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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
Date Mon, 25 Aug 2014 21:08:31 GMT
It logs it as a warn, but fails the test.
Should there it assertNotNull only if UMLS setup else, pass the test?  
That way, for those folks are doing a default 'maven clean install, they won't have to skipTests?
// UMLSDaoTest .testGetAllAuiStr() - Check to see if UMLS is setup before checking?
Assert.assertNotNull(auis);
CTAKES-308

> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Monday, August 25, 2014 4:30 PM
> To: dev@ctakes.apache.org
> Subject: Re: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
> 
> That is an expected error having to do with the fact that UMLS isn't installed
> in the test database that get's fired up for unit tests.  That is actually a
> warning (and should be interpreted as an error only if you do have UMLS set
> up)
> 
> 
> On Mon, Aug 25, 2014 at 9:02 PM, Pei Chen <chenpei@apache.org> wrote:
> 
> > Hi VJ,
> > While on the subject of unit tests-
> >
> > I didn't get a chance to dig deeper and was hoping you would know the
> > cause of this unit test failure: > mvn clean install
> >
> > 2014-08-25 13:33:50,830 WARN  net.sf.ehcache.CacheManager  - Creating
> > a new instance of CacheManager using the diskStorePath
> > "/var/folders/qc/d7xd4zzs0_xcybv88skt5_7m0000gn/T/" which is already
> > used by an existing CacheManager.
> >
> > The source of the configuration was
> >
> >
> net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigura
> tionSource@7433a719.
> >
> > The diskStore path for this CacheManager will be set to
> >
> >
> /var/folders/qc/d7xd4zzs0_xcybv88skt5_7m0000gn/T//ehcache_auto_creat
> ed_1408988030830.
> >
> > To avoid this warning consider using the CacheManager factory methods
> > to create a singleton CacheManager or specifying a separate ehcache
> > configuration (ehcache.xml) for each CacheManager instance.
> >
> > 2014-08-25 13:33:51,082 WARN
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper  - SQL Error: 62,
> > SQLState: S0010
> >
> > 2014-08-25 13:33:51,082 ERROR
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper  - Unknown JDBC
> > escape sequence: {{db.schema}.MRCONSO mrconso0_ where
> mrconso0_.aui>?
> > and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
> > mrconso0_.lat='ENG' order by mrconso0_.aui
> >
> > 2014-08-25 13:33:51,085 WARN
> > org.apache.ctakes.ytex.umls.dao.UMLSDaoTest  - sql exception - mrconso
> > probably doesn't exist, check error
> >
> > org.hibernate.exception.SQLGrammarException: could not prepare
> > statement
> >
> > at
> > org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQ
> > LStateConversionDelegate.java:123)
> >
> > at
> > org.hibernate.exception.internal.StandardSQLExceptionConverter.convert
> > (StandardSQLExceptionConverter.java:49)
> >
> > at
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionH
> > elper.java:125)
> >
> > at
> >
> org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPrep
> > arationTemplate.prepareStatement(StatementPreparerImpl.java:188)
> >
> > at
> > org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryS
> > tatement(StatementPreparerImpl.java:159)
> >
> > at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
> >
> > at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
> >
> > at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
> >
> > at org.hibernate.loader.Loader.doQuery(Loader.java:900)
> >
> > at
> > org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loa
> > der.java:342)
> >
> > at org.hibernate.loader.Loader.doList(Loader.java:2526)
> >
> > at org.hibernate.loader.Loader.doList(Loader.java:2512)
> >
> > at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
> >
> > at org.hibernate.loader.Loader.list(Loader.java:2337)
> >
> > at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
> >
> > at
> > org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslato
> > rImpl.java:357)
> >
> > at
> >
> org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.j
> > ava:195)
> >
> > at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
> >
> > at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
> >
> > at
> >
> org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getAllAuiStr(UMLSDaoImpl.j
> > ava:106)
> >
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.j
> > ava:57)
> >
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
> s
> > orImpl.java:43)
> >
> > at java.lang.reflect.Method.invoke(Method.java:606)
> >
> > at
> > org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflectio
> > n(AopUtils.java:319)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoi
> > npoint(ReflectiveMethodInvocation.java:183)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> R
> > eflectiveMethodInvocation.java:150)
> >
> > at
> > org.springframework.transaction.interceptor.TransactionInterceptor.inv
> > oke(TransactionInterceptor.java:110)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> R
> > eflectiveMethodInvocation.java:172)
> >
> > at
> > org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke
> > (ExposeInvocationInterceptor.java:90)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> R
> > eflectiveMethodInvocation.java:172)
> >
> > at
> >
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDyna
> mic
> > AopProxy.java:202)
> >
> > at com.sun.proxy.$Proxy11.getAllAuiStr(Unknown Source)
> >
> > at
> >
> org.apache.ctakes.ytex.umls.dao.UMLSDaoTest.testGetAllAuiStr(UMLSDaoT
> e
> > st.java:53)
> >
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.j
> > ava:57)
> >
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
> s
> > orImpl.java:43)
> >
> > at java.lang.reflect.Method.invoke(Method.java:606)
> >
> > at
> >
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(Framework
> M
> > ethod.java:45)
> >
> > at
> > org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCall
> > able.java:15)
> >
> > at
> >
> org.junit.runners.model.FrameworkMethod.invokeExplosively(Framework
> Met
> > hod.java:42)
> >
> > at
> >
> org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMeth
> > od.java:20)
> >
> > at
> > org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.j
> > ava:28)
> >
> > at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
> >
> > at
> > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunn
> > er.java:68)
> >
> > at
> > org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunn
> > er.java:47)
> >
> > at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
> >
> > at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
> >
> > at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
> >
> > at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
> >
> > at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
> >
> > at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
> >
> > at
> > org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider
> > .java:249)
> >
> > at
> > org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4P
> > rovider.java:142)
> >
> > at
> > org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.
> > java:113)
> >
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.j
> > ava:57)
> >
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
> s
> > orImpl.java:43)
> >
> > at java.lang.reflect.Method.invoke(Method.java:606)
> >
> > at
> > org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(R
> > eflectionUtils.java:189)
> >
> > at
> > org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(
> > ProviderFactory.java:165)
> >
> > at
> > org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(Provid
> > erFactory.java:85)
> >
> > at
> >
> org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(Forke
> > dBooter.java:104)
> >
> > at
> >
> org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:7
> > 5)
> >
> > Caused by: java.sql.SQLException: Unknown JDBC escape sequence:
> > {{db.schema}.MRCONSO mrconso0_ where mrconso0_.aui>? and
> > length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
> > mrconso0_.lat='ENG' order by mrconso0_.aui
> >
> > at org.hsqldb.jdbc.jdbcConnection.onStartEscapeSequence(Unknown
> > Source)
> >
> > at org.hsqldb.jdbc.jdbcConnection.nativeSQL(Unknown Source)
> >
> > at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source)
> >
> > at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source)
> >
> > at
> >
> org.apache.commons.dbcp.DelegatingConnection.prepareStatement(Delega
> ti
> > ngConnection.java:281)
> >
> > at
> >
> org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapp
> er.p
> > repareStatement(PoolingDataSource.java:313)
> >
> > at
> > org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(S
> > tatementPreparerImpl.java:161)
> >
> > at
> >
> org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPrep
> > arationTemplate.prepareStatement(StatementPreparerImpl.java:182)
> >
> > ... 60 more
> >
> > Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.202
> > sec
> >
> >
> > Results :
> >
> >
> > Tests in error:
> >
> >   setSchema(org.apache.ctakes.jdl.data.xml.ValidationTest)
> >
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