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:[email protected]] Sent: Sunday, April 27, 2014 10:56 PM To: [email protected] 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
