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From Pei Chen <chen...@apache.org>
Subject Re: query
Date Tue, 17 Jun 2014 21:29:22 GMT
Harpreet,
Are you using the CVD GUI? or within Eclipse IDE?
Also which version cTAKES are you using? trunk?
--Pei


On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja <hsk5004@rit.edu> wrote:

> Hello Pei,
>   I would really appreciate if you could help me again.
>   After talking to you and reading other email archives. I have done almost
> everything I could, but I am not able to use
> AggregatePlainTextUMLSProcessor.xml using
> UIMA_CVD----clinical-pipeline.launch.
>
>   Just to be sure.
>   The resources folder that from <
>
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
> >
> url
>   is used to replace the resources folder which is already inside
> ctakes/ctakes-dictionary-lookup/ -- directory            or
>          ctakes/ctakes-dictionary-lookup-res/source/main/ -- directory.
>
>  And then which directory is used as a classpath to
> ctakes-clinical-pipeline project.
>
> I still get the same exception that I was getting earlier. I looked into
> the exception deeply and I found that the exception is thrown
> while creating a connection object ( iv_conn ) in
>  JdbcConnectionResourceImpl.java (   line 109 or 110 ) which is inside
>                       ctakes- core/
>                             > src/main/java
>                                 > org.apache.ctakes.core.resource
>                                                     package.
>
> Thank you very much.
> Harpreet
>
>
> On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> >
> wrote:
>
> > Harpreet,
> > Just curious- is maven able to connect to the internet (maven central
> > repositories)? i.e. did you have to set your ~/.m2/settings.xml with
> proxy
> > info if behind a firewall?
> > If it was an intermittent issue, you can try clearing out the local
> > ~/.m2/repository?
> > --Pei
> >
> > > -----Original Message-----
> > > From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> > > Sent: Wednesday, June 11, 2014 3:54 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: query
> > >
> > > 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-resou
> > > > > > rces
> > > > > > -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(Jdbc
> > > > > Co
> > > > > > 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.initializeExter
> > > > > > nalR
> > > > > > esources(ResourceManager_impl.java:442)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_Imp
> > > > > > lBas
> > > > > > e.java:153)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initia
> > > > > > lize
> > > > > > (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(Anal
> > > > > ys
> > > > > > 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:37
> > > > > > 5)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > > > init
> > > > > > ialize(AggregateAnalysisEngine_impl.java:185)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
> > > > > ys
> > > > > > 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:37
> > > > > > 5)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > > > > > init
> > > > > > ialize(AggregateAnalysisEngine_impl.java:185)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
> > > > > ys
> > > > > > 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(Analysis
> > > > > > Engi
> > > > > > neFactory.java:424)
> > > > > > > at
> > > > > >
> org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav
> > > > > > a:16
> > > > > > 5)
> > > > > > > at
> > > > > >
> org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav
> > > > > > a:19
> > > > > > 0)
> > > > > > > at
> > > > > > >
> > > > > > >
> > > > > >
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(Cl
> > > > > > inic
> > > > > > 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(Jdbc
> > > > > Co
> > > > > > nnectionResourceImpl.java:109)
> > > > > > > ... 30 more
> > > > > > >
> > > > > >
> > > >
> >
>

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