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From Thilo Goetz <twgo...@gmx.de>
Subject Re: question about InterOP between Apache UIMA and Omnifind Annotators (CAS2JDBC)
Date Wed, 24 Jun 2009 07:05:45 GMT
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.


> 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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