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owl2_java_owlapi.pl
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/* -*- Mode: Prolog -*- */
:- module(owl2_java_owlapi,
[
version_info/1,
create_manager/1,
create_factory/2,
create_ontology/3,
build_ontology/1,
build_ontology/3,
save_ontology/3,
create_reasoner/3,
reasoner_classify/1,
reasoner_classify/2,
reasoner_classify/3,
reasoner_classify_using/3,
is_consistent/1,
inconsistent_class/2,
unsatisfiable_class/2,
inferred_axiom/3,
reasoner_nr_subClassOf/4,
reasoner_subClassOf/4,
reasoner_subClassOf/5,
reasoner_equivalent_to/4,
reasoner_individualOf/4,
reasoner_nr_individualOf/4,
reasoner_objectPropertyAssertion/5,
add_axiom/5,
show_java_memory_info/0
]).
:- use_module(library(jpl)).
:- use_module(owl2_model).
:- use_module(owl2_metamodel).
:- multifile owlterm_java/4.
prefix('org.semanticweb.owlapi.model').
nothing('http://www.w3.org/2002/07/owl#Nothing').
version_info(Info) :-
jpl_call('org.semanticweb.owlapi.util.VersionInfo',getVersionInfo,[],VI),
jpl_call(VI,getVersion,[],Info).
atom_javaIRI('owl:Thing',U):-
!,
atom_javaIRI('http://www.w3.org/2002/07/owl#Thing',U).
atom_javaIRI('owl:Nothing',U):-
!,
atom_javaIRI('http://www.w3.org/2002/07/owl#Nothing',U).
atom_javaIRI(X,U):-
sub_atom(X,_,_,_,':'),
!,
jpl_call('org.semanticweb.owlapi.model.IRI',create,[X],U).
atom_javaIRI(X,U):-
ontology(Ont),
!,
concat_atom([Ont,X],'#',X2),
jpl_call('org.semanticweb.owlapi.model.IRI',create,[X2],U).
atom_javaIRI(X,U):-
concat_atom(['http://foo.org',X],'#',X2),
jpl_call('org.semanticweb.owlapi.model.IRI',create,[X2],U).
%% create_manager(?Manager)
create_manager(Manager) :-
jpl_call('org.semanticweb.owlapi.apibinding.OWLManager',createOWLOntologyManager,[],Manager).
require_manager(Manager) :-
var(Manager),
!,
create_manager(Manager).
require_manager(_).
%% create_ontology(?Manager,+Name,?Ont)
% @param Manager - manager instance will be created unless this is ground
create_ontology(Manager,Name,Ont) :-
require_manager(Manager),
atom_javaIRI(Name,IRI),
jpl_call(Manager,createOntology,[IRI],Ont).
%% build_ontology(?Ont)
% create an ontology from the current prolog db
build_ontology(Ont) :-
create_factory(Man,Fac),
build_ontology(Man,Fac,Ont).
%% build_ontology(+Man,+Fac,?Ont)
% create an ontology from the current prolog db
build_ontology(Man,Fac,Ont) :-
require_manager(Man),
( ontology(OntName)
-> true
; OntName='http://example.org'),
create_ontology(Man,OntName,Ont),
forall(axiom(Ax),
add_axiom_noerror(Man,Fac,Ont,Ax,_)),
debug(owl2,'Built ontology',[]).
add_axiom_noerror(Manager,Factory,Ont,Axiom,JAx) :-
debug(owl2,'[[Adding axiom: ~p', [Axiom]),
add_axiom(Manager,Factory,Ont,Axiom,JAx), !,
debug(owl2,' /Added axiom: ~p]]',[Axiom]).
add_axiom_noerror(_Manager,_Factory,_Ont,Axiom,_JAx) :-
print_message(warning, thea(failed(add_axiom(Axiom)))).
build_single_ontology(Man,Fac,OntIRI,Ont) :-
require_manager(Man),
create_ontology(Man,OntIRI,Ont),
forall(ontologyAxiom(OntIRI,Ax),
( debug(owl2,'[[Adding axiom: ~w',[Ax]),
add_axiom(Man,Fac,Ont,Ax,_),
debug(owl2,' /Added axiom: ~w]]',[Ax]))),
debug(owl2,'Built ontology',[]).
:- multifile owl2_io:load_axioms_hook/3.
owl2_io:load_axioms_hook(File,owlapi,Opts) :-
owl2_io:load_axioms_hook(File,owlapi(_),Opts).
owl2_io:load_axioms_hook(File,owlapi(_Fmt),_Opts) :-
create_factory(Man,_Fac),
load_ontology(Man,_Ont,File).
:- multifile owl2_io:save_axioms_hook/3.
owl2_io:save_axioms_hook(File,owlapi,Opts) :-
!,
owl2_io:save_axioms_hook(File,owlapi(''),Opts).
owl2_io:save_axioms_hook(File,owlapi(Fmt),Opts) :-
member(ontology(OntIRI),Opts),
!,
create_factory(Man,Fac),
build_single_ontology(Man,Fac,OntIRI,Ont),
save_ontology(Man,Ont,Fmt,File).
owl2_io:save_axioms_hook(File,owlapi(Fmt),_Opts) :-
create_factory(Man,Fac),
build_ontology(Man,Fac,Ont),
save_ontology(Man,Ont,Fmt,File).
