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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Tue, 17 Jun 2014 21:36:18 GMT
Pei,

  Thank you for the quick reply.
  I am using CVD GUI within eclipse which is under
                           >ctakes-clinical-pipeline project..
                             > resources
                                >launch
                                    >
UIMA_CVD---clinical_documents_pipeline.launch.

  I am using ctakes 3.1.1 and resouces also 3.1

 I used this link for svn : https://svn.apache.org/repos/asf/ctakes/trunk
 when I downloaded ctakes using Eclipse.

 isn't this svn for ctakes 3.1.1?

 Thank you,

Harpreet


On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen <chenpei@apache.org> wrote:

> 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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