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Date: Thu, 31 Oct 2013 09:33:28 -0400
From: Marshall Schor <msa@schor.com>
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To: user@uima.apache.org
Subject: Re: XmiCasSerializer error in UIMA-AS
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Hi,

This is I think a plain and simple bug.

Here's the Jira I created:  https://issues.apache.org/jira/browse/UIMA-3396

I'll do a fix...

-Marshall
On 10/30/2013 9:11 AM, Eddie Epstein wrote:
> 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 Kl�gl <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 Kl�gl <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)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>