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From "srinivasa.rao kundeti" <srinivas1...@gmail.com>
Subject I am New to CTakes 3.2.2 : Need Help
Date Thu, 28 Jan 2016 04:07:15 GMT
Hi Sean/Pie,
             I am trying to run a sample to invoke UMLS DictionaryLookup
Annotator in my mac. Getting the following exception
             1. I have provided UMLS licensced user name and password.

             Do I need to set any classpath ?

As I am new to CTakes, Is there a post/document, on the pre-requisites to
perform, before using UMLS Dictionary Lookup Annotator.

Exception when running from Intellij/Eclipse is pasted below. Please help.
The example , that I am trying to run is attached.

with regards
Sriniwaas



Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator" failed.
(Descriptor: <unknown>)

at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(
PrimitiveAnalysisEngine_impl.java:254)

at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(
PrimitiveAnalysisEngine_impl.java:158)

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:279)

at org.apache.uima.UIMAFramework.produceAnalysisEngine(
UIMAFramework.java:405)

at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:255
)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(
AggregateAnalysisEngine_impl.java:429)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(
AggregateAnalysisEngine_impl.java:373)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(
AggregateAnalysisEngine_impl.java:186)

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:279)

at org.apache.uima.UIMAFramework.produceAnalysisEngine(
UIMAFramework.java:405)

at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:255
)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(
AggregateAnalysisEngine_impl.java:429)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(
AggregateAnalysisEngine_impl.java:373)

at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(
AggregateAnalysisEngine_impl.java:186)

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:279)

at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:329)

at org.apache.uima.UIMAFramework.produceAnalysisEngine(
UIMAFramework.java:446)

at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(
AnalysisEngineFactory.java:205)

at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(
SimplePipeline.java:226)

at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(
SimplePipeline.java:259)

at sparkapps.ctakes.CtakesTermAnalyzer$.analyze(CtakesTermAnalyzer.scala:116
)

at sparkapps.ctakes.CtakesTermAnalyzer$.main(CtakesTermAnalyzer.scala:143)

at sparkapps.ctakes.CtakesTermAnalyzer.main(CtakesTermAnalyzer.scala)

Caused by: org.apache.uima.resource.ResourceInitializationException

at
org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.configInit(
DictionaryLookupAnnotator.java:91)

at
org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.initialize(
DictionaryLookupAnnotator.java:74)

at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(
PrimitiveAnalysisEngine_impl.java:252)

... 28 more

Caused by: java.lang.reflect.InvocationTargetException

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(
NativeConstructorAccessorImpl.java:57)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:526)

at
org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.parseLookupBindingXml(
LookupParseUtilities.java:274)

at
org.apache.ctakes.dictionary.lookup.ae.LookupParseUtilities.parseDescriptor(
LookupParseUtilities.java:83)

at
org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.configInit(
DictionaryLookupAnnotator.java:88)

... 30 more

Caused by: java.sql.SQLException: Table not found in statement [select code
from umls_snomed_map where cui=?]

at org.hsqldb.jdbc.Util.throwError(Unknown Source)

at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source)

at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source)

at org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl.<init>(
UmlsToSnomedDbConsumerImpl.java:58)

at org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl.<init>(
UmlsToSnomedDbConsumerImpl.java:64)

... 37 more

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