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 static org.semanticweb.owlapi.util.OWLAPIStreamUtils.add;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.atomic.AtomicBoolean;
import javax.annotation.Nullable;
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.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLObjectHasValue;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
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);
protected final OWLOntology inputOntology;
protected final OWLOntologyManager manager;
protected final Visitor visitor;
protected final AbstractDataVisitorEx dataVisitor;
protected final boolean shouldAddExpansionMarker;
protected boolean shouldTransferAnnotations = false;
protected Set extraAnnotations;
/**
* @param ontology ontology to use
*/
public MacroExpansionVisitor(OWLOntology ontology) {
this(ontology, AbstractMacroExpansionVisitor.EMPTY_ANNOTATIONS, false, false);
}
/**
* @param ontology ontology to use
* @param shouldAddExpansionMarker true if expansions should be added
*/
public MacroExpansionVisitor(OWLOntology ontology, boolean shouldAddExpansionMarker) {
this(ontology, AbstractMacroExpansionVisitor.EMPTY_ANNOTATIONS, false,
shouldAddExpansionMarker);
}
/**
* @param ontology ontology to use
* @param shouldTransferAnnotations true if annotations should be transferred
* @param shouldAddExpansionMarker true if expansions should be added
*/
public MacroExpansionVisitor(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 expansions should be added
*/
public MacroExpansionVisitor(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);
visitor.rebuild(inputOntology);
manager = inputOntology.getOWLOntologyManager();
dataVisitor = new AbstractDataVisitorEx(manager.getOWLDataFactory());
}
/**
* @return new MacroExpansions
*/
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();
inputOntology.add(newAxioms);
inputOntology.remove(rmAxioms);
return inputOntology;
}
/**
* @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() {
visitor.getTool().dispose();
}
private class MacroExpansions {
private final Set newAxioms = new HashSet<>();
private final Set rmAxioms = new HashSet<>();
public MacroExpansions() {
inputOntology.axioms(AxiomType.SUBCLASS_OF).forEach(axiom -> {
OWLAxiom newAxiom = axiom.accept(visitor);
replaceIfDifferent(axiom, newAxiom);
});
inputOntology.axioms(AxiomType.EQUIVALENT_CLASSES).forEach(axiom -> {
OWLAxiom newAxiom = axiom.accept(visitor);
replaceIfDifferent(axiom, newAxiom);
});
inputOntology.axioms(AxiomType.CLASS_ASSERTION).forEach(axiom -> {
OWLAxiom newAxiom = axiom.accept(visitor);
replaceIfDifferent(axiom, newAxiom);
});
add(rmAxioms,
inputOntology.axioms(AxiomType.ANNOTATION_ASSERTION).filter(this::expand));
}
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<>();
AtomicBoolean expandedSomething = new AtomicBoolean(false);
try {
if (expandTo != null) {
Set annotations = new HashSet<>(extraAnnotations);
if (shouldAddExpansionMarker) {
annotations.add(visitor.getExpansionMarkerAnnotation());
}
if (shouldTransferAnnotations()) {
add(annotations, axiom.annotations());
}
// 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();
OWLDataFactory dataFactory = visitor.df;
OWLClass axValClass = dataFactory.getOWLClass(axValIRI);
if (asList(inputOntology.declarationAxioms(axValClass)).isEmpty()) {
OWLDeclarationAxiom declarationAxiom =
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
visitor.rebuild(inputOntology);
}
LOG.info("Template to Expand {}", expandTo);
expandTo = expandTo.replaceAll("\\?X",
visitor.getTool().getId((IRI) axiom.getSubject()));
expandTo = expandTo.replaceAll("\\?Y", visitor.getTool().getId(axValIRI));
LOG.info("Expanding {}", expandTo);
try {
expandAndAddAnnotations(expandTo, expandedSomething, annotations);
} catch (Exception ex) {
LOG.error(ex.getMessage(), ex);
}
// TODO:
}
} finally {
inputOntology.remove(declarations);
}
return expandedSomething.get();
}
protected void expandAndAddAnnotations(String expandTo, AtomicBoolean expandedSomething,
Set annotations) {
visitor.getTool().parseManchesterExpressionFrames(expandTo).stream()
.map(axp -> axp.getAxiom())
.map(ax -> shouldTransferAnnotations() ? ax.getAnnotatedAxiom(annotations) : ax)
.forEach(expandedAxiom -> {
newAxioms.add(expandedAxiom);
expandedSomething.set(true);
});
}
}
private class Visitor extends AbstractMacroExpansionVisitor {
Visitor(OWLOntology inputOntology, boolean shouldAddExpansionMarker) {
super(inputOntology, shouldAddExpansionMarker);
rangeVisitor = dataVisitor;
classVisitor = new AbstractMacroExpansionVisitor.AbstractClassExpressionVisitorEx() {
@Override
@Nullable
protected OWLClassExpression expandOWLObjSomeVal(OWLClassExpression filler,
OWLObjectPropertyExpression p) {
return expandObject(filler, p);
}
@Override
@Nullable
protected OWLClassExpression expandOWLObjHasVal(OWLObjectHasValue desc,
OWLIndividual filler, OWLObjectPropertyExpression p) {
OWLClassExpression result = expandObject(filler, p);
if (result != null) {
result = df.getOWLObjectSomeValuesFrom(desc.getProperty(), result);
}
return result;
}
};
}
}
}
