[CTAKES-435] AE descriptors for processing CDA input is using deprecated assertion annotators

• Type: Bug
• Status: Resolved
• Priority: Minor
• Resolution: Fixed
• Affects Version/s: 4.0.0
• Fix Version/s: future enhancement
• Component/s: ctakes-assertion, ctakes-clinical-pipeline
• Assignee: James Joseph Masanz
• Reporter: James Joseph Masanz
• Created: 20/Apr/17 18:37
• Updated: 20/Apr/17 18:43
• Resolved: 20/Apr/17 18:43

Description

Found while testing rc3 for 4.0.0. This looks like something that can be fixed in the next point release. Users can get an updated .xml file if they need a fix for this, which will use the later version of the assertion annotators

Symptoms:
Using AggregateCdaUMLSProcessor.xml or AggregateCdaProcessor.xml

Might notice the following warnings while loading the AE:

WARN BatchRunner - This class cannot be used until CTAKES-76 is implemented.
WARN JarafeMEDecoder - This class cannot be used until CTAKES-76 is implemented.

The following occur when running the AE against a document:
WARN SingleDocumentProcessor - This class cannot be used until CTAKES-76 is implemented.
WARN SingleDocumentProcessor - This class cannot be used until CTAKES-76 is implemented.
WARN SingleDocumentProcessor - This class cannot be used until CTAKES-76 is implemented.

And when run the AE, a stack trace that includes:

Caused by: java.lang.NullPointerException
at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.process(AssertionAnalysisEngine.java:213)
at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
... 51 more