%% load_ontology(+Man,?Ont,+File) is det
% TODO - need to maps java axioms to owlpl axioms
load_ontology(Man,Ont,File) :-
atom_javaIRI(File,IRI),
jpl_call(Man,loadOntologyFromPhysicalIRI,[IRI],Ont).
%% save_ontology(+Man,+Ont,+File) is det
save_ontology(Man,Ont,File) :-
save_ontology(Man,Ont,'',File).
save_ontology(Man,Ont,Fmt,File) :-
( var(File)
-> tmp_file(owl,File),
Tmp=true
; Tmp=fail),
atom_concat('file://',File,FileIRI),
atom_javaIRI(FileIRI,IRI),
fmt_cls(Fmt,FmtCls),
jpl_new(FmtCls,[],FmtObj),
jpl_call(Man,saveOntology,[Ont,FmtObj,IRI],_),
( Tmp
-> sformat(Cmd,'cat ~w',[File]),
shell(Cmd)
; true).
fmt_cls(owlxml,'org.semanticweb.owlapi.io.OWLXMLOntologyFormat') :- !.
fmt_cls(manchester,'org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat') :- !.
fmt_cls(_,'org.semanticweb.owlapi.io.RDFXMLOntologyFormat') :- !.
%% create_factory(?Manager,?Factory) is det
% @param Manager - manager instance will be created unless this is ground
create_factory(Manager,Fac) :-
require_manager(Manager),
jpl_call(Manager,getOWLDataFactory,[],Fac).
%% create_reasoner(?Ont,?Type,?Reasoner) is nondet
% if Type is ground then this predicate is deterministic
% @param Type - factpp or pellet
create_reasoner(Ont,RN,Reasoner) :-
reasoner_factory(RN,RFacClass),
jpl_new(RFacClass,[],RFac),
debug(owl2,'got reasoner factory: ~w',[RFac]),
jpl_call(RFac,createReasoner,[Ont],Reasoner).
reasoner_factory(pellet,'com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory').
reasoner_factory(hermit,'org.semanticweb.HermiT.Reasoner$ReasonerFactory').
reasoner_factory(factpp,'uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory').
% DEPRECATED
reasoner_classify(Reasoner) :-
throw(deprecated('no need to call classify with owlapi v3')),
debug(owl2,'classifying...',[]),
jpl_call(Reasoner,classify,[],_).
% DEPRECATED
reasoner_classify(Reasoner,Ont) :-
throw(deprecated('no need to call classify with owlapi v3')),
reasoner_classify(Reasoner,_Man,Ont).
% DEPRECATED
reasoner_classify(Reasoner,Man,_Ont) :-
throw(deprecated('no need to call classify with owlapi v3')),
require_manager(Man),
%jpl_call(Man,getImportsClosure,[Ont],IC),
%jpl_call(Reasoner,loadOntologies,[IC],_),
reasoner_classify(Reasoner).
% DEPRECATED
reasoner_classify_using(Reasoner,Ont,RN) :-
throw(deprecated('no need to call classify with owlapi v3')),
require_manager(Man),
create_reasoner(Ont,RN,Reasoner),
reasoner_classify(Reasoner,Man,Ont).
is_consistent(Reasoner) :-
jpl_call(Reasoner,isConsistent,[],'@'(true)).
inconsistent_class(Reasoner,Class) :-
jpl_call(Reasoner,getInconsistentClasses,[],JOWLClasses),
member(JOWLClass,JOWLClasses),
java_namedentity(JOWLClass,Class).
unsatisfiable_class(Reasoner,Class) :-
jpl_call(Reasoner,getUnsatisfiableClasses,[],Node),
jpl_call(Node,getEntities,[],ESet),
jpl_call(ESet,toArray,[],EArr),
jpl_array_to_list(EArr,PList),
member(JOWLClass,PList),
java_namedentity(JOWLClass,Class).
java_namedentity(J,C) :-
jpl_call(J,getIRI,[],IRI),
jpl_call(IRI,toString,[],C).
%% nodeset_entity(+NodeSet,?E) is nondet
nodeset_entity(NodeSet,E) :-
jpl_call(NodeSet,'getNodes',[],NodeSetG),
jpl_call(NodeSetG,'toArray',[],NodeArr),
jpl_array_to_list(NodeArr,Nodes),
member(Node,Nodes),
jpl_call(Node,getEntities,[],ESet),
jpl_call(ESet,toArray,[],EArr),
jpl_array_to_list(EArr,Es),
( Es=[JE],
java_namedentity(JE,E)
-> true
; Es=[]
-> fail
; maplist(java_namedentity,Es,PEs),
E=equivalentClasses(PEs)).
%% ecsets_class(+JPSetSet,?P) is nondet
% Set<Set<OWLClass>> --> class expression
% class expression will be
% equivalentClasses(ECL) |
% other class expression
ecsets_class(JPSetSet,P) :-
jpl_call(JPSetSet,toArray,[],JPSetArr),
jpl_array_to_list(JPSetArr,JPSets),
member(JPSet,JPSets),
jpl_call(JPSet,toArray,[],JPArr),
jpl_array_to_list(JPArr,JPs),
( JPs=[JP],
java_namedentity(JP,P)
-> true
; JPs=[]
-> fail
; maplist(java_namedentity,JPs,Ps),
P=equivalentClasses(Ps)).
