au.csiro.ontology.importer.owl.OWLImporter Maven / Gradle / Ivy
/**
* Copyright CSIRO Australian e-Health Research Centre (http://aehrc.com).
* All rights reserved. Use is subject to license terms and conditions.
*/
package au.csiro.ontology.importer.owl;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.EmptyStackException;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.Stack;
import javax.xml.bind.DatatypeConverter;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
import org.semanticweb.owlapi.model.OWLDataExactCardinality;
import org.semanticweb.owlapi.model.OWLDataHasValue;
import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
import org.semanticweb.owlapi.model.OWLDataMinCardinality;
import org.semanticweb.owlapi.model.OWLDataOneOf;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDataPropertyExpression;
import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom;
import org.semanticweb.owlapi.model.OWLDataRange;
import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom;
import org.semanticweb.owlapi.model.OWLFacetRestriction;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
import org.semanticweb.owlapi.model.OWLObjectHasSelf;
import org.semanticweb.owlapi.model.OWLObjectHasValue;
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
import org.semanticweb.owlapi.model.OWLObjectOneOf;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectUnionOf;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLFacet;
import au.csiro.ontology.Ontology;
import au.csiro.ontology.importer.BaseImporter;
import au.csiro.ontology.importer.ImportException;
import au.csiro.ontology.model.Axiom;
import au.csiro.ontology.model.BigIntegerLiteral;
import au.csiro.ontology.model.Concept;
import au.csiro.ontology.model.ConceptInclusion;
import au.csiro.ontology.model.Conjunction;
import au.csiro.ontology.model.Datatype;
import au.csiro.ontology.model.DateLiteral;
import au.csiro.ontology.model.DecimalLiteral;
import au.csiro.ontology.model.Existential;
import au.csiro.ontology.model.FloatLiteral;
import au.csiro.ontology.model.IntegerLiteral;
import au.csiro.ontology.model.Literal;
import au.csiro.ontology.model.NamedConcept;
import au.csiro.ontology.model.NamedFeature;
import au.csiro.ontology.model.NamedRole;
import au.csiro.ontology.model.Operator;
import au.csiro.ontology.model.Role;
import au.csiro.ontology.model.RoleInclusion;
import au.csiro.ontology.model.StringLiteral;
import au.csiro.ontology.util.IProgressMonitor;
import au.csiro.ontology.util.Statistics;
/**
* Imports axioms in OWL format into the internal representation used by
* Snorocket. This initial implementation does not support versions.
*
* @author Alejandro Metke
*
*/
public class OWLImporter extends BaseImporter {
public static final String THING_IRI = "http://www.w3.org/2002/07/owl#Thing";
public static final String NOTHING_IRI = "http://www.w3.org/2002/07/owl#Nothing";
private final Set dprAxioms = new HashSet();
private final List problems = new ArrayList();
private OWLOntology ontology;
private List axioms;
private SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd");
/**
* The OWL EL spec only allows using the following types: owl:real, owl:rational, xsd:decimal, xsd:integer,
* xsd:nonNegativeInteger. The Java types that most naturally correspond to these types are BigInteger and
* BigDecimal. However, the memory consumption increases and the performance decreases when using these types
* instead of the Java built-in types. When the following flags are set to true, the transformation uses the
* built-in data types instead of the math types.
*/
private boolean useSimpleInts = true;
private boolean useSimpleFloats = true;
public OWLImporter(OWLOntology ontology) {
this();
this.ontology = ontology;
}
public OWLImporter(List axioms) {
this();
this.axioms = axioms;
}
/**
* Private constructor.
