Hello,
I am trying to use ctakes as a developer. I am not able to use UMLS
resources when I run
the AEs which use UMLS Dictionary.
I have signed up on the UMLS website and I am using the correct email and
password.
I have specified username and password in
Dictionary Lookup: <cTAKES_HOME>/desc/ctakes-dictionary-
lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
But I keep getting the exception. I would really appreciate any help on
this.
OUTPUT THAT I GET on running AggregatePlaintextUMLSProcessor.xml :
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].
11 Jun 2014 13:07:01 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
11 Jun 2014 13:07:01 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
11 Jun 2014 13:07:01 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
11 Jun 2014 13:07:01 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
11 Jun 2014 13:07:03 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - config file absolute
path =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cwd =
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:04 INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
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.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:165)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:190)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(ClinicalPipelineFactory.java:116)
Caused by: java.sql.SQLException: File input/output error:
java.io.IOException: Stream closed
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(Unknown Source)
at java.sql.DriverManager.getConnection(Unknown Source)
at
org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)
... 30 more
