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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Thu, 19 Jun 2014 00:31:27 GMT
Hello Pei,

It didn't work for me.
If it works for you,
please let me know.

Thank you,
Harpreet



On Wed, Jun 18, 2014 at 8:02 PM, Pei Chen <chenpei@apache.org> wrote:

> Harpreet,
> looks like resources just made it to the maven central mirrors.  But I
> didn't not get a chance to try it out or fully test it yet.
> If you would like to give it a whirl, you can update
> ctakes-dictionary-lookup-res/pom.xml to use the latest.
> If EclipseIDE doesn't unpack the resources automatically to target/classes,
> you can force it to run mvn clean compile.
>
>  <!-- cTAKES Resources -->
>
>  <dependency>
>
>  <groupId>net.sourceforge.ctakesresources</groupId>
>
>  <artifactId>ctakes-resources-umls2011ab</artifactId>
>
>  <version>3.1.3</version>
>
>  </dependency>
>
>  <dependency>
>
>  <groupId>net.sourceforge.ctakesresources</groupId>
>
>  <artifactId>ctakes-resources-rxnorm-hsqldb-2011ab</artifactId>
>
>  <version>3.1.3</version>
>
>  </dependency>
>
>  <dependency>
>
>  <groupId>net.sourceforge.ctakesresources</groupId>
>
>  <artifactId>ctakes-resources-orangebook-hsqldb</artifactId>
>
>  <version>3.1.3</version>
>
>  </dependency>
>
>
> On Wed, Jun 18, 2014 at 6:58 PM, Harpreet Khanduja <hsk5004@rit.edu>
> wrote:
>
> > Hello Pei,
> >   Are you able to use trunk now?
> >
> > Thank you,
> > Harpreet
> >
> >
> > On Wed, Jun 18, 2014 at 12:47 PM, Harpreet Khanduja <hsk5004@g.rit.edu>
> > wrote:
> >
> > > Hello Pei,
> > >
> > > Thank you so much for helping.
> > >
> > >
> > > Harpreet
> > >
> > >
> > > On Wed, Jun 18, 2014 at 11:08 AM, Pei Chen <chenpei@apache.org> wrote:
> > >
> > >> Harpreet,
> > >> I just did a fresh checkout of trunk and could recreate the error.  I
> > >> think
> > >> I see the issue- the orangebook hsqldb resource is empty on maven
> > central.
> > >>  I'm hoping to fix that up today.
> > >>
> > >> --Pei
> > >>
> > >>
> > >> On Tue, Jun 17, 2014 at 6:22 PM, Harpreet Khanduja <hsk5004@rit.edu>
> > >> wrote:
> > >>
> > >> > Hello Pei,
> > >> >
> > >> > I also ran from cmd line same exception
> > >> > and I checked pom.xml file on this location.
> > >> > https://svn.apache.org/repos/asf/ctakes/trunk
> > >> > The version mentioned in the file is 3.1.1.
> > >> > .
> > >> >
> > >> > Could you please tell me about the resources directory problem
> which I
> > >> > mentioned in the last email?
> > >> >
> > >> > Thank you so much for your time.
> > >> >
> > >> > Harpreet
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei <
> > >> Pei.Chen@childrens.harvard.edu
> > >> > >
> > >> > wrote:
> > >> >
> > >> > > If this is trunk, Can you do an 'svn update' to ensure you have
> the
> > >> > latest?
> > >> > > If this is trunk you won't need to do a separate download- maven
> > >> should
> > >> > > download and unpack it automatically for you.
> > >> > > Also try the command line alternative:
> > >> > > 'mvn -PrunCVD compile' from the root dir. Let me know.
> > >> > >
> > >> > >
> > >> > > Sent from my iPhone
> > >> > >
> > >> > > > On Jun 17, 2014, at 5:37 PM, "Harpreet Khanduja" <
> hsk5004@rit.edu
> > >
> > >> > > wrote:
> > >> > > >
> > >> > > > 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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