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refactor unsat object-checking to leverage object hierarchy, for reasoners that support that #1100

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May 3, 2023
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refactor unsat object-checking to leverage object hierarchy, for reasoners that support that #1100

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19bc219
refactor unsatisfiable object-checking to leverage object hierarchy, …
jclerman Feb 28, 2023
514a006
Describe #1100 in CHANGELOG
jclerman Feb 28, 2023
0b747a5
remove redundant logger lines
jclerman Mar 1, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

### Changed
- Speed up unsatisfiable object-property check on certain reasoners including HermiT [#1100]

## [1.9.3] - 2023-02-16

### Added
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103 changes: 72 additions & 31 deletions robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java
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Expand Up @@ -13,6 +13,7 @@
import org.obolibrary.robot.reason.InferredSubObjectPropertyAxiomGeneratorIncludingIndirect;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.util.*;
import org.slf4j.Logger;
Expand All @@ -36,6 +37,72 @@ public class ReasonerHelper {
/** Logger. */
private static final Logger logger = LoggerFactory.getLogger(ReasonerHelper.class);

/**
* Check an ontology for unsatisfiable object properties.
*
* @param reasoner OWLReasoner being used.
* @return A set of unsatisfiable OWLObjectProperty objects (will be empty if none are found).
*/
public static Set<OWLObjectProperty> getUnsatisfiableObjectProperties(OWLReasoner reasoner) {
Set<OWLObjectProperty> unsatObjectProps = new HashSet<>();

if (reasoner
.getPrecomputableInferenceTypes()
.contains(InferenceType.OBJECT_PROPERTY_HIERARCHY)) {
// Fast object-unsat check
logger.info(
"Object-property precomputation is supported; using that to find unsatisfiable object properties...");
reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);
Set<OWLObjectPropertyExpression> unsatObjPropExps =
reasoner.getBottomObjectPropertyNode().getEntitiesMinusBottom();
for (OWLObjectPropertyExpression uOPE : unsatObjPropExps) {
if (uOPE.isNamed()) {
unsatObjectProps.add(uOPE.asOWLObjectProperty());
}
}
} else {
// Have to do this the slow way
OWLOntology ont = reasoner.getRootOntology();
OWLOntologyManager manager = ont.getOWLOntologyManager();
OWLDataFactory dataFactory = manager.getOWLDataFactory();
OWLClass thing = dataFactory.getOWLThing();
Set<OWLAxiom> tempAxioms = new HashSet<>();
Map<OWLClass, OWLObjectProperty> probeFor = new HashMap<>();

for (OWLObjectProperty p : ont.getObjectPropertiesInSignature(Imports.INCLUDED)) {
UUID uuid = UUID.randomUUID();
IRI probeIRI = IRI.create(p.getIRI().toString() + "-" + uuid.toString());
OWLClass probe = dataFactory.getOWLClass(probeIRI);
probeFor.put(probe, p);
tempAxioms.add(dataFactory.getOWLDeclarationAxiom(probe));
tempAxioms.add(
dataFactory.getOWLSubClassOfAxiom(
probe, dataFactory.getOWLObjectSomeValuesFrom(p, thing)));
}
manager.addAxioms(ont, tempAxioms);
reasoner.flush();

Set<OWLClass> unsatisfiableProbeClasses =
reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();

// leave no trace
manager.removeAxioms(ont, tempAxioms);
reasoner.flush();

if (unsatisfiableProbeClasses.size() > 0) {
logger.error(
"There are {} unsatisfiable properties in the ontology.",
unsatisfiableProbeClasses.size());
for (OWLClass cls : unsatisfiableProbeClasses) {
OWLObjectProperty unsatP = probeFor.get(cls);
unsatObjectProps.add(unsatP);
logger.error(" unsatisfiable property: " + unsatP.getIRI());
}
}
}
return unsatObjectProps;
}

/**
* Validates ontology.
*
Expand Down Expand Up @@ -118,40 +185,14 @@ public static void validate(
throw new IncoherentTBoxException(unsatisfiableClasses);
}

// TODO: can this be done by checking for equivalence to bottomObjectProperty?
logger.info("Checking for unsatisfiable object properties...");

