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From Pei Chen <chen...@apache.org>
Subject Re: query
Date Wed, 18 Jun 2014 15:08:38 GMT
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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