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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Wed, 18 Jun 2014 22:58:55 GMT
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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