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Posted to dev@ctakes.apache.org by Pankaj Shinde <pa...@krixi.com> on 2015/05/27 15:38:17 UTC

Apache cTAKES - ResourceInitializationException

Hi,

I want to parse clinical documents using Apache cTAKES. I have a set of
clinical documents as plain texts.
For this, I am using BagOfCUIsGenerator.java and cTAKES jars.
I configured this in IntelliJ IDEA as a java project.

When I try to run, I am getting exception and error as follows.
Output:

*log4j:WARN No appenders could be found for logger
(org.springframework.validation.DataBinder).*
*log4j:WARN Please initialize the log4j system properly.*
*log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
<http://logging.apache.org/log4j/1.2/faq.html#noconfig> for more info.*
*Loading configuration.*
*Loading feature templates.*
*Loading lexica.*
*Loading model:*
*........................................................................................*
*Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine"
failed.  (Descriptor:
file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)*
* at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)*
* at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)*
* 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:21)*
* at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)*
* 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: java.lang.NullPointerException*
* at java.io.Reader.<init>(Reader.java:78)*
* at java.io.InputStreamReader.<init>(InputStreamReader.java:72)*
* at java.util.Scanner.<init>(Scanner.java:608)*
* at
org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.<init>(ContextWordWindowExtractor.java:55)*
* at
org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)*
* at
org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)*
* at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)*
* ... 24 more*

*Process finished with exit code 1*

Please help.
Thanks
Pankaj Shinde

Re: Apache cTAKES - ResourceInitializationException

Posted by "HARPREET KHANDUJA (RIT Student)" <hs...@rit.edu>.

Pankaj,

  Caused by: java.lang.NullPointerException*
* at java.io.Reader.<init>(Reader.java:78)*
* at java.io.InputStreamReader.<init>(InputStreamReader.java:72)*

My guess is you are trying to read something which is null. Hope it helps.

Regards,
Harpreet

On Wednesday, May 27, 2015, Pankaj Shinde <pa...@krixi.com> wrote:

> Hi,
>
> I want to parse clinical documents using Apache cTAKES. I have a set of
> clinical documents as plain texts.
> For this, I am using BagOfCUIsGenerator.java and cTAKES jars.
> I configured this in IntelliJ IDEA as a java project.
>
> When I try to run, I am getting exception and error as follows.
> Output:
>
> *log4j:WARN No appenders could be found for logger
> (org.springframework.validation.DataBinder).*
> *log4j:WARN Please initialize the log4j system properly.*
> *log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
> <http://logging.apache.org/log4j/1.2/faq.html#noconfig> for more info.*
> *Loading configuration.*
> *Loading feature templates.*
> *Loading lexica.*
> *Loading model:*
>
> *........................................................................................*
> *Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> annotator class
> "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine"
> failed.  (Descriptor:
>
> file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)*
> * at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)*
> * at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)*
> * 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:21)*
> * at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)*
> * 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: java.lang.NullPointerException*
> * at java.io.Reader.<init>(Reader.java:78)*
> * at java.io.InputStreamReader.<init>(InputStreamReader.java:72)*
> * at java.util.Scanner.<init>(Scanner.java:608)*
> * at
>
> org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.<init>(ContextWordWindowExtractor.java:55)*
> * at
>
> org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)*
> * at
>
> org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)*
> * at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)*
> * ... 24 more*
>
> *Process finished with exit code 1*
>
> Please help.
> Thanks
> Pankaj Shinde
>