +++ b/owlrl/XsdDatatypes.py @@ -3,7 +3,7 @@ """ Lists of XSD datatypes and their mutual relationships -**Requires**: `RDFLib`_, 4.0.0 and higher. +**Requires**: `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib diff --git a/owlrl/__init__.py b/owlrl/__init__.py index 3d41d12..7e95ac0 100755 --- a/owlrl/__init__.py +++ b/owlrl/__init__.py @@ -132,13 +132,13 @@ **Requires**: - * `RDFLib`_, 4.0.0 and higher. + * `RDFLib`_, 7.5.0 and higher. .. _RDFLib: https://github.com/RDFLib/rdflib - * `rdflib_jsonld`_ + * Optional: `PyOxigraph`_ (install with ``pip install owlrl[oxigraph]``) to use an Oxigraph store as the graph backend. - .. _rdflib_jsonld: https://github.com/RDFLib/rdflib-jsonld + .. _PyOxigraph: https://pyoxigraph.readthedocs.io/ **License**: This software is available for use under the `W3C Software License`_ @@ -155,7 +155,7 @@ """ # Examples: LangString is disjoint from String -__version__ = "7.1.4" +__version__ = "7.5.0" __author__ = "Ivan Herman" __contact__ = "Ivan Herman, ivan@w3.org" __license__ = "W3C® SOFTWARE NOTICE AND LICENSE, http://www.w3.org/Consortium/Legal/2002/copyright-software-20021231" diff --git a/owlrl/graph_abstraction.py b/owlrl/graph_abstraction.py new file mode 100644 index 0000000..6220b63 --- /dev/null +++ b/owlrl/graph_abstraction.py @@ -0,0 +1,612 @@ +try: + from pyoxigraph import ( + Store as ox_Store, + DefaultGraph as ox_DefaultGraph, + Quad as ox_Quad, + Literal as ox_Literal, + BlankNode as ox_BlankNode, + NamedNode as ox_NamedNode, + ) + + has_oxigraph = True +except ImportError: + has_oxigraph = False + ox_Store = None + ox_DefaultGraph = None + ox_Quad = None + ox_Literal = None + ox_BlankNode = None + ox_NamedNode = None + +from collections.abc import Generator +from rdflib import Graph as rdf_Graph, Dataset as rdf_Dataset +from rdflib.term import ( + IdentifiedNode as rdf_IdentifiedNode, + Literal as rdf_Literal, + BNode as rdf_BNode, + URIRef as rdf_URIRef, +) +from rdflib.namespace import RDF +from typing import Union, Any, Tuple +import warnings + +ALLOWED_GRAPH_TYPES = Union[rdf_Graph, rdf_Dataset, ox_Store] + + +class DataGraph: + + is_oxigraph: bool + _default_union: bool + + def __new__( + cls, + store: ALLOWED_GRAPH_TYPES, + locked_context: Union[rdf_Graph, str, None] = None, + ): + self = super().__new__(cls) + self.is_oxigraph = has_oxigraph and isinstance(store, ox_Store) + self.impl = store + + self._default_union = False + if self.is_oxigraph: + self.triples = self.triples_in_oxigraph + self.add = self.add_to_oxigraph + self.remove = self.remove_from_oxigraph + self.subject_objects = self.subject_objects_in_oxigraph + self.subjects = self.subjects_in_oxigraph + self.objects = self.objects_in_oxigraph + self.predicate_objects = self.predicate_objects_in_oxigraph + self.subject_predicates = self.subject_predicates_in_oxigraph + if isinstance(locked_context, rdf_Graph): + self.locked_context = ox_NamedNode(locked_context.identifier) + elif isinstance(locked_context, str): + self.locked_context = ox_NamedNode(locked_context) + else: + self.locked_context = None + else: + self.triples = self.triples_in_rdflib + self.add = self.add_to_rdflib + self.remove = self.remove_from_rdflib + self.subject_objects = self.subject_objects_in_rdflib + self.subjects = self.subjects_in_rdflib + self.objects = self.objects_in_rdflib + self.predicate_objects = self.predicate_objects_in_rdflib + self.subject_predicates = self.subject_predicates_in_rdflib + if