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dev.ikm.reasoner.hybrid.SubsumptionNormalFormBuilder Maven / Gradle / Ivy
package dev.ikm.reasoner.hybrid;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Stream;
import java.util.stream.Collectors;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLProperty;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
public class SubsumptionNormalFormBuilder {
private OWLOntology kernelOntology;
private OWLReasoner kernelOwlReasoner;
private OWLOntology statementOntology;
private OWLReasoner statementOwlReasoner;
private HybridReasonerProperties properties;
private HybridSubsumptionTester subsumptionTester;
private List concepts = new ArrayList<>();
private HashMap chained = new HashMap<>();
private HashSet transitive = new HashSet<>();
private HashMap> superProps = new HashMap<>();
private HashMap> unmergedSubsumptionNormalFormsSHIELD = new HashMap<>();
private HashMap subsumptionNormalFormsSHIELD = new HashMap<>();
private int countNormalized = 0;
public List getConcepts() {
return concepts;
}
public List getUnmergedSubsumptionNormalFormsSHIELD(OWLClass con) {
return unmergedSubsumptionNormalFormsSHIELD.get(con);
}
public HashMap getSubsumptionNormalFormsSHIELD() {
return subsumptionNormalFormsSHIELD;
}
public SubsumptionNormalForm getSNF(OWLClass con) {
return subsumptionNormalFormsSHIELD.get(con);
}
public SubsumptionNormalFormBuilder(OWLOntology kernelOntology, OWLReasoner kernelOwlReasoner,
OWLOntology statementOntology, OWLReasoner statementOwlReasoner, HybridReasonerProperties properties) {
super();
this.kernelOntology = kernelOntology;
this.kernelOwlReasoner = kernelOwlReasoner;
this.statementOntology = statementOntology;
this.statementOwlReasoner = statementOwlReasoner;
this.properties = properties;
this.subsumptionTester = new HybridSubsumptionTester(kernelOntology, properties.temporalAnnotationOwlIri());
}
// This method was for debugging only
// public void testSubsumptionsPairwise() {
// for (Map.Entry entry : subsumptionNormalFormsSHIELD.entrySet()) {
// OWLClass key = entry.getKey();
// SubsumptionNormalFormSHIELD value = entry.getValue();
//// DEBUG System.out.println("SNF Key=" + key + ", \nSNF Value=\n" + value);
// }
//// CustomSubsumptionTesterSHIELD subsumptionTester = new CustomSubsumptionTesterSHIELD();
// for (OWLClass superConcept : statementOntology.getClassesInSignature()) {
// for (OWLClass subConcept : statementOntology.getClassesInSignature()) {
// if (StatementClassifierSHIELD.logicallyDefinedInOntology(superConcept, statementOntology) &&
// StatementClassifierSHIELD.logicallyDefinedInOntology(subConcept, statementOntology)) {
//
//// "if" statement select a particular concept or pair of concepts to check subsumption with respect to.
//// If the statement is omitted, this will test subsumption with respect to all pairs of SNFs
// if (superConcept.getIRI().toString()
// .contains("#ABSENT_History-of-Allergic-Asthma-in-Patient-in-Past") &&
// subConcept.getIRI().toString()
// .contains("#ABSENT_Respiratory-Disease-in-Patient-in-Past") ) {
//
// SubsumptionNormalFormSHIELD superSNF = subsumptionNormalFormsSHIELD.get(superConcept);
// SubsumptionNormalFormSHIELD subSNF = subsumptionNormalFormsSHIELD.get(subConcept);
//
//// DEBUG System.out.println("Super Class: " + superConcept);
//// DEBUG System.out.println(superSNF.toString());
//// DEBUG System.out.println("Sub Class: " + subConcept);
//// DEBUG System.out.println(subSNF.toString());
// boolean isSnfSubsumedBy = subsumptionTester.isSubsumedBy(subSNF, superSNF, kernelOwlReasoner, statementOwlReasoner);
//// DEBUG System.out.println(" Is Subsumed: " + isSnfSubsumedBy);
//// DEBUG System.out.println();
// }
// }
// }
// }
// }
public void init() {
//ReasonerExplorer.pause("about to initialize concepts");
initConcepts();
//ReasonerExplorer.pause("about to initialize roles");
initRoles();
for (OWLAxiom ax : statementOntology.getAxioms()) {
// if( ax.getAxiomType().getName().equals("Declaration")) {
// System.out.println("Axiom type name is Declaration!");
// }
switch (ax.getAxiomType().getName()) {
case "Declaration": {
}
case "SubClassOf": {
}
case "EquivalentClasses": {
}
case "SubObjectPropertyOf": {
}
case "SubPropertyChainOf": {
}
case "TransitiveObjectProperty": {
}
case "ReflexiveObjectProperty": {
}
// TODO: Not recognizing "Declaration" for some reason and throwing this exception...
