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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 15:04:42 GMT
Brandon, thank you.

I just did a quick mailing archive search and it looks like this is known issue, which presumably
was fixed a while ago:

http://mail-archives.apache.org/mod_mbox/ctakes-dev/201510.mbox/%3CD8F818BA-50FD-4A08-95EA-4E841FF6FBDF@childrens.harvard.edu%3E

Thanks again,

Dima

> On Jun 28, 2016, at 09:50, Geise, Brandon D. <bdgeise@geisinger.edu> wrote:
> 
> Hi Dima,
> 
> I believe this is related to the path of LVG.  You can try coping the LVG data folder
to the same directory (This is at least how I've gotten around it) when running a compiled
jar.  You can also search the mailing list for additional discussion on this issue.
> 
> Thanks,
> Brandon
> 
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu] 
> Sent: Tuesday, June 28, 2016 10:45 AM
> To: cTAKES Developer list <dev@ctakes.apache.org>
> Subject: URI is not hierarchical
> 
> 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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