isinstance(locked_context, rdf_Graph): + self.locked_context = locked_context + elif isinstance(locked_context, str): + self.locked_context = self.impl.get_context(rdf_URIRef(locked_context)) + else: + self.locked_context = None + return self + + @classmethod + def convert_triple_to_oxigraph( + cls, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal, None], + Union[rdf_IdentifiedNode, None], + Union[rdf_Literal, rdf_IdentifiedNode, None], + ], + ): + in_s, in_p, in_o = triple + + if in_s is None: + out_s = None + elif isinstance(in_s, rdf_BNode): + out_s = ox_BlankNode(str(in_s)) + elif isinstance(in_s, rdf_Literal): + data_type = in_s.datatype + if data_type is not None: + data_type = ox_NamedNode(str(data_type)) + out_s = ox_Literal(in_s.value, datatype=data_type, language=in_s.language) + else: + out_s = ox_NamedNode(str(in_s)) + if in_p is None: + out_p = None + elif isinstance(in_p, rdf_BNode): + out_p = ox_BlankNode(str(in_p)) + else: + out_p = ox_NamedNode(str(in_p)) + if in_o is None: + out_o = None + elif isinstance(in_o, rdf_BNode): + out_o = ox_BlankNode(str(in_o)) + elif isinstance(in_o, rdf_Literal): + data_type = in_o.datatype + if data_type is not None: + data_type = ox_NamedNode(str(data_type)) + out_o = ox_Literal(in_o.value, datatype=data_type, language=in_o.language) + else: + out_o = ox_NamedNode(str(in_o)) + return out_s, out_p, out_o + + @classmethod + def to_ox( + cls, term: Union[rdf_IdentifiedNode, rdf_Literal, None] + ) -> Union[ox_NamedNode, ox_BlankNode, ox_Literal, None]: + if term is None: + return None + elif isinstance(term, rdf_BNode): + return ox_BlankNode(str(term)) + elif isinstance(term, rdf_Literal): + data_type = term.datatype + if data_type is not None: + data_type = ox_NamedNode(str(data_type)) + return ox_Literal(term.value, datatype=data_type, language=term.language) + else: + return ox_NamedNode(str(term)) + + @classmethod + def to_rdf( + cls, term: Union[ox_NamedNode, ox_BlankNode, ox_Literal, None] + ) -> Union[rdf_IdentifiedNode, rdf_Literal, None]: + if term is None: + return None + elif isinstance(term, ox_BlankNode): + return rdf_BNode(term.value) + elif isinstance(term, ox_Literal): + data_type = term.datatype + if data_type is not None: + data_type = rdf_URIRef(data_type.value) + return rdf_Literal(term.value, datatype=data_type, language=term.language) + else: + return rdf_URIRef(term.value) + + @classmethod + def convert_quad_to_rdflib(cls, quad: ox_Quad): + s, p, o, g = quad + if s is None: + out_s = None + elif isinstance(s, ox_BlankNode): + out_s = rdf_BNode(s.value) + elif isinstance(s, ox_Literal): + # Technically a subject can never be a Literal + # in Oxigraph, but this is here for completeness + data_type = s.datatype + if data_type is not None: + data_type = rdf_URIRef(data_type.value) + out_s = rdf_Literal(s.value, datatype=data_type, language=s.language) + else: + out_s = rdf_URIRef(s.value) + if p is None: + out_p = None + elif isinstance(p, ox_BlankNode): + out_p = rdf_BNode(p.value) + else: + out_p = rdf_URIRef(p.value) + if o is None: + out_o = None + elif isinstance(o, ox_Literal): + data_type = o.datatype + if data_type is not None: + data_type = rdf_URIRef(data_type.value) + out_o = rdf_Literal(o.value, datatype=data_type, language=o.language) + elif isinstance(o, ox_BlankNode): + out_o = rdf_BNode(o.value) + else: + out_o = rdf_URIRef(o.value) + if g is None: + out_g = None + elif isinstance(g, ox_DefaultGraph): + out_g = None + else: + out_g = rdf_URIRef(g.value) + return