protege4.1 elk-plugin 0.3.2 java 7 compatibility?

95 views
Skip to first unread message

Onur Deniz

unread,
Mar 4, 2013, 3:39:48 AM3/4/13
to elk-reasone...@googlegroups.com
hi all,

Is elk-reasoner compatible with java-7, or is there another reason for the following error? 

starting protege:

onur@deniz:~/Protege_4.1$ ./run.sh
Starting Protege 4 OWL Editor (Version 4.1.0, Build = 239)
Platform:
    Java: JVM 1.7.0_15-b03 Memory: 3728M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: linux (3.2.0-38-generic)
    Processor: x86-64
Installed plugin Owlviz Plug-in
Installed plugin ELK Reasoner Protege Plug-in
Installed plugin The Protege 4 OWL Editor
Installed plugin The OWL API
Installed plugin OntoGraf Plug-in
Installed plugin Factplusplus Plug-in
Installed plugin Dlquery
Installed plugin HermiT Reasoner
Using OWL API version 3.2.3.1824
Rebuilding entity indices...
... rebuilt in 16 ms



Loading SNOMED owl ontology, (I obtained the OWL SNOMED using the script in SNOMED distro.), then trying to reasoning it with elk, I get the following error windows:

Reasoner Error
InterruptedException: null

ELK Error
Could not start workers required for reasoner computation

--
an here is the regarding logs:

ELK reasoner was created
Loading of Axioms started
Loading of Axioms finished in 3456 ms
Initializing the reasoner by performing the following steps:
class hierarchy
class assertions
Loading of Changes started
Loading of Changes finished in 0 ms
Object Property Hierarchy Computation started
Object Property Hierarchy Computation using 8 workers
Object Property Hierarchy Computation finished in 11 ms
Object Property Hierarchy Computation started

<for each worker, I guess, i get the following error>
Error logged
org.semanticweb.elk.util.concurrent.computation.ComputationRuntimeException: Uncought exception in a worker thread:
at org.semanticweb.elk.util.concurrent.computation.ComputationExecutor$Worker.run(ComputationExecutor.java:184)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.RuntimeException: java.lang.InterruptedException
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.findClass(BundleWiringImpl.java:2055)
at org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1472)
at org.apache.felix.framework.BundleWiringImpl.access$400(BundleWiringImpl.java:75)
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.loadClass(BundleWiringImpl.java:1923)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
at org.semanticweb.elk.reasoner.saturation.properties.SaturatedPropertyChain.<init>(SaturatedPropertyChain.java:54)
at org.semanticweb.elk.reasoner.saturation.properties.ObjectPropertyHierarchyComputationFactory$Engine.submit(ObjectPropertyHierarchyComputationFactory.java:70)
at org.semanticweb.elk.reasoner.saturation.properties.ObjectPropertyHierarchyComputationFactory$Engine.submit(ObjectPropertyHierarchyComputationFactory.java:60)
at org.semanticweb.elk.util.concurrent.computation.ConcurrentComputation$Worker.run(ConcurrentComputation.java:219)
at org.semanticweb.elk.util.concurrent.computation.ComputationExecutor$Worker.run(ComputationExecutor.java:182)
... 3 more
Caused by: java.lang.InterruptedException
at java.lang.Object.wait(Native Method)
at java.lang.Object.wait(Object.java:503)
at org.apache.felix.framework.BundleWiringImpl$BundleClassLoader.findClass(BundleWiringImpl.java:2050)
... 12 more
Object Property Hierarchy Computation using 8 workers
Could not start workers required for reasoner computation!
INTERRUPTED while loading Image
Object Property Hierarchy Computation finished in 7 ms
Exception thrown by listener: org.protege.editor.owl.model.OWLWorkspace$1.  Detatching bad listener!
Error logged
org.semanticweb.owlapi.reasoner.ReasonerInternalException: org.semanticweb.elk.owl.exceptions.ElkRuntimeException: Could not start workers required for reasoner computation!
at org.semanticweb.elk.owlapi.ElkExceptionConverter.convert(ElkExceptionConverter.java:80)
at org.semanticweb.elk.owlapi.ElkConverter.convert(ElkConverter.java:119)
at org.semanticweb.elk.owlapi.ElkReasoner.isConsistent(ElkReasoner.java:827)
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl.getReasonerStatus(OWLReasonerManagerImpl.java:225)
at org.protege.editor.owl.model.OWLWorkspace.updateReasonerStatus(OWLWorkspace.java:704)
at org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:314)
at org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:129)
at org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:227)
at org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:787)
at org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$ClassificationRunner$1.run(OWLReasonerManagerImpl.java:371)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:727)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.awt.EventQueue$3.run(EventQueue.java:686)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
at java.awt.Dialog.show(Dialog.java:1082)
at java.awt.Component.show(Component.java:1651)
at java.awt.Component.setVisible(Component.java:1603)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.protege.editor.owl.ui.inference.ReasonerProgressUI$2.run(ReasonerProgressUI.java:148)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:727)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.awt.EventQueue$3.run(EventQueue.java:686)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:697)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: org.semanticweb.elk.owl.exceptions.ElkRuntimeException: Could not start workers required for reasoner computation!
at org.semanticweb.elk.reasoner.ReasonerComputation.process(ReasonerComputation.java:96)
at org.semanticweb.elk.reasoner.stages.ObjectPropertyHierarchyComputationStage.execute(ObjectPropertyHierarchyComputationStage.java:83)
at org.semanticweb.elk.reasoner.stages.LoggingStageExecutor.complete(LoggingStageExecutor.java:56)
at org.semanticweb.elk.reasoner.stages.LoggingStageExecutor.complete(LoggingStageExecutor.java:51)
at org.semanticweb.elk.reasoner.stages.LoggingStageExecutor.complete(LoggingStageExecutor.java:51)
at org.semanticweb.elk.reasoner.stages.AbstractReasonerState.isConsistent(AbstractReasonerState.java:247)
at org.semanticweb.elk.owlapi.ElkReasoner.isConsistent(ElkReasoner.java:821)
... 42 more

