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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Wed, 11 Jun 2014 19:53:42 GMT
Pei,
   I had provided the classpath = ctakes-dictionay-look-up/resources to all
the projects in ctakes.
   as it says in the documentation but there was nothing inside my target
folder in ctakes-clinical-pipeline directory.
   So, then I ran maven compile and I got following error.


 [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could
not resolve dependencies for project
org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to
collect dependencies for
[org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile),
jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test),
org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT
(compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed to
read artifact descriptor for
org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: Failure to find
org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in
http://repository.apache.org/snapshots was cached in the local repository,
resolution will not be reattempted until the update interval of
apache.snapshots has elapsed or updates are forced -> [Help 1]
[ERROR]



On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> 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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