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Jeff Headley commented on CTAKES-370: ------------------------------------- I'm using version 3.2.2 and trying to do this in my application. It was previously working with the AggregatePlaintextFastUMLSProcessor. I tried using the one attached to this issue and made the import changes as mentioned in the description, but I am getting the below error: {code:java} org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed. (Descriptor: file:/D:/Software/Epividian/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 {code} The error happens in {{FileLocator}} at method {{private static File locateOnClasspath( final String relativePath )}} and the passed in parameter is: org/apache/ctakes/smokingstatus/data/KU/keywords.txt > Include smoking status in clinical pipeline > ------------------------------------------- > > Key: CTAKES-370 > URL: https://issues.apache.org/jira/browse/CTAKES-370 > Project: cTAKES > Issue Type: Improvement > Components: ctakes-clinical-pipeline, ctakes-smoking-status > Affects Versions: 3.2.2 > Environment: Linux > Reporter: Tomasz Oliwa > Priority: Minor > Attachments: AggregatePlaintextFastUMLSProcessor.xml > > > The smoking status detection can be included in the clinical pipeline. > Attached is a AggregatePlaintextFastUMLSProcessor.xml that has the clinical > pipeline + the smoking status detection integrated. > Currently cTAKES has smoking status resources that need to have > their imports adjusted for any smoking status detection to work. As a > workaround, in: > ProductionPostSentenceAggregate_step1.xml > change: > <import name="org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"/> > <import > name="org.apache.ctakes.core.analysis_engine.SentenceDetectorAnnotator"/> > to the absolute or relative path (depends on the installed system, on my > machine it is) of these annotators: > <import > location="../../../../../../desc/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/> > <import > location="../../../../../../desc/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/> -- This message was sent by Atlassian JIRA (v6.4.14#64029)