ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 16:02:10 GMT
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
>>>> 
>>>> 
>> 

Mime
View raw message