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Date: Tue, 29 Oct 2013 12:36:59 -0400
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Subject: Re: XmiCasSerializer error in UIMA-AS
From: Eddie Epstein <eaepstein@gmail.com>
To: user@uima.apache.org
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Hi Peter,

Things like  XmiCasDeserializer.deserialize(new FileInputStream(each), cas,
true) in RutaInterpreterRunner?
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.

Eddie


On Tue, Oct 29, 2013 at 9:39 AM, Peter Kl=FCgl <pkluegl@uni-wuerzburg.de>wr=
ote:

> 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 whi=
ch
> > 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 com=
e
> 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. Whe=
n
> 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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