default: {
} // throw new UnsupportedOperationException("Unexpected Axiom Type: " + ax + "
// **" + ax.getAxiomType().getName() + "**");
// TODO: Figure out why this case statement is not recognizing "Declaration"
// Axioms...
}
}
}
private void initConcepts() {
// DEBUG System.out.println("STATEMENT REASONER TAXONOMY - IN SNF BUILDER");
// DEBUG ReasonerExplorer.printCurrentReasonerTaxonomy((StructuralReasoner) statementOwlReasoner, false);
for (OWLClass concept : statementOntology.getClassesInSignature()) {
// NodeSet supers = statementOwlReasoner.getSuperClasses(concept, false);
// for (Iterator> iterator = supers.iterator(); iterator.hasNext();) {
// OWLClassNode owlClassNode = (OWLClassNode) iterator.next();
// }
concepts.add(concept);
}
}
@SuppressWarnings("unused")
private void initRoles() {
for (OWLSubPropertyChainOfAxiom ax : kernelOntology.getAxioms(AxiomType.SUB_PROPERTY_CHAIN_OF)) {
if (ax.getPropertyChain().size() != 2) {
throw new UnsupportedOperationException("Unexpected: " + ax);
}
OWLObjectProperty prop1 = ax.getPropertyChain().get(0).asOWLObjectProperty();
OWLObjectProperty prop2 = ax.getPropertyChain().get(1).asOWLObjectProperty();
OWLObjectProperty sup = ax.getSuperProperty().asOWLObjectProperty();
if (!prop1.equals(sup)) {
throw new UnsupportedOperationException("Unexpected: " + ax);
}
if (chained.get(prop1) != null) {
throw new UnsupportedOperationException(
"Two chains for: " + prop1 + " " + ax + " " + chained.get(prop1));
}
chained.put(prop1, prop2);
}
for (Entry es : chained.entrySet()) {
}
for (OWLTransitiveObjectPropertyAxiom ax : kernelOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY)) {
OWLObjectProperty prop = ax.getProperty().asOWLObjectProperty();
transitive.add(prop);
}
for (OWLObjectProperty prop : transitive) {
// LOG LOG.info("Transitive: " + prop);
}
for (Iterator iterator = concepts.iterator(); iterator.hasNext();) {
OWLClass owlClass = (OWLClass) iterator.next();
}
Set allObjectProperties = kernelOntology.getObjectPropertiesInSignature();
for (Iterator iterator = allObjectProperties.iterator(); iterator.hasNext();) {
OWLObjectProperty prop = (OWLObjectProperty) iterator.next();
// for (OWLObjectProperty prop : kernelOntology.getObjectPropertiesInSignature()) {
superProps.put(prop, new HashSet<>());
superProps.get(prop).add(prop);
// TODO Why does this this cause incompleteness warnings
// TODO: Elk does not support getSuperObjectProperties method! So, commented
// out.
