Hi Chris, Sorry, could you please clarify which environment variable I am missing?
Thanks, Dima > On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) > <chris.a.mattm...@jpl.nasa.gov> wrote: > > 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 >> >>
