use of org.semanticweb.owlapi.reasoner.ReasonerProgressMonitor in project goci by EBISPOT.
the class ReasonedOntologyLoader method indexOntology.
protected OWLOntology indexOntology(OWLOntology ontology) throws OWLOntologyCreationException {
getLog().debug("Trying to create a reasoner over ontology '" + getOntologyURI() + "'");
OWLReasonerFactory factory = new Reasoner.ReasonerFactory();
ReasonerProgressMonitor progressMonitor = new LoggingReasonerProgressMonitor(getLog());
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
this.reasoner = factory.createReasoner(ontology, config);
getLog().debug("Precomputing inferences...");
reasoner.precomputeInferences();
getLog().debug("Checking ontology consistency...");
reasoner.isConsistent();
getLog().debug("Checking for unsatisfiable classes...");
if (reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size() > 0) {
throw new OWLOntologyCreationException("Once classified, unsatisfiable classes were detected in '" + getOntologyIRI() + "'");
} else {
getLog().debug("Reasoning complete! ");
}
Set<OWLClass> allClasses = ontology.getClassesInSignature();
removeExcludedClasses(ontology, allClasses, superclass -> reasoner.getSubClasses(superclass, false).getFlattened());
int labelCount = 0;
int labelledClassCount = 0;
int synonymCount = 0;
int synonymedClassCount = 0;
getLog().debug("Loading " + allClasses.size() + " classes...");
for (OWLClass ontologyClass : allClasses) {
IRI clsIri = ontologyClass.getIRI();
// get IRI fragment/path
Optional<String> accession = evaluateAccessionValue(ontology, ontologyClass);
if (accession.isPresent()) {
addClassAccession(clsIri, accession.get());
}
// get label annotations
Optional<String> label = evaluateLabelAnnotationValue(ontology, ontologyClass);
if (label.isPresent()) {
addClassLabel(clsIri, label.get());
labelledClassCount++;
labelCount++;
}
// get all synonym annotations
getLog().trace("Loading synonyms of " + clsIri.toString() + "...");
Set<String> synonyms = evaluateSynonymAnnotationValues(ontology, ontologyClass);
if (!synonyms.isEmpty()) {
addSynonyms(clsIri, synonyms);
synonymCount += synonyms.size();
synonymedClassCount++;
}
// get parent labels
getLog().trace("Loading parents of " + clsIri.toString() + "...");
Set<OWLClass> parents = reasoner.getSuperClasses(ontologyClass, false).getFlattened();
// only add type if the parent isn't excluded
Set<String> parentLabelSet = parents.stream().filter(allClasses::contains).peek(parent -> getLog().trace("Next parent of " + label + ": " + parent)).map(parent -> evaluateLabelAnnotationValue(ontology, parent)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
// always also add current class to the parents
label.ifPresent(parentLabelSet::add);
addClassParentLabels(clsIri, parentLabelSet);
// get child labels
getLog().trace("Loading children of " + clsIri.toString() + "...");
Set<OWLClass> children = reasoner.getSubClasses(ontologyClass, false).getFlattened();
// only add type if the child isn't excluded
Set<String> childLabelSet = children.stream().filter(allClasses::contains).peek(child -> getLog().trace("Next child of " + label + ": " + child)).map(child -> evaluateLabelAnnotationValue(ontology, child)).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toSet());
// always also add current class to the parents
label.ifPresent(childLabelSet::add);
addClassChildLabels(clsIri, childLabelSet);
}
getLog().debug("Successfully indexed " + labelCount + " labels on " + labelledClassCount + " classes and " + synonymCount + " synonyms on " + synonymedClassCount + " classes!");
return ontology;
}
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