%% pimap_property_individual(PIMap,P,I) is nondet
% Map<OWLObjectProperty, Set<OWLNamedIndividual>> --> ?Property ?Individual
% (currently object properties only?)
pimap_property_individual(PIMap,P,I) :-
jpl_call(PIMap,keySet,[],JPSet),
jpl_call(JPSet,toArray,[],JPArr),
jpl_array_to_list(JPArr,JPs),
member(JP,JPs),
jpl_call(PIMap,get,[JP],JISet),
jpl_call(JISet,toArray,[],JIArr),
jpl_array_to_list(JIArr,JIs),
member(JI,JIs),
java_namedentity(JP,P),
java_namedentity(JI,I).
% converts prolog reference to java
pl2javaref(Fac,C,JC) :-
( atom(C)
-> owlterm_java(Fac,_,C,JC)
; translate_arg_to_java(Fac,C,_,JC)).
%% inferred_axiom(+R,+Fac,?Axiom)
inferred_axiom(R,Fac,subClassOf(A,B)) :-
reasoner_subClassOf(R,Fac,A,B).
inferred_axiom(R,Fac,classAssertion(C,I)) :-
reasoner_individualOf(R,Fac,I,C).
inferred_axiom(R,Fac,classAssertion(C,I)) :-
reasoner_nr_individualOf(R,Fac,I,C).
inferred_axiom(R,Fac,propertyAssertion(P,I,I2)) :-
reasoner_objectPropertyAssertion(R,Fac,I,P,I2).
%% reasoner_nr_subClassOf(+R,+Fac,?C,?P)
% ?C ?P - find superclasses for all named classes C
% +C ?P - find superclasses
% ?C +P - find subclasses
%
% an unbound variable may be bound to a named class
% or to a class expression using equivalentClasses/1 -- TODO - this is an axiom not expression
%
% DEPRECATED - use reasoner_nr_subClassOf/5 with final argument 'true'
% reasoner_nr_subClassOf(+R,+Fac,?C,?P)
reasoner_nr_subClassOf(R,Fac,C,P) :-
throw(not_implemented),
var(C),
var(P),
!,
class(C),
reasoner_nr_subClassOf(R,Fac,C,P).
% reasoner_nr_subClassOf(+R,+Fac,+C,?P)
reasoner_nr_subClassOf(R,Fac,C,P) :-
throw(not_implemented),
nonvar(C),
!,
pl2javaref(Fac,C,JC),
jpl_call(R,getSuperClasses,[JC],JPSetSet),
ecsets_class(JPSetSet,P).
% reasoner_nr_subClassOf(+R,+Fac,?C,+P)
reasoner_nr_subClassOf(R,Fac,C,P) :-
throw(not_implemented),
nonvar(P),
!,
pl2javaref(Fac,P,JP),
jpl_call(R,getSubClasses,[JP,@(true)],JCSetSet),
nodeset_entity(JCSetSet,C).
%% reasoner_subClassOf(+R,+Fac,?C,?P)
% ?C ?P - find superclasses for all named classes C
% +C ?P - find superclasses
% ?C +P - find subclasses
reasoner_subClassOf(R,Fac,C,P) :-
reasoner_subClassOf(R,Fac,C,P,false).
%% reasoner_subClassOf(+R,+Fac,?C,?P,+IsDirect)
% ?C ?P - find superclasses for all named classes C
% +C ?P - find superclasses
% ?C +P - find subclasses
% IsDirect - true or false
% reasoner_subClassOf(+R,+Fac,?C,?P,+IsDirect)
reasoner_subClassOf(R,Fac,C,P,IsDirect) :-
var(C),
var(P),
!,
class(C),
reasoner_subClassOf(R,Fac,C,P,IsDirect).
% reasoner_subClassOf(+R,+Fac,+C,?P,+IsDirect)
reasoner_subClassOf(R,Fac,C,P,IsDirect) :-
nonvar(C),
!,
pl2javaref(Fac,C,JC),
jpl_call(R,getSuperClasses,[JC,@(IsDirect)],JPSetSet),
nodeset_entity(JPSetSet,P).
% reasoner_subClassOf(+R,+Fac,?C,+P,+IsDirect)
reasoner_subClassOf(R,Fac,C,P,IsDirect) :-
nonvar(P),
!,
debug(reasoner,'getSubClasses( ~w )',[P]),
pl2javaref(Fac,P,JP),
jpl_call(R,getSubClasses,[JP,@(IsDirect)],JCSetSet),
debug(reasoner,'getSubClasses( ~w ) = ~w',[P,JCSetSet]),
nodeset_entity(JCSetSet,C).
%% reasoner_nr_individualOf(+R,+Fac,?I,?C)
% ?I ?C - find classes for all named individuals I
% +I ?C - find classes
% ?I +C - find individuals
reasoner_nr_individualOf(R,Fac,I,C) :-
reasoner_individualOf(R,Fac,I,C,true).