out_s, out_p, out_o, out_g + + @property + def default_union(self) -> bool: + return self._default_union + + @property + def store(self) -> Any: + if self.is_oxigraph: + return self.impl + else: + return self.impl.store + + @default_union.setter + def default_union(self, value: bool): + self._default_union = value + if self.is_oxigraph: + pass + elif isinstance(self.impl, rdf_Dataset): + self.impl.default_union = value + + def add_to_oxigraph( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_Literal, rdf_IdentifiedNode], + ], + ): + if isinstance(triple[1], rdf_BNode) or isinstance(triple[1], rdf_Literal): + # Oxigraph does not support BNode or Literal in the predicate position + # Cannot add the triple + warnings.warn( + "OWL-RL inferencer tried to add a triple with a BNode or Literal in the predicate position", + ) + return + if isinstance(triple[0], rdf_Literal): + # Oxigraph does not support Literal in the subject position + # Cannot add the triple + warnings.warn( + "OWL-RL inferencer tried to add a triple with a Literal in the subject position", + ) + return + ox_s, ox_p, ox_o = self.convert_triple_to_oxigraph(triple) + if self.locked_context is not None: + ox_g = self.locked_context + else: + ox_g = None + return self.impl.add(ox_Quad(ox_s, ox_p, ox_o, ox_g)) + + def remove_from_oxigraph( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_Literal, rdf_IdentifiedNode], + ], + ): + ox_triples = self.convert_triple_to_oxigraph(triple) + if isinstance(ox_triples[1], ox_BlankNode) or isinstance( + ox_triples[1], ox_Literal + ): + return + if isinstance(ox_triples[0], ox_Literal): + return + if self.locked_context is not None: + to_remove = list( + self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], self.locked_context + ) + ) + elif self._default_union: + to_remove = list( + self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], None + ) + ) + else: + to_remove = list( + self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], ox_DefaultGraph() + ) + ) + for q in to_remove: + self.impl.remove(q) + + def triples_in_oxigraph( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal, None], + Union[rdf_IdentifiedNode, None], + Union[rdf_IdentifiedNode, rdf_Literal, None], + ], + ) -> Generator[ + Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_IdentifiedNode, rdf_Literal], + ], + None, + None, + ]: + ox_triples = self.convert_triple_to_oxigraph(triple) + if isinstance(ox_triples[1], ox_BlankNode) or isinstance( + ox_triples[1], ox_Literal + ): + # Oxigraph does not support BNode or Literal in the predicate position + # Cannot yield any results + return + if isinstance(ox_triples[0], ox_Literal): + # Oxigraph does not support Literal in the subject position + # Cannot yield any results + return + if self.locked_context is not None: + for q in self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], self.locked_context + ): + yield self.convert_quad_to_rdflib(q)[:3] + elif self._default_union: + for q in self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], None + ): + yield self.convert_quad_to_rdflib(q)[:3] + else: + default_graph = ox_DefaultGraph() + for q in self.impl.quads_for_pattern( + ox_triples[0], ox_triples[1], ox_triples[2], default_graph + ): + yield self.convert_quad_to_rdflib(q)[:3] + + def subject_objects_in_oxigraph( + self, predicate: Union[rdf_IdentifiedNode, None] + ) -> Generator[ + Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + Union[rdf_IdentifiedNode, rdf_Literal], + ], + None, + None, + ]: + if isinstance(predicate, rdf_BNode) or isinstance(predicate, rdf_Literal): + # Oxigraph does not support BNode or Literal in the predicate position + # Cannot yield any results + return + _p = self.to_ox(predicate) + if self.locked_context is not None: + for q in self.impl.quads_for_pattern(None, _p, None, self.locked_context): + s, _, o, _ = self.convert_quad_to_rdflib(q) + yield s, o + elif self._default_union: + for q in self.impl.quads_for_pattern(None, _p, None, None): + s, _, o, _ = self.convert_quad_to_rdflib(q) + yield s, o + else: + for q in self.impl.quads_for_pattern(None, _p, None, ox_DefaultGraph()): + s, _, o, _ = self.convert_quad_to_rdflib(q) + yield s, o + + def subject_predicates_in_oxigraph( + self, object_: Union[rdf_IdentifiedNode, rdf_Literal, None] + ) -> Generator[ + Tuple[Union[rdf_IdentifiedNode, rdf_Literal], rdf_IdentifiedNode], None, None + ]: + _o = self.to_ox(object_) + if self.locked_context is not None: + for q in self.impl.quads_for_pattern(None, None, _o, self.locked_context): + s, p, _, _ = self.convert_quad_to_rdflib(q) + yield s, p + elif self._default_union: + for q in self.impl.quads_for_pattern(None, None, _o, None): + s, p, _, _ = self.convert_quad_to_rdflib(q) + yield s, p + else: + for q in self.impl.quads_for_pattern(None, None, _o, ox_DefaultGraph()): + s, p, _, _ = self.convert_quad_to_rdflib(q) + yield s, p + + def predicate_objects_in_oxigraph( + self, subject: Union[rdf_IdentifiedNode, rdf_Literal, None] + ) -> Generator[ + Tuple[rdf_IdentifiedNode, Union[rdf_IdentifiedNode, rdf_Literal]], None, None + ]: + _s = self.to_ox(subject) + if self.locked_context is not None: + for q in self.impl.quads_for_pattern(_s, None, None, self.locked_context): + _, p, o, _ = self.convert_quad_to_rdflib(q) + yield p, o + elif self._default_union: + for q in self.impl.quads_for_pattern(_s, None, None, None): + _, p, o, _ = self.convert_quad_to_rdflib(q) + yield p, o + else: + for q in self.impl.quads_for_pattern(_s, None, None, ox_DefaultGraph()): + _, p, o, _ = self.convert_quad_to_rdflib(q) + yield p, o + + def subjects_in_oxigraph( + self, + predicate: rdf_IdentifiedNode, + object_: Union[rdf_IdentifiedNode, rdf_Literal, None], + ) -> Generator[Union[rdf_IdentifiedNode, rdf_Literal], None, None]: + _p = self.to_ox(predicate) + _o = self.to_ox(object_) + if self.locked_context is not None: + for s, _, _, _ in self.impl.quads_for_pattern( + None, _p, _o, self.locked_context + ): + yield self.to_rdf(s) + elif self._default_union: + for s, _, _, _ in self.impl.quads_for_pattern(None, _p, _o, None): + yield self.to_rdf(s) + else: + for s, _, _, _ in self.impl.quads_for_pattern( + None, _p, _o, ox_DefaultGraph() + ): + yield self.to_rdf(s) + + def objects_in_oxigraph( + self, + subject: Union[rdf_IdentifiedNode, rdf_Literal], + predicate: Union[rdf_IdentifiedNode, None], + ) -> Generator[Union[rdf_IdentifiedNode, rdf_Literal], None, None]: + _s = self.to_ox(subject) + _p = self.to_ox(predicate) + if self.locked_context is not None: + for _, _, o, _ in self.impl.quads_for_pattern( + _s, _p, None, self.locked_context + ): + yield self.to_rdf(o) + elif self._default_union: + for _, _, o, _ in self.impl.quads_for_pattern(_s, _p, None, None): + yield self.to_rdf(o) + else: + for _, _, o, _ in self.impl.quads_for_pattern( + _s, _p, None, ox_DefaultGraph() + ): + yield self.to_rdf(o) + + def add_to_rdflib( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_Literal, rdf_IdentifiedNode], + ], + ): + if