[Pellet-users] null pointer exception in Individual.getRNeighborEdges(Individual.java: 690)

[Henk-Jan Lebbink]

Dear list,

Thanks Evren, I think I’ve remedied the problem. It was most likely, as
indicated, a URI that was not defined as a property. The problem was
introduced by Protégé (3.4) that allowed an annotation in a class
restriction. Protégé does not allow creating such restrictions with
annotations; however, by changing object properties into annotations, it
is possible.

Would that explain the exception?

Greetings Henk-Jan.

---
On Thu, March 13, 2008 13:35, Evren Sirin wrote:
> Usually this kind of exception is due to a URI that is not defined
> explicitly as a property but used in a restriction as a property. This
> is not allowed in OWL-DL and Pellet generally does a good job of
> catching and patching such untyped resources. But I'm guessing automatic
> patching failed in this case. Running the species validator would
> indicate which URI is the problem.
>
> Or I'm completely wrong at my guess and something else is wrong :)
> Trying to extract a minimal ontology (or worst case the whole ontology
> itself) showing the problem would help us identify the problem.
>
> Cheers,
> Evren
>
> On 3/13/08 6:46 AM, Henk-Jan Lebbink wrote:
>> Dear List,
>>
>> I’m a dedicated Protégé and recently also a Pellet user. I and some
>> colleagues use Pellet in combination with Protégé 3.4 to do consistency
>> checks on our ontologies. However, we stumbled on a null pointer
>> exception
>> that, for the moment, we could not circumvent. The ontology is large,
>> the
>> expression was something with needles and haystacks - you get the point.
>>
>> Question: does someone know how to circumvent the exception (see below),
>> or how can I submit some sort of bug report.
>>
>> With regards, and thanks in advance!
>> Henk-Jan Lebbink.
>>
>> ---
>> C:\Documents and Settings\Bo\Bureaublad\pellet 1.5.1 (8081)>rem  java
>> -Xss4m
>> -Xms30m -Xmx1600m -clas
>> spath lib\pellet.jar org.mindswap.pellet.dig.PelletDIGServer
>>
>> C:\Documents and Settings\Bo\Bureaublad\pellet 1.5.1 (8081)>"C:\Program
>> Files\Java\jre1.6.0_05\bin\j
>> ava.exe" -Xss4m -Xms30m -Xmx2000000000 -classpath lib\pellet.jar -
>> Dpellet.configuration=file:pellet.
>> properties org.mindswap.pellet.dig.PelletDIGServer
>>
>> PelletDIGServer Version 1.5.1 (October 26 2007)
>> Port: 8081
>> java.lang.NullPointerException
>>         at
>> org.mindswap.pellet.Individual.getRNeighborEdges(Individual.java
>> :690)
>>         at org.mindswap.pellet.CompletionStrategy.applyAllValues(
>> CompletionStrategy.java:920)
>>         at org.mindswap.pellet.CompletionStrategy.addType(
>> CompletionStrategy.java:273)
>>         at org.mindswap.pellet.CompletionStrategy.applyUnfoldingRule(
>> CompletionStrategy.java:643)
>>         at org.mindswap.pellet.CompletionStrategy.applyUnfoldingRule(
>> CompletionStrategy.java:614)
>>         at org.mindswap.pellet.CompletionStrategy.initialize(
>> CompletionStrategy.java:170)
>>         at org.mindswap.pellet.SROIQStrategy.complete(SROIQStrategy.java
>> :120)
>>         at org.mindswap.pellet.ABox.isConsistent(ABox.java:1605)
>>         at org.mindswap.pellet.ABox.isConsistent(ABox.java:1489)
>>         at
>> org.mindswap.pellet.KnowledgeBase.consistency(KnowledgeBase.java
>> :1568)
>>         at
>> org.mindswap.pellet.KnowledgeBase.isConsistent(KnowledgeBase.java
>> :1589)
>>         at
>> org.mindswap.pellet.dig.DIGAskHandler.asks(DIGAskHandler.java:54)
>>         at org.mindswap.pellet.dig.PelletDIGReasoner.process(
>> PelletDIGReasoner.java:160)
>>         at org.mindswap.pellet.dig.PelletDIGReasoner.process(
>> PelletDIGReasoner.java:112)
>>         at org.mindswap.pellet.dig.PelletDIGReasoner.process(
>> PelletDIGReasoner.java:102)
>>         at org.mindswap.pellet.dig.PelletDIGServer.handle(
>> PelletDIGServer.java:74)
>>         at org.mortbay.http.HttpContext.handle(HttpContext.java:1565)
>>         at org.mortbay.http.HttpContext.handle(HttpContext.java:1517)
>>         at org.mortbay.http.HttpServer.service(HttpServer.java:954)
>>         at
>> org.mortbay.http.HttpConnection.service(HttpConnection.java:816)
>>         at
>> org.mortbay.http.HttpConnection.handleNext(HttpConnection.java
>> :983)
>>         at
>> org.mortbay.http.HttpConnection.handle(HttpConnection.java:833)
>>         at org.mortbay.http.SocketListener.handleConnection(
>> SocketListener.java:244)
>>         at
>> org.mortbay.util.ThreadedServer.handle(ThreadedServer.java:357)
>>         at
>> org.mortbay.util.ThreadPool$PoolThread.run(ThreadPool.java:534)
>>
>>
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