Looks to me like a missing environment variable.. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Chris Mattmann, Ph.D. Chief Architect Instrument Software and Science Data Systems Section (398) NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA Office: 168-519, Mailstop: 168-527 Email: chris.a.mattm...@nasa.gov WWW: http://sunset.usc.edu/~mattmann/ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Director, Information Retrieval and Data Science Group (IRDS) Adjunct Associate Professor, Computer Science Department University of Southern California, Los Angeles, CA 90089 USA WWW: http://irds.usc.edu/ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <ddlig...@luc.edu> wrote: >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 > >
