ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From vijay garla <vnga...@gmail.com>
Subject Re: ytex merged into trunk
Date Mon, 28 Apr 2014 17:26:30 GMT
sorry about that.  I will investigate.

-vj


On Mon, Apr 28, 2014 at 11:00 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Vijay,
>
> I did a checkout this morning and I'm getting compile errors from Maven.
>
> If I just run mvn compile then I get an error while building ytex claiming
> that the package has not been created.  Is there a reversed dependency?
>
> If I run mvn compile package then ytex seems to run through, but there is
> an error in the test of ytex-uima (see below).
>
> Any ideas?
>
> Thanks,
> Sean
>
>
> Running org.apache.ctakes.ytex.uima.annotators.SparseDataExporterTest
> ...
> 2014-04-28 10:50:43,074 INFO  org.hibernate.dialect.Dialect  - HHH000400:
> Using dialect: org.hibernate.dialect.HSQLDialect
> 2014-04-28 10:50:43,112 WARN
>  org.hibernate.engine.jdbc.spi.SqlExceptionHelper  - SQL Error: -22,
> SQLState: S0002
> 2014-04-28 10:50:43,112 ERROR
> org.hibernate.engine.jdbc.spi.SqlExceptionHelper  - Table not found in
> statement [select uimatype0_.ui
> ma_type_id as uima_typ1_21_, uimatype0_.uima_type_name as uima_typ2_21_,
> uimatype0_.table_name as table_na3_21_ from PUBLIC.ref_uima
> _type uimatype0_]
> ...
> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 6.277 sec
> <<< FAILURE!
>
> Results :
>
> Tests in error:
>   test(org.apache.ctakes.ytex.uima.annotators.DBCollectionReaderTest):
> Unable to initialize group definition. Group resource name [c
> lasspath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested exception is org.springframe
> work.beans.factory.BeanCreationException: Error creating bean with name
> 'ytexApplicationContext' defined in URL [file:/C:/Spiffy/Dev
> /ApacheCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed;
>  nested exception is org.springframework.beans.BeanInstantiationException:
> Could not instantiate bean class [org.springframework.con
> text.support.ClassPathXmlApplicationContext]: Constructor threw exception;
> nested exception is org.springframework.beans.factory.Bea
> nCreationException: Error creating bean with name 'documentMapperService'
> defined in class path resource [org/apache/ctakes/ytex/uim
> a/beans-uima-mapper.xml]: Invocation of init method failed; nested
> exception is org.hibernate.exception.SQLGrammarException: could n
> ot prepare statement
>   org.apache.ctakes.ytex.uima.annotators.DBConsumerTest: Unable to
> initialize group definition. Group resource name [classpath*:org/
> apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested exception is org.springframework.beans.fac
> tory.BeanCreationException: Error creating bean with name
> 'ytexApplicationContext' defined in URL [file:/C:/Spiffy/Dev/ApacheCtakesT
> runk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; nested except
> ion is org.springframework.beans.BeanInstantiationException: Could not
> instantiate bean class [org.springframework.context.support.C
> lassPathXmlApplicationContext]: Constructor threw exception; nested
> exception is org.springframework.beans.factory.BeanCreationExcep
> tion: Error creating bean with name 'documentMapperService' defined in
> class path resource [org/apache/ctakes/ytex/uima/beans-uima-m
> apper.xml]: Invocation of init method failed; nested exception is
> org.hibernate.exception.SQLGrammarException: could not prepare sta
> tement
>   org.apache.ctakes.ytex.uima.annotators.DBConsumerTest
>
> testDictionaryLookupIntegrated(org.apache.ctakes.ytex.uima.annotators.DictionaryLookupAnnotatorTest):
> Initialization of annotator
> class "org.apache.ctakes.ytex.uima.annotators.SegmentRegexAnnotator"
> failed.  (Descriptor: file:/C:/Spiffy/Dev/ApacheCtakesTrunk/cta
> kes-ytex-uima/desc/analysis_engine/SegmentRegexAnnotator.xml)
>
> testDictionaryLookupSimple(org.apache.ctakes.ytex.uima.annotators.DictionaryLookupAnnotatorTest)
>
> testDisambiguate(org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotatorTest):
> Unable to initialize group definition. G
> roup resource name
> [classpath*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested excepti
> on is org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'ytexApplicationContext' defined in URL
>  [file:/C:/Spiffy/Dev/ApacheCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instanti
> ation of bean failed; nested exception is
> org.springframework.beans.BeanInstantiationException: Could not instantiate
> bean class [or
> g.springframework.context.support.ClassPathXmlApplicationContext]:
> Constructor threw exception; nested exception is org.springframew
> ork.beans.factory.BeanCreationException: Error creating bean with name
> 'documentMapperService' defined in class path resource [org/a
> pache/ctakes/ytex/uima/beans-uima-mapper.xml]: Invocation of init method
> failed; nested exception is org.hibernate.exception.SQLGram
> marException: could not prepare statement
>   org.apache.ctakes.ytex.uima.annotators.SparseDataExporterTest: Unable to
> initialize group definition. Group resource name [classpa
> th*:org/apache/ctakes/ytex/uima/beanRefContext.xml], factory key
> [ytexApplicationContext]; nested exception is org.springframework.b
> eans.factory.BeanCreationException: Error creating bean with name
> 'ytexApplicationContext' defined in URL [file:/C:/Spiffy/Dev/Apach
> eCtakesTrunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/uima/beanRefContext.xml]:
> Instantiation of bean failed; neste
> d exception is org.springframework.beans.BeanInstantiationException: Could
> not instantiate bean class [org.springframework.context.s
> upport.ClassPathXmlApplicationContext]: Constructor threw exception;
> nested exception is org.springframework.beans.factory.BeanCreat
> ionException: Error creating bean with name 'documentMapperService'
> defined in class path resource [org/apache/ctakes/ytex/uima/bean
> s-uima-mapper.xml]: Invocation of init method failed; nested exception is
> org.hibernate.exception.SQLGrammarException: could not pre
> pare statement
>
> Tests run: 12, Failures: 0, Errors: 7, Skipped: 0
> ...
>
> [INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [
>  1.089 s]
> [INFO] Apache cTAKES YTEX ................................ SUCCESS [
> 14.592 s]
> [INFO] Apache cTAKES YTEX UIMA ........................... FAILURE [01:34
> min]
> [INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
> [INFO] Apache cTAKES YTEX Web ............................ SKIPPED
>
> ...
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-surefire-plugin:2.12:test (default-test) on
> project ctakes-ytex-uima:
> There are test failures.
>
>
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Sunday, April 27, 2014 10:56 PM
> To: dev@ctakes.apache.org
> Subject: ytex merged into trunk
>
> Hello All,
>
> I have merged YTEX into trunk, will keep the branch around a little while
> then delete it.  Some non-ytex related changes (I will gladly change/revert
> if there are objections):
> * ctakes-temporal does not compile; from the email threads I take it that
> this is under development and the compilation failures are to be expected.
>  I have commented out these modules from the root pom.xml so that ctakes
> builds.  I wasn't able to use maven profiles to exclude ctakes-temporal,
> not sure why.
> * default max memory runctakesCPE/CVD.bat: I have increased this to 2G
> (was 1G).  I do not think it is possible to run cTAKES with less memory
> (definitely not in a 64-bit jdk) when loading the assertion models (which
> is the 'default' pipeline).
>
> I will clean up the ytex docs shortly.
>
> Best,
>
> VJ
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message