%% reasoner_individualOf(+R,+Fac,?I,?C)
reasoner_individualOf(R,Fac,I,C) :-
reasoner_individualOf(R,Fac,I,C,false).
reasoner_individualOf(R,Fac,I,C,IsDirect) :-
var(C),
var(I),
!,
is_class(C),
reasoner_individualOf(R,Fac,I,C,IsDirect).
reasoner_individualOf(R,Fac,I,C,IsDirect) :-
nonvar(C),
!,
pl2javaref(Fac,C,JC),
( IsDirect
-> Bool='@'(true)
; Bool='@'(false)),
jpl_call(R,getInstances,[JC,Bool],ISet),
nodeset_entity(ISet,I).
reasoner_individualOf(R,Fac,I,C,IsDirect) :-
nonvar(I),
!,
pl2javaref(Fac,I,JI),
( IsDirect
-> Bool='@'(true)
; Bool='@'(false)),
jpl_call(R,getTypes,[JI,Bool],JCSetSet),
ecsets_class(JCSetSet,C).
reasoner_objectPropertyAssertion(R,Fac,P,I,I2) :-
( var(I)
-> classAssertion(_,I), % TODO - better way to get enumerate individuals?
\+ objectProperty(I), % see issue 16 - hack for now
\+ is_class(I)
; true),
( var(P)
-> objectProperty(P)
; true),
debug(reasoner,'I=~w',[I]),
pl2javaref(Fac,I,JI),
pl2javaref(Fac,P,JP),
jpl_call(R,getObjectPropertyValues,[JI,JP],NodeSet),
nodeset_entity(NodeSet,I2).
% java util
jset_member(JPSet,JP) :-
jpl_call(JPSet,toArray,[],JPArr),
jpl_array_to_list(JPArr,JPs),
member(JP,JPs).
%% reasoner_equivalent_to(+R,+Fac,+C,?P)
reasoner_equivalent_to(R,Fac,C,P) :-
( var(C)
-> is_class(C)
; true),
owlterm_java(Fac,_,class(C),JC),
jpl_call(R,getEquivalentClasses,[JC],JPSet),
jset_member(JPSet,JP),
java_namedentity(JP,P).
%% add_axiom(+Manager,+Factory,+Ont,+Axiom,?Obj) is det
% adds an axiom to Ont from the prolog databases
add_axiom(Manager,Factory,Ont,Axiom,JAx) :-
debug(owl2,' converting axiom: ~w ',[Axiom]),
owlterm_java(Factory,_,Axiom,JAx),
debug(owl2,' axiom ~w = ~w',[Axiom,JAx]),
( owl2_model:declarationAxiom(Axiom)
-> true
; JAx=ignore
-> true
; jpl_new('org.semanticweb.owlapi.model.AddAxiom',[Ont,JAx],AddAxiom),
jpl_call(Manager,applyChange,[AddAxiom],_)).
%% owlterm_java(+Factory,?Type,+OWLTerm,?Obj) is det
% translate OWL Axiom or OWL Expression from prolog term to java object
% --------
% SPECIAL CASES
% --------
% special rules for ontology declarations - should have been handled previously
owlterm_java(_,_,ontology(_),_) :- !.
% special rules for ontologyAnnotations
% TODO: this can go when we have sorted out ontologyAnnotation/2. See issue#17.
% also - not currently clear to me how to make an axiom for ontologyAnnotation/2 in the owlapi
owlterm_java(_,_,propertyAssertion(_,Sub,_),ignore) :-
ontology(Sub),
!.
owlterm_java(_,_,propertyAssertion(P,S,V),ignore) :-
\+ property(P),
print_message(warning,no_translation(propertyAssertion(P,S,V),'property is of unknown type')),
!.
owlterm_java(_,_,annotationAssertion(_,Sub,_),ignore) :-
ontology(Sub),
!.
% disable this for now whilst we figure out owlapi3
% (not required for reasoning anyway)
owlterm_java(_,_,annotationAssertion(_,_,_),ignore) :-
!.
% special rules for annotationAssertions
owlterm_java(Fac,_,annotationAssertion(AP,Sub,Val),Obj) :-
!,
%( atom(Val)
%-> trace
%; true),
%( Sub='http://www.obofoundry.org/ro/ro.owl#part_of'
%-> trace
%; true),
%owlterm_java(Fac,_,Sub,JEntity), % e.g. "fred"
( translate_arg_to_java(Fac,Val,literal,JVal)
-> true,
debug(owl2,'~w is liter => ~w',[Val,JVal])
; atom_javaIRI(Val,JVal),
debug(owl2,'treating ~w as IRI ~w',[Val,JVal])),
%translate_arg_to_java(Fac,Val,literal,JVal), % e.g. "fred"
%translate_arg_to_java(Fac,Sub,entity,JEntity), % e.g. db:fred
%atom_javaIRI(Sub,JEntity), % e.g. db:fred
% force argument to be an annotation property
atom_javaIRI(Sub,JEntity), % e.g. label
atom_javaIRI(AP,AP_IRI), % e.g. label
jpl_call(Fac,getOWLAnnotationProperty,[AP_IRI],JAP),
debug(owl2,'ap(~w) => ~w',[AP,JAP]),
%owlterm_java(Fac,_,AP,JAP),
debug(owl2,'annot assertion(~w ~w ~w)',[JAP,JEntity,JVal]),
jpl_call(Fac,getOWLAnnotationAssertionAxiom,[JAP,JEntity,JVal],Obj).