/******
* superProps of every property will be empty set; later figure out how to
* handle them, given above Set propsSuperProps =
* kernelReasoner.getSuperObjectProperties(prop, false).getFlattened(); for
* (Iterator iterator2 = propsSuperProps.iterator(); iterator2.hasNext();) {
* OWLObjectPropertyExpression superProp = (OWLObjectPropertyExpression)
* iterator2 .next(); if (!superProp.isOWLTopObjectProperty()) {
* superProps.get(prop).add(superProp.asOWLObjectProperty()); } }
*******/
}
for (Entry> es : superProps.entrySet()) {
if (es.getValue().size() > 1) {
// LOG LOG.info("Super props: " + es.getKey());
for (OWLObjectProperty prop : es.getValue()) {
if (!prop.equals(es.getKey())) {
// LOG LOG.info("\t" + prop);
}
}
}
}
}
public void generate() { // was public void generate(Roles roles)
// Needed?? Reasoner.processingSubsumptionNormalFormSHIELD = true;
//ReasonerExplorer.pause("about to generate subsumptionNormalizedConcepts");
for (OWLClass concept : concepts) {
for (OWLClassAxiom axiom : getLogicalAxioms(concept, statementOntology)) {
unmergedSubsumptionNormalFormsSHIELD.put(concept, new ArrayList<>());
SubsumptionNormalForm expr = createExpression(concept, axiom);
unmergedSubsumptionNormalFormsSHIELD.get(concept).add(expr);
// DEBUG System.out.println("Initial SNF for " + concept + " is :");
// DEBUG System.out.println(" " + expr.toString());
simplify(expr.getUngroupedProps());
}
if (!getLogicalAxioms(concept, statementOntology).isEmpty()) {
subsumptionNormalFormsSHIELD.put(concept, mergeNNFs(unmergedSubsumptionNormalFormsSHIELD.get(concept)));
// DEBUG System.out.println("Simplified/Merged SNF for " + concept + " is :");
// DEBUG System.out.println(" " + subsumptionNormalFormSHIELD.get(concept));
}
if (++countNormalized % 50 == 0)
System.out.println("Normalized " + countNormalized);
}
// Needed?? Reasoner.processingSubsumptionNormalFormSHIELD = false;
}
private SubsumptionNormalForm mergeNNFs(List nnfs) {
SubsumptionNormalForm merged_nnf = new SubsumptionNormalForm();
// TODO subClassOf
merged_nnf.setUngroupedProps(new HashSet<>());
merged_nnf.setFocusConcepts(new HashSet<>());
for (SubsumptionNormalForm nnf : nnfs) {
merged_nnf.getUngroupedProps().addAll(nnf.getUngroupedProps());
merged_nnf.getFocusConcepts().addAll(nnf.getFocusConcepts());
}
simplify(merged_nnf.getUngroupedProps());
simplifyFocusConcepts(merged_nnf.getFocusConcepts());
if (isAbsentConcept(merged_nnf))
merged_nnf.setIsAbsent(true);
else
merged_nnf.setIsAbsent(false);
return merged_nnf;
}
private OWLClassExpression getDefinition(OWLClass concept, OWLClassAxiom axiom) {
// DEBUG System.out.println("The Axiom: " + axiom);
// DEBUG System.out.println("The Concept: " + concept);
// switch (axiom) {
// case OWLEquivalentClassesAxiom {
if (axiom instanceof OWLEquivalentClassesAxiom) {
Set class_exprs = ((OWLEquivalentClassesAxiom) axiom).getClassExpressions();
if (class_exprs.size() != 2)
throw new UnsupportedOperationException("Unexpected: " + class_exprs.size() + " " + class_exprs);
Iterator iterator = class_exprs.iterator();
@SuppressWarnings("unused") // Only included to get to 2nd item
OWLClassExpression clazz = iterator.next();
OWLClassExpression def = iterator.next();
return def;
}
// case OWLSubClassOfAxiom x -> {
else if (axiom instanceof OWLSubClassOfAxiom) {
OWLClassExpression def = ((OWLSubClassOfAxiom) axiom).getSuperClass();
return def;
}
// default -> throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
else {
throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
}
}
private SubsumptionNormalForm createExpression(OWLClass concept, OWLClassAxiom axiom) {
SubsumptionNormalForm expr = new SubsumptionNormalForm();
{
// switch (axiom) {
// case OWLEquivalentClassesAxiom x -> expr.setSubClassOf(false);
if (axiom instanceof OWLEquivalentClassesAxiom)
expr.setSubClassOf(false);
// case OWLSubClassOfAxiom x -> expr.setSubClassOf(true);
