org.obolibrary.macro.ManchesterSyntaxTool Maven / Gradle / Ivy
package org.obolibrary.macro;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.atomic.AtomicBoolean;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.obolibrary.obo2owl.OWLAPIObo2Owl;
import org.obolibrary.oboformat.model.OBODoc;
import org.semanticweb.owlapi.OWLAPIConfigProvider;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
import org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl;
import org.semanticweb.owlapi.manchestersyntax.renderer.ParserException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationSubject;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.util.BidirectionalShortFormProviderAdapter;
import org.semanticweb.owlapi.util.IRIShortFormProvider;
import org.semanticweb.owlapi.util.OntologyAxiomPair;
import org.semanticweb.owlapi.util.ShortFormProvider;
import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
import org.semanticweb.owlapi.util.mansyntax.ManchesterOWLSyntaxParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* wrapper for parsing Manchester Syntax.
*
* @author heiko
*/
public class ManchesterSyntaxTool {
private static final Logger LOG = LoggerFactory
.getLogger(ManchesterSyntaxTool.class);
@Nonnull
protected final IRIShortFormProvider iriShortFormProvider = new SimpleIRIShortFormProvider();
@Nonnull
private final OWLDataFactory dataFactory;
@Nonnull
private final AdvancedEntityChecker entityChecker;
@Nonnull
private final ShortFormProvider shortFormProvider = new ShortFormProvider() {
@Override
public void dispose() {
// do nothing
}
@Override
public String getShortForm(@Nonnull OWLEntity entity) {
return iriShortFormProvider.getShortForm(entity.getIRI());
}
};
private final AtomicBoolean disposed = new AtomicBoolean(false);
/**
* Create a new parser instance for the given ontology. By default, this
* parser will also try to resolve OWLObjects via their identifier or
* rdfs:label.
*
* @param inputOntology
* inputOntology
*/
public ManchesterSyntaxTool(@Nonnull OWLOntology inputOntology) {
this(inputOntology, null);
}
/**
* Create a new parser instance for the given ontologies. By default, this
* parser will also try to resolve OWLObjects via their identifier or
* rdfs:label.
*
* @param inputOntology
* inputOntology
* @param auxiliaryOntologies
* set of additional ontologies or null
*/
public ManchesterSyntaxTool(@Nonnull OWLOntology inputOntology,
@Nullable Collection auxiliaryOntologies) {
OWLOntologyManager manager = inputOntology.getOWLOntologyManager();
dataFactory = manager.getOWLDataFactory();
Set ontologies = new HashSet<>(
inputOntology.getImportsClosure());
if (auxiliaryOntologies != null && !auxiliaryOntologies.isEmpty()) {
for (OWLOntology auxOnt : auxiliaryOntologies) {
ontologies.addAll(auxOnt.getImportsClosure());
}
}
ShortFormEntityChecker defaultInstance = new ShortFormEntityChecker(
new BidirectionalShortFormProviderAdapter(manager, ontologies,
shortFormProvider));
entityChecker = new AdvancedEntityChecker(defaultInstance, ontologies,
inputOntology.getOWLOntologyManager());
}
/**
* Parse frame expressions in Manchester syntax.
*
* @param expression
* expression
* @return set of {@link OntologyAxiomPair}
* @throws ParserException
* parser exception
*/
public Set parseManchesterExpressionFrames(
@Nonnull String expression) {
ManchesterOWLSyntaxParser parser = createParser(expression);
return parser.parseFrames();
}
/**
* Parse a class expression in Manchester syntax.
