[jamesaoverton]

The Protégé project is upgrading to OWL API 5.5.1 and we want ROBOT to stay in sync. protegeproject/protege#1351

Here is the OWL API migration guide.

The code is compiling and the unit tests are passing, with the exception of some now marked @Ignored (see below). The command line integration tests are not yet passing.

Done:

• migrate from Guava Optional to java,utl.Optional
  • replace .or() with orElse()
  • replace .orNull() with .orElse(null)
  • sometimes use .orElseThrow(...)
• convert EntitySearcher streams back into collections by adding .collect(Collectors.toList())
• update HermiT to 1.4.5.519 -- but see this issue Update and verify bundled HermiT for Protégé 6 protegeproject/protege#1352
• update JFact to 5.0.3
• update owlexplanation to 5.0.1 and make minor API changes
• rename *PrefixOWLOntologyFormat to *PrefixOWLDocumentFormat
• replace various Set<_> with Stream<_>, and replace .size() with .count()
• remove ReferencedEntitySetProvider and replace with ontology.getSignature(Imports.INCLUDED)
• remove try/catch when certain exceptions can no longer be thrown, e.g. RioRenderer no longer throws IOException
• rename OntologyHelper.getObjects(OWLAxiom) to getAxiomObjects(OWLAxiom), avoiding an ambiguity with getObjects(OWLOntology) -- this breaks our japicmp backwards compatibility checks, but I don't think it can be helped
• replace OWLOntologyLoaderConfiguration with OntologyConfigurator
• update owl-diff @balhoff -- many of our tests rely on diffs, and these are all disabled for now

To Do:

• update ELK Provide and verify an OWL API 5-compatible ELK plugin for Protégé 6 protegeproject/protege#1356
• update Whelk @balhoff
• update obographs for some JSON formats @matentzn
• update relation graph for extract subset (specifically scowl?) @balhoff
• update org.geneontology.reasoner.ExpressionMaterializingReasonerFactory from https://github.com/owlcollab/expression-materializing-reasoner @matentzn
• fix null pointer errors in MeasureOperation @matentzn
• fix all @Ignore tests
• restore japicmp tests for backwards compatibility

[jamesaoverton]

This method is required to implement HasGetOntologies.