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From Arohi Kumar <ar...@mobipulse.in>
Subject Problem Regarding Running cTAKES UI from Eclipse()
Date Sun, 01 Sep 2013 20:31:23 GMT
Hello,

I am trying to run the cTAKES UI from Eclipse. I have followed the
installation guidelines provided in
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide
However, I am not able to run the CVD launcher. The stack trace that I get
is

Started org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls at Mon
Sep 02 01:52:44 IST 2013
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
Reading from directory:
/home/arohi-sigmoid/Desktop/ctakes-clinical-test-data/data/plaintext
Outputting to directory:
/home/arohi-sigmoid/Desktop/ctakes-clinical-test-data/data/processing_output_aka_eval_output
02 Sep 2013 01:52:48  INFO ClearNLPDependencyParserAE - using Morphy
analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
02 Sep 2013 01:53:59  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
02 Sep 2013 01:53:59  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
02 Sep 2013 01:54:00  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
02 Sep 2013 01:54:00  INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
02 Sep 2013 01:54:00  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
02 Sep 2013 01:54:00  INFO StatusContextAnalyzer - initBoundaryData()
called for ContextInitializer
02 Sep 2013 01:54:00  INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
02 Sep 2013 01:54:01  INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
Loading configuration.
Loading feature templates.
Loading model:
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02 Sep 2013 01:54:19  INFO Chunker - Chunker model file:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-chunker-res/target/classes/org/apache/ctakes/chunker/models/chunker-model.zip
02 Sep 2013 01:54:20  INFO AssertionAnalysisEngine - scope model file:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/assertion/models/scope.model
02 Sep 2013 01:54:20  INFO AssertionAnalysisEngine - cue model file:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/assertion/models/cue.model
scope model:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/assertion/models/scope.model
02 Sep 2013 01:54:23  INFO AssertionAnalysisEngine - pos model file:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/assertion/models/pos.model
2 Sep, 2013 1:54:23 AM org.mitre.medfacts.i2b2.cli.BatchRunner
loadEnabledFeaturesFromFile
INFO: opening enabled features file:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/assertion/models/featureFile11b

2 Sep, 2013 1:54:24 AM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named assertionModelResourceImpl has been
declared multiple times with different definitions. The definition of the
resource in component /null-0/AssertionAnnotator/assertionAnalysisEngine/
will be used.  The definition in component
/null-0/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored.
2 Sep, 2013 1:54:24 AM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named scopeModelResourceImpl has been
declared multiple times with different definitions. The definition of the
resource in component /null-0/AssertionAnnotator/assertionAnalysisEngine/
will be used.  The definition in component
/null-0/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored.
2 Sep, 2013 1:54:24 AM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named cueModelResourceImpl has been declared
multiple times with different definitions. The definition of the resource
in component /null-0/AssertionAnnotator/assertionAnalysisEngine/ will be
used.  The definition in component
/null-0/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored.
2 Sep, 2013 1:54:24 AM org.apache.uima.resource.impl.ResourceManager_impl
initializeExternalResources
WARNING: The external resource named enabledFeaturesResourceImpl has been
declared multiple times with different definitions. The definition of the
resource in component /null-0/AssertionAnnotator/assertionAnalysisEngine/
will be used.  The definition in component
/null-0/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored.
02 Sep 2013 01:54:24  INFO LuceneIndexReaderResourceImpl -
indexDir=org/apache/ctakes/dictionary/lookup/drug_index  exists.
02 Sep 2013 01:54:24  INFO LuceneIndexReaderResourceImpl - Loading Lucene
Index into memory:
/home/arohi-sigmoid/final_workspace/ctakes/ctakes-dictionary-lookup/resources/org/apache/ctakes/dictionary/lookup/drug_index
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
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.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.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:74)
Caused by: org.apache.lucene.index.IndexFormatTooOldException: Format
version is not supported (resource:
ChecksumIndexInput(RAMInputStream(name=segments))): -1 (needs to be between
-9 and -11). This version of Lucene only supports indexes created with
release 3.0 and later.
at
org.apache.lucene.codecs.lucene3x.Lucene3xSegmentInfoReader.readLegacySegmentInfo(Lucene3xSegmentInfoReader.java:128)
at
org.apache.lucene.codecs.lucene3x.Lucene3xSegmentInfoReader.readLegacyInfos(Lucene3xSegmentInfoReader.java:54)
at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:312)
at
org.apache.lucene.index.StandardDirectoryReader$1.doBody(StandardDirectoryReader.java:56)
at
org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:783)
at
org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:52)
at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:65)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:291)
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:70)
... 29 more

Please help me understand where I am going wrong.

Thank you
Arohi Kumar

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