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From Eddie Epstein <eaepst...@gmail.com>
Subject Re: XmiCasSerializer error in UIMA-AS
Date Wed, 30 Oct 2013 13:11:44 GMT
Other than reordering the CAS within an annotator via CAS
serialization/deserialization, nothing else comes to mind. So the next idea
would be to pursue a UIMA bug.

Looking at the exception stack shows the problem is associated with
deleting an FS from the index repository. Code in ruta-core does
cas.addFsToIndexes and cas.removeFsFromIndexes. Perhaps there is a bug in
UIMA delta CAS processing associated with this scenario. Much as I would
like to,
can't think of any way to blade Ruta code for this.

Eddie


On Wed, Oct 30, 2013 at 4:38 AM, Peter Klügl <pkluegl@uni-wuerzburg.de>wrote:

> On 29.10.2013 17:36, Eddie Epstein wrote:
> > Hi Peter,
> >
> > Things like  XmiCasDeserializer.deserialize(new FileInputStream(each),
> cas,
> > true) in RutaInterpreterRunner?
>
> Ah ok, that shouldn't cause any problems. It's code of the eclipse-based
> tooling and should not be used in a normal pipeline. The problem (if
> ruta causes it) has to be in ruta-core, I think.
>
> > I am only looking for things that would do something unexpected to a
> CAS. I
> > would not be so concerned with the new Ruta annotations as with changes
> to
> > previously existing annotations.
>
> Are there any known modifications that cause problems?
>
> Peter
>
> > Eddie
> >
> >
> >
> >
> >
> > On Tue, Oct 29, 2013 at 9:39 AM, Peter Klügl <pkluegl@uni-wuerzburg.de
> >wrote:
> >
> >> On 28.10.2013 13:47, Eddie Epstein wrote:
> >>> Assuming you would rather not share the CAS files, what I'd be looking
> >> for
> >>> is the xmi:id values changing between the before and after files. There
> >> is
> >>> some code in ruta that replaces CASes with serialization from files
> which
> >>> could be the cause of this problem.
> >> What code do you mean?
> >>
> >> I have no idea what the problem could be. I would have bet that the
> >> RutaBasic annotation cause the problem, but the problem apparently still
> >> exists if all ruta specific annotations are yet removed in the analysis
> >> engine.
> >>
> >> Peter
> >>
> >>> Eddie
> >>>
> >>>
> >>> On Tue, Oct 22, 2013 at 10:21 AM, Eddie Epstein <eaepstein@gmail.com>
> >> wrote:
> >>>> Can you share the before and after XmiCas files for a case where
> UIMA-AS
> >>>> service serialization failed? No confidential info please!
> >>>>
> >>>> Eddie
> >>>>
> >>>>
> >>>>
> >>>> On Tue, Oct 22, 2013 at 2:27 AM, Prokopis Prokopidis <
> prokopis@ilsp.gr
> >>> wrote:
> >>>>> No, this is not an easily reproduced error: I have noticed it so
far
> >> only
> >>>>> upon application of typesystem-specific ruta rules. I will try to
> come
> >> up
> >>>>> with an easily reproducible example.
> >>>>>
> >>>>> In the meantime, I followed your suggestions and added 2 XMI
> >>>>> serialization calls at the end of the AE processing for the failing
> >> case,
> >>>>> just before and just after using the ruta rules for modifying the
> >>>>> annotations in my CAS. In both cases, serialization to file
> succeeded,
> >> with
> >>>>> the second file containing the expected results of rule application.
> >>>>>
> >>>>> Unfortunately, the UIMA-AS serialization still produces the error
in
> my
> >>>>> original mail.
> >>>>>
> >>>>> Prokopis
> >>>>>
> >>>>>
> >>>>> On 10/18/2013 07:09 PM, Eddie Epstein wrote:
> >>>>>
> >>>>>> Is this a solid error that is easily reproduced?
> >>>>>>
> >>>>>> The error is occurring when UIMA-AS is returning the CAS from
the
> >>>>>> service.
> >>>>>> You could add XMI serialization to file at the end of AE processing,
> >> for
> >>>>>> the good and failing cases. If so lucky to have that serialization
> >> fail
> >>>>>> too, could try inserting the serialization at points earlier.
> >>>>>>
> >>>>>> Note that the UIMA-AS serialization is only serializing the
delta
> >> changes
> >>>>>> from the input CAS, different from what you would do.
> >>>>>>
> >>>>>> Eddie
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Thu, Oct 17, 2013 at 12:19 PM, Prokopis Prokopidis <
> >> prokopis@ilsp.gr
> >>>>>>> wrote:
> >>>>>>  Hi all,
> >>>>>>> I have an AE that produces the error below when deployed
as a
> UIMA-AS
> >>>>>>> 2.4.0 service. The same AE as part of a UIMA 2.4.2 CPE or
a uimafit
> >> 2.*
> >>>>>>> pipeline does not produce any errors and works as expected.
> >>>>>>>
> >>>>>>> Among other things, this AE uses ruta rules to process the
CAS.
> When
> >> the
> >>>>>>> rules are not used,  the AE works as expected in both UIMA
and
> >> UIMA-AS.
> >>>>>>> I have tried to log all annotations generated by the AE
when the
> >> rules
> >>>>>>> are
> >>>>>>> used and just before the AE processing is finished. The