% --------
% DECLARATIONS
% --------
owlterm_java(Fac,_,OWLTerm,Obj) :-
OWLTerm =.. [P,X],
decl_method(P,M), % declaration axiom
!,
debug(owl2,'decl(~w,~w) -- converting to IRI: ~w',[P,M,X]),
atom_javaIRI(X,U),
debug(owl2,'calling: ~w . ~w( ~w )',[Fac,M,U]),
jpl_call(Fac,M,[U],Obj),
debug(owl2,'called: ~w . ~w( ~w ) = ~w',[Fac,M,U,Obj]).
% --------
% ATOMS
% --------
owlterm_java(Fac,_,OWLTerm,Obj) :-
atom(OWLTerm), % undeclared atom; TODO; numbers eg card
!,
debug(owl2,'converting to IRI: ~w',[OWLTerm]),
atom_javaIRI(OWLTerm,U),
( is_class(OWLTerm)
-> M=getOWLClass
; objectProperty(OWLTerm)
-> M=getOWLObjectProperty
; \+ \+ classAssertion(_,_M) % JW: was `M`, but that makes no sense
-> M=getOWLNamedIndividual
; throw(OWLTerm)),
debug(owl2,' using: ~w',[M]),
jpl_call(Fac,M,[U],Obj). % TODO
% --------
% UNTYPED AXIOMS
% --------
% some axioms such as subClassOf are effectively untyped
owlterm_java(Fac,_Type,OWLTerm,Obj) :- % e.g subClassOf
OWLTerm =.. [P|Args],
axiom_method(P,M),
!,
axiom_arguments(P,ArgTypes),
debug(owl2,'using java method: ~w, expecting arguments: ~w',[M,ArgTypes]),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
jpl_call(Fac,M,Objs,Obj).
% as above, but we must re-order
owlterm_java(Fac,_Type,OWLTerm,Obj) :- % e.g classAssertion
OWLTerm =.. [P|Args],
axiom_method(P,M,Objs,ReorderedObjs),
!,
axiom_arguments(P,ArgTypes),
debug(owl2,'using java method: ~w, expecting arguments: ~w',[M,ArgTypes]),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
jpl_call(Fac,M,ReorderedObjs,Obj).
% special case translation for property chains
owlterm_java(Fac,_,subPropertyOf(propertyChain(PL),P),Obj) :- % e.g. subObjectPropertyOf
!,
debug(owl2,' translating chain ~w',[PL]),
translate_args_to_java(Fac,[PL,P],[list(objectPropertyExpression),objectPropertyExpression],Objs),
debug(owl2,' translated chain to: ~w',[Objs]),
jpl_call(Fac,getOWLSubPropertyChainOfAxiom,Objs,Obj).
% --------
% TYPED AXIOMS
% --------
% axioms such as subPropertyOf have two typed variants.
% we use type checking which may require the axiom declaration
% to be asserted in the prolog owl2_model database
owlterm_java(Fac,_,UntypedAxiom,Obj) :- % e.g. subObjectPropertyOf
UntypedAxiom =.. [UntypedPred|Args], % e.g subPropertyOf p1 p2
nonvar(UntypedPred),
owlpredicate_typed(UntypedPred,TypedPred),
axiom_method(TypedPred,M), % e.g. subObjectPropertyOf
TypeCheckGoal =.. [TypedPred|Args],
%( UntypedPred=propertyAssertion
%-> trace
%; true),
TypeCheckGoal,
!,
debug(owl2,'typed axiom: if ~w is ~w',[UntypedAxiom,TypedPred]),
owlpredicate_arguments(TypedPred,ArgTypes),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
debug(owl2,' translated ~w :: ~w method: ~w',[Args,ArgTypes,M]),
jpl_call(Fac,M,Objs,Obj).
% on occasion the owlapi has a different ordering of arguments...
owlterm_java(Fac,_,UntypedAxiom,Obj) :-
UntypedAxiom =.. [UntypedPred|Args],
nonvar(UntypedPred),
owlpredicate_typed(UntypedPred,TypedPred),
TypeCheckGoal =.. [TypedPred|Args],
TypeCheckGoal,
debug(owl2,'typed axiom: if ~w is ~w',[UntypedAxiom,TypedPred]),
owlpredicate_arguments(TypedPred,ArgTypes),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
axiom_method(TypedPred,M,Objs,ObjsReordered), % e.g. subObjectPropertyOf
debug(owl2,' translated ~w :: ~w method: ~w',[Args,ArgTypes,M]),
jpl_call(Fac,M,ObjsReordered,Obj).
%% translate_arg_to_java(+Fac,+X,+Type,?Obj)
translate_args_to_java(_Fac,[],[],[]).
translate_args_to_java(Fac,[A|Args],[T|ArgTypes],[Obj|Objs]) :-
debug(owl2,' translating: ~w :: ~w',[A,T]),
translate_arg_to_java(Fac,A,T,Obj),
debug(owl2,' translated: ~w --> ~w',[A,Obj]),
translate_args_to_java(Fac,Args,ArgTypes,Objs).
translate_arg_to_java(Fac,L,set(T),Set) :-
is_list(L),
!,
findall(T,member(_,L),Ts),
translate_args_to_java(Fac,L,Ts,Objs),
jpl_new('java.util.HashSet',[],Set),
debug(owl2,' new set: ~w = ~w -- adding objs ~w',[L,Set,Objs]),
forall(member(Obj,Objs),
jpl_call(Set,add,[Obj],_)),
debug(owl2,' made set: ~w ',[Set]).
