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Throws exceptions if ontology logically incoherent, fixes #40
Includes incoherent OPs in logical tests, fixes #104 Note these two tickets are coupled, so were tackled together. To handle validation checks a new ReasonerHelper class was created. This implements - inconsistency - incoherent TBox (ie unsat classes) - incoherent RBox (using probe classes) Exceptions are thrown on encountering any of these. Currently there is no way to allow the user to ignore exceptions; this could in theory be added but would likely be a very bady idea
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106 changes: 106 additions & 0 deletions
106
robot-core/src/main/java/org/obolibrary/robot/ReasonerHelper.java
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| package org.obolibrary.robot; | ||
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| import java.util.HashMap; | ||
| import java.util.HashSet; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
| import java.util.UUID; | ||
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| import org.obolibrary.robot.exceptions.IncoherentTBoxException; | ||
| import org.obolibrary.robot.exceptions.IncoherentRBoxException; | ||
| import org.obolibrary.robot.exceptions.InconsistentOntologyException; | ||
| import org.semanticweb.owlapi.model.IRI; | ||
| import org.semanticweb.owlapi.model.OWLAxiom; | ||
| import org.semanticweb.owlapi.model.OWLClass; | ||
| import org.semanticweb.owlapi.model.OWLDataFactory; | ||
| import org.semanticweb.owlapi.model.OWLObjectProperty; | ||
| import org.semanticweb.owlapi.model.OWLOntology; | ||
| import org.semanticweb.owlapi.model.OWLOntologyManager; | ||
| import org.semanticweb.owlapi.model.parameters.Imports; | ||
| import org.semanticweb.owlapi.reasoner.InferenceType; | ||
| import org.semanticweb.owlapi.reasoner.Node; | ||
| import org.semanticweb.owlapi.reasoner.OWLReasoner; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| /** | ||
| * | ||
| * Provides convenience methods for working with OWL reasoning. | ||
| * | ||
| * @author cjm | ||
| * | ||
| */ | ||
| public class ReasonerHelper { | ||
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| /** | ||
| * Logger. | ||
| */ | ||
| private static final Logger logger = | ||
| LoggerFactory.getLogger(ReasonerHelper.class); | ||
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| public static void validate(OWLReasoner reasoner) throws IncoherentTBoxException, InconsistentOntologyException, IncoherentRBoxException { | ||
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| OWLOntology ont = reasoner.getRootOntology(); | ||
| OWLOntologyManager manager = ont.getOWLOntologyManager(); | ||
| OWLDataFactory dataFactory = manager.getOWLDataFactory(); | ||
| OWLClass nothing = dataFactory.getOWLNothing(); | ||
| OWLClass thing = dataFactory.getOWLThing(); | ||
| logger.info("Checking for inconsistencies"); | ||
| if (!reasoner.isConsistent()) { | ||
| throw new InconsistentOntologyException(); | ||
| } | ||
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| logger.info("Checking for unsatisfiable classes..."); | ||
| Set<OWLClass> unsatisfiableClasses = | ||
| reasoner.getUnsatisfiableClasses().getEntitiesMinus(nothing); | ||
| if (unsatisfiableClasses.size() > 0) { | ||
| logger.error("There are {} unsatisfiable classes in the ontology.", | ||
| unsatisfiableClasses.size()); | ||
| for (OWLClass cls : unsatisfiableClasses) { | ||
| logger.error(" unsatisfiable: " + cls.getIRI()); | ||
| } | ||
| throw new IncoherentTBoxException(unsatisfiableClasses); | ||
| } | ||
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| logger.info("Checking for unsatisfiable object properties..."); | ||
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| 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(); | ||
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| Set<OWLClass> unsatisfiableProbeClasses = | ||
| reasoner.getUnsatisfiableClasses().getEntitiesMinus(nothing); | ||
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| // leave no trace | ||
| manager.removeAxioms(ont, tempAxioms); | ||
| reasoner.flush(); | ||
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| 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()); | ||
| } | ||
| throw new IncoherentRBoxException(unsatPs); | ||
| } | ||
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| } | ||
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| } |
22 changes: 22 additions & 0 deletions
22
robot-core/src/main/java/org/obolibrary/robot/exceptions/IncoherentRBoxException.java
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| @@ -0,0 +1,22 @@ | ||
| package org.obolibrary.robot.exceptions; | ||
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| import java.util.Set; | ||
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| import org.semanticweb.owlapi.model.OWLClass; | ||
| import org.semanticweb.owlapi.model.OWLEntity; | ||
| import org.semanticweb.owlapi.model.OWLObject; | ||
| import org.semanticweb.owlapi.model.OWLObjectProperty; | ||
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| /** | ||
| * Ontology contains unsatisfiable properties | ||
| * | ||
| * @author cjm | ||
| * | ||
| */ | ||
| public class IncoherentRBoxException extends OntologyLogicException { | ||
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| public IncoherentRBoxException(Set<OWLObjectProperty> unsatisfiableProperties) { | ||
| // TODO Auto-generated constructor stub | ||
| } | ||
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| } |
21 changes: 21 additions & 0 deletions
21
robot-core/src/main/java/org/obolibrary/robot/exceptions/IncoherentTBoxException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,21 @@ | ||
| package org.obolibrary.robot.exceptions; | ||
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| import java.util.Set; | ||
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| import org.semanticweb.owlapi.model.OWLClass; | ||
| import org.semanticweb.owlapi.model.OWLEntity; | ||
| import org.semanticweb.owlapi.model.OWLObject; | ||
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| /** | ||
| * Ontology contains unsatisfiable classes | ||
| * | ||
| * @author cjm | ||
| * | ||
| */ | ||
| public class IncoherentTBoxException extends OntologyLogicException { | ||
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| public IncoherentTBoxException(Set<OWLClass> unsatisfiableClasses) { | ||
| // TODO Auto-generated constructor stub | ||
| } | ||
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| } |
13 changes: 13 additions & 0 deletions
13
robot-core/src/main/java/org/obolibrary/robot/exceptions/InconsistentOntologyException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| package org.obolibrary.robot.exceptions; | ||
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| /** | ||
| * Ontology contains logical inconsistencies | ||
| * | ||
| * Note inconsistency is not the same as incoherency | ||
| * | ||
| * @author cjm | ||
| * | ||
| */ | ||
| public class InconsistentOntologyException extends OntologyLogicException { | ||
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| } |
11 changes: 11 additions & 0 deletions
11
robot-core/src/main/java/org/obolibrary/robot/exceptions/OntologyLogicException.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| package org.obolibrary.robot.exceptions; | ||
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| /** | ||
| * Ontology contains unsatisfiable classes, properties or inconsistencies | ||
| * | ||
| * @author cjm | ||
| * | ||
| */ | ||
| public class OntologyLogicException extends Exception { | ||
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| } |
8 changes: 8 additions & 0 deletions
8
robot-core/src/main/java/org/obolibrary/robot/exceptions/package-info.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,8 @@ | ||
| /** | ||
| * | ||
| */ | ||
| /** | ||
| * @author cjm | ||
| * | ||
| */ | ||
| package org.obolibrary.robot.exceptions; |
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