Re: [OWLAPI-developer] Problem with loadOntologyFromOntologyDocument method

[Ignazio P. <ipa...@gm...>]

On 22 Apr 2013 13:19, "Alejandro Rodríguez González" <
ale...@gm...> wrote:
>
> Hello all,
>
> I'm writing a code which, basically, do the next steps:
>
> - Create a set of pairs (input/output) URIs of classes
> - For each pair, I create two OWLOntology objects and I load the ontology
which correspondo to each class using loadOntologyFromOntologyDocument()
method (I create the IRI from a String)
> - In one of the ontologies (input one), I create several individuals
under one of the classess, merge both and perform reasoning using HermiT to
see if the indiviuals are classified under a concrete class of the output
ontology.
>
> This process should be executed about 25.000 times (because I create 25k
pairs in-out). My problem is, that my program is getting freeze randomly.
Sometimes get freeze with pair 77, others with pair 300, others with the
pair 3.452.. I mean, the number of pair always (or near always change).
>

It's a bit hard to tell what's wrong. One thing you can try is to use
separate managers for different pairs.

Are you calling dispose() on the reasoner when you are done with an
ontology?

Hth,
I.

> I debug my program and I find that the problem is that it enters in the
line of code where I load the ontology
using loadOntologyFromOntologyDocument() method, but never exit.
>
> So I understand that something is happenning with this method which is
getting freeze (memory problem? connection error?) but is not returning
anything, so I can't continue the process.
>
> I can upload some parts of the code if necessary but I would like to know
if someone can give me an explanation about why can be happening this. The
code is too large to upload it entirely (I've summarized the process but
several other things are done, and there are several classes and objects
involved). However, the problem is isolated in the execution of this method.
>
> Hoping someone can help me. I don't know if it can be some bug on OWL
API..
>
> The concretely code is the following:
>
> private Result loadInputOntologyOWLAPI() {
> try {
> inputNamespace = IRI.create(this.outputInputPair.getInput()
> .getObject());
> logger.log("inputNamespace created.. OWL API [ " +
inputNamespace.toString() + " ]");
> inputOntology = manager
> .loadOntologyFromOntologyDocument(inputNamespace);
> logger.log("Input ontology loaded in the object.. OWL API");
> } catch (Exception e) {
> return new Result(false, e.getMessage());
> }
> return new Result(true);
> }
>
> I can get the message "inputNamespace created.." but when gets freeze,
never execute the next one ("Input ontology loaded..").
>
> Thanks
>
> --
> Dr. Alejandro Rodríguez González - PhD
>
> Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
> Polytechnic University of Madrid
> http://www.alejandrorg.com
> Phone: +34 914524900 . Ext: 25550
>
>
> Once the game is over, the king and the pawn go back in the same box. -
Italian proverb
>
>
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