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From Marshall Schor <...@schor.com>
Subject Re: question about InterOP between Apache UIMA and Omnifind Annotators (CAS2JDBC)
Date Wed, 24 Jun 2009 15:51:31 GMT
There is some sample code that is part of Apache UIMA distribution that
is a cas consumer that does a Cas to JDBC operation; you might be able
to use this to guide you in developing your own cas consumer, if you want. 

The sample code is in
uimaj-examples/src/main/java/org/apache/uima/examples/cpe/PersonTitleDBWriterCasConsumer.java
- here's a link to this in our SVN: 
http://svn.apache.org/viewvc/incubator/uima/uimaj/trunk/uimaj-examples/src/main/java/org/apache/uima/examples/cpe/PersonTitleDBWriterCasConsumer.java?view=co


HTH.  -Marshall

Thilo Goetz wrote:
> Hi Chengmin,
>
> please don't cross post.  Answers below.
>
> Chengmin Ding wrote:
>   
>> Hello,
>>
>> We have used the UIMA Adapter for IBM annotators and it worked for some of
>> our testing annotators.  However, when we tried it on cas2jdbc, we got the
>> following error:
>>
>> We have a CPE pipeline and the CAS2JDBC is the only consumer/engine based on
>> IBM UIMA framework. We are using Apache UIMA 2.2 for the entire pipeline. We
>> were thinking this was caused by missing Omnifind specific annotator which
>> fills out the DocumentAnnotation or the omnifind specific
>> com.ibm.es.tt.DocumentMetaData feature structure (which contains documentid
>> etc features). We then added the base annotator from Omnifind
>> (OF_Tokenization.xml etc) and also wrapped it up with the adapter. But we
>> still got the same error. Our questions are:
>>
>> 1) Is the error indeed caused by missing some Omnifind specific annotator
>> that fills out the DocumentAnnotation feature structure?
>>     
>
> Not quite sure from the error message, but very likely yes.  I suppose
> that cas2jdbc was never intended to be run outside the OF UIMA pipeline.
> OF has an internal document model that is shared between its annotators,
> and I assume that cas2jdbc relies on that model.  Seems reasonable, given
> that you will later need to identify documents in the DB based on some ID
> or other.
>
>   
>> 2) Is there any way to further isolate the problem via any tools considering
>> we do not have the source code for cas2jdbc?
>>     
>
> I can't think of any.  A better place to ask would be the IBM OF
> support forum.
>
>   
>> 3) Can the IBM UIMA Adapter be used the same way to wrap regular annotator,
>> aggregated analysis engine and consumers ?
>>     
>
> Yes for primitive and aggregate AEs.  Consumers I actually don't know,
> they used to have a special status in IBM UIMA.  It doesn't look like
> that's your problem, though.
>
>   
>> 4) Does Apache UIMA have any plan to come up with a CAS2JDBC compatible db
>> consumer?
>>     
>
> If there is one, I don't know of it.
>
> --Thilo
>
>   
>> Thanks a lot!
>> ================================================
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>> at
>> com.ibm.uima.adapter.ibm.IBMAnalysisEngineWrapper.processAndOutputNewCASes(Unknown
>> Source)
>> at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:218)
>> at
>> org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:892)
>> at
>> org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577)
>> Caused by: com.ibm.uima.analysis_engine.AnalysisEngineProcessException: The
>> common analysis structure cannot be processed. See the previous exception
>> for details.
>> at
>> com.ibm.uima.reference_impl.analysis_engine.compatibility.CasConsumerAdapter.process(CasConsumerAdapter.java:93)
>> at
>> com.ibm.uima.reference_impl.analysis_engine.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:392)
>> at
>> com.ibm.uima.reference_impl.analysis_engine.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:297)
>> at
>> com.ibm.uima.reference_impl.analysis_engine.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:218)
>> ... 4 more
>> Caused by: com.ibm.uima.resource.ResourceProcessException: The common
>> analysis structure cannot be processed. See the previous exception for
>> details.
>> at
>> com.ibm.uima.consumer.cas2jdbc.utils.Cas2JdbcLogger.log_PROCESS_CAS__SEVERE(Unknown
>> Source)
>> at com.ibm.uima.consumer.cas2jdbc.Cas2Jdbc.processCas(Unknown Source)
>> at
>> com.ibm.uima.reference_impl.analysis_engine.compatibility.CasConsumerAdapter.process(CasConsumerAdapter.java:89)
>> ... 7 more
>> Caused by: com.ibm.uima.resource.ResourceProcessException: The document's ID
>> cannot be parsed. See the previous exception for details.
>> at
>> com.ibm.uima.consumer.cas2jdbc.utils.Cas2JdbcLogger.log_BAD_DOCID__SEVERE(Unknown
>> Source)
>> at com.ibm.uima.consumer.cas2jdbc.Cas2Jdbc.parseDocID(Unknown Source)
>> ... 9 more
>> Caused by: java.lang.NullPointerException
>> ... 10 more
>>
>> -Chengmin
>>
>>     
>
>
>
>   

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