ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: I am New to CTakes 3.2.2 : Need Help
Date Thu, 28 Jan 2016 13:31:35 GMT
Hi Sriniwaas,

I haven’t used the old lookup module for a while, so I’ll need to look further into this,
but it looks like your umls credentials passed muster and the dictionary is being used, the
dictionary resources are present, but ctakes cannot find the umls_snomed_map Table.  Perhaps
the dictionary that you downloaded got corrupted during the transfer?  That is a little strange,
but I suppose that you could try to download it again.  Some time this afternoon I will inspect
the old databases and see what is there.

As an aside, you could always try the –fast lookup module.  :^)

Sean
From: srinivasa.rao kundeti [mailto:srinivas1106@gmail.com]
Sent: Wednesday, January 27, 2016 11:07 PM
To: dev@ctakes.apache.org; Finan, Sean; Pei.Chen@childrens.harvard.edu; srinivasa.rao@philips.com;
bruce.tietjen@imatsolutions.com
Subject: I am New to CTakes 3.2.2 : Need Help

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
Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message