OWLAPI 4.5.24 throws seemingly irrelevant error

[matentzn]

When processing OWL constructs outside of OBO spec, a nasty error is through which pollutes our Log files:

Minimal example:

Prefix(:=<urn:unnamed:ontology#ont1>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/fbbt/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/fbbt/releases/2023-02-08/patterns/definitions.owl>

SubClassOf(<http://purl.obolibrary.org/obo/FBbt_00001599> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00052517> <http://purl.obolibrary.org/obo/FBbt_00111673>))

)

Run for example:

robot convert -i error-log-test.owl -f obo -o error-log.obo

And you will see a nasty error message:

ERROR No instantiation found for org.semanticweb.owlapi.model.OWLOntologyBuilder arg0
ERROR Instantiation failed
java.lang.reflect.InvocationTargetException: null
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
        at org.semanticweb.owlapi.utilities.Injector.instantiate(Injector.java:364)
        at org.semanticweb.owlapi.utilities.Injector.lambda$load$5(Injector.java:297)
        at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
        at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1655)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
        at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
        at org.semanticweb.owlapi.utilities.Injector.inject(Injector.java:209)
        at org.obolibrary.obo2owl.OwlStringTools.translate(OwlStringTools.java:71)
        at org.obolibrary.obo2owl.OWLAPIOwl2Obo.tr(OWLAPIOwl2Obo.java:321)
        at org.obolibrary.obo2owl.OWLAPIOwl2Obo.convert(OWLAPIOwl2Obo.java:286)
        at org.semanticweb.owlapi.oboformat.OBOFormatRenderer.render(OBOFormatRenderer.java:55)
        at org.semanticweb.owlapi.oboformat.OBOFormatStorer.storeOntology(OBOFormatStorer.java:42)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:99)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:64)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1527)
        at org.obolibrary.robot.IOHelper.saveOntologyFile(IOHelper.java:1752)
        at org.obolibrary.robot.IOHelper.saveOntology(IOHelper.java:866)
        at org.obolibrary.robot.CommandLineHelper.maybeSaveOutput(CommandLineHelper.java:667)
        at org.obolibrary.robot.ConvertCommand.execute(ConvertCommand.java:141)
        at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
        at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
        at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
        at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:61)
Caused by: java.lang.IllegalStateException: value cannot be null at this stage
        at org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull(OWLAPIPreconditions.java:61)
        at org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull(OWLAPIPreconditions.java:40)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.<init>(OWLOntologyFactoryImpl.java:59)
        ... 30 common frames omitted

The OBO result looks correct though:

format-version: 1.2
data-version: fbbt/releases/2023-02-08/patterns/definitions.owl
ontology: fbbt/patterns/definitions
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/FBbt_00001599>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/FBbt_00052517>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/FBbt_00111673>))\n############################\n#   Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/FBbt_00001599> (<http://purl.obolibrary.org/obo/FBbt_00001599>)\n\nSubClassOf(<http://purl.obolibrary.org/obo/FBbt_00001599> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/FBbt_00052517> <http://purl.obolibrary.org/obo/FBbt_00111673>))\n\n\n)

[Term]
id: FBbt:00001599

This needs to be fixed in OWL API, keeping this here only for tracking.

[hkir-dev]

Fix PR created: owlcs/owlapi#1091

[jamesaoverton]

Resolved by #1093