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