translate_arg_to_java(Fac,L,list(T),List) :-
is_list(L),
!,
findall(T,member(_,L),Ts),
translate_args_to_java(Fac,L,Ts,Objs),
jpl_new('java.util.ArrayList',[],List),
debug(owl2,' new set: ~w = ~w -- adding objs ~w',[L,List,Objs]),
forall(member(Obj,Objs),
jpl_call(List,add,[Obj],_)),
debug(owl2,' made list: ~w ',[List]).
translate_arg_to_java(_Fac,X,T,X) :- nonvar(T),T=int,!.
translate_arg_to_java(Fac,X,classExpression,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,class(X),Obj).
translate_arg_to_java(Fac,X,objectPropertyExpressionOrChain,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,objectProperty(X),Obj).
translate_arg_to_java(Fac,X,objectPropertyExpression,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,objectProperty(X),Obj).
translate_arg_to_java(Fac,X,dataPropertyExpression,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,dataProperty(X),Obj).
translate_arg_to_java(Fac,X,objectProperty,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,objectProperty(X),Obj).
translate_arg_to_java(Fac,X,individual,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,individual(X),Obj).
translate_arg_to_java(Fac,X,entity,Obj) :-
atom(X),
!,
owlterm_java(Fac,_,entity(X),Obj).
translate_arg_to_java(Fac,Val,literal,Obj) :- % todo - caused by bug in rdf parser
atom(Val),
sub_atom(Val,0,_,_,'_:'),
!,
translate_arg_to_java(Fac,literal(''),literal,Obj).
translate_arg_to_java(Fac,literal(lang(_,Val)),literal,Obj) :- % todo - LANG
!,
jpl_call(Fac,getOWLStringLiteral,[Val],Obj).
translate_arg_to_java(Fac,literal(type(_,Val)),literal,Obj) :- % todo - typed constants
!,
jpl_call(Fac,getOWLStringLiteral,[Val],Obj).
translate_arg_to_java(Fac,literal(Val),literal,Obj) :- % todo - typed constants
!,
jpl_call(Fac,getOWLStringLiteral,[Val],Obj).
translate_arg_to_java(_Fac,X,T,Obj) :- % TODO
atom(X),
!,
atom_javaIRI(X,U),
jpl_new(T,U,Obj).
translate_arg_to_java(Fac,X,_T,Obj) :-
atom(X),
is_class(X),
!,
debug(owl2,'converting to IRI: ~w',[X]),
atom_javaIRI(X,U),
jpl_call(Fac,getOWLClass,U,Obj).
translate_arg_to_java(Fac,X,_T,Obj) :-
atom(X),
\+ \+ classAssertion(_,X),
!,
atom_javaIRI(X,U),
jpl_call(Fac,getOWLNamedIndividual,U,Obj).
translate_arg_to_java(Fac,X,_T,Obj) :-
atom(X),
objectProperty(X),
!,
atom_javaIRI(X,U),
jpl_call(Fac,getOWLObjectProperty,U,Obj).
% typed expressions
translate_arg_to_java(Fac,UntypedExpr,_T,Obj) :-
UntypedExpr =.. [UntypedPred|Args], % eg intersectionOf(L)
owlpredicate_typed(UntypedPred,TypedPred),
owlpredicate_arguments(TypedPred,ArgTypes),
debug(owl2,' testing for java expr method ~w',[TypedPred]),
expr_method(TypedPred,Method),
Check =.. [TypedPred,UntypedExpr], % eg objectIntersectionOf(intersectionOf(L))
debug(owl2,' checking expr ~w',[Check]),
Check,
!,
debug(owl2,' typed expr ~w -> ~w :: ~w',[UntypedExpr,TypedPred,ArgTypes]),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
debug(owl2,' expr ~w -> java ~w.~w',[UntypedExpr,Method,Objs]),
jpl_call(Fac,Method,Objs,Obj),
debug(owl2,' made obj for ~w = ~w',[UntypedExpr,Obj]).
translate_arg_to_java(Fac,UntypedExpr,_T,Obj) :-
UntypedExpr =.. [UntypedPred|Args], % eg intersectionOf(L)
owlpredicate_typed(UntypedPred,TypedPred),
owlpredicate_arguments(TypedPred,ArgTypes),
Check =.. [TypedPred,UntypedExpr], % eg objectIntersectionOf(intersectionOf(L))
debug(owl2,' checking expr ~w',[Check]),
Check,
debug(owl2,' typed expr ~w -> ~w :: ~w',[UntypedExpr,TypedPred,ArgTypes]),
translate_args_to_java(Fac,Args,ArgTypes,Objs),
debug(owl2,' testing for REORDERED java expr method ~w',[TypedPred]),
expr_method(TypedPred,Method,Objs,ReorderedObjs),
!,
debug(owl2,' expr ( reordered ) ~w -> java ~w.~w',[UntypedExpr,Method,ReorderedObjs]),
jpl_call(Fac,Method,ReorderedObjs,Obj),
debug(owl2,' made obj for ~w = ~w',[UntypedExpr,Obj]).
translate_arg_to_java(Fac,Expr,_T,Obj) :-
Expr =.. [Pred|Args], % eg oneOf(L)
owlpredicate_arguments(Pred,ArgTypes),
expr_method(Pred,Method),
!,
translate_args_to_java(Fac,Args,ArgTypes,Objs),
jpl_call(Fac,Method,Objs,Obj).
