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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject URI is not hierarchical
Date Tue, 28 Jun 2016 14:45:23 GMT
Dear cTAKES developers,

I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a
group of people to cTAKES. This pipeline:

ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java

seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I
run it from command line:

mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”

It begins to run but then crashes. I am including the error messages below. Any clues?

Thank you in advance,

Dima

ava.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
	at java.io.File.<init>(File.java:418)
	at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
	at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
	at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
	at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
	at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
	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: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.produceResource(UIMAFramework.java:314)
	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
	at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
	at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
	at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
	... 6 more


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