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Problem after upgrading to 5.1.0

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The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.
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Problem after upgrading to 5.1.0

Postby tpengo » Fri Apr 03, 2015 6:26 pm

Hi,

I was running OMERO.server-5.0.6-ice34-b53 on Windows with PostgreSQL 9.4 on Windows and upgraded to OMERO.server-5.1.0-ice34-b40.

I followed the instructions in
http://www.openmicroscopy.org/site/supp ... grade.html.

After starting the server, I got the following error in the Blitz log:

Code: Select all
2015-04-03 12:56:27,517 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2015-04-03 12:56:27,517 INFO  [    ome.services.util.ServerVersionCheck] (      main) OMERO Version: 5.1.0-ice34-b40 Ready.
2015-04-03 12:56:27,549 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2015-04-03 12:56:28,377 INFO  [                 ome.system.UpgradeCheck] (      main) no update needed
2015-04-03 12:56:28,408 INFO  [    ome.tools.hibernate.ExtendedMetadata] (      main) Calculating ExtendedMetadata...
2015-04-03 12:56:29,502 INFO  [       ome.services.graphs.GraphPathBean] (      main) initialized graph path bean with 702 properties
2015-04-03 12:56:29,502 INFO  [      o.s.scheduler.SchedulerFactoryBean] (      main) Starting Quartz Scheduler now
2015-04-03 12:56:29,502 INFO  [        ome.services.util.ServiceHandler] (      main)  Executor.doWork -- ome.services.util.NamespaceCheck.namespaceCheck[]
2015-04-03 12:56:29,502 INFO  [        ome.services.util.ServiceHandler] (      main)  Args:   [null, InternalSF@603475441]
2015-04-03 12:56:29,611 INFO  [                 org.perf4j.TimingLogger] (      main) start[1428083789502] time[97] tag[omero.call.exception]
2015-04-03 12:56:29,611 WARN  [        ome.services.util.ServiceHandler] (      main) InvalidDataAccessResourceUsageException thrown.

