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From "Mattmann, Chris A (3980)" <chris.a.mattm...@jpl.nasa.gov>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 16:07:50 GMT
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 I’ve
had that same bug (in another project), that was the cause. You may
try looking for URIs in config file in which the property isn’t 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:  http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Director, Information Retrieval and Data Science Group (IRDS)
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
WWW: http://irds.usc.edu/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++









On 6/28/16, 9:02 AM, "Dligach, Dmitriy" <ddligach@luc.edu> wrote:

>Thanks, Chris.
>
>I didn’t 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 isn’t 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:  http://sunset.usc.edu/~mattmann/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Director, Information Retrieval and Data Science Group (IRDS)
>> Adjunct Associate Professor, Computer Science Department
>> University of Southern California, Los Angeles, CA 90089 USA
>> WWW: http://irds.usc.edu/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 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:  http://sunset.usc.edu/~mattmann/
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>> Director, Information Retrieval and Data Science Group (IRDS)
>>>> Adjunct Associate Professor, Computer Science Department
>>>> University of Southern California, Los Angeles, CA 90089 USA
>>>> WWW: http://irds.usc.edu/
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 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/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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