*/
private OWLImporter() {
}
/**
* @return the useSimpleInts
*/
public boolean isUseSimpleInts() {
return useSimpleInts;
}
/**
* @param useSimpleInts the useSimpleInts to set
*/
public void setUseSimpleInts(boolean useSimpleInts) {
this.useSimpleInts = useSimpleInts;
}
/**
* @return the useSimpleFloats
*/
public boolean isUseSimpleFloats() {
return useSimpleFloats;
}
/**
* @param useSimpleFloats the useSimpleFloats to set
*/
public void setUseSimpleFloats(boolean useSimpleFloats) {
this.useSimpleFloats = useSimpleFloats;
}
private Axiom transformOWLSubPropertyChainOfAxiom(OWLSubPropertyChainOfAxiom a) {
List sub = a.getPropertyChain();
OWLObjectPropertyExpression sup = a.getSuperProperty();
int size = sub.size();
Role[] lhss = new Role[size];
for (int i = 0; i < size; i++) {
lhss[i] = new NamedRole(sub.get(i).asOWLObjectProperty().toStringID());
}
Role rhs = new NamedRole(sup.asOWLObjectProperty().toStringID());
if (lhss.length == 1 || lhss.length == 2) {
return new RoleInclusion(lhss, rhs);
} else {
problems.add("Unable to import axiom "+a.toString()+". RoleChains longer than 2 not supported.");
return null;
}
}
private Axiom transformOWLSubObjectPropertyOfAxiom(OWLSubObjectPropertyOfAxiom a) {
OWLObjectPropertyExpression sub = a.getSubProperty();
OWLObjectPropertyExpression sup = a.getSuperProperty();
Role lhs = new NamedRole(sub.asOWLObjectProperty().toStringID());
Role rhs = new NamedRole(sup.asOWLObjectProperty().toStringID());
return new RoleInclusion(new Role[]{lhs}, rhs);
}
private Axiom transformOWLReflexiveObjectPropertyAxiom(OWLReflexiveObjectPropertyAxiom a) {
OWLObjectPropertyExpression exp = a.getProperty();
return new RoleInclusion(new Role[] {}, new NamedRole(exp.asOWLObjectProperty().toStringID()));
}
private Axiom transformOWLTransitiveObjectPropertyAxiom(OWLTransitiveObjectPropertyAxiom a) {
OWLObjectPropertyExpression exp = a.getProperty();
Role r = new NamedRole(exp.asOWLObjectProperty().toStringID());
return new RoleInclusion(new Role[] { r, r }, r);
}
private Axiom transformOWLSubClassOfAxiom(OWLSubClassOfAxiom a) {
OWLClassExpression sub = a.getSubClass();
OWLClassExpression sup = a.getSuperClass();
try {
Concept subConcept = getConcept(sub);
Concept superConcept = getConcept(sup);
return new ConceptInclusion(subConcept, superConcept);
} catch(UnsupportedOperationException e) {
problems.add(e.getMessage());
return null;
}
}
private List transformOWLEquivalentClassesAxiom(
OWLEquivalentClassesAxiom a) {
List axioms = new ArrayList();
List exps = a.getClassExpressionsAsList();
int size = exps.size();
for (int i = 0; i < size - 1; i++) {
try {
OWLClassExpression e1 = exps.get(i);
Concept concept1 = getConcept(e1);
for (int j = i; j < size; j++) {
OWLClassExpression e2 = exps.get(j);
if (e1 == e2)
continue;
Concept concept2 = getConcept(e2);
axioms.add(new ConceptInclusion(concept1, concept2));
axioms.add(new ConceptInclusion(concept2, concept1));
}
} catch(UnsupportedOperationException e) {
problems.add(e.getMessage());
}
}
return axioms;
}
private Axiom transformOWLDisjointClassesAxiom(OWLDisjointClassesAxiom a) {
try {
List exps = a.getClassExpressionsAsList();
List concepts = new ArrayList();
for (OWLClassExpression exp : exps) {
concepts.add(getConcept(exp));
}
Concept[] conjs = new Concept[concepts.size()];
int i = 0;
for (; i < concepts.size(); i++) {
conjs[i] = concepts.get(i);
}
return new ConceptInclusion(new Conjunction(conjs), NamedConcept.BOTTOM_CONCEPT);
} catch(UnsupportedOperationException e) {
problems.add(e.getMessage());
return null;
}
}
private List transformOWLEquivalentObjectPropertiesAxiom(
OWLEquivalentObjectPropertiesAxiom a) {
List axioms = new ArrayList();
for (OWLSubObjectPropertyOfAxiom ax : a.asSubObjectPropertyOfAxioms()) {
OWLObjectPropertyExpression sub = ax.getSubProperty();
OWLObjectPropertyExpression sup = ax.getSuperProperty();
axioms.add(
new RoleInclusion(new NamedRole(sub.asOWLObjectProperty().toStringID()),
new NamedRole(sup.asOWLObjectProperty().toStringID()))
);
}
return axioms;
}
private Set transform(List axioms, IProgressMonitor monitor) throws ImportException {
monitor.taskStarted("Loading axioms");
final Set res = new HashSet();
int totalAxioms = axioms.size();
int workDone = 0;
for (OWLAxiom axiom : axioms) {
if (axiom instanceof OWLDeclarationAxiom) {
OWLDeclarationAxiom a = (OWLDeclarationAxiom)axiom;
OWLEntity ent = a.getEntity();
if (ent.isOWLClass()) {
res.add(new ConceptInclusion(
new NamedConcept(ent.asOWLClass().toStringID()), NamedConcept.TOP_CONCEPT));
} else if (ent.isOWLObjectProperty()) {
// Do nothing for now.
