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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: cTakes - hsqldb connection problem
Date Tue, 02 Jun 2015 14:39:47 GMT
Hi Pankaj,

I haven't seen this exact error before.  I guess that my first steps toward a possible remedy
would be:
- check for existence of /org/apache/ctakes/dictionary/lookup/umls2011ab/umls.properties
- make sure that it (resources/) is in your classpath
- see if it looks like any of the umls2011ab/ files were not fully downloaded (ls -l : 99069136,
410610240, 1295, 705)

I looked at the hsql source a little bit and can't really make heads or tails of why you'd
get a 452 error (file input/output) associated with a null pointer exception (NPE) with the
file path actually listed.  I didn't look too far into the tree but it doesn't look like it
is thrown by any of the main entry points.

Do you have more than one version of hsql installed?  I only ask because the single report
of a similar error message( 452: NPE)  that I found on the web reported it solved when they
equalized all the versions.  It doesn't make sense to me, but it is something to check.

Sean


-----Original Message-----
From: Pankaj Shinde [mailto:pankaj.shinde@krixi.com] 
Sent: Tuesday, June 02, 2015 2:46 AM
To: dev@ctakes.apache.org
Subject: cTakes - hsqldb connection problem

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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