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_-7Ematt >mann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4usw >NF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr2EEENN >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=CwIGaQ >&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m= >bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3FhhH1RYX >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_-7Ema >>>ttmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF >>>4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr >>>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=CwIG >>>aQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm1 >>>0&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3Fh >>>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_-7E >>>>>mattmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTj >>>>>wuVF4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TV >>>>>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=Cw >>>>>IGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5 >>>>>Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkern >>>>>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/clinicalpipe >>>>>>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.ClinicalPipeline >>>>>>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(DelegatingMethodAcces >>>>>>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(LvgCmdApiRe >>>>>>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.initializeExternal >>>>>>Resources(ResourceManager_impl.java:442) > >>>>>> at >>>>>>org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBa >>>>>>se.java:153) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initializ >>>>>>e(AnalysisEngineImplBase.java:157) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini >>>>>>tialize(PrimitiveAnalysisEngine_impl.java:123) > >>>>>> at >>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy >>>>>>sisEngineFactory_impl.java:94) > >>>>>> at >>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co >>>>>>mpositeResourceFactory_impl.java:62) > >>>>>> at >>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > >>>>>> at >>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav >>>>>>a: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.ini >>>>>>tASB(AggregateAnalysisEngine_impl.java:431) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini >>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini >>>>>>tialize(AggregateAnalysisEngine_impl.java:185) > >>>>>> at >>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy >>>>>>sisEngineFactory_impl.java:94) > >>>>>> at >>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co >>>>>>mpositeResourceFactory_impl.java:62) > >>>>>> at >>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) > >>>>>> at >>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav >>>>>>a: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.ini >>>>>>tASB(AggregateAnalysisEngine_impl.java:431) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini >>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > >>>>>> at >>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini >>>>>>tialize(AggregateAnalysisEngine_impl.java:185) > >>>>>> at >>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy >>>>>>sisEngineFactory_impl.java:94) > >>>>>> at >>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co >>>>>>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.jav >>>>>>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(Clin >>>>>>icalPipelineWithUmls.java:68) > >>>>>> ... 6 more > >>>>>> > >>>>>> > >>>> > >> >
