Harpreet, Ensure that you have downloaded the dictionaries (umls) per download page: http://ctakes.apache.org/downloads.cgi Resources
Resources are required to run most of cTAKES. They are available for download from SourceForge: ctakes-resources-3.1.0.zip <http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download> . Please download, unzip and add/merge the contents to the existing resources directory. Follow the User <https://cwiki.apache.org/confluence/x/oxAHAg> or Developer <https://cwiki.apache.org/confluence/x/nxAHAg> Install Guide to direct you through the installation process. On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja <hsk5...@rit.edu> wrote: > 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 >
