ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Mattmann, Chris A (3980)" <chris.a.mattm...@jpl.nasa.gov>
Subject Re: URI is not hierarchical
Date Tue, 28 Jun 2016 15:26:23 GMT
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