*
* @param expression
* expression
* @return {@link OWLClassExpression}
* @throws ParserException
* parser exception
*/
public OWLClassExpression parseManchesterExpression(
@Nonnull String expression) {
ManchesterOWLSyntaxParser parser = createParser(expression);
return parser.parseClassExpression();
}
@Nonnull
private ManchesterOWLSyntaxParser createParser(@Nonnull String expression) {
if (disposed.get()) {
throw new OWLRuntimeException(
"Illegal State: Trying to use an disposed instance.");
}
ManchesterOWLSyntaxParser parser = new ManchesterOWLSyntaxParserImpl(
new OWLAPIConfigProvider(), dataFactory);
parser.setStringToParse(expression);
parser.setOWLEntityChecker(entityChecker);
LOG.info("parsing: {}", expression);
return parser;
}
/**
* Translate the {@link IRI} into the short form as expected by the parser.
*
* @param iri
* iri
* @return short form
*/
public String getId(@Nonnull IRI iri) {
if (disposed.get()) {
throw new OWLRuntimeException(
"Illegal State: Trying to use an disposed instance.");
}
return iriShortFormProvider.getShortForm(iri);
}
/**
* Translate the {@link OWLEntity} identifier into the short form as
* expected by the parser.
*
* @param entity
* entity
* @return short form
*/
public String getId(@Nonnull OWLEntity entity) {
if (disposed.get()) {
throw new OWLRuntimeException(
"Illegal State: Trying to use an disposed instance.");
}
return shortFormProvider.getShortForm(entity);
}
/**
* {@link OWLEntityChecker} which additionally checks for corresponding
* identifiers and labels to retrieve entities. The intended behavior is
* specified as follows:
*
* - If the string is enclosed with matching single quotes, try to resolve
* as label
* - Otherwise, try to resolve as identifier
*
*/
static class AdvancedEntityChecker implements OWLEntityChecker {
private final OWLEntityChecker defaultInstance;
private final Set ontologies;
private final OWLOntologyManager manager;
/**
* @param defaultInstance
* defaultInstance
* @param ontologies
* ontologies
* @param manager
* manager
*/
AdvancedEntityChecker(OWLEntityChecker defaultInstance,
Set ontologies, OWLOntologyManager manager) {
this.defaultInstance = defaultInstance;
this.ontologies = ontologies;
this.manager = manager;
}
@Nullable
@Override
public OWLClass getOWLClass(@Nonnull String name) {
OWLClass owlClass = defaultInstance.getOWLClass(name);
if (owlClass == null) {
IRI iri = getIRI(name);
if (iri != null) {
owlClass = getOWLClass(iri);
}
}
return owlClass;
}
@Nullable
@Override
public OWLObjectProperty getOWLObjectProperty(@Nonnull String name) {
OWLObjectProperty owlObjectProperty = defaultInstance
.getOWLObjectProperty(name);
if (owlObjectProperty == null) {
IRI iri = getIRI(name);
if (iri != null) {
owlObjectProperty = getOWLObjectProperty(iri);
}
}
return owlObjectProperty;
}
@Override
public OWLDataProperty getOWLDataProperty(String name) {
return defaultInstance.getOWLDataProperty(name);
}
@Nullable
@Override
public OWLNamedIndividual getOWLIndividual(@Nonnull String name) {
OWLNamedIndividual owlIndividual = defaultInstance
.getOWLIndividual(name);
if (owlIndividual == null) {
IRI iri = getIRI(name);
if (iri != null) {
owlIndividual = getOWLIndividual(iri);
}
}
return owlIndividual;
}
@Override
public OWLDatatype getOWLDatatype(String name) {
return defaultInstance.getOWLDatatype(name);
}
@Override
public OWLAnnotationProperty getOWLAnnotationProperty(String name) {
return defaultInstance.getOWLAnnotationProperty(name);
}
@SuppressWarnings("null")
@Nullable
IRI getIRI(@Nonnull String name) {
if (isQuoted(name)) {
// anything in '....' quotes is a label
return getIRIByLabel(name.substring(1, name.length() - 1));
}
if (name.length() > 2 && name.charAt(0) == '<'
&& name.charAt(name.length() - 1) == '>') {
// anything between <...> brackets is a complete IRI
return IRI.create(name.substring(1, name.length() - 1));
}
return getIRIByIdentifier(name);
}
private static boolean isQuoted(@Nonnull String s) {
int length = s.length();
if (length >= 2) {
return s.charAt(0) == '\'' && s.charAt(length - 1) == '\'';
}
return false;
}
@Nullable
IRI getIRIByIdentifier(@Nonnull String id) {
OWLAPIObo2Owl b = new OWLAPIObo2Owl(manager);
b.setObodoc(new OBODoc());
return b.oboIdToIRI(id);
}
/**
* Retrieve an {@link IRI} by rdfs:label.
