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From Pei Chen <chen...@apache.org>
Subject Re: query
Date Wed, 11 Jun 2014 17:49:11 GMT
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 <hsk5004@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
>

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