} else if (ent.isOWLDataProperty()) {
// Do nothing for now.
}
} else if (axiom instanceof OWLSubPropertyChainOfAxiom) {
OWLSubPropertyChainOfAxiom a = (OWLSubPropertyChainOfAxiom) axiom;
Axiom ax = transformOWLSubPropertyChainOfAxiom(a);
if(ax != null) res.add(ax);
monitor.step(workDone, totalAxioms);
} else if (axiom instanceof OWLSubObjectPropertyOfAxiom) {
OWLSubObjectPropertyOfAxiom a = (OWLSubObjectPropertyOfAxiom) axiom;
res.add(transformOWLSubObjectPropertyOfAxiom(a));
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLReflexiveObjectPropertyAxiom) {
OWLReflexiveObjectPropertyAxiom a = (OWLReflexiveObjectPropertyAxiom) axiom;
res.add(transformOWLReflexiveObjectPropertyAxiom(a));
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLTransitiveObjectPropertyAxiom) {
OWLTransitiveObjectPropertyAxiom a = (OWLTransitiveObjectPropertyAxiom) axiom;
res.add(transformOWLTransitiveObjectPropertyAxiom(a));
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLSubClassOfAxiom) {
OWLSubClassOfAxiom a = (OWLSubClassOfAxiom) axiom;
Axiom ax = transformOWLSubClassOfAxiom(a);
if(ax != null) res.add(ax);
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLEquivalentClassesAxiom) {
OWLEquivalentClassesAxiom a = (OWLEquivalentClassesAxiom) axiom;
res.addAll(transformOWLEquivalentClassesAxiom(a));
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLDisjointClassesAxiom) {
OWLDisjointClassesAxiom a = (OWLDisjointClassesAxiom) axiom;
Axiom ax = transformOWLDisjointClassesAxiom(a);
if(ax != null) res.add(ax);
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLEquivalentObjectPropertiesAxiom) {
OWLEquivalentObjectPropertiesAxiom a = (OWLEquivalentObjectPropertiesAxiom) axiom;
res.addAll(transformOWLEquivalentObjectPropertiesAxiom(a));
monitor.step(++workDone, totalAxioms);
} else if (axiom instanceof OWLAnnotationAssertionAxiom) {
// Do nothing
monitor.step(++workDone, totalAxioms);
} else {
problems.add("The axiom " + axiom.toString() + " is not currently supported by Snorocket.");
}
}
// TODO: deal with other axioms types even if Snorocket does not
// currently support them
monitor.taskEnded();
/*
if(!problems.isEmpty()) {
throw new ImportException("Problems occurred during import. See getProblems()");
}
*/
return res;
}
private Set transform(OWLOntology ont, IProgressMonitor monitor) throws ImportException {
return transform(Collections.list(Collections.enumeration(ont.getAxioms())), monitor);
}
/**
*
* @param l
* @return
*/
private Literal getLiteral(OWLLiteral l) {
OWLDatatype dt = l.getDatatype();
String literal = l.getLiteral();
Literal res = null;
if(dt.isBuiltIn()) {
OWL2Datatype odt = dt.getBuiltInDatatype();
switch (odt) {
case RDF_PLAIN_LITERAL:
case RDF_XML_LITERAL:
case XSD_STRING:
case XSD_NORMALIZED_STRING:
case XSD_NAME:
case XSD_NCNAME:
case XSD_NMTOKEN:
case XSD_HEX_BINARY:
case XSD_BASE_64_BINARY:
case XSD_ANY_URI:
case XSD_TOKEN:
res = new StringLiteral(literal);
break;
case XSD_INTEGER:
case XSD_NON_NEGATIVE_INTEGER:
if(useSimpleInts) {
res = new IntegerLiteral(Integer.parseInt(literal));
} else {
res = new BigIntegerLiteral(new BigInteger(literal));
}
break;
case XSD_DATE_TIME:
res = new DateLiteral(DatatypeConverter.parseDateTime(literal));
break;
case OWL_RATIONAL:
case OWL_REAL:
case XSD_DECIMAL:
if(useSimpleFloats) {
res = new FloatLiteral(Float.parseFloat(literal));
} else {
res = new DecimalLiteral(new BigDecimal(literal));
}
break;
default:
problems.add("Unsupported literal " + l);
}
} else {
problems.add("Datatype is not built in: " + dt);
}
return res;
}
private void checkInconsistentProperty(OWLDataProperty dp, OWLDatatype type) {
for (OWLDataPropertyRangeAxiom a : dprAxioms) {
OWLDataPropertyExpression pe = a.getProperty();
OWLDataRange r = a.getRange();
// TODO: check DataOneOf
// TODO: check OWLDataIntersectionOf
OWLDatatype otype = r.asOWLDatatype();
if (!pe.isAnonymous()) {
