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Task #2492 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: SQL errors after new config?

Reported by: cxallan Owned by:
Priority: minor Milestone: OMERO-Beta4.2
Component: General Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2010-05-27 (10)

Description

On Blitz startup after the configuration commits I now have SQL errors.

Change History (4)

comment:1 Changed 9 years ago by cxallan 

2010-06-09 08:57:44,696 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:/Users/callan/code/OMERO-TRUNK/dist/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:/Users/callan/code/OMERO-TRUNK/dist/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 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409)
	at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
	at ome.services.blitz.Entry.start(Entry.java:203)
	at ome.services.blitz.Entry.main(Entry.java:121)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/Users/callan/code/OMERO-TRUNK/dist/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:/Users/callan/code/OMERO-TRUNK/dist/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 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
	at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:586)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
	at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048)
	at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397)
	... 3 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/Users/callan/code/OMERO-TRUNK/dist/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 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
	at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
	... 16 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141)
	at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107)
	at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273)
	... 25 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Invocation of init method failed; nested exception is java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
	at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
	at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
	at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105)
	at ome.system.OmeroContext.<init>(OmeroContext.java:98)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
	... 27 more
Caused by: java.lang.RuntimeException:           =====================================================
Data access exception: Did you create your database? 
=====================================================

	at ome.services.sessions.SessionManagerImpl.init(SessionManagerImpl.java:181)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1527)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1468)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400)
	... 44 more
Caused by: org.springframework.dao.DataIntegrityViolationException: PreparedStatementCallback; SQL [insert into session (id,permissions,timetoidle,timetolive,started,closed,defaulteventtype,uuid,owner,node)values (?,-35,?,?,?,null,?,?,?,?)]; ERROR: null value in column "defaultpermissions" violates not-null constraint; nested exception is org.postgresql.util.PSQLException: ERROR: null value in column "defaultpermissions" violates not-null constraint
	at org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:245)
	at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:72)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:602)
	at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:811)
	at org.springframework.jdbc.core.JdbcTemplate.update(JdbcTemplate.java:833)
	at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.update(NamedParameterJdbcTemplate.java:233)
	at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.update(NamedParameterJdbcTemplate.java:237)
	at org.springframework.jdbc.core.simple.SimpleJdbcTemplate.update(SimpleJdbcTemplate.java:239)
	at ome.services.sessions.SessionManagerImpl$10.doWork(SessionManagerImpl.java:1023)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	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:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at $Proxy48.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.executeStateless(Executor.java:390)
	at ome.services.sessions.SessionManagerImpl.executeInternalSession(SessionManagerImpl.java:984)
	at ome.services.sessions.SessionManagerImpl.init(SessionManagerImpl.java:177)
	... 51 more
Caused by: org.postgresql.util.PSQLException: ERROR: null value in column "defaultpermissions" violates not-null constraint
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1608)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1343)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:194)
	at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:451)
	at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:350)
	at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:304)
	at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:817)
	at org.springframework.jdbc.core.JdbcTemplate$2.doInPreparedStatement(JdbcTemplate.java:1)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:586)
	... 71 more

comment:2 Changed 9 years ago by jmoore

From devteam log (below) it looks like the prefs upgrade took place, but to the wrong file (OMERO-TRUNK/etc/grid/config.xml rather than OMERO-TRUNK/dist/etc/grid/config.xml).

$ dist/bin/omero admin start
Creating directory /Users/callan/code/OMERO-TRUNK/dist/var
Importing pre-4.2 preferences
Creating /Users/callan/code/OMERO-TRUNK/dist/var/master
Initializing /Users/callan/code/OMERO-TRUNK/dist/var/log
Creating /Users/callan/code/OMERO-TRUNK/dist/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes

$ dist/bin/omero config get
etc/grid/config.xml not found; using /Users/callan/omero/config.xml
$ ls -al ~/omero/config.xml
-rw-r--r--  1 callan  staff  524  9 Jun 09:06 /Users/callan/omero/config.xml
$ cat ~/omero/config.xml
<?xml version="1.0" ?>
<icegrid>
  <!-- 

    This file was generated at Wed Jun  9 09:06:52 2010 by the OmeroConfig system.
    Do not edit directly but see bin/omero config for details.
    This file may be included into your IceGrid application.

 -->
  <properties id="__ACTIVE__">
    <property name="omero.config.profile" value="default"/>
    <property name="omero.config.version" value="4.2.0"/>
  </properties>
  <properties id="default">
    <property name="omero.config.version" value="4.2.0"/>
  </properties>
</icegrid>

comment:3 Changed 9 years ago by jmoore

(In [7231]) Adding log statement of config.xml creation. See #2492

comment:4 Changed 9 years ago by cxallan

  • Resolution set to invalid
  • Status changed from new to closed

Possible issue with OMERO_CONFIG and/or database oddities. drop/create resolved the problem.

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