else if (axiom instanceof OWLSubClassOfAxiom)
expr.setSubClassOf(false);
// default -> throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
else
throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
// }
}
Set focusConcepts = processDefinitionFocusConcepts(concept, axiom);
expr.setFocusConcepts(focusConcepts);
Set roles = processDefinitionProperties(concept, axiom);
;
expr.setUngroupedProps(roles);
return expr;
}
@SuppressWarnings("deprecation")
private Set processDefinitionProperties(OWLClass concept, OWLClassAxiom axiom) {
Set properties = new HashSet<>();
OWLClassExpression classDefinition = getDefinition(concept, axiom);
// switch (axiom) { // Just a safety check
// case OWLSubClassOfAxiom x -> { }
// case OWLEquivalentClassesAxiom x -> { }
// default -> throw new UnsupportedOperationException("Unexpected Axiom Type: " + axiom.getAxiomType());
if (axiom instanceof OWLSubClassOfAxiom) {
} else if (axiom instanceof OWLEquivalentClassesAxiom) {
} else {
throw new UnsupportedOperationException("Unexpected Axiom Type: " + axiom.getAxiomType());
}
// switch (classDefinition) {
// case OWLClass y -> {
if (classDefinition instanceof OWLClass) {
for (OWLClassAxiom superAxiom : statementOntology.getAxioms((OWLClass) classDefinition)) {
properties.addAll(processDefinitionProperties(getDefinedClass(superAxiom), superAxiom));
}
}
// case OWLObjectSomeValuesFrom y -> {
else if (classDefinition instanceof OWLObjectSomeValuesFrom) {
properties.add((OWLObjectSomeValuesFrom) classDefinition);
}
// case OWLObjectIntersectionOf y -> {
else if (classDefinition instanceof OWLObjectIntersectionOf) {
OWLObjectIntersectionOf y = (OWLObjectIntersectionOf) classDefinition;
properties.addAll(processIntersectionProperties(y.getOperands(), axiom));
}
// default -> throw new UnsupportedOperationException(
else {
throw new UnsupportedOperationException(
"Unexpected: " + classDefinition + " " + classDefinition.getClassExpressionType());
}
return properties;
}
@SuppressWarnings("deprecation")
private Set processIntersectionProperties(Set class_exprs,
OWLClassAxiom axiom) {
Set properties = new HashSet<>();
for (Iterator iterator = class_exprs.iterator(); iterator.hasNext();) {
OWLClassExpression class_expr = (OWLClassExpression) iterator.next();
// switch (class_expr) {
// case OWLClass z -> {
if (class_expr instanceof OWLClass) {
for (OWLClassAxiom superAxiom : statementOntology.getAxioms((OWLClass) class_expr)) {
properties.addAll(processDefinitionProperties(getDefinedClass(superAxiom), superAxiom));
}
}
// case OWLObjectSomeValuesFrom z -> {
else if (class_expr instanceof OWLObjectSomeValuesFrom) {
properties.add((OWLObjectSomeValuesFrom) class_expr);
}
// default -> throw new UnsupportedOperationException(
else {
throw new UnsupportedOperationException(
"Unexpected: " + class_expr + " " + class_expr.getClassExpressionType());
// TODO: This method will not handle intersections within intersections; needed?
// Would need to recurse to do that
}
}
return properties;
}
@SuppressWarnings("deprecation")
private Set processDefinitionFocusConcepts(OWLClass concept, OWLClassAxiom axiom) {
Set focusConcepts = new HashSet<>();
OWLClassExpression classDefinition = getDefinition(concept, axiom);
// DEBUG if (concept.getIRI().toString().contains("#ABSENT_History-of-Allergic-Asthma-in-Patient-Recently_COPY"))
// DEBUG System.out.print("");
{
// switch (axiom) {
// case OWLSubClassOfAxiom x -> {
if (axiom instanceof OWLSubClassOfAxiom) {
focusConcepts.add(concept); // And don't walk further up the stated hierarchy
}
// case OWLEquivalentClassesAxiom x -> {
else if (axiom instanceof OWLEquivalentClassesAxiom) {
// switch (classDefinition) {
// case OWLClass y -> {
if (classDefinition instanceof OWLClass) {
// for (OWLClassAxiom superAxiom : statementOntology.getAxioms(classDefinition)) {
for (OWLClassAxiom superAxiom : statementOntology.getAxioms((OWLClass) classDefinition)) {
