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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: ytex merged into trunk
Date Mon, 28 Apr 2014 20:03:08 GMT
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 <vngarla@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
>>
>
>
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