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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: query
Date Wed, 11 Jun 2014 18:17:56 GMT
Harpreet,
I had a closer look at your log file and it looks like you were actually trying to run it
from Eclipse IDE?
If so, just ensure that the resources do exist in the classpath.
If it's within eclipse ide, the plugin should download and unpack the umls dictionaries automatically
actually. (you can check the below to ensure it exists
target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
You can also try running 'mvn clean compile' from the command line as well.



> -----Original Message-----
> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> Sent: Wednesday, June 11, 2014 2:09 PM
> To: dev@ctakes.apache.org
> Subject: Re: query
> 
> Hello,
>    Thanks for the reply, but I have already done that and I made sure that
>    these resources are there all over again.
> 
> Harpreet
> 
> 
> 
> On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen <chenpei@apache.org> wrote:
> 
> > 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\resourc
> > es\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\resourc
> > es\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\resourc
> > es\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(JdbcCo
> > nnectionResourceImpl.java:130)
> > > at
> > >
> > >
> >
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(Re
> > sourceManager_impl.java:603)
> > > at
> > >
> > >
> > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalR
> > esources(ResourceManager_impl.java:442)
> > > at
> > >
> > >
> > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBas
> > e.java:153)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize
> > (AnalysisEngineImplBase.java:157)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> > ialize(PrimitiveAnalysisEngine_impl.java:123)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > isEngineFactory_impl.java:94)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> om
> > positeResourceFactory_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.init
> > ASB(AggregateAnalysisEngine_impl.java:431)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ialize(AggregateAnalysisEngine_impl.java:185)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > isEngineFactory_impl.java:94)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> om
> > positeResourceFactory_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.init
> > ASB(AggregateAnalysisEngine_impl.java:431)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> > > at
> > >
> > >
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ialize(AggregateAnalysisEngine_impl.java:185)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > isEngineFactory_impl.java:94)
> > > at
> > >
> > >
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> om
> > positeResourceFactory_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(AnalysisEngi
> > neFactory.java:424)
> > > at
> > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:16
> > 5)
> > > at
> > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:19
> > 0)
> > > at
> > >
> > >
> > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(Clinic
> > alPipelineFactory.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(JdbcCo
> > nnectionResourceImpl.java:109)
> > > ... 30 more
> > >
> >
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