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From Peter Klügl <pklu...@uni-wuerzburg.de>
Subject Re: XmiCasSerializer error in UIMA-AS
Date Wed, 30 Oct 2013 08:38:47 GMT
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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