org.springframework.dao.InvalidDataAccessResourceUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:629) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:411) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at ome.logic.QueryImpl.get(QueryImpl.java:159) ~[server.jar:na]
   at ome.logic.AdminImpl.groupProxy(AdminImpl.java:195) ~[server.jar:na]
   at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:383) ~[server.jar:na]
   at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) ~[server.jar:na]
   at ome.security.basic.EventHandler.invoke(EventHandler.java:146) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) ~[org.springframework.transaction.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
   at com.sun.proxy.$Proxy72.doWork(Unknown Source) [na:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:447) [server.jar:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:391) [server.jar:na]
   at ome.services.util.NamespaceCheck.handleContextRefreshedEvent(NamespaceCheck.java:55) [server.jar:na]
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:67) [server.jar:na]
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:25) [server.jar:na]
   at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:97) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at ome.services.messages.GlobalMulticaster.multicastEvent(GlobalMulticaster.java:55) [server.jar:na]
   at ome.system.OmeroContext.publishEvent(OmeroContext.java:327) [common.jar:na]
   at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:887) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:426) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.<init>(OmeroContext.java:98) [common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [na:1.7.0_71]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) [na:1.7.0_71]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) [na:1.7.0_71]
   at java.lang.reflect.Constructor.newInstance(Unknown Source) [na:1.7.0_71]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:586) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) [org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) [org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) [common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:194) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:151) [blitz.jar:na]
Caused by: org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:92) ~[hibernate-core.jar:na]
   at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) ~[hibernate-core.jar:na]
   at org.hibernate.loader.Loader.loadEntity(Loader.java:1957) ~[hibernate-core.jar:na]
   at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:86) ~[hibernate-core.jar:na]
   at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:76) ~[hibernate-core.jar:na]
   at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3270) ~[hibernate-core.jar:na]
   at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:496) ~[hibernate-core.jar:na]
   at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:477) ~[hibernate-core.jar:na]
   at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:227) ~[hibernate-core.jar:na]
   at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:147) ~[hibernate-core.jar:na]
   at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:1082) ~[hibernate-core.jar:na]
   at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:1020) ~[hibernate-core.jar:na]
   at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:176) ~[hibernate-core.jar:na]
   at org.hibernate.Hibernate.initialize(Hibernate.java:428) ~[hibernate-core.jar:na]
   at ome.logic.QueryImpl$1.doInHibernate(QueryImpl.java:176) ~[server.jar:na]
   at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   ... 62 common frames omitted
Caused by: org.postgresql.util.PSQLException: ERROR: permission denied for relation experimentergroup_config
   at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2270) ~[postgresql.jar:9.4]
   at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1998) ~[postgresql.jar:9.4]
   at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255) ~[postgresql.jar:9.4]
   at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:570) ~[postgresql.jar:9.4]
   at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:420) ~[postgresql.jar:9.4]
   at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:305) ~[postgresql.jar:9.4]
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_71]
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:1.7.0_71]
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:1.7.0_71]
   at java.lang.reflect.Method.invoke(Unknown Source) ~[na:1.7.0_71]
   at bitronix.tm.resource.jdbc.BaseProxyHandlerClass.invoke(BaseProxyHandlerClass.java:64) ~[btm.jar:2.1.3]
   at com.sun.proxy.$Proxy7.executeQuery(Unknown Source) ~[na:na]
   at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208) ~[hibernate-core.jar:na]
   at org.hibernate.loader.Loader.getResultSet(Loader.java:1869) ~[hibernate-core.jar:na]
   at org.hibernate.loader.Loader.doQuery(Loader.java:718) ~[hibernate-core.jar:na]
   at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270) ~[hibernate-core.jar:na]
   at org.hibernate.loader.Loader.loadEntity(Loader.java:1953) ~[hibernate-core.jar:na]
   ... 75 common frames omitted
2015-04-03 12:56:29,611 INFO  [        ome.services.util.ServiceHandler] (      main)  Excp:   org.springframework.dao.InvalidDataAccessResourceUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
2015-04-03 12:56:29,627 ERROR [                ome.services.blitz.Entry] (      main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/C:/OMERO.server-5.1.0-ice34-b40/lib/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/C:/OMERO.server-5.1.0-ice34-b40/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is ome.conditions.ApiUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203) ~[common.jar:na]
   at ome.services.blitz.Entry.start(Entry.java:194) [blitz.jar:na]
   at ome.services.blitz.Entry.main(Entry.java:151) [blitz.jar:na]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/C:/OMERO.server-5.1.0-ice34-b40/lib/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/C:/OMERO.server-5.1.0-ice34-b40/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is ome.conditions.ApiUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:586) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 3 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/C:/OMERO.server-5.1.0-ice34-b40/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is ome.conditions.ApiUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 16 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is ome.conditions.ApiUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 25 common frames omitted
Caused by: ome.conditions.ApiUsageException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]; SQL [select experiment0_.id as id34_0_, experiment0_.description as descript2_34_0_, experiment0_.external_id as external7_34_0_, experiment0_.permissions as permissi3_34_0_, experiment0_.ldap as ldap34_0_, experiment0_.name as name34_0_, experiment0_.version as version34_0_, config1_.experimentergroup_id as experime1_34_2_, config1_.name as name2_, config1_.value as value2_, config1_.index as index2_ from experimentergroup experiment0_ left outer join experimentergroup_config config1_ on experiment0_.id=config1_.experimentergroup_id where experiment0_.id=?]; nested exception is org.hibernate.exception.SQLGrammarException: could not load an entity: [ome.model.meta.ExperimenterGroup#0]
   at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:629) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:411) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at ome.logic.QueryImpl.get(QueryImpl.java:159) ~[server.jar:na]
   at ome.logic.AdminImpl.groupProxy(AdminImpl.java:195) ~[server.jar:na]
   at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:383) ~[server.jar:na]
   at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) ~[server.jar:na]
   at ome.security.basic.EventHandler.invoke(EventHandler.java:146) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) ~[org.springframework.transaction.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) ~[server.jar:na]
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) ~[org.springframework.aop.jar:3.0.1.RELEASE-A]
   at com.sun.proxy.$Proxy72.doWork(Unknown Source) ~[na:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:447) ~[server.jar:na]
   at ome.services.util.Executor$Impl.execute(Executor.java:391) ~[server.jar:na]
   at ome.services.util.NamespaceCheck.handleContextRefreshedEvent(NamespaceCheck.java:55) ~[server.jar:na]
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:67) ~[server.jar:na]
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:25) ~[server.jar:na]
   at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:97) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at ome.services.messages.GlobalMulticaster.multicastEvent(GlobalMulticaster.java:55) ~[server.jar:na]
   at ome.system.OmeroContext.publishEvent(OmeroContext.java:327) ~[common.jar:na]
   at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:887) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:426) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105) ~[org.springframework.context.jar:3.0.1.RELEASE-A]
   at ome.system.OmeroContext.<init>(OmeroContext.java:98) ~[common.jar:na]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_71]
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[na:1.7.0_71]
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) ~[na:1.7.0_71]
   at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[na:1.7.0_71]
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126) ~[org.springframework.beans.jar:3.0.1.RELEASE-A]
   ... 27 common frames omitted


