On second thought... This might be useful http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical
On 6/28/16, 9:24 AM, "Abramowitsch, Peter" <pabramowit...@hearst.com> wrote: >Dima > >Although I'm not an expert, I don't think Ctakes relies on any Environment >variables a priori, unless you have a Ctakes extensions that has added a >dependency. Depending on your error you may need to look in AE or >TypeSystem definition files or in the uimafit types.txt file where search >paths are defined for locating the TypeSystem files themselves. > >But looking specifically at the exception being thrown (URI not >heirarchical), I'm wondering if there's a path to the LVG resources that >has accidentally been written with dots as in a Java import, instead of >slashes. Have you looked at the engine descriptor for LVG? > >- p > >On 6/28/16, 9:07 AM, "Mattmann, Chris A (3980)" ><chris.a.mattm...@jpl.nasa.gov> wrote: > >>Hi Dima, >> >> >> >>Might be a red herring - I am not 100% positive that there is an env >> >>var in cTAKES that you are missing just that in the past when I¹ve >> >>had that same bug (in another project), that was the cause. You may >> >>try looking for URIs in config file in which the property isn¹t being >> >>resolved or it ends up as file://NULL/some/path/that/doesnt/exist >> >> >> >>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: >>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Emat >>t >>mann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4us >>w >>NF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr2EEEN >>N >>3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e= >> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>Director, Information Retrieval and Data Science Group (IRDS) >> >>Adjunct Associate Professor, Computer Science Department >> >>University of Southern California, Los Angeles, CA 90089 USA >> >>WWW: >>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwIGa >>Q >>&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m >>= >>bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3FhhH1RY >>X >>hU7RpzHFREfscxk&e= >> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>On 6/28/16, 9:02 AM, "Dligach, Dmitriy" <ddlig...@luc.edu> wrote: >> >> >> >>>Thanks, Chris. >> >>> >> >>>I didn¹t 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 isn¹t 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: >>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Em >>>>a >>>>ttmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuV >>>>F >>>>4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlq >>>>r >>>>2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e= >> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>>> Director, Information Retrieval and Data Science Group (IRDS) >> >>>> Adjunct Associate Professor, Computer Science Department >> >>>> University of Southern California, Los Angeles, CA 90089 USA >> >>>> WWW: >>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwI >>>>G >>>>aQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm >>>>1 >>>>0&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3F >>>>h >>>>hH1RYXhU7RpzHFREfscxk&e= >> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> >>>> 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: >>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7 >>>>>>E >>>>>>mattmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjT >>>>>>j >>>>>>wuVF4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=T >>>>>>V >>>>>>AwAlqr2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e= >> >>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>>>>> Director, Information Retrieval and Data Science Group (IRDS) >> >>>>>> Adjunct Associate Professor, Computer Science Department >> >>>>>> University of Southern California, Los Angeles, CA 90089 USA >> >>>>>> WWW: >>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=C >>>>>>w >>>>>>IGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK >>>>>>5 >>>>>>Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwker >>>>>>n >>>>>>B6S3FhhH1RYXhU7RpzHFREfscxk&e= >> >>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> 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/clinicalpip >>>>>>>e >>>>>>>line/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=³org.apache.ctakes.clinicalpipeline.ClinicalPipelin >>>>>>>e >>>>>>>WithUmls² >> >>>>>>> >> >>>>>>> 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(DelegatingMethodAcce >>>>>>>s >>>>>>>sorImpl.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(LvgCmdApiR >>>>>>>e >>>>>>>sourceImpl.java:65) >> >>>>>>> at >>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.registerResource( >>>>>>>R >>>>>>>esourceManager_impl.java:603) >> >>>>>>> at >>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.initializeExterna >>>>>>>l >>>>>>>Resources(ResourceManager_impl.java:442) >> >>>>>>> at >>>>>>>org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplB >>>>>>>a >>>>>>>se.java:153) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initiali >>>>>>>z >>>>>>>e(AnalysisEngineImplBase.java:157) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.in >>>>>>>i >>>>>>>tialize(PrimitiveAnalysisEngine_impl.java:123) >> >>>>>>> at >>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal >>>>>>>y >>>>>>>sisEngineFactory_impl.java:94) >> >>>>>>> at >>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C >>>>>>>o >>>>>>>mpositeResourceFactory_impl.java:62) >> >>>>>>> at >>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269 >>>>>>>) >> >>>>>>> at >>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja >>>>>>>v >>>>>>>a:387) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.jav >>>>>>>a >>>>>>>:254) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tASB(AggregateAnalysisEngine_impl.java:431) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375 >>>>>>>) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tialize(AggregateAnalysisEngine_impl.java:185) >> >>>>>>> at >>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal >>>>>>>y >>>>>>>sisEngineFactory_impl.java:94) >> >>>>>>> at >>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C >>>>>>>o >>>>>>>mpositeResourceFactory_impl.java:62) >> >>>>>>> at >>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269 >>>>>>>) >> >>>>>>> at >>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja >>>>>>>v >>>>>>>a:387) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.jav >>>>>>>a >>>>>>>:254) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tASB(AggregateAnalysisEngine_impl.java:431) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375 >>>>>>>) >> >>>>>>> at >>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in >>>>>>>i >>>>>>>tialize(AggregateAnalysisEngine_impl.java:185) >> >>>>>>> at >>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal >>>>>>>y >>>>>>>sisEngineFactory_impl.java:94) >> >>>>>>> at >>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C >>>>>>>o >>>>>>>mpositeResourceFactory_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.ja >>>>>>>v >>>>>>>a: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(Cli >>>>>>>n >>>>>>>icalPipelineWithUmls.java:68) >> >>>>>>> ... 6 more >> >>>>>>> >> >>>>>>> >> >>>>> >> >>> >> >