%add_axiom_method(AP,M) :-
% atom_chars(AP,[C|Chars]),
% upcase_atom(AP,AP2),
% atom_chars(AP2,[C2|Chars]),
% sformat(M,'get~wAxiom',[AP2]).
%% decl_method(?Predicate,?JavaMethod)
% maps a declaration axiom predicate to the java factory method that will instantiate an instance
decl_method(P,M) :-
decl_method(P,M,_).
decl_method(class,getOWLClass,classExpression).
decl_method(objectProperty,getOWLObjectProperty,propertyExpression).
decl_method(annotationProperty,getOWLAnnotationProperty,iri).
decl_method(dataType,getOWLDatatype,datatype).
decl_method(dataProperty,getOWLDataProperty,_).
decl_method(individual,getOWLNamedIndividual,_). % anonymous individuals?
decl_method(entity,getOWLNamedIndividual,_). % anonymous individuals?
:- discontiguous axiom_method/2,axiom_method/4.
% ----------------------------------------
% untyped axioms
% ----------------------------------------
axiom_method(subClassOf,getOWLSubClassOfAxiom).
axiom_method(equivalentClasses,getOWLEquivalentClassesAxiom).
axiom_method(disjointClasses,getOWLDisjointClassesAxiom).
axiom_method(inverseProperties,getOWLInverseObjectPropertiesAxiom).
axiom_method(symmetricProperty,getOWLSymmetricObjectPropertyAxiom).
axiom_method(asymmetricProperty,getOWLAsymmetricObjectPropertyAxiom).
axiom_method(reflexiveProperty,getOWLReflexiveObjectPropertyAxiom).
axiom_method(irreflexiveProperty,getOWLIrreflexiveObjectPropertyAxiom).
axiom_method(functionalObjectProperty,getOWLFunctionalObjectPropertyAxiom).
axiom_method(dataObjectProperty,getOWLFunctionalDataPropertyAxiom).
axiom_method(objectPropertyAssertion,getOWLObjectPropertyAssertionAxiom).
axiom_method(dataPropertyAssertion,getOWLDataPropertyAssertionAxiom).
axiom_method(differentIndividuals,getOWLDifferentIndividualsAxiom).
% ----------------------------------------
% typed axioms
% ----------------------------------------
%% axiom_method(?Pred,?JavaGetMethod)
axiom_method(subObjectPropertyOf,getOWLSubObjectPropertyOfAxiom).
axiom_method(subDataPropertyOf,getOWLSubDataPropertyOfAxiom).
axiom_method(disjointObjectProperties,getOWLDisjointObjectPropertiesAxiom).
axiom_method(disjointDataProperties,getOWLDisjointDataPropertiesAxiom).
axiom_method(equivalentObjectProperties,getOWLEquivalentObjectPropertiesAxiom).
axiom_method(equivalentDataProperties,getOWLEquivalentDataPropertiesAxiom).
axiom_method(transitiveProperty,getOWLTransitiveObjectPropertyAxiom).
axiom_method(inverseFunctionalProperty,getOWLInverseFunctionalObjectPropertyAxiom).
axiom_method(symmetricProperty,getOWLSymmetricObjectPropertyAxiom).
axiom_method(dataPropertyDomain,getOWLDataPropertyDomainAxiom).
axiom_method(objectPropertyDomain,getOWLObjectPropertyDomainAxiom).
axiom_method(dataPropertyRange,getOWLDataPropertyRangeAxiom).
axiom_method(objectPropertyRange,getOWLObjectPropertyRangeAxiom).
axiom_method(classAssertion,getOWLClassAssertionAxiom).
expr_method(objectIntersectionOf,getOWLObjectIntersectionOf).
expr_method(dataIntersectionOf,getOWLObjectIntersectionOf).
expr_method(objectSomeValuesFrom,getOWLObjectSomeValuesFrom).
expr_method(dataSomeValuesFrom,getOWLDataSomeValiesFrom).
expr_method(objectHasValue,getOWLObjectHasValue).
expr_method(dataHasValue,getOWLDataHasValue).
expr_method(objectAllValuesFrom,getOWLObjectAllValuesFrom).
expr_method(dataAllValuesFrom,getOWLDataAllValuesFrom).
expr_method(objectComplementOf,getOWLObjectComplementOf).
expr_method(dataComplementOf,getOWLDataComplementOf).
expr_method(objectUnionOf,getOWLObjectUnionOf).
expr_method(dataUnionOf,getOWLDataUnionOf).
expr_method(objectOneOf,getOWLObjectOneOf).
expr_method(dataOneOf,getOWLDataOneOf).
expr_method(inverseOf,getOWLObjectPropertyInverse).
