Error in loading ontologies

[rpgoldman]

Previously, I had a single main ontology that imported all of the others, and I used that ontology's IRI in the owlery configuration file.

I now have two such ontologies, so instead of having the IRI of the single "leaf" ontology, I replaced that with the pathname of the directory holding all of my OWL files.

Now I get the following error trying to start up Owlery:

Exception in thread "main" java.lang.ExceptionInInitializerError
	at org.phenoscape.owlery.Main$.initializeReasoners(Main.scala:81)
	at org.phenoscape.owlery.Main$.delayedEndpoint$org$phenoscape$owlery$Main$1(Main.scala:83)
	at org.phenoscape.owlery.Main$delayedInit$body.apply(Main.scala:23)
	at scala.Function0.apply$mcV$sp(Function0.scala:39)
	at scala.Function0.apply$mcV$sp$(Function0.scala:39)
	at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
	at scala.App.$anonfun$main$1(App.scala:76)
	at scala.App.$anonfun$main$1$adapted(App.scala:76)
	at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563)
	at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:919)
	at scala.App.main(App.scala:76)
	at scala.App.main$(App.scala:74)
	at org.phenoscape.owlery.Main$.main(Main.scala:23)
	at org.phenoscape.owlery.Main.main(Main.scala)
Caused by: org.semanticweb.owlapi.model.OWLOntologyDocumentAlreadyExistsException
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1130)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1097)
	at org.phenoscape.owlery.Owlery$.$anonfun$loadOntologyFromFolder$2(Owlery.scala:69)
	at scala.collection.StrictOptimizedIterableOps.map(StrictOptimizedIterableOps.scala:99)
	at scala.collection.StrictOptimizedIterableOps.map$(StrictOptimizedIterableOps.scala:86)
	at scala.collection.mutable.ArrayBuffer.map(ArrayBuffer.scala:42)
	at org.phenoscape.owlery.Owlery$.loadOntologyFromFolder(Owlery.scala:69)
	at org.phenoscape.owlery.Owlery$.loadKnowledgebase(Owlery.scala:54)
	at org.phenoscape.owlery.Owlery$.$anonfun$loadKnowledgebases$1(Owlery.scala:48)
	at scala.collection.StrictOptimizedIterableOps.map(StrictOptimizedIterableOps.scala:99)
	at scala.collection.StrictOptimizedIterableOps.map$(StrictOptimizedIterableOps.scala:86)
	at scala.collection.immutable.Set$Set1.map(Set.scala:156)
	at org.phenoscape.owlery.Owlery$.loadKnowledgebases(Owlery.scala:48)
	at org.phenoscape.owlery.Owlery$.<clinit>(Owlery.scala:23)
	... 15 more

I'm kind of at a loss for how to diagnose and repair this, since owlapi isn't telling me what ontology it thinks already exists (nor why it's a problem to load an ontology twice -- shouldn't that be an idempotent operation?).

I'm inclined to try to fix this by making a dummy leaf ontology that just loads the two leaf ontologies, provide that IRI, and leave it at that. But this seems yucky.

As a follow-up:

Any chance Owlery could log the contents of any OWLAPI exceptions it sees? This one has an ontologyDocumentIRI property that would be super helpful to see..

[rpgoldman]

I'm going to close this, because I think I have figured it out.