Include smoking status in clinical pipeline

[Jeff Headley <je...@gmail.com>]

Using ctakes 3.2.2 and I'm trying to include the smoking status in the
clinical pipeline as outlined in
https://issues.apache.org/jira/browse/CTAKES-370 and could use some help
please. I downloaded the pipeline xml, I modified the 2 imports, and now I
get this stack trace:

org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed.
 (Descriptor:
file:/D:/Software/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at
com.epividian.ctakes.utils.CTAKESUtils.getAnalysisEngine(CTAKESUtils.java:143)
at
com.epividian.ctakes.processors.CommandLineProcessor.processLine(CommandLineProcessor.java:144)
at
java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at
java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at
com.epividian.ctakes.processors.CommandLineProcessor.run(CommandLineProcessor.java:112)
at com.epividian.ctakes.App.main(App.java:109)
Caused by: org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:74)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 19 more
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(File.java:418)
at
org.apache.ctakes.core.resource.FileLocator.locateOnClasspath(FileLocator.java:182)
at
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:125)
at
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:67)
... 20 more


I have tried modifying that import in a similar way as the others with no
luck.
<import
location="../../../../../../desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml"/>

Thanks,
Jeff