focusConcepts.addAll(processDefinitionFocusConcepts(getDefinedClass(superAxiom), superAxiom));
return focusConcepts;
}
}
// case OWLObjectSomeValuesFrom y -> {
else if (classDefinition instanceof OWLObjectSomeValuesFrom) {
// ignore this type of expression; ; return null Set
}
// case OWLObjectIntersectionOf y -> {
else if (classDefinition instanceof OWLObjectIntersectionOf) {
OWLObjectIntersectionOf y = (OWLObjectIntersectionOf) classDefinition;
focusConcepts = processIntersectionFocusConcepts(y.getOperands(), axiom);
return focusConcepts;
}
// default -> throw new UnsupportedOperationException(
else {
throw new UnsupportedOperationException(
"Unexpected: " + classDefinition + " " + classDefinition.getClassExpressionType());
}
}
// default -> throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
else {
throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
}
}
return focusConcepts;
}
@SuppressWarnings("deprecation")
private Set processIntersectionFocusConcepts(Set class_exprs, OWLClassAxiom axiom) {
Set focusConcepts = new HashSet<>();
for (OWLClassExpression class_expr : class_exprs) {
// switch (axiom) {
// case OWLSubClassOfAxiom x -> {
if (axiom instanceof OWLSubClassOfAxiom) {
// switch (class_expr) {
// case OWLClass z -> {
if (class_expr instanceof OWLClass) {
focusConcepts.add((OWLClass) class_expr); // Don't walk further up the stated hierarchy
return focusConcepts;
}
// case OWLObjectSomeValuesFrom z -> {
else if (class_expr instanceof OWLObjectSomeValuesFrom) {
// Ignore; add no focus concepts
}
// default -> throw new UnsupportedOperationException(
else {
throw new UnsupportedOperationException(
"Unexpected: " + class_expr + " " + class_expr.getClassExpressionType());
// TODO: This method will not handle intersections within intersections; would
// need to recurse
}
}
// case OWLEquivalentClassesAxiom x -> {
else if (axiom instanceof OWLEquivalentClassesAxiom) {
// switch (class_expr) {
// case OWLClass z -> {
if (class_expr instanceof OWLClass) {
OWLClass z = (OWLClass) class_expr;
for (OWLClassAxiom superAxiom : statementOntology.getAxioms(z)) {
focusConcepts.addAll(processDefinitionFocusConcepts(getDefinedClass(superAxiom), superAxiom));
return focusConcepts;
}
}
// case OWLObjectSomeValuesFrom z -> {
else if (class_expr instanceof OWLObjectSomeValuesFrom) {
// Ignore; add no focus concepts
}
// default -> throw new UnsupportedOperationException(
else {
throw new UnsupportedOperationException(
"Unexpected: " + class_expr + " " + class_expr.getClassExpressionType());
// TODO: This method will not handle intersections within intersections; would
// need to recurse
}
}
// default -> throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
else {
throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
}
}
return focusConcepts;
}
private OWLClass getDefinedClass(OWLClassAxiom axiom) {
// switch (axiom) {
// case OWLEquivalentClassesAxiom x -> {
// Set class_exprs = x.getClassExpressions();
if (axiom instanceof OWLEquivalentClassesAxiom) {
Set class_exprs = ((OWLEquivalentClassesAxiom) axiom).getClassExpressions();
if (class_exprs.size() != 2)
throw new UnsupportedOperationException("Unexpected: " + class_exprs.size() + " " + class_exprs);
OWLClassExpression definedClass = class_exprs.iterator().next();
return (OWLClass) definedClass;
}
// case OWLSubClassOfAxiom x -> {
// OWLClassExpression definedClass = x.getSubClass();
else if (axiom instanceof OWLSubClassOfAxiom) {
OWLClassExpression definedClass = ((OWLSubClassOfAxiom) axiom).getSubClass();
return (OWLClass) definedClass;
}
// default -> throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
else {
throw new UnsupportedOperationException("Unexpected: " + axiom.getAxiomType());
}
}
// Only needed to handle subsumption w.r.t. chained properties for purposes of creating the SNF
// TODO: CustomSubsumptionTesterSHIELD does not support subsumption w.r.t. chained properties. Should we add?
