All Downloads are FREE. Search and download functionalities are using the official Maven repository.
Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance.
Project price only 1 $
You can buy this project and download/modify it how often you want.
org.obolibrary.macro.MacroExpansionVisitor Maven / Gradle / Ivy
package org.obolibrary.macro;
import java.util.HashSet;
import java.util.Set;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLNamedObject;
import org.semanticweb.owlapi.model.OWLObjectHasValue;
import org.semanticweb.owlapi.model.OWLObjectOneOf;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.util.OntologyAxiomPair;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* @author cjm TODO - allow use of prefixes
*/
public class MacroExpansionVisitor {
protected static final Logger LOG =
LoggerFactory.getLogger(MacroExpansionVisitor.class.getName());
@Nonnull
protected final OWLOntology inputOntology;
protected final OWLOntologyManager manager;
protected final Visitor visitor;
protected ManchesterSyntaxTool manchesterSyntaxTool;
protected boolean shouldTransferAnnotations = false;
protected final boolean shouldAddExpansionMarker;
protected Set extraAnnotations;
/**
* @param ontology ontology to visit
*/
public MacroExpansionVisitor(@Nonnull OWLOntology ontology) {
this(ontology, AbstractMacroExpansionVisitor.EMPTY_ANNOTATIONS, false, false);
}
/**
* @param ontology ontology to visit
* @param shouldAddExpansionMarker true if expansion should be added
*/
public MacroExpansionVisitor(@Nonnull OWLOntology ontology, boolean shouldAddExpansionMarker) {
this(ontology, AbstractMacroExpansionVisitor.EMPTY_ANNOTATIONS, false,
shouldAddExpansionMarker);
}
/**
* @param ontology ontology to visit
* @param shouldTransferAnnotations true if annotations should be transferred
* @param shouldAddExpansionMarker true if expansion should be added
*/
public MacroExpansionVisitor(@Nonnull OWLOntology ontology, boolean shouldTransferAnnotations,
boolean shouldAddExpansionMarker) {
this(ontology, AbstractMacroExpansionVisitor.EMPTY_ANNOTATIONS, shouldTransferAnnotations,
shouldAddExpansionMarker);
}
/**
* @param inputOntology input ontology
* @param extraAnnotations extra annotations to add
* @param shouldTransferAnnotations true if annotations should be transferred
* @param shouldAddExpansionMarker true if expansion should be added
*/
public MacroExpansionVisitor(@Nonnull OWLOntology inputOntology,
Set extraAnnotations, boolean shouldTransferAnnotations,
boolean shouldAddExpansionMarker) {
this.inputOntology = inputOntology;
this.extraAnnotations = extraAnnotations;
this.shouldTransferAnnotations = shouldTransferAnnotations;
this.shouldAddExpansionMarker = shouldAddExpansionMarker;
visitor = new Visitor(inputOntology, shouldAddExpansionMarker);
manchesterSyntaxTool = new ManchesterSyntaxTool(inputOntology);
manager = inputOntology.getOWLOntologyManager();
}
/**
* @return macro expansions
*/
@Nonnull
public MacroExpansions getMacroExpansions() {
return new MacroExpansions();
}
/**
* @return ontology with expanded macros
*/
public OWLOntology expandAll() {
MacroExpansions macroExpansions = new MacroExpansions();
Set newAxioms = macroExpansions.getNewAxioms();
Set rmAxioms = macroExpansions.getRmAxioms();
manager.addAxioms(inputOntology, newAxioms);
manager.removeAxioms(inputOntology, rmAxioms);
return inputOntology;
}
private class MacroExpansions {
private final Set newAxioms = new HashSet<>();
private final Set rmAxioms = new HashSet<>();
public MacroExpansions() {
for (OWLSubClassOfAxiom axiom : inputOntology.getAxioms(AxiomType.SUBCLASS_OF)) {
OWLAxiom newAxiom = visitor.visit(axiom);
replaceIfDifferent(axiom, newAxiom);
}
for (OWLEquivalentClassesAxiom axiom : inputOntology
.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
OWLAxiom newAxiom = visitor.visit(axiom);
replaceIfDifferent(axiom, newAxiom);
}
for (OWLClassAssertionAxiom axiom : inputOntology
.getAxioms(AxiomType.CLASS_ASSERTION)) {
OWLAxiom newAxiom = visitor.visit(axiom);
replaceIfDifferent(axiom, newAxiom);
}
for (OWLAnnotationAssertionAxiom axiom : inputOntology
.getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
if (expand(axiom)) {
rmAxioms.add(axiom);
}
}
}
private void replaceIfDifferent(OWLAxiom ax, OWLAxiom exAx) {
if (!ax.equals(exAx)) {