--
I tried whether the problem comes from protege-reasoning api but pizza ontology has been successfully reasoned with both hermit and fact++ reasoners. So, I guess the problem is an incompatibility issue of elk with java7.

By the way, I just switched to java7. With java6 reasoning process was flawless. (after switching to java7, I applied http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Bug-and-fix-4-1-and-4-2-won-t-start-with-Java-7-javax-swing-BundleException-td4080682.html in order to run protege)





Yevgeny Kazakov

unread,
Mar 4, 2013, 5:01:00 AM3/4/13
to elk-reasone...@googlegroups.com
Dear Onur,

indeed there seems to be some problem with Apache Felix in Protege 4.1
for Java 7. For me the stock Protege 4.1 does not start as well
(Java(TM) SE Runtime Environment (build 1.7.0_07-b10) on Mac OS X
10.8.2).

Any reason why you cannot use Protege 4.2?

Anyway, I did not manage to download the "Felix Framework
Distribution" from http://felix.apache.org/site/downloads.cgi as in
the fix you linked (all links appear to be broken for me?), but I just
copied felix.jar from Protege_4.2/bin/ to Protege_4.1/bin/, and after
that Protege has started (except that I had to remove FaCT++ because
it was not able to find native libraries) and ELK worked fine for me
on Snomed. I guess there are some incompatibilities between various
versions of Apache Felix (Protege uses one version, but ELK was
compiled against another version). Using the latest version of Protege
would probably be more safe.

Please, let me know if switching to Protege 4.2 and / or copying
felix.jar fixes the problem. If not, we will try to reproduce it on a
linux box.

Best regards,

Yevgeny
> --
> You received this message because you are subscribed to the Google Groups
> "elk-reasoner-discussion" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to elk-reasoner-disc...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>

Onur Deniz

unread,
Mar 5, 2013, 5:11:27 AM3/5/13
to elk-reasone...@googlegroups.com

dear Yevgeny,

actually there was no reason to switching 4.2 and that did worked for the previous errors..

thank you for really quick response and advice.

the correct link for apache-felix is http://felix.apache.org/downloads.cgi . the link in the bug-fix comment is broken since apache's converting the web site i guess. (http://felix.apache.org/)


by the way thanks for the really fast reasoner. 


onur deniz


You received this message because you are subscribed to a topic in the Google Groups "elk-reasoner-discussion" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/elk-reasoner-discussion/G4FBldoc0LI/unsubscribe?hl=en.
To unsubscribe from this group and all its topics, send an email to elk-reasoner-disc...@googlegroups.com.