*
* @param label
* label
* @return {@link IRI} or null
*/
@Nullable
IRI getIRIByLabel(@Nonnull String label) {
for (OWLOntology o : ontologies) {
Set aas = o
.getAxioms(AxiomType.ANNOTATION_ASSERTION);
for (OWLAnnotationAssertionAxiom aa : aas) {
OWLAnnotationValue v = aa.getValue();
OWLAnnotationProperty property = aa.getProperty();
if (isMatchingLabel(label, v, property)) {
OWLAnnotationSubject obj = aa.getSubject();
if (obj instanceof IRI) {
return (IRI) obj;
}
}
}
}
return null;
}
/**
* @param label
* label to match
* @param v
* annotation value
* @param property
* property to check
* @return true if property is a label, v is a literal and v matches
* label
*/
protected boolean isMatchingLabel(String label, OWLAnnotationValue v,
OWLAnnotationProperty property) {
return property.isLabel() && v instanceof OWLLiteral
&& label.equals(((OWLLiteral) v).getLiteral());
}
/**
* Retrieve the {@link OWLClass} for a given {@link IRI}, if it has at
* least one {@link OWLDeclarationAxiom}.
*
* @param iri
* iri
* @return {@link OWLClass} or null
*/
@Nullable
OWLClass getOWLClass(@Nonnull IRI iri) {
for (OWLOntology o : ontologies) {
OWLClass c = o.getOWLOntologyManager().getOWLDataFactory()
.getOWLClass(iri);
if (!o.getDeclarationAxioms(c).isEmpty()) {
return c;
}
if (o.getOWLOntologyManager().getOWLDataFactory()
.getOWLNothing().equals(c)) {
return c;
}
}
return null;
}
/**
* Retrieve the {@link OWLNamedIndividual} for a given {@link IRI}, if
* it has at least one corresponding {@link OWLDeclarationAxiom}.
*
* @param iri
* iri
* @return {@link OWLNamedIndividual} or null
*/
@Nullable
OWLNamedIndividual getOWLIndividual(@Nonnull IRI iri) {
for (OWLOntology o : ontologies) {
OWLNamedIndividual c = o.getOWLOntologyManager()
.getOWLDataFactory().getOWLNamedIndividual(iri);
for (OWLDeclarationAxiom da : o.getDeclarationAxioms(c)) {
if (da.getEntity() instanceof OWLNamedIndividual) {
return (OWLNamedIndividual) da.getEntity();
}
}
}
return null;
}
/**
* Retrieve the {@link OWLObjectProperty} for a given {@link IRI}, if it
* has at least one {@link OWLDeclarationAxiom}.
*
* @param iri
* iri
* @return {@link OWLObjectProperty} or null
*/
@Nullable
OWLObjectProperty getOWLObjectProperty(@Nonnull IRI iri) {
for (OWLOntology o : ontologies) {
OWLObjectProperty p = o.getOWLOntologyManager()
.getOWLDataFactory().getOWLObjectProperty(iri);
if (!o.getDeclarationAxioms(p).isEmpty()) {
return p;
}
}
return null;
}
}
/**
* Call this method to dispose the internal data structures. This will
* remove also the listeners registered with the ontology manager.
*/
public void dispose() {
if (!disposed.getAndSet(true)) {
shortFormProvider.dispose();
}
}
}