% TODO: is this still required? holdover from owlapi<3, when args were not in same order
expr_method(objectMinCardinality,getOWLObjectMinCardinality,[N,P,CE],[N,P,CE]).
expr_method(objectMinCardinality,getOWLObjectMinCardinality,[N,P],[N,P]).
expr_method(dataMinCardinality,getOWLDataMinCardinality,[N,P,CE],[N,P,CE]).
expr_method(dataMinCardinality,getOWLDataMinCardinality,[N,P],[N,P]).
expr_method(objectMaxCardinality,getOWLObjectMaxCardinality,[N,P,CE],[N,P,CE]).
expr_method(objectMaxCardinality,getOWLObjectMaxCardinality,[N,P],[N,P]).
expr_method(dataMaxCardinality,getOWLDataMaxCardinality,[N,P,CE],[N,P,CE]).
expr_method(dataMaxCardinality,getOWLDataMaxCardinality,[N,P],[N,P]).
expr_method(objectExactCardinality,getOWLObjectExactCardinality,[N,P,CE],[N,P,CE]).
expr_method(objectExactCardinality,getOWLObjectExactCardinality,[N,P],[N,P]).
expr_method(dataExactCardinality,getOWLDataExactCardinality,[N,P,CE],[N,P,CE]).
expr_method(dataExactCardinality,getOWLDataExactCardinality,[N,P],[N,P]).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% incrememntal classifier %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
/*
TODO - need to detect which changes have been applied
add reasoner_reclassify_hook
new_incremental_classifier(pellet_incremental(R)) :-
require_manager(Man),
create_factory(Man,Fac),
build_ontology(Man,Fac,Ont),
jpl_new('com.clarkparsia.modularity.IncrementalClassifier',[Ont],R),
jpl_call(R,classify,[],_).
*/
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Hooks for owl2_reasoner.pl %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
:- multifile owl2_reasoner:initialize_reasoner_hook/3.
:- multifile owl2_reasoner:reasoner_tell_hook/2.
:- multifile owl2_reasoner:reasoner_tell_all_hook/1.
:- multifile owl2_reasoner:reasoner_ask_hook/2.
:- multifile owl2_reasoner:reasoner_check_consistency_hook/2.
:- multifile owl2_reasoner:reasoner_unsatisfiable_class_hook/2.
wrapped_reasoner(pellet).
wrapped_reasoner(hermit).
wrapped_reasoner(factpp).
owl2_reasoner:initialize_reasoner_hook(Type,R,Opts) :-
wrapped_reasoner(Type), % choose arbitrary if not defined
!,
owl2_reasoner:initialize_reasoner_hook(owlapi(Type),R,Opts).
owl2_reasoner:initialize_reasoner_hook(owlapi(Type),owlapi_reasoner(R,Fac,Opts),Opts) :-
!,
require_manager(Man),
create_factory(Man,Fac),
statistics(cputime,T1),
print_message(informational,bench(reasoner,T1)),
build_ontology(Man,Fac,Ont),
create_reasoner(Ont,Type,R),
statistics(cputime,T2),
print_message(informational,bench(reasoner,T1,T2)).
%reasoner_tell_hook(R,Axiom) :- foo.
owl2_reasoner:reasoner_tell_all_hook(owlapi_reasoner(OWLReasoner,Fac,_Opts)) :-
build_ontology(Man,Fac,Ont),
reasoner_classify(OWLReasoner,Man,Ont).
%owl2_reasoner:reasoner_ask_hook(R,Axiom) :-
% var(Axiom), % allow all?
% !,
% throw(error(reasoner(R,Axiom))).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),subClassOf(A,B)) :-
reasoner_subClassOf(R,Fac,A,B),
\+ nothing(A).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),subClassOf(A,B),IsDirect) :-
reasoner_subClassOf(R,Fac,A,B,IsDirect),
\+ nothing(A).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),directSubClassOf(A,B)) :-
reasoner_subClassOf(R,Fac,A,B,true),
\+ nothing(A).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),classAssertion(C,I)) :-
reasoner_individualOf(R,Fac,I,C).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),classAssertion(C,I),IsDirect) :-
reasoner_individualOf(R,Fac,I,C,IsDirect).
owl2_reasoner:reasoner_ask_hook(owlapi_reasoner(R,Fac,_Opts),propertyAssertion(P,A,B)) :-
reasoner_objectPropertyAssertion(R,Fac,P,A,B).
owl2_reasoner:reasoner_unsatisfiable_class_hook(owlapi_reasoner(R,_Fac,_Opts),C) :-
unsatisfiable_class(R,C).
owl2_reasoner:reasoner_check_consistency_hook(owlapi_reasoner(R,_Fac,_Opts),V) :-
debug(reasoner,'checking consistency',[]),
( is_consistent(R)
-> V=true
; V=false).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% utils %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
show_java_memory_info :-
java_memory_info(M,TM,FM,MM),
Mb is M/(1024*1024),
MMb is MM/(1024*1024),
format(user_error,'Mem: ~2fMb (~Db) // Max: ~2fMb (~Db) // ~D - ~D',[Mb,M,MMb,MM,TM,FM]).
%print_message(informational,memory(M,TM,FM)).
java_memory_info(M,TM,FM,MM) :-
java_gc,
java_gc,
java_gc,
jpl_call('java.lang.Runtime',getRuntime,[],RunTime),
jpl_call(RunTime,totalMemory,[],TM),
jpl_call(RunTime,freeMemory,[],FM),
jpl_call(RunTime,maxMemory,[],MM),
M is TM-FM.
java_gc :- jpl_call('java.lang.System',gc,[],_).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% messages %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
prolog:message(bench(M,T1)) -->
['initializing: ',M,' ',T1].
prolog:message(bench(M,T1,T2)) -->
{TD is T2-T1},
['completed: ',M,' ',T2,' time: ',TD].
/** <module> bridge to java OWLAPI
---+ Synopsis