Thanks, Chris. I didn’t realize cTAKES was relying on environment variables for locating resources. Do you know which environment variable might be the issue?
Thanks again for your help, Dima > On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980) > <chris.a.mattm...@jpl.nasa.gov> wrote: > > 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 >>>> >>>> >>
