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From "Mattmann, Chris A (3980)" <chris.a.mattm...@jpl.nasa.gov>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 14:49:50 GMT
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.mattmann@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" <ddligach@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
>
>
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