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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: ytex merged into trunk
Date Mon, 28 Apr 2014 15:00:38 GMT
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
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