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-4e841ff6f...@childrens.harvard.edu%3E Thanks again, Dima > On Jun 28, 2016, at 09:50, Geise, Brandon D. <bdge...@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:ddlig...@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 > > > > > IMPORTANT WARNING: The information in this message (and the documents > attached to it, if any) is confidential and may be legally privileged. It is > intended solely for the addressee. Access to this message by anyone else is > unauthorized. If you are not the intended recipient, any disclosure, copying, > distribution or any action taken, or omitted to be taken, in reliance on it > is prohibited and may be unlawful. If you have received this message in > error, please delete all electronic copies of this message (and the documents > attached to it, if any), destroy any hard copies you may have created and > notify me immediately by replying to this email. Thank you. > > Geisinger Health System utilizes an encryption process to safeguard Protected > Health Information and other confidential data contained in external e-mail > messages. If email is encrypted, the recipient will receive an e-mail > instructing them to sign on to the Geisinger Health System Secure E-mail > Message Center to retrieve the encrypted e-mail.
