Re: [OWLAPI-developer] strange NullPointerException while loading ontology

[Raghava M. <m.v...@gm...>]

Thank you for looking into it :).

Regards,
Raghava.


On Fri, Jun 28, 2013 at 12:28 PM, Ignazio Palmisano <
ipa...@gm...> wrote:

>
> On 28 Jun 2013 10:07, "Raghava Mutharaju" <m.v...@gm...>
> wrote:
> >
> > Yes, it is strange. Following is the output of java -version on my
> machine.
> >
> > Java(TM) SE Runtime Environment (build
> pxa6460sr13ifix-20130303_02(SR13+IV37419))
> > IBM J9 VM (build 2.4, JRE 1.6.0 IBM J9 2.4 Linux amd64-64
> jvmxa6460sr13-20130114_134867 (JIT enabled, AOT enabled)
> > J9VM - 20130114_134867
> > JIT  - r9_20130108_31100
> > GC   - 20121212_AA)
> > JCL  - 20130303_02
> >
> > Regards,
> > Raghava.
> >
>
> I'll try to reproduce, although I foresee this being hard :-)
> I.
>
> >
> > On Thu, Jun 27, 2013 at 11:25 PM, Ignazio Palmisano <
> ipa...@gm...> wrote:
> >>
> >> On 27 June 2013 10:52, Raghava Mutharaju <m.v...@gm...>
> wrote:
> >> > I tried with version 3.4.4. I ran into the same issue after 1001. For
> now, I
> >> > am merging couple of owl files and then I will try again with lesser
> number
> >> > of files.
> >> >
> >>
> >> I'm having troubles replicating this - I just tried with two thousand
> >> files and parsing went well. Input streams are closed correctly after
> >> parsing is complete, in a finally block. The null pointer exception is
> >> thrown inside a simple setter method in XMLInputSource:
> >>
> >>  public void setSystemId(String paramString)   {
> >>      this.fSystemId = paramString;
> >>    }
> >>
> >> So there is no obvious reason why it should be thrown there.
> >>
> >> I'm running this on Oracle Java 7 - what's the VM you're using?
> >> Cheers,
> >> I.
> >>
> >> > Regards,
> >> > Raghava.
> >> >
> >> >
> >> > On Thu, Jun 27, 2013 at 10:42 AM, Ignazio Palmisano
> >> > <ipa...@gm...> wrote:
> >> >>
> >> >>
> >> >> On 27 Jun 2013 10:02, "Raghava Mutharaju" <m.v...@gm...
> >
> >> >> wrote:
> >> >> >
> >> >> > Hello Ignazio,
> >> >> >
> >> >> > At this point only this piece of code is running in my
> application. I
> >> >> > used a new manager for each iteration but the result is the same,
> it gives a
> >> >> > NullPointerException after processing 1001 files. loadOntology()
> and
> >> >> > saveOntology() should do the opening and closing of files. Can you
> please
> >> >> > check and let me know? Also, I am not using the latest version of
> OWL API.
> >> >> > Would it help in switching to the current release?
> >> >> >
> >> >> > Regards,
> >> >> > Raghava.
> >> >> >
> >> >>
> >> >> It's worth trying while I debug the issue. The latest release should
> >> >> create one less file per save operation, so it's likely to work
> until 2001
> >> >> files :-)
> >> >> I.
> >> >>
> >> >> >
> >> >> > On Thu, Jun 27, 2013 at 9:19 AM, Ignazio Palmisano
> >> >> > <ipa...@gm...> wrote:
> >> >> >>
> >> >> >>
> >> >> >> On 26 Jun 2013 20:57, "Raghava Mutharaju" <
> m.v...@gm...>
> >> >> >> wrote:
> >> >> >> >
> >> >> >> > Yes, thats why I had a hard time in figuring out the cause of
> this
> >> >> >> > exception. I haven't opened any files.
> >> >> >>
> >> >> >> I didn't mean explicitly in your code, I meant overall in your
> >> >> >> application. There must be at least two streams opened, one for
> reading and
> >> >> >> one for writing. As you don't pass streams explicitly to the
> manager, it
> >> >> >> should take care to close any streams it opens - this might have
> been
> >> >> >> neglected. I'll check.
> >> >> >> I.
> >> >> >>
> >> >> >> > There might be some in saveOntology(), but I guess closing the
> files
> >> >> >> > would have been appropriately handled there. I will try out
> with a new
> >> >> >> > manager in each iteration.
> >> >> >> >
> >> >> >> > Thank you.
> >> >> >> >
> >> >> >> > Regards,
> >> >> >> > Raghava.
> >> >> >> >
> >> >> >> >
> >> >> >> > On Wed, Jun 26, 2013 at 6:06 PM, Ignazio Palmisano
> >> >> >> > <ipa...@gm...> wrote:
> >> >> >> >>
> >> >> >> >> On 26 June 2013 17:52, Raghava Mutharaju <
> m.v...@gm...>
