{"action":"closed","issue":{"url":"https://api.github.com/repos/molgenis/molgenis/issues/4490","repository_url":"https://api.github.com/repos/molgenis/molgenis","labels_url":"https://api.github.com/repos/molgenis/molgenis/issues/4490/labels{/name}","comments_url":"https://api.github.com/repos/molgenis/molgenis/issues/4490/comments","events_url":"https://api.github.com/repos/molgenis/molgenis/issues/4490/events","html_url":"https://github.com/molgenis/molgenis/issues/4490","id":133696026,"number":4490,"title":"Migration from 1.16.2 to 1.17.0 fails","user":{"login":"Mark-de-Haan","id":3625016,"avatar_url":"https://avatars.githubusercontent.com/u/3625016?v=3","gravatar_id":"","url":"https://api.github.com/users/Mark-de-Haan","html_url":"https://github.com/Mark-de-Haan","followers_url":"https://api.github.com/users/Mark-de-Haan/followers","following_url":"https://api.github.com/users/Mark-de-Haan/following{/other_user}","gists_url":"https://api.github.com/users/Mark-de-Haan/gists{/gist_id}","starred_url":"https://api.github.com/users/Mark-de-Haan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Mark-de-Haan/subscriptions","organizations_url":"https://api.github.com/users/Mark-de-Haan/orgs","repos_url":"https://api.github.com/users/Mark-de-Haan/repos","events_url":"https://api.github.com/users/Mark-de-Haan/events{/privacy}","received_events_url":"https://api.github.com/users/Mark-de-Haan/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/molgenis/molgenis/labels/1.17.0-RC","name":"1.17.0-RC","color":"fbca04"},{"url":"https://api.github.com/repos/molgenis/molgenis/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-15T12:01:14Z","updated_at":"2016-02-16T12:47:48Z","closed_at":"2016-02-16T12:47:48Z","body":"```\r\n12:59:43.292 [ajp-bio-8009-exec-6] INFO  o.m.m.v.v.Step27MetaDataAttributeRoles - Updated metadata from version 26 to 27\r\n12:59:43.300 [ajp-bio-8009-exec-6] INFO  o.m.m.v.MolgenisUpgradeServiceImpl - MetaData upgrade done.\r\n12:59:43.411 [ajp-bio-8009-exec-6] INFO  o.m.a.WebAppConfig$$EnhancerBySpringCGLIB$$1275ab7d - Reindexing repositories due to MOLGENIS upgrade...\r\n12:59:43.703 [ajp-bio-8009-exec-6] WARN  o.s.w.c.s.AnnotationConfigWebApplicationContext - Exception encountered during context initialization - cancelling refresh attempt\r\norg.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webAppConfig': Invocation of init method failed; nested exception is org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [SELECT this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, GROUP_CONCAT(DISTINCT(`lookupAttributes`.`lookupAttributes`) ORDER BY `lookupAttributes`.`order`) AS `lookupAttributes`, this.`abstract`, this.`label`, this.`extends`, this.`description`, GROUP_CONCAT(DISTINCT(`tags`.`tags`) ORDER BY `tags`.`order`) AS `tags`, GROUP_CONCAT(DISTINCT(`attributes`.`attributes`) ORDER BY `attributes`.`order`) AS `attributes`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl` FROM `entities` AS this LEFT JOIN `entities_lookupAttributes` AS `lookupAttributes` ON (this.`fullName` = `lookupAttributes`.`fullName`) LEFT JOIN `entities_tags` AS `tags` ON (this.`fullName` = `tags`.`fullName`) LEFT JOIN `entities_attributes` AS `attributes` ON (this.`fullName` = `attributes`.`fullName`) GROUP BY this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, this.`abstract`, this.`label`, this.`extends`, this.`description`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl`  LIMIT 1000]; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1564) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:755) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:759) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:434) [molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306) [molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106) [molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5014) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:553) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.check(HostConfig.java:1668) [catalina.jar:7.0.59]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Method.invoke(Method.java:483) ~[na:1.8.0_31]\r\n\tat org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301) [tomcat-coyote.jar:7.0.59]\r\n\tat com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819) [na:1.8.0_31]\r\n\tat com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801) [na:1.8.0_31]\r\n\tat org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1516) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:739) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:457) [catalina.jar:7.0.59]\r\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:649) [servlet-api.jar:na]\r\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:727) [servlet-api.jar:na]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:613) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:334) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:119) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:421) [catalina.jar:7.0.59]\r\n\tat org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.59]\r\n\tat org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611) [tomcat-coyote.jar:7.0.59]\r\n\tat org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314) [tomcat-coyote.jar:7.0.59]\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_31]\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_31]\r\n\tat org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.59]\r\n\tat java.lang.Thread.run(Thread.java:745) [na:1.8.0_31]\r\nCaused by: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [SELECT this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, GROUP_CONCAT(DISTINCT(`lookupAttributes`.`lookupAttributes`) ORDER BY `lookupAttributes`.`order`) AS `lookupAttributes`, this.`abstract`, this.`label`, this.`extends`, this.`description`, GROUP_CONCAT(DISTINCT(`tags`.`tags`) ORDER BY `tags`.`order`) AS `tags`, GROUP_CONCAT(DISTINCT(`attributes`.