if (!otype.equals(type)) {
problems.add("The literal value restriction " + dp + " is inconsistent with the data property " +
"range axiom " + a);
}
} else {
problems.add("Found anonymous data property expression in data property range axiom: " + pe);
}
}
}
/**
*
* @param desc
* @return
*/
private Concept getConcept(OWLClassExpression desc) {
final Stack stack = new Stack();
desc.accept(new OWLClassExpressionVisitor() {
private void unimplemented(OWLClassExpression e) {
String message = "The class expression "+ e.getClassExpressionType().getName()+
" is not currently supported by Snorocket.";
throw new UnsupportedOperationException(message);
}
private Concept pop() {
return stack.pop();
}
private void push(Concept concept) {
stack.push(concept);
}
public void visit(OWLDataMaxCardinality e) {
unimplemented(e);
}
public void visit(OWLDataExactCardinality e) {
unimplemented(e);
}
public void visit(OWLDataMinCardinality e) {
unimplemented(e);
}
public void visit(OWLDataHasValue e) {
OWLDataPropertyExpression dpe = e.getProperty();
// TODO: consider the case where dpe is anonymous
OWLDataProperty dp = dpe.asOWLDataProperty();
OWLLiteral l = e.getValue();
OWLDatatype type = l.getDatatype();
checkInconsistentProperty(dp, type);
NamedFeature f = new NamedFeature(dp.toStringID());
Literal lit = getLiteral(l);
if(lit != null) {
push(new Datatype(f, Operator.EQUALS,lit));
} else {
problems.add("Axiom " + e + " will be ignored because of the unsupported literal.");
}
}
public void visit(OWLDataAllValuesFrom e) {
unimplemented(e);
}
public void visit(OWLDataSomeValuesFrom e) {
OWLDataProperty dp = e.getProperty().asOWLDataProperty();
OWLDataRange range = e.getFiller();
/*
* An OWLDataRange can be one of the following:
* Datatype | DataIntersectionOf | DataUnionOf |
* DataComplementOf | DataOneOf | DatatypeRestriction
*
* We initially support only DataOneOf.
*/
if(range instanceof OWLDataOneOf) {
OWLDataOneOf doo = (OWLDataOneOf)range;
Set values = doo.getValues();
if(values.size() != 1) {
problems.add("Expected only a single literal in "+e);
return;
}
OWLLiteral l = (OWLLiteral)values.toArray()[0];
OWLDatatype type = l.getDatatype();
checkInconsistentProperty(dp, type);
NamedFeature f = new NamedFeature(dp.toStringID());
Literal lit = getLiteral(l);
if(lit != null) {
push(new Datatype(f, Operator.EQUALS, lit));
} else {
problems.add("Axiom " + e + " will be ignored because of the unsupported literal.");
}
} else if(range instanceof OWLDatatypeRestriction) {
NamedFeature f = new NamedFeature(dp.toStringID());
OWLDatatypeRestriction dtr = (OWLDatatypeRestriction)range;
Set frs = dtr.getFacetRestrictions();
List conjuncts = new ArrayList();
for(OWLFacetRestriction fr : frs) {
OWLLiteral l = fr.getFacetValue();
Literal lit = getLiteral(l);
if(lit != null) {
checkInconsistentProperty(dp, l.getDatatype());
OWLFacet facet = fr.getFacet();
switch(facet) {
case MAX_EXCLUSIVE:
conjuncts.add(new Datatype(f, Operator.LESS_THAN, lit));
break;
case MAX_INCLUSIVE:
conjuncts.add(new Datatype(f, Operator.LESS_THAN_EQUALS, lit));
break;
case MIN_EXCLUSIVE:
conjuncts.add(new Datatype(f, Operator.GREATER_THAN, lit));
break;
case MIN_INCLUSIVE:
conjuncts.add(new Datatype(f, Operator.GREATER_THAN_EQUALS, lit));
break;
default:
throw new RuntimeException("Unsupported facet "+facet);
}
} else {
problems.add("Axiom " + e + " will be ignored because of the unsupported literal.");
}
}
// Create conjunctions with all restrictions
if(conjuncts.size() == 1) {
push(conjuncts.get(0));
} else if(!conjuncts.isEmpty()){
push(new Conjunction(conjuncts));
}
} else {
throw new RuntimeException("Unsupporter OWLDataRange: "+
range.getClass().getName());
}
}
public void visit(OWLObjectOneOf e) {
// TODO: implement to support EL profile
unimplemented(e);
}
public void visit(OWLObjectHasSelf e) {
// TODO: implement to support EL profile
// There is no model object to support this.