annotations
> >> seem
> >>>>>>> the same in both the UIMA and the UIMA-AS processing scenarios.
> >>>>>>>
> >>>>>>> Does anyone have hints on what the cause of this might be
or how I
> >>>>>>> should
> >>>>>>> proceed in debugging?
> >>>>>>>
> >>>>>>> Many thanks in advance,
> >>>>>>>
> >>>>>>> Prokopis
> >>>>>>>
> >>>>>>> WARNING:
> >>>>>>> java.lang.****ArrayIndexOutOfBoundsException
> >>>>>>>          at org.apache.uima.internal.util.**
> >>>>>>> **IntVector.remove(IntVector.****
> >>>>>>> java:207)
> >>>>>>>          at org.apache.uima.internal.util.**
> >>>>>>> **IntSet.remove(IntSet.java:**77)
> >>>>>>>          at org.apache.uima.cas.impl.****FSIndexRepositoryImpl.**
> >>>>>>> processIndexUpdates(****FSIndexRepositoryImpl.java:****1756)
> >>>>>>>          at org.apache.uima.cas.impl.****FSIndexRepositoryImpl.****
> >>>>>>> isModified(*
> >>>>>>> *FSIndexRepositoryImpl.java:****1800)
> >>>>>>>          at org.apache.uima.cas.impl.****XmiCasSerializer$**
> >>>>>>> XmiCasDocSerializer.serialize(****XmiCasSerializer.java:256)
> >>>>>>>          at org.apache.uima.cas.impl.****XmiCasSerializer$**
> >>>>>>> XmiCasDocSerializer.access$****700(XmiCasSerializer.java:108)
> >>>>>>>          at
> >> org.apache.uima.cas.impl.****XmiCasSerializer.serialize(**
> >>>>>>> XmiCasSerializer.java:1566)
> >>>>>>>          at org.apache.uima.aae.****UimaSerializer.****
> >>>>>>> serializeCasToXmi(**
> >>>>>>> UimaSerializer.java:160)
> >>>>>>>          at org.apache.uima.adapter.jms.****
> >>>>>>> activemq.JmsOutputChannel.**
> >>>>>>> serializeCAS(JmsOutputChannel.****java:237)
> >>>>>>>          at org.apache.uima.adapter.jms.****
> >>>>>>> activemq.JmsOutputChannel.**
> >>>>>>> getSerializedCas(****JmsOutputChannel.java:1223)
> >>>>>>>          at org.apache.uima.adapter.jms.****
> >>>>>>> activemq.JmsOutputChannel.**
> >>>>>>> sendReply(JmsOutputChannel.****java:786)
> >>>>>>>          at org.apache.uima.aae.****controller.**
> >>>>>>> PrimitiveAnalysisEngineControl****ler_impl.process(**
> >>>>>>> PrimitiveAnalysisEngineControl****ler_impl.java:1036)
> >>>>>>>          at org.apache.uima.aae.handler.****
> >>>>>>> HandlerBase.invokeProcess(**
> >>>>>>> HandlerBase.java:121)
> >>>>>>>          at org.apache.uima.aae.handler.****
> >>>>>>> input.ProcessRequestHandler_**
> >>>>>>> impl.****handleProcessRequestFromRemote****Client(**
> >>>>>>> ProcessRequestHandler_**
> >>>>>>> impl.java:542)
> >>>>>>>          at org.apache.uima.aae.handler.****
> >>>>>>> input.ProcessRequestHandler_**
> >>>>>>> impl.handle(****ProcessRequestHandler_impl.****java:1041)
> >>>>>>>          at org.apache.uima.aae.handler.****
> >>>>>>> input.MetadataRequestHandler_****
> >>>>>>> impl.handle(****MetadataRequestHandler_impl.****java:78)
> >>>>>>>          at
> >> org.apache.uima.adapter.jms.****activemq.JmsInputChannel.**
> >>>>>>> onMessage(JmsInputChannel.****java:706)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>> AbstractMessageListenerContain****er.doInvokeListener(**
> >>>>>>> AbstractMessageListenerContain****er.java:535)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>> AbstractMessageListenerContain****er.invokeListener(**
> >>>>>>> AbstractMessageListenerContain****er.java:495)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>> AbstractMessageListenerContain****er.doExecuteListener(**
> >>>>>>> AbstractMessageListenerContain****er.java:467)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>>
> AbstractPollingMessageListener****Container.**doReceiveAndExecute(**
> >>>>>>> AbstractPollingMessageListener****Container.java:325)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>> AbstractPollingMessageListener****Container.receiveAndExecute(****
> >>>>>>> AbstractPollingMessageListener****Container.java:263)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>>
> DefaultMessageListenerContaine****r$**AsyncMessageListenerInvoker.**
> >>>>>>> invokeListener(****DefaultMessageListenerContaine****r.java:1058)
> >>>>>>>          at org.springframework.jms.****listener.**
> >>>>>>>
> >> DefaultMessageListenerContaine****r$**AsyncMessageListenerInvoker.****
> >>>>>>> run(**
> >>>>>>> DefaultMessageListenerContaine****r.java:952)
> >>>>>>>          at
> >> java.util.concurrent.****ThreadPoolExecutor.runWorker(****
> >>>>>>> ThreadPoolExecutor.java:1145)
> >>>>>>>          at
> >> java.util.concurrent.****ThreadPoolExecutor$Worker.run(****
> >>>>>>> ThreadPoolExecutor.java:615)
> >>>>>>>          at org.apache.uima.aae.****UimaAsThreadFactory$1.run(**
> >>>>>>> UimaAsThreadFactory.java:118)
> >>>>>>>          at java.lang.Thread.run(Thread.****java:724)
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>
>
>

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