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Posted to dev@ctakes.apache.org by vijay garla <vn...@gmail.com> on 2014/04/28 04:55:16 UTC
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
RE: ytex merged into trunk
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Completely new error. I have taken this offline until we figure out what is going on.
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Monday, April 28, 2014 1:47 PM
To: dev@ctakes.apache.org
Subject: Re: ytex merged into trunk
Hello All,
I can't reproduce this build error. It appears that maven does not want to run copy-dependencies in the compile phase. However, I have tried building this with maven 3.2.1 and maven 3.1.0 and it works fine for both.
@Sean - can you send me the output of mvn -x clean install -pl ctakes-ytex (executed from ctakes root dir)
This is the plugin that maven is complaining about:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>compile</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
On Mon, Apr 28, 2014 at 1:26 PM, vijay garla <vn...@gmail.com> wrote:
> 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.Dic
>> tionaryLookupAnnotatorTest)
>>
>> 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
>>
>
>
Re: ytex merged into trunk
Posted by vijay garla <vn...@gmail.com>.
Hello All,
I can't reproduce this build error. It appears that maven does not want to
run copy-dependencies in the compile phase. However, I have tried building
this with maven 3.2.1 and maven 3.1.0 and it works fine for both.
@Sean - can you send me the output of mvn -x clean install -pl ctakes-ytex
(executed from ctakes root dir)
This is the plugin that maven is complaining about:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>compile</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
On Mon, Apr 28, 2014 at 1:26 PM, vijay garla <vn...@gmail.com> wrote:
> 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
>>
>
>
Re: ytex merged into trunk
Posted by vijay garla <vn...@gmail.com>.
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
>
RE: ytex merged into trunk
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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