/*
* A self-restriction ObjectHasSelf( OPE ) consists of an object
* property expression OPE, and it contains all those
* individuals that are connected by OPE to themselves.
*/
/*Role r = new Role<>(e.getProperty().asOWLObjectProperty().toStringID());*/
unimplemented(e);
}
public void visit(OWLObjectMaxCardinality e) {
unimplemented(e);
}
public void visit(OWLObjectExactCardinality e) {
unimplemented(e);
}
public void visit(OWLObjectMinCardinality e) {
unimplemented(e);
}
public void visit(OWLObjectHasValue e) {
// TODO: implement to support EL profile
// We do not support individuals
unimplemented(e);
}
public void visit(OWLObjectAllValuesFrom e) {
unimplemented(e);
}
public void visit(OWLObjectSomeValuesFrom e) {
NamedRole r = new NamedRole(e.getProperty().asOWLObjectProperty().toStringID());
e.getFiller().accept(this);
try {
push(new Existential(r, pop()));
} catch(EmptyStackException ex) {
problems.add("Unable to add axiom " + e + " because of previous problems.");
}
}
public void visit(OWLObjectComplementOf e) {
unimplemented(e);
}
public void visit(OWLObjectUnionOf e) {
unimplemented(e);
}
public void visit(OWLObjectIntersectionOf e) {
List items = new ArrayList();
for (OWLClassExpression desc : e.getOperands()) {
desc.accept(this);
try {
items.add(pop());
} catch(EmptyStackException ex) {
problems.add("Unable to add conjunct " + desc + " because of previous problems.");
}
}
if(!items.isEmpty()) {
Conjunction conj = new Conjunction(items);
push(conj);
}
}
public void visit(OWLClass e) {
String id = e.toStringID();
if (("<"+THING_IRI+">").equals(id) || THING_IRI.equals(id))
push(NamedConcept.TOP_CONCEPT);
else if (("<"+NOTHING_IRI+">").equals(id) || NOTHING_IRI.equals(id))
push(NamedConcept.BOTTOM_CONCEPT);
else
push(new NamedConcept(id));
}
});
if (stack.size() != 1) {
throw new RuntimeException("Stack size should be 1 but is " + stack.size());
}
return stack.pop();
}
/**
* Clears all the state in the importer.
*/
public void clear() {
dprAxioms.clear();
problems.clear();
}
/**
* @return the problems
*/
public List getProblems() {
return problems;
}
public Iterator getOntologyVersions(IProgressMonitor monitor) {
return new OntologyInterator(monitor);
}
class OntologyInterator implements Iterator {
private boolean accessed = false;
private IProgressMonitor monitor;
public OntologyInterator(IProgressMonitor monitor) {
this.monitor = monitor;
}
public boolean hasNext() {
return !accessed;
}
public Ontology next() throws IllegalArgumentException, RuntimeException {
long start = System.currentTimeMillis();
Set ont = null;
try {
if(ontology != null) {
ont = transform(ontology, monitor);
} else if(axioms != null) {
ont = transform(axioms, monitor);
} else {
throw new IllegalArgumentException("No OWL ontology to transform.");
}
} catch (ImportException e) {
throw new RuntimeException(e);
}
String id = null;
if(ontology != null) {
id = ontology.getOntologyID().toString();
} else {
id = "incremental";
}
String version = sdf.format(new Date());
Ontology res = new Ontology(id, version, ont, null);
Statistics.INSTANCE.setTime("owl loading", System.currentTimeMillis() - start);
accessed = true;
return res;
}
public void remove() {
throw new UnsupportedOperationException();
}
}
}
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