@SuppressWarnings("unused")
private boolean isSubClassOfEntailed(OWLObjectSomeValuesFrom prop1, OWLObjectSomeValuesFrom prop2) {
boolean isSubClassOf = false;
if (superProps.get(prop1.getProperty().asOWLObjectProperty())
.contains(prop2.getProperty().asOWLObjectProperty())) {
if (chained.get(prop1.getProperty()) == null && chained.get(prop2.getProperty()) == null
&& !transitive.contains(prop1.getProperty()) && !transitive.contains(prop2.getProperty())) {
OWLClass con1 = prop1.getFiller().asOWLClass();
OWLClass con2 = prop2.getFiller().asOWLClass();
isSubClassOf = con1.equals(con2) || subsumptionTester.isSubsumedBy(con1, con2, kernelOwlReasoner);
} else {
}
}
return isSubClassOf;
}
// This subclass is only needed to handle chained properties. Currently not handled by classification process
// TODO: Determine if we need to add support for subsumption w.r.t. chained properties to CustomSubsumptionTesterSHIELD
private static class SVF {
private OWLObjectProperty prop;
private OWLClassExpression filler;
public SVF(OWLObjectProperty prop, OWLClassExpression filler) {
super();
this.prop = prop;
this.filler = filler;
}
@Override
public int hashCode() {
return Objects.hash(filler, prop);
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
SVF other = (SVF) obj;
return Objects.equals(filler, other.filler) && Objects.equals(prop, other.prop);
}
@Override
public String toString() {
return "SVF(" + prop + " " + filler + ")";
}
}
@SuppressWarnings("unused")
private HashSet expandChain(OWLObjectProperty prop, OWLClass filler) {
HashSet svfs = new HashSet<>();
svfs.add(new SVF(prop, filler));
while (true) {
ArrayList svfs_l = new ArrayList<>(svfs);
for (SVF svf : svfs_l) {
List chain_exps = expandChain1(svf);
svfs.addAll(chain_exps);
List prop_exps = expandSuperProps(svf);
svfs.addAll(prop_exps);
}
if (svfs.size() == svfs_l.size())
break;
}
return svfs;
}
private List expandChain1(SVF svf) {
ArrayList chained_props = new ArrayList<>();
if (chained.get(svf.prop) != null) {
chained_props.add(chained.get(svf.prop));
}
if (transitive.contains(svf.prop))
chained_props.add(svf.prop);
// List chained_cons = subsumptionNormalFormsSHIELD.get(svf.filler).getUngroupedProps().stream()
// .filter(x -> chained_props.contains(x.getProperty().asOWLObjectProperty()))
// .map(x -> x.getFiller().asOWLClass()).distinct().toList();
Stream chained_cons_stream = subsumptionNormalFormsSHIELD.get(svf.filler).getUngroupedProps().stream()
.filter(x -> chained_props.contains(x.getProperty().asOWLObjectProperty()))
.map(x -> x.getFiller().asOWLClass()).distinct();
List chained_cons = chained_cons_stream.collect(Collectors.toList());
// return chained_cons.stream().map(x -> new SVF(svf.prop, x)).toList();
return chained_cons.stream().map(x -> new SVF(svf.prop, x)).collect(Collectors.toList());
}
private List expandSuperProps(SVF svf) {
// return superProps.get(svf.prop).stream().filter(x -> !x.equals(svf.prop)).map(x -> new SVF(x, svf.filler))
// .toList();
Stream superPropsStream = (Stream) superProps.get(svf.prop).stream().filter(x -> !x.equals(svf.prop))
.map(x -> new SVF(x, svf.filler));
return superPropsStream.collect(Collectors.toList());
}
@SuppressWarnings("unused")
private boolean isSubsumedBy(SVF svf1, SVF svf2, OWLReasoner owlReasoner) {
return subsumptionTester.isSubsumedBy(svf1.prop, svf2.prop)
&& isSubsumedBy(svf1.filler, svf2.filler, owlReasoner);
}
private boolean isSubsumedBy(OWLClassExpression expr1, OWLClassExpression expr2, OWLReasoner owlReasoner) {
return subsumptionTester.isSubsumedBy(expr1, expr2, owlReasoner);
}
private void simplifyFocusConcepts(Set cons) {
if (cons.isEmpty())
return;
ArrayList to_remove = new ArrayList<>();