> >> >> >> >> wrote:
> >> >> >> >> > Hello all,
> >> >> >> >> >
> >> >> >> >> > I have the following code using which, in each iteration, I
> load
> >> >> >> >> > one
> >> >> >> >> > ontology, work on it and save it.
> >> >> >> >> >
> >> >> >> >> >          for(File owlFile : allFiles) {
> >> >> >> >> >        IRI documentIRI = IRI.create(owlFile);
> >> >> >> >> >        System.out.println("Working on file: " +
> >> >> >> >> > owlFile.getName());
> >> >> >> >> >        OWLOntology ontology =
> manager.loadOntology(documentIRI);
> >> >> >> >> >     Normalizer normalizer = new Normalizer(manager,
> ontology);
> >> >> >> >> >     OWLOntology normalizedOntology = normalizer.Normalize();
> >> >> >> >> >     OWLXMLOntologyFormat owlxmlFormat = new
> >> >> >> >> > OWLXMLOntologyFormat();
> >> >> >> >> >    File file = new File(args[1] + File.separator +
> >> >> >> >> >     "Norm-" + owlFile.getName());
> >> >> >> >> >    if(file.exists())
> >> >> >> >> >     file.delete();
> >> >> >> >> >    manager.saveOntology(normalizedOntology,
> >> >> >> >> >     owlxmlFormat, IRI.create(file));
> >> >> >> >> >    manager.removeOntology(ontology);
> >> >> >> >> >     }
> >> >> >> >> >
> >> >> >> >> > After processing 1001 ontologies in this way, it gives out a
> >> >> >> >> > NullPointerException at the line where ontology is loaded
> using
> >> >> >> >> > loadOntology(). If I try it separately, just on that ontology
> >> >> >> >> > file, I don't
> >> >> >> >> > get a NullPointerException. The owl file seems to be fine. In
> >> >> >> >> > fact, it
> >> >> >> >> > doesn't seem to be a problem with that particular owl file.
> If I
> >> >> >> >> > remove that
> >> >> >> >> > owl file from the list, even then I get the same exception
> after
> >> >> >> >> > processing
> >> >> >> >> > 1001 files.
> >> >> >> >> >
> >> >> >> >> > Any help is highly appreciated.
> >> >> >> >> >
> >> >> >> >> > Here is the exception
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >> The null pointer itself is deep inside Xerces, so hard to make
> sense
> >> >> >> >> of it. Since it happens after one thousand iterations, I
> wonder if
> >> >> >> >> you
> >> >> >> >> might have too many open files and therefore running out of
> file
> >> >> >> >> handlers. I'd also try creating a new manager for each ontology
> >> >> >> >> instead of reusing the same manager.
> >> >> >> >> HTH,
> >> >> >> >> I.
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> > Exception in thread "main" java.lang.NullPointerException
> >> >> >> >> >         at
> >> >> >> >> >
> org.apache.xerces.xni.parser.XMLInputSource.setSystemId(Unknown
> >> >> >> >> > Source)
> >> >> >> >> >         at
> >> >> >> >> > java.io.FilterInputStream.read(FilterInputStream.java:101)
> >> >> >> >> >         at
> >> >> >> >> > org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
> Source)
> >> >> >> >> >         at
> >> >> >> >> >
> org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown
> >> >> >> >> > Source)
> >> >> >> >> >         at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown
> >> >> >> >> > Source)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> org.semanticweb.owlapi.rdf.syntax.RDFParser.parse(RDFParser.java:173)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> org.coode.owlapi.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:120)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:204)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:726)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:667)
> >> >> >> >> >         at
> >> >> >> >> >
> >> >> >> >> >
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:641)
> >> >> >> >> >
> >> >> >> >> > Thank you.
> >> >> >> >> >
> >> >> >> >> > Regards,
> >> >> >> >> > Raghava.
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
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> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
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> >> >> >> >
> >> >> >> >
> >> >> >> >
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