Set<OWLAxiom> tempAxioms = new HashSet<>();
Map<OWLClass, OWLObjectProperty> probeFor = new HashMap<>();
for (OWLObjectProperty p : ont.getObjectPropertiesInSignature(Imports.INCLUDED)) {
UUID uuid = UUID.randomUUID();
IRI probeIRI = IRI.create(p.getIRI().toString() + "-" + uuid.toString());
OWLClass probe = dataFactory.getOWLClass(probeIRI);
probeFor.put(probe, p);
tempAxioms.add(dataFactory.getOWLDeclarationAxiom(probe));
tempAxioms.add(
dataFactory.getOWLSubClassOfAxiom(
probe, dataFactory.getOWLObjectSomeValuesFrom(p, thing)));
}
manager.addAxioms(ont, tempAxioms);
reasoner.flush();

Set<OWLClass> unsatisfiableProbeClasses =
reasoner.getUnsatisfiableClasses().getEntitiesMinus(nothing);

// leave no trace
manager.removeAxioms(ont, tempAxioms);
reasoner.flush();
Set<OWLObjectProperty> unsatPs = getUnsatisfiableObjectProperties(reasoner);

if (unsatisfiableProbeClasses.size() > 0) {
logger.error(
"There are {} unsatisfiable properties in the ontology.",
unsatisfiableProbeClasses.size());
Set<OWLObjectProperty> unsatPs = new HashSet<>();
for (OWLClass cls : unsatisfiableProbeClasses) {
OWLObjectProperty unsatP = probeFor.get(cls);
unsatPs.add(unsatP);
logger.error(" unsatisfiable property: " + unsatP.getIRI());
if (unsatPs.size() > 0) {
logger.error("There are {} unsatisfiable properties in the ontology.", unsatPs.size());
for (OWLObjectProperty p : unsatPs) {
logger.error(" unsatisfiable property: " + p.getIRI());
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Isnt this log output redundant with the one in the end of getUnsatisfiableObjectProperties?

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Thanks @matentzn - yes indeed. Fixed in a new commit.

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Nice :)

}
throw new IncoherentRBoxException(unsatPs);
}
Expand Down
44 changes: 28 additions & 16 deletions robot-core/src/test/java/org/obolibrary/robot/ReasonerHelperTest.java
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Expand Up @@ -3,6 +3,8 @@
import static org.junit.Assert.*;

import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Set;
import org.junit.Test;
import org.obolibrary.robot.exceptions.IncoherentRBoxException;
Expand Down Expand Up @@ -34,16 +36,21 @@ public class ReasonerHelperTest extends CoreTest {
public void testIncoherentRBox()
throws IOException, IncoherentTBoxException, InconsistentOntologyException {
OWLOntology ontology = loadOntology("/incoherent-rbox.owl");
OWLReasonerFactory reasonerFactory = new org.semanticweb.elk.owlapi.ElkReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
boolean isCaughtException = false;
try {
ReasonerHelper.validate(reasoner);
List<OWLReasonerFactory> factories =
Arrays.asList(
new org.semanticweb.elk.owlapi.ElkReasonerFactory(),
new org.semanticweb.HermiT.ReasonerFactory());
for (OWLReasonerFactory reasonerFactory : factories) {
OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
boolean isCaughtException = false;
try {
ReasonerHelper.validate(reasoner);

} catch (IncoherentRBoxException e) {
isCaughtException = true;
} catch (IncoherentRBoxException e) {
isCaughtException = true;
}
assertTrue(isCaughtException);
}
assertTrue(isCaughtException);
}

/**
Expand All @@ -57,16 +64,21 @@ public void testIncoherentRBox()
public void testIncoherentTBox()
throws IOException, InconsistentOntologyException, IncoherentRBoxException {
OWLOntology ontology = loadOntology("/incoherent-tbox.owl");
OWLReasonerFactory reasonerFactory = new org.semanticweb.elk.owlapi.ElkReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
boolean isCaughtException = false;
try {
ReasonerHelper.validate(reasoner);
List<OWLReasonerFactory> factories =
Arrays.asList(
new org.semanticweb.elk.owlapi.ElkReasonerFactory(),
new org.semanticweb.HermiT.ReasonerFactory());
for (OWLReasonerFactory reasonerFactory : factories) {
OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
boolean isCaughtException = false;
try {
ReasonerHelper.validate(reasoner);

} catch (IncoherentTBoxException e) {
isCaughtException = true;
} catch (IncoherentTBoxException e) {
isCaughtException = true;
}
assertTrue(isCaughtException);
}
assertTrue(isCaughtException);
}

/**
Expand Down