NullPointer while classifying the EL fragment of galen

[naditina]

I am working with ELK (elk-distribution-0.4.3-owlapi-library) on the EL fragment of some version of galen. I added and subsequently removed several axioms that introduce fresh concept symbols as a shortcut for conjunctions built from subconcepts of that ontology. I get the following exception with the following stack trace:

Exception in thread "main" java.lang.NullPointerException
at org.semanticweb.elk.util.collections.ArrayHashMap.get(ArrayHashMap.java:203)
at org.semanticweb.elk.util.collections.chains.AbstractChain$1.next(AbstractChain.java:105)
at org.semanticweb.elk.util.collections.chains.AbstractChain$1.next(AbstractChain.java:101)
at org.semanticweb.elk.util.collections.chains.AbstractChain.find(AbstractChain.java:42)
at org.semanticweb.elk.reasoner.indexing.hierarchy.IndexedSubClassOfAxiom$ThisCompositionRule.removeFrom(IndexedSubClassOfAxiom.java:162)
at org.semanticweb.elk.reasoner.indexing.hierarchy.DifferentialIndex.add(DifferentialIndex.java:172)
at org.semanticweb.elk.reasoner.indexing.hierarchy.IndexedSubClassOfAxiom.updateOccurrenceNumbers(IndexedSubClassOfAxiom.java:85)
at org.semanticweb.elk.reasoner.indexing.hierarchy.MainAxiomIndexerVisitor$AxiomOccurrenceUpdateFilter.update(MainAxiomIndexerVisitor.java:384)
at org.semanticweb.elk.reasoner.indexing.hierarchy.MainAxiomIndexerVisitor$AxiomOccurrenceUpdateFilter.visit(MainAxiomIndexerVisitor.java:394)
at org.semanticweb.elk.reasoner.indexing.hierarchy.MainAxiomIndexerVisitor$AxiomOccurrenceUpdateFilter.visit(MainAxiomIndexerVisitor.java:373)
at org.semanticweb.elk.reasoner.indexing.hierarchy.MainAxiomIndexerVisitor.indexSubClassOfAxiom(MainAxiomIndexerVisitor.java:148)
at org.semanticweb.elk.reasoner.indexing.hierarchy.AbstractElkAxiomIndexerVisitor.visit(AbstractElkAxiomIndexerVisitor.java:166)
at org.semanticweb.elk.reasoner.indexing.hierarchy.AbstractElkAxiomIndexerVisitor.visit(AbstractElkAxiomIndexerVisitor.java:63)
at org.semanticweb.elk.owlapi.wrapper.ElkEquivalentClassesAxiomWrap.accept(ElkEquivalentClassesAxiomWrap.java:61)
at org.semanticweb.elk.owlapi.wrapper.ElkClassAxiomWrap.accept(ElkClassAxiomWrap.java:51)
at org.semanticweb.elk.reasoner.indexing.hierarchy.DelegatingElkAxiomVisitor.visit(DelegatingElkAxiomVisitor.java:103)
at org.semanticweb.elk.reasoner.indexing.hierarchy.DelegatingElkAxiomVisitor.visit(DelegatingElkAxiomVisitor.java:74)
at org.semanticweb.elk.owlapi.wrapper.ElkEquivalentClassesAxiomWrap.accept(ElkEquivalentClassesAxiomWrap.java:61)
at org.semanticweb.elk.owlapi.wrapper.ElkClassAxiomWrap.accept(ElkClassAxiomWrap.java:51)
at org.semanticweb.elk.reasoner.indexing.hierarchy.ChangeIndexingProcessor.visit(ChangeIndexingProcessor.java:57)
at org.semanticweb.elk.owlapi.OwlOntologyChangeProcessorVisitor.visit(OwlOntologyChangeProcessorVisitor.java:78)
at org.semanticweb.elk.owlapi.OwlOntologyChangeProcessorVisitor.visit(OwlOntologyChangeProcessorVisitor.java:39)
at org.semanticweb.owlapi.model.AddAxiom.accept(AddAxiom.java:76)
at org.semanticweb.elk.owlapi.OwlChangesLoader.load(OwlChangesLoader.java:90)
at org.semanticweb.elk.reasoner.stages.AxiomLoadingStage.executeStage(AxiomLoadingStage.java:121)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerStage.execute(AbstractReasonerStage.java:165)
at org.semanticweb.elk.reasoner.stages.AxiomLoadingStage.execute(AxiomLoadingStage.java:45)
at org.semanticweb.elk.reasoner.stages.LoggingStageExecutor.execute(LoggingStageExecutor.java:53)
at org.semanticweb.elk.reasoner.stages.AbstractStageExecutor.complete(AbstractStageExecutor.java:55)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerState.complete(AbstractReasonerState.java:145)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerState.loadAxioms(AbstractReasonerState.java:306)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerState.isInconsistent(AbstractReasonerState.java:284)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerState.getTaxonomy(AbstractReasonerState.java:324)
at org.semanticweb.elk.owlapi.ElkReasoner.precomputeInferences(ElkReasoner.java:942)
at simplification.ConceptMinimizer.computeConjunctions(ConceptMinimizer.java:254)

Nadeschda

[ykazakov]

Hi & thanks for reporting!
Unfortunately I cannot reproduce this. I need more input.

Can you paste the log output of ELK? Are there any warning / error messages?

Also, can you try to pinpoint which exactly axiom addition triggers the error? As I can see from the stack trace, it is triggered when an equivalence axiom is being added. I need to know which one.

Ideally, could you provide a small example like the one here (with concrete ontology and class expressions) that triggers the problem in your case?

[ykazakov]

Hi Nadeschda,
we were able to reproduce your error message if we query for the empty conjunctions, i.e., add axioms like:

EquivalentClasses(:tmp ObjectIntersectionOf())

Do you by chance create such expressions?

Although it is not a valid OWL 2 expression, OWL API allows to create expressions like this (probably to be backward compatible with the previous version of OWL).
This should be related to issue #35

[naditina]

Hi Yevgeny,

indeed this was the cause. Thank you for looking into it.

Nadeschda

[ykazakov]

Reopening this to avoid similar problems in the future.
Should treat empty conjunction as owl:Thing, empty disjunction as owl:Nothing, etc.