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From "Abramowitsch, Peter" <pabramowit...@hearst.com>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 16:33:54 GMT
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" <pabramowitsch@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.mattmann@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.mattmann@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" <ddligach@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.mattmann@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.mattmann@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" <ddligach@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.mattmann@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.mattmann@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" <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/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
>>
>>>>>>> 
>>
>>>>>>> 
>>
>>>>> 
>>
>>>
>>
>

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