@Grapes([
          @Grab(group='org.semanticweb.elk', module='elk-owlapi', version='0.4.2'),
          @Grab(group='net.sourceforge.owlapi', module='owlapi-api', version='4.1.0'),
          @Grab(group='net.sourceforge.owlapi', module='owlapi-apibinding', version='4.1.0'),
          @Grab(group='net.sourceforge.owlapi', module='owlapi-impl', version='4.1.0'),
          @Grab(group='net.sourceforge.owlapi', module='owlapi-parsers', version='4.1.0'),
          @GrabConfig(systemClassLoader=true)
        ])

import org.semanticweb.owlapi.model.parameters.*
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.elk.owlapi.ElkReasonerConfiguration
import org.semanticweb.elk.reasoner.config.*
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.reasoner.*
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.io.*;
import org.semanticweb.owlapi.owllink.*;
import org.semanticweb.owlapi.util.*;
import org.semanticweb.owlapi.search.*;
import org.semanticweb.owlapi.manchestersyntax.renderer.*;
import org.semanticweb.owlapi.reasoner.structural.*

OWLOntologyManager manager = OWLManager.createOWLOntologyManager()
def ont = manager.loadOntologyFromOntologyDocument(new File("ontology/flopo.owl"))
OWLDataFactory fac = manager.getOWLDataFactory()
ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor()
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor)
ElkReasonerFactory f1 = new ElkReasonerFactory()
OWLReasoner reasoner = f1.createReasoner(ont,config)

reasoner.getEquivalentClasses(fac.getOWLNothing()).each { cl ->
  EntitySearcher.getEquivalentClasses(cl, ont).each { equiv ->
    manager.removeAxiom(ont, fac.getOWLEquivalentClassesAxiom(cl, equiv))
  }
  def anno = fac.getOWLAnnotation(fac.getOWLDeprecated(), fac.getOWLLiteral(true))
  manager.addAxiom(ont, fac.getOWLAnnotationAssertionAxiom(cl.getIRI(), anno))
}

manager.saveOntology(ont, IRI.create("file:/tmp/flopo-clean.owl"))