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OWLTools
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Help required: Nullpointer in TableToAxiomConverter #284

Closed matentzn closed 5 years ago

matentzn commented 5 years ago

I am trying to figure out why running this command fails:

cleaned/hp_hp.owl: sources
    owltools $(HP) $(MP) $(ZP) $(MP_G2P) $(HP_D2P) $(ZP_G2P) --merge-imports-closure --load-instances $(HP_D2P) --load-labels $(HP_DL) --merge-support-ontologies -o $@.tmp.owl && \
    owltools $@.tmp.owl --merge-import-closure --remove-disjoints --remove-equivalent-to-nothing-axioms -o $@

I don't need a solution, just a pointer on what to look for. All files referenced by the query exist and are parseable. My suspicion is that the problem appears here, and somehow an empty row parsed from a table causes the whole issue. But before I launch myself into debugging, I wanted to give it another set of eyes before poking in the dark.

Exception in thread "main" java.lang.NullPointerException
        at com.carrotsearch.hppcrt.IteratorPool.borrow(IteratorPool.java:83)
        at com.carrotsearch.hppcrt.sets.ObjectHashSet.iterator(ObjectHashSet.java:808)
        at uk.ac.manchester.cs.owl.owlapi.HPPCSet.iterator(MapPointer.java:466)
        at uk.ac.manchester.cs.owl.owlapi.HPPCSet.addAll(MapPointer.java:514)
        at uk.ac.manchester.cs.owl.owlapi.HPPCSet.<init>(MapPointer.java:445)
        at uk.ac.manchester.cs.owl.owlapi.MapPointer.putInternal(MapPointer.java:324)
        at uk.ac.manchester.cs.owl.owlapi.MapPointer.put(MapPointer.java:239)
        at uk.ac.manchester.cs.owl.owlapi.Internals$1.visit(Internals.java:653)
        at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.accept(OWLClassImpl.java:253)
        at uk.ac.manchester.cs.owl.owlapi.AbstractEntityRegistrationManager.visit(AbstractEntityRegistrationManager.java:298)
        at uk.ac.manchester.cs.owl.owlapi.OWLClassAssertionAxiomImpl.accept(OWLClassAssertionAxiomImpl.java:123)
        at uk.ac.manchester.cs.owl.owlapi.Internals.addAxiom(Internals.java:649)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:141)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl$OWLOntologyChangeFilter.visit(OWLOntologyImpl.java:114)
        at org.semanticweb.owlapi.model.AddAxiom.accept(AddAxiom.java:76)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.applyChange(OWLOntologyImpl.java:64)
        at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.applyChange(ConcurrentOWLOntologyImpl.java:2194)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:640)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChanges(OWLOntologyManagerImpl.java:667)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:817)
        at owltools.io.TableToAxiomConverter.addRow(TableToAxiomConverter.java:229)
        at owltools.io.TableToAxiomConverter.addRow(TableToAxiomConverter.java:224)
        at owltools.io.TableToAxiomConverter.parse(TableToAxiomConverter.java:109)
        at owltools.io.TableToAxiomConverter.parse(TableToAxiomConverter.java:95)
        at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4063)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
        at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)
make: *** [Makefile:121: cleaned/hp_hp.owl] Error 1
matentzn commented 5 years ago

Empty row was not the issue. Is there anyone here at owltools that could help me with this?

matentzn commented 5 years ago

Closing because I cant replicate in some environments. Maybe docker image related issue?