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From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject RE: URI is not hierarchical
Date Tue, 28 Jun 2016 14:50:20 GMT
Hi Dima,

I believe this is related to the path of LVG.  You can try coping the LVG data folder to the
same directory (This is at least how I've gotten around it) when running a compiled jar. 
You can also search the mailing list for additional discussion on this issue.

Thanks,
Brandon

-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu] 
Sent: Tuesday, June 28, 2016 10:45 AM
To: cTAKES Developer list <dev@ctakes.apache.org>
Subject: URI is not hierarchical

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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