`attributes`) ORDER BY `attributes`.`order`) AS `attributes`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl` FROM `entities` AS this LEFT JOIN `entities_lookupAttributes` AS `lookupAttributes` ON (this.`fullName` = `lookupAttributes`.`fullName`) LEFT JOIN `entities_tags` AS `tags` ON (this.`fullName` = `tags`.`fullName`) LEFT JOIN `entities_attributes` AS `attributes` ON (this.`fullName` = `attributes`.`fullName`) GROUP BY this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, this.`abstract`, this.`label`, this.`extends`, this.`description`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl`  LIMIT 1000]; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:660) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:695) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:727) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:737) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:787) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.mysql.MysqlRepository$3.getBatch(MysqlRepository.java:750) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.support.BatchingQueryResult.getBatch(BatchingQueryResult.java:36) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.support.BatchingQueryResult.getBatch(BatchingQueryResult.java:14) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.util.BatchingIterable$1.nextBatch(BatchingIterable.java:138) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.util.BatchingIterable$1.hasNext(BatchingIterable.java:58) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1811) ~[na:1.8.0_31]\r\n\tat java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) ~[na:1.8.0_31]\r\n\tat org.molgenis.data.meta.EntityMetaDataRepository.fillEntityMetaDataCache(EntityMetaDataRepository.java:81) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.meta.MetaDataServiceImpl.bootstrapMetaRepos(MetaDataServiceImpl.java:171) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.meta.MetaDataServiceImpl.setDefaultBackend(MetaDataServiceImpl.java:116) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.app.WebAppConfig.addReposToReindex(WebAppConfig.java:128) ~[WebAppConfig.class:na]\r\n\tat org.molgenis.ui.MolgenisWebAppConfig.reindex(MolgenisWebAppConfig.java:424) ~[molgenis-core-ui-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.ui.MolgenisWebAppConfig.initRepositories(MolgenisWebAppConfig.java:473) ~[molgenis-core-ui-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Method.invoke(Method.java:483) ~[na:1.8.0_31]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:349) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:300) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:133) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\t... 60 common frames omitted\r\nCaused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Constructor.newInstance(Constructor.java:408) ~[na:1.8.0_31]\r\n\tat com.mysql.jdbc.Util.handleNewInstance(Util.java:411) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.Util.getInstance(Util.java:386) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1054) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2825) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2313) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) ~[c3p0-0.9.1.1.jar:0.9.1.1]\r\n\tat org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:703) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:644) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\t... 84 common frames omitted\r\n12:59:43.773 [ajp-bio-8009-exec-6] INFO  o.m.d.e.f.EmbeddedElasticSearchServiceFactory - Elastic search server stopped\r\n12:59:43.784 [ajp-bio-8009-exec-6] ERROR o.s.web.context.ContextLoader - Context initialization failed\r\norg.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webAppConfig': Invocation of init method failed; nested exception is org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [SELECT this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, GROUP_CONCAT(DISTINCT(`lookupAttributes`.`lookupAttributes`) ORDER BY `lookupAttributes`.`order`) AS `lookupAttributes`, this.`abstract`, this.`label`, this.`extends`, this.`description`, GROUP_CONCAT(DISTINCT(`tags`.`tags`) ORDER BY `tags`.`order`) AS `tags`, GROUP_CONCAT(DISTINCT(`attributes`.`attributes`) ORDER BY `attributes`.`order`) AS `attributes`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl` FROM `entities` AS this LEFT JOIN `entities_lookupAttributes` AS `lookupAttributes` ON (this.`fullName` = `lookupAttributes`.`fullName`) LEFT JOIN `entities_tags` AS `tags` ON (this.`fullName` = `tags`.`fullName`) LEFT JOIN `entities_attributes` AS `attributes` ON (this.`fullName` = `attributes`.`fullName`) GROUP BY this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, this.`abstract`, this.`label`, this.`extends`, this.`description`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl`  LIMIT 1000]; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1564) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:303) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:299) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:194) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:755) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:759) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:434) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106) [molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5014) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:553) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.startup.HostConfig.check(HostConfig.java:1668) [catalina.jar:7.0.59]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Method.invoke(Method.java:483) ~[na:1.8.0_31]\r\n\tat org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301) [tomcat-coyote.jar:7.0.59]\r\n\tat com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819) [na:1.8.0_31]\r\n\tat