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From Harpreet Khanduja <hsk5...@rit.edu>
Subject Re: query
Date Tue, 17 Jun 2014 22:22:06 GMT
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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