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From Sangram Patil <sangr...@figmd.com>
Subject Re: Exception when running BagOfCUIsGenerator.java
Date Wed, 20 May 2015 14:42:41 GMT
I have downloaded 3.2.2 bin. In InteliJ IDE, I have added all JAR's from
\lib, and trying to run
/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java.

For running the code, I right click on BagOfCUIsGenerator.java file
and select run option. Here is the log -->


Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
20 May 2015 15:20:11  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
20 May 2015 15:20:11  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
20 May 2015 15:20:11  INFO ConstituencyParser - Initializing parser...
20 May 2015 15:20:16  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
20 May 2015 15:20:16  INFO StatusContextAnalyzer - initBoundaryData()
called for ContextInitializer
20 May 2015 15:20:16  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
20 May 2015 15:20:16  INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine"
failed.  (Descriptor:
file:/E:/ctakes-assertion/desc/analysis_engine/SubjectCleartkAnalysisEngine.xml)
 at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
 at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
 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.factory.AnalysisEngineFactory.createEngineFromPath(AnalysisEngineFactory.java:773)
 at
org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:60)
 at
org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.<init>(BagOfAnnotationsGenerator.java:54)
 at BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:20)
 at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:54)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
 at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:606)
 at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)
Caused by: org.apache.uima.resource.ResourceInitializationException
 at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:137)
 at
org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.initialize(AssertionCleartkAnalysisEngine.java:192)
 at
org.apache.ctakes.assertion.medfacts.cleartk.SubjectCleartkAnalysisEngine.initialize(SubjectCleartkAnalysisEngine.java:44)
 at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
 ... 24 more
Caused by: java.io.FileNotFoundException:
\org\apache\ctakes\assertion\models\subject\model.jar (The system cannot
find the path specified)
 at java.io.FileInputStream.open(Native Method)
 at java.io.FileInputStream.<init>(FileInputStream.java:146)
 at java.io.FileInputStream.<init>(FileInputStream.java:101)
 at
org.cleartk.ml.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:69)
 at
org.cleartk.ml.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35)
 at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:135)
 ... 27 more
Process finished with exit code 1

On Wed, May 20, 2015 at 7:48 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

>  What version are you using? Did you download src or bin? And what command
> did you use to run it?
> Thanks
> Tim
>
>
> On 05/20/2015 01:24 AM, Sangram Patil wrote:
>
>  Hi,
>
>  I pretty new to Java and cTakes !!!
>
> I am trying to run
> /ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java,
> but I am getting error -
> org.apache.uima.resource.ResourceInitializationException: Initialization
> of annotator class
> "org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE"
> failed.  (Descriptor:
> file:/E:/ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml
> )
>
>  I have tried to run example in Intellij and Eclipse as well. I am
> getting the same error. When I googled, the reason showed is classpath need
> to be mentioned, that didn't solve the problem.
>
>  Could you please provide me any direction and information.
>
> --
>
>  Sincerely,
> Sangram Patil
>
>
>
>
>
>
>


-- 
** Please include your practice ID in your correspondence.*

Sincerely,

Sangram Patil
Team Lead-Core Dev
Cell: +91 992 293 9497


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