com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801) [na:1.8.0_31]\r\n\tat org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1516) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.manager.ManagerServlet.deploy(ManagerServlet.java:739) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.manager.ManagerServlet.doPut(ManagerServlet.java:457) [catalina.jar:7.0.59]\r\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:649) [servlet-api.jar:na]\r\n\tat javax.servlet.http.HttpServlet.service(HttpServlet.java:727) [servlet-api.jar:na]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:613) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:334) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.RemoteAddrValve.invoke(RemoteAddrValve.java:119) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.59]\r\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:421) [catalina.jar:7.0.59]\r\n\tat org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.59]\r\n\tat org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611) [tomcat-coyote.jar:7.0.59]\r\n\tat org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314) [tomcat-coyote.jar:7.0.59]\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_31]\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_31]\r\n\tat org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.59]\r\n\tat java.lang.Thread.run(Thread.java:745) [na:1.8.0_31]\r\nCaused by: org.springframework.jdbc.BadSqlGrammarException: PreparedStatementCallback; bad SQL grammar [SELECT this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, GROUP_CONCAT(DISTINCT(`lookupAttributes`.`lookupAttributes`) ORDER BY `lookupAttributes`.`order`) AS `lookupAttributes`, this.`abstract`, this.`label`, this.`extends`, this.`description`, GROUP_CONCAT(DISTINCT(`tags`.`tags`) ORDER BY `tags`.`order`) AS `tags`, GROUP_CONCAT(DISTINCT(`attributes`.`attributes`) ORDER BY `attributes`.`order`) AS `attributes`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl` FROM `entities` AS this LEFT JOIN `entities_lookupAttributes` AS `lookupAttributes` ON (this.`fullName` = `lookupAttributes`.`fullName`) LEFT JOIN `entities_tags` AS `tags` ON (this.`fullName` = `tags`.`fullName`) LEFT JOIN `entities_attributes` AS `attributes` ON (this.`fullName` = `attributes`.`fullName`) GROUP BY this.`fullName`, this.`simpleName`, this.`backend`, this.`package`, this.`idAttribute`, this.`labelAttribute`, this.`abstract`, this.`label`, this.`extends`, this.`description`, this.`description-de`, this.`description-en`, this.`description-nl`, this.`label-de`, this.`label-en`, this.`label-nl`  LIMIT 1000]; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:231) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:660) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:695) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:727) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:737) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:787) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.mysql.MysqlRepository$3.getBatch(MysqlRepository.java:750) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.support.BatchingQueryResult.getBatch(BatchingQueryResult.java:36) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.support.BatchingQueryResult.getBatch(BatchingQueryResult.java:14) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.util.BatchingIterable$1.nextBatch(BatchingIterable.java:138) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.util.BatchingIterable$1.hasNext(BatchingIterable.java:58) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1811) ~[na:1.8.0_31]\r\n\tat java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681) ~[na:1.8.0_31]\r\n\tat org.molgenis.data.meta.EntityMetaDataRepository.fillEntityMetaDataCache(EntityMetaDataRepository.java:81) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.meta.MetaDataServiceImpl.bootstrapMetaRepos(MetaDataServiceImpl.java:171) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.data.meta.MetaDataServiceImpl.setDefaultBackend(MetaDataServiceImpl.java:116) ~[molgenis-data-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.app.WebAppConfig.addReposToReindex(WebAppConfig.java:128) ~[WebAppConfig.class:na]\r\n\tat org.molgenis.ui.MolgenisWebAppConfig.reindex(MolgenisWebAppConfig.java:424) ~[molgenis-core-ui-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.molgenis.ui.MolgenisWebAppConfig.initRepositories(MolgenisWebAppConfig.java:473) ~[molgenis-core-ui-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Method.invoke(Method.java:483) ~[na:1.8.0_31]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:349) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:300) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:133) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\t... 60 common frames omitted\r\nCaused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'omx.entities_lookupAttributes' doesn't exist\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_31]\r\n\tat sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_31]\r\n\tat sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_31]\r\n\tat java.lang.reflect.Constructor.newInstance(Constructor.java:408) ~[na:1.8.0_31]\r\n\tat com.mysql.jdbc.Util.handleNewInstance(Util.java:411) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.Util.getInstance(Util.java:386) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1054) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2825) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2313) ~[mysql-connector-java-5.1.28.jar:na]\r\n\tat com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) ~[c3p0-0.9.1.1.jar:0.9.1.1]\r\n\tat org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:703) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\tat org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:644) ~[molgenis-data-annotators-1.17.0-SNAPSHOT.jar:1.17.0-SNAPSHOT]\r\n\t... 84 common frames omitted\r\n```"}}