Any idea what could I have done wrong?

My wild guess is that is has something to do with the schema change..?

Thanks in advance
Thomas
tpengo
 
Posts: 9
Joined: Wed Aug 06, 2014 8:37 am
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Re: Problem after upgrading to 5.1.0

Postby tpengo » Fri Apr 03, 2015 7:56 pm

Hi,

I found the problem.

Instead of using the command line, I used pgAdmin III and the SQL console. This meant that the user performing the queries was 'postgres'. This result in a number of tables, sequences and views to be created under the user 'postgres', leaving poor OMERO being 'omero' out of the game.

Following http://stackoverflow.com/questions/1348 ... postgresql I used these three meta-queries (runned to file w/unquoted strings, then run the file) to correct my blunder:

Code: Select all
SELECT 'ALTER TABLE '|| schemaname || '.' || tablename ||' OWNER TO omero;'
FROM pg_tables WHERE NOT schemaname IN ('pg_catalog', 'information_schema')
ORDER BY schemaname, tablename;

Code: Select all
SELECT 'ALTER SEQUENCE '|| sequence_schema || '.' || sequence_name ||' OWNER TO omero;'
FROM information_schema.sequences WHERE NOT sequence_schema IN ('pg_catalog', 'information_schema')
ORDER BY sequence_schema, sequence_name;

Code: Select all
SELECT 'ALTER VIEW '|| table_schema || '.' || table_name ||' OWNER TO omero;'
FROM information_schema.views WHERE NOT table_schema IN ('pg_catalog', 'information_schema')
ORDER BY table_schema, table_name;


I posted this in case someone run into the same problem...

Cheers
Thomas
tpengo
 
Posts: 9
Joined: Wed Aug 06, 2014 8:37 am
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Re: Problem after upgrading to 5.1.0

Postby sbesson » Mon Apr 06, 2015 8:34 am

Hi Thomas,

glad you found the solution to the upgrade problem. In addition to your forum post, it would be possible to amend the current server upgrade documentation and add a warning about database upgrade via graphical clients. Let us know if you think this would be worth it or if you can think of a better placeholder to add this information.

Best regards,
Sebastien
User avatar
sbesson
Team Member
 
Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm
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Re: Problem after upgrading to 5.1.0

Postby tpengo » Mon Apr 06, 2015 2:49 pm

Hi Sebastien,

yes, I think it would help users who are not aware of this issue. It mostly affects Windows users as the default is not to have the psql tool in the PATH (at least in my case), which would tend to favor the use of the graphical tool. On the other hand, there might be a way to connect to the database as another user in the graphical tool, but I am not sure how.

One thing I was wondering, in the docs: did you really mean "The example below assumes you are upgrading from a 4.4 server."?

Cheers
Thomas
tpengo
 
Posts: 9
Joined: Wed Aug 06, 2014 8:37 am
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Re: Problem after upgrading to 5.1.0

Postby sbesson » Mon Apr 06, 2015 4:54 pm

Hi Thomas,

you are right, the 4.4 mention is not expected in the 5.1 upgrade page. This Pull Request should fix this erroneous line and add a note warning system administrators about the connection user while using SQL Shell for the upgrade.

Thanks for all the feedback,
Sebastien
User avatar
sbesson
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Posts: 421
Joined: Tue Feb 28, 2012 7:20 pm
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