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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject Re: query
Date Tue, 17 Jun 2014 21:45:04 GMT
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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