self.locked_context is not None: + return self.impl.add((triple[0], triple[1], triple[2], self.locked_context)) + else: + return self.impl.add((triple[0], triple[1], triple[2])) + + def remove_from_rdflib( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_Literal, rdf_IdentifiedNode], + ], + ): + if self.locked_context is not None: + return self.impl.remove( + (triple[0], triple[1], triple[2], self.locked_context) + ) + else: + return self.impl.remove((triple[0], triple[1], triple[2])) + + def triples_in_rdflib( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal, None], + Union[rdf_IdentifiedNode, None], + Union[rdf_IdentifiedNode, rdf_Literal, None], + ], + ) -> Generator[ + Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal], + rdf_IdentifiedNode, + Union[rdf_IdentifiedNode, rdf_Literal], + ], + None, + None, + ]: + if self.locked_context is not None: + for t in self.impl.triples(triple, context=self.locked_context): + yield t + else: + for t in self.impl.triples(triple): + yield t + + def subject_objects_in_rdflib( + self, predicate: Union[rdf_IdentifiedNode, None] + ) -> Generator[tuple, None, None]: + if self.locked_context is not None: + for t in self.impl.subject_objects(predicate, context=self.locked_context): + yield t + else: + for t in self.impl.subject_objects(predicate): + yield t + + def subject_predicates_in_rdflib( + self, object_: Union[rdf_IdentifiedNode, rdf_Literal, None] + ) -> Generator[Any, None, None]: + if self.locked_context is not None: + for t in self.impl.subject_predicates(object_, context=self.locked_context): + yield t + else: + for t in self.impl.subject_predicates(object_): + yield t + + def predicate_objects_in_rdflib( + self, subject: Union[rdf_IdentifiedNode, rdf_Literal, None] + ) -> Generator[tuple, None, None]: + if self.locked_context is not None: + for t in self.impl.predicate_objects(subject, context=self.locked_context): + yield t + else: + for t in self.impl.predicate_objects(subject): + yield t + + def subjects_in_rdflib( + self, + predicate: rdf_IdentifiedNode, + object_: Union[rdf_IdentifiedNode, rdf_Literal, None], + ) -> Generator[rdf_IdentifiedNode, None, None]: + if self.locked_context is not None: + for t in self.impl.subjects( + predicate, object_, context=self.locked_context + ): + yield t + else: + for t in self.impl.subjects(predicate, object_): + yield t + + def objects_in_rdflib( + self, + subject: Union[rdf_IdentifiedNode, rdf_Literal], + predicate: Union[rdf_IdentifiedNode, None], + ) -> Generator[Union[rdf_IdentifiedNode, rdf_Literal], None, None]: + if self.locked_context is not None: + for t in self.impl.objects(subject, predicate, context=self.locked_context): + yield t + else: + for t in self.impl.objects(subject, predicate): + yield t + + def get_context(self, identifier: Union[rdf_URIRef, str]) -> "DataGraph": + if self.is_oxigraph: + return DataGraph(self.impl, str(identifier)) + else: + return DataGraph(self.impl, self.impl.get_context(rdf_URIRef(identifier))) + + def __contains__( + self, + triple: Tuple[ + Union[rdf_IdentifiedNode, rdf_Literal, None], + Union[rdf_IdentifiedNode, None], + Union[rdf_IdentifiedNode, rdf_Literal, None], + ], + ) -> bool: + if self.is_oxigraph: + triple_ = self.convert_triple_to_oxigraph(triple) + if self.locked_context is not None: + quad = ox_Quad(triple_[0], triple_[1], triple_[2], self.locked_context) + elif self._default_union: + quad = ox_Quad(triple_[0], triple_[1], triple_[2], None) + else: + quad = ox_Quad(triple_[0], triple_[1], triple_[2], ox_DefaultGraph()) + return quad in self.impl + else: + if self.locked_context is not None: + quad = (triple[0], triple[1], triple[2], self.locked_context) + return quad in self.impl + else: + return triple in self.impl + + def items( + self, list_: rdf_IdentifiedNode + ) -> Generator[Union[rdf_IdentifiedNode, rdf_Literal], None, None]: + """Generator over all items in the resource specified by list + + Args: + list: An RDF collection. + """ + if not self.is_oxigraph: + for i in self.impl.items(list_): + yield i + return + if isinstance(list_, rdf_URIRef): + next_list = ox_NamedNode(str(list_)) + elif isinstance(list_, rdf_BNode): + next_list = ox_BlankNode(str(list_)) + else: + raise ValueError("List must be a URIRef, or BNode") + chain = set[ox_NamedNode]([next_list]) + FIRST = ox_NamedNode(RDF.first) + REST = ox_NamedNode(RDF.rest) + while next_list: + firsts = list(self.impl.quads_for_pattern(next_list, FIRST, None, None)) + if len(firsts) == 0: + item = None + else: + item = firsts[0][2] + if item is not None: + yield self.to_rdf(item) + rests = list(self.impl.quads_for_pattern(next_list, REST, None, None)) + if len(rests) == 0: + next_list = None + else: + next_list = rests[0][2] + if next_list in chain: + raise ValueError("List contains a recursive rdf:rest reference") + chain.add(next_list) + + def bind(self, prefix: str, namespace: str, **kwargs) -> None: + if self.is_oxigraph: + pass + else: + self.impl.bind(prefix, namespace, **kwargs) diff --git a/poetry.lock b/poetry.lock index bf0425c..ac191c5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,27 +1,27 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.3.3 and should not be changed by hand. 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"more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] type = ["pytest-mypy"] +[extras] +oxigraph = ["pyoxigraph"] + [metadata] lock-version = "2.1" -python-versions = ">=3.9,<4.0" -content-hash = "21295d04cc780525e82f6de98a984a56dd82468e1754440dca99c058ce44bbdc" +python-versions = ">=3.9" +content-hash = "5068558e59a3146375c3a85fc15f1128dcb27000890ca7140e2465ce86f0b08f" diff --git a/pyproject.toml b/pyproject.toml index 28a6fc5..35f861f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,15 +1,32 @@ -[tool.poetry] +[project] name = "owlrl" -version = "7.1.4" +version = "7.5.0" description = "A simple implementation of the OWL2 RL Profile, as well as a basic RDFS inference, on top of RDFLib. Based mechanical forward chaining." -authors = ["Nicholas Car "] -license = "W3C software and Document Notice License" +authors = [ + {name="Nicholas Car", email="nick@kurrawong.ai"}, + {name="Ashley Sommer", email="ashleysommer@gmail.com"} +] +license = "W3C-20150513" readme = "README.rst" -packages = [{include = "owlrl"}] +requires-python = ">=3.9" +dependencies = [ + "rdflib>=7.5.0", +] + +[project.urls] +homepage = "https://github.com/RDFLib/OWL-RL" +source = "https://github.com/RDFLib/OWL-RL" +issues = "https://github.com/RDFLib/OWL-RL/issues" +download = "https://github.com/RDFLib/OWL-RL/releases" -[tool.poetry.dependencies] -python = ">=3.9,<4.0" -rdflib = ">=7.1.4" +[project.optional-dependencies] +# These are equivalent to python package "extras" +oxigraph = [ + "pyoxigraph>=0.5.6" +] + +[tool.poetry] +packages = [{include = "owlrl"}] [tool.poetry.group.dev.dependencies] black = "24.4.2" @@ -17,5 +34,5 @@ sphinx = ">=7.1.2,<8" pytest = ">=7.1.3,<9.0.0" [build-system] -requires = ["poetry-core"] +requires = ["poetry-core>=2.0"] build-backend = "poetry.core.masonry.api" diff --git a/setup.py b/setup.py index 665832e..65dc981 100755 --- a/setup.py +++ b/setup.py @@ -70,11 +70,10 @@ def open_local(paths, mode="r", encoding="utf8"): "Natural Language :: English", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: Implementation :: CPython", "Programming Language :: Python :: Implementation :: PyPy", diff --git a/test/test_dataset_oxigraph.py b/test/test_dataset_oxigraph.py new file mode 100644 index 0000000..51369b5 --- /dev/null +++ b/test/test_dataset_oxigraph.py @@ -0,0 +1,84 @@ +from rdflib import Namespace, URIRef +from rdflib.namespace import RDF +import sys +from pathlib import Path + +import pytest + +pytest.importorskip("pyoxigraph") +from pyoxigraph import Store, DefaultGraph, NamedNode, RdfFormat + + +sys.path.append(str(Path(__file__).parent.parent)) +import owlrl + +RELS = Namespace("http://example.org/relatives#") + + +def test_dataset(): + # create an RDF graph, load a simple OWL ontology and data + s = Store() + try: + s.bulk_load(None, path="relatives.ttl", format=RdfFormat.TURTLE) + except FileNotFoundError: + # This test might be run from the parent directory root + s.bulk_load(None, path="test/relatives.ttl", format=RdfFormat.TURTLE) + + # count no. rels:Person class instances, no inferencing, should find 14 results (one Child) + cnt = 0 + + + person_instances = s.quads_for_pattern(None, NamedNode(RDF.type), NamedNode(RELS.Person), None) + for _ in person_instances: + cnt += 1 + + assert cnt == 14 + + + dest_uri = NamedNode("urn:test:dest") + # count no. of hasGrandparent predicates, no inferencing, should find 0 results + cnt = 0 + has_grandparent_predicates = s.quads_for_pattern(None, NamedNode(RELS.hasGrandparent), None, dest_uri) + for _ in has_grandparent_predicates: + cnt += 1 + assert cnt == 0 + + # expand the graph with OWL-RL semantics + owlrl.DeductiveClosure(owlrl.OWLRL_Semantics).expand(s, destination=URIRef("urn:test:dest")) + + # count no. rels:Person class instances, after inferencing, should find 1 result in the Dest graph + cnt = 0 + has_person_instances = s.quads_for_pattern(None, NamedNode(RDF.type), NamedNode(RELS.Person), dest_uri) + for _ in has_person_instances: + cnt += 1 + + assert cnt == 1 + + # count no. rels:Person class instances, after inferencing, should find 15 results in the whole dataset + cnt = 0 + has_person_instances = s.quads_for_pattern(None, NamedNode(RDF.type), NamedNode(RELS.Person), None) + for _ in has_person_instances: + cnt += 1 + + assert cnt == 15 + + # count no. of hasGrandparent predicates, after inferencing, should find 7 results in the Dest graph + cnt = 0 + has_grandparent_predicates = s.quads_for_pattern(None, NamedNode(RELS.hasGrandparent), None, dest_uri) + for _ in has_grandparent_predicates: + cnt += 1 + assert cnt == 7 + + # count no. of hasGrandparent predicates, after inferencing, should find 7 results in the whole dataset + cnt = 0 + has_grandparent_predicates = s.quads_for_pattern(None, NamedNode(RELS.hasGrandparent), None, None) + for _ in has_grandparent_predicates: + cnt += 1 + assert cnt == 7 + + # count no. of hasGrandparent predicates, after inferencing, should find 0 results in the default graph + cnt = 0 + has_grandparent_predicates = s.quads_for_pattern(None, NamedNode(RELS.hasGrandparent), None, DefaultGraph()) + for _ in has_grandparent_predicates: + cnt += 1 + assert cnt == 0