newAxioms.add(exAx);
rmAxioms.add(ax);
}
}
public Set getNewAxioms() {
return newAxioms;
}
public Set getRmAxioms() {
return rmAxioms;
}
private boolean expand(OWLAnnotationAssertionAxiom axiom) {
OWLAnnotationProperty prop = axiom.getProperty();
String expandTo = visitor.expandAssertionToMap.get(prop.getIRI());
HashSet declarations = new HashSet<>();
boolean expandedSomething = false;
try {
if (expandTo != null) {
Set annotations = new HashSet<>(extraAnnotations);
if (shouldAddExpansionMarker) {
annotations.add(visitor.getExpansionMarkerAnnotation());
}
if (shouldTransferAnnotations()) {
annotations.addAll(axiom.getAnnotations());
}
// when expanding assertions, the axiom is an annotation
// assertion,
// and the value may be not be explicitly declared. If it is
// not,
// we assume it is a class
IRI axValIRI = (IRI) axiom.getValue();
OWLClass axValClass = visitor.dataFactory.getOWLClass(axValIRI);
if (inputOntology.getDeclarationAxioms(axValClass).isEmpty()) {
OWLDeclarationAxiom declarationAxiom =
visitor.dataFactory.getOWLDeclarationAxiom(axValClass, annotations);
declarations.add(declarationAxiom);
newAxioms.add(declarationAxiom);
manager.addAxiom(inputOntology, declarationAxiom);
// we need to sync the MST entity checker with the new
// ontology
// plus declarations;
// we do this by creating a new MST - this is not
// particularly
// efficient, a better
// way might be to first scan the ontology for all
// annotation
// axioms that will be expanded,
// then add the declarations at this point
manchesterSyntaxTool = new ManchesterSyntaxTool(inputOntology);
}
LOG.info("Template to Expand {}", expandTo);
expandTo = expandTo.replaceAll("\\?X",
manchesterSyntaxTool.getId((IRI) axiom.getSubject()));
expandTo = expandTo.replaceAll("\\?Y", manchesterSyntaxTool.getId(axValIRI));
LOG.info("Expanding {}", expandTo);
try {
Set setAxp =
manchesterSyntaxTool.parseManchesterExpressionFrames(expandTo);
for (OntologyAxiomPair axp : setAxp) {
OWLAxiom expandedAxiom = axp.getAxiom();
if (shouldTransferAnnotations()) {
expandedAxiom = expandedAxiom.getAnnotatedAxiom(annotations);
}
newAxioms.add(expandedAxiom);
expandedSomething = true;
}
} catch (Exception ex) {
LOG.error(ex.getMessage(), ex);
}
// TODO:
}
} finally {
manager.removeAxioms(inputOntology, declarations);
}
return expandedSomething;
}
}
private class Visitor extends AbstractMacroExpansionVisitor {
Visitor(OWLOntology inputOntology, boolean shouldAddExpansionMarker) {
super(inputOntology, shouldAddExpansionMarker);
}
@Override
protected OWLClassExpression expandOWLObjSomeVal(OWLClassExpression filler,
OWLObjectPropertyExpression p) {
return expandObject(filler, p);
}
@Override
protected OWLClassExpression expandOWLObjHasVal(OWLObjectHasValue desc,
OWLIndividual filler, OWLObjectPropertyExpression p) {
OWLClassExpression result = expandObject(filler, p);
if (result != null) {
result = dataFactory.getOWLObjectSomeValuesFrom(desc.getProperty(), result);
}
return result;
}
@Nullable
OWLClassExpression expandObject(Object filler, OWLObjectPropertyExpression p) {
OWLClassExpression result = null;
IRI iri = ((OWLObjectProperty) p).getIRI();
IRI templateVal = null;
if (expandExpressionMap.containsKey(iri)) {
if (filler instanceof OWLObjectOneOf) {
Set inds = ((OWLObjectOneOf) filler).getIndividuals();
if (inds.size() == 1) {
OWLIndividual ind = inds.iterator().next();
if (ind instanceof OWLNamedIndividual) {
templateVal = ((OWLNamedObject) ind).getIRI();
}
}
}
if (filler instanceof OWLNamedObject) {
templateVal = ((OWLNamedObject) filler).getIRI();
}
if (templateVal != null) {
String tStr = expandExpressionMap.get(iri);
String exStr = tStr.replaceAll("\\?Y", manchesterSyntaxTool.getId(templateVal));
try {
result = manchesterSyntaxTool.parseManchesterExpression(exStr);
} catch (OWLParserException e) {
LOG.error(e.getMessage(), e);
}
}
}
return result;
}
}
/**
* @return true if annotations should be transferred
*/
public boolean shouldTransferAnnotations() {
return shouldTransferAnnotations;
}
/**
* @param shouldTransferAnnotations new value
*/
public void setShouldTransferAnnotations(boolean shouldTransferAnnotations) {
this.shouldTransferAnnotations = shouldTransferAnnotations;
}
/** Call this method to clear internal references. */
public void dispose() {
manchesterSyntaxTool.dispose();
}
}