Yevgeny Kazakov

unread,
Mar 5, 2013, 10:55:52 AM3/5/13
to elk-reasone...@googlegroups.com
Der Onur,

On Tue, Mar 5, 2013 at 11:11 AM, Onur Deniz <onur...@gmail.com> wrote:
>
> dear Yevgeny,
>
> actually there was no reason to switching 4.2 and that did worked for the
> previous errors..
>
> thank you for really quick response and advice.

Could you, please, update us if you still have the same problem with
Protege 4.2 and / or after copying felix.jar from Protege 4.2 to
Protege 4.1?

> the correct link for apache-felix is http://felix.apache.org/downloads.cgi .
> the link in the bug-fix comment is broken since apache's converting the web
> site i guess. (http://felix.apache.org/)

Thanks for the suggestion! I have now tried felix.jar from the
official distribution and it works for me fine with Protege 4.1 and
SNOMED.
Can you reproduce the problem reliably? Does it happen on other
ontologies than SNOMED, e.g., on pizza with ELK?

> by the way thanks for the really fast reasoner.

You are welcomed!
Just out of curiosity, can you tell us what do you do with ELK? If you
use it in any application, we will be happy to mention it in our wiki:
http://code.google.com/p/elk-reasoner/wiki/Projects

Best regards,

Yevgeny

Onur Deniz

unread,
Mar 6, 2013, 6:59:04 AM3/6/13
to elk-reasone...@googlegroups.com

>Could you, please, update us if you still have the same problem with
>Protege 4.2 and / or after copying felix.jar from Protege 4.2 to
>Protege 4.1?
with protege4.2 i don't have the same problem. but, another problem (i think stems from protege itself) has been occured: after reasoning process, the informative window does not halt. as i said its mostly from protege i guess, because with other reasoners same problem has been repeated.
beside un-halting problem, the reasoning process is ok in protege 4.2

>Can you reproduce the problem reliably? Does it happen on other
>ontologies than SNOMED, e.g., on pizza with ELK?
protege4.1 + latest felix.jar (from its website) + pizza ontology ; same error with elk, no problem with fact++ and hermit
protege4.1 + felix.jar from protege4.2 + pizza ontology ; no problem with both elk, fact++ and hermit


the project is in an early phase for now. but in summary, we are trying to find snomed concepts in free-text medical discharge notes and than map to relevant icd-10 codes. (besides using US-NLM snomed-icd mapping, we are trying to model our own mapping with representing icd-10 codes and rules using granular snomed concepts.)

for finding snomed concepts, i'm using elk-reasoner for detecting most specific concepts in ontology...

anyway, after some progress i will gladly share the project hopefully with some publications...


kind regards.

onur

Yevgeny Kazakov

unread,
Mar 6, 2013, 4:06:43 PM3/6/13
to elk-reasone...@googlegroups.com
Dear Onur,

On Wed, Mar 6, 2013 at 12:59 PM, Onur Deniz <onur...@gmail.com> wrote:
>
>>Can you reproduce the problem reliably? Does it happen on other
>>ontologies than SNOMED, e.g., on pizza with ELK?
> protege4.1 + latest felix.jar (from its website) + pizza ontology ; same
> error with elk, no problem with fact++ and hermit
> protege4.1 + felix.jar from protege4.2 + pizza ontology ; no problem with
> both elk, fact++ and hermit

Thanks for checking!
Finally I was able to reproduce the problem with the latest felix.jar
from the website and Protege 4.1 both with pizza.owl and SNOMED.
This surely looks as some felix incompatibility. I am afraid, there is
nothing that we can do about it now (as a workaround, you can just use
the jar from Protege 4.2), but for the next release of ELK we will try
to make sure that ELK works with the latest release of Apache Felix.

Thanks a lot for reporting the problem!

>
> the project is in an early phase for now. but in summary, we are trying to
> find snomed concepts in free-text medical discharge notes and than map to
> relevant icd-10 codes. (besides using US-NLM snomed-icd mapping, we are
> trying to model our own mapping with representing icd-10 codes and rules
> using granular snomed concepts.)
>
> for finding snomed concepts, i'm using elk-reasoner for detecting most
> specific concepts in ontology...
>
> anyway, after some progress i will gladly share the project hopefully with
> some publications...

I don't know much about icd-10 codes, but surely, this looks
interesting. Please, keep us posted about your progress!

Cheers,

Yevgeny
Reply all
Reply to author
Forward
0 new messages