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From Pankaj Shinde <pankaj.shi...@krixi.com>
Subject cTakes - hsqldb connection problem
Date Tue, 02 Jun 2015 06:44:05 GMT
Hi,

I have done following to get cTakes working.

1. Created java project
2. Created java class
3. Instanciated BagOfCUIsGenerator class with two arguments, input folder
and output folder.
4. Added all required files in this java project.

When I try to run application I am getting following error.
I ran application in 'Debug' mode and I traced exception.
I found out that exception is raised in JdbcConnectionResourceImpl.java
file at line number 109, iv_conn is null.
It seems that application is not properly connecting to hsqldb database.

Error is as follows

*Loading model:*
*.*
*Loading configuration.*
*Loading feature templates.*
*Loading lexica.*
*Loading model:*
*................................*
*Loading model:*
*.............................*
*Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException*
* at
org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)*
* 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.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
org.apache.ctakes.clinicalpipeline.runtime.BagOfCUIsGenerator.<init>(BagOfCUIsGenerator.java:34)*
* at com.krixi.cTakesDemo.main(cTakesDemo.java:12)*
* 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.sql.SQLException: File input/output error
/org/apache/ctakes/dictionary/lookup/umls2011ab/umls.properties
java.lang.NullPointerException*
* at org.hsqldb.jdbc.Util.sqlException(Unknown Source)*
* at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)*
* at org.hsqldb.jdbcDriver.getConnection(Unknown Source)*
* at org.hsqldb.jdbcDriver.connect(Unknown Source)*
* at java.sql.DriverManager.getConnection(DriverManager.java:571)*
* at java.sql.DriverManager.getConnection(DriverManager.java:215)*
* at
org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)*
* ... 28 more*

*Process finished with exit code 1*


Please help me.

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