Return-Path: X-Original-To: apmail-ctakes-notifications-archive@www.apache.org Delivered-To: apmail-ctakes-notifications-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 1DE2811586 for ; Tue, 26 Aug 2014 14:50:59 +0000 (UTC) Received: (qmail 91439 invoked by uid 500); 26 Aug 2014 14:50:59 -0000 Delivered-To: apmail-ctakes-notifications-archive@ctakes.apache.org Received: (qmail 91366 invoked by uid 500); 26 Aug 2014 14:50:59 -0000 Mailing-List: contact notifications-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list notifications@ctakes.apache.org Received: (qmail 91224 invoked by uid 99); 26 Aug 2014 14:50:58 -0000 Received: from arcas.apache.org (HELO arcas.apache.org) (140.211.11.28) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 26 Aug 2014 14:50:58 +0000 Date: Tue, 26 Aug 2014 14:50:58 +0000 (UTC) From: "Pei Chen (JIRA)" To: notifications@ctakes.apache.org Message-ID: In-Reply-To: References: Subject: [jira] [Commented] (CTAKES-308) ytex unit tests fixes MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-JIRA-FingerPrint: 30527f35849b9dde25b450d4833f0394 [ https://issues.apache.org/jira/browse/CTAKES-308?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14110774#comment-14110774 ] Pei Chen commented on CTAKES-308: --------------------------------- DAOTest is just a warning. The real error is coming from: Hi However, earlier in the ytex tests, I did get another error: Running org.apache.ctakes.jdl.data.xml.ValidationTest org.xml.sax.SAXParseException; schema_reference.4: Failed to read schema document 'file:/C:/Users/oconnell/workspace/cTakes%20Projects/ctakes/ctakes-ytex/file:/C:/Users/oconnell/workspace/cTakes%2520Projects/ctakes/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd', because 1) could not find the document; 2) the document could not be read; 3) the root element of the document is not . at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198) ... Caused by: java.io.FileNotFoundException: C:\Users\oconnell\workspace\cTakes Projects\ctakes\ctakes-ytex\file:\C:\Users\oconnell\workspace\cTakes%20Projects\ctakes\ctakes-ytex-res\target\ctakes-ytex-res-3.2.1-SNAPSHOT.jar!\org\apache\ctakes\jdl\xdl.xsd (The filename, directory name, or volume label syntax is incorrect) ... Tests run: 3, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.624 sec <<< FAILURE! The test that is failing has nothing to do with the MRCONSO not found warning. ValidationTest failed because it couldn't find the XSD. The XSD is in the ctakes-ytex-resources, but the corresponding maven artifact is an empty jar. I think it would be best to modify the resource jars to actually contain resources. I'm not too privy to the ytex config details, but yes you're right, it's caused by the xdl.xsd being null. However it looks like it exists in ytex-res.jar but the call being made uses Class.getResource which won't be able to read in from the jar as an InputStream. 1) We can make ytex read in resources directly from jars (as maven central artifacts). We can make AppJdl.class.getResourceAsStream() instead of getResource(). However, are there any other local physical File dependencies? 2) Alternatively, we can add a step to have maven unpack res.jar if required. I think 1 would be nice, but not sure how involved it will be. Caused by: java.io.FileNotFoundException: /Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex/file:/Users/pei/workspace/apache-ctakes/trunk/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:146) at java.io.FileInputStream.<init>(FileInputStream.java:101) at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90) Anyhow- https://issues.apache.org/jira/browse/CTAKES-308 opened to track this > ytex unit tests fixes > --------------------- > > Key: CTAKES-308 > URL: https://issues.apache.org/jira/browse/CTAKES-308 > Project: cTAKES > Issue Type: Bug > Components: ctakes-ytex > Reporter: Pei Chen > Priority: Minor > > 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$InputStreamConfigurationSource@7433a719. > The diskStore path for this CacheManager will be set to /var/folders/qc/d7xd4zzs0_xcybv88skt5_7m0000gn/T//ehcache_auto_created_1408988030830. > To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a separate ehcache configuration (ehcache.xml) for each CacheManager instance. > 2014-08-25 13:33:51,082 WARN > org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 62, > SQLState: S0010 > 2014-08-25 13:33:51,082 ERROR > org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Unknown JDBC escape sequence: {{db.schema}.MRCONSO mrconso0_ where mrconso0_.aui>? > and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and mrconso0_.lat='ENG' order by mrconso0_.aui > 2014-08-25 13:33:51,085 WARN > org.apache.ctakes.ytex.umls.dao.UMLSDaoTest - sql exception - mrconso probably doesn't exist, check error > org.hibernate.exception.SQLGrammarException: could not prepare statement > at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:123) > at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49) > at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125) > at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:188) > at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(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(Loader.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(QueryTranslatorImpl.java:357) > at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java: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.java:106) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319) > at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) > at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) > at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110) > at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) > at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90) > at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) > at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) > at com.sun.proxy.$Proxy11.getAllAuiStr(Unknown Source) > at org.apache.ctakes.ytex.umls.dao.UMLSDaoTest.testGetAllAuiStr(UMLSDaoTest.java:53) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45) > at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15) > at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42) > at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20) > at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28) > at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263) > at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68) > at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.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$2.evaluate(ParentRunner.java:222) > at org.junit.runners.ParentRunner.run(ParentRunner.java:300) > at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249) > at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142) > at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189) > at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165) > at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85) > at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104) > at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75) > 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.(Unknown Source) > at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source) > at org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281) > at org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313) > at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:161) > at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.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) -- This message was sent by Atlassian JIRA (v6.2#6252)