for (OWLClass con1 : cons) {
for (OWLClass con2 : cons) {
if (con1 == con2)
continue;
if (subsumptionTester.isSubsumedBy(con1, con2, statementOwlReasoner)) {
to_remove.add(con2);
}
}
}
cons.removeAll(to_remove);
}
private void simplify(Set props) {
if (props.isEmpty())
return;
ArrayList to_remove = new ArrayList<>();
for (OWLObjectSomeValuesFrom prop1 : props) {
for (OWLObjectSomeValuesFrom prop2 : props) {
// DEBUG System.out.println("Prop1: " + prop1);
// DEBUG System.out.println("Prop2: " + prop2);
if (prop1 == prop2)
continue;
if (subsumptionTester.isSubsumedBy(prop1, prop2, kernelOwlReasoner))
to_remove.add(prop2);
}
}
props.removeAll(to_remove);
}
/**
* SPECIFIED MODELING OF AN 'ABSENT' CONCEPT: The SubsumptionNormalForm of the
* concept has the 'ObjectSomeValuesFrom' constraint defined by
* 'createAbsentSomeValuesFrom()';
*/
private boolean isAbsentConcept(SubsumptionNormalForm merged_nnf) {
// OWLObjectSomeValuesFrom absentProperty = createAbsentProperty();
OWLObjectSomeValuesFrom absentProperty = createAbsentSomeValuesFrom();
// if (merged_nnf.getUngroupedProps().contains(absentProperty))
if (containsAbsentProperty(merged_nnf.getUngroupedProps(), absentProperty))
return true;
else
return false;
}
// ROLE_GROUP_PROPERTY_NAMESPACE = "http://www.hhs.fda.org/shield/SWEC-Ontology#";
// public static final String ROLE_GROUP_PROPERTY_NAME)
private boolean containsAbsentProperty(Set ungroupedProps,
OWLObjectSomeValuesFrom absentProperty) {
// Test if absentProperty is among top-level class expressions
if (ungroupedProps.contains(absentProperty))
return true;
// Test if absentProperty is among intersection of class expressions within a
// top-level role group
IRI roleGroupPropertyIri = IRI.create(properties.roleGroupProperty());
for (OWLObjectSomeValuesFrom prop : ungroupedProps) {
if (prop.getProperty().getNamedProperty().getIRI().equals(roleGroupPropertyIri)) {
OWLClassExpression propertyValue = prop.getFiller();
if (propertyValue instanceof OWLObjectSomeValuesFrom) {
if (((OWLObjectSomeValuesFrom) propertyValue).equals(absentProperty))
return true;
} else if (propertyValue instanceof OWLObjectIntersectionOf) {
Set intersectedClassExpressions = ((OWLObjectIntersectionOf) propertyValue)
.getOperands();
for (OWLClassExpression classExpression : intersectedClassExpressions) {
if (classExpression instanceof OWLObjectSomeValuesFrom)
if (((OWLObjectSomeValuesFrom) classExpression).equals(absentProperty))
return true;
}
} else {
// throw exception; filler of role group must either be a single
// OWLObjectSomeValuesFrom
// constraint or an intersection of OWLObjectSomeValuesFrom constraints
throw new RuntimeException("Error: Filler of the Role-Group property "
+ roleGroupPropertyIri.toString()
+ " must be either an OWLObjectSomeValuesFrom or an OWLObjectIntersectionOf object");
}
}
}
return false;
};
/**
* Specifies the ObjectSomeValuesFrom constraint that defines an 'absent'
* concept in the input OWL ontology. For example, the following parameter
* values for this method:
*
* absenceNamespace = "http://www.hhs.fda.org/shield/SWEC-Ontology"
* absenceProperty = "Situation-Presence" absenceValueNamesapce =
* "http://www.hhs.fda.org/shield/SWEC-Ontology" absenceValueName = "Absent"
*
* would specify that the following ObjectSomeValuesFrom constraint defines an
* 'absent' concept (i.e., a concept is an 'absent' concept if and only if it
* has the following ObjectSomeValuesFrom constraint):
*
* getLogicalAxioms(OWLClass concept, OWLOntology statementOntology) {
Set logicalAxioms = new HashSet();
for (OWLClassAxiom axiom : statementOntology.getAxioms(concept)) {
if (axiom.isLogicalAxiom()) {
logicalAxioms.add(axiom);
}
}
return logicalAxioms;
}
}
