Hi Dima, In Apache OODT, when we do environment variable replacement on a URI, e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that error like you had below so that was the source of my suggestion sorry for not clarifying.
Cheers, Chris ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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, 8:03 AM, "Dligach, Dmitriy" <ddlig...